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Sample records for 2d fluorescence difference

  1. Comparing the heterogeneity of copper-binding characteristics for two different-sized soil humic acid fractions using fluorescence quenching combined with 2D-COS.

    PubMed

    Hur, Jin; Lee, Bo-Mi

    2011-01-01

    Heterogeneous distributions of copper-binding characteristics were compared for two ultrafiltered size fractions of a soil HA using fluorescence quenching combined with two-dimensional correlation spectroscopy (2D-COS). The apparent shapes of the original synchronous fluorescence spectra and the extent of the fluorescence quenching upon the addition of copper were similar for the two fractions. The stability constants calculated at their highest peaks were not significantly different. However, the 2D-COS results revealed that the fluorescence quenching behaviors were strongly affected by the associated wavelengths and the fraction's size. The spectral change preferentially occurred in the wavelength order of 467 nm → 451 nm → 357 nm for the 1-10 K fraction and of 376 nm → 464 nm for the >100 K fraction. The extent of the binding affinities exactly followed the sequential orders interpreted from the 2D-COS, and they exhibited the distinctive ranges of the logarithmic values from 5.86 to 4.91 and from 6.48 to 5.95 for the 1-10 K and the >100 K fractions, respectively. Our studies demonstrated that fluorescence quenching combined with 2D-COS could be successfully utilized to give insight into the chemical heterogeneity associated with metal-binding sites within the relatively homogeneous HA size fractions.

  2. Rapid-scan coherent 2D fluorescence spectroscopy.

    PubMed

    Draeger, Simon; Roeding, Sebastian; Brixner, Tobias

    2017-02-20

    We developed pulse-shaper-assisted coherent two-dimensional (2D) electronic spectroscopy in liquids using fluorescence detection. A customized pulse shaper facilitates shot-to-shot modulation at 1 kHz and is employed for rapid scanning over all time delays. A full 2D spectrum with 15 × 15 pixels is obtained in approximately 6 s of measurement time (plus further averaging if needed). Coherent information is extracted from the incoherent fluorescence signal via 27-step phase cycling. We exemplify the technique on cresyl violet in ethanol and recover literature-known oscillations as a function of population time. Signal-to-noise behavior is analyzed as a function of the amount of averaging. Rapid scanning provides a 2D spectrum with a root-mean-square error of < 0.05 after 1 min of measurement time.

  3. Solution conformation of 2-aminopurine (2-AP) dinucleotide determined by ultraviolet 2D fluorescence spectroscopy (UV-2D FS).

    PubMed

    Widom, Julia R; Johnson, Neil P; von Hippel, Peter H; Marcus, Andrew H

    2013-02-01

    We have observed the conformation-dependent electronic coupling between the monomeric subunits of a dinucleotide of 2-aminopurine (2-AP), a fluorescent analog of the nucleic acid base adenine. This was accomplished by extending two-dimensional fluorescence spectroscopy (2D FS) - a fluorescence-detected variation of 2D electronic spectroscopy - to excite molecular transitions in the ultraviolet (UV) regime. A collinear sequence of four ultrafast laser pulses centered at 323 nm was used to resonantly excite the coupled transitions of 2-AP dinucleotide. The phases of the optical pulses were continuously swept at kilohertz frequencies, and the ensuing nonlinear fluorescence was phase-synchronously detected at 370 nm. Upon optimization of a point-dipole coupling model to our data, we found that in aqueous buffer the 2-AP dinucleotide adopts an average conformation in which the purine bases are non-helically stacked (center-to-center distance R12 = 3.5 Å ± 0.5 Å, twist angle θ12 = 5° ± 5°), which differs from the conformation of such adjacent bases in duplex DNA. These experiments establish UV-2D FS as a method for examining the local conformations of an adjacent pair of fluorescent nucleotides substituted into specific DNA or RNA constructs, which will serve as a powerful probe to interpret, in structural terms, biologically significant local conformational changes within the nucleic acid framework of protein-nucleic acid complexes.

  4. Quantum process tomography by 2D fluorescence spectroscopy

    SciTech Connect

    Pachón, Leonardo A.; Marcus, Andrew H.; Aspuru-Guzik, Alán

    2015-06-07

    Reconstruction of the dynamics (quantum process tomography) of the single-exciton manifold in energy transfer systems is proposed here on the basis of two-dimensional fluorescence spectroscopy (2D-FS) with phase-modulation. The quantum-process-tomography protocol introduced here benefits from, e.g., the sensitivity enhancement ascribed to 2D-FS. Although the isotropically averaged spectroscopic signals depend on the quantum yield parameter Γ of the doubly excited-exciton manifold, it is shown that the reconstruction of the dynamics is insensitive to this parameter. Applications to foundational and applied problems, as well as further extensions, are discussed.

  5. Application of highly sensitive fluorescent dyes (CyDye DIGE Fluor saturation dyes) to laser microdissection and two-dimensional difference gel electrophoresis (2D-DIGE) for cancer proteomics.

    PubMed

    Kondo, Tadashi; Hirohashi, Setsuo

    2006-01-01

    Proteome data combined with histopathological information provides important, novel clues for understanding cancer biology and reveals candidates for tumor markers and therapeutic targets. We have established an application of a highly sensitive fluorescent dye (CyDye DIGE Fluor saturation dye), developed for two-dimensional difference gel electrophoresis (2D-DIGE), to the labeling of proteins extracted from laser microdissected tissues. The use of the dye dramatically decreases the protein amount and, in turn, the number of cells required for 2D-DIGE; the cells obtained from a 1 mm2 area of an 8-12 microm thick tissue section generate up to 5,000 protein spots in a large-format 2D gel. This protocol allows the execution of large-scale proteomics in a more efficient, accurate and reproducible way. The protocol can be used to examine a single sample in 5 d or to examine hundreds of samples in large-scale proteomics.

  6. 2-D fluorescence lifetime imaging using a time-gated image intensifier

    NASA Astrophysics Data System (ADS)

    Dowling, K.; Hyde, S. C. W.; Dainty, J. C.; French, P. M. W.; Hares, J. D.

    1997-02-01

    We report a 2-D fluorescence lifetime imaging system based on a time-gated image intensifier and a Cr:LiSAF regenerative amplifier. We have demonstrated 185 ps temporal resolution. The deleterious effects of optical scattering are demonstrated.

  7. Direct Formation of Large-Area 2D Nanosheets from Fluorescent Semiconducting Homopolymer with Orthorhombic Crystalline Orientation.

    PubMed

    Yang, Sanghee; Shin, Suyong; Choi, Inho; Lee, Jaeho; Choi, Tae-Lim

    2017-03-01

    Semiconducting polymers have been widely investigated due to their intriguing optoelectronic properties and their high crystallinity that provides a strong driving force for self-assembly. Although there are various reports of successful self-assembly of nanostructures using semiconducting polymers, direct in situ self-assembly of these polymers into two-dimensional (2D) nanostructures has proven difficult, despite their importance for optoelectronics applications. Here, we report the synthesis of a simple conjugated homopolymer by living cyclopolymerization of a 1,6-heptadiyne (having a fluorene moiety) and its efficient in situ formation of large-area 2D fluorescent semiconducting nanostructures. Using high-resolution imaging tools such as atomic force microscopy and transmission electron microscopy, we observed the solvent-dependent self-assembly behaviors of this homopolymer; the identical starting polymer formed 2D nanosheets with different shapes, such as rectangle, raft, and leaf, when dissolved in different solvents. Furthermore, super-resolution optical microscopy enabled the real-time imaging of the fluorescent 2D nanosheets, revealing their stable and uniform shapes, fluorescence, and solution dynamics. Notably, we propose an orthorhombic crystalline packing model to explain the direct formation of 2D nanostructures based on various diffraction patterns, providing important insight for their shape modulation during the self-assembly.

  8. 2D map projections for visualization and quantitative analysis of 3D fluorescence micrographs

    PubMed Central

    Sendra, G. Hernán; Hoerth, Christian H.; Wunder, Christian; Lorenz, Holger

    2015-01-01

    We introduce Map3-2D, a freely available software to accurately project up to five-dimensional (5D) fluorescence microscopy image data onto full-content 2D maps. Similar to the Earth’s projection onto cartographic maps, Map3-2D unfolds surface information from a stack of images onto a single, structurally connected map. We demonstrate its applicability for visualization and quantitative analyses of spherical and uneven surfaces in fixed and dynamic live samples by using mammalian and yeast cells, and giant unilamellar vesicles. Map3-2D software is available at http://www.zmbh.uni-heidelberg.de//Central_Services/Imaging_Facility/Map3-2D.html. PMID:26208256

  9. Investigation on the spectral properties of 2D asynchronous fluorescence spectra generated by using variable excitation wavelengths as a perturbation

    NASA Astrophysics Data System (ADS)

    Wang, Jingdan; He, Anqi; Guo, Ran; Wei, Yongju; Feng, Juan; Xu, Yizhuang; Noda, Isao; Wu, Jinguang

    2016-11-01

    Properties of 2D asynchronous spectra generated from a series of fluorescence emission spectra are investigated. Variable excitation wavelengths are utilized as an external perturbation. Based on the results of mathematical analysis and computer simulation, we find that no cross peak will be produced on the 2D asynchronous spectrum if the fluorescent solute under investigation occurs in a single micro-environment. The observation of cross peaks implies that the fluorescent molecule may occur in different micro-environments in a solution. Based on these results, we use 2D asynchronous spectra to investigate the emission spectra of anthracene dissolved in cyclohexane. When the concentration of anthracene is low, no cross peak is produced in the resultant 2D asynchronous spectrum, confirming that anthracene is dissolved as single molecule in the solution. As the concentration elevated, cross peaks appear in the corresponding 2D asynchronous spectra. A plausible explanation of this phenomenon is that anthracene may undergo aggregation via π-π interaction or π-C-H interaction.

  10. Temperature-dependent conformations of a membrane supported zinc porphyrin tweezer by 2D fluorescence spectroscopy.

    PubMed

    Widom, Julia R; Lee, Wonbae; Perdomo-Ortiz, Alejandro; Rappoport, Dmitrij; Molinski, Tadeusz F; Aspuru-Guzik, Alán; Marcus, Andrew H

    2013-07-25

    We studied the equilibrium conformations of a zinc porphyrin tweezer composed of two carboxylphenyl-functionalized zinc tetraphenyl porphyrin subunits connected by a 1,4-butyndiol spacer, which was suspended inside the amphiphilic regions of 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) liposomes. By combining phase-modulation two-dimensional fluorescence spectroscopy (2D FS) with linear absorbance and fluorimetry, we determined that the zinc porphyrin tweezer adopts a mixture of folded and extended conformations in the membrane. By fitting an exciton-coupling model to a series of data sets recorded over a range of temperatures (17-85 °C) and at different laser center wavelengths, we determined that the folded form of the tweezer is stabilized by a favorable change in the entropy of the local membrane environment. Our results provide insights toward understanding the balance of thermodynamic factors that govern molecular assembly in membranes.

  11. Protein profiling using two-dimensional difference gel electrophoresis (2-D DIGE).

    PubMed

    Feret, Renata; Lilley, Kathryn S

    2014-02-03

    2-D DIGE relies on pre-electrophoretic labeling of samples with one of three spectrally distinct fluorescent dyes, followed by electrophoresis of all samples in one 2-D gel. The dye-labeled samples are then viewed individually by scanning the gel at different wavelengths, which circumvents problems with gel-to-gel variation and spot matching between gels. Image analysis programs are used to generate volume ratios for each spot, which essentially describe the intensity of a particular spot in each test sample, and thus enable protein abundance level changes to be identified and quantified. This unit describes the 2-D DIGE procedure including sample preparation from various cell types, labeling of proteins, and points to consider in the downstream processing of fluorescently labeled samples.

  12. 2D fluorescence spectroscopy for monitoring ion-exchange membrane based technologies - Reverse electrodialysis (RED).

    PubMed

    Pawlowski, Sylwin; Galinha, Claudia F; Crespo, João G; Velizarov, Svetlozar

    2016-01-01

    Reverse electrodialysis (RED) is one of the emerging, membrane-based technologies for harvesting salinity gradient energy. In RED process, fouling is an undesirable operation constraint since it leads to a decrease of the obtainable net power density due to increasing stack electric resistance and pressure drop. Therefore, early fouling detection is one of the main challenges for successful RED technology implementation. In the present study, two-dimensional (2D) fluorescence spectroscopy was used, for the first time, as a tool for fouling monitoring in RED. Fluorescence excitation-emission matrices (EEMs) of ion-exchange membrane surfaces and of natural aqueous streams were acquired during one month of a RED stack operation. Fouling evolvement on the ion-exchange membrane surfaces was successfully followed by 2D fluorescence spectroscopy and quantified using principal components analysis (PCA). Additionally, the efficiency of cleaning strategy was assessed by measuring the membrane fluorescence emission intensity before and after cleaning. The anion-exchange membrane (AEM) surface in contact with river water showed to be significantly affected due to fouling by humic compounds, which were found to cross through the membrane from the lower salinity (river water) to higher salinity (sea water) stream. The results obtained show that the combined approach of using 2D fluorescence spectroscopy and PCA has a high potential for studying fouling development and membrane cleaning efficiency in ion exchange membrane processes.

  13. Laser irradiated fluorescent perfluorocarbon microparticles in 2-D and 3-D breast cancer cell models

    NASA Astrophysics Data System (ADS)

    Niu, Chengcheng; Wang, Long; Wang, Zhigang; Xu, Yan; Hu, Yihe; Peng, Qinghai

    2017-03-01

    Perfluorocarbon (PFC) droplets were studied as new generation ultrasound contrast agents via acoustic or optical droplet vaporization (ADV or ODV). Little is known about the ODV irradiated vaporization mechanisms of PFC-microparticle complexs and the stability of the new bubbles produced. In this study, fluorescent perfluorohexane (PFH) poly(lactic-co-glycolic acid) (PLGA) particles were used as a model to study the process of particle vaporization and bubble stability following excitation in two-dimensional (2-D) and three-dimensional (3-D) cell models. We observed localization of the fluorescent agent on the microparticle coating material initially and after vaporization under fluorescence microscopy. Furthermore, the stability and growth dynamics of the newly created bubbles were observed for 11 min following vaporization. The particles were co-cultured with 2-D cells to form 3-D spheroids and could be vaporized even when encapsulated within the spheroids via laser irradiation, which provides an effective basis for further work.

  14. Targeted fluorescence imaging enhanced by 2D materials: a comparison between 2D MoS2 and graphene oxide.

    PubMed

    Xie, Donghao; Ji, Ding-Kun; Zhang, Yue; Cao, Jun; Zheng, Hu; Liu, Lin; Zang, Yi; Li, Jia; Chen, Guo-Rong; James, Tony D; He, Xiao-Peng

    2016-08-04

    Here we demonstrate that 2D MoS2 can enhance the receptor-targeting and imaging ability of a fluorophore-labelled ligand. The 2D MoS2 has an enhanced working concentration range when compared with graphene oxide, resulting in the improved imaging of both cell and tissue samples.

  15. 2D to 3D conversion implemented in different hardware

    NASA Astrophysics Data System (ADS)

    Ramos-Diaz, Eduardo; Gonzalez-Huitron, Victor; Ponomaryov, Volodymyr I.; Hernandez-Fragoso, Araceli

    2015-02-01

    Conversion of available 2D data for release in 3D content is a hot topic for providers and for success of the 3D applications, in general. It naturally completely relies on virtual view synthesis of a second view given by original 2D video. Disparity map (DM) estimation is a central task in 3D generation but still follows a very difficult problem for rendering novel images precisely. There exist different approaches in DM reconstruction, among them manually and semiautomatic methods that can produce high quality DMs but they demonstrate hard time consuming and are computationally expensive. In this paper, several hardware implementations of designed frameworks for an automatic 3D color video generation based on 2D real video sequence are proposed. The novel framework includes simultaneous processing of stereo pairs using the following blocks: CIE L*a*b* color space conversions, stereo matching via pyramidal scheme, color segmentation by k-means on an a*b* color plane, and adaptive post-filtering, DM estimation using stereo matching between left and right images (or neighboring frames in a video), adaptive post-filtering, and finally, the anaglyph 3D scene generation. Novel technique has been implemented on DSP TMS320DM648, Matlab's Simulink module over a PC with Windows 7, and using graphic card (NVIDIA Quadro K2000) demonstrating that the proposed approach can be applied in real-time processing mode. The time values needed, mean Similarity Structural Index Measure (SSIM) and Bad Matching Pixels (B) values for different hardware implementations (GPU, Single CPU, and DSP) are exposed in this paper.

  16. Low-frequency phased-array 2D fluorescence localization in breast cancer detection

    NASA Astrophysics Data System (ADS)

    Liu, Qian; Chen, Yu; Chance, Britton; Luo, Qingming

    2003-12-01

    A method for rapid, non-invasive 2D fluorescence localization of breast cancer using low frequency phased array near-infrared technique is presented in this article. In our study, we have developed a dual-channel fluorescence detection system to locate breast cancer. This system consists two pair of in-phase and out-of-phase light emitting diodes (LEDs) as the light sources and Photomultiplier Tube (PMT) as the detector. Two null planes generated by cancellation of diffusion photon density waves (DPDW) will indicate the 2D position of breast cancer with exogenous contrast agents. The fluorescent contrast agent used in this study is Indocyanine Green (ICG) and the minimum amount of ICG detected by our system is 0.5 μM. With the 2 cm separation of sources and detector, the maximum depth our system can detect is 10 mm. The whole system is in compact size and portable. Phantom experiments show that the system can provide real time detection and localization of small hidden absorbing-fluorescent objects inside the highly scattering medium with high accuracy of +/-3 mm. The potential application is that it is low-cost and can be used for breast cancer localization as operation aid and self-examination.

  17. Fluorescence Intensity and Polarization from Photodissociated H2, D2 and HD

    NASA Astrophysics Data System (ADS)

    Machacek, J. R.; Andrianarijaona, V. M.; Furst, J. E.; Gay, T. J.; Kilcoyne, A. L. D.; Landers, A. L.; McLaughlin, K. W.

    2009-05-01

    We have measured the intensity and linear polarization of Hα (n=3->n=2) 656.3 nm fluorescence resulting from H and D atoms created by photodissociation of H2, D2 and HD using linearly-polarized photons with energies ranging from 16.5 to 17.6 eV. Between the threshold for atomic n=3 production at 16.6 eV and the n=4 production threshold at 17.3 eV, the relative cross section and polarization data are free from cascade contributions due to higher-lying atomic states. The photon beam energy width used for this work was 3 meV. Comparison of relative intensities to previous measurements [1] show marked differences. However, the polarization is in qualitative agreement. [1] H. Frohlich et al., Z. Phys. D 34, 119 (1995). Support provided by the NSF (Grant PHY-0653379), DOE (LBNL/ALS) and ANSTO (Access to Major Research Facilities Programme).

  18. Laser irradiated fluorescent perfluorocarbon microparticles in 2-D and 3-D breast cancer cell models

    PubMed Central

    Niu, Chengcheng; Wang, Long; Wang, Zhigang; Xu, Yan; Hu, Yihe; Peng, Qinghai

    2017-01-01

    Perfluorocarbon (PFC) droplets were studied as new generation ultrasound contrast agents via acoustic or optical droplet vaporization (ADV or ODV). Little is known about the ODV irradiated vaporization mechanisms of PFC-microparticle complexs and the stability of the new bubbles produced. In this study, fluorescent perfluorohexane (PFH) poly(lactic-co-glycolic acid) (PLGA) particles were used as a model to study the process of particle vaporization and bubble stability following excitation in two-dimensional (2-D) and three-dimensional (3-D) cell models. We observed localization of the fluorescent agent on the microparticle coating material initially and after vaporization under fluorescence microscopy. Furthermore, the stability and growth dynamics of the newly created bubbles were observed for 11 min following vaporization. The particles were co-cultured with 2-D cells to form 3-D spheroids and could be vaporized even when encapsulated within the spheroids via laser irradiation, which provides an effective basis for further work. PMID:28262671

  19. A Two-Dimensional Difference Gel Electrophoresis (2D-DIGE) Protocol for Studies of Neural Precursor Cells.

    PubMed

    Guest, Paul C

    2017-01-01

    This chapter describes the basics of two-dimensional difference gel electrophoresis (2D-DIGE) for multiplex analysis of up to distinct proteomes. The example given describes the analysis of undifferentiated and differentiated neural precursor cells labelled with fluorescent Cy3 and Cy5 dyes in comparison to a pooled standard labelled with Cy2. After labelling, the proteomes are mixed together and electrophoresed on the same 2D gels. Scanning the gels at wavelengths specific for each dye allows direct overlay of the two different proteomes and the differences in abundance of specific protein spots can be determined through comparison to the pooled standard.

  20. Parallel online multi-wavelength (2D) fluorescence spectroscopy in each well of a continuously shaken microtiter plate.

    PubMed

    Ladner, Tobias; Beckers, Mario; Hitzmann, Bernd; Büchs, Jochen

    2016-12-01

    Small-scale high-throughput screening devices are becoming increasingly important in bioprocess development. Conventional dipping probes for process monitoring are often too large to be used in these devices. Thus, optical measurements are often the method of choice. Even some parameters that cannot directly be measured by fluorescence become accessible via sensitive fluorescence dyes. However, not all compounds of interest are measurable by this technique. Recent studies applying multi-wavelength (2D) fluorescence spectroscopy in combination with chemometrics have shown that information on numerous analytes is obscured by the fluorescence data. Hitherto, this measurement technique has only been available on the scale of stirred tank fermenters. This work introduces a new device for multi-wavelength (2D) fluorescence spectroscopy in each well of a continuously shaken microtiter plate. Using a combination of spectrograph and CCD detector, the required time per measurement cycle in a 48-well microtiter plate was 0.5 h. Cultures of Hansenula polymorpha and Escherichia coli are monitored. The concentrations of glycerol, glucose and acetate as well as pH are determined using partial least square (PLS) models. Because a pH-sensitive fluorescence dye was not required, no dependency of the pKa of a fluorescence dye exists, and measurements in the low pH range can be obtained.

  1. Model-based segmentation and quantification of subcellular structures in 2D and 3D fluorescent microscopy images

    NASA Astrophysics Data System (ADS)

    Wörz, Stefan; Heinzer, Stephan; Weiss, Matthias; Rohr, Karl

    2008-03-01

    We introduce a model-based approach for segmenting and quantifying GFP-tagged subcellular structures of the Golgi apparatus in 2D and 3D microscopy images. The approach is based on 2D and 3D intensity models, which are directly fitted to an image within 2D circular or 3D spherical regions-of-interest (ROIs). We also propose automatic approaches for the detection of candidates, for the initialization of the model parameters, and for adapting the size of the ROI used for model fitting. Based on the fitting results, we determine statistical information about the spatial distribution and the total amount of intensity (fluorescence) of the subcellular structures. We demonstrate the applicability of our new approach based on 2D and 3D microscopy images.

  2. Melting of Boltzmann particles in different 2D trapping potential

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Dyuti; Filinov, Alexei; Ghosal, Amit; Bonitz, Michael

    2015-03-01

    We analyze the quantum melting of two dimensional Wigner solid in several confined geometries and compare them with corresponding thermal melting in a purely classical system. Our results show that the geometry play little role in deciding the crossover quantum parameter nX, as the effects from boundary is well screened by the quantum zero point motion. The unique phase diagram in the plane of thermal and quantum fluctuations determined from independent melting criteria separates out the Wigner molecule ``phase'' from the classical and quantum ``liquids''. An intriguing signature of weakening liquidity with increasing temperature T have been found in the extreme quantum regime (n). This crossover is associated with production of defects, just like in case of thermal melting, though the role of them in determining the mechanism of the crossover appears different. Our study will help comprehending melting in a variety of experimental realization of confined system - from quantum dots to complex plasma.

  3. CYP2D6 Genetic Polymorphisms and Phenotypes in Different Ethnicities of Malaysian Breast Cancer Patients.

    PubMed

    Chin, Fee Wai; Chan, Soon Choy; Abdul Rahman, Sabariah; Noor Akmal, Sharifah; Rosli, Rozita

    2016-01-01

    The cytochrome P450, family 2, subfamily D, polypeptide 6 (CYP2D6) is an enzyme that is predominantly involved in the metabolism of tamoxifen. Genetic polymorphisms of the CYP2D6 gene may contribute to inter-individual variability in tamoxifen metabolism, which leads to the differences in clinical response to tamoxifen among breast cancer patients. In Malaysia, the knowledge on CYP2D6 genetic polymorphisms as well as metabolizer status in Malaysian breast cancer patients remains unknown. Hence, this study aimed to comprehensively identify CYP2D6 genetic polymorphisms among 80 Malaysian breast cancer patients. The genetic polymorphisms of all the 9 exons of CYP2D6 gene were identified using high-resolution melting analysis and confirmed by DNA sequencing. Seven CYP2D6 alleles consisting of CYP2D6*1, CYP2D6*2, CYP2D6*4, CYP2D6*10, CYP2D6*39, CYP2D6*49, and CYP2D6*75 were identified in this study. Among these alleles, CYP2D6*10 is the most common allele in both Malaysian Malay (54.8%) and Chinese (71.4%) breast cancer patients, whereas CYP2D6*4 in Malaysian Indian (28.6%) breast cancer patients. In relation to CYP2D6 genotype, CYP2D6*10/*10 is more frequently observed in both Malaysian Malay (28.9%) and Chinese (57.1%) breast cancer patients, whereas CYP2D6*4/*10 is more frequently observed in Malaysian Indian (42.8%) breast cancer patients. In terms of CYP2D6 phenotype, 61.5% of Malaysian Malay breast cancer patients are predicted as extensive metabolizers in which they are most likely to respond well to tamoxifen therapy. However, 57.1% of Chinese as well as Indian breast cancer patients are predicted as intermediate metabolizers and they are less likely to gain optimal benefit from the tamoxifen therapy. This is the first report of CYP2D6 genetic polymorphisms and phenotypes in Malaysian breast cancer patients for different ethnicities. These data may aid clinicians in selecting an optimal drug therapy for Malaysian breast cancer patients, hence improve the

  4. Conformation and electronic population transfer in membrane-supported self-assembled porphyrin dimers by 2D fluorescence spectroscopy.

    PubMed

    Perdomo-Ortiz, Alejandro; Widom, Julia R; Lott, Geoffrey A; Aspuru-Guzik, Alán; Marcus, Andrew H

    2012-09-06

    Two-dimensional fluorescence spectroscopy (2D FS) is applied to determine the conformation and femtosecond electronic population transfer in a dimer of magnesium meso tetraphenylporphyrin. The dimers are prepared by self-assembly of the monomer within the amphiphilic regions of 1,2-distearoyl-sn-glycero-3-phosphocholine liposomes. A theoretical framework to describe 2D FS experiments is presented, and a direct comparison is made between the observables of this measurement and those of 2D electronic spectroscopy (2D ES). The sensitivity of the method to varying dimer conformation is explored. A global multivariable fitting analysis of linear and 2D FS data indicates that the dimer adopts a "bent T-shaped" conformation. Moreover, the manifold of singly excited excitons undergoes rapid electronic dephasing and downhill population transfer on the time scale of ∼95 fs. The open conformation of the dimer suggests that its self-assembly is favored by an increase in entropy of the local membrane environment.

  5. Cloning and characterization of a novel human phosphatidic acid phosphatase type 2, PAP2d, with two different transcripts PAP2d_v1 and PAP2d_v2.

    PubMed

    Sun, Liyun; Gu, Shaohua; Sun, Yaqiong; Zheng, Dan; Wu, Qihan; Li, Xin; Dai, Jianfeng; Dai, Jianliang; Ji, Chaoneng; Xie, Yi; Mao, Yumin

    2005-04-01

    This study reports the cloning and characterization of a novel human phosphatidic acid phosphatase type 2 isoform cDNAs (PAP2d) from the foetal brain cDNA library. The PAP2d gene is localized on chromosome 1p21.3. It contains six exons and spans 112 kb of the genomic DNA. By large-scale cDNA sequencing we found two splice variants of PAP2d, PAP2d_v1 and PAP2d_v2. The PAP2d_v1 cDNA is 1722 bp in length and spans an open reading frame from nucleotide 56 to 1021, encoding a 321aa protein. The PAP2d_v2 cDNA is 1707 bp in length encoding a 316aa protein from nucleotide 56-1006. The PAP2d_v1 cDNA is 15 bp longer than the PAP2d_v2 cDNA in the terminal of the fifth exon and it creates different ORF. Both of the proteins contain a well-conserved PAP2 motif. The PAP2d_v1 is mainly expressed in human brain, lung, kidney, testis and colon, while PAP2d_v2 is restricted to human placenta, skeletal muscle, and kidney. The two splice variants are co-expressed only in kidney.

  6. 2D ratiometric fluorescent pH sensor for tracking of cells proliferation and metabolism.

    PubMed

    Ma, Jun; Ding, Changqin; Zhou, Jie; Tian, Yang

    2015-08-15

    Extracellular pH plays a vital role no matter in physiological or pathological studies. In this work, a hydrogel, CD@Nile-FITC@Gel (Gel sensor), entrapping the ratiometric fluorescent probe CD@Nile-FITC was developed. The Gel sensor was successfully used for real-time extracellular pH monitoring. In the case of CD@Nile-FITC, pH-sensitive fluorescent dye fluorescein isothiocyanate (FITC) was chosen as the response signal for H(+) and Nile blue chloride (Nile) as the reference signal. The developed fluorescent probe exhibited high selectivity for pH over other metal ions and amino acids. Meanwhile, the carbon-dots-based inorganic-organic probe demonstrated excellent photostability against long-term light illumination. In order to study the extracellular pH change in processes of cell proliferation and metabolism, CD@Nile-FITC probe was entrapped in sodium alginate gel and consequently formed CD@Nile-FITC@Gel. The MTT assay showed low cytotoxicity of the Gel and the pH titration indicated that it could monitor the pH fluctuations linearly and rapidly within the pH range of 6.0-9.0, which is valuable for physiological pH determination. As expected, the real-time bioimaging of the probe was successfully achieved.

  7. An algorithm to correct 2D near-infrared fluorescence signals using 3D intravascular ultrasound architectural information

    NASA Astrophysics Data System (ADS)

    Mallas, Georgios; Brooks, Dana H.; Rosenthal, Amir; Vinegoni, Claudio; Calfon, Marcella A.; Razansky, R. Nika; Jaffer, Farouc A.; Ntziachristos, Vasilis

    2011-03-01

    Intravascular Near-Infrared Fluorescence (NIRF) imaging is a promising imaging modality to image vessel biology and high-risk plaques in vivo. We have developed a NIRF fiber optic catheter and have presented the ability to image atherosclerotic plaques in vivo, using appropriate NIR fluorescent probes. Our catheter consists of a 100/140 μm core/clad diameter housed in polyethylene tubing, emitting NIR laser light at a 90 degree angle compared to the fiber's axis. The system utilizes a rotational and a translational motor for true 2D imaging and operates in conjunction with a coaxial intravascular ultrasound (IVUS) device. IVUS datasets provide 3D images of the internal structure of arteries and are used in our system for anatomical mapping. Using the IVUS images, we are building an accurate hybrid fluorescence-IVUS data inversion scheme that takes into account photon propagation through the blood filled lumen. This hybrid imaging approach can then correct for the non-linear dependence of light intensity on the distance of the fluorescence region from the fiber tip, leading to quantitative imaging. The experimental and algorithmic developments will be presented and the effectiveness of the algorithm showcased with experimental results in both saline and blood-like preparations. The combined structural and molecular information obtained from these two imaging modalities are positioned to enable the accurate diagnosis of biologically high-risk atherosclerotic plaques in the coronary arteries that are responsible for heart attacks.

  8. 2D laser-collision induced fluorescence in low-pressure argon discharges

    SciTech Connect

    Barnat, E. V.; Weatherford, B. R.

    2015-09-25

    Development and application of laser-collision induced fluorescence (LCIF) diagnostic technique is presented for the use of interrogating argon plasma discharges. Key atomic states of argon utilized for the LCIF method are identified. A simplified two-state collisional radiative model is then used to establish scaling relations between the LCIF, electron density, and reduced electric fields (E/N). The procedure used to generate, detect and calibrate the LCIF in controlled plasma environments is discussed in detail. LCIF emanating from an argon discharge is then presented for electron densities spanning 109 e cm–3 to 1012 e cm–3 and reduced electric fields spanning 0.1 Td to 40 Td. Lastly, application of the LCIF technique for measuring the spatial distribution of both electron densities and reduced electric field is demonstrated.

  9. 2D laser-collision induced fluorescence in low-pressure argon discharges

    DOE PAGES

    Barnat, E. V.; Weatherford, B. R.

    2015-09-25

    Development and application of laser-collision induced fluorescence (LCIF) diagnostic technique is presented for the use of interrogating argon plasma discharges. Key atomic states of argon utilized for the LCIF method are identified. A simplified two-state collisional radiative model is then used to establish scaling relations between the LCIF, electron density, and reduced electric fields (E/N). The procedure used to generate, detect and calibrate the LCIF in controlled plasma environments is discussed in detail. LCIF emanating from an argon discharge is then presented for electron densities spanning 109 e cm–3 to 1012 e cm–3 and reduced electric fields spanning 0.1 Tdmore » to 40 Td. Lastly, application of the LCIF technique for measuring the spatial distribution of both electron densities and reduced electric field is demonstrated.« less

  10. Spatial Solitons in 2D Graded-Index Waveguides with Different Distributed Transverse Diffractions

    NASA Astrophysics Data System (ADS)

    Chen, Yi-Xiang

    2014-02-01

    We discuss the nonlinear Schrödinger equation with variable coefficients in 2D graded-index waveguides with different distributed transverse diffractions and obtain exact bright and dark soliton solutions. Based on these solutions, we mainly investigate the dynamical behaviors of solitons in three different diffraction decreasing waveguides with the hyperbolic, Gaussian and Logarithmic profiles. Results indicate that for the same parameters, the amplitude of bright solitons in the Logarithmic profile and the amplitude of dark solitons in the Gaussian profile are biggest respectively, and the amplitude in the hyperbolic profile is smallest, while the width of solitons has the opposite case.

  11. Interfractional trend analysis of dose differences based on 2D transit portal dosimetry

    NASA Astrophysics Data System (ADS)

    Persoon, L. C. G. G.; Nijsten, S. M. J. J. G.; Wilbrink, F. J.; Podesta, M.; Snaith, J. A. D.; Lustberg, T.; van Elmpt, W. J. C.; van Gils, F.; Verhaegen, F.

    2012-10-01

    Dose delivery of a radiotherapy treatment can be influenced by a number of factors. It has been demonstrated that the electronic portal imaging device (EPID) is valuable for transit portal dosimetry verification. Patient related dose differences can emerge at any time during treatment and can be categorized in two types: (1) systematic—appearing repeatedly, (2) random—appearing sporadically during treatment. The aim of this study is to investigate how systematic and random information appears in 2D transit dose distributions measured in the EPID plane over the entire course of a treatment and how this information can be used to examine interfractional trends, building toward a methodology to support adaptive radiotherapy. To create a trend overview of the interfractional changes in transit dose, the predicted portal dose for the different beams is compared to a measured portal dose using a γ evaluation. For each beam of the delivered fraction, information is extracted from the γ images to differentiate systematic from random dose delivery errors. From the systematic differences of a fraction for a projected anatomical structures, several metrics are extracted like percentage pixels with |γ| > 1. We demonstrate for four example cases the trends and dose difference causes which can be detected with this method. Two sample prostate cases show the occurrence of a random and systematic difference and identify the organ that causes the difference. In a lung cancer case a trend is shown of a rapidly diminishing atelectasis (lung fluid) during the course of treatment, which was detected with this trend analysis method. The final example is a breast cancer case where we show the influence of set-up differences on the 2D transit dose. A method is presented based on 2D portal transit dosimetry to record dose changes throughout the course of treatment, and to allow trend analysis of dose discrepancies. We show in example cases that this method can identify the causes of

  12. 2D:4D Asymmetry and Gender Differences in Academic Performance

    PubMed Central

    Nye, John V. C.; Androuschak, Gregory; Desierto, Desirée; Jones, Garett; Yudkevich, Maria

    2012-01-01

    Exposure to prenatal androgens affects both future behavior and life choices. However, there is still relatively limited evidence on its effects on academic performance. Moreover, the predicted effect of exposure to prenatal testosterone (T)–which is inversely correlated with the relative length of the second to fourth finger lengths (2D:4D)–would seem to have ambiguous effects on academic achievement since traits like aggressiveness or risk-taking are not uniformly positive for success in school. We provide the first evidence of a non-linear, quadratic, relationship between 2D:4D and academic achievement using samples from Moscow and Manila. We also find that there is a gender differentiated link between various measures of academic achievement and measured digit ratios. These effects are different depending on the field of study, choice of achievement measure, and use of the right hand or left digit ratios. The results seem to be asymmetric between Moscow and Manila where the right (left) hand generates inverted-U (U-shaped) curves in Moscow while the pattern for hands reverses in Manila. Drawing from unusually large and detailed samples of university students in two countries not studied in the digit literature, our work is the first to have a large cross country comparison that includes two groups with very different ethnic compositions. PMID:23056282

  13. 2D:4D asymmetry and gender differences in academic performance.

    PubMed

    Nye, John V C; Androuschak, Gregory; Desierto, Desirée; Jones, Garett; Yudkevich, Maria

    2012-01-01

    Exposure to prenatal androgens affects both future behavior and life choices. However, there is still relatively limited evidence on its effects on academic performance. Moreover, the predicted effect of exposure to prenatal testosterone (T)-which is inversely correlated with the relative length of the second to fourth finger lengths (2D:4D)-would seem to have ambiguous effects on academic achievement since traits like aggressiveness or risk-taking are not uniformly positive for success in school. We provide the first evidence of a non-linear, quadratic, relationship between 2D:4D and academic achievement using samples from Moscow and Manila. We also find that there is a gender differentiated link between various measures of academic achievement and measured digit ratios. These effects are different depending on the field of study, choice of achievement measure, and use of the right hand or left digit ratios. The results seem to be asymmetric between Moscow and Manila where the right (left) hand generates inverted-U (U-shaped) curves in Moscow while the pattern for hands reverses in Manila. Drawing from unusually large and detailed samples of university students in two countries not studied in the digit literature, our work is the first to have a large cross country comparison that includes two groups with very different ethnic compositions.

  14. 2D ion velocity distribution function measurements by laser-induced fluorescence above a radio-frequency biased silicon wafer

    NASA Astrophysics Data System (ADS)

    Moore, Nathaniel; Gekelman, Walter; Pribyl, Patrick; Zhang, Yiting; Kushner, Mark

    2012-10-01

    Ion dynamics have been measured in the sheath above a 30 cm diameter, 2.2 MHz-biased silicon wafer in a plasma processing etch tool using laser-induced fluorescence (LIF). The velocity distribution function of argon ions was measured at thousands of positions above and radially along the edge of the wafer by sending a planar laser sheet from a pulsed, tunable dye laser into the tool. The RF sheath is clearly resolved. The laser sheet entered the machine both parallel and perpendicular to the wafer in order to measure the distribution function for both parallel and perpendicular velocities/energies (0.4 eV < Emax<600 eV). The resulting fluorescence was recorded using a fast CCD camera, which provided spatial (0.4 mm) and temporal (30 ns) resolution. Data was taken at eight different phases of the 2.2 MHz cycle. The distribution functions were found to be spatially non-uniform near the edge of the wafer and the distribution of energies extremely phase-dependent. Several cm above the wafer the distribution is Maxwellian and independent of phase. Results are compared with simulations; for example, the experimental time-averaged ion energy distribution function compares favorably with a computer model carefully constructed to emulate the device.

  15. 2D ion velocity distribution function measurements by laser-induced fluorescence above a radio-frequency biased silicon wafer

    NASA Astrophysics Data System (ADS)

    Moore, Nathaniel; Gekelman, Walter; Pribyl, Patrick; Zhang, Yiting; Kushner, Mark

    2012-10-01

    Ion dynamics have been measured in the sheath above a 30 cm diameter, 2.2 MHz-biased silicon wafer in a plasma processing etch tool using laser-induced fluorescence (LIF). The velocity distribution function of argon ions was measured at thousands of positions above and radially along the edge of the wafer by sending a planar laser sheet from a pulsed, tunable dye laser into the tool. The RF sheath is clearly resolved. The laser sheet entered the machine both parallel and perpendicular to the wafer in order to measure the distribution function for both parallel and perpendicular velocities/energies (0.4 eV < Emax< 600 eV). The resulting fluorescence was recorded using a fast CCD camera, which provided spatial (0.4 mm) and temporal (30 ns) resolution. Data was taken at eight different phases of the 2.2 MHz cycle. The distribution functions were found to be spatially non-uniform near the edge of the wafer and the distribution of energies extremely phase-dependent. Several cm above the wafer the distribution is Maxwellian and independent of phase. Results are compared with simulations; for example, the experimental time-averaged ion energy distribution function compares favorably with a computer model carefully constructed to emulate the device.

  16. M2Di: Concise and efficient MATLAB 2-D Stokes solvers using the Finite Difference Method

    NASA Astrophysics Data System (ADS)

    Räss, Ludovic; Duretz, Thibault; Podladchikov, Yury Y.; Schmalholz, Stefan M.

    2017-02-01

    Recent development of many multiphysics modeling tools reflects the currently growing interest for studying coupled processes in Earth Sciences. The core of such tools should rely on fast and robust mechanical solvers. Here we provide M2Di, a set of routines for 2-D linear and power law incompressible viscous flow based on Finite Difference discretizations. The 2-D codes are written in a concise vectorized MATLAB fashion and can achieve a time to solution of 22 s for linear viscous flow on 10002 grid points using a standard personal computer. We provide application examples spanning from finely resolved crystal-melt dynamics, deformation of heterogeneous power law viscous fluids to instantaneous models of mantle flow in cylindrical coordinates. The routines are validated against analytical solution for linear viscous flow with highly variable viscosity and compared against analytical and numerical solutions of power law viscous folding and necking. In the power law case, both Picard and Newton iterations schemes are implemented. For linear Stokes flow and Picard linearization, the discretization results in symmetric positive-definite matrix operators on Cartesian grids with either regular or variable grid spacing allowing for an optimized solving procedure. For Newton linearization, the matrix operator is no longer symmetric and an adequate solving procedure is provided. The reported performance of linear and power law Stokes flow is finally analyzed in terms of wall time. All MATLAB codes are provided and can readily be used for educational as well as research purposes. The M2Di routines are available from Bitbucket and the University of Lausanne Scientific Computing Group website, and are also supplementary material to this article.

  17. Expression of green fluorescent protein in human foreskin fibroblasts for use in 2D and 3D culture models.

    PubMed

    Chao, Jie; Peña, Tiffany; Heimann, Dean G; Hansen, Chris; Doyle, David A; Yanala, Ujwal R; Guenther, Timothy M; Carlson, Mark A

    2014-01-01

    The availability of fibroblasts that express green fluorescent protein (GFP) would be of interest for the monitoring of cell growth, migration, contraction, and other processes within the fibroblast-populated collagen matrix and other culture systems. A plasmid lentiviral vector-GFP (pLV-GFP) was utilized for gene delivery to produce primary human foreskin fibroblasts (HFFs) that stably express GFP. Cell morphology, cell migration, and collagen contraction were compared between nontransduced HFFs and transduced GFP-HFFs; no differences were observed. Immunocytochemical staining showed no differences in cell morphology between nontransduced and GFP-HFFs in both two-dimensional and three-dimensional culture systems. Furthermore, there was no significant difference in cellular population growth within the collagen matrix populated with nontransduced vs. GFP-HFFs. Within the limits of our assays, we conclude that transduction of GFP into HFFs did not alter the observed properties of HFFs compared with nontransduced fibroblasts. The GFP-HFFs may represent a new tool for the convenient monitoring of living primary fibroblast processes in two-dimensional or three-dimensional culture.

  18. Full 2D observation of water surface elevation from SWOT under different flow conditions

    NASA Astrophysics Data System (ADS)

    Domeneghetti, Alessio; Schumann, Guy; Rui, Wei; Durand, Michael; Pavelsky, Tamlin

    2016-04-01

    The upcoming Surface Water and Ocean Topography (SWOT) satellite mission is a joint project of NASA, Centre National d'Etudes Spatiales (CNES, France), the Canadian Space Agency, and the Space Agency of the UK that will provide a first global, high-resolution observation of ocean and terrestrial water surface heights. Characterized by an observation swath of 120 km and an orbit repeat interval of about 21 days, SWOT will provide unprecedented bi-dimensional observations of rivers wider than 50-100 m. Despite many research activities that have investigated potential uses of remotely sensed data from SWOT, potentials and limitations of the spatial observations provided by the satellite mission for flood modeling still remain poorly understood and investigated. In this study we present a first analysis of the spatial observation of water surface elevation that is expected from SWOT for a 140 km reach of the middle-lower portion of the Po River, in Northern Italy. The river stretch is characterized by a main channel varying from 200-500 m in width and a floodplain that can be as wide as 5 km and that is delimited by a system of major embankments. The reconstruction of the hydraulic behavior of the Po River is performed by means of a quasi-2d model built with detailed topographic and bathymetric information (LiDAR, 2 m resolution), while the simulation of the spatial observation sensed by SWOT is performed with a SWOT simulator that mimics the satellite sensor characteristics. Referring to water surface elevations associated with different flow conditions (maximum, minimum and average flow reproduced by means of the quasi-2d numerical model) this work provides a first characterization of the spatial observations provided by SWOT and highlights the strengths and limitations of the expected products. By referring to a real river reach the analysis provides a credible example of the type of spatial observations that will be available after launch of SWOT and offers a first

  19. Binding of 7-methoxy-4-(aminomethyl)-coumarin to wild-type and W128F mutant cytochrome P450 2D6 studied by time-resolved fluorescence spectroscopy

    PubMed Central

    Stortelder, Aike; Keizers, Peter H. J.; Oostenbrink, Chris; De Graaf, Chris; De Kruijf, Petra; Vermeulen, Nico P. E.; Gooijer, Cees; Commandeur, Jan N. M.; Van Der Zwan, Gert

    2005-01-01

    Enzyme structure and dynamics may play a main role in substrate binding and the subsequent steps in the CYP (cytochrome P450) catalytic cycle. In the present study, changes in the structure of human CYP2D6 upon binding of the substrate are studied using steady-state and time-resolved fluorescence methods, focusing not only on the emission of the tryptophan residues, but also on emission of the substrate. As a substrate, MAMC [7-methoxy-4-(aminomethyl)-coumarin] was selected, a compound exhibiting native fluorescence. As well as the wild-type, the W128F (Trp128→Phe) mutant of CYP2D6 was studied. After binding, a variety of energy transfer possibilities exist, and molecular dynamics simulations were performed to calculate distances and relative orientations of donors and acceptors. Energy transfer from Trp128 to haem appeared to be important; its emission was related to the shortest of the three average tryptophan fluorescence lifetimes observed for CYP2D6. MAMC to haem energy transfer was very efficient as well: when bound in the active site, the emission of MAMC was fully quenched. Steady-state anisotropy revealed that besides the MAMC in the active site, another 2.4% of MAMC was bound outside of the active site to wild-type CYP2D6. The tryptophan residues in CYP2D6 appeared to be less accessible for the external quenchers iodide and acrylamide in presence of MAMC, indicating a tightening of the enzyme structure upon substrate binding. However, the changes in the overall enzyme structure were not very large, since the emission characteristics of the enzyme were not very different in the presence of MAMC. PMID:16190863

  20. Optimal implicit 2-D finite differences to model wave propagation in poroelastic media

    NASA Astrophysics Data System (ADS)

    Itzá, Reymundo; Iturrarán-Viveros, Ursula; Parra, Jorge O.

    2016-08-01

    Numerical modeling of seismic waves in heterogeneous porous reservoir rocks is an important tool for the interpretation of seismic surveys in reservoir engineering. We apply globally optimal implicit staggered-grid finite differences (FD) to model 2-D wave propagation in heterogeneous poroelastic media at a low-frequency range (<10 kHz). We validate the numerical solution by comparing it to an analytical-transient solution obtaining clear seismic wavefields including fast P and slow P and S waves (for a porous media saturated with fluid). The numerical dispersion and stability conditions are derived using von Neumann analysis, showing that over a wide range of porous materials the Courant condition governs the stability and this optimal implicit scheme improves the stability of explicit schemes. High-order explicit FD can be replaced by some lower order optimal implicit FD so computational cost will not be as expensive while maintaining the accuracy. Here, we compute weights for the optimal implicit FD scheme to attain an accuracy of γ = 10-8. The implicit spatial differentiation involves solving tridiagonal linear systems of equations through Thomas' algorithm.

  1. Comparison of different sets of array configurations for multichannel 2D ERT acquisition

    NASA Astrophysics Data System (ADS)

    Martorana, R.; Capizzi, P.; D'Alessandro, A.; Luzio, D.

    2017-02-01

    Traditional electrode arrays such Wenner-Schlumberger or dipole-dipole are still widely used thanks to their well-known properties but the array configurations are generally not optimized for multi-channel resistivity measures. Synthetic datasets relating to four different arrays, dipole-dipole (DD), pole-dipole (PD), Wenner-Schlumberger (WS) and a modified version of multiple gradient (MG), have been made for a systematic comparison between 2D resistivity models and their inverted images. Different sets of array configurations generated from simple combinations of geometric parameters (potential dipole lengths and dipole separation factors) were tested with synthetic and field data sets, even considering the influence of errors and the acquisition velocity. The purpose is to establish array configurations capable to provide reliable results but, at the same time, not involving excessive survey costs, even linked to the acquiring time and therefore to the number of current dipoles used. For DD, PD and WS arrays a progression of different datasets were considered increasing the number of current dipoles trying to get about the same amount of measures. A multi-coverage MG array configuration is proposed by increasing the lateral coverage and so the number of current dipoles. Noise simulating errors both on the electrode positions and on the electric potential was added. The array configurations have been tested on field data acquired in the landfill site of Bellolampo (Palermo, Italy), to detect and locate the leachate plumes and to identify the HDPE bottom of the landfill. The inversion results were compared using a quantitative analysis of data misfit, relative model resolution and model misfit. The results show that the trends of the first two parameters are linked on the array configuration and that a cumulative analysis of these parameters can help to choose the best array configuration in order to obtain a good resolution and reliability of a survey, according

  2. Characterization and quantification of humic substances 2D-Fluorescence by usage of extended size exclusion chromatography.

    PubMed

    Wagner, Martin; Schmidt, Wido; Imhof, Lutz; Grübel, Anika; Jähn, Camilla; Georgi, Denise; Petzoldt, Heike

    2016-04-15

    In this article, two methods for in-depth analysis of humic substances fluorescence are presented. The first one allows the combined analysis of fluorescence excitation-emission matrix (EEM) with chromatography technique. The main issue is the coupling of size exclusion chromatography (SEC) with spectroscopy by the use of an absorption and a fluorescence spectrometer as additional detectors. These allow a detailed characterization of humic substances depending on their molecular size, concentration and optical properties. For the evaluation of the resulting complex data, a model based on non-negative matrix factorization, which is also presented in this article, was developed. From the results of the examined humic substances standards, the second method was developed. It allows the characterization and quantification of humic substances fluorescence of a natural water sample solely on the basis of an excitation-emission matrix. The validation of the model is carried out within the framework of extensive analysis of real water samples.

  3. Crystal structures and fluorescence properties of two 2D MnII/CdII trimellitic complexes containing terpyridine

    NASA Astrophysics Data System (ADS)

    Ren, Yixia; Chai, Hongmei; Hou, Xiangyang; Wang, Jijiang; Fu, Feng

    2015-12-01

    Hydrothermal reactions of manganese (II)/cadmium(II) salts with 1,2,4-trimellitic acid (H3tma) and 2,2‧:6‧,2-terpyridine (tpy) result in two novel complexes formulated with [M(Htma)(tpy)]·H2O (M = Mn(1) and Cd(2)). X-ray diffraction structural analyses of two complexes reveal they are isomorphic except for the different center metal ions and crystallize in the monoclinic crystal system of P(2)/n space group. The metal ion lies in a six-coordinated distorted octahedral environment coordinated with three Htma2- anions and one tpy ligand. There is an infinite two-dimensional rhombic network based on the metallic dimmers and Htma2- anions with the tpy ligands in void. Furthermore, the tpy ligands from the adjacent network weakly interact each other by π⋯π packing interactions into 3D supramolecular structure. The fluorescence properties could be assigned to the π - π* transition of organic ligands.

  4. 2D/3D cryo x-ray fluorescence imaging at the bionanoprobe at the advanced photon source

    SciTech Connect

    Chen, S. Vine, D. J.; Lai, B.; Paunesku, T.; Yuan, Y.; Woloschak, G. E.; Deng, J.; Jin, Q.; Hong, Y. P.; Flachenecker, C.; Hornberger, B.; Brister, K.; Jacobsen, C.; Vogt, S.

    2016-01-28

    Trace elements, particularly metals, play very important roles in biological systems. Synchrotron-based hard X-ray fluorescence microscopy offers the most suitable capabilities to quantitatively study trace metals in thick biological samples, such as whole cells and tissues. In this manuscript, we have demonstrated X-ray fluorescence imaging of frozen-hydrated whole cells using the recent developed Bionanoprobe (BNP). The BNP provides spatial resolution down to 30 nm and cryogenic capabilities. Frozen-hydrated biological cells have been directly examined on a sub-cellular level at liquid nitrogen temperatures with minimal sample preparation.

  5. 2D warp-and-woof interwoven networks constructed by helical chains with different chirality.

    PubMed

    Feng, Yuhua; Guo, Yang; OuYang, Yan; Liu, Zhanquan; Liao, Daizheng; Cheng, Peng; Yan, Shiping; Jiang, Zonghui

    2007-09-21

    Two unprecedented 2D entangled layers of warp-and-woof threads interwoven by left- and right-handed helical chains, {[Mn(salen)Au(CN)2]4(H2O)}n (salen = N,N'-ethylenebis(salicylideneaminato)) and {Mn(acacen)Ag(CN)2}n (acacen = N,N'-ethylenebis(acetylacetonylideneiminate)) 2, have been synthesized and characterized.

  6. Mean cell size and collagen orientation from 2D Fourier analysis on confocal laser scanning microscopy and two-photon fluorescence microscopy on human skin in vivo

    NASA Astrophysics Data System (ADS)

    Lucassen, Gerald W.; Bakker, Bernard L.; Neerken, Sieglinde; Hendriks, Rob F. M.

    2003-07-01

    We present results from 2D Fourier analysis on 3D stacks of images obtained by confocal laser scanning reflectance microscopy (CLSM) and two-photon fluorescence microscopy (2PM) on human skin in vivo. CLSM images were obtained with a modified commercial system (Vivascope1000, Lucid Inc, excitation wavelength 830 nm) equipped with a piezo-focusing element (350 μm range) for depth positioning of the objective lens. 2PM was performed with a specially designed set-up with excitation wavelength 730 nm. Mean cell size in the epidermal layer and structural orientation in the dermal layer have been determined as a function of depth by 2D Fourier analysis. Fourier analysis on microscopic images enables automatic non-invasive quantitative structural analysis (mean cell size and orientation) of living human skin.

  7. Electron momentum distribution and singlet-singlet annihilation in the organic anthracene molecular crystals using positron 2D-ACAR and fluorescence spectroscopy.

    PubMed

    Selvakumar, Sellaiyan; Sivaji, Krishnan; Arulchakkaravarthi, Arjunan; Sankar, Sambasivam

    2014-08-14

    We present the mapping of electron momentum distribution (EMD) in a single crystal of anthracene by two-dimensional angular correlation of positron annihilation radiation (2D-ACAR). The projected EMD is explained on the basis of the crystallographic features of the material. The EMD spectra provide information about the positron states and their behavior and also about the hindrance of the positronium (Ps) formation in this material. The EMD has exhibited evidence for the absence of free volume defects. The characteristic EMD features regarding the delocalized electronic states are explained. Further, scintillation characteristics such as fluorescence and time-correlated single photon counting have also been studied. The emission peaks are attributed to vibrational bands of fluorescence emission from the singlet excitons and lifetime components are observed to be due to singlet fission and the singlet-singlet excitons annihilation.

  8. Protein quantification and its tolerance for different interfering reagents using the BCA-method with regard to 2D SDS PAGE.

    PubMed

    Krieg, Rene C; Dong, Yan; Schwamborn, Kristina; Knuechel, Ruth

    2005-10-31

    Measuring the protein content of a sample is a mandatory and frequently practiced procedure in the lab. Although the procedure is quite simple and convenient to perform with commercially available kits, incompatible reagents in the lysate can cause problems in the quality of measurement. Unfortunately these reagents are cornerstones of high efficiency lysing buffers, e.g. high amounts of urea or beta-mercaptoethanol. In this study we addressed the tolerance of the well-known BCA-assay (bicinchoninic acid) to various reagents in different concentrations, with special regard to a subsequent 2D-gelelectrophoresis. As a result, the kit is incompatible with the recipes of regular 2D-buffers. Also, when mixing two different reagents interfering effects will occur in a non-predictable way. Therefore we established a new method to quantify protein content in lysates ready for 2D-gelelectrophoresis: by mixing an aliquot with SDS, an equilibration is performed to that the sample can be run on a regular 1D SDS PAGE. Image analysis following fluorescence staining (SYPRO Ruby) reveals the absolute protein content in comparison to a BSA dilution curve processed accordingly.

  9. Nuclear Resonance Fluorescence Using Different Photon Sources

    SciTech Connect

    Warren, Glen A.; Caggiano, Joseph A.; Ahmed, Mohammad; Bertozzi, William; Hunt, Alan W.; Johnson, James; Jones, James L.; Korbly, Steve; Reedy, Edward; Seipel, Heather; Stave, Sean; Watson, Scott; Weller, Henry

    2008-11-14

    Abstract–Nuclear resonance fluorescence (NRF) is a photon-based active interrogation approach that provides isotope-specific signatures that can be used to detect and characterize samples. As NRF systems are designed to address specific appli¬cations, an obvious first question to address is the type of photon source to be employed for the application. Our collaboration has conducted a series of NRF measurements using different photon sources to begin to examine this issue. The measurements were designed to be as similar as possible to facilitate a straightforward comparison of the different sources. Measurements were conducted with a high-duty factor electron accelerator using bremsstrahlung photons, with a pulsed linear accelerator using bremsstrahlung photons, and with a narrow bandwidth photon source using Compton backscattered photons. We present our observations on the advantages and disadvantages of each photon source type. Issues such as signal rate, the signal-to-noise ratio, and absorbed dose are discussed.

  10. On the uniqueness of quantitative DNA difference descriptors in 2D graphical representation models

    NASA Astrophysics Data System (ADS)

    Nandy, A.; Nandy, P.

    2003-01-01

    The rapid growth in additions to databases of DNA primary sequence data have led to searches for methods to numerically characterize these data and help in fast identification and retrieval of relevant sequences. The DNA descriptors derived from the 2D graphical representation technique have already been proposed to index chemical toxicity and single nucleotide polymorphic (SNP) genes but the inherent degeneracies in this representation have given rise to doubts about their suitability. We prove in this paper that such degeneracies will exist only in very restricted cases and that the method can be relied upon to provide unique descriptors for, in particular, the SNP genes and several other classes of DNA sequences.

  11. Differences in the Toxicological Potential of 2D versus Aggregated Molybdenum Disulfide in the Lung.

    PubMed

    Wang, Xiang; Mansukhani, Nikhita D; Guiney, Linda M; Ji, Zhaoxia; Chang, Chong Hyun; Wang, Meiying; Liao, Yu-Pei; Song, Tze-Bin; Sun, Bingbing; Li, Ruibin; Xia, Tian; Hersam, Mark C; Nel, André E

    2015-10-01

    2D molybdenum disulfide (MoS2 ) has distinct optical and electronic properties compared to aggregated MoS2 , enabling wide use of these materials for electronic and biomedical applications. However, the hazard potential of MoS2 has not been studied extensively. Here, a comprehensive analysis of the pulmonary hazard potential of three aqueous suspended forms of MoS2 -aggregated MoS2 (Agg-MoS2 ), MoS2 exfoliated by lithiation (Lit-MoS2 ), and MoS2 dispersed by Pluronic F87 (PF87-MoS2 )-is presented. No cytotoxicity is detected in THP-1 and BEAS-2B cell lines. However, Agg-MoS2 induces strong proinflammatory and profibrogenic responses in vitro. In contrast, Lit- and PF87-MoS2 have little or no effect. In an acute toxicity study in mice, Agg-MoS2 induces acute lung inflammation, while Lit-MoS2 and PF87-MoS2 have little or no effect. In a subchronic study, there is no evidence of pulmonary fibrosis in response to all forms of MoS2 . These data suggest that exfoliation attenuates the toxicity of Agg-MoS2 , which is an important consideration toward the safety evaluation and use of nanoscale MoS2 materials for industrial and biological applications.

  12. 2-D difference gel electrophoresis approach to assess protein expression profiles in Bathymodiolus azoricus from Mid-Atlantic Ridge hydrothermal vents.

    PubMed

    Company, Rui; Antúnez, Oreto; Bebianno, Maria João; Cajaraville, Miren P; Torreblanca, Amparo

    2011-11-18

    Hydrothermal vent mussels Bathymodiolus azoricus are naturally exposed to toxic chemical species originated directly from vent chimneys. The amount of toxic elements varies significantly among vent sites along the Mid-Atlantic Ridge and B. azoricus must be able to adapt to changes in hydrothermal fluid composition, temperature and pressure. The aim of this work was to study changes in the proteome in the "gill-bacteria complex" of mussels B. azoricus from three hydrothermal vent sites with distinct environmental characteristics using 2-D Fluorescence Difference Gel Electrophoresis (2-D DIGE). Results showed that 31 proteins had different expression profiles among vent sites and both cluster and principal component analysis confirm a clear separation of mussels between sites. This suggests the existence of specific parameters grouping individuals from the same hydrothermal site. Protein spots of the more abundant differentially expressed proteins were excised, digested with trypsin and identified by mass spectrometry. All identified proteins (actin, ubiquinone, S-adenosylhomocysteine hydrolase, cysteine peptidases, chaperonin and catalase) have been related previously with oxidative stress conditions and are known to be affected by ROS inducing stressors, including metals. Results point out to specific adaptations at the proteome level of B. azoricus depending on the level of toxicants present in their environment.

  13. High Order Finite Difference Methods with Subcell Resolution for 2D Detonation Waves

    NASA Technical Reports Server (NTRS)

    Wang, W.; Shu, C. W.; Yee, H. C.; Sjogreen, B.

    2012-01-01

    In simulating hyperbolic conservation laws in conjunction with an inhomogeneous stiff source term, if the solution is discontinuous, spurious numerical results may be produced due to different time scales of the transport part and the source term. This numerical issue often arises in combustion and high speed chemical reacting flows.

  14. Digit ratio (2D:4D), sex differences, allometry, and finger length of 12-30-year olds: evidence from the British Broadcasting Corporation (BBC) Internet study.

    PubMed

    Manning, John T

    2010-01-01

    Many studies have reported digit ratio (2D:4D) to be sexually dimorphic, (males lower 2D:4D than females). However, Kratochvíl and Flegr ([2009]: Biol Lett 5:643-646) have suggested that 2D regressed on 4D has an allometric regression line with nonzero Y-intercept that is shared by males and females. Thus, 2D is shorter than expected when 4D is long, and males have lower 2D:4D than females because they have longer fingers. In this study, it is shown that this suggestion may be incorrect because sex differences in slope were not considered. Participants were recruited in an Internet study and had an age range of 12-30 years. The expected sex difference in 2D:4D was found, and the regression of 2D on 4D showed a significant sex difference in slope (males lower than females). A comparison of 10 age groups (12 years, 13 years..., 21-30 years) showed that sexual dimorphism for fingers was age dependent, varying from monomorphic to very dimorphic. Changes in sexual dimorphism of 2D:4D were much less marked, but there was a significant reduction in mean 2D:4D with age. The tendency for slopes of 2D regressed on 4D to be lower in males compared with females was significant in eight age groups. Sex difference in 2D:4D varied across the age groups and was positively related to the magnitude of the difference in female and male slopes. In contrast to the report of Kratochvíl and Flegr, it was found that the regression of 2D on 4D showed sex differences in slope, and such differences gave rise to the sexual dimorphism in 2D:4D.

  15. 2D-PAGE protein analysis of dinoflagellate Alexandrium minutum based on three different temperatures

    NASA Astrophysics Data System (ADS)

    Latib, Norhidayu Abdul; Norshaha, Safida Anira; Usup, Gires; Yusof, Nurul Yuziana Mohd

    2015-09-01

    Harmful algae bloom or red tide seems to be considered as threat to ecosystem, especially to human consumption because of the production of neurotoxin by dinoflagellates species such as Alexandrium minutum which can lead to paralytic shellfish poisoning. The aim of this study is to determine the most suitable method for protein extraction of A. minutum followed by determination of differential protein expression of A. minutum on three different temperatures (15°C, 26°C and 31.5°C). After the optimization, the protein extract was subjected to two-dimensional polyacrylamide gel electrophoresis (2-DE) to compare the intensity and distribution of the protein spots. Based on quantitative and qualitative protein assessment, use of Trizol reagent is the most suitable method to extract protein from A. minutum. 2-DE analysis of the samples results in different distribution and intensity of the protein spots were compared between 15°C, 26°C and 31.5°C.

  16. Two-Dimensional Fluorescence Difference Spectroscopy to Characterize Nanoparticles and their Interactions.

    PubMed

    Hurst, Miranda N; DeLong, Robert K

    2016-09-14

    Two dimensional fluorescence difference spectroscopy (2D FDS) detects nanoparticle interactions following surface functionalization and biomolecule loading by generating a spectral signature of the fluorescent intensity per excitation and emission wavelengths. Comparing metal oxide nanoparticles revealed a unique spectral signature per material composition. 2D FDS showed to be sensitive to changes in surface properties between ZnO NPs synthesized by different methods. ZnO NP loaded with glycol chitosan, polyacrylic acid (PAA), or methoxy polyethylene glycol (mPEG) exhibited a distinct spectral signature shift. ZnO NP loaded with Torula Yeast RNA (TYRNA)(640 nm), polyinosinic: polycytidylic acid (pIC)(680 nm), or splice switching oligonucleotide (SSO)(650 nm) each revealed a shift in emission. Ras-Binding domain (RBD) at three concentrations (25, 37.5, 50 μg/mL) showed that fluorescent intensity was inversely related to the concentration of protein loaded. These data support 2D FDS as a novel technique in identifying nanoparticles and their surface interactions as a quality assurance tool.

  17. Two-Dimensional Fluorescence Difference Spectroscopy to Characterize Nanoparticles and their Interactions

    PubMed Central

    Hurst, Miranda N.; DeLong, Robert K.

    2016-01-01

    Two dimensional fluorescence difference spectroscopy (2D FDS) detects nanoparticle interactions following surface functionalization and biomolecule loading by generating a spectral signature of the fluorescent intensity per excitation and emission wavelengths. Comparing metal oxide nanoparticles revealed a unique spectral signature per material composition. 2D FDS showed to be sensitive to changes in surface properties between ZnO NPs synthesized by different methods. ZnO NP loaded with glycol chitosan, polyacrylic acid (PAA), or methoxy polyethylene glycol (mPEG) exhibited a distinct spectral signature shift. ZnO NP loaded with Torula Yeast RNA (TYRNA)(640 nm), polyinosinic: polycytidylic acid (pIC)(680 nm), or splice switching oligonucleotide (SSO)(650 nm) each revealed a shift in emission. Ras-Binding domain (RBD) at three concentrations (25, 37.5, 50 μg/mL) showed that fluorescent intensity was inversely related to the concentration of protein loaded. These data support 2D FDS as a novel technique in identifying nanoparticles and their surface interactions as a quality assurance tool. PMID:27624316

  18. Two-Dimensional Fluorescence Difference Spectroscopy to Characterize Nanoparticles and their Interactions

    NASA Astrophysics Data System (ADS)

    Hurst, Miranda N.; Delong, Robert K.

    2016-09-01

    Two dimensional fluorescence difference spectroscopy (2D FDS) detects nanoparticle interactions following surface functionalization and biomolecule loading by generating a spectral signature of the fluorescent intensity per excitation and emission wavelengths. Comparing metal oxide nanoparticles revealed a unique spectral signature per material composition. 2D FDS showed to be sensitive to changes in surface properties between ZnO NPs synthesized by different methods. ZnO NP loaded with glycol chitosan, polyacrylic acid (PAA), or methoxy polyethylene glycol (mPEG) exhibited a distinct spectral signature shift. ZnO NP loaded with Torula Yeast RNA (TYRNA)(640 nm), polyinosinic: polycytidylic acid (pIC)(680 nm), or splice switching oligonucleotide (SSO)(650 nm) each revealed a shift in emission. Ras-Binding domain (RBD) at three concentrations (25, 37.5, 50 μg/mL) showed that fluorescent intensity was inversely related to the concentration of protein loaded. These data support 2D FDS as a novel technique in identifying nanoparticles and their surface interactions as a quality assurance tool.

  19. An energy stable, hexagonal finite difference scheme for the 2D phase field crystal amplitude equations

    NASA Astrophysics Data System (ADS)

    Guan, Zhen; Heinonen, Vili; Lowengrub, John; Wang, Cheng; Wise, Steven M.

    2016-09-01

    In this paper we construct an energy stable finite difference scheme for the amplitude expansion equations for the two-dimensional phase field crystal (PFC) model. The equations are formulated in a periodic hexagonal domain with respect to the reciprocal lattice vectors to achieve a provably unconditionally energy stable and solvable scheme. To our knowledge, this is the first such energy stable scheme for the PFC amplitude equations. The convexity of each part in the amplitude equations is analyzed, in both the semi-discrete and fully-discrete cases. Energy stability is based on a careful convexity analysis for the energy (in both the spatially continuous and discrete cases). As a result, unique solvability and unconditional energy stability are available for the resulting scheme. Moreover, we show that the scheme is point-wise stable for any time and space step sizes. An efficient multigrid solver is devised to solve the scheme, and a few numerical experiments are presented, including grain rotation and shrinkage and grain growth studies, as examples of the strength and robustness of the proposed scheme and solver.

  20. A Pedestrian Detection Scheme Using a Coherent Phase Difference Method Based on 2D Range-Doppler FMCW Radar.

    PubMed

    Hyun, Eugin; Jin, Young-Seok; Lee, Jong-Hun

    2016-01-20

    For an automotive pedestrian detection radar system, fast-ramp based 2D range-Doppler Frequency Modulated Continuous Wave (FMCW) radar is effective for distinguishing between moving targets and unwanted clutter. However, when a weak moving target such as a pedestrian exists together with strong clutter, the pedestrian may be masked by the side-lobe of the clutter even though they are notably separated in the Doppler dimension. To prevent this problem, one popular solution is the use of a windowing scheme with a weighting function. However, this method leads to a spread spectrum, so the pedestrian with weak signal power and slow Doppler may also be masked by the main-lobe of clutter. With a fast-ramp based FMCW radar, if the target is moving, the complex spectrum of the range- Fast Fourier Transform (FFT) is changed with a constant phase difference over ramps. In contrast, the clutter exhibits constant phase irrespective of the ramps. Based on this fact, in this paper we propose a pedestrian detection for highly cluttered environments using a coherent phase difference method. By detecting the coherent phase difference from the complex spectrum of the range-FFT, we first extract the range profile of the moving pedestrians. Then, through the Doppler FFT, we obtain the 2D range-Doppler map for only the pedestrian. To test the proposed detection scheme, we have developed a real-time data logging system with a 24 GHz FMCW transceiver. In laboratory tests, we verified that the signal processing results from the proposed method were much better than those expected from the conventional 2D FFT-based detection method.

  1. A Pedestrian Detection Scheme Using a Coherent Phase Difference Method Based on 2D Range-Doppler FMCW Radar

    PubMed Central

    Hyun, Eugin; Jin, Young-Seok; Lee, Jong-Hun

    2016-01-01

    For an automotive pedestrian detection radar system, fast-ramp based 2D range-Doppler Frequency Modulated Continuous Wave (FMCW) radar is effective for distinguishing between moving targets and unwanted clutter. However, when a weak moving target such as a pedestrian exists together with strong clutter, the pedestrian may be masked by the side-lobe of the clutter even though they are notably separated in the Doppler dimension. To prevent this problem, one popular solution is the use of a windowing scheme with a weighting function. However, this method leads to a spread spectrum, so the pedestrian with weak signal power and slow Doppler may also be masked by the main-lobe of clutter. With a fast-ramp based FMCW radar, if the target is moving, the complex spectrum of the range- Fast Fourier Transform (FFT) is changed with a constant phase difference over ramps. In contrast, the clutter exhibits constant phase irrespective of the ramps. Based on this fact, in this paper we propose a pedestrian detection for highly cluttered environments using a coherent phase difference method. By detecting the coherent phase difference from the complex spectrum of the range-FFT, we first extract the range profile of the moving pedestrians. Then, through the Doppler FFT, we obtain the 2D range-Doppler map for only the pedestrian. To test the proposed detection scheme, we have developed a real-time data logging system with a 24 GHz FMCW transceiver. In laboratory tests, we verified that the signal processing results from the proposed method were much better than those expected from the conventional 2D FFT-based detection method. PMID:26805835

  2. Verification of a non-hydrostatic dynamical core using horizontally spectral element vertically finite difference method: 2-D aspects

    NASA Astrophysics Data System (ADS)

    Choi, S.-J.; Giraldo, F. X.; Kim, J.; Shin, S.

