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Sample records for automated two-dimensional protein

  1. A Chip-Capillary Hybrid Device for Automated Transfer of Sample Pre-Separated by Capillary Isoelectric Focusing to Parallel Capillary Gel Electrophoresis for Two-Dimensional Protein Separation

    Science.gov (United States)

    Lu, Joann J.; Wang, Shili; Li, Guanbin; Wang, Wei; Pu, Qiaosheng; Liu, Shaorong

    2012-01-01

    In this report, we introduce a chip-capillary hybrid device to integrate capillary isoelectric focusing (CIEF) with parallel capillary sodium dodecyl sulfate – polyacrylamide gel electrophoresis (SDS-PAGE) or capillary gel electrophoresis (CGE) toward automating two-dimensional (2D) protein separations. The hybrid device consists of three chips that are butted together. The middle chip can be moved between two positions to re-route the fluidic paths, which enables the performance of CIEF and injection of proteins partially resolved by CIEF to CGE capillaries for parallel CGE separations in a continuous and automated fashion. Capillaries are attached to the other two chips to facilitate CIEF and CGE separations and to extend the effective lengths of CGE columns. Specifically, we illustrate the working principle of the hybrid device, develop protocols for producing and preparing the hybrid device, and demonstrate the feasibility of using this hybrid device for automated injection of CIEF-separated sample to parallel CGE for 2D protein separations. Potentials and problems associated with the hybrid device are also discussed. PMID:22830584

  2. Automated multi-dimensional purification of tagged proteins.

    Science.gov (United States)

    Sigrell, Jill A; Eklund, Pär; Galin, Markus; Hedkvist, Lotta; Liljedahl, Pia; Johansson, Christine Markeland; Pless, Thomas; Torstenson, Karin

    2003-01-01

    The capacity for high throughput purification (HTP) is essential in fields such as structural genomics where large numbers of protein samples are routinely characterized in, for example, studies of structural determination, functionality and drug development. Proteins required for such analysis must be pure and homogenous and available in relatively large amounts. AKTA 3D system is a powerful automated protein purification system, which minimizes preparation, run-time and repetitive manual tasks. It has the capacity to purify up to 6 different His6- or GST-tagged proteins per day and can produce 1-50 mg protein per run at >90% purity. The success of automated protein purification increases with careful experimental planning. Protocol, columns and buffers need to be chosen with the final application area for the purified protein in mind.

  3. Automated Processing of Two-Dimensional Correlation Spectra

    Science.gov (United States)

    Sengstschmid; Sterk; Freeman

    1998-04-01

    An automated scheme is described which locates the centers of cross peaks in two-dimensional correlation spectra, even under conditions of severe overlap. Double-quantum-filtered correlation (DQ-COSY) spectra have been investigated, but the method is also applicable to TOCSY and NOESY spectra. The search criterion is the intrinsic symmetry (or antisymmetry) of cross-peak multiplets. An initial global search provides the preliminary information to build up a two-dimensional "chemical shift grid." All genuine cross peaks must be centered at intersections of this grid, a fact that reduces the extent of the subsequent search program enormously. The program recognizes cross peaks by examining the symmetry of signals in a test zone centered at a grid intersection. This "symmetry filter" employs a "lowest value algorithm" to discriminate against overlapping responses from adjacent multiplets. A progressive multiplet subtraction scheme provides further suppression of overlap effects. The processed two-dimensional correlation spectrum represents cross peaks as points at the chemical shift coordinates, with some indication of their relative intensities. Alternatively, the information is presented in the form of a correlation table. The authenticity of a given cross peak is judged by a set of "confidence criteria" expressed as numerical parameters. Experimental results are presented for the 400-MHz double-quantum-filtered COSY spectrum of 4-androsten-3,17-dione, a case where there is severe overlap. Copyright 1998 Academic Press.

  4. Binding Direction-Based Two-Dimensional Flattened Contact Area Computing Algorithm for Protein-Protein Interactions.

    Science.gov (United States)

    Kang, Beom Sik; Pugalendhi, GaneshKumar; Kim, Ku-Jin

    2017-10-13

    Interactions between protein molecules are essential for the assembly, function, and regulation of proteins. The contact region between two protein molecules in a protein complex is usually complementary in shape for both molecules and the area of the contact region can be used to estimate the binding strength between two molecules. Although the area is a value calculated from the three-dimensional surface, it cannot represent the three-dimensional shape of the surface. Therefore, we propose an original concept of two-dimensional contact area which provides further information such as the ruggedness of the contact region. We present a novel algorithm for calculating the binding direction between two molecules in a protein complex, and then suggest a method to compute the two-dimensional flattened area of the contact region between two molecules based on the binding direction.

  5. Procedures for two-dimensional electrophoresis of proteins

    Energy Technology Data Exchange (ETDEWEB)

    Tollaksen, S.L.; Giometti, C.S.

    1996-10-01

    High-resolution two-dimensional gel electrophoresis (2DE) of proteins, using isoelectric focusing in the first dimension and sodium dodecyl sulfate/polyacrylamide gel electrophoresis (SDS-PAGE) in the second, was first described in 1975. In the 20 years since those publications, numerous modifications of the original method have evolved. The ISO-DALT system of 2DE is a high-throughput approach that has stood the test of time. The problem of casting many isoelectric focusing gels and SDS-PAGE slab gels (up to 20) in a reproducible manner has been solved by the use of the techniques and equipment described in this manual. The ISO-DALT system of two-dimensional gel electrophoresis originated in the late 1970s and has been modified many times to improve its high-resolution, high-throughput capabilities. This report provides the detailed procedures used with the current ISO-DALT system to prepare, run, stain, and photograph two-dimensional gels for protein analysis.

  6. Two-dimensional polyacrylamide gel electrophoresis of intracellular proteins

    International Nuclear Information System (INIS)

    Ojima, N.; Sakamoto, T.; Yamashita, M.

    1996-01-01

    Since two-dimensional electrophoresis was established by O'Farrell for analysis of intracellular proteins of Escherichia coli, it has been applied to separation of proteins of animal cells and tissues, and especially to identification of stress proteins. Using this technique, proteins are separated by isoelectric focusing containing 8 m urea in the first dimension and by SDS-PAGE in the second dimension. The gels are stained with Coomassie Blue R-250 dye, followed by silver staining. In the case of radio-labeled proteins, the gels are dried and then autoradiographed. In order to identify a specific protein separated by two-dimensional electrophoresis, a technique determining the N-terminal amino acid sequence of the protein has been developed recently. After the proteins in the gel were electrotransferred to a polyvinylidene difluoride membrane, the membrane was stained for protein with Commassie Blue and a stained membrane fragment was applied to a protein sequencer. Our recent studies demonstrated that fish cells newly synthesized various proteins in response to heat shock, cold nd osmotic stresses. For example, when cellular proteins extracted from cold-treated rainbow trout cells were subjected to two-dimensional gel electrophoresis, the 70 kDa protein was found to be synthesized during the cold-treatment. N-Terminal sequence analysis showed that the cold-inducible protein was a homolog of mammalian valosin-containing protein and yeast cell division cycle gene product CDC48p. Furthermore, the sequence data were useful for preparing PCR primers and a rabbit antibody against a synthetic peptide to analyze a role for the protein in the function of trout cells and mechanisms for regulation

  7. Femtosecond X-ray diffraction from two-dimensional protein crystals

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    Matthias Frank

    2014-03-01

    Full Text Available X-ray diffraction patterns from two-dimensional (2-D protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permit a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy approach at the Linac Coherent Light Source, Bragg diffraction was acquired to better than 8.5 Å resolution for two different 2-D protein crystal samples each less than 10 nm thick and maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.

  8. Crystallization of SHARPIN using an automated two-dimensional grid screen for optimization

    International Nuclear Information System (INIS)

    Stieglitz, Benjamin; Rittinger, Katrin; Haire, Lesley F.

    2012-01-01

    The expression, purification and crystallization of an N-terminal fragment of SHARPIN are reported. Diffraction-quality crystals were obtained using a two-dimensional grid-screen seeding technique. An N-terminal fragment of human SHARPIN was recombinantly expressed in Escherichia coli, purified and crystallized. Crystals suitable for X-ray diffraction were obtained by a one-step optimization of seed dilution and protein concentration using a two-dimensional grid screen. The crystals belonged to the primitive tetragonal space group P4 3 2 1 2, with unit-cell parameters a = b = 61.55, c = 222.81 Å. Complete data sets were collected from native and selenomethionine-substituted protein crystals at 100 K to 2.6 and 2.0 Å resolution, respectively

  9. Binding Direction-Based Two-Dimensional Flattened Contact Area Computing Algorithm for Protein–Protein Interactions

    Directory of Open Access Journals (Sweden)

    Beom Sik Kang

    2017-10-01

    Full Text Available Interactions between protein molecules are essential for the assembly, function, and regulation of proteins. The contact region between two protein molecules in a protein complex is usually complementary in shape for both molecules and the area of the contact region can be used to estimate the binding strength between two molecules. Although the area is a value calculated from the three-dimensional surface, it cannot represent the three-dimensional shape of the surface. Therefore, we propose an original concept of two-dimensional contact area which provides further information such as the ruggedness of the contact region. We present a novel algorithm for calculating the binding direction between two molecules in a protein complex, and then suggest a method to compute the two-dimensional flattened area of the contact region between two molecules based on the binding direction.

  10. Explorative data analysis of two-dimensional electrophoresis gels

    DEFF Research Database (Denmark)

    Schultz, J.; Gottlieb, D.M.; Petersen, Marianne Kjerstine

    2004-01-01

    of gels is presented. First, an approach is demonstrated in which no prior knowledge of the separated proteins is used. Alignment of the gels followed by a simple transformation of data makes it possible to analyze the gels in an automated explorative manner by principal component analysis, to determine......Methods for classification of two-dimensional (2-DE) electrophoresis gels based on multivariate data analysis are demonstrated. Two-dimensional gels of ten wheat varieties are analyzed and it is demonstrated how to classify the wheat varieties in two qualities and a method for initial screening...... if the gels should be further analyzed. A more detailed approach is done by analyzing spot volume lists by principal components analysis and partial least square regression. The use of spot volume data offers a mean to investigate the spot pattern and link the classified protein patterns to distinct spots...

  11. Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal.

    Science.gov (United States)

    Bordoli, Lorenza; Schwede, Torsten

    2012-01-01

    Comparative protein structure modeling is a computational approach to build three-dimensional structural models for proteins using experimental structures of related protein family members as templates. Regular blind assessments of modeling accuracy have demonstrated that comparative protein structure modeling is currently the most reliable technique to model protein structures. Homology models are often sufficiently accurate to substitute for experimental structures in a wide variety of applications. Since the usefulness of a model for specific application is determined by its accuracy, model quality estimation is an essential component of protein structure prediction. Comparative protein modeling has become a routine approach in many areas of life science research since fully automated modeling systems allow also nonexperts to build reliable models. In this chapter, we describe practical approaches for automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal.

  12. Advancements of two dimensional correlation spectroscopy in protein researches

    Science.gov (United States)

    Tao, Yanchun; Wu, Yuqing; Zhang, Liping

    2018-05-01

    The developments of two-dimensional correlation spectroscopy (2DCOS) applications in protein studies are discussed, especially for the past two decades. The powerful utilities of 2DCOS combined with various analytical techniques in protein studies are summarized. The emphasis is on the vibration spectroscopic techniques including IR, NIR, Raman and optical activity (ROA), as well as vibration circular dichroism (VCD) and fluorescence spectroscopy. In addition, some new developments, such as hetero-spectral 2DCOS, moving-window correlation, and model based correlation, are also reviewed for their utility in the investigation of the secondary structure, denaturation, folding and unfolding changes of protein. Finally, the new possibility and challenges of 2DCOS in protein research are highlighted as well.

  13. Human muscle proteins: analysis by two-dimensional electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Giometti, C.S.; Danon, M.J.; Anderson, N.G.

    1983-09-01

    Proteins from single frozen sections of human muscle were separated by two-dimensional gel electrophoresis and detected by fluorography or Coomassie Blue staining. The major proteins were identical in different normal muscles obtained from either sex at different ages, and in Duchenne and myotonic dystrophy samples. Congenital myopathy denervation atrophy, polymyositis, and Becker's muscular dystrophy samples, however, showed abnormal myosin light chain compositions, some with a decrease of fast-fiber myosin light chains and others with a decrease of slow-fiber light chains. These protein alterations did not correlate with any specific disease, and may be cause by generalized muscle-fiber damage.

  14. Consistent two-dimensional visualization of protein-ligand complex series

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    Stierand Katrin

    2011-06-01

    Full Text Available Abstract Background The comparative two-dimensional graphical representation of protein-ligand complex series featuring different ligands bound to the same active site offers a quick insight in their binding mode differences. In comparison to arbitrary orientations of the residue molecules in the individual complex depictions a consistent placement improves the legibility and comparability within the series. The automatic generation of such consistent layouts offers the possibility to apply it to large data sets originating from computer-aided drug design methods. Results We developed a new approach, which automatically generates a consistent layout of interacting residues for a given series of complexes. Based on the structural three-dimensional input information, a global two-dimensional layout for all residues of the complex ensemble is computed. The algorithm incorporates the three-dimensional adjacencies of the active site residues in order to find an universally valid circular arrangement of the residues around the ligand. Subsequent to a two-dimensional ligand superimposition step, a global placement for each residue is derived from the set of already placed ligands. The method generates high-quality layouts, showing mostly overlap-free solutions with molecules which are displayed as structure diagrams providing interaction information in atomic detail. Application examples document an improved legibility compared to series of diagrams whose layouts are calculated independently from each other. Conclusions The presented method extends the field of complex series visualizations. A series of molecules binding to the same protein active site is drawn in a graphically consistent way. Compared to existing approaches these drawings substantially simplify the visual analysis of large compound series.

  15. Assembly of positioner of automated two-dimensional scan coupled to X-ray fluorescence spectrometry

    International Nuclear Information System (INIS)

    Silva, Leonardo Santiago Melgaço

    2011-01-01

    This work describes the design and assembling of a prototype automated positioner two-dimensional scanning coupled to X-ray fluorescence spectrometry. The work aims to achieve a portable and easy to use, device of broad utility in the analysis of samples by X-ray fluorescence area of expertise and research. The two-dimensional scanning of the positioner is by means of two stepper motors controlled by a microcontroller PIC 16F877A, encoder and optical sensors. The user interacts with the XY table through an interface program for the Windows operating system, which communicates with the microcontroller through the serial port. The system of Fluorescence Spectroscopy incorporated into the positioner consists of a system commercially available system from the company AMPTEK, where the primary source of excitation of the sample was a source of 241 Am of 59.5 KeV emissions. Resolution and accuracy of tests were performed in the XY scanning process and reproducibility of the same kit with the fluorescence spectrometry X-ray. Qualitative tests by X-ray fluorescence spectrometry in samples were performed to demonstrate the applicability and versatility of the project. It follows that the prototype illustrates a possible adequately to portable device for X-ray spectrometry of two-dimensional. (author)

  16. The Utilization of Triton X-100 for Enhanced Two-Dimensional Liquid-Phase Proteomics

    OpenAIRE

    Kim, Mina; Lee, Sang-Hee; Min, Jiho; Kobayashi, Fumihisa; Um, Hyun-Ju; Kim, Yang-Hoon

    2011-01-01

    One of the main challenges in proteomics lies in obtaining a high level of reproducible fractionation of the protein samples. Automated two-dimensional liquid phase fractionation (PF2D) system manufactured by Beckman Coulter provides a process well suited for proteome studies. However, the protein recovery efficiency of such system is low when a protocol recommended by the manufacturer is used for metaproteome profiling of environmental sample. In search of an alternative method that can over...

  17. Crystallization of SHARPIN using an automated two-dimensional grid screen for optimization.

    Science.gov (United States)

    Stieglitz, Benjamin; Rittinger, Katrin; Haire, Lesley F

    2012-07-01

    An N-terminal fragment of human SHARPIN was recombinantly expressed in Escherichia coli, purified and crystallized. Crystals suitable for X-ray diffraction were obtained by a one-step optimization of seed dilution and protein concentration using a two-dimensional grid screen. The crystals belonged to the primitive tetragonal space group P4(3)2(1)2, with unit-cell parameters a = b = 61.55, c = 222.81 Å. Complete data sets were collected from native and selenomethionine-substituted protein crystals at 100 K to 2.6 and 2.0 Å resolution, respectively.

  18. A Robust Identification of the Protein Standard Bands in Two-Dimensional Electrophoresis Gel Images

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    Serackis Artūras

    2017-12-01

    Full Text Available The aim of the investigation presented in this paper was to develop a software-based assistant for the protein analysis workflow. The prior characterization of the unknown protein in two-dimensional electrophoresis gel images is performed according to the molecular weight and isoelectric point of each protein spot estimated from the gel image before further sequence analysis by mass spectrometry. The paper presents a method for automatic and robust identification of the protein standard band in a two-dimensional gel image. In addition, the method introduces the identification of the positions of the markers, prepared by using pre-selected proteins with known molecular mass. The robustness of the method was achieved by using special validation rules in the proposed original algorithms. In addition, a self-organizing map-based decision support algorithm is proposed, which takes Gabor coefficients as image features and searches for the differences in preselected vertical image bars. The experimental investigation proved the good performance of the new algorithms included into the proposed method. The detection of the protein standard markers works without modification of algorithm parameters on two-dimensional gel images obtained by using different staining and destaining procedures, which results in different average levels of intensity in the images.

  19. Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high-throughput structural studies on proteins.

    Science.gov (United States)

    Reddy, Jithender G; Kumar, Dinesh; Hosur, Ramakrishna V

    2015-02-01

    Protein NMR spectroscopy has expanded dramatically over the last decade into a powerful tool for the study of their structure, dynamics, and interactions. The primary requirement for all such investigations is sequence-specific resonance assignment. The demand now is to obtain this information as rapidly as possible and in all types of protein systems, stable/unstable, soluble/insoluble, small/big, structured/unstructured, and so on. In this context, we introduce here two reduced dimensionality experiments – (3,2)D-hNCOcanH and (3,2)D-hNcoCAnH – which enhance the previously described 2D NMR-based assignment methods quite significantly. Both the experiments can be recorded in just about 2-3 h each and hence would be of immense value for high-throughput structural proteomics and drug discovery research. The applicability of the method has been demonstrated using alpha-helical bovine apo calbindin-D9k P43M mutant (75 aa) protein. Automated assignment of this data using AUTOBA has been presented, which enhances the utility of these experiments. The backbone resonance assignments so derived are utilized to estimate secondary structures and the backbone fold using Web-based algorithms. Taken together, we believe that the method and the protocol proposed here can be used for routine high-throughput structural studies of proteins. Copyright © 2014 John Wiley & Sons, Ltd.

  20. Automated protein identification by the combination of MALDI MS and MS/MS spectra from different instruments.

    Science.gov (United States)

    Levander, Fredrik; James, Peter

    2005-01-01

    The identification of proteins separated on two-dimensional gels is most commonly performed by trypsin digestion and subsequent matrix-assisted laser desorption ionization (MALDI) with time-of-flight (TOF). Recently, atmospheric pressure (AP) MALDI coupled to an ion trap (IT) has emerged as a convenient method to obtain tandem mass spectra (MS/MS) from samples on MALDI target plates. In the present work, we investigated the feasibility of using the two methodologies in line as a standard method for protein identification. In this setup, the high mass accuracy MALDI-TOF spectra are used to calibrate the peptide precursor masses in the lower mass accuracy AP-MALDI-IT MS/MS spectra. Several software tools were developed to automate the analysis process. Two sets of MALDI samples, consisting of 142 and 421 gel spots, respectively, were analyzed in a highly automated manner. In the first set, the protein identification rate increased from 61% for MALDI-TOF only to 85% for MALDI-TOF combined with AP-MALDI-IT. In the second data set the increase in protein identification rate was from 44% to 58%. AP-MALDI-IT MS/MS spectra were in general less effective than the MALDI-TOF spectra for protein identification, but the combination of the two methods clearly enhanced the confidence in protein identification.

  1. Protein profile analysis of Malaysian snake venoms by two-dimensional gel electrophoresis

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    J Vejayan

    2010-01-01

    Full Text Available Snake venoms comprise a highly complex mixture of proteins, which requires for their characterization the use of versatile two-dimensional electrophoresis techniques. In the present study, venoms obtained from eight snakes (Ophiophagus hannah, Naja kaouthia, Naja sumatrana, Bungarus fasciatus, Trimeresurus sumatranus, Tropidolaemus wagleri, Enhydrina schistosa and Calloselasma rhodostoma commonly found in Malaysia were separated based on two independent properties, isoelectric point (pI and molecular weight (MW. Many differences in snake venoms at the inter-family, inter-subfamily, inter-genus and inter-species levels were revealed. Notably, proteins from individuals of the Viperidae family - Trimeresurus sumatranus, Tropidolaemus wagleri and Calloselasma rhodostoma - were found to be numerous and scattered by the two-dimensional gel electrophoresis (2DE specifically in regions between 37 and 100 kDa compared to the Elapidae venom proteins. The latter were clustered at the basic and lower molecular mass region (less than 20 kDa. Trains of spots were commonly observed, indicating that these proteins may be derived from post-translational modifications. Ophiophagus hannah (Elapidae revealed a great amount of protein spots in the higher molecular mass range when compared to Enhydrina schistosa, Naja kaouthia, Naja sumatrana and Bungarus fasciatus. Overall 2DE showed large differences in the venom profile of each species, which might be employed as an ancillary tool to the identification of venomous snake species.

  2. Measuring protein dynamics with ultrafast two-dimensional infrared spectroscopy

    International Nuclear Information System (INIS)

    Adamczyk, Katrin; Candelaresi, Marco; Hunt, Neil T; Robb, Kirsty; Hoskisson, Paul A; Tucker, Nicholas P; Gumiero, Andrea; Walsh, Martin A; Parker, Anthony W

    2012-01-01

    Recent advances in the methodology and application of ultrafast two-dimensional infrared (2D-IR) spectroscopy to biomolecular systems are reviewed. A description of the 2D-IR technique and the molecular contributions to the observed spectra are presented followed by a discussion of recent literature relating to the use of 2D-IR and associated approaches for measuring protein dynamics. In particular, these include the use of diatomic ligand groups for measuring haem protein dynamics, isotopic labelling strategies and the use of vibrational probe groups. The final section reports on the current state of the art regarding the use of 2D-IR methods to provide insights into biological reaction mechanisms. (topical review)

  3. NMRKIN: Simulating line shapes from two-dimensional spectra of proteins upon ligand binding

    International Nuclear Information System (INIS)

    Guenther, Ulrich L.; Schaffhausen, Brian

    2002-01-01

    The analysis of the shape of signals in NMR spectra is a powerful tool to study exchange and reaction kinetics. Line shapes in two-dimensional spectra of proteins recorded for titrations with ligands provide information about binding rates observed at individual residues. Here we describe a fast method to simulate a series of line shapes derived from two-dimensional spectra of a protein during a ligand titration. This procedure, which takes the mutual effects of two dimensions into account, has been implemented in MATLAB as an add-on to NMRLab (Guenther et al., 2000). In addition, more complex kinetic models, including sequential and parallel reactions, were simulated to demonstrate common features of more complex line shapes which could be encountered in protein-ligand interactions. As an example of this method, we describe its application to line shapes obtained for a titration of the p85 N-SH2 domain of PI3-kinase with a peptide derived from polyomavirus middle T antigen (MT)

  4. [Analysis of total proteins in the seed of almond (Prunus dulcis) by two-dimensional electrophoresis].

    Science.gov (United States)

    Li, Dong-dong; He, Shao-heng

    2004-07-01

    To analyse the total proteins in the seeds of almond (Prunus dulcis), one of the popular ingestent allergens in China, by two-dimensional electrophoresis. The total proteins of the seeds were extracted by trichloracetic acid (TCA) method, and then separated by isoelectric focusing as first dimension and SDS-PAGE as the second dimension. The spots of proteins were visualized by staining with Coomassie Brilliant Blue R-250. After analysis with software (ImageMaster 2D), 188 different proteins were detected. The isoelectric points (pI) for approximately 28% of total proteins were between 4.5-5.5, and the relative molecular mass (M(r)) of approximately 62% total proteins were between (20-25)x10(3). This was the first high-resolution, two-dimensional protein map of the seed of almond (Prunus dulcis) in China. Our finding has laid a solid foundation for further identification, characterization, gene cloning and standardization of allergenic proteins in the seed of almond (Prunus dulcis).

  5. Proteomic analysis of Bacillus thuringiensis at different growth phases by using an automated online two-dimensional liquid chromatography-tandem mass spectrometry strategy.

    Science.gov (United States)

    Huang, Shaoya; Ding, Xuezhi; Sun, Yunjun; Yang, Qi; Xiao, Xiuqing; Cao, Zhenping; Xia, Liqiu

    2012-08-01

    The proteome of a new Bacillus thuringiensis subsp. kurstaki strain, 4.0718, from the middle vegetative (T(1)), early sporulation (T(2)), and late sporulation (T(3)) phases was analyzed using an integrated liquid chromatography (LC)-based protein identification system. The system comprised two-dimensional (2D) LC coupled with nanoscale electrospray ionization (ESI) tandem mass spectrometry (MS/MS) on a high-resolution hybrid mass spectrometer with an automated data analysis system. After deletion of redundant proteins from the different batches and B. thuringiensis subspecies, 918, 703, and 778 proteins were identified in the respective three phases. Their molecular masses ranged from 4.6 Da to 477.4 Da, and their isoelectric points ranged from 4.01 to 11.84. Function clustering revealed that most of the proteins in the three phases were functional metabolic proteins, followed by proteins participating in cell processes. Small molecular and macromolecular metabolic proteins were further classified according to the Kyoto Encyclopedia of Genes and Genome and BioCyc metabolic pathway database. Three protoxins (Cry2Aa, Cry1Aa, and Cry1Ac) as well as a series of potential intracellular active factors were detected. Many significant proteins related to spore and crystal formation, including sporulation proteins, help proteins, chaperones, and so on, were identified. The expression patterns of two identified proteins, CotJc and glutamine synthetase, were validated by Western blot analysis, which further confirmed the MS results. This study is the first to use shotgun technology to research the proteome of B. thuringiensis. Valuable experimental data are provided regarding the methodology of analyzing the B. thuringiensis proteome (which can be used to produce insecticidal crystal proteins) and have been added to the related protein database.

  6. Introduction to the conformational investigation of peptides and proteins by using two-dimensional proton NMR experiments

    International Nuclear Information System (INIS)

    Neumann, J.M.; Macquaire, F.

    1991-01-01

    This report presents the elementary bases for an initiation to the conformational study of peptides and proteins by using two-dimensional proton NMR experiments. First, some general features of protein structures are summarized. A second chapter is devoted to the basic NMR experiments and to the spectral parameters which provide a structural information. This description is illustrated by NMR spectra of peptides. The third chapter concerns the most standard two-dimensional proton NMR experiments and their use for a conformational study of peptides and proteins. Lastly, an example of NMR structural investigation of a peptide is reported [fr

  7. Additional band broadening of peptides in the first size-exclusion chromatographic dimension of an automated stop-flow two-dimensional high performance liquid chromatography.

    Science.gov (United States)

    Xu, Jucai; Sun-Waterhouse, Dongxiao; Qiu, Chaoying; Zhao, Mouming; Sun, Baoguo; Lin, Lianzhu; Su, Guowan

    2017-10-27

    The need to improve the peak capacity of liquid chromatography motivates the development of two-dimensional analysis systems. This paper presented a fully automated stop-flow two-dimensional liquid chromatography system with size exclusion chromatography followed by reversed phase liquid chromatography (SEC×RPLC) to efficiently separate peptides. The effects of different stop-flow operational parameters (stop-flow time, peak parking position, number of stop-flow periods and column temperature) on band broadening in the first dimension (1 st D) SEC column were quantitatively evaluated by using commercial small proteins and peptides. Results showed that the effects of peak parking position and the number of stop-flow periods on band broadening were relatively small. Unlike stop-flow analysis of large molecules with a long running time, additional band broadening was evidently observed for small molecule analytes due to the relatively high effective diffusion coefficient (D eff ). Therefore, shorter analysis time and lower 1 st D column temperature were suggested for analyzing small molecules. The stop-flow two-dimensional liquid chromatography (2D-LC) system was further tested on peanut peptides and an evidently improved resolution was observed for both stop-flow heart-cutting and comprehensive 2D-LC analysis (in spite of additional band broadening in SEC). The stop-flow SEC×RPLC, especially heart-cutting analysis with shorter analysis time and higher 1 st D resolution for selected fractions, offers a promising approach for efficient analysis of complex samples. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Comparison of Yeast Cell Protein Solubilization Procedures for Two-dimensional Electrophoresis

    DEFF Research Database (Denmark)

    Harder, A; Wildgruber, R; Nawrocki, A

    1999-01-01

    Three different procedures for the solubilization of yeast (S. cerevisiae) cell proteins were compared on the basis of the obtained two-dimensional (2-D) polypeptide patterns. Major emphasis was laid on minimizing handling steps, protein modification or degradation, and quantitative loss of high...... with sodium dodecyl sulfate (SDS) buffer, consisting of 1% SDS and 100 mM tris(hydroxymethyl)aminomethane (Tris)-HCl, pH 7.0, followed by dilution with "standard" lysis buffer, and (iii) boiling the sample with SDS during cell lysis, followed by dilution with thiourea/urea lysis buffer (2 M thiourea/ 7 M urea...

  9. Approaches to automated protein crystal harvesting

    Energy Technology Data Exchange (ETDEWEB)

    Deller, Marc C., E-mail: mdeller@scripps.edu; Rupp, Bernhard, E-mail: mdeller@scripps.edu

    2014-01-28

    Approaches to automated and robot-assisted harvesting of protein crystals are critically reviewed. While no true turn-key solutions for automation of protein crystal harvesting are currently available, systems incorporating advanced robotics and micro-electromechanical systems represent exciting developments with the potential to revolutionize the way in which protein crystals are harvested.

  10. Efficient extraction of proteins from recalcitrant plant tissue for subsequent analysis by two-dimensional gel electrophoresis.

    Science.gov (United States)

    Parkhey, Suruchi; Chandrakar, Vibhuti; Naithani, S C; Keshavkant, S

    2015-10-01

    Protein extraction for two-dimensional electrophoresis from tissues of recalcitrant species is quite problematic and challenging due to the low protein content and high abundance of contaminants. Proteomics in Shorea robusta is scarcely conducted due to the lack of a suitable protein preparation procedure. To establish an effective protein extraction protocol suitable for two-dimensional electrophoresis in Shorea robusta, four procedures (borate buffer/trichloroacetic acid extraction, organic solvent/trichloroacetic acid precipitation, sucrose/Tris/phenol, and organic solvent/phenol/sodium dodecyl sulfate) were evaluated. Following these, proteins were isolated from mature leaves and were analyzed for proteomics, and also for potential contaminants, widely reported to hinder proteomics. The borate buffer/trichloroacetic acid extraction had the lowest protein yield and did not result in any banding even in one-dimensional electrophoresis. In contrast, organic solvent/phenol/sodium dodecyl sulfate extraction allowed the highest protein yield. Moreover, during proteomics, organic solvent/phenol/sodium dodecyl sulfate extracted protein resolved the maximum number (144) of spots. Further, when proteins were evaluated for contaminants, significant (77-95%) reductions in the nucleic acids, phenol, and sugars were discernible with refinement in extraction procedure. Accumulated data suggested that the organic solvent/phenol/sodium dodecyl sulfate extraction was the most effective protocol for protein isolation for proteomics of Shorea robusta and can be used for plants that have a similar set of contaminants. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Expression of Leaf Proteins in Two Cultivars of Bread Wheat under Cadmium and Mercury Stress Using Two-Dimensional Gel Electrophoresis

    Directory of Open Access Journals (Sweden)

    S. Y. Raeesi Sadati

    2016-02-01

    Full Text Available Wheat is an important source of human food. Cadmium and mercury bind to sulfhydryl groups of structural proteins and enzymes and cause inhibition in activity and decrease in protein production or interfere with the regulation of the enzymes. To study the effect of protein expression under different levels of cadmium and mercury, the experiment was conducted in a completely randomized design with three replications in Mohaghegh Ardabili University, Ardabil, Iran. Experimental factors consisted of two Gonbad and Tajan bread what cultivars, heavy metals in seven levels (four concentrations of mercuric chloride in 5, 10, 15 and 20 µM and cadmium chloride at two concentrations of 0.25 and 0.5 mM and sampling time after 8 and 16 hours of treatment. The Bradford method was used for quantitative analysis of proteins and 12% SDS-PAGE and two dimensional electrophorese techniques were hired for analysis of their expression. The results showed that under cadmium and mercury stresses, the total protein content increased compared to the control. Two-dimensional electrophoresis of proteins under cadmium stress showed differential expression of the protein spots on the plant leaves, than the control. In general, changes in the expression of proteins under the effect of cadmium stress were divided into two main categories: Spots 9, 10, 13, 14 and 16 belonged to proteins with reduced expression and the spots 1, 2, 8, 19 and 20 belonged to proteins with increased expression, in comparison to non-stressed control. These spots of up regulated proteins were directly related to the defense system against the heavy metal stress.

  12. PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination.

    Science.gov (United States)

    Lee, Woonghee; Kim, Jin Hae; Westler, William M; Markley, John L

    2011-06-15

    PONDEROSA (Peak-picking Of Noe Data Enabled by Restriction of Shift Assignments) accepts input information consisting of a protein sequence, backbone and sidechain NMR resonance assignments, and 3D-NOESY ((13)C-edited and/or (15)N-edited) spectra, and returns assignments of NOESY crosspeaks, distance and angle constraints, and a reliable NMR structure represented by a family of conformers. PONDEROSA incorporates and integrates external software packages (TALOS+, STRIDE and CYANA) to carry out different steps in the structure determination. PONDEROSA implements internal functions that identify and validate NOESY peak assignments and assess the quality of the calculated three-dimensional structure of the protein. The robustness of the analysis results from PONDEROSA's hierarchical processing steps that involve iterative interaction among the internal and external modules. PONDEROSA supports a variety of input formats: SPARKY assignment table (.shifts) and spectrum file formats (.ucsf), XEASY proton file format (.prot), and NMR-STAR format (.star). To demonstrate the utility of PONDEROSA, we used the package to determine 3D structures of two proteins: human ubiquitin and Escherichia coli iron-sulfur scaffold protein variant IscU(D39A). The automatically generated structural constraints and ensembles of conformers were as good as or better than those determined previously by much less automated means. The program, in the form of binary code along with tutorials and reference manuals, is available at http://ponderosa.nmrfam.wisc.edu/.

  13. A two-dimensionally coincident second difference cosmic ray spike removal method for the fully automated processing of Raman spectra.

    Science.gov (United States)

    Schulze, H Georg; Turner, Robin F B

    2014-01-01

    Charge-coupled device detectors are vulnerable to cosmic rays that can contaminate Raman spectra with positive going spikes. Because spikes can adversely affect spectral processing and data analyses, they must be removed. Although both hardware-based and software-based spike removal methods exist, they typically require parameter and threshold specification dependent on well-considered user input. Here, we present a fully automated spike removal algorithm that proceeds without requiring user input. It is minimally dependent on sample attributes, and those that are required (e.g., standard deviation of spectral noise) can be determined with other fully automated procedures. At the core of the method is the identification and location of spikes with coincident second derivatives along both the spectral and spatiotemporal dimensions of two-dimensional datasets. The method can be applied to spectra that are relatively inhomogeneous because it provides fairly effective and selective targeting of spikes resulting in minimal distortion of spectra. Relatively effective spike removal obtained with full automation could provide substantial benefits to users where large numbers of spectra must be processed.

  14. Comparison of ethanol-soluble proteins from different rye (Secale cereale) varieties by two-dimensional electrophoresis

    DEFF Research Database (Denmark)

    Radzikowski, Louise; Nesic, Ljiljana; Hansen, H.B.

    2002-01-01

    The major storage proteins from six rye varieties, grown under the same conditions in 1997 and 1998 in Ronhave, Denmark, were analyzed by two-dimensional (2-D) polyacrylamide gel electrophoresis. The proteins were extracted from ground rye kernels with 70% ethanol and separated by 2-D electrophor......The major storage proteins from six rye varieties, grown under the same conditions in 1997 and 1998 in Ronhave, Denmark, were analyzed by two-dimensional (2-D) polyacrylamide gel electrophoresis. The proteins were extracted from ground rye kernels with 70% ethanol and separated by 2-D...... electrophoresis. The gels were scanned, compared using ImageMaster(R) software and the data sets were analyzed by principal component analysis (PCA) using THE UNSCRAMBLER software. Afterwards MATLAB was used to make a cluster analysis of the varieties based on PCA. The analysis of the gels showed...... separately. When the results were combined from the two years five varieties could be differentiated. The results from the PCA confirmed the finding of the unique spots and cluster analysis was made in order to illustrate the results. The combination of the results from 2-D electrophoresis and other grain...

  15. Two-dimensional electrophoretic analysis of nuclear matrix proteins in human colon adenocarcinoma.

    Science.gov (United States)

    Toumpanaki, A; Baltatzis, G E; Gaitanarou, E; Seretis, E; Toumpanakis, C; Aroni, K; Kittas, Christos; Voloudakis-Baltatzis, I E

    2009-01-01

    The aim of the present study was to observe possible qualitative and quantitative expression differences between nuclear matrix proteins (NMPs) of human colon adenocarcinoma and their mirror biopsies, using the technique of two-dimensional gel electrophoresis, in order to identify the existence of specific NMP fingerprints for colon cancer. Colon tissues were examined ultrastructurally and NMPs were isolated biochemically, by serial extraction of lipids, soluble proteins, DNA, RNA, and intermediate filaments and were separated according to their isoelectric point (pI) and their molecular weight (MW) by high-resolution two-dimensional electrophoresis (2D). By comparing the 2D electropherograms of colon cancer tissues and mirror biopsy tissues we observed qualitative and quantitative expression differences between their NMPs but also a differentiation of NMP composition between the stages of malignancy. Moreover, despite the similarities between mirror biopsy samples, a highlight percentage of exception was observed. Electrophoretic results provided in this study demonstrated that the examined NMPs could be further investigated as potential markers for detection of colorectal cancer in an early stage, for the assessment of the disease progression, as well as useful tools for individual therapy and for preventing a possible recurrence of cancer and metastasis.

  16. Automated three-dimensional X-ray analysis using a dual-beam FIB

    International Nuclear Information System (INIS)

    Schaffer, Miroslava; Wagner, Julian; Schaffer, Bernhard; Schmied, Mario; Mulders, Hans

    2007-01-01

    We present a fully automated method for three-dimensional (3D) elemental analysis demonstrated using a ceramic sample of chemistry (Ca)MgTiO x . The specimen is serially sectioned by a focused ion beam (FIB) microscope, and energy-dispersive X-ray spectrometry (EDXS) is used for elemental analysis of each cross-section created. A 3D elemental model is reconstructed from the stack of two-dimensional (2D) data. This work concentrates on issues arising from process automation, the large sample volume of approximately 17x17x10 μm 3 , and the insulating nature of the specimen. A new routine for post-acquisition data correction of different drift effects is demonstrated. Furthermore, it is shown that EDXS data may be erroneous for specimens containing voids, and that back-scattered electron images have to be used to correct for these errors

  17. Two- and three-dimensional proton NMR studies of apo-neocarzinostatin

    International Nuclear Information System (INIS)

    Xiaolian Gao; Burkhart, W.

    1991-01-01

    Neocarzinostatin (NCS) is an antitumor protein from Streptomyces carzinostaticus that is identical in apo-protein sequence with mitomalcin (MMC) from Streptomyces malayensis. The authors describe the use of apo-NCS as a model system for applying combined two-and three-dimensional (2D and 3D) proton NMR spectroscopy to the structure determination of proteins without isotope labeling. Strategies aimed at accurately assigning overlapped 2D cross-peaks by using semiautomated combined 2D and 3D data analysis are developed. Using this approach, they have assigned 99% of the protons, including those of the side chains, and identified about 1,270 intra- and interresidue proton-proton interactions (fixed distances are not included) in apo-NCS. Comparing these results with those reported recently on 2D NMR studies of apo-NCS demonstrated advantages of proton 3D NMR spectroscopy in protein spectral assignments. They are able to obtain more complete proton resonance and secondary structural assignments and find several misassignments in the earlier report. Strategies utilized in this work should be useful for developing automation procedures for spectral assignments

  18. Characterization and identification of early proteins in Chlamydia trachomatis serovar L2 by two-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Lundemose, AG; Birkelund, Svend; Larsen, PM

    1990-01-01

    The synthesis of early proteins from Chlamydia trachomatis serovar L2 was analyzed by two-dimensional gel electrophoresis. By pulse-label experiments, the synthesis of seven proteins was observed at 2 to 8 h postinfection before the major outer membrane protein was detected at 8 to 10 h after...

  19. Protein composition of wheat gluten polymer fractions determined by quantitative two-dimensional gel electrophoresis and tandem mass spectrometry

    Science.gov (United States)

    Flour proteins from the US bread wheat Butte 86 were extracted in 0.5% SDS using a two-step procedure with and without sonication and further separated by size exclusion chromatography into monomeric and polymeric fractions. Proteins in each fraction were analyzed by quantitative two-dimensional gel...

  20. Two-dimensional gel electrophoresis of selenized yeast and autoradiography of 75Se-containing proteins

    International Nuclear Information System (INIS)

    Chery, C.C.; Dumont, E.; Cornelis, R.; Moens, L.

    2001-01-01

    Two-dimensional high-resolution gel electrophoresis (2DE) has been applied to the fractionation of 75 Se-containing proteins in yeast, grown in 75 Se-containing medium, and autoradiography was used for detection of the 75 Se-containing proteins. Gel filtration and ultrafiltration were used to check whether the selenium side-chains were stable in the presence of the chemicals used for lysis and 2DE. The mass distribution of the selenium-containing proteins was estimated by use of gel filtration and the results were compared with the distribution obtained by 2DE. A 2DE map of selenium-containing proteins in yeast is presented, and compared with a total protein map of yeast. (orig.)

  1. Characterization of royal jelly proteins in both Africanized and European honeybees (Apis mellifera) by two-dimensional gel electrophoresis.

    Science.gov (United States)

    Sano, Osamu; Kunikata, Toshio; Kohno, Keizo; Iwaki, Kanso; Ikeda, Masao; Kurimoto, Masashi

    2004-01-14

    In this study, the proteins contained in royal jelly (RJ) produced by Africanized honeybees and European honeybees (Apis mellifera) haven been analyzed in detail and compared using two-dimensional gel electrophoresis, and the N-terminal amino acid sequence of each spot has been determined. Most spots were assigned to major royal jelly proteins (MRJPs). Remarkable differences were found in the heterogeneity of the MRJPs, in particular MRJP3, in terms of molecular weights and isoelectric points between the two species of RJ. Furthermore, during the determination of the N-terminal amino acid sequence of each spot, for the first time, MRJP4 protein has been identified, the existence of which had been only implied by cloning of its cDNA sequence. The presence of heterogeneous bands of glucose oxidase was also identified. Thus, the results suggest that two-dimensional gel electrophoresis provides a suitable method for the qualitative analysis of the proteins contained in RJ derived from different honeybee species.

  2. Simplification and improvement of protein detection in two-dimensional electrophoresis gels with SERVA HPE™ lightning red.

    Science.gov (United States)

    Griebel, Anja; Obermaier, Christian; Westermeier, Reiner; Moche, Martin; Büttner, Knut

    2013-07-01

    A new fluorescent amino-reactive dye has been tested for both labelling proteins prior to electrophoretic separations and between the two steps of two-dimensional electrophoresis. A series of experiments showed, that the labelling of lysines with this dye is compatible with all standard additives used for sample preparation, including reducing substances and carrier ampholytes. Using this dye for pre-labelling considerably simplifies the electrophoresis and detection workflow and provides highly sensitive and quantitative visualisation of proteins.