    2014-06-01

    The non-hydrostatic (NH) compressible Euler equations of dry atmosphere are solved in a simplified two dimensional (2-D) slice framework employing a spectral element method (SEM) for the horizontal discretization and a finite difference method (FDM) for the vertical discretization. The SEM uses high-order nodal basis functions associated with Lagrange polynomials based on Gauss-Lobatto-Legendre (GLL) quadrature points. The FDM employs a third-order upwind biased scheme for the vertical flux terms and a centered finite difference scheme for the vertical derivative terms and quadrature. The Euler equations used here are in a flux form based on the hydrostatic pressure vertical coordinate, which are the same as those used in the Weather Research and Forecasting (WRF) model, but a hybrid sigma-pressure vertical coordinate is implemented in this model. We verified the model by conducting widely used standard benchmark tests: the inertia-gravity wave, rising thermal bubble, density current wave, and linear hydrostatic mountain wave. The results from those tests demonstrate that the horizontally spectral element vertically finite difference model is accurate and robust. By using the 2-D slice model, we effectively show that the combined spatial discretization method of the spectral element and finite difference method in the horizontal and vertical directions, respectively, offers a viable method for the development of a NH dynamical core.

  3. Assessing HYDRUS-2D model to estimate soil water contents and olive tree transpiration fluxes under different water distribution systems

    NASA Astrophysics Data System (ADS)

    Autovino, Dario; Negm, Amro; Rallo, Giovanni; Provenzano, Giuseppe

    2016-04-01

    In Mediterranean countries characterized by limited water resources for agricultural and societal sectors, irrigation management plays a major role to improve water use efficiency at farm scale, mainly where irrigation systems are correctly designed to guarantee a suitable application efficiency and the uniform water distribution throughout the field. In the last two decades, physically-based agro-hydrological models have been developed to simulate mass and energy exchange processes in the soil-plant-atmosphere (SPA) system. Mechanistic models like HYDRUS 2D/3D (Šimunek et al., 2011) have been proposed to simulate all the components of water balance, including actual crop transpiration fluxes estimated according to a soil potential-dependent sink term. Even though the suitability of these models to simulate the temporal dynamics of soil and crop water status has been reported in the literature for different horticultural crops, a few researches have been considering arboreal crops where the higher gradients of root water uptake are the combination between the localized irrigation supply and the three dimensional root system distribution. The main objective of the paper was to assess the performance of HYDRUS-2D model to evaluate soil water contents and transpiration fluxes of an olive orchard irrigated with two different water distribution systems. Experiments were carried out in Castelvetrano (Sicily) during irrigation seasons 2011 and 2012, in a commercial farm specialized in the production of table olives (Olea europaea L., var. Nocellara del Belice), representing the typical variety of the surrounding area. During the first season, irrigation water was provided by a single lateral placed along the plant row with four emitters per plant (ordinary irrigation), whereas during the second season a grid of emitters laid on the soil was installed in order to irrigate the whole soil surface around the selected trees. The model performance was assessed based on the

  4. Analysis of the high Reynolds number 2D tests on a wind turbine airfoil performed at two different wind tunnels

    NASA Astrophysics Data System (ADS)

    Pires, O.; Munduate, X.; Ceyhan, O.; Jacobs, M.; Madsen, J.; Schepers, J. G.

    2016-09-01

    2D wind tunnel tests at high Reynolds numbers have been done within the EU FP7 AVATAR project (Advanced Aerodynamic Tools of lArge Rotors) on the DU00-W-212 airfoil and at two different test facilities: the DNW High Pressure Wind Tunnel in Gottingen (HDG) and the LM Wind Power in-house wind tunnel. Two conditions of Reynolds numbers have been performed in both tests: 3 and 6 million. The Mach number and turbulence intensity values are similar in both wind tunnels at the 3 million Reynolds number test, while they are significantly different at 6 million Reynolds number. The paper presents a comparison of the data obtained from the two wind tunnels, showing good repeatability at 3 million Reynolds number and differences at 6 million Reynolds number that are consistent with the different Mach number and turbulence intensity values.

  5. Analysis of Leishmania chagasi by 2-D difference gel electrophoresis (2-D DIGE) and immunoproteomic: identification of novel candidate antigens for diagnostic tests and vaccine.

    PubMed

    Costa, Míriam M; Andrade, Hélida M; Bartholomeu, Daniella C; Freitas, Leandro M; Pires, Simone F; Chapeaurouge, Alexander D; Perales, Jonas; Ferreira, André T; Giusta, Mário S; Melo, Maria N; Gazzinelli, Ricardo T

    2011-05-06

    Identification of novel antigens is essential for developing new diagnostic tests and vaccines. We used DIGE to compare protein expression in amastigote and promastigote forms of Leishmania chagasi. Nine hundred amastigote and promastigote spots were visualized. Five amastigote-specific, 25 promastigote-specific, and 10 proteins shared by the two parasite stages were identified. Furthermore, 41 proteins were identified in the Western blot employing 2-DE and sera from infected dogs. From these proteins, 3 and 38 were reactive with IgM and total IgG, respectively. The proteins recognized by total IgG presented different patterns in terms of their recognition by IgG1 and/or IgG2 isotypes. All the proteins selected by Western blot were mapped for B-cell epitopes. One hundred and eighty peptides were submitted to SPOT synthesis and immunoassay. A total of 25 peptides were shown of interest for serodiagnosis to visceral leishmaniasis. In addition, all proteins identified in this study were mapped for T cell epitopes by using the NetCTL software, and candidates for vaccine development were selected. Therefore, a large-scale screening of L. chagasi proteome was performed to identify new B and T cell epitopes with potential use for developing diagnostic tests and vaccines.

  6. Analysis of Telomere-Homologous DNA with Different Conformations Using 2D Agarose Electrophoresis and In-Gel Hybridization.

    PubMed

    Zhang, Zepeng; Hu, Qian; Zhao, Yong

    2017-01-01

    In mammalian cells, in addition to double-stranded telomeric DNA at chromosome ends, extra telomere-homologous DNA is present that adopts different conformations, including single-stranded G- or C-rich DNA, extrachromosomal circular DNA (T-circle), and telomeric complex (T-complex) with an unidentified structure. The formation of such telomere-homologous DNA is closely related to telomeric DNA metabolism and chromosome end protection by telomeres. Conventional agarose gel electrophoresis is unable to separate DNA based on conformation. Here, we introduce the method of two-dimensional (2D) agarose electrophoresis in combination with in-gel native/denatured hybridization to determine different conformations formed by telomere-homologous DNA.

  7. Breaking the Diffraction Barrier Using Fluorescence Emission Difference Microscopy

    PubMed Central

    Kuang, Cuifang; Li, Shuai; Liu, Wei; Hao, Xiang; Gu, Zhaotai; Wang, Yifan; Ge, Jianhong; Li, Haifeng; Liu, Xu

    2013-01-01

    We propose a novel physical mechanism for breaking the diffraction barrier in the far field. Termed fluorescence emission difference microscopy (FED), our approach is based on the intensity difference between two differently acquired images. When fluorescence saturation is applied, the resolving ability of FED can be further enhanced. A detailed theoretical analysis and a series of simulation tests are performed. The validity of FED in practical use is demonstrated by experiments on fluorescent nanoparticles and biological cells in which a spatial resolution of <λ/4 is achieved. Featuring the potential to realize a high imaging speed, this approach may be widely applied in nanoscale investigations. PMID:23486546

  8. SWAT and River-2D Modelling of Pinder River for Analysing Snow Trout Habitat under Different Flow Abstraction Scenarios

    NASA Astrophysics Data System (ADS)

    Nale, J. P.; Gosain, A. K.; Khosa, R.

    2015-12-01

    Pinder River, one of major headstreams of River Ganga, originates in Pindari Glaciers of Kumaon Himalayas and after passing through rugged gorges meets Alaknanda at Karanprayag forming one of the five celestial confluences of Upper Ganga region. While other sub-basins of Upper Ganga are facing severe ecological losses, Pinder basin is still in its virginal state and is well known for its beautiful valleys besides being host to unique and rare biodiversity. A proposed 252 MW run-of-river hydroelectric project at Devsari on this river has been a major concern on account of its perceived potential for egregious environmental and social impacts. In this context, the study presented tries to analyse the expected changes in aquatic habitat conditions after this project is operational (with different operation policies). SWAT hydrological modelling platform has been used to derive stream flow simulations under various scenarios ranging from the present to the likely future conditions. To analyse the habitat conditions, a two dimensional hydraulic-habitat model 'River-2D', a module of iRIC software, is used. Snow trout has been identified as the target keystone species and its habitat preferences, in the form of flow depths, flow velocity and substrate condition, are obtained from diverse sources of related literature and are provided as Habitat Suitability Indices to River-2D. Bed morphology constitutes an important River-2D input and has been obtained, for the designated 1 km long study reach of Pinder upto Karanprayag, from a combination of actual field observations and supplemented by SRTM 1 Arc-Second Global digital elevation data. Monthly Weighted Usable Area for three different life stages (Spawning, Juvenile and Adult) of Snow Trout are obtained corresponding to seven different flow discharges ranging from 10 cumec to 1000 cumec. Comparing the present and proposed future river flow conditions obtained from SWAT modelling, losses in Weighted Usable Area, for the

  9. SU-E-T-422: Correlation Between 2D Passing Rates and 3D Dose Differences for Pretreatment VMAT QA

    SciTech Connect

    Jin, X; Xie, C

    2014-06-01

    Purpose: Volumetric modulated arc therapy (VMAT) quality assurance (QA) is typically using QA methods and action levels taken from fixedbeam intensity-modulated radiotherapy (IMRT) QA methods. However, recent studies demonstrated that there is no correlation between the percent gamma passing rate (%GP) and the magnitude of dose discrepancy between the planned dose and the actual delivered dose for IMRT. The purpose of this study is to investigate whether %GP is correlated with clinical dosimetric difference for VMAT. Methods: Twenty nasopharyngeal cancer (NPC) patients treated with dual-arc simultaneous integrated boost VMAT and 20 esophageal cancer patients treated with one-arc VMAT were enrolled in this study. Pretreatment VMAT QA was performed by a 3D diode array ArcCheck. Acceptance criteria of 2%/2mm, 3%/3mm, and 4%/4mm were applied for 2D %GP. Dose values below 10% of the per-measured normalization maximum dose were ignored.Mean DVH values obtained from 3DVH software and TPS were calculated and percentage dose differences were calculated. Statistical correlation between %GP and percent dose difference was studied by using Pearson correlation. Results: The %GP for criteria 2%/2mm, 3%/3mm, and 4%/4mm were 82.33±4.45, 93.47±2.31, 97.13±2.41, respectively. Dose differences calculated from 3DVH and TPS for beam isocenter, mean dose of PTV, maximum dose of PTV, D2 of PTV and D98 of PTV were -1.04±3.24, -0.74±1.71, 2.92±3.62, 0.89±3.29, -1.46±1.97, respectively. No correction were found between %GP and dose differences. Conclusion: There are weak correlations between the 2D %GP and dose differences calculated from 3DVH. The %GP acceptance criteria of 3%/3mm usually applied for pretreatment QA of IMRT and VMAT is not indicating strong clinical correlation with 3D dose difference. 3D dose reconstructions on patient anatomy may be necessary for physicist to predict the accuracy of delivered dose for VMAT QA.

  10. Wheat quality related differential expressions of albumins and globulins revealed by two-dimensional difference gel electrophoresis (2-D DIGE).

    PubMed

    Gao, Liyan; Wang, Aili; Li, Xiaohui; Dong, Kun; Wang, Ke; Appels, Rudi; Ma, Wujun; Yan, Yueming

    2009-12-01

    Comparative proteomics analysis offers a new approach to identify differential proteins among different wheat genotypes and developmental stages. In this study, the non-prolamin expression profiles during grain development of two common or bread wheat cultivars (Triticum aestivum L.), Jing 411 and Sunstate, with different quality properties were analyzed using two-dimensional difference gel electrophoresis (2-D DIGE). Five grain developmental stages during the post-anthesis period were sampled corresponding to the cumulative averages of daily temperatures ( degrees C: 156 degrees C, 250 degrees C, 354 degrees C, 447 degrees C and 749.5 degrees C). More than 400 differential protein spots detected at one or more of the developmental stages of the two cultivars were monitored, among which 230 proteins were identified by MS. Of the identified proteins, more than 85% were enzymes possessing different physiological functions. A total of 36 differential proteins were characterized between the two varieties, which are likely to be related to wheat quality attributes. About one quarter of the proteins identified expressed in multiple spots with different pIs and molecular masses, implying certain post-translational modifications (PTMs) of proteins such as phosphorylations and glycosylations. The results provide new insights into biochemical mechanisms for grain development and quality.

  11. Digit ratio (2D:4D) in Lithuania once and now: testing for sex differences, relations with eye and hair color, and a possible secular change.

    PubMed

    Voracek, Martin; Bagdonas, Albinas; Dressler, Stefan G

    2007-09-01

    The second-to-fourth digit ratio (2D:4D) is a sexually dimorphic somatic trait and has been proposed as a biomarker for the organizational, i.e., permanent, effects of prenatal testosterone on the human brain. Accordingly, recent research has related 2D:4D to a variety of sex-dependent, hormonally influenced traits and phenotypes. The geographical variation in typical 2D:4D is marked and presently poorly understood. This study presents the first investigation into the 2D:4D ratio in a Baltic country. A contemporary sample of 109 Lithuanian men and women was compared with data from a historical sample of 100 Lithuanian men and women, collected and published in the 1880s and rediscovered only now. The findings included the following lines of evidence: (i) seen in an international perspective, the average 2D:4D in Lithuania is low; (ii) there was a sex difference in 2D:4D in the expected direction in both samples; (iii) a previously adduced hypothesis of an association of lighter eye and hair color with higher, i.e., more feminized, 2D:4D received no support in both samples; and (iv) the average 2D:4D in the contemporary sample was higher than in the historical sample. In view of a hypothesized increase in 2D:4D in modern populations, owing to increased environmental levels of endocrine disruptors such as xenoestrogens, this latter finding appears to be of particular notice. However, because finger-length measurement methods differed across the samples, it cannot be safely ruled out that the apparent time trend in Lithuanian 2D:4D in truth is an artifact. The puzzling geographical pattern seen in the 2D:4D ratio and the question of possible time trends therein deserve further investigations.

  12. Effective finite-difference modelling methods with 2-D acoustic wave equation using a combination of cross and rhombus stencils

    NASA Astrophysics Data System (ADS)

    Wang, Enjiang; Liu, Yang; Sen, Mrinal K.

    2016-09-01

    The 2-D acoustic wave equation is commonly solved numerically by finite-difference (FD) methods in which the accuracy of solution is significantly affected by the FD stencils. The commonly used cross stencil can reach either only second-order accuracy for space domain dispersion-relation-based FD method or (2M)th-order accuracy along eight specific propagation directions for time-space domain dispersion-relation-based FD method, if the conventional (2M)th-order spatial FD and second-order temporal FD are used to discretize the equation. One other newly developed rhombus stencil can reach arbitrary even-order accuracy. However, this stencil adds significantly to computational cost when the operator length is large. To achieve a balance between the solution accuracy and efficiency, we develop a new FD stencil to solve the 2-D acoustic wave equation. This stencil is a combination of the cross stencil and rhombus stencil. A cross stencil with an operator length parameter M is used to approximate the spatial partial derivatives while a rhombus stencil with an operator length parameter N together with the conventional second-order temporal FD is employed in approximating the temporal partial derivatives. Using this stencil, a new FD scheme is developed; we demonstrate that this scheme can reach (2M)th-order accuracy in space and (2N)th-order accuracy in time when spatial FD coefficients and temporal FD coefficients are derived from respective dispersion relation using Taylor-series expansion (TE) method. To further increase the accuracy, we derive the FD coefficients by employing the time-space domain dispersion relation of this FD scheme using TE. We also use least-squares (LS) optimization method to reduce dispersion at high wavenumbers. Dispersion analysis, stability analysis and modelling examples demonstrate that our new scheme has greater accuracy and better stability than conventional FD schemes, and thus can adopt large time steps. To reduce the extra

  13. Large eddy simulations for quasi-2D turbulence in shallow flows: A comparison between different subgrid scale models

    NASA Astrophysics Data System (ADS)

    Awad, Esam; Toorman, Erik; Lacor, Chris

    2009-06-01

    In this study, the performance of the horizontal large eddy simulation module, developed at the University of Leuven (HLES-KULeuven module) is assessed. A comparison between different subgrid scale models has been carried out. The study is concerned with the non-rotating and unstratified flows. The results of the simulation for an oscillatory backward facing (BFS) flow are presented in case of an expanding flume based on a one-length scale approach and a two-length scale approach. Three subgrid scale (SGS) models have been tested: Smagorinsky SGS model (Smagorinsky, J., (1963). General circulation experiments with the primitive equations, I. the basic experiments. Monthly Weather Review, 91(3), 99-164), Uittenbogaard SGS model (Uittenbogaard, R.E., and van Vossen, B., (2004). Subgrid-scale model for quasi-2D turbulence in shallow water. Shallow Flows. Jirka and Uijttewaal (Eds.), Taylor & Francis Group, London, ISBN 90 5809 700 5) and a proposed two-length scale approach. The first two models are considered to be a one-length scale models. A simulation without a subgrid scale model for the horizontal mixing has also been conducted. In all simulations, a quadratic friction model parameterizes the dissipation produced by the 3D-subdepth scale turbulence. The two-length scale concept uses a newly mixing length formulation for the quasi-2D turbulence and doesn't depend on the filter width in contrast to the one-length scale approach, in which the mixing length is function of the filter width. The outputs of the HLES-KULeuven module have been compared with the experimental data taken from Stelling, G.S., and Wang, L.X., (1984). Experiments and computations on separating flow in an expanding flume. Dept. Civil Engineering, Delft University of Technology, Report 2-84.). The two-length scale approach has been validated with experimental data from SERC Flood Channel Facility at HR Wallingford. In general, there is a qualitative agreement with the experimental data. It has

  14. Simulations of P-SV wave scattering due to cracks by the 2-D finite difference method

    NASA Astrophysics Data System (ADS)

    Suzuki, Yuji; Shiina, Takahiro; Kawahara, Jun; Okamoto, Taro; Miyashita, Kaoru

    2013-12-01

    We simulate P-SV wave scattering by 2-D parallel cracks using the finite difference method (FDM). Here, special emphasis is put on simplicity; we apply a standard FDM (second-order velocity-stress scheme with a staggered grid) to media including traction-free, infinitesimally thin cracks, which are expressed in a simple manner. As an accuracy test of the present method, we calculate the displacement discontinuity along an isolated crack caused by harmonic waves using the method, which is compared with the corresponding results based on a reliable boundary integral equation method. The test resultantly indicates that the present method yields sufficient accuracy. As an application of this method, we also simulate wave propagation in media with randomly distributed cracks. We experimentally determine the attenuation and velocity dispersion induced by scattering from the synthetic seismograms, using a waveform averaging technique. It is shown that the results are well explained by a theory based on the Foldy approximation, if the crack density is sufficiently low. The theory appears valid with a crack density up to at least 0.1 for SV wave incidence, whereas the validity limit appears lower for P wave incidence.

  15. Characterization of Phenotypic and Transcriptional Differences in Human Pluripotent Stem Cells under 2D and 3D Culture Conditions.

    PubMed

    Kamei, Ken-Ichiro; Koyama, Yoshie; Tokunaga, Yumie; Mashimo, Yasumasa; Yoshioka, Momoko; Fockenberg, Christopher; Mosbergen, Rowland; Korn, Othmar; Wells, Christine; Chen, Yong

    2016-11-01

    Human pluripotent stem cells hold great promise for applications in drug discovery and regenerative medicine. Microfluidic technology is a promising approach for creating artificial microenvironments; however, although a proper 3D microenvironment is required to achieve robust control of cellular phenotypes, most current microfluidic devices provide only 2D cell culture and do not allow tuning of physical and chemical environmental cues simultaneously. Here, the authors report a 3D cellular microenvironment plate (3D-CEP), which consists of a microfluidic device filled with thermoresponsive poly(N-isopropylacrylamide)-β-poly(ethylene glycol) hydrogel (HG), which enables systematic tuning of both chemical and physical environmental cues as well as in situ cell monitoring. The authors show that H9 human embryonic stem cells (hESCs) and 253G1 human induced pluripotent stem cells in the HG/3D-CEP system maintain their pluripotent marker expression under HG/3D-CEP self-renewing conditions. Additionally, global gene expression analyses are used to elucidate small variations among different test environments. Interestingly, the authors find that treatment of H9 hESCs under HG/3D-CEP self-renewing conditions results in initiation of entry into the neural differentiation process by induction of PAX3 and OTX1 expression. The authors believe that this HG/3D-CEP system will serve as a versatile platform for developing targeted functional cell lines and facilitate advances in drug screening and regenerative medicine.

  16. Prevalence of the CYP2D6*10 (C100T), *4 (G1846A), and *14 (G1758A) alleles among Iranians of different ethnicities.

    PubMed

    Bagheri, Ali; Kamalidehghan, Behnam; Haghshenas, Maryam; Azadfar, Parisa; Akbari, Leila; Sangtarash, Mohammad Hossein; Vejdandoust, Faramarz; Ahmadipour, Fatemeh; Meng, Goh Yong; Houshmand, Massoud

    2015-01-01

    The presence of polymorphisms in the CYP2D6 gene may modulate enzyme level and activity, thereby affecting individual responses to pharmacological treatment. Here, we compared the prevalence of the CYP2D6*10, *4, and 14* alleles in an Iranian population of different ethnicities with those of other populations. Allele and genotype frequency distributions of CYP2D6*10 variants and predicted phenotypes including extensive metabolizers, intermediate metabolizers, and poor metabolizers were analysed in blood samples of 300 unrelated healthy individuals in an Iranian population using polymerase chain reaction (PCR)-restriction fragment length polymorphism, PCR-single-strand conformation polymorphism, and direct genomic DNA sequencing. The CYP2D6*4 (G1846A) and *14 (G1758A) allelic frequencies were not detected in different ethnicities, demonstrating the absence of a significant contribution of these alleles in Iranian populations. However, the T/T, C/T, and C/C genotype frequencies of the CYP2D6*10 allele were significantly different (P<0.01) in all Iranian ethnic groups. Additionally, the frequency of the homozygous T/T variant of the CYP2D6*10 allele was significantly high in the Lure (P<0.017) and low in the Kurd (P<0.002) ethnicities. The frequency of the T/T variant of the CYP2D6*10 allele in central Iran was the highest (P<0.001), while the south of Iran had the lowest frequency (P<0.001). The frequency of the C/T variant of the CYP2D6*10 allele was significantly a bit high (P<0.001) in females compare to males, while the frequencies of the T/T variant in females is similar to males, which are 24.4% and 24.3%, respectively. In contrast to absence of the CYP2D6*4 (G1846A) and *14 (G1758A) alleles in Iranian populations of different ethnicities, the prediction of the CYP2D6*10 allele is required in drug research and routine treatment, where the information would be helpful for clinicians to optimize therapy or identify persons at risk of adverse drug reactions before

  17. Sex differences in college students' free drawings and their relationship to 2D:4D ratio and recalled childhood play behavior.

    PubMed

    Rothkopf, Ian; Turgeon, Sarah M

    2014-02-01

    In a prior study, we observed that female-typical characteristics in elementary school girls' drawings were correlated with a feminized digit ratio (2D:4D), a marker for prenatal androgen exposure. However, this observation was limited to older girls, suggesting that social factors mediate the relationship between 2D:4D and drawing. To examine the hypothesis that the influence of prenatal androgen on girls' drawing is mediated by an effect of early androgens on sex-typical behavior, we examined 2D:4D, free drawings, and scores on the Recalled Childhood Gender Identity (RCGI) Questionnaire in a population of college students. Characteristics of participants' free drawings were assessed and those that showed sex differences were compared with 2D:4D and RCGI scores. Men had smaller 2D:4D ratios than women, used fewer total colors, used fewer pinks, purples, and blues, and had higher gender-typical scores on the RCGI. Women's drawings were more likely to contain flowers and animals and men's drawings were more likely to represent sports. Within-sex RCGI and 2D:4D scores were not significantly correlated. Significant within-sex relationships between 2D:4D and RCGI and drawing behavior were observed but the effects appeared to be independent; the hypothesis that gender-typical childhood behavior mediates the effect of prenatal androgen on drawing characteristics was not supported.

  18. Comparison of Different 2D and 3D-QSAR Methods on Activity Prediction of Histamine H3 Receptor Antagonists.

    PubMed

    Dastmalchi, Siavoush; Hamzeh-Mivehroud, Maryam; Asadpour-Zeynali, Karim

    2012-01-01

    Histamine H3 receptor subtype has been the target of several recent drug development programs. Quantitative structure-activity relationship (QSAR) methods are used to predict the pharmaceutically relevant properties of drug candidates whenever it is applicable. The aim of this study was to compare the predictive powers of three different QSAR techniques, namely, multiple linear regression (MLR), artificial neural network (ANN), and HASL as a 3D QSAR method, in predicting the receptor binding affinities of arylbenzofuran histamine H3 receptor antagonists. Genetic algorithm coupled partial least square as well as stepwise multiple regression methods were used to select a number of calculated molecular descriptors to be used in MLR and ANN-based QSAR studies. Using the leave-group-out cross-validation technique, the performances of the MLR and ANN methods were evaluated. The calculated values for the mean absolute percentage error (MAPE), ranging from 2.9 to 3.6, and standard deviation of error of prediction (SDEP), ranging from 0.31 to 0.36, for both MLR and ANN methods were statistically comparable, indicating that both methods perform equally well in predicting the binding affinities of the studied compounds toward the H3 receptors. On the other hand, the results from 3D-QSAR studies using HASL method were not as good as those obtained by 2D methods. It can be concluded that simple traditional approaches such as MLR method can be as reliable as those of more advanced and sophisticated methods like ANN and 3D-QSAR analyses.

  19. Estimation of percentage breast tissue density: comparison between digital mammography (2D full field digital mammography) and digital breast tomosynthesis according to different BI-RADS categories

    PubMed Central

    Cavagnetto, F; Calabrese, M; Houssami, N

    2013-01-01

    Objective: To compare breast density estimated from two-dimensional full-field digital mammography (2D FFDM) and from digital breast tomosynthesis (DBT) according to different Breast Imaging–Reporting and Data System (BI-RADS) categories, using automated software. Methods: Institutional review board approval and written informed patient consent were obtained. DBT and 2D FFDM were performed in the same patients to allow within-patient comparison. A total of 160 consecutive patients (mean age: 50±14 years; mean body mass index: 22±3) were included to create paired data sets of 40 patients for each BI-RADS category. Automatic software (MedDensity©, developed by Giulio Tagliafico) was used to compare the percentage breast density between DBT and 2D FFDM. The estimated breast percentage density obtained using DBT and 2D FFDM was examined for correlation with the radiologists' visual BI-RADS density classification. Results: The 2D FFDM differed from DBT by 16.0% in BI-RADS Category 1, by 11.9% in Category 2, by 3.5% in Category 3 and by 18.1% in Category 4. These differences were highly significant (p<0.0001). There was a good correlation between the BI-RADS categories and the density evaluated using 2D FFDM and DBT (r=0.56, p<0.01 and r=0.48, p<0.01, respectively). Conclusion: Using DBT, breast density values were lower than those obtained using 2D FFDM, with a non-linear relationship across the BI-RADS categories. These data are relevant for clinical practice and research studies using density in determining the risk. Advances in knowledge: On DBT, breast density values were lower than with 2D FFDM, with a non-linear relationship across the classical BI-RADS categories. PMID:24029631

  20. Individual Recognition in Domestic Cattle (Bos taurus): Evidence from 2D-Images of Heads from Different Breeds

    PubMed Central

    Coulon, Marjorie; Deputte, Bertrand L.; Heyman, Yvan; Baudoin, Claude

    2009-01-01

    Background In order to maintain cohesion of groups, social animals need to process social information efficiently. Visual individual recognition, which is distinguished from mere visual discrimination, has been studied in only few mammalian species. In addition, most previous studies used either a small number of subjects or a few various views as test stimuli. Dairy cattle, as a domestic species allow the testing of a good sample size and provide a large variety of test stimuli due to the morphological diversity of breeds. Hence cattle are a suitable model for studying individual visual recognition. This study demonstrates that cattle display visual individual recognition and shows the effect of both familiarity and coat diversity in discrimination. Methodology/Principal Findings We tested whether 8 Prim'Holstein heifers could recognize 2D-images of heads of one cow (face, profiles, ¾ views) from those of other cows. Experiments were based on a simultaneous discrimination paradigm through instrumental conditioning using food rewards. In Experiment 1, all images represented familiar cows (belonging to the same social group) from the Prim'Holstein breed. In Experiments 2, 3 and 4, images were from unfamiliar (unknown) individuals either from the same breed or other breeds. All heifers displayed individual recognition of familiar and unfamiliar individuals from their own breed. Subjects reached criterion sooner when recognizing a familiar individual than when recognizing an unfamiliar one (Exp 1: 3.1±0.7 vs. Exp 2: 5.2±1.2 sessions; Z = 1.99, N = 8, P = 0.046). In addition almost all subjects recognized unknown individuals from different breeds, however with greater difficulty. Conclusions/Significance Our results demonstrated that cattle have efficient individual recognition based on categorization capacities. Social familiarity improved their performance. The recognition of individuals with very different coat characteristics from the subjects was

  1. Origin of the different energetic ion populations in the quasi-perpendicular Ion Foreshock: 2D Full-particle simulation

    NASA Astrophysics Data System (ADS)

    Savoini, P.; Lembege, B.; Stienlet, J.

    2012-04-01

    The foreshock region is located upstream of the terrestrial bow shock and is characterized by energetic backstreaming particles (electrons and ions) issued from the shock and by an important wave activity as observed by many space missions. In order to analyse the foreshock region, a curved shock is simulated with the help of a 2 - D full particle (PIC) code, where full curvature and time of flight effects, and where both electrons and ions dynamics are fully described by a self consistent approach. The analysis is presently restricted to the quasi-perpendicular angular range defined by 45°≤ θBn ≤ 90°, where θBn is the angle between the shock normal and the upstream magnetostatic field, and we focus only on the ion foreshock. In a good agreement with experimental data, present preliminary results evidence two distinct ion populations collimated along the interplanetary magnetic field (IMF): (i) the Field-Aligned Beam population (hereafter named "FAB") and (ii) the gyro-phase bunch population (hereafter named "GPB") which differ from each other by their gyrotropic or non-gyrotropic behavior, respectively. Additionally, the "FAB" population is observed at the edge of the ion foreshock and near the curved shock front, while the "'GPB" population is observed deeper in the foreshock and further from the shock front. The analysis shows that no pitch angle scattering mechanism needs to be invoked to account for the generation of the "GPB", but rather additional criteria are necessary namely: the interaction time Δtint of backstreaming ions with the shock front and their downstream penetration depth. These criteria allow to evidence that (i) the "FAB" population corresponds to particles which move back and forth between the upstream edge of the front and the overshoot, and are characterized by a quite large Δtint (covering several local gyro-periods, 4 ≤ τci ≤ 12). In contrast, (ii) the "GPB" ions have suffered a very short interaction time (i.e. Δtint < 1

  2. Multiplexed Spectral Imaging of 120 Different Fluorescent Labels

    PubMed Central

    Valm, Alex M.; Oldenbourg, Rudolf; Borisy, Gary G.

    2016-01-01

    The number of fluorescent labels that can unambiguously be distinguished in a single image when acquired through band pass filters is severely limited by the spectral overlap of available fluorophores. The recent development of spectral microscopy and the application of linear unmixing algorithms to spectrally recorded image data have allowed simultaneous imaging of fluorophores with highly overlapping spectra. However, the number of distinguishable fluorophores is still limited by the unavoidable decrease in signal to noise ratio when fluorescence signals are fractionated over multiple wavelength bins. Here we present a spectral image analysis algorithm to greatly expand the number of distinguishable objects labeled with binary combinations of fluorophores. Our algorithm utilizes a priori knowledge about labeled specimens and imposes a binary label constraint on the unmixing solution. We have applied our labeling and analysis strategy to identify microbes labeled by fluorescence in situ hybridization and here demonstrate the ability to distinguish 120 differently labeled microbes in a single image. PMID:27391327

  3. Simultaneous measurement of J(HH) and two different (n)J(CH) coupling constants from a single multiply edited 2D cross-peak.

    PubMed

    Saurí, Josep; Parella, Teodor

    2013-07-01

    Three different J-editing methods (IPAP, E.COSY and J-resolved) are implemented in a single NMR experiment to provide spin-state-edited 2D cross-peaks from which a simultaneous measurement of different homonuclear and heteronuclear coupling constants can be performed. A new J-selHSQMBC-IPAP experiment is proposed for the independent measurement of two different (n)J(CH) coupling constants along the F2 and F1 dimensions of the same 2D cross-peak. In addition, the E.COSY pattern provides additional information about the magnitude and relative sign between J(HH) and (n)J(CH) coupling constants.

  4. Differences in growth properties of endometrial cancer in three dimensional (3D) culture and 2D cell monolayer

    SciTech Connect

    Chitcholtan, Kenny; Asselin, Eric; Parent, Sophie; Sykes, Peter H.; Evans, John J.

    2013-01-01

    Three-dimensional (3D) in vitro models have an invaluable role in understanding the behaviour of tumour cells in a well defined microenvironment. This is because some aspects of tumour characteristics cannot be fully recapitulated in a cell monolayer (2D). In the present study, we compared growth patterns, expression of signalling molecules, and metabolism-associated proteins of endometrial cancer cell lines in 3D and 2D cell cultures. Cancer cells formed spherical structures in 3D reconstituted basement membrane (3D rBM), and the morphological appearance was cell line dependent. Cell differentiation was observed after 8 days in the 3D rBM. There was reduced proliferation, detected by less expression of PCNA in 3D rBM than in 2D cell monolayers. The addition of exogenous epidermal growth factor (EGF) to cancer cells induced phosphorylation of EGFR and Akt in both cell culture conditions. The uptake of glucose was selectively altered in the 3D rBM, but there was a lack of association with Glut-1 expression. The secretion of vascular endothelial growth factor (VEGF) and prostaglandin E{sub 2} (PGE{sub 2}) was selectively altered in 3D rBM, and it was cell line dependent. Our data demonstrated that 3D rBM as an in vitro model can influence proliferation and metabolism of endometrial cancer cell behaviour compared to 2D cell monolayer. Changes are specific to individual cell types. The use of 3D rBM is, therefore, important in the in vitro study of targeted anticancer therapies.

  5. SEX DIFFERENCES IN DIGIT RATIO (2D:4D) AMONG MILITARY AND CIVIL COHORTS AT A MILITARY ACADEMY IN WROCŁAW, POLAND.

    PubMed

    Kociuba, Marek; Kozieł, Slawomir; Chakraborty, Raja

    2016-09-01

    The ratio of second-to-fourth digit length (2D:4D), which is generally higher in women compared with men, is a putative marker of prenatal testosterone (PT) exposure. Lower 2D:4D is linked with greater physical ability and strength, better sporting performance and a propensity towards jobs demanding greater physical ability. The objectives of this paper were to examine the sexual dimorphism in 2D:4D in both hands 1and compare this dimorphism in the students of military and civil courses at the General Kuściuszko Military Academy of Land Forces in Wrocław. The cross-sectional study compared 59 female and 118 male students from the military courses and 53 females and 64 male students from the civil courses. Besides calculating 2D:4D (2D/4D) for each hand, height and weight were also recorded. Physical fitness and endurance were assessed using Eurofit tests. Handgrip strength was measured using a standardized isometric dynamometer. In almost all physical tests, students in the military cohort showed highly significant greater physical ability and strength (e.g. handgrip strength) when compared with the civil cohort. Male participants had a significantly lower 2D:4D than females for each hand, as well as for the average value for both hands. The sexual dimorphism was, however, a little more pronounced in the right hand than in the left. Both sex and course type were significant predictors of 2D:4D. There were significant interactions between sex and the student type. Among females, but not in males, the military cohort had a significantly lower, i.e. more 'masculine', 2D:4D for the left hand and right hand and average for both hands (t=3.290, p<0.001) than the civil cohort. This was not the case in males. However, the sex difference in 2D:4D was only significant among the civil students, and not among the military cadets. In conclusion, higher PT exposure, as represented by a lower 2D:4D, among the Polish females might be an indicator of relatively increased physical

  6. 2D and 3D imaging of the gas phase close to an operating model catalyst by planar laser induced fluorescence

    NASA Astrophysics Data System (ADS)

    Blomberg, Sara; Zhou, Jianfeng; Gustafson, Johan; Zetterberg, Johan; Lundgren, Edvin

    2016-11-01

    In recent years, efforts have been made in catalysis related surface science studies to explore the possibilities to perform experiments at conditions closer to those of a technical catalyst, in particular at increased pressures. Techniques such as high pressure scanning tunneling/atomic force microscopy (HPSTM/AFM), near ambient pressure x-ray photoemission spectroscopy (NAPXPS), surface x-ray diffraction (SXRD) and polarization-modulation infrared reflection absorption spectroscopy (PM-IRAS) at semi-realistic conditions have been used to study the surface structure of model catalysts under reaction conditions, combined with simultaneous mass spectrometry (MS). These studies have provided an increased understanding of the surface dynamics and the structure of the active phase of surfaces and nano particles as a reaction occurs, providing novel information on the structure/activity relationship. However, the surface structure detected during the reaction is sensitive to the composition of the gas phase close to the catalyst surface. Therefore, the catalytic activity of the sample itself will act as a gas-source or gas-sink, and will affect the surface structure, which in turn may complicate the assignment of the active phase. For this reason, we have applied planar laser induced fluorescence (PLIF) to the gas phase in the vicinity of an active model catalysts. Our measurements demonstrate that the gas composition differs significantly close to the catalyst and at the position of the MS, which indeed should have a profound effect on the surface structure. However, PLIF applied to catalytic reactions presents several beneficial properties in addition to investigate the effect of the catalyst on the effective gas composition close to the model catalyst. The high spatial and temporal resolution of PLIF provides a unique tool to visualize the on-set of catalytic reactions and to compare different model catalysts in the same reactive environment. The technique can be

  7. 2D and 3D imaging of the gas phase close to an operating model catalyst by planar laser induced fluorescence.

    PubMed

    Blomberg, Sara; Zhou, Jianfeng; Gustafson, Johan; Zetterberg, Johan; Lundgren, Edvin

    2016-11-16

    In recent years, efforts have been made in catalysis related surface science studies to explore the possibilities to perform experiments at conditions closer to those of a technical catalyst, in particular at increased pressures. Techniques such as high pressure scanning tunneling/atomic force microscopy (HPSTM/AFM), near ambient pressure x-ray photoemission spectroscopy (NAPXPS), surface x-ray diffraction (SXRD) and polarization-modulation infrared reflection absorption spectroscopy (PM-IRAS) at semi-realistic conditions have been used to study the surface structure of model catalysts under reaction conditions, combined with simultaneous mass spectrometry (MS). These studies have provided an increased understanding of the surface dynamics and the structure of the active phase of surfaces and nano particles as a reaction occurs, providing novel information on the structure/activity relationship. However, the surface structure detected during the reaction is sensitive to the composition of the gas phase close to the catalyst surface. Therefore, the catalytic activity of the sample itself will act as a gas-source or gas-sink, and will affect the surface structure, which in turn may complicate the assignment of the active phase. For this reason, we have applied planar laser induced fluorescence (PLIF) to the gas phase in the vicinity of an active model catalysts. Our measurements demonstrate that the gas composition differs significantly close to the catalyst and at the position of the MS, which indeed should have a profound effect on the surface structure. However, PLIF applied to catalytic reactions presents several beneficial properties in addition to investigate the effect of the catalyst on the effective gas composition close to the model catalyst. The high spatial and temporal resolution of PLIF provides a unique tool to visualize the on-set of catalytic reactions and to compare different model catalysts in the same reactive environment. The technique can be

  8. Effects of Spatial Ability, Gender Differences, and Pictorial Training on Children Using 2-D and 3-D Environments to Recall Landmark Locations from Memory

    ERIC Educational Resources Information Center

    Kopcha, Theodore J.; Otumfuor, Beryl A.; Wang, Lu

    2015-01-01

    This study examines the effects of spatial ability, gender differences, and pictorial training on fourth grade students' ability to recall landmark locations from memory. Ninety-six students used Google Earth over a 3-week period to locate landmarks (3-D) and mark their location on a 2-D topographical map. Analysis of covariance on posttest scores…

  9. Reliability Criteria for Liver Stiffness Measurements with Real-Time 2D Shear Wave Elastography in Different Clinical Scenarios of Chronic Liver Disease.

    PubMed

    Thiele, M; Madsen, B S; Procopet, B; Hansen, J F; Møller, L M S; Detlefsen, S; Berzigotti, A; Krag, A

    2016-06-07

    Purpose: Liver stiffness measurement by real-time 2-dimensional shear wave elastography (2D-SWE) lacks universal reliability criteria. We sought to assess whether previously published 2D-SWE reliability criteria for portal hypertension were applicable for the evaluation of liver fibrosis and cirrhosis, and to look for criteria that minimize the risk of misclassification in this setting. Materials and Methods: In a biopsy-controlled diagnostic study, we obtained five 2D-SWE measurements of optimal image quality. Correctly classified cases of fibrosis and cirrhosis were compared to misclassified cases. We compared reliability predictors (standard deviation (SD), SD/mean, size of region of interest (ROI) and difference between a single measurement and the patient's median) with those obtained in a prior study on clinically significant portal hypertension. Results: We obtained 678 2D-SWE measurements from 142 patients. Overall, the variability in liver stiffness within single 2D-SWE measurements was low (SD = 1.1 ± 1.5kPa; SD/mean = 12 ± 9 %). Intra-observer analysis showed almost perfect concordance (intraclass correlation coefficient = 0.95; 95 % CI 0.94 - 0.96; average difference from median = 0.4 ± 0.9kPa). For the diagnosis of cirrhosis, a smaller SD (optimally ≤ 1.75 kPa) and larger ROI size (optimally ≥ 18 mm) were associated with higher accuracy. Similarly, within the published cohort of patients assessed for portal hypertension, a low variability of measurements was associated with high reliability. Conclusion: A high quality 2D-SWE elastogram ensures low variability and high reliability, regardless of indication. We recommend aiming for a combination of low standard deviation and large ROI.

  10. Molar concentration from sequential 2-D water-window X-ray ptychography and X-ray fluorescence in hydrated cells

    PubMed Central

    Jones, M. W. M.; Elgass, K. D.; Junker, M. D.; de Jonge, M. D.; van Riessen, G. A.

    2016-01-01

    Recent developments in biological X-ray microscopy have allowed structural information and elemental distribution to be simultaneously obtained by combining X-ray ptychography and X-ray fluorescence microscopy. Experimentally, these methods can be performed simultaneously; however, the optimal conditions for each measurement may not be compatible. Here, we combine two distinct measurements of ultrastructure and elemental distribution, with each measurement performed under optimised conditions. By combining optimised ptychography and fluorescence information we are able to determine molar concentrations from two-dimensional images, allowing an investigation into the interactions between the environment sensing filopodia in fibroblasts and extracellular calcium. Furthermore, the biological ptychography results we present illustrate a point of maturity where the technique can be applied to solve significant problems in structural biology. PMID:27067957

  11. Lifetime measurements on electronically excited C 2(A 1Π u) and C 2(d 3Π g) by laser-induced fluorescence

    NASA Astrophysics Data System (ADS)

    Bauer, W.; Becker, K. H.; Bielefeld, M.; Meuser, R.

    1986-01-01

    The radiative lifetimes of C 2(A 1Π u, ν'= 0 and 3) were determined by laser-induced fluorescence to be τ 0(0) = 18.5 ± 3 and τ 0(3) = 11.4 ± 2 μs. In addition, the lifetimes of C 2C 2(A 1Π u,ν' = 0 and 1) were measured as τ 0 = 106 ± 15 ns and 105 ± 15 ns, respectively. The error is 3σ.

  12. Quantifying the flow dynamics of supercritical CO2-water displacement in a 2D porous micromodel using fluorescent microscopy and microscopic PIV

    NASA Astrophysics Data System (ADS)

    Kazemifar, Farzan; Blois, Gianluca; Kyritsis, Dimitrios C.; Christensen, Kenneth T.

    2016-09-01

    The multi-phase flow of liquid/supercritical CO2 and water (non-wetting and wetting phases, respectively) in a two-dimensional silicon micromodel was investigated at reservoir conditions (80 bar, 24 °C and 40 °C). The fluorescent microscopy and microscopic particle image velocimetry (micro-PIV) techniques were combined to quantify the flow dynamics associated with displacement of water by CO2 (drainage) in the porous matrix. To this end, water was seeded with fluorescent tracer particles, CO2 was tagged with a fluorescent dye and each phase was imaged independently using spectral separation in conjunction with microscopic imaging. This approach allowed simultaneous measurement of the spatially-resolved instantaneous velocity field in the water and quantification of the spatial configuration of the two fluid phases. The results, acquired with sufficient time resolution to follow the dynamic progression of both phases, provide a comprehensive picture of the flow physics during the migration of the CO2 front, the temporal evolution of individual menisci, and the growth of fingers within the porous microstructure. During that growth process, velocity jumps 20-25 times larger in magnitude than the bulk velocity were measured in the water phase and these bursts of water flow occurred both in-line with and against the bulk flow direction. These unsteady velocity events support the notion of pressure bursts and Haines jumps during pore drainage events as previously reported in the literature [1-3]. After passage of the CO2 front, shear-induced flow was detected in the trapped water ganglia in the form of circulation zones near the CO2-water interfaces as well as in the thin water films wetting the surfaces of the silicon micromodel. To our knowledge, the results presented herein represent the first quantitative spatially and temporally resolved velocity-field measurements at high pressure for water displacement by liquid/supercritical CO2 injection in a porous micromodel.

  13. Rapid authentication of different ages of tissue-cultured and wild Dendrobium huoshanense as well as wild Dendrobium henanense using FTIR and 2D-COS IR

    NASA Astrophysics Data System (ADS)

    Chen, Nai-Dong; Chen, Nai-Fu; Li, Jun; Cao, Cai-Yun; Wang, Jin-Mei

    2015-12-01

    The accumulating of pharmaceutical chemicals in medicinal plants would greatly be affected by their ages and establishing a fast quality-identification method to evaluate the similarity of medicinal herbs at different cultivated ages is a critical step for assurance of quality and safety in the TCM industry. In this work, tri-step IR macro-fingerprinting and 2D-COS IR spectrum techniques combined with statistical pattern recognition were applied for discrimination and similarity evaluation of different ages of tissue-cultured and wild Dendrobium huoshanense C. Z. Tang et S. J. Cheng as well as Dendrobium henanense J.L.Lu et L.X Gao. Both tissue-cultured and wild D. huoshanense were easily differentiated from D. henanense by FTIR and SD-IR spectra, while it's quite difficult to discriminate different cultivated years of the three investigated Dendrobiums. In 2D-COS IR spectra, 1-5 auto-peaks with different indensity and positions were located in the region 1160-1030 cm-1 of the twelve Dendrobium samples and thus could be used to identify Dendrobium samples at different ages. Principle component analysis (PCA) of synchronous 2D-COS data showed that the twelve samples were effectively identified and evaluated. The results indicated that the tri-step infrared macro-fingerprinting combined with PCA method was suitable to differentiate the cultivated ages of Dendrobiums with species and orgins rapidly and nondestructively.

  14. Comparison of the effect of simple and complex acquisition trajectories on the 2D SPR and 3D voxelized differences for dedicated breast CT imaging

    NASA Astrophysics Data System (ADS)

    Shah, Jainil P.; Mann, Steve D.; McKinley, Randolph L.; Tornai, Martin P.

    2014-03-01

    The 2D scatter-to-primary (SPR) ratios and 3D voxelized difference volumes were characterized for a cone beam breast CT scanner capable of arbitrary (non-traditional) 3D trajectories. The CT system uses a 30x30cm2 flat panel imager with 197 micron pixellation and a rotating tungsten anode x-ray source with 0.3mm focal spot, with an SID of 70cm. Data were acquired for two cylindrical phantoms (12.5cm and 15cm diameter) filled with three different combinations of water and methanol yielding a range of uniform densities. Projections were acquired with two acquisition trajectories: 1) simple-circular azimuthal orbit with fixed tilt; and 2) saddle orbit following a +/-15° sinusoidal trajectory around the object. Projection data were acquired in 2x2 binned mode. Projections were scatter corrected using a beam stop array method, and the 2D SPR was measured on the projections. The scatter corrected and uncorrected data were then reconstructed individually using an iterative ordered subsets convex algorithm, and the 3D difference volumes were calculated as the absolute difference between the two. Results indicate that the 2D SPR is ~7-15% higher on projections with greatest tilt for the saddle orbit, due to the longer x-ray path length through the volume, compared to the 0° tilt projections. Additionally, the 2D SPR increases with object diameter as well as density. The 3D voxelized difference volumes are an estimate of the scatter contribution to the reconstructed attenuation coefficients on a voxel level. They help visualize minor deficiencies and artifacts in the volumes due to correction methods.

  15. Volatility-dependent 2D IR correlation analysis of traditional Chinese medicine ‘Red Flower Oil’ preparation from different manufacturers

    NASA Astrophysics Data System (ADS)

    Wu, Yan-Wen; Sun, Su-Qin; Zhou, Qun; Tao, Jia-Xun; Noda, Isao

    2008-06-01

    As a traditional Chinese medicine (TCM), 'Red Flower Oil' preparation is widely used as a household remedy in China and Southeast Asia. Usually, the preparation is a mixture of several plant essential oils with different volatile features, such as wintergreen oil, turpentine oil and clove oil. The proportions of these plant essential oils in 'Red Flower Oil' vary from different manufacturers. Thus, it is important to develop a simple and rapid evaluation method for quality assurance of the preparations. Fourier transform infrared (FT-IR) was applied and two-dimensional correlation infrared spectroscopy (2D IR) based on the volatile characteristic of samples was used to enhance the resolution of FT-IR spectra. 2D IR technique could, not only easily provide the composition and their volatile sequences in 'Red flower Oil' preparations, but also rapidly discriminate the subtle differences in products from different manufacturers. Therefore, FT-IR combined with volatility-dependent 2D IR correlation analysis provides a very fast and effective method for the quality control of essential oil mixtures in TCM.

  16. Vertical 2D Heterostructures

    NASA Astrophysics Data System (ADS)

    Lotsch, Bettina V.

    2015-07-01

    Graphene's legacy has become an integral part of today's condensed matter science and has equipped a whole generation of scientists with an armory of concepts and techniques that open up new perspectives for the postgraphene area. In particular, the judicious combination of 2D building blocks into vertical heterostructures has recently been identified as a promising route to rationally engineer complex multilayer systems and artificial solids with intriguing properties. The present review highlights recent developments in the rapidly emerging field of 2D nanoarchitectonics from a materials chemistry perspective, with a focus on the types of heterostructures available, their assembly strategies, and their emerging properties. This overview is intended to bridge the gap between two major—yet largely disjunct—developments in 2D heterostructures, which are firmly rooted in solid-state chemistry or physics. Although the underlying types of heterostructures differ with respect to their dimensions, layer alignment, and interfacial quality, there is common ground, and future synergies between the various assembly strategies are to be expected.

  17. The basics of 2D DIGE.

    PubMed

    Beckett, Phil

    2012-01-01

    The technique of two-dimensional (2D) gel electrophoresis is a powerful tool for separating complex mixtures of proteins, but since its inception in the mid 1970s, it acquired the stigma of being a very difficult application to master and was generally used to its best effect by experts. The introduction of commercially available immobilized pH gradients in the early 1990s provided enhanced reproducibility and easier protocols, leading to a pronounced increase in popularity of the technique. However gel-to-gel variation was still difficult to control without the use of technical replicates. In the mid 1990s (at the same time as the birth of "proteomics"), the concept of multiplexing fluorescently labeled proteins for 2D gel separation was realized by Jon Minden's group and has led to the ability to design experiments to virtually eliminate gel-to-gel variation, resulting in biological replicates being used for statistical analysis with the ability to detect very small changes in relative protein abundance. This technology is referred to as 2D difference gel electrophoresis (2D DIGE).

  18. A new method to make 2-D wear measurements less sensitive to projection differences of cemented THAs.

    PubMed

    The, Bertram; Flivik, Gunnar; Diercks, Ron L; Verdonschot, Nico

    2008-03-01

    Wear curves from individual patients often show unexplained irregular wear curves or impossible values (negative wear). We postulated errors of two-dimensional wear measurements are mainly the result of radiographic projection differences. We tested a new method that makes two-dimensional wear measurements less sensitive for radiograph projection differences of cemented THAs. The measurement errors that occur when radiographically projecting a three-dimensional THA were modeled. Based on the model, we developed a method to reduce the errors, thus approximating three-dimensional linear wear values, which are less sensitive for projection differences. An error analysis was performed by virtually simulating 144 wear measurements under varying conditions with and without application of the correction: the mean absolute error was reduced from 1.8 mm (range, 0-4.51 mm) to 0.11 mm (range, 0-0.27 mm). For clinical validation, radiostereometric analysis was performed on 47 patients to determine the true wear at 1, 2, and 5 years. Subsequently, wear was measured on conventional radiographs with and without the correction: the overall occurrence of errors greater than 0.2 mm was reduced from 35% to 15%. Wear measurements are less sensitive to differences in two-dimensional projection of the THA when using the correction method.

  19. A comparative method for protein extraction and 2-D gel electrophoresis from different tissues of Cajanus cajan

    PubMed Central

    Singh, Nisha; Jain, Neha; Kumar, Ram; Jain, Ajay; Singh, Nagendra K.; Rai, Vandna

    2015-01-01

    Pigeonpea is an important legume crop with high protein content. However, it is often subjected to various abiotic and biotic stresses. Proteomics is a state-of-the-art technique used to analyze the protein profiling of a tissue for deciphering the molecular entities that could be manipulated for developing crops resistant to these stresses. In this context, developing a comprehensive proteome profile from different vegetative and reproductive tissues has become mandatory. Although several protein extraction protocols from different tissues of diverse plant species have been reported, there is no report for pigeonpea. Here, we report tissue-specific protein extraction protocols representing vegetative (young leaves), and reproductive (flowers and seeds) organs and their subsequent analysis on 2-dimensional gel electrophoresis. The study explicitly demonstrated that the efficacy of a particular protein extraction protocol is dependent on the different tissues, such as leaves, flowers and seeds that differ in their structure and metabolic constituents. For instance, phenol-based protocol showed an efficacy toward higher protein yield, better spot resolution and a minimal streaking on 2-DE gel for both leaves and flowers. Protein extraction from seeds was best achieved by employing phosphate-TCA-acetone protocol. PMID:26300903

  20. A comparative method for protein extraction and 2-D gel electrophoresis from different tissues of Cajanus cajan.

    PubMed

    Singh, Nisha; Jain, Neha; Kumar, Ram; Jain, Ajay; Singh, Nagendra K; Rai, Vandna

    2015-01-01

    Pigeonpea is an important legume crop with high protein content. However, it is often subjected to various abiotic and biotic stresses. Proteomics is a state-of-the-art technique used to analyze the protein profiling of a tissue for deciphering the molecular entities that could be manipulated for developing crops resistant to these stresses. In this context, developing a comprehensive proteome profile from different vegetative and reproductive tissues has become mandatory. Although several protein extraction protocols from different tissues of diverse plant species have been reported, there is no report for pigeonpea. Here, we report tissue-specific protein extraction protocols representing vegetative (young leaves), and reproductive (flowers and seeds) organs and their subsequent analysis on 2-dimensional gel electrophoresis. The study explicitly demonstrated that the efficacy of a particular protein extraction protocol is dependent on the different tissues, such as leaves, flowers and seeds that differ in their structure and metabolic constituents. For instance, phenol-based protocol showed an efficacy toward higher protein yield, better spot resolution and a minimal streaking on 2-DE gel for both leaves and flowers. Protein extraction from seeds was best achieved by employing phosphate-TCA-acetone protocol.

  1. Comparison of different fluorescence fluctuation methods for their use in FRET assays: monitoring a protease reaction.

    PubMed

    Eggeling, C; Jäger, S; Winkler, D; Kask, Peet

    2005-10-01

    We compare the accuracy of a variety of Fluorescence Fluctuation Spectroscopy (FFS) methods for the study of Förster Resonance Energy Transfer (FRET) assays. As an example, the cleavage of a doubly labeled, FRET-active peptide substrate by the protease Trypsin is monitored and analyzed using methods based on fluorescence intensity, Fluorescence Correlation Spectroscopy (FCS) and Fluorescence Intensity Distribution Analysis (FIDA). The presented fluorescence data are compared to High-Pressure Liquid Chromatography (HPLC) data obtained from the same assay. The HPLC analysis discloses general disadvantages of the FRET approach, such as incomplete labeling and the need for aliquots. However, the simultaneous use of two photon detectors monitoring the fluorescence signal of both labels significantly improves the analysis. In particular, the two global analysis tools Two-Dimensional Fluorescence Intensity Distribution Analysis (2D-FIDA) and Two-Color Global Fluorescence Correlation Spectroscopy (2CG-FCS) highlight the potential of a combination of FFS and FRET. While conventional FIDA and FCS auto- or cross-correlation analysis leaves the user with drawbacks inherent in two-color and FRET applications, these effects are overcome by the global analysis on the molecular level. Furthermore, it is advantageous to analyze the unnormalized as opposed to the normalized correlation data when combining any fluorescence correlation method with FRET, since the analysis of the unnormalized data introduces more accuracy and is less sensitive to the experimental drawbacks.

  2. Differences in serum protein 2D gel electrophoresis patterns of Przewalski's (Mongolian wild horse) and thoroughbred horses.

    PubMed

    Barsuren, Enkhbolor; Namkhai, Bandi; Kong, Hong Sik

    2015-04-01

    The objective of this study was to assess differences in serum protein expression profiles of Przewalski's (Mongolian wild horse) and thoroughbred horses using proteome analysis. The serum proteins were separated by two-dimensional electrophoresis (2-DE) and five different gene products were identified. Proteins represented by the five spots were identified by matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry (MS)/MS technology. The identities of all proteins were deduced based on their similarity to proteins in the human plasma protein database. Three proteins (a haptoglobin-2 alpha glycoprotein and two haptoglobin-2beta glycoproteins with different accession numbers) were downregulated in Przewalski's horse sera compared to thoroughbred horse sera. Moreover, two proteins (tetraspanin-18 and pM5) were upregulated in Przewalski's horses compared to thoroughbred horses. Haptoglobin-2 alpha and haptoglobin-2beta may serve as candidate molecules in future studies of inflammation, coagulation, immune modulation and pro-oxidant and antioxidant activity with consequential effects on the entire metabolism of the horse.

  3. One-step construction of two different kinds of pores in a 2D covalent organic framework.

    PubMed

    Zhou, Tian-You; Xu, Shun-Qi; Wen, Qiang; Pang, Zhong-Fu; Zhao, Xin

    2014-11-12

    Covalent organic frameworks (COFs) are crystalline porous materials bearing microporous or mesoporous pores. The type and size of pores play crucial roles in regulating the properties of COFs. In this work, a novel COF, which bears two different kinds of ordered pores with controllable sizes: one within microporous range (7.1 Å) and the other in mesoporous range (26.9 Å), has been constructed via one-step synthesis. The structure of the dual-pore COF was confirmed by PXRD investigation, nitrogen adsorption-desorption study, and theoretical calculations.

  4. 2D nano-Y2O3:Eu3+ photoluminescence with different preparation methods and annealing temperatures

    NASA Astrophysics Data System (ADS)

    Zhou, Jun; Zhu, Yanhua; Liu, Huangqing; Chai, Yifeng; Yang, Yibo; Zhang, Qingjun; Wang, Lingling

    2017-03-01

    Y2O3:Eu3+ (YOE) material is an important photoluminescence (PL) material. In this paper, YOE nano-powder was prepared by the low-temperature combustion method (LTC) and sol-gel method (SG), and annealed with different temperatures, respectively. The influence of the preparation methods and annealing temperature on the optical properties of YOE were well studied. The as-synthesized nano-YOE samples were characterized by x-ray diffraction (XRD), PL spectra, and Fourier transform infrared spectroscopy (FTIR). Results show that with the increase in annealing temperature, the charge transfer band (CTB) of samples blue-shifts and shows higher intensity. FTIR results indicate that low emission intensity decreases luminescence intensity and deteriorates the optical properties of nano-YOE. We also studied the spectral intensity changes before and after laser-induced, which shows the intensity of significant changes over time.

  5. High velocity impact on different hybrid architectures of 2D laminated and 3D warp interlock fabric composite

    NASA Astrophysics Data System (ADS)

    Provost, B.; Boussu, F.; Coutellier, D.; Vallee, D.; Rondot, F.

    2012-08-01

    For decades, conventional amour shield is mainly oriented on metallic materials which are today well-known. Since the use of non conventional threats as IEDs, performances of those protections are required to be upgraded. The expected improvements that manufacturers are looking for are mainly oriented to the weight reduction which is the key parameter to reduce the fuel consumption, increase the payload, and offer more manoeuvrability to vehicles [1]. However, the difficulty is to reduce as cautiously as possible the total mass of the protection solution while ensuring the safety of the vehicle. One of the possible solutions is to use new combinations of materials, able to be more efficient against new threats and lighter than the traditional steel armour. It is in this context that the combination between some well-known ballistic alloys and textile composite material appear as a high potential solution for armour plated protection. Indeed, used as a backing, textile composite material present some interesting properties such as a very low density compared with steel and good behaviour in term of ballistic efficiency. This study proposes to test and compare the behaviour and efficiency of three different textile composite backings.

  6. SU-E-T-83: A Study On Evaluating the Directional Dependency of 2D Seven 29 Ion Chamber Array Clinically with Different IMRT Plans

    SciTech Connect

    Kumar, Syam; Aswathi, C.P.

    2015-06-15

    Purpose: To evaluate the directional dependency of 2D seven 29 ion chamber array clinically with different IMRT plans. Methods: 25 patients already treated with IMRT plans were selected for the study. Verification plans were created for each treatment plan in eclipse 10 treatment planning system using the AAA algorithm with the 2D array and the Octavius CT phantom. Verification plans were done 2 times for a single patient. First plan with real IMRT (plan-related approach) and second plan with zero degree gantry angle (field-related approach). Measurements were performed on a Varian Clinac-iX, linear accelerator equipped with a millennium 120 multileaf collimator. Fluence was measured for all the delivered plans and analyzed using the verisoft software. Comparison was done by selecting the fluence delivered in static gantry (zero degree gantry) versus IMRT with real gantry angles. Results: The gamma pass percentage is greater than 97 % for all IMRT delivered with zero gantry angle and between 95%–98% for real gantry angles. Dose difference between the TPS calculated and measured for IMRT delivered with zero gantry angle was found to be between (0.03 to 0.06Gy) and with real gantry angles between (0.02 to 0.05Gy). There is a significant difference between the gamma analysis between the zero degree and true angle with a significance of 0.002. Standard deviation of gamma pass percentage between the IMRT plans with zero gantry angle was 0.68 and for IMRT with true gantry angle was found to be 0.74. Conclusion: The gamma analysis for IMRT with zero degree gantry angles shows higher pass percentage than IMRT delivered with true gantry angles. Verification plans delivered with true gantry angles lower the verification accuracy when 2D array is used for measurement.

  7. [Comparative proteomics study of different processing technology for pilose antler using iTRAQ technology coupled with 2D LC-MS].

    PubMed

    Jin, Meng-ya; Dong, Ling; Luo, Yuan-ming; Yu, Li; Mo, Mei; Hou, Cheng-bo; Li, Zhi-yuan

    2015-12-01

    This study was designed to use iTRAQ technology coupled with 2D LC-MS/MS to study the comparative proteomics of different processing technology for pilose antler. 1015 proteins were identified with 2D LC combined with MOLDI TOF/TOF mass spectrometry. Comparative analysis with Protein Pilot (Version 4.5) revealed that 87 proteins were changed (P ≤ 0.05, the ratio of > 1.50 or < 0.60 as the threshold selection of difference proteins), of which 24 were up regulated and 33 were down regulated in the traditional frying process (TFP) compared with the fresh pilose antler (P ≤ 0.05). 7 significant different proteins (P ≤ 0.001), most of these significantly changed proteins were found to be involved in calcium ion binding and ATP binding associated with human healthy. Freeze drying with protective agent (FDP) (Trehalose) can improve the content of significantly different proteins (P ≤ 0.001) including Collagen alpha-1 (XII) chain (COL12A1) and Collagen alpha-1 (II) chain (COL2A1). The significant function involves in platelets activating, maintenance of spermatogonium, and disorder expression in tumor cells. The functional annotation by Hierarchical clustering and GO (gene ontology) showed that the main molecule functions of the proteins significantly changed in these processes were involved in binding (52.7%), catalytic (25.3%), structural molecule and transporter (6.6%).

  8. 2D and 3D Stem Cell Models of Primate Cortical Development Identify Species-Specific Differences in Progenitor Behavior Contributing to Brain Size.

    PubMed

    Otani, Tomoki; Marchetto, Maria C; Gage, Fred H; Simons, Benjamin D; Livesey, Frederick J

    2016-04-07

    Variation in cerebral cortex size and complexity is thought to contribute to differences in cognitive ability between humans and other animals. Here we compare cortical progenitor cell output in humans and three nonhuman primates using directed differentiation of pluripotent stem cells (PSCs) in adherent two-dimensional (2D) and organoid three-dimensional (3D) culture systems. Clonal lineage analysis showed that primate cortical progenitors proliferate for a protracted period of time, during which they generate early-born neurons, in contrast to rodents, where this expansion phase largely ceases before neurogenesis begins. The extent of this additional cortical progenitor expansion differs among primates, leading to differences in the number of neurons generated by each progenitor cell. We found that this mechanism for controlling cortical size is regulated cell autonomously in culture, suggesting that primate cerebral cortex size is regulated at least in part at the level of individual cortical progenitor cell clonal output.

  9. 2D and 3D Stem Cell Models of Primate Cortical Development Identify Species-Specific Differences in Progenitor Behavior Contributing to Brain Size

    PubMed Central

    Otani, Tomoki; Marchetto, Maria C.; Gage, Fred H.; Simons, Benjamin D.; Livesey, Frederick J.

    2016-01-01

    Summary Variation in cerebral cortex size and complexity is thought to contribute to differences in cognitive ability between humans and other animals. Here we compare cortical progenitor cell output in humans and three nonhuman primates using directed differentiation of pluripotent stem cells (PSCs) in adherent two-dimensional (2D) and organoid three-dimensional (3D) culture systems. Clonal lineage analysis showed that primate cortical progenitors proliferate for a protracted period of time, during which they generate early-born neurons, in contrast to rodents, where this expansion phase largely ceases before neurogenesis begins. The extent of this additional cortical progenitor expansion differs among primates, leading to differences in the number of neurons generated by each progenitor cell. We found that this mechanism for controlling cortical size is regulated cell autonomously in culture, suggesting that primate cerebral cortex size is regulated at least in part at the level of individual cortical progenitor cell clonal output. PMID:27049876

  10. Motion corrected photoacoustic difference imaging of fluorescent contrast agents

    NASA Astrophysics Data System (ADS)

    Märk, Julia; Wagener, Asja; Pönick, Sarah; Grötzinger, Carsten; Zhang, Edward; Laufer, Jan

    2016-03-01

    In fluorophores, such as exogenous dyes and genetically expressed proteins, the excited state lifetime can be modulated using pump-probe excitation at wavelengths corresponding to the absorption and fluorescence spectra. Simultaneous pump-probe pulses induce stimulated emission (SE) which, in turn, modulates the thermalized energy, and hence the photoacoustic (PA) signal amplitude. For time-delayed pulses, by contrast, SE is suppressed. Since this is not observed in endogenous chromophores, the location of the fluorophore can be determined by subtracting images acquired using simultaneous and time-delayed pump-probe excitation. This simple experimental approach exploits a fluorophorespecific contrast mechanism, and has the potential to enable deep-tissue molecular imaging at fluences below the MPE. In this study, some of the challenges to its in vivo implementation are addressed. First, the PA signal amplitude generated in fluorophores in vivo is often much smaller than that in blood. Second, tissue motion can give rise to artifacts that correspond to endogenous chromophores in the difference image. This would not allow the unambiguous detection of fluorophores. A method to suppress motion artifacts based on fast switching between simultaneous and time-delayed pump-probe excitation was developed. This enables the acquisition of PA signals using the two excitation modes with minimal time delay (20 ms), thus minimizing the effects of tissue motion. The feasibility of this method is demonstrated by visualizing a fluorophore (Atto680) in tissue phantoms, which were moved during the image acquisition to mimic tissue motion.

  11. Plasmonic spectrum on 1D and 2D periodic arrays of rod-shape metal nanoparticle pairs with different core patterns for biosensor and solar cell applications

    NASA Astrophysics Data System (ADS)

    Kumara, N. T. R. N.; Chou Chau, Yuan-Fong; Huang, Jin-Wei; Huang, Hung Ji; Lin, Chun-Ting; Chiang, Hai-Pang

    2016-11-01

    Simulations of surface plasmon resonance (SPR) on the near field intensity and absorption spectra of one-dimensional (1D) and two-dimensional (2D) periodic arrays of rod-shape metal nanoparticle (MNP) pairs using the finite element method (FEM) and taking into account the different core patterns for biosensor and solar cell applications are investigated. A tunable optical spectrum corresponding to the transverse SPR modes is observed. The peak resonance wavelength (λ res) can be shifted to red as the core patterns in rod-shape MNPs have been changed. We find that the 2D periodic array of core-shell MNP pairs (case 2) exhibit a red shifted SPR that can be tuned the gap enhancement and absorption efficiency simultaneously over an extended wavelength range. The tunable optical performances give us a qualitative idea of the geometrical properties of the periodic array of rod-shape MNP pairs on SPRs that can be as a promising candidate for plasmonic biosensor and solar cell applications.

  12. In situ hybridization study of CYP2D mRNA in the common marmoset brain

    PubMed Central

    Shimamoto, Yoshinori; Niimi, Kimie; Kitamura, Hiroshi; Tsubakishita, Sae; Takahashi, Eiki

    2016-01-01

    The common marmoset is a non-human primate that has increasingly employed in the biomedical research including the fields of neuroscience and behavioral studies. Cytochrome P450 (CYP) 2D has been speculated to be involved in psycho-neurologic actions in the human brain. In the present study, to clarify the role of CYP2D in the marmoset brain, we investigated the expression patterns of CYP2D mRNA in the brain using in situ hybridization (ISH). In addition, to identify the gene location of CYP2D19, a well-studied CYP2D isoform in the common marmoset, a fluorescence in situ hybridization (FISH) study was performed. Consistent with findings for the human brain, CYP2D mRNA was localized in the neuronal cells of different brain regions; e.g., the cerebral cortex, hippocampus, substantia nigra, and cerebellum. FISH analysis showed that the CYP2D19 gene was located on chromosome 1q, which is homologous to human chromosome 22 on which the CYP2D6 gene exists. These results suggest that CYP2D in the marmoset brain may play the same role as human CYP2D6 in terms of brain actions, and that the CYP2D19 gene is conserved in a syntenic manner. Taken together, these findings suggest that the common marmoset is a useful model for studying psychiatric disorders related to CYP2D dysfunction in the brain. PMID:27356856

  13. Hydrothermal synthesis of zinc(II)-phosphonate coordination polymers with different dimensionality (0D, 2D, 3D) and dimensionality change in the solid phase (0D→3D) induced by temperature

    SciTech Connect

    Fernández-Zapico, Eva; Montejo-Bernardo, Jose; Fernández-González, Alfonso; García, José R. García-Granda, Santiago

    2015-05-15

    Three new zinc(II) coordination polymers, [Zn(HO{sub 3}PCH{sub 2}CH{sub 2}COO)(C{sub 12}H{sub 8}N{sub 2})(H{sub 2}O)] (1), [Zn{sub 3}(O{sub 3}PCH{sub 2}CH{sub 2}COO){sub 2}(C{sub 12}H{sub 8}N{sub 2})](H{sub 2}O){sub 3.40} (2) and [Zn{sub 5}(HO{sub 3}PCH{sub 2}CH{sub 2}COO){sub 2}(O{sub 3}PCH{sub 2}CH{sub 2}COO){sub 2}(C{sub 12}H{sub 8}N{sub 2}){sub 4}](H{sub 2}O){sub 0.32} (3), with different structural dimensionality (0D, 2D and 3D, respectively) have been prepared by hydrothermal synthesis, and their structures were determined by single-crystal X-ray diffraction. Compound 1 crystallizes in the monoclinic system (P2{sub 1}/c) forming discrete dimeric units bonded through H-bonds, while compounds 2 and 3 crystallize in the triclinic (P−1) and the monoclinic (C2/c) systems, respectively. Compound 3, showing three different coordination numbers (4, 5 and 6) for the zinc atoms, has also been obtained by thermal treatment of 1 (probed by high-temperature XRPD experiments). The crystalline features of these compounds, related to the coordination environments for the zinc atoms in each structure, provoke the increase of the relative fluorescence for 2 and 3, compared to the free phenanthroline. Thermal analysis (TG and DSC) and XPS studies have been also carried out for all compounds. - Graphical abstract: Three new coordination compounds of zinc with 2-carboxyethylphosphonic acid (H{sub 2}PPA) and phenanthroline have been obtained by hydrothermal synthesis. The crystalline structure depends on the different coordination environments of the zinc atoms (see two comparative Zn{sub 6}-moieties). The influence of the different coordination modes of H{sub 2}PPA with the central atom in all structures have been studied, being found new coordination modes for this ligand. Several compounds show a significant increase in relative fluorescence with respect to the free phenanthroline. - Highlights: • Compounds have been obtained modifying the reaction time and the rate of

  14. Growth mechanisms of 2D organic assemblies generated from dialkylated melaminium derivatives: the length difference of the two alkyl chains that matters.