  3. Suitability of two-dimensional electrophoretic protein separations for quantitative detection of mutations

    International Nuclear Information System (INIS)

    Taylor, J.; Anderson, N.L.; Anderson, N.G.; Gemmell, A.; Giometti, C.S.; Nance, S.L.; Tollaksen, S.L.

    1986-01-01

    Separation of proteins by two-dimensional electrophoresis (2DE) provides a powerful method for mutagenesis studies, since hundreds of proteins can be monitored simultaneously. In previous mutation studies in which 2DE has been used, only qualitative protein differences were monitored; quantitative protein variations were not evaluated. Although significant differences in protein abundance can be detected by eye, the large number of protein spots present in 2DE patterns together with the large number of individual patterns required for a mutagenesis study would necessitate the use of a computerized analysis system to detect the rare quantitative protein changes indicative of gene deletions or inactivation of genes by point mutations in regulatory genes. A pilot study to search for heritable mutations induced by treatment of mice with either ethylnitrosourea or gamma radiation is underway. Samples are being monitored for quantitative changes that reduce the amount of protein by about 50%. The results of this study indicate that the key methods to improve the application of 2DE to mutation screening are to increase the number of measurable spots (i.e., improve stain sensitivity) and to decrease the spread of values for the volume measurements. Even small improvements in these areas could greatly increase the number of monitorable spots. 9 refs., 4 figs

  4. Automated protein structure calculation from NMR data

    International Nuclear Information System (INIS)

    Williamson, Mike P.; Craven, C. Jeremy

    2009-01-01

    Current software is almost at the stage to permit completely automatic structure determination of small proteins of <15 kDa, from NMR spectra to structure validation with minimal user interaction. This goal is welcome, as it makes structure calculation more objective and therefore more easily validated, without any loss in the quality of the structures generated. Moreover, it releases expert spectroscopists to carry out research that cannot be automated. It should not take much further effort to extend automation to ca 20 kDa. However, there are technological barriers to further automation, of which the biggest are identified as: routines for peak picking; adoption and sharing of a common framework for structure calculation, including the assembly of an automated and trusted package for structure validation; and sample preparation, particularly for larger proteins. These barriers should be the main target for development of methodology for protein structure determination, particularly by structural genomics consortia

  5. Facilitating the Hyphenation of CIEF and MALDI-MS for Two-Dimensional Separation of Proteins

    Science.gov (United States)

    Cheng, Chang; Lu, Joann J.; Wang, Xiayan; Roberts, Jonathan; Liu, Shaorong

    2011-01-01

    Both CIEF and MALDI-MS are frequently used in protein analysis, but hyphenation of the two is not investigated proportionally. One of the major reasons is that the additives (such as carrier ampholytes and detergent) in CIEF severely suppress the MALDI-MS signal, which hampers the hyphenation of the two. In this paper, we develop a simple means to alleviate the above signal-suppressing effect. We first deposit 1 µL of water onto a MALDI-MS target, deliver a fraction of CIEF-separated protein (~0.1 µL) to the water droplet, evaporate the solvent, add 0.5 µL of MALDI matrix to the sample spot, dry the matrix, and move the target plate to a MALDI-TOF-MS for mass spectrum measurement. We optimize the droplet volume and the laser-ablation region. Under the optimized conditions, we improve the signal to noise ratio by 2–10 fold. We also apply this method for two-dimensional separations of standard proteins and Apolipoprotein A-I, a membrane protein expressed in E. Coli cells. PMID:20603827

  6. Automated 3D-Printed Unibody Immunoarray for Chemiluminescence Detection of Cancer Biomarker Proteins

    Science.gov (United States)

    Tang, C. K.; Vaze, A.; Rusling, J. F.

    2017-01-01

    A low cost three-dimensional (3D) printed clear plastic microfluidic device was fabricated for fast, low cost automated protein detection. The unibody device features three reagent reservoirs, an efficient 3D network for passive mixing, and an optically transparent detection chamber housing a glass capture antibody array for measuring chemiluminescence output with a CCD camera. Sandwich type assays were built onto the glass arrays using a multi-labeled detection antibody-polyHRP (HRP = horseradish peroxidase). Total assay time was ~30 min in a complete automated assay employing a programmable syringe pump so that the protocol required minimal operator intervention. The device was used for multiplexed detection of prostate cancer biomarker proteins prostate specific antigen (PSA) and platelet factor 4 (PF-4). Detection limits of 0.5 pg mL−1 were achieved for these proteins in diluted serum with log dynamic ranges of four orders of magnitude. Good accuracy vs ELISA was validated by analyzing human serum samples. This prototype device holds good promise for further development as a point-of-care cancer diagnostics tool. PMID:28067370

  7. Proteomic study of muscle sarcoplasmic proteins using AUT-PAGE/SDS-PAGE as two-dimensional gel electrophoresis.

    Science.gov (United States)

    Picariello, Gianluca; De Martino, Alessandra; Mamone, Gianfranco; Ferranti, Pasquale; Addeo, Francesco; Faccia, Michele; Spagnamusso, Salvatore; Di Luccia, Aldo

    2006-03-20

    In the present study, an alternative procedure for two-dimensional (2D) electrophoretic analysis in proteomic investigation of the most represented basic muscle water-soluble proteins is suggested. Our method consists of Acetic acid-Urea-Triton polyacrylamide gel (AUT-PAGE) analysis in the first dimension and standard sodium dodecyl sulphate polyacrylamide gel (SDS-PAGE) in the second dimension. Although standard two-dimensional Immobilized pH Gradient-Sodium Dodecyl-Sulphate (2D IPG-SDS) gel electrophoresis has been successfully used to study these proteins, most of the water-soluble proteins are spread on the alkaline part of the 2D map and are poorly focused. Furthermore, the similarity in their molecular weights impairs resolution of the classical approach. The addition of Triton X-100, a non-ionic detergent, into the gel induces a differential electrophoretic mobility of proteins as a result of the formation of mixed micelles between the detergent and the hydrophobic moieties of polypeptides, separating basic proteins with a criterion similar to reversed phase chromatography based on their hydrophobicity. The acid pH induces positive net charges, increasing with the isoelectric point of proteins, thus allowing enhanced resolution in the separation. By using 2D AUT-PAGE/SDS electrophoresis approach to separate water-soluble proteins from fresh pork and from dry-cured products, we could spread proteins over a greater area, achieving a greater resolution than that obtained by IPG in the pH range 3-10 and 6-11. Sarcoplasmic proteins undergoing proteolysis during the ripening of products were identified by Matrix Assisted Laser Desorption/Ionization-Time of Flight (MALDI-ToF) mass spectrometry peptide mass fingerprinting in a easier and more effective way. Two-dimensional AUT-PAGE/SDS electrophoresis has allowed to simplify separation of sarcoplasmic protein mixtures making this technique suitable in the defining of quality of dry-cured pork products by immediate

  8. Two-dimensional analysis of human lymphocyte proteins. III. Preliminary report on a marker for the early detection and diagnosis of infectious mononucleosis

    International Nuclear Information System (INIS)

    Willard, K.E.

    1982-01-01

    Two-dimensional gel electrophoretic patterns of human peripheral blood leukocytes from 12 patients with infectious mononucleosis were prepared by use of the ISO-DALT system. Before the two-dimensional separation, the leukocytes were purified by Ficoll-Paque gradient centrifugation and labeled overnight with [ 35 S] methionine. Quantitative increases in two proteins were detected in the patterns of infected leukocytes from the patients as compared with controls. Fluorescence-activated cell sorting of leukocytes from normal human peripheral blood before subsequent two-dimensional gel analysis revealed that the dramatic increase in one of these proteins (Inmono:2) could be due to shifts in the population ratios of lymphocytes, monocytes, and granulocytes. In contrast, the appearance in the infected leukocytes of a second protein, Inmono:1, could not be accounted for by cell-population shifts. Increased amounts of these two proteins have been found in every patient studied who had clinically detectable infectious mononucleosis. In addition, a patient who displayed symptoms of infectious mononucleosis but who did not have a positive result in the MONOSPOT test (Ortho) until three weeks after our analysis also demonstrated increased relative amounts of these proteins in his leukocyte pattern

  9. Two-dimensional liquid chromatography consisting of twelve second-dimension columns for comprehensive analysis of intact proteins.

    Science.gov (United States)

    Ren, Jiangtao; Beckner, Matthew A; Lynch, Kyle B; Chen, Huang; Zhu, Zaifang; Yang, Yu; Chen, Apeng; Qiao, Zhenzhen; Liu, Shaorong; Lu, Joann J

    2018-05-15

    A comprehensive two-dimensional liquid chromatography (LCxLC) system consisting of twelve columns in the second dimension was developed for comprehensive analysis of intact proteins in complex biological samples. The system consisted of an ion-exchange column in the first dimension and the twelve reverse-phase columns in the second dimension; all thirteen columns were monolithic and prepared inside 250 µm i.d. capillaries. These columns were assembled together through the use of three valves and an innovative configuration. The effluent from the first dimension was continuously fractionated and sequentially transferred into the twelve second-dimension columns, while the second-dimension separations were carried out in a series of batches (six columns per batch). This LCxLC system was tested first using standard proteins followed by real-world samples from E. coli. Baseline separation was observed for eleven standard proteins and hundreds of peaks were observed for the real-world sample analysis. Two-dimensional liquid chromatography, often considered as an effective tool for mapping proteins, is seen as laborious and time-consuming when configured offline. Our online LCxLC system with increased second-dimension columns promises to provide a solution to overcome these hindrances. Copyright © 2018 Elsevier B.V. All rights reserved.

  10. Mapping and identification of interferon gamma-regulated HeLa cell proteins separated by immobilized pH gradient two-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Shaw, A.; Larsen, M.; Roepstorff, P.

    1999-01-01

    magnitude of IFN-gamma responsive genes has been reported previously. Our goal is to identify and map IFN-gamma-regulated HeLa cell proteins to the two-dimensional polyacrylamide gel electrophoresis with the immobilized pH gradient (IPG) two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) system...

  11. Velocity and Dispersion for a Two-Dimensional Random Walk

    International Nuclear Information System (INIS)

    Li Jinghui

    2009-01-01

    In the paper, we consider the transport of a two-dimensional random walk. The velocity and the dispersion of this two-dimensional random walk are derived. It mainly show that: (i) by controlling the values of the transition rates, the direction of the random walk can be reversed; (ii) for some suitably selected transition rates, our two-dimensional random walk can be efficient in comparison with the one-dimensional random walk. Our work is motivated in part by the challenge to explain the unidirectional transport of motor proteins. When the motor proteins move at the turn points of their tracks (i.e., the cytoskeleton filaments and the DNA molecular tubes), some of our results in this paper can be used to deal with the problem. (general)

  12. The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Woonghee, E-mail: whlee@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison and Biochemistry Department (United States); Petit, Chad M. [University of Alabama at Birmingham, Department of Biochemistry and Molecular Genetics (United States); Cornilescu, Gabriel; Stark, Jaime L.; Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison and Biochemistry Department (United States)

    2016-06-15

    We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25 kDa that had 27–98 % sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models.

  13. The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data

    International Nuclear Information System (INIS)

    Lee, Woonghee; Petit, Chad M.; Cornilescu, Gabriel; Stark, Jaime L.; Markley, John L.

    2016-01-01

    We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25 kDa that had 27–98 % sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models.

  14. Automated DBS microsampling, microscale automation and microflow LC-MS for therapeutic protein PK.

    Science.gov (United States)

    Zhang, Qian; Tomazela, Daniela; Vasicek, Lisa A; Spellman, Daniel S; Beaumont, Maribel; Shyong, BaoJen; Kenny, Jacqueline; Fauty, Scott; Fillgrove, Kerry; Harrelson, Jane; Bateman, Kevin P

    2016-04-01

    Reduce animal usage for discovery-stage PK studies for biologics programs using microsampling-based approaches and microscale LC-MS. We report the development of an automated DBS-based serial microsampling approach for studying the PK of therapeutic proteins in mice. Automated sample preparation and microflow LC-MS were used to enable assay miniaturization and improve overall assay throughput. Serial sampling of mice was possible over the full 21-day study period with the first six time points over 24 h being collected using automated DBS sample collection. Overall, this approach demonstrated comparable data to a previous study using single mice per time point liquid samples while reducing animal and compound requirements by 14-fold. Reduction in animals and drug material is enabled by the use of automated serial DBS microsampling for mice studies in discovery-stage studies of protein therapeutics.

  15. Automated, non-linear registration between 3-dimensional brain map and medical head image

    International Nuclear Information System (INIS)

    Mizuta, Shinobu; Urayama, Shin-ichi; Zoroofi, R.A.; Uyama, Chikao

    1998-01-01

    In this paper, we propose an automated, non-linear registration method between 3-dimensional medical head image and brain map in order to efficiently extract the regions of interest. In our method, input 3-dimensional image is registered into a reference image extracted from a brain map. The problems to be solved are automated, non-linear image matching procedure, and cost function which represents the similarity between two images. Non-linear matching is carried out by dividing the input image into connected partial regions, transforming the partial regions preserving connectivity among the adjacent images, evaluating the image similarity between the transformed regions of the input image and the correspondent regions of the reference image, and iteratively searching the optimal transformation of the partial regions. In order to measure the voxelwise similarity of multi-modal images, a cost function is introduced, which is based on the mutual information. Some experiments using MR images presented the effectiveness of the proposed method. (author)

  16. The master two-dimensional gel database of human AMA cell proteins: towards linking protein and genome sequence and mapping information (update 1991)

    DEFF Research Database (Denmark)

    Celis, J E; Leffers, H; Rasmussen, H H

    1991-01-01

    autoantigens" and "cDNAs". For convenience we have included an alphabetical list of all known proteins recorded in this database. In the long run, the main goal of this database is to link protein and DNA sequencing and mapping information (Human Genome Program) and to provide an integrated picture......The master two-dimensional gel database of human AMA cells currently lists 3801 cellular and secreted proteins, of which 371 cellular polypeptides (306 IEF; 65 NEPHGE) were added to the master images during the last 10 months. These include: (i) very basic and acidic proteins that do not focus...

  17. Initial proteome analysis of caffeine-induced proteins in Aspergillus tamarii using two-dimensional fluorescence difference gel electrophoresis.

    Science.gov (United States)

    Gutiérrez-Sánchez, Gerardo; Atwood, James; Kolli, V S Kumar; Roussos, Sévastianos; Augur, Christopher

    2012-04-01

    Caffeine is toxic to most microorganisms. However, some filamentous fungi, such as Aspergillus tamarii, are able to metabolize this alkaloid when fed caffeine as the sole nitrogen source. The aim of the present work was to identify intracellular A. tamarii proteins, regulated by caffeine, using fluorescence difference two-dimensional gel electrophoresis. Specific proteins from two culture media of A. tamarii grown either on ammonium sulfate or caffeine as the sole nitrogen source were analysed by mass spectrometry. Thirteen out of a total of 85 differentially expressed spots were identified after database search. Identified up-regulated proteins include phosphoglycerate kinase, malate dehydrogenase, dyp-type peroxidase family protein, heat shock protein, Cu, Zn superoxidase dismutase and xanthine dehydrogenase. Some of the proteins identified in this study are involved in the caffeine degradation pathway as well as in stress response, suggesting that stress proteins could be involved in caffeine metabolism in filamentous fungi.

  18. Relationship between recombinant protein expression and host metabolome as determined by two-dimensional NMR spectroscopy.

    Directory of Open Access Journals (Sweden)

    Young Kee Chae

    Full Text Available Escherichia coli has been the most widely used host to produce large amounts of heterologous proteins. However, given an input plasmid DNA, E. coli may produce soluble protein, produce only inclusion bodies, or yield little or no protein at all. Many efforts have been made to surmount these problems, but most of them have involved time-consuming and labor-intensive trial-and-error. We hypothesized that different metabolomic fingerprints might be associated with different protein production outcomes. If so, then it might be possible to change the expression pattern by manipulating the metabolite environment. As a first step in testing this hypothesis, we probed a subset of the intracellular metabolites by partially labeling it with 13C-glucose. We tested 71 genes and identified 17 metabolites by employing the two-dimensional NMR spectroscopy. The statistical analysis showed that there existed the metabolite compositions favoring protein production. We hope that this work would help devise a systematic and predictive approach to the recombinant protein production.

  19. Avoiding acidic region streaking in two-dimensional gel electrophoresis: case study with two bacterial whole cell protein extracts.

    Science.gov (United States)

    Roy, Arnab; Varshney, Umesh; Pal, Debnath

    2014-09-01

    Acidic region streaking (ARS) is one of the lacunae in two-dimensional gel electrophoresis (2DE) of bacterial proteome. This streaking is primarily caused by nucleic acid (NuA) contamination and poses major problem in the downstream processes like image analysis and protein identification. Although cleanup and nuclease digestion are practiced as remedial options, these strategies may incur loss in protein recovery and perform incomplete removal of NuA. As a result, ARS has remained a common observation across publications, including the recent ones. In this work, we demonstrate how ultrasound wave can be used to shear NuA in plain ice-cooled water, facilitating the elimination of ARS in the 2DE gels without the need for any additional sample cleanup tasks. In combination with a suitable buffer recipe, IEF program and frequent paper-wick changing approach, we are able to reproducibly demonstrate the production of clean 2DE gels with improved protein recovery and negligible or no ARS. We illustrate our procedure using whole cell protein extracts from two diverse organisms, Escherichia coli and Mycobacterium smegmatis. Our designed protocols are straightforward and expected to provide good 2DE gels without ARS, with comparable times and significantly lower cost.

  20. Comparison of a three-dimensional and two-dimensional camera system for automated measurement of back posture in dairy cows

    NARCIS (Netherlands)

    Viazzi, S.; Bahr, C.; Hertem, van T.; Schlageter-Tello, A.; Romanini, C.E.B.; Halachmi, I.; Lokhorst, C.; Berckmans, D.

    2014-01-01

    In this study, two different computer vision techniques to automatically measure the back posture in dairy cows were tested and evaluated. A two-dimensional and a three-dimensional camera system were used to extract the back posture from walking cows, which is one measurement used by experts to

  1. Electrophoretic analysis of proteins from Mycoplasma hominis strains detected by SDS-PAGE, two-dimensional gel electrophoresis and immunoblotting

    DEFF Research Database (Denmark)

    Andersen, H; Birkelund, Svend; Christiansen, Gunna

    1987-01-01

    The proteins of 14 strains of Mycoplasma hominis were compared by SDS-PAGE in gradient gels, by two-dimensional (2D) gel electrophoresis of extracts of 35S-labelled cells and by immunoblot analysis of cell proteins. The strains examined included the M. hominis type strain PG21 and 13 others...... isolated variously from genital tract, mouth, blood, upper urinary tract and a wound. These 14 strains shared 76-99% of proteins in SDS-gradient gel analysis and 41-72% in the 2D gels. As expected, the immunoblot analysis likewise revealed the existence of an extensive common protein pattern in M. hominis...

  2. Evaluation of training nurses to perform semi-automated three-dimensional left ventricular ejection fraction using a customised workstation-based training protocol.

    Science.gov (United States)

    Guppy-Coles, Kristyan B; Prasad, Sandhir B; Smith, Kym C; Hillier, Samuel; Lo, Ada; Atherton, John J

    2015-06-01

    We aimed to determine the feasibility of training cardiac nurses to evaluate left ventricular function utilising a semi-automated, workstation-based protocol on three dimensional echocardiography images. Assessment of left ventricular function by nurses is an attractive concept. Recent developments in three dimensional echocardiography coupled with border detection assistance have reduced inter- and intra-observer variability and analysis time. This could allow abbreviated training of nurses to assess cardiac function. A comparative, diagnostic accuracy study evaluating left ventricular ejection fraction assessment utilising a semi-automated, workstation-based protocol performed by echocardiography-naïve nurses on previously acquired three dimensional echocardiography images. Nine cardiac nurses underwent two brief lectures about cardiac anatomy, physiology and three dimensional left ventricular ejection fraction assessment, before a hands-on demonstration in 20 cases. We then selected 50 cases from our three dimensional echocardiography library based on optimal image quality with a broad range of left ventricular ejection fractions, which was quantified by two experienced sonographers and the average used as the comparator for the nurses. Nurses independently measured three dimensional left ventricular ejection fraction using the Auto lvq package with semi-automated border detection. The left ventricular ejection fraction range was 25-72% (70% with a left ventricular ejection fraction nurses showed excellent agreement with the sonographers. Minimal intra-observer variability was noted on both short-term (same day) and long-term (>2 weeks later) retest. It is feasible to train nurses to measure left ventricular ejection fraction utilising a semi-automated, workstation-based protocol on previously acquired three dimensional echocardiography images. Further study is needed to determine the feasibility of training nurses to acquire three dimensional echocardiography

  3. Non-Uniform Sampling and J-UNIO Automation for Efficient Protein NMR Structure Determination.

    Science.gov (United States)

    Didenko, Tatiana; Proudfoot, Andrew; Dutta, Samit Kumar; Serrano, Pedro; Wüthrich, Kurt

    2015-08-24

    High-resolution structure determination of small proteins in solution is one of the big assets of NMR spectroscopy in structural biology. Improvements in the efficiency of NMR structure determination by advances in NMR experiments and automation of data handling therefore attracts continued interest. Here, non-uniform sampling (NUS) of 3D heteronuclear-resolved [(1)H,(1)H]-NOESY data yielded two- to three-fold savings of instrument time for structure determinations of soluble proteins. With the 152-residue protein NP_372339.1 from Staphylococcus aureus and the 71-residue protein NP_346341.1 from Streptococcus pneumonia we show that high-quality structures can be obtained with NUS NMR data, which are equally well amenable to robust automated analysis as the corresponding uniformly sampled data. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Evaluation of different protein extraction methods for banana (Musa spp.) root proteome analysis by two-dimensional electrophoresis.

    Science.gov (United States)

    Vaganan, M Mayil; Sarumathi, S; Nandakumar, A; Ravi, I; Mustaffa, M M

    2015-02-01

    Four protocols viz., the trichloroacetic acid-acetone (TCA), phenol-ammonium acetate (PAA), phenol/SDS-ammonium acetate (PSA) and trisbase-acetone (TBA) were evaluated with modifications for protein extraction from banana (Grand Naine) roots, considered as recalcitrant tissues for proteomic analysis. The two-dimensional electrophoresis (2-DE) separated proteins were compared based on protein yield, number of resolved proteins, sum of spot quantity, average spot intensity and proteins resolved in 4-7 pI range. The PAA protocol yielded more proteins (0.89 mg/g of tissues) and protein spots (584) in 2-DE gel than TCA and other protocols. Also, the PAA protocol was superior in terms of sum of total spot quantity and average spot intensity than TCA and other protocols, suggesting phenol as extractant and ammonium acetate as precipitant of proteins were the most suitable for banana rooteomics analysis by 2-DE. In addition, 1:3 ratios of root tissue to extraction buffer and overnight protein precipitation were most efficient to obtain maximum protein yield.

  5. Mapping of Chlamydia trachomatis proteins by immobiline-polyacrylamide two-dimensional electrophoresis: spot identification by N-terminal sequencing and immunoblotting

    DEFF Research Database (Denmark)

    Bini, L; Sanchez-Campillo, M; Santucci, A

    1996-01-01

    Proteins from purified elementary bodies of Chlamydia trachomatis were separated by two-dimensional gel electrophoresis on nonlinear wide-range immobilized pH gradients in the first dimension and polyacrylamide gradient gels in the second dimension. The maps obtained with this system are highly...

  6. Zero in on Key Open Problems in Automated NMR Protein Structure Determination

    KAUST Repository

    Abbas, Ahmed

    2015-11-12

    Nuclear magnetic resonance (NMR) is one of the main approaches for protein struc- ture determination. The biggest advantage of this approach is that it can determine the three-dimensional structure of the protein in the solution phase. Thus, the natural dynamics of the protein can be studied. However, NMR protein structure determina- tion is an expertise intensive and time-consuming process. If the structure determi- nation process can be accelerated or even automated by computational methods, that will significantly advance the structural biology field. Our goal in this dissertation is to propose highly efficient and error tolerant methods that can work well on real and noisy data sets of NMR. Our first contribution in this dissertation is the development of a novel peak pick- ing method (WaVPeak). First, WaVPeak denoises the NMR spectra using wavelet smoothing. A brute force method is then used to identify all the candidate peaks. Af- ter that, the volume of each candidate peak is estimated. Finally, the peaks are sorted according to their volumes. WaVPeak is tested on the same benchmark data set that was used to test the state-of-the-art method, PICKY. WaVPeak shows significantly better performance than PICKY in terms of recall and precision. Our second contribution is to propose an automatic method to select peaks pro- duced by peak picking methods. This automatic method is used to overcome the limitations of fixed number-based methods. Our method is based on the Benjamini- Hochberg (B-H) algorithm. The method is used with both WaVPeak and PICKY to automatically select the number of peaks to return from out of hundreds of candidate peaks. The volume (in WaVPeak) and the intensity (in PICKY) are converted into p-values. Peaks that have p-values below some certain threshold are selected. Ex- perimental results show that the new method is better than the fixed number-based method in terms of recall. To improve precision, we tried to eliminate false peaks using

  7. Toponomics method for the automated quantification of membrane protein translocation.

    Science.gov (United States)

    Domanova, Olga; Borbe, Stefan; Mühlfeld, Stefanie; Becker, Martin; Kubitz, Ralf; Häussinger, Dieter; Berlage, Thomas

    2011-09-19

    Intra-cellular and inter-cellular protein translocation can be observed by microscopic imaging of tissue sections prepared immunohistochemically. A manual densitometric analysis is time-consuming, subjective and error-prone. An automated quantification is faster, more reproducible, and should yield results comparable to manual evaluation. The automated method presented here was developed on rat liver tissue sections to study the translocation of bile salt transport proteins in hepatocytes. For validation, the cholestatic liver state was compared to the normal biological state. An automated quantification method was developed to analyze the translocation of membrane proteins and evaluated in comparison to an established manual method. Firstly, regions of interest (membrane fragments) are identified in confocal microscopy images. Further, densitometric intensity profiles are extracted orthogonally to membrane fragments, following the direction from the plasma membrane to cytoplasm. Finally, several different quantitative descriptors were derived from the densitometric profiles and were compared regarding their statistical significance with respect to the transport protein distribution. Stable performance, robustness and reproducibility were tested using several independent experimental datasets. A fully automated workflow for the information extraction and statistical evaluation has been developed and produces robust results. New descriptors for the intensity distribution profiles were found to be more discriminative, i.e. more significant, than those used in previous research publications for the translocation quantification. The slow manual calculation can be substituted by the fast and unbiased automated method.

  8. Muscle protein analysis. II. Two-dimensional electrophoresis of normal and diseased human skeletal muscle

    Energy Technology Data Exchange (ETDEWEB)

    Giometti, C.S. (Argonne National Lab., IL); Barany, M.; Danon, M.J.; Anderson, N.G.

    1980-07-01

    High-resolution two-dimensional electrophoresis was used to analyze the major proteins of normal and pathological human-muscle samples. The normal human-muscle pattern contains four myosin light chains: three that co-migrate with the myosin light chains from rabbit fast muscle (extensor digitorum longus), and one that co-migrates with the light chain 2 from rabbit slow muscle (soleus). Of seven Duchenne muscular dystrophy samples, four yielded patterns with decreased amounts of actin and myosin relative to normal muscle, while three samples gave patterns comparable to that for normal muscle. Six samples from patients with myotonic dystrophy also gave normal patterns. In nemaline rod myopathy, in contrast, the pattern was deficient in two of the fast-type myosin light chains.

  9. Comparison of protein patterns after two-dimensional gel electrophoresis from leaves of in vitro cultures and seedlings of Rubus chamaemorus L.

    Directory of Open Access Journals (Sweden)

    Barbara Thiem

    2014-01-01

    Full Text Available Proteins from leaves of Rubus chamaemorus propagated in vitro were subjected to miniaturized 2-D electrophoresis. The 2-DE patterns of proteins showed qualitative differences between plants propagated in vitro and control seedlings. More proteins of a high molecular weight were observed in leaves of plants from in vitro culture. A two-dimensional map of proteins from leaves provides detailed data concerning both polymorphism and protein patterns of this species. This makes it possible to start constructing a protein map of R. chamaemorus. The reasons for qualitative differences are discussed.

  10. 4D experiments measured with APSY for automated backbone resonance assignments of large proteins

    International Nuclear Information System (INIS)

    Krähenbühl, Barbara; Boudet, Julien; Wider, Gerhard

    2013-01-01

    Detailed structural and functional characterization of proteins by solution NMR requires sequence-specific resonance assignment. We present a set of transverse relaxation optimization (TROSY) based four-dimensional automated projection spectroscopy (APSY) experiments which are designed for resonance assignments of proteins with a size up to 40 kDa, namely HNCACO, HNCOCA, HNCACB and HN(CO)CACB. These higher-dimensional experiments include several sensitivity-optimizing features such as multiple quantum parallel evolution in a ‘just-in-time’ manner, aliased off-resonance evolution, evolution-time optimized APSY acquisition, selective water-handling and TROSY. The experiments were acquired within the concept of APSY, but they can also be used within the framework of sparsely sampled experiments. The multidimensional peak lists derived with APSY provided chemical shifts with an approximately 20 times higher precision than conventional methods usually do, and allowed the assignment of 90 % of the backbone resonances of the perdeuterated primase-polymerase ORF904, which contains 331 amino acid residues and has a molecular weight of 38.4 kDa.

  11. Automated multivariate analysis of comprehensive two-dimensional gas chromatograms of petroleum

    DEFF Research Database (Denmark)

    Skov, Søren Furbo

    of separated compounds makes the analysis of GCGC chromatograms tricky, as there are too much data for manual analysis , and automated analysis is not always trouble-free: Manual checking of the results is often necessary. In this work, I will investigate the possibility of another approach to analysis of GCGC...... impossible to find it. For a special class of models, multi-way models, unique solutions often exist, meaning that the underlying phenomena can be found. I have tested this class of models on GCGC data from petroleum and conclude that more work is needed before they can be automated. I demonstrate how...

  12. Analysis of Two-Dimensional Electrophoresis Gel Images

    DEFF Research Database (Denmark)

    Pedersen, Lars

    2002-01-01

    This thesis describes and proposes solutions to some of the currently most important problems in pattern recognition and image analysis of two-dimensional gel electrophoresis (2DGE) images. 2DGE is the leading technique to separate individual proteins in biological samples with many biological...

  13. Two Dimensional Electrophoresis of Proteins from Cultures of Erysiphe graminis f.sp. hordei

    DEFF Research Database (Denmark)

    Torp, J.; Andersen, Brian

    1982-01-01

    Conidial proteins from barley powdery mildew, Erysiphe graminis f. sp. hordei, were separated by 2-dimensional electrophoresis in polyacrylamide slab gels. Isoelectric focusing was used in the first dimension and separation according to molecular weight in a gel containing sodium dodecyl sulphate...

  14. Separation and identification of Musa acuminate Colla (banana) leaf proteins by two-dimensional gel electrophoresis and mass spectrometry.

    Science.gov (United States)

    Lu, Y; Qi, Y X; Zhang, H; Zhang, H Q; Pu, J J; Xie, Y X

    2013-12-19

    To establish a proteomic reference map of Musa acuminate Colla (banana) leaf, we separated and identified leaf proteins using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Tryptic digests of 44 spots were subjected to peptide mass fingerprinting (PMF) by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS. Three spots that were not identified by MALDI-TOF MS analysis were identified by searching against the NCBInr, SwissProt, and expressed sequence tag (EST) databases. We identified 41 unique proteins. The majority of the identified leaf proteins were found to be involved in energy metabolism. The results indicate that 2D-PAGE is a sensitive and powerful technique for the separation and identification of Musa leaf proteins. A summary of the identified proteins and their putative functions is discussed.

  15. Optimized Protocol for Protein Extraction from the Breast Tissue that is Compatible with Two-Dimensional Gel Electrophoresis

    Directory of Open Access Journals (Sweden)

    Olena Zakharchenko

    2011-01-01

    Full Text Available Proteomics is a highly informative approach to analyze cancer-associated transformation in tissues. The main challenge to use a tissue for proteomics studies is the small sample size and difficulties to extract and preserve proteins. The choice of a buffer compatible with proteomics applications is also a challenge. Here we describe a protocol optimized for the most efficient extraction of proteins from the human breast tissue in a buffer compatible with two-dimensional gel electrophoresis (2D-GE. This protocol is based on mechanically assisted disintegration of tissues directly in the 2D-GE buffer. Our method is simple, robust and easy to apply in clinical practice. We demonstrate high quality of separation of proteins prepared according to the reported here protocol.

  16. Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH

    International Nuclear Information System (INIS)

    Volk, Jochen; Herrmann, Torsten; Wuethrich, Kurt

    2008-01-01

    MATCH (Memetic Algorithm and Combinatorial Optimization Heuristics) is a new memetic algorithm for automated sequence-specific polypeptide backbone NMR assignment of proteins. MATCH employs local optimization for tracing partial sequence-specific assignments within a global, population-based search environment, where the simultaneous application of local and global optimization heuristics guarantees high efficiency and robustness. MATCH thus makes combined use of the two predominant concepts in use for automated NMR assignment of proteins. Dynamic transition and inherent mutation are new techniques that enable automatic adaptation to variable quality of the experimental input data. The concept of dynamic transition is incorporated in all major building blocks of the algorithm, where it enables switching between local and global optimization heuristics at any time during the assignment process. Inherent mutation restricts the intrinsically required randomness of the evolutionary algorithm to those regions of the conformation space that are compatible with the experimental input data. Using intact and artificially deteriorated APSY-NMR input data of proteins, MATCH performed sequence-specific resonance assignment with high efficiency and robustness

  17. PINE-SPARKY.2 for automated NMR-based protein structure research.

    Science.gov (United States)

    Lee, Woonghee; Markley, John L

    2018-05-01

    Nuclear magnetic resonance (NMR) spectroscopy, along with X-ray crystallography and cryoelectron microscopy, is one of the three major tools that enable the determination of atomic-level structural models of biological macromolecules. Of these, NMR has the unique ability to follow important processes in solution, including conformational changes, internal dynamics and protein-ligand interactions. As a means for facilitating the handling and analysis of spectra involved in these types of NMR studies, we have developed PINE-SPARKY.2, a software package that integrates and automates discrete tasks that previously required interaction with separate software packages. The graphical user interface of PINE-SPARKY.2 simplifies chemical shift assignment and verification, automated detection of secondary structural elements, predictions of flexibility and hydrophobic cores, and calculation of three-dimensional structural models. PINE-SPARKY.2 is available in the latest version of NMRFAM-SPARKY from the National Magnetic Resonance Facility at Madison (http://pine.nmrfam.wisc.edu/download_packages.html), the NMRbox Project (https://nmrbox.org) and to subscribers to the SBGrid (https://sbgrid.org). For a detailed description of the program, see http://www.nmrfam.wisc.edu/pine-sparky2.htm. whlee@nmrfam.wisc.edu or markley@nmrfam.wisc.edu. Supplementary data are available at Bioinformatics online.

  18. Correlation of acidic and basic carrier ampholyte and immobilized pH gradient two-dimensional gel electrophoresis patterns based on mass spectrometric protein identification

    DEFF Research Database (Denmark)

    Nawrocki, A; Larsen, Martin Røssel; Podtelejnikov, A V

    1998-01-01

    Separation of proteins on either carrier ampholyte-based or immobilized pH gradient-based two-dimensional (2-D) gels gives rise to electrophoretic patterns that are difficult to compare visually. In this paper we have used matrix-assisted laser desorption/ionization mass spectrometry (MALDI......-MS) to determine the identities of 335 protein spots in these two 2-D gel systems, including a substantial number of basic proteins which had never been identified before. Proteins that were identified in both gel systems allowed us to cross-reference the gel patterns. Vector analysis of these cross...

  19. Human lymphocyte polymorphisms detected by quantitative two-dimensional electrophoresis

    International Nuclear Information System (INIS)

    Goldman, D.; Merril, C.R.

    1983-01-01

    A survey of 186 soluble lymphocyte proteins for genetic polymorphism was carried out utilizing two-dimensional electrophoresis of 14 C-labeled phytohemagglutinin (PHA)-stimulated human lymphocyte proteins. Nineteen of these proteins exhibited positional variation consistent with independent genetic polymorphism in a primary sample of 28 individuals. Each of these polymorphisms was characterized by quantitative gene-dosage dependence insofar as the heterozygous phenotype expressed approximately 50% of each allelic gene product as was seen in homozygotes. Patterns observed were also identical in monozygotic twins, replicate samples, and replicate gels. The three expected phenotypes (two homozygotes and a heterozygote) were observed in each of 10 of these polymorphisms while the remaining nine had one of the homozygous classes absent. The presence of the three phenotypes, the demonstration of gene-dosage dependence, and our own and previous pedigree analysis of certain of these polymorphisms supports the genetic basis of these variants. Based on this data, the frequency of polymorphic loci for man is: P . 19/186 . .102, and the average heterozygosity is .024. This estimate is approximately 1/3 to 1/2 the rate of polymorphism previously estimated for man in other studies using one-dimensional electrophoresis of isozyme loci. The newly described polymorphisms and others which should be detectable in larger protein surveys with two-dimensional electrophoresis hold promise as genetic markers of the human genome for use in gene mapping and pedigree analyses

  20. Electron cryomicroscopy of two-dimensional crystals of the H+-ATPase from chloroplasts

    NARCIS (Netherlands)

    Böttcher, Bettina; Gräber, Peter; Boekema, Egbert J.; Lücken, Uwe

    1995-01-01

    The H+-ATPase from spinach chloroplasts was isolated and purified. Two-dimensional crystals were obtained from the protein/lipid/detergent micelles by treatment with phospholipase and simultaneous removal of detergent and fatty acids by Biobeads. The resulting two-dimensionally ordered arrays were

  1. Two-dimensional servo control of surface motor; Surface motor no nijigen servo control

    Energy Technology Data Exchange (ETDEWEB)

    Ebihara, D; Takahashi, T; Watada, M [Musashi Institute of Technology, Tokyo (Japan)

    1995-08-20

    Two dimensional (2D) drive system is needed in many aspects of factory automation (FA) and office automation (OA) machines, such as pen drivers in X-Y plotters, X-Y stage for machining, 2D moving robots, etc. Conventional 2D drive systems are consisted from two sets of rotational motor drive and several types of rotary-to-linear transform mechanisms. Linear motors, in these days, have become to be effective as the requirement for high speed increases. We have been studying about Surface Motor which enables 2D drive on a surface by single mover, and the characteristics are measured. Main difficulty of the actuator is that it is short of thrust forces. Also the feasibility is limited because of its vocational uncertainty caused by the open loop control. Our interest is to introduce the closed loop digital control, to obtain required thrust force at any point on the stator. Since open loop control is used, that is, stability point where the thrust force is zero is moved one after another, generated thrust force within the range of synchronization is small. We have been studying about the peculiar expression of exciting currents to generate required direction at all the stator. On the basis of results, two dimensional position feedback system is assembled, which detect the two dimensional location of the mover by optical sensors and direct current instructions are generated for all the four phases of the mover. 14 refs., 11 figs., 1 tab.

  2. Proteome analysis of barley seeds: Identification of major proteins from two-dimensional gels (pl 4-7)

    DEFF Research Database (Denmark)

    Østergaard, O.; Finnie, Christine; Laugesen, S.

    2004-01-01

    inhibitors), and proteins related to desiccation and oxidative stress. Sixty-four of the identifications were made using expressed sequence tags (ESTs). Numerous spots in the 2-D gel pattern changed during germination (micromalting) and an intensely stained area which contained large amounts of the serpin......Germination of monocotyledonous plants involves activation and de novo synthesis of enzymes that degrade cell walls and starch and mobilize stored endosperm reserves for embryo growth. Two-dimensional (2-D) gel electrophoresis and mass spectrometry were applied to identify major water...

  3. Two-dimensional errors

    International Nuclear Information System (INIS)

    Anon.

    1991-01-01

    This chapter addresses the extension of previous work in one-dimensional (linear) error theory to two-dimensional error analysis. The topics of the chapter include the definition of two-dimensional error, the probability ellipse, the probability circle, elliptical (circular) error evaluation, the application to position accuracy, and the use of control systems (points) in measurements

  4. Non-parametric comparison of histogrammed two-dimensional data distributions using the Energy Test

    International Nuclear Information System (INIS)

    Reid, Ivan D; Lopes, Raul H C; Hobson, Peter R

    2012-01-01

    When monitoring complex experiments, comparison is often made between regularly acquired histograms of data and reference histograms which represent the ideal state of the equipment. With the larger HEP experiments now ramping up, there is a need for automation of this task since the volume of comparisons could overwhelm human operators. However, the two-dimensional histogram comparison tools available in ROOT have been noted in the past to exhibit shortcomings. We discuss a newer comparison test for two-dimensional histograms, based on the Energy Test of Aslan and Zech, which provides more conclusive discrimination between histograms of data coming from different distributions than methods provided in a recent ROOT release.

  5. Automating data analysis for two-dimensional gas chromatography/time-of-flight mass spectrometry non-targeted analysis of comparative samples.

    Science.gov (United States)

    Titaley, Ivan A; Ogba, O Maduka; Chibwe, Leah; Hoh, Eunha; Cheong, Paul H-Y; Simonich, Staci L Massey

    2018-03-16

    Non-targeted analysis of environmental samples, using comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC × GC/ToF-MS), poses significant data analysis challenges due to the large number of possible analytes. Non-targeted data analysis of complex mixtures is prone to human bias and is laborious, particularly for comparative environmental samples such as contaminated soil pre- and post-bioremediation. To address this research bottleneck, we developed OCTpy, a Python™ script that acts as a data reduction filter to automate GC × GC/ToF-MS data analysis from LECO ® ChromaTOF ® software and facilitates selection of analytes of interest based on peak area comparison between comparative samples. We used data from polycyclic aromatic hydrocarbon (PAH) contaminated soil, pre- and post-bioremediation, to assess the effectiveness of OCTpy in facilitating the selection of analytes that have formed or degraded following treatment. Using datasets from the soil extracts pre- and post-bioremediation, OCTpy selected, on average, 18% of the initial suggested analytes generated by the LECO ® ChromaTOF ® software Statistical Compare feature. Based on this list, 63-100% of the candidate analytes identified by a highly trained individual were also selected by OCTpy. This process was accomplished in several minutes per sample, whereas manual data analysis took several hours per sample. OCTpy automates the analysis of complex mixtures of comparative samples, reduces the potential for human error during heavy data handling and decreases data analysis time by at least tenfold. Copyright © 2018 Elsevier B.V. All rights reserved.

  6. Two-dimensional polyacrylamide gel analysis of Plodia interpunctella granulosis virus

    International Nuclear Information System (INIS)

    Russell, D.L.; Consigli, R.A.