    PubMed

    Xu, Jun; Wu, Guanglu; Wang, Zhiqiang; Zhang, Xi

    2013-08-27

    This research is aimed to understand the growth mechanisms for self-assembly of dialkylated melamine derivatives. The dialkylated melamine derivatives with different alkyl chains (Mela-m-n) are able to self-assemble with hydrochloric acid in dichloromethane to form 2D organic assemblies, exhibiting similar lamellar structures as Mela-n·HCl with identical alkyl chains. The most interesting finding is that the growth mechanism of Mela-n·HCl with identical alkyl chains is revealed to be layer growth, while Mela-m-n·HCl with asymmetric alkyl chains adopts a spiral growth mechanism. The asymmetric alkyl chains in Mela-m-n may lead to the formation of dislocation, which is responsible for the spiral growth mechanism.

  15. Fluorescence: An Interdisciplinary Phenomenon for Different Education Levels

    ERIC Educational Resources Information Center

    García, J. A.; Moreno, J. M.; Perales, F. J.; Romero, J.; Sánchez, P.; Gómez-Robledo, L.

    2012-01-01

    This paper shows the scientific foundations of a natural phenomenon of undoubted interest and applicability in our day, fluorescence, and its possibilities for teaching at three educational levels: primary, secondary and university. It begins by describing the nature of the phenomenon and continues by explaining how we work with students of the…

  16. Verification of a non-hydrostatic dynamical core using the horizontal spectral element method and vertical finite difference method: 2-D aspects

    NASA Astrophysics Data System (ADS)

    Choi, S.-J.; Giraldo, F. X.; Kim, J.; Shin, S.

    2014-11-01

    The non-hydrostatic (NH) compressible Euler equations for dry atmosphere were solved in a simplified two-dimensional (2-D) slice framework employing a spectral element method (SEM) for the horizontal discretization and a finite difference method (FDM) for the vertical discretization. By using horizontal SEM, which decomposes the physical domain into smaller pieces with a small communication stencil, a high level of scalability can be achieved. By using vertical FDM, an easy method for coupling the dynamics and existing physics packages can be provided. The SEM uses high-order nodal basis functions associated with Lagrange polynomials based on Gauss-Lobatto-Legendre (GLL) quadrature points. The FDM employs a third-order upwind-biased scheme for the vertical flux terms and a centered finite difference scheme for the vertical derivative and integral terms. For temporal integration, a time-split, third-order Runge-Kutta (RK3) integration technique was applied. The Euler equations that were used here are in flux form based on the hydrostatic pressure vertical coordinate. The equations are the same as those used in the Weather Research and Forecasting (WRF) model, but a hybrid sigma-pressure vertical coordinate was implemented in this model. We validated the model by conducting the widely used standard tests: linear hydrostatic mountain wave, tracer advection, and gravity wave over the Schär-type mountain, as well as density current, inertia-gravity wave, and rising thermal bubble. The results from these tests demonstrated that the model using the horizontal SEM and the vertical FDM is accurate and robust provided sufficient diffusion is applied. The results with various horizontal resolutions also showed convergence of second-order accuracy due to the accuracy of the time integration scheme and that of the vertical direction, although high-order basis functions were used in the horizontal. By using the 2-D slice model, we effectively showed that the combined spatial

  17. Self-assembly and morphology change of four organic-polyoxometalate hybrids with different solid structures from 2D lamellar to 3D hexagonal forms

    NASA Astrophysics Data System (ADS)

    TAN, Chunxia

    2017-02-01

    A series of organic-polyoxometalate hybrids L-EuW11, L-EuW10, L-EuW22 and L-Mo132 were fabricated by the same organic cations with different polyoxometalate anions from K5[Eu(SiW11O39)(H2O)2], K13[Eu(SiW11O39)2]·15H2O, Na9[EuW10O36]·36H2O to "Keplerate" -type (NH4)72[Mo132O372(SO4)30(H2O)72]. The structures of hybrids were characterized by elemental analysis, thermogravimetric analysis (TGA), infrared spectra (IR) and small-angle X-ray scattering (SAXS). Self-assembly behaviors and aggregates morphology of these hybrids in mixed solution of chloroform-methanol are obtained by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). L-EuW11, L-EuW10 and L-EuW22 have different aggregation morphology but the similarly layered structures. Micron-sized vesicular structures of L-Mo132 rupture in solvent and eventually turn into approximate hexagon. SAXS analysis of L-EuW11, L-EuW10 and L-EuW22 shows that these hybrids aggregates change from two-dimensional (2D) lamellar to three-dimensional (3D) hexagonal structure in solid state.

  18. Physiologically Based Pharmacokinetic Predictions of Tramadol Exposure Throughout Pediatric Life: an Analysis of the Different Clearance Contributors with Emphasis on CYP2D6 Maturation.

    PubMed

    T'jollyn, Huybrecht; Snoeys, Jan; Vermeulen, An; Michelet, Robin; Cuyckens, Filip; Mannens, Geert; Van Peer, Achiel; Annaert, Pieter; Allegaert, Karel; Van Bocxlaer, Jan; Boussery, Koen

    2015-11-01

    This paper focuses on the retrospective evaluation of physiologically based pharmacokinetic (PBPK) techniques used to mechanistically predict clearance throughout pediatric life. An intravenous tramadol retrograde PBPK model was set up in Simcyp® using adult clearance values, qualified for CYP2D6, CYP3A4, CYP2B6, and renal contributions. Subsequently, the model was evaluated for mechanistic prediction of total, CYP2D6-related, and renal clearance predictions in very early life. In two in vitro pediatric human liver microsomal (HLM) batches (1 and 3 months), O-desmethyltramadol and N-desmethyltramadol formation rates were compared with CYP2D6 and CYP3A4 activity, respectively. O-desmethyltramadol formation was mediated only by CYP2D6, while N-desmethyltramadol was mediated in part by CYP3A4. Additionally, the clearance maturation of the PBPK model predictions was compared to two in vivo maturation models (Hill and exponential) based on plasma concentration data, and to clearance estimations from a WinNonlin® fit of plasma concentration and urinary excretion data. Maturation of renal and CYP2D6 clearance is captured well in the PBPK model predictions, but total tramadol clearance is underpredicted. The most pronounced underprediction of total and CYP2D6-mediated clearance was observed in the age range of 2-13 years. In conclusion, the PBPK technique showed to be a powerful mechanistic tool capable of predicting maturation of CYP2D6 and renal tramadol clearance in early infancy, although some underprediction occurs between 2 and 13 years for total and CYP2D6-mediated tramadol clearance.

  19. Characterization of metabolites in different kiwifruit varieties by NMR and fluorescence spectroscopy.

    PubMed

    Abdul Hamid, Nur Ashikin; Mediani, Ahmed; Maulidiani, M; Abas, Faridah; Park, Yong Seo; Leontowicz, Hanna; Leontowicz, Maria; Namiesnik, Jacek; Gorinstein, S

    2017-05-10

    It is known from our previous studies that kiwifruits, which are used in common human diet, have preventive properties of coronary artery disease. This study describes a combination of (1)H NMR spectroscopy, multivariate data analyses and fluorescence measurements in differentiating of some kiwifruit varieties, their quenching and antioxidant properties. A total of 41 metabolites were identified by comparing with literature data Chenomx database and 2D NMR. The binding properties of the extracted polyphenols against HSA showed higher reactivity of studied two cultivars in comparison with the common Hayward. The results showed that the fluorescence of HSA was quenched by Bidan as much as twice than by other fruits. The correlation between the binding properties of polyphenols in the investigated fruits, their relative quantification and suggested metabolic pathway was established. These results can provide possible application of fruit extracts in pharmaceutical industry.

  20. 2D DIGE analysis of the bursa of Fabricius reveals characteristic proteome profiles for different stages of chicken B-cell development.

    PubMed

    Korte, Julia; Fröhlich, Thomas; Kohn, Marina; Kaspers, Bernd; Arnold, Georg J; Härtle, Sonja

    2013-01-01

    Antibody producing B-cells are an essential component of the immune system. In contrast to human and mice where B-cells develop in the bone marrow, chicken B-cells develop in defined stages in the bursa of Fabricius, a gut associated lymphoid tissue. In order to gain a better understanding of critical biological processes like immigration of B-cell precursors into the bursa anlage, their differentiation and final emigration from the bursa we analyzed the proteome dynamics of this organ during embryonic and posthatch development. Samples were taken from four representative developmental stages (embryonic day (ED) 10, ED18, day 2, and day 28) and compared in an extensive 2D DIGE approach comprising six biological replicates per time point. Cluster analysis and PCA demonstrated high reliability and reproducibility of the obtained data set and revealed distinctive proteome profiles for the selected time points, which precisely reflect the differentiation processes. One hundred fifty three protein spots with significantly different intensities were identified by MS. We detected alterations in the abundance of several proteins assigned to retinoic acid metabolism (e.g. retinal-binding protein 5) and the actin-cytoskeleton (e.g. vinculin and gelsolin). By immunohistochemistry, desmin was identified as stromal cell protein associated with the maturation of B-cell follicles. Strongest protein expression difference (10.8-fold) was observed for chloride intracellular channel 2. This protein was thus far not associated with B-cell biology but our data suggest an important function in bursa B-cell development.

  1. Assembly of 1D nanofibers into a 2D bi-layered composite nanofibrous film with different functionalities at the two layers via layer-by-layer electrospinning.

    PubMed

    Wang, Zijiao; Ma, Qianli; Dong, Xiangting; Li, Dan; Xi, Xue; Yu, Wensheng; Wang, Jinxian; Liu, Guixia

    2016-12-21

    A two-dimensional (2D) bi-layered composite nanofibrous film assembled by one-dimensional (1D) nanofibers with trifunctionality of electrical conduction, magnetism and photoluminescence has been successfully fabricated by layer-by-layer electrospinning. The composite film consists of a polyaniline (PANI)/Fe3O4 nanoparticle (NP)/polyacrylonitrile (PAN) tuned electrical-magnetic bifunctional layer on one side and a Tb(TTA)3(TPPO)2/polyvinylpyrrolidone (PVP) photoluminescent layer on the other side, and the two layers are tightly combined face-to-face together into the novel bi-layered composite film of trifunctionality. The brand-new film has totally different characteristics at the double layers. The electrical conductivity and magnetism of the electrical-magnetic bifunctional layer can be, respectively, tunable via modulating the PANI and Fe3O4 NP contents, and the highest electrical conductivity can reach up to the order of 10(-2) S cm(-1), and predominant intense green emission at 545 nm is obviously observed in the photoluminescent layer under the excitation of 357 nm single-wavelength ultraviolet light. More importantly, the luminescence intensity of the photoluminescent layer remains almost unaffected by the electrical-magnetic bifunctional layer because the photoluminescent materials have been successfully isolated from dark-colored PANI and Fe3O4 NPs. By comparing with the counterpart single-layered composite nanofibrous film, it is found that the bi-layered composite nanofibrous film has better performance. The novel bi-layered composite nanofibrous film with trifunctionality has potential in the fields of nanodevices, molecular electronics and biomedicine. Furthermore, the design conception and fabrication technique for the bi-layered multifunctional film provide a new and facile strategy towards other films of multifunctionality.

  2. Accurate modeling of fluorescence line narrowing difference spectra: Direct measurement of the single-site fluorescence spectrum

    NASA Astrophysics Data System (ADS)

    Reppert, Mike; Naibo, Virginia; Jankowiak, Ryszard

    2010-07-01

    Accurate lineshape functions for modeling fluorescence line narrowing (FLN) difference spectra (ΔFLN spectra) in the low-fluence limit are derived and examined in terms of the physical interpretation of various contributions, including photoproduct absorption and emission. While in agreement with the earlier results of Jaaniso [Proc. Est. Acad. Sci., Phys., Math. 34, 277 (1985)] and Fünfschilling et al. [J. Lumin. 36, 85 (1986)], the derived formulas differ substantially from functions used recently [e.g., M. Rätsep et al., Chem. Phys. Lett. 479, 140 (2009)] to model ΔFLN spectra. In contrast to traditional FLN spectra, it is demonstrated that for most physically reasonable parameters, the ΔFLN spectrum reduces simply to the single-site fluorescence lineshape function. These results imply that direct measurement of a bulk-averaged single-site fluorescence lineshape function can be accomplished with no complicated extraction process or knowledge of any additional parameters such as site distribution function shape and width. We argue that previous analysis of ΔFLN spectra obtained for many photosynthetic complexes led to strong artificial lowering of apparent electron-phonon coupling strength, especially on the high-energy side of the pigment site distribution function.

  3. Fluorescently tuned nitrogen-doped carbon dots from carbon source with different content of carboxyl groups

    SciTech Connect

    Wang, Hao; Wang, Yun; Dai, Xiao; Zou, Guifu E-mail: zouguifu@suda.edu.cn; Gao, Peng; Zhang, Ke-Qin E-mail: zouguifu@suda.edu.cn; Du, Dezhuang; Guo, Jun

    2015-08-01

    In this study, fluorescent nitrogen-doped carbon dots (NCDs) were tuned via varying the sources with different number of carboxyl groups. Owing to the interaction between amino and carboxyl, more amino groups conjugate the surface of the NCDs by the source with more carboxyl groups. Fluorescent NCDs were tuned via varying the sources with different content of carboxyl groups. Correspondingly, the nitrogen content, fluorescence quantum yields and lifetime of NCDs increases with the content of carboxyl groups from the source. Furthermore, cytotoxicity assay and cell imaging test indicate that the resultant NCDs possess low cytotoxicity and excellent biocompatibility.

  4. Molecular environments of divinyl chlorophylls in Prochlorococcus and Synechocystis: differences in fluorescence properties with chlorophyll replacement.

    PubMed

    Mimuro, Mamoru; Murakami, Akio; Tomo, Tatsuya; Tsuchiya, Tohru; Watabe, Kazuyuki; Yokono, Makio; Akimoto, Seiji

    2011-05-01

    A marine cyanobacterium, Prochlorococcus, is a unique oxygenic photosynthetic organism, which accumulates divinyl chlorophylls instead of the monovinyl chlorophylls. To investigate the molecular environment of pigments after pigment replacement but before optimization of the protein moiety in photosynthetic organisms, we compared the fluorescence properties of the divinyl Chl a-containing cyanobacteria, Prochlorococcus marinus (CCMP 1986, CCMP 2773 and CCMP 1375), by a Synechocystis sp. PCC 6803 (Synechocystis) mutant in which monovinyl Chl a was replaced with divinyl Chl a. P. marinus showed a single fluorescence band for photosystem (PS) II at 687nm at 77K; this was accompanied with change in pigment, because the Synechocystis mutant showed the identical shift. No fluorescence bands corresponding to the PS II 696-nm component and PS I longer-wavelength component were detected in P. marinus, although the presence of the former was suggested using time-resolved fluorescence spectra. Delayed fluorescence (DF) was detected at approximately 688nm with a lifetime of approximately 29ns. In striking contrast, the Synechocystis mutant showed three fluorescence bands at 687, 696, and 727nm, but suppressed DF. These differences in fluorescence behaviors might not only reflect differences in the molecular structure of pigments but also differences in molecular environments of pigments, including pigment-pigment and/or pigment-protein interactions, in the antenna and electron transfer systems.

  5. Calculation of effective conductivity of 2D and 3D composite materials with anisotropic constituents and different inclusion shapes in Mathematica

    NASA Astrophysics Data System (ADS)

    Gómez-Muñoz, José Luis; Bravo-Castillero, Julián

    2008-08-01

    The study of the effective properties of composite materials with anisotropic constituents and different inclusion shapes has motivated the development of the Mathematica 6.0 package "CompositeMaterials". This package can be used to calculate the effective anisotropic conductivity tensor of two-phase composites. Any fiber cross section, even percolating ones, can be studied in the 2D composites. "Rectangular Prism" and "Ellipsoidal" inclusion shapes with arbitrary orientations can be investigated in the 3D composites. This package combines the Asymptotic Homogenization Method and the Finite Element Method in order to obtain the effective conductivity tensor. The commands and options of the package are illustrated with two sample applications for two- and three-dimensional composites. Program summaryProgram title:CompositeMaterials Catalogue identifier:AEAU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAU_v1_0.html Program obtainable from:CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions:Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.:132 183 No. of bytes in distributed program, including test data, etc.:1 334 908 Distribution format:tar.gz Programming language:Mathematica 6.0 Computer:Any that can run Mathematica 6.0 and where the open-source free C-programs Triangle ( http://www.cs.cmu.edu/ quake/triangle.html) and TetGen ( http://tetgen.berlios.de/) can be compiled and executed. Tested in Intel Pentium computers. Operating system:Any that can run Mathematica 6.0 and where the open-source free C-programs Triangle ( http://www.cs.cmu.edu/ quake/triangle.html) and TetGen ( http://tetgen.berlios.de/) can be compiled and executed. Tested in Windows XP. RAM:Small two-dimensional calculations require less than 100 MB. Large three-dimensional calculations require 500 MB or more. Classification:7.9 External routines:One Mathematica Add-on and

  6. 2D semiconductor optoelectronics

    NASA Astrophysics Data System (ADS)

    Novoselov, Kostya

    The advent of graphene and related 2D materials has recently led to a new technology: heterostructures based on these atomically thin crystals. The paradigm proved itself extremely versatile and led to rapid demonstration of tunnelling diodes with negative differential resistance, tunnelling transistors, photovoltaic devices, etc. By taking the complexity and functionality of such van der Waals heterostructures to the next level we introduce quantum wells engineered with one atomic plane precision. Light emission from such quantum wells, quantum dots and polaritonic effects will be discussed.

  7. Variable-temperature Fourier-transform infrared studies of poly(L-lactic acid) in different states of order: A 2DCOS and PCMW2D analysis

    NASA Astrophysics Data System (ADS)

    Zhang, Pudun; Unger, Miriam; Pfeifer, Frank; Siesler, Heinz W.

    2016-11-01

    Variable-temperature Fourier-transform infrared (FT-IR) spectra of a predominantly amorphous and a semi-crystalline poly(L-lactic acid) (PLLA) film were measured between 30 °C and 170 °C in order to investigate their temperature-dependent structural changes as a function of the initial state of order. For an in-depth analysis of the spectral variations in the carbonyl stretching band region (1803-1722 cm-1) two-dimensional correlation spectroscopy (2DCOS) and perturbation-correlation moving-window two-dimensional (PCMW2D) analyses were applied. Significant spectral changes were observed during heating of the amorphous PLLA sample whereas the semi-crystalline specimen showed only slight band shifts as a function of the external perturbation. The PCMW2D results suggested that for efficient 2DCOS analyses the heating process should be split up in two temperature intervals. These analyses then provided information on the recrystallization of the amorphous regions, the presence of an intermediate state of order and a sequence scenario for the observed spectral changes.

  8. 2D and 3D bimetallic oxalate-based ferromagnets prepared by insertion of different Fe(III) spin crossover complexes.

    PubMed

    Clemente-León, Miguel; Coronado, Eugenio; López-Jordà, Maurici

    2010-05-28

    The syntheses, structures and magnetic properties of the compounds of formula [Fe(III)(5-NO(2)sal(2)-trien)][Mn(II)Cr(III)(ox)(3)]·CH(3)NO(2).0.5H(2)O (1) and [Fe(III)(5-CH(3)Osal(2)-trien)][Mn(II)Cr(III)(ox)(3)] (2) are reported. The structure of 1, that crystallizes in the P2(1) chiral space group, presents a 2D honeycomb anionic layer formed by Mn(II) and Cr(III) ions linked through oxalate ligands and a cationic layer of [Fe(III)(5-NO(2)sal(2)-trien)](+) complexes intercalated between the 2D oxalate network. The structure of 2, that crystallizes in the Pna2(1) acentric space group, presents a 3D achiral anionic network formed by Mn(II) and Cr(III) ions linked through oxalate ligands with [Fe(5-CH(3)Osal(2)-trien)](+) complexes intercalated within the 3D oxalate network. The magnetic properties of 1 and 2 indicate that both compounds undergo a long-range ferromagnetic ordering at ca. 5 K. On the other hand, the inserted Fe(III) cations remain mainly in the low-spin (LS) state in the case of 1 and in the high-spin (HS) state in the case of 2.

  9. Quantitative 2D liquid-state NMR.

    PubMed

    Giraudeau, Patrick

    2014-06-01

    Two-dimensional (2D) liquid-state NMR has a very high potential to simultaneously determine the absolute concentration of small molecules in complex mixtures, thanks to its capacity to separate overlapping resonances. However, it suffers from two main drawbacks that probably explain its relatively late development. First, the 2D NMR signal is strongly molecule-dependent and site-dependent; second, the long duration of 2D NMR experiments prevents its general use for high-throughput quantitative applications and affects its quantitative performance. Fortunately, the last 10 years has witnessed an increasing number of contributions where quantitative approaches based on 2D NMR were developed and applied to solve real analytical issues. This review aims at presenting these recent efforts to reach a high trueness and precision in quantitative measurements by 2D NMR. After highlighting the interest of 2D NMR for quantitative analysis, the different strategies to determine the absolute concentrations from 2D NMR spectra are described and illustrated by recent applications. The last part of the manuscript concerns the recent development of fast quantitative 2D NMR approaches, aiming at reducing the experiment duration while preserving - or even increasing - the analytical performance. We hope that this comprehensive review will help readers to apprehend the current landscape of quantitative 2D NMR, as well as the perspectives that may arise from it.

  10. ON THE STAINING OF PARAAGGLUTINATING E. COLI STRAINS WITH FLUORESCENT SERA OF DIFFERENT SPECIFICITY,

    DTIC Science & Technology

    Paraagglutinizing E . coli strains, both isolated naturally and obtained experimentally, were able in different degrees to adsorb serum proteins of...various specificity. In staining E . coli parastrains with fluorescent sera of different specificity (through the direct and indirect method), microbe

  11. Denaturation studies reveal significant differences between GFP and blue fluorescent protein.

    PubMed

    Saeed, Ibtesam A; Ashraf, S Salman

    2009-10-01

    Green fluorescent protein (GFP) is an unusually stable fluorescent protein that belongs to a family of related auto-fluorescent proteins (AFPs). These AFPs have been generated from jellyfish GFP by mutating the amino acids in the chromophore or its vicinity. Variants that emit light in the blue region (Blue Fluorescent Protein, BFP), red region, or yellow region are readily available and are widely used in diverse applications. Previously, we had used fluorescence spectroscopy to study the effect of pH on the denaturation of GFP with SDS, urea, and heat. Surprisingly, we found that SDS, urea or heat, did not have any significant effect on the fluorescence of GFP at pH 7.5 or 8.5, however, at pH 6.5, the protein lost all fluorescence within a very short period of time. These results suggested that GFP undergoes a structural/stability shift between pH 6.5 and 7.5, with the GFP structure at pH 6.5 being very sensitive to denaturation by SDS, urea, and heat. In the present study, we wanted to explore whether the stability or structure of the closely related BFP is also pH dependent. As expected, we found heat-induced denaturation and renaturation of BFP to be pH dependent, very much like GFP. However, when exposed to other denaturants like urea/heat or SDS we found BFP to behave very differently than GFP. Unlike GFP, which at pH 8.5 and 7.5 is very resistant to SDS-induced denaturation, BFP readily lost about 20% of its fluorescence at pH 8.5 and about 60% fluorescence at pH 7.5. Also, our denaturation and renaturation studies show that under certain conditions, BFP is more stable than GFP, such that under conditions where GFP is completely denatured, BFP still retained significant fluorescence. Taken together, our preliminary results show that despite being very similar in both amino acid sequences and overall structures, there may be subtle and important structural/conformational differences between BFP and GFP.

  12. Fluorescence quenching of 7-amino-4-methylcoumarin by different TEMPO derivatives

    NASA Astrophysics Data System (ADS)

    Żamojć, Krzysztof; Wiczk, Wiesław; Zaborowski, Bartłomiej; Jacewicz, Dagmara; Chmurzyński, Lech

    2015-02-01

    The fluorescence quenching of 7-amino-4-methylcoumarin by different TEMPO derivatives was studied in aqueous solutions with the use of steady-state, time-resolved fluorescence spectroscopy as well as UV-VIS absorption spectroscopy methods. In order to distinguish each TEMPO derivative from the others and to understand the mechanism of quenching, the absorption and fluorescence emission spectra as well as decays of the fluorescence of 7-amino-4-methylcoumarin were registered as a function of each TEMPO derivative concentration. There were no deviations from a linearity in the Stern-Volmer plots (determined from both, steady-state and time-resolved measurements). The fluorescence quenching mechanism was found to be entirely collisional, what was additionally confirmed by the registration of Stern-Volmer plots at 5 temperatures ranging from 15 to 55 °C. Based on theoretical calculations of molecular radii and ionization potentials of all TEMPO derivatives the mechanism of electron transfer was rejected. The fluorescence quenching which was being studied seems to be diffusion-limited and caused by the increase of non-radiative processes, such as an internal conversion and an intersystem crossing. The Stern-Volmer quenching constants and bimolecular quenching constants were determined at the room temperature for all TEMPO derivatives studied. Among all TEMPO derivatives studied TEMPO-4-amino-4-carboxylic acid (TOAC) was found to be the most effective quencher of 7-amino-4-methylcoumarin fluorescence (kq for TOAC was approximately 1.5 higher than kq for other TEMPO compounds studied). The findings demonstrate the possibility of developing an analytical method for the quantitative determination of TOAC, which incorporation into membrane proteins may provide a direct detection of peptide backbone dynamics.

  13. Variability in chlorophyll fluorescence spectra of eggplant fruit grown under different light environments: a case study.

    PubMed

    Ospina Calvo, Brian; Parapugna, Tamara L; Lagorio, M Gabriela

    2017-03-13

    The main goal of the present work was to clarify physiological strategies in plants whose chloroplasts were developed under different light environments. The specific objective was to elucidate the influence of the spectral distribution of light on the chlorophyll fluorescence ratio and on photosynthetic parameters. To achieve this purpose, three species of eggplant fruit (black, purple and white striped and white) were used as a case study and their chlorophyll fluorescence was analyzed in detail. Spectra of the non-variable fluorescence in each part of the fruit were corrected for distortions by light reabsorption processes using a physical model. The main conclusion of this work was that the corrected fluorescence ratio was dependent on the contribution of each photosystem to the fluorescence and consequently on the environmental lighting conditions, becoming higher when illumination was rich in long wavelengths. Variable chlorophyll fluorescence, similar to that observed from plant leaves, was detected for the pulp of the black eggplant, for the pulp of the purple and white striped eggplant and for the intact fruit of the black eggplant. The maximum quantum efficiency of photosystem II in the light-adapted state (F'v/F'm), the quantum efficiency of photosystem II (ΦPSII), and the photochemical and non-photochemical quenching coefficients (qP and qNP/NPQ respectively) were determined in each case. The results could be explained very interestingly, in relation with the proportion of exciting light reaching each photosystem (I and II). The photochemical parameters obtained from variable chlorophyll fluorescence, allowed us to monitor non-destructively the physiological state of the black fruit during storage under both chilled or room-temperature conditions.

  14. Fluorescence quenching of 7-amino-4-methylcoumarin by different TEMPO derivatives.

    PubMed

    Żamojć, Krzysztof; Wiczk, Wiesław; Zaborowski, Bartłomiej; Jacewicz, Dagmara; Chmurzyński, Lech

    2015-02-05

    The fluorescence quenching of 7-amino-4-methylcoumarin by different TEMPO derivatives was studied in aqueous solutions with the use of steady-state, time-resolved fluorescence spectroscopy as well as UV-VIS absorption spectroscopy methods. In order to distinguish each TEMPO derivative from the others and to understand the mechanism of quenching, the absorption and fluorescence emission spectra as well as decays of the fluorescence of 7-amino-4-methylcoumarin were registered as a function of each TEMPO derivative concentration. There were no deviations from a linearity in the Stern-Volmer plots (determined from both, steady-state and time-resolved measurements). The fluorescence quenching mechanism was found to be entirely collisional, what was additionally confirmed by the registration of Stern-Volmer plots at 5 temperatures ranging from 15 to 55°C. Based on theoretical calculations of molecular radii and ionization potentials of all TEMPO derivatives the mechanism of electron transfer was rejected. The fluorescence quenching which was being studied seems to be diffusion-limited and caused by the increase of non-radiative processes, such as an internal conversion and an intersystem crossing. The Stern-Volmer quenching constants and bimolecular quenching constants were determined at the room temperature for all TEMPO derivatives studied. Among all TEMPO derivatives studied TEMPO-4-amino-4-carboxylic acid (TOAC) was found to be the most effective quencher of 7-amino-4-methylcoumarin fluorescence (kq for TOAC was approximately 1.5 higher than kq for other TEMPO compounds studied). The findings demonstrate the possibility of developing an analytical method for the quantitative determination of TOAC, which incorporation into membrane proteins may provide a direct detection of peptide backbone dynamics.

  15. Histologic differences between orthotopic xenograft pancreas models affect Verteporfin uptake measured by fluorescence microscopy and spectroscopy

    NASA Astrophysics Data System (ADS)

    O'Hara, Julia A.; Samkoe, Kimberley S.; Chen, Alina; Isabelle, Martin; Hoopes, P. J.; Hasan, Tayyaba; Pogue, Brian W.

    2012-02-01

    Photodynamic therapy (PDT) that uses the second generation photosensitizer, verteporfin (VP), is a developing therapy for pancreatic cancer. The optimal timing of light delivery related to VP uptake and distribution in pancreatic tumors will be important information to obtain to improve treatment for this intractable disease. In this work we examined uptake and distribution of VP in two orthotopic pancreatic tumors with different histological structure. ASPC-1 (fast-growing) and Panc-1 (slower growing) tumors were implanted in SCID mice and studied when tumors were approximately 100mm3. In a pilot study, these tumors had been shown to differ in uptake of VP using lightinduced fluorescence spectroscopy (LIFS) in vivo and fluorescence imaging ex vivo and that work is extended here. In vivo fluorescence mean readings of tumor and liver increased rapidly up to 15 minutes after photosensitizer injection for both tumor types, and then continued to increase up to 60 minutes post injection to a higher level in ASPC-1 than in Panc-1. There was variability among animals with the same tumor type, in both liver and tumor uptake and no selectivity of tumor over liver. In this work we further examined VP uptake at multiple time points in relation to microvascular density and perfusion, using DiOC7 (to mark blood vessels) and VP fluorescence in the same tissue slices. Analysis of DiOC7 fluorescence indicates that AsPC-1 and Panc-1 have different vascular densities but AsPC-1 vasculature is more perfusive. Analysis of colocalized DiOC7 and VP fluorescence showed ASPC-1 with higher accumulation of VP 3 hrs after injection and more VP at a distance from blood vessels compared to Panc-1. This work shows the need for techniques to analyze photosensitizer distribution in order to optimize photodynamic therapy as an effective treatment for pancreatic tumors.

  16. Different scenarios for inverse estimation of soil hydraulic parameters from double-ring infiltrometer data using HYDRUS-2D/3D

    NASA Astrophysics Data System (ADS)

    Mashayekhi, Parisa; Ghorbani-Dashtaki, Shoja; Mosaddeghi, Mohammad Reza; Shirani, Hossein; Nodoushan, Ali Reza Mohammadi

    2016-04-01

    In this study, HYDRUS-2D/3D was used to simulate ponded infiltration through double-ring infiltrometers into a hypothetical loamy soil profile. Twelve scenarios of inverse modelling (divided into three groups) were considered for estimation of Mualem-van Genuchten hydraulic parameters. In the first group, simulation was carried out solely using cumulative infiltration data. In the second group, cumulative infiltration data plus water content at h = -330 cm (field capacity) were used as inputs. In the third group, cumulative infiltration data plus water contents at h = -330 cm (field capacity) and h = -15 000 cm (permanent wilting point) were used simultaneously as predictors. The results showed that numerical inverse modelling of the double-ring infiltrometer data provided a reliable alternative method for determining soil hydraulic parameters. The results also indicated that by reducing the number of hydraulic parameters involved in the optimization process, the simulation error is reduced. The best one in infiltration simulation which parameters α, n, and Ks were optimized using the infiltration data and field capacity as inputs. Including field capacity as additional data was important for better optimization/definition of soil hydraulic functions, but using field capacity and permanent wilting point simultaneously as additional data increased the simulation error.

  17. Fluorescent probe ABM and estimation of immune state in patients with different pathologies (review article).

    PubMed

    Kalnina, Inta; Bruvere, Ruta; Zvagule, Tija; Gabruseva, Natalija; Klimkane, Laura; Kirilova, Elena; Meirovics, Imants; Kizane, Gunta

    2010-01-01

    The fluorescent probe ABM (3-aminobenzanthrone derivative) one of the fluorescent probes synthesized in Riga Technical University proved to be an excellent, independent model for studying cell membranes. In our work we have investigated the possibility of using the fluorescent probe ABM for detection of immune state in patients with different pathologies. There is a strong correlation among all studied ABM spectral parameters, immunological characteristics, clinical and laboratory investigations of the all observed patients groups. The obtained results suggest that ABM spectral parameters in cell suspension reflect the alterations of the cellular mechanisms of immunity. Therefore fluorescent method could be used as preliminary screening test in immune diagnostics instead of more expensive, time consuming methods (subset detection, radioisotope method etc.) used as routine in clinics. Spectral parameters of ABM reflect a wide range of interrelated (interdependent) characteristics of cells (physico-chemical state and microviscosity of membrane, proliferating and lipid metabolic activity of cells, distribution of cells among subsets). The observed change of the studied parameters reflects alterations of the cellular mechanisms of immunity which is a main focus for its application as preliminary screening test in immune diagnostics. The fluorescence based method is sensitive, less expensive and time consuming, technically simple and convenient.

  18. Syntheses, structures and properties of two 2-D layered hybrid organic-inorganic materials based on different V4O12 building units.

    PubMed

    Hou, Wentao; Guo, Jiuyu; Xu, Xiao; Wang, Zuoxiang; Zhang, Deng; Wan, Hongxiang; Song, You; Zhu, Dunru; Xu, Yan

    2014-01-14

    Two new layered hybrid organic-inorganic compounds [Zn(pyim)]2V4O12 () (pyim = 2-(2-pyridyl)imidazole) and [Cu(bim)2]2V4O12(H2O)·CH3CH2OH () (bim = bis(1-imidazolyl)methane) based on polyoxovanadates (POVs) and organic ligands decorated transition metal units have been synthesized by hydrothermal and solvothermal methods respectively. Single crystal XRD, fluorescence spectrum, magnetic measurement, IR spectra, powder XRD and thermogravimetric (TG) measurements were performed to analyze the structures and properties of and . The structural analysis reveals that compound features a two-dimensional {[Zn(pyim)]2V4O12}n layered structure, constructed by sine wave-like {V4O12}n(4n-) chains, Zn(2+) ions and pyim ligands. In the layered structure of , {V4O12}(4-) circles are connected by Cu(2+) ions to form {Cu(V4O12)}n(2n-) chains, which are further linked by {Cu(bim)4}(2+) subunits to generate a hybrid layer of . The magnetic susceptibility measurement indicates strong antiferromagnetic interactions between Cu(2+) ions in .

  19. Precise diagnosis in different scenarios using photoacoustic and fluorescence imaging with dual-modality nanoparticles

    NASA Astrophysics Data System (ADS)

    Peng, Dong; Du, Yang; Shi, Yiwen; Mao, Duo; Jia, Xiaohua; Li, Hui; Zhu, Yukun; Wang, Kun; Tian, Jie

    2016-07-01

    Photoacoustic imaging and fluorescence molecular imaging are emerging as important research tools for biomedical studies. Photoacoustic imaging offers both strong optical absorption contrast and high ultrasonic resolution, and fluorescence molecular imaging provides excellent superficial resolution, high sensitivity, high throughput, and the ability for real-time imaging. Therefore, combining the imaging information of both modalities can provide comprehensive in vivo physiological and pathological information. However, currently there are limited probes available that can realize both fluorescence and photoacoustic imaging, and advanced biomedical applications for applying this dual-modality imaging approach remain underexplored. In this study, we developed a dual-modality photoacoustic-fluorescence imaging nanoprobe, ICG-loaded Au@SiO2, which was uniquely designed, consisting of gold nanorod cores and indocyanine green with silica shell spacer layers to overcome fluorophore quenching. This nanoprobe was examined by both PAI and FMI for in vivo imaging on tumor and ischemia mouse models. Our results demonstrated that the nanoparticles can specifically accumulate at the tumor and ischemic areas and be detected by both imaging modalities. Moreover, this dual-modality imaging strategy exhibited superior advantages for a precise diagnosis in different scenarios. The new nanoprobe with the dual-modality imaging approach holds great potential for diagnosis and stage classification of tumor and ischemia related diseases.Photoacoustic imaging and fluorescence molecular imaging are emerging as important research tools for biomedical studies. Photoacoustic imaging offers both strong optical absorption contrast and high ultrasonic resolution, and fluorescence molecular imaging provides excellent superficial resolution, high sensitivity, high throughput, and the ability for real-time imaging. Therefore, combining the imaging information of both modalities can provide

  20. Can Sex Differences in Science Be Tied to the Long Reach of Prenatal Hormones? Brain Organization Theory, Digit Ratio (2D/4D), and Sex Differences in Preferences and Cognition

    PubMed Central

    Valla, Jeffrey; Ceci, Stephen J.

    2011-01-01

    Brain organization theory posits a cascade of physiological and behavioral changes initiated and shaped by prenatal hormones. Recently, this theory has been associated with outcomes including gendered toy preference, 2D/4D digit ratio, personality characteristics, sexual orientation, and cognitive profile (spatial, verbal, and mathematical abilities). We examine the evidence for this claim, focusing on 2D/4D and its putative role as a biomarker for organizational features that influence cognitive abilities/interests predisposing males toward mathematically and spatially intensive careers. Although massive support exists for early brain organization theory overall, there are myriad inconsistencies, alternative explanations, and outright contradictions that must be addressed while still taking the entire theory into account. Like a fractal within the larger theory, the 2D/4D hypothesis mirrors this overall support on a smaller scale while likewise suffering from inconsistencies (positive, negative, and sex-dependent correlations), alternative explanations (2D/4D related to spatial preferences rather than abilities per se), and contradictions (feminine 2D/4D in men associated with higher spatial ability). Using the debate over brain organization theory as the theoretical stage, we focus on 2D/4D evidence as an increasingly important player on this stage, a demonstrative case in point of the evidential complexities of the broader debate, and an increasingly important topic in its own right. PMID:22164187

  1. Diffusion behavior of the fluorescent proteins eGFP and Dreiklang in solvents of different viscosity monitored by fluorescence correlation spectroscopy

    NASA Astrophysics Data System (ADS)

    Junghans, Cornelia; Schmitt, Franz-Josef; Vukojević, Vladana; Friedrich, Thomas

    2016-12-01

    Fluorescence correlation spectroscopy relies on temporal autocorrelation analysis of fluorescence intensity fluctuations that spontaneously arise in systems at equilibrium due to molecular motion and changes of state that cause changes in fluorescence, such as triplet state transition, photoisomerization and other photophysical transformations, to determine the rates of these processes. The stability of a fluorescent molecule against dark state conversion is of particular concern for chromophores intended to be used as reference tags for comparing diffusion processes on multiple time scales. In this work, we analyzed properties of two fluorescent proteins, the photoswitchable Dreiklang and its parental eGFP, in solvents of different viscosity to vary the diffusion time through the observation volume element by several orders of magnitude. In contrast to eGFP, Dreiklang undergoes a dark-state conversion on the time scale of tens to hundreds of microseconds under conditions of intense fluorescence excitation, which results in artificially shortened diffusion times if the diffusional motion through the observation volume is sufficiently slowed down. Such photophysical quenching processes have also been observed in FCS studies on other photoswitchable fluorescent proteins including Citrine, from which Dreiklang was derived by genetic engineering. This property readily explains the discrepancies observed previously between the diffusion times of eGFP- and Dreiklang-labeled plasma membrane protein complexes.

  2. E-2D Advanced Hawkeye Aircraft (E-2D AHE)

    DTIC Science & Technology

    2015-12-01

    Selected Acquisition Report (SAR) RCS: DD-A&T(Q&A)823-364 E-2D Advanced Hawkeye Aircraft (E-2D AHE) As of FY 2017 President’s Budget Defense...Office Estimate RDT&E - Research, Development, Test, and Evaluation SAR - Selected Acquisition Report SCP - Service Cost Position TBD - To Be Determined

  3. 2D quasiperiodic plasmonic crystals

    PubMed Central

    Bauer, Christina; Kobiela, Georg; Giessen, Harald

    2012-01-01

    Nanophotonic structures with irregular symmetry, such as quasiperiodic plasmonic crystals, have gained an increasing amount of attention, in particular as potential candidates to enhance the absorption of solar cells in an angular insensitive fashion. To examine the photonic bandstructure of such systems that determines their optical properties, it is necessary to measure and model normal and oblique light interaction with plasmonic crystals. We determine the different propagation vectors and consider the interaction of all possible waveguide modes and particle plasmons in a 2D metallic photonic quasicrystal, in conjunction with the dispersion relations of a slab waveguide. Using a Fano model, we calculate the optical properties for normal and inclined light incidence. Comparing measurements of a quasiperiodic lattice to the modelled spectra for angle of incidence variation in both azimuthal and polar direction of the sample gives excellent agreement and confirms the predictive power of our model. PMID:23209871

  4. Identification of glycoprotein receptors within the human salivary proteome for the lectin-like BabA and SabA adhesins of Helicobacter pylori by fluorescence-based 2-D bacterial overlay.

    PubMed

    Walz, Anke; Odenbreit, Stefan; Stühler, Kai; Wattenberg, Andreas; Meyer, Helmut E; Mahdavi, Jafar; Borén, Thomas; Ruhl, Stefan

    2009-03-01

    Because gastric infection by Helicobacter pylori takes place via the oral route, possible interactions of this bacterium with human salivary proteins could occur. By using modified 1- and 2-D bacterial overlay, binding of H. pylori adhesins BabA and SabA to the whole range of salivary proteins was explored. Bound salivary receptor molecules were identified by MALDI-MS and by comparison to previously established proteome maps of whole and glandular salivas. By use of adhesin-deficient mutants, binding of H. pylori to MUC7 and gp-340 could be linked to the SabA and BabA adhesins, respectively, whereas binding to MUC5B was associated with both adhesins. Binding of H. pylori to the proline-rich glycoprotein was newly detected and assigned to BabA adhesin whereas the SabA adhesin was found to mediate binding to newly detected receptor molecules, including carbonic anhydrase VI, secretory component, heavy chain of secretory IgA1, parotid secretory protein and zinc-alpha(2)-glycoprotein. Some of these salivary glycoproteins are known to act as scavenger molecules or are involved in innate immunity whereas others might come to modify the pathogenetic properties of this organism. In general, this 2-D bacterial overlay technique represents a useful supplement in adhesion studies of bacteria with complex protein mixtures.

  5. Fluorescent sensing and electrocatalytic properties of three Zn(II)/Co(II) coordination complexes containing two different dicarboxylates and two various bis(pyridyl)-bis(amide) ligands

    NASA Astrophysics Data System (ADS)

    Lin, Hongyan; Rong, Xing; Liu, Guocheng; Wang, Xiang; Wang, Xiuli; Duan, Surui

    2016-09-01

    Three new transition metal(II) coordination complexes constructed from two different dicarboxylates (1,3-H2BDC = 1,3-benzenedicarboxylic acid, 1,4-H2NDC = 1,4-naphthalenedicarboxylic acid) and two bis(pyridyl)-bis(amide) ligands (3-bpcd = N,N‧-bis(3-pyridyl)cyclohexane-1,4-dicarboxamide, 3-bpod = N,N‧-bis(3-pyridyl)octandiamide), [Zn(1,3-BDC)(3-bpcd)0.5(H2O)]·H2O (1), [Zn(1,3-BDC)(3-bpod)0.5(H2O)] (2) and [Co(1,4-NDC)(3-bpod)1.5(H2O)] (3) have been synthesized in the hydrothermal environments and structurally characterized by IR, TG and single crystal X-ray diffraction. Complexes 1 and 2 possess the similar 1D ladder-like chain based on [Zn(1,3-BDC)]n zigzag chain and the bidentate ligands 3-bpcd/or 3-bpod. Complex 3 shows a 2D layered structure with a 5-connected {410} topology, which consists of 1D linear [Co(1,4-NDC)]n chain and [Co(3-bpod)1.5]n chain with alternating arrangement of 3-bpod ligands and Co2(3-bpod)2 dinuclear loops. The adjacent 1D chains for 1-2 or the 2D layers for 3 are further extended into 2D or 3D supramolecular frameworks through the hydrogen bonding interactions. Additionally, the solid state fluorescent properties for the title complexes 1-3, the fluorescent sensing behaviors of complexes 1-2 and the electrochemical behaviour of complex 3 have been investigated.

  6. [Fluorescence parameters of chlorophyll in leaves of caules plants in different environmental conditions].

    PubMed

    Iakovleva, O V; Talipova, E V; Kukarskikh, G P; Krendeleeva, T E; Rubin, A B

    2005-01-01

    The functional state of medicinal plants of Convallaria majalis L., Vaccinium vitis-idaeae L., Arctostaphylos uva-ursi L. in connection with heavy metal accumulation in their leaves under man impact was studied by the pulse-amplitude-modulation (PAM) fluorometric method. The relative yield of variable fluorescence (F(v)/F(m)), induction of fluorescence of chlorophyll, and fluorescence quenching processes in leaves at different distances from the local Kirov-Sovetsk, Kirov-Omutninsk road in Kirov region were analyzed. Changes in biophysical characteristics with the increasing content of heavy metals in leaves were demonstrated. The most informative characteristic is F(v)/F(m). Its value correlates with the activity of the photosynthetic apparatus and reflects the potential effeciency of photosynthesis. The better are the environmental conditions of plant growth, the higher is the F(v)/F(m) ratio and the lower is its average statistical deviation. Fluorescence induction curves do not always vary in shape under our ecological conditions, indicating relatively favorable conditions at places of plant growth investigated. The rate of the environmental pollution in the investigated region is not critical, since the content of heavy metal in leaves does not change considerably with the distance from the road.

  7. Analysis of the Fluorescence Correlation Function of Quantum Rods with Different Lengths.

    PubMed

    Lee, Jaeran; Kim, Sok Won

    2015-11-01

    We built a polarization fluorescence correlation spectroscopy system to analyze the variation of the correlation function in rotational diffusion based on the length of rod-like fluorescent particles. Because the rotational diffusion of particles in liquid depends on the relative polarization states of the laser source and particle fluorescence, we compared the amplitudes of the rotational diffusion using the autocorrelation function in different polarization states. For experiments that depend on the length of the fluorescent particles, we prepared three kinds of quantum rod samples with a width of 6.5 ± 0.5 nm and lengths of 17 ± 3, 40 ± 3, and 46 ± 3 nm. Through the experiment, we obtained the hydrodynamic radii of each particle using the rotational diffusion coefficient: 10.7 ± 0.8, 13.4 ± 0.7, and 14.1 ± 0.4 nm with the length of the particles. All the obtained values for radii are 3 nm larger than the calculated equivalent radii of spheres with the same volume as the rod samples. Through a fraction analysis by polarization state, we confirmed that the ratio of rotational fraction for polarization increases with the aspect ratio of the actual particle.

  8. Brittle damage models in DYNA2D

    SciTech Connect

    Faux, D.R.

    1997-09-01

    DYNA2D is an explicit Lagrangian finite element code used to model dynamic events where stress wave interactions influence the overall response of the system. DYNA2D is often used to model penetration problems involving ductile-to-ductile impacts; however, with the advent of the use of ceramics in the armor-anti-armor community and the need to model damage to laser optics components, good brittle damage models are now needed in DYNA2D. This report will detail the implementation of four brittle damage models in DYNA2D, three scalar damage models and one tensor damage model. These new brittle damage models are then used to predict experimental results from three distinctly different glass damage problems.

  9. Influence of different environments on the excited-state proton transfer and dual fluorescence of fisetin

    NASA Astrophysics Data System (ADS)

    Guharay, Jayanti; Dennison, S. Moses; Sengupta, Pradeep K.

    1999-05-01

    The influence of different protic and aprotic solvent environments on the excited-state intramolecular proton transfer (ESIPT) leading to a dual fluorescence behaviour of a biologically important, naturally occurring, polyhydroxyflavone, fisetin (3,3',4',7-tetrahydroxyflavone), has been investigated. The normal fluorescence band, in particular, is extremely sensitive to solvent polarity with νmax shifting from 24 510 cm -1 in dioxane ( ET(30)=36.0) to 20 790 cm -1 in methanol ( ET(30)=55.5). This is rationalized in terms of solvent dipolar relaxation process, which also accounts for the red edge excitation shifts (REES) observed in viscous environments such as glycerol at low temperatures. Significant solvent dependence of the tautomer fluorescence properties ( νmax, yield and decay kinetics) reveals the influence of external hydrogen bonding perturbation on the internal hydrogen bond of the molecule. These excited-state relaxation phenomena and their relevant parameters have been used to probe the microenvironment of fisetin in a membrane mimetic system, namely AOT reverse micelles in n-heptane at different water/surfactant molar ratio ( w0).

  10. Photosensitizer fluorescence dynamics at its diffusion in blood flow for different means of cells concentrations

    NASA Astrophysics Data System (ADS)

    Maryakhina, V. S.; Gun'kov, V. V.

    2016-04-01

    In the paper the mathematical model of kinetics of interaction of the injected compound with biological liquid flow has been described for different means of cells concentrations connected on packed cell volume. It is considered that biological liquid contains a three phases such as water, peptides and cells. At the time, the injected compound can interact with peptides and cells which are "trap" for him. The obtained distribution of the compound connects on changes of its fluorescence spectra. It is shown that fluorescence intensivity change is different at 560, 580 and 590 nm. The curves do not have monotonic nature. There is a sharp curves decline in the first few seconds, next, it are increasing. Curves inflection time slightly depends on the cells concentration and is 7-9 seconds. At the time stationary concentration significantly depends on this parameter in contrast to blood viscosity. As long s cells concentration is primarily mean of the packed cell volume, the model can be important for pharmacokinetics and preparations delivery. It can be also used for fluorescent biomedical diagnostics of cancer tumour.

  11. Mismatch discrimination in fluorescent in situ hybridization using different types of nucleic acids.

    PubMed

    Fontenete, Silvia; Silvia, Fontenete; Barros, Joana; Joana, Barros; Madureira, Pedro; Pedro, Madureira; Figueiredo, Céu; Céu, Figueiredo; Wengel, Jesper; Jesper, Wengel; Azevedo, Nuno Filipe; Filipe, Azevedo Nuno

    2015-05-01

    In the past few years, several researchers have focused their attention on nucleic acid mimics due to the increasing necessity of developing a more robust recognition of DNA or RNA sequences. Fluorescence in situ hybridization (FISH) is an example of a method where the use of these novel nucleic acid monomers might be crucial to the success of the analysis. To achieve the expected accuracy in detection, FISH probes should have high binding affinity towards their complementary strands and discriminate effectively the noncomplementary strands. In this study, we investigate the effect of different chemical modifications in fluorescent probes on their ability to successfully detect the complementary target and discriminate the mismatched base pairs by FISH. To our knowledge, this paper presents the first study where this analysis is performed with different types of FISH probes directly in biological targets, Helicobacter pylori and Helicobacter acinonychis. This is also the first study where unlocked nucleic acids (UNA) were used as chemistry modification in oligonucleotides for FISH methodologies. The effectiveness in detecting the specific target and in mismatch discrimination appears to be improved using locked nucleic acids (LNA)/2'-O-methyl RNA (2'OMe) or peptide nucleic acid (PNA) in comparison to LNA/DNA, LNA/UNA, or DNA probes. Further, the use of LNA modifications together with 2'OMe monomers allowed the use of shorter fluorescent probes and increased the range of hybridization temperatures at which FISH would work.

  12. Simulation of seismic wave propagation in 2-D poroelastic media using weighted-averaging finite difference stencils in the frequency-space domain

    NASA Astrophysics Data System (ADS)

    Yang, Qingjie; Mao, Weijian

    2017-01-01

    The poroelastodynamic equations are used to describe the dynamic solid-fluid interaction in the reservoir. To obtain the intrinsic properties of reservoir rocks from geophysical data measured in both laboratory and field, we need an accurate solution of the wave propagation in porous media. At present, the poroelastic wave equations are mostly solved in the time domain, which involves a difficult and complicated time convolution. In order to avoid the issues caused by the time convolution, we propose a frequency-space domain method. The poroelastic wave equations are composed of a linear system in the frequency domain, which easily takes into account the effects of all frequencies on the dispersion and attenuation of seismic wave. A 25-point weighted-averaging finite different scheme is proposed to discretize the equations. For the finite model, the perfectly matched layer technique is applied at the model boundaries. We validated the proposed algorithm by testing three numerical examples of poroelastic models, which are homogenous, two-layered and heterogeneous with different fluids, respectively. The testing results are encouraging in the aspects of both computational accuracy and efficiency.

  13. The antioxidative power AP—A new quantitative time dependent (2D) parameter for the determination of the antioxidant capacity and reactivity of different plants

    NASA Astrophysics Data System (ADS)

    Jung, Katinka; Richter, J.; Kabrodt, K.; Lücke, I. M.; Schellenberg, I.; Herrling, Th.

    2006-03-01

    In the last decade, naturally occurring antioxidants continue to play an important role in the food-supplement industry. The content of antioxidants in a plant depends on the species, temperature, humidity, period of growth, harvest month, part of the plant used and many other variables. Herein, we present a new method able to determine the all over antioxidative power (AP) of plant extracts or lyophilised plant parts based on the reducing activity against a stable test radical. The method is performed by ESR spectroscopy and is based on the well-known 1,1-diphenyl-2-picryl-hydrazil (DPPH) method with the major difference that both the antioxidative capacity and the antioxidative activity are used to characterise an antioxidant. The resulting antioxidative power is expressed in antioxidative units (AU), where 1 AU corresponds to the activity of a 1 ppm solution of Vitamin C as a benchmark. This method allows a rapid, unexpensive and general applicable technique for the measurement of the antioxidative power of very different kinds of substances. The inclusion of the kinetic behaviour of the reducing process of the antioxidant for the determination of the AP allows the identification of the main antioxidant present in a sample. Herein, we present the application example of seeds, sprouts and adult parts of dandelion, amaranth, quinoa, fenugreek, broccoli, red clover and mugwort, where the AP method permits to characterise the plants with the highest antioxidant capacity and reaction velocity. The method permits to select active plant extracts for the food and nutrition industry.

  14. Convergent validity and sex differences in healthy elderly adults for performance on 3D virtual reality navigation learning and 2D hidden maze tasks.

    PubMed

    Tippett, William J; Lee, Jang-Han; Mraz, Richard; Zakzanis, Konstantine K; Snyder, Peter J; Black, Sandra E; Graham, Simon J

    2009-04-01

    This study assessed the convergent validity of a virtual environment (VE) navigation learning task, the Groton Maze Learning Test (GMLT), and selected traditional neuropsychological tests performed in a group of healthy elderly adults (n = 24). The cohort was divided equally between males and females to explore performance variability due to sex differences, which were subsequently characterized and reported as part of the analysis. To facilitate performance comparisons, specific "efficiency" scores were created for both the VE navigation task and the GMLT. Men reached peak performance more rapidly than women during VE navigation and on the GMLT and significantly outperformed women on the first learning trial in the VE. Results suggest reasonable convergent validity across the VE task, GMLT, and selected neuropsychological tests for assessment of spatial memory.

  15. Caffeine and sulfadiazine interact differently with human serum albumin: A combined fluorescence and molecular docking study

    NASA Astrophysics Data System (ADS)

    Islam, Mullah Muhaiminul; Sonu, Vikash K.; Gashnga, Pynsakhiat Miki; Moyon, N. Shaemningwar; Mitra, Sivaprasad

    2016-01-01

    The interaction and binding behavior of the well-known drug sulfadiazine (SDZ) and psychoactive stimulant caffeine (CAF) with human serum albumin (HSA) was monitored by in vitro fluorescence titration and molecular docking calculations under physiological condition. The quenching of protein fluorescence on addition of CAF is due to the formation of protein-drug complex in the ground state; whereas in case of SDZ, the experimental results were explained on the basis of sphere of action model. Although both these compounds bind preferentially in Sudlow's site 1 of the protein, the association constant is approximately two fold higher in case of SDZ (∼4.0 × 104 M-1) in comparison with CAF (∼9.3 × 102 M-1) and correlates well with physico-chemical properties like pKa and lipophilicity of the drugs. Temperature dependent fluorescence study reveals that both SDZ and CAF bind spontaneously with HSA. However, the binding of SDZ with the protein is mainly governed by the hydrophobic forces in contrast with that of CAF; where, the interaction is best explained in terms of electrostatic mechanism. Molecular docking calculation predicts the binding of these drugs in different location of sub-domain IIA in the protein structure.

  16. Caffeine and sulfadiazine interact differently with human serum albumin: A combined fluorescence and molecular docking study.

    PubMed

    Islam, Mullah Muhaiminul; Sonu, Vikash K; Gashnga, Pynsakhiat Miki; Moyon, N Shaemningwar; Mitra, Sivaprasad

    2016-01-05

    The interaction and binding behavior of the well-known drug sulfadiazine (SDZ) and psychoactive stimulant caffeine (CAF) with human serum albumin (HSA) was monitored by in vitro fluorescence titration and molecular docking calculations under physiological condition. The quenching of protein fluorescence on addition of CAF is due to the formation of protein-drug complex in the ground state; whereas in case of SDZ, the experimental results were explained on the basis of sphere of action model. Although both these compounds bind preferentially in Sudlow's site 1 of the protein, the association constant is approximately two fold higher in case of SDZ (∼4.0×10(4)M(-1)) in comparison with CAF (∼9.3×10(2)M(-1)) and correlates well with physico-chemical properties like pKa and lipophilicity of the drugs. Temperature dependent fluorescence study reveals that both SDZ and CAF bind spontaneously with HSA. However, the binding of SDZ with the protein is mainly governed by the hydrophobic forces in contrast with that of CAF; where, the interaction is best explained in terms of electrostatic mechanism. Molecular docking calculation predicts the binding of these drugs in different location of sub-domain IIA in the protein structure.

  17. Application of multiplexed cysteine-labeled complex protein sample for 2D electrophoretic gel alignment.

    PubMed

    Haimi, Perttu; Sikorskaite-Gudziuniene, Sidona; Baniulis, Danas

    2015-06-01

    The analysis of cellular subproteomes by 2DE is hampered by the difficulty of aligning gel images from samples that have very different protein composition. Here, we present a sensitive and cost-effective fluorescent labeling method for analyzing protein samples that is not dependent on their composition. The alignment is guided by inclusion of a complex mixture of proteins that is co-run with the sample. Maleimide-conjugated fluorescent dyes Dy-560 and Dy-635 are used to label the cysteine residues of the sample of interest and the alignment standard, respectively. The two differently labeled mixtures are then combined and separated on a 2D gel and, after selective fluorescence detection, an unsupervised image registration process is used to align the protein patters. In a pilot study, this protocol significantly improved the accuracy of alignment of nuclear proteins with total cellular proteins.

  18. Application of 2D Non-Graphene Materials and 2D Oxide Nanostructures for Biosensing Technology

    PubMed Central

    Shavanova, Kateryna; Bakakina, Yulia; Burkova, Inna; Shtepliuk, Ivan; Viter, Roman; Ubelis, Arnolds; Beni, Valerio; Starodub, Nickolaj; Yakimova, Rositsa; Khranovskyy, Volodymyr

    2016-01-01

    The discovery of graphene and its unique properties has inspired researchers to try to invent other two-dimensional (2D) materials. After considerable research effort, a distinct “beyond graphene” domain has been established, comprising the library of non-graphene 2D materials. It is significant that some 2D non-graphene materials possess solid advantages over their predecessor, such as having a direct band gap, and therefore are highly promising for a number of applications. These applications are not limited to nano- and opto-electronics, but have a strong potential in biosensing technologies, as one example. However, since most of the 2D non-graphene materials have been newly discovered, most of the research efforts are concentrated on material synthesis and the investigation of the properties of the material. Applications of 2D non-graphene materials are still at the embryonic stage, and the integration of 2D non-graphene materials into devices is scarcely reported. However, in recent years, numerous reports have blossomed about 2D material-based biosensors, evidencing the growing potential of 2D non-graphene materials for biosensing applications. This review highlights the recent progress in research on the potential of using 2D non-graphene materials and similar oxide nanostructures for different types of biosensors (optical and electrochemical). A wide range of biological targets, such as glucose, dopamine, cortisol, DNA, IgG, bisphenol, ascorbic acid, cytochrome and estradiol, has been reported to be successfully detected by biosensors with transducers made of 2D non-graphene materials. PMID:26861346

  19. Application of 2D Non-Graphene Materials and 2D Oxide Nanostructures for Biosensing Technology.

    PubMed

    Shavanova, Kateryna; Bakakina, Yulia; Burkova, Inna; Shtepliuk, Ivan; Viter, Roman; Ubelis, Arnolds; Beni, Valerio; Starodub, Nickolaj; Yakimova, Rositsa; Khranovskyy, Volodymyr

    2016-02-06

    The discovery of graphene and its unique properties has inspired researchers to try to invent other two-dimensional (2D) materials. After considerable research effort, a distinct "beyond graphene" domain has been established, comprising the library of non-graphene 2D materials. It is significant that some 2D non-graphene materials possess solid advantages over their predecessor, such as having a direct band gap, and therefore are highly promising for a number of applications. These applications are not limited to nano- and opto-electronics, but have a strong potential in biosensing technologies, as one example. However, since most of the 2D non-graphene materials have been newly discovered, most of the research efforts are concentrated on material synthesis and the investigation of the properties of the material. Applications of 2D non-graphene materials are still at the embryonic stage, and the integration of 2D non-graphene materials into devices is scarcely reported. However, in recent years, numerous reports have blossomed about 2D material-based biosensors, evidencing the growing potential of 2D non-graphene materials for biosensing applications. This review highlights the recent progress in research on the potential of using 2D non-graphene materials and similar oxide nanostructures for different types of biosensors (optical and electrochemical). A wide range of biological targets, such as glucose, dopamine, cortisol, DNA, IgG, bisphenol, ascorbic acid, cytochrome and estradiol, has been reported to be successfully detected by biosensors with transducers made of 2D non-graphene materials.

  20. Effect of fluorescence characteristics and different algorithms on the estimation of leaf nitrogen content based on laser-induced fluorescence lidar in paddy rice.

    PubMed

    Yang, Jian; Sun, Jia; Du, Lin; Chen, Biwu; Zhang, Zhenbing; Shi, Shuo; Gong, Wei

    2017-02-20

    Paddy rice is one of the most significant food sources and an important part of the ecosystem. Thus, accurate monitoring of paddy rice growth is highly necessary. Leaf nitrogen content (LNC) serves as a crucial indicator of growth status of paddy rice and determines the dose of nitrogen (N) fertilizer to be used. This study aims to compare the predictive ability of the fluorescence spectra excited by different excitation wavelengths (EWs) combined with traditional multivariate analysis algorithms, such as principal component analysis (PCA), back-propagation neural network (BPNN), and support vector machine (SVM), for estimating paddy rice LNC from the leaf level with three different fluorescence characteristics as input variables. Then, six estimation models were proposed. Compared with the five other models, PCA-BPNN was the most suitable model for the estimation of LNC by improving R2 and reducing RMSE and RE. For 355, 460 and 556 nm EWs, R2 was 0.89, 0.80 and 0.88, respectively. Experimental results demonstrated that the fluorescence spectra excited by 355 and 556 nm EWs were superior to those excited by 460 nm for the estimation of LNC with different models. BPNN algorithm combined with PCA may provide a helpful exploratory and predictive tool for fluorescence spectra excited by appropriate EW based on practical application requirements for monitoring the N status of crops.

  1. Optoelectronics with 2D semiconductors

    NASA Astrophysics Data System (ADS)

    Mueller, Thomas

    2015-03-01

    Two-dimensional (2D) atomic crystals, such as graphene and layered transition-metal dichalcogenides, are currently receiving a lot of attention for applications in electronics and optoelectronics. In this talk, I will review our research activities on electrically driven light emission, photovoltaic energy conversion and photodetection in 2D semiconductors. In particular, WSe2 monolayer p-n junctions formed by electrostatic doping using a pair of split gate electrodes, type-II heterojunctions based on MoS2/WSe2 and MoS2/phosphorene van der Waals stacks, 2D multi-junction solar cells, and 3D/2D semiconductor interfaces will be presented. Upon optical illumination, conversion of light into electrical energy occurs in these devices. If an electrical current is driven, efficient electroluminescence is obtained. I will present measurements of the electrical characteristics, the optical properties, and the gate voltage dependence of the device response. In the second part of my talk, I will discuss photoconductivity studies of MoS2 field-effect transistors. We identify photovoltaic and photoconductive effects, which both show strong photoconductive gain. A model will be presented that reproduces our experimental findings, such as the dependence on optical power and gate voltage. We envision that the efficient photon conversion and light emission, combined with the advantages of 2D semiconductors, such as flexibility, high mechanical stability and low costs of production, could lead to new optoelectronic technologies.

  2. Two-dimensional fluorescence difference gel electrophoresis analysis of Listeria monocytogenes submitted to a redox shock.

    PubMed

    Ignatova, Maria; Guével, Blandine; Com, Emmanuelle; Haddad, Nabila; Rossero, Albert; Bogard, Philippe; Prévost, Hervé; Guillou, Sandrine

    2013-02-21

    The influence of redox alteration on the growth and proteomic pattern of Listeria monocytogenes was investigated. A redox shock was induced in cultures by addition of 3mM ferricyanide (FeCN) and 6mM dithiothreitol (DTT) to increase or to decrease respectively the redox potential naturally occurring at the beginning of growth. In both conditions, the reducing and oxidizing redox shock had a strong influence, decreasing the maximum growth rate by half compared to a control culture. The proteomic analysis of L. monocytogenes performed by two-dimensional difference gel electrophoresis (2D-DIGE) exhibited twenty-three proteins differentially expressed (P<0.05), among these, many were oxidoreductases, and proteins involved in cellular metabolism (glycolysis, protein synthesis), detoxification (kat) or adhesion (Lmo1634).

  3. Interregional difference in spring neap variations in stratification and chlorophyll fluorescence during summer in a tidal sea (Yatsushiro Sea, Japan)

    NASA Astrophysics Data System (ADS)

    Aoki, Kazuhiro; Onitsuka, Goh; Shimizu, Manabu; Matsuo, Hitoshi; Kitadai, Yuuki; Ochiai, Hironori; Yamamoto, Takeshi; Furukawa, Shinpei

    2016-10-01

    Spring neap variations in stratification and chlorophyll fluorescence were studied during the summers of 2011-2014 in a tidal sea (Yatsushiro Sea, Japan) using monitoring data and hydrodynamic models. Vertical profiles of salinity, temperature and chlorophyll fluorescence were collected nearly weekly from nine stations in this sea during the same period. Composite analysis using vertical profiles of density clearly indicated enhancement of the stratification during the neap tide and a vertically mixed water column during the spring tide in the tidal area. Interregional differences were revealed in the variation of chlorophyll fluorescence with the spring neap tidal cycle. More notable increases in chlorophyll fluorescence were observed during the neap tide in the tidal area around the narrow strait than in the inner area. Temporal stratification led to an increase in the chlorophyll fluorescence in the tidal strait during the neap tide.

  4. Results from an indirect fluorescent antibody test using three different strains of Ehrlichia canis.

    PubMed

    Aguirre, Enara; Ayllón, Tania; Sainz, Angel; Amusategui, Inmaculada; Villaescusa, Alejandra; Rodríguez-Franco, Fernando; Tesouro, Miguel A

    2009-11-01

    An indirect fluorescent antibody (IFA) test is usually performed to detect antibodies in dogs naturally infected by Ehrlichia canis. In this work, results obtained using three different E. canis strains as antigen (a commercial antigen, the E. canis Oklahoma strain and the E. canis Madrid strain) were compared. One hundred and forty-nine serum samples obtained from dogs living in the centre of Spain were analysed. When qualitative results were evaluated, identical results were detected in 87.2% of samples for the three antigens tested. When comparing antibody titre results, differences between the Madrid strain and the commercial antigen, and between the Madrid and Oklahoma strains were statistically significant (P<0.0001). No differences were found when comparing the Oklahoma strain with the commercial antigen (P=0.562). Subtle intra-laboratory variations shown in this study suggest a higher sensitivity of the IFA test when an autochthonous strain is used as antigen.

  5. Comparison of different fluorescence spectrum analysis techniques to characterize humification levels of waste-derived dissolved organic matter.

    PubMed

    Shao, L M; Zhang, C Y; He, P J; Lü, F

    2012-12-01

    In the present work, the humification level of waste-derived dissolved organic matter (DOM) at different waste biostability was investigated, by using fluorescent excitation-emission matrix (EEM) scanning. Different fluorescence spectrum analysis techniques were applied and compared. Experimental results demonstrate that parallel factor (PARAFAC) analysis was sensitive to reflect DOM humification, and the most reasonable to deconstruct DOM compositions, when compared with other spectrum analysis techniques. It suggests applying the DOM-EEM-PARAFAC pipeline for rapid estimation of waste biostability.

  6. The application of fluorescence in situ hybridization in different ploidy levels cross-breeding of lily.

    PubMed

    Wang, Qing; Wang, Jingmao; Zhang, Yiying; Zhang, Yue; Xu, Shunchao; Lu, Yingmin

    2015-01-01

    21 crossing were conducted between Asiatic Lily with different ploidy levels, the results showed that the interploidy hybridization between diploid and tetraploid lilies was not as successful as intraploidy hybridization. Regardless of male sterility, triploid lilies could be used as female parents in the hybridization which the progenies were aneuploidy. 3x×4x crosses could be cultured more successfully than 3x×2x crosses. 45S rDNA was mapped on the chromosomes of seven Lilium species and their progenies using fluorescence in situ hybridization (FISH). FISH revealed six to sixteen 45S rDNA gene loci, and normally the sites were not in pairs. The asymmetry indexes of LA (Longiflorum hybrids × Asiatic hybrids) hybrids was higher than Asiatic hybrids, the evolution degree was LA hybrids > Asiatic hybrids. 45S rDNA distributed variably on chromosome 1-10 and 12 among Asiatic hybrids. Chromosome 1 had invariable sites of 45S rDNA in all Asiatic hybrids, which could be considered as the characteristic of Asiatic hybrids. LA hybrid 'Freya' had two sites of 45S rDNA on one homologous chromosome 5, and also it could be found in the progenies. The karyotype and fluorescence in situ hybridization with 45S rDNA as probe were applied to identify the different genotypes of 9 hybrids. Typical chromosomes with parental signal sites could be observed in all the genotypes of hybrids, it was confirmed that all the hybrids were true.

  7. Inter-ethnic differences in genetic polymorphisms of xenobiotic-metabolizing enzymes (CYP1A1, CYP2D6, NAT1 and NAT2) in healthy populations: correlation with the functional in silico prediction.

    PubMed

    Khlifi, Rim; Ben Salah, Ghada; Chakroun, Amine; Hamza-Chaffai, Amel; Rebai, Ahmed

    2014-09-01

    Several studies have shown that many polymorphisms of the xenobiotic-metabolizing enzymes (XME) affect either enzymatic functions or are associated with various aspects of human health. Owing to the presence of these single nucleotide variants (SNVs), differences in detoxification capacity have been observed between many ethnicities. The aim of this investigation was to study the prevalence of four polymorphisms in XME among various ethnic groups. Attention was focused on polymorphisms of CYP2D6 (rs1058172, G>A, p.Arg365His), CYP1A1 (rs4646421, c.-26-728C>T), NAT1 (rs4921880, c.-85-1014T>A) and NAT2 (rs1208, A>G, p.Arg268Lys). These polymorphisms were analyzed in 261 healthy Tunisians individuals in comparison with different ethnic backgrounds from hapmap database. In addition, in silico functional prediction was also performed to determine the loss of function variants. Our results demonstrated that population's origins widely affect the genetic variability of XME enzymes and Tunisians show a characteristic pattern. In silico predictions showed a deleterious effect for p.Arg268Lys substitution on CYP2D6 function, findings confirmed its key role played in cancer susceptibility. These data show that detoxification genes structures depend on the studied population. This suggests that ethnic differences impact on disease risk or response to drugs and therefore should be taken into consideration in genetic association studies focusing on XME enzymes. Our results provide the first report on these SNV in Tunisian population and could be useful for further epidemiological investigations including targeted therapy.

  8. Method for determining surface coverage by materials exhibiting different fluorescent properties

    NASA Technical Reports Server (NTRS)

    Chappelle, Emmett W. (Inventor); Daughtry, Craig S. T. (Inventor); Mcmurtrey, James E., III (Inventor)

    1995-01-01

    An improved method for detecting, measuring, and distinguishing crop residue, live vegetation, and mineral soil is presented. By measuring fluorescence in multiple bands, live and dead vegetation are distinguished. The surface of the ground is illuminated with ultraviolet radiation, inducing fluorescence in certain molecules. The emitted fluorescent emission induced by the ultraviolet radiation is measured by means of a fluorescence detector, consisting of a photodetector or video camera and filters. The spectral content of the emitted fluorescent emission is characterized at each point sampled, and the proportion of the sampled area covered by residue or vegetation is calculated.

  9. Highly crystalline 2D superconductors

    NASA Astrophysics Data System (ADS)

    Saito, Yu; Nojima, Tsutomu; Iwasa, Yoshihiro

    2016-12-01

    Recent advances in materials fabrication have enabled the manufacturing of ordered 2D electron systems, such as heterogeneous interfaces, atomic layers grown by molecular beam epitaxy, exfoliated thin flakes and field-effect devices. These 2D electron systems are highly crystalline, and some of them, despite their single-layer thickness, exhibit a sheet resistance more than an order of magnitude lower than that of conventional amorphous or granular thin films. In this Review, we explore recent developments in the field of highly crystalline 2D superconductors and highlight the unprecedented physical properties of these systems. In particular, we explore the quantum metallic state (or possible metallic ground state), the quantum Griffiths phase observed in out-of-plane magnetic fields and the superconducting state maintained in anomalously large in-plane magnetic fields. These phenomena are examined in the context of weakened disorder and/or broken spatial inversion symmetry. We conclude with a discussion of how these unconventional properties make highly crystalline 2D systems promising platforms for the exploration of new quantum physics and high-temperature superconductors.

  10. Extensions of 2D gravity

    SciTech Connect

    Sevrin, A.

    1993-06-01

    After reviewing some aspects of gravity in two dimensions, I show that non-trivial embeddings of sl(2) in a semi-simple (super) Lie algebra give rise to a very large class of extensions of 2D gravity. The induced action is constructed as a gauged WZW model and an exact expression for the effective action is given.

  11. Absorption and fluorescence properties of aryl substituted porphyrins in different media

    NASA Astrophysics Data System (ADS)

    Bozkurt, Serap Seyhan; Merdivan, Melek; Ayata, Sevda

    2010-02-01

    Absorption and fluorescence properties of aryl substituted porphyrins, 5,10,15,20-tetra-4-oxy(aceticacid)phenylporphyrin (TAPP), 5,10,15,20-tetra-(4-phenoxyphenyl) porphyrin (TPPP), 5,10,15,20-tetra-(3-bromo-4-hydroxyphenyl) porphyrin (TBHPP), and 5,10,15,20-tetra-p-chloromethylphenyl porphyrin (CMPP) were investigated. The UV/vis absorption, fluorescence and excited spectra as the fluorescence quantum yields and fluorescence lifetimes for the compounds were measured in organic solvents (chloroform (CHCl 3), tetrahydrofuran (THF)) and immobilized media (PVC film, sol-gel matrix). The fluorescence quantum yields of TAPP and TPPP were higher than the others. The fluorescence lifetimes of all studied porphyrin derivates were found to be fifty percent lower and their fluorescence intensities were increased fifty percent more in both of immobilized mediums, as compared to organic solvents.

  12. Super-resolution microscopy based on fluorescence emission difference of cylindrical vector beams

    NASA Astrophysics Data System (ADS)

    Rong, Zihao; Kuang, Cuifang; Fang, Yue; Zhao, Guangyuan; Xu, Yingke; Liu, Xu

    2015-11-01

    We propose a novel fluorescence emission difference microscopy (FED) system based on focusing cylindrical vector beams. In conventional FED, a Gaussian beam and a 0-2π vortex phase plate are used to generate solid and hollow spots. We focus radially polarized and azimuthally polarized cylindrical vector beams to obtain an expanded solid spot and a shrunken hollow spot, taking advantage of the optical properties of cylindrical vector beams to improve the conventional FED performance. Our novel method enhances FED performance because the hollow spot size determines the FED resolution and an expanded solid spot effectively reduces negative side-lobe emergence during image processing. We demonstrate improved performance theoretically and experimentally using an in-house built FED. Our FED achieved resolution of less than λ/4 in test images of 100 nm nanoparticles, better than the confocal image resolution by a factor of approximately 1/3. We also discuss detailed simulation analyses and FED imaging of biological cells.

  13. Differences in in vivo fluorescence yield between three phytoplankton size classes

    USGS Publications Warehouse

    Alpine, Andrea E.; Cloern, James E.

    1985-01-01

    The size-dependent relationship between in vivo fluorescence (IVF) and chlorophyll a was determined for monthly phytoplankton samples from the San Francisco Bay estuary. Chlorophyll a and IVF were both measured on netplankton (>22 μm), nanoplankton (5–22 μm), and ultraplankton (<5 μm) samples that were separated with screens. IVF and chlorophyll a were linearly related for each size class, but the IVF per unit chlorophyll a (R) was significantly different between these three size classes. The ultraplankton R was twice that of the nanoplankton which was in turn twice the netplankton R. Hence, accurate size fractionation of phytoplankton biomass from measures of IVF requires correction for size-dependent variations in R.

  14. The Application of Fluorescence In Situ Hybridization in Different Ploidy Levels Cross-Breeding of Lily

    PubMed Central

    Wang, Qing; Wang, Jingmao; Zhang, Yiying; Zhang, Yue; Xu, Shunchao; Lu, Yingmin

    2015-01-01

    21 crossing were conducted between Asiatic Lily with different ploidy levels, the results showed that the interploidy hybridization between diploid and tetraploid lilies was not as successful as intraploidy hybridization. Regardless of male sterility, triploid lilies could be used as female parents in the hybridization which the progenies were aneuploidy. 3x×4x crosses could be cultured more successfully than 3x×2x crosses. 45S rDNA was mapped on the chromosomes of seven Lilium species and their progenies using fluorescence in situ hybridization (FISH). FISH revealed six to sixteen 45S rDNA gene loci, and normally the sites were not in pairs. The asymmetry indexes of LA (Longiflorum hybrids × Asiatic hybrids) hybrids was higher than Asiatic hybrids, the evolution degree was LA hybrids > Asiatic hybrids. 45S rDNA distributed variably on chromosome 1-10 and 12 among Asiatic hybrids. Chromosome 1 had invariable sites of 45S rDNA in all Asiatic hybrids, which could be considered as the characteristic of Asiatic hybrids. LA hybrid ‘Freya’ had two sites of 45S rDNA on one homologous chromosome 5, and also it could be found in the progenies. The karyotype and fluorescence in situ hybridization with 45S rDNA as probe were applied to identify the different genotypes of 9 hybrids. Typical chromosomes with parental signal sites could be observed in all the genotypes of hybrids, it was confirmed that all the hybrids were true. PMID:26010356

  15. Different mechanisms of action of antimicrobial peptides: insights from fluorescence spectroscopy experiments and molecular dynamics simulations.

    PubMed

    Bocchinfuso, Gianfranco; Palleschi, Antonio; Orioni, Barbara; Grande, Giacinto; Formaggio, Fernando; Toniolo, Claudio; Park, Yoonkyung; Hahm, Kyung-Soo; Stella, Lorenzo

    2009-09-01

    Most antimicrobial peptides exert their activity by interacting with bacterial membranes, thus perturbing their permeability. They are investigated as a possible solution to the insurgence of bacteria resistant to the presently available antibiotic drugs. However, several different models have been proposed for their mechanism of membrane perturbation, and the molecular details of this process are still debated. Here, we compare fluorescence spectroscopy experiments and molecular dynamics (MD) simulations regarding the association with lipid bilayers and lipid perturbation for two different amphiphilic helical antimicrobial peptides, PMAP-23 and trichogin GA IV. PMAP-23, a cationic peptide member of the cathelicidin family, is considered to induce membrane permeability according to the Shai-Matsuzaki-Huang "carpet" model, while trichogin GA IV is a neutral peptide, member of the peptaibol family. Although several lines of evidence suggest a "barrel-stave" mechanism of pore formation for the latter peptide, its length is only half the normal thickness of a lipid bilayer. Both fluorescence spectroscopy experiments and MD simulations indicated that PMAP-23 associates with membranes close to their surface and parallel to it, and in this arrangement it causes a severe perturbation to the bilayer, both regarding its surface tension and lipid order. By contrast, trichogin GA IV can undergo a transition from a surface-bound state to a transmembrane orientation. In the first arrangement, it does not cause any strong membrane perturbation, while in the second orientation it might be able to span the bilayer from one side to the other, despite its relatively short length, by causing a significant thinning of the membrane.

  16. Differential CYP 2D6 metabolism alters primaquine pharmacokinetics.

    PubMed

    Potter, Brittney M J; Xie, Lisa H; Vuong, Chau; Zhang, Jing; Zhang, Ping; Duan, Dehui; Luong, Thu-Lan T; Bandara Herath, H M T; Dhammika Nanayakkara, N P; Tekwani, Babu L; Walker, Larry A; Nolan, Christina K; Sciotti, Richard J; Zottig, Victor E; Smith, Philip L; Paris, Robert M; Read, Lisa T; Li, Qigui; Pybus, Brandon S; Sousa, Jason C; Reichard, Gregory A; Marcsisin, Sean R

    2015-04-01

    Primaquine (PQ) metabolism by the cytochrome P450 (CYP) 2D family of enzymes is required for antimalarial activity in both humans (2D6) and mice (2D). Human CYP 2D6 is highly polymorphic, and decreased CYP 2D6 enzyme activity has been linked to decreased PQ antimalarial activity. Despite the importance of CYP 2D metabolism in PQ efficacy, the exact role that these enzymes play in PQ metabolism and pharmacokinetics has not been extensively studied in vivo. In this study, a series of PQ pharmacokinetic experiments were conducted in mice with differential CYP 2D metabolism characteristics, including wild-type (WT), CYP 2D knockout (KO), and humanized CYP 2D6 (KO/knock-in [KO/KI]) mice. Plasma and liver pharmacokinetic profiles from a single PQ dose (20 mg/kg of body weight) differed significantly among the strains for PQ and carboxy-PQ. Additionally, due to the suspected role of phenolic metabolites in PQ efficacy, these were probed using reference standards. Levels of phenolic metabolites were highest in mice capable of metabolizing CYP 2D6 substrates (WT and KO/KI 2D6 mice). PQ phenolic metabolites were present in different quantities in the two strains, illustrating species-specific differences in PQ metabolism between the human and mouse enzymes. Taking the data together, this report furthers understanding of PQ pharmacokinetics in the context of differential CYP 2D metabolism and has important implications for PQ administration in humans with different levels of CYP 2D6 enzyme activity.

  17. A fluorescent probe for the efficient discrimination of Cys, Hcy and GSH based on different cascade reactions.

    PubMed

    Li, Ying; Liu, Weimin; Zhang, Panpan; Zhang, Hongyan; Wu, Jiasheng; Ge, Jiechao; Wang, Pengfei

    2017-04-15

    A fluorescent probe (1) for distinguishing amongst biothiols, including cysteine (Cys), homocysteine (Hcy) and glutathione (GSH), is developed based on different cascade reactions. The key design feature of fluorescent probe 1 is the integration of two potential reaction groups for the thiol and amino groups of biothiols in one molecule. By reacting with the halogen atom and α, β-unsaturated malonitrile in probe 1, Cys, Hcy and GSH can generate a total of three main products with distinct photophysical properties. Probe 1 shows a strong fluorescence turn-on response to Cys with blue-green emission by using an excitation wavelength of 390nm. At an excitation wavelength of 500nm, probe 1 responds to GSH over Cys and Hcy and emits strong orange fluorescence. The discrimination of biothiols can be demonstrated by cell imaging experiments, indicating that probe 1 can be a useful tool for the selective imaging of Cys and GSH in living cells.

  18. Ultrasensitive detection of genetically modified maize DNA by capillary gel electrophoresis with laser-induced fluorescence using different fluorescent intercalating dyes.

    PubMed

    García-Cañas, Virginia; González, Ramón; Cifuentes, Alejandro

    2002-07-31

    In this work, four different fluorescent intercalating dyes are compared for the ultrasensitive CGE-LIF detection of DNA from transgenic maize in flours. The fluorescent intercalating dyes compared are YOPRO-1, SYBR-Green-I, Ethidium bromide (EthBr), and EnhanCE. For all the four dyes optimum concentrations are established, and efficient separations of DNA fragments ranging in size from 80 to 1000 bp are obtained. The comparative study demonstrates that SYBR-Green-I and YOPRO-1 provide better limits of detection (LODs) than EnhanCE or EthBr (i.e., LODs are, respectively, 700, 1000, 11300, and 97400 zmol, calculated for a 200-bp DNA fragment). Separations using YOPRO-1 are faster than those using SYBR-Green-I (30 min vs 47 min for the analysis of the 80-1000 bp DNA fragments). Also, separations using YOPRO-1 are more efficient than those using SYBR-Green-I (e.g., 2.4 x 10(6) plates/m vs 1.6 x 10(6) plates/m, respectively, calculated for the 200-bp fragment). Also, buffer depletion and cost per analysis are worse with SYBR-Green-I than with YOPRO-1. Therefore, YOPRO-1 was selected as the preferred intercalating dye. Using this fluorescent compound, analysis time reproducibility for the CGE-LIF separation of the DNA fragments is determined to be better than 1.7% (% RSD, n = 10) within the same day, and better than 1.9% (% RSD, n = 30) for three different days. Moreover, the fluorescence signal obtained using this dye is shown to vary linearly with the DNA concentration in the range studied, i.e., 1-500 ng/microL. It is demonstrated that by using this method 0.01% of transgenic maize can be detected in flour by direct injection of the PCR-amplified sample.

  19. Monitoring the Photosynthetic Apparatus During Space Flight: Interspecific Variation in Chlorophyll Fluorescence Signatures Induced by Different Root Zone Stresses

    NASA Technical Reports Server (NTRS)

    Bubenheim, David L.; Patterson, Mark T.; Kliss, Mark H. (Technical Monitor)

    1996-01-01

    Chlorophyll fluorescence has been used extensively as a tool to indicate stress to the photosynthetic apparatus in green plants. A rise in fluorescence has been attributed to the blockage of photosystem II photochemistry, and patterns of fluorescence decay (quenching) from dark adapted leaves can be related to specific photochemical and non-photochemical deexcitation pathways of light trapped by the photosynthetic apparatus and thus result in characteristically different fluorescence signatures. Four distantly related plant species, Hypocharis radicata (Asteraceae), Brassica rapa (Brassicaceae), Spinacea oleracea (Chenopodiaceae) and Triticum aestivum (Poaceae), were grown hydroponically for three weeks before the initiation of three different root zone stresses (10 mM Cu, 100 mM NaCl and nitrogen deficient nutrition). After 10 days, characteristic fluorescence signatures for each stress could be noted although the degree varied between species. Fast kinetics analysis showed a reduction in plastoquinone pool size for copper and nitrogen stress for all species but a more species specific result with NaCl stress. Photochemical quenching kinetics varied between species and stress treatments from no quenching in S. oleracea in copper treatments to increased photochemical quenching in NaCl treatments. Non-photochemical quenching kinetics demonstrated a distinct pattern between stresses for all species. Copper treatments characteristically exhibited a shallow, flat non-photochemical quenching profile suggesting a general blockage of electron transport whereas NaCl treatments exhibited a slow rising profile that suggested damage to thylakoid acidification kinetics and nitrogen deficiency exhibited a fast rising and declining profile that suggested an altered state 1-state 2 transition regulated by the phosphorylation of LHCII. These results demonstrate characteristic fluorescence signatures for specific plant stresses that may be applied to different, unrelated plant

  20. Genomic diversity amongst Vibrio isolates from different sources determined by fluorescent amplified fragment length polymorphism.

    PubMed

    Thompson, F L; Hoste, B; Vandemeulebroecke, K; Swings, J

    2001-12-01

    The genomic diversity among 506 strains of the family Vibrionaceae was analysed using Fluorescent Amplified Fragments Length Polymorphisms (FAFLP). Isolates were from different sources (e.g. fish, mollusc, shrimp, rotifers, artemia, and their culture water) in different countries, mainly from the aquacultural environment. Clustering of the FAFLP band patterns resulted in 69 clusters. A majority of the actually known species of the family Vibrionaceae formed separate clusters. Certain species e.g. V. alginolyticus, V. cholerae, V. cincinnatiensis, V. diabolicus, V. diazotrophicus, V. harveyi, V. logei, V. natriegens, V. nereis, V. splendidus and V. tubiashii were found to be ubiquitous, whereas V. halioticoli, V. ichthyoenteri, V. pectenicida and V. wodanis appear to be exclusively associated with a particular host or geographical region. Three main categories of isolates could be distinguished: (1) isolates with genomes related (i.e. with > or =45% FAFLP pattern similarity) to one of the known type strains; (2) isolates clustering (> or =45% pattern similarity) with more than one type strain; (3) isolates with genomes unrelated (<45% pattern similarity) to any of the type strains. The latter group consisted of 236 isolates distributed in 31 clusters indicating that many culturable taxa of the Vibrionaceae remain as yet to be described.

  1. [Discussion of the characteristic indexs in using three-dimensional fluorescence method to identify different crude oils].

    PubMed

    Zhao, Yan; Zhang, Shi-Yuan; Ling, Ping; Li, Si-Yuan; Huang, Kai-Sheng; Zhou, Yong-Sheng; Xie, Yue-Liang

    2009-12-01

    The present paper investigates the influence of solvent purity on the test of three-dimensional fluorescence spectra, determines the process of its pre-purification, and studies the influence of the concentrations on the three-dimensional fluorescence characteristic indexes such as the characteristic peaks position, fluorescence intensity (F), and ratio (R) of fluorescence intensity when the phenomena of fluorescence quenching won't appear. The result shows that the concentration affects the value F and value R largely but its effect on the relative peak intensity (R(s)) is relatively small. Different crude oils has different value R(s). According to those characteristics, this paper presents that the value R(s) can be used as a new characteristic index for identification of crude oil. This conclusion was confirmed by testing many crude oils stably and reliably from different areas with their concentrations at 5 mg x L(-1). This method can be applied to identify most crude oils preliminary and further accurate analysis can be carried out together with other index.

  2. Two-dimensional fluorescence intensity distribution analysis: theory and applications.

    PubMed

    Kask, P; Palo, K; Fay, N; Brand, L; Mets, U; Ullmann, D; Jungmann, J; Pschorr, J; Gall, K

    2000-04-01

    A method of sample analysis is presented which is based on fitting a joint distribution of photon count numbers. In experiments, fluorescence from a microscopic volume containing a fluctuating number of molecules is monitored by two detectors, using a confocal microscope. The two detectors may have different polarizational or spectral responses. Concentrations of fluorescent species together with two specific brightness values per species are determined. The two-dimensional fluorescence intensity distribution analysis (2D-FIDA), if used with a polarization cube, is a tool that is able to distinguish fluorescent species with different specific polarization ratios. As an example of polarization studies by 2D-FIDA, binding of 5'-(6-carboxytetramethylrhodamine) (TAMRA)-labeled theophylline to an anti-theophylline antibody has been studied. Alternatively, if two-color equipment is used, 2D-FIDA can determine concentrations and specific brightness values of fluorescent species corresponding to individual labels alone and their complex. As an example of two-color 2D-FIDA, binding of TAMRA-labeled somatostatin-14 to the human type-2 high-affinity somatostatin receptors present in stained vesicles has been studied. The presented method is unusually accurate among fluorescence fluctuation methods. It is well suited for monitoring a variety of molecular interactions, including receptors and ligands or antibodies and antigens.

  3. Extrinsic Cation Selectivity of 2D Membranes

    PubMed Central

    2017-01-01

    From a systematic study of the concentration driven diffusion of positive and negative ions across porous 2D membranes of graphene and hexagonal boron nitride (h-BN), we prove their cation selectivity. Using the current–voltage characteristics of graphene and h-BN monolayers separating reservoirs of different salt concentrations, we calculate the reversal potential as a measure of selectivity. We tune the Debye screening length by exchanging the salt concentrations and demonstrate that negative surface charge gives rise to cation selectivity. Surprisingly, h-BN and graphene membranes show similar characteristics, strongly suggesting a common origin of selectivity in aqueous solvents. For the first time, we demonstrate that the cation flux can be increased by using ozone to create additional pores in graphene while maintaining excellent selectivity. We discuss opportunities to exploit our scalable method to use 2D membranes for applications including osmotic power conversion. PMID:28157333

  4. Standoff laser-induced fluorescence of suspensions from different bacterial strains

    NASA Astrophysics Data System (ADS)

    Duschek, Frank; Walter, Arne; Fellner, Lea; Grünewald, Karin; Pargmann, Carsten; Handke, Jürgen; Tomaso, Herbert

    2016-10-01

    Biological hazardous substances like certain fungi and bacteria represent a high risk for the broad public if fallen into wrong hands. Incidents based on bio agents are commonly considered to have incalculable and complex consequences for first responders and people. The impact of such an event can be minimized by a combination of different sensor technologies that have been developed to detect bio-threats and to gather information after an incident. Sensors for bio-agents can be grouped into two categories. Sampling devices collect material from locations supposed to be contaminated, and they are able to identify biological material with high sensitivity and selectivity. However, these point sensors need to be positioned correctly in advance of an attack, and moving sources of biological material cannot be tracked. A different approach is based on optical standoff detection. For biological samples laser induced florescence (LIF) has been proven to get real time data on location and type of hazards without being in contact with the suspicious substance. This work is based on a bio-detector developed at the DLR Lampoldshausen. The LIF detection has been designed for outdoor operation at standoff distances from 20 m up to more than 100 m. The detector acquires LIF spectral data for two different excitation wavelengths (280 and 355 nm) as well as time resolved information for the fluorescence decay which can be used to classify suspicious samples. While the classification device had been trained on uncritical samples (like amino acids, NADH, yeast, chemicals, oils), this work presents the progress to more relevant, living bacteria of different strains. The low risk and non-pathogenic bacteria Bacillus thuringensis, Bacillus atrophaeus, Bacillus subtilis, Brevibacillus brevis, Micrococcus luteus, Oligella urethralis, Paenibacillus polymyxa and Escherichia coli (K12) have been investigated with the above set-up at both excitation wavelengths

  5. Quasiparticle interference in unconventional 2D systems

    NASA Astrophysics Data System (ADS)

    Chen, Lan; Cheng, Peng; Wu, Kehui

    2017-03-01

    At present, research of 2D systems mainly focuses on two kinds of materials: graphene-like materials and transition-metal dichalcogenides (TMDs). Both of them host unconventional 2D electronic properties: pseudospin and the associated chirality of electrons in graphene-like materials, and spin-valley-coupled electronic structures in the TMDs. These exotic electronic properties have attracted tremendous interest for possible applications in nanodevices in the future. Investigation on the quasiparticle interference (QPI) in 2D systems is an effective way to uncover these properties. In this review, we will begin with a brief introduction to 2D systems, including their atomic structures and electronic bands. Then, we will discuss the formation of Friedel oscillation due to QPI in constant energy contours of electron bands, and show the basic concept of Fourier-transform scanning tunneling microscopy/spectroscopy (FT-STM/STS), which can resolve Friedel oscillation patterns in real space and consequently obtain the QPI patterns in reciprocal space. In the next two parts, we will summarize some pivotal results in the investigation of QPI in graphene and silicene, in which systems the low-energy quasiparticles are described by the massless Dirac equation. The FT-STM experiments show there are two different interference channels (intervalley and intravalley scattering) and backscattering suppression, which associate with the Dirac cones and the chirality of quasiparticles. The monolayer and bilayer graphene on different substrates (SiC and metal surfaces), and the monolayer and multilayer silicene on a Ag(1 1 1) surface will be addressed. The fifth part will introduce the FT-STM research on QPI in TMDs (monolayer and bilayer of WSe2), which allow us to infer the spin texture of both conduction and valence bands, and present spin-valley coupling by tracking allowed and forbidden scattering channels.

  6. Computational Screening of 2D Materials for Photocatalysis.

    PubMed

    Singh, Arunima K; Mathew, Kiran; Zhuang, Houlong L; Hennig, Richard G

    2015-03-19

    Two-dimensional (2D) materials exhibit a range of extraordinary electronic, optical, and mechanical properties different from their bulk counterparts with potential applications for 2D materials emerging in energy storage and conversion technologies. In this Perspective, we summarize the recent developments in the field of solar water splitting using 2D materials and review a computational screening approach to rapidly and efficiently discover more 2D materials that possess properties suitable for solar water splitting. Computational tools based on density-functional theory can predict the intrinsic properties of potential photocatalyst such as their electronic properties, optical absorbance, and solubility in aqueous solutions. Computational tools enable the exploration of possible routes to enhance the photocatalytic activity of 2D materials by use of mechanical strain, bias potential, doping, and pH. We discuss future research directions and needed method developments for the computational design and optimization of 2D materials for photocatalysis.

  7. Fabrication of 2D sheet-like BiOCl/carbon quantum dot hybrids via a template-free coprecipitation method and their tunable visible-light photocatalytic activities derived from different size distributions of carbon quantum dots

    NASA Astrophysics Data System (ADS)

    Deng, Fang; Lu, Xiaoying; Zhong, Fei; Pei, Xule; Luo, Xubiao; Luo, Shenglian; Dionysiou, Dionysios D.; Au, Chaktong

    2016-02-01

    A series of two-dimensional (2D) interlaced BiOCl/carbon quantum dot composites (denoted as BiOCl/CQD composites) were synthesized by a template-free coprecipitation method at room temperature, and the influence of different particle size distributions of the CQDs on the physiochemical properties and photocatalytic activities of the BiOCl/CQD composites was studied. CQDs can change the morphology and increase the specific surface area of the BiOCl/CQD composites. Moreover, the particle size distribution of the CQDs (CQD loading amount) has some effect on the light absorption, separation of photogenerated charge carriers, and photocatalytic performance of the BiOCl/CQD composites. The optimized size distribution of the CQDs is 50-150 nm. BiOCl/CQD (50-150 nm) composites showed the best improvement of light absorption and the highest photocurrent density of 0.44 μA cm-2, and exhibited the highest photocatalytic activity with almost 100% 2-nitrophenol removal under visible-light irradiation. The high efficacy of BiOCl/CQD (50-150 nm) composites could be attributed to their excellent light absorption and highly effective separation of photogenerated charge carriers.

  8. [Vermicomposting of different organic materials and three-dimensional excitation emission matrix fluorescence spectroscopic characterization of their dissolved organic matter].

    PubMed

    Yang, Wei; Wang, Dong-sheng; Liu, Man-qiang; Hu, Feng; Li, Hui-xin; Huang, Zhong-yang; Chang, Yi-jun; Jiao, Jia-guo

    2015-10-01

    In this experiment, different proportions of the cattle manure, tea-leaf, herb and mushroom residues, were used as food for earthworm (Eisenia fetida) to study the growth of the earth-worm. Then the characteristics and transformation of nutrient content and three-dimensional excitation emission matrix fluorescence (3DEEM) of dissolved organic matter (DOM) during vermistabilization were investigated by means of chemical and spectroscopic methods. The result showed that the mixture of different ratios of cattle manure with herb residue, and cattle manure with tea-leaf were conducive to the growth of earthworm, while the materials compounded with mushroom residue inhibited the growth of earthworm. With the increasing time of verimcomposting, the pH in vermicompost tended to be circumneutral and weakly acidic, and there were increases in electrical conductivity, and the contents of total nitrogen, total phosphorus, available nitrogen, and available phosphorus, while the total potassium and available potassium increased first and then decreased, and the organic matter content decreased. 3DEEM and fluorescence regional integration results indicated that, the fluorescence of protein-like fluorescence peaks declined significantly, while the intensity of humic-like fluorescence peak increased significantly in DOM. Vermicomposting process might change the compositions of DOM with elevated concentrations of humic acid and fulvic acid in the organics. In all, this study suggested the suitability of 3DEEM for monitoring the organics transformation and assessing the maturity in the vermicomposting.

  9. 2D imaging and 3D sensing data acquisition and mutual registration for painting conservation

    NASA Astrophysics Data System (ADS)

    Fontana, Raffaella; Gambino, Maria Chiara; Greco, Marinella; Marras, Luciano; Pampaloni, Enrico M.; Pelagotti, Anna; Pezzati, Luca; Poggi, Pasquale

    2004-12-01

    We describe the application of 2D and 3D data acquisition and mutual registration to the conservation of paintings. RGB color image acquisition, IR and UV fluorescence imaging, together with the more recent hyperspectral imaging (32 bands) are among the most useful techniques in this field. They generally are meant to provide information on the painting materials, on the employed techniques and on the object state of conservation. However, only when the various images are perfectly registered on each other and on the 3D model, no ambiguity is possible and safe conclusions may be drawn. We present the integration of 2D and 3D measurements carried out on two different paintings: "Madonna of the Yarnwinder" by Leonardo da Vinci, and "Portrait of Lionello d'Este", by Pisanello, both painted in the XV century.

  10. 2D imaging and 3D sensing data acquisition and mutual registration for painting conservation

    NASA Astrophysics Data System (ADS)

    Fontana, Raffaella; Gambino, Maria Chiara; Greco, Marinella; Marras, Luciano; Pampaloni, Enrico M.; Pelagotti, Anna; Pezzati, Luca; Poggi, Pasquale

    2005-01-01

    We describe the application of 2D and 3D data acquisition and mutual registration to the conservation of paintings. RGB color image acquisition, IR and UV fluorescence imaging, together with the more recent hyperspectral imaging (32 bands) are among the most useful techniques in this field. They generally are meant to provide information on the painting materials, on the employed techniques and on the object state of conservation. However, only when the various images are perfectly registered on each other and on the 3D model, no ambiguity is possible and safe conclusions may be drawn. We present the integration of 2D and 3D measurements carried out on two different paintings: "Madonna of the Yarnwinder" by Leonardo da Vinci, and "Portrait of Lionello d'Este", by Pisanello, both painted in the XV century.

  11. Different crystal morphologies lead to slightly different conformations of light-harvesting complex II as monitored by variations of the intrinsic fluorescence lifetime.

    PubMed

    van Oort, Bart; Maréchal, Amandine; Ruban, Alexander V; Robert, Bruno; Pascal, Andrew A; de Ruijter, Norbert C A; van Grondelle, Rienk; van Amerongen, Herbert

    2011-07-21

    In 2005, it was found that the fluorescence of crystals of the major light-harvesting complex LHCII of green plants is significantly quenched when compared to the fluorescence of isolated LHCII (A. A. Pascal et al., Nature, 2005, 436, 134-137). The Raman spectrum of crystallized LHCII was also found to be different from that of isolated LHCII but very similar to that of aggregated LHCII, which has often been considered a good model system for studying nonphotochemical quenching (NPQ), the major protection mechanism of plants against photodamage in high light. It was proposed that in the crystal LHCII adopts a similar (quenching) conformation as during NPQ and indeed similar changes in the Raman spectrum were observed during NPQ in vivo (A. V. Ruban et al., Nature, 2007, 450, 575-579). We now compared the fluorescence of various types of crystals, differing in morphology and age. Each type gave rise to its own characteristic mono-exponential fluorescence lifetime, which was 5 to 10 times shorter than that of isolated LHCII. This indicates that fluorescence is not quenched by random impurities and packing defects (as proposed recently by T. Barros et al., EMBO Journal, 2009, 28, 298-306), but that LHCII adopts a particular structure in each crystal type, that leads to fluorescence quenching. Most interestingly, the extent of quenching appears to depend on the crystal morphology, indicating that also the crystal structure depends on this crystal morphology but at the moment no data are available to correlate the crystals' structural changes to changes in fluorescence lifetime.

  12. Valleytronics in 2D materials

    NASA Astrophysics Data System (ADS)

    Schaibley, John R.; Yu, Hongyi; Clark, Genevieve; Rivera, Pasqual; Ross, Jason S.; Seyler, Kyle L.; Yao, Wang; Xu, Xiaodong

    2016-11-01

    Semiconductor technology is currently based on the manipulation of electronic charge; however, electrons have additional degrees of freedom, such as spin and valley, that can be used to encode and process information. Over the past several decades, there has been significant progress in manipulating electron spin for semiconductor spintronic devices, motivated by potential spin-based information processing and storage applications. However, experimental progress towards manipulating the valley degree of freedom for potential valleytronic devices has been limited until very recently. We review the latest advances in valleytronics, which have largely been enabled by the isolation of 2D materials (such as graphene and semiconducting transition metal dichalcogenides) that host an easily accessible electronic valley degree of freedom, allowing for dynamic control.

  13. Unparticle example in 2D.

    PubMed

    Georgi, Howard; Kats, Yevgeny

    2008-09-26

    We discuss what can be learned about unparticle physics by studying simple quantum field theories in one space and one time dimension. We argue that the exactly soluble 2D theory of a massless fermion coupled to a massive vector boson, the Sommerfield model, is an interesting analog of a Banks-Zaks model, approaching a free theory at high energies and a scale-invariant theory with nontrivial anomalous dimensions at low energies. We construct a toy standard model coupling to the fermions in the Sommerfield model and study how the transition from unparticle behavior at low energies to free particle behavior at high energies manifests itself in interactions with the toy standard model particles.

  14. Irreversibility-inversions in 2D turbulence

    NASA Astrophysics Data System (ADS)

    Bragg, Andrew; de Lillo, Filippo; Boffetta, Guido

    2016-11-01

    We consider a recent theoretical prediction that for inertial particles in 2D turbulence, the nature of the irreversibility of their pair dispersion inverts when the particle inertia exceeds a certain value. In particular, when the particle Stokes number, St , is below a certain value, the forward-in-time (FIT) dispersion should be faster than the backward-in-time (BIT) dispersion, but for St above this value, this should invert so that BIT becomes faster than FIT dispersion. This non-trivial behavior arises because of the competition between two physically distinct irreversibility mechanisms that operate in different regimes of St . In 3D turbulence, both mechanisms act to produce faster BIT than FIT dispersion, but in 2D, the two mechanisms have opposite effects because of the inverse energy cascade in the turbulent velocity field. We supplement the qualitative argument given by Bragg et al. by deriving quantitative predictions of this effect in the short-time dispersion limit. These predictions are then confirmed by results of inertial particle dispersion in a direct numerical simulation of 2D turbulence.

  15. Realistic and efficient 2D crack simulation

    NASA Astrophysics Data System (ADS)

    Yadegar, Jacob; Liu, Xiaoqing; Singh, Abhishek

    2010-04-01

    Although numerical algorithms for 2D crack simulation have been studied in Modeling and Simulation (M&S) and computer graphics for decades, realism and computational efficiency are still major challenges. In this paper, we introduce a high-fidelity, scalable, adaptive and efficient/runtime 2D crack/fracture simulation system by applying the mathematically elegant Peano-Cesaro triangular meshing/remeshing technique to model the generation of shards/fragments. The recursive fractal sweep associated with the Peano-Cesaro triangulation provides efficient local multi-resolution refinement to any level-of-detail. The generated binary decomposition tree also provides efficient neighbor retrieval mechanism used for mesh element splitting and merging with minimal memory requirements essential for realistic 2D fragment formation. Upon load impact/contact/penetration, a number of factors including impact angle, impact energy, and material properties are all taken into account to produce the criteria of crack initialization, propagation, and termination leading to realistic fractal-like rubble/fragments formation. The aforementioned parameters are used as variables of probabilistic models of cracks/shards formation, making the proposed solution highly adaptive by allowing machine learning mechanisms learn the optimal values for the variables/parameters based on prior benchmark data generated by off-line physics based simulation solutions that produce accurate fractures/shards though at highly non-real time paste. Crack/fracture simulation has been conducted on various load impacts with different initial locations at various impulse scales. The simulation results demonstrate that the proposed system has the capability to realistically and efficiently simulate 2D crack phenomena (such as window shattering and shards generation) with diverse potentials in military and civil M&S applications such as training and mission planning.

  16. Quantum coherence selective 2D Raman–2D electronic spectroscopy

    PubMed Central

    Spencer, Austin P.; Hutson, William O.; Harel, Elad

    2017-01-01

    Electronic and vibrational correlations report on the dynamics and structure of molecular species, yet revealing these correlations experimentally has proved extremely challenging. Here, we demonstrate a method that probes correlations between states within the vibrational and electronic manifold with quantum coherence selectivity. Specifically, we measure a fully coherent four-dimensional spectrum which simultaneously encodes vibrational–vibrational, electronic–vibrational and electronic–electronic interactions. By combining near-impulsive resonant and non-resonant excitation, the desired fifth-order signal of a complex organic molecule in solution is measured free of unwanted lower-order contamination. A critical feature of this method is electronic and vibrational frequency resolution, enabling isolation and assignment of individual quantum coherence pathways. The vibronic structure of the system is then revealed within an otherwise broad and featureless 2D electronic spectrum. This method is suited for studying elusive quantum effects in which electronic transitions strongly couple to phonons and vibrations, such as energy transfer in photosynthetic pigment–protein complexes. PMID:28281541

  17. Quantum coherence selective 2D Raman-2D electronic spectroscopy

    NASA Astrophysics Data System (ADS)

    Spencer, Austin P.; Hutson, William O.; Harel, Elad

    2017-03-01

    Electronic and vibrational correlations report on the dynamics and structure of molecular species, yet revealing these correlations experimentally has proved extremely challenging. Here, we demonstrate a method that probes correlations between states within the vibrational and electronic manifold with quantum coherence selectivity. Specifically, we measure a fully coherent four-dimensional spectrum which simultaneously encodes vibrational-vibrational, electronic-vibrational and electronic-electronic interactions. By combining near-impulsive resonant and non-resonant excitation, the desired fifth-order signal of a complex organic molecule in solution is measured free of unwanted lower-order contamination. A critical feature of this method is electronic and vibrational frequency resolution, enabling isolation and assignment of individual quantum coherence pathways. The vibronic structure of the system is then revealed within an otherwise broad and featureless 2D electronic spectrum. This method is suited for studying elusive quantum effects in which electronic transitions strongly couple to phonons and vibrations, such as energy transfer in photosynthetic pigment-protein complexes.

  18. Quantum coherence selective 2D Raman-2D electronic spectroscopy.

    PubMed

    Spencer, Austin P; Hutson, William O; Harel, Elad

    2017-03-10

    Electronic and vibrational correlations report on the dynamics and structure of molecular species, yet revealing these correlations experimentally has proved extremely challenging. Here, we demonstrate a method that probes correlations between states within the vibrational and electronic manifold with quantum coherence selectivity. Specifically, we measure a fully coherent four-dimensional spectrum which simultaneously encodes vibrational-vibrational, electronic-vibrational and electronic-electronic interactions. By combining near-impulsive resonant and non-resonant excitation, the desired fifth-order signal of a complex organic molecule in solution is measured free of unwanted lower-order contamination. A critical feature of this method is electronic and vibrational frequency resolution, enabling isolation and assignment of individual quantum coherence pathways. The vibronic structure of the system is then revealed within an otherwise broad and featureless 2D electronic spectrum. This method is suited for studying elusive quantum effects in which electronic transitions strongly couple to phonons and vibrations, such as energy transfer in photosynthetic pigment-protein complexes.

  19. Plant chlorophyll fluorescence: active and passive measurements at canopy and leaf scales with different nitrogen treatments

    PubMed Central

    Cendrero-Mateo, M. Pilar; Moran, M. Susan; Papuga, Shirley A.; Thorp, K.R.; Alonso, L.; Moreno, J.; Ponce-Campos, G.; Rascher, U.; Wang, G.

    2016-01-01

    Most studies assessing chlorophyll fluorescence (ChlF) have examined leaf responses to environmental stress conditions using active techniques. Alternatively, passive techniques are able to measure ChlF at both leaf and canopy scales. However, the measurement principles of both techniques are different, and only a few datasets concerning the relationships between them are reported in the literature. In this study, we investigated the potential for interchanging ChlF measurements using active techniques with passive measurements at different temporal and spatial scales. The ultimate objective was to determine the limits within which active and passive techniques are comparable. The results presented in this study showed that active and passive measurements were highly correlated over the growing season across nitrogen treatments at both canopy and leaf-average scale. At the single-leaf scale, the seasonal relation between techniques was weaker, but still significant. The variability within single-leaf measurements was largely related to leaf heterogeneity associated with variations in CO2 assimilation and stomatal conductance, and less so to variations in leaf chlorophyll content, leaf size or measurement inputs (e.g. light reflected and emitted by the leaf and illumination conditions and leaf spectrum). This uncertainty was exacerbated when single-leaf analysis was limited to a particular day rather than the entire season. We concluded that daily measurements of active and passive ChlF at the single-leaf scale are not comparable. However, canopy and leaf-average active measurements can be used to better understand the daily and seasonal behaviour of passive ChlF measurements. In turn, this can be used to better estimate plant photosynthetic capacity and therefore to provide improved information for crop management. PMID:26482242

  20. Use of fluorescent proteins and color-coded imaging to visualize cancer cells with different genetic properties.

    PubMed

    Hoffman, Robert M

    2016-03-01

    Fluorescent proteins are very bright and available in spectrally-distinct colors, enable the imaging of color-coded cancer cells growing in vivo and therefore the distinction of cancer cells with different genetic properties. Non-invasive and intravital imaging of cancer cells with fluorescent proteins allows the visualization of distinct genetic variants of cancer cells down to the cellular level in vivo. Cancer cells with increased or decreased ability to metastasize can be distinguished in vivo. Gene exchange in vivo which enables low metastatic cancer cells to convert to high metastatic can be color-coded imaged in vivo. Cancer stem-like and non-stem cells can be distinguished in vivo by color-coded imaging. These properties also demonstrate the vast superiority of imaging cancer cells in vivo with fluorescent proteins over photon counting of luciferase-labeled cancer cells.

  1. The Fluorescent Properties of Dissolved Organic Matter and Assessment of Total Nitrogen in Overlying Water with Different Dissolved Oxygen Conditions.

    PubMed

    Zhang Hua; Kuan, Wang; Song, Jian; Zhang, Yong; Huang, Ming; Huang, Jian; Zhu, Jing; Huang, Shan; Wang, Meng

    2016-03-01

    This paper used excitation-emission matrix spectroscopy (EEMs) to probe the fluorescence properties of dissolved organic matter (DOM) in the overlying water with different dissolved oxygen (DO) conditions, investigating the relationship between protein-like fluorescence intensity and total nitrogen concentration. The resulting fluorescence spectra revealed three protein-like components (high-excitation wavelength tyrosine, low-excitation wavelength tyrosine, low-excitation wavelength tryptophan) and two fulvic-like components (ultraviolet fulvic-like components, visible fulvic-like components) in the overlying water. Moreover, the protein-like components were dominant in the overlying water's DOM. The fluorescence intensity of the protein-like components decreased significantly after aeration. Two of the protein-like components--the low-excitation wavelength tyrosine and the low-excitation wavelength tryptophan--were more susceptible to degradation by microorganisms within the degradable organic matter with respect to the high-excitation wavelength tyrosine. In contrast, the ultraviolet and visible fulvic-like fluorescence intensity increased along with increasing DO concentration, indicating that the fulvic-like components were part of the refractory organics. The fluorescence indices of the DOM in the overlying water were between 1.65-1.80, suggesting that the sources of the DOM were related to terrigenous sediments and microbial metabolic processes, with the primary source being the contribution from microbial metabolism. The fluorescence indices increased along with DO growth, which showed that microbial biomass and microbial activity gradually increased with increasing DO while microbial metabolism also improved, which also increased the biogenic components in the overlying water. The fluorescence intensity of the high-excitation wavelength tyrosine peak A showed a good linear relationship with the total nitrogen concentration at higher DO concentrations of 2

  2. RRM1, TUBB3, TOP2A, CYP19A1, CYP2D6: Difference between mRNA and protein expression in predicting prognosis of breast cancer patients.

    PubMed

    Xu, Ying-Chun; Zhang, Feng-Chun; Li, Jun-Jian; Dai, Jia-Qi; Liu, Qiang; Tang, Lei; Ma, Yue; Xu, Qi; Lin, Xiao-Lin; Fan, Hong-Bin; Wang, Hong-Xia

    2015-10-01

    The study investigated the clinical significance of RRM1 (ribonucleoside reductase subunit M1), TUBB3 (tubulin-β-III), TOP2A (DNA topoisomerase II), CYP19A1 (cytochrome P450, family 19, subfamily A, polypeptide 1) and CYP2D6 (cytochrome P450, family 2, subfamily D, polypeptide 6) for the diagnosis and possible predictive roles in breast cancer. Tissue microarray detected the expression of RRM1, tubulin-β-III, Topo IIα, CYP19A1 and CYP2D6 protein in breast cancer tissue and tissue adjacent to tumors (TATs). In addition, a publically available tool, was used to assess the prognostic value of their gene expression in breast cancer (http://kmplot.com). Analysis for relapse-free survival (RFS), disease-free survival (DFS) and overall survival (OS) was performed. Cytoplasmic RRM1, tubulin-β-III, CYP19A1 and Topo IIα staining were significantly higher in breast cancer tissues compared with TATs (P<0.050). Significant correlation occurred between RRM1 expression with pathological classification (P=0.018), lymph node involvement (P=0.035) and ER status (P=0.003). Tubulin-β-III and CYP2D6 expression correlated significantly with tumor grade (P=0.021 for tubulin-β-III and P=0.029 for CYP2D6, respectively). Cox analysis showed that the protein expression of CYP2D6, CYP19A1, RRM1, Topo IIα or tubulin-β-III was not an independent prognostic factor. A significant association occurred between RFS and TUBB3, TOP2A, CYP19A1, and CYP2D6 mRNA expression. With CYP19A1 (P<0.001) and CYP2D6 (P<0.001), a high expression was associated with good clinical outcome. Conversely, a low expression of TUBB3 (P<0.001) and TOP2A (P<0.001) was associated with good clinical outcome. TUBB3 (P=0.0004) and TOP2A (P<0.001) were significant prognostic factors in predicting the patient OS. The expression of RRM1, tubulin-β-III, Topo IIα and CYP19A1 in tumor tissues was significantly higher than that in TATs. TUBB3, TOP2A, CYP19A1 and CYP2D6 gene expression, but not protein expression, was

  3. Fluorescent Beads Are a Versatile Tool for Staging Caenorhabditis elegans in Different Life Histories.

    PubMed

    Nika, Liberta; Gibson, Taylor; Konkus, Rebecca; Karp, Xantha

    2016-07-07

    Precise staging of Caenorhabditis elegans is essential for developmental studies in different environmental conditions. In favorable conditions, larvae develop continuously through four larval stages separated by molting periods. Distinguishing molting from intermolt larvae has been achieved using transgenes with molting reporters, therefore requiring strain constructions, or careful observation of individuals for pharyngeal pumping or behavioral quiescence. In unfavorable conditions, larvae can enter the stress-resistant and developmentally arrested dauer larva stage. Identifying dauer larvae has been based on their ability to withstand detergent selection, precluding identification of recovering animals or of mutants with defects in dauer morphogenesis. Here, we describe a simple method to distinguish molting larvae or dauer larvae from intermolt larvae that bypasses the limitations of current methods. Fluorescent latex beads are mixed with the bacterial food source and ingested by intermolt larvae and adults. Molting and dauer larvae do not feed, and therefore lack beads in their digestive tract. The presence of beads can be determined using a dissecting microscope at magnifications as low as 100 ×, or by using a wormsorter for high-throughput experiments. We find that continuously developing bead-lacking larvae display hallmarks of molting, including expression of the mlt-10::gfp molting marker and a lack of pharyngeal pumping. Furthermore, wild-type and mutant dauer larvae produced by any of three common methods are accurately identified by a lack of beads. Importantly, this method is effective in SDS-sensitive mutant backgrounds and can identify recovering dauer larvae, a stage for which there is no other method of positive selection.

  4. Fluorescent Beads Are a Versatile Tool for Staging Caenorhabditis elegans in Different Life Histories

    PubMed Central

    Nika, Liberta; Gibson, Taylor; Konkus, Rebecca; Karp, Xantha

    2016-01-01

    Precise staging of Caenorhabditis elegans is essential for developmental studies in different environmental conditions. In favorable conditions, larvae develop continuously through four larval stages separated by molting periods. Distinguishing molting from intermolt larvae has been achieved using transgenes with molting reporters, therefore requiring strain constructions, or careful observation of individuals for pharyngeal pumping or behavioral quiescence. In unfavorable conditions, larvae can enter the stress-resistant and developmentally arrested dauer larva stage. Identifying dauer larvae has been based on their ability to withstand detergent selection, precluding identification of recovering animals or of mutants with defects in dauer morphogenesis. Here, we describe a simple method to distinguish molting larvae or dauer larvae from intermolt larvae that bypasses the limitations of current methods. Fluorescent latex beads are mixed with the bacterial food source and ingested by intermolt larvae and adults. Molting and dauer larvae do not feed, and therefore lack beads in their digestive tract. The presence of beads can be determined using a dissecting microscope at magnifications as low as 100 ×, or by using a wormsorter for high-throughput experiments. We find that continuously developing bead-lacking larvae display hallmarks of molting, including expression of the mlt-10::gfp molting marker and a lack of pharyngeal pumping. Furthermore, wild-type and mutant dauer larvae produced by any of three common methods are accurately identified by a lack of beads. Importantly, this method is effective in SDS-sensitive mutant backgrounds and can identify recovering dauer larvae, a stage for which there is no other method of positive selection. PMID:27172224

  5. Comparison of Fluorescence Microscopy and Different Growth Media Culture Methods for Acanthamoeba Keratitis Diagnosis

    PubMed Central

    Peretz, Avi; Geffen, Yuval; Socea, Soergiu D.; Pastukh, Nina; Graffi, Shmuel

    2015-01-01

    Acanthamoeba keratitis (AK), a potentially blinding infection of the cornea, is caused by a free-living protozoan. Culture and microscopic examination of corneal scraping tissue material is the conventional method for identifying Acanthamoeba. In this article, we compared several methods for AK diagnosis of 32 patients: microscopic examination using fluorescent dye, specific culture on growth media—non-nutrient agar (NNA), culture on liquid growth media—peptone yeast glucose (PYG), and TYI-S-33. AK was found in 14 patients. Thirteen of the specimens were found AK positive by fluorescence microscopic examination, 11 specimens were found AK positive on PYG growth media, and 9 specimens were found AK positive on TYI-S-33 growth media. Only five specimens were found AK positive on NNA growth media. Therefore, we recommend using fluorescence microscopy technique and culture method, especially PYG liquid media. PMID:25962772

  6. Optical and fluorescence properties of corn leaves from different nitrogen regimes

    NASA Astrophysics Data System (ADS)

    Middleton, Elizabeth M.; McMurtrey, James E., III; Entcheva Campbell, Petya K.; Corp, Lawrence A.; Butcher, L. M.; Chappelle, Emmett W.

    2003-03-01

    The important role of nitrogen (N) in limiting or enhancing vegetation productivity is relatively well understood, although the interaction of N with other environmental variables in natural and agricultural ecosystems needs more study. In 2001, a suite of optical, fluorescence, and biophysical measurements were collected on leaves of corn (Zea Mays L.) from field plots provided four N fertilizer application rates: 20%, 50%, 100% and 150% of optimal N levels. Two complementary sets of high-resolution (< 2 nm) optical spectra were acquired for both adaxial and abaxial leaf surfaces. The first was comprised of leaf optical properties (350-2500 nm) for reflectance, transmittance, and absorptance. The second was comprised of reflectance spectra (500-1000 nm) acquired with and without a long pass 665 nm filter to determine the fluorescence contribution to "apparent reflectance" in the 670-750 nm spectrum that includes the 685 and 740 nm chlorophyll fluorescence (ChlF) peaks. Two types of fluorescence measurements were also made on adaxial and abaxial surfaces: 1) fluorescence images in four 10 nm bands (blue, green, red, far-red) resulting from broadband irradiance excitation; and 2) emission spectra at 5 nm resolution produced by three excitation wavelengths (280, 380, and 532 nm). The strongest relationships between optical properties and foliar chemistry were obtained for a "red-edge" optical parameter versus C/N and chlorophyll b. Select optical indices and ChlF parameters were correlated. A significant contribution of steady-state ChlF to apparent reflectance was observed, averaging 10-25% at 685 nm and 2-6% at 740 nm over the range of N treatments. From all measurements assessing fluorescence, higher ChlF was measured from the abaxial leaf surfaces.

  7. Codon Constraints on Closed 2D Shapes,

    DTIC Science & Technology

    2014-09-26

    19843$ CODON CONSTRAINTS ON CLOSED 2D SHAPES Go Whitman Richards "I Donald D. Hoffman’ D T 18 Abstract: Codons are simple primitives for describing plane...RSONAL AUT"ORtIS) Richards, Whitman & Hoffman, Donald D. 13&. TYPE OF REPORT 13b. TIME COVERED N/A P8 AT F RRrT t~r. Ago..D,) is, PlE COUNT Reprint...outlines, if figure and ground are ignored. Later, we will address the problem of indexing identical codon descriptors that have different figure

  8. Production and laser-induced fluorescence spectroscopy (L.I.F.S.) of different Hypericum perforatum L. extracts

    NASA Astrophysics Data System (ADS)

    Skalkos, Dimitris; Filippidis, George; Kapsokalyvas, Dimitris; Meyer, Heiko; Papazoglou, Theodore; Karentzou, Eleni; Dimitriou, Heleni; Kalmanti, M.

    2005-04-01

    We are reporting elsewhere, the promising photodynamic effect of Hypericum perforatum L. extract (PMF) against T24, NBT-II tumor bladder cells, and HL-60 leukemic cells (using 630nm, and 530nm laser light respectively). The main advantages of the extract as a photosensitizer are its low cost, extensive availability, adequate solubility, minimal toxicity, and use with a range of wavelengths. Extraction of dry herb with methanol yields the methanolic extract (ME) in 11%, which is then fractionated using liquid / liquid extraction, yielding the polar methanolic fraction (PMF) in 9,9% overall yield. Hypericin, a photosensitizing ingredient of the herb, was found in these extracts in concentrations as low as 0,51%, and 0,57% respectively. Laser induced fluorescence spectra from the ME and PMF were recorded in order to evaluate their photodiagnostic capacity. An Argon-ion laser was employed for the excitation of the samples. It was shown that the extracts resulted in different fluorescence spectra related both to their intensity, and shape. The intensities of these spectra were only 8 times less compared to the fluorescence of pure hypericin. The dependence of the signal on the pH of the medium of pure hypericin and of PMF was also investigated in order to determine specific spectra variations. According to the results hypericin fluorescence signal fades smoothly in highly acidic medium, while it decreases sharply in highly basic environment. On the contrary PMF gives a slow decrease of fluorescence in both acidic and basic medium. These data suggest that PMF-induced fluorescence is highly sensitive in basic and acidic environment.

  9. Comparison of 2D and 3D gamma analyses

    SciTech Connect

    Pulliam, Kiley B.; Huang, Jessie Y.; Howell, Rebecca M.; Followill, David; Kry, Stephen F.; Bosca, Ryan; O’Daniel, Jennifer

    2014-02-15

    Purpose: As clinics begin to use 3D metrics for intensity-modulated radiation therapy (IMRT) quality assurance, it must be noted that these metrics will often produce results different from those produced by their 2D counterparts. 3D and 2D gamma analyses would be expected to produce different values, in part because of the different search space available. In the present investigation, the authors compared the results of 2D and 3D gamma analysis (where both datasets were generated in the same manner) for clinical treatment plans. Methods: Fifty IMRT plans were selected from the authors’ clinical database, and recalculated using Monte Carlo. Treatment planning system-calculated (“evaluated dose distributions”) and Monte Carlo-recalculated (“reference dose distributions”) dose distributions were compared using 2D and 3D gamma analysis. This analysis was performed using a variety of dose-difference (5%, 3%, 2%, and 1%) and distance-to-agreement (5, 3, 2, and 1 mm) acceptance criteria, low-dose thresholds (5%, 10%, and 15% of the prescription dose), and data grid sizes (1.0, 1.5, and 3.0 mm). Each comparison was evaluated to determine the average 2D and 3D gamma, lower 95th percentile gamma value, and percentage of pixels passing gamma. Results: The average gamma, lower 95th percentile gamma value, and percentage of passing pixels for each acceptance criterion demonstrated better agreement for 3D than for 2D analysis for every plan comparison. The average difference in the percentage of passing pixels between the 2D and 3D analyses with no low-dose threshold ranged from 0.9% to 2.1%. Similarly, using a low-dose threshold resulted in a difference between the mean 2D and 3D results, ranging from 0.8% to 1.5%. The authors observed no appreciable differences in gamma with changes in the data density (constant difference: 0.8% for 2D vs 3D). Conclusions: The authors found that 3D gamma analysis resulted in up to 2.9% more pixels passing than 2D analysis. It must

  10. WE-AB-BRA-07: Quantitative Evaluation of 2D-2D and 2D-3D Image Guided Radiation Therapy for Clinical Trial Credentialing, NRG Oncology/RTOG

    SciTech Connect

    Giaddui, T; Yu, J; Xiao, Y; Jacobs, P; Manfredi, D; Linnemann, N

    2015-06-15

    Purpose: 2D-2D kV image guided radiation therapy (IGRT) credentialing evaluation for clinical trial qualification was historically qualitative through submitting screen captures of the fusion process. However, as quantitative DICOM 2D-2D and 2D-3D image registration tools are implemented in clinical practice for better precision, especially in centers that treat patients with protons, better IGRT credentialing techniques are needed. The aim of this work is to establish methodologies for quantitatively reviewing IGRT submissions based on DICOM 2D-2D and 2D-3D image registration and to test the methodologies in reviewing 2D-2D and 2D-3D IGRT submissions for RTOG/NRG Oncology clinical trials qualifications. Methods: DICOM 2D-2D and 2D-3D automated and manual image registration have been tested using the Harmony tool in MIM software. 2D kV orthogonal portal images are fused with the reference digital reconstructed radiographs (DRR) in the 2D-2D registration while the 2D portal images are fused with DICOM planning CT image in the 2D-3D registration. The Harmony tool allows alignment of the two images used in the registration process and also calculates the required shifts. Shifts calculated using MIM are compared with those submitted by institutions for IGRT credentialing. Reported shifts are considered to be acceptable if differences are less than 3mm. Results: Several tests have been performed on the 2D-2D and 2D-3D registration. The results indicated good agreement between submitted and calculated shifts. A workflow for reviewing these IGRT submissions has been developed and will eventually be used to review IGRT submissions. Conclusion: The IROC Philadelphia RTQA center has developed and tested a new workflow for reviewing DICOM 2D-2D and 2D-3D IGRT credentialing submissions made by different cancer clinical centers, especially proton centers. NRG Center for Innovation in Radiation Oncology (CIRO) and IROC RTQA center continue their collaborative efforts to enhance

  11. Dental fluorosis in populations from Chiang Mai, Thailand with different fluoride exposures - Paper 2: The ability of fluorescence imaging to detect differences in fluorosis prevalence and severity for different fluoride intakes from water

    PubMed Central

    2012-01-01

    Background To assess the ability of fluorescence imaging to detect a dose response relationship between fluorosis severity and different levels of fluoride in water supplies compared to remote photographic scoring in selected populations participating in an observational, epidemiological survey in Chiang Mai, Thailand. Methods Subjects were male and female lifetime residents aged 8-13 years. For each child the fluoride content of cooking water samples (CWS) was assessed to create categorical intervals of water fluoride concentration. Fluorescence images were taken of the maxillary central incisors and analyzed for dental fluorosis using two different software techniques. Output metrics for the fluorescence imaging techniques were compared to TF scores from blinded photographic scores obtained from the survey. Results Data from 553 subjects were available. Both software analysis techniques demonstrated significant correlations with the photographic scores. The metrics for area effected by fluorosis and the overall fluorescence loss had the strongest association with the photographic TF score (Spearman’s rho 0.664 and 0.652 respectively). Both software techniques performed well for comparison of repeat fluorescence images with ICC values of 0.95 and 0.85 respectively. Conclusions This study supports the potential use of fluorescence imaging for the objective quantification of dental fluorosis. Fluorescence imaging was able to discriminate between populations with different fluoride exposures on a comparable level to remote photographic scoring with acceptable levels of repeatability. PMID:22908997

  12. Estrogen-Induced Cholestasis Leads to Repressed CYP2D6 Expression in CYP2D6-Humanized Mice.

    PubMed

    Pan, Xian; Jeong, Hyunyoung

    2015-07-01

    Cholestasis activates bile acid receptor farnesoid X receptor (FXR) and subsequently enhances hepatic expression of small heterodimer partner (SHP). We previously demonstrated that SHP represses the transactivation of cytochrome P450 2D6 (CYP2D6) promoter by hepatocyte nuclear factor (HNF) 4α. In this study, we investigated the effects of estrogen-induced cholestasis on CYP2D6 expression. Estrogen-induced cholestasis occurs in subjects receiving estrogen for contraception or hormone replacement, or in susceptible women during pregnancy. In CYP2D6-humanized transgenic (Tg-CYP2D6) mice, cholestasis triggered by administration of 17α-ethinylestradiol (EE2) at a high dose led to 2- to 3-fold decreases in CYP2D6 expression. This was accompanied by increased hepatic SHP expression and subsequent decreases in the recruitment of HNF4α to CYP2D6 promoter. Interestingly, estrogen-induced cholestasis also led to increased recruitment of estrogen receptor (ER) α, but not that of FXR, to Shp promoter, suggesting a predominant role of ERα in transcriptional regulation of SHP in estrogen-induced cholestasis. EE2 at a low dose (that does not cause cholestasis) also increased SHP (by ∼ 50%) and decreased CYP2D6 expression (by 1.5-fold) in Tg-CYP2D6 mice, the magnitude of differences being much smaller than that shown in EE2-induced cholestasis. Taken together, our data indicate that EE2-induced cholestasis increases SHP and represses CYP2D6 expression in Tg-CYP2D6 mice in part through ERα transactivation of Shp promoter.

  13. Structural investigation of nuclear RNP particles containing pre-mRNA by different fluorescence techniques.

    PubMed Central

    Borissova, O F; Krichevskaya, A A; Samarina, O P

    1981-01-01

    Ethidium bromide (EB) adsorption isotherms on 30S nuclear RNP particles isolated from liver nuclei has revealed 6% of double-stranded regions in pre-mRNA (dsRNA). It has been established by measurements of the EB fluorescence polarization that the bulk of dsRNA regions in RNP is rigidly attached to RNP. They are longer than 45 degree A. The increase of NaCl concentration from 0.1 up to 0.4 M causes a significant loosening of dsRNA-protein bonds. As a result the dsRNA segments become more flexible. Measurements of energy transfer from fluorescamine (covalently bound to the protein) to EB (adsorbed on dsRNA) have yielded information about dsRNA location. The fact that absorbtion of exciting light by fluorescamine causes pronounced increase of EB fluorescence is consistent with the idea that helical regions of RNA are located outside the RNP particles. PMID:7220348

  14. NKG2D ligands as therapeutic targets

    PubMed Central

    Spear, Paul; Wu, Ming-Ru; Sentman, Marie-Louise; Sentman, Charles L.

    2013-01-01

    The Natural Killer Group 2D (NKG2D) receptor plays an important role in protecting the host from infections and cancer. By recognizing ligands induced on infected or tumor cells, NKG2D modulates lymphocyte activation and promotes immunity to eliminate ligand-expressing cells. Because these ligands are not widely expressed on healthy adult tissue, NKG2D ligands may present a useful target for immunotherapeutic approaches in cancer. Novel therapies targeting NKG2D ligands for the treatment of cancer have shown preclinical success and are poised to enter into clinical trials. In this review, the NKG2D receptor and its ligands are discussed in the context of cancer, infection, and autoimmunity. In addition, therapies targeting NKG2D ligands in cancer are also reviewed. PMID:23833565

  15. Remarks on thermalization in 2D CFT

    NASA Astrophysics Data System (ADS)

    de Boer, Jan; Engelhardt, Dalit

    2016-12-01

    We revisit certain aspects of thermalization in 2D conformal field theory (CFT). In particular, we consider similarities and differences between the time dependence of correlation functions in various states in rational and non-rational CFTs. We also consider the distinction between global and local thermalization and explain how states obtained by acting with a diffeomorphism on the ground state can appear locally thermal, and we review why the time-dependent expectation value of the energy-momentum tensor is generally a poor diagnostic of global thermalization. Since all 2D CFTs have an infinite set of commuting conserved charges, generic initial states might be expected to give rise to a generalized Gibbs ensemble rather than a pure thermal ensemble at late times. We construct the holographic dual of the generalized Gibbs ensemble and show that, to leading order, it is still described by a Banados-Teitelboim-Zanelli black hole. The extra conserved charges, while rendering c <1 theories essentially integrable, therefore seem to have little effect on large-c conformal field theories.

  16. Joint 2D and 3D phase processing for quantitative susceptibility mapping: application to 2D echo-planar imaging.

    PubMed

    Wei, Hongjiang; Zhang, Yuyao; Gibbs, Eric; Chen, Nan-Kuei; Wang, Nian; Liu, Chunlei

    2017-04-01

    Quantitative susceptibility mapping (QSM) measures tissue magnetic susceptibility and typically relies on time-consuming three-dimensional (3D) gradient-echo (GRE) MRI. Recent studies have shown that two-dimensional (2D) multi-slice gradient-echo echo-planar imaging (GRE-EPI), which is commonly used in functional MRI (fMRI) and other dynamic imaging techniques, can also be used to produce data suitable for QSM with much shorter scan times. However, the production of high-quality QSM maps is difficult because data obtained by 2D multi-slice scans often have phase inconsistencies across adjacent slices and strong susceptibility field gradients near air-tissue interfaces. To address these challenges in 2D EPI-based QSM studies, we present a new data processing procedure that integrates 2D and 3D phase processing. First, 2D Laplacian-based phase unwrapping and 2D background phase removal are performed to reduce phase inconsistencies between slices and remove in-plane harmonic components of the background phase. This is followed by 3D background phase removal for the through-plane harmonic components. The proposed phase processing was evaluated with 2D EPI data obtained from healthy volunteers, and compared against conventional 3D phase processing using the same 2D EPI datasets. Our QSM results were also compared with QSM values from time-consuming 3D GRE data, which were taken as ground truth. The experimental results show that this new 2D EPI-based QSM technique can produce quantitative susceptibility measures that are comparable with those of 3D GRE-based QSM across different brain regions (e.g. subcortical iron-rich gray matter, cortical gray and white matter). This new 2D EPI QSM reconstruction method is implemented within STI Suite, which is a comprehensive shareware for susceptibility imaging and quantification. Copyright © 2016 John Wiley & Sons, Ltd.

  17. Exciton energy transfer-based quantum dot fluorescence sensing array: "chemical noses" for discrimination of different nucleobases.

    PubMed

    Liu, Jianbo; Li, Gui; Yang, Xiaohai; Wang, Kemin; Li, Li; Liu, Wei; Shi, Xing; Guo, Yali

    2015-01-20

    A novel exciton energy transfer-based fluorescence sensing array for the discrimination of different nucleobases was developed through target nucleobase-triggered self-assembly of quantum dots (QDs). Four QD nanoprobes with different ligand receptors, including mercaptoethylamine, N-acetyl-l-cysteine, 2-dimethyl-aminethanethiol, and thioglycolic acid, were created to detect and identify nucleobase targets. These QDs served as both selective recognition scaffolds and signal transduction elements for a biomolecule target. The extent of particle assembly, induced by the analyte-triggered self-assembly of QDs, led to an exciton energy transfer effect between interparticles that gave a readily detectable fluorescence quenching and distinct fluorescence response patterns. These patterns are characteristic for each nucleobase and can be quantitatively differentiated by linear discriminate analysis. Furthermore, a fingerprint-based barcode was established to conveniently discriminate the nucleobases. This pattern sensing was successfully used to identify nucleobase samples at unknown concentrations and five rare bases. In this "chemical noses" strategy, the robust characteristics of QD nanoprobes, coupled with the diversity of surface functionality that can be readily obtained using nanoparticles, provides a simple and label-free biosensing approach that shows great promise for biomedical applications.

  18. Synchrotron-induced X-ray fluorescence from rat bone and lumber vertebra of different age groups

    NASA Astrophysics Data System (ADS)

    Rao, Donepudi V.; Swapna, Medasani; Cesareo, Roberto; Brunetti, Antonio; Akatsuka, Tako; Yuasa, Tetsuya; Takeda, Tohoru; Tromba, Giuliana; Gigante, Giovanni E.

    2009-02-01

    The fluorescence spectra from rat bones of different age groups (8, 56 and 78 weeks) and lumber vertebra were measured with 8, 10 and 12 keV synchrotron X-rays. We have utilized the new hard X-ray micro-spectroscopy beamline facility, X27A, available at NSLS with a primary beam spot size of the order of ˜10 μm. With this spatial resolution and high flux throughput, X-ray fluorescent intensities for Ca and other trace elements were measured using a liquid-nitrogen-cooled 13-element energy-dispersive high-purity germanium detector. Regarding the lumber vertebra, we acquired the fluorescence spectra from the left, right and middle portions and calcium accumulation was evaluated and compared with the other samples. We have identified the major trace elements of Ca, Ni, Fe and Zn and minor trace elements of Ti, Cr and Mn in the sample. The percentage of scattered radiation and trace element contributions from these samples were highlighted at different energies.

  19. Compact and cost effective instrument for detecting drug precursors in different environments based on fluorescence polarization

    NASA Astrophysics Data System (ADS)

    Antolín-Urbaneja, J. C.; Eguizabal, I.; Briz, N.; Dominguez, A.; Estensoro, P.; Secchi, A.; Varriale, A.; Di Giovanni, S.; D'Auria, S.

    2013-05-01

    Several techniques for detecting chemical drug precursors have been developed in the last decade. Most of them are able to identify molecules at very low concentration under lab conditions. Other commercial devices are able to detect a fixed number and type of target substances based on a single detection technique providing an absence of flexibility with respect to target compounds. The construction of compact and easy to use detection systems providing screening for a large number of compounds being able to discriminate them with low false alarm rate and high probability of detection is still an open concern. Under CUSTOM project, funded by the European Commission within the FP7, a stand-alone portable sensing device based on multiple techniques is being developed. One of these techniques is based on the LED induced fluorescence polarization to detect Ephedrine and Benzyl Methyl Keton (BMK) as a first approach. This technique is highly selective with respect to the target compounds due to the generation of properly engineered fluorescent proteins which are able to bind the target analytes, as it happens in an "immune-type reaction". This paper deals with the advances in the design, construction and validation of the LED induced fluorescence sensor to detect BMK analytes. This sensor includes an analysis module based on high performance LED and PMT detector, a fluidic system to dose suitable quantities of reagents and some printed circuit boards, all of them fixed in a small structure (167mm × 193mm × 228mm) with the capability of working as a stand-alone application.

  20. Absorption, Fluorescence and Emission Anisotropy Spectra of 4-Cyano-N,N-dimethylaniline in Different Media and at Different Temperatures

    NASA Astrophysics Data System (ADS)

    Kawski, A.; Piszczek, G.

    1997-05-01

    The effect of temperature on fluorescence and emission anisotropy spectra of 4-cyano-N,N-dimethylaniline (CDMA) was investigated in viscous (glycerol and paraffin oil) and rigid (polyvinyl alcohol) PVA and polyvinyl chloride) PVC) media. A strong effect of temperature on the intensity of a and b emission bands was observed. It was also found that the emission anisotropy, r, does not vary in the longwave emission band a at a fixed temperature but decreases in the emission band b together with the decreasing wavelength. The latter effect is due to the fact that the transition moment in this band is perpendicular to the long axis of the CDMA molecule. For CDMA in paraffin oil, a normal b band with negative emission anisotropy only occurs. In all other media used, the emission anisotropy has lower values, approaching zero, which results from the considerable covering of band b with a broad emission band a.

  1. Computational analysis of fluorescence induction curves in intact spinach leaves treated at different pH.

    PubMed

    Tongra, Teena; Mehta, Pooja; Mathur, Sonal; Agrawal, Divya; Bharti, Sudhakar; Los, Dmitry A; Allakhverdiev, Suleyman I; Jajoo, Anjana

    2011-02-01

    Effects of change in pH have been investigated on spinach leaf discs by measuring fluorescence induction kinetics using plant efficiency analyzer (PEA). On the basis of computational analysis of the results, we have reported that acidic pH causes a significant inhibition of the donor and the acceptor side of PS II. Energy flux models have been presented using the software Biolyzer HP 3. Effects of pH were investigated on the antenna size heterogeneity of PS II and a relative change in the proportions of α, β, and γ centers was observed.