    1986-01-01

    The structural polypeptides of purified Plodia interpunctella granulosis virus were analyzed by three different two-dimensional gel systems. Isoelectric focusing followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis allowed resolution of 53 acidic polypeptides in the enveloped nucleocapsid of the virus ranging in molecular weight from 97,300 to 8000. Nine of these polypeptides were shown to be glycoproteins by the technique of radiolabeled lectin blotting. Separation of the granulin in this system allowed resolution of five species, all of which have identical tryptic peptide maps. This matrix protein was demonstrated to be a phosphoglycoprotein by radiolabeled lectin blotting and acid phosphatase dephosphorylation. Nonequilibrium pH gel electrophoresis followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis allowed resolution of the major basic protein of the virus, VP12, from a more acidic protein of the same molecular weight. Tryptic peptide analysis demonstrated that these two proteins were indeed different and acid urea gels followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis allowed localization of the acidic protein to the envelope and the basic protein to the nucleocapsid of the virus. Finally, probing of the separated envelope nucleocapsid proteins in both the isoelectric focusing and nonequilibrium pH gel electrophoresis two-dimensional systems after transfer to nitrocellulose with iodinated, purified viral proteins allowed further insight into reactions which may be important in the maintenance of the virion structure

  7. Automated backbone assignment of labeled proteins using the threshold accepting algorithm

    International Nuclear Information System (INIS)

    Leutner, Michael; Gschwind, Ruth M.; Liermann, Jens; Schwarz, Christian; Gemmecker, Gerd; Kessler, Horst

    1998-01-01

    The sequential assignment of backbone resonances is the first step in the structure determination of proteins by heteronuclear NMR. For larger proteins, an assignment strategy based on proton side-chain information is no longer suitable for the use in an automated procedure. Our program PASTA (Protein ASsignment by Threshold Accepting) is therefore designed to partially or fully automate the sequential assignment of proteins, based on the analysis of NMR backbone resonances plus C β information. In order to overcome the problems caused by peak overlap and missing signals in an automated assignment process, PASTA uses threshold accepting, a combinatorial optimization strategy, which is superior to simulated annealing due to generally faster convergence and better solutions. The reliability of this algorithm is shown by reproducing the complete sequential backbone assignment of several proteins from published NMR data. The robustness of the algorithm against misassigned signals, noise, spectral overlap and missing peaks is shown by repeating the assignment with reduced sequential information and increased chemical shift tolerances. The performance of the program on real data is finally demonstrated with automatically picked peak lists of human nonpancreatic synovial phospholipase A 2 , a protein with 124 residues

  8. Mobile home automation-merging mobile value added services and home automation technologies

    OpenAIRE

    Rosendahl, Andreas; Hampe, Felix J.; Botterweck, Goetz

    2007-01-01

    non-peer-reviewed In this paper we study mobile home automation, a field that emerges from an integration of mobile application platforms and home automation technologies. In a conceptual introduction we first illustrate the need for such applications by introducing a two-dimensional conceptual model of mobility. Subsequently we suggest an architecture and discuss different options of how a user might access a mobile home automation service and the controlled devices. As another contrib...

  9. ONE-DIMENSIONAL AND TWO-DIMENSIONAL LEADERSHIP STYLES

    Directory of Open Access Journals (Sweden)

    Nikola Stefanović

    2007-06-01

    Full Text Available In order to motivate their group members to perform certain tasks, leaders use different leadership styles. These styles are based on leaders' backgrounds, knowledge, values, experiences, and expectations. The one-dimensional styles, used by many world leaders, are autocratic and democratic styles. These styles lie on the two opposite sides of the leadership spectrum. In order to precisely define the leadership styles on the spectrum between the autocratic leadership style and the democratic leadership style, leadership theory researchers use two dimensional matrices. The two-dimensional matrices define leadership styles on the basis of different parameters. By using these parameters, one can identify two-dimensional styles.

  10. Two Dimensional Electrophoresis of Galactosidase Relating to the Disappearance of Bombyx Lectin Activity

    OpenAIRE

    カトウ, ヤスオ; Yasuo, Kato

    2004-01-01

    "Two dimensional polyacrylamide gel electroporesis (2 D-PAGE) analysis on the haemolymph of Bombyx mori was performed using the Mini-PROTEAN mini tube gel two dimensional polyacrylamide gel electrophoresis system (Bio-Rad Laboratories, Inc.). The result on various electrophoretical conditions using the haemolymph-protein showed the possibility that the haemolymph-protein was separated actually by means of this method. Moreover, the result of 2 D-PAGE analysis on Fraction II obtained by gel fi...

  11. Automated Quantification of Pneumothorax in CT

    Science.gov (United States)

    Do, Synho; Salvaggio, Kristen; Gupta, Supriya; Kalra, Mannudeep; Ali, Nabeel U.; Pien, Homer

    2012-01-01

    An automated, computer-aided diagnosis (CAD) algorithm for the quantification of pneumothoraces from Multidetector Computed Tomography (MDCT) images has been developed. Algorithm performance was evaluated through comparison to manual segmentation by expert radiologists. A combination of two-dimensional and three-dimensional processing techniques was incorporated to reduce required processing time by two-thirds (as compared to similar techniques). Volumetric measurements on relative pneumothorax size were obtained and the overall performance of the automated method shows an average error of just below 1%. PMID:23082091

  12. Current status and future prospects of an automated sample exchange system PAM for protein crystallography

    Science.gov (United States)

    Hiraki, M.; Yamada, Y.; Chavas, L. M. G.; Matsugaki, N.; Igarashi, N.; Wakatsuki, S.

    2013-03-01

    To achieve fully-automated and/or remote data collection in high-throughput X-ray experiments, the Structural Biology Research Centre at the Photon Factory (PF) has installed PF automated mounting system (PAM) for sample exchange robots at PF macromolecular crystallography beamlines BL-1A, BL-5A, BL-17A, AR-NW12A and AR-NE3A. We are upgrading the experimental systems, including the PAM for stable and efficient operation. To prevent human error in automated data collection, we installed a two-dimensional barcode reader for identification of the cassettes and sample pins. Because no liquid nitrogen pipeline in the PF experimental hutch is installed, the users commonly add liquid nitrogen using a small Dewar. To address this issue, an automated liquid nitrogen filling system that links a 100-liter tank to the robot Dewar has been installed on the PF macromolecular beamline. Here we describe this new implementation, as well as future prospects.

  13. Sex-specific and blood meal-induced proteins of Anopheles gambiae midguts: analysis by two-dimensional gel electrophoresis

    Directory of Open Access Journals (Sweden)

    Laurent-Winter C

    2003-02-01

    Full Text Available Abstract Background Anopheles gambiae is the main vector of Plasmodium falciparum in Africa. The mosquito midgut constitutes a barrier that the parasite must cross if it is to develop and be transmitted. Despite the central role of the mosquito midgut in the host/parasite interaction, little is known about its protein composition. Characterisation of An. gambiae midgut proteins may identify the proteins that render An. gambiae receptive to the malaria parasite. Methods We carried out two-dimensional gel electrophoresis of An. gambiae midgut proteins and compared protein profiles for midguts from males, sugar-fed females and females fed on human blood. Results Very few differences were detected between male and female mosquitoes for the approximately 375 silver-stained proteins. Male midguts contained ten proteins not detected in sugar-fed or blood-fed females, which are therefore probably involved in male-specific functions; conversely, female midguts contained twenty-three proteins absent from male midguts. Eight of these proteins were specific to sugar-fed females, and another ten, to blood-fed females. Conclusion Mass spectrometry analysis of the proteins found only in blood-fed female midguts, together with data from the recent sequencing of the An. gambiae genome, should make it possible to determine the role of these proteins in blood digestion or parasite receptivity.

  14. Effects of interferon gamma on Chlamydia trachomatis serovar A and L2 protein expression investigated by two-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Shaw, A; Christiansen, Gunna; Birkelund, Svend

    1999-01-01

    ]methionine and two-dimensional gel electrophoresis with immobilized pH gradients in order to investigate changes in the protein expression of C. trachomatis serovar A and L2 caused by treatment with IFN-gamma. In contrast to what was observed in C. trachomatis L2, our results showed that, in C. trachomatis A, down...

  15. Identification of liver protein targets modified by tienilic acid metabolites using a two-dimensional Western blot-mass spectrometry approach

    Science.gov (United States)

    Methogo, Ruth Menque; Dansette, Patrick M.; Klarskov, Klaus

    2007-12-01

    A combined approach based on two-dimensional electrophoresis-immuno-blotting and nanoliquid chromatography coupled on-line with electrospray ionization mass spectrometry (nLC-MS/MS) was used to identify proteins modified by a reactive intermediate of tienilic acid (TA). Liver homogenates from rats exposed to TA were fractionated using ultra centrifugation; four fractions were obtained and subjected to 2D electrophoresis. Following transfer to PVDF membranes, modified proteins were visualized after India ink staining, using an anti-serum raised against TA and ECL detection. Immuno-reactive spots were localized on the PVDF membrane by superposition of the ECL image, protein spots of interest were excised, digested on the membrane with trypsin followed by nLC-MS/MS analysis and protein identification. A total of 15 proteins were identified as likely targets modified by a TA reactive metabolite. These include selenium binding protein 2, senescence marker protein SMP-30, adenosine kinase, Acy1 protein, adenosylhomocysteinase, capping protein (actin filament), protein disulfide isomerase, fumarylacetoacetase, arginase chain A, ketohexokinase, proteasome endopeptidase complex, triosephosphate isomerase, superoxide dismutase, dna-type molecular chaperone hsc73 and malate dehydrogenase.

  16. Proteomic analysis of differential protein expression of achilles tendon in a rabbit model by two-dimensional polyacrylamide gel electrophoresis at 21 days postoperation.

    Science.gov (United States)

    Jielile, Jiasharete; Jialili, Ainuer; Sabirhazi, Gulnur; Shawutali, Nuerai; Redati, Darebai; Chen, Jiangtao; Tang, Bin; Bai, Jingping; Aldyarhan, Kayrat

    2011-10-01

    Postoperative early kinesitherapy has been advocated as an optimal method for treating Achilles tendon rupture. However, an insight into the rationale of how early kinesitherapy contributes to healing of Achilles tendon remains to be achieved, and research in the area of proteomic analysis of Achilles tendon has so far been lacking. Forty-two rabbits were randomized into control group, immobilization group, and early motion group, and received postoperative cast immobilization and early motion treatments. Achilles tendon samples were prepared 21 days following microsurgery, and the proteins were separated with two-dimensional polyacrylamide gel electrophoresis. Differentially expressed proteins were first recognized by PDQuest software, and then identified using peptide mass fingerprinting, tandem mass spectrometry, and database searching. A total of 463  ±  12, 511  ±  39, and 513  ±  80 protein spots were successfully detected in the two-dimensional polyacrylamide gels for the Achilles tendon samples of rabbits in the control group, immobilization group, and early motion group, respectively. There were 15, 8, and 9 unique proteins in these three groups, respectively, and some differentially expressed proteins were also identified in each group. It was indicated that some of the differentially expressed proteins were involved in various metabolism pathways and may play an important role in healing of Achilles tendon rupture. Postoperative early kinesitherapy resulted in differentially expressed proteins in ruptured Achilles tendon compared with those treated with postoperative cast immobilization. These differentially expressed proteins may contribute to healing of Achilles tendon rupture through a mechanobiological mechanism due to the application of postoperative early kinesitherapy.

  17. Subspace Dimensionality: A Tool for Automated QC in Seismic Array Processing

    Science.gov (United States)

    Rowe, C. A.; Stead, R. J.; Begnaud, M. L.

    2013-12-01

    Because of the great resolving power of seismic arrays, the application of automated processing to array data is critically important in treaty verification work. A significant problem in array analysis is the inclusion of bad sensor channels in the beamforming process. We are testing an approach to automated, on-the-fly quality control (QC) to aid in the identification of poorly performing sensor channels prior to beam-forming in routine event detection or location processing. The idea stems from methods used for large computer servers, when monitoring traffic at enormous numbers of nodes is impractical on a node-by node basis, so the dimensionality of the node traffic is instead monitoried for anomalies that could represent malware, cyber-attacks or other problems. The technique relies upon the use of subspace dimensionality or principal components of the overall system traffic. The subspace technique is not new to seismology, but its most common application has been limited to comparing waveforms to an a priori collection of templates for detecting highly similar events in a swarm or seismic cluster. In the established template application, a detector functions in a manner analogous to waveform cross-correlation, applying a statistical test to assess the similarity of the incoming data stream to known templates for events of interest. In our approach, we seek not to detect matching signals, but instead, we examine the signal subspace dimensionality in much the same way that the method addresses node traffic anomalies in large computer systems. Signal anomalies recorded on seismic arrays affect the dimensional structure of the array-wide time-series. We have shown previously that this observation is useful in identifying real seismic events, either by looking at the raw signal or derivatives thereof (entropy, kurtosis), but here we explore the effects of malfunctioning channels on the dimension of the data and its derivatives, and how to leverage this effect for

  18. Two-dimensional chromatographic analysis using three second-dimension columns for continuous comprehensive analysis of intact proteins.

    Science.gov (United States)

    Zhu, Zaifang; Chen, Huang; Ren, Jiangtao; Lu, Juan J; Gu, Congying; Lynch, Kyle B; Wu, Si; Wang, Zhe; Cao, Chengxi; Liu, Shaorong

    2018-03-01

    We develop a new two-dimensional (2D) high performance liquid chromatography (HPLC) approach for intact protein analysis. Development of 2D HPLC has a bottleneck problem - limited second-dimension (second-D) separation speed. We solve this problem by incorporating multiple second-D columns to allow several second-D separations to be proceeded in parallel. To demonstrate the feasibility of using this approach for comprehensive protein analysis, we select ion-exchange chromatography as the first-dimension and reverse-phase chromatography as the second-D. We incorporate three second-D columns in an innovative way so that three reverse-phase separations can be performed simultaneously. We test this system for separating both standard proteins and E. coli lysates and achieve baseline resolutions for eleven standard proteins and obtain more than 500 peaks for E. coli lysates. This is an indication that the sample complexities are greatly reduced. We see less than 10 bands when each fraction of the second-D effluents are analyzed by sodium dodecyl sulfate - polyacrylamide gel electrophoresis (SDS-PAGE), compared to hundreds of SDS-PAGE bands as the original sample is analyzed. This approach could potentially be an excellent and general tool for protein analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Two-dimensional NMR spectrometry

    International Nuclear Information System (INIS)

    Farrar, T.C.

    1987-01-01

    This article is the second in a two-part series. In part one (ANALYTICAL CHEMISTRY, May 15) the authors discussed one-dimensional nuclear magnetic resonance (NMR) spectra and some relatively advanced nuclear spin gymnastics experiments that provide a capability for selective sensitivity enhancements. In this article and overview and some applications of two-dimensional NMR experiments are presented. These powerful experiments are important complements to the one-dimensional experiments. As in the more sophisticated one-dimensional experiments, the two-dimensional experiments involve three distinct time periods: a preparation period, t 0 ; an evolution period, t 1 ; and a detection period, t 2

  20. Integration of two-dimensional LC-MS with multivariate statistics for comparative analysis of proteomic samples

    NARCIS (Netherlands)

    Gaspari, M.; Verhoeckx, K.C.M.; Verheij, E.R.; Greef, J. van der

    2006-01-01

    LC-MS-based proteomics requires methods with high peak capacity and a high degree of automation, integrated with data-handling tools able to cope with the massive data produced and able to quantitatively compare them. This paper describes an off-line two-dimensional (2D) LC-MS method and its

  1. Automated local bright feature image analysis of nuclear protein distribution identifies changes in tissue phenotype

    International Nuclear Information System (INIS)

    Knowles, David; Sudar, Damir; Bator, Carol; Bissell, Mina

    2006-01-01

    The organization of nuclear proteins is linked to cell and tissue phenotypes. When cells arrest proliferation, undergo apoptosis, or differentiate, the distribution of nuclear proteins changes. Conversely, forced alteration of the distribution of nuclear proteins modifies cell phenotype. Immunostaining and fluorescence microscopy have been critical for such findings. However, there is an increasing need for quantitative analysis of nuclear protein distribution to decipher epigenetic relationships between nuclear structure and cell phenotype, and to unravel the mechanisms linking nuclear structure and function. We have developed imaging methods to quantify the distribution of fluorescently-stained nuclear protein NuMA in different mammary phenotypes obtained using three-dimensional cell culture. Automated image segmentation of DAPI-stained nuclei was generated to isolate thousands of nuclei from three-dimensional confocal images. Prominent features of fluorescently-stained NuMA were detected using a novel local bright feature analysis technique, and their normalized spatial density calculated as a function of the distance from the nuclear perimeter to its center. The results revealed marked changes in the distribution of the density of NuMA bright features as non-neoplastic cells underwent phenotypically normal acinar morphogenesis. In contrast, we did not detect any reorganization of NuMA during the formation of tumor nodules by malignant cells. Importantly, the analysis also discriminated proliferating non-neoplastic cells from proliferating malignant cells, suggesting that these imaging methods are capable of identifying alterations linked not only to the proliferation status but also to the malignant character of cells. We believe that this quantitative analysis will have additional applications for classifying normal and pathological tissues

  2. The time-course of agonist-induced solubilization of trimeric Gqα/G11α proteins resolved by two-dimensional electrophoresis

    Czech Academy of Sciences Publication Activity Database

    Durchánková, Dana; Novotný, Jiří; Svoboda, Petr

    2008-01-01

    Roč. 57, č. 2 (2008), s. 195-203 ISSN 0862-8408 R&D Projects: GA MŠk(CZ) LC554; GA MŠk(CZ) LC06063; GA ČR(CZ) GA309/06/0121 Institutional research plan: CEZ:AV0Z50110509 Keywords : G proteins * solubilization * two-dimensional electrophoresis Subject RIV: CE - Biochemistry Impact factor: 1.653, year: 2008

  3. Noise-induced drift in two-dimensional anisotropic systems

    Science.gov (United States)

    Farago, Oded

    2017-10-01

    We study the isothermal Brownian dynamics of a particle in a system with spatially varying diffusivity. Due to the heterogeneity of the system, the particle's mean displacement does not vanish even if it does not experience any physical force. This phenomenon has been termed "noise-induced drift," and has been extensively studied for one-dimensional systems. Here, we examine the noise-induced drift in a two-dimensional anisotropic system, characterized by a symmetric diffusion tensor with unequal diagonal elements. A general expression for the mean displacement vector is derived and presented as a sum of two vectors, depicting two distinct drifting effects. The first vector describes the tendency of the particle to drift toward the high diffusivity side in each orthogonal principal diffusion direction. This is a generalization of the well-known expression for the noise-induced drift in one-dimensional systems. The second vector represents a novel drifting effect, not found in one-dimensional systems, originating from the spatial rotation in the directions of the principal axes. The validity of the derived expressions is verified by using Langevin dynamics simulations. As a specific example, we consider the relative diffusion of two transmembrane proteins, and demonstrate that the average distance between them increases at a surprisingly fast rate of several tens of micrometers per second.

  4. Assembly of positioner of automated two-dimensional scan coupled to X-ray fluorescence spectrometry; Montagem de posicionador de varredura bidimensional automatizada acoplado a espectrometria de fluorescência de raios-X

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Leonardo Santiago Melgaço

    2011-07-01

    This work describes the design and assembling of a prototype automated positioner two-dimensional scanning coupled to X-ray fluorescence spectrometry. The work aims to achieve a portable and easy to use, device of broad utility in the analysis of samples by X-ray fluorescence area of expertise and research. The two-dimensional scanning of the positioner is by means of two stepper motors controlled by a microcontroller PIC 16F877A, encoder and optical sensors. The user interacts with the XY table through an interface program for the Windows operating system, which communicates with the microcontroller through the serial port. The system of Fluorescence Spectroscopy incorporated into the positioner consists of a system commercially available system from the company AMPTEK, where the primary source of excitation of the sample was a source of {sup 241}Am of 59.5 KeV emissions. Resolution and accuracy of tests were performed in the XY scanning process and reproducibility of the same kit with the fluorescence spectrometry X-ray. Qualitative tests by X-ray fluorescence spectrometry in samples were performed to demonstrate the applicability and versatility of the project. It follows that the prototype illustrates a possible adequately to portable device for X-ray spectrometry of two-dimensional. (author)

  5. ProteinSplit: splitting of multi-domain proteins using prediction of ordered and disordered regions in protein sequences for virtual structural genomics

    International Nuclear Information System (INIS)

    Wyrwicz, Lucjan S; Koczyk, Grzegorz; Rychlewski, Leszek; Plewczynski, Dariusz

    2007-01-01

    The annotation of protein folds within newly sequenced genomes is the main target for semi-automated protein structure prediction (virtual structural genomics). A large number of automated methods have been developed recently with very good results in the case of single-domain proteins. Unfortunately, most of these automated methods often fail to properly predict the distant homology between a given multi-domain protein query and structural templates. Therefore a multi-domain protein should be split into domains in order to overcome this limitation. ProteinSplit is designed to identify protein domain boundaries using a novel algorithm that predicts disordered regions in protein sequences. The software utilizes various sequence characteristics to assess the local propensity of a protein to be disordered or ordered in terms of local structure stability. These disordered parts of a protein are likely to create interdomain spacers. Because of its speed and portability, the method was successfully applied to several genome-wide fold annotation experiments. The user can run an automated analysis of sets of proteins or perform semi-automated multiple user projects (saving the results on the server). Additionally the sequences of predicted domains can be sent to the Bioinfo.PL Protein Structure Prediction Meta-Server for further protein three-dimensional structure and function prediction. The program is freely accessible as a web service at http://lucjan.bioinfo.pl/proteinsplit together with detailed benchmark results on the critical assessment of a fully automated structure prediction (CAFASP) set of sequences. The source code of the local version of protein domain boundary prediction is available upon request from the authors

  6. The analysis of carbohydrates in milk powder by a new "heart-cutting" two-dimensional liquid chromatography method.

    Science.gov (United States)

    Ma, Jing; Hou, Xiaofang; Zhang, Bing; Wang, Yunan; He, Langchong

    2014-03-01

    In this study, a new"heart-cutting" two-dimensional liquid chromatography method for the simultaneous determination of carbohydrate contents in milk powder was presented. In this two dimensional liquid chromatography system, a Venusil XBP-C4 analysis column was used in the first dimension ((1)D) as a pre-separation column, a ZORBAX carbohydrates analysis column was used in the second dimension ((2)D) as a final-analysis column. The whole process was completed in less than 35min without a particular sample preparation procedure. The capability of the new two dimensional HPLC method was demonstrated in the determination of carbohydrates in various brands of milk powder samples. A conventional one dimensional chromatography method was also proposed. The two proposed methods were both validated in terms of linearity, limits of detection, accuracy and precision. The comparison between the results obtained with the two methods showed that the new and completely automated two dimensional liquid chromatography method is more suitable for milk powder sample because of its online cleanup effect involved. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

  7. Application of zwitterionic detergent to the solubilization of Klebsiella pneumoniae outer membrane proteins for two-dimensional gel electrophoresis.

    Science.gov (United States)

    Bednarz-Misa, I; Serek, P; Dudek, B; Pawlak, A; Bugla-Płoskońska, G; Gamian, A

    2014-12-01

    Klebsiella pneumoniae is a frequent cause of nosocomial respiratory, urinary and gastrointestinal tract infections and septicemia with the multidrug-resistant K. pneumoniae being a major public health concern. Outer membrane proteins (OMPs) are important virulence factors responsible for the appropriate adaptation to the host environment. They constitute of the antigens being the first in contact with infected organism. However, K. pneumoniae strains are heavily capsulated and it is important to establish the OMPs isolation procedure prior to proteomics extensive studies. In this study we used Zwittergent Z 3-14® as a detergent to isolate the OMPs from K. pneumoniae cells and resolve them using two-dimensional electrophoresis (2-DE). As a result we identified 134 protein spots. The OMPs identified in this study are possible candidates for the development of a protein-based vaccine against K. pneumoniae infections. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. High-resolution two-dimensional gel analysis of proteins in wing imaginal discs: A data base of Drosophila

    International Nuclear Information System (INIS)

    Santaren, J.F.; Garcia-Bellido, A.

    1990-01-01

    An improved method of high-resolution two-dimensional gel electrophoresis has been used to study the patterns of protein synthesis in wing imaginal discs of late instar larvae of Drosophila melanogaster. A small number of discs were radiolabeled with a mixture of 14 C-labeled amino acids or with [ 35 S]methionine and the pattern of labeled proteins was analyzed. One thousand and twenty-five polypeptides (787 acidic (IEF) and 238 basic (NEPHGE)) from wing discs of several wild-type strains have so far been separated and cataloged. All these polypeptides have been numbered and presented in a reference map for further studies. When comparing patterns of label we have found small quantitative differences in rate of synthesis between individuals of the same strain, not due to sexual differences, and very few quantitative and qualitative differences between groups of individuals of different strains

  9. Proteomic analysis of halotolerant proteins under high and low salt stress in Dunaliella salina using two-dimensional differential in-gel electrophoresis

    Directory of Open Access Journals (Sweden)

    Yan-Long Jia

    2016-01-01

    Full Text Available Abstract Dunaliella salina, a single-celled marine alga with extreme salt tolerance, is an important model organism for studying fundamental extremophile survival mechanisms and their potential practical applications. In this study, two-dimensional differential in-gel electrophoresis (2D-DIGE was used to investigate the expression of halotolerant proteins under high (3 M NaCl and low (0.75 M NaCl salt concentrations. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF/TOF MS and bioinformatics were used to identify and characterize the differences among proteins. 2D-DIGE analysis revealed 141 protein spots that were significantly differentially expressed between the two salinities. Twenty-four differentially expressed protein spots were successfully identified by MALDI-TOF/TOF MS, including proteins in the following important categories: molecular chaperones, proteins involved in photosynthesis, proteins involved in respiration and proteins involved in amino acid synthesis. Expression levels of these proteins changed in response to the stress conditions, which suggests that they may be involved in the maintenance of intracellular osmotic pressure, cellular stress responses, physiological changes in metabolism, continuation of photosynthetic activity and other aspects of salt stress. The findings of this study enhance our understanding of the function and mechanisms of various proteins in salt stress.

  10. Insights into the Structural Changes Occurring upon Photoconversion in the Orange Carotenoid Protein from Broadband Two-Dimensional Electronic Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    De Re, Eleonora; Schlau-Cohen, Gabriela S.; Leverenz, Ryan L.; Huxter, Vanessa M.; Oliver, Thomas A. A.; Mathies, Richard A.; Fleming, Graham R.

    2014-05-22

    Carotenoids play an essential role in photoprotection, interacting with other pigments to safely dissipate excess absorbed energy as heat. In cyanobacteria, the short time scale photoprotective mechanisms involve the photoactive orange carotenoid protein (OCP), which binds a single carbonyl carotenoid. Blue-green light induces the photoswitching of OCP from its ground state form (OCPO) to a metastable photoproduct (OCPR). OCPR can bind to the phycobilisome antenna and induce fluorescence quenching. The photoswitching is accompanied by structural and functional changes at the level of the protein and of the bound carotenoid. In this study, we use broadband two-dimensional electronic spectroscopy to look at the differences in excited state dynamics of the carotenoid in the two forms of OCP. Our results provide insight into the origin of the pronounced vibrational lineshape and oscillatory dynamics observed in linear absorption and 2D electronic spectroscopy of OCPO and the large inhomogeneous broadening in OCPR, with consequences for the chemical function of the two forms.

  11. MannDB – A microbial database of automated protein sequence analyses and evidence integration for protein characterization

    Directory of Open Access Journals (Sweden)

    Kuczmarski Thomas A

    2006-10-01

    Full Text Available Abstract Background MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. Description MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS, CDC, HHS, NIAID, USDA, USFDA, and WHO. Conclusion MannDB comprises a large number of genomes and comprehensive protein

  12. Integrated Automation of High-Throughput Screening and Reverse Phase Protein Array Sample Preparation

    DEFF Research Database (Denmark)

    Pedersen, Marlene Lemvig; Block, Ines; List, Markus

    into automated robotic high-throughput screens, which allows subsequent protein quantification. In this integrated solution, samples are directly forwarded to automated cell lysate preparation and preparation of dilution series, including reformatting to a protein spotter-compatible format after the high......-throughput screening. Tracking of huge sample numbers and data analysis from a high-content screen to RPPAs is accomplished via MIRACLE, a custom made software suite developed by us. To this end, we demonstrate that the RPPAs generated in this manner deliver reliable protein readouts and that GAPDH and TFR levels can...

  13. Proteomic analysis of plasma proteins in diabetic retinopathy patients by two dimensional electrophoresis and MALDI-Tof-MS.

    Science.gov (United States)

    Gopalakrishnan, Vidhya; Purushothaman, Parthiban; Bhaskar, Anusha

    2015-01-01

    Diabetic retinopathy is a highly specific vascular complication of diabetes mellitus and progresses from mild non-proliferative abnormalities characterized by increased vascular permeability to moderate and severe proliferative diabetic retinopathy characterized by the growth of blood vessels on the retina. The aim of the study was to identify the differentially expressed proteins in diabetic retinopathy using two-dimensional electrophoresis. Blood sample was drawn from subjects with diabetes mellitus (without retinopathy) who served as controls and patients with diabetic retinopathy in tubes containing EDTA as anticoagulant. Albumin and immunoglobulin IgG collectively removed to enrich proteins of lower abundance. 2de was carried out to see if there are any differentially expressed proteins. Approximately 48 and 61 spots were identified in control and diabetic retinopathy respectively, of which three protein spots RBP1 (retinol-binding protein 1), NUD10 (Diphosphoinositol polyphosphohydrolase 3 alpha), NGB (neuroglobin) were down regulated and HBG2 (hemoglobin) and BY55 (CD 160 antigen) were upregulated in diabetic retinopathy. These five protein spots were excised and were subjected to in-gel tryptic digestion, and their identities were determined by ultraflex MALDI-TOF-MS. We report a comprehensive patient-based plasma proteomic approach to the identification of potential biomarkers for diabetic retinopathy screening and detection. We identified 5 different proteins that were differentially expressed in the plasma of control diabetic patients (without retinopathy). Among these five proteins the expression of neuroglobin (NGB) protein varied significantly and may be a potential biomarker in diabetic retinopathy. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Validation of a prefractionation method followed by two-dimensional electrophoresis – Applied to cerebrospinal fluid proteins from frontotemporal dementia patients

    Directory of Open Access Journals (Sweden)

    Sjögren Magnus

    2004-11-01

    Full Text Available Abstract Background The aim of this study was firstly, to improve and validate a cerebrospinal fluid (CSF prefractionation method followed by two-dimensional electrophoresis (2-DE and secondly, using this strategy to investigate differences between the CSF proteome of frontotemporal dementia (FTD patients and controls. From each subject three ml of CSF was prefractionated using liquid phase isoelectric focusing prior to 2-DE. Results With respect to protein recovery and purification potential, ethanol precipitation of the prefractionated CSF sample was found superior, after testing several sample preparation methods. The reproducibility of prefractionated CSF analyzed on 2-D gels was comparable to direct 2-DE analysis of CSF. The protein spots on the prefractionated 2-D gels had an increased intensity, indicating a higher protein concentration, compared to direct 2-D gels. Prefractionated 2-DE analysis of FTD and control CSF showed that 26 protein spots were changed at least two fold. Using mass spectrometry, 13 of these protein spots were identified, including retinol-binding protein, Zn-α-2-glycoprotein, proapolipoproteinA1, β-2-microglobulin, transthyretin, albumin and alloalbumin. Conclusion The results suggest that the prefractionated 2-DE method can be useful for enrichment of CSF proteins and may provide a new tool to investigate the pathology of neurodegenerative diseases. This study confirmed reduced levels of retinol-binding protein and revealed some new biomarker candidates for FTD.

  15. Efficient method of protein extraction from Theobroma cacao L. roots for two-dimensional gel electrophoresis and mass spectrometry analyses.

    Science.gov (United States)

    Bertolde, F Z; Almeida, A-A F; Silva, F A C; Oliveira, T M; Pirovani, C P

    2014-07-04

    Theobroma cacao is a woody and recalcitrant plant with a very high level of interfering compounds. Standard protocols for protein extraction were proposed for various types of samples, but the presence of interfering compounds in many samples prevented the isolation of proteins suitable for two-dimensional gel electrophoresis (2-DE). An efficient method to extract root proteins for 2-DE was established to overcome these problems. The main features of this protocol are: i) precipitation with trichloroacetic acid/acetone overnight to prepare the acetone dry powder (ADP), ii) several additional steps of sonication in the ADP preparation and extractions with dense sodium dodecyl sulfate and phenol, and iii) adding two stages of phenol extractions. Proteins were extracted from roots using this new protocol (Method B) and a protocol described in the literature for T. cacao leaves and meristems (Method A). Using these methods, we obtained a protein yield of about 0.7 and 2.5 mg per 1.0 g lyophilized root, and a total of 60 and 400 spots could be separated, respectively. Through Method B, it was possible to isolate high-quality protein and a high yield of roots from T. cacao for high-quality 2-DE gels. To demonstrate the quality of the extracted proteins from roots of T. cacao using Method B, several protein spots were cut from the 2-DE gels, analyzed by tandem mass spectrometry, and identified. Method B was further tested on Citrus roots, with a protein yield of about 2.7 mg per 1.0 g lyophilized root and 800 detected spots.

  16. A comprehensive two-dimensional gel protein database of noncultured unfractionated normal human epidermal keratinocytes: towards an integrated approach to the study of cell proliferation, differentiation and skin diseases

    DEFF Research Database (Denmark)

    Celis, J E; Madsen, Peder; Rasmussen, H H

    1991-01-01

    A two-dimensional (2-D) gel database of cellular proteins from noncultured, unfractionated normal human epidermal keratinocytes has been established. A total of 2651 [35S]methionine-labeled cellular proteins (1868 isoelectric focusing, 783 nonequilibrium pH gradient electrophoresis) were resolved...

  17. Cytoskeletal proteins from human skin fibroblasts, peripheral blood leukocytes, and a lymphoblastoid cell line compared by two-dimensional gel electrophoresis

    International Nuclear Information System (INIS)

    Giometti, C.S.; Willard, K.E.; Anderson, N.L.

    1982-01-01

    Differences in proteins between cells grown as suspension cultures and those grown as attached cultures were studied by comparing the proteins of detergent-resistant cytoskeletons prepared from peripheral blood leukocytes and a lymphoblastoid cell line (GM607) (both grown as suspension cultures) and those of human skin fibroblasts (grown as attached cultures) by two-dimensional gel electrophoresis. The major cytoskeletal proteins of the leukocytes were also present in the protein pattern of GM607 cytoskeletons. In contrast, the fibroblast cytoskeletal protein pattern contained four groups of proteins that differed from the patterns of the leukocytes and GM607. In addition, surface labeling of GM607 and human fibroblasts with 125 I demonstrated that substantial amounts of vimentin and actin are exposed at the surface of the attached fibroblasts, but there is little evidence of similar exposure at the surface of the suspension-grown GM607. These results demonstrate some differences in cytoskeletal protein composition between different types of cells could be related to their ability or lack of ability to grow as attached cells in tissue culture

  18. Background-free, high sensitivity staining of proteins in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gels using a luminescent ruthenium complex.

    Science.gov (United States)

    Berggren, K; Chernokalskaya, E; Steinberg, T H; Kemper, C; Lopez, M F; Diwu, Z; Haugland, R P; Patton, W F

    2000-07-01

    SYPRO Ruby dye is a permanent stain comprised of ruthenium as part of an organic complex that interacts noncovalently with proteins. SYPRO Ruby Protein Gel Stain provides a sensitive, gentle, fluorescence-based method for detecting proteins in one-dimensional and two-dimensional sodium dodecyl sulfate-polyacrylamide gels. Proteins are fixed, stained from 3h to overnight and then rinsed in deionized water or dilute methanol/acetic acid solution for 30 min. The stain can be visualized using a wide range of excitation sources commonly used in image analysis systems including a 302 nm UV-B transilluminator, 473 nm second harmonic generation (SHG) laser, 488 nm argon-ion laser, 532 nm yttrium-aluminum-garnet (YAG) laser, xenon arc lamp, blue fluorescent light bulb or blue light-emitting diode (LED). The sensitivity of SYPRO Ruby Protein Gel Stain is superior to colloidal Coomassie Brilliant Blue (CBB) stain or monobromobimane labeling and comparable with the highest sensitivity silver or zinc-imidazole staining procedures available. The linear dynamic range of SYPRO Ruby Protein Gel stain extends over three orders of magnitude, which is vastly superior to silver, zinc-imidazole, monobromobimane and CBB stain. The fluorescent stain does not contain superfluous chemicals (formaldehyde, glutaraldehyde, Tween-20) that frequently interfere with peptide identification in mass spectrometry. While peptide mass profiles are severely altered in protein samples prelabeled with monobromobimane, successful identification of proteins by peptide mass profiling using matrix-assisted laser desorption/ionization mass spectrometry was easily performed after protein detection with SYPRO Ruby Protein Gel stain.

  19. Ocular Proteomics with Emphasis on Two-Dimensional Gel Electrophoresis and Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Honoré Bent

    2010-01-01

    Full Text Available Abstract The intention of this review is to provide an overview of current methodologies employed in the rapidly developing field of ocular proteomics with emphasis on sample preparation, two-dimensional polyacrylamide gel electrophoresis (2D-PAGE and mass spectrometry (MS. Appropriate sample preparation for the diverse range of cells and tissues of the eye is essential to ensure reliable results. Current methods of protein staining for 2D-PAGE, protein labelling for two-dimensional difference gel electrophoresis, gel-based expression analysis and protein identification by MS are summarised. The uses of gel-free MS-based strategies (MuDPIT, iTRAQ, ICAT and SILAC are also discussed. Proteomic technologies promise to shed new light onto ocular disease processes that could lead to the discovery of strong novel biomarkers and therapeutic targets useful in many ophthalmic conditions.

  20. Application of Tandem Two-Dimensional Mass Spectrometry for Top-Down Deep Sequencing of Calmodulin.

    Science.gov (United States)

    Floris, Federico; Chiron, Lionel; Lynch, Alice M; Barrow, Mark P; Delsuc, Marc-André; O'Connor, Peter B

    2018-06-04

    Two-dimensional mass spectrometry (2DMS) involves simultaneous acquisition of the fragmentation patterns of all the analytes in a mixture by correlating their precursor and fragment ions by modulating precursor ions systematically through a fragmentation zone. Tandem two-dimensional mass spectrometry (MS/2DMS) unites the ultra-high accuracy of Fourier transform ion cyclotron resonance (FT-ICR) MS/MS and the simultaneous data-independent fragmentation of 2DMS to achieve extensive inter-residue fragmentation of entire proteins. 2DMS was recently developed for top-down proteomics (TDP), and applied to the analysis of calmodulin (CaM), reporting a cleavage coverage of about ~23% using infrared multiphoton dissociation (IRMPD) as fragmentation technique. The goal of this work is to expand the utility of top-down protein analysis using MS/2DMS in order to extend the cleavage coverage in top-down proteomics further into the interior regions of the protein. In this case, using MS/2DMS, the cleavage coverage of CaM increased from ~23% to ~42%. Graphical Abstract Two-dimensional mass spectrometry, when applied to primary fragment ions from the source, allows deep-sequencing of the protein calmodulin.

  1. Structures of larger proteins in solution: Three- and four-dimensional heteronuclear NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Gronenborn, A.M.; Clore, G.M. [National Institutes of Health, Bethesda, MD (United States)

    1994-12-01

    Complete understanding of a protein`s function and mechanism of action can only be achieved with a knowledge of its three-dimensional structure at atomic resolution. At present, there are two methods available for determining such structures. The first method, which has been established for many years, is x-ray diffraction of protein single crystals. The second method has blossomed only in the last 5 years and is based on the application of nuclear magnetic resonance (NMR) spectroscopy to proteins in solution. This review paper describes three- and four-dimensional NMR methods applied to protein structure determination and was adapted from Clore and Gronenborn. The review focuses on the underlying principals and practice of multidimensional NMR and the structural information obtained.

  2. The Protein Maker: an automated system for high-throughput parallel purification

    International Nuclear Information System (INIS)

    Smith, Eric R.; Begley, Darren W.; Anderson, Vanessa; Raymond, Amy C.; Haffner, Taryn E.; Robinson, John I.; Edwards, Thomas E.; Duncan, Natalie; Gerdts, Cory J.; Mixon, Mark B.; Nollert, Peter; Staker, Bart L.; Stewart, Lance J.

    2011-01-01

    The Protein Maker instrument addresses a critical bottleneck in structural genomics by allowing automated purification and buffer testing of multiple protein targets in parallel with a single instrument. Here, the use of this instrument to (i) purify multiple influenza-virus proteins in parallel for crystallization trials and (ii) identify optimal lysis-buffer conditions prior to large-scale protein purification is described. The Protein Maker is an automated purification system developed by Emerald BioSystems for high-throughput parallel purification of proteins and antibodies. This instrument allows multiple load, wash and elution buffers to be used in parallel along independent lines for up to 24 individual samples. To demonstrate its utility, its use in the purification of five recombinant PB2 C-terminal domains from various subtypes of the influenza A virus is described. Three of these constructs crystallized and one diffracted X-rays to sufficient resolution for structure determination and deposition in the Protein Data Bank. Methods for screening lysis buffers for a cytochrome P450 from a pathogenic fungus prior to upscaling expression and purification are also described. The Protein Maker has become a valuable asset within the Seattle Structural Genomics Center for Infectious Disease (SSGCID) and hence is a potentially valuable tool for a variety of high-throughput protein-purification applications

  3. Human cellular protein patterns and their link to genome DNA sequence data: usefulness of two-dimensional gel electrophoresis and microsequencing

    DEFF Research Database (Denmark)

    Celis, J E; Rasmussen, H H; Leffers, H

    1991-01-01

    a global approach to the study of the cell. Using the integrated approach offered by 2-dimensional gel protein databases it is now possible to reveal phenotype specific protein (or proteins), to microsequence them, to search for homology with previously identified proteins, to clone the cDNAs, to assign...

  4. Sample preparation guidelines for two-dimensional electrophoresis.

    Science.gov (United States)

    Posch, Anton

    2014-12-01

    Sample preparation is one of the key technologies for successful two-dimensional electrophoresis (2DE). Due to the great diversity of protein sample types and sources, no single sample preparation method works with all proteins; for any sample the optimum procedure must be determined empirically. This review is meant to provide a broad overview of the most important principles in sample preparation in order to avoid a multitude of possible pitfalls. Sample preparation protocols from the expert in the field were screened and evaluated. On the basis of these protocols and my own comprehensive practical experience important guidelines are given in this review. The presented guidelines will facilitate straightforward protocol development for researchers new to gel-based proteomics. In addition the available choices are rationalized in order to successfully prepare a protein sample for 2DE separations. The strategies described here are not limited to 2DE and can also be applied to other protein separation techniques.

  5. Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal

    OpenAIRE

    Bordoli, Lorenza; Schwede, Torsten

    2012-01-01

    Comparative protein structure modeling is a computational approach to build three-dimensional structural models for proteins using experimental structures of related protein family members as templates. Regular blind assessments of modeling accuracy have demonstrated that comparative protein structure modeling is currently the most reliable technique to model protein structures. Homology models are often sufficiently accurate to substitute for experimental structures in a wide variety of appl...

  6. Specific proteins synthesized during the viral lytic cycle in vaccinia virus-infected HeLa cells: analysis by high-resolution, two-dimensional gel electrophoresis

    International Nuclear Information System (INIS)

    Carrasco, L.; Bravo, R.

    1986-01-01

    The proteins synthesized in vaccinia-infected HeLa cells have been analyzed at different times after infection by using two-dimensional gel electrophoresis. Vaccinia-infected cells present up to 198 polypeptides (138 acidic, isoelectric focusing; 60 basic, nonequilibrium pH gradient electrophoresis) not detected in control cells. Cells infected in the presence of cycloheximide show 81 additional polypeptides after cycloheximide removal, resulting in a total estimate of 279 proteins induced after vaccinia infection. The glycoproteins made at various time postinfection were also analyzed. At least 13 proteins labeled with [ 3 H]glucosamine were detected in vaccinia-infected HeLa cells

  7. Improved protein hydrogen/deuterium exchange mass spectrometry platform with fully automated data processing.

    Science.gov (United States)

    Zhang, Zhongqi; Zhang, Aming; Xiao, Gang

    2012-06-05

    Protein hydrogen/deuterium exchange (HDX) followed by protease digestion and mass spectrometric (MS) analysis is accepted as a standard method for studying protein conformation and conformational dynamics. In this article, an improved HDX MS platform with fully automated data processing is described. The platform significantly reduces systematic and random errors in the measurement by introducing two types of corrections in HDX data analysis. First, a mixture of short peptides with fast HDX rates is introduced as internal standards to adjust the variations in the extent of back exchange from run to run. Second, a designed unique peptide (PPPI) with slow intrinsic HDX rate is employed as another internal standard to reflect the possible differences in protein intrinsic HDX rates when protein conformations at different solution conditions are compared. HDX data processing is achieved with a comprehensive HDX model to simulate the deuterium labeling and back exchange process. The HDX model is implemented into the in-house developed software MassAnalyzer and enables fully unattended analysis of the entire protein HDX MS data set starting from ion detection and peptide identification to final processed HDX output, typically within 1 day. The final output of the automated data processing is a set (or the average) of the most possible protection factors for each backbone amide hydrogen. The utility of the HDX MS platform is demonstrated by exploring the conformational transition of a monoclonal antibody by increasing concentrations of guanidine.