  2. 2D vs. 3D mammography observer study

    NASA Astrophysics Data System (ADS)

    Fernandez, James Reza F.; Hovanessian-Larsen, Linda; Liu, Brent

    2011-03-01

    Breast cancer is the most common type of non-skin cancer in women. 2D mammography is a screening tool to aid in the early detection of breast cancer, but has diagnostic limitations of overlapping tissues, especially in dense breasts. 3D mammography has the potential to improve detection outcomes by increasing specificity, and a new 3D screening tool with a 3D display for mammography aims to improve performance and efficiency as compared to 2D mammography. An observer study using a mammography phantom was performed to compare traditional 2D mammography with this ne 3D mammography technique. In comparing 3D and 2D mammography there was no difference in calcification detection, and mass detection was better in 2D as compared to 3D. There was a significant decrease in reading time for masses, calcifications, and normals in 3D compared to 2D, however, as well as more favorable confidence levels in reading normal cases. Given the limitations of the mammography phantom used, however, a clearer picture in comparing 3D and 2D mammography may be better acquired with the incorporation of human studies in the future.

  3. Development of a MEMS 2D separations device

    NASA Astrophysics Data System (ADS)

    Bloschock, Kristen P.; Flyer, Jonathan N.; Schneider, Thomas W.; Hussam, Abul; Van Keuren, Edward R.

    2004-12-01

    A polymer based biochip for rapid 2D separations of peptides, proteins, and other biomedically relevant molecules was designed and fabricated. Like traditional 2D polyacrylamide gel electrophoresis (2D-PAGE) methods, the device will allow molecules to separate based on isoelectric point (pI) and molecular weight (MW). Our design, however, integrates both an initial capillary isoelectric focusing (cIEF) step followed by capillary electrophoresis (CE) in multiple parallel channels, all on a single microfluidic chip. Not only is the "lab-on-a-chip" design easier to use and less expensive, but the miniaturization of the device produces very rapid separations. Compared to traditional 2D-PAGE, which can take hours to complete, we estimate separation times on the order of seconds. Fluorescence detection will be used in the preliminary stages of testing, but the device also is equipped with integrated electrodes in the electrophoresis channels to perform multiplexed electrochemical detection for quantitative analysis. We will present preliminary results of the chip development and testing.

  4. Application of 2-D graphical representation of DNA sequence

    NASA Astrophysics Data System (ADS)

    Liao, Bo; Tan, Mingshu; Ding, Kequan

    2005-10-01

    Recently, we proposed a 2-D graphical representation of DNA sequence [Bo Liao, A 2-D graphical representation of DNA sequence, Chem. Phys. Lett. 401 (2005) 196-199]. Based on this representation, we consider properties of mutations and compute the similarities among 11 mitochondrial sequences belonging to different species. The elements of the similarity matrix are used to construct phylogenic tree. Unlike most existing phylogeny construction methods, the proposed method does not require multiple alignment.

  5. Phylogenetic tree construction based on 2D graphical representation

    NASA Astrophysics Data System (ADS)

    Liao, Bo; Shan, Xinzhou; Zhu, Wen; Li, Renfa

    2006-04-01

    A new approach based on the two-dimensional (2D) graphical representation of the whole genome sequence [Bo Liao, Chem. Phys. Lett., 401(2005) 196.] is proposed to analyze the phylogenetic relationships of genomes. The evolutionary distances are obtained through measuring the differences among the 2D curves. The fuzzy theory is used to construct phylogenetic tree. The phylogenetic relationships of H5N1 avian influenza virus illustrate the utility of our approach.

  6. Recovering fluorescent spectra with an RGB digital camera and color filters using different matrix factorizations.

    PubMed

    Nieves, Juan L; Valero, Eva M; Hernández-Andrés, Javier; Romero, Javier

    2007-07-01

    The aim of a multispectral system is to recover a spectral function at each image pixel, but when a scene is digitally imaged under a light of unknown spectral power distribution (SPD), the image pixels give incomplete information about the spectral reflectances of objects in the scene. We have analyzed how accurately the spectra of artificial fluorescent light sources can be recovered with a digital CCD camera. The red-green-blue (RGB) sensor outputs are modified by the use of successive cutoff color filters. Four algorithms for simplifying the spectra datasets are used: nonnegative matrix factorization (NMF), independent component analysis (ICA), a direct pseudoinverse method, and principal component analysis (PCA). The algorithms are tested using both simulated data and data from a real RGB digital camera. The methods are compared in terms of the minimum rank of factorization and the number of sensors required to derive acceptable spectral and colorimetric SPD estimations; the PCA results are also given for the sake of comparison. The results show that all the algorithms surpass the PCA when a reduced number of sensors is used. The experimental results suggest a significant loss of quality when more than one color filter is used, which agrees with the previous results for reflectances. Nevertheless, an RGB digital camera with or without a prefilter is found to provide good spectral and colorimetric recovery of indoor fluorescent lighting and can be used for color correction without the need of a telespectroradiometer.

  7. Numerical Evaluation of 2D Ground States

    NASA Astrophysics Data System (ADS)

    Kolkovska, Natalia

    2016-02-01

    A ground state is defined as the positive radial solution of the multidimensional nonlinear problem \\varepsilon propto k_ bot 1 - ξ with the function f being either f(u) =a|u|p-1u or f(u) =a|u|pu+b|u|2pu. The numerical evaluation of ground states is based on the shooting method applied to an equivalent dynamical system. A combination of fourth order Runge-Kutta method and Hermite extrapolation formula is applied to solving the resulting initial value problem. The efficiency of this procedure is demonstrated in the 1D case, where the maximal difference between the exact and numerical solution is ≈ 10-11 for a discretization step 0:00025. As a major application, we evaluate numerically the critical energy constant. This constant is defined as a functional of the ground state and is used in the study of the 2D Boussinesq equations.

  8. Endogenous and exogenous fluorescence of gastrointestinal tumors: initial clinical observations

    NASA Astrophysics Data System (ADS)

    Borisova, Ekaterina; Plamenova, Lilia; Keremedchiev, Momchil; Vladimirov, Borislav; Avramov, Latchezar

    2013-03-01

    The limitations of standard endoscopy for detection and evaluation of cancerous changes in gastrointestinal tract (GIT) are significant challenge and initiate development of new diagnostic modalities. Therefore many spectral and optical techniques are applied recently into the clinical practice for obtaining qualitatively and quantitatively new data from gastrointestinal neoplasia with different level of clinical applicability and diagnostic success. One of the most promising approaches is fluorescence detection using naturally existing fluorescent molecules or added fluorescent markers. Deltaaminolevulinic acid / protoporphyrin IX is applied for exogenous fluorescent tumor detection in the upper part of gastrointestinal tract. The 5-ALA is administered per os six hours before measurements at dose 20mg/kg weight. Highpower light-emitting diode at 405 nm is used as a source and the excitation light is passed through the light-guide of standard video-endoscopic system to obtain 2-D visualization. Both kinds of spectra - autofluorescence signals and protoporphyrin IX signal are recorded and stored using a fiber-optic microspectrometer, as in endoscopy instrumental channel a fiber is applied to return information about fluorescence signals. In such way 1-D detection and 2-D visualization of the lesions' fluorescence are received. The results from in vivo detection show significant differentiation between normal and abnormal tissues in 1-D spectroscopic regime, but only moderate discrimination in 2-D imaging.

  9. Regulation of NKG2D ligand gene expression.

    PubMed

    Eagle, Robert A; Traherne, James A; Ashiru, Omodele; Wills, Mark R; Trowsdale, John

    2006-03-01

    The activating immunoreceptor NKG2D has seven known host ligands encoded by the MHC class I chain-related MIC and ULBP/RAET genes. Why there is such diversity of NKG2D ligands is not known but one hypothesis is that they are differentially expressed in different tissues in response to different stresses. To explore this, we compared expression patterns and promoters of NKG2D ligand genes. ULBP/RAET genes were transcribed independent of each other in a panel of cell lines. ULBP/RAET gene expression was upregulated on infection with human cytomegalovirus; however, a clinical strain, Toledo, induced expression more slowly than did a laboratory strain, AD169. ULBP4/RAET1E was not induced by infection with either strain. To investigate the mechanisms behind the similarities and differences in NKG2D ligand gene expression a comparative sequence analysis of NKG2D ligand gene putative promoter regions was conducted. Sequence alignments demonstrated that there was significant sequence diversity; however, one region of high similarity between most of the genes is evident. This region contains a number of potential transcription factor binding sites, including those involved in shock responses and sites for retinoic acid-induced factors. Promoters of some NKG2D ligand genes are polymorphic and several sequence alterations in these alleles abolished putative transcription factor binding.

  10. Total-reflection X-ray fluorescence — a tool to obtain information about different air masses and air pollution

    NASA Astrophysics Data System (ADS)

    Schmeling, Martina

    2001-11-01

    Atmospheric aerosols are solid particles dissolved in air and change their chemical composition frequently depending on various parameters. In order to identify regional air circulation atmospheric aerosol filter samples were taken at Loyola University Chicago's Lake Shore Campus during the months of July and August 2000 with sampling times ranging between 1 and 2 h. The samples were digested in a microwave oven and analyzed by total-reflection X-ray fluorescence (TXRF) spectrometry. One diurnal variation comprising five consecutive sampling events was selected and discussed as well as 4 days experiencing different meteorology were compared to exemplify the variation in trace elemental concentration according to air mass movements and highlight the capability of total-reflection X-ray fluorescence analysis. It was found that due to changes in meteorological conditions particularly wind direction and wind speed, trace elemental compositions varied rapidly and could be used to distinguish between 'Lake Michigan air' and 'metropolitan Chicago air' on such short-term time scale like one hour. Back trajectory analysis was applied to support and corroborate the results. The outcome of this study clearly shows that total-reflection X-ray fluorescence is an optimal tool for analysis of atmospheric aerosols.

  11. Calibration of the response of 9-amino acridine fluorescence to transmembrane pH differences in bacterial chromatophores.

    PubMed

    Casadio, R; Melandri, B A

    1985-04-01

    The spectral characteristics of absorption and fluorescence emission of 9-amino acridine are not altered by the interaction with bacterial chromatophores, except for the attenuation of both the absorption and emission following the formation of a protonic gradient. The lifetime of fluorescence of the dye is significantly affected in the presence of membranes, and even more following illumination. The shortening of the lifetime induced by light is reversible and prevented by nigericin and K+. The onset kinetics of the fluorescence quenching following the generation of an artificial transmembrane pH difference is temperature dependent, with an activation energy of 17 +/- 3 kcal/mol. The effect of pH on the rate constants is consistent with a model assuming that the diffusion of the unprotonated species is the limiting step in the quenching phenomenon. The response of 9-amino acridine to artificially imposed delta pH's has been utilized as a calibration method for the measurements of the light-induced protonic gradient. The apparent inner volume of chromatophores, evaluated from the extraplation of the response at delta pH = 0, was found to be much larger (15- to 40-fold) than the true osmotic volume, indicating that most of the dye is bound to the membrane when accumulated into the inner lumen.

  12. Stability of curcumin in different solvent and solution media: UV-visible and steady-state fluorescence spectral study.

    PubMed

    Mondal, Satyajit; Ghosh, Soumen; Moulik, Satya P

    2016-05-01

    In aqueous solution, curcumin is photodegradable (light sensitive), it is also self-degradable in the dark. In basic medium, the second process is enhanced. The dark process has been studied in water and also in a number of protic and aprotic solvents, and aqueous solutions of ionic liquids, pluronics, reverse micelles and salt. The kinetics of the process followed the first order rate law; a comparative as well as individual assessment of which has been made. The kinetics of curcumin self-degradation has been found to be fairly dependent on salt (NaCl) concentration. Curcumin molecules in solution may remain in the enol or keto-enol form. From the visible spectral analysis, an estimate of the proportions of these forms in aqueous ethanol medium has been made. The temperature effect on the visible and fluorescence spectra of curcumin has been also studied. The steady state fluorescence anisotropy of the photoactive curcumin has been evaluated in different solvent and solution media. The reversibility of the steady state fluorescence anisotropy of curcumin on heating and cooling conditions has been examined. The results herein presented are new and ought to be useful as the study of physicochemistry of curcumin has been gaining importance in the light of its biological importance.

  13. Recovering 3D particle size distributions from 2D sections

    NASA Astrophysics Data System (ADS)

    Cuzzi, Jeffrey N.; Olson, Daniel M.

    2017-03-01

    We discuss different ways to convert observed, apparent particle size distributions from 2D sections (thin sections, SEM maps on planar surfaces, etc.) into true 3D particle size distributions. We give a simple, flexible, and practical method to do this; show which of these techniques gives the most faithful conversions; and provide (online) short computer codes to calculate both 2D-3D recoveries and simulations of 2D observations by random sectioning. The most important systematic bias of 2D sectioning, from the standpoint of most chondrite studies, is an overestimate of the abundance of the larger particles. We show that fairly good recoveries can be achieved from observed size distributions containing 100-300 individual measurements of apparent particle diameter.

  14. Phonon thermal conduction in novel 2D materials

    NASA Astrophysics Data System (ADS)

    Xu, Xiangfan; Chen, Jie; Li, Baowen

    2016-12-01

    Recently, there has been increasing interest in phonon thermal transport in low-dimensional materials, due to the crucial importance of dissipating and managing heat in micro- and nano-electronic devices. Significant progress has been achieved for one-dimensional (1D) systems, both theoretically and experimentally. However, the study of heat conduction in two-dimensional (2D) systems is still in its infancy due to the limited availability of 2D materials and the technical challenges of fabricating suspended samples that are suitable for thermal measurements. In this review, we outline different experimental techniques and theoretical approaches for phonon thermal transport in 2D materials, discuss the problems and challenges of phonon thermal transport measurements and provide a comparison between existing experimental data. Special attention will be given to the effects of size, dimensionality, anisotropy and mode contributions in novel 2D systems, including graphene, boron nitride, MoS2, black phosphorous and silicene.

  15. Recent developments in 2D layered inorganic nanomaterials for sensing

    NASA Astrophysics Data System (ADS)

    Kannan, Padmanathan Karthick; Late, Dattatray J.; Morgan, Hywel; Rout, Chandra Sekhar

    2015-08-01

    Two dimensional layered inorganic nanomaterials (2D-LINs) have recently attracted huge interest because of their unique thickness dependent physical and chemical properties and potential technological applications. The properties of these layered materials can be tuned via both physical and chemical processes. Some 2D layered inorganic nanomaterials like MoS2, WS2 and SnS2 have been recently developed and employed in various applications, including new sensors because of their layer-dependent electrical properties. This article presents a comprehensive overview of recent developments in the application of 2D layered inorganic nanomaterials as sensors. Some of the salient features of 2D materials for different sensing applications are discussed, including gas sensing, electrochemical sensing, SERS and biosensing, SERS sensing and photodetection. The working principles of the sensors are also discussed together with examples.

  16. Phonon thermal conduction in novel 2D materials.

    PubMed

    Xu, Xiangfan; Chen, Jie; Li, Baowen

    2016-12-07

    Recently, there has been increasing interest in phonon thermal transport in low-dimensional materials, due to the crucial importance of dissipating and managing heat in micro- and nano-electronic devices. Significant progress has been achieved for one-dimensional (1D) systems, both theoretically and experimentally. However, the study of heat conduction in two-dimensional (2D) systems is still in its infancy due to the limited availability of 2D materials and the technical challenges of fabricating suspended samples that are suitable for thermal measurements. In this review, we outline different experimental techniques and theoretical approaches for phonon thermal transport in 2D materials, discuss the problems and challenges of phonon thermal transport measurements and provide a comparison between existing experimental data. Special attention will be given to the effects of size, dimensionality, anisotropy and mode contributions in novel 2D systems, including graphene, boron nitride, MoS2, black phosphorous and silicene.

  17. Reconstruction-based 3D/2D image registration.

    PubMed

    Tomazevic, Dejan; Likar, Bostjan; Pernus, Franjo

    2005-01-01

    In this paper we present a novel 3D/2D registration method, where first, a 3D image is reconstructed from a few 2D X-ray images and next, the preoperative 3D image is brought into the best possible spatial correspondence with the reconstructed image by optimizing a similarity measure. Because the quality of the reconstructed image is generally low, we introduce a novel asymmetric mutual information similarity measure, which is able to cope with low image quality as well as with different imaging modalities. The novel 3D/2D registration method has been evaluated using standardized evaluation methodology and publicly available 3D CT, 3DRX, and MR and 2D X-ray images of two spine phantoms, for which gold standard registrations were known. In terms of robustness, reliability and capture range the proposed method outperformed the gradient-based method and the method based on digitally reconstructed radiographs (DRRs).

  18. Dominant 2D magnetic turbulence in the solar wind

    NASA Technical Reports Server (NTRS)

    Bieber, John W.; Wanner, Wolfgang; Matthaeus, William H.

    1995-01-01

    There have been recent suggestions that solar wind magnetic turbulence may be a composite of slab geometry (wavevector aligned with the mean magnetic field) and 2D geometry (wavevectors perpendicular to the mean field). We report results of two new tests of this hypothesis using Helios measurements of inertial ranged magnetic spectra in the solar wind. The first test is based upon a characteristic difference between perpendicular and parallel reduced power spectra which is expected for the 2D component but not for the slab component. The second test examines the dependence of power spectrum density upon the magnetic field angle (i.e., the angle between the mean magnetic field and the radial direction), a relationship which is expected to be in opposite directions for the slab and 2D components. Both tests support the presence of a dominant (approximately 85 percent by energy) 2D component in solar wind magnetic turbulence.

  19. Revealing Invisible Beauty, Ultra Detailed: The Influence of Low Cost UV Exposure on Natural History Specimens in 2D+ Digitization

    PubMed Central

    Brecko, Jonathan; Mathys, Aurore; Dekoninck, Wouter; De Ceukelaire, Marleen; VandenSpiegel, Didier; Semal, Patrick

    2016-01-01

    Digitization of the natural history specimens usually occurs by taking detailed pictures from different sides or producing 3D models. Additionally this is normally limited to imaging the specimen while exposed by light of the visual spectrum. However many specimens can see in or react to other spectra as well. Fluorescence is a well known reaction to the ultraviolet (UV) spectrum by animals, plants, minerals etc. but rarely taken into account while examining natural history specimens. Our tests show that museum specimens still fluoresce when exposed to UV light of 395 nm and 365 nm, even after many years of preservation. When the UV exposure is used in the digitization of specimens using our low cost focus stacking (2D+) setup, the resulting pictures reveal more detail than the conventional 2D+ images. Differences in fluorescence using 395 nm or 365 nm UV lights were noticed, however there isn’t a preferred wavelength as some specimens react more to the first, while others have better results with the latter exposure. Given the increased detail and the low cost of the system, UV exposure should be considered while digitizing natural history museum collections. PMID:27536993

  20. Revealing Invisible Beauty, Ultra Detailed: The Influence of Low Cost UV Exposure on Natural History Specimens in 2D+ Digitization.

    PubMed

    Brecko, Jonathan; Mathys, Aurore; Dekoninck, Wouter; De Ceukelaire, Marleen; VandenSpiegel, Didier; Semal, Patrick

    2016-01-01

    Digitization of the natural history specimens usually occurs by taking detailed pictures from different sides or producing 3D models. Additionally this is normally limited to imaging the specimen while exposed by light of the visual spectrum. However many specimens can see in or react to other spectra as well. Fluorescence is a well known reaction to the ultraviolet (UV) spectrum by animals, plants, minerals etc. but rarely taken into account while examining natural history specimens. Our tests show that museum specimens still fluoresce when exposed to UV light of 395 nm and 365 nm, even after many years of preservation. When the UV exposure is used in the digitization of specimens using our low cost focus stacking (2D+) setup, the resulting pictures reveal more detail than the conventional 2D+ images. Differences in fluorescence using 395 nm or 365 nm UV lights were noticed, however there isn't a preferred wavelength as some specimens react more to the first, while others have better results with the latter exposure. Given the increased detail and the low cost of the system, UV exposure should be considered while digitizing natural history museum collections.

  1. Ultrathin 2D Metal-Organic Framework Nanosheets.

    PubMed

    Zhao, Meiting; Wang, Yixian; Ma, Qinglang; Huang, Ying; Zhang, Xiao; Ping, Jianfeng; Zhang, Zhicheng; Lu, Qipeng; Yu, Yifu; Xu, Huan; Zhao, Yanli; Zhang, Hua

    2015-12-02

    A facile surfactant-assisted bottom-up synthetic method to prepare a series of freestanding ultrathin 2D M-TCPP (M = Zn, Cu, Cd or Co, TCPP = tetrakis(4-carboxyphenyl)porphyrin) nanosheets with a thickness of sub-10 nm is developed. As a proof-of-concept application, some of them are successfully used as new platforms for DNA detection. The Cu-TCPP nanosheet-based sensor shows excellent fluorescent sensing performance and is used for the simultaneous detection of multiple DNA targets.

  2. Annotated Bibliography of EDGE2D Use

    SciTech Connect

    J.D. Strachan and G. Corrigan

    2005-06-24

    This annotated bibliography is intended to help EDGE2D users, and particularly new users, find existing published literature that has used EDGE2D. Our idea is that a person can find existing studies which may relate to his intended use, as well as gain ideas about other possible applications by scanning the attached tables.

  3. Staring 2-D hadamard transform spectral imager

    DOEpatents

    Gentry, Stephen M.; Wehlburg, Christine M.; Wehlburg, Joseph C.; Smith, Mark W.; Smith, Jody L.

    2006-02-07

    A staring imaging system inputs a 2D spatial image containing multi-frequency spectral information. This image is encoded in one dimension of the image with a cyclic Hadamarid S-matrix. The resulting image is detecting with a spatial 2D detector; and a computer applies a Hadamard transform to recover the encoded image.

  4. Quantitative determinations and imaging in different structures of buried human bones from the XVIII-XIXth centuries by energy dispersive X-ray fluorescence - Postmortem evaluation.

    PubMed

    Guimarães, D; Dias, A A; Carvalho, M; Carvalho, M L; Santos, J P; Henriques, F R; Curate, F; Pessanha, S

    2016-08-01

    In this work, a non-commercial triaxial geometry energy dispersive X-ray Fluorescence (EDXRF) setup and a benchtop µ-XRF system were used to identify postmortem contamination in buried bones. For two of the individuals, unusually high concentrations of Cu and Pb, but also Zn (in one individual) were observed. The pigments of the burial shroud coverings have been identified as the source of contamination. Accurate and precise quantitative results were obtained by nondestructive process using fundamental parameters method taking into account the matrix absorption effects. A total of 30 bones from 13 individuals, buried between the mid-XVIIIth to early XIXth centuries, were analyzed to study the elemental composition and elemental distribution. The bones were collected from a church in Almada (Portugal), called Ermida do Espírito Santo, located near the Tagus River and at the sea neighbourhood. The triaxial geometry setup was used to quantify Ca, Fe, Cu, Zn, Br, Sr and Pb of powder pressed bone pellets (n=9 for each bone). Cluster analysis was performed considering the elemental concentrations for the different bones. There was a clear association between some bones regarding Fe, Cu, Zn, Br and Pb content but not a categorization between cortical and trabecular bones. The elemental distribution of Cu, Zn and Pb were assessed by the benchtop μ-analysis, the M4 Tornado, based on a polycapillary system which provides multi-elemental 2D maps. The results showed that contamination was mostly on the surface of the bone confirming that it was related to the burial shroud covering the individuals.

  5. DNA interaction with DAPI fluorescent dye: Force spectroscopy decouples two different binding modes.

    PubMed

    Reis, L A; Rocha, M S

    2017-05-01

    In this work, we use force spectroscopy to investigate the interaction between the DAPI fluorescent dye and the λ-DNA molecule under high (174 mM) and low (34 mM) ionic strengths. Firstly, we have measured the changes on the mechanical properties (persistence and contour lengths) of the DNA-DAPI complexes as a function of the dye concentration in the sample. Then, we use recently developed models in order to connect the behavior of both mechanical properties to the physical chemistry of the interaction. Such analysis has allowed us to identify and to decouple two main binding modes, determining the relevant physicochemical (binding) parameters for each of these modes: minor groove binding, which saturates at very low DAPI concentrations ( CT ∼ 0.50 μM) and presents equilibrium binding constants of the order of ∼10(7) M(-1) for the two ionic strengths studied; and intercalation, which starts to play a significant role only after the saturation of the first mode, presenting much smaller equilibrium binding constants (∼10(5) M(-1) ).

  6. Evaluation of different synchrotron beamline configurations for X-ray fluorescence analysis of environmental samples.

    PubMed

    Barberie, Sean R; Iceman, Christopher R; Cahill, Catherine F; Cahill, Thomas M

    2014-08-19

    Synchrotron radiation X-ray fluorescence (SR-XRF) is a powerful elemental analysis tool, yet synchrotrons are large, multiuser facilities that are generally not amenable to modification. However, the X-ray beamlines from synchrotrons can be modified by simply including X-ray filters or removing monochromators to improve the SR-XRF analysis. In this study, we evaluated four easily applied beamline configurations for the analysis of three representative environmental samples, namely a thin aerosol sample, an intermediate thickness biological sample, and a thick rare earth mineral specimen. The results showed that the "white beam" configuration, which was simply the full, polychromatic output of the synchrotron, was the optimal configuration for the analysis of thin samples with little mass. The "filtered white beam" configuration removed the lower energy X-rays from the excitation beam so it gave better sensitivity for elements emitting more energetic X-rays. The "filtered white beam-filtered detector" configuration sacrifices the lower energy part of the spectrum (<15 keV) for improved sensitivity in the higher end (∼26 to 48 keV range). The use of a monochromatic beam, which tends to be the standard mode of operation for most SR-XRF analyses reported in the literature, gave the least sensitive analysis.

  7. CYP2D6 variability in populations from Venezuela.

    PubMed

    Moreno, Nancy; Flores-Angulo, Carlos; Villegas, Cecilia; Mora, Yuselin

    2016-12-01

    CYP2D6 is an important cytochrome P450 enzyme that plays an important role in the metabolism of about 25% of currently prescribed drugs. The presence of polymorphisms in the CYP2D6 gene may modulate enzyme level and activity, thereby affecting individual responses to pharmacological treatments. The most prevalent diseases in the admixed population from Venezuela are cardiovascular and cancer, whereas viral, bacterial and parasitic diseases, particularly malaria, are prevalent in Amerindian populations; in the treatment of these diseases, several drugs that are metabolized by CYP2D6 are used. In this work, we reviewed the data on CYP2D6 variability and predicted metabolizer phenotypes, in healthy volunteers of two admixed and five Amerindian populations from Venezuela. The Venezuelan population is very heterogeneous as a result of the genetic admixture of three major ethnical components: Europeans, Africans and Amerindians. There are noticeable inter-regional and inter-population differences in the process of mixing of this population. Hitherto, there are few published studies in Venezuela on CYP2D6; therefore, it is necessary to increase research in this regard, in particular to develop studies with a larger sample size. There is a considerable amount of work remaining before CYP2D6 is integrated into clinical practice in Venezuela.

  8. Capturing tumor complexity in vitro: Comparative analysis of 2D and 3D tumor models for drug discovery

    PubMed Central

    Stock, Kristin; Estrada, Marta F.; Vidic, Suzana; Gjerde, Kjersti; Rudisch, Albin; Santo, Vítor E.; Barbier, Michaël; Blom, Sami; Arundkar, Sharath C.; Selvam, Irwin; Osswald, Annika; Stein, Yan; Gruenewald, Sylvia; Brito, Catarina; van Weerden, Wytske; Rotter, Varda; Boghaert, Erwin; Oren, Moshe; Sommergruber, Wolfgang; Chong, Yolanda; de Hoogt, Ronald; Graeser, Ralph

    2016-01-01

    Two-dimensional (2D) cell cultures growing on plastic do not recapitulate the three dimensional (3D) architecture and complexity of human tumors. More representative models are required for drug discovery and validation. Here, 2D culture and 3D mono- and stromal co-culture models of increasing complexity have been established and cross-comparisons made using three standard cell carcinoma lines: MCF7, LNCaP, NCI-H1437. Fluorescence-based growth curves, 3D image analysis, immunohistochemistry and treatment responses showed that end points differed according to cell type, stromal co-culture and culture format. The adaptable methodologies described here should guide the choice of appropriate simple and complex in vitro models. PMID:27364600

  9. Influence of amino acid residue 374 of cytochrome P-450 2D6 (CYP2D6) on the regio- and enantio-selective metabolism of metoprolol.

    PubMed Central

    Ellis, S W; Rowland, K; Ackland, M J; Rekka, E; Simula, A P; Lennard, M S; Wolf, C R; Tucker, G T

    1996-01-01

    Cytochrome P-450 2D6 (CYP2D6) is an important human drug-metabolizing enzyme responsible for the oxidation of more than 30 widely used therapeutic agents. The enzymes encoded by the published genomic [Kimura, Umeno, Skoda, Meyer and Gonzalez (1989) Am. J. Hum. Genet. 45, 889-904] and cDNA [Gonzalez, Skoda, Kimura, Umeno, Zanger, Nebert, Gelboin, Hardwick and Meyer (1988) Nature 331, 442-446] sequences of CYP2D6, and presumed to represent wild-type sequences, differ at residue 374 and encode valine (CYP2D6-Val) and methionine (CYP2D6-Met) respectively. The influence of this amino acid difference on cytochrome P-450 expression, ligand binding, catalysis and stereoselective oxidation of metoprolol was investigated by the heterologous expression of the corresponding cDNAs in the yeast Saccharomyces cerevisiae. The level of expression of apo- and holo-protein was similar with each form of CYP2D6 cDNA, and the binding affinities of a series of ligands to CYP2D6-Val and CYP2D6-Met were identical. The enantioselective O-demethylation and alpha-hydroxylation of metoprolol were also similar with each form of CYP2D6, O-demethylation being R-(+)- enantioselective (CYP2D6-Val: R/S, 1.6; CYP2D6-Met: R/S, 1.4), whereas alpha-hydroxylation showed a preference for S-(-)-metoprolol (CYP2D6-Val: R/S, 0.7; CYP2D6-Met: R/S, 0.8). However, although the favoured regiomer overall was O-demethylmetoprolol (ODM), the regioselectivity for O-demethylation of each metoprolol enantiomer was significantly greater for CYP2D6-Val [R-(+)-: ODM/alpha-hydroxymetoprolol (alpha OH), 5.9; S-(-)-: ODM/alpha OH, 2.5) than that observed for CYP2D6-Met [R-(+)-: ODM/alpha OH, 2.2; S-(-)-: ODM/alpha OH, 1.4]. The stereoselective properties of CYP2D6-Val were consistent with those observed for CYP2D6 in human liver microsomes. The difference in the stereoselective properties of CYP2D6-Val and CYP2D6-Met were rationalized with respect to a homology model of the active site of CYP2D6 based on an alignment with

  10. Impact of two different types of heat stress on chloroplast movement and fluorescence signal of tobacco leaves.

    PubMed

    Frolec, Jirí; Rebícek, Jirí; Lazár, Dusan; Naus, Jan

    2010-07-01

    Although the chloroplast movement can be strongly affected by ambient temperature, the information about chloroplast movement especially related to high temperatures is scarce. For detailed investigation of the effects of heat stress (HS) on tobacco leaves (Nicotiana tabacum L. cv. Samsun), we used two different HS treatments in dark with wide range of elevated temperatures (25-45 degrees C). The leaf segments were either linearly heated in water bath at heating rate of 2 degrees C min(-1) from room temperature up to maximal temperature (T (m)) and then linearly cooled down to 25 degrees C or incubated for 5 min in water bath at the same T (m) followed by 5 min incubation at 25 degrees C (T-jump). The changes in light-induced chloroplast movement caused by the HS pretreatment were detected after the particular heating regime at 25 degrees C using a method of time-dependent collimated transmittance (CT) and compared with the chlorophyll O-J-I-P fluorescence rise (FLR) measurements. The inhibition of chloroplast movement started at about 40 degrees C while the fluorescence parameters responded generally at higher T (m). This difference in sensitivity of CT and FLR was higher for the T-jump than for the linear HS indicating importance of applied heating regime. A possible influence of chloroplast movement on the FLR measurement and a physiological role of the HS-impaired chloroplast movement are discussed.

  11. Persistence Measures for 2d Soap Froth

    NASA Astrophysics Data System (ADS)

    Feng, Y.; Ruskin, H. J.; Zhu, B.

    Soap froths as typical disordered cellular structures, exhibiting spatial and temporal evolution, have been studied through their distributions and topological properties. Recently, persistence measures, which permit representation of the froth as a two-phase system, have been introduced to study froth dynamics at different length scales. Several aspects of the dynamics may be considered and cluster persistence has been observed through froth experiment. Using a direct simulation method, we have investigated persistent properties in 2D froth both by monitoring the persistence of survivor cells, a topologically independent measure, and in terms of cluster persistence. It appears that the area fraction behavior for both survivor and cluster persistence is similar for Voronoi froth and uniform froth (with defects). Survivor and cluster persistent fractions are also similar for a uniform froth, particularly when geometries are constrained, but differences observed for the Voronoi case appear to be attributable to the strong topological dependency inherent in cluster persistence. Survivor persistence, on the other hand, depends on the number rather than size and position of remaining bubbles and does not exhibit the characteristic decay to zero.

  12. Differential mitochondrial calcium responses in different cell types detected with a mitochondrial calcium fluorescent indicator, mito-GCaMP2.

    PubMed

    Chen, Min; Wang, Yanru; Hou, Tingting; Zhang, Huiliang; Qu, Aijuan; Wang, Xianhua

    2011-10-01

    Mitochondrial calcium plays a crucial role in mitochondrial metabolism, cell calcium handling, and cell death. However, some mechanisms concerning mitochondrial calcium regulation are still unknown, especially how mitochondrial calcium couples with cytosolic calcium. In this work, we constructed a novel mitochondrial calcium fluorescent indicator (mito-GCaMP2) by genetic manipulation. Mito-GCaMP2 was imported into mitochondria with high efficiency and the fluorescent signals co-localized with that of tetramethyl rhodamine methyl ester, a mitochondrial membrane potential indicator. The mitochondrial inhibitors specifically decreased the signals of mito-GCaMP2. The apparent K(d) of mito-GCaMP2 was 195.0 nmol/L at pH 8.0 in adult rat cardiomyocytes. Furthermore, we observed that mito-GCaMP2 preferred the alkaline pH surrounding of mitochondria. In HeLa cells, we found that mitochondrial calcium ([Ca(2+)](mito)) responded to the changes of cytosolic calcium ([Ca(2+)](cyto)) induced by histamine or thapasigargin. Moreover, external Ca(2+) (100 μmol/L) directly induced an increase of [Ca(2+)](mito) in permeabilized HeLa cells. However, in rat cardiomyocytes [Ca(2+)](mito) did not respond to cytosolic calcium transients stimulated by electric pacing or caffeine. In permeabilized cardiomyocytes, 600 nmol/L free Ca(2+) repeatedly increased the fluorescent signals of mito-GCaMP2, which excluded the possibility that mito-GCaMP2 lost its function in cardiomyocytes mitochondria. These results showed that the response of mitochondrial calcium is diverse in different cell lineages and suggested that mitochondria in cardiomyocytes may have a special defense mechanism to control calcium flux.

  13. Live fluorescent RNA-based detection of pluripotency gene expression in embryonic and induced pluripotent stem cells of different species.

    PubMed

    Lahm, Harald; Doppler, Stefanie; Dreßen, Martina; Werner, Astrid; Adamczyk, Klaudia; Schrambke, Dominic; Brade, Thomas; Laugwitz, Karl-Ludwig; Deutsch, Marcus-André; Schiemann, Matthias; Lange, Rüdiger; Moretti, Alessandra; Krane, Markus

    2015-02-01

    The generation of induced pluripotent stem (iPS) cells has successfully been achieved in many species. However, the identification of truly reprogrammed iPS cells still remains laborious and the detection of pluripotency markers requires fixation of cells in most cases. Here, we report an approach with nanoparticles carrying Cy3-labeled sense oligonucleotide reporter strands coupled to gold-particles. These molecules are directly added to cultured cells without any manipulation and gene expression is evaluated microscopically after overnight incubation. To simultaneously detect gene expression in different species, probe sequences were chosen according to interspecies homology. With a common target-specific probe we could successfully demonstrate expression of the GAPDH house-keeping gene in somatic cells and expression of the pluripotency markers NANOG and GDF3 in embryonic stem cells and iPS cells of murine, human, and porcine origin. The population of target gene positive cells could be purified by fluorescence-activated cell sorting. After lentiviral transduction of murine tail-tip fibroblasts Nanog-specific probes identified truly reprogrammed murine iPS cells in situ during development based on their Cy3-fluorescence. The intensity of Nanog-specific fluorescence correlated positively with an increased capacity of individual clones to differentiate into cells of all three germ layers. Our approach offers a universal tool to detect intracellular gene expression directly in live cells of any desired origin without the need for manipulation, thus allowing conservation of the genetic background of the target cell. Furthermore, it represents an easy, scalable method for efficient screening of pluripotency which is highly desirable during high-throughput cell reprogramming and after genomic editing of pluripotent stem cells.

  14. The agreement between 3D, standard 2D and triplane 2D speckle tracking: effects of image quality and 3D volume rate.

    PubMed

    Trache, Tudor; Stöbe, Stephan; Tarr, Adrienn; Pfeiffer, Dietrich; Hagendorff, Andreas

    2014-12-01

    Comparison of 3D and 2D speckle tracking performed on standard 2D and triplane 2D datasets of normal and pathological left ventricular (LV) wall-motion patterns with a focus on the effect that 3D volume rate (3DVR), image quality and tracking artifacts have on the agreement between 2D and 3D speckle tracking. 37 patients with normal LV function and 18 patients with ischaemic wall-motion abnormalities underwent 2D and 3D echocardiography, followed by offline speckle tracking measurements. The values of 3D global, regional and segmental strain were compared with the standard 2D and triplane 2D strain values. Correlation analysis with the LV ejection fraction (LVEF) was also performed. The 3D and 2D global strain values correlated good in both normally and abnormally contracting hearts, though systematic differences between the two methods were observed. Of the 3D strain parameters, the area strain showed the best correlation with the LVEF. The numerical agreement of 3D and 2D analyses varied significantly with the volume rate and image quality of the 3D datasets. The highest correlation between 2D and 3D peak systolic strain values was found between 3D area and standard 2D longitudinal strain. Regional wall-motion abnormalities were similarly detected by 2D and 3D speckle tracking. 2DST of triplane datasets showed similar results to those of conventional 2D datasets. 2D and 3D speckle tracking similarly detect normal and pathological wall-motion patterns. Limited image quality has a significant impact on the agreement between 3D and 2D numerical strain values.

  15. Matrix models of 2d gravity

    SciTech Connect

    Ginsparg, P.

    1991-01-01

    These are introductory lectures for a general audience that give an overview of the subject of matrix models and their application to random surfaces, 2d gravity, and string theory. They are intentionally 1.5 years out of date.

  16. Matrix models of 2d gravity

    SciTech Connect

    Ginsparg, P.

    1991-12-31

    These are introductory lectures for a general audience that give an overview of the subject of matrix models and their application to random surfaces, 2d gravity, and string theory. They are intentionally 1.5 years out of date.

  17. 2D/3D switchable displays

    NASA Astrophysics Data System (ADS)

    Dekker, T.; de Zwart, S. T.; Willemsen, O. H.; Hiddink, M. G. H.; IJzerman, W. L.

    2006-02-01

    A prerequisite for a wide market acceptance of 3D displays is the ability to switch between 3D and full resolution 2D. In this paper we present a robust and cost effective concept for an auto-stereoscopic switchable 2D/3D display. The display is based on an LCD panel, equipped with switchable LC-filled lenticular lenses. We will discuss 3D image quality, with the focus on display uniformity. We show that slanting the lenticulars in combination with a good lens design can minimize non-uniformities in our 20" 2D/3D monitors. Furthermore, we introduce fractional viewing systems as a very robust concept to further improve uniformity in the case slanting the lenticulars and optimizing the lens design are not sufficient. We will discuss measurements and numerical simulations of the key optical characteristics of this display. Finally, we discuss 2D image quality, the switching characteristics and the residual lens effect.

  18. 2-d Finite Element Code Postprocessor

    SciTech Connect

    Sanford, L. A.; Hallquist, J. O.

    1996-07-15

    ORION is an interactive program that serves as a postprocessor for the analysis programs NIKE2D, DYNA2D, TOPAZ2D, and CHEMICAL TOPAZ2D. ORION reads binary plot files generated by the two-dimensional finite element codes currently used by the Methods Development Group at LLNL. Contour and color fringe plots of a large number of quantities may be displayed on meshes consisting of triangular and quadrilateral elements. ORION can compute strain measures, interface pressures along slide lines, reaction forces along constrained boundaries, and momentum. ORION has been applied to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

  19. Closed-shell and open-shell 2D nanographenes.

    PubMed

    Sun, Zhe; Wu, Jishan

    2014-01-01

    This chapter describes a series of two-dimensional (2D) expanded arene networks, also known as nanographenes, with either closed-shell or open-shell electronic structure in the ground state. These systems are further categorized into three classes on a basis of different edge structures: those with zigzag edges only, those with armchair edges only, and those possessing both. Distinctive physical properties of these 2D aromatic systems are closely related to their structural characteristics and provide great potential for them as materials for different applications.

  20. Chemical Approaches to 2D Materials.

    PubMed

    Samorì, Paolo; Palermo, Vincenzo; Feng, Xinliang

    2016-08-01

    Chemistry plays an ever-increasing role in the production, functionalization, processing and applications of graphene and other 2D materials. This special issue highlights a selection of enlightening chemical approaches to 2D materials, which nicely reflect the breadth of the field and convey the excitement of the individuals involved in it, who are trying to translate graphene and related materials from the laboratory into a real, high-impact technology.

  1. Application of X-Ray Fluorescence Analysis to Determine the Elemental Composition of Tissues from Different Ovarian Neoplasms

    NASA Astrophysics Data System (ADS)

    Motevich, I. G.; Strekal, N. D.; Papko, N. M.; Glebovich, M. I.; Shulha, A. V.; Maskevich, S. A.

    2015-03-01

    We present the results of x-ray fluorescence analysis of tissues from healthy ovaries and from ovaries with different pathologies: benign and borderline tumors, mucinous and endometrioid cancers, serous carcinomas. We determine the average copper, zinc, calcium, selenium, cadmium, lead, and mercury levels. We observed that in the benign ovarian tumors, we see a significant decrease in the cadmium, mercury, and lead levels compared with healthy tissues. In the borderline neoplasms, the copper level is reduced relative to zinc (Cu/Zn), cadmium, mercury, and lead, and also the zinc concentration is increased. In the ovarian carcinomas, we observed changes in the ratio of the chemical elements in the tumor tissues, depending on the histologic type. The results obtained can be used for differentiation, diagnosis, and adjustment of treatment for different ovarian neoplasms.

  2. Different Ligands of the TRPV3 Cation Channel Cause Distinct Conformational Changes as Revealed by Intrinsic Tryptophan Fluorescence Quenching*

    PubMed Central

    Billen, Bert; Brams, Marijke; Debaveye, Sarah; Remeeva, Alina; Alpizar, Yeranddy A.; Waelkens, Etienne; Kreir, Mohamed; Brüggemann, Andrea; Talavera, Karel; Nilius, Bernd; Voets, Thomas; Ulens, Chris

    2015-01-01

    TRPV3 is a thermosensitive ion channel primarily expressed in epithelial tissues of the skin, nose, and tongue. The channel has been implicated in environmental thermosensation, hyperalgesia in inflamed tissues, skin sensitization, and hair growth. Although transient receptor potential (TRP) channel research has vastly increased our understanding of the physiological mechanisms of nociception and thermosensation, the molecular mechanics of these ion channels are still largely elusive. In order to better comprehend the functional properties and the mechanism of action in TRP channels, high-resolution three-dimensional structures are indispensable, because they will yield the necessary insights into architectural intimacies at the atomic level. However, structural studies of membrane proteins are currently hampered by difficulties in protein purification and in establishing suitable crystallization conditions. In this report, we present a novel protocol for the purification of membrane proteins, which takes advantage of a C-terminal GFP fusion. Using this protocol, we purified human TRPV3. We show that the purified protein is a fully functional ion channel with properties akin to the native channel using planar patch clamp on reconstituted channels and intrinsic tryptophan fluorescence spectroscopy. Using intrinsic tryptophan fluorescence spectroscopy, we reveal clear distinctions in the molecular interaction of different ligands with the channel. Altogether, this study provides powerful tools to broaden our understanding of ligand interaction with TRPV channels, and the availability of purified human TRPV3 opens up perspectives for further structural and functional studies. PMID:25829496

  3. Competing coexisting phases in 2D water

    NASA Astrophysics Data System (ADS)

    Zanotti, Jean-Marc; Judeinstein, Patrick; Dalla-Bernardina, Simona; Creff, Gaëlle; Brubach, Jean-Blaise; Roy, Pascale; Bonetti, Marco; Ollivier, Jacques; Sakellariou, Dimitrios; Bellissent-Funel, Marie-Claire

    2016-05-01

    The properties of bulk water come from a delicate balance of interactions on length scales encompassing several orders of magnitudes: i) the Hydrogen Bond (HBond) at the molecular scale and ii) the extension of this HBond network up to the macroscopic level. Here, we address the physics of water when the three dimensional extension of the HBond network is frustrated, so that the water molecules are forced to organize in only two dimensions. We account for the large scale fluctuating HBond network by an analytical mean-field percolation model. This approach provides a coherent interpretation of the different events experimentally (calorimetry, neutron, NMR, near and far infra-red spectroscopies) detected in interfacial water at 160, 220 and 250 K. Starting from an amorphous state of water at low temperature, these transitions are respectively interpreted as the onset of creation of transient low density patches of 4-HBonded molecules at 160 K, the percolation of these domains at 220 K and finally the total invasion of the surface by them at 250 K. The source of this surprising behaviour in 2D is the frustration of the natural bulk tetrahedral local geometry and the underlying very significant increase in entropy of the interfacial water molecules.

  4. Competing coexisting phases in 2D water

    PubMed Central

    Zanotti, Jean-Marc; Judeinstein, Patrick; Dalla-Bernardina, Simona; Creff, Gaëlle; Brubach, Jean-Blaise; Roy, Pascale; Bonetti, Marco; Ollivier, Jacques; Sakellariou, Dimitrios; Bellissent-Funel, Marie-Claire

    2016-01-01

    The properties of bulk water come from a delicate balance of interactions on length scales encompassing several orders of magnitudes: i) the Hydrogen Bond (HBond) at the molecular scale and ii) the extension of this HBond network up to the macroscopic level. Here, we address the physics of water when the three dimensional extension of the HBond network is frustrated, so that the water molecules are forced to organize in only two dimensions. We account for the large scale fluctuating HBond network by an analytical mean-field percolation model. This approach provides a coherent interpretation of the different events experimentally (calorimetry, neutron, NMR, near and far infra-red spectroscopies) detected in interfacial water at 160, 220 and 250 K. Starting from an amorphous state of water at low temperature, these transitions are respectively interpreted as the onset of creation of transient low density patches of 4-HBonded molecules at 160 K, the percolation of these domains at 220 K and finally the total invasion of the surface by them at 250 K. The source of this surprising behaviour in 2D is the frustration of the natural bulk tetrahedral local geometry and the underlying very significant increase in entropy of the interfacial water molecules. PMID:27185018

  5. Characterization of a 2D soft x-ray tomography camera with discrimination in energy bands

    SciTech Connect

    Romano, A.; Pacella, D.; Gabellieri, L.; Tilia, B.; Piergotti, V.; Mazon, D.; Malard, P.

    2010-10-15

    A gas detector with a 2D pixel readout is proposed for a future soft x-ray (SXR) tomography with discrimination in energy bands separately per pixel. The detector has three gas electron multiplier foils for the electron amplification and it offers the advantage, compared with the single stage, to be less sensitive to neutrons and gammas. The energy resolution and the detection efficiency of the detector have been accurately studied in the laboratory with continuous SXR spectra produced by an electronic tube and line emissions produced by fluorescence (K, Fe, and Mo) in the range of 3-17 keV. The front-end electronics, working in photon counting mode with a selectable threshold for pulse discrimination, is optimized for high rates. The distribution of the pulse amplitude has been indirectly derived by means of scans of the threshold. Scans in detector gain have also been performed to assess the capability of selecting different energy ranges.

  6. Digit ratio (2D:4D) and hand preference for writing in the BBC Internet Study.

    PubMed

    Manning, J T; Peters, M

    2009-09-01

    The ratio of the length of the second to the fourth digit (2D:4D) may be negatively correlated with prenatal testosterone. Hand preference has been linked with prenatal testosterone and 2D:4D. Here we show that 2D:4D is associated with hand preference for writing in a large internet sample (n>170,000) in which participants self-reported their finger lengths. We replicated a significant association between right 2D:4D and writing hand preference (low right 2D:4D associated with left hand preference) as well as a significant correlation between writing hand preference and the difference between left and right 2D:4D or Dr-l (low Dr-l associated with left hand preference). A new significant correlation between left 2D:4D and writing hand preference was also shown (high left 2D:4D associated with left hand preference). There was a clear interaction between writing hand preference and 2D:4D: The left 2D:4D was significantly larger than the right 2D:4D in male and female left-handed writers, and the right hand 2D:4D was significantly larger than the left hand 2D:4D in male and female right-handed writers.

  7. Mechanical characterization of 2D, 2D stitched, and 3D braided/RTM materials

    NASA Technical Reports Server (NTRS)

    Deaton, Jerry W.; Kullerd, Susan M.; Portanova, Marc A.

    1993-01-01

    Braided composite materials have potential for application in aircraft structures. Fuselage frames, floor beams, wing spars, and stiffeners are examples where braided composites could find application if cost effective processing and damage tolerance requirements are met. Another important consideration for braided composites relates to their mechanical properties and how they compare to the properties of composites produced by other textile composite processes being proposed for these applications. Unfortunately, mechanical property data for braided composites do not appear extensively in the literature. Data are presented in this paper on the mechanical characterization of 2D triaxial braid, 2D triaxial braid plus stitching, and 3D (through-the-thickness) braid composite materials. The braided preforms all had the same graphite tow size and the same nominal braid architectures, (+/- 30 deg/0 deg), and were resin transfer molded (RTM) using the same mold for each of two different resin systems. Static data are presented for notched and unnotched tension, notched and unnotched compression, and compression after impact strengths at room temperature. In addition, some static results, after environmental conditioning, are included. Baseline tension and compression fatigue results are also presented, but only for the 3D braided composite material with one of the resin systems.

  8. Change in the amount of epsilon-hexosyllysine, UV absorbance, and fluorescence of collagen with age in different animal species

    SciTech Connect

    Miksik, I.; Deyl, Z. )

    1991-05-01

    Skin and aorta collagen specimens of Wistar rats, white mice, beagle dogs, cats, horses, and human necropsies of different ages were examined with respect to the content of glycated products. The data presented show that (a) glycation and accumulation of the chromophore(s) are comparable in collagen samples from different species of comparable age; (b) glycation and pigmented accumulation increase markedly during the first 5-10 years of age; (c) the extent of glycation is different in different tissues (in particular, glycation of aortal collagen is about twice that of skin collagen); and (d) collagen pigmentation as followed by fluorescence is comparable in aortal and skin collagen (except below 10 years); pigmentation measured by absorbance at 350 nm is, on the contrary, lower in aortal than in skin collagen. Based on the assumption of constant blood glucose level during the life span, it appears feasible to conclude that the degree of nonenzymatic collagen glycation reflects the time period for which the protein was exposed to the action of sugars. This period, because of increased cross-linking, is likely to be extended in older animals. Other factors, such as differences in collagen turnover between different tissues and the intensity of the removal process of the glycated products, should be taken into consideration as well.

  9. Fluorescent-increase kinetics of different fluorescent reporters used for qPCR depend on monitoring chemistry, targeted sequence, type of DNA input and PCR efficiency.

    PubMed

    Ruijter, Jan M; Lorenz, Peter; Tuomi, Jari M; Hecker, Michael; van den Hoff, Maurice J B

    2014-01-01

    The analysis of quantitative PCR data usually does not take into account the fact that the increase in fluorescence depends on the monitoring chemistry, the input of ds-DNA or ss-cDNA, and the directionality of the targeting of probes or primers. The monitoring chemistries currently available can be categorized into six groups: (A) DNA-binding dyes; (B) hybridization probes; (C) hydrolysis probes; (D) LUX primers; (E) hairpin primers; and (F) the QZyme system. We have determined the kinetics of the increase in fluorescence for each of these groups with respect to the input of both ds-DNA and ss-cDNA. For the latter, we also evaluated mRNA and cDNA targeting probes or primers. This analysis revealed three situations. Hydrolysis probes and LUX primers, compared to DNA-binding dyes, do not require a correction of the observed quantification cycle. Hybridization probes and hairpin primers require a correction of -1 cycle (dubbed C-lag), while the QZyme system requires the C-lag correction and an efficiency-dependent C-shift correction. A PCR efficiency value can be derived from the relative increase in fluorescence in the exponential phase of the amplification curve for all monitoring chemistries. In case of hydrolysis probes, LUX primers and hairpin primers, however, this should be performed after cycle 12, and for the QZyme system after cycle 19, to keep the overestimation of the PCR efficiency below 0.5 %. FigureThe qPCR monitoring chemistries form six groups with distinct fluorescence kinetics. The displacement of the amplification curve depends on the chemistry, DNA input and probe-targeting. The observed shift in Cq values can be corrected and PCR efficiencies can be derived.

  10. Spatial discrimination against background with different optical systems for collection of fluorescence in laser-excited atomic fluorescence spectrometry with a graphite tube electrothermal atomizer.

    PubMed

    Yuzefovsky, A I; Lonardo, R F; Michel, R G

    1995-07-01

    A single 90 degrees off-axis ellipsoidal mirror fragment was used in a dispersive detection system for electrothermal atomization laser-excited atomic fluorescence spectrometry. The performance of the new optical arrangement was compared with those of optical arrangements that employed a plane mirror in combination with biconvex or plano-convex lenses. All the optical arrangements collected fluorescence in a scheme called front surface illustration. BEAM-4, an optical ray tracing program, was used for calculations of spatial ray distributions and optical collection efficiency for the various optical configurations. Experimentally, the best collection efficiency was obtained by use of the ellipsoidal mirror, in qualitative agreement with simulations done by use of the BEAM-4 software. The best detection limit for cobalt with the new optical arrangement was 20 fg, which was a factor of 5 better than that obtained with conventional optical arrangements with otherwise the same instrumentation. The signal-to-background ratio and the fluorescence collection efficiency were also studied as a function of position of the optical components for the various optical arrangements. For both cobalt and phosphorus, the signal-to-background ratio with the new optical arrangement remained stable within 10-20% during +/- 8 mm shifts in the position of the detection system from the focal plane of the optics. Overall, the new optical arrangement offered high collection efficiency, excellent sensitivity, and facile optical alignment due to efficient spatial separation between the fluorescence signal and the background radiation. The advantages of the new optical arrangement were particularly important during measurements in the presence of high levels of blackbody radiation.

  11. Regulation of ligands for the activating receptor NKG2D

    PubMed Central

    Mistry, Anita R; O'Callaghan, Chris A

    2007-01-01

    The outcome of an encounter between a cytotoxic cell and a potential target cell depends on the balance of signals from inhibitory and activating receptors. Natural Killer group 2D (NKG2D) has recently emerged as a major activating receptor on T lymphocytes and natural killer cells. In both humans and mice, multiple different genes encode ligands for NKG2D, and these ligands are non-classical major histocompatibility complex class I molecules. The NKG2D–ligand interaction triggers an activating signal in the cell expressing NKG2D and this promotes cytotoxic lysis of the cell expressing the ligand. Most normal tissues do not express ligands for NKG2D, but ligand expression has been documented in tumour and virus-infected cells, leading to lysis of these cells. Tight regulation of ligand expression is important. If there is inappropriate expression in normal tissues, this will favour autoimmune processes, whilst failure to up-regulate the ligands in pathological conditions would favour cancer development or dissemination of intracellular infection. PMID:17614877

  12. 2D Materials for Optical Modulation: Challenges and Opportunities.

    PubMed

    Yu, Shaoliang; Wu, Xiaoqin; Wang, Yipei; Guo, Xin; Tong, Limin

    2017-02-21

    Owing to their atomic layer thickness, strong light-material interaction, high nonlinearity, broadband optical response, fast relaxation, controllable optoelectronic properties, and high compatibility with other photonic structures, 2D materials, including graphene, transition metal dichalcogenides and black phosphorus, have been attracting increasing attention for photonic applications. By tuning the carrier density via electrical or optical means that modifies their physical properties (e.g., Fermi level or nonlinear absorption), optical response of the 2D materials can be instantly changed, making them versatile nanostructures for optical modulation. Here, up-to-date 2D material-based optical modulation in three categories is reviewed: free-space, fiber-based, and on-chip configurations. By analysing cons and pros of different modulation approaches from material and mechanism aspects, the challenges faced by using these materials for device applications are presented. In addition, thermal effects (e.g., laser induced damage) in 2D materials, which are critical to practical applications, are also discussed. Finally, the outlook for future opportunities of these 2D materials for optical modulation is given.

  13. Reliability of aneuploidy estimates in human sperm: Results of fluorescence in situ hybridization studies using two different scoring criteria

    SciTech Connect

    Martin, R.H. |; Rademaker, A.

    1994-09-01

    Aneuploidy estimates for individual chromosomes in human sperm have varied more than 10-fold in different laboratories using fluorescence in situ hybridization (FISH). These laboratories use different scoring criteria in the assessment of a disomic sperm. In order to determine reliable estimates of aneuploidy, we have investigated whether scoring criteria affect the aneuploidy frequency in human sperm. Aneuploidy estimates for chromosomes 1(pUC1.77), 12(pBR12), X(XC) and Y(DYZ3Z) were obtained in human sperm from five donors using multicolor FISH analysis to provide an internal control to differentiate between nullisomy and lack of hybridization and between disomy and diploidy. Disomy frequencies were obtained by scoring a minimum of 10,000 sperm for each chromosome probe per donor. This analysis was replicated for two scoring criteria: one scoring criterion used one-half a signal domain as the minimum distance between two signals to be counted as two and thus disomic; the other scoring criterion set one signal domain as the minimum distance between two signals. A total of 120,870 sperm were assessed using one half domain as the scoring criterion and 113,478 were scored using one domain as the criterion. The mean percent disomy for chromosomes 1, 12, X, Y and XY was .18, .16, .15, .19, .25 respectively using the one-half domain criterion and .08, .17, .07, .12, .16 respectively using the one domain criterion. The percent disomy decreased significantly with use of one domain as the minimum distance for signal separation for all chromosomes except chromosome number 12. These lower disomy frequencies correlated well with frequencies derived from human sperm karyotypes analyzed in our laboratory. This suggests that the fluorescent signals for chromosomes 1, X and Y split into more than one domain in decondensed interphase sperm and use of the one-half domain criterion leads to an overestimate of aneuploidy frequencies.

  14. Microscale 2D separation systems for proteomic analysis

    PubMed Central

    Xu, Xin; Liu, Ke; Fan, Z. Hugh

    2012-01-01

    Microscale 2D separation systems have been implemented in capillaries and microfabricated channels. They offer advantages of faster analysis, higher separation efficiency and less sample consumption than the conventional methods, such as liquid chromatography (LC) in a column and slab gel electrophoresis. In this article, we review their recent advancement, focusing on three types of platforms, including 2D capillary electrophoresis (CE), CE coupling with capillary LC, and microfluidic devices. A variety of CE and LC modes have been employed to construct 2D separation systems via sophistically designed interfaces. Coupling of different separation modes has also been realized in a number of microfluidic devices. These separation systems have been applied for the proteomic analysis of various biological samples, ranging from a single cell to tumor tissues. PMID:22462786

  15. 2D-3D transition of gold cluster anions resolved

    NASA Astrophysics Data System (ADS)

    Johansson, Mikael P.; Lechtken, Anne; Schooss, Detlef; Kappes, Manfred M.; Furche, Filipp

    2008-05-01

    Small gold cluster anions Aun- are known for their unusual two-dimensional (2D) structures, giving rise to properties very different from those of bulk gold. Previous experiments and calculations disagree about the number of gold atoms nc where the transition to 3D structures occurs. We combine trapped ion electron diffraction and state of the art electronic structure calculations to resolve this puzzle and establish nc=12 . It is shown that theoretical studies using traditional generalized gradient functionals are heavily biased towards 2D structures. For a correct prediction of the 2D-3D crossover point it is crucial to use density functionals yielding accurate jellium surface energies, such as the Tao-Perdew-Staroverov-Scuseria (TPSS) functional or the Perdew-Burke-Ernzerhof functional modified for solids (PBEsol). Further, spin-orbit effects have to be included, and large, flexible basis sets employed. This combined theoretical-experimental approach is promising for larger gold and other metal clusters.

  16. IUPAP Award: Ion transport in 2D materials

    NASA Astrophysics Data System (ADS)

    Bao, Wenzhong

    Intercalation in 2D materials drastically influences both physical and chemical properties, which leads to a new degree of freedom for fundamental studies and expands the potential applications of 2D materials. In this talk, I will discuss our work in the past two years related to ion intercalation of 2D materials, including insertion of Li and Na ions in graphene and MoS2. We focused on both fundamental mechanism and potential application, e.g. we measured in-situ optical transmittance spectra and electrical transport properties of few-layer graphene (FLG) nanostructures upon electrochemical lithiation/delithiation. By observing a simultaneous increase of both optical transmittance and DC conductivity, strikingly different from other materials, we proposed its application as a next generation transparent electrode.

  17. 2-D Finite Element Cable and Box IEMP Analysis

    SciTech Connect

    Scivner, G.J.; Turner, C.D.

    1998-12-17

    A 2-D finite element code has been developed for the solution of arbitrary geometry cable SGEMP and box IEMP problems. The quasi- static electric field equations with radiation- induced charge deposition and radiation-induced conductivity y are numerically solved on a triangular mesh. Multiple regions of different dielectric materials and multiple conductors are permitted.

  18. Orthotropic Piezoelectricity in 2D Nanocellulose

    NASA Astrophysics Data System (ADS)

    García, Y.; Ruiz-Blanco, Yasser B.; Marrero-Ponce, Yovani; Sotomayor-Torres, C. M.

    2016-10-01

    The control of electromechanical responses within bonding regions is essential to face frontier challenges in nanotechnologies, such as molecular electronics and biotechnology. Here, we present Iβ-nanocellulose as a potentially new orthotropic 2D piezoelectric crystal. The predicted in-layer piezoelectricity is originated on a sui-generis hydrogen bonds pattern. Upon this fact and by using a combination of ab-initio and ad-hoc models, we introduce a description of electrical profiles along chemical bonds. Such developments lead to obtain a rationale for modelling the extended piezoelectric effect originated within bond scales. The order of magnitude estimated for the 2D Iβ-nanocellulose piezoelectric response, ~pm V‑1, ranks this material at the level of currently used piezoelectric energy generators and new artificial 2D designs. Such finding would be crucial for developing alternative materials to drive emerging nanotechnologies.

  19. Orthotropic Piezoelectricity in 2D Nanocellulose

    PubMed Central

    García, Y.; Ruiz-Blanco, Yasser B.; Marrero-Ponce, Yovani; Sotomayor-Torres, C. M.

    2016-01-01

    The control of electromechanical responses within bonding regions is essential to face frontier challenges in nanotechnologies, such as molecular electronics and biotechnology. Here, we present Iβ-nanocellulose as a potentially new orthotropic 2D piezoelectric crystal. The predicted in-layer piezoelectricity is originated on a sui-generis hydrogen bonds pattern. Upon this fact and by using a combination of ab-initio and ad-hoc models, we introduce a description of electrical profiles along chemical bonds. Such developments lead to obtain a rationale for modelling the extended piezoelectric effect originated within bond scales. The order of magnitude estimated for the 2D Iβ-nanocellulose piezoelectric response, ~pm V−1, ranks this material at the level of currently used piezoelectric energy generators and new artificial 2D designs. Such finding would be crucial for developing alternative materials to drive emerging nanotechnologies. PMID:27708364

  20. Orthotropic Piezoelectricity in 2D Nanocellulose.

    PubMed

    García, Y; Ruiz-Blanco, Yasser B; Marrero-Ponce, Yovani; Sotomayor-Torres, C M

    2016-10-06

    The control of electromechanical responses within bonding regions is essential to face frontier challenges in nanotechnologies, such as molecular electronics and biotechnology. Here, we present Iβ-nanocellulose as a potentially new orthotropic 2D piezoelectric crystal. The predicted in-layer piezoelectricity is originated on a sui-generis hydrogen bonds pattern. Upon this fact and by using a combination of ab-initio and ad-hoc models, we introduce a description of electrical profiles along chemical bonds. Such developments lead to obtain a rationale for modelling the extended piezoelectric effect originated within bond scales. The order of magnitude estimated for the 2D Iβ-nanocellulose piezoelectric response, ~pm V(-1), ranks this material at the level of currently used piezoelectric energy generators and new artificial 2D designs. Such finding would be crucial for developing alternative materials to drive emerging nanotechnologies.

  1. 2D microwave imaging reflectometer electronics

    SciTech Connect

    Spear, A. G.; Domier, C. W. Hu, X.; Muscatello, C. M.; Ren, X.; Luhmann, N. C.; Tobias, B. J.

    2014-11-15

    A 2D microwave imaging reflectometer system has been developed to visualize electron density fluctuations on the DIII-D tokamak. Simultaneously illuminated at four probe frequencies, large aperture optics image reflections from four density-dependent cutoff surfaces in the plasma over an extended region of the DIII-D plasma. Localized density fluctuations in the vicinity of the plasma cutoff surfaces modulate the plasma reflections, yielding a 2D image of electron density fluctuations. Details are presented of the receiver down conversion electronics that generate the in-phase (I) and quadrature (Q) reflectometer signals from which 2D density fluctuation data are obtained. Also presented are details on the control system and backplane used to manage the electronics as well as an introduction to the computer based control program.

  2. Large Area Synthesis of 2D Materials

    NASA Astrophysics Data System (ADS)

    Vogel, Eric

    Transition metal dichalcogenides (TMDs) have generated significant interest for numerous applications including sensors, flexible electronics, heterostructures and optoelectronics due to their interesting, thickness-dependent properties. Despite recent progress, the synthesis of high-quality and highly uniform TMDs on a large scale is still a challenge. In this talk, synthesis routes for WSe2 and MoS2 that achieve monolayer thickness uniformity across large area substrates with electrical properties equivalent to geological crystals will be described. Controlled doping of 2D semiconductors is also critically required. However, methods established for conventional semiconductors, such as ion implantation, are not easily applicable to 2D materials because of their atomically thin structure. Redox-active molecular dopants will be demonstrated which provide large changes in carrier density and workfunction through the choice of dopant, treatment time, and the solution concentration. Finally, several applications of these large-area, uniform 2D materials will be described including heterostructures, biosensors and strain sensors.

  3. 2D microwave imaging reflectometer electronics.

    PubMed

    Spear, A G; Domier, C W; Hu, X; Muscatello, C M; Ren, X; Tobias, B J; Luhmann, N C

    2014-11-01

    A 2D microwave imaging reflectometer system has been developed to visualize electron density fluctuations on the DIII-D tokamak. Simultaneously illuminated at four probe frequencies, large aperture optics image reflections from four density-dependent cutoff surfaces in the plasma over an extended region of the DIII-D plasma. Localized density fluctuations in the vicinity of the plasma cutoff surfaces modulate the plasma reflections, yielding a 2D image of electron density fluctuations. Details are presented of the receiver down conversion electronics that generate the in-phase (I) and quadrature (Q) reflectometer signals from which 2D density fluctuation data are obtained. Also presented are details on the control system and backplane used to manage the electronics as well as an introduction to the computer based control program.

  4. Assessing 2D electrophoretic mobility spectroscopy (2D MOSY) for analytical applications.

    PubMed

    Fang, Yuan; Yushmanov, Pavel V; Furó, István

    2016-12-08

    Electrophoretic displacement of charged entity phase modulates the spectrum acquired in electrophoretic NMR experiments, and this modulation can be presented via 2D FT as 2D mobility spectroscopy (MOSY) spectra. We compare in various mixed solutions the chemical selectivity provided by 2D MOSY spectra with that provided by 2D diffusion-ordered spectroscopy (DOSY) spectra and demonstrate, under the conditions explored, a superior performance of the former method. 2D MOSY compares also favourably with closely related LC-NMR methods. The shape of 2D MOSY spectra in complex mixtures is strongly modulated by the pH of the sample, a feature that has potential for areas such as in drug discovery and metabolomics. Copyright © 2016 The Authors. Magnetic Resonance in Chemistry published by John Wiley & Sons Ltd. StartCopTextCopyright © 2016 The Authors. Magnetic Resonance in Chemistry published by John Wiley & Sons Ltd.

  5. Origin of pronounced differences in 77 K fluorescence of the green alga Chlamydomonas reinhardtii in state 1 and 2.

    PubMed

    Ünlü, Caner; Polukhina, Iryna; van Amerongen, Herbert

    2016-04-01

    In response to changes in the reduction state of the plastoquinone pool in its thylakoid membrane, the green alga Chlamydomonas reinhardtti is performing state transitions: remodelling of its thylakoid membrane leads to a redistribution of excitations over photosystems I and II (PSI and PSII). These transitions are accompanied by marked changes in the 77 K fluorescence spectrum, which form the accepted signature of state transitions. The changes are generally thought to reflect a redistribution of light-harvesting complexes (LHCs) over PSII (fluorescing below 700 nm) and PSI (fluorescing above 700 nm). Here we studied the picosecond fluorescence properties of C. reinhardtti over a broad range of wavelengths with very low excitation intensities (0.2 nJ per laser pulse). Cells were directly used for time-resolved fluorescence measurements at 77 K without further treatment, such as medium exchange with glycerol. It is observed that upon going from state 1 (relatively more fluorescence below 700 nm) to state 2 (relatively more fluorescence above 700 nm), a large part of the fluorescence of LHC/PSII becomes substantially quenched in concurrence with LHC detachment from PSII, whereas the absolute amount of PSI fluorescence hardly changes. These results are in agreement with the recent proposal that the amount of LHC moving from PSII to PSI upon going from state 1 to state 2 is rather limited (Unlu et al. Proc Natl Acad Sci USA 111 (9):3460-3465, 2014).

  6. 2D Distributed Sensing Via TDR

    DTIC Science & Technology

    2007-11-02

    plate VEGF CompositeSensor Experimental Setup Air 279 mm 61 78 VARTM profile: slope RTM profile: rectangle 22 1 Jul 2003© 2003 University of Delaware...2003 University of Delaware All rights reserved Vision: Non-contact 2D sensing ü VARTM setup constructed within TL can be sensed by its EM field: 2D...300.0 mm/ns. 1 2 1 Jul 2003© 2003 University of Delaware All rights reserved Model Validation “ RTM Flow” TDR Response to 139 mm VEGC

  7. Inkjet printing of 2D layered materials.

    PubMed

    Li, Jiantong; Lemme, Max C; Östling, Mikael

    2014-11-10

    Inkjet printing of 2D layered materials, such as graphene and MoS2, has attracted great interests for emerging electronics. However, incompatible rheology, low concentration, severe aggregation and toxicity of solvents constitute critical challenges which hamper the manufacturing efficiency and product quality. Here, we introduce a simple and general technology concept (distillation-assisted solvent exchange) to efficiently overcome these challenges. By implementing the concept, we have demonstrated excellent jetting performance, ideal printing patterns and a variety of promising applications for inkjet printing of 2D layered materials.

  8. Parallel Stitching of 2D Materials.

    PubMed

    Ling, Xi; Lin, Yuxuan; Ma, Qiong; Wang, Ziqiang; Song, Yi; Yu, Lili; Huang, Shengxi; Fang, Wenjing; Zhang, Xu; Hsu, Allen L; Bie, Yaqing; Lee, Yi-Hsien; Zhu, Yimei; Wu, Lijun; Li, Ju; Jarillo-Herrero, Pablo; Dresselhaus, Mildred; Palacios, Tomás; Kong, Jing

    2016-03-23

    Diverse parallel stitched 2D heterostructures, including metal-semiconductor, semiconductor-semiconductor, and insulator-semiconductor, are synthesized directly through selective "sowing" of aromatic molecules as the seeds in the chemical vapor deposition (CVD) method. The methodology enables the large-scale fabrication of lateral heterostructures, which offers tremendous potential for its application in integrated circuits.

  9. Parallel stitching of 2D materials

    DOE PAGES

    Ling, Xi; Wu, Lijun; Lin, Yuxuan; ...

    2016-01-27

    Diverse parallel stitched 2D heterostructures, including metal–semiconductor, semiconductor–semiconductor, and insulator–semiconductor, are synthesized directly through selective “sowing” of aromatic molecules as the seeds in the chemical vapor deposition (CVD) method. Lastly, the methodology enables the large-scale fabrication of lateral heterostructures, which offers tremendous potential for its application in integrated circuits.

  10. An Intercomparison of 2-D Models Within a Common Framework

    NASA Technical Reports Server (NTRS)

    Weisenstein, Debra K.; Ko, Malcolm K. W.; Scott, Courtney J.; Jackman, Charles H.; Fleming, Eric L.; Considine, David B.; Kinnison, Douglas E.; Connell, Peter S.; Rotman, Douglas A.; Bhartia, P. K. (Technical Monitor)

    2002-01-01

    A model intercomparison among the Atmospheric and Environmental Research (AER) 2-D model, the Goddard Space Flight Center (GSFC) 2-D model, and the Lawrence Livermore National Laboratory 2-D model allows us to separate differences due to model transport from those due to the model's chemical formulation. This is accomplished by constructing two hybrid models incorporating the transport parameters of the GSFC and LLNL models within the AER model framework. By comparing the results from the native models (AER and e.g. GSFC) with those from the hybrid model (e.g. AER chemistry with GSFC transport), differences due to chemistry and transport can be identified. For the analysis, we examined an inert tracer whose emission pattern is based on emission from a High Speed Civil Transport (HSCT) fleet; distributions of trace species in the 2015 atmosphere; and the response of stratospheric ozone to an HSCT fleet. Differences in NO(y) in the upper stratosphere are found between models with identical transport, implying different model representations of atmospheric chemical processes. The response of O3 concentration to HSCT aircraft emissions differs in the models from both transport-dominated differences in the HSCT-induced perturbations of H2O and NO(y) as well as from differences in the model represent at ions of O3 chemical processes. The model formulations of cold polar processes are found to be the most significant factor in creating large differences in the calculated ozone perturbations

  11. A chimeric virus created by DNA shuffling of the capsid genes of different subtypes of porcine circovirus type 2 (PCV2) in the backbone of the non-pathogenic PCV1 induces protective immunity against the predominant PCV2b and the emerging PCV2d in pigs.

    PubMed

    Matzinger, Shannon R; Opriessnig, Tanja; Xiao, Chao-Ting; Catanzaro, Nicholas; Beach, Nathan M; Slade, David E; Nitzel, Gregory P; Meng, Xiang-Jin

    2016-11-01

    Porcine circovirus type 2 (PCV2) is the primary causative agent of porcine circovirus-associated disease (PCVAD). Available commercial vaccines all target PCV2a subtype, although the circulating predominant subtype worldwide is PCV2b, and the emerging PCV2d subtype is also increasingly associated with PCVAD. Here we molecularly bred genetically-divergent strains representing PCV2a, PCV2b, PCV2c, PCV2d, and "divergent PCV2a" subtypes by DNA-shuffling of the capsid genes to produce a chimeric virus representing PCV2 global genetic diversity. When placed in the PCV2a backbone, one chimeric virus (PCV2-3cl14) induced higher neutralizing antibody titers against different PCV2 subtypes. Subsequently, a candidate vaccine (PCV1-3cl14) was produced by cloning the shuffled 3cl14 capsid into the backbone of the non-pathogenic PCV1. A vaccine efficacy study revealed that chimeric virus PCV1-3cl14 induces protective immunity against challenge with PCV2b or PCV2d in pigs. The chimeric PCV1-3cl14 virus is a strong candidate for a novel vaccine in pigs infected with variable PCV2 strains.

  12. E-2D Advanced Hawkeye: primary flight display

    NASA Astrophysics Data System (ADS)

    Paolillo, Paul W.; Saxena, Ragini; Garruba, Jonathan; Tripathi, Sanjay; Blanchard, Randy

    2006-05-01

    This paper is a response to the challenge of providing a large area avionics display for the E-2D AHE aircraft. The resulting display design provides a pilot with high-resolution visual information content covering an image area of almost three square feet (Active Area of Samsung display = 33.792cm x 27.0336 cm = 13.304" x 10.643" = 141.596 square inches = 0.983 sq. ft x 3 = 2.95 sq. ft). The avionics display application, design and performance being described is the Primary Flight Display for the E-2D Advanced Hawkeye aircraft. This cockpit display has a screen diagonal size of 17 inches. Three displays, with minimum bezel width, just fit within the available instrument panel area. The significant design constraints of supporting an upgrade installation have been addressed. These constraints include a display image size that is larger than the mounting opening in the instrument panel. This, therefore, requires that the Electromagnetic Interference (EMI) window, LCD panel and backlight all fit within the limited available bezel depth. High brightness and a wide dimming range are supported with a dual mode Cold Cathode Fluorescent Tube (CCFT) and LED backlight. Packaging constraints dictated the use of multiple U shaped fluorescent lamps in a direct view backlight design for a maximum display brightness of 300 foot-Lamberts. The low intensity backlight levels are provided by remote LEDs coupled through a fiber optic mesh. This architecture generates luminous uniformity within a minimum backlight depth. Cross-cockpit viewing is supported with ultra-wide field-of-view performance including contrast and the color stability of an advanced LCD cell design supports. Display system design tradeoffs directed a priority to high optical efficiency for minimum power and weight.

  13. A gluten-free diet lowers NKG2D and ligand expression in BALB/c and non-obese diabetic (NOD) mice.

    PubMed

    Adlercreutz, E H; Weile, C; Larsen, J; Engkilde, K; Agardh, D; Buschard, K; Antvorskov, J C

    2014-08-01

    The interplay between diet and immune parameters which could affect type 1 diabetes (T1D) pathogenesis is not sufficiently clarified. Intestinal up-regulation of the activating receptor natural killer group 2D (NKG2D) (CD314) and its ligands is a hallmark of coeliac disease. However, the direct effect of gluten on NKG2D expression is not known. We studied, by fluorescence activated cell sorter (lymphoid tissues) and reverse transcription-quantitative polymerase chain reaction (intestine and pancreatic islets), if a gluten-free diet (GF diet) from 4 weeks of age or a gluten-free diet introduced in breeding pairs (SGF diet), induced changes in NKG2D expression on DX5(+) (CD49b) natural killer (NK) cells, CD8(+) T cells and in intestinal and islet levels of NKG2D and ligands in BALB/c and non-obese diabetic (NOD) mice. Gluten-free NOD mice had lower insulitis (P < 0·0001); reduced expression of NKG2D on DX5(+) NK cells in spleen and auricular lymph nodes (P < 0·05); and on CD8(+) T cells in pancreas-associated lymph nodes (P = 0·04). Moreover, the level of CD71 on DX5(+) NK cells and CD8(+) T cells (P < 0·005) was markedly reduced. GF and SGF mice had reduced expression of NKG2D and DX5 mRNA in intestine (P < 0·05). Differences in intestinal mRNA expression were found in mice at 8, 13 and 20 weeks. Intestinal expression of NKG2D ligands was reduced in SGF mice with lower expression of all ligands. In isolated islets, a SGF diet induced a higher expression of specific NKG2D ligands. Our data show that a gluten-free diet reduces the level of NKG2D and the expression of NKG2D ligands. These immunological changes may contribute to the lower T1D incidence associated with a gluten-free diet.

  14. Graphene and graphene-like 2D materials for optical biosensing and bioimaging: a review

    NASA Astrophysics Data System (ADS)

    Zhu, Chengzhou; Du, Dan; Lin, Yuehe

    2015-09-01

    The increasing demands of bioassay and biomedical applications have significantly promoted the rational design and fabrication of a wide range of functional nanomaterials. Coupling these advanced nanomaterials with biomolecule recognition events leads to novel sensing and diagnostic platforms. Because of their unique structures and multifunctionalities, two-dimensional nanomaterials, such as graphene and graphene-like materials (e.g., graphitic carbon nitride, transition metal dichalcogenides, boron nitride, and transition metal oxides), have stimulated great interest in the field of optical biosensors and imaging because of their innovative mechanical, physicochemical and optical properties. Depending on the different applications, the graphene and graphene-like nanomaterials can be tailored to form either fluorescent emitters or efficient fluorescence quenchers, making them powerful platforms for fabricating a series of optical biosensors to sensitively detect various targets including ions, small biomolecules, DNA/RNA and proteins. This review highlights the recent progress in optical biosensors based on graphene and graphene-like 2D materials and their imaging applications. Finally, the opportunities and some critical challenges in this field are also addressed.

  15. Fluorescence of the various red antenna states in photosystem I complexes from cyanobacteria is affected differently by the redox state of P700.

    PubMed

    Schlodder, Eberhard; Hussels, Martin; Cetin, Marianne; Karapetyan, Navassard V; Brecht, Marc

    2011-11-01

    Photosystem I of cyanobacteria contains different spectral pools of chlorophylls called red or long-wavelength chlorophylls that absorb at longer wavelengths than the primary electron donor P700. We measured the fluorescence spectra at the ensemble and the single-molecule level at low temperatures in the presence of oxidized and reduced P700. In accordance with the literature, it was observed that the fluorescence is quenched by P700(+). However, the efficiency of the fluorescence quenching by oxidized P700(+) was found to be extremely different for the various red states in PS I from different cyanobacteria. The emission of the longest-wavelength absorbing antenna state in PS I trimers from Thermosynechococcus elongatus (absorption maximum at 5K: ≈ 719nm; emission maximum at 5K: ≈ 740nm) was found to be strongly quenched by P700(+) similar to the reddest state in PS I trimers from Arthrospira platensis emitting at 760nm at 5K. The fluorescence of these red states is diminished by more than a factor of 10 in the presence of oxidized P700. For the first time, the emission of the reddest states in A. platensis and T. elongatus has been monitored using single-molecule fluorescence techniques.

  16. Vector correlations study of the reaction N(2D)+H2(X1Σg+)→NH(a1Δ)+H(2S) with different collision energies and reagent vibration excitations

    NASA Astrophysics Data System (ADS)

    Li, Yong-Qing; Zhang, Yong-Jia; Zhao, Jin-Feng; Zhao, Mei-Yu; Ding, Yong

    2015-11-01

    Vector correlations of the reaction are studied based on a recent DMBE-SEC PES for the first excited state of NH2 [J. Phys. Chem. A 114 9644 (2010)] by using a quasi-classical trajectory method. The effects of collision energy and the reagent initial vibrational excitation on cross section and product polarization are investigated for v = 0-5 and j = 0 states in a wide collision energy range (10-50 kcal/mol). The integral cross section could be increased by H2 vibration excitation remarkably based on the DMBE-SEC PES. The different phenomena of differential cross sections with different collision energies and reagent vibration excitations are explained. Particularly, the NH molecules are scattered mainly in the backward hemisphere at low vibration quantum number and evolve from backward to forward direction with increasing vibration quantum number, which could be explained by the fact that the vibrational excitation enlarges the H-H distance in the entrance channel, thus enhancing the probability of collision between N atom and H atom. A further study on product polarization demonstrates that the collision energy and vibrational excitation of the reagent remarkably influence the distributions of P(θr), P(ϕr), and P(θr, ϕr). Project supported by the National Natural Science Foundation of China (Grant Nos. 11474141 and 11404080), the Special Fund Based Research New Technology of Methanol conversion and Coal Instead of Oil, the China Postdoctoral Science Foundation (Grant No. 2014M550158) , the Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry of China (Grant No. 2014-1685), and the Program for Liaoning Excellent Talents in University, China (Grant Nos. LJQ2015040 and LJQ2014001).

  17. Optoelectronics of supported and suspended 2D semiconductors

    NASA Astrophysics Data System (ADS)

    Bolotin, Kirill

    2014-03-01

    Two-dimensional semiconductors, materials such monolayer molybdenum disulfide (MoS2) are characterized by strong spin-orbit and electron-electron interactions. However, both electronic and optoelectronic properties of these materials are dominated by disorder-related scattering. In this talk, we investigate approaches to reduce scattering and explore physical phenomena arising in intrinsic 2D semiconductors. First, we discuss fabrication of pristine suspended monolayer MoS2 and use photocurrent spectroscopy measurements to study excitons in this material. We observe band-edge and van Hove singularity excitons and estimate their binding energies. Furthermore, we study dissociation of these excitons and uncover the mechanism of their contribution to photoresponse of MoS2. Second, we study strain-induced modification of bandstructures of 2D semiconductors. With increasing strain, we find large and controllable band gap reduction of both single- and bi-layer MoS2. We also detect experimental signatures consistent with strain-induced transition from direct to indirect band gap in monolayer MoS2. Finally, we fabricate heterostructures of dissimilar 2D semiconductors and study their photoresponse. For closely spaced 2D semiconductors we detect charge transfer, while for separation larger than 10nm we observe Forster-like energy transfer between excitations in different layers.

  18. Rheological Properties of Quasi-2D Fluids in Microgravity

    NASA Technical Reports Server (NTRS)

    Stannarius, Ralf; Trittel, Torsten; Eremin, Alexey; Harth, Kirsten; Clark, Noel; Maclennan, Joseph; Glaser, Matthew; Park, Cheol; Hall, Nancy; Tin, Padetha

    2015-01-01

    In recent years, research on complex fluids and fluids in restricted geometries has attracted much attention in the scientific community. This can be attributed not only to the development of novel materials based on complex fluids but also to a variety of important physical phenomena which have barely been explored. One example is the behavior of membranes and thin fluid films, which can be described by two-dimensional (2D) rheology behavior that is quite different from 3D fluids. In this study, we have investigated the rheological properties of freely suspended films of a thermotropic liquid crystal in microgravity experiments. This model system mimics isotropic and anisotropic quasi 2D fluids [46]. We use inkjet printing technology to dispense small droplets (inclusions) onto the film surface. The motion of these inclusions provides information on the rheological properties of the films and allows the study of a variety of flow instabilities. Flat films have been investigated on a sub-orbital rocket flight and curved films (bubbles) have been studied in the ISS project OASIS. Microgravity is essential when the films are curved in order to avoid sedimentation. The experiments yield the mobility of the droplets in the films as well as the mutual mobility of pairs of particles. Experimental results will be presented for 2D-isotropic (smectic-A) and 2D-nematic (smectic-C) phases.

  19. Compatible embedding for 2D shape animation.

    PubMed

    Baxter, William V; Barla, Pascal; Anjyo, Ken-Ichi

    2009-01-01

    We present new algorithms for the compatible embedding of 2D shapes. Such embeddings offer a convenient way to interpolate shapes having complex, detailed features. Compared to existing techniques, our approach requires less user input, and is faster, more robust, and simpler to implement, making it ideal for interactive use in practical applications. Our new approach consists of three parts. First, our boundary matching algorithm locates salient features using the perceptually motivated principles of scale-space and uses these as automatic correspondences to guide an elastic curve matching algorithm. Second, we simplify boundaries while maintaining their parametric correspondence and the embedding of the original shapes. Finally, we extend the mapping to shapes' interiors via a new compatible triangulation algorithm. The combination of our algorithms allows us to demonstrate 2D shape interpolation with instant feedback. The proposed algorithms exhibit a combination of simplicity, speed, and accuracy that has not been achieved in previous work.

  20. Schottky diodes from 2D germanane

    NASA Astrophysics Data System (ADS)

    Sahoo, Nanda Gopal; Esteves, Richard J.; Punetha, Vinay Deep; Pestov, Dmitry; Arachchige, Indika U.; McLeskey, James T.

    2016-07-01

    We report on the fabrication and characterization of a Schottky diode made using 2D germanane (hydrogenated germanene). When compared to germanium, the 2D structure has higher electron mobility, an optimal band-gap, and exceptional stability making germanane an outstanding candidate for a variety of opto-electronic devices. One-atom-thick sheets of hydrogenated puckered germanium atoms have been synthesized from a CaGe2 framework via intercalation and characterized by XRD, Raman, and FTIR techniques. The material was then used to fabricate Schottky diodes by suspending the germanane in benzonitrile and drop-casting it onto interdigitated metal electrodes. The devices demonstrate significant rectifying behavior and the outstanding potential of this material.

  1. Static & Dynamic Response of 2D Solids

    SciTech Connect

    Lin, Jerry

    1996-07-15

    NIKE2D is an implicit finite-element code for analyzing the finite deformation, static and dynamic response of two-dimensional, axisymmetric, plane strain, and plane stress solids. The code is fully vectorized and available on several computing platforms. A number of material models are incorporated to simulate a wide range of material behavior including elasto-placicity, anisotropy, creep, thermal effects, and rate dependence. Slideline algorithms model gaps and sliding along material interfaces, including interface friction, penetration and single surface contact. Interactive-graphics and rezoning is included for analyses with large mesh distortions. In addition to quasi-Newton and arc-length procedures, adaptive algorithms can be defined to solve the implicit equations using the solution language ISLAND. Each of these capabilities and more make NIKE2D a robust analysis tool.

  2. Explicit 2-D Hydrodynamic FEM Program

    SciTech Connect

    Lin, Jerry

    1996-08-07

    DYNA2D* is a vectorized, explicit, two-dimensional, axisymmetric and plane strain finite element program for analyzing the large deformation dynamic and hydrodynamic response of inelastic solids. DYNA2D* contains 13 material models and 9 equations of state (EOS) to cover a wide range of material behavior. The material models implemented in all machine versions are: elastic, orthotropic elastic, kinematic/isotropic elastic plasticity, thermoelastoplastic, soil and crushable foam, linear viscoelastic, rubber, high explosive burn, isotropic elastic-plastic, temperature-dependent elastic-plastic. The isotropic and temperature-dependent elastic-plastic models determine only the deviatoric stresses. Pressure is determined by one of 9 equations of state including linear polynomial, JWL high explosive, Sack Tuesday high explosive, Gruneisen, ratio of polynomials, linear polynomial with energy deposition, ignition and growth of reaction in HE, tabulated compaction, and tabulated.

  3. Compact 2-D graphical representation of DNA

    NASA Astrophysics Data System (ADS)

    Randić, Milan; Vračko, Marjan; Zupan, Jure; Novič, Marjana

    2003-05-01

    We present a novel 2-D graphical representation for DNA sequences which has an important advantage over the existing graphical representations of DNA in being very compact. It is based on: (1) use of binary labels for the four nucleic acid bases, and (2) use of the 'worm' curve as template on which binary codes are placed. The approach is illustrated on DNA sequences of the first exon of human β-globin and gorilla β-globin.

  4. 2D Metals by Repeated Size Reduction.

    PubMed

    Liu, Hanwen; Tang, Hao; Fang, Minghao; Si, Wenjie; Zhang, Qinghua; Huang, Zhaohui; Gu, Lin; Pan, Wei; Yao, Jie; Nan, Cewen; Wu, Hui

    2016-10-01

    A general and convenient strategy for manufacturing freestanding metal nanolayers is developed on large scale. By the simple process of repeatedly folding and calendering stacked metal sheets followed by chemical etching, free-standing 2D metal (e.g., Ag, Au, Fe, Cu, and Ni) nanosheets are obtained with thicknesses as small as 1 nm and with sizes of the order of several micrometers.

  5. Characterization of a versatile reference instrument for traceable fluorescence measurements using different illumination and viewing geometries specified in practical colorimetry—part 1: bidirectional geometry (45:0)

    NASA Astrophysics Data System (ADS)

    Zwinkels, Joanne; Neil, William; Noël, Mario

    2016-10-01

    For highest accuracy fluorescence colorimetry, standardizing organizations recommend the use of a two-monochromator method with a bidirectional illumination and viewing geometry (45:0 or 0:45). For this reason, reference fluorescence instruments developed by National Measurement Institutes (NMIs) have largely conformed to this bidirectional geometry. However, for many practical applications in colorimetry where the samples exhibit texture, surface roughness or other spatial non-uniformities, the relevant standard test methods specify a sphere geometry with diffuse illumination or viewing (e.g. d:8 or 8:d) which gives improved measurement precision. This difference in the measurement geometry between the primary instrument used to realize the fluorescence scale and the secondary testing instruments used for practical measurements, compromises the traceability of these fluorescence calibrations. To address this metrology issue, a two-monochromator goniospectrofluorimeter instrument has been developed at the National Research Council of Canada (NRC). This instrument can be configured for different illumination and viewing geometries to conform with international standards for different colorimetric applications. To improve the traceability chain for measurements using different geometries, the instrument has been thoroughly characterized and validated by means of comparison measurements with NRC’s other spectrophotometric and fluorescence reference instruments. This uncertainty analysis has been carried out in a step-wise manner; first, for a bidirectional geometry (45:0) and then for a sphere geometry (8:d) to provide an uninterrupted traceability to primary radiometric scales. The first paper in this two paper series reviews the background to this work and provides details of the basic design of the new instrument and its characterization for measurements using a bidirectional geometry (45:0), including a representative uncertainty budget. In part 2, the major

  6. Determining cyclooxygenase-2 activity in three different test systems utilizing online-solid phase extraction-liquid chromatography-mass spectrometry for parallel quantification of prostaglandin E(2), D(2) and thromboxane B(2).

    PubMed

    Willenberg, Ina; Meschede, Anna K; Schebb, Nils Helge

    2015-04-24

    Cyclooxygenase-2 (COX-2) catalyzes the formation of PGH2 from arachidonic acid. PGH2 is further converted to different prostaglandins (PG), such as PGE2, PGD2 and TxB2. In this study a rapid online-SPE-LC-MS method for the simultaneous quantification of PGE2, PGD2 and TxB2 streamlined for COX-2 enzyme assays is presented. Baseline separation of all analytes was achieved in only 7.1 min per sample, including sample preparation by online SPE. The method showed high sensitivity (LODs of 0.65-1.25 fmol on column) and accuracy (89-113%) in protein containing media. Because of online-SPE, no manual sample preparation was required, except for addition of IS solution, allowing to use the approach as rapid read-out in COX-2 activity assays. This was demonstrated by applying the method on three in vitro test systems: a cell-free enzyme assay, an assay using HCA-7 cells constitutively expressing COX-2 and primary human monocytes. In these assays, the potency of three popular drugs celecoxib, indomethacin and dexamethasone was successfully characterized with the new online-LC-MS method. The comparison of the results showed that the inhibitory effects of PG formation strongly depend on the test system. Thus we suggest that the modulation of COX-2 activity of a test compound should be at least characterized in two assay systems. With the online-SPE-LC-MS described in here we present a versatile tool as read-out for these types of assays.

  7. Engineering light outcoupling in 2D materials.

    PubMed

    Lien, Der-Hsien; Kang, Jeong Seuk; Amani, Matin; Chen, Kevin; Tosun, Mahmut; Wang, Hsin-Ping; Roy, Tania; Eggleston, Michael S; Wu, Ming C; Dubey, Madan; Lee, Si-Chen; He, Jr-Hau; Javey, Ali

    2015-02-11

    When light is incident on 2D transition metal dichalcogenides (TMDCs), it engages in multiple reflections within underlying substrates, producing interferences that lead to enhancement or attenuation of the incoming and outgoing strength of light. Here, we report a simple method to engineer the light outcoupling in semiconducting TMDCs by modulating their dielectric surroundings. We show that by modulating the thicknesses of underlying substrates and capping layers, the interference caused by substrate can significantly enhance the light absorption and emission of WSe2, resulting in a ∼11 times increase in Raman signal and a ∼30 times increase in the photoluminescence (PL) intensity of WSe2. On the basis of the interference model, we also propose a strategy to control the photonic and optoelectronic properties of thin-layer WSe2. This work demonstrates the utilization of outcoupling engineering in 2D materials and offers a new route toward the realization of novel optoelectronic devices, such as 2D LEDs and solar cells.

  8. Elemental changes in the hippocampal formation following two different formulas of ketogenic diet: an X-ray fluorescence microscopy study.

    PubMed

    Chwiej, J; Patulska, A; Skoczen, A; Janeczko, K; Ciarach, M; Simon, R; Setkowicz, Z

    2015-12-01

    The main purpose of the following study was the determination of elemental changes occurring within hippocampal formation as a result of high-fat and carbohydrate-restricted ketogenic diet (KD). To realize it, X-ray fluorescence microscopy was applied for topographic and quantitative analysis of P, S, K, Ca, Fe, Cu, Zn and Se in hippocampal formations taken from rats fed with two different KDs and naive controls. The detailed comparisons were done for sectors 1 and 3 of the Ammon's, the dentate gyrus and hilus of dentate gyrus. The results of elemental analysis showed that the KDs induced statistically significant changes in the accumulation of P, K, Ca, Zn and Se in particular areas of hippocampal formation and these alterations strongly depended on the composition of the diets. Much greater influence on the hippocampal areal densities of examined elements was found for the KD which was characterized by a lower content of carbohydrates, higher content of fats and increased proportion of unsaturated fatty acids. The levels of P, K and Zn decreased whilst those of Ca and Se increased as a result of the treatment with the KDs.

  9. Effect of Different Light Qualities on Growth, Pigment Content, Chlorophyll Fluorescence, and Antioxidant Enzyme Activity in the Red Alga Pyropia haitanensis (Bangiales, Rhodophyta).

    PubMed

    Wu, Huanyang

    2016-01-01

    Spectral light changes evoke different morphogenetic and photosynthetic responses that can vary among different algae species. The aim of this study is to investigate the photosynthetic characteristics of the red macroalgae grown under different spectrum environments. In this study, Pyropia haitanensis were cultured under blue, red, and green LED and fluorescent tubes light. The growth rate, photopigment composition, chlorophyll fluorescence, and antioxidative enzymes activities in different light spectrums were investigated. The results revealed that growth rate was significantly higher in the thalli grown under blue, green, and fluorescent tubes light. Contents of Chl a and phycobiliprotein in red light were lower among all the growth conditions. Furthermore, a striking increase in SOD and CAT activity was observed in red light treatment along with the NPQ increase. The results revealed that the photosynthetic efficiency and increased growth rate of P. haitanensis benefitted from light spectrums such as blue, green, and fluorescent tubes light by pigment composition and photochemical efficiency manipulation, whereas red light has disadvantageous effects. Accordingly, the results for improving quality and the economic yield of algae species in some extent and the combination of different wavelengths could allow better economic resource exploitation.

  10. Effect of Different Light Qualities on Growth, Pigment Content, Chlorophyll Fluorescence, and Antioxidant Enzyme Activity in the Red Alga Pyropia haitanensis (Bangiales, Rhodophyta)

    PubMed Central

    2016-01-01

    Spectral light changes evoke different morphogenetic and photosynthetic responses that can vary among different algae species. The aim of this study is to investigate the photosynthetic characteristics of the red macroalgae grown under different spectrum environments. In this study, Pyropia haitanensis were cultured under blue, red, and green LED and fluorescent tubes light. The growth rate, photopigment composition, chlorophyll fluorescence, and antioxidative enzymes activities in different light spectrums were investigated. The results revealed that growth rate was significantly higher in the thalli grown under blue, green, and fluorescent tubes light. Contents of Chl a and phycobiliprotein in red light were lower among all the growth conditions. Furthermore, a striking increase in SOD and CAT activity was observed in red light treatment along with the NPQ increase. The results revealed that the photosynthetic efficiency and increased growth rate of P. haitanensis benefitted from light spectrums such as blue, green, and fluorescent tubes light by pigment composition and photochemical efficiency manipulation, whereas red light has disadvantageous effects. Accordingly, the results for improving quality and the economic yield of algae species in some extent and the combination of different wavelengths could allow better economic resource exploitation. PMID:27642603

  11. Analytic signal extraction approach based on 2D Grating Interferometer and systematic comparison between 2D GI and 1D case

    NASA Astrophysics Data System (ADS)

    Ju, Z.; Wang, Y.; Li, P.; Zhu, Z.; Zhang, K.; Huang, W.; Yuan, Q.; Wu, Z.; Zhu, P.

    2016-03-01

    X-ray imaging method based on 2D grating interferometer was proposed and studied recently, to overcome the limitations in signal extraction and phase retrieval when using 1D grating interferometer. In this paper, the concept of angle-signal response function is proposed, and different surfaces of different 2D setups under the condition of parallel coherent light are calculated and depicted with Matlab. Based on this concept, performance of 2D grating interferometer is systematically analyzed and an analytic 2D signal extraction approach is theoretically proposed. Besides, signal extraction, phase retrieval and feasibility of using conventional source are also briefly discussed and compared between 2D grating interferometer and 1D case.

  12. 2D superconductivity by ionic gating

    NASA Astrophysics Data System (ADS)

    Iwasa, Yoshi

    2D superconductivity is attracting a renewed interest due to the discoveries of new highly crystalline 2D superconductors in the past decade. Superconductivity at the oxide interfaces triggered by LaAlO3/SrTiO3 has become one of the promising routes for creation of new 2D superconductors. Also, the MBE grown metallic monolayers including FeSe are also offering a new platform of 2D superconductors. In the last two years, there appear a variety of monolayer/bilayer superconductors fabricated by CVD or mechanical exfoliation. Among these, electric field induced superconductivity by electric double layer transistor (EDLT) is a unique platform of 2D superconductivity, because of its ability of high density charge accumulation, and also because of the versatility in terms of materials, stemming from oxides to organics and layered chalcogenides. In this presentation, the following issues of electric filed induced superconductivity will be addressed; (1) Tunable carrier density, (2) Weak pinning, (3) Absence of inversion symmetry. (1) Since the sheet carrier density is quasi-continuously tunable from 0 to the order of 1014 cm-2, one is able to establish an electronic phase diagram of superconductivity, which will be compared with that of bulk superconductors. (2) The thickness of superconductivity can be estimated as 2 - 10 nm, dependent on materials, and is much smaller than the in-plane coherence length. Such a thin but low resistance at normal state results in extremely weak pinning beyond the dirty Boson model in the amorphous metallic films. (3) Due to the electric filed, the inversion symmetry is inherently broken in EDLT. This feature appears in the enhancement of Pauli limit of the upper critical field for the in-plane magnetic fields. In transition metal dichalcogenide with a substantial spin-orbit interactions, we were able to confirm the stabilization of Cooper pair due to its spin-valley locking. This work has been supported by Grant-in-Aid for Specially

  13. Estimating chlorophyll content and photochemical yield of photosystem II (ΦPSII) using solar-induced chlorophyll fluorescence measurements at different growing stages of attached leaves

    PubMed Central

    Tubuxin, Bayaer; Rahimzadeh-Bajgiran, Parinaz; Ginnan, Yusaku; Hosoi, Fumiki; Omasa, Kenji

    2015-01-01

    This paper illustrates the possibility of measuring chlorophyll (Chl) content and Chl fluorescence parameters by the solar-induced Chl fluorescence (SIF) method using the Fraunhofer line depth (FLD) principle, and compares the results with the standard measurement methods. A high-spectral resolution HR2000+ and an ordinary USB4000 spectrometer were used to measure leaf reflectance under solar and artificial light, respectively, to estimate Chl fluorescence. Using leaves of Capsicum annuum cv. ‘Sven’ (paprika), the relationships between the Chl content and the steady-state Chl fluorescence near oxygen absorption bands of O2B (686nm) and O2A (760nm), measured under artificial and solar light at different growing stages of leaves, were evaluated. The Chl fluorescence yields of ΦF 686nm/ΦF 760nm ratios obtained from both methods correlated well with the Chl content (steady-state solar light: R2 = 0.73; artificial light: R2 = 0.94). The SIF method was less accurate for Chl content estimation when Chl content was high. The steady-state solar-induced Chl fluorescence yield ratio correlated very well with the artificial-light-induced one (R2 = 0.84). A new methodology is then presented to estimate photochemical yield of photosystem II (ΦPSII) from the SIF measurements, which was verified against the standard Chl fluorescence measurement method (pulse-amplitude modulated method). The high coefficient of determination (R2 = 0.74) between the ΦPSII of the two methods shows that photosynthesis process parameters can be successfully estimated using the presented methodology. PMID:26071530

  14. Structural Complexity and Phonon Physics in 2D Arsenenes.

    PubMed

    Carrete, Jesús; Gallego, Luis J; Mingo, Natalio

    2017-03-15

    In the quest for stable 2D arsenic phases, four different structures have been recently claimed to be stable. We show that, due to phonon contributions, the relative stability of those structures differs from previous reports and depends crucially on temperature. We also show that one of those four phases is in fact mechanically unstable. Furthermore, our results challenge the common assumption of an inverse correlation between structural complexity and thermal conductivity. Instead, a richer picture emerges from our results, showing how harmonic interactions, anharmonicity, and symmetries all play a role in modulating thermal conduction in arsenenes. More generally, our conclusions highlight how vibrational properties are an essential element to be carefully taken into account in theoretical searches for new 2D materials.

  15. Synthesis of fluorescent C24-ceramide: evidence for acyl chain length dependent differences in penetration of exogenous NBD-ceramides into human skin.

    PubMed

    Novotný, Jakub; Pospechová, Katerina; Hrabálek, Alexandr; Cáp, Robert; Vávrová, Katerina

    2009-12-15

    Topical skin lipid supplementation may provide opportunities for controlling ceramide (Cer) deficiency in skin diseases such as atopic dermatitis or psoriasis. Here we describe the synthesis of a long-chain 7-nitrobenzo[c][1,2,5]oxadiazol-4-yl (NBD)-labeled Cer and its different penetration through human skin compared to widely used short-chain fluorescent Cer tools.

  16. FASTWO - A 2-D interactive algebraic grid generator

    NASA Technical Reports Server (NTRS)

    Luh, Raymond Ching-Chung; Lombard, C. K.

    1988-01-01

    This paper presents a very simple and effective computational procedure, FASTWO, for generating patched composite finite difference grids in 2-D for any geometry. Major components of the interactive graphics based method that is closely akin to and borrows many tools from transfinite interpolation are highlighted. Several grids produced by FASTWO are shown to illustrate its powerful capability. Comments about extending the methodology to 3-D are also given.

  17. [3D display of sequential 2D medical images].

    PubMed

    Lu, Yisong; Chen, Yazhu

    2003-12-01

    A detailed review is given in this paper on various current 3D display methods for sequential 2D medical images and the new development in 3D medical image display. True 3D display, surface rendering, volume rendering, 3D texture mapping and distributed collaborative rendering are discussed in depth. For two kinds of medical applications: Real-time navigation system and high-fidelity diagnosis in computer aided surgery, different 3D display methods are presented.

  18. Study on the Mechanism of Interaction Between Tubeimoside I and Human Serum Albumin at Different Temperatures by Three-Dimensional Fluorescence Spectrum

    NASA Astrophysics Data System (ADS)

    Lin, Xiaogang; Li, Wenchao; Ye, Changbin; Liu, Zhiyuan

    2015-06-01

    Tubeimoside (TBMS), the bulb of Bolbostemma paniculatum (Maxim.) Franquet (Cucurbitaceae), is one of the traditional Chinese medicines often used for the treatment of tumors as well as for detoxication. Tubeimoside I (TBMS I) is one of the main active ingredients of TBMS, the mechanism of action of which remains unknown. Human serum albumin (HSA) is the most abundant carrier protein in blood circulation. Three-dimensional (3D) fluorescence spectra and the excitation-emission matrix of interaction between TBMS I and HSA were measured at different temperatures. The results showed that HSA fluorescence was quenched by TBMS I through a static quenching mechanism. Also, the HSA fluorescence was quenched with the temperature increase from 283 K to 353 K. 3D spectral results revealed the changes in the secondary structure of HSA upon interaction with TBMS I.

  19. Volumetric elasticity imaging with a 2-D CMUT array.

    PubMed

    Fisher, Ted G; Hall, Timothy J; Panda, Satchi; Richards, Michael S; Barbone, Paul E; Jiang, Jingfeng; Resnick, Jeff; Barnes, Steve

    2010-06-01

    This article reports the use of a two-dimensional (2-D) capacitive micro-machined ultrasound transducer (CMUT) to acquire radio-frequency (RF) echo data from relatively large volumes of a simple ultrasound phantom to compare three-dimensional (3-D) elasticity imaging methods. Typical 2-D motion tracking for elasticity image formation was compared with three different methods of 3-D motion tracking, with sum-squared difference (SSD) used as the similarity measure. Differences among the algorithms were the degree to which they tracked elevational motion: not at all (2-D search), planar search, combination of multiple planes and plane independent guided search. The cross-correlation between the predeformation and motion-compensated postdeformation RF echo fields was used to quantify motion tracking accuracy. The lesion contrast-to-noise ratio was used to quantify image quality. Tracking accuracy and strain image quality generally improved with increased tracking sophistication. When used as input for a 3-D modulus reconstruction, high quality 3-D displacement estimates yielded accurate and low noise modulus reconstruction.

  20. Volumetric Elasticity Imaging with a 2D CMUT Array

    PubMed Central

    Fisher, Ted G.; Hall, Timothy J.; Panda, Satchi; Richards, Michael S.; Barbone, Paul E.; Jiang, Jingfeng; Resnick, Jeff; Barnes, Steve

    2010-01-01

    This paper reports the use of a two-dimensional (2D) capacitive micro-machined ultrasound transducer (CMUT) to acquire radio frequency (RF) echo data from relatively large volumes of a simple ultrasound phantom to compare 3D elasticity imaging methods. Typical 2D motion tracking for elasticity image formation was compared to three different methods of 3D motion tracking, with sum-squared difference (SSD) used as the similarity measure. Differences among the algorithms were the degree to which they tracked elevational motion: not at all (2D search), planar search, combination of multiple planes, and plane independent guided search. The cross correlation between the pre-deformation and motion-compensated post-deformation RF echo fields was used to quantify motion tracking accuracy. The lesion contrast-to-noise ratio was used to quantify image quality. Tracking accuracy and strain image quality generally improved with increased tracking sophistication. When used as input for a 3D modulus reconstruction, high quality 3D displacement estimates yielded accurate and low noise modulus reconstruction. PMID:20510188

  1. Periodically sheared 2D Yukawa systems

    SciTech Connect

    Kovács, Anikó Zsuzsa; Hartmann, Peter; Donkó, Zoltán

    2015-10-15

    We present non-equilibrium molecular dynamics simulation studies on the dynamic (complex) shear viscosity of a 2D Yukawa system. We have identified a non-monotonic frequency dependence of the viscosity at high frequencies and shear rates, an energy absorption maximum (local resonance) at the Einstein frequency of the system at medium shear rates, an enhanced collective wave activity, when the excitation is near the plateau frequency of the longitudinal wave dispersion, and the emergence of significant configurational anisotropy at small frequencies and high shear rates.

  2. ENERGY LANDSCAPE OF 2D FLUID FORMS

    SciTech Connect

    Y. JIANG; ET AL

    2000-04-01

    The equilibrium states of 2D non-coarsening fluid foams, which consist of bubbles with fixed areas, correspond to local minima of the total perimeter. (1) The authors find an approximate value of the global minimum, and determine directly from an image how far a foam is from its ground state. (2) For (small) area disorder, small bubbles tend to sort inwards and large bubbles outwards. (3) Topological charges of the same sign repel while charges of opposite sign attract. (4) They discuss boundary conditions and the uniqueness of the pattern for fixed topology.

  3. Gold-standard performance for 2D hydrodynamic modeling

    NASA Astrophysics Data System (ADS)

    Pasternack, G. B.; MacVicar, B. J.

    2013-12-01

    Two-dimensional, depth-averaged hydrodynamic (2D) models are emerging as an increasingly useful tool for environmental water resources engineering. One of the remaining technical hurdles to the wider adoption and acceptance of 2D modeling is the lack of standards for 2D model performance evaluation when the riverbed undulates, causing lateral flow divergence and convergence. The goal of this study was to establish a gold-standard that quantifies the upper limit of model performance for 2D models of undulating riverbeds when topography is perfectly known and surface roughness is well constrained. A review was conducted of published model performance metrics and the value ranges exhibited by models thus far for each one. Typically predicted velocity differs from observed by 20 to 30 % and the coefficient of determination between the two ranges from 0.5 to 0.8, though there tends to be a bias toward overpredicting low velocity and underpredicting high velocity. To establish a gold standard as to the best performance possible for a 2D model of an undulating bed, two straight, rectangular-walled flume experiments were done with no bed slope and only different bed undulations and water surface slopes. One flume tested model performance in the presence of a porous, homogenous gravel bed with a long flat section, then a linear slope down to a flat pool bottom, and then the same linear slope back up to the flat bed. The other flume had a PVC plastic solid bed with a long flat section followed by a sequence of five identical riffle-pool pairs in close proximity, so it tested model performance given frequent undulations. Detailed water surface elevation and velocity measurements were made for both flumes. Comparing predicted versus observed velocity magnitude for 3 discharges with the gravel-bed flume and 1 discharge for the PVC-bed flume, the coefficient of determination ranged from 0.952 to 0.987 and the slope for the regression line was 0.957 to 1.02. Unsigned velocity

  4. Study of heavy metals in wild edible mushrooms under different pollution conditions by X-ray fluorescence spectrometry.

    PubMed

    Carvalho, M L; Pimentel, A C; Fernandes, B

    2005-07-01

    In this work we studied and compared the metal uptake in edible mushrooms (Lepiota procera, Boletus badius, Boletus edulis, Tricholoma equestry, Lactarius deliciosus, Cantarelus tubalformis and Cantarelus edulis), relative to sampling sites submitted to different pollution conditions: car traffic, soil pollution due to pesticides and fertilizers used in old vineyards, and incineration of hospital waste. Soil was also collected in some places, and its content was correlated to the corresponding one in some mushrooms species. All samples, without any chemical treatment, were analyzed by an X-ray fluorescence set-up. This technique is based on a monochromatic X-ray beam ionizing the atoms of the sample. Following this ionization, the emitted radiation is characteristic of the element, allowing its identification and quantification. Vineyards are normally submitted to very high amounts of sulfating, containing high copper concentrations. This metal is accumulated on the soil, and can be up-taken by vegetation. Very high levels of Fe and Cu were found in Lepiota procera species in old vineyards. Zinc was found to be always higher than Cu by factors ranging from 1.5 to 8 in clean wood taken as a reference for the whole analyzed species, while in old vineyards the ratio Zn/Cu reach 0.25 for Lepiota procera. This is correlated to the soil content for both elements. In addition, pollution induced by car traffic was checked in some samples, collected in the proximity of highways. Pb was the main contaminant in these areas, and presenting values 10 times higher than the corresponding ones in sites not submitted to pollution, for some species. Mushrooms contamination due to incineration of hospital waste was also studied, but we did not observe any contamination involving heavy metals in the several analyzed species around these areas. This is in agreement with what was expected, taking into account that hospital waste is mostly organic and, in principle, no heavy metals would

  5. [Influence of different concentration Ni and Cu on the photosynthesis and chlorophyll fluorescence characteristics of Peganum harmala].

    PubMed

    Lu, Yan; Li, Xin-rong; He, Ming-zhu; Su, Yan-gui; Zeng, Fan-jiang

    2011-04-01

    A pot experiment was conducted to study the influence of different concentration (0, 50, 100, 200, and 400 mg kg(-1)) Ni and Cu on the growth, photosynthesis, and chlorophyll fluorescence characteristics of Peganum harmala seedlings. With increasing concentration Ni in the medium, the seedlings growth parameters, photosynthetic pigment content, net photosynthetic rate (P(n)), stomatal conductance (G(s)), transpiration rate (T(r)), maximal photochemical efficiency of PS II (F(v)/F(m)), quantum efficiency of electric transport of PS II (phi (PS II)), and coefficient of photochemical quenching (q(P)) of P. harmala decreased significantly, while the intercellular CO2 concentration (C(i)) and the coefficient of non-photochemical quenching (q(N)) were in adverse. The decrease of P(n) under Ni stress was mainly caused by non-stomatal limitation. At 50 mg kg(-1) Cu, the growth parameters, photosynthetic pigment content, P(n), G(s), T(r), C(i), F(v)/F(m), phi(PS II), and q(P) reached their peak values; at 100 mg kg(-1) Cu, the growth parameters, chlorophyll a and b contents, P(n), G(s), T(r), C(i), and F(v)/F(m) were still slightly higher than the control; while with the further increasing Cu concentration in the medium, all the test indices except q(N) tended to decrease. The decrease of P(n) under Cu stress was mainly caused by stomatal limitation.

  6. The role of the cytoskeleton in cellular force generation in 2D and 3D environments

    NASA Astrophysics Data System (ADS)

    Kraning-Rush, Casey M.; Carey, Shawn P.; Califano, Joseph P.; Smith, Brooke N.; Reinhart-King, Cynthia A.

    2011-02-01

    To adhere and migrate, cells generate forces through the cytoskeleton that are transmitted to the surrounding matrix. While cellular force generation has been studied on 2D substrates, less is known about cytoskeletal-mediated traction forces of cells embedded in more in vivo-like 3D matrices. Recent studies have revealed important differences between the cytoskeletal structure, adhesion, and migration of cells in 2D and 3D. Because the cytoskeleton mediates force, we sought to directly compare the role of the cytoskeleton in modulating cell force in 2D and 3D. MDA-MB-231 cells were treated with agents that perturbed actin, microtubules, or myosin, and analyzed for changes in cytoskeletal organization and force generation in both 2D and 3D. To quantify traction stresses in 2D, traction force microscopy was used; in 3D, force was assessed based on single cell-mediated collagen fibril reorganization imaged using confocal reflectance microscopy. Interestingly, even though previous studies have observed differences in cell behaviors like migration in 2D and 3D, our data indicate that forces generated on 2D substrates correlate with forces within 3D matrices. Disruption of actin, myosin or microtubules in either 2D or 3D microenvironments disrupts cell-generated force. These data suggest that despite differences in cytoskeletal organization in 2D and 3D, actin, microtubules and myosin contribute to contractility and matrix reorganization similarly in both microenvironments.

  7. Microwave Assisted 2D Materials Exfoliation

    NASA Astrophysics Data System (ADS)

    Wang, Yanbin

    Two-dimensional materials have emerged as extremely important materials with applications ranging from energy and environmental science to electronics and biology. Here we report our discovery of a universal, ultrafast, green, solvo-thermal technology for producing excellent-quality, few-layered nanosheets in liquid phase from well-known 2D materials such as such hexagonal boron nitride (h-BN), graphite, and MoS2. We start by mixing the uniform bulk-layered material with a common organic solvent that matches its surface energy to reduce the van der Waals attractive interactions between the layers; next, the solutions are heated in a commercial microwave oven to overcome the energy barrier between bulk and few-layers states. We discovered the minutes-long rapid exfoliation process is highly temperature dependent, which requires precise thermal management to obtain high-quality inks. We hypothesize a possible mechanism of this proposed solvo-thermal process; our theory confirms the basis of this novel technique for exfoliation of high-quality, layered 2D materials by using an as yet unknown role of the solvent.

  8. Changes in fluorescent emission of cationic fluorophores in the presence of n-alkanes and alcohols in different polarity solvents

    NASA Astrophysics Data System (ADS)

    Delgado-Camón, Arantzazu; Garriga, Rosa; Mateos, Elena; Cebolla, Vicente L.; Galbán, Javier; Membrado, Luis; Marcos, Susana de; Gálvez, Eva M.

    2011-01-01

    Berberine and coralyne experience either fluorescence enhancement or quenching when long hydrocarbon chain compounds (e.g., n-alkanes or alcohols) are added to their solutions, depending on solvent polarity. In polar solvents, as methanol or acetonitrile, the added compounds provide an apolar microenvironment that hinders alternative relaxation mechanisms, favouring fluorescence emission. However, alkane additions produce quenching in dichloromethane, which has been explained taking into account ion pairing between cationic fluorophore and counterion. The strong quenching measured after alcohol additions in dichloromethane suggests reversed micelle formation. Procedures and results described here may find practical applications in the development of analytical methods.

  9. Report of the 1988 2-D Intercomparison Workshop, chapter 3

    NASA Technical Reports Server (NTRS)

    Jackman, Charles H.; Brasseur, Guy; Soloman, Susan; Guthrie, Paul D.; Garcia, Rolando; Yung, Yuk L.; Gray, Lesley J.; Tung, K. K.; Ko, Malcolm K. W.; Isaken, Ivar

    1989-01-01

    Several factors contribute to the errors encountered. With the exception of the line-by-line model, all of the models employ simplifying assumptions that place fundamental limits on their accuracy and range of validity. For example, all 2-D modeling groups use the diffusivity factor approximation. This approximation produces little error in tropospheric H2O and CO2 cooling rates, but can produce significant errors in CO2 and O3 cooling rates at the stratopause. All models suffer from fundamental uncertainties in shapes and strengths of spectral lines. Thermal flux algorithms being used in 2-D tracer tranport models produce cooling rates that differ by as much as 40 percent for the same input model atmosphere. Disagreements of this magnitude are important since the thermal cooling rates must be subtracted from the almost-equal solar heating rates to derive the net radiative heating rates and the 2-D model diabatic circulation. For much of the annual cycle, the net radiative heating rates are comparable in magnitude to the cooling rate differences described. Many of the models underestimate the cooling rates in the middle and lower stratosphere. The consequences of these errors for the net heating rates and the diabatic circulation will depend on their meridional structure, which was not tested here. Other models underestimate the cooling near 1 mbar. Suchs errors pose potential problems for future interactive ozone assessment studies, since they could produce artificially-high temperatures and increased O3 destruction at these levels. These concerns suggest that a great deal of work is needed to improve the performance of thermal cooling rate algorithms used in the 2-D tracer transport models.

  10. Fluorescence study of sugars

    NASA Astrophysics Data System (ADS)

    Thongjamroon, Sunida; Pattanaporkratana, Apichart

    2015-07-01

    We studied photoemission of monosaccharides and disaccharides using laser-induced fluorescence spectroscopy. A 532- nm, 10 mW, laser was used to excite the samples and back-scattering signals were collected by a spectrometer. We found that most sugars show weak fluorescence in solid phase but do not fluoresce when dissolved in water solutions. The emission spectra show similar peak intensity at 590 nm, but they are different in emission intensities. We suggest that the fluorescence spectra may be used to differentiate sugar type, even though the origin of the fluorescence is unclear and needed further study.

  11. 2-D or not 2-D, that is the question: A Northern California test

    SciTech Connect

    Mayeda, K; Malagnini, L; Phillips, W S; Walter, W R; Dreger, D

    2005-06-06

    Reliable estimates of the seismic source spectrum are necessary for accurate magnitude, yield, and energy estimation. In particular, how seismic radiated energy scales with increasing earthquake size has been the focus of recent debate within the community and has direct implications on earthquake source physics studies as well as hazard mitigation. The 1-D coda methodology of Mayeda et al. has provided the lowest variance estimate of the source spectrum when compared against traditional approaches that use direct S-waves, thus making it ideal for networks that have sparse station distribution. The 1-D coda methodology has been mostly confined to regions of approximately uniform complexity. For larger, more geophysically complicated regions, 2-D path corrections may be required. The complicated tectonics of the northern California region coupled with high quality broadband seismic data provides for an ideal ''apples-to-apples'' test of 1-D and 2-D path assumptions on direct waves and their coda. Using the same station and event distribution, we compared 1-D and 2-D path corrections and observed the following results: (1) 1-D coda results reduced the amplitude variance relative to direct S-waves by roughly a factor of 8 (800%); (2) Applying a 2-D correction to the coda resulted in up to 40% variance reduction from the 1-D coda results; (3) 2-D direct S-wave results, though better than 1-D direct waves, were significantly worse than the 1-D coda. We found that coda-based moment-rate source spectra derived from the 2-D approach were essentially identical to those from the 1-D approach for frequencies less than {approx}0.7-Hz, however for the high frequencies (0.7{le} f {le} 8.0-Hz), the 2-D approach resulted in inter-station scatter that was generally 10-30% smaller. For complex regions where data are plentiful, a 2-D approach can significantly improve upon the simple 1-D assumption. In regions where only 1-D coda correction is available it is still preferable over 2

  12. Effects of 22 CYP2D6 Genetic Variations Newly Identified in Chinese Population on Olanzapine Metabolism in vitro.

    PubMed

    Zhou, Hong-Yu; Gu, Er-Min; Chen, Qiu-Lei; Zhan, Yun-Yun; Wang, Shuang-Hu; Liang, Bing-Qing; Dai, Da-Peng; Cai, Jian-Ping; Hu, Guo-Xin

    2016-01-01

    The objective of this study was to assess the catalytic activity of 22 novel CYP2D6 allelic variants (2D6*87-*98, R25Q, F164L, E215K, F219S, V327M, D336N, V342M, R344Q, R440C and R497C) to olanzapine in vitro. Their protein products expressed in Spodoptera frugiperda 21 (Sf21) insect cells were incubated with olanzapine 100-2,000 μmol/l for 30 min. The kinetic parameters of Km, Vmax and intrinsic clearance were determined by 2-hydroxymethylolanzapine, the metabolite of olanzapine mediated by CYP2D6, using ultra-performance liquid chromatography tandem mass spectrometry. Results showed that the kinetic parameters of 2 alleles, CYP2D6*92 and 2D6*96, could not be detected; 17 allelic variants, CYP2D6*87-*88, 2D6*90-*91, 2D6*93-*95, 2D6*97, R25Q, F164L, E215K, F219S, V327M, V342M, R344Q, R440C and R497C, significantly reduced the intrinsic clearance of olanzapine; 2 variants, CYP2D6*89 and 2D6*98, increased the intrinsic clearance of olanzapine; no difference was found in intrinsic clearance of D336N. Furthermore, 6 alleles, CYP2D6*87, 2D6*88, 2D6*91, 2D6*93, 2D6*97 and R497C, exhibited higher Km values in a range of 120.80-217.56% relative to wild-type CYP2D6*1. The research demonstrated the metabolic phenotype of the 22 novel CYP2D6 variants for olanzapine that were different from probe drugs we used previously and might provide beneficial information to the personalized medicine of olanzapine.

  13. Variation in the inhibitory potency of terbinafine among genetic variants of CYP2D6.

    PubMed

    Akiyoshi, Takeshi; Ishiuchi, Miho; Imaoka, Ayuko; Ohtani, Hisakazu

    2015-08-01

    Cytochrome P450 2D6 (CYP2D6) is a highly polymorphic enzyme that is involved in the metabolism of many drugs. Terbinafine (TER) is a CYP2D6 inhibitor and causes persistent drug interactions in the clinical setting; however, its inhibitory mechanism and the differences in its inhibitory potency among genetic variants of CYP2D6 remain to be investigated. This study aimed to investigate the inhibitory mechanism of TER and the differences in its inhibitory potency among three CYP2D6 variants, CYP2D6.1, CYP2D6.2, and CYP2D6.10. In a competitive inhibition study, the metabolic activity of the CYP2D6 was assessed based on their demethylation of dextromethorphan in the presence or absence of TER, and the time-dependency of the inhibitory effects were examined by preincubating the enzymes with TER. TER had weaker inhibitory effects on CYP2D6.2 and CYP2D6.10 than on CYP2D6.1; i.e., TER exhibited Ki values (the concentration of inhibitor that results in half-maximal inhibition) of 0.0525, 0.355, and 1.85 μM for CYP2D6.1, CYP2D6.2, and CYP2D6.10, respectively. The inhibitory effects of TER were not time-dependent. Since TER's Ki value for CYP2D6.10 was 35.2-fold higher than its Ki value for CYP2D6.1, the CYP2D6 genotype of subjects should be taken into account when estimating the severity of drug interactions involving TER.

  14. Transition to turbulence: 2D directed percolation

    NASA Astrophysics Data System (ADS)

    Chantry, Matthew; Tuckerman, Laurette; Barkley, Dwight

    2016-11-01

    The transition to turbulence in simple shear flows has been studied for well over a century, yet in the last few years has seen major leaps forward. In pipe flow, this transition shows the hallmarks of (1 + 1) D directed percolation, a universality class of continuous phase transitions. In spanwisely confined Taylor-Couette flow the same class is found, suggesting the phenomenon is generic to shear flows. However in plane Couette flow the largest simulations and experiments to-date find evidence for a discrete transition. Here we study a planar shear flow, called Waleffe flow, devoid of walls yet showing the fundamentals of planar transition to turbulence. Working with a quasi-2D yet Navier-Stokes derived model of this flow we are able to attack the (2 + 1) D transition problem. Going beyond the system sizes previously possible we find all of the required scalings of directed percolation and thus establish planar shears flow in this class.

  15. 2D quantum gravity from quantum entanglement.

    PubMed

    Gliozzi, F

    2011-01-21

    In quantum systems with many degrees of freedom the replica method is a useful tool to study the entanglement of arbitrary spatial regions. We apply it in a way that allows them to backreact. As a consequence, they become dynamical subsystems whose position, form, and extension are determined by their interaction with the whole system. We analyze, in particular, quantum spin chains described at criticality by a conformal field theory. Its coupling to the Gibbs' ensemble of all possible subsystems is relevant and drives the system into a new fixed point which is argued to be that of the 2D quantum gravity coupled to this system. Numerical experiments on the critical Ising model show that the new critical exponents agree with those predicted by the formula of Knizhnik, Polyakov, and Zamolodchikov.

  16. Simulation of Yeast Cooperation in 2D.

    PubMed

    Wang, M; Huang, Y; Wu, Z

    2016-03-01

    Evolution of cooperation has been an active research area in evolutionary biology in decades. An important type of cooperation is developed from group selection, when individuals form spatial groups to prevent them from foreign invasions. In this paper, we study the evolution of cooperation in a mixed population of cooperating and cheating yeast strains in 2D with the interactions among the yeast cells restricted to their small neighborhoods. We conduct a computer simulation based on a game theoretic model and show that cooperation is increased when the interactions are spatially restricted, whether the game is of a prisoner's dilemma, snow drifting, or mutual benefit type. We study the evolution of homogeneous groups of cooperators or cheaters and describe the conditions for them to sustain or expand in an opponent population. We show that under certain spatial restrictions, cooperator groups are able to sustain and expand as group sizes become large, while cheater groups fail to expand and keep them from collapse.

  17. 2D Electrostatic Actuation of Microshutter Arrays

    NASA Technical Reports Server (NTRS)

    Burns, Devin E.; Oh, Lance H.; Li, Mary J.; Jones, Justin S.; Kelly, Daniel P.; Zheng, Yun; Kutyrev, Alexander S.; Moseley, Samuel H.

    2015-01-01

    An electrostatically actuated microshutter array consisting of rotational microshutters (shutters that rotate about a torsion bar) were designed and fabricated through the use of models and experiments. Design iterations focused on minimizing the torsional stiffness of the microshutters, while maintaining their structural integrity. Mechanical and electromechanical test systems were constructed to measure the static and dynamic behavior of the microshutters. The torsional stiffness was reduced by a factor of four over initial designs without sacrificing durability. Analysis of the resonant behavior of the microshutter arrays demonstrates that the first resonant mode is a torsional mode occurring around 3000 Hz. At low vacuum pressures, this resonant mode can be used to significantly reduce the drive voltage necessary for actuation requiring as little as 25V. 2D electrostatic latching and addressing was demonstrated using both a resonant and pulsed addressing scheme.

  18. Graphene suspensions for 2D printing

    NASA Astrophysics Data System (ADS)

    Soots, R. A.; Yakimchuk, E. A.; Nebogatikova, N. A.; Kotin, I. A.; Antonova, I. V.

    2016-04-01

    It is shown that, by processing a graphite suspension in ethanol or water by ultrasound and centrifuging, it is possible to obtain particles with thicknesses within 1-6 nm and, in the most interesting cases, 1-1.5 nm. Analogous treatment of a graphite suspension in organic solvent yields eventually thicker particles (up to 6-10 nm thick) even upon long-term treatment. Using the proposed ink based on graphene and aqueous ethanol with ethylcellulose and terpineol additives for 2D printing, thin (~5 nm thick) films with sheet resistance upon annealing ~30 MΩ/□ were obtained. With the ink based on aqueous graphene suspension, the sheet resistance was ~5-12 kΩ/□ for 6- to 15-nm-thick layers with a carrier mobility of ~30-50 cm2/(V s).

  19. Canard configured aircraft with 2-D nozzle

    NASA Technical Reports Server (NTRS)

    Child, R. D.; Henderson, W. P.

    1978-01-01

    A closely-coupled canard fighter with vectorable two-dimensional nozzle was designed for enhanced transonic maneuvering. The HiMAT maneuver goal of a sustained 8g turn at a free-stream Mach number of 0.9 and 30,000 feet was the primary design consideration. The aerodynamic design process was initiated with a linear theory optimization minimizing the zero percent suction drag including jet effects and refined with three-dimensional nonlinear potential flow techniques. Allowances were made for mutual interference and viscous effects. The design process to arrive at the resultant configuration is described, and the design of a powered 2-D nozzle model to be tested in the LRC 16-foot Propulsion Wind Tunnel is shown.

  20. A novel point cloud registration using 2D image features

    NASA Astrophysics Data System (ADS)

    Lin, Chien-Chou; Tai, Yen-Chou; Lee, Jhong-Jin; Chen, Yong-Sheng

    2017-01-01

    Since a 3D scanner only captures a scene of a 3D object at a time, a 3D registration for multi-scene is the key issue of 3D modeling. This paper presents a novel and an efficient 3D registration method based on 2D local feature matching. The proposed method transforms the point clouds into 2D bearing angle images and then uses the 2D feature based matching method, SURF, to find matching pixel pairs between two images. The corresponding points of 3D point clouds can be obtained by those pixel pairs. Since the corresponding pairs are sorted by their distance between matching features, only the top half of the corresponding pairs are used to find the optimal rotation matrix by the least squares approximation. In this paper, the optimal rotation matrix is derived by orthogonal Procrustes method (SVD-based approach). Therefore, the 3D model of an object can be reconstructed by aligning those point clouds with the optimal transformation matrix. Experimental results show that the accuracy of the proposed method is close to the ICP, but the computation cost is reduced significantly. The performance is six times faster than the generalized-ICP algorithm. Furthermore, while the ICP requires high alignment similarity of two scenes, the proposed method is robust to a larger difference of viewing angle.

  1. Resolving 2D Amorphous Materials with Scanning Probe Microscopy

    NASA Astrophysics Data System (ADS)

    Burson, Kristen M.; Buechner, Christin; Lewandowski, Adrian; Heyde, Markus; Freund, Hans-Joachim

    Novel two-dimensional (2D) materials have garnered significant scientific interest due to their potential technological applications. Alongside the emphasis on crystalline materials, such as graphene and hexagonal BN, a new class of 2D amorphous materials must be pursued. For amorphous materials, a detailed understanding of the complex structure is necessary. Here we present a structural study of 2D bilayer silica on Ru(0001), an insulating material which is weakly coupled to the substrate. Atomic structure has been determined with a dual mode atomic force microscopy (AFM) and scanning tunneling microscopy (STM) sensor in ultra-high vacuum (UHV) at low temperatures, revealing a network of different ring sizes. Liquid AFM measurements with sub-nanometer resolution bridge the gap between clean UHV conditions and the environments that many material applications demand. Samples are grown and characterized in vacuum and subsequently transferred to the liquid AFM. Notably, the key structural features observed, namely nanoscale ring networks and larger holes to the substrate, show strong quantitative agreement between the liquid and UHV microscopy measurements. This provides direct evidence for the structural stability of these silica films for nanoelectronics and other applications. KMB acknowledges support from the Alexander von Humboldt Foundation.

  2. F-theory and 2d (0, 2) theories

    NASA Astrophysics Data System (ADS)

    Schäfer-Nameki, Sakura; Weigand, Timo

    2016-05-01

    F-theory compactified on singular, elliptically fibered Calabi-Yau five-folds gives rise to two-dimensional gauge theories preserving N = (0 , 2) supersymmetry. In this paper we initiate the study of such compactifications and determine the dictionary between the geometric data of the elliptic fibration and the 2d gauge theory such as the matter content in terms of (0 , 2) superfields and their supersymmetric couplings. We study this setup both from a gauge-theoretic point of view, in terms of the partially twisted 7-brane theory, and provide a global geometric description based on the structure of the elliptic fibration and its singularities. Global consistency conditions are determined and checked against the dual M-theory compactification to one dimension. This includes a discussion of gauge anomalies, the structure of the Green-Schwarz terms and the Chern-Simons couplings in the dual M-theory supersymmetric quantum mechanics. Furthermore, by interpreting the resulting 2d (0 , 2) theories as heterotic worldsheet theories, we propose a correspondence between the geometric data of elliptically fibered Calabi-Yau five-folds and the target space of a heterotic gauged linear sigma-model (GLSM). In particular the correspondence between the Landau-Ginsburg and sigma-model phase of a 2d (0 , 2) GLSM is realized via different T-branes or gluing data in F-theory.

  3. 2D depiction of nonbonding interactions for protein complexes.

    PubMed

    Zhou, Peng; Tian, Feifei; Shang, Zhicai

    2009-04-30

    A program called the 2D-GraLab is described for automatically generating schematic representation of nonbonding interactions across the protein binding interfaces. The input file of this program takes the standard PDB format, and the outputs are two-dimensional PostScript diagrams giving intuitive and informative description of the protein-protein interactions and their energetics properties, including hydrogen bond, salt bridge, van der Waals interaction, hydrophobic contact, pi-pi stacking, disulfide bond, desolvation effect, and loss of conformational entropy. To ensure these interaction information are determined accurately and reliably, methods and standalone programs employed in the 2D-GraLab are all widely used in the chemistry and biology community. The generated diagrams allow intuitive visualization of the interaction mode and binding specificity between two subunits in protein complexes, and by providing information on nonbonding energetics and geometric characteristics, the program offers the possibility of comparing different protein binding profiles in a detailed, objective, and quantitative manner. We expect that this 2D molecular graphics tool could be useful for the experimentalists and theoreticians interested in protein structure and protein engineering.

  4. Metrology for graphene and 2D materials

    NASA Astrophysics Data System (ADS)

    Pollard, Andrew J.

    2016-09-01

    The application of graphene, a one atom-thick honeycomb lattice of carbon atoms with superlative properties, such as electrical conductivity, thermal conductivity and strength, has already shown that it can be used to benefit metrology itself as a new quantum standard for resistance. However, there are many application areas where graphene and other 2D materials, such as molybdenum disulphide (MoS2) and hexagonal boron nitride (h-BN), may be disruptive, areas such as flexible electronics, nanocomposites, sensing and energy storage. Applying metrology to the area of graphene is now critical to enable the new, emerging global graphene commercial world and bridge the gap between academia and industry. Measurement capabilities and expertise in a wide range of scientific areas are required to address this challenge. The combined and complementary approach of varied characterisation methods for structural, chemical, electrical and other properties, will allow the real-world issues of commercialising graphene and other 2D materials to be addressed. Here, examples of metrology challenges that have been overcome through a multi-technique or new approach are discussed. Firstly, the structural characterisation of defects in both graphene and MoS2 via Raman spectroscopy is described, and how nanoscale mapping of vacancy defects in graphene is also possible using tip-enhanced Raman spectroscopy (TERS). Furthermore, the chemical characterisation and removal of polymer residue on chemical vapour deposition (CVD) grown graphene via secondary ion mass spectrometry (SIMS) is detailed, as well as the chemical characterisation of iron films used to grow large domain single-layer h-BN through CVD growth, revealing how contamination of the substrate itself plays a role in the resulting h-BN layer. In addition, the role of international standardisation in this area is described, outlining the current work ongoing in both the International Organization of Standardization (ISO) and the

  5. Fully automated 2D-3D registration and verification.

    PubMed

    Varnavas, Andreas; Carrell, Tom; Penney, Graeme

    2015-12-01

    Clinical application of 2D-3D registration technology often requires a significant amount of human interaction during initialisation and result verification. This is one of the main barriers to more widespread clinical use of this technology. We propose novel techniques for automated initial pose estimation of the 3D data and verification of the registration result, and show how these techniques can be combined to enable fully automated 2D-3D registration, particularly in the case of a vertebra based system. The initialisation method is based on preoperative computation of 2D templates over a wide range of 3D poses. These templates are used to apply the Generalised Hough Transform to the intraoperative 2D image and the sought 3D pose is selected with the combined use of the generated accumulator arrays and a Gradient Difference Similarity Measure. On the verification side, two algorithms are proposed: one using normalised features based on the similarity value and the other based on the pose agreement between multiple vertebra based registrations. The proposed methods are employed here for CT to fluoroscopy registration and are trained and tested with data from 31 clinical procedures with 417 low dose, i.e. low quality, high noise interventional fluoroscopy images. When similarity value based verification is used, the fully automated system achieves a 95.73% correct registration rate, whereas a no registration result is produced for the remaining 4.27% of cases (i.e. incorrect registration rate is 0%). The system also automatically detects input images outside its operating range.

  6. Off-on Fluorescent Sensor from On-off Sensor: Exploiting Silver Nanoparticles Influence on the Organic Fluorophore Fluorescence.

    PubMed

    Hariharan, P S; Sivasubramanian, Arvind; Anthony, Savarimuthu Philip

    2014-03-01

    Turn-off fluorescence of organic fluorophore, 2-{[4-(2H-Naphtho[1,2-d][1,2,3]triazol-2-yl)-phenyl]carboxylic acid (NTPC), with metal ions (Fe(3+), Cu(2+), Pb(2+)) was converted into turn-on fluorescent sensor for biologically important Zn(2+), Cu(2+) and Fe(3+) metal ions in aqueous solution at ppb level by exploiting strong fluorescence quenching phenomena of metal nanoparticles when organic fluorophores assembled in the vicinity of metallic surface. Amino acid attached phenolic ligands (L) were used as reducing as well as functional capping agents in the synthesis of silver nanoparticles (AgNPs). The hydrogen bonding functionality of L facilitated the assembling of NTPC in the vicinity of metallic surfaces that leads to complete quenching of NTPC fluorescence. The strong and selective coordination of L with metal ions (Zn(2+), Cu(2+) and Fe(3+)) separates the NTPC from the AgNPs surface that turn-on the NTPC fluorescence. HR-TEM and absorption studies confirm the metal coordination with L and separation of NTPC from the AgNPs surface. Mn(2+) showed selective red shifting of NTPC fluorescence after 12 h with all sample. Effects of different amino acid attached phenolic ligands were explored in the metal ion sensitivity and selectivity. This approach demonstrates the multifunctional utility of metal NPs in the development of turn-on fluorescence sensor for paramagnetic heavy metal ions in aqueous solution. ᅟ

  7. A novel hybrid motion detection algorithm based on 2D histogram

    NASA Astrophysics Data System (ADS)

    Su, Xiaomeng; Wang, Haiying

    2015-03-01

    This article proposes a novel hybrid motion detection algorithm based on 2-D (2-Dimensional) spatio-temporal states histogram. The new algorithm combines the idea of image change detection based on 2-D histogram and spatio-temporal entropy image segmentation. It quantifies the continuity of pixel state in time and space domain which are called TDF (Time Domain Filter) and SDF (Space Domain Filter) respectively. After this, put both channels of output data from TDF and SDF into a 2-D histogram. In the 2-D histogram, a curve division method helps to separate the foreground state points and the background ones more accurately. Innovatively, the new algorithm converts the video sequence to its histogram sequence, and transforms the difference of pixel's value in the video sequence into the difference of pixel's position in the 2-D histogram. Experimental results on different types of scenes added Gaussian noise shows that the proposed technique has strong ability of detecting moving objects.

  8. Extraction of tetracyclinic antibiotic residues from fish filet: comparison and optimization of different procedures using liquid chromatography with fluorescence detection.

    PubMed

    Orlando, Eduardo Adilson; Simionato, Ana Valéria C

    2013-09-13

    Anti-microbials have been used to control the quality of the aquatic environment for both prophylactic and therapeutic purposes. Tetracyclines are among the main antimicrobials used in aquaculture, and present a particular difficulty for extraction, due to a complex structure and high interaction with components of the biological matrix. In this study, different techniques of extraction and clean-up of antimicrobials of the tetracycline class in tilapia filets have been optimized and compared, followed by validation of the methodology using the best procedure. Oxytetracycline, doxycycline, tetracycline and chlortetracycline were analyzed by HPLC-fluorescence under the following conditions: organic mobile phase composed of methanol:acetonitrile (1:1, v/v) and aqueous mobile phase containing sodium acetate (0.0375molL(-1)), calcium chloride (0.0175molL(-1)) and EDTA (0.0125molL(-1)) at pH 7.00. The chromatographic analysis was performed using a mobile phase gradient with a flow rate of 1mLmin(-1) and detection wavelength of 385/528nm (λexc/λem). Four extraction methods have been evaluated, namely: liquid-liquid partition; solid phase extraction (SPE) using phenyl, C18 and polymeric Oasis-HLB stationary phases; dispersive SPE (dSPE) using polymeric adsorbent XAD 16 resin; and QuEChERS. The methods have been optimized with fractional factorial experimental design and compared by the extraction efficiency. The liquid-liquid extraction and the QuEChERS methods showed low extraction efficiencies (14-30%) for the analytes. The use of dSPE showed good efficiency (40-60%), but with low precision and high consumption of time. Among the evaluated extraction techniques the use of SPE showed the best results, with emphasis on the phenyl phase (58-76%), and has been validated for analysis of residues of tetracyclines in tilapia muscle regarding selectivity, linearity, precision and limits of detection and quantification. The validated method was adequate for the investigation

  9. Detection of aneuploid human sperm by fluorescence in situ hybridization: Evidence for a donor difference in frequency of sperm disomic for chromosomes 1 and Y

    SciTech Connect

    Robbins, W.A. Lawrence Livermore National Lab., CA ); Segraves, R.; Pinkel, D. ); Wyrobek, A.J. )

    1993-04-01

    Fluorescence in situ hybridization with repetitive-sequence DNA probes was used to detect human sperm disomic for chromosomes 1 and Y in three healthy men. Data on these same men had been obtained previously, using the human-sperm/hamster-egg cytogenetic technique, providing a cytogenetic reference for validating sperm hybridization measurements. Air-dried smears were prepared from semen samples and treated with DTT and lithium diiodosalicylate to expand sperm chromatin. Hybridization with fluorescently tagged DNA probes for chromosomes 1 (pUC177) or Y (pY3.4) yielded average frequencies of sperm with two fluorescent domains of 14.2[+-]2.4/10,000 and 5.6[+-]1.6/10,000 sperm, respectively. These frequencies did not differ statistically from frequencies of hyperploidy observed for these chromosomes with the hamster technique. In addition, frequencies of disomic sperm from one donor were elevated [approximately]2.5-fold above those of other donors, for both chromosomes 1 (P = .045) and Y (P = .01), consistent with a trend found with the hamster technique. The authors conclude that fluorescence in situ hybridization to sperm chromosomes provides a valid and promising measure of the frequency of disomic human sperm. 43 refs., 1 fig., 4 tabs.