  8. Optimized sample preparation for two-dimensional gel electrophoresis of soluble proteins from chicken bursa of Fabricius

    Directory of Open Access Journals (Sweden)

    Zheng Xiaojuan

    2009-10-01

    Full Text Available Abstract Background Two-dimensional gel electrophoresis (2-DE is a powerful method to study protein expression and function in living organisms and diseases. This technique, however, has not been applied to avian bursa of Fabricius (BF, a central immune organ. Here, optimized 2-DE sample preparation methodologies were constructed for the chicken BF tissue. Using the optimized protocol, we performed further 2-DE analysis on a soluble protein extract from the BF of chickens infected with virulent avibirnavirus. To demonstrate the quality of the extracted proteins, several differentially expressed protein spots selected were cut from 2-DE gels and identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS. Results An extraction buffer containing 7 M urea, 2 M thiourea, 2% (w/v 3-[(3-cholamidopropyl-dimethylammonio]-1-propanesulfonate (CHAPS, 50 mM dithiothreitol (DTT, 0.2% Bio-Lyte 3/10, 1 mM phenylmethylsulfonyl fluoride (PMSF, 20 U/ml Deoxyribonuclease I (DNase I, and 0.25 mg/ml Ribonuclease A (RNase A, combined with sonication and vortex, yielded the best 2-DE data. Relative to non-frozen immobilized pH gradient (IPG strips, frozen IPG strips did not result in significant changes in the 2-DE patterns after isoelectric focusing (IEF. When the optimized protocol was used to analyze the spleen and thymus, as well as avibirnavirus-infected bursa, high quality 2-DE protein expression profiles were obtained. 2-DE maps of BF of chickens infected with virulent avibirnavirus were visibly different and many differentially expressed proteins were found. Conclusion These results showed that method C, in concert extraction buffer IV, was the most favorable for preparing samples for IEF and subsequent protein separation and yielded the best quality 2-DE patterns. The optimized protocol is a useful sample preparation method for comparative proteomics analysis of chicken BF tissues.

  9. Two-dimensional gel electrophoresis pattern (pH 6-11) and identification of water-soluble barley seed and malt proteins by mass spectrometry

    DEFF Research Database (Denmark)

    Bak-Jensen, K.S.; Laugesen, S.; Roepstorff, P.

    2004-01-01

    A protocol was established for two-dimensional gel electrophoresis (2-DE) of barley seed and malt proteins in the pH range of 6-11. Proteins extracted from flour in a low-salt buffer were focused after cup-loading onto IPG strips. Successful separation in the second dimension was achieved using...... gradient gels in a horizontal SDS-PAGE system. Silver staining of gels visualized around 380 (seed) and 500 (malt) spots. Thirty-seven different proteins from seeds were identified in 60 spots, among these 46 were visualized also in the malt 2-D pattern. Proteins were identified by peptide mass...... in defence against pathogens (21 spots), 4 in storage, folding, and synthesis of proteins, and in nitrogen metabolism (5 spots), 6 in carbohydrate metabolism (11 spots), and 4 in stress and detoxification (9 spots). Six proteins (7 spots) were not grouped in these categories, and 3 were not ascribed...

  10. Two-Dimensional Electrophoresis Study of Lactobacillus delbrueckii subsp. bulgaricus Thermotolerance

    OpenAIRE

    Gouesbet, Gwenola; Jan, Gwenael; Boyaval, Patrick

    2002-01-01

    The response of Lactobacillus delbrueckii subsp. bulgaricus cells to heat stress was studied by use of a chemically defined medium. Two-dimensional electrophoresis (2-DE) analysis was used to correlate the kinetics of heat shock protein (HSP) induction with cell recovery from heat injury. We demonstrated that enhanced viability, observed after 10 min at 65°C, resulted from the overexpression of HSP and from mechanisms not linked to protein synthesis. In order to analyze the thermoadaptation m...

  11. The human keratinocyte two-dimensional protein database (update 1994): towards an integrated approach to the study of cell proliferation, differentiation and skin diseases

    DEFF Research Database (Denmark)

    Celis, J E; Rasmussen, H H; Olsen, E

    1994-01-01

    The master two-dimensional (2-D) gel database of human keratinocytes currently lists 3087 cellular proteins (2168 isoelectric focusing, IEF; and 919 none-quilibrium pH gradient electrophoresis, NEPHGE), many of which correspond to posttranslational modifications, 890 polypeptides have been...... in the database. We also report a database of proteins recovered from the medium of noncultured, unfractionated keratinocytes. This database lists 398 polypeptides (309 IEF; 89 NEPHGE) of which 76 have been identified. The aim of the comprehensive databases is to gather, through a systematic study...

  12. Proton transport in a membrane protein channel: two-dimensional infrared spectrum modeling.

    NARCIS (Netherlands)

    Liang, C.; Knoester, J.; Jansen, T.L.Th.A.

    2012-01-01

    We model the two-dimensional infrared (2DIR) spectrum of a proton channel to investigate its applicability as a spectroscopy tool to study the proton transport process in biological systems. Proton transport processes in proton channels are involved in numerous fundamental biochemical reactions.

  13. Automated three-dimensional morphology-based clustering of human erythrocytes with regular shapes: stomatocytes, discocytes, and echinocytes

    Science.gov (United States)

    Ahmadzadeh, Ezat; Jaferzadeh, Keyvan; Lee, Jieun; Moon, Inkyu

    2017-07-01

    We present unsupervised clustering methods for automatic grouping of human red blood cells (RBCs) extracted from RBC quantitative phase images obtained by digital holographic microscopy into three RBC clusters with regular shapes, including biconcave, stomatocyte, and sphero-echinocyte. We select some good features related to the RBC profile and morphology, such as RBC average thickness, sphericity coefficient, and mean corpuscular volume, and clustering methods, including density-based spatial clustering applications with noise, k-medoids, and k-means, are applied to the set of morphological features. The clustering results of RBCs using a set of three-dimensional features are compared against a set of two-dimensional features. Our experimental results indicate that by utilizing the introduced set of features, two groups of biconcave RBCs and old RBCs (suffering from the sphero-echinocyte process) can be perfectly clustered. In addition, by increasing the number of clusters, the three RBC types can be effectively clustered in an automated unsupervised manner with high accuracy. The performance evaluation of the clustering techniques reveals that they can assist hematologists in further diagnosis.

  14. Equivalence of two-dimensional gravities

    International Nuclear Information System (INIS)

    Mohammedi, N.

    1990-01-01

    The authors find the relationship between the Jackiw-Teitelboim model of two-dimensional gravity and the SL(2,R) induced gravity. These are shown to be related to a two-dimensional gauge theory obtained by dimensionally reducing the Chern-Simons action of the 2 + 1 dimensional gravity. The authors present an explicit solution to the equations of motion of the auxiliary field of the Jackiw-Teitelboim model in the light-cone gauge. A renormalization of the cosmological constant is also given

  15. Two-dimensional metamaterial optics

    International Nuclear Information System (INIS)

    Smolyaninov, I I

    2010-01-01

    While three-dimensional photonic metamaterials are difficult to fabricate, many new concepts and ideas in the metamaterial optics can be realized in two spatial dimensions using planar optics of surface plasmon polaritons. In this paper we review recent progress in this direction. Two-dimensional photonic crystals, hyperbolic metamaterials, and plasmonic focusing devices are demonstrated and used in novel microscopy and waveguiding schemes

  16. General Protein Data Bank-Based Collective Variables for Protein Folding.

    Science.gov (United States)

    Ardevol, Albert; Palazzesi, Ferruccio; Tribello, Gareth A; Parrinello, Michele

    2016-01-12

    New, automated forms of data analysis are required to understand the high-dimensional trajectories that are obtained from molecular dynamics simulations on proteins. Dimensionality reduction algorithms are particularly appealing in this regard as they allow one to construct unbiased, low-dimensional representations of the trajectory using only the information encoded in the trajectory. The downside of this approach is that a different set of coordinates are required for each different chemical system under study precisely because the coordinates are constructed using information from the trajectory. In this paper, we show how one can resolve this problem by using the sketch-map algorithm that we recently proposed to construct a low-dimensional representation of the structures contained in the protein data bank. We show that the resulting coordinates are as useful for analyzing trajectory data as coordinates constructed using landmark configurations taken from the trajectory and that these coordinates can thus be used for understanding protein folding across a range of systems.

  17. Two-Dimensional Spectroscopy Is Being Used to Address Core Scientific Questions in Biology and Materials Science.

    Science.gov (United States)

    Petti, Megan K; Lomont, Justin P; Maj, Michał; Zanni, Martin T

    2018-02-15

    Two-dimensional spectroscopy is a powerful tool for extracting structural and dynamic information from a wide range of chemical systems. We provide a brief overview of the ways in which two-dimensional visible and infrared spectroscopies are being applied to elucidate fundamental details of important processes in biological and materials science. The topics covered include amyloid proteins, photosynthetic complexes, ion channels, photovoltaics, batteries, as well as a variety of promising new methods in two-dimensional spectroscopy.

  18. Structural organization of the human glucocorticoid receptor determined by one- and two-dimensional gel electrophoresis of proteolytic receptor fragments

    International Nuclear Information System (INIS)

    Smith, A.C.; Harmon, J.M.

    1987-01-01

    The structural organization of the steroid-binding protein of the IM-9 cell glucocorticoid receptor was investigated by using one- and two-dimensional gel electrophoresis of proteolytic receptor fragments. One-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of receptor fragments isolated after trypsin digestion of immunopurified [ 3 H]dexamethasone 21-mesylate ([ 3 H]DM-) labeled receptor revealed the presence of a stable 26.5-kilodalton (kDa) steroid-containing non-DNA-binding fragment, derived from a larger, less stable, 29-kDa fragment. The 26.5-kDa tryptic fragment appeared to be completely contained within a 41-kDa, steroid-containing, DNA-binding species isolated after chymotrypsin digestion of the intact protein. Two-dimensional electrophoretic analysis of the [ 3 H]DM-labeled tryptic fragments resolved two 26.5-kDa and two 29-kDa components. This was the same number of isoforms seen in the intact protein, indicating that the charge heterogeneity of the steroid-binding protein is the result of modification within the steroid-containing, non-DNA-binding, 26.5-kDa tryptic fragment. Two-dimensional analysis of the 41-kDa [ 3 H]DM-labeled chymotryptic species revealed a pattern of isoforms more complex than that seen either in the intact protein or in the steroid-containing tryptic fragments. These results suggest that the 41-kDa [ 3 H]DM-labeled species resolved by one-dimensional SDS-PAGE after chymotrypsin digestion may be composed of several distinct proteolytic fragments

  19. Fish proteins as targets of ferrous-catalyzed oxidation: identification of protein carbonyls by fluorescent labeling on two-dimensional gels and MALDI-TOF/TOF mass spectrometry.

    Science.gov (United States)

    Pazos, Manuel; da Rocha, Angela Pereira; Roepstorff, Peter; Rogowska-Wrzesinska, Adelina

    2011-07-27

    Protein oxidation in fish meat is considered to affect negatively the muscle texture. An important source of free radicals taking part in this process is Fenton's reaction dependent on ferrous ions present in the tissue. The aim of this study was to investigate the susceptibility of cod muscle proteins in sarcoplasmic and myofibril fractions to in vitro metal-catalyzed oxidation and to point out protein candidates that might play a major role in the deterioration of fish quality. Extracted control proteins and proteins subjected to free radicals generated by Fe(II)/ascorbate mixture were labeled with fluorescein-5-thiosemicarbazide (FTSC) to tag carbonyl groups and separated by two-dimensional gel electrophoresis. Consecutive visualization of protein carbonyl levels by capturing the FTSC signal and total protein levels by capturing the SyproRuby staining signal allowed us to quantify the relative change in protein carbonyl levels corrected for changes in protein content. Proteins were identified using MALDI-TOF/TOF mass spectrometry and homology-based searches. The results show that freshly extracted cod muscle proteins exhibit a detectable carbonylation background and that the incubation with Fe(II)/ascorbate triggers a further oxidation of both sarcoplasmic and myofibril proteins. Different proteins exhibited various degrees of sensitivity to oxidation processes. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), nucleoside diphosphate kinase B (NDK), triosephosphate isomerase, phosphoglycerate mutase, lactate dehydrogenase, creatine kinase, and enolase were the sarcoplasmic proteins most vulnerable to ferrous-catalyzed oxidation. Moreover, NDK, phosphoglycerate mutase, and GAPDH were identified in several spots differing by their pI, and those forms showed different susceptibilities to metal-catalyzed oxidation, indicating that post-translational modifications may change the resistance of proteins to oxidative damage. The Fe(II)/ascorbate treatment significantly

  20. Identification of differentially expressed proteins between human esophageal immortalized and carcinomatous cell lines by two-dimensional electrophoresis and MALDI-TOF-mass spectrometry

    Institute of Scientific and Technical Information of China (English)

    Xing-Dong Xiong; Li-Yan Xu; Zhong-Ying Shen; Wei-Jia Cai; Jian-Min Luo; Ya-Li Han; En-Min Li

    2002-01-01

    AIM: To identify the differentially expressed proteins between the human immortalized esophageal epithelial cell line (SHEE) and the malignant transformed esophageal carcinoma cell line (SHEEC), and to explore new ways for studying esophageal carcinoma associated genes. METHODS: SHEE and SHEEC cell lines were used to separate differentially expressed proteins by two-dimensional electrophoresis/The silver-stained 2-D gels was scanned with EDAS290 digital camera system and analyzed with the PDQuest 6.2 Software. Six spots in which the differentially expressed protein was more obvious were selected and analyzed with matrix-assisted laser desorption/ionization time of flying mass spectrometry (MALDI-TOF-MS).RESULTS: There were 107±4.58 and 115±9.91 protein spots observed in SHEE and SHEEC respectively, and the majority of these spots between the two cell lines matched each other (r=-0.772), only a few were expressed differentially. After analyzed by MALDI-TOF-MS and database search for the six differentially expressed proteins, One new protein as well as other five sequence-known proteins including RNPEP-like protein, human rRNA gene upstream sequence binding transcription factor, uracil DNA glycosylase,Annexin A2 and p300/CBP-associated factor were preliminarily identified.CONCLUSION: These differentially expressed proteins might play an importance role during malignant transformation of SHEEC from SHEE. The identification of these proteins may serve as a new way for studying esophageal carcinoma associated genes.

  1. PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination.

    Science.gov (United States)

    Lee, Woonghee; Stark, Jaime L; Markley, John L

    2014-11-01

    Peak-picking Of Noe Data Enabled by Restriction Of Shift Assignments-Client Server (PONDEROSA-C/S) builds on the original PONDEROSA software (Lee et al. in Bioinformatics 27:1727-1728. doi: 10.1093/bioinformatics/btr200, 2011) and includes improved features for structure calculation and refinement. PONDEROSA-C/S consists of three programs: Ponderosa Server, Ponderosa Client, and Ponderosa Analyzer. PONDEROSA-C/S takes as input the protein sequence, a list of assigned chemical shifts, and nuclear Overhauser data sets ((13)C- and/or (15)N-NOESY). The output is a set of assigned NOEs and 3D structural models for the protein. Ponderosa Analyzer supports the visualization, validation, and refinement of the results from Ponderosa Server. These tools enable semi-automated NMR-based structure determination of proteins in a rapid and robust fashion. We present examples showing the use of PONDEROSA-C/S in solving structures of four proteins: two that enable comparison with the original PONDEROSA package, and two from the Critical Assessment of automated Structure Determination by NMR (Rosato et al. in Nat Methods 6:625-626. doi: 10.1038/nmeth0909-625 , 2009) competition. The software package can be downloaded freely in binary format from http://pine.nmrfam.wisc.edu/download_packages.html. Registered users of the National Magnetic Resonance Facility at Madison can submit jobs to the PONDEROSA-C/S server at http://ponderosa.nmrfam.wisc.edu, where instructions, tutorials, and instructions can be found. Structures are normally returned within 1-2 days.

  2. Verification of Single-Peptide Protein Identifications by the Application of Complementary Database Search Algorithms

    National Research Council Canada - National Science Library

    Rohrbough, James G; Breci, Linda; Merchant, Nirav; Miller, Susan; Haynes, Paul A

    2005-01-01

    .... One such technique, known as the Multi-Dimensional Protein Identification Technique, or MudPIT, involves the use of computer search algorithms that automate the process of identifying proteins...

  3. Comparison of liver mitochondrial proteins derived from newborn cloned calves and from cloned adult cattle by two-dimensional differential gel electrophoresis.

    Science.gov (United States)

    Takeda, Kumiko; Tasai, Mariko; Akagi, Satoshi; Watanabe, Shinya; Oe, Mika; Chikuni, Koichi; Ohnishi-Kameyama, Mayumi; Hanada, Hirofumi; Nakamura, Yoshiaki; Tagami, Takahiro; Nirasawa, Keijiro

    2011-04-01

    Aberrant reprogramming of donor somatic cell nuclei may result in many severe problems in animal cloning. The inability to establish functional interactions between donor nucleus and recipient mitochondria is also likely responsible for such a developmental deficiency. However, detailed knowledge of protein expression during somatic cell nuclear transfer (SCNT) in cattle is lacking. In the present study, variations in mitochondrial protein levels between SCNT-derived and control cattle, and from calves derived by artificial insemination were investigated. Mitochondrial fractions were prepared from frozen liver samples and subjected to two-dimensional (2-D) fluorescence differential gel electrophoresis (DIGE) using CyDye™ dyes. Protein expression changes were confirmed with a volume ratio greater than 2.0 (P result implicates mitochondrial-related gene expression in early developmental loss of SCNT embryos. Comparative proteomic analysis represents an important tool for further studies on SCNT animals. Copyright © 2011 Wiley-Liss, Inc.

  4. On the two-dimensional Saigo-Maeda fractional calculus asociated with two-dimensional Aleph TRANSFORM

    Directory of Open Access Journals (Sweden)

    Dinesh Kumar

    2013-11-01

    Full Text Available This paper deals with the study of two-dimensional Saigo-Maeda operators of Weyl type associated with Aleph function defined in this paper. Two theorems on these defined operators are established. Some interesting results associated with the H-functions and generalized Mittag-Leffler functions are deduced from the derived results. One dimensional analog of the derived results is also obtained.

  5. Smartnotebook: A semi-automated approach to protein sequential NMR resonance assignments

    International Nuclear Information System (INIS)

    Slupsky, Carolyn M.; Boyko, Robert F.; Booth, Valerie K.; Sykes, Brian D.

    2003-01-01

    Complete and accurate NMR spectral assignment is a prerequisite for high-throughput automated structure determination of biological macromolecules. However, completely automated assignment procedures generally encounter difficulties for all but the most ideal data sets. Sources of these problems include difficulty in resolving correlations in crowded spectral regions, as well as complications arising from dynamics, such as weak or missing peaks, or atoms exhibiting more than one peak due to exchange phenomena. Smartnotebook is a semi-automated assignment software package designed to combine the best features of the automated and manual approaches. The software finds and displays potential connections between residues, while the spectroscopist makes decisions on which connection is correct, allowing rapid and robust assignment. In addition, smartnotebook helps the user fit chains of connected residues to the primary sequence of the protein by comparing the experimentally determined chemical shifts with expected shifts derived from a chemical shift database, while providing bookkeeping throughout the assignment procedure

  6. Trimodal Mixed Mode Chromatography That Enables Efficient Offline Two-Dimensional Peptide Fractionation for Proteome Analysis.

    Science.gov (United States)

    Yu, Peng; Petzoldt, Svenja; Wilhelm, Mathias; Zolg, Daniel Paul; Zheng, Runsheng; Sun, Xuefei; Liu, Xiaodong; Schneider, Günter; Huhmer, Andreas; Kuster, Bernhard

    2017-09-05

    Offline two-dimensional chromatography is a common means to achieve deep proteome coverage. To reduce sample complexity and dynamic range and to utilize mass spectrometer (MS) time efficiently, high chromatographic resolution of and good orthogonality between the two dimensions are needed. Ion exchange and high pH reversed phase chromatography are often used for this purpose. However, the former requires desalting to be MS-compatible, and the latter requires fraction pooling to create orthogonality. Here, we report an alternative first-dimension separation technique using a commercial trimodal phase incorporating polar embedded reversed phase, weak anion exchange, and strong cation exchange material. The column is capable of retaining polar and nonpolar peptides alike without noticeable breakthrough. It allows separating ordinary and TMT-labeled peptides under mild acidic conditions using an acetonitrile gradient. The direct MS compatibility of solvents and good orthogonality to online coupled C18 columns enable a straightforward workflow without fraction pooling and desalting while showing comparable performance to the other techniques. The method scales from low to high microgram sample quantity and is amenable to full automation. To demonstrate practical utility, we analyzed the proteomes of 10 human pancreatic cancer cell lines to a depth of >8,700 quantified proteins.

  7. New Approach for Segmentation and Quantification of Two-Dimensional Gel Electrophoresis Images

    DEFF Research Database (Denmark)

    Anjo, Antonio dos; Laurell Blom Møller, Anders; Ersbøll, Bjarne Kjær

    2011-01-01

    Motivation: Detection of protein spots in two-dimensional gel electrophoresis images (2-DE) is a very complex task and current approaches addressing this problem still suffer from significant shortcomings. When quantifying a spot, most of the current software applications include a lot of backgro...

  8. NMRNet: A deep learning approach to automated peak picking of protein NMR spectra.

    Science.gov (United States)

    Klukowski, Piotr; Augoff, Michal; Zieba, Maciej; Drwal, Maciej; Gonczarek, Adam; Walczak, Michal J

    2018-03-14

    Automated selection of signals in protein NMR spectra, known as peak picking, has been studied for over 20 years, nevertheless existing peak picking methods are still largely deficient. Accurate and precise automated peak picking would accelerate the structure calculation, and analysis of dynamics and interactions of macromolecules. Recent advancement in handling big data, together with an outburst of machine learning techniques, offer an opportunity to tackle the peak picking problem substantially faster than manual picking and on par with human accuracy. In particular, deep learning has proven to systematically achieve human-level performance in various recognition tasks, and thus emerges as an ideal tool to address automated identification of NMR signals. We have applied a convolutional neural network for visual analysis of multidimensional NMR spectra. A comprehensive test on 31 manually-annotated spectra has demonstrated top-tier average precision (AP) of 0.9596, 0.9058 and 0.8271 for backbone, side-chain and NOESY spectra, respectively. Furthermore, a combination of extracted peak lists with automated assignment routine, FLYA, outperformed other methods, including the manual one, and led to correct resonance assignment at the levels of 90.40%, 89.90% and 90.20% for three benchmark proteins. The proposed model is a part of a Dumpling software (platform for protein NMR data analysis), and is available at https://dumpling.bio/. michaljerzywalczak@gmail.compiotr.klukowski@pwr.edu.pl. Supplementary data are available at Bioinformatics online.

  9. New apparatus for direct counting of β particles from two-dimensional gels and an application to changes in protein synthesis due to cell density

    International Nuclear Information System (INIS)

    Anderson, H.L.; Puck, T.T.; Shera, E.B.

    1987-07-01

    A new method is described for scanning two-dimensional gels by the direct counting of β particles instead of autoradiography. The methodology is described; results are compared with autoradiographic results; and data are presented demonstrating changed patterns of protein synthesis accompanying changes in cell density. The method is rapid and permits identification of differences in protein abundance of approximately 10% for a substantial fraction of the more prominent proteins. A modulation effect of more than 5 standard deviations, accompanying contact inhibition of cell growth, is shown to occur for an appreciable number of these proteins. The method promises to be applicable to a variety of biochemical and genetic experiments designed to delineate changes in protein synthesis accompanying changes in genome, molecular environment, history, and state of differentiation of the cell populations studied. 13 refs., 8 figs., 4 tabs

  10. Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.

    Science.gov (United States)

    Niklasson, Markus; Ahlner, Alexandra; Andresen, Cecilia; Marsh, Joseph A; Lundström, Patrik

    2015-01-01

    The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available.

  11. Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.

    Directory of Open Access Journals (Sweden)

    Markus Niklasson

    2015-01-01

    Full Text Available The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available.

  12. Two-dimensional nuclear magnetic resonance spectroscopy

    International Nuclear Information System (INIS)

    Bax, A.; Lerner, L.

    1986-01-01

    Great spectral simplification can be obtained by spreading the conventional one-dimensional nuclear magnetic resonance (NMR) spectrum in two independent frequency dimensions. This so-called two-dimensional NMR spectroscopy removes spectral overlap, facilitates spectral assignment, and provides a wealth of additional information. For example, conformational information related to interproton distances is available from resonance intensities in certain types of two-dimensional experiments. Another method generates 1 H NMR spectra of a preselected fragment of the molecule, suppressing resonances from other regions and greatly simplifying spectral appearance. Two-dimensional NMR spectroscopy can also be applied to the study of 13 C and 15 N, not only providing valuable connectivity information but also improving sensitivity of 13 C and 15 N detection by up to two orders of magnitude. 45 references, 10 figures

  13. Identification of proteins of human colorectal carcinoma cell line SW480 by two-dimensional electrophoresis and MALDI-TOF mass spectrometry

    Institute of Scientific and Technical Information of China (English)

    Ying-Tao Zhang; Yi-Ping Geng; Le Zhou; Bao-Chang Lai; Lv-Sheng Si; Yi-Li Wang

    2005-01-01

    AIM: To conduct the proteomic analysis of human colorectal carcinoma cell line, SW480 by using two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption /ionization-time of flight mass spectrometry (MALDITOFMS).METHODS: The total proteins of human colorectal carcinoma cell line, SW480 were separated with 2-DE by using immobilized pH gradient strips and visualized by staining with silver nitrate. The gel images were acquired by scanner and 2-DE analysis software, Image Master 2D Elite. Nineteen distinct protein spots were excised from gel randomly and digested in gel by TPCK-trypsin. Mass analysis ofthe tryptic digest peptides mixture was performed by using MALDI-TOF MS. Peptide mass fingerprints (PMFs) obtained by the MALDI-TOF analysis were used to search NCBI,SWISS-PROT and MSDB databases by using Mascot software.RESULTS: PMF maps of all spots were obtained by MALDI-TOF MS and thirteen proteins were preliminarily identified.CONCLUSION: The methods of analysis and identification of protein spots of tumor cells in 2-DE gel with silver staining by MALDI-TOF MS derived PMF have been established.Protein expression profile of SW480 has been obtained.It is demonstrated that a combination of proteomics and cell culture is a useful approach to comprehend the process of colon carcinogenesis.

  14. FireProt: web server for automated design of thermostable proteins

    Science.gov (United States)

    Musil, Milos; Stourac, Jan; Brezovsky, Jan; Prokop, Zbynek; Zendulka, Jaroslav; Martinek, Tomas

    2017-01-01

    Abstract There is a continuous interest in increasing proteins stability to enhance their usability in numerous biomedical and biotechnological applications. A number of in silico tools for the prediction of the effect of mutations on protein stability have been developed recently. However, only single-point mutations with a small effect on protein stability are typically predicted with the existing tools and have to be followed by laborious protein expression, purification, and characterization. Here, we present FireProt, a web server for the automated design of multiple-point thermostable mutant proteins that combines structural and evolutionary information in its calculation core. FireProt utilizes sixteen tools and three protein engineering strategies for making reliable protein designs. The server is complemented with interactive, easy-to-use interface that allows users to directly analyze and optionally modify designed thermostable mutants. FireProt is freely available at http://loschmidt.chemi.muni.cz/fireprot. PMID:28449074

  15. Automated measurement of serum thyroxine with the ''AIRA II,'' as compared with competitive protein binding and radioimmunoassay

    International Nuclear Information System (INIS)

    Reese, M.G.; Johnson, L.V.R.

    1978-01-01

    Two conventional serum thyroxine assays, run in separate laboratories, one by competitive protein binding and one by radioimmunoassay, were used to evaluate the automated ARIA II (Becton Dickinson Immunodiagnostics) serum thyroxine assay. Competitive protein binding as compared to ARIA II with 111 clinical serum samples gave a slope of 1.04 and a correlation coefficient of 0.94. The radioimmunoassay comparison to ARIA II with 53 clinical serum samples gave a slope of 1.05 and a correlation coefficient of 0.92. The ARIA II inter-assay coefficient of variation for 10 replicates of low, medium, and high thyroxine serum samples was 6.2, 6.0, and 2.9%, respectively, with an inter-assay coefficient of variation among 15 different assays of 15.5, 10.1, and 7.9%. The automated ARIA II, with a 2.2-min cycle per sample, gives results that compare well with those by manual methodology

  16. On some classes of two-dimensional local models in discrete two-dimensional monatomic FPU lattice with cubic and quartic potential

    International Nuclear Information System (INIS)

    Quan, Xu; Qiang, Tian

    2009-01-01

    This paper discusses the two-dimensional discrete monatomic Fermi–Pasta–Ulam lattice, by using the method of multiple-scale and the quasi-discreteness approach. By taking into account the interaction between the atoms in the lattice and their nearest neighbours, it obtains some classes of two-dimensional local models as follows: two-dimensional bright and dark discrete soliton trains, two-dimensional bright and dark line discrete breathers, and two-dimensional bright and dark discrete breather. (condensed matter: structure, thermal and mechanical properties)

  17. [Establishment of two-dimensional differential gel electrophoresis using cerebrospinal fluid from neurocysticercosis patients].

    Science.gov (United States)

    Li, Jing-Yi; Tian, Xiao-Jun; Huang, Yong; Yang, Yan-Jun; Ma, Qiao-Rong; Xue, Yan-Ping

    2008-06-30

    To establish the method of two-dimensional differential gel electrophoresis and obtain high resolution 2D images from cerebrospinal fluid (CSF) of patients with neurocysticercosis. CSF samples were collected from four patients diagnosed as neurocysticercosis clinically and by ELISA, computed tomography (CT) or magnetic resonance imaging (MRI), and from four healthy subjects without neurological disorders. The CSF samples were precipitated with cold acetone, then pooled by equal amount as patients and controls. The internal standard comprised equal amounts of proteins extracted from both groups. Internal standard, and proteins from the two groups were labeled prior to electrophoresis with spectrally resolvable fluorescent dyes, cyanein dye2 (Cy2), Cy3 and Cy5. Sodium dodecylsulfonate polyacrylamide gel chromatography (SDS-PAGE) and two-dimensional differential in-gel electrophoresis (2-D DIGE) of labeled samples were then run. The differential expressed proteins showed in the images of SDS-PAGE and 2-D DIGE gels scanned with 488 nm, 532 nm and 633 nm wavelength laser were analyzed by ImageQuant and DeCyde 5.0 respectively. Spot detection and quantification was performed for the differential in-gel analysis (DIA) module of DeCyder. Biological variation analysis (BVA) module of DeCyder was matched gel 1 and gel 2 images to provide data on differential protein expression levels between the two groups. The ImageQuant result displayed that the CSF protein was compatible with the dye, and the difference of protein amount was revealed by the difference of fluorescence intensity. DIA indicated that there were 896 and 894 protein dots on gel 1 and gel 2 respectively, and 90% of them were matched each other. BVA showed that there were 55 protein spots with different expressional level between neurocysticercosis and control groups. Protein spots with two-fold increase or decrease were 47 and 8 respectively in neurocysticercosis patients compared with healthy controls. The

  18. Two-dimensional models

    International Nuclear Information System (INIS)

    Schroer, Bert; Freie Universitaet, Berlin

    2005-02-01

    It is not possible to compactly review the overwhelming literature on two-dimensional models in a meaningful way without a specific viewpoint; I have therefore tacitly added to the above title the words 'as theoretical laboratories for general quantum field theory'. I dedicate this contribution to the memory of J. A. Swieca with whom I have shared the passion of exploring 2-dimensional models for almost one decade. A shortened version of this article is intended as a contribution to the project 'Encyclopedia of mathematical physics' and comments, suggestions and critical remarks are welcome. (author)

  19. Exploration of beer proteome using OFFGEL prefractionation in combination with two-dimensional gel electrophoresis with narrow pH range gradients.

    Science.gov (United States)

    Konečná, Hana; Müller, Lukáš; Dosoudilová, Hana; Potěšil, David; Buršíková, Jana; Sedo, Ondrej; Márová, Ivana; Zdráhal, Zbyněk

    2012-03-14

    Two-dimensional gel electrophoresis in combination with mass spectrometry has already been applied successfully to study beer proteome. Due to the abundance of protein Z in beer samples, prefractionation techniques might help to improve beer proteome coverage. Proteins from four lager beers of different origins were separated by two-dimensional electrophoresis (2-DE) followed by tandem mass spectrometric analysis. Initially 52 proteins mostly from Hordeum vulgare (22 proteins) and Saccharomyces species (25 proteins) were identified. Preparative isoelectric focusing by OFFGEL Fractionator was applied prior to 2-DE to improve its resolution power. As a result of this combined approach, a total of 70 beer proteins from Hordeum vulgare (30 proteins), from Saccharomyces species (31 proteins), and from other sources (9 proteins) were identified. Of these, 37 proteins have not been previously reported in beer samples.

  20. Two-dimensional multifractal cross-correlation analysis

    International Nuclear Information System (INIS)

    Xi, Caiping; Zhang, Shuning; Xiong, Gang; Zhao, Huichang; Yang, Yonghong

    2017-01-01

    Highlights: • We study the mathematical models of 2D-MFXPF, 2D-MFXDFA and 2D-MFXDMA. • Present the definition of the two-dimensional N 2 -partitioned multiplicative cascading process. • Do the comparative analysis of 2D-MC by 2D-MFXPF, 2D-MFXDFA and 2D-MFXDMA. • Provide a reference on the choice and parameter settings of these methods in practice. - Abstract: There are a number of situations in which several signals are simultaneously recorded in complex systems, which exhibit long-term power-law cross-correlations. This paper presents two-dimensional multifractal cross-correlation analysis based on the partition function (2D-MFXPF), two-dimensional multifractal cross-correlation analysis based on the detrended fluctuation analysis (2D-MFXDFA) and two-dimensional multifractal cross-correlation analysis based on the detrended moving average analysis (2D-MFXDMA). We apply these methods to pairs of two-dimensional multiplicative cascades (2D-MC) to do a comparative study. Then, we apply the two-dimensional multifractal cross-correlation analysis based on the detrended fluctuation analysis (2D-MFXDFA) to real images and unveil intriguing multifractality in the cross correlations of the material structures. At last, we give the main conclusions and provide a valuable reference on how to choose the multifractal algorithms in the potential applications in the field of SAR image classification and detection.

  1. Application of Fluorescence Two-Dimensional Difference In-Gel Electrophoresis as a Proteomic Biomarker Discovery Tool in Muscular Dystrophy Research

    Science.gov (United States)

    Carberry, Steven; Zweyer, Margit; Swandulla, Dieter; Ohlendieck, Kay

    2013-01-01

    In this article, we illustrate the application of difference in-gel electrophoresis for the proteomic analysis of dystrophic skeletal muscle. The mdx diaphragm was used as a tissue model of dystrophinopathy. Two-dimensional gel electrophoresis is a widely employed protein separation method in proteomic investigations. Although two-dimensional gels usually underestimate the cellular presence of very high molecular mass proteins, integral membrane proteins and low copy number proteins, this method is extremely powerful in the comprehensive analysis of contractile proteins, metabolic enzymes, structural proteins and molecular chaperones. This gives rise to two-dimensional gel electrophoretic separation as the method of choice for studying contractile tissues in health and disease. For comparative studies, fluorescence difference in-gel electrophoresis has been shown to provide an excellent biomarker discovery tool. Since aged diaphragm fibres from the mdx mouse model of Duchenne muscular dystrophy closely resemble the human pathology, we have carried out a mass spectrometry-based comparison of the naturally aged diaphragm versus the senescent dystrophic diaphragm. The proteomic comparison of wild type versus mdx diaphragm resulted in the identification of 84 altered protein species. Novel molecular insights into dystrophic changes suggest increased cellular stress, impaired calcium buffering, cytostructural alterations and disturbances of mitochondrial metabolism in dystrophin-deficient muscle tissue. PMID:24833232

  2. Two-dimensional beam profiles and one-dimensional projections

    Science.gov (United States)

    Findlay, D. J. S.; Jones, B.; Adams, D. J.

    2018-05-01

    One-dimensional projections of improved two-dimensional representations of transverse profiles of particle beams are proposed for fitting to data from harp-type monitors measuring beam profiles on particle accelerators. Composite distributions, with tails smoothly matched on to a central (inverted) parabola, are shown to give noticeably better fits than single gaussian and single parabolic distributions to data from harp-type beam profile monitors all along the proton beam transport lines to the two target stations on the ISIS Spallation Neutron Source. Some implications for inferring beam current densities on the beam axis are noted.

  3. Progress in two-dimensional polyacrylamide gel electrophoresis and application in radiation research

    International Nuclear Information System (INIS)

    Wang Zhidong; Chen Xiaohua

    2003-01-01

    Two-dimensional polyacrylamide gel electrophoresis is the key separation technique in proteomics research, which is designed by protein character: molecular weight and PI. Some progress has been made in disease mechanism detection, tumor indicator research and drug development. This technique also has some potential application in radiation research

  4. Automated design evolution of stereochemically randomized protein foldamers

    Science.gov (United States)

    Ranbhor, Ranjit; Kumar, Anil; Patel, Kirti; Ramakrishnan, Vibin; Durani, Susheel

    2018-05-01

    Diversification of chain stereochemistry opens up the possibilities of an ‘in principle’ increase in the design space of proteins. This huge increase in the sequence and consequent structural variation is aimed at the generation of smart materials. To diversify protein structure stereochemically, we introduced L- and D-α-amino acids as the design alphabet. With a sequence design algorithm, we explored the usage of specific variables such as chirality and the sequence of this alphabet in independent steps. With molecular dynamics, we folded stereochemically diverse homopolypeptides and evaluated their ‘fitness’ for possible design as protein-like foldamers. We propose a fitness function to prune the most optimal fold among 1000 structures simulated with an automated repetitive simulated annealing molecular dynamics (AR-SAMD) approach. The highly scored poly-leucine fold with sequence lengths of 24 and 30 amino acids were later sequence-optimized using a Dead End Elimination cum Monte Carlo based optimization tool. This paper demonstrates a novel approach for the de novo design of protein-like foldamers.

  5. FPGA Implementation of one-dimensional and two-dimensional cellular automata

    International Nuclear Information System (INIS)

    D'Antone, I.

    1999-01-01

    This report describes the hardware implementation of one-dimensional and two-dimensional cellular automata (CAs). After a general introduction to the cellular automata, we consider a one-dimensional CA used to implement pseudo-random techniques in built-in self test for VLSI. Due to the increase in digital ASIC complexity, testing is becoming one of the major costs in the VLSI production. The high electronics complexity, used in particle physics experiments, demands higher reliability than in the past time. General criterions are given to evaluate the feasibility of the circuit used for testing and some quantitative parameters are underlined to optimize the architecture of the cellular automaton. Furthermore, we propose a two-dimensional CA that performs a peak finding algorithm in a matrix of cells mapping a sub-region of a calorimeter. As in a two-dimensional filtering process, the peaks of the energy clusters are found in one evolution step. This CA belongs to Wolfram class II cellular automata. Some quantitative parameters are given to optimize the architecture of the cellular automaton implemented in a commercial field programmable gate array (FPGA)

  6. Automating the application of smart materials for protein crystallization

    International Nuclear Information System (INIS)

    Khurshid, Sahir; Govada, Lata; EL-Sharif, Hazim F.; Reddy, Subrayal M.; Chayen, Naomi E.

    2015-01-01

    The first semi-liquid, non-protein nucleating agent for automated protein crystallization trials is described. This ‘smart material’ is demonstrated to induce crystal growth and will provide a simple, cost-effective tool for scientists in academia and industry. The fabrication and validation of the first semi-liquid nonprotein nucleating agent to be administered automatically to crystallization trials is reported. This research builds upon prior demonstration of the suitability of molecularly imprinted polymers (MIPs; known as ‘smart materials’) for inducing protein crystal growth. Modified MIPs of altered texture suitable for high-throughput trials are demonstrated to improve crystal quality and to increase the probability of success when screening for suitable crystallization conditions. The application of these materials is simple, time-efficient and will provide a potent tool for structural biologists embarking on crystallization trials

  7. Lie algebra contractions on two-dimensional hyperboloid

    International Nuclear Information System (INIS)

    Pogosyan, G. S.; Yakhno, A.

    2010-01-01

    The Inoenue-Wigner contraction from the SO(2, 1) group to the Euclidean E(2) and E(1, 1) group is used to relate the separation of variables in Laplace-Beltrami (Helmholtz) equations for the four corresponding two-dimensional homogeneous spaces: two-dimensional hyperboloids and two-dimensional Euclidean and pseudo-Euclidean spaces. We show how the nine systems of coordinates on the two-dimensional hyperboloids contracted to the four systems of coordinates on E 2 and eight on E 1,1 . The text was submitted by the authors in English.

  8. Quasi-two-dimensional holography

    International Nuclear Information System (INIS)

    Kutzner, J.; Erhard, A.; Wuestenberg, H.; Zimpfer, J.

    1980-01-01

    The acoustical holography with numerical reconstruction by area scanning is memory- and time-intensive. With the experiences by the linear holography we tried to derive a scanning for the evaluating of the two-dimensional flaw-sizes. In most practical cases it is sufficient to determine the exact depth extension of a flaw, whereas the accuracy of the length extension is less critical. For this reason the applicability of the so-called quasi-two-dimensional holography is appropriate. The used sound field given by special probes is divergent in the inclined plane and light focussed in the perpendicular plane using cylindrical lenses. (orig.) [de

  9. Automated mass correction and data interpretation for protein open-access liquid chromatography-mass spectrometry.

    Science.gov (United States)

    Wagner, Craig D; Hall, John T; White, Wendy L; Miller, Luke A D; Williams, Jon D

    2007-02-01

    Characterization of recombinant protein purification fractions and final products by liquid chromatography-mass spectrometry (LC/MS) are requested more frequently each year. A protein open-access (OA) LC/MS system was developed in our laboratory to meet this demand. This paper compares the system that we originally implemented in our facilities in 2003 to the one now in use, and discusses, in more detail, recent enhancements that have improved its robustness, reliability, and data reporting capabilities. The system utilizes instruments equipped with reversed-phase chromatography and an orthogonal accelerated time-of-flight mass spectrometer fitted with an electrospray source. Sample analysis requests are accomplished using a simple form on a web-enabled laboratory information management system (LIMS). This distributed form is accessible from any intranet-connected company desktop computer. Automated data acquisition and processing are performed using a combination of in-house (OA-Self Service, OA-Monitor, and OA-Analysis Engine) and vendor-supplied programs (AutoLynx, and OpenLynx) located on acquisition computers and off-line processing workstations. Analysis results are then reported via the same web-based LIMS. Also presented are solutions to problems not addressed on commercially available, small-molecule OA-LC/MS systems. These include automated transforming of mass-to-charge (m/z) spectra to mass spectra and automated data interpretation that considers minor variants to the protein sequence-such as common post-translational modifications (PTMs). Currently, our protein OA-LC/MS platform runs on five LC/MS instruments located in three separate GlaxoSmithKline R&D sites in the US and UK. To date, more than 8000 protein OA-LC/MS samples have been analyzed. With these user friendly and highly automated OA systems in place, mass spectrometry plays a key role in assessing the quality of recombinant proteins, either produced at our facilities or bought from external

  10. Topology optimization of two-dimensional waveguides

    DEFF Research Database (Denmark)

    Jensen, Jakob Søndergaard; Sigmund, Ole

    2003-01-01

    In this work we use the method of topology optimization to design two-dimensional waveguides with low transmission loss.......In this work we use the method of topology optimization to design two-dimensional waveguides with low transmission loss....