  10. 2D-Visualization of metabolic activity with planar optical chemical sensors (optodes)

    NASA Astrophysics Data System (ADS)

    Meier, R. J.; Liebsch, G.

    2015-12-01

    Microbia plays an outstandingly important role in many hydrologic compartments, such as e.g. the benthic community in sediments, or biologically active microorganisms in the capillary fringe, in ground water, or soil. Oxygen, pH, and CO2 are key factors and indicators for microbial activity. They can be measured using optical chemical sensors. These sensors record changing fluorescence properties of specific indicator dyes. The signals can be measured in a non-contact mode, even through transparent walls, which is important for many lab-experiments. They can measure in closed (transparent) systems, without sampling or intruding into the sample. They do not consume the analytes while measuring, are fully reversible and able to measure in non-stirred solutions. These sensors can be applied as high precision fiberoptic sensors (for profiling), robust sensor spots, or as planar sensors for 2D visualization (imaging). Imaging enables to detect thousands of measurement spots at the same time and generate 2D analyte maps over a region of interest. It allows for comparing different regions within one recorded image, visualizing spatial analyte gradients, or more important to identify hot spots of metabolic activity. We present ready-to-use portable imaging systems for the analytes oxygen, pH, and CO2. They consist of a detector unit, planar sensor foils and a software for easy data recording and evaluation. Sensors foils for various analytes and measurement ranges enable visualizing metabolic activity or analyte changes in the desired range. Dynamics of metabolic activity can be detected in one shot or over long time periods. We demonstrate the potential of this analytical technique by presenting experiments on benthic disturbance-recovery dynamics in sediments and microbial degradation of organic material in the capillary fringe. We think this technique is a new tool to further understand how microbial and geochemical processes are linked in (not solely) hydrologic

  11. Design and characterization of low-loss 2D grating couplers for silicon photonics integrated circuits

    NASA Astrophysics Data System (ADS)

    Lacava, C.; Carrol, L.; Bozzola, A.; Marchetti, R.; Minzioni, P.; Cristiani, I.; Fournier, M.; Bernabe, S.; Gerace, D.; Andreani, L. C.

    2016-03-01

    We present the characterization of Silicon-on-insulator (SOI) photonic-crystal based 2D grating-couplers (2D-GCs) fabricated by CEA-Leti in the frame of the FP7 Fabulous project, which is dedicated to the realization of devices and systems for low-cost and high-performance passives-optical-networks. On the analyzed samples different test structures are present, including 2D-GC connected to another 2D-GC by different waveguides (in a Mach-Zehnder like configuration), and 2D-GC connected to two separate 2D-GCs, so as to allow a complete assessment of different parameters. Measurements were carried out using a tunable laser source operating in the extended telecom bandwidth and a fiber-based polarization controlling system at the input of device-under-test. The measured data yielded an overall fiber-to-fiber loss of 7.5 dB for the structure composed by an input 2D-GC connected to two identical 2D-GCs. This value was obtained at the peak wavelength of the grating, and the 3-dB bandwidth of the 2D-GC was assessed to be 43 nm. Assuming that the waveguide losses are negligible, so as to make a worst-case analysis, the coupling efficiency of the single 2D-GC results to be equal to -3.75 dB, constituting, to the best of our knowledge, the lowest value ever reported for a fully CMOS compatible 2D-GC. It is worth noting that both the obtained values are in good agreement with those expected by the numerical simulations performed using full 3D analysis by Lumerical FDTD-solutions.

  12. Graphene-like 2D nanomaterial-based biointerfaces for biosensing applications.

    PubMed

    Zhu, Chengzhou; Du, Dan; Lin, Yuehe

    2017-03-15

    Due to their unique structures and multifunctionalities, two-dimensional (2D) nanomaterials have aroused increasing interest in the construction of the novel biointerfaces for biosensing applications. Efforts in constructing novel biointerfaces led to exploit the more versatile and tunable graphene-like 2D nanomaterials (e.g. graphitic carbon nitride, boron nitride, transition metal dichalcogenides, and transition metal oxides) with various structural and compositional characteristics. This review highlights recent efforts in the design of graphene-like 2D nanomaterials and their derived biointerfaces and exploitation of their research on fluorescent sensors and a series of electrochemical sensors, including amperometric, electrochemiluminescence, photoelectrochemical and field-effect transistor sensors. Finally, we discuss some critical challenges and future perspectives in this field.

  13. 2D light scattering label-free cytometry using light-sheet illumination

    NASA Astrophysics Data System (ADS)

    Lin, Meiai; Su, Xuantao

    2016-10-01

    Two-dimensional (2D) light scattering cytometry has been demonstrated as an effective label-free technology for cell analysis. Here we develop the light-sheet illumination in 2D light scattering static cytometry. In our cytometer, a cylindrical lens is used to form the light-sheet for better excitation of the static cells under an inverted microscope. The thickness of the light-sheet measured in fluorescent solution is about 13 μm. Two-dimensional light scattering patterns of standard microspheres and yeast cells are obtained by using a complementary metal oxide semiconductor (CMOS) detector via a low numerical aperture (NA 0.4) optical objective. The experimental patterns characterized with fringe structures agree well with Mie theory simulated ones. Our results suggest that the light-sheet illumination is an effective excitation method for 2D light scattering label-free cytometry.

  14. Development of wide-angle 2D light scattering static cytometry

    NASA Astrophysics Data System (ADS)

    Xie, Linyan; Liu, Qiao; Shao, Changshun; Su, Xuantao

    2016-10-01

    We have recently developed a 2D light scattering static cytometer for cellular analysis in a label-free manner, which measures side scatter (SSC) light in the polar angular range from 79 to 101 degrees. Compared with conventional flow cytometry, our cytometric technique requires no fluorescent labeling of the cells, and static cytometry measurements can be performed without flow control. In this paper we present an improved label-free static cytometer that can obtain 2D light scattering patterns in a wider angular range. By illuminating the static microspheres on chip with a scanning optical fiber, wide-angle 2D light scattering patterns of single standard microspheres with a mean diameter of 3.87 μm are obtained. The 2D patterns of 3.87 μm microspheres contain both large-angle forward scatter (FSC) and SSC light in the polar angular range from 40 to 100 degrees, approximately. Experimental 2D patterns of 3.87 μm microspheres are in good agreement with Mie theory simulated ones. The wide-angle light scattering measurements may provide a better resolution for particle analysis as compared with the SSC measurements. Two dimensional light scattering patterns of HL-60 human acute leukemia cells are obtained by using our static cytometer. Compared with SSC 2D light scattering patterns, wide-angle 2D patterns contain richer information of the HL-60 cells. The obtaining of 2D light scattering patterns in a wide angular range could help to enhance the capabilities of our label-free static cytometry for cell analysis.

  15. Differential patterns of 2D location versus depth decoding along the visual hierarchy.

    PubMed

    Finlayson, Nonie J; Zhang, Xiaoli; Golomb, Julie D

    2017-02-15

    Visual information is initially represented as 2D images on the retina, but our brains are able to transform this input to perceive our rich 3D environment. While many studies have explored 2D spatial representations or depth perception in isolation, it remains unknown if or how these processes interact in human visual cortex. Here we used functional MRI and multi-voxel pattern analysis to investigate the relationship between 2D location and position-in-depth information. We stimulated different 3D locations in a blocked design: each location was defined by horizontal, vertical, and depth position. Participants remained fixated at the center of the screen while passively viewing the peripheral stimuli with red/green anaglyph glasses. Our results revealed a widespread, systematic transition throughout visual cortex. As expected, 2D location information (horizontal and vertical) could be strongly decoded in early visual areas, with reduced decoding higher along the visual hierarchy, consistent with known changes in receptive field sizes. Critically, we found that the decoding of position-in-depth information tracked inversely with the 2D location pattern, with the magnitude of depth decoding gradually increasing from intermediate to higher visual and category regions. Representations of 2D location information became increasingly location-tolerant in later areas, where depth information was also tolerant to changes in 2D location. We propose that spatial representations gradually transition from 2D-dominant to balanced 3D (2D and depth) along the visual hierarchy.

  16. Screening and transport in 2D semiconductor systems at low temperatures.

    PubMed

    Das Sarma, S; Hwang, E H

    2015-11-17

    Low temperature carrier transport properties in 2D semiconductor systems can be theoretically well-understood within RPA-Boltzmann theory as being limited by scattering from screened Coulomb disorder arising from random quenched charged impurities in the environment. In this work, we derive a number of analytical formula, supported by realistic numerical calculations, for the relevant density, mobility, and temperature range where 2D transport should manifest strong intrinsic (i.e., arising purely from electronic effects) metallic temperature dependence in different semiconductor materials arising entirely from the 2D screening properties, thus providing an explanation for why the strong temperature dependence of the 2D resistivity can only be observed in high-quality and low-disorder 2D samples and also why some high-quality 2D materials manifest much weaker metallicity than other materials. We also discuss effects of interaction and disorder on the 2D screening properties in this context as well as compare 2D and 3D screening functions to comment why such a strong intrinsic temperature dependence arising from screening cannot occur in 3D metallic carrier transport. Experimentally verifiable predictions are made about the quantitative magnitude of the maximum possible low-temperature metallicity in 2D systems and the scaling behavior of the temperature scale controlling the quantum to classical crossover.

  17. The Relationship Between Digit Ratio (2D:4D) and Sexual Orientation in Men from China.

    PubMed

    Xu, Yin; Zheng, Yong

    2016-04-01

    We examined the relationship between 2D:4D digit ratio and sexual orientation in men from China and analyzed the influences of the components used to assess sexual orientation and the criteria used to classify individuals as homosexual on this relationship. A total of 309 male and 110 female participants took part in a web-based survey. Our results showed that heterosexual men had a significantly lower 2D:4D than heterosexual women and exclusively homosexual men had a significantly higher left 2D:4D than heterosexual men whereas only exclusively homosexual men had a significantly higher right 2D:4D than heterosexual men when sexual orientation was assessed via sexual attraction. The left 2D:4D showed a significant positive correlation with sexual identity, sexual attraction, and sexual behavior, and the right 2D:4D showed a significant positive correlation with sexual attraction. The effect sizes for differences in 2D:4D between homosexual and heterosexual men varied according to criteria used to classify individuals as homosexual and sexual orientation components; the more stringent the criteria (scores closer to the homosexual category), the larger the effect sizes; further, sexual attraction yielded the largest effect size. There were no significant effects of age and latitude on Chinese 2D:4D. This study contributes to the current understanding of the relationship between 2D:4D and male sexual orientation.

  18. Screening and transport in 2D semiconductor systems at low temperatures

    PubMed Central

    Das Sarma, S.; Hwang, E. H.

    2015-01-01

    Low temperature carrier transport properties in 2D semiconductor systems can be theoretically well-understood within RPA-Boltzmann theory as being limited by scattering from screened Coulomb disorder arising from random quenched charged impurities in the environment. In this work, we derive a number of analytical formula, supported by realistic numerical calculations, for the relevant density, mobility, and temperature range where 2D transport should manifest strong intrinsic (i.e., arising purely from electronic effects) metallic temperature dependence in different semiconductor materials arising entirely from the 2D screening properties, thus providing an explanation for why the strong temperature dependence of the 2D resistivity can only be observed in high-quality and low-disorder 2D samples and also why some high-quality 2D materials manifest much weaker metallicity than other materials. We also discuss effects of interaction and disorder on the 2D screening properties in this context as well as compare 2D and 3D screening functions to comment why such a strong intrinsic temperature dependence arising from screening cannot occur in 3D metallic carrier transport. Experimentally verifiable predictions are made about the quantitative magnitude of the maximum possible low-temperature metallicity in 2D systems and the scaling behavior of the temperature scale controlling the quantum to classical crossover. PMID:26572738

  19. The effects of aging on haptic 2D shape recognition.

    PubMed

    Overvliet, Krista E; Wagemans, J; Krampe, Ralf T

    2013-12-01

    We use the image-mediation model (Klatzky & Lederman, 1987) as a framework to investigate potential sources of adult age differences in the haptic recognition of two-dimensional (2D) shapes. This model states that the low-resolution, temporally sequential, haptic input is translated into a visual image, which is then reperceived through the visual processors, before it is matched against a long-term memory representation and named. In three experiments we tested groups of 12 older (mean age 73.11) and three groups of 12 young adults (mean age 22.80) each. In Experiment 1 we confirm age-related differences in haptic 2D shape recognition, and we show the typical age × complexity interaction. In Experiment 2 we show that if we facilitate the visual translation process, age differences become smaller, but only with simple shapes and not with the more complex everyday objects. In Experiment 3 we target the last step in the model (matching and naming) for complex stimuli. We found that age differences in exploration time were considerably reduced when this component process was facilitated by providing a category name. We conclude that the image-mediation model can explain adult-age differences in haptic recognition, particularly if the role of working memory in forming the transient visual image is considered. Our findings suggest that sensorimotor skills thought to rely on peripheral processes for the most part are critically constrained by age-related changes in central processing capacity in later adulthood.

  20. Red/blue spectral shifts of laser-induced fluorescence emission due to different nanoparticle suspensions in various dye solutions.

    PubMed

    Bavali, A; Parvin, P; Mortazavi, S Z; Mohammadian, M; Mousavi Pour, M R

    2014-08-20

    Red/blue shifts of laser-induced fluorescence (LIF) are investigated using several guest dielectric nanoscatterers, such as TiO2, ZnO, Al2O3, and SiO2, in the host Rd6G, RdB, Coumarin 4, and Coumarin 7 ethanolic solutions. A couple of inflection points are identified varying nanoparticle (NP) density into dye solutions based on LIF spectroscopy. The inflection of the spectral shift exhibits that the suspension of NPs in dye solutions significantly involves a couple of competitive chemical and optical mechanisms during photon traveling in scattering media regarding ballistic and diffusive transport. It is shown that the low, medium, and high NP additives in fluorescent suspension induce blue, red, and blue spectral shifts, respectively.

  1. Assembly of 3D coordination polymers from 2D sheets by [2+2] cycloaddition reaction.

    PubMed

    Medishetty, Raghavender; Tandiana, Rika; Koh, Lip Lin; Vittal, Jagadese J

    2014-01-27

    The synthesis of three 2D interdigitated Zn(II) coordination polymers (CPs), by using three monotopic ligands containing C=C bonds, is reported. Among these, two CPs with 4spy (4-styryl pyridine) and 2F-4spy (a 2'-fluoro derivative of 4spy) ligands showed quantitative formation of cyclobutane rings, thus demonstrating a unique synthetic procedure to synthesize metal-organic frameworks (MOFs) by using this photochemical reaction. Interestingly, these compounds can also be synthesized by mechanochemical grinding procedures by using Zn(OAc)2. In contrast, Zn(NO3)2 did not yield the required product, unlike in the solution route. In addition, compounds with 4vpy (4-vinylpyridine), 4spy and 2F-4spy ligands created different units in the CPs; 4vpy and 2F-4spy furnished paddle wheel units, whereas 4spy yielded tetrahedral Zn(II) repeating units. Furthermore, the change in coordination geometry manifests in the photoluminescence properties, attributed to the difference in charge-transfer and ligand-centered fluorescent phenomenon.

  2. Different visible colors and green fluorescence were obtained from the mutated purple chromoprotein isolated from sea anemone.

    PubMed

    Chiang, Cheng-Yi; Chen, Yi-Lin; Tsai, Huai-Jen

    2014-08-01

    Green fluorescent protein (GFP)-like proteins have been studied with the aim of developing fluorescent proteins. Since the property of color variation is understudied, we isolated a novel GFP-like chromoprotein from the carpet anemone Stichodactyla haddoni, termed shCP. Its maximum absorption wavelength peak (λ(max)) is located at 574 nm, resulting in a purple color. The shCP protein consists of 227 amino acids (aa), sharing 96 % identity with the GFP-like chromoprotein of Heteractis crispa. We mutated aa residues to examine any alteration in color. When E63, the first aa of the chromophore, was replaced by serine (E63S), the λ(max) of the mutated protein shCP-E63S was shifted to 560 nm and exhibited a pink color. When Q39, T194, and I196, which reside in the surrounding 5 Å of the chromophore's microenvironment, were mutated, we found that (1) the λ(max) of the mutated protein shCP-Q39S was shifted to 518 nm and exhibited a red color, (2) shCP-T194I exhibited a purple-blue color, and (3) an additional mutation at I196H of the mutated protein shCP-E63L exhibited green fluorescence. In contrast, when the aa located neither at the chromophore nor within its microenvironment were mutated, the resultant proteins shCP-L122H, -E138G, -S137D, -T95I, -D129N, -T194V, -E138Q, -G75E, -I183V, and -I70V never altered their purple color, suggesting that mutations at the shCP chromophore and the surrounding 5 Å microenvironment mostly control changes in color expression or cause fluorescence to develop. Additionally, we found that the cDNAs of shCP and its mutated varieties are faithfully and stably expressed both in Escherichia coli and zebrafish embryos.

  3. Impact of CYP2D6 polymorphisms on clinical efficacy and tolerability of metoprolol tartrate.

    PubMed

    Hamadeh, I S; Langaee, T Y; Dwivedi, R; Garcia, S; Burkley, B M; Skaar, T C; Chapman, A B; Gums, J G; Turner, S T; Gong, Y; Cooper-DeHoff, R M; Johnson, J A

    2014-08-01

    Metoprolol is a selective β-1 adrenergic receptor blocker that undergoes extensive metabolism by the polymorphic enzyme cytochrome P450 2D6 (CYP2D6). Our objective was to investigate the influence of CYP2D6 polymorphisms on the efficacy and tolerability of metoprolol tartrate. Two hundred and eighty-one participants with uncomplicated hypertension received 50 mg of metoprolol twice daily followed by response-guided titration to 100 mg twice daily. Phenotypes were assigned based on results of CYP2D6 genotyping and copy number variation assays. Clinical response to metoprolol and adverse effect rates were analyzed in relation to CYP2D6 phenotypes using appropriate statistical tests. Heart rate response differed significantly by CYP2D6 phenotype (P < 0.0001), with poor and intermediate metabolizers showing greater reduction. However, blood pressure response and adverse effect rates were not significantly different by CYP2D6 phenotype. Other than a significant difference in heart rate response, CYP2D6 polymorphisms were not determinants of variability in metoprolol response or tolerability.

  4. Solution conformation of 2-aminopurine dinucleotide determined by ultraviolet two-dimensional fluorescence spectroscopy

    NASA Astrophysics Data System (ADS)

    Widom, Julia R.; Johnson, Neil P.; von Hippel, Peter H.; Marcus, Andrew H.

    2013-02-01

    We have observed the conformation-dependent electronic coupling between the monomeric subunits of a dinucleotide of 2-aminopurine (2-AP), a fluorescent analogue of the nucleic acid base adenine. This was accomplished by extending two-dimensional fluorescence spectroscopy (2D FS)—a fluorescence-detected variation of 2D electronic spectroscopy—to excite molecular transitions in the ultraviolet (UV) regime. A collinear sequence of four ultrafast laser pulses centered at 323 nm was used to resonantly excite the coupled transitions of 2-AP dinucleotide. The phases of the optical pulses were continuously swept at kilohertz frequencies, and the ensuing nonlinear fluorescence was phase-synchronously detected at 370 nm. Upon optimization of a point-dipole coupling model to our data, we found that in aqueous buffer the 2-AP dinucleotide adopts an average conformation in which the purine bases are non-helically stacked (center-to-center distance R12 = 3.5 ± 0.5 Å , twist angle θ12 = 5° ± 5° ), which differs from the conformation of such adjacent bases in duplex DNA. These experiments establish UV-2D FS as a method for examining the local conformations of an adjacent pair of fluorescent nucleotides substituted into specific DNA or RNA constructs, which will serve as a powerful probe to interpret, in structural terms, biologically significant local conformational changes within the nucleic acid framework of protein-nucleic acid complexes.

  5. [Three-dimensional Fluorescence Spectral Characteristics of Different Molecular Weight Fractionations of Dissolved Organic Matter in the Water-level Fluctuation Zones of Three Gorges Reservoir Areas].

    PubMed

    Chen, Xue-shuang; Jiang, Tao; Lu, Song; Wei, Shi-qiang; Wang, Ding-yong; Yan, Jin-long

    2016-03-15

    The study of the molecular weight (MW) fractions of dissolved organic matter (DOM) in aquatic environment is of interests because the size plays an important role in deciding the biogeochemical characteristics of DOM. Thus, using ultrafiltration ( UF) technique combined with three-dimensional fluorescence spectroscopy, DOM samples from four sampling sites in typical water-level fluctuation zones of Three Gorge Reservoir areas were selected to investigate the differences of properties and sources of different DOM MW fractions. The results showed that in these areas, the distribution of MW fractions was highly dispersive, but the approximately equal contributions from colloidal (Mr 1 x 10³-0.22 µm) and true dissolved fraction (Mr < 1 x 10³) to the total DOC concentration were found. Four fluorescence signals (humic-like A and C; protein-like B and T) were observed in all MW fractions including bulk DOM, which showed the same distribution trend: true dissolved > low MW (Mr 1 x 10³-10 x 10³) > medium MW (Mr 10 x 10³-30 x 10³) > high MW (Mr 30 x 10³-0.22 µm). Additionally, with decreasing MW fraction, fluorescence index (FI) and freshness index (BIX) increased suggesting enhanced signals of autochthonous inputs, whereas humification index ( HIX) decreased indicating lowe humification degree. It strongly suggested that terrestrial input mainly affected the composition and property of higher MW fractions of DOM, as compared to lower MW and true dissolved fractions that were controlled by autochthonous sources such as microbial and alga activities, instead of allochthonous sources. Meanwhile, the riparian different land-use types also affected obviously on the characteristics of DOM. Therefore, higher diversity of land-use types, and also higher complexity of ecosystem and landscapes, induced higher heterogeneity of fluorescence components in different MW fraction of DOM.

  6. High resolution fluorescence microscopy evidence on the transport of immunoglobulins. Differences between mammalian IgG, F(ab')2 and avian IgY.

    PubMed

    Sevcik, Carlos; Salazar, Víctor; Díaz, Patricia; D'Suze, Gina; Vázquez, Hilda

    2013-03-01

    We describe the subcellular localization of horse F(ab')(2) and IgG, and ostrich IgY labeled with fluorescein isothiocyanate (FITC) administered IV to mice. We used wide field high sensitivity fluorescence microscopy deblurred by 3-dimensional blind deconvolution of kidney, liver, lungs and brain sections. Sections were obtained from mice sacrificed 15 min, 1 or 5 h after receiving FITC-immunoproteins, counter-stained with DAPI (4',6'-diamidino-2-phenylindole) and Evans blue. FITC-IgG and its fractions are rapidly taken up and extravasated by vascular endothelium. FITC-IgG and FITC-F(ab')(2) appear to be quickly secreted by glomeruli endothelium and to be reabsorbed along all nephron segments. FITC-IgG and FITC-F(ab')(2) appeared 15 min after IV injection within bronchial, alveolar and bile duct epithelium. Hepatocytes were loaded with fluorescence after 15 min of administration. Fluorescence was absent from brain slices, except for the endothelium of some vessels in brain ventricles which appeared intensely fluorescent. Fluorescence appeared in intracellular vesicles which conferred the tissues a glowing foamy aspect for up to 5 h after inoculation. Arterial elastic layers were intensely green after horse FITC-Ig inoculation. Ostrich FITC-IgY behaved completely differently to horse Ig's; only 1 h after injection it was possible to observe small brightly green scarce vesicles in vascular endothelium of arteries, interstitial kidney capillaries between nephron tubules and were also scarce in glomeruli endothelium; FITC-IgY appeared only in hepatic sinusoids in the liver. No IgY was seen in bronchial and alveolar endothelium, in bile ducts or in hepatocytes.

  7. 2D and 3D Chromosome Painting in Malaria Mosquitoes

    PubMed Central

    George, Phillip; Sharma, Atashi; Sharakhov, Igor V

    2014-01-01

    Fluorescent in situ hybridization (FISH) of whole arm chromosome probes is a robust technique for mapping genomic regions of interest, detecting chromosomal rearrangements, and studying three-dimensional (3D) organization of chromosomes in the cell nucleus. The advent of laser capture microdissection (LCM) and whole genome amplification (WGA) allows obtaining large quantities of DNA from single cells. The increased sensitivity of WGA kits prompted us to develop chromosome paints and to use them for exploring chromosome organization and evolution in non-model organisms. Here, we present a simple method for isolating and amplifying the euchromatic segments of single polytene chromosome arms from ovarian nurse cells of the African malaria mosquito Anopheles gambiae. This procedure provides an efficient platform for obtaining chromosome paints, while reducing the overall risk of introducing foreign DNA to the sample. The use of WGA allows for several rounds of re-amplification, resulting in high quantities of DNA that can be utilized for multiple experiments, including 2D and 3D FISH. We demonstrated that the developed chromosome paints can be successfully used to establish the correspondence between euchromatic portions of polytene and mitotic chromosome arms in An. gambiae. Overall, the union of LCM and single-chromosome WGA provides an efficient tool for creating significant amounts of target DNA for future cytogenetic and genomic studies. PMID:24429496

  8. Repression of multiple CYP2D genes in mouse primary hepatocytes with a single siRNA construct.

    PubMed

    Elraghy, Omaima; Baldwin, William S

    2015-01-01

    The Cyp2d subfamily is the second most abun-dant subfamily of hepatic drug-metabolizing CYPs. In mice, there are nine Cyp2d members that are believed to have redundant catalytic activity. We are testing and optimizing the ability of one short interfering RNA (siRNA) construct to knockdown the expression of multiple mouse Cyp2ds in primary hepatocytes. Expression of Cyp2d10, Cyp2d11, Cyp2d22, and Cyp2d26 was observed in the primary male mouse hepatocytes. Cyp2d9, which is male-specific and growth hormone-dependent, was not expressed in male primary hepatocytes, potentially because of its dependence on pulsatile growth hormone release from the anterior pituitary. Several different siRNAs at different concentrations and with different reagents were used to knockdown Cyp2d expression. siRNA constructs designed to repress only one construct often mildly repressed several Cyp2d isoforms. A construct designed to knockdown every Cyp2d isoform provided the best results, especially when incubated with transfection reagents designed specifically for primary cell culture. Interestingly, a construct designed to knockdown all Cyp2d isoforms, except Cyp2d10, caused a 2.5× increase in Cyp2d10 expression, presumably because of a compensatory response. However, while RNA expression is repressed 24 h after siRNA treatment, associated changes in Cyp2d-mediated metabolism are tenuous. Overall, this study provides data on the expression of murine Cyp2ds in primary cell lines, valuable information on designing siRNAs for silencing multiple murine CYPs, and potential pros and cons of using siRNA as a tool for repressing Cyp2d and estimating Cyp2d's role in murine xenobiotic metabolism.

  9. SEM signal emulation for 2D patterns

    NASA Astrophysics Data System (ADS)

    Sukhov, Evgenii; Muelders, Thomas; Klostermann, Ulrich; Gao, Weimin; Braylovska, Mariya

    2016-03-01

    The application of accurate and predictive physical resist simulation is seen as one important use model for fast and efficient exploration of new patterning technology options, especially if fully qualified OPC models are not yet available at an early pre-production stage. The methodology of using a top-down CD-SEM metrology to extract the 3D resist profile information, such as the critical dimension (CD) at various resist heights, has to be associated with a series of presumptions which may introduce such small, but systematic CD errors. Ideally, the metrology effects should be carefully minimized during measurement process, or if possible be taken into account through proper metrology modeling. In this paper we discuss the application of a fast SEM signal emulation describing the SEM image formation. The algorithm is applied to simulated resist 3D profiles and produces emulated SEM image results for 1D and 2D patterns. It allows estimating resist simulation quality by comparing CDs which were extracted from the emulated and from the measured SEM images. Moreover, SEM emulation is applied for resist model calibration to capture subtle error signatures through dose and defocus. Finally, it should be noted that our SEM emulation methodology is based on the approximation of physical phenomena which are taking place in real SEM image formation. This approximation allows achieving better speed performance compared to a fully physical model.

  10. Radiofrequency Spectroscopy and Thermodynamics of Fermi Gases in the 2D to Quasi-2D Dimensional Crossover

    NASA Astrophysics Data System (ADS)

    Cheng, Chingyun; Kangara, Jayampathi; Arakelyan, Ilya; Thomas, John

    2016-05-01

    We tune the dimensionality of a strongly interacting degenerate 6 Li Fermi gas from 2D to quasi-2D, by adjusting the radial confinement of pancake-shaped clouds to control the radial chemical potential. In the 2D regime with weak radial confinement, the measured pair binding energies are in agreement with 2D-BCS mean field theory, which predicts dimer pairing energies in the many-body regime. In the qausi-2D regime obtained with increased radial confinement, the measured pairing energy deviates significantly from 2D-BCS theory. In contrast to the pairing energy, the measured radii of the cloud profiles are not fit by 2D-BCS theory in either the 2D or quasi-2D regimes, but are fit in both regimes by a beyond mean field polaron-model of the free energy. Supported by DOE, ARO, NSF, and AFOSR.

  11. Surface Tension Components Based Selection of Cosolvents for Efficient Liquid Phase Exfoliation of 2D Materials.

    PubMed

    Shen, Jianfeng; Wu, Jingjie; Wang, Man; Dong, Pei; Xu, Jingxuan; Li, Xiaoguang; Zhang, Xiang; Yuan, Junhua; Wang, Xifan; Ye, Mingxin; Vajtai, Robert; Lou, Jun; Ajayan, Pulickel M

    2016-05-01

    A proper design of direct liquid phase exfoliation (LPE) for 2D materials as graphene, MoS2 , WS2 , h-BN, Bi2 Se3 , MoSe2 , SnS2 , and TaS2 with common cosolvents is carried out based on considering the polar and dispersive components of surface tensions of various cosolvents and 2D materials. It has been found that the exfoliation efficiency is enhanced by matching the ratio of surface tension components of cosolvents to that of the targeted 2D materials, based on which common cosolvents composed of IPA/water, THF/water, and acetone/water can be designed for sufficient LPE process. In this context, the library of low-toxic and low-cost solvents with low boiling points for LPE is infinitely enlarged when extending to common cosolvents. Polymer-based composites reinforced with a series of different 2D materials are compared with each other. It is demonstrated that the incorporation of cosolvents-exfoliated 2D materials can substantially improve the mechanical and thermal properties of polymer matrices. Typically, with the addition of 0.5 wt% of such 2D material as MoS2 nanosheets, the tensile strength and Young's modulus increased up to 74.85% and 136.97%, respectively. The different enhancement effect of 2D materials is corresponded to the intrinsic properties and LPE capacity of 2D materials.

  12. Local conformations and excited state dynamics of porphyrins and nucleic acids by 2-dimensional fluorescence spectroscopy

    NASA Astrophysics Data System (ADS)

    Widom, Julia R.

    Biological systems present many challenges to researchers attempting to study them using spectroscopy. Low specificity, low sensitivity, and broad and overlapping lineshapes limit the amount of information that can be obtained in experiments. Two-dimensional fluorescence spectroscopy (2D FS) is a highly sensitive and information-rich spectroscopic technique that was developed to study the conformations and excited state dynamics of systems exhibiting exciton coupling. In this dissertation, I describe a variety of extensions of 2D FS that further increase its utility for the study of biological systems. I describe experiments on a dimer of zinc tetraphenylporphyrin embedded in a membrane, in which the signals from two conformational subpopulations were separated in order to study the thermodynamics of their interconversion. I present proof-of-principle experiments on nucleic acids that utilize fluorescence resonance energy transfer to separate signals from different subpopulations. I also describe experiments in which 2D FS was performed using ultraviolet excitation to determine the conformation of a dinucleotide of a fluorescent analogue of the nucleic acid base adenine. I discuss experiments on porphyrin dimers in which 2D FS was used as a probe of excited state dynamics. Finally, I present model calculations for a proposed variation of 2D FS in which entangled photons would be used as the excitation source. These calculations suggest that this approach has the potential to yield significantly narrower spectral lineshapes than conventional 2D FS. These experiments and calculations yield new insight into the systems investigated and establish a `toolbox' of variations of 2D FS that can be used to gain as much information as possible from experiments on challenging systems such as protein-DNA complexes.

  13. Further insights into metal-DOM interaction: consideration of both fluorescent and non-fluorescent substances.

    PubMed

    Xu, Huacheng; Zhong, Jicheng; Yu, Guanghui; Wu, Jun; Jiang, Helong; Yang, Liuyan

    2014-01-01

    Information on metal binding with fluorescent substances has been widely studied. By contrast, information on metal binding with non-fluorescent substances remains lacking despite the dominance of these substances in aquatic systems. In this study, the metal binding properties of both fluorescent and non-fluorescent substances were investigated by using metal titration combined with two-dimensional correlation spectroscopy (2D-COS) analysis. The organic matters in the eutrophic algae-rich lake, including natural organic matters (NOM) and algae-induced extracellular polymeric substances (EPS), both contained fluorescent and non-fluorescent substances. The peaks in the one-dimensional spectra strongly overlapped, while 2D-COS can decompose the overlapped peaks and thus enhanced the spectral resolution. Moreover, 2D FTIR COS demonstrated that the binding susceptibility of organic ligands in both NOM and algal EPS matrices followed the order: 3400>1380>1650 cm-1, indicative the significant contribution of non-fluorescent ligands in metal binding. The modified Stern-Volmer equation also revealed a substantial metal binding potential for the non-fluorescent substances (logKM: 3.57∼4.92). As for the effects of organic ligands on metal binding, EPS was characterized with higher binding ability than NOM for both fluorescent and non-fluorescent ligands. Algae-induced EPS and the non-fluorescent substances in eutrophic algae-rich lakes should not be overlooked because of their high metal binding potential.

  14. 3D surface configuration modulates 2D symmetry detection.

    PubMed

    Chen, Chien-Chung; Sio, Lok-Teng

    2015-02-01

    We investigated whether three-dimensional (3D) information in a scene can affect symmetry detection. The stimuli were random dot patterns with 15% dot density. We measured the coherence threshold, or the proportion of dots that were the mirror reflection of the other dots in the other half of the image about a central vertical axis, at 75% accuracy with a 2AFC paradigm under various 3D configurations produced by the disparity between the left and right eye images. The results showed that symmetry detection was difficult when the corresponding dots across the symmetry axis were on different frontoparallel or inclined planes. However, this effect was not due to a difference in distance, as the observers could detect symmetry on a slanted surface, where the depth of the two sides of the symmetric axis was different. The threshold was reduced for a hinge configuration where the join of two slanted surfaces coincided with the axis of symmetry. Our result suggests that the detection of two-dimensional (2D) symmetry patterns is subject to the 3D configuration of the scene; and that coplanarity across the symmetry axis and consistency between the 2D pattern and 3D structure are important factors for symmetry detection.

  15. Influence of Elevation Data Source on 2D Hydraulic Modelling

    NASA Astrophysics Data System (ADS)

    Bakuła, Krzysztof; StĘpnik, Mateusz; Kurczyński, Zdzisław

    2016-08-01

    The aim of this paper is to analyse the influence of the source of various elevation data on hydraulic modelling in open channels. In the research, digital terrain models from different datasets were evaluated and used in two-dimensional hydraulic models. The following aerial and satellite elevation data were used to create the representation of terrain-digital terrain model: airborne laser scanning, image matching, elevation data collected in the LPIS, EuroDEM, and ASTER GDEM. From the results of five 2D hydrodynamic models with different input elevation data, the maximum depth and flow velocity of water were derived and compared with the results of the most accurate ALS data. For such an analysis a statistical evaluation and differences between hydraulic modelling results were prepared. The presented research proved the importance of the quality of elevation data in hydraulic modelling and showed that only ALS and photogrammetric data can be the most reliable elevation data source in accurate 2D hydraulic modelling.

  16. Digit ratio (2D:4D), salivary testosterone, and handedness.

    PubMed

    Beaton, Alan A; Rudling, Nick; Kissling, Christian; Taurines, Regine; Thome, Johannes

    2011-03-01

    The length of the index finger relative to that of the ring finger, the 2D:4D ratio, has been taken to be a marker of the amount of testosterone (T) that was present in the foetal environment (Manning, Scutt, Wilson, & Lewis-Jones, 1998). It has also been suggested (Geschwind & Galaburda, 1987) that elevated levels of foetal T are associated with left-handedness and that adult levels of circulating T might relate to foetal levels (Jamison, Meier, & Campbell, 1993). We used multiple regression analyses to investigate whether there is any relationship between either left or right hand 2D:4D ratio and handedness. We also examined whether adult levels of salivary T (or cortisol, used as a control hormone) predict digit ratio and/or handedness. Although the 2D:4D ratio of neither the left nor the right hand was related to handedness, the difference between the digit ratios of the right and left hands, D(R-L), was a significant predictor of handedness and of the performance difference between the hands on a peg-moving task, supporting previous findings (Manning & Peters, 2009; Manning et al., 1998; Manning, Trivers, Thornhill, & Singh, 2000; Stoyanov, Marinov, & Pashalieva, 2009). Adult circulating T levels did not predict the digit ratio of the left or right hand; nor was there a significant relationship between concentrations of salivary T (or cortisol) and either hand preference or asymmetry in manual skill. We suggest that the association between D(R-L) and hand preference arises because D(R-L) is a correlate of sensitivity to T in the developing foetus.

  17. 2D discrete Fourier transform on sliding windows.

    PubMed

    Park, Chun-Su

    2015-03-01

    Discrete Fourier transform (DFT) is the most widely used method for determining the frequency spectra of digital signals. In this paper, a 2D sliding DFT (2D SDFT) algorithm is proposed for fast implementation of the DFT on 2D sliding windows. The proposed 2D SDFT algorithm directly computes the DFT bins of the current window using the precalculated bins of the previous window. Since the proposed algorithm is designed to accelerate the sliding transform process of a 2D input signal, it can be directly applied to computer vision and image processing applications. The theoretical analysis shows that the computational requirement of the proposed 2D SDFT algorithm is the lowest among existing 2D DFT algorithms. Moreover, the output of the 2D SDFT is mathematically equivalent to that of the traditional DFT at all pixel positions.

  18. An Optimized Fluorescence-Based Bidimensional Immunoproteomic Approach for Accurate Screening of Autoantibodies

    PubMed Central

    Launay, David; Sobanski, Vincent; Dussart, Patricia; Chafey, Philippe; Broussard, Cédric; Duban-Deweer, Sophie; Vermersch, Patrick; Prin, Lionel; Lefranc, Didier

    2015-01-01

    Serological proteome analysis (SERPA) combines classical proteomic technology with effective separation of cellular protein extracts on two-dimensional gel electrophoresis, western blotting, and identification of the antigenic spot of interest by mass spectrometry. A critical point is related to the antigenic target characterization by mass spectrometry, which depends on the accuracy of the matching of antigenic reactivities on the protein spots during the 2D immunoproteomic procedures. The superimposition, based essentially on visual criteria of antigenic and protein spots, remains the major limitation of SERPA. The introduction of fluorescent dyes in proteomic strategies, commonly known as 2D-DIGE (differential in-gel electrophoresis), has boosted the qualitative capabilities of 2D electrophoresis. Based on this 2D-DIGE strategy, we have improved the conventional SERPA by developing a new and entirely fluorescence-based bi-dimensional immunoproteomic (FBIP) analysis, performed with three fluorescent dyes. To optimize the alignment of the different antigenic maps, we introduced a landmark map composed of a combination of specific antibodies. This methodological development allows simultaneous revelation of the antigenic, landmark and proteomic maps on each immunoblot. A computer-assisted process using commercially available software automatically leads to the superimposition of the different maps, ensuring accurate localization of antigenic spots of interest. PMID:26132557

  19. MAGNUM2D. Radionuclide Transport Porous Media

    SciTech Connect

    Langford, D.W.; Baca, R.G.

    1989-03-01

    MAGNUM2D was developed to analyze thermally driven fluid motion in the deep basalts below the Paco Basin at the Westinghouse Hanford Site. Has been used in the Basalt Waste Isolation Project to simulate nonisothermal groundwater flow in a heterogeneous anisotropic medium and heat transport in a water/rock system near a high level nuclear waste repository. Allows three representations of the hydrogeologic system: an equivalent porous continuum, a system of discrete, unfilled, and interconnecting fractures separated by impervious rock mass, and a low permeability porous continuum with several discrete, unfilled fractures traversing the medium. The calculations assume local thermodynamic equilibrium between the rock and groundwater, nonisothermal Darcian flow in the continuum portions of the rock, and nonisothermal Poiseuille flow in discrete unfilled fractures. In addition, the code accounts for thermal loading within the elements, zero normal gradient and fixed boundary conditions for both temperature and hydraulic head, and simulation of the temperature and flow independently. The Q2DGEOM preprocessor was developed to generate, modify, plot and verify quadratic two dimensional finite element geometries. The BCGEN preprocessor generates the boundary conditions for head and temperature and ICGEN generates the initial conditions. The GRIDDER postprocessor interpolates nonregularly spaced nodal flow and temperature data onto a regular rectangular grid. CONTOUR plots and labels contour lines for a function of two variables and PARAM plots cross sections and time histories for a function of time and one or two spatial variables. NPRINT generates data tables that display the data along horizontal or vertical cross sections. VELPLT differentiates the hydraulic head and buoyancy data and plots the velocity vectors. The PATH postprocessor plots flow paths and computes the corresponding travel times.

  20. MAGNUM2D. Radionuclide Transport Porous Media

    SciTech Connect

    Langford, D.W.; Baca, R.G.

    1988-08-01

    MAGNUM2D was developed to analyze thermally driven fluid motion in the deep basalts below the Paco Basin at the Westinghouse Hanford Site. Has been used in the Basalt Waste Isolation Project to simulate nonisothermal groundwater flow in a heterogeneous anisotropic medium and heat transport in a water/rock system near a high level nuclear waste repository. Allows three representations of the hydrogeologic system: an equivalent porous continuum, a system of discrete, unfilled, and interconnecting fractures separated by impervious rock mass, and a low permeability porous continuum with several discrete, unfilled fractures traversing the medium. The calculation assumes local thermodynamic equilibrium between the rock and groundwater, nonisothermal Darcian flow in the continuum portions of the rock, and nonisothermal Poiseuille flow in discrete unfilled fractures. In addition, the code accounts for thermal loading within the elements, zero normal gradient and fixed boundary conditions for both temperature and hydraulic head, and simulation of the temperature and flow independently. The Q2DGEOM preprocessor was developed to generate, modify, plot and verify quadratic two dimensional finite element geometries. The BCGEN preprocessor generates the boundary conditions for head and temperature and ICGEN generates the initial conditions. The GRIDDER postprocessor interpolates nonregularly spaced nodal flow and temperature data onto a regular rectangular grid. CONTOUR plots and labels contour lines for a function of two variables and PARAM plots cross sections and time histories for a function of time and one or two spatial variables. NPRINT generates data tables that display the data along horizontal or vertical cross sections. VELPLT differentiates the hydraulic head and buoyancy data and plots the velocity vectors. The PATH postprocessor plots flow paths and computes the corresponding travel times.

  1. Generates 2D Input for DYNA NIKE & TOPAZ

    SciTech Connect

    Hallquist, J. O.; Sanford, Larry

    1996-07-15

    MAZE is an interactive program that serves as an input and two-dimensional mesh generator for DYNA2D, NIKE2D, TOPAZ2D, and CHEMICAL TOPAZ2D. MAZE also generates a basic template for ISLAND input. MAZE has been applied to the generation of input data to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

  2. MAZE96. Generates 2D Input for DYNA NIKE & TOPAZ

    SciTech Connect

    Sanford, L.; Hallquist, J.O.

    1992-02-24

    MAZE is an interactive program that serves as an input and two-dimensional mesh generator for DYNA2D, NIKE2D, TOPAZ2D, and CHEMICAL TOPAZ2D. MAZE also generates a basic template for ISLAND input. MAZE has been applied to the generation of input data to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

  3. NIKE2D96. Static & Dynamic Response of 2D Solids

    SciTech Connect

    Raboin, P.; Engelmann, B.; Halquist, J.O.

    1992-01-24

    NIKE2D is an implicit finite-element code for analyzing the finite deformation, static and dynamic response of two-dimensional, axisymmetric, plane strain, and plane stress solids. The code is fully vectorized and available on several computing platforms. A number of material models are incorporated to simulate a wide range of material behavior including elasto-placicity, anisotropy, creep, thermal effects, and rate dependence. Slideline algorithms model gaps and sliding along material interfaces, including interface friction, penetration and single surface contact. Interactive-graphics and rezoning is included for analyses with large mesh distortions. In addition to quasi-Newton and arc-length procedures, adaptive algorithms can be defined to solve the implicit equations using the solution language ISLAND. Each of these capabilities and more make NIKE2D a robust analysis tool.

  4. Extending Ripley’s K-Function to Quantify Aggregation in 2-D Grayscale Images

    PubMed Central

    Amgad, Mohamed; Itoh, Anri; Tsui, Marco Man Kin

    2015-01-01

    In this work, we describe the extension of Ripley’s K-function to allow for overlapping events at very high event densities. We show that problematic edge effects introduce significant bias to the function at very high densities and small radii, and propose a simple correction method that successfully restores the function’s centralization. Using simulations of homogeneous Poisson distributions of events, as well as simulations of event clustering under different conditions, we investigate various aspects of the function, including its shape-dependence and correspondence between true cluster radius and radius at which the K-function is maximized. Furthermore, we validate the utility of the function in quantifying clustering in 2-D grayscale images using three modalities: (i) Simulations of particle clustering; (ii) Experimental co-expression of soluble and diffuse protein at varying ratios; (iii) Quantifying chromatin clustering in the nuclei of wt and crwn1 crwn2 mutant Arabidopsis plant cells, using a previously-published image dataset. Overall, our work shows that Ripley’s K-function is a valid abstract statistical measure whose utility extends beyond the quantification of clustering of non-overlapping events. Potential benefits of this work include the quantification of protein and chromatin aggregation in fluorescent microscopic images. Furthermore, this function has the potential to become one of various abstract texture descriptors that are utilized in computer-assisted diagnostics in anatomic pathology and diagnostic radiology. PMID:26636680

  5. [Analysis of Three Polycyclic Aromatic Hydrocarbons in Solution Based on Two-Dimensional Fluorescence Correlation Spectroscopy].

    PubMed

    Zhou, Chang-hong; Zhao, Mei-rong; Yang, Ren-jie; Zhu, Wen-bi; Dong, Gui-mei

    2016-02-01

    Polycyclic aromatic hydrocarbons (PAHs) are listed as the priority pollutants. It is difficult to resolve effectively the peaks of PAHs by conventional one-dimensional fluorescence spectroscopy due to its low content and the overlapping fluorescence three mixed ystems and a total of 27 samples, are to be prepared with different concentrations of three PAHs. Concentrations of three PAHS are monotonically increasing or decreasing in each mixed system. Then the 2D fluorescence correlation spectrum of each mixed systems will be calculated under the perturbation of the concentration of anthracene, phenanthrene and pyrene in solution. There are seven strong autopeaks at 425, 402, 381, 373, 365, 393 and 347 nm in synchronous 2D correlation spectrum. The fluorescence peak of phenanthrene at 347 nm is uncovered in three mixed systems, so the band at 347 nm is to be used as clues for further assignment. According to positive or negative cross peaks at 347 nm in synchronous 2D correlation spectrum, we can know that the peaks at 402, 381, 425 and 452 nm are assigned to anthracene, the peaks at 373 and 393 nm are assigned to pyrene, and the peaks at 365, 356 and 347 nm are assigned to phenanthrene. The fluorescence peak of phenanthrene at 385 nm is shown in asynchronous 2D correlation spectrum; it means the spectral resolution of asynchronous spectrum is better than the synchronous spectrum. The results are that it is feasible to analyze serious overlapping multi-component PAHs using two-dimensional fluorescence correlation spectroscopy, which can be extended to the detection of other pollutants in the air.

  6. Hybrid 2D-nanomaterials-based electrochemical immunosensing strategies for clinical biomarkers determination.

    PubMed

    Campuzano, S; Pedrero, M; Nikoleli, G-P; Pingarrón, J M; Nikolelis, D P

    2017-03-15

    Owing to the outstanding conductivity and biocompatibility as well as numerous other fascinating properties of two-dimensional (2D)-nanomaterials, 2D-based nanohybrids have shown unparalleled superiorities in the field of electrochemical biosensors. This review highlights latest advances in electrochemical immunosensors for clinical biomarkers based on different hybrid 2D-nanomaterials. Particular attention will be given to hybrid nanostructures involving graphene and other graphene-like 2D-layered nanomaterials (GLNs). Several recent strategies for using such 2D-nanomaterial heterostructures in the development of modern immunosensors, both for tagging or modifying electrode transducers, are summarized and discussed. These hybrid nanocomposites, quite superior than their rival materials, will undoubtedly have an important impact within the near future and not only in clinical areas. Current challenges and future perspectives in this rapidly growing field are also outlined.

  7. One-atom-thick 2D copper oxide clusters on graphene.

    PubMed

    Kano, Emi; Kvashnin, Dmitry G; Sakai, Seiji; Chernozatonskii, Leonid A; Sorokin, Pavel B; Hashimoto, Ayako; Takeguchi, Masaki

    2017-03-17

    The successful isolation and remarkable properties of graphene have recently triggered investigation of two-dimensional (2D) materials from layered compounds; however, one-atom-thick 2D materials without bulk layered counterparts are scarcely reported. Here we report the structure and properties of novel 2D copper oxide studied by experimental and theoretical methods. Electron microscopy observations reveal that copper oxide can form monoatomic layers with an unusual square lattice on graphene. Density functional theory calculations suggest that oxygen atoms at the centre of the square lattice stabilizes the 2D Cu structure, and that the 2D copper oxide sheets have unusual electronic and magnetic properties different from 3D bulk copper oxide.

  8. One-step synthesis of intrinsically functionalized fluorescent carbon nanoparticles by hydrothermal carbonization from different carbon sources

    NASA Astrophysics Data System (ADS)

    Shen, Chen; Yao, Wei; Lu, Yun

    2013-10-01

    Highly functionalized carbon nanoparticles (F-CNPs) with average sizes of 5-30 nm were fabricated by hydrothermal carbonization of specific carbon sources at a mild temperature without usual strong acid treatment or surface modification. The morphology, structure, and fluorescent properties of the nanoparticles were characterized by transmission electron microscopy, dynamic light scattering, Fourier-transform infrared spectra, X-ray photoelectron spectroscopy, Raman spectra and fluorescent spectrophotometer. As a result, the abundant carboxylic, sulfonic, amine, or ethanamide groups were furnished on the surface of these carbon nanoparticles, offering the reaction sites for their possible further functionalization, and these functional groups also enhance the dispersion of carbon nanoparticles which are kept without precipitation for months. The hydrothermal treatment which is simple, green, and economical, also can endow the F-CNPs much more carboxyl groups, thus improving the quantum efficiency of as-prepared products. These functionalized carbon nanoparticles demonstrate the excitation wavelength-independent photoluminescence behavior, implying their potential applications in biological labeling, imaging, and chromatography.

  9. Integrated Fluorescence

    NASA Technical Reports Server (NTRS)

    Tuma, Margaret (Inventor); Gruhlke, Russell W. (Inventor)

    1998-01-01

    A detection method is integrated with a filtering method and an enhancement method to create a fluorescence sensor that can be miniaturized. The fluorescence sensor comprises a thin film geometry including a waveguide layer, a metal film layer and sensor layer. The thin film geometry of the fluorescence sensor allows the detection of fluorescent radiation over a narrow wavelength interval. This enables wavelength discrimination and eliminates the detection of unwanted light from unknown or spurious sources.

  10. Two-dimensional difference gel electrophoresis applied for analytical proteomics: fundamentals and applications to the study of plant proteomics.

    PubMed

    Arruda, Sandra Cristina Capaldi; Barbosa, Herbert de Sousa; Azevedo, Ricardo Antunes; Arruda, Marco Aurélio Zezzi

    2011-10-21

    The present review reports the principles, fundamentals and some applications of two-dimensional difference gel electrophoresis for analytical proteomics based on plant proteome analysis, also emphasizing some advantages of 2-D DIGE over 2-D PAGE techniques. Some fluorescent protein labeling reagents, methods of protein labeling, models of 2-D DIGE experiments, and some limitations of this technique are presented and discussed in terms of 2-D DIGE plant proteomes. Finally, some practical applications of this technique are pointed out, emphasizing its potentialities in plant proteomics.

  11. Measurement and modelling of magnetic properties of soft magnetic composite material under 2D vector magnetisations

    NASA Astrophysics Data System (ADS)

    Guo, Y. G.; Zhu, J. G.; Zhong, J. J.

    2006-07-01

    This paper reports the measurement and modelling of magnetic properties of SOMALOY TM 500, a soft magnetic composite (SMC) material, under different 2D vector magnetisations, such as alternating along one direction, circularly and elliptically rotating in a 2D plane. By using a 2D magnetic property tester, the B- H curves and core losses of the SMC material have been measured with different flux density patterns on a single sheet square sample. The measurements can provide useful information for modelling of the magnetic properties, such as core losses. The core loss models have been successfully applied in the design of rotating electrical machines with SMC core.

  12. Interferometric Motion Detection in Atomic Layer 2D Nanostructures: Visualizing Signal Transduction Efficiency and Optimization Pathways

    PubMed Central

    Wang, Zenghui; Feng, Philip X.-L.

    2016-01-01

    Atomic layer crystals are emerging building blocks for enabling new two-dimensional (2D) nanomechanical systems, whose motions can be coupled to other attractive physical properties in such 2D systems. Optical interferometry has been very effective in reading out the infinitesimal motions of these 2D structures and spatially resolving different modes. To quantitatively understand the detection efficiency and its dependence on the device parameters and interferometric conditions, here we present a systematic study of the intrinsic motion responsivity in 2D nanomechanical systems using a Fresnel-law-based model. We find that in monolayer to 14-layer structures, MoS2 offers the highest responsivity among graphene, h-BN, and MoS2 devices and for the three commonly used visible laser wavelengths (633, 532, and 405 nm). We also find that the vacuum gap resulting from the widely used 300 nm-oxide substrate in making 2D devices, fortunately, leads to close-to-optimal responsivity for a wide range of 2D flakes. Our results elucidate and graphically visualize the dependence of motion transduction responsivity upon 2D material type and number of layers, vacuum gap, oxide thickness, and detecting wavelength, thus providing design guidelines for constructing 2D nanomechanical systems with optimal optical motion readout. PMID:27464908

  13. Interferometric Motion Detection in Atomic Layer 2D Nanostructures: Visualizing Signal Transduction Efficiency and Optimization Pathways

    NASA Astrophysics Data System (ADS)

    Wang, Zenghui; Feng, Philip X.-L.

    2016-07-01

    Atomic layer crystals are emerging building blocks for enabling new two-dimensional (2D) nanomechanical systems, whose motions can be coupled to other attractive physical properties in such 2D systems. Optical interferometry has been very effective in reading out the infinitesimal motions of these 2D structures and spatially resolving different modes. To quantitatively understand the detection efficiency and its dependence on the device parameters and interferometric conditions, here we present a systematic study of the intrinsic motion responsivity in 2D nanomechanical systems using a Fresnel-law-based model. We find that in monolayer to 14-layer structures, MoS2 offers the highest responsivity among graphene, h-BN, and MoS2 devices and for the three commonly used visible laser wavelengths (633, 532, and 405 nm). We also find that the vacuum gap resulting from the widely used 300 nm-oxide substrate in making 2D devices, fortunately, leads to close-to-optimal responsivity for a wide range of 2D flakes. Our results elucidate and graphically visualize the dependence of motion transduction responsivity upon 2D material type and number of layers, vacuum gap, oxide thickness, and detecting wavelength, thus providing design guidelines for constructing 2D nanomechanical systems with optimal optical motion readout.

  14. Interferometric Motion Detection in Atomic Layer 2D Nanostructures: Visualizing Signal Transduction Efficiency and Optimization Pathways.

    PubMed

    Wang, Zenghui; Feng, Philip X-L

    2016-07-28

    Atomic layer crystals are emerging building blocks for enabling new two-dimensional (2D) nanomechanical systems, whose motions can be coupled to other attractive physical properties in such 2D systems. Optical interferometry has been very effective in reading out the infinitesimal motions of these 2D structures and spatially resolving different modes. To quantitatively understand the detection efficiency and its dependence on the device parameters and interferometric conditions, here we present a systematic study of the intrinsic motion responsivity in 2D nanomechanical systems using a Fresnel-law-based model. We find that in monolayer to 14-layer structures, MoS2 offers the highest responsivity among graphene, h-BN, and MoS2 devices and for the three commonly used visible laser wavelengths (633, 532, and 405 nm). We also find that the vacuum gap resulting from the widely used 300 nm-oxide substrate in making 2D devices, fortunately, leads to close-to-optimal responsivity for a wide range of 2D flakes. Our results elucidate and graphically visualize the dependence of motion transduction responsivity upon 2D material type and number of layers, vacuum gap, oxide thickness, and detecting wavelength, thus providing design guidelines for constructing 2D nanomechanical systems with optimal optical motion readout.

  15. Representativeness of 2D models to simulate 3D unstable variable density flow in porous media

    NASA Astrophysics Data System (ADS)

    Knorr, Bastian; Xie, Yueqing; Stumpp, Christine; Maloszewski, Piotr; Simmons, Craig T.

    2016-11-01

    Variable density flow in porous media has been studied primarily using numerical models because it is a semi-chaotic and transient process. Most of these studies have been 2D, owing to the computational restrictions on 3D simulations, and the ability to observe variable density flow in 2D experimentation. However, it is recognised that variable density flow is a three-dimensional process. A 3D system may cause weaker variable density flow than a 2D system due to stronger dispersion, but may also result in bigger fingers and hence stronger variable density flow because of more space for fingers to coalesce. This study aimed to determine the representativeness of 2D modelling to simulate 3D variable density flow. 3D homogeneous sand column experiments were conducted at three different water flow velocities with three different bromide tracer solutions mixed with methanol resulting in different density ratios. Both 2D axisymmetric and 3D numerical simulations were performed to reproduce experimental data. Experimental results showed that the magnitude of variable density flow increases with decreasing flow rates and decreasing density ratios. The shapes of the observed breakthrough curves differed significantly from those produced by 2D axisymmetric and 3D simulations. Compared to 2D simulations, the onset of instabilities was delayed but the growth was more pronounced in 3D simulations. Despite this difference, both 2D axisymmetric and 3D models successfully simulated mass recovery with high efficiency (between 77% and 99%). This study indicates that 2D simulations are sufficient to understand integrated features of variable density flow in homogeneous sand column experiments.

  16. Distribution of CYP2D6 alleles and phenotypes in the Brazilian population.

    PubMed

    Friedrich, Deise C; Genro, Júlia P; Sortica, Vinicius A; Suarez-Kurtz, Guilherme; de Moraes, Maria Elizabete; Pena, Sergio D J; dos Santos, Andrea K Ribeiro; Romano-Silva, Marco A; Hutz, Mara H

    2014-01-01

    The CYP2D6 enzyme is one of the most important members of the cytochrome P450 superfamily. This enzyme metabolizes approximately 25% of currently prescribed medications. The CYP2D6 gene presents a high allele heterogeneity that determines great inter-individual variation. The aim of this study was to evaluate the variability of CYP2D6 alleles, genotypes and predicted phenotypes in Brazilians. Eleven single nucleotide polymorphisms and CYP2D6 duplications/multiplications were genotyped by TaqMan assays in 1020 individuals from North, Northeast, South, and Southeast Brazil. Eighteen CYP2D6 alleles were identified in the Brazilian population. The CYP2D6*1 and CYP2D6*2 alleles were the most frequent and widely distributed in different geographical regions of Brazil. The highest number of CYPD6 alleles observed was six and the frequency of individuals with more than two copies ranged from 6.3% (in Southern Brazil) to 10.2% (Northern Brazil). The analysis of molecular variance showed that CYP2D6 is homogeneously distributed across different Brazilian regions and most of the differences can be attributed to inter-individual differences. The most frequent predicted metabolic status was EM (83.5%). Overall 2.5% and 3.7% of Brazilians were PMs and UMs respectively. Genomic ancestry proportions differ only in the prevalence of intermediate metabolizers. The IM predicted phenotype is associated with a higher proportion of African ancestry and a lower proportion of European ancestry in Brazilians. PM and UM classes did not vary among regions and/or ancestry proportions therefore unique CYP2D6 testing guidelines for Brazilians are possible and could potentially avoid ineffective or adverse events outcomes due to drug prescriptions.

  17. Distribution of CYP2D6 Alleles and Phenotypes in the Brazilian Population

    PubMed Central

    Sortica, Vinicius A.; Suarez-Kurtz, Guilherme; de Moraes, Maria Elizabete; Pena, Sergio D. J.; dos Santos, Ândrea K. Ribeiro; Romano-Silva, Marco A.; Hutz, Mara H.

    2014-01-01

    Abstract The CYP2D6 enzyme is one of the most important members of the cytochrome P450 superfamily. This enzyme metabolizes approximately 25% of currently prescribed medications. The CYP2D6 gene presents a high allele heterogeneity that determines great inter-individual variation. The aim of this study was to evaluate the variability of CYP2D6 alleles, genotypes and predicted phenotypes in Brazilians. Eleven single nucleotide polymorphisms and CYP2D6 duplications/multiplications were genotyped by TaqMan assays in 1020 individuals from North, Northeast, South, and Southeast Brazil. Eighteen CYP2D6 alleles were identified in the Brazilian population. The CYP2D6*1 and CYP2D6*2 alleles were the most frequent and widely distributed in different geographical regions of Brazil. The highest number of CYPD6 alleles observed was six and the frequency of individuals with more than two copies ranged from 6.3% (in Southern Brazil) to 10.2% (Northern Brazil). The analysis of molecular variance showed that CYP2D6 is homogeneously distributed across different Brazilian regions and most of the differences can be attributed to inter-individual differences. The most frequent predicted metabolic status was EM (83.5%). Overall 2.5% and 3.7% of Brazilians were PMs and UMs respectively. Genomic ancestry proportions differ only in the prevalence of intermediate metabolizers. The IM predicted phenotype is associated with a higher proportion of African ancestry and a lower proportion of European ancestry in Brazilians. PM and UM classes did not vary among regions and/or ancestry proportions therefore unique CYP2D6 testing guidelines for Brazilians are possible and could potentially avoid ineffective or adverse events outcomes due to drug prescriptions. PMID:25329392

  18. 2D Gridded Surface Data Value-Added Product

    SciTech Connect

    Tang, Q; Xie, S

    2015-08-30

    This report describes the Atmospheric Radiation Measurement (ARM) Best Estimate (ARMBE) 2-dimensional (2D) gridded surface data (ARMBE2DGRID) value-added product. Spatial variability is critically important to many scientific studies, especially those that involve processes of great spatial variations at high temporal frequency (e.g., precipitation, clouds, radiation, etc.). High-density ARM sites deployed at the Southern Great Plains (SGP) allow us to observe the spatial patterns of variables of scientific interests. The upcoming megasite at SGP with its enhanced spatial density will facilitate the studies at even finer scales. Currently, however, data are reported only at individual site locations at different time resolutions for different datastreams. It is difficult for users to locate all the data they need and requires extra effort to synchronize the data. To address these problems, the ARMBE2DGRID value-added product merges key surface measurements at the ARM SGP sites and interpolates the data to a regular 2D grid to facilitate the data application.

  19. Spectroscopic properties of multilayered gold nanoparticle 2D sheets.

    PubMed

    Yoshida, Akihito; Imazu, Keisuke; Li, Xinheng; Okamoto, Koichi; Tamada, Kaoru

    2012-12-11

    We report the fabrication technique and optical properties of multilayered two-dimensional (2D) gold nanoparticle sheets ("Au nanosheet"). The 2D crystalline monolayer sheet composed of Au nanoparticles shows an absorption peak originating from a localized surface plasmon resonance (LSPR). It was found that the absorption spectra dramatically change when the monolayers are assembled into the multilayers on different substrates (quartz or Au). In the case of the multilayers on Au thin film (d = 200 nm), the LSPR peak is shifted to longer wavelength at the near-IR region by increasing the number of layers. The absorbance also depends on the layer number and shows the nonlinear behavior. On the other hand, the multilayers on quartz substrate show neither such LSPR peak shift nor nonlinear response of absorbance. The layer number dependence on metal surfaces can be interpreted as the combined effects between the near-field coupling of the LSPR and the far-field optics of the stratified metamaterial films, as proposed in our previous study. We also report the spectroscopic properties of hybrid multilayers composed of two kinds of monolayers, i.e., Au nanosheet and Ag nanosheet. The combination of the different metal nanoparticle sheets realizes more flexible plasmonic color tuning.

  20. Application Perspective of 2D+SCALE Dimension

    NASA Astrophysics Data System (ADS)

    Karim, H.; Rahman, A. Abdul

    2016-09-01

    Different applications or users need different abstraction of spatial models, dimensionalities and specification of their datasets due to variations of required analysis and output. Various approaches, data models and data structures are now available to support most current application models in Geographic Information System (GIS). One of the focuses trend in GIS multi-dimensional research community is the implementation of scale dimension with spatial datasets to suit various scale application needs. In this paper, 2D spatial datasets that been scaled up as the third dimension are addressed as 2D+scale (or 3D-scale) dimension. Nowadays, various data structures, data models, approaches, schemas, and formats have been proposed as the best approaches to support variety of applications and dimensionality in 3D topology. However, only a few of them considers the element of scale as their targeted dimension. As the scale dimension is concerned, the implementation approach can be either multi-scale or vario-scale (with any available data structures and formats) depending on application requirements (topology, semantic and function). This paper attempts to discuss on the current and new potential applications which positively could be integrated upon 3D-scale dimension approach. The previous and current works on scale dimension as well as the requirements to be preserved for any given applications, implementation issues and future potential applications forms the major discussion of this paper.

  1. Remote Sensing Study of the Influence of Different Herbicides on the Leaf Spectral Reflectance and Fluorescence of Pea Plants (Pisum sativum L.)

    NASA Astrophysics Data System (ADS)

    Krezhova, Dora; Yanev, Tony; Iliev, Ilko; Alexieva, Vera; Tsaneva, Mariana

    The effective use of airborne and satellite-based remote sensor systems in resource management, agriculture, mineral exploration and environmental monitoring requires an understanding of the nature and limitations of the high-resolution remote sensing data and of various strategies for processing and interpreting it. In developing the necessary knowledge base, ground-based measurements are the expedient source of information. In this study, remote sensing techniques were applied in laboratory for detection of the influence of herbicides 2.4-D, glyphosate, fluridone and acifluorfen on the leaf spectral reflectance and fluorescence of pea plants (Pisum sativum L.). According to the classification of the Herbicide Resistance Action Committee with reference to their mode of action they belong to different groups: synthetic auxins - O (2.4-D), inhibition of EPSP synthase - G (glyphosate), photobleaching - F1 (fluridone), and inhibition of PPO - E (acifluorfen). During the last 40 years, these herbicides are among the ones used most widely in agriculture worldwide. The plants studied were grown hydroponically in a growth chamber in a nutritious medium to which every herbicide was added at two low concentrations (1 µM, 0.1 µM) with respect to the field dose applied in the agricultural practice. High-resolution spectral data for leaf spectral reflectance and fluorescence were collected from freshly detached leaves using three multichannel spectrometers. Spectral reflectance characteristics were obtained from the leaf reflectance referenced against a standard (white diffuse screen) in the visible and near infrared ranges of the electromagnetic spectrum (450÷850 nm). Fluorescence spectra were taken in the spectral range 650-850 nm. To assess the changes arising in leaf spectral reflectance under the herbicide action we developed and applied an analytical approach based on discriminant analysis and other statistical methods. The spectral characteristics were analyzed in

  2. Fluorescence imaging spectrometer optical design

    NASA Astrophysics Data System (ADS)

    Taiti, A.; Coppo, P.; Battistelli, E.

    2015-09-01

    The optical design of the FLuORescence Imaging Spectrometer (FLORIS) studied for the Fluorescence Explorer (FLEX) mission is discussed. FLEX is a candidate for the ESA's 8th Earth Explorer opportunity mission. FLORIS is a pushbroom hyperspectral imager foreseen to be embarked on board of a medium size satellite, flying in tandem with Sentinel-3 in a Sun synchronous orbit at a height of about 815 km. FLORIS will observe the vegetation fluorescence and reflectance within a spectral range between 500 and 780 nm. Multi-frames acquisitions on matrix detectors during the satellite movement will allow the production of 2D Earth scene images in two different spectral channels, called HR and LR with spectral resolution of 0.3 and 2 nm respectively. A common fore optics is foreseen to enhance by design the spatial co-registration between the two spectral channels, which have the same ground spatial sampling (300 m) and swath (150 km). An overlapped spectral range between the two channels is also introduced to simplify the spectral coregistration. A compact opto-mechanical solution with all spherical and plane optical elements is proposed, and the most significant design rationales are described. The instrument optical architecture foresees a dual Babinet scrambler, a dioptric telescope and two grating spectrometers (HR and LR), each consisting of a modified Offner configuration. The developed design is robust, stable vs temperature, easy to align, showing very high optical quality along the whole field of view. The system gives also excellent correction for transverse chromatic aberration and distortions (keystone and smile).

  3. Three-dimensional fluorescence excitation-emission matrix (EEM) spectroscopy with regional integration analysis for assessing waste sludge hydrolysis at different pretreated temperatures.

    PubMed

    Sun, Jian; Guo, Liang; Li, Qianqian; Zhao, Yangguo; Gao, Mengchun; She, Zonglian; Jin, Chunji

    2016-12-01

    Heat pretreatment process can promote sludge hydrolysis and enhance the degradability of waste sludge. The effect of heat pretreatment at different temperatures on the changes of soluble chemical oxygen demand (SCOD), carbohydrates, and proteins and the structural and functional properties of organics in extracellular polymeric substances (EPS) and dissolved organic matters (DOM) were systematically investigated. Heat pretreatment was conducted at 65, 80, 100, and 121 °C for 30 min. The SCOD in DOM increased with pretreated temperatures. Three-dimensional excitation-emission matrix (3D-EEM) fluorescence spectroscopy was utilized to evaluate the biodegradable and non-biodegradable components in EPS and DOM. Moreover, the humification index (HIX) and the fluorescence index (FI) were used to evaluate the humification and DOM source. At 80 °C, the percent fluorescence response (P i,n ) of easily biodegradable soluble microbial by-product substance was higher than others; meanwhile, little non-biodegradable humic acid-like substance was accumulated. In order to enhance sludge biodegradability, 80 °C was chosen as the optimal temperature for heat pretreatment.

  4. A comparative study of ZnAl2O4 nanoparticles synthesized from different aluminum salts for use as fluorescence materials

    PubMed Central

    Wang, Shi-Fa; Sun, Guang-Zhuang; Fang, Lei-Ming; Lei, Li; Xiang, Xia; Zu, Xiao-Tao

    2015-01-01

    Three ZnAl2O4 samples were prepared via a modified polyacrylamide gel method using a citric acid solution with different aluminum salt starting materials, including AlCl3∙6H2O, Al2(SO4)3∙18H2O, and Al(NO3)3∙9H2O under identical conditions. The influence of different aluminum salts on the morphologies, phase purity, and optical and fluorescence properties of the as-prepared ZnAl2O4 nanoparticles were studied. The experimental results demonstrate that the phase purity, particle size, morphology, and optical and fluorescence properties of ZnAl2O4 nanoparticles can be manipulated by the use of different aluminum salts as starting materials. The energy bandgap (Eg) values of ZnAl2O4 nanoparticles increase with a decrease in particle size. The fluorescence spectra show that a major blue emission band around 400 nm and two weaker side bands located at 410 and 445 nm are observed when the excitation wavelength is 325 nm. The ZnAl2O4 nanoparticles prepared from Al(NO3)3∙9H2O exhibit the largest emission intensity among the three ZnAl2O4 samples, followed in turn by the ZnAl2O4 nanoparticles prepared from Al2(SO4)3∙18H2O and AlCl3∙6H2O. These differences are attributed to combinational changes in Eg and the defect types of the ZnAl2O4 nanoparticles. PMID:26238034

  5. 2D Seismic Reflection Data across Central Illinois

    SciTech Connect

    Smith, Valerie; Leetaru, Hannes

    2014-09-30

    In a continuing collaboration with the Midwest Geologic Sequestration Consortium (MGSC) on the Evaluation of the Carbon Sequestration Potential of the Cambro-Ordovician Strata of the Illinois and Michigan Basins project, Schlumberger Carbon Services and WesternGeco acquired two-dimensional (2D) seismic data in the Illinois Basin. This work included the design, acquisition and processing of approximately 125 miles of (2D) seismic reflection surveys running west to east in the central Illinois Basin. Schlumberger Carbon Services and WesternGeco oversaw the management of the field operations (including a pre-shoot planning, mobilization, acquisition and de-mobilization of the field personnel and equipment), procurement of the necessary permits to conduct the survey, post-shoot closure, processing of the raw data, and provided expert consultation as needed in the interpretation of the delivered product. Three 2D seismic lines were acquired across central Illinois during November and December 2010 and January 2011. Traversing the Illinois Basin, this 2D seismic survey was designed to image the stratigraphy of the Cambro-Ordovician sections and also to discern the basement topography. Prior to this survey, there were no regionally extensive 2D seismic data spanning this section of the Illinois Basin. Between the NW side of Morgan County and northwestern border of Douglas County, these seismic lines ran through very rural portions of the state. Starting in Morgan County, Line 101 was the longest at 93 miles in length and ended NE of Decatur, Illinois. Line 501 ran W-E from the Illinois Basin – Decatur Project (IBDP) site to northwestern Douglas County and was 25 miles in length. Line 601 was the shortest and ran N-S past the IBDP site and connected lines 101 and 501. All three lines are correlated to well logs at the IBDP site. Originally processed in 2011, the 2D seismic profiles exhibited a degradation of signal quality below ~400 millisecond (ms) which made

  6. Are Temporal Differences in GDNF and NOS Isoform Induction Contributors to Neurodegeneration? A Fluorescence Microscopy-Based Study

    PubMed Central

    Doursout, Marie-Francoise; Liang, Yangyan; Schiess, Mya C.; Padilla, Angelica; Poindexter, Brian J.; Hickson-Bick, Diane L. M.; Bick, Roger J.