  11. Traditional Semiconductors in the Two-Dimensional Limit.

    Science.gov (United States)

    Lucking, Michael C; Xie, Weiyu; Choe, Duk-Hyun; West, Damien; Lu, Toh-Ming; Zhang, S B

    2018-02-23

    Interest in two-dimensional materials has exploded in recent years. Not only are they studied due to their novel electronic properties, such as the emergent Dirac fermion in graphene, but also as a new paradigm in which stacking layers of distinct two-dimensional materials may enable different functionality or devices. Here, through first-principles theory, we reveal a large new class of two-dimensional materials which are derived from traditional III-V, II-VI, and I-VII semiconductors. It is found that in the ultrathin limit the great majority of traditional binary semiconductors studied (a series of 28 semiconductors) are not only kinetically stable in a two-dimensional double layer honeycomb structure, but more energetically stable than the truncated wurtzite or zinc-blende structures associated with three dimensional bulk. These findings both greatly increase the landscape of two-dimensional materials and also demonstrate that in the double layer honeycomb form, even ordinary semiconductors, such as GaAs, can exhibit exotic topological properties.

  12. Sufficient Controllability Condition for Affine Systems with Two-Dimensional Control and Two-Dimensional Zero Dynamics

    Directory of Open Access Journals (Sweden)

    D. A. Fetisov

    2015-01-01

    Full Text Available The controllability conditions are well known if we speak about linear stationary systems: a linear stationary system is controllable if and only if the dimension of the state vector is equal to the rank of the controllability matrix. The concept of the controllability matrix is extended to affine systems, but relations between affine systems controllability and properties of this matrix are more complicated. Various controllability conditions are set for affine systems, but they deal as usual either with systems of some special form or with controllability in some small neighborhood of the concerned point. An affine system is known to be controllable if the system is equivalent to a system of a canonical form, which is defined and regular in the whole space of states. In this case, the system is said to be feedback linearizable in the space of states. However there are examples, which illustrate that a system can be controllable even if it is not feedback linearizable in any open subset in the space of states. In this article we deal with such systems.Affine systems with two-dimensional control are considered. The system in question is assumed to be equivalent to a system of a quasicanonical form with two-dimensional zero dynamics which is defined and regular in the whole space of states. Therefore the controllability of the original system is equivalent to the controllability of the received system of a quasicanonical form. In this article the sufficient condition for an available solution of the terminal problem is proven for systems of a quasicanonical form with two-dimensional control and two-dimensional zero dynamics. The condition is valid in the case of an arbitrary time interval and arbitrary initial and finite states of the system. Therefore the controllability condition is set for systems of a quasicanonical form with two-dimensional control and two-dimensional zero dynamics. An example is given which illustrates how the proved

  13. Automated computation of autonomous spectral submanifolds for nonlinear modal analysis

    Science.gov (United States)

    Ponsioen, Sten; Pedergnana, Tiemo; Haller, George

    2018-04-01

    We discuss an automated computational methodology for computing two-dimensional spectral submanifolds (SSMs) in autonomous nonlinear mechanical systems of arbitrary degrees of freedom. In our algorithm, SSMs, the smoothest nonlinear continuations of modal subspaces of the linearized system, are constructed up to arbitrary orders of accuracy, using the parameterization method. An advantage of this approach is that the construction of the SSMs does not break down when the SSM folds over its underlying spectral subspace. A further advantage is an automated a posteriori error estimation feature that enables a systematic increase in the orders of the SSM computation until the required accuracy is reached. We find that the present algorithm provides a major speed-up, relative to numerical continuation methods, in the computation of backbone curves, especially in higher-dimensional problems. We illustrate the accuracy and speed of the automated SSM algorithm on lower- and higher-dimensional mechanical systems.

  14. ANALOGIES IN THE 2-DIMENSIONAL SPATIAL ARRANGEMENT OF ADSORBED PROTEINS AND ADHERING BACTERIA - BOVINE SERUM-ALBUMIN AND STREPTOCOCCUS-SANGUIS-12

    NARCIS (Netherlands)

    BUSSCHER, HJ; VANDERMEI, HC; SCHAKENRAAD, JM

    1991-01-01

    Neither proteins nor bacteria adsorb or adhere homogeneously to a substratum surface. The final two-dimensional spatial arrangement depends on a complicated interplay between protein-protein (bacterium-bacterium) and protein (bacterium)-substratum interactions and the prevailing hydrodynamic

  15. Two-dimensional flexible nanoelectronics

    Science.gov (United States)

    Akinwande, Deji; Petrone, Nicholas; Hone, James

    2014-12-01

    2014/2015 represents the tenth anniversary of modern graphene research. Over this decade, graphene has proven to be attractive for thin-film transistors owing to its remarkable electronic, optical, mechanical and thermal properties. Even its major drawback--zero bandgap--has resulted in something positive: a resurgence of interest in two-dimensional semiconductors, such as dichalcogenides and buckled nanomaterials with sizeable bandgaps. With the discovery of hexagonal boron nitride as an ideal dielectric, the materials are now in place to advance integrated flexible nanoelectronics, which uniquely take advantage of the unmatched portfolio of properties of two-dimensional crystals, beyond the capability of conventional thin films for ubiquitous flexible systems.

  16. Automated 3-D Radiation Mapping

    International Nuclear Information System (INIS)

    Tarpinian, J. E.

    1991-01-01

    This work describes an automated radiation detection and imaging system which combines several state-of-the-art technologies to produce a portable but very powerful visualization tool for planning work in radiation environments. The system combines a radiation detection system, a computerized radiation imaging program, and computerized 3-D modeling to automatically locate and measurements are automatically collected and imaging techniques are used to produce colored, 'isodose' images of the measured radiation fields. The isodose lines from the images are then superimposed over the 3-D model of the area. The final display shows the various components in a room and their associated radiation fields. The use of an automated radiation detection system increases the quality of radiation survey obtained measurements. The additional use of a three-dimensional display allows easier visualization of the area and associated radiological conditions than two-dimensional sketches

  17. Enhanced detergent extraction for analysis of membrane proteomes by two-dimensional gel electrophoresis

    Directory of Open Access Journals (Sweden)

    Hsu Kimberly K

    2005-06-01

    Full Text Available Abstract Background The analysis of hydrophobic membrane proteins by two-dimensional gel electrophoresis has long been hampered by the concept of inherent difficulty due to solubility issues. We have optimized extraction protocols by varying the detergent composition of the solubilization buffer with a variety of commercially available non-ionic and zwitterionic detergents and detergent-like phospholipids. Results After initial analyses by one-dimensional SDS-PAGE, quantitative two-dimensional analyses of human erythrocyte membranes, mouse liver membranes, and mouse brain membranes, extracted with buffers that included the zwitterionic detergent MEGA 10 (decanoyl-N-methylglucamide and the zwitterionic lipid LPC (1-lauroyl lysophosphatidylcholine, showed selective improvement over extraction with the common 2-DE detergent CHAPS (3 [(3-cholamidopropyldimethylammonio]-1-propanesulfonate. Mixtures of the three detergents showed additive improvements in spot number, density, and resolution. Substantial improvements in the analysis of a brain membrane proteome were observed. Conclusion This study demonstrates that an optimized detergent mix, coupled with rigorous sample handling and electrophoretic protocols, enables simple and effective analysis of membrane proteomes using two-dimensional electrophoresis.

  18. A metrological study of autoradiographs from two-dimensional gel electrophoresis.

    Science.gov (United States)

    Valiron, O; Lefkovits, I; Garderet, P; Steinberg, C

    1984-12-01

    Samples prepared from a single batch of labeled cells were subjected to two-dimensional gel electrophoresis and autoradiography. Three factors were varied: total quantity of protein, quantity of labeled protein, and exposure time. The mean background absorbance of the film remained identical (about 0.5 A) for all the treated series, whatever the exposure time and whether or not there were unlabeled proteins in the sample. Hence any spot with a peak A of the same order of magnitude can be seen. The standard deviation was about 0.05 A. Thus, the measurement precision is 2.5% of full scale for digitalization over 0 to 2 A. We derived experimental calibration curves, which are neither linear nor logarithmic because of the film response and which can be used on randomly chosen spots.

  19. Automation in biological crystallization.

    Science.gov (United States)

    Stewart, Patrick Shaw; Mueller-Dieckmann, Jochen

    2014-06-01

    Crystallization remains the bottleneck in the crystallographic process leading from a gene to a three-dimensional model of the encoded protein or RNA. Automation of the individual steps of a crystallization experiment, from the preparation of crystallization cocktails for initial or optimization screens to the imaging of the experiments, has been the response to address this issue. Today, large high-throughput crystallization facilities, many of them open to the general user community, are capable of setting up thousands of crystallization trials per day. It is thus possible to test multiple constructs of each target for their ability to form crystals on a production-line basis. This has improved success rates and made crystallization much more convenient. High-throughput crystallization, however, cannot relieve users of the task of producing samples of high quality. Moreover, the time gained from eliminating manual preparations must now be invested in the careful evaluation of the increased number of experiments. The latter requires a sophisticated data and laboratory information-management system. A review of the current state of automation at the individual steps of crystallization with specific attention to the automation of optimization is given.

  20. Semi-automated analysis of three-dimensional track images

    International Nuclear Information System (INIS)

    Meesen, G.; Poffijn, A.

    2001-01-01

    In the past, three-dimensional (3-d) track images in solid state detectors were difficult to obtain. With the introduction of the confocal scanning laser microscope it is now possible to record 3-d track images in a non-destructive way. These 3-d track images can latter be used to measure typical track parameters. Preparing the detectors and recording the 3-d images however is only the first step. The second step in this process is enhancing the image quality by means of deconvolution techniques to obtain the maximum possible resolution. The third step is extracting the typical track parameters. This can be done on-screen by an experienced operator. For large sets of data however, this manual technique is not desirable. This paper will present some techniques to analyse 3-d track data in an automated way by means of image analysis routines. Advanced thresholding techniques guarantee stable results in different recording situations. By using pre-knowledge about the track shape, reliable object identification is obtained. In case of ambiguity, manual intervention is possible

  1. A modified strategy for sequence specific assignment of protein NMR spectra based on amino acid type selective experiments

    International Nuclear Information System (INIS)

    Schubert, Mario; Labudde, Dirk; Leitner, Dietmar; Oschkinat, Hartmut; Schmieder, Peter

    2005-01-01

    The determination of the three-dimensional structure of a protein or the study of protein-ligand interactions requires the assignment of all relevant nuclei as an initial step. This is nowadays almost exclusively performed using triple-resonance experiments. The conventional strategy utilizes one or more pairs of three dimensional spectra to obtain redundant information and thus reliable assignments. Here, a modified strategy for obtaining sequence specific assignments based on two dimensional amino acid type selective triple-resonance experiments is proposed. These experiments can be recorded with good resolution in a relatively short time. They provide very specific and redundant information, in particular on sequential connectivities, that drastically increases the ease and reliability of the assignment procedure, done either manually or in an automated fashion. The new strategy is demonstrated with the protein domain PB1 from yeast CDC24p

  2. Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces.

    Directory of Open Access Journals (Sweden)

    Ching-Tai Chen

    Full Text Available Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins and were tested on an independent dataset (consisting of 142 proteins. The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted

  3. Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces

    Science.gov (United States)

    Chen, Ching-Tai; Peng, Hung-Pin; Jian, Jhih-Wei; Tsai, Keng-Chang; Chang, Jeng-Yih; Yang, Ei-Wen; Chen, Jun-Bo; Ho, Shinn-Ying; Hsu, Wen-Lian; Yang, An-Suei

    2012-01-01

    Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI) sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins) and were tested on an independent dataset (consisting of 142 proteins). The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted correctly with

  4. Characterization of the supersonic flowing microwave discharge using two dimensional plasma tomography

    Energy Technology Data Exchange (ETDEWEB)

    Nikolic, M.; Samolov, A.; Popovic, S.; Vuskovic, L.; Godunov, A. [Department of Physics, Center for Accelerator Science, Old Dominion University, Norfolk, Virginia 23529 (United States); Cuckov, F. [Department of Electrical and Computer Engineering, Old Dominion University, Norfolk, Virginia 23529 (United States)

    2013-03-14

    A tomographic numerical method based on the two-dimensional Radon formula for a cylindrical cavity has been employed for obtaining spatial distributions of the argon excited levels. The spectroscopy measurements were taken at different positions and directions to observe populations of excited species in the plasmoid region and the corresponding excitation temperatures. Excited argon states are concentrated near the tube walls, thus, confirming the assumption that the post discharge plasma is dominantly sustained by travelling surface wave. An automated optical measurement system has been developed for reconstruction of local plasma parameters of the plasmoid structure formed in an argon supersonic flowing microwave discharge. The system carries out angle and distance measurements using a rotating, flat mirror, as well as two high precision stepper motors operated by a microcontroller-based system and several sensors for precise feedback control.

  5. Electron crystallography of three dimensional protein crystals

    NARCIS (Netherlands)

    Georgieva, Dilyana

    2008-01-01

    This thesis describes an investigation of the potential of electron diffraction for studying three dimensional sub-micro-crystals of proteins and pharmaceuticals. A prerequisite for using electron diffraction for structural studies is the predictable availability of tiny crystals. A method for

  6. CASA: An Efficient Automated Assignment of Protein Mainchain NMR Data Using an Ordered Tree Search Algorithm

    International Nuclear Information System (INIS)

    Wang Jianyong; Wang Tianzhi; Zuiderweg, Erik R. P.; Crippen, Gordon M.

    2005-01-01

    Rapid analysis of protein structure, interaction, and dynamics requires fast and automated assignments of 3D protein backbone triple-resonance NMR spectra. We introduce a new depth-first ordered tree search method of automated assignment, CASA, which uses hand-edited peak-pick lists of a flexible number of triple resonance experiments. The computer program was tested on 13 artificially simulated peak lists for proteins up to 723 residues, as well as on the experimental data for four proteins. Under reasonable tolerances, it generated assignments that correspond to the ones reported in the literature within a few minutes of CPU time. The program was also tested on the proteins analyzed by other methods, with both simulated and experimental peaklists, and it could generate good assignments in all relevant cases. The robustness was further tested under various situations

  7. Three-dimensional rotation electron diffraction: software RED for automated data collection and data processing.

    Science.gov (United States)

    Wan, Wei; Sun, Junliang; Su, Jie; Hovmöller, Sven; Zou, Xiaodong

    2013-12-01

    Implementation of a computer program package for automated collection and processing of rotation electron diffraction (RED) data is described. The software package contains two computer programs: RED data collection and RED data processing. The RED data collection program controls the transmission electron microscope and the camera. Electron beam tilts at a fine step (0.05-0.20°) are combined with goniometer tilts at a coarse step (2.0-3.0°) around a common tilt axis, which allows a fine relative tilt to be achieved between the electron beam and the crystal in a large tilt range. An electron diffraction (ED) frame is collected at each combination of beam tilt and goniometer tilt. The RED data processing program processes three-dimensional ED data generated by the RED data collection program or by other approaches. It includes shift correction of the ED frames, peak hunting for diffraction spots in individual ED frames and identification of these diffraction spots as reflections in three dimensions. Unit-cell parameters are determined from the positions of reflections in three-dimensional reciprocal space. All reflections are indexed, and finally a list with hkl indices and intensities is output. The data processing program also includes a visualizer to view and analyse three-dimensional reciprocal lattices reconstructed from the ED frames. Details of the implementation are described. Data collection and data processing with the software RED are demonstrated using a calcined zeolite sample, silicalite-1. The structure of the calcined silicalite-1, with 72 unique atoms, could be solved from the RED data by routine direct methods.

  8. Approximate solutions for the two-dimensional integral transport equation. Solution of complex two-dimensional transport problems

    International Nuclear Information System (INIS)

    Sanchez, Richard.

    1980-11-01

    This work is divided into two parts: the first part deals with the solution of complex two-dimensional transport problems, the second one (note CEA-N-2166) treats the critically mixed methods of resolution. A set of approximate solutions for the isotropic two-dimensional neutron transport problem has been developed using the interface current formalism. The method has been applied to regular lattices of rectangular cells containing a fuel pin, cladding, and water, or homogenized structural material. The cells are divided into zones that are homogeneous. A zone-wise flux expansion is used to formulate a direct collision probability problem within a cell. The coupling of the cells is effected by making extra assumptions on the currents entering and leaving the interfaces. Two codes have been written: CALLIOPE uses a cylindrical cell model and one or three terms for the flux expansion, and NAUSICAA uses a two-dimensional flux representation and does a truly two-dimensional calculation inside each cell. In both codes, one or three terms can be used to make a space-independent expansion of the angular fluxes entering and leaving each side of the cell. The accuracies and computing times achieved with the different approximations are illustrated by numerical studies on two benchmark problems and by calculations performed in the APOLLO multigroup code [fr

  9. Two-dimensional topological field theories coupled to four-dimensional BF theory

    International Nuclear Information System (INIS)

    Montesinos, Merced; Perez, Alejandro

    2008-01-01

    Four-dimensional BF theory admits a natural coupling to extended sources supported on two-dimensional surfaces or string world sheets. Solutions of the theory are in one to one correspondence with solutions of Einstein equations with distributional matter (cosmic strings). We study new (topological field) theories that can be constructed by adding extra degrees of freedom to the two-dimensional world sheet. We show how two-dimensional Yang-Mills degrees of freedom can be added on the world sheet, producing in this way, an interactive (topological) theory of Yang-Mills fields with BF fields in four dimensions. We also show how a world sheet tetrad can be naturally added. As in the previous case the set of solutions of these theories are contained in the set of solutions of Einstein's equations if one allows distributional matter supported on two-dimensional surfaces. These theories are argued to be exactly quantizable. In the context of quantum gravity, one important motivation to study these models is to explore the possibility of constructing a background-independent quantum field theory where local degrees of freedom at low energies arise from global topological (world sheet) degrees of freedom at the fundamental level

  10. Digital Three-Dimensional Automation of the Modified Huddart and Bodenham Scoring System for Patients With Cleft Lip and Palate.

    Science.gov (United States)

    Ma, Xinhui; Martin, Catherine; McIntyre, Grant; Lin, Ping; Mossey, Peter

    2017-07-01

    The modified Huddart and Bodenham scoring system assesses maxillary arch constriction and surgical outcomes in cleft lip and palate. This project automates modified Huddart and Bodenham scoring using three-dimensional digital models. Development of a novel software tool. The design, construction, development, and testing of the system was carried out at Dundee Dental Hospital. Subjects with cleft lip and palate. A plug-in has been developed using an open three-dimensional development platform: Rhinoceros, version 5 ( http://www.rhino3d.co.uk ). Users select cusps on mandibular and maxillary teeth on three-dimensional digital models. A three-dimensional cubic spline generates a mandibular curve, and a best-fit horizontal mandibular reference plane is produced using a least-squares method. Horizontal distances projected from the shortest three-dimensional distances were subsequently calculated between the maxillary cusps and the mandibular curve to calculate the modified Huddart and Bodenham score. Automatic scoring of digital models using the modified Huddart and Bodenham system produces similar results to manual scoring. By standardizing outcome assessment in cleft care, multicenter comparisons for audit and research can be simplified, allowing centers throughout the world to upload three-dimensional digital models or intraoral scans of the dental arches for remote scoring. Thereafter, these data can feed back into the global database on orofacial clefting as part of the World Health Organization's international collaborative "Global Burden of Disease" research project for craniofacial anomalies. The automated system facilitates quicker and more reliable outcome assessments by minimizing human errors.

  11. [Study on the method of two dimensional polycrylamide gel electrophoresis on rat condylar chondrocyte].

    Science.gov (United States)

    Wu, Tuo-jiang; Li, Huang; Ma, Qiao-lin; Wang, Wen-mei

    2010-08-01

    To investigate the protein profile by two dimensional polycrylamide gel electrophoresis on the rat condylar chondrocyte in vitro. The third-passage chondrocytes were harvested from the mandibular condyles of 2-day-old rats in this study. The protein profile of the rat mandibular condylar chondrocytes was examined by two dimensional polycrylamide gel electrophoresis (2-DE-PAGE). The 2-DE gel maps on different pH gradients were obtained. The result of modified coomassi blue-sliver staining and sliver staining was compared using Pdquest 7.1 image analysis software. The results showed that the good protein profile of the condylar chondrocytes was obtained by standard Bio-Rad manual. The protein was mainly in the field from pH4 to pH7. The 1203±86 protein points were examined on 2-DE gel map by modified coomassi blue-sliver staining, and 1769±97 protein points was examined by sliver staining. The silver staining map showed more distinctly but higher background than modified coomassi blue-sliver staining. The protein profile of the condylar chondrocytes enriches the proteomic database and gives evidence to further proteomic research. The 2-DE map obtained by modified coomassi blue-sliver staining is more suitable for MALDI-TOF mass identification. Supported by National Natural Science Foundation of China (Grant No. C30700963), China Postdoctoral Science Foundation(Grant No.20090461088), Jiangsu Provincial Postdoctoral Science Foundation (Grant No.0802003C) and Nanjing City's Science and Technology Foundation (Grant No.200905011).

  12. Beginning Introductory Physics with Two-Dimensional Motion

    Science.gov (United States)

    Huggins, Elisha

    2009-01-01

    During the session on "Introductory College Physics Textbooks" at the 2007 Summer Meeting of the AAPT, there was a brief discussion about whether introductory physics should begin with one-dimensional motion or two-dimensional motion. Here we present the case that by starting with two-dimensional motion, we are able to introduce a considerable…

  13. Two-dimensional thermofield bosonization

    International Nuclear Information System (INIS)

    Amaral, R.L.P.G.; Belvedere, L.V.; Rothe, K.D.

    2005-01-01

    The main objective of this paper was to obtain an operator realization for the bosonization of fermions in 1 + 1 dimensions, at finite, non-zero temperature T. This is achieved in the framework of the real-time formalism of Thermofield Dynamics. Formally, the results parallel those of the T = 0 case. The well-known two-dimensional Fermion-Boson correspondences at zero temperature are shown to hold also at finite temperature. To emphasize the usefulness of the operator realization for handling a large class of two-dimensional quantum field-theoretic problems, we contrast this global approach with the cumbersome calculation of the fermion-current two-point function in the imaginary-time formalism and real-time formalisms. The calculations also illustrate the very different ways in which the transmutation from Fermi-Dirac to Bose-Einstein statistics is realized

  14. Two-dimensional x-ray diffraction

    CERN Document Server

    He, Bob B

    2009-01-01

    Written by one of the pioneers of 2D X-Ray Diffraction, this useful guide covers the fundamentals, experimental methods and applications of two-dimensional x-ray diffraction, including geometry convention, x-ray source and optics, two-dimensional detectors, diffraction data interpretation, and configurations for various applications, such as phase identification, texture, stress, microstructure analysis, crystallinity, thin film analysis and combinatorial screening. Experimental examples in materials research, pharmaceuticals, and forensics are also given. This presents a key resource to resea

  15. Smart multi-channel two-dimensional micro-gas chromatography for rapid workplace hazardous volatile organic compounds measurement.

    Science.gov (United States)

    Liu, Jing; Seo, Jung Hwan; Li, Yubo; Chen, Di; Kurabayashi, Katsuo; Fan, Xudong

    2013-03-07

    We developed a novel smart multi-channel two-dimensional (2-D) micro-gas chromatography (μGC) architecture that shows promise to significantly improve 2-D μGC performance. In the smart μGC design, a non-destructive on-column gas detector and a flow routing system are installed between the first dimensional separation column and multiple second dimensional separation columns. The effluent from the first dimensional column is monitored in real-time and decision is then made to route the effluent to one of the second dimensional columns for further separation. As compared to the conventional 2-D μGC, the greatest benefit of the smart multi-channel 2-D μGC architecture is the enhanced separation capability of the second dimensional column and hence the overall 2-D GC performance. All the second dimensional columns are independent of each other, and their coating, length, flow rate and temperature can be customized for best separation results. In particular, there is no more constraint on the upper limit of the second dimensional column length and separation time in our architecture. Such flexibility is critical when long second dimensional separation is needed for optimal gas analysis. In addition, the smart μGC is advantageous in terms of elimination of the power intensive thermal modulator, higher peak amplitude enhancement, simplified 2-D chromatogram re-construction and potential scalability to higher dimensional separation. In this paper, we first constructed a complete smart 1 × 2 channel 2-D μGC system, along with an algorithm for automated control/operation of the system. We then characterized and optimized this μGC system, and finally employed it in two important applications that highlight its uniqueness and advantages, i.e., analysis of 31 workplace hazardous volatile organic compounds, and rapid detection and identification of target gas analytes from interference background.

  16. Autonomy and Automation

    Science.gov (United States)

    Shively, Jay

    2017-01-01

    A significant level of debate and confusion has surrounded the meaning of the terms autonomy and automation. Automation is a multi-dimensional concept, and we propose that Remotely Piloted Aircraft Systems (RPAS) automation should be described with reference to the specific system and task that has been automated, the context in which the automation functions, and other relevant dimensions. In this paper, we present definitions of automation, pilot in the loop, pilot on the loop and pilot out of the loop. We further propose that in future, the International Civil Aviation Organization (ICAO) RPAS Panel avoids the use of the terms autonomy and autonomous when referring to automated systems on board RPA. Work Group 7 proposes to develop, in consultation with other workgroups, a taxonomy of Levels of Automation for RPAS.

  17. Piezoelectricity in Two-Dimensional Materials

    KAUST Repository

    Wu, Tao

    2015-02-25

    Powering up 2D materials: Recent experimental studies confirmed the existence of piezoelectricity - the conversion of mechanical stress into electricity - in two-dimensional single-layer MoS2 nanosheets. The results represent a milestone towards embedding low-dimensional materials into future disruptive technologies. © 2015 Wiley-VCH Verlag GmbH & Co. KGaA.

  18. Two-dimensional confinement of heavy fermions

    International Nuclear Information System (INIS)

    Shishido, Hiroaki; Shibauchi, Takasada; Matsuda, Yuji; Terashima, Takahito

    2010-01-01

    Metallic systems with the strongest electron correlations are realized in certain rare-earth and actinide compounds whose physics are dominated by f-electrons. These materials are known as heavy fermions, so called because the effective mass of the conduction electrons is enhanced via correlation effects up to as much as several hundreds times the free electron mass. To date the electronic structure of all heavy-fermion compounds is essentially three-dimensional. Here we report on the first realization of a two-dimensional heavy-fermion system, where the dimensionality is adjusted in a controllable fashion by fabricating heterostructures using molecular beam epitaxy. The two-dimensional heavy fermion system displays striking deviations from the standard Fermi liquid low-temperature electronic properties. (author)

  19. Two-dimensional topological photonics

    Science.gov (United States)

    Khanikaev, Alexander B.; Shvets, Gennady

    2017-12-01

    Originating from the studies of two-dimensional condensed-matter states, the concept of topological order has recently been expanded to other fields of physics and engineering, particularly optics and photonics. Topological photonic structures have already overturned some of the traditional views on wave propagation and manipulation. The application of topological concepts to guided wave propagation has enabled novel photonic devices, such as reflection-free sharply bent waveguides, robust delay lines, spin-polarized switches and non-reciprocal devices. Discrete degrees of freedom, widely used in condensed-matter physics, such as spin and valley, are now entering the realm of photonics. In this Review, we summarize the latest advances in this highly dynamic field, with special emphasis on the experimental work on two-dimensional photonic topological structures.

  20. Structures of two-dimensional three-body systems

    International Nuclear Information System (INIS)

    Ruan, W.Y.; Liu, Y.Y.; Bao, C.G.

    1996-01-01

    Features of the structure of L = 0 states of a two-dimensional three-body model system have been investigated. Three types of permutation symmetry of the spatial part, namely symmetric, antisymmetric, and mixed, have been considered. A comparison has been made between the two-dimensional system and the corresponding three-dimensional one. The effect of symmetry on microscopic structures is emphasized. (author)

  1. An automated framework for NMR resonance assignment through simultaneous slice picking and spin system forming

    KAUST Repository

    Abbas, Ahmed

    2014-04-19

    Despite significant advances in automated nuclear magnetic resonance-based protein structure determination, the high numbers of false positives and false negatives among the peaks selected by fully automated methods remain a problem. These false positives and negatives impair the performance of resonance assignment methods. One of the main reasons for this problem is that the computational research community often considers peak picking and resonance assignment to be two separate problems, whereas spectroscopists use expert knowledge to pick peaks and assign their resonances at the same time. We propose a novel framework that simultaneously conducts slice picking and spin system forming, an essential step in resonance assignment. Our framework then employs a genetic algorithm, directed by both connectivity information and amino acid typing information from the spin systems, to assign the spin systems to residues. The inputs to our framework can be as few as two commonly used spectra, i.e., CBCA(CO)NH and HNCACB. Different from the existing peak picking and resonance assignment methods that treat peaks as the units, our method is based on \\'slices\\', which are one-dimensional vectors in three-dimensional spectra that correspond to certain (N, H) values. Experimental results on both benchmark simulated data sets and four real protein data sets demonstrate that our method significantly outperforms the state-of-the-art methods while using a less number of spectra than those methods. Our method is freely available at http://sfb.kaust.edu.sa/Pages/Software.aspx. © 2014 Springer Science+Business Media.

  2. X-ray imaging device for one-dimensional and two-dimensional radioscopy

    International Nuclear Information System (INIS)

    1978-01-01

    The X-ray imaging device for the selectable one-dimensional or two-dimensional pictures of objects illuminated by X-rays, comprising an X-ray source, an X-ray screen, and an opto-electrical picture development device placed behind the screen, is characterized by an anamorphotic optical system, which is positioned with a one-dimensional illumination between the X-ray screen and the opto-electrical device and that a two-dimensional illumination will be developed, and that in view of the lens system which forms part of the opto-electrical device, there is placed an X-ray screen in a specified beam direction so that a magnified image may be formed by equalisation of the distance between the X-ray screen and the lens system. (G.C.)

  3. Hamiltonian formalism of two-dimensional Vlasov kinetic equation.

    Science.gov (United States)

    Pavlov, Maxim V

    2014-12-08

    In this paper, the two-dimensional Benney system describing long wave propagation of a finite depth fluid motion and the multi-dimensional Russo-Smereka kinetic equation describing a bubbly flow are considered. The Hamiltonian approach established by J. Gibbons for the one-dimensional Vlasov kinetic equation is extended to a multi-dimensional case. A local Hamiltonian structure associated with the hydrodynamic lattice of moments derived by D. J. Benney is constructed. A relationship between this hydrodynamic lattice of moments and the two-dimensional Vlasov kinetic equation is found. In the two-dimensional case, a Hamiltonian hydrodynamic lattice for the Russo-Smereka kinetic model is constructed. Simple hydrodynamic reductions are presented.

  4. Novel target design algorithm for two-dimensional optical storage (TwoDOS)

    NARCIS (Netherlands)

    Huang, Li; Chong, T.C.; Vijaya Kumar, B.V.K.; Kobori, H.

    2004-01-01

    In this paper we introduce the Hankel transform based channel model of Two-Dimensional Optical Storage (TwoDOS) system. Based on this model, the two-dimensional (2D) minimum mean-square error (MMSE) equalizer has been derived and applied to some simple but common cases. The performance of the 2D

  5. Two-dimensional ferroelectrics

    Energy Technology Data Exchange (ETDEWEB)

    Blinov, L M; Fridkin, Vladimir M; Palto, Sergei P [A.V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Moscow, Russian Federaion (Russian Federation); Bune, A V; Dowben, P A; Ducharme, Stephen [Department of Physics and Astronomy, Behlen Laboratory of Physics, Center for Materials Research and Analysis, University of Nebraska-Linkoln, Linkoln, NE (United States)

    2000-03-31

    The investigation of the finite-size effect in ferroelectric crystals and films has been limited by the experimental conditions. The smallest demonstrated ferroelectric crystals had a diameter of {approx}200 A and the thinnest ferroelectric films were {approx}200 A thick, macroscopic sizes on an atomic scale. Langmuir-Blodgett deposition of films one monolayer at a time has produced high quality ferroelectric films as thin as 10 A, made from polyvinylidene fluoride and its copolymers. These ultrathin films permitted the ultimate investigation of finite-size effects on the atomic thickness scale. Langmuir-Blodgett films also revealed the fundamental two-dimensional character of ferroelectricity in these materials by demonstrating that there is no so-called critical thickness; films as thin as two monolayers (1 nm) are ferroelectric, with a transition temperature near that of the bulk material. The films exhibit all the main properties of ferroelectricity with a first-order ferroelectric-paraelectric phase transition: polarization hysteresis (switching); the jump in spontaneous polarization at the phase transition temperature; thermal hysteresis in the polarization; the increase in the transition temperature with applied field; double hysteresis above the phase transition temperature; and the existence of the ferroelectric critical point. The films also exhibit a new phase transition associated with the two-dimensional layers. (reviews of topical problems)

  6. Complex mixture analysis of peptides using LC/LC-MS/MS and data-dependent protein identification

    International Nuclear Information System (INIS)

    Wasinger, V.; Corthals, G.

    2001-01-01

    The comprehensive identification of proteins within complex solutions by mass-spectrometry largely depends on the sensitivity, resolving power and sampling efficiency of the technology. An integrated orthogonal approach using Strong Cation Exchange-Reverse Phase-MS/MS (SCX-RP-MS/MS) was used to evaluate the data-dependent Collision Induced Dissociation (CID) of yeast peptides. Reverse phase gradient times of 4, 10. 30, 90, and 180 minutes allowed the identification of hundreds of proteins in a nearly automated fashion from nuclear, membrane, and cytosolic distributions. Many proteins from typically difficult to resolve regions of two-dimensional gels, such as >100kDa, > pI 9.0 and Codon Adaptation Index < 0.2, were also identified using this multi-dimensional separation technology. Few low mass proteins (<10kDa) were identified. The impact of scan-range and duty-cycle on CID of peptides will be discussed

  7. Protein identification from two-dimensional gel electrophoresis analysis of Klebsiella pneumoniae by combined use of mass spectrometry data and raw genome sequences

    Directory of Open Access Journals (Sweden)

    Zeng An-Ping

    2003-12-01

    Full Text Available Abstract Separation of proteins by two-dimensional gel electrophoresis (2-DE coupled with identification of proteins through peptide mass fingerprinting (PMF by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS is the widely used technique for proteomic analysis. This approach relies, however, on the presence of the proteins studied in public-accessible protein databases or the availability of annotated genome sequences of an organism. In this work, we investigated the reliability of using raw genome sequences for identifying proteins by PMF without the need of additional information such as amino acid sequences. The method is demonstrated for proteomic analysis of Klebsiella pneumoniae grown anaerobically on glycerol. For 197 spots excised from 2-DE gels and submitted for mass spectrometric analysis 164 spots were clearly identified as 122 individual proteins. 95% of the 164 spots can be successfully identified merely by using peptide mass fingerprints and a strain-specific protein database (ProtKpn constructed from the raw genome sequences of K. pneumoniae. Cross-species protein searching in the public databases mainly resulted in the identification of 57% of the 66 high expressed protein spots in comparison to 97% by using the ProtKpn database. 10 dha regulon related proteins that are essential for the initial enzymatic steps of anaerobic glycerol metabolism were successfully identified using the ProtKpn database, whereas none of them could be identified by cross-species searching. In conclusion, the use of strain-specific protein database constructed from raw genome sequences makes it possible to reliably identify most of the proteins from 2-DE analysis simply through peptide mass fingerprinting.

  8. Two-Dimensional Materials for Sensing: Graphene and Beyond

    Directory of Open Access Journals (Sweden)

    Seba Sara Varghese

    2015-09-01

    Full Text Available Two-dimensional materials have attracted great scientific attention due to their unusual and fascinating properties for use in electronics, spintronics, photovoltaics, medicine, composites, etc. Graphene, transition metal dichalcogenides such as MoS2, phosphorene, etc., which belong to the family of two-dimensional materials, have shown great promise for gas sensing applications due to their high surface-to-volume ratio, low noise and sensitivity of electronic properties to the changes in the surroundings. Two-dimensional nanostructured semiconducting metal oxide based gas sensors have also been recognized as successful gas detection devices. This review aims to provide the latest advancements in the field of gas sensors based on various two-dimensional materials with the main focus on sensor performance metrics such as sensitivity, specificity, detection limit, response time, and reversibility. Both experimental and theoretical studies on the gas sensing properties of graphene and other two-dimensional materials beyond graphene are also discussed. The article concludes with the current challenges and future prospects for two-dimensional materials in gas sensor applications.

  9. Two-dimensional calculus

    CERN Document Server

    Osserman, Robert

    2011-01-01

    The basic component of several-variable calculus, two-dimensional calculus is vital to mastery of the broader field. This extensive treatment of the subject offers the advantage of a thorough integration of linear algebra and materials, which aids readers in the development of geometric intuition. An introductory chapter presents background information on vectors in the plane, plane curves, and functions of two variables. Subsequent chapters address differentiation, transformations, and integration. Each chapter concludes with problem sets, and answers to selected exercises appear at the end o

  10. Phase transitions in two-dimensional systems

    International Nuclear Information System (INIS)

    Salinas, S.R.A.

    1983-01-01

    Some experiences are related using synchrotron radiation beams, to characterize solid-liquid (fusion) and commensurate solid-uncommensurate solid transitions in two-dimensional systems. Some ideas involved in the modern theories of two-dimensional fusion are shortly exposed. The systems treated consist of noble gases (Kr,Ar,Xe) adsorbed in the basal plane of graphite and thin films formed by some liquid crystal shells. (L.C.) [pt

  11. The theory of critical phenomena in two-dimensional systems

    International Nuclear Information System (INIS)

    Olvera de la C, M.

    1981-01-01

    An exposition of the theory of critical phenomena in two-dimensional physical systems is presented. The first six chapters deal with the mean field theory of critical phenomena, scale invariance of the thermodynamic functions, Kadanoff's spin block construction, Wilson's renormalization group treatment of critical phenomena in configuration space, and the two-dimensional Ising model on a triangular lattice. The second part of this work is made of four chapters devoted to the application of the ideas expounded in the first part to the discussion of critical phenomena in superfluid films, two-dimensional crystals and the two-dimensional XY model of magnetic systems. Chapters seven to ten are devoted to the following subjects: analysis of long range order in one, two, and three-dimensional physical systems. Topological defects in the XY model, in superfluid films and in two-dimensional crystals. The Thouless-Kosterlitz iterated mean field theory of the dipole gas. The renormalization group treatment of the XY model, superfluid films and two-dimensional crystal. (author)

  12. Development of automated endoscopes for dimensional micro-measurements

    Science.gov (United States)

    Hrebabetzky, Frank

    2013-04-01

    Increasing demands for product quality and outsourcing of production in the automobile industry lead to in­ creasingly tight tolerances for the components. In the area of metal-mechanics these are largely dimensional and require frequently uncertainties in the micron region. For optical instruments this means microscopical resolu­ tion. Dimensional measurement with uncertainties of some microns is nothing new, state of the art equipment in fact goes far below. The task becomes difficult if the measurements have to be carried out in an industrial production environment - and deep inside a bore hole. This paper describes the development of an automatic measurement system for internal dimensions of brake master cylinders, specifically the development of endoscopes, illuminations for edge detection, and integration with other sensors, actuators and controllers. The most demanding part was the endoscope development, because, surprisingly, no commercial product for microscopic view and precision measurements was found on the market. As the market for such measurement machines is very small, and as the requirements were different for each endoscope, the budget allowed only the development of prototypes, using readily available optical components. Borders between faces with different orientation of metallic structures can be difficult do detect. A satisfactory metrological performance can be achieved only with carefully shaped illumination, even if the source is a simple LED (light emitting diode). The automation was responsible for the largest part of the overall cost, coming from the desire for a high throughput of the measurement machine, even when operated by not highly qualified personnel. With the safety requirements satisfied, such a device ends up as a pretty complex equipment. Nevertheless, these aspects will be mentioned only for completeness, because standard components and methods were applied.

  13. The two capsid proteins of maize rayado fino virus contain common peptide sequences.

    Science.gov (United States)

    Falk, B W; Tsai, J H

    1986-01-01

    Virions of maize rayado fino virus (MRFV) were purified and two major capsid proteins (ca. Mr 29,000 and 22,000) were resolved by SDS-PAGE. When the two major capsid proteins were isolated from gels and compared by one-dimensional peptide mapping after digestion with Staphylococcus aureus V-8 protease, indistinguishable peptide maps were obtained, suggesting that these two proteins contain common peptide sequences. Some preparations also showed minor protein components that were intermediate between the Mr 22,000 and Mr 29,000 capsid proteins. One of the minor proteins, ca. Mr 27,000, gave a peptide map indistinguishable from the major capsid proteins. In vitro ageing of partially purified preparations or virion treatment with proteolytic enzymes failed to show conversion of the Mr 29,000 protein to a Mr 22,000. Protease inhibitors added to the buffers used for virion purification did not affect the apparent 1:3 ratio of 29,000 to 22,000 proteins in the purified preparations.

  14. Two- and three-dimensional CT analysis of ankle fractures

    International Nuclear Information System (INIS)

    Magid, D.; Fishman, E.K.; Ney, D.R.; Kuhlman, J.E.

    1988-01-01

    CT with coronal and sagittal reformatting (two-dimensional CT) and animated volumetric image rendering (three-dimensional CT) was used to assess ankle fractures. Partial volume limits transaxial CT in assessments of horizontally oriented structures. Two-dimensional CT, being orthogonal to the plafond, superior mortise, talar dome, and tibial epiphysis, often provides the most clinically useful images. Two-dimensional CT is most useful in characterizing potentially confusing fractures, such as Tillaux (anterior tubercle), triplane, osteochondral talar dome, or nondisplaced talar neck fractures, and it is the best study to confirm intraarticular fragments. Two-and three-dimensional CT best indicate the percentage of articular surface involvement and best demonstrate postoperative results or complications (hardware migration, residual step-off, delayed union, DJD, AVN, etc). Animated three-dimensional images are the preferred means of integrating the two-dimensional findings for surgical planning, as these images more closely simulate the clinical problem

  15. On two-dimensionalization of three-dimensional turbulence in shell models

    DEFF Research Database (Denmark)

    Chakraborty, Sagar; Jensen, Mogens Høgh; Sarkar, A.

    2010-01-01

    Applying a modified version of the Gledzer-Ohkitani-Yamada (GOY) shell model, the signatures of so-called two-dimensionalization effect of three-dimensional incompressible, homogeneous, isotropic fully developed unforced turbulence have been studied and reproduced. Within the framework of shell m......-similar PDFs for longitudinal velocity differences are also presented for the rotating 3D turbulence case....

  16. Two-dimensional turbulent convection

    Science.gov (United States)

    Mazzino, Andrea

    2017-11-01

    We present an overview of the most relevant, and sometimes contrasting, theoretical approaches to Rayleigh-Taylor and mean-gradient-forced Rayleigh-Bénard two-dimensional turbulence together with numerical and experimental evidences for their support. The main aim of this overview is to emphasize that, despite the different character of these two systems, especially in relation to their steadiness/unsteadiness, turbulent fluctuations are well described by the same scaling relationships originated from the Bolgiano balance. The latter states that inertial terms and buoyancy terms balance at small scales giving rise to an inverse kinetic energy cascade. The main difference with respect to the inverse energy cascade in hydrodynamic turbulence [R. H. Kraichnan, "Inertial ranges in two-dimensional turbulence," Phys. Fluids 10, 1417 (1967)] is that the rate of cascade of kinetic energy here is not constant along the inertial range of scales. Thanks to the absence of physical boundaries, the two systems here investigated turned out to be a natural physical realization of the Kraichnan scaling regime hitherto associated with the elusive "ultimate state of thermal convection" [R. H. Kraichnan, "Turbulent thermal convection at arbitrary Prandtl number," Phys. Fluids 5, 1374-1389 (1962)].

  17. PASA - A Program for Automated Protein NMR Backbone Signal Assignment by Pattern-Filtering Approach

    International Nuclear Information System (INIS)

    Xu Yizhuang; Wang Xiaoxia; Yang Jun; Vaynberg, Julia; Qin Jun

    2006-01-01

    We present a new program, PASA (Program for Automated Sequential Assignment), for assigning protein backbone resonances based on multidimensional heteronuclear NMR data. Distinct from existing programs, PASA emphasizes a per-residue-based pattern-filtering approach during the initial stage of the automated 13 C α and/or 13 C β chemical shift matching. The pattern filter employs one or multiple constraints such as 13 C α /C β chemical shift ranges for different amino acid types and side-chain spin systems, which helps to rule out, in a stepwise fashion, improbable assignments as resulted from resonance degeneracy or missing signals. Such stepwise filtering approach substantially minimizes early false linkage problems that often propagate, amplify, and ultimately cause complication or combinatorial explosion of the automation process. Our program (http://www.lerner.ccf.org/moleccard/qin/) was tested on four representative small-large sized proteins with various degrees of resonance degeneracy and missing signals, and we show that PASA achieved the assignments efficiently and rapidly that are fully consistent with those obtained by laborious manual protocols. The results demonstrate that PASA may be a valuable tool for NMR-based structural analyses, genomics, and proteomics

  18. Protein solution structure determination using distances from two-dimensional nuclear Overhauser effect experiments: Effect of approximations on the accuracy of derived structures

    International Nuclear Information System (INIS)

    Thomas, P.D.; Basus, V.J.; James, T.L.

    1991-01-01

    Solution structures for many proteins have been determined to date utilizing interproton distance constraints estimated from two-dimensional nuclear Overhauser effect (2D NOE) spectra. Although the simple isolated spin pair approximation (ISPA) generally used can result in systematic errors in distances, the large number of constraints enables proteins structure to be defined with reasonably high resolution. Effects of these systematic errors on the resulting protein structure are examined. Iterative relaxation matrix calculations, which account for dipolar interactions between all protons in a molecule, can accurately determine internuclear distances with little or no a priori knowledge of the molecular structure. The value of this additional complexity is also addressed. To assess these distance determination methods, hypothetical experimental data, including random noise and peak overlap, are calculated for an arbitrary true protein structure. Three methods of obtaining distance constraints from 2D NOE peak intensities are examined: one entails a conservative use of ISPA, one assumes the ISPA to be fairly accurate, and on utilizes an iterative relaxation matrix method called MARDIGRAS (matrix analysis of relaxation for discerning the geometry of an aqueous structure), developed in this laboratory. An R factor for evaluating fit between experimental and calculated 2D NOE intensities is proposed

  19. Extracting information from two-dimensional electrophoresis gels by partial least squares regression

    DEFF Research Database (Denmark)

    Jessen, Flemming; Lametsch, R.; Bendixen, E.

    2002-01-01

    of all proteins/spots in the gels. In the present study it is demonstrated how information can be extracted by multivariate data analysis. The strategy is based on partial least squares regression followed by variable selection to find proteins that individually or in combination with other proteins vary......Two-dimensional gel electrophoresis (2-DE) produces large amounts of data and extraction of relevant information from these data demands a cautious and time consuming process of spot pattern matching between gels. The classical approach of data analysis is to detect protein markers that appear...... or disappear depending on the experimental conditions. Such biomarkers are found by comparing the relative volumes of individual spots in the individual gels. Multivariate statistical analysis and modelling of 2-DE data for comparison and classification is an alternative approach utilising the combination...

  20. The jellyfish and its polyp: a comparative study of gene expression monitored by the protein patterns using two-dimensional gels with double-label autoradiography

    International Nuclear Information System (INIS)

    Bally, Andreas; Schmid, Volker

    1988-01-01

    The life cycle of Podocoryne carnea (Coelenterata. Anthomedusae) shows several distinct stages which differ considerably in terms of their ecology, morphology, cellular composition and ultra structure. Using two-dimensional gel electrophoresis and a new method of double-label autoradiography, we show here for the first time for metagenic hydrozoans that only minor differences in gene expression exist between the various life cycle stages. Our results demonstrate the high resolution power of these techniques and show that the different life stages of P. carnea remain rather similar on the protein level (author)

  1. Automated Hydrophobic Interaction Chromatography Column Selection for Use in Protein Purification

    Science.gov (United States)

    Murphy, Patrick J. M.; Stone, Orrin J.; Anderson, Michelle E.

    2011-01-01

    In contrast to other chromatographic methods for purifying proteins (e.g. gel filtration, affinity, and ion exchange), hydrophobic interaction chromatography (HIC) commonly requires experimental determination (referred to as screening or "scouting") in order to select the most suitable chromatographic medium for purifying a given protein 1. The method presented here describes an automated approach to scouting for an optimal HIC media to be used in protein purification. HIC separates proteins and other biomolecules from a crude lysate based on differences in hydrophobicity. Similar to affinity chromatography (AC) and ion exchange chromatography (IEX), HIC is capable of concentrating the protein of interest as it progresses through the chromatographic process. Proteins best suited for purification by HIC include those with hydrophobic surface regions and able to withstand exposure to salt concentrations in excess of 2 M ammonium sulfate ((NH4)2SO4). HIC is often chosen as a purification method for proteins lacking an affinity tag, and thus unsuitable for AC, and when IEX fails to provide adequate purification. Hydrophobic moieties on the protein surface temporarily bind to a nonpolar ligand coupled to an inert, immobile matrix. The interaction between protein and ligand are highly dependent on the salt concentration of the buffer flowing through the chromatography column, with high ionic concentrations strengthening the protein-ligand interaction and making the protein immobile (i.e. bound inside the column) 2. As salt concentrations decrease, the protein-ligand interaction dissipates, the protein again becomes mobile and elutes from the column. Several HIC media are commercially available in pre-packed columns, each containing one of several hydrophobic ligands (e.g. S-butyl, butyl, octyl, and phenyl) cross-linked at varying densities to agarose beads of a specific diameter 3. Automated column scouting allows for an efficient approach for determining which HIC media

  2. Multi-perspective views of students’ difficulties with one-dimensional vector and two-dimensional vector

    Science.gov (United States)

    Fauzi, Ahmad; Ratna Kawuri, Kunthi; Pratiwi, Retno

    2017-01-01

    Researchers of students’ conceptual change usually collects data from written tests and interviews. Moreover, reports of conceptual change often simply refer to changes in concepts, such as on a test, without any identification of the learning processes that have taken place. Research has shown that students have difficulties with vectors in university introductory physics courses and high school physics courses. In this study, we intended to explore students’ understanding of one-dimensional and two-dimensional vector in multi perspective views. In this research, we explore students’ understanding through test perspective and interviews perspective. Our research study adopted the mixed-methodology design. The participants of this research were sixty students of third semester of physics education department. The data of this research were collected by testand interviews. In this study, we divided the students’ understanding of one-dimensional vector and two-dimensional vector in two categories, namely vector skills of the addition of one-dimensionaland two-dimensional vector and the relation between vector skills and conceptual understanding. From the investigation, only 44% of students provided correct answer for vector skills of the addition of one-dimensional and two-dimensional vector and only 27% students provided correct answer for the relation between vector skills and conceptual understanding.

  3. Optimizing separations in online comprehensive two-dimensional liquid chromatography.

    Science.gov (United States)

    Pirok, Bob W J; Gargano, Andrea F G; Schoenmakers, Peter J

    2018-01-01

    Online comprehensive two-dimensional liquid chromatography has become an attractive option for the analysis of complex nonvolatile samples found in various fields (e.g. environmental studies, food, life, and polymer sciences). Two-dimensional liquid chromatography complements the highly popular hyphenated systems that combine liquid chromatography with mass spectrometry. Two-dimensional liquid chromatography is also applied to the analysis of samples that are not compatible with mass spectrometry (e.g. high-molecular-weight polymers), providing important information on the distribution of the sample components along chemical dimensions (molecular weight, charge, lipophilicity, stereochemistry, etc.). Also, in comparison with conventional one-dimensional liquid chromatography, two-dimensional liquid chromatography provides a greater separation power (peak capacity). Because of the additional selectivity and higher peak capacity, the combination of two-dimensional liquid chromatography with mass spectrometry allows for simpler mixtures of compounds to be introduced in the ion source at any given time, improving quantitative analysis by reducing matrix effects. In this review, we summarize the rationale and principles of two-dimensional liquid chromatography experiments, describe advantages and disadvantages of combining different selectivities and discuss strategies to improve the quality of two-dimensional liquid chromatography separations. © 2017 The Authors. Journal of Separation Science published by WILEY-VCH Verlag GmbH & Co. KGaA.

  4. 78 FR 53466 - Modification of Two National Customs Automation Program (NCAP) Tests Concerning Automated...

    Science.gov (United States)

    2013-08-29

    ... Customs Automation Program (NCAP) Tests Concerning Automated Commercial Environment (ACE) Document Image... National Customs Automation Program (NCAP) tests concerning document imaging, known as the Document Image... the National Customs Automation Program (NCAP) tests concerning document imaging, known as the...

  5. Two-dimensional liquid chromatography

    DEFF Research Database (Denmark)

    Græsbøll, Rune

    -dimensional separation space. Optimization of gradients in online RP×RP is more difficult than in normal HPLC as a result of the increased number of parameters and their influence on each other. Modeling the coverage of the compounds across the two-dimensional chromatogram as a result of a change in gradients could...... be used for optimization purposes, and reduce the time spend on optimization. In this thesis (chapter 6), and manuscript B, a measure of the coverage of the compounds in the twodimensional separation space is defined. It is then shown that this measure can be modeled for changes in the gradient in both...

  6. Two-dimensional simulation of sintering process

    International Nuclear Information System (INIS)

    Vasconcelos, Vanderley de; Pinto, Lucio Carlos Martins; Vasconcelos, Wander L.

    1996-01-01

    The results of two-dimensional simulations are directly applied to systems in which one of the dimensions is much smaller than the others, and to sections of three dimensional models. Moreover, these simulations are the first step of the analysis of more complex three-dimensional systems. In this work, two basic features of the sintering process are studied: the types of particle size distributions related to the powder production processes and the evolution of geometric parameters of the resultant microstructures during the solid-state sintering. Random packing of equal spheres is considered in the sintering simulation. The packing algorithm does not take into account the interactive forces between the particles. The used sintering algorithm causes the densification of the particle set. (author)

  7. Two-dimensional patterning of thin coatings for the control of tissue outgrowth

    DEFF Research Database (Denmark)

    Thissen, H.; Johnson, G.; Hartley, P.G.

    2006-01-01

    were used to provide evidence of successful surface modifications. Adsorption of the extracellular matrix protein collagen I followed by tissue outgrowth experiments with bovine corneal epithelial tissue for up to 21 days showed that two-dimensional control over tissue outgrowth is achievable with our......Control of the precise location and extent of cellular attachment and proliferation, and of tissue outgrowth is important in a number of biomedical applications, including biomaterials and tissue engineered medical devices. Here we describe a method to control and direct the location and define...... boundaries of tissue growth on surfaces in two dimensions. The method relies on the generation of a spatially defined surface chemistry comprising protein adsorbing and non-adsorbing areas that allow control over the adsorption of cell-adhesive glycoproteins. Surface modification was carried out...

  8. Chaotic dynamics in two-dimensional noninvertible maps

    CERN Document Server

    Mira, Christian; Cathala, Jean-Claude; Gardini, Laura

    1996-01-01

    This book is essentially devoted to complex properties (Phase plane structure and bifurcations) of two-dimensional noninvertible maps, i.e. maps having either a non-unique inverse, or no real inverse, according to the plane point. They constitute models of sets of discrete dynamical systems encountered in Engineering (Control, Signal Processing, Electronics), Physics, Economics, Life Sciences. Compared to the studies made in the one-dimensional case, the two-dimensional situation remained a long time in an underdeveloped state. It is only since these last years that the interest for this resea

  9. Application of a method for comparing one-dimensional and two-dimensional models of a ground-water flow system

    International Nuclear Information System (INIS)

    Naymik, T.G.

    1978-01-01

    To evaluate the inability of a one-dimensional ground-water model to interact continuously with surrounding hydraulic head gradients, simulations using one-dimensional and two-dimensional ground-water flow models were compared. This approach used two types of models: flow-conserving one-and-two dimensional models, and one-dimensional and two-dimensional models designed to yield two-dimensional solutions. The hydraulic conductivities of controlling features were varied and model comparison was based on the travel times of marker particles. The solutions within each of the two model types compare reasonably well, but a three-dimensional solution is required to quantify the comparison

  10. Assessment of automated disease detection in diabetic retinopathy screening using two-field photography.

    Science.gov (United States)

    Goatman, Keith; Charnley, Amanda; Webster, Laura; Nussey, Stephen

    2011-01-01

    To assess the performance of automated disease detection in diabetic retinopathy screening using two field mydriatic photography. Images from 8,271 sequential patient screening episodes from a South London diabetic retinopathy screening service were processed by the Medalytix iGrading™ automated grading system. For each screening episode macular-centred and disc-centred images of both eyes were acquired and independently graded according to the English national grading scheme. Where discrepancies were found between the automated result and original manual grade, internal and external arbitration was used to determine the final study grades. Two versions of the software were used: one that detected microaneurysms alone, and one that detected blot haemorrhages and exudates in addition to microaneurysms. Results for each version were calculated once using both fields and once using the macula-centred field alone. Of the 8,271 episodes, 346 (4.2%) were considered unassessable. Referable disease was detected in 587 episodes (7.1%). The sensitivity of the automated system for detecting unassessable images ranged from 97.4% to 99.1% depending on configuration. The sensitivity of the automated system for referable episodes ranged from 98.3% to 99.3%. All the episodes that included proliferative or pre-proliferative retinopathy were detected by the automated system regardless of configuration (192/192, 95% confidence interval 98.0% to 100%). If implemented as the first step in grading, the automated system would have reduced the manual grading effort by between 2,183 and 3,147 patient episodes (26.4% to 38.1%). Automated grading can safely reduce the workload of manual grading using two field, mydriatic photography in a routine screening service.

  11. Optimized set of two-dimensional experiments for fast sequential assignment, secondary structure determination, and backbone fold validation of 13C/15N-labelled proteins

    International Nuclear Information System (INIS)

    Bersch, Beate; Rossy, Emmanuel; Coves, Jacques; Brutscher, Bernhard

    2003-01-01

    NMR experiments are presented which allow backbone resonance assignment, secondary structure identification, and in favorable cases also molecular fold topology determination from a series of two-dimensional 1 H- 15 N HSQC-like spectra. The 1 H- 15 N correlation peaks are frequency shifted by an amount ± ω X along the 15 N dimension, where ω X is the C α , C β , or H α frequency of the same or the preceding residue. Because of the low dimensionality (2D) of the experiments, high-resolution spectra are obtained in a short overall experimental time. The whole series of seven experiments can be performed in typically less than one day. This approach significantly reduces experimental time when compared to the standard 3D-based methods. The here presented methodology is thus especially appealing in the context of high-throughput NMR studies of protein structure, dynamics or molecular interfaces

  12. Two-dimensional analytic weighting functions for limb scattering

    Science.gov (United States)

    Zawada, D. J.; Bourassa, A. E.; Degenstein, D. A.

    2017-10-01

    Through the inversion of limb scatter measurements it is possible to obtain vertical profiles of trace species in the atmosphere. Many of these inversion methods require what is often referred to as weighting functions, or derivatives of the radiance with respect to concentrations of trace species in the atmosphere. Several radiative transfer models have implemented analytic methods to calculate weighting functions, alleviating the computational burden of traditional numerical perturbation methods. Here we describe the implementation of analytic two-dimensional weighting functions, where derivatives are calculated relative to atmospheric constituents in a two-dimensional grid of altitude and angle along the line of sight direction, in the SASKTRAN-HR radiative transfer model. Two-dimensional weighting functions are required for two-dimensional inversions of limb scatter measurements. Examples are presented where the analytic two-dimensional weighting functions are calculated with an underlying one-dimensional atmosphere. It is shown that the analytic weighting functions are more accurate than ones calculated with a single scatter approximation, and are orders of magnitude faster than a typical perturbation method. Evidence is presented that weighting functions for stratospheric aerosols calculated under a single scatter approximation may not be suitable for use in retrieval algorithms under solar backscatter conditions.

  13. Uniform and selective deuteration in two-dimensional NMR of proteins

    International Nuclear Information System (INIS)

    LeMaster, D.M.

    1990-01-01

    This paper reports on the practicality of isotopic labeling, particularly deuteration, that has received considerable impetus from advances in molecular biology, which have allowed ready production of NMR quantities of labeled proteins. Protein expression in Escherichia coli allows use of the considerable metabolic genetics known for the organism in shaping the biosynthetic process to meet the labeling demands of the NMR experiments. In addition to deuteration's common use in spectral assignment problems, it also offers considerable potential for enhancing the quality of the nuclear Overhauser effect (NOE) distance and dihedral angle constraints used for solution structural analysis of proteins. Recent reviews emphasize the sample preparation and spectral benefits of protein deuteration

  14. Three-dimensional, automated, real-time video system for tracking limb motion in brain-machine interface studies.

    Science.gov (United States)

    Peikon, Ian D; Fitzsimmons, Nathan A; Lebedev, Mikhail A; Nicolelis, Miguel A L

    2009-06-15

    Collection and analysis of limb kinematic data are essential components of the study of biological motion, including research into biomechanics, kinesiology, neurophysiology and brain-machine interfaces (BMIs). In particular, BMI research requires advanced, real-time systems capable of sampling limb kinematics with minimal contact to the subject's body. To answer this demand, we have developed an automated video tracking system for real-time tracking of multiple body parts in freely behaving primates. The system employs high-contrast markers painted on the animal's joints to continuously track the three-dimensional positions of their limbs during activity. Two-dimensional coordinates captured by each video camera are combined and converted to three-dimensional coordinates using a quadratic fitting algorithm. Real-time operation of the system is accomplished using direct memory access (DMA). The system tracks the markers at a rate of 52 frames per second (fps) in real-time and up to 100fps if video recordings are captured to be later analyzed off-line. The system has been tested in several BMI primate experiments, in which limb position was sampled simultaneously with chronic recordings of the extracellular activity of hundreds of cortical cells. During these recordings, multiple computational models were employed to extract a series of kinematic parameters from neuronal ensemble activity in real-time. The system operated reliably under these experimental conditions and was able to compensate for marker occlusions that occurred during natural movements. We propose that this system could also be extended to applications that include other classes of biological motion.

  15. Depth-enhanced three-dimensional-two-dimensional convertible display based on modified integral imaging.

    Science.gov (United States)

    Park, Jae-Hyeung; Kim, Hak-Rin; Kim, Yunhee; Kim, Joohwan; Hong, Jisoo; Lee, Sin-Doo; Lee, Byoungho

    2004-12-01

    A depth-enhanced three-dimensional-two-dimensional convertible display that uses a polymer-dispersed liquid crystal based on the principle of integral imaging is proposed. In the proposed method, a lens array is located behind a transmission-type display panel to form an array of point-light sources, and a polymer-dispersed liquid crystal is electrically controlled to pass or to scatter light coming from these point-light sources. Therefore, three-dimensional-two-dimensional conversion is accomplished electrically without any mechanical movement. Moreover, the nonimaging structure of the proposed method increases the expressible depth range considerably. We explain the method of operation and present experimental results.

  16. Automated Patient Identification and Localization Error Detection Using 2-Dimensional to 3-Dimensional Registration of Kilovoltage X-Ray Setup Images

    International Nuclear Information System (INIS)

    Lamb, James M.; Agazaryan, Nzhde; Low, Daniel A.

    2013-01-01

    Purpose: To determine whether kilovoltage x-ray projection radiation therapy setup images could be used to perform patient identification and detect gross errors in patient setup using a computer algorithm. Methods and Materials: Three patient cohorts treated using a commercially available image guided radiation therapy (IGRT) system that uses 2-dimensional to 3-dimensional (2D-3D) image registration were retrospectively analyzed: a group of 100 cranial radiation therapy patients, a group of 100 prostate cancer patients, and a group of 83 patients treated for spinal lesions. The setup images were acquired using fixed in-room kilovoltage imaging systems. In the prostate and cranial patient groups, localizations using image registration were performed between computed tomography (CT) simulation images from radiation therapy planning and setup x-ray images corresponding both to the same patient and to different patients. For the spinal patients, localizations were performed to the correct vertebral body, and to an adjacent vertebral body, using planning CTs and setup x-ray images from the same patient. An image similarity measure used by the IGRT system image registration algorithm was extracted from the IGRT system log files and evaluated as a discriminant for error detection. Results: A threshold value of the similarity measure could be chosen to separate correct and incorrect patient matches and correct and incorrect vertebral body localizations with excellent accuracy for these patient cohorts. A 10-fold cross-validation using linear discriminant analysis yielded misclassification probabilities of 0.000, 0.0045, and 0.014 for the cranial, prostate, and spinal cases, respectively. Conclusions: An automated measure of the image similarity between x-ray setup images and corresponding planning CT images could be used to perform automated patient identification and detection of localization errors in radiation therapy treatments

  17. Automated Patient Identification and Localization Error Detection Using 2-Dimensional to 3-Dimensional Registration of Kilovoltage X-Ray Setup Images

    Energy Technology Data Exchange (ETDEWEB)

    Lamb, James M., E-mail: jlamb@mednet.ucla.edu; Agazaryan, Nzhde; Low, Daniel A.

    2013-10-01

    Purpose: To determine whether kilovoltage x-ray projection radiation therapy setup images could be used to perform patient identification and detect gross errors in patient setup using a computer algorithm. Methods and Materials: Three patient cohorts treated using a commercially available image guided radiation therapy (IGRT) system that uses 2-dimensional to 3-dimensional (2D-3D) image registration were retrospectively analyzed: a group of 100 cranial radiation therapy patients, a group of 100 prostate cancer patients, and a group of 83 patients treated for spinal lesions. The setup images were acquired using fixed in-room kilovoltage imaging systems. In the prostate and cranial patient groups, localizations using image registration were performed between computed tomography (CT) simulation images from radiation therapy planning and setup x-ray images corresponding both to the same patient and to different patients. For the spinal patients, localizations were performed to the correct vertebral body, and to an adjacent vertebral body, using planning CTs and setup x-ray images from the same patient. An image similarity measure used by the IGRT system image registration algorithm was extracted from the IGRT system log files and evaluated as a discriminant for error detection. Results: A threshold value of the similarity measure could be chosen to separate correct and incorrect patient matches and correct and incorrect vertebral body localizations with excellent accuracy for these patient cohorts. A 10-fold cross-validation using linear discriminant analysis yielded misclassification probabilities of 0.000, 0.0045, and 0.014 for the cranial, prostate, and spinal cases, respectively. Conclusions: An automated measure of the image similarity between x-ray setup images and corresponding planning CT images could be used to perform automated patient identification and detection of localization errors in radiation therapy treatments.

  18. Automated patient identification and localization error detection using 2-dimensional to 3-dimensional registration of kilovoltage x-ray setup images.

    Science.gov (United States)

    Lamb, James M; Agazaryan, Nzhde; Low, Daniel A

    2013-10-01

    To determine whether kilovoltage x-ray projection radiation therapy setup images could be used to perform patient identification and detect gross errors in patient setup using a computer algorithm. Three patient cohorts treated using a commercially available image guided radiation therapy (IGRT) system that uses 2-dimensional to 3-dimensional (2D-3D) image registration were retrospectively analyzed: a group of 100 cranial radiation therapy patients, a group of 100 prostate cancer patients, and a group of 83 patients treated for spinal lesions. The setup images were acquired using fixed in-room kilovoltage imaging systems. In the prostate and cranial patient groups, localizations using image registration were performed between computed tomography (CT) simulation images from radiation therapy planning and setup x-ray images corresponding both to the same patient and to different patients. For the spinal patients, localizations were performed to the correct vertebral body, and to an adjacent vertebral body, using planning CTs and setup x-ray images from the same patient. An image similarity measure used by the IGRT system image registration algorithm was extracted from the IGRT system log files and evaluated as a discriminant for error detection. A threshold value of the similarity measure could be chosen to separate correct and incorrect patient matches and correct and incorrect vertebral body localizations with excellent accuracy for these patient cohorts. A 10-fold cross-validation using linear discriminant analysis yielded misclassification probabilities of 0.000, 0.0045, and 0.014 for the cranial, prostate, and spinal cases, respectively. An automated measure of the image similarity between x-ray setup images and corresponding planning CT images could be used to perform automated patient identification and detection of localization errors in radiation therapy treatments. Copyright © 2013 Elsevier Inc. All rights reserved.

  19. Multivariate data analysis of two-dimensional gel electrophoresis protein patterns from few samples

    DEFF Research Database (Denmark)

    Jensen, Kristina Nedenskov; Jessen, Flemming; Jørgensen, Bo

    2008-01-01

    One application of 2D gel electrophoresis is to reveal differences in protein pattern between two or more groups of individuals, attributable to their group membership. Multivariate data analytical methods are useful in pinpointing the spots relevant for discrimination by focusing not only...... on single spot differences, but on the covariance structure between proteins. However, their outcome is dependent on data scaling, and they may fail in producing valid multivariate models due to the much higher number of "irrelevant" spots present in the gels. The case where only few gels are available...... and where the aim is to find as many as possible of the group-dependent proteins seems particularly difficult to handle. The present paper investigates such a case regarding the effect of scaling and of prefiltering by univariate nonparametric statistics on the selection of spots. Besides, a modified...

  20. Fully Automated Data Collection Using PAM and the Development of PAM/SPACE Reversible Cassettes

    Science.gov (United States)

    Hiraki, Masahiko; Watanabe, Shokei; Chavas, Leonard M. G.; Yamada, Yusuke; Matsugaki, Naohiro; Igarashi, Noriyuki; Wakatsuki, Soichi; Fujihashi, Masahiro; Miki, Kunio; Baba, Seiki; Ueno, Go; Yamamoto, Masaki; Suzuki, Mamoru; Nakagawa, Atsushi; Watanabe, Nobuhisa; Tanaka, Isao

    2010-06-01

    To remotely control and automatically collect data in high-throughput X-ray data collection experiments, the Structural Biology Research Center at the Photon Factory (PF) developed and installed sample exchange robots PAM (PF Automated Mounting system) at PF macromolecular crystallography beamlines; BL-5A, BL-17A, AR-NW12A and AR-NE3A. We developed and installed software that manages the flow of the automated X-ray experiments; sample exchanges, loop-centering and X-ray diffraction data collection. The fully automated data collection function has been available since February 2009. To identify sample cassettes, PAM employs a two-dimensional bar code reader. New beamlines, BL-1A at the Photon Factory and BL32XU at SPring-8, are currently under construction as part of Targeted Proteins Research Program (TPRP) by the Ministry of Education, Culture, Sports, Science and Technology of Japan. However, different robots, PAM and SPACE (SPring-8 Precise Automatic Cryo-sample Exchanger), will be installed at BL-1A and BL32XU, respectively. For the convenience of the users of both facilities, pins and cassettes for PAM and SPACE are developed as part of the TPRP.

  1. Automated builder and database of protein/membrane complexes for molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Sunhwan Jo

    2007-09-01

    Full Text Available Molecular dynamics simulations of membrane proteins have provided deeper insights into their functions and interactions with surrounding environments at the atomic level. However, compared to solvation of globular proteins, building a realistic protein/membrane complex is still challenging and requires considerable experience with simulation software. Membrane Builder in the CHARMM-GUI website (http://www.charmm-gui.org helps users to build such a complex system using a web browser with a graphical user interface. Through a generalized and automated building process including system size determination as well as generation of lipid bilayer, pore water, bulk water, and ions, a realistic membrane system with virtually any kinds and shapes of membrane proteins can be generated in 5 minutes to 2 hours depending on the system size. Default values that were elaborated and tested extensively are given in each step to provide reasonable options and starting points for both non-expert and expert users. The efficacy of Membrane Builder is illustrated by its applications to 12 transmembrane and 3 interfacial membrane proteins, whose fully equilibrated systems with three different types of lipid molecules (DMPC, DPPC, and POPC and two types of system shapes (rectangular and hexagonal are freely available on the CHARMM-GUI website. One of the most significant advantages of using the web environment is that, if a problem is found, users can go back and re-generate the whole system again before quitting the browser. Therefore, Membrane Builder provides the intuitive and easy way to build and simulate the biologically important membrane system.

  2. Identification of proteins in a human pleural exudate using two-dimensional preparative liquid-phase electrophoresis and matrix-assisted laser desorption/ionization mass spectrometry.

    Science.gov (United States)

    Nilsson, C L; Puchades, M; Westman, A; Blennow, K; Davidsson, P

    1999-01-01

    Pleural effusion may occur in patients suffering from physical trauma or systemic disorders such as infection, inflammation, or cancer. In order to investigate proteins in a pleural exudate from a patient with severe pneumonia, we used a strategy that combined preparative two-dimensional liquid-phase electrophoresis (2-D LPE), matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and Western blotting. Preparative 2-D LPE is based on the same principles as analytical 2-D gel electrophoresis, except that the proteins remain in liquid phase during the entire procedure. In the first dimension, liquid-phase isoelectric focusing allows for the enrichment of proteins in liquid fractions. In the Rotofor cell, large volumes (up to 55 mL) and protein amounts (up to 1-2 g) can be loaded. Several low abundance proteins, cystatin C, haptoglobin, transthyretin, beta2-microglobulin, and transferrin, were detected after liquid-phase isoelectric focusing, through Western blotting analysis, in a pleural exudate (by definition, >25 g/L total protein). Direct MALDI-TOF-MS analysis of proteins in a Rotofor fraction is demonstrated as well. MALDI-TOF-MS analysis of a tryptic digest of a continuous elution sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) fraction confirmed the presence of cystatin C. By applying 2-D LPE, MALDI-TOF-MS, and Western blotting to the analysis of this pleural exudate, we were able to confirm the identity of proteins of potential diagnostic value. Our findings serve to illustrate the usefulness of this combination of methods in the analysis of pathological fluids.

  3. Comparison of protein patterns of xrs-5, a radiosensitive Chinese hamster ovary cell line, and CHO-K1, its radioresistant parent, using two-dimensional gel-electrophoresis

    International Nuclear Information System (INIS)

    Kramer, J.M.

    1991-01-01

    X-ray sensitive strains of Chinese hamster ovary cell lines have been used to analyze radiation repair mechanisms. One cell line, xrs-5, has been shown to be very sensitive to ionizing radiation and radical forming chemical mutagens. This sensitivity is thought to be a result a mutation in the DNA double strand break (DSB) repair mechanism, and its characterization has been a goal of several repair mechanism studies. Using two-dimensional gel electrophoresis, we have detected a protein (MW approximately 55KD) in the DNA/Nuclear Matrix (nucleoid) cell fraction of CHO-Kl cells that is absent in the nucleoid fraction of xrs-5. This protein is present, however, in both CHO-Kl and xrs-5 whole cell protein maps. To determine whether the 55KD protein is responsible for the radiosensitive and defective DSB repair phenotype of xrs-5 cells, studies are now underway to analyze revertants of xrs-5 that are proficient in DSB repair. Furthermore, an effort to sequence the protein in question is planned. 23 refs., 2 figs

  4. Insulin as a model to teach three-dimensional structure of proteins

    Directory of Open Access Journals (Sweden)

    João Batista Teixeira da Rocha

    2018-02-01

    Proteins are the most ubiquitous macromolecules found in the living cells and have innumerous physiological functions. Therefore, it is fundamental to build a solid knowledge about the proteins three dimensional structure to better understand the living state. The hierarchical structure of proteins is usually studied in the undergraduate discipline of Biochemistry. Here we described pedagogical interventions designed to increase the preservice teacher chemistry students’ knowledge about protein structure. The activities were made using alternative and cheap materials to encourage the application of these simple methodologies by the future teachers in the secondary school. From the primary structure of insulin chains, students had to construct a three-dimensional structure of insulin. After the activities, the students highlighted an improvement of their previous knowledge about proteins structure. The construction of a tridimensional model together with other activities seems to be an efficient way to promote the learning about the structure of proteins to undergraduate students. The methodology used was inexpensiveness and simple and it can be used both in the university and in the high-school.

  5. Functional inks and printing of two-dimensional materials.

    Science.gov (United States)

    Hu, Guohua; Kang, Joohoon; Ng, Leonard W T; Zhu, Xiaoxi; Howe, Richard C T; Jones, Christopher G; Hersam, Mark C; Hasan, Tawfique

    2018-05-08

    Graphene and related two-dimensional materials provide an ideal platform for next generation disruptive technologies and applications. Exploiting these solution-processed two-dimensional materials in printing can accelerate this development by allowing additive patterning on both rigid and conformable substrates for flexible device design and large-scale, high-speed, cost-effective manufacturing. In this review, we summarise the current progress on ink formulation of two-dimensional materials and the printable applications enabled by them. We also present our perspectives on their research and technological future prospects.

  6. One and two-dimensional electrophoresis of fast axonally-transported proteins in rat nerves following acrylamide and 2,5-hexanedione exposure

    International Nuclear Information System (INIS)

    Sickles, D.W.

    1990-01-01

    Transient and repeated deficiencies in protein delivery to the axon are observed following injections of acrylamide (ACR) and 2,5-hexanedione (2,5-HD) (Sickles DW, Neurotoxicology 10: 91;103, 1989; Neurosci Abstr 14:1219, 1988). We have furthered these studies by measuring the effects of single 50 mg/kg ACR and 4 nmole/kg 2,5-HD injections on the quantity of select fast-transported proteins. Proteins were radiolabelled with 3H-leucine injections of the DRG; 1 and 2 dimensional gels were used for separation of the sciatic nerve (9-45mm distal to the ganglion) homogenates. Scintillation counting demonstrated that transport of all proteins studied were affected by both toxicants. Some variation in effect was observed; a direct correlation between molecular weight (r=0.71) and original quantity of radiolabel (r=0.80) with the percent reduction in transport was observed. Some apparent increases in transport of certain proteins were observed on the 2D gels; but this may indicate a change in the isoelectric points of these transported proteins

  7. K-FIX: a computer program for transient, two-dimensional, two-fluid flow. THREED: an extension of the K-FIX code for three-dimensional calculations

    International Nuclear Information System (INIS)

    Rivard, W.C.; Torrey, M.D.

    1978-10-01

    The transient, two-dimensional, two-fluid code K-FIX has been extended to perform three-dimensional calculations. This capability is achieved by adding five modification sets of FORTRAN statements to the basic two-dimensional code. The modifications are listed and described, and a complete listing of the three-dimensional code is provided. Results of an example problem are provided for verification

  8. Characterisation of ribosomal proteins from HeLa and Krebs II mouse ascites tumor cells by different two-dimensional polyacrylamide gel electrophoresis techniques

    DEFF Research Database (Denmark)

    Issinger, O G; Beier, H

    1978-01-01

    Electrophoresis of ribosomal proteins according to Kaltschmidt and Wittmann, 1970a, b (pH 8.6/pH 4.5 urea system) yielded 29 proteins for the small subunits and 35 and 37 proteins for the large subunits of Krebs II ascites and HeLa ribosomes, respectively. Analysis of the proteins according...... to a modified technique by Mets and Bogorad (1974) (pH 4.5/pH 8.6 SDS system) revealed 28 and 29 proteins in the small subunits and 37 and 38 proteins in the large subunits of Krebs II ascites and HeLa ribosomes. The molecular weights of the individual proteins were determined by: 1. "three-dimensional" gel...... using the pH 4.5/pH 8.6 SDS system. The molecular weights Krebs II ascites and HeLa ribosomal proteins are compared with those obtained by other authors for different mammalian species....

  9. Two-dimensional critical phenomena

    International Nuclear Information System (INIS)

    Saleur, H.

    1987-09-01

    Two dimensional critical systems are studied using transformation to free fields and conformal invariance methods. The relations between the two approaches are also studied. The analytical results obtained generally depend on universality hypotheses or on renormalization group trajectories which are not established rigorously, so numerical verifications, mainly using the transfer matrix approach, are presented. The exact determination of critical exponents; the partition functions of critical models on toruses; and results as the critical point is approached are discussed [fr

  10. Comparative two-dimensional gel analysis and microsequencing identifies gelsolin as one of the most prominent downregulated markers of transformed human fibroblast and epithelial cells

    DEFF Research Database (Denmark)

    Vandekerckhove, J; Bauw, G; Vancompernolle, K

    1990-01-01

    A systematic comparison of the protein synthesis patterns of cultured normal and transformed human fibroblasts and epithelial cells, using two-dimensional gel protein analysis combined with computerized imaging and data acquisition, identified a 90-kD protein (SSP 5714) as one of the most striking...... downregulated markers typical of the transformed state. Using the information stored in the comprehensive human cellular protein database, we found this protein strongly expressed in several fetal tissues and one of them, epidermis, served as a source for preparative two-dimensional gel electrophoresis. Partial...... and by coelectrophoresis with purified human gelsolin. These results suggest that an important regulatory protein of the microfilament system may play a role in defining the phenotype of transformed human fibroblast and epithelial cells in culture. Udgivelsesdato: 1990-Jul...

  11. Comparative two-dimensional gel analysis and microsequencing identifies gelsolin as one of the most prominent downregulated markers of transformed human fibroblast and epithelial cells

    DEFF Research Database (Denmark)

    Vandekerckhove, J; Bauw, G; Vancompernolle, K

    1990-01-01

    downregulated markers typical of the transformed state. Using the information stored in the comprehensive human cellular protein database, we found this protein strongly expressed in several fetal tissues and one of them, epidermis, served as a source for preparative two-dimensional gel electrophoresis. Partial......A systematic comparison of the protein synthesis patterns of cultured normal and transformed human fibroblasts and epithelial cells, using two-dimensional gel protein analysis combined with computerized imaging and data acquisition, identified a 90-kD protein (SSP 5714) as one of the most striking...... and by coelectrophoresis with purified human gelsolin. These results suggest that an important regulatory protein of the microfilament system may play a role in defining the phenotype of transformed human fibroblast and epithelial cells in culture. Udgivelsesdato: 1990-Jul...

  12. Comparing the photophysics of the two forms of the Orange Carotenoid Protein using 2D electronic spectroscopy

    Directory of Open Access Journals (Sweden)

    Mathies R.A.

    2013-03-01

    Full Text Available Broadband two-dimensional electronic spectroscopy is applied to investigate the photophysics of the photoactive orange carotenoid protein, which is involved in nonphotochemical quenching in cyanobacteria. Differences in dynamics between the light and dark forms arise from the different structure of the carotenoid in the protein pocket, with consequences for the biological role of the two forms.

  13. Automated extraction of pleural effusion in three-dimensional thoracic CT images

    Science.gov (United States)

    Kido, Shoji; Tsunomori, Akinori

    2009-02-01

    It is important for diagnosis of pulmonary diseases to measure volume of accumulating pleural effusion in threedimensional thoracic CT images quantitatively. However, automated extraction of pulmonary effusion correctly is difficult. Conventional extraction algorithm using a gray-level based threshold can not extract pleural effusion from thoracic wall or mediastinum correctly, because density of pleural effusion in CT images is similar to those of thoracic wall or mediastinum. So, we have developed an automated extraction method of pulmonary effusion by use of extracting lung area with pleural effusion. Our method used a template of lung obtained from a normal lung for segmentation of lungs with pleural effusions. Registration process consisted of two steps. First step was a global matching processing between normal and abnormal lungs of organs such as bronchi, bones (ribs, sternum and vertebrae) and upper surfaces of livers which were extracted using a region-growing algorithm. Second step was a local matching processing between normal and abnormal lungs which were deformed by the parameter obtained from the global matching processing. Finally, we segmented a lung with pleural effusion by use of the template which was deformed by two parameters obtained from the global matching processing and the local matching processing. We compared our method with a conventional extraction method using a gray-level based threshold and two published methods. The extraction rates of pleural effusions obtained from our method were much higher than those obtained from other methods. Automated extraction method of pulmonary effusion by use of extracting lung area with pleural effusion is promising for diagnosis of pulmonary diseases by providing quantitative volume of accumulating pleural effusion.

  14. Characterization of pH titration shifts for all the nonlabile proton resonances in a protein by two-dimensional NMR: The case of mouse epidermal growth factor

    International Nuclear Information System (INIS)

    Kohda, Daisuke; Sawada, Toshie; Inagaki, Fuyuhiko

    1991-01-01

    The pH titration shifts for all the nonlabile proton resonances in a 53-residue protein (mouse epidermal growth factor) were measured in the p 2 H range 1.5-9 with two-dimensional (2D) 1 H NMR. The 2D NMR pH titration experiment made it possible to determine the pK values for all the ionizable group which were titrated in the pH range 1.5-9 in the protein. The pK values of the nine ionizable groups (α-amino group, four Asp, two Glu, one His, and α-carboxyl group) were found to be near their normal values. The 2D titration experiment also provided a detailed description of the pH-dependent behavior of the proton chemical shifts and enabled us to characterize the pH-dependent changes of protein conformation. Analysis of the pH-dependent shifts of ca. 200 proton resonances offered evidence of conformational changes in slightly basic pH solution: The deprotonation of the N-terminal α-amino group induced a widespread conformational change over the β-sheet structure in the protein, while the effects of deprotonation of the His22 imidazole group were relatively localized. The authors found that the 2D NMR pH titration experiment is a powerful tool for investigating the structural and dynamic properties of proteins

  15. Two-dimensional capillary origami

    Energy Technology Data Exchange (ETDEWEB)

    Brubaker, N.D., E-mail: nbrubaker@math.arizona.edu; Lega, J., E-mail: lega@math.arizona.edu

    2016-01-08

    We describe a global approach to the problem of capillary origami that captures all unfolded equilibrium configurations in the two-dimensional setting where the drop is not required to fully wet the flexible plate. We provide bifurcation diagrams showing the level of encapsulation of each equilibrium configuration as a function of the volume of liquid that it contains, as well as plots representing the energy of each equilibrium branch. These diagrams indicate at what volume level the liquid drop ceases to be attached to the endpoints of the plate, which depends on the value of the contact angle. As in the case of pinned contact points, three different parameter regimes are identified, one of which predicts instantaneous encapsulation for small initial volumes of liquid. - Highlights: • Full solution set of the two-dimensional capillary origami problem. • Fluid does not necessarily wet the entire plate. • Global energy approach provides exact differential equations satisfied by minimizers. • Bifurcation diagrams highlight three different regimes. • Conditions for spontaneous encapsulation are identified.

  16. Two-dimensional capillary origami

    International Nuclear Information System (INIS)

    Brubaker, N.D.; Lega, J.

    2016-01-01

    We describe a global approach to the problem of capillary origami that captures all unfolded equilibrium configurations in the two-dimensional setting where the drop is not required to fully wet the flexible plate. We provide bifurcation diagrams showing the level of encapsulation of each equilibrium configuration as a function of the volume of liquid that it contains, as well as plots representing the energy of each equilibrium branch. These diagrams indicate at what volume level the liquid drop ceases to be attached to the endpoints of the plate, which depends on the value of the contact angle. As in the case of pinned contact points, three different parameter regimes are identified, one of which predicts instantaneous encapsulation for small initial volumes of liquid. - Highlights: • Full solution set of the two-dimensional capillary origami problem. • Fluid does not necessarily wet the entire plate. • Global energy approach provides exact differential equations satisfied by minimizers. • Bifurcation diagrams highlight three different regimes. • Conditions for spontaneous encapsulation are identified.