    2016-01-01

    Background: Specific factors in Parkinson’s disease have become targets as to their protective and degenerative effects. We have demonstrated that cytokines and PD-CSF detrimentally affect microglia and astrocyte growth. While glial cell-derived neurotrophic factor (GDNF) has been recognized as a possible neuron-rescue agent, nitric oxide synthase (NOS) has been implicated in neurodegenerative processes. Objective: To demonstrate that glial cell activation, cytokine production, and NOS induction, play an intimate role in the loss of dopaminergic signaling, via mechanisms that are a result of inflammation and inflammatory stimuli. Methods: Study animals were sacrificed following endotoxin treatment and tissue sections were harvested and probed for GDNF and NOS isomers by fluorescence deconvolution microscopy. Fluorescence was mapped and quantified for each probe Results: An immune cell influx into ‘vulnerable’ areas of the brain was seen, and three NOS isomers, inducible (iNOS), neuronal (nNOS) and endothelial (eNOS), were synthesized in the brains, a finding which suggests that each isomer has a role in neurodegeneration. eNOS was found associated with blood vessels, while iNOS was associated with glial and matrix cells and nNOS was located with both glia and neurons. Following endotoxin treatment, serum levels of nitric oxide were higher at 6-8 hours, while tissue levels of NOS were elevated for much longer. Thus, induction of NOS occurred earlier than the induction of GDNF. Conclusion: Our findings suggest that the protective abilities of GDNF to combat neural destruction are not available rapidly enough, and do not remain at sufficiently high levels long enough to assert its protective effects. (250). PMID:27651844

  7. CYP2D7 Sequence Variation Interferes with TaqMan CYP2D6*15 and *35 Genotyping

    PubMed Central

    Riffel, Amanda K.; Dehghani, Mehdi; Hartshorne, Toinette; Floyd, Kristen C.; Leeder, J. Steven; Rosenblatt, Kevin P.; Gaedigk, Andrea

    2016-01-01

    TaqMan™ genotyping assays are widely used to genotype CYP2D6, which encodes a major drug metabolizing enzyme. Assay design for CYP2D6 can be challenging owing to the presence of two pseudogenes, CYP2D7 and CYP2D8, structural and copy number variation and numerous single nucleotide polymorphisms (SNPs) some of which reflect the wild-type sequence of the CYP2D7 pseudogene. The aim of this study was to identify the mechanism causing false-positive CYP2D6*15 calls and remediate those by redesigning and validating alternative TaqMan genotype assays. Among 13,866 DNA samples genotyped by the CompanionDx® lab on the OpenArray platform, 70 samples were identified as heterozygotes for 137Tins, the key SNP of CYP2D6*15. However, only 15 samples were confirmed when tested with the Luminex xTAG CYP2D6 Kit and sequencing of CYP2D6-specific long range (XL)-PCR products. Genotype and gene resequencing of CYP2D6 and CYP2D7-specific XL-PCR products revealed a CC>GT dinucleotide SNP in exon 1 of CYP2D7 that reverts the sequence to CYP2D6 and allows a TaqMan assay PCR primer to bind. Because CYP2D7 also carries a Tins, a false-positive mutation signal is generated. This CYP2D7 SNP was also responsible for generating false-positive signals for rs769258 (CYP2D6*35) which is also located in exon 1. Although alternative CYP2D6*15 and *35 assays resolved the issue, we discovered a novel CYP2D6*15 subvariant in one sample that carries additional SNPs preventing detection with the alternate assay. The frequency of CYP2D6*15 was 0.1% in this ethnically diverse U.S. population sample. In addition, we also discovered linkage between the CYP2D7 CC>GT dinucleotide SNP and the 77G>A (rs28371696) SNP of CYP2D6*43. The frequency of this tentatively functional allele was 0.2%. Taken together, these findings emphasize that regardless of how careful genotyping assays are designed and evaluated before being commercially marketed, rare or unknown SNPs underneath primer and/or probe regions can impact

  8. CYP2D7 Sequence Variation Interferes with TaqMan CYP2D6 (*) 15 and (*) 35 Genotyping.

    PubMed

    Riffel, Amanda K; Dehghani, Mehdi; Hartshorne, Toinette; Floyd, Kristen C; Leeder, J Steven; Rosenblatt, Kevin P; Gaedigk, Andrea

    2015-01-01

    TaqMan™ genotyping assays are widely used to genotype CYP2D6, which encodes a major drug metabolizing enzyme. Assay design for CYP2D6 can be challenging owing to the presence of two pseudogenes, CYP2D7 and CYP2D8, structural and copy number variation and numerous single nucleotide polymorphisms (SNPs) some of which reflect the wild-type sequence of the CYP2D7 pseudogene. The aim of this study was to identify the mechanism causing false-positive CYP2D6 (*) 15 calls and remediate those by redesigning and validating alternative TaqMan genotype assays. Among 13,866 DNA samples genotyped by the CompanionDx® lab on the OpenArray platform, 70 samples were identified as heterozygotes for 137Tins, the key SNP of CYP2D6 (*) 15. However, only 15 samples were confirmed when tested with the Luminex xTAG CYP2D6 Kit and sequencing of CYP2D6-specific long range (XL)-PCR products. Genotype and gene resequencing of CYP2D6 and CYP2D7-specific XL-PCR products revealed a CC>GT dinucleotide SNP in exon 1 of CYP2D7 that reverts the sequence to CYP2D6 and allows a TaqMan assay PCR primer to bind. Because CYP2D7 also carries a Tins, a false-positive mutation signal is generated. This CYP2D7 SNP was also responsible for generating false-positive signals for rs769258 (CYP2D6 (*) 35) which is also located in exon 1. Although alternative CYP2D6 (*) 15 and (*) 35 assays resolved the issue, we discovered a novel CYP2D6 (*) 15 subvariant in one sample that carries additional SNPs preventing detection with the alternate assay. The frequency of CYP2D6 (*) 15 was 0.1% in this ethnically diverse U.S. population sample. In addition, we also discovered linkage between the CYP2D7 CC>GT dinucleotide SNP and the 77G>A (rs28371696) SNP of CYP2D6 (*) 43. The frequency of this tentatively functional allele was 0.2%. Taken together, these findings emphasize that regardless of how careful genotyping assays are designed and evaluated before being commercially marketed, rare or unknown SNPs underneath primer

  9. Cervical cancer cell lines expressing NKG2D-ligands are able to down-modulate the NKG2D receptor on NKL cells with functional implications

    PubMed Central

    2012-01-01

    Background Cervical cancer represents the third most commonly diagnosed cancer and the fourth leading cause of cancer-related deaths in women worldwide. Natural killer (NK) cells play an important role in the defense against viruses, intracellular bacteria and tumors. NKG2D, an activating receptor on NK cells, recognizes MHC class I chain-related molecules, such as MICA/B and members of the ULBP/RAET1 family. Tumor-derived soluble NKG2D-ligands have been shown to down-modulate the expression of NKG2D on NK cells. In addition to the down-modulation induced by soluble NKG2D-ligands, it has recently been described that persistent cell-cell contact can also down-modulate NKG2D expression. The goal of this study was to determine whether the NKG2D receptor is down-modulated by cell-cell contact with cervical cancer cells and whether this down-modulation might be associated with changes in NK cell activity. Results We demonstrate that NKG2D expressed on NKL cells is down-modulated by direct cell contact with cervical cancer cell lines HeLa, SiHa, and C33A, but not with non-tumorigenic keratinocytes (HaCaT). Moreover, this down-modulation had functional implications. We found expression of NKG2D-ligands in all cervical cancer cell lines, but the patterns of ligand distribution were different in each cell line. Cervical cancer cell lines co-cultured with NKL cells or fresh NK cells induced a marked diminution of NKG2D expression on NKL cells. Additionally, the cytotoxic activity of NKL cells against K562 targets was compromised after co-culture with HeLa and SiHa cells, while co-culture with C33A increased the cytotoxic activity of the NKL cells. Conclusions Our results suggest that differential expression of NKG2D-ligands in cervical cancer cell lines might be associated with the down-modulation of NKG2D, as well as with changes in the cytotoxic activity of NKL cells after cell-cell contact with the tumor cells. PMID:22316211

  10. Discrimination of rewetted / renaturated habitats from natural moist habitat in a mire by means of DOM quality differences using fluorescence indices

    NASA Astrophysics Data System (ADS)

    Herzsprung, Peter; Osterloh, Katja; von Tümpling, Wolf; Harir, Mourad; Hertkorn, Norbert; Meissner, Ralf; Friese, Kurt; Bernsdorf, Sabine; Schmitt-Kopplin, Philippe

    2015-04-01

    Discrimination of rewetted / renaturated habitats from natural moist habitat in a mire by means of DOM quality differences using fluorescence indices Mires can be a potential source of dissolved organic matter load (DOC) in fresh water catchment areas. Renaturation and rewetting of formerly drained mire sites is often debated in terms of nature protection aspects as well as in terms of climatic and adjacent water protection. Latter aspect is closely connected with the drinking water supply and thus of major human interest. In this case the Central German uplands play an important role. For estimation of potential leaching of humic substances the principal comparison of natural habitat with artificially rewetted habitats concerning dissolved organic matter quality can be of interest. In this regard a partly rewetted mire in the Harz Mountains, Germany was investigated. Seven locations, one oligotrophic natural, one mesotrophic natural, and together 5 rewetted locations were investigated. The soil water of all sites was sampled monthly and its quality was analysed by bulk parameters like DOC and bulk optical parameters like excitation emission matrix fluorescence (EEM) and UV spectra. Water was pumped from piezometers and immediately filtered. Each site consisted of four parallel piezometers in the peat soil. Samples were stored at 4° C before analysis. All spectroscopic data, both UV spectra and EEM were recorded simultaneously. Fluorescence EEMs were collected using a spectrofluorometer (AQUALOG, HORIBA Jobin Yvon, USA). Fluorescence intensity was measured during emission scans (240 nm - 600 nm every 3.27 nm, 8 pixel) at set excitation wavelength in 3 nm increments from 240 nm to 600 nm. The fluorescence indices freshness (ß/α), Fluorescence Index (FI), and Humification Index (HIX) were calculated [1] from the inner filter effect (IFE) corrected EEM spectra. The natural habitat could be clearly discriminated from the rewetted sites. The DOC, UV absorption at 254

  11. TOPAZ2D heat transfer code users manual and thermal property data base

    SciTech Connect

    Shapiro, A.B.; Edwards, A.L.

    1990-05-01

    TOPAZ2D is a two dimensional implicit finite element computer code for heat transfer analysis. This user's manual provides information on the structure of a TOPAZ2D input file. Also included is a material thermal property data base. This manual is supplemented with The TOPAZ2D Theoretical Manual and the TOPAZ2D Verification Manual. TOPAZ2D has been implemented on the CRAY, SUN, and VAX computers. TOPAZ2D can be used to solve for the steady state or transient temperature field on two dimensional planar or axisymmetric geometries. Material properties may be temperature dependent and either isotropic or orthotropic. A variety of time and temperature dependent boundary conditions can be specified including temperature, flux, convection, and radiation. Time or temperature dependent internal heat generation can be defined locally be element or globally by material. TOPAZ2D can solve problems of diffuse and specular band radiation in an enclosure coupled with conduction in material surrounding the enclosure. Additional features include thermally controlled reactive chemical mixtures, thermal contact resistance across an interface, bulk fluid flow, phase change, and energy balances. Thermal stresses can be calculated using the solid mechanics code NIKE2D which reads the temperature state data calculated by TOPAZ2D. A three dimensional version of the code, TOPAZ3D is available. The material thermal property data base, Chapter 4, included in this manual was originally published in 1969 by Art Edwards for use with his TRUMP finite difference heat transfer code. The format of the data has been altered to be compatible with TOPAZ2D. Bob Bailey is responsible for adding the high explosive thermal property data.

  12. GEO2D - Two-Dimensional Computer Model of a Ground Source Heat Pump System

    SciTech Connect

    James Menart

    2013-06-07

    This file contains a zipped file that contains many files required to run GEO2D. GEO2D is a computer code for simulating ground source heat pump (GSHP) systems in two-dimensions. GEO2D performs a detailed finite difference simulation of the heat transfer occurring within the working fluid, the tube wall, the grout, and the ground. Both horizontal and vertical wells can be simulated with this program, but it should be noted that the vertical wall is modeled as a single tube. This program also models the heat pump in conjunction with the heat transfer occurring. GEO2D simulates the heat pump and ground loop as a system. Many results are produced by GEO2D as a function of time and position, such as heat transfer rates, temperatures and heat pump performance. On top of this information from an economic comparison between the geothermal system simulated and a comparable air heat pump systems or a comparable gas, oil or propane heating systems with a vapor compression air conditioner. The version of GEO2D in the attached file has been coupled to the DOE heating and cooling load software called ENERGYPLUS. This is a great convenience for the user because heating and cooling loads are an input to GEO2D. GEO2D is a user friendly program that uses a graphical user interface for inputs and outputs. These make entering data simple and they produce many plotted results that are easy to understand. In order to run GEO2D access to MATLAB is required. If this program is not available on your computer you can download the program MCRInstaller.exe, the 64 bit version, from the MATLAB website or from this geothermal depository. This is a free download which will enable you to run GEO2D..

  13. 2D vibrational properties of epitaxial silicene on Ag(111)

    NASA Astrophysics Data System (ADS)

    Solonenko, Dmytro; Gordan, Ovidiu D.; Le Lay, Guy; Sahin, Hasan; Cahangirov, Seymur; Zahn, Dietrich R. T.; Vogt, Patrick

    2017-03-01

    The two-dimensional silicon allotrope, silicene, could spur the development of new and original concepts in Si-based nanotechnology. Up to now silicene can only be epitaxially synthesized on a supporting substrate such as Ag(111). Even though the structural and electronic properties of these epitaxial silicene layers have been intensively studied, very little is known about its vibrational characteristics. Here, we present a detailed study of epitaxial silicene on Ag(111) using in situ Raman spectroscopy, which is one of the most extensively employed experimental techniques to characterize 2D materials, such as graphene, transition metal dichalcogenides, and black phosphorous. The vibrational fingerprint of epitaxial silicene, in contrast to all previous interpretations, is characterized by three distinct phonon modes with A and E symmetries. Both, energies and symmetries of theses modes are confirmed by ab initio theory calculations. The temperature dependent spectral evolution of these modes demonstrates unique thermal properties of epitaxial silicene and a significant electron-phonon coupling. These results unambiguously support the purely two-dimensional character of epitaxial silicene up to about 300 °C, whereupon a 2D-to-3D phase transition takes place. The detailed fingerprint of epitaxial silicene will allow us to identify it in different environments or to study its modifications.

  14. Dynamics of quasi 2D co-rotating vortex merger

    NASA Astrophysics Data System (ADS)

    Khandekar, Akshay G.

    Merger of vortices is examined experimentally to compare the merger of slender parallel vortices generated coincidentally. It is known that like-sign vortices rotate around a common center of circulation and merger between the vortices may occur under certain conditions. This merger is dependent on the strength of the vortex circulation, distance of separation between the centers of the two vortices, ReGamma, and vorticity distribution. Quasi-2D experimental data is examined and merger relations are derived. The 2D experiments conducted in a vortex generator tank uses high aspect ratio rotating paddles. The vortex merger tank generates slender co-rotating vortices and are examined using PIV (Particle Image Velocimetry). Merger characteristics are compared at centerline, 25% span and 5% span for different circulation strengths. Symmetric and asymmetric mergers are studied and it is found that in both cases, the vortex pair rotates around an axis perpendicular to the plane of the vortex pair. Symmetric merger is seen to occur at the center between the two vortices whereas in asymmetric merger the stronger vortex breaks the weaker vortex filaments and continues to follow its path. Wall effects seem to have an effect of vortex braiding and vortex stretching. Closer to the wall, the merger time increases while the merged vortex dissipates faster than at the centerline.

  15. Microwave Imaging with Infrared 2-D Lock-in Amplifier

    NASA Astrophysics Data System (ADS)

    Chiyo, Noritaka; Arai, Mizuki; Tanaka, Yasuhiro; Nishikata, Atsuhiro; Maeno, Takashi

    We have developed a 3-D electromagnetic field measurement system using 2-D lock-in amplifier. This system uses an amplitude modulated electromagnetic wave source to heat a resistive screen. A very small change of temperature on a screen illuminated with the modulated electromagnetic wave is measured using an infrared thermograph camera. In this paper, we attempted to apply our system to microwave imaging. By placing conductor patches in front of the resistive screen and illuminating with microwave, the shape of each conductor was clearly observed as the temperature difference image of the screen. In this way, the conductor pattern inside the non-contact type IC card could be visualized. Moreover, we could observe the temperature difference image reflecting the shape of a Konnyaku (a gelatinous food made from devil's-tonge starch) or a dried fishbone, both as non-conducting material resembling human body. These results proved that our method is applicable to microwave see-through imaging.

  16. Robust 2D phase unwrapping based on multiresolution

    NASA Astrophysics Data System (ADS)

    Davidson, Gordon W.; Bamler, Richard

    1996-12-01

    An approach to 2D phase unwrapping for SAR interferometry is presented, based on separate steps of coarse phase and fine phase estimation. The coarse phase is constructed from instantaneous frequency estimates obtained using adaptive multiresolution, in which estimation is done of difference frequencies between resolution levels, and the frequency differences are summed over resolution levels such that a conservative phase gradient field is maintained. This allows a smoothed coarse unwrapped phase, which achieves the full terrain height, to be obtained with an unweighted least squares phase construction. The coarse phase is used to remove the bulk of the phase variation of the interferogram, allowing more accurate multilooking, and the resulting fine phase in unwrapped with weighted least squares. The unwrapping approach is verified on simulated interferograms.

  17. Feasibility of different cleaning methods for silver-copper alloys by X-ray fluorescence: Application to ancient Greek silver coins

    NASA Astrophysics Data System (ADS)

    Moreno-Suárez, A. I.; Ager, F. J.; Rodríquez-Segovia, C.; Gómez-Morón, A.; Chaves, F.; Scrivano, S.; Gómez-Tubío, B.; Pliego, R.; Respaldiza, M. A.

    2016-02-01

    Archeological pieces with high Ag concentrations often have a surface enrichment of Ag. Usually, researchers in this field do not agree on the causes of these enrichments, one of which could be the cleaning procedures. In this work, a set of 18 ancient Greek silver coins was selected to study the effects of different cleaning procedures in terms of producing a surface Ag enrichment. The aim of this study is to find and select the less aggressive one in terms of the lower modification of Ag concentrations and visual aspect. These coins were analyzed by X-ray fluorescence (XRF) before and after each cleaning procedure.

  18. Application of the total reflection X-ray fluorescence method to the elemental analysis of brain tumors of different types and grades of malignancy

    NASA Astrophysics Data System (ADS)

    Lankosz, M. W.; Grzelak, M.; Ostachowicz, B.; Wandzilak, A.; Szczerbowska-Boruchowska, M.; Wrobel, P.; Radwanska, E.; Adamek, D.

    2014-11-01

    The process of carcinogenesis may influence normal biochemical reactions leading to alterations in the elemental composition of the tissue. Total reflection X-ray fluorescence analysis (TXRF) was applied to the elemental analysis of different brain tumors. The following elements were present in all the neoplastic tissues analyzed: K, Ca, Fe, Cu, Zn and Rb. The results of the analysis showed that the elemental composition of a relatively small fragment of tissue represents satisfactorily the biochemical “signature” of a cancer. On the basis of the element concentrations determined, it was possible to differentiate between some types of brain tumors.

  19. [Effects of different water potentials on leaf gas exchange and chlorophyll fluorescence parameters of cucumber during post-flowering growth stage].

    PubMed

    Lin, Lu; Tang, Yun; Zhang, Ji-tao; Yan, Wan-li; Xiao, Jian-hong; Ding, Chao; Dong, Chuan; Ji, Zeng-shun

    2015-07-01

    Impacts of different substrate water potentials (SWP) on leaf gas exchange and chlorophyll fluorescence parameters of greenhouse cucumber during its post-flowering growth stage were analyzed in this study. The results demonstrated that -10 and -30 kPa were the critical values for initiating stomatal and non-stomatal limitation of drought stress, respectively. During the stage of no drought stress (-10 kPa < SWP ≤ 0 kPa), gas exchange parameters and chlorophyll fluorescence parameters were not different significantly among treatments. During the stage of stomatal limitation of drought stress (-30 kPafluorescence parameters and differed significantly among treatments. During the stage of non-stomatal limitation of drought stress (-45 kPa≤SWP ≤ -30 kPa), with the decrease of SWP, light saturation point (LSP), Rd, CE, Vcmax, VTPU, LS, WUEi, ΦpPSII, Fv/Fm and qp decreased, while CCP, Ci and qN increased. In this stage, chlorophyll fluorescence parameters changed faster than gas exchange parameters and differed significantly among treatments. In production of greenhouse cucumber, -10 and -5 kPa should be the lower and upper limit value of irrigation, respectively. The stomatal

  20. Scale-free behavior of a 2D complex plasma during rapid cooling.

    PubMed

    Knapek, C A; Durniak, C; Samsonov, D; Morfill, G E

    2013-01-18

    Experimental evidence is presented for a scale-free transition from an unordered to an ordered state in a 2D complex plasma that differs from the KTHNY theory of phase transitions in 2D systems. The transition is characterized by the formation and growth of ordered domains. A fractal relationship is found between the domain areas and domain boundary lengths, which can be explained by a recent theoretical model. The experimental findings are supported by a molecular dynamics simulation of a 2D particle system.

  1. Efficient screening of 2D molecular polymorphs at the solution-solid interface

    NASA Astrophysics Data System (ADS)

    Lee, Shern-Long; Adisoejoso, Jinne; Fang, Yuan; Tahara, Kazukuni; Tobe, Yoshito; Mali, Kunal S.; de Feyter, Steven

    2015-03-01

    Formation of multiple polymorphs during two-dimensional (2D) crystallization of organic molecules is more of a routine occurrence than rarity. Although such diverse crystalline structures provide exciting possibilities for studying crystal engineering in 2D, predicting the occurrence of polymorphs for a given building block is often non-trivial. Moreover, there is scarcity of methods that can experimentally verify the presence of such crystalline polymorphs in a straightforward fashion. Here we demonstrate a relatively simple experimental approach for screening of 2D polymorphs formed at the solution-solid interface. The strategy involves use of solution flow produced by contacting a piece of tissue paper to the sample to generate a lateral density gradient along the substrate surface. In situ generation of such gradient allows rapid discovery and nanoscale separation of multiple 2D polymorphs in a single experiment. The concept is demonstrated using three structurally different building blocks that differ in terms of intermolecular interactions responsible for 2D crystal formation. The method described here represents a powerful tool for efficient screening of 2D polymorphs formed at the solution-solid interface.Formation of multiple polymorphs during two-dimensional (2D) crystallization of organic molecules is more of a routine occurrence than rarity. Although such diverse crystalline structures provide exciting possibilities for studying crystal engineering in 2D, predicting the occurrence of polymorphs for a given building block is often non-trivial. Moreover, there is scarcity of methods that can experimentally verify the presence of such crystalline polymorphs in a straightforward fashion. Here we demonstrate a relatively simple experimental approach for screening of 2D polymorphs formed at the solution-solid interface. The strategy involves use of solution flow produced by contacting a piece of tissue paper to the sample to generate a lateral density

  2. Relationship between CYP 2D6 metabolic status and sexual dysfunction in paroxetine treatment.

    PubMed

    Zourková, Alexandra; Hadasová, Eva

    2002-01-01

    This article describes the incidence of sexual dysfunction in 30 patients subjected to long-term treatment by paroxetine in dependence on the P 450 CYP 2D6 isoenzyme metabolic status. Measured on the Arizona Sexual Experience Scale (ASEX; McGahuey, Delgado, & Gelenberg, 1999), the incidence of sexual dysfunction in patients converted to CYP 2D6 poor metabolizers was markedly higher compared with patients who had no history of such conversion, a difference that reached the level of statistical significance. Our article discusses the incidence of sexual dysfunction in connection with reduced CYP 2D6 capacity.

  3. Residual lens effects in 2D mode of auto-stereoscopic lenticular-based switchable 2D/3D displays

    NASA Astrophysics Data System (ADS)

    Sluijter, M.; IJzerman, W. L.; de Boer, D. K. G.; de Zwart, S. T.

    2006-04-01

    We discuss residual lens effects in multi-view switchable auto-stereoscopic lenticular-based 2D/3D displays. With the introduction of a switchable lenticular, it is possible to switch between a 2D mode and a 3D mode. The 2D mode displays conventional content, whereas the 3D mode provides the sensation of depth to the viewer. The uniformity of a display in the 2D mode is quantified by the quality parameter modulation depth. In order to reduce the modulation depth in the 2D mode, birefringent lens plates are investigated analytically and numerically, by ray tracing. We can conclude that the modulation depth in the 2D mode can be substantially decreased by using birefringent lens plates with a perfect index match between lens material and lens plate. Birefringent lens plates do not disturb the 3D performance of a switchable 2D/3D display.

  4. Effects of repeated treatment with the dopamine D2/D3 receptor partial agonist aripiprazole on striatal D2/D3 receptor availability in monkeys

    PubMed Central

    Czoty, Paul W.; Gage, H. Donald; Garg, Pradeep K.; Garg, Sudha; Nader, Michael A.

    2013-01-01

    Rationale Chronic treatment with dopamine (DA) receptor agonists and antagonists can differentially affect measures of DA D2/D3 receptor number and function, but the effects of chronic treatment with a partial D2/D3 receptor agonist are not clear. Objective We used a within-subjects design in male cynomolgus monkeys to determine the effects of repeated (17-day) treatment with the D2/D3 receptor partial agonist aripiprazole (ARI; 0.03 mg/kg and 0.1 mg/kg i.m.) on food-reinforced behavior (n=5) and on D2/D3 receptor availability as measured with positron emission tomography (PET; n=9). Methods Five monkeys responded under a fixed-ratio 50 schedule of food reinforcement and D2/D3 receptor availability was measured before and four days after ARI treatment using PET and the D2/D3 receptor-selective radioligand [18F]fluoroclebopride (FCP). Four additional monkeys were studied using [11C]raclopride and treated sequentially with each dose of ARI for 17 days. Results ARI decreased food-maintained responding with minimal evidence of tolerance. Repeated ARI administration increased FCP and raclopride distribution volume ratios (DVRs) in the caudate nucleus and putamen in most monkeys, but decreases were observed in monkeys with the highest baseline DVRs. Conclusions The results indicate that repeated treatment with a low efficacy DA receptor partial agonist produces effects on brain D2/D3 receptor availability that are qualitatively different from those of both high-efficacy receptor agonists and antagonists, and suggest that the observed individual differences in response to ARI treatment may reflect its partial agonist activity. PMID:24077804

  5. How to characterize thermal transport capability of 2D materials fairly? - Sheet thermal conductance and the choice of thickness

    NASA Astrophysics Data System (ADS)

    Wu, Xufei; Varshney, Vikas; Lee, Jonghoon; Pang, Yunsong; Roy, Ajit K.; Luo, Tengfei

    2017-02-01

    Thermal transport capability of monolayer 2D materials has been under constant spotlight. However, different definitions of thickness in literature have led to ambiguity towards predicting thermal conductivity values and thus in understanding the heat transfer capability of different monolayer 2D materials. We argue that the same thickness should be used and a 'sheet thermal conductance' should be defined as an intensive 2D material property when characterizing the heat transfer capability of 2D materials. When converting literature thermal conductivity values of monolayer materials to this new property, some new features that were not displayed when using different thicknesses show up.

  6. Different PS application methods for laserlight-induced fluorescence diagnostics (LIFD) of dysplasia and early cancer of the colon

    NASA Astrophysics Data System (ADS)

    Gahlen, Johannes; Pressmar, Jochen; Stern, Josef; Boehm, J.; Sinn, Hanns-joerg; Born, I. A.; Holle, R.; Herfarth, Christian

    1997-12-01

    Conventional diagnostics fail to trace dysplasias and early cancers of the colon. By means of Laserlight Induced Fluorescence Diagnostics (LIFD) macroscopically not visible malignant tumors and dysplasias of the colon can be detected. The main side effect of systemically applicated photosensitizers is a general photosensibilization of the organism which provokes an increased photosensitivity of the body. Local application of (delta) -aminolevulinic acid (ALA) reduces systemic uptake without impairment of the quality of investigation. Colorectal cancer in male wistar rats was induced by weekly subcutaneous (s.c.) injections of 1,2- dimethylhydrazine (DMH) for 17 weeks. After s.c. DMH injection the wistar rats (n equals 25) developed in average 5.6 macroscopically visible colon carcinomas. 80% of these tumor were detected by LIFD after photosensibilization with Photofrin II intravenously (i.v.), 29% after application of mTHPC (i.v.), 13% after ALA (i.v.), 20% after intraperitoneal application of ALA (i.p.) and 57% after local application of ALA in the colon. LIFD is a capable method for the detection of macroscopically not visible dysplasias and colon carcinomas of the rat induced by DMH. The applied PS and the method of application influences the detection of carcinomas and dysplasias. Systemic photosensibilization of the whole organism can be avoided by the local application of ALA without limiting the quality of investigation.

  7. Crossing barriers: the new dimension of 2D cell migration assays.

    PubMed

    Van Horssen, Remco; ten Hagen, Timo L M

    2011-01-01

    In our body cells move in three dimensions, embedded in an extracellular matrix that varies in composition, density and stiffness, and this movement is fundamental to life. Next to 3D cell migration assays, representing these physiological circumstances, still we need 2D migrations assays to perform detailed studies on the contribution of matrix-components and (extra)cellular proteins to cell movements. Next to the debate on differences between 3D and 2D migration, there also are many new perspectives on the use and development of novel or modified 2D cell migration assays. Of special significance is the introduction of so-called barrier migration assays, methods that avoid cell and matrix damage, as complementation or replacement of scratch/wound healing assays. Here, we discuss the possibilities and limitations of different 2D barrier migration assays.

  8. The Effect of CYP2D6 Drug-Drug Interactions on Hydrocodone Effectiveness

    PubMed Central

    Monte, Andrew A.; Heard, Kennon J.; Campbell, Jenny; Hamamura, D.; Weinshilboum, Richard M.; Vasiliou, Vasilis

    2014-01-01

    Objectives The hepatic cytochrome 2D6 (CYP2D6) is a saturable enzyme responsible for metabolism of approximately 25% of known pharmaceuticals. CYP interactions can alter the efficacy of prescribed medications. Hydrocodone is largely dependent on CYP2D6 metabolism for analgesia, ondansetron is inactivated by CYP2D6, and oxycodone analgesia is largely independent of CYP2D6. The objective was to determine if CYP2D6 medication co-ingestion decreases the effectiveness of hydrocodone. Methods This was a prospective observational study conducted in an academic U.S. emergency department (ED). Subjects were included if they had self-reported pain or nausea; and were excluded if they were unable to speak English, were less than 18 years of age, had liver or renal failure, or carried diagnoses of chronic pain or cyclic vomiting. Detailed drug ingestion histories for the preceding 48 hours prior to the ED visit were obtained. The patient's pain and nausea were quantified using a 100-millimeter visual analogue scale (VAS) at baseline prior to drug administration and following doses of hydrocodone, oxycodone, or ondansetron. We used a mixed model with random subject effect to determine the interaction between CYP2D6 drug ingestion and study drug effectiveness. Odds ratios (OR) were calculated to compare clinically significant VAS changes between CYP2D6 users and non-users. Results Two hundred fifty (49.8%) of the 502 subjects enrolled had taken at least one CYP2D6 substrate, inhibitor, or inducing pharmaceutical, supplement, or illicit drug in the 48 hours prior to ED presentation. CYP2D6-drug users were one third as likely to respond to hydrocodone (OR 0.33, 95% CI = 0.1 to 0.8), and more than three times as likely as non-users to respond to ondansetron (OR 3.4, 95% CI = 1.3 to 9.1). There was no significant difference in oxycodone effectiveness between CYP2D6 users and non-users (OR 0.53, 95% CI = 0.3 to 1.1). Conclusions CYP2D6 drug-drug interactions appear to change

  9. CYP2D6 polymorphisms and their influence on risperidone treatment

    PubMed Central

    Puangpetch, Apichaya; Vanwong, Natchaya; Nuntamool, Nopphadol; Hongkaew, Yaowaluck; Chamnanphon, Monpat; Sukasem, Chonlaphat

    2016-01-01

    Cytochrome P450 enzyme especially CYP2D6 plays a major role in biotransformation. The interindividual variations of treatment response and toxicity are influenced by the polymorphisms of this enzyme. This review emphasizes the effect of CYP2D6 polymorphisms in risperidone treatment in terms of basic knowledge, pharmacogenetics, effectiveness, adverse events, and clinical practice. Although the previous studies showed different results, the effective responses in risperidone treatment depend on the CYP2D6 polymorphisms. Several studies suggested that CYP2D6 polymorphisms were associated with plasma concentration of risperidone, 9-hydroxyrisperidone, and active moiety but did not impact on clinical outcomes. In addition, CYP2D6 poor metabolizer showed more serious adverse events such as weight gain and prolactin than other predicted phenotype groups. The knowledge of pharmacogenomics of CYP2D6 in risperidone treatment is increasing, and it can be used for the development of personalized medication in term of genetic-based dose recommendation. Moreover, the effects of many factors in risperidone treatment are still being investigated. Both the CYP2D6 genotyping and therapeutic drug monitoring are the important steps to complement the genetic-based risperidone treatment. PMID:27942231

  10. Divergences in KIR2D+ natural killer and KIR2D+CD8+ T-cell reconstitution following liver transplantation.

    PubMed

    López-Álvarez, M R; Campillo, J A; Legaz, I; Blanco-García, R M; Salgado-Cecilia, G; Bolarín, J M; Gimeno, L; Gil, J; García-Alonso, A M; Muro, M; Alvarez-López, M R; Miras, M; Minguela, A

    2011-03-01

    Natural killer (NK) and CD8(+) T cells may be active elements in the allograft response, but little is known about their role in liver transplantation. Some of these cells express killer immunoglobulin-like receptors (KIRs), which after binding specific ligands may transmit inhibitory/activating signals. In this study, circulating NK and CD8(+) T cells expressing CD158a/h (KIR2DL1/S1) or CD158b/j (KIR2DL2/3/S(2)) receptors were analyzed in 142 liver recipients by flow cytometry. They were underrepresented in patients before transplantation, but following transplantation, whereas the KIR2D(+) NK subsets experienced a late recuperation (day 365) mainly in C2-homozygous patients developing early acute rejection, recovery of the 2 CD8(+)KIR2D(+) T cells started earlier, showing significant differences on day 365 between patients without acute rejection and those suffering from it (p = 0.004 and p < 0.0001, respectively). These differences were also evident when the human leukocute antigen-C genotypes of the recipient were considered. In conclusion, whereas the late recovery of KIR2D(+) NK cells in C2/C2 patients appears to be linked to acute rejection, the increase in early CD8(+)KIR2D(+) T cells in overall liver recipients correlates with a most successful early graft outcome. Therefore, monitoring of KIR2D(+) cells appears to be a useful tool for liver transplant follow-up.

  11. Fractal dimension as a measure of altered actin cytoskeleton in MC3T3-E1 cells under simulated microgravity using 3-D/2-D clinostats.

    PubMed

    Qian, A R; Li, D; Han, J; Gao, X; Di, S M; Zhang, W; Hu, L F; Shang, Peng

    2012-05-01

    Osteoblasts, the bone-forming cells, respond to various mechanical forces, such as stretch and fluid shear force in essentially similar ways. The cytoskeleton, as the load-bearing architecture of the cell, is sensitive to altered inertial forces. Disruption of the cytoskeleton will result in alteration of cellular structure and function. However, it is difficult to quantitatively illustrate cytoskeletal rearrangement because of the complexity of cytoskeletal structure. Usually, the morphological changes in actin organization caused by external stimulus are basically descriptive. In this study, fractal dimensions (D) analysis was used to quantify the morphological changes in the actin cytoskeleton of osteoblast-like cells (MC3T3-E1) under simulated microgravity using 3-D/2-D clinostats. The ImageJ software was used to count the fractal dimension of actin cytoskeleton by box-counting methods. Real-time PCR and immunofluroscent assays were used to further confirm the results obtained by fractal dimension analysis. The results showed significant decreases in D value of actin cytoskeleton, β-actin mRNA expression, and the mean fluorescence intensity of F-actin in osteoblast-like cells after 24 or 48 h of incubation under 3-D/2-D clinorotation condition compared with control. The findings indicate that 3-D/2-D clinorotation affects both actin cytoskeleton architecture and mRNA expression, and fractal may be a promising approach for quantitative analysis of the changes in cytoskeleton in different environments.

  12. Eurasian Seismic Surveillance - 2D FD Seismic Synthetics and Event Discrimination

    DTIC Science & Technology

    1993-12-22

    for 2D finite difference (FD) synthetic seismogram experiments . The results here are encouraging in the sense that models incorporating small scale... ProMAX screendump of synthetic seismograms generated for the model shown in Fig. 2.4.1. The receivers were placed with 3 km intervals in the range x=13 to...our 2D FD synthetic seismogram experiments is that a simple lithosphere model, being moderately heterogeneous, gives rise to complex seismograms which

  13. Synthetic Covalent and Non-Covalent 2D Materials.

    PubMed

    Boott, Charlotte E; Nazemi, Ali; Manners, Ian

    2015-11-16

    The creation of synthetic 2D materials represents an attractive challenge that is ultimately driven by their prospective uses in, for example, electronics, biomedicine, catalysis, sensing, and as membranes for separation and filtration. This Review illustrates some recent advances in this diverse field with a focus on covalent and non-covalent 2D polymers and frameworks, and self-assembled 2D materials derived from nanoparticles, homopolymers, and block copolymers.

  14. Controllable self-assembly of NaREF4 upconversion nanoparticles and their distinctive fluorescence properties

    NASA Astrophysics Data System (ADS)

    Liu, Xiaoxia; Ni, Yaru; Zhu, Cheng; Fang, Liang; Kou, Jiahui; Lu, Chunhua; Xu, Zhongzi

    2016-07-01

    The paper presents the growth of hexagonal NaYF4:Yb3+, Tm3+ nanocrystals with tunable sizes induced by different contents of doped Yb3+ ions (10%-99.5%) using the thermal decomposition method. These nanoparticles, which have different sizes, are then self-assembled at the interface of cyclohexane and ethylene and transferred onto a normal glass slide. It is found that the size of nanoparticles directs their self-assembly. Due to the appropriate size of 40.5 nm, 15% Yb3+ ions doped nanoparticles are able to be self-assembled into an ordered inorganic monolayer membrane with a large area of about 10 × 10 μm2. More importantly, the obvious short-wave (300-500 nm) fluorescence improvement of the ordered 2D self-assembly structure is observed to be relative to disordered nanoparticles, which is because intrinsic absorption and scattering of upconversion nanoparticles leads to the self-loss of fluorescence, especially the short-wave fluorescence inside the disordered structure, and the relative emission of short-wave fluorescence is reduced. The construction of a 2D self-assembly structure can effectively avoid this and improve the radiated short-wave fluorescence, especially UV photons, and is able to direct the design of new types of solid-state optical materials in many fields.

  15. 2D ultrasonic elastography with lateral displacement estimation using statistics.

    PubMed

    Zhang, Zhihong; Liu, Haolin; Cheng, Yangjie

    2014-01-01

    Ultrasound elastography is the method of obtaining relative stiffness information of biological tissue, which plays an important role in early diagnosis. Generally, a gradient-based strain imaging algorithm assumes that motion only occurs in an axial direction. However, because tissue has different relative stiffness, the scatter presents lateral motion under high freehand compression. Therefore, errors occur in estimating the cross-correlation phase in the calculation window. A 2D elastography algorithm with lateral displacement estimation using statistics was proposed to reduce errors. The new method was investigated through simulation, and the experiment confirmed that errors introduced by lateral tissue movement have been greatly reduced with no sacrifice of real-time ultrasonic imaging quality.

  16. Comparison of the effect of anti-hyperlipidemic drugs from different groups on the phase profile of liposomal membrane-a fluorescence anisotropy study

    NASA Astrophysics Data System (ADS)

    Bhandary, Suman; Basu, Ruma; Das, Sukhen; Nandy, Papiya

    2010-07-01

    The study compares the effect of incorporation of three different groups of anti-hyperlipidemic drugs, namely niacin, simvastatin, and fenofibrate on the phase profile of liposomal membranes of dipalmitoylphosphatidylcholine (DPPC). The fluorescence anisotropy studies, using 1,6-diphenyl-1,3,5-hexatriene as fluorescent probe, have shown that the lipophilic molecule fenofibrate changes phase behavior of DPPC liposomal membrane to a greater extent compared to the changes produced by amphiphilic simvastatin and hydrophilic niacin. This variation in effect can be attributed to the nature of the drug molecules and hence their location in different parts of the liposomal membrane. We have also calculated the changes in van't Hoff enthalpy values in all these three cases and observed that these values decreased with increase in drug concentrations in the case of simvastatin but for fenofibrate and niacin the effect is completely the reverse. In order to get a better insight, the fraction of motionally restricted lipid molecules has been calculated.

  17. Theoretical modelling of X-ray fluorescence signals for different lunar compositions and dependence on solar activity

    NASA Astrophysics Data System (ADS)

    Banerjee, D.; Vadawale, S.

    2010-09-01

    We present a forward modelling technique for calculating the surface X-ray spectra for a variety of lunar terrains. Our calculations considered variations in solar fluxes from solar quiescent condition to large flare activity (M1 flare), and expected elemental concentrations in the target, as well as yield, instrumental, and viewing geometry parameters for X-ray induced fluorescence from the lunar surface. Additionally, we present estimates of anticipated XRF signals from prominent K α lines observable by a collimated 14 cm 2 X-ray detector from a 100 km lunar orbit with ˜20 km spatial resolution. Our results show that Mg, Al and Si characteristic K α lines can be observed for all solar conditions. The Ca K α lines line can be differentiated from a fixed background during more energetic solar conditions such as C1 and M1 flares, whereas Ti and Fe lines are identifiable only during C1 and M1 solar flare conditions for Apollo 12 site composition. Both the K α X-ray intensity ratios of Mg/Si and Al/Si correlate well with concentration ratios of Mg/Si and Al/Si, respectively, for B1 and M1 solar conditions. The K α X-ray intensity ratios of Fe/Si and Ca/Si correlates with concentration ratios of Fe/Si and Ca/Si, respectively, for M1 solar condition. In principle, the modelling technique outlined here can be used to determine absolute elemental abundances (Mg, Al, Si, Ca, Ti and Fe) from X-ray spectra measured during recent and future lunar missions.

  18. Thermocapillary bubble dynamics in a 2D axis swirl domain

    NASA Astrophysics Data System (ADS)

    Alhendal, Yousuf; Turan, Ali

    2014-09-01

    The lack of significant buoyancy effects in zero-gravity conditions poses an issue with fluid transfer in a stagnant liquid. In this paper, bubble movement in a stagnant liquid is analysed and presented numerically using a computational fluid dynamics approach. The governing continuum and conservation equations for two-phase flow are solved using the commercial software package Ansys-Fluent v.13. The volume of fluid method is used to track the liquid/gas interface in 2D and 3D domains, which has been found to be a valuable tool for studying the phenomenon of gas-liquid interaction, and the validation results are in reasonable agreement with earlier experimental observations. The flow is driven via Marangoni influence induced by the temperature difference, which in turn drives the bubble from the cold to the hot region. The results indicate that the inherent velocity of bubbles decreases with an increase in Marangoni number; this is in agreement with the results of previous experiments conducted in Kang et al. (Microgravity Sci Technol 20:67-71, 2008). Some three-dimensional simulations will also be performed to compare and examine the results with two-dimensional simulations. The thermocapillary bubble flow in a 2D swirl axisymmetry driven by the rotation of the walls was also carried out for different angular velocities in zero gravity. The bubble migration speed was found to decrease with increasing angular velocity. This occurrence is due to an increase in the pressure gradient between the cylinder's outer wall and the axis of rotation, which forces the lowest pressure region to shift from the sides of the bubble to the axis of rotation. A deformation of the bubble and the formation of the two vortices inside the bubble are also observed. These new and original findings aim to help support research into space applications.

  19. Thermocapillary bubble dynamics in a 2D axis swirl domain

    NASA Astrophysics Data System (ADS)

    Alhendal, Yousuf; Turan, Ali

    2015-04-01

    The lack of significant buoyancy effects in zero-gravity conditions poses an issue with fluid transfer in a stagnant liquid. In this paper, bubble movement in a stagnant liquid is analysed and presented numerically using a computational fluid dynamics approach. The governing continuum and conservation equations for two-phase flow are solved using the commercial software package Ansys-Fluent v.13. The volume of fluid method is used to track the liquid/gas interface in 2D and 3D domains, which has been found to be a valuable tool for studying the phenomenon of gas-liquid interaction, and the validation results are in reasonable agreement with earlier experimental observations. The flow is driven via Marangoni influence induced by the temperature difference, which in turn drives the bubble from the cold to the hot region. The results indicate that the inherent velocity of bubbles decreases with an increase in Marangoni number; this is in agreement with the results of previous experiments conducted in Kang et al. (Microgravity Sci Technol 20:67-71, 2008). Some three-dimensional simulations will also be performed to compare and examine the results with two-dimensional simulations. The thermocapillary bubble flow in a 2D swirl axisymmetry driven by the rotation of the walls was also carried out for different angular velocities in zero gravity. The bubble migration speed was found to decrease with increasing angular velocity. This occurrence is due to an increase in the pressure gradient between the cylinder's outer wall and the axis of rotation, which forces the lowest pressure region to shift from the sides of the bubble to the axis of rotation. A deformation of the bubble and the formation of the two vortices inside the bubble are also observed. These new and original findings aim to help support research into space applications.

  20. Epitaxial 2D SnSe2/ 2D WSe2 van der Waals Heterostructures.

    PubMed

    Aretouli, Kleopatra Emmanouil; Tsoutsou, Dimitra; Tsipas, Polychronis; Marquez-Velasco, Jose; Aminalragia Giamini, Sigiava; Kelaidis, Nicolaos; Psycharis, Vassilis; Dimoulas, Athanasios

    2016-09-07

    van der Waals heterostructures of 2D semiconductor materials can be used to realize a number of (opto)electronic devices including tunneling field effect devices (TFETs). It is shown in this work that high quality SnSe2/WSe2 vdW heterostructure can be grown by molecular beam epitaxy on AlN(0001)/Si(111) substrates using a Bi2Se3 buffer layer. A valence band offset of 0.8 eV matches the energy gap of SnSe2 in such a way that the VB edge of WSe2 and the CB edge of SnSe2 are lined up, making this materials combination suitable for (nearly) broken gap TFETs.

  1. Crystal Structure of Human Cytochrome P450 2D6 with Prinomastat Bound*

    PubMed Central

    Wang, An; Savas, Uzen; Hsu, Mei-Hui; Stout, C. David; Johnson, Eric F.

    2012-01-01

    Human cytochrome P450 2D6 contributes to the metabolism of >15% of drugs used in clinical practice. This study determined the structure of P450 2D6 complexed with a substrate and potent inhibitor, prinomastat, to 2.85 Å resolution by x-ray crystallography. Prinomastat binding is well defined by electron density maps with its pyridyl nitrogen bound to the heme iron. The structure of ligand-bound P450 2D6 differs significantly from the ligand-free structure reported for the P450 2D6 Met-374 variant (Protein Data Bank code 2F9Q). Superposition of the structures reveals significant differences for β sheet 1, helices A, F, F′, G″, G, and H as well as the helix B-C loop. The structure of the ligand complex exhibits a closed active site cavity that conforms closely to the shape of prinomastat. The closure of the open cavity seen for the 2F9Q structure reflects a change in the direction and pitch of helix F and introduction of a turn at Gly-218, which is followed by a well defined helix F′ that was not observed in the 2F9Q structure. These differences reflect considerable structural flexibility that is likely to contribute to the catalytic versatility of P450 2D6, and this new structure provides an alternative model for in silico studies of substrate interactions with P450 2D6. PMID:22308038

  2. Unusual dimensionality effects and surface charge density in 2D Mg(OH)2.

    PubMed

    Suslu, Aslihan; Wu, Kedi; Sahin, Hasan; Chen, Bin; Yang, Sijie; Cai, Hui; Aoki, Toshihiro; Horzum, Seyda; Kang, Jun; Peeters, Francois M; Tongay, Sefaattin

    2016-02-05

    We present two-dimensional Mg(OH)2 sheets and their vertical heterojunctions with CVD-MoS2 for the first time as flexible 2D insulators with anomalous lattice vibration and chemical and physical properties. New hydrothermal crystal growth technique enabled isolation of environmentally stable monolayer Mg(OH)2 sheets. Raman spectroscopy and vibrational calculations reveal that the lattice vibrations of Mg(OH)2 have fundamentally different signature peaks and dimensionality effects compared to other 2D material systems known to date. Sub-wavelength electron energy-loss spectroscopy measurements and theoretical calculations show that Mg(OH)2 is a 6 eV direct-gap insulator in 2D, and its optical band gap displays strong band renormalization effects from monolayer to bulk, marking the first experimental confirmation of confinement effects in 2D insulators. Interestingly, 2D-Mg(OH)2 sheets possess rather strong surface polarization (charge) effects which is in contrast to electrically neutral h-BN materials. Using 2D-Mg(OH)2 sheets together with CVD-MoS2 in the vertical stacking shows that a strong change transfer occurs from n-doped CVD-MoS2 sheets to Mg(OH)2, naturally depleting the semiconductor, pushing towards intrinsic doping limit and enhancing overall optical performance of 2D semiconductors. Results not only establish unusual confinement effects in 2D-Mg(OH)2, but also offer novel 2D-insulating material with unique physical, vibrational, and chemical properties for potential applications in flexible optoelectronics.

  3. Unusual dimensionality effects and surface charge density in 2D Mg(OH)2

    PubMed Central

    Suslu, Aslihan; Wu, Kedi; Sahin, Hasan; Chen, Bin; Yang, Sijie; Cai, Hui; Aoki, Toshihiro; Horzum, Seyda; Kang, Jun; Peeters, Francois M.; Tongay, Sefaattin

    2016-01-01

    We present two-dimensional Mg(OH)2 sheets and their vertical heterojunctions with CVD-MoS2 for the first time as flexible 2D insulators with anomalous lattice vibration and chemical and physical properties. New hydrothermal crystal growth technique enabled isolation of environmentally stable monolayer Mg(OH)2 sheets. Raman spectroscopy and vibrational calculations reveal that the lattice vibrations of Mg(OH)2 have fundamentally different signature peaks and dimensionality effects compared to other 2D material systems known to date. Sub-wavelength electron energy-loss spectroscopy measurements and theoretical calculations show that Mg(OH)2 is a 6 eV direct-gap insulator in 2D, and its optical band gap displays strong band renormalization effects from monolayer to bulk, marking the first experimental confirmation of confinement effects in 2D insulators. Interestingly, 2D-Mg(OH)2 sheets possess rather strong surface polarization (charge) effects which is in contrast to electrically neutral h-BN materials. Using 2D-Mg(OH)2 sheets together with CVD-MoS2 in the vertical stacking shows that a strong change transfer occurs from n-doped CVD-MoS2 sheets to Mg(OH)2, naturally depleting the semiconductor, pushing towards intrinsic doping limit and enhancing overall optical performance of 2D semiconductors. Results not only establish unusual confinement effects in 2D-Mg(OH)2, but also offer novel 2D-insulating material with unique physical, vibrational, and chemical properties for potential applications in flexible optoelectronics. PMID:26846617

  4. Presynaptic GluN2D receptors detect glutamate spillover and regulate cerebellar GABA release

    PubMed Central

    Dubois, Christophe J.; Lachamp, Philippe M.; Sun, Lu; Mishina, Masayoshi

    2015-01-01

    Glutamate directly activates N-methyl-d-aspartate (NMDA) receptors on presynaptic inhibitory interneurons and enhances GABA release, altering the excitatory-inhibitory balance within a neuronal circuit. However, which class of NMDA receptors is involved in the detection of glutamate spillover is not known. GluN2D subunit-containing NMDA receptors are ideal candidates as they exhibit a high affinity for glutamate. We now show that cerebellar stellate cells express both GluN2B and GluN2D NMDA receptor subunits. Genetic deletion of GluN2D subunits prevented a physiologically relevant, stimulation-induced, lasting increase in GABA release from stellate cells [long-term potentiation of inhibitory transmission (I-LTP)]. NMDA receptors are tetramers composed of two GluN1 subunits associated to either two identical subunits (di-heteromeric receptors) or to two different subunits (tri-heteromeric receptors). To determine whether tri-heteromeric GluN2B/2D NMDA receptors mediate I-LTP, we tested the prediction that deletion of GluN2D converts tri-heteromeric GluN2B/2D to di-heteromeric GluN2B NMDA receptors. We find that prolonged stimulation rescued I-LTP in GluN2D knockout mice, and this was abolished by GluN2B receptor blockers that failed to prevent I-LTP in wild-type mice. Therefore, NMDA receptors that contain both GluN2D and GluN2B mediate the induction of I-LTP. Because these receptors are not present in the soma and dendrites, presynaptic tri-heteromeric GluN2B/2D NMDA receptors in inhibitory interneurons are likely to mediate the cross talk between excitatory and inhibitory transmission. PMID:26510761

  5. Enhanced sampling of 2D interference patterns.

    PubMed

    Schwartz, Eyal; Ribak, Erez N

    2017-03-01

    We propose a simple analysis to improve the resolution of interference patterns which consist of straight fringes. As the pattern is rotated with respect to the detector, each row or column in the camera perceives it in a slightly shifted manner. We support this proposed method by analyzing both simulated and experimental interference patterns, and verify it using an interferogram obtained from a spectrally complex light source. The results imply that this technique could be implemented in different aspects of image analysis common in many fields in physics.

  6. Detection of Leptomeningeal Metastasis by Contrast-Enhanced 3D T1-SPACE: Comparison with 2D FLAIR and Contrast-Enhanced 2D T1-Weighted Images

    PubMed Central

    Gil, Bomi; Hwang, Eo-Jin; Lee, Song; Jang, Jinhee; Jung, So-Lyung; Ahn, Kook-Jin; Kim, Bum-soo

    2016-01-01

    Introduction To compare the diagnostic accuracy of contrast-enhanced 3D(dimensional) T1-weighted sampling perfection with application-optimized contrasts by using different flip angle evolutions (T1-SPACE), 2D fluid attenuated inversion recovery (FLAIR) images and 2D contrast-enhanced T1-weighted image in detection of leptomeningeal metastasis except for invasive procedures such as a CSF tapping. Materials and Methods Three groups of patients were included retrospectively for 9 months (from 2013-04-01 to 2013-12-31). Group 1 patients with positive malignant cells in CSF cytology (n = 22); group 2, stroke patients with steno-occlusion in ICA or MCA (n = 16); and group 3, patients with negative results on MRI, whose symptom were dizziness or headache (n = 25). A total of 63 sets of MR images are separately collected and randomly arranged: (1) CE 3D T1-SPACE; (2) 2D FLAIR; and (3) CE T1-GRE using a 3-Tesla MR system. A faculty neuroradiologist with 8-year-experience and another 2nd grade trainee in radiology reviewed each MR image- blinded by the results of CSF cytology and coded their observations as positives or negatives of leptomeningeal metastasis. The CSF cytology result was considered as a gold standard. Sensitivity and specificity of each MR images were calculated. Diagnostic accuracy was compared using a McNemar’s test. A Cohen's kappa analysis was performed to assess inter-observer agreements. Results Diagnostic accuracy was not different between 3D T1-SPACE and CSF cytology by both raters. However, the accuracy test of 2D FLAIR and 2D contrast-enhanced T1-weighted GRE was inconsistent by the two raters. The Kappa statistic results were 0.657 (3D T1-SPACE), 0.420 (2D FLAIR), and 0.160 (2D contrast-enhanced T1-weighted GRE). The 3D T1-SPACE images showed the highest inter-observer agreements between the raters. Conclusions Compared to 2D FLAIR and 2D contrast-enhanced T1-weighted GRE, contrast-enhanced 3D T1 SPACE showed a better detection rate of

  7. Chlorophyll fluorescence kinetics, photosynthetic activity, and pigment composition of blue-shade and half-shade leaves as compared to sun and shade leaves of different trees.

    PubMed

    Lichtenthaler, Hartmut K; Babani, Fatbardha; Navrátil, Martin; Buschmann, Claus

    2013-11-01

    The chlorophyll (Chl) fluorescence induction kinetics, net photosynthetic CO2 fixation rates P N, and composition of photosynthetic pigments of differently light exposed leaves of several trees were comparatively measured to determine the differences in photosynthetic activity and pigment adaptation of leaves. The functional measurements were carried out with sun, half-shade and shade leaves of seven different trees species. These were: Acer platanoides L., Ginkgo biloba L., Fagus sylvatica L., Platanus x acerifolia Willd., Populus nigra L., Quercus robur L., Tilia cordata Mill. In three cases (beech, ginkgo, and oak), we compared the Chl fluorescence kinetics and photosynthetic rates of blue-shade leaves of the north tree crown receiving only blue sky light but no direct sunlight with that of sun leaves. In these cases, we also determined in detail the pigment composition of all four leaf types. In addition, we determined the quantum irradiance and spectral irradiance of direct sunlight, blue skylight as well as the irradiance in half shade and full shade. The results indicate that sun leaves possess significantly higher mean values for the net CO2 fixation rates P N (7.8-10.7 μmol CO2 m(-2) s(-1) leaf area) and the Chl fluorescence ratio R Fd (3.85-4.46) as compared to shade leaves (mean P N of 2.6-3.8 μmol CO2 m(-2) s(-1) leaf area.; mean R Fd of 1.94-2.56). Sun leaves also exhibit higher mean values for the pigment ratio Chl a/b (3.14-3.31) and considerably lower values for the weight ratio total chlorophylls to total carotenoids, (a + b)/(x + c), (4.07-4.25) as compared to shade leaves (Chl a/b 2.62-2.72) and (a + b)/(x + c) of 5.18-5.54. Blue-shade and half-shade leaves have an intermediate position between sun and shade leaves in all investigated parameters including the ratio F v/F o (maximum quantum yield of PS2 photochemistry) and are significantly different from sun and shade leaves but could not be differentiated from each other. The

  8. Circular photogalvanic effect caused by the transitions between edge and 2D states in a 2D topological insulator

    NASA Astrophysics Data System (ADS)

    Magarill, L. I.; Entin, M. V.

    2016-12-01

    The electron absorption and the edge photocurrent of a 2D topological insulator are studied for transitions between edge states to 2D states. The circular polarized light is found to produce the edge photocurrent, the direction of which is determined by light polarization and edge orientation. It is shown that the edge-state current is found to exceed the 2D current owing to the topological protection of the edge states.

  9. Silicene, a promising new 2D material

    NASA Astrophysics Data System (ADS)

    Oughaddou, Hamid; Enriquez, Hanna; Tchalala, Mohammed Rachid; Yildirim, Handan; Mayne, Andrew J.; Bendounan, Azzedine; Dujardin, Gérald; Ait Ali, Mustapha; Kara, Abdelkader

    2015-02-01

    Silicene is emerging as a two-dimensional material with very attractive electronic properties for a wide range of applications; it is a particularly promising material for nano-electronics in silicon-based technology. Over the last decade, the existence and stability of silicene has been the subject of much debate. Theoretical studies were the first to predict a puckered honeycomb structure with electronic properties resembling those of graphene. Though these studies were for free-standing silicene, experimental fabrication of silicene has been achieved so far only through epitaxial growth on crystalline surfaces. Indeed, it was only in 2010 that researchers presented the first experimental evidence of the formation of silicene on Ag(1 1 0) and Ag(1 1 1), which has launched silicene in a similar way to graphene. This very active field has naturally led to the recent growth of silicene on Ir(1 1 1), ZrB2(0 0 0 1) and Au(1 1 0) substrates. However, the electronic properties of epitaxially grown silicene on metal surfaces are influenced by the strong silicene-metal interactions. This has prompted experimental studies of the growth of multi-layer silicene, though the nature of its "silicene" structure remains questionable. Of course, like graphene, synthesizing free-standing silicene represents the ultimate challenge. A first step towards this has been reported recently through chemical exfoliation from calcium disilicide (CaSi2). In this review, we discuss the experimental and theoretical studies of silicene performed to date. Special attention is given to different experimental studies of the electronic properties of silicene on metal substrates. New avenues for the growth of silicene on other substrates with different chemical characteristics are presented along with foreseeable applications such as nano-devices and novel batteries.

  10. Single-molecule catalysis mapping quantifies site-specific activity and uncovers radial activity gradient on single 2D nanocrystals.

    PubMed

    Andoy, Nesha May; Zhou, Xiaochun; Choudhary, Eric; Shen, Hao; Liu, Guokun; Chen, Peng

    2013-02-06

    Shape-controlled metal nanocrystals are a new generation of nanoscale catalysts. Depending on their shapes, these nanocrystals exhibit various surface facets, and the assignments of their surface facets have routinely been used to rationalize or predict their catalytic activity in a variety of chemical transformations. Recently we discovered that for 1-dimensional (1D) nanocrystals (Au nanorods), the catalytic activity is not constant along the same side facets of single nanorods but rather differs significantly and further shows a gradient along its length, which we attributed to an underlying gradient of surface defect density resulting from their linear decay in growth rate during synthesis (Nat. Nanotechnol.2012, 7, 237-241). Here we report that this behavior also extends to 2D nanocrystals, even for a different catalytic reaction. By using super-resolution fluorescence microscopy to map out the locations of catalytic events within individual triangular and hexagonal Au nanoplates in correlation with scanning electron microscopy, we find that the catalytic activity within the flat {111} surface facet of a Au nanoplate exhibits a 2D radial gradient from the center toward the edges. We propose that this activity gradient results from a growth-dependent surface defect distribution. We also quantify the site-specific activity at different regions within a nanoplate: The corner regions have the highest activity, followed by the edge regions and then the flat surface facets. These discoveries highlight the spatial complexity of catalytic activity at the nanoscale as well as the interplay amid nanocrystal growth, morphology, and surface defects in determining nanocatalyst properties.

  11. Fluorescence response of a dipolar organic solute in a dicationic ionic liquid (IL): is the behavior of dicationic IL different from that of usual monocationic IL?

    PubMed

    Sahu, Prabhat Kumar; Das, Sudhir Kumar; Sarkar, Moloy

    2014-07-07

    The solvation and rotational relaxation dynamics of coumarin 153 have been investigated in a dicationic ionic liquid (IL), 1,6-bis-(3-methylimidazolium-1-yl)hexane bis-(trifluoromethylsulfonyl)amide ([C6(MIm)2][NTf2]2), for the first time to provide a comprehensive and a quantitative understanding of the nature of the ionic fluid and its influence on the average solvation and rotational relaxation time. On several occasions, the photophysical data obtained in the present dicationic IL have also been compared with the monocationic imidazolium-based ionic liquid so as to find out the difference between their behaviors. The dicationic ionic liquid has been synthesized via a two step process and subsequently characterized by conventional spectroscopic methods. Steady state absorption and fluorescence measurements reveal that the polarity of the ionic liquid is close to that of dichloromethane. Steady state excitation wavelength dependent fluorescence measurement indicates the micro-heterogeneous nature of the ionic liquid. However, the steady state excitation wavelength dependent fluorescence response is found to be similar for both the dicationic and a structurally similar monocationic ionic liquid. In the time-resolved fluorescence studies, contrary to the monocationic imidazolium-based ionic liquid, no missing ultra-fast component of solvation has been observed in the present dicationic IL. Excitation wavelength dependence of the average solvation and rotation times also indicates the micro-heterogeneous nature of these media. When viscosity dependence (η) of the measured average solvation 〈τs〉 and rotation 〈τr〉 times are verified by the relation: 〈τx〉 ∝ (η/T)(p) (where 'x' is solvation or rotation, p is the exponent and T is the temperature), the fractional dependence of both average solvation and rotational times with the medium viscosity have been observed. The recent findings (J. Chem. Phys., 2012, 136, 174503; Chem. Phys. Lett., 2011, 517

  12. Development of an Implicit, Charge and Energy Conserving 2D Electromagnetic PIC Code on Advanced Architectures

    NASA Astrophysics Data System (ADS)

    Payne, Joshua; Taitano, William; Knoll, Dana; Liebs, Chris; Murthy, Karthik; Feltman, Nicolas; Wang, Yijie; McCarthy, Colleen; Cieren, Emanuel

    2012-10-01

    In order to solve problems such as the ion coalescence and slow MHD shocks fully kinetically we developed a fully implicit 2D energy and charge conserving electromagnetic PIC code, PlasmaApp2D. PlasmaApp2D differs from previous implicit PIC implementations in that it will utilize advanced architectures such as GPUs and shared memory CPU systems, with problems too large to fit into cache. PlasmaApp2D will be a hybrid CPU-GPU code developed primarily to run on the DARWIN cluster at LANL utilizing four 12-core AMD Opteron CPUs and two NVIDIA Tesla GPUs per node. MPI will be used for cross-node communication, OpenMP will be used for on-node parallelism, and CUDA will be used for the GPUs. Development progress and initial results will be presented.

  13. Controllable liquid crystal gratings for an adaptive 2D/3D auto-stereoscopic display

    NASA Astrophysics Data System (ADS)

    Zhang, Y. A.; Jin, T.; He, L. C.; Chu, Z. H.; Guo, T. L.; Zhou, X. T.; Lin, Z. X.

    2017-02-01

    2D/3D switchable, viewpoint controllable and 2D/3D localizable auto-stereoscopic displays based on controllable liquid crystal gratings are proposed in this work. Using the dual-layer staggered structure on the top substrate and bottom substrate as driven electrodes within a liquid crystal cell, the ratio between transmitting region and shielding region can be selectively controlled by the corresponding driving circuit, which indicates that 2D/3D switch and 3D video sources with different disparity images can reveal in the same auto-stereoscopic display system. Furthermore, the controlled region in the liquid crystal gratings presents 3D model while other regions maintain 2D model in the same auto-stereoscopic display by the corresponding driving circuit. This work demonstrates that the controllable liquid crystal gratings have potential applications in the field of auto-stereoscopic display.

  14. Two lead(II) 2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate complexes exhibiting different topologies and fluorescent properties

    SciTech Connect

    Chen Zilu; Yan Jiehua; Xing Huihui; Zhang Zhong; Liang Fupei

    2011-05-15

    The reactions of PbCl{sub 2} with 2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylic acid (H{sub 3}iso) gave two complexes [Pb(H{sub 2}iso){sub 2}(H{sub 2}O)]{sub n} (1) and [Pb(Hiso)(H{sub 2}O)]{sub n} (2), which were characterized by IR spectroscopy, elemental analysis, thermogravimetric analysis, powder X-ray diffraction and single crystal X-ray diffraction analysis. The two complexes display different topologies. 1 shows a three-dimensional framework with the Schlaefli symbol (4.8{sup 5})(4.8{sup 2}) no matter if the weak Pb-O bonds are included or not. However, 2 presents a 3,3-connected two-dimensional sheet with the Schlaefli symbol (4.8{sup 2})(4.8{sup 2}) based on the calculation of only the normal Pb-O bonds and a 5,5-connected 3D network with the Schlaefli symbol (4{sup 15}.6{sup 4})(4{sup 4}.6{sup 8}.8{sup 2}) when the weak Pb-O bonds are also included. The fluorescent studies reveal an emission attributed to intraligand emission for 1 and an emission assigned to LMCT for 2. -- Graphical abstract: The reactions of PbCl{sub 2} with 2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylic acid (H{sub 3}iso) gave two complexes [Pb(H{sub 2}iso){sub 2}(H{sub 2}O)]{sub n} (1) and [Pb(Hiso)(H{sub 2}O)]{sub n} (2), which display different topologies and fluorescent properties. Display Omitted Highlights: {yields} Two Pb(II) complexes were prepared from the reactions of PbCl{sub 2} with the same ligand. {yields} The two title complexes display different topologies. {yields} Both normal and weak Pb-O bonds are discussed in the manuscript.{yields} The title two complexes show different fluorescent properties.

  15. 2-d Packing of Prolate Granular Materials

    NASA Astrophysics Data System (ADS)

    Franklin, Scott

    2002-11-01

    Piles of extremely prolate (aspect ratio α=L/D>10) granular materials are qualitatively different than lower aspect-ratio particles. One can run a hand through sand, for example, but not through nails. In three dimensions this transition occurs at α ˜ 35. We investigate the two-dimensional packing of particles with aspect ratios ranging from 10-44, comparing experiments with Monte-Carlo simulations. Particle alignment can quantified by an orientational order correlation function and related to the packing fraction. In both simulation and experiment the correlation between particle orientation decays after a distance of two particle lengths. We also quantify the distribution of voids in the pile, finding it to follow a power law with exponent -β=-2.370.05. Dynamic experiments involve rotating the pile. Particles with aspect ratio as low as 10 do not appear to have a well defined angle of repose, suggesting that the transition to rigidity occurs at a far lower aspect ratio in two dimensions. Preliminary results from this experiment will be presented.

  16. 2D kinematic signatures of boxy/peanut bulges

    NASA Astrophysics Data System (ADS)

    Iannuzzi, Francesca; Athanassoula, E.

    2015-07-01

    We study the imprints of boxy/peanut structures on the 2D line-of-sight kinematics of simulated disc galaxies. The models under study belong to a family with varying initial gas fraction and halo triaxiality, plus few other control runs with different structural parameters; the kinematic information was extracted using the Voronoi-binning technique and parametrized up to the fourth order of a Gauss-Hermite series. Building on a previous work for the long-slit case, we investigate the 2D kinematic behaviour in the edge-on projection as a function of the boxy/peanut strength and position angle; we find that for the strongest structures the highest moments show characteristic features away from the mid-plane in a range of position angles. We also discuss the masking effect of a classical bulge and the ambiguity in discriminating kinematically this spherically symmetric component from a boxy/peanut bulge seen end-on. Regarding the face-on case, we extend existing results to encompass the effect of a second buckling and find that this phenomenon spurs an additional set of even deeper minima in the fourth moment. Finally, we show how the results evolve when inclining the disc away from perfectly edge-on and face-on. The behaviour of stars born during the course of the simulations is discussed and confronted to that of the pre-existing disc. The general aim of our study is providing a handle to identify boxy/peanut structures and their properties in latest generation Integral Field Unit observations of nearby disc galaxies.

  17. ''Super 2D,'' Innovative seismic reprocessing: A case history

    SciTech Connect

    Conne, D.K.M.; Bolander, A.G.; MacDonald, R.J.; Strelioff, D.M.

    1988-01-01

    The ''Super 2D'' processing sequence involves taking a randomly oriented grid of multivintage two-dimensional seismic data and reprocessing to tie the data where required, then interpolating the data set to a regular grid suitable for three-dimensional processing and interpretation. A data set from Alberta, provided by a Canadian oil company, comprises 15 two-dimensional seismic lines collected and processed over a period of 6 years by various contractors. Field conditions, advances in technology, and changing objectives combined to result in a data set that densely sampled a small area, but did not tie in well enough to be interpreted as a whole. The data mistied in time, phase, and frequency, as well as having a problem with multiples in the zone of interest that had been partly attenuated in varying degrees. Therefore, the first objective of reprocessing was to resolve these problems. The authors' current land data processing sequence, which includes frequency balancing followed by source wavelet designature, F/K multiple attenuation, trim statics, and F-X filtering, as well as close attention to statics and velocity control, resolved all the mistie issues and produced a standardized data volume. This data volume was now suitable for the second stage of this sequence (i.e., interpolating to a regular grid and subsequent three-dimensional processing). The volume was three-dimensionally migrated (finite difference), filtered, and scaled. The full range of three-dimensional display and interpretational options, including loading on an interactive system, are now possible. This, along with standardizing the data set and improving the spatial location of events via three-dimensional migration are the key results of the ''Super 2D'' sequence.

  18. Energy Efficiency of D2D Multi-User Cooperation.

    PubMed

    Zhang, Zufan; Wang, Lu; Zhang, Jie

    2017-03-28

    The Device-to-Device (D2D) communication system is an important part of heterogeneous networks. It has great potential to improve spectrum efficiency, throughput and energy efficiency cooperation of multiple D