  17. Two-dimensional black holes and non-commutative spaces

    International Nuclear Information System (INIS)

    Sadeghi, J.

    2008-01-01

    We study the effects of non-commutative spaces on two-dimensional black hole. The event horizon of two-dimensional black hole is obtained in non-commutative space up to second order of perturbative calculations. A lower limit for the non-commutativity parameter is also obtained. The observer in that limit in contrast to commutative case see two horizon

  18. Two-Dimensional Raman Correlation Analysis of Diseased Esophagus in a Rat

    Science.gov (United States)

    Takanezawa, Sota; Morita, Shin-ichi; Maruyama, Atsushi; Murakami, Takurou N.; Kawashima, Norimichi; Endo, Hiroyuki; Iijima, Katsunori; Asakura, Tohru; Shimosegawa, Tooru; Sato, Hidetoshi

    2010-07-01

    Generalized two-dimensional (2D) Raman correlation analysis effectively distinguished a benign tumor from normal tissue. Line profiling Raman spectra of a rat esophagus, including a benign tumor, were measured and the generalized 2D synchronous and asynchronous spectra were calculated. In the autocorrelation area of the amide I band of proteins in the asynchronous map, a cross-like pattern was observed. A simulation study indicated that the pattern was caused by a sharp band component in the amide I band region. We considered that the benign tumor corresponded to the sharp component.

  19. Robust and automated three-dimensional segmentation of densely packed cell nuclei in different biological specimens with Lines-of-Sight decomposition.

    Science.gov (United States)

    Mathew, B; Schmitz, A; Muñoz-Descalzo, S; Ansari, N; Pampaloni, F; Stelzer, E H K; Fischer, S C

    2015-06-08

    Due to the large amount of data produced by advanced microscopy, automated image analysis is crucial in modern biology. Most applications require reliable cell nuclei segmentation. However, in many biological specimens cell nuclei are densely packed and appear to touch one another in the images. Therefore, a major difficulty of three-dimensional cell nuclei segmentation is the decomposition of cell nuclei that apparently touch each other. Current methods are highly adapted to a certain biological specimen or a specific microscope. They do not ensure similarly accurate segmentation performance, i.e. their robustness for different datasets is not guaranteed. Hence, these methods require elaborate adjustments to each dataset. We present an advanced three-dimensional cell nuclei segmentation algorithm that is accurate and robust. Our approach combines local adaptive pre-processing with decomposition based on Lines-of-Sight (LoS) to separate apparently touching cell nuclei into approximately convex parts. We demonstrate the superior performance of our algorithm using data from different specimens recorded with different microscopes. The three-dimensional images were recorded with confocal and light sheet-based fluorescence microscopes. The specimens are an early mouse embryo and two different cellular spheroids. We compared the segmentation accuracy of our algorithm with ground truth data for the test images and results from state-of-the-art methods. The analysis shows that our method is accurate throughout all test datasets (mean F-measure: 91%) whereas the other methods each failed for at least one dataset (F-measure≤69%). Furthermore, nuclei volume measurements are improved for LoS decomposition. The state-of-the-art methods required laborious adjustments of parameter values to achieve these results. Our LoS algorithm did not require parameter value adjustments. The accurate performance was achieved with one fixed set of parameter values. We developed a novel and

  20. Two-dimensional Navier-Stokes turbulence in bounded domains

    NARCIS (Netherlands)

    Clercx, H.J.H.; van Heijst, G.J.F.

    In this review we will discuss recent experimental and numerical results of quasi-two-dimensional decaying and forced Navier–Stokes turbulence in bounded domains. We will give a concise overview of developments in two-dimensional turbulence research, with emphasis on the progress made during the

  1. Two-dimensional Navier-Stokes turbulence in bounded domains

    NARCIS (Netherlands)

    Clercx, H.J.H.; Heijst, van G.J.F.

    2009-01-01

    In this review we will discuss recent experimental and numerical results of quasi-two-dimensional decaying and forced Navier–Stokes turbulence in bounded domains. We will give a concise overview of developments in two-dimensional turbulence research, with emphasis on the progress made during the

  2. Piezoelectricity in Two-Dimensional Materials

    KAUST Repository

    Wu, Tao; Zhang, Hua

    2015-01-01

    Powering up 2D materials: Recent experimental studies confirmed the existence of piezoelectricity - the conversion of mechanical stress into electricity - in two-dimensional single-layer MoS2 nanosheets. The results represent a milestone towards

  3. Solution of the two-dimensional spectral factorization problem

    Science.gov (United States)

    Lawton, W. M.

    1985-01-01

    An approximation theorem is proven which solves a classic problem in two-dimensional (2-D) filter theory. The theorem shows that any continuous two-dimensional spectrum can be uniformly approximated by the squared modulus of a recursively stable finite trigonometric polynomial supported on a nonsymmetric half-plane.

  4. Quantitative real-time PCR as a sensitive protein-protein interaction quantification method and a partial solution for non-accessible autoactivator and false-negative molecule analysis in the yeast two-hybrid system.

    Science.gov (United States)

    Maier, Richard H; Maier, Christina J; Hintner, Helmut; Bauer, Johann W; Onder, Kamil

    2012-12-01

    Many functional proteomic experiments make use of high-throughput technologies such as mass spectrometry combined with two-dimensional polyacrylamide gel electrophoresis and the yeast two-hybrid (Y2H) system. Currently there are even automated versions of the Y2H system available that can be used for proteome-wide research. The Y2H system has the capacity to deliver a profusion of Y2H positive colonies from a single library screen. However, subsequent analysis of these numerous primary candidates with complementary methods can be overwhelming. Therefore, a method to select the most promising candidates with strong interaction properties might be useful to reduce the number of candidates requiring further analysis. The method described here offers a new way of quantifying and rating the performance of positive Y2H candidates. The novelty lies in the detection and measurement of mRNA expression instead of proteins or conventional Y2H genetic reporters. This method correlates well with the direct genetic reporter readouts usually used in the Y2H system, and has greater sensitivity for detecting and quantifying protein-protein interactions (PPIs) than the conventional Y2H system, as demonstrated by detection of the Y2H false-negative PPI of RXR/PPARG. Approximately 20% of all proteins are not suitable for the Y2H system, the so-called autoactivators. A further advantage of this method is the possibility to evaluate molecules that usually cannot be analyzed in the Y2H system, exemplified by a VDR-LXXLL motif peptide interaction. Copyright © 2012 Elsevier Inc. All rights reserved.

  5. Development of Two-Dimensional NMR

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 11. Development of Two-Dimensional NMR: Strucure Determination of Biomolecules in Solution. Anil Kumar. General Article Volume 20 Issue 11 November 2015 pp 995-1002 ...

  6. ONE-DIMENSIONAL AND TWO-DIMENSIONAL LEADERSHIP STYLES

    OpenAIRE

    Nikola Stefanović

    2007-01-01

    In order to motivate their group members to perform certain tasks, leaders use different leadership styles. These styles are based on leaders' backgrounds, knowledge, values, experiences, and expectations. The one-dimensional styles, used by many world leaders, are autocratic and democratic styles. These styles lie on the two opposite sides of the leadership spectrum. In order to precisely define the leadership styles on the spectrum between the autocratic leadership style and the democratic ...

  7. 78 FR 44142 - Modification of Two National Customs Automation Program (NCAP) Tests Concerning Automated...

    Science.gov (United States)

    2013-07-23

    ... Customs Automation Program (NCAP) Tests Concerning Automated Commercial Environment (ACE) Document Image... (CBP's) plan to modify the National Customs Automation Program (NCAP) tests concerning document imaging... entry process by reducing the number of data elements required to obtain release for cargo transported...

  8. Infrared magneto-spectroscopy of two-dimensional and three-dimensional massless fermions: A comparison

    Energy Technology Data Exchange (ETDEWEB)

    Orlita, M., E-mail: milan.orlita@lncmi.cnrs.fr [Laboratoire National des Champs Magnétiques Intenses, CNRS-UJF-UPS-INSA, 38042 Grenoble (France); Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2 (Czech Republic); Faugeras, C.; Barra, A.-L.; Martinez, G.; Potemski, M. [Laboratoire National des Champs Magnétiques Intenses, CNRS-UJF-UPS-INSA, 38042 Grenoble (France); Basko, D. M. [LPMMC UMR 5493, Université Grenoble 1/CNRS, B.P. 166, 38042 Grenoble (France); Zholudev, M. S. [Laboratoire Charles Coulomb (L2C), UMR CNRS 5221, GIS-TERALAB, Université Montpellier II, 34095 Montpellier (France); Institute for Physics of Microstructures, RAS, Nizhny Novgorod GSP-105 603950 (Russian Federation); Teppe, F.; Knap, W. [Laboratoire Charles Coulomb (L2C), UMR CNRS 5221, GIS-TERALAB, Université Montpellier II, 34095 Montpellier (France); Gavrilenko, V. I. [Institute for Physics of Microstructures, RAS, Nizhny Novgorod GSP-105 603950 (Russian Federation); Mikhailov, N. N.; Dvoretskii, S. A. [A.V. Rzhanov Institute of Semiconductor Physics, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090 (Russian Federation); Neugebauer, P. [Institut für Physikalische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart (Germany); Berger, C. [School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332 (United States); Institut Néel/CNRS-UJF BP 166, F-38042 Grenoble Cedex 9 (France); Heer, W. A. de [School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332 (United States)

    2015-03-21

    Here, we report on a magneto-optical study of two distinct systems hosting massless fermions—two-dimensional graphene and three-dimensional HgCdTe tuned to the zero band gap condition at the point of the semiconductor-to-semimetal topological transition. Both materials exhibit, in the quantum regime, a fairly rich magneto-optical response, which is composed from a series of intra- and interband inter-Landau level resonances with for massless fermions typical √(B) dependence. The impact of the system's dimensionality and of the strength of the spin-orbit interaction on the optical response is also discussed.

  9. One-dimensional versus two-dimensional electronic states in vicinal surfaces

    International Nuclear Information System (INIS)

    Ortega, J E; Ruiz-Oses, M; Cordon, J; Mugarza, A; Kuntze, J; Schiller, F

    2005-01-01

    Vicinal surfaces with periodic arrays of steps are among the simplest lateral nanostructures. In particular, noble metal surfaces vicinal to the (1 1 1) plane are excellent test systems to explore the basic electronic properties in one-dimensional superlattices by means of angular photoemission. These surfaces are characterized by strong emissions from free-electron-like surface states that scatter at step edges. Thereby, the two-dimensional surface state displays superlattice band folding and, depending on the step lattice constant d, it splits into one-dimensional quantum well levels. Here we use high-resolution, angle-resolved photoemission to analyse surface states in a variety of samples, in trying to illustrate the changes in surface state bands as a function of d

  10. Quantitative two-dimensional gel electrophoresis analysis of human fibroblasts transformed by ras oncogenes.

    Science.gov (United States)

    Miller, M J; Maher, V M; McCormick, J J

    1992-11-01

    Quantitative two-dimensional gel electrophoresis was used to compare the cellular protein patterns of a normal foreskin-derived human fibroblasts cell line (LG1) and three immortal derivatives of LG1. One derivative, designated MSU-1.1 VO, was selected for its ability to grow in the absence of serum and is non-tumorigenic in athymic mice. The other two strains were selected for focus-formation following transfection with either Ha-ras or N-ras oncogenes and form high grade malignant tumors. Correspondence and cluster analysis provided a nonbiased estimate of the relative similarity of the different two-dimensional patterns. These techniques separated the gel patterns into three distinct classes: LG1, MSU-1.1 VO, and the ras transformed cell strains. The MSU-1.1 VO cells were more closely related to the parental LG1 than to the ras-transformed cells. The differences between the three classes were primarily quantitative in nature: 16% of the spots demonstrated statistically significant changes (P 2) in the rate of incorporation of radioactive amino acids. The patterns from the two ras-transformed cell strains were similar, and variations in the expression of proteins that occurred between the separate experiments obscured consistent differences between the Ha-ras and N-ras transformed cells. However, while only 9 out of 758 spots were classified as different (1%), correspondence analysis could consistently separate the two ras transformants. One of these spots was five times more intense in the Ha-ras transformed cells than the N-ras.(ABSTRACT TRUNCATED AT 250 WORDS)

  11. Densis. Densimetric representation of two-dimensional matrices

    International Nuclear Information System (INIS)

    Los Arcos Merino, J.M.

    1978-01-01

    Densis is a Fortran V program which allows off-line control of a Calcomp digital plotter, to represent a two-dimensional matrix of numerical elements in the form of a variable shading intensity map in two colours. Each matrix element is associated to a square of a grid which is traced over by lines whose number is a function of the element value according to a selected scale. Program features, subroutine structure and running instructions, are described. Some typical results, for gamma-gamma coincidence experimental data and a sampled two-dimensional function, are indicated. (author)

  12. Full automation and validation of a flexible ELISA platform for host cell protein and protein A impurity detection in biopharmaceuticals.

    Science.gov (United States)

    Rey, Guillaume; Wendeler, Markus W

    2012-11-01

    Monitoring host cell protein (HCP) and protein A impurities is important to ensure successful development of recombinant antibody drugs. Here, we report the full automation and validation of an ELISA platform on a robotic system that allows the detection of Chinese hamster ovary (CHO) HCPs and residual protein A of in-process control samples and final drug substance. The ELISA setup is designed to serve three main goals: high sample throughput, high quality of results, and sample handling flexibility. The processing of analysis requests, determination of optimal sample dilutions, and calculation of impurity content is performed automatically by a spreadsheet. Up to 48 samples in three unspiked and spiked dilutions each are processed within 24 h. The dilution of each sample is individually prepared based on the drug concentration and the expected impurity content. Adaptable dilution protocols allow the analysis of sample dilutions ranging from 1:2 to 1:2×10(7). The validity of results is assessed by automatic testing for dilutional linearity and spike recovery for each sample. This automated impurity ELISA facilitates multi-project process development, is easily adaptable to other impurity ELISA formats, and increases analytical capacity by combining flexible sample handling with high data quality. Copyright © 2012 Elsevier B.V. All rights reserved.

  13. Resonance fluorescence based two- and three-dimensional atom localization

    Science.gov (United States)

    Wahab, Abdul; Rahmatullah; Qamar, Sajid

    2016-06-01

    Two- and three-dimensional atom localization in a two-level atom-field system via resonance fluorescence is suggested. For the two-dimensional localization, the atom interacts with two orthogonal standing-wave fields, whereas for the three-dimensional atom localization, the atom interacts with three orthogonal standing-wave fields. The effect of the detuning and phase shifts associated with the corresponding standing-wave fields is investigated. A precision enhancement in position measurement of the single atom can be noticed via the control of the detuning and phase shifts.

  14. Toward two-dimensional search engines

    International Nuclear Information System (INIS)

    Ermann, L; Shepelyansky, D L; Chepelianskii, A D

    2012-01-01

    We study the statistical properties of various directed networks using ranking of their nodes based on the dominant vectors of the Google matrix known as PageRank and CheiRank. On average PageRank orders nodes proportionally to a number of ingoing links, while CheiRank orders nodes proportionally to a number of outgoing links. In this way, the ranking of nodes becomes two dimensional which paves the way for the development of two-dimensional search engines of a new type. Statistical properties of information flow on the PageRank–CheiRank plane are analyzed for networks of British, French and Italian universities, Wikipedia, Linux Kernel, gene regulation and other networks. A special emphasis is done for British universities networks using the large database publicly available in the UK. Methods of spam links control are also analyzed. (paper)

  15. Subjective figure reversal in two- and three-dimensional perceptual space.

    Science.gov (United States)

    Radilová, J; Radil-Weiss, T

    1984-08-01

    A permanently illuminated pattern of Mach's truncated pyramid can be perceived according to the experimental instruction given, either as a three-dimensional reversible figure with spontaneously changing convex and concave interpretation (in one experiment), or as a two-dimensional reversible figure-ground pattern (in another experiment). The reversal rate was about twice as slow, without the subjects being aware of it, if it was perceived as a three-dimensional figure compared to the situation when it was perceived as two-dimensional. It may be hypothetized that in the three-dimensional case, the process of perception requires more sequential steps than in the two-dimensional one.

  16. Protein-Based Three-Dimensional Memories and Associative Processors

    Science.gov (United States)

    Birge, Robert

    2008-03-01

    The field of bioelectronics has benefited from the fact that nature has often solved problems of a similar nature to those which must be solved to create molecular electronic or photonic devices that operate with efficiency and reliability. Retinal proteins show great promise in bioelectronic devices because they operate with high efficiency (˜0.65%), high cyclicity (>10^7), operate over an extended wavelength range (360 -- 630 nm) and can convert light into changes in voltage, pH, absorption or refractive index. This talk will focus on a retinal protein called bacteriorhodopsin, the proton pump of the organism Halobacterium salinarum. Two memories based on this protein will be described. The first is an optical three-dimensional memory. This memory stores information using volume elements (voxels), and provides as much as a thousand-fold improvement in effective capacity over current technology. A unique branching reaction of a variant of bacteriorhodopsin is used to turn each protein into an optically addressed latched AND gate. Although three working prototypes have been developed, a number of cost/performance and architectural issues must be resolved prior to commercialization. The major issue is that the native protein provides a very inefficient branching reaction. Genetic engineering has improved performance by nearly 500-fold, but a further order of magnitude improvement is needed. Protein-based holographic associative memories will also be discussed. The human brain stores and retrieves information via association, and human intelligence is intimately connected to the nature and enormous capacity of this associative search and retrieval process. To a first order approximation, creativity can be viewed as the association of two seemingly disparate concepts to form a totally new construct. Thus, artificial intelligence requires large scale associative memories. Current computer hardware does not provide an optimal environment for creating artificial

  17. Completion of autobuilt protein models using a database of protein fragments

    International Nuclear Information System (INIS)

    Cowtan, Kevin

    2012-01-01

    Two developments in the process of automated protein model building in the Buccaneer software are described: the use of a database of protein fragments in improving the model completeness and the assembly of disconnected chain fragments into complete molecules. Two developments in the process of automated protein model building in the Buccaneer software are presented. A general-purpose library for protein fragments of arbitrary size is described, with a highly optimized search method allowing the use of a larger database than in previous work. The problem of assembling an autobuilt model into complete chains is discussed. This involves the assembly of disconnected chain fragments into complete molecules and the use of the database of protein fragments in improving the model completeness. Assembly of fragments into molecules is a standard step in existing model-building software, but the methods have not received detailed discussion in the literature

  18. Two multi-dimensional uncertainty relations

    International Nuclear Information System (INIS)

    Skala, L; Kapsa, V

    2008-01-01

    Two multi-dimensional uncertainty relations, one related to the probability density and the other one related to the probability density current, are derived and discussed. Both relations are stronger than the usual uncertainty relations for the coordinates and momentum

  19. Mechanical exfoliation of two-dimensional materials

    Science.gov (United States)

    Gao, Enlai; Lin, Shao-Zhen; Qin, Zhao; Buehler, Markus J.; Feng, Xi-Qiao; Xu, Zhiping

    2018-06-01

    Two-dimensional materials such as graphene and transition metal dichalcogenides have been identified and drawn much attention over the last few years for their unique structural and electronic properties. However, their rise begins only after these materials are successfully isolated from their layered assemblies or adhesive substrates into individual monolayers. Mechanical exfoliation and transfer are the most successful techniques to obtain high-quality single- or few-layer nanocrystals from their native multi-layer structures or their substrate for growth, which involves interfacial peeling and intralayer tearing processes that are controlled by material properties, geometry and the kinetics of exfoliation. This procedure is rationalized in this work through theoretical analysis and atomistic simulations. We propose a criterion to assess the feasibility for the exfoliation of two-dimensional sheets from an adhesive substrate without fracturing itself, and explore the effects of material and interface properties, as well as the geometrical, kinetic factors on the peeling behaviors and the torn morphology. This multi-scale approach elucidates the microscopic mechanism of the mechanical processes, offering predictive models and tools for the design of experimental procedures to obtain single- or few-layer two-dimensional materials and structures.

  20. The Buccaneer software for automated model building. 1. Tracing protein chains.

    Science.gov (United States)

    Cowtan, Kevin

    2006-09-01

    A new technique for the automated tracing of protein chains in experimental electron-density maps is described. The technique relies on the repeated application of an oriented electron-density likelihood target function to identify likely C(alpha) positions. This function is applied both in the location of a few promising ;seed' positions in the map and to grow those initial C(alpha) positions into extended chain fragments. Techniques for assembling the chain fragments into an initial chain trace are discussed.

  1. A novel approach to sequence validating protein expression clones with automated decision making

    Directory of Open Access Journals (Sweden)

    Mohr Stephanie E

    2007-06-01

    Full Text Available Abstract Background Whereas the molecular assembly of protein expression clones is readily automated and routinely accomplished in high throughput, sequence verification of these clones is still largely performed manually, an arduous and time consuming process. The ultimate goal of validation is to determine if a given plasmid clone matches its reference sequence sufficiently to be "acceptable" for use in protein expression experiments. Given the accelerating increase in availability of tens of thousands of unverified clones, there is a strong demand for rapid, efficient and accurate software that automates clone validation. Results We have developed an Automated Clone Evaluation (ACE system – the first comprehensive, multi-platform, web-based plasmid sequence verification software package. ACE automates the clone verification process by defining each clone sequence as a list of multidimensional discrepancy objects, each describing a difference between the clone and its expected sequence including the resulting polypeptide consequences. To evaluate clones automatically, this list can be compared against user acceptance criteria that specify the allowable number of discrepancies of each type. This strategy allows users to re-evaluate the same set of clones against different acceptance criteria as needed for use in other experiments. ACE manages the entire sequence validation process including contig management, identifying and annotating discrepancies, determining if discrepancies correspond to polymorphisms and clone finishing. Designed to manage thousands of clones simultaneously, ACE maintains a relational database to store information about clones at various completion stages, project processing parameters and acceptance criteria. In a direct comparison, the automated analysis by ACE took less time and was more accurate than a manual analysis of a 93 gene clone set. Conclusion ACE was designed to facilitate high throughput clone sequence

  2. Two-dimensional gel electrophoresis data in support of leaf comparative proteomics of two citrus species differing in boron-tolerance

    Directory of Open Access Journals (Sweden)

    Wen Sang

    2015-09-01

    Full Text Available Here, we provide the data from a comparative proteomics approach used to investigate the response of boron (B-tolerant ‘Xuegan’ (Citrus sinensis and B-intolerant ‘Sour pummelo’ (Citrus grandis leaves to B-toxicity. Using two-dimensional gel electrophoresis (2-DE technique, we identified 50 and 45 protein species with a fold change of more than 1.5 and a P-value of less than 0.05 from B-toxic C. sinensis and C. grandis leaves. These B-toxicity-responsive protein species were mainly involved in carbohydrate and energy metabolism, antioxidation and detoxification, stress responses, coenzyme biosynthesis, protein and amino acid metabolism, signal transduction, cell transport, cytoskeleton, nucleotide metabolism, and cell cycle and DNA processing. A detailed analysis of this data may be obtained from Sang et al. (J. Proteomics 114 (2015[1].

  3. Proteomic profiling of human pleural effusion using two-dimensional nano liquid chromatography tandem mass spectrometry.

    Science.gov (United States)

    Tyan, Yu-Chang; Wu, Hsin-Yi; Lai, Wu-Wei; Su, Wu-Chou; Liao, Pao-Chi

    2005-01-01

    Pleural effusion, an accumulation of pleural fluid, contains proteins originated from plasma filtrate and, especially when tissues are damaged, parenchyma interstitial spaces of lungs and/or other organs. This study details protein profiles in human pleural effusion from 43 lung adenocarcinoma patients by a two-dimensional nano-high performance liquid chromatography electrospray ionization tandem mass spectrometry (2D nano-HPLC-ESI-MS/MS) system. The experimental results revealed the identification of 1415 unique proteins from human pleural effusion. Among these 124 proteins identified with higher confidence levels, some proteins have not been reported in plasma and may represent proteins specifically present in pleural effusion. These proteins are valuable for mass identification of differentially expressed proteins involved in proteomics database and screening biomarker to further study in human lung adenocarcinoma. The significance of the use of proteomics analysis of human pleural fluid for the search of new lung cancer marker proteins, and for their simultaneous display and analysis in patients suffering from lung disorders has been examined.

  4. Finding protein sites using machine learning methods

    Directory of Open Access Journals (Sweden)

    Jaime Leonardo Bobadilla Molina

    2003-07-01

    Full Text Available The increasing amount of protein three-dimensional (3D structures determined by x-ray and NMR technologies as well as structures predicted by computational methods results in the need for automated methods to provide inital annotations. We have developed a new method for recognizing sites in three-dimensional protein structures. Our method is based on a previosly reported algorithm for creating descriptions of protein microenviroments using physical and chemical properties at multiple levels of detail. The recognition method takes three inputs: 1. A set of control nonsites that share some structural or functional role. 2. A set of control nonsites that lack this role. 3. A single query site. A support vector machine classifier is built using feature vectors where each component represents a property in a given volume. Validation against an independent test set shows that this recognition approach has high sensitivity and specificity. We also describe the results of scanning four calcium binding proteins (with the calcium removed using a three dimensional grid of probe points at 1.25 angstrom spacing. The system finds the sites in the proteins giving points at or near the blinding sites. Our results show that property based descriptions along with support vector machines can be used for recognizing protein sites in unannotated structures.

  5. Asymptotics for Two-dimensional Atoms

    DEFF Research Database (Denmark)

    Nam, Phan Thanh; Portmann, Fabian; Solovej, Jan Philip

    2012-01-01

    We prove that the ground state energy of an atom confined to two dimensions with an infinitely heavy nucleus of charge $Z>0$ and $N$ quantum electrons of charge -1 is $E(N,Z)=-{1/2}Z^2\\ln Z+(E^{\\TF}(\\lambda)+{1/2}c^{\\rm H})Z^2+o(Z^2)$ when $Z\\to \\infty$ and $N/Z\\to \\lambda$, where $E^{\\TF}(\\lambd......We prove that the ground state energy of an atom confined to two dimensions with an infinitely heavy nucleus of charge $Z>0$ and $N$ quantum electrons of charge -1 is $E(N,Z)=-{1/2}Z^2\\ln Z+(E^{\\TF}(\\lambda)+{1/2}c^{\\rm H})Z^2+o(Z^2)$ when $Z\\to \\infty$ and $N/Z\\to \\lambda$, where $E......^{\\TF}(\\lambda)$ is given by a Thomas-Fermi type variational problem and $c^{\\rm H}\\approx -2.2339$ is an explicit constant. We also show that the radius of a two-dimensional neutral atom is unbounded when $Z\\to \\infty$, which is contrary to the expected behavior of three-dimensional atoms....

  6. Two Automated Techniques for Carotid Lumen Diameter Measurement: Regional versus Boundary Approaches.

    Science.gov (United States)

    Araki, Tadashi; Kumar, P Krishna; Suri, Harman S; Ikeda, Nobutaka; Gupta, Ajay; Saba, Luca; Rajan, Jeny; Lavra, Francesco; Sharma, Aditya M; Shafique, Shoaib; Nicolaides, Andrew; Laird, John R; Suri, Jasjit S

    2016-07-01

    The degree of stenosis in the carotid artery can be predicted using automated carotid lumen diameter (LD) measured from B-mode ultrasound images. Systolic velocity-based methods for measurement of LD are subjective. With the advancement of high resolution imaging, image-based methods have started to emerge. However, they require robust image analysis for accurate LD measurement. This paper presents two different algorithms for automated segmentation of the lumen borders in carotid ultrasound images. Both algorithms are modeled as a two stage process. Stage one consists of a global-based model using scale-space framework for the extraction of the region of interest. This stage is common to both algorithms. Stage two is modeled using a local-based strategy that extracts the lumen interfaces. At this stage, the algorithm-1 is modeled as a region-based strategy using a classification framework, whereas the algorithm-2 is modeled as a boundary-based approach that uses the level set framework. Two sets of databases (DB), Japan DB (JDB) (202 patients, 404 images) and Hong Kong DB (HKDB) (50 patients, 300 images) were used in this study. Two trained neuroradiologists performed manual LD tracings. The mean automated LD measured was 6.35 ± 0.95 mm for JDB and 6.20 ± 1.35 mm for HKDB. The precision-of-merit was: 97.4 % and 98.0 % w.r.t to two manual tracings for JDB and 99.7 % and 97.9 % w.r.t to two manual tracings for HKDB. Statistical tests such as ANOVA, Chi-Squared, T-test, and Mann-Whitney test were conducted to show the stability and reliability of the automated techniques.

  7. Comprehensive two-dimensional gas chromatography and food sensory properties: potential and challenges.

    Science.gov (United States)

    Cordero, Chiara; Kiefl, Johannes; Schieberle, Peter; Reichenbach, Stephen E; Bicchi, Carlo

    2015-01-01

    Modern omics disciplines dealing with food flavor focus the analytical efforts on the elucidation of sensory-active compounds, including all possible stimuli of multimodal perception (aroma, taste, texture, etc.) by means of a comprehensive, integrated treatment of sample constituents, such as physicochemical properties, concentration in the matrix, and sensory properties (odor/taste quality, perception threshold). Such analyses require detailed profiling of known bioactive components as well as advanced fingerprinting techniques to catalog sample constituents comprehensively, quantitatively, and comparably across samples. Multidimensional analytical platforms support comprehensive investigations required for flavor analysis by combining information on analytes' identities, physicochemical behaviors (volatility, polarity, partition coefficient, and solubility), concentration, and odor quality. Unlike other omics, flavor metabolomics and sensomics include the final output of the biological phenomenon (i.e., sensory perceptions) as an additional analytical dimension, which is specifically and exclusively triggered by the chemicals analyzed. However, advanced omics platforms, which are multidimensional by definition, pose challenging issues not only in terms of coupling with detection systems and sample preparation, but also in terms of data elaboration and processing. The large number of variables collected during each analytical run provides a high level of information, but requires appropriate strategies to exploit fully this potential. This review focuses on advances in comprehensive two-dimensional gas chromatography and analytical platforms combining two-dimensional gas chromatography with olfactometry, chemometrics, and quantitative assays for food sensory analysis to assess the quality of a given product. We review instrumental advances and couplings, automation in sample preparation, data elaboration, and a selection of applications.

  8. Fully automated reconstruction of three-dimensional vascular tree structures from two orthogonal views using computational algorithms and productionrules

    Science.gov (United States)

    Liu, Iching; Sun, Ying

    1992-10-01

    A system for reconstructing 3-D vascular structure from two orthogonally projected images is presented. The formidable problem of matching segments between two views is solved using knowledge of the epipolar constraint and the similarity of segment geometry and connectivity. The knowledge is represented in a rule-based system, which also controls the operation of several computational algorithms for tracking segments in each image, representing 2-D segments with directed graphs, and reconstructing 3-D segments from matching 2-D segment pairs. Uncertain reasoning governs the interaction between segmentation and matching; it also provides a framework for resolving the matching ambiguities in an iterative way. The system was implemented in the C language and the C Language Integrated Production System (CLIPS) expert system shell. Using video images of a tree model, the standard deviation of reconstructed centerlines was estimated to be 0.8 mm (1.7 mm) when the view direction was parallel (perpendicular) to the epipolar plane. Feasibility of clinical use was shown using x-ray angiograms of a human chest phantom. The correspondence of vessel segments between two views was accurate. Computational time for the entire reconstruction process was under 30 s on a workstation. A fully automated system for two-view reconstruction that does not require the a priori knowledge of vascular anatomy is demonstrated.

  9. Spin dynamics in a two-dimensional quantum gas

    DEFF Research Database (Denmark)

    Pedersen, Poul Lindholm; Gajdacz, Miroslav; Deuretzbacher, Frank

    2014-01-01

    We have investigated spin dynamics in a two-dimensional quantum gas. Through spin-changing collisions, two clouds with opposite spin orientations are spontaneously created in a Bose-Einstein condensate. After ballistic expansion, both clouds acquire ring-shaped density distributions with superimp......We have investigated spin dynamics in a two-dimensional quantum gas. Through spin-changing collisions, two clouds with opposite spin orientations are spontaneously created in a Bose-Einstein condensate. After ballistic expansion, both clouds acquire ring-shaped density distributions...

  10. Quantum oscillations in quasi-two-dimensional conductors

    CERN Document Server

    Galbova, O

    2002-01-01

    The electronic absorption of sound waves in quasi-two-dimensional conductors in strong magnetic fields, is investigated theoretically. A longitudinal acoustic wave, propagating along the normal n-> to the layer of quasi-two-dimensional conductor (k-> = left brace 0,0,k right brace; u-> = left brace 0,0,u right brace) in magnetic field (B-> = left brace 0, 0, B right brace), is considered. The quasiclassical approach for this geometry is of no interest, due to the absence of interaction between electromagnetic and acoustic waves. The problem is of interest in strong magnetic field when quantization of the charge carriers energy levels takes place. The quantum oscillations in the sound absorption coefficient, as a function of the magnetic field, are theoretically observed. The experimental study of the quantum oscillations in quasi-two-dimensional conductors makes it possible to solve the inverse problem of determining from experimental data the extrema closed sections of the Fermi surface by a plane p sub z = ...

  11. Third sound in one and two dimensional modulated structures

    International Nuclear Information System (INIS)

    Komuro, T.; Kawashima, H., Shirahama, K.; Kono, K.

    1996-01-01

    An experimental technique is developed to study acoustic transmission in one and two dimensional modulated structures by employing third sound of a superfluid helium film. In particular, the Penrose lattice, which is a two dimensional quasiperiodic structure, is studied. In two dimensions, the scattering of third sound is weaker than in one dimension. Nevertheless, the authors find that the transmission spectrum in the Penrose lattice, which is a two dimensional prototype of the quasicrystal, is observable if the helium film thickness is chosen around 5 atomic layers. The transmission spectra in the Penrose lattice are explained in terms of dynamical theory of diffraction

  12. The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013

    Energy Technology Data Exchange (ETDEWEB)

    Rosato, Antonio [University of Florence, Department of Chemistry and Magnetic Resonance Center (Italy); Vranken, Wim [Vrije Universiteit Brussel, Structural Biology Brussels (Belgium); Fogh, Rasmus H.; Ragan, Timothy J. [University of Leicester, Department of Biochemistry, School of Biological Sciences (United Kingdom); Tejero, Roberto [Universidad de Valencia, Departamento de Química Física (Spain); Pederson, Kari; Lee, Hsiau-Wei; Prestegard, James H. [University of Georgia, Complex Carbohydrate Research Center and Northeast Structural Genomics Consortium (United States); Yee, Adelinda; Wu, Bin; Lemak, Alexander; Houliston, Scott; Arrowsmith, Cheryl H. [University of Toronto, Department of Medical Biophysics, Cancer Genomics and Proteomics, Ontario Cancer Institute, Northeast Structural Genomics Consortium (Canada); Kennedy, Michael [Miami University, Department of Chemistry and Biochemistry, Northeast Structural Genomics Consortium (United States); Acton, Thomas B.; Xiao, Rong; Liu, Gaohua; Montelione, Gaetano T., E-mail: guy@cabm.rutgers.edu [The State University of New Jersey, Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers (United States); Vuister, Geerten W., E-mail: gv29@le.ac.uk [University of Leicester, Department of Biochemistry, School of Biological Sciences (United Kingdom)

    2015-08-15

    The second round of the community-wide initiative Critical Assessment of automated Structure Determination of Proteins by NMR (CASD-NMR-2013) comprised ten blind target datasets, consisting of unprocessed spectral data, assigned chemical shift lists and unassigned NOESY peak and RDC lists, that were made available in both curated (i.e. manually refined) or un-curated (i.e. automatically generated) form. Ten structure calculation programs, using fully automated protocols only, generated a total of 164 three-dimensional structures (entries) for the ten targets, sometimes using both curated and un-curated lists to generate multiple entries for a single target. The accuracy of the entries could be established by comparing them to the corresponding manually solved structure of each target, which was not available at the time the data were provided. Across the entire data set, 71 % of all entries submitted achieved an accuracy relative to the reference NMR structure better than 1.5 Å. Methods based on NOESY peak lists achieved even better results with up to 100 % of the entries within the 1.5 Å threshold for some programs. However, some methods did not converge for some targets using un-curated NOESY peak lists. Over 90 % of the entries achieved an accuracy better than the more relaxed threshold of 2.5 Å that was used in the previous CASD-NMR-2010 round. Comparisons between entries generated with un-curated versus curated peaks show only marginal improvements for the latter in those cases where both calculations converged.

  13. The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013

    International Nuclear Information System (INIS)

    Rosato, Antonio; Vranken, Wim; Fogh, Rasmus H.; Ragan, Timothy J.; Tejero, Roberto; Pederson, Kari; Lee, Hsiau-Wei; Prestegard, James H.; Yee, Adelinda; Wu, Bin; Lemak, Alexander; Houliston, Scott; Arrowsmith, Cheryl H.; Kennedy, Michael; Acton, Thomas B.; Xiao, Rong; Liu, Gaohua; Montelione, Gaetano T.; Vuister, Geerten W.

    2015-01-01

    The second round of the community-wide initiative Critical Assessment of automated Structure Determination of Proteins by NMR (CASD-NMR-2013) comprised ten blind target datasets, consisting of unprocessed spectral data, assigned chemical shift lists and unassigned NOESY peak and RDC lists, that were made available in both curated (i.e. manually refined) or un-curated (i.e. automatically generated) form. Ten structure calculation programs, using fully automated protocols only, generated a total of 164 three-dimensional structures (entries) for the ten targets, sometimes using both curated and un-curated lists to generate multiple entries for a single target. The accuracy of the entries could be established by comparing them to the corresponding manually solved structure of each target, which was not available at the time the data were provided. Across the entire data set, 71 % of all entries submitted achieved an accuracy relative to the reference NMR structure better than 1.5 Å. Methods based on NOESY peak lists achieved even better results with up to 100 % of the entries within the 1.5 Å threshold for some programs. However, some methods did not converge for some targets using un-curated NOESY peak lists. Over 90 % of the entries achieved an accuracy better than the more relaxed threshold of 2.5 Å that was used in the previous CASD-NMR-2010 round. Comparisons between entries generated with un-curated versus curated peaks show only marginal improvements for the latter in those cases where both calculations converged

  14. Two-dimensional membranes in motion

    NARCIS (Netherlands)

    Davidovikj, D.

    2018-01-01

    This thesis revolves around nanomechanical membranes made of suspended two - dimensional materials. Chapters 1-3 give an introduction to the field of 2D-based nanomechanical devices together with an overview of the underlying physics and the measurementtools used in subsequent chapters. The research

  15. Comparison of first dimension IPG and NEPHGE techniques in two-dimensional gel electrophoresis experiment with cytosolic unfolded protein response in Saccharomyces cerevisiae

    Science.gov (United States)

    2013-01-01

    Background Two-dimensional gel electrophoresis (2DE) is one of the most popular methods in proteomics. Currently, most 2DE experiments are performed using immobilized pH gradient (IPG) in the first dimension; however, some laboratories still use carrier ampholytes-based isoelectric focusing technique. The aim of this study was to directly compare IPG-based and non-equilibrium pH gradient electrophoresis (NEPHGE)-based 2DE techniques by using the same samples and identical second dimension procedures. We have used commercially available Invitrogen ZOOM IPGRunner and WITAvision systems for IPG and NEPHGE, respectively. The effectiveness of IPG-based and NEPHGE-based 2DE methods was compared by analysing differential protein expression during cytosolic unfolded protein response (UPR-Cyto) in Saccharomyces cerevisiae. Results Protein loss during 2DE procedure was higher in IPG-based method, especially for basic (pI > 7) proteins. Overall reproducibility of spots was slightly better in NEPHGE-based method; however, there was a marked difference when evaluating basic and acidic protein spots. Using Coomassie staining, about half of detected basic protein spots were not reproducible by IPG-based 2DE, whereas NEPHGE-based method showed excellent reproducibility in the basic gel zone. The reproducibility of acidic proteins was similar in both methods. Absolute and relative volume variability of separate protein spots was comparable in both 2DE techniques. Regarding proteomic analysis of UPR-Cyto, the results exemplified parameters of general comparison of the methods. New highly basic protein Sis1p, overexpressed during UPR-Cyto stress, was identified by NEPHGE-based 2DE method, whereas IPG-based method showed unreliable results in the basic pI range and did not provide any new information on basic UPR-Cyto proteins. In the acidic range, the main UPR-Cyto proteins were detected and quantified by both methods. The drawback of NEPHGE-based 2DE method is its failure to

  16. Automation of C-terminal sequence analysis of 2D-PAGE separated proteins

    Directory of Open Access Journals (Sweden)

    P.P. Moerman

    2014-06-01

    Full Text Available Experimental assignment of the protein termini remains essential to define the functional protein structure. Here, we report on the improvement of a proteomic C-terminal sequence analysis method. The approach aims to discriminate the C-terminal peptide in a CNBr-digest where Met-Xxx peptide bonds are cleaved in internal peptides ending at a homoserine lactone (hsl-derivative. pH-dependent partial opening of the lactone ring results in the formation of doublets for all internal peptides. C-terminal peptides are distinguished as singlet peaks by MALDI-TOF MS and MS/MS is then used for their identification. We present a fully automated protocol established on a robotic liquid-handling station.

  17. Numerical calculation on a two-step subdiffusion behavior of lateral protein movement in plasma membranes

    Science.gov (United States)

    Sumi, Tomonari; Okumoto, Atsushi; Goto, Hitoshi; Sekino, Hideo

    2017-10-01

    A two-step subdiffusion behavior of lateral movement of transmembrane proteins in plasma membranes has been observed by using single-molecule experiments. A nested double-compartment model where large compartments are divided into several smaller ones has been proposed in order to explain this observation. These compartments are considered to be delimited by membrane-skeleton "fences" and membrane-protein "pickets" bound to the fences. We perform numerical simulations of a master equation using a simple two-dimensional lattice model to investigate the heterogeneous diffusion dynamics behavior of transmembrane proteins within plasma membranes. We show that the experimentally observed two-step subdiffusion process can be described using fence and picket models combined with decreased local diffusivity of transmembrane proteins in the vicinity of the pickets. This allows us to explain the two-step subdiffusion behavior without explicitly introducing nested double compartments.

  18. Solving structures of protein complexes by molecular replacement with Phaser

    International Nuclear Information System (INIS)

    McCoy, Airlie J.

    2006-01-01

    Four case studies in using maximum-likelihood molecular replacement, as implemented in the program Phaser, to solve structures of protein complexes are described. Molecular replacement (MR) generally becomes more difficult as the number of components in the asymmetric unit requiring separate MR models (i.e. the dimensionality of the search) increases. When the proportion of the total scattering contributed by each search component is small, the signal in the search for each component in isolation is weak or non-existent. Maximum-likelihood MR functions enable complex asymmetric units to be built up from individual components with a ‘tree search with pruning’ approach. This method, as implemented in the automated search procedure of the program Phaser, has been very successful in solving many previously intractable MR problems. However, there are a number of cases in which the automated search procedure of Phaser is suboptimal or encounters difficulties. These include cases where there are a large number of copies of the same component in the asymmetric unit or where the components of the asymmetric unit have greatly varying B factors. Two case studies are presented to illustrate how Phaser can be used to best advantage in the standard ‘automated MR’ mode and two case studies are used to show how to modify the automated search strategy for problematic cases

  19. Incorrectness of conventional one-dimensional parallel thermal resistance circuit model for two-dimensional circular composite pipes

    International Nuclear Information System (INIS)

    Wong, K.-L.; Hsien, T.-L.; Chen, W.-L.; Yu, S.-J.

    2008-01-01

    This study is to prove that two-dimensional steady state heat transfer problems of composite circular pipes cannot be appropriately solved by the conventional one-dimensional parallel thermal resistance circuits (PTRC) model because its interface temperatures are not unique. Thus, the PTRC model is definitely different from its conventional recognized analogy, parallel electrical resistance circuits (PERC) model, which has unique node electric voltages. Two typical composite circular pipe examples are solved by CFD software, and the numerical results are compared with those obtained by the PTRC model. This shows that the PTRC model generates large error. Thus, this conventional model, introduced in most heat transfer text books, cannot be applied to two-dimensional composite circular pipes. On the contrary, an alternative one-dimensional separately series thermal resistance circuit (SSTRC) model is proposed and applied to a two-dimensional composite circular pipe with isothermal boundaries, and acceptable results are returned

  20. Determination of steroids, caffeine and methylparaben in water using solid phase microextraction-comprehensive two dimensional gas chromatography-time of flight mass spectrometry.

    Science.gov (United States)

    Lima Gomes, Paulo C F; Barnes, Brian B; Santos-Neto, Álvaro J; Lancas, Fernando M; Snow, Nicholas H

    2013-07-19

    Analysis of several emerging contaminants (steroids, caffeine and methylparaben) in water using automated solid-phase microextraction with comprehensive two dimensional gas chromatography coupled to time of flight mass spectrometry (SPME-GCxGC-ToF/MS) is presented. Experimental design was used to determine the best SPME extraction conditions and the steroids were not derivatized prior to injection. SPME-GCxGC-ToF/MS provided linear ranges from 0.6 to 1200μgL(-1) and limits of detection and quantitation from 0.02 to 100μgL(-1). A series of river water samples obtained locally were subjected to analysis. SPME-GCxGC-ToF/MS is readily automated, straightforward and competitive with other methods for low level analysis of emerging contaminants. Copyright © 2013 Elsevier B.V. All rights reserved.

  1. Investigation of two different anoxia models by 2-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Wulff, Tune; Jessen, Flemming; Hoffmann, Else Kay

    2006-01-01

    anoxia obtained by NaN3 is a widely used model for simulating anoxia (Ossum et al., 2004). The effects of anoxia were studied by protein expression analysis using 2-dimensional gel electrophoresis followed by MS/MS. In this way we were able to separate more than 1500 protein spots with an apparent range...

  2. Chiral anomaly, fermionic determinant and two dimensional models

    International Nuclear Information System (INIS)

    Rego Monteiro, M.A. do.

    1985-01-01

    The chiral anomaly in random pair dimension is analysed. This anomaly is perturbatively calculated by dimensional regularization method. A new method for non-perturbative Jacobian calculation of a general chiral transformation, 1.e., finite and non-Abelian, is developed. This method is used for non-perturbative chiral anomaly calculation, as an alternative to bosonization of two-dimensional theories for massless fermions and to study the phenomenum of fermion number fractionalization. The fermionic determinant from two-dimensional quantum chromodynamics is also studied, and calculated, exactly, as in decoupling gauge as with out reference to a particular gauge. (M.C.K.) [pt

  3. A two-dimensional Zn coordination polymer with a three-dimensional supramolecular architecture

    Directory of Open Access Journals (Sweden)

    Fuhong Liu

    2017-10-01

    Full Text Available The title compound, poly[bis{μ2-4,4′-bis[(1,2,4-triazol-1-ylmethyl]biphenyl-κ2N4:N4′}bis(nitrato-κOzinc(II], [Zn(NO32(C18H16N62]n, is a two-dimensional zinc coordination polymer constructed from 4,4′-bis[(1H-1,2,4-triazol-1-ylmethyl]-1,1′-biphenyl units. It was synthesized and characterized by elemental analysis and single-crystal X-ray diffraction. The ZnII cation is located on an inversion centre and is coordinated by two O atoms from two symmetry-related nitrate groups and four N atoms from four symmetry-related 4,4′-bis[(1H-1,2,4-triazol-1-ylmethyl]-1,1′-biphenyl ligands, forming a distorted octahedral {ZnN4O2} coordination geometry. The linear 4,4′-bis[(1H-1,2,4-triazol-1-ylmethyl]-1,1′-biphenyl ligand links two ZnII cations, generating two-dimensional layers parallel to the crystallographic (132 plane. The parallel layers are connected by C—H...O, C—H...N, C—H...π and π–π stacking interactions, resulting in a three-dimensional supramolecular architecture.

  4. Theory of the one- and two-dimensional electron gas

    International Nuclear Information System (INIS)

    Emery, V.J.

    1987-01-01

    Two topics are discussed: (1) the competition between 2k/sub F/ and 4k/sub F/ charge state waves in a one-dimensional electron gas and (2) a two-dimensional model of high T/sub c/ superconductivity in the oxides

  5. The inaccuracy of conventional one-dimensional parallel thermal resistance circuit model for two-dimensional composite walls

    International Nuclear Information System (INIS)

    Wong, K.-L.; Hsien, T.-L.; Hsiao, M.-C.; Chen, W.-L.; Lin, K.-C.

    2008-01-01

    This investigation is to show that two-dimensional steady state heat transfer problems of composite walls should not be solved by the conventionally one-dimensional parallel thermal resistance circuits (PTRC) model because the interface temperatures are not unique. Thus PTRC model cannot be used like its conventional recognized analogy, parallel electrical resistance circuits (PERC) model which has the unique node electric voltage. Two typical composite wall examples, solved by CFD software, are used to demonstrate the incorrectness. The numerical results are compared with those obtained by PTRC model, and very large differences are observed between their results. This proves that the application of conventional heat transfer PTRC model to two-dimensional composite walls, introduced in most heat transfer text book, is totally incorrect. An alternative one-dimensional separately series thermal resistance circuit (SSTRC) model is proposed and applied to the two-dimensional composite walls with isothermal boundaries. Results with acceptable accuracy can be obtained by the new model

  6. Two-dimensional fourier transform spectrometer

    Science.gov (United States)

    DeFlores, Lauren; Tokmakoff, Andrei

    2013-09-03

    The present invention relates to a system and methods for acquiring two-dimensional Fourier transform (2D FT) spectra. Overlap of a collinear pulse pair and probe induce a molecular response which is collected by spectral dispersion of the signal modulated probe beam. Simultaneous collection of the molecular response, pulse timing and characteristics permit real time phasing and rapid acquisition of spectra. Full spectra are acquired as a function of pulse pair timings and numerically transformed to achieve the full frequency-frequency spectrum. This method demonstrates the ability to acquire information on molecular dynamics, couplings and structure in a simple apparatus. Multi-dimensional methods can be used for diagnostic and analytical measurements in the biological, biomedical, and chemical fields.

  7. Topological aspect of disclinations in two-dimensional crystals

    International Nuclear Information System (INIS)

    Wei-Kai, Qi; Tao, Zhu; Yong, Chen; Ji-Rong, Ren

    2009-01-01

    By using topological current theory, this paper studies the inner topological structure of disclinations during the melting of two-dimensional systems. From two-dimensional elasticity theory, it finds that there are topological currents for topological defects in homogeneous equation. The evolution of disclinations is studied, and the branch conditions for generating, annihilating, crossing, splitting and merging of disclinations are given. (the physics of elementary particles and fields)

  8. Two-dimensional ranking of Wikipedia articles

    Science.gov (United States)

    Zhirov, A. O.; Zhirov, O. V.; Shepelyansky, D. L.

    2010-10-01

    The Library of Babel, described by Jorge Luis Borges, stores an enormous amount of information. The Library exists ab aeterno. Wikipedia, a free online encyclopaedia, becomes a modern analogue of such a Library. Information retrieval and ranking of Wikipedia articles become the challenge of modern society. While PageRank highlights very well known nodes with many ingoing links, CheiRank highlights very communicative nodes with many outgoing links. In this way the ranking becomes two-dimensional. Using CheiRank and PageRank we analyze the properties of two-dimensional ranking of all Wikipedia English articles and show that it gives their reliable classification with rich and nontrivial features. Detailed studies are done for countries, universities, personalities, physicists, chess players, Dow-Jones companies and other categories.

  9. A two-dimensional proteome reference map of Herbaspirillum seropedicae proteins.

    Science.gov (United States)

    Chaves, Daniela Fojo Seixas; Ferrer, Pércio Pereira; de Souza, Emanuel Maltempi; Gruz, Leonardo Magalhães; Monteiro, Rose Adele; de Oliveira Pedrosa, Fábio

    2007-10-01

    Herbaspirillum seropedicae is an endophytic diazotroph associated with economically important crops such as rice, sugarcane, and wheat. Here, we present a 2-D reference map for H. seropedicae. Using MALDI-TOF-MS we identified 205 spots representing 173 different proteins with a calculated average of 1.18 proteins/gene. Seventeen hypothetical or conserved hypothetical ORFs were shown to code for true gene products. These data will support the genome annotation process and provide a basis on which to undertake comparative proteomic studies.

  10. Finding two-dimensional peaks

    International Nuclear Information System (INIS)

    Silagadze, Z.K.

    2007-01-01

    Two-dimensional generalization of the original peak finding algorithm suggested earlier is given. The ideology of the algorithm emerged from the well-known quantum mechanical tunneling property which enables small bodies to penetrate through narrow potential barriers. We merge this 'quantum' ideology with the philosophy of Particle Swarm Optimization to get the global optimization algorithm which can be called Quantum Swarm Optimization. The functionality of the newborn algorithm is tested on some benchmark optimization problems

  11. Quantum Communication Through a Two-Dimensional Spin Network

    International Nuclear Information System (INIS)

    Wang Zhaoming; Gu Yongjian

    2012-01-01

    We investigate the state or entanglement transfer through a two-dimensional spin network. We show that for state transfer, better fidelity can be gained along the diagonal direction but for entanglement transfer, when the initial entanglement is created along the boundary, the concurrence is more inclined to propagate along the boundary. This behavior is produced by quantum mechanical interference and the communication quality depends on the precise size of the network. For some number of sites, the fidelity in a two-dimensional channel is higher than one-dimensional case. This is an important result for realizing quantum communication through high dimension spin chain networks.

  12. Two-dimensional wave propagation in layered periodic media

    KAUST Repository

    Quezada de Luna, Manuel

    2014-09-16

    We study two-dimensional wave propagation in materials whose properties vary periodically in one direction only. High order homogenization is carried out to derive a dispersive effective medium approximation. One-dimensional materials with constant impedance exhibit no effective dispersion. We show that a new kind of effective dispersion may arise in two dimensions, even in materials with constant impedance. This dispersion is a macroscopic effect of microscopic diffraction caused by spatial variation in the sound speed. We analyze this dispersive effect by using highorder homogenization to derive an anisotropic, dispersive effective medium. We generalize to two dimensions a homogenization approach that has been used previously for one-dimensional problems. Pseudospectral solutions of the effective medium equations agree to high accuracy with finite volume direct numerical simulations of the variable-coeffi cient equations.

  13. Modelling of oscillations in two-dimensional echo-spectra of the Fenna-Matthews-Olson complex

    International Nuclear Information System (INIS)

    Hein, Birgit; Kreisbeck, Christoph; Kramer, Tobias; Rodríguez, Mirta

    2012-01-01

    Recent experimental observations of time-dependent beatings in the two-dimensional echo-spectra of light-harvesting complexes at ambient temperatures have opened up the question of whether coherence and wave-like behaviour play a significant role in photosynthesis. We carry out a numerical study of the absorption and echo-spectra of the Fenna-Matthews-Olson (FMO) complex in Chlorobium tepidum and analyse the requirements in the theoretical model needed to reproduce beatings in the calculated spectra. The energy transfer in the FMO pigment-protein complex is theoretically described by an exciton Hamiltonian coupled to a phonon bath which accounts for the pigments' electronic and vibrational excitations, respectively. We use the hierarchical equations of motions method to treat the strong couplings in a non-perturbative way. We show that the oscillations in the two-dimensional echo-spectra persist in the presence of thermal noise and static disorder. (paper)

  14. Lorentz covariant tempered distributions in two-dimensional space-time

    International Nuclear Information System (INIS)

    Zinov'ev, Yu.M.

    1989-01-01

    The problem of describing Lorentz covariant distributions without any spectral condition has hitherto remained unsolved even for two-dimensional space-time. Attempts to solve this problem have already been made. Zharinov obtained an integral representation for the Laplace transform of Lorentz invariant distributions with support in the product of two-dimensional future light cones. However, this integral representation does not make it possible to obtain a complete description of the corresponding Lorentz invariant distributions. In this paper the author gives a complete description of Lorentz covariant distributions for two-dimensional space-time. No spectral conditions is assumed

  15. Solution-Based Processing and Applications of Two-Dimensional Heterostructures

    Science.gov (United States)

    Hersam, Mark

    Two-dimensional materials have emerged as promising candidates for next-generation electronics and optoelectronics, but advances in scalable nanomanufacturing are required to exploit this potential in real-world technology. This talk will explore methods for improving the uniformity of solution-processed two-dimensional materials with an eye toward realizing dispersions and inks that can be deposited into large-area thin-films. In particular, density gradient ultracentrifugation allows the solution-based isolation of graphene, boron nitride, montmorillonite, and transition metal dichalcogenides (e.g., MoS2, WS2, ReS2, MoSe2, WSe2) with homogeneous thickness down to the atomically thin limit. Similarly, two-dimensional black phosphorus is isolated in organic solvents or deoxygenated aqueous surfactant solutions with the resulting phosphorene nanosheets showing field-effect transistor mobilities and on/off ratios that are comparable to micromechanically exfoliated flakes. By adding cellulosic polymer stabilizers to these dispersions, the rheological properties can be tuned by orders of magnitude, thereby enabling two-dimensional material inks that are compatible with a range of additive manufacturing methods including inkjet, gravure, screen, and 3D printing. The resulting solution-processed two-dimensional heterostructures show promise in several device applications including photodiodes, anti-ambipolar transistors, gate-tunable memristors, and heterojunction photovoltaics.

  16. Validation of commercially available automated canine-specific immunoturbidimetric method for measuring canine C-reactive protein

    DEFF Research Database (Denmark)

    Hillström, Anna; Hagman, Ragnvi; Tvedten, Harold

    2014-01-01

    BACKGROUND: Measurement of C-reactive protein (CRP) is used for diagnosing and monitoring systemic inflammatory disease in canine patients. An automated human immunoturbidimetric assay has been validated for measuring canine CRP, but cross-reactivity with canine CRP is unpredictable. OBJECTIVE......: The purpose of the study was to validate a new automated canine-specific immunoturbidimetric CRP method (Gentian cCRP). METHODS: Studies of imprecision, accuracy, prozone effect, interference, limit of quantification, and stability under different storage conditions were performed. The new method was compared...... with a human CRP assay previously validated for canine CRP determination. Samples from 40 healthy dogs were analyzed to establish a reference interval. RESULTS: Total imprecision was

  17. Assessing the accuracy and reliability of ultrasonographic three-dimensional parathyroid volume measurement in a patient with secondary hyperparathyroidism: a comparison with the two-dimensional conventional method

    Energy Technology Data Exchange (ETDEWEB)

    You, Sung Hye; Son, Gyu Ri; Lee, Nam Joon [Dept. of Radiology, Korea University Anam Hospital, Seoul (Korea, Republic of); Suh, Sangil; Ryoo, In Seon; Seol, Hae Young [Dept. of Radiology, Korea University Guro Hospital, Seoul (Korea, Republic of); Lee, Young Hen; Seo, Hyung Suk [Dept. of Radiology, Korea University Ansan Hospital, Ansan (Korea, Republic of)

    2017-01-15

    The purpose of this study was to investigate the accuracy and reliability of the semi-automated ultrasonographic volume measurement tool, virtual organ computer-aided analysis (VOCAL), for measuring the volume of parathyroid glands. Volume measurements for 40 parathyroid glands were performed in patients with secondary hyperparathyroidism caused by chronic renal failure. The volume of the parathyroid glands was measured twice by experienced radiologists by two-dimensional (2D) and three-dimensional (3D) methods using conventional sonograms and the VOCAL with 30°angle increments before parathyroidectomy. The specimen volume was also measured postoperatively. Intraclass correlation coefficients (ICCs) and the absolute percentage error were used for estimating the reproducibility and accuracy of the two different methods. The ICC value between two measurements of the 2D method and the 3D method was 0.956 and 0.999, respectively. The mean absolute percentage error of the 2D method and the 3D VOCAL technique was 29.56% and 5.78%, respectively. For accuracy and reliability, the plots of the 3D method showed a more compact distribution than those of the 2D method on the Bland-Altman graph. The rotational VOCAL method for measuring the parathyroid gland is more accurate and reliable than the conventional 2D measurement. This VOCAL method could be used as a more reliable follow-up imaging modality in a patient with hyperparathyroidism.

  18. Assessing the accuracy and reliability of ultrasonographic three-dimensional parathyroid volume measurement in a patient with secondary hyperparathyroidism: a comparison with the two-dimensional conventional method

    International Nuclear Information System (INIS)

    You, Sung Hye; Son, Gyu Ri; Lee, Nam Joon; Suh, Sangil; Ryoo, In Seon; Seol, Hae Young; Lee, Young Hen; Seo, Hyung Suk

    2017-01-01

    The purpose of this study was to investigate the accuracy and reliability of the semi-automated ultrasonographic volume measurement tool, virtual organ computer-aided analysis (VOCAL), for measuring the volume of parathyroid glands. Volume measurements for 40 parathyroid glands were performed in patients with secondary hyperparathyroidism caused by chronic renal failure. The volume of the parathyroid glands was measured twice by experienced radiologists by two-dimensional (2D) and three-dimensional (3D) methods using conventional sonograms and the VOCAL with 30°angle increments before parathyroidectomy. The specimen volume was also measured postoperatively. Intraclass correlation coefficients (ICCs) and the absolute percentage error were used for estimating the reproducibility and accuracy of the two different methods. The ICC value between two measurements of the 2D method and the 3D method was 0.956 and 0.999, respectively. The mean absolute percentage error of the 2D method and the 3D VOCAL technique was 29.56% and 5.78%, respectively. For accuracy and reliability, the plots of the 3D method showed a more compact distribution than those of the 2D method on the Bland-Altman graph. The rotational VOCAL method for measuring the parathyroid gland is more accurate and reliable than the conventional 2D measurement. This VOCAL method could be used as a more reliable follow-up imaging modality in a patient with hyperparathyroidism

  19. A Comparison of Two Scoring Methods for an Automated Speech Scoring System

    Science.gov (United States)

    Xi, Xiaoming; Higgins, Derrick; Zechner, Klaus; Williamson, David

    2012-01-01

    This paper compares two alternative scoring methods--multiple regression and classification trees--for an automated speech scoring system used in a practice environment. The two methods were evaluated on two criteria: construct representation and empirical performance in predicting human scores. The empirical performance of the two scoring models…

  20. Inter-layer Cooper pairing of two-dimensional electrons

    International Nuclear Information System (INIS)

    Inoue, Masahiro; Takemori, Tadashi; Yoshizaki, Ryozo; Sakudo, Tunetaro; Ohtaka, Kazuo

    1987-01-01

    The authors point out the possibility that the high transition temperatures of the recently discovered oxide superconductors are dominantly caused by the inter-layer Cooper pairing of two-dimensional electrons that are coupled through the exchange of three-dimensional phonons. (author)

  1. A three-dimensional image processing program for accurate, rapid, and semi-automated segmentation of neuronal somata with dense neurite outgrowth

    Science.gov (United States)

    Ross, James D.; Cullen, D. Kacy; Harris, James P.; LaPlaca, Michelle C.; DeWeerth, Stephen P.

    2015-01-01

    Three-dimensional (3-D) image analysis techniques provide a powerful means to rapidly and accurately assess complex morphological and functional interactions between neural cells. Current software-based identification methods of neural cells generally fall into two applications: (1) segmentation of cell nuclei in high-density constructs or (2) tracing of cell neurites in single cell investigations. We have developed novel methodologies to permit the systematic identification of populations of neuronal somata possessing rich morphological detail and dense neurite arborization throughout thick tissue or 3-D in vitro constructs. The image analysis incorporates several novel automated features for the discrimination of neurites and somata by initially classifying features in 2-D and merging these classifications into 3-D objects; the 3-D reconstructions automatically identify and adjust for over and under segmentation errors. Additionally, the platform provides for software-assisted error corrections to further minimize error. These features attain very accurate cell boundary identifications to handle a wide range of morphological complexities. We validated these tools using confocal z-stacks from thick 3-D neural constructs where neuronal somata had varying degrees of neurite arborization and complexity, achieving an accuracy of ≥95%. We demonstrated the robustness of these algorithms in a more complex arena through the automated segmentation of neural cells in ex vivo brain slices. These novel methods surpass previous techniques by improving the robustness and accuracy by: (1) the ability to process neurites and somata, (2) bidirectional segmentation correction, and (3) validation via software-assisted user input. This 3-D image analysis platform provides valuable tools for the unbiased analysis of neural tissue or tissue surrogates within a 3-D context, appropriate for the study of multi-dimensional cell-cell and cell-extracellular matrix interactions. PMID

  2. Automated selected reaction monitoring software for accurate label-free protein quantification.

    Science.gov (United States)

    Teleman, Johan; Karlsson, Christofer; Waldemarson, Sofia; Hansson, Karin; James, Peter; Malmström, Johan; Levander, Fredrik

    2012-07-06

    Selected reaction monitoring (SRM) is a mass spectrometry method with documented ability to quantify proteins accurately and reproducibly using labeled reference peptides. However, the use of labeled reference peptides becomes impractical if large numbers of peptides are targeted and when high flexibility is desired when selecting peptides. We have developed a label-free quantitative SRM workflow that relies on a new automated algorithm, Anubis, for accurate peak detection. Anubis efficiently removes interfering signals from contaminating peptides to estimate the true signal of the targeted peptides. We evaluated the algorithm on a published multisite data set and achieved results in line with manual data analysis. In complex peptide mixtures from whole proteome digests of Streptococcus pyogenes we achieved a technical variability across the entire proteome abundance range of 6.5-19.2%, which was considerably below the total variation across biological samples. Our results show that the label-free SRM workflow with automated data analysis is feasible for large-scale biological studies, opening up new possibilities for quantitative proteomics and systems biology.

  3. Automated lung nodule classification following automated nodule detection on CT: A serial approach

    International Nuclear Information System (INIS)

    Armato, Samuel G. III; Altman, Michael B.; Wilkie, Joel; Sone, Shusuke; Li, Feng; Doi, Kunio; Roy, Arunabha S.

    2003-01-01

    We have evaluated the performance of an automated classifier applied to the task of differentiating malignant and benign lung nodules in low-dose helical computed tomography (CT) scans acquired as part of a lung cancer screening program. The nodules classified in this manner were initially identified by our automated lung nodule detection method, so that the output of automated lung nodule detection was used as input to automated lung nodule classification. This study begins to narrow the distinction between the 'detection task' and the 'classification task'. Automated lung nodule detection is based on two- and three-dimensional analyses of the CT image data. Gray-level-thresholding techniques are used to identify initial lung nodule candidates, for which morphological and gray-level features are computed. A rule-based approach is applied to reduce the number of nodule candidates that correspond to non-nodules, and the features of remaining candidates are merged through linear discriminant analysis to obtain final detection results. Automated lung nodule classification merges the features of the lung nodule candidates identified by the detection algorithm that correspond to actual nodules through another linear discriminant classifier to distinguish between malignant and benign nodules. The automated classification method was applied to the computerized detection results obtained from a database of 393 low-dose thoracic CT scans containing 470 confirmed lung nodules (69 malignant and 401 benign nodules). Receiver operating characteristic (ROC) analysis was used to evaluate the ability of the classifier to differentiate between nodule candidates that correspond to malignant nodules and nodule candidates that correspond to benign lesions. The area under the ROC curve for this classification task attained a value of 0.79 during a leave-one-out evaluation

  4. Automating tasks in protein structure determination with the clipper python module.

    Science.gov (United States)

    McNicholas, Stuart; Croll, Tristan; Burnley, Tom; Palmer, Colin M; Hoh, Soon Wen; Jenkins, Huw T; Dodson, Eleanor; Cowtan, Kevin; Agirre, Jon

    2018-01-01

    Scripting programming languages provide the fastest means of prototyping complex functionality. Those with a syntax and grammar resembling human language also greatly enhance the maintainability of the produced source code. Furthermore, the combination of a powerful, machine-independent scripting language with binary libraries tailored for each computer architecture allows programs to break free from the tight boundaries of efficiency traditionally associated with scripts. In the present work, we describe how an efficient C++ crystallographic library such as Clipper can be wrapped, adapted and generalized for use in both crystallographic and electron cryo-microscopy applications, scripted with the Python language. We shall also place an emphasis on best practices in automation, illustrating how this can be achieved with this new Python module. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

  5. Two-dimensional capillary electrophoresis: capillary isoelectric focusing and capillary zone electrophoresis with laser-induced fluorescence detection

    Science.gov (United States)

    Dickerson, Jane A.; Ramsay, Lauren M.; Dada, Oluwatosin O.; Cermak, Nathan

    2011-01-01

    Capillary isoelectric focusing and capillary zone electrophoresis are coupled with laser-induced fluorescence detection to create an ultrasensitive two-dimensional separation method for proteins. In this method, two capillaries are joined through a buffer filled interface. Separate power supplies control the potential at the injection end of the first capillary and at the interface; the detector is held at ground potential. Proteins are labeled with the fluorogenic reagent Chromeo P503, which preserves the isoelectric point of the labeled protein. The labeled proteins were mixed with ampholytes and injected into the first dimension capillary. A focusing step was performed with the injection end of the capillary at high pH and the interface at low pH. To mobilize components, the interface was filled with a high pH buffer, which was compatible with the second dimension separation. A fraction was transferred to the second dimension capillary for separation. The process of fraction transfer and second dimension separation was repeated two dozen times. The separation produced a spot capacity of 125. PMID:20603830

  6. Optimal Padding for the Two-Dimensional Fast Fourier Transform

    Science.gov (United States)

    Dean, Bruce H.; Aronstein, David L.; Smith, Jeffrey S.

    2011-01-01

    One-dimensional Fast Fourier Transform (FFT) operations work fastest on grids whose size is divisible by a power of two. Because of this, padding grids (that are not already sized to a power of two) so that their size is the next highest power of two can speed up operations. While this works well for one-dimensional grids, it does not work well for two-dimensional grids. For a two-dimensional grid, there are certain pad sizes that work better than others. Therefore, the need exists to generalize a strategy for determining optimal pad sizes. There are three steps in the FFT algorithm. The first is to perform a one-dimensional transform on each row in the grid. The second step is to transpose the resulting matrix. The third step is to perform a one-dimensional transform on each row in the resulting grid. Steps one and three both benefit from padding the row to the next highest power of two, but the second step needs a novel approach. An algorithm was developed that struck a balance between optimizing the grid pad size with prime factors that are small (which are optimal for one-dimensional operations), and with prime factors that are large (which are optimal for two-dimensional operations). This algorithm optimizes based on average run times, and is not fine-tuned for any specific application. It increases the amount of times that processor-requested data is found in the set-associative processor cache. Cache retrievals are 4-10 times faster than conventional memory retrievals. The tested implementation of the algorithm resulted in faster execution times on all platforms tested, but with varying sized grids. This is because various computer architectures process commands differently. The test grid was 512 512. Using a 540 540 grid on a Pentium V processor, the code ran 30 percent faster. On a PowerPC, a 256x256 grid worked best. A Core2Duo computer preferred either a 1040x1040 (15 percent faster) or a 1008x1008 (30 percent faster) grid. There are many industries that

  7. Surface representations of two- and three-dimensional fluid flow topology

    Science.gov (United States)

    Helman, James L.; Hesselink, Lambertus

    1990-01-01

    We discuss our work using critical point analysis to generate representations of the vector field topology of numerical flow data sets. Critical points are located and characterized in a two-dimensional domain, which may be either a two-dimensional flow field or the tangential velocity field near a three-dimensional body. Tangent curves are then integrated out along the principal directions of certain classes of critical points. The points and curves are linked to form a skeleton representing the two-dimensional vector field topology. When generated from the tangential velocity field near a body in a three-dimensional flow, the skeleton includes the critical points and curves which provide a basis for analyzing the three-dimensional structure of the flow separation. The points along the separation curves in the skeleton are used to start tangent curve integrations to generate surfaces representing the topology of the associated flow separations.

  8. Quasi-integrability and two-dimensional QCD

    International Nuclear Information System (INIS)

    Abdalla, E.; Mohayaee, R.

    1996-10-01

    The notion of integrability in two-dimensional QCD is discussed. We show that in spite of an infinite number of conserved charges, particle production is not entirely suppressed. This phenomenon, which we call quasi-integrability, is explained in terms of quantum corrections to the combined algebra of higher-conserved and spectrum-generating currents. We predict the qualitative form of particle production probabilities and verify that they are in agreement with numerical data. We also discuss four-dimensional self-dual Yang-Mills theory in the light of our results. (author). 25 refs, 4 figs, 1 tab

  9. Two-dimensional QCD in the Coulomb gauge

    International Nuclear Information System (INIS)

    Kalashnikova, Yu.S.; Nefed'ev, A.V.

    2002-01-01

    Various aspects of the 't Hooft model for two-dimensional QCD in the limit of infinite number of colours in the Coulomb gauge are discussed. The properties of mesonic excitations are studied, with special emphasis on the pion. Attention is paid to the dual role of the pion. which, while a genuine qq-bar state, is a Goldstone boson of two-dimensional QCD as well. In particular, the validity of the soft-pion theorems is demonstrated. It is shown that the Coulomb gauge is the most suitable choice for the study of hadronic observables involving pions [ru

  10. Sensitivity analysis explains quasi-one-dimensional current transport in two-dimensional materials

    DEFF Research Database (Denmark)

    Boll, Mads; Lotz, Mikkel Rønne; Hansen, Ole

    2014-01-01

    We demonstrate that the quasi-one-dimensional (1D) current transport, experimentally observed in graphene as measured by a collinear four-point probe in two electrode configurations A and B, can be interpreted using the sensitivity functions of the two electrode configurations (configurations...... A and B represents different pairs of electrodes chosen for current sources and potential measurements). The measured sheet resistance in a four-point probe measurement is averaged over an area determined by the sensitivity function. For a two-dimensional conductor, the sensitivity functions for electrode...... configurations A and B are different. But when the current is forced to flow through a percolation network, e.g., graphene with high density of extended defects, the two sensitivity functions become identical. This is equivalent to a four-point measurement on a line resistor, hence quasi-1D transport...

  11. A humidity sensitive two-dimensional tunable amorphous photonic structure in the outer layer of bivalve ligament from Sunset Siliqua

    International Nuclear Information System (INIS)

    Zhang, Weigang; Zhang, Gangsheng

    2015-01-01

    A humidity sensitive two-dimensional tunable amorphous photonic structure (2D TAPS) in the outer layer of bivalve ligament from Sunset Siliqua (OLLS) was reported in this paper. The structural color and microstructure of OLLS were investigated by reflection spectra and scanning electron microscopy, respectively. The results indicate that the reflection peak wavelength of the wet OLLS blue-shifts from 454 nm to 392 nm with the increasing of air drying time from 0 to 40 min, while the reflectivity decreases gradually and vanishes at last, relevant color changes from blue to black background color. The structural color in the OLLS is produced by a two-dimensional amorphous photonic structure consisting of aligned protein fibers, in which the diameter of protein fiber and the inter-fiber spacing are 101 ± 12 nm. Water can reversibly tune the reflection peak wavelength and reflectivity of this photonic structure, and the regulation achieved through dynamically tuning the interaction between inter-fiber spacing and average refractive index. - Highlights: • A humidity sensitive two-dimensional tunable amorphous photonic structure • Water can reversibly tune the reflection peak wavelength and reflectivity of this photonic structure. • This photonic structure may yield very useful template for artificial structures

  12. A humidity sensitive two-dimensional tunable amorphous photonic structure in the outer layer of bivalve ligament from Sunset Siliqua

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Weigang, E-mail: abczwg15@163.com [College of Materials and Chemical Engineering, Chuzhou University, Chuzhou 239000 (China); Zhang, Gangsheng [College of Material Science and Technology, Guangxi University, Nanning 530004 (China)

    2015-07-01

    A humidity sensitive two-dimensional tunable amorphous photonic structure (2D TAPS) in the outer layer of bivalve ligament from Sunset Siliqua (OLLS) was reported in this paper. The structural color and microstructure of OLLS were investigated by reflection spectra and scanning electron microscopy, respectively. The results indicate that the reflection peak wavelength of the wet OLLS blue-shifts from 454 nm to 392 nm with the increasing of air drying time from 0 to 40 min, while the reflectivity decreases gradually and vanishes at last, relevant color changes from blue to black background color. The structural color in the OLLS is produced by a two-dimensional amorphous photonic structure consisting of aligned protein fibers, in which the diameter of protein fiber and the inter-fiber spacing are 101 ± 12 nm. Water can reversibly tune the reflection peak wavelength and reflectivity of this photonic structure, and the regulation achieved through dynamically tuning the interaction between inter-fiber spacing and average refractive index. - Highlights: • A humidity sensitive two-dimensional tunable amorphous photonic structure • Water can reversibly tune the reflection peak wavelength and reflectivity of this photonic structure. • This photonic structure may yield very useful template for artificial structures.

  13. Advances in establishment and analysis of three-dimensional tumor spheroid-based functional assays for target validation and drug evaluation

    Directory of Open Access Journals (Sweden)

    Vinci Maria

    2012-03-01

    Full Text Available Abstract Background There is overwhelming evidence that in vitro three-dimensional tumor cell cultures more accurately reflect the complex in vivo microenvironment than simple two-dimensional cell monolayers, not least with respect to gene expression profiles, signaling pathway activity and drug sensitivity. However, most currently available three-dimensional techniques are time consuming and/or lack reproducibility; thus standardized and rapid protocols are urgently needed. Results To address this requirement, we have developed a versatile toolkit of reproducible three-dimensional tumor spheroid models for dynamic, automated, quantitative imaging and analysis that are compatible with routine high-throughput preclinical studies. Not only do these microplate methods measure three-dimensional tumor growth, but they have also been significantly enhanced to facilitate a range of functional assays exemplifying additional key hallmarks of cancer, namely cell motility and matrix invasion. Moreover, mutual tissue invasion and angiogenesis is accommodated by coculturing tumor spheroids with murine embryoid bodies within which angiogenic differentiation occurs. Highly malignant human tumor cells were selected to exemplify therapeutic effects of three specific molecularly-targeted agents: PI-103 (phosphatidylinositol-3-kinase (PI3K-mammalian target of rapamycin (mTOR inhibitor, 17-N-allylamino-17-demethoxygeldanamycin (17-AAG (heat shock protein 90 (HSP90 inhibitor and CCT130234 (in-house phospholipase C (PLCγ inhibitor. Fully automated analysis using a Celigo cytometer was validated for tumor spheroid growth and invasion against standard image analysis techniques, with excellent reproducibility and significantly increased throughput. In addition, we discovered key differential sensitivities to targeted agents between two-dimensional and three-dimensional cultures, and also demonstrated enhanced potency of some agents against cell migration

  14. Three-dimensional echocardiography of normal and pathologic mitral valve: a comparison with two-dimensional transesophageal echocardiography

    NARCIS (Netherlands)

    Salustri, A.; Becker, A. E.; van Herwerden, L.; Vletter, W. B.; ten Cate, F. J.; Roelandt, J. R.

    1996-01-01

    This study was done to ascertain whether three-dimensional echocardiography can facilitate the diagnosis of mitral valve abnormalities. The value of the additional information provided by three-dimensional echocardiography compared with two-dimensional multiplane transesophageal echocardiography for

  15. Activación automática de las dimensiones de competencia y sociabilidad en el caso de los estereotipos de género

    Directory of Open Access Journals (Sweden)

    Juan Lupiáñez

    2008-01-01

    Full Text Available Se realizó un estudio experimental, en el que participaron 43 estudiantes de Psicología voluntarios, con el fin de medir la activación de las dimensiones estereotípicas de género, mediante un paradigma de priming como medida indirecta de la estereotipia de género, y bajo condiciones experimentales que limitaban los recursos cognitivos disponibles, maximizando el procesamiento automático. Se utilizaron como dimensiones estereotípicas respecto al género la sociabilidad o expresividad (propia de las mujeres y la competencia o instrumentalidad (propia de los hombres. Se utilizó una tarea de priming en la que los rasgos de competencia y sociabilidad, que los participantes debían categorizar como positivos o negativos, eran precedidos de fotografías de hombres y mujeres. Los resultados mostraron efectos de facilitación para la información estereotípica, apoyando así la hipótesis acerca de la activación automática de las dimensiones estereotípicas (competencia y sociabilidad y demostrando la relevancia de la evaluación de las personas en una determinada dimensión u otra en función de su grupo de género.

  16. Two-Dimensional Motions of Rockets

    Science.gov (United States)

    Kang, Yoonhwan; Bae, Saebyok

    2007-01-01

    We analyse the two-dimensional motions of the rockets for various types of rocket thrusts, the air friction and the gravitation by using a suitable representation of the rocket equation and the numerical calculation. The slope shapes of the rocket trajectories are discussed for the three types of rocket engines. Unlike the projectile motions, the…

  17. Two-Dimensional Theory of Scientific Representation

    Directory of Open Access Journals (Sweden)

    A Yaghmaie

    2013-03-01

    Full Text Available Scientific representation is an interesting topic for philosophers of science, many of whom have recently explored it from different points of view. There are currently two competing approaches to the issue: cognitive and non-cognitive, and each of them claims its own merits over the other. This article tries to provide a hybrid theory of scientific representation, called Two-Dimensional Theory of Scientific Representation, which has the merits of the two accounts and is free of their shortcomings. To do this, we will argue that although scientific representation needs to use the notion of intentionality, such a notion is defined and realized in a simply structural form contrary to what cognitive approach says about intentionality. After a short introduction, the second part of the paper is devoted to introducing theories of scientific representation briefly. In the third part, the structural accounts of representation will be criticized. The next step is to introduce the two-dimensional theory which involves two key components: fixing and structural fitness. It will be argued that fitness is an objective and non-intentional relation, while fixing is intentional.

  18. Comparison of one- and two-dimensional liquid chromatography approaches in the label-free quantitative analysis of Methylocella silvestris.

    Science.gov (United States)

    Patel, Nisha A; Crombie, Andrew; Slade, Susan E; Thalassinos, Konstantinos; Hughes, Chris; Connolly, Joanne B; Langridge, James; Murrell, J Colin; Scrivens, James H

    2012-09-07

    The proteome of the bacterium Methylocella silvestris has been characterized using reversed phase ultra high pressure liquid chromatography (UPLC) and two-dimensional reversed phase (high pH)-reversed phase (low pH) UPLC prior to mass spectrometric analysis. Variations in protein expression levels were identified with the aid of label-free quantification in a study of soluble protein extracts from the organism grown using methane, succinate, or propane as a substrate. The number of first dimensional fractionation steps has been varied for 2D analyses, and the impact on data throughput and quality has been demonstrated. Comparisons have been made regarding required experimental considerations including total loading of biological samples required, instrument time, and resulting data file sizes. The data obtained have been evaluated with respect to number of protein identifications, confidence of assignments, sequence coverage, relative levels of proteins, and dynamic range. Good qualitative and quantitative agreement was observed between the different approaches, and the potential benefits and limitations of the reversed phase-reversed phase UPLC technique in label-free analysis are discussed. A preliminary screen of the protein regulation data has also been performed, providing evidence for a possible propane assimilation route.

  19. Two dimensional crystals of LH2 light-harvesting complexes from Ectothiorhodospira sp. and Rhodobacter capsulatus investigated by electron microscopy

    NARCIS (Netherlands)

    Oling, Frank; Boekema, EJ; deZarate, IO; Visschers, R; vanGrondelle, R; Keegstra, W; Brisson, A; Picorel, R

    1996-01-01

    Two-dimensional crystals of LH2 (B800-850) light-harvesting complexes from Ectothiorhodospira sp, and Rhodobacter capsulatus were obtained by reconstitution of purified protein into phospholipid vesicles and characterized by electron microscopy. The size of the crystals was up to several

  20. Two-dimensional crystals of LH2 light-harvesting complexes from Ectothiorhodospira sp. and Rhodobacter capsulatus investigated by electron microscopy.

    NARCIS (Netherlands)

    Oling, F.; Boekema, E.J.; Ortiz de Zarate, I.; Visschers, R.W.; van Grondelle, R.; Keegstra, W.; Brisson, A.; Picorel, R.

    1996-01-01

    Two-dimensional crystals of LH2 (B800-850) light-harvesting complexes from Ectothiorhodospira sp. and Rhodobacter capsulatus were obtained by reconstitution of purified protein into phospholipid vesicles and characterized by electron microscopy. The size of the crystals was up to several

  1. Two-dimensional Simulations of Correlation Reflectometry in Fusion Plasmas

    International Nuclear Information System (INIS)

    Valeo, E.J.; Kramer, G.J.; Nazikian, R.

    2001-01-01

    A two-dimensional wave propagation code, developed specifically to simulate correlation reflectometry in large-scale fusion plasmas is described. The code makes use of separate computational methods in the vacuum, underdense and reflection regions of the plasma in order to obtain the high computational efficiency necessary for correlation analysis. Simulations of Tokamak Fusion Test Reactor (TFTR) plasma with internal transport barriers are presented and compared with one-dimensional full-wave simulations. It is shown that the two-dimensional simulations are remarkably similar to the results of the one-dimensional full-wave analysis for a wide range of turbulent correlation lengths. Implications for the interpretation of correlation reflectometer measurements in fusion plasma are discussed

  2. Volume scanning three-dimensional display with an inclined two-dimensional display and a mirror scanner

    Science.gov (United States)

    Miyazaki, Daisuke; Kawanishi, Tsuyoshi; Nishimura, Yasuhiro; Matsushita, Kenji

    2001-11-01

    A new three-dimensional display system based on a volume-scanning method is demonstrated. To form a three-dimensional real image, an inclined two-dimensional image is rapidly moved with a mirror scanner while the cross-section patterns of a three-dimensional object are displayed sequentially. A vector-scan CRT display unit is used to obtain a high-resolution image. An optical scanning system is constructed with concave mirrors and a galvanometer mirror. It is confirmed that three-dimensional images, formed by the experimental system, satisfy all the criteria for human stereoscopic vision.

  3. Molecular phylogeny of the hominoid primates as indicated by two-dimensional protein electrophoresis

    International Nuclear Information System (INIS)

    Goldman, D.; Giri, P.R.; O'Brien, J.O.

    1987-01-01

    A molecular phylogeny for the hominoid primates was constructed by using genetic distances from a survey of 383 radiolabeled fibroblast polypeptides resolved by two-dimensional electrophoresis (2DE). An internally consistent matrix of Nei genetic distances was generated on the basis of variants in electrophoretic position. The derived phylogenetic tree indicated a branching sequence, from oldest to most recent, of cercopithecoids (Macaca fascicularis), gibbon-siamang, orangutan, gorilla, and human-chimpanzee. A cladistic analysis of 240 electrophoretic characters that varied between ape species produced an identical tree. Genetic distance measures obtained by 2DE are largely consistent with those generated by other molecular procedures. In addition, the 2DE data set appears to resolve the human-chimpanzee-gorilla trichotomy in favor of a more recent association of chimpanzees and humans

  4. Three-dimensional tokamak equilibria and stellarators with two-dimensional magnetic symmetry

    International Nuclear Information System (INIS)

    Garabedian, P.R.

    1997-01-01

    Three-dimensional computer codes have been developed to simulate equilibrium, stability and transport in tokamaks and stellarators. Bifurcated solutions of the tokamak problem suggest that three-dimensional effects may be more important than has generally been thought. Extensive calculations have led to the discovery of a stellarator configuration with just two field periods and with aspect ratio 3.2 that has a magnetic field spectrum B mn with toroidal symmetry. Numerical studies of equilibrium, stability and transport for this new device, called the Modular Helias-like Heliac 2 (MHH2), will be presented. (author)

  5. A two-stage preventive maintenance optimization model incorporating two-dimensional extended warranty

    International Nuclear Information System (INIS)

    Su, Chun; Wang, Xiaolin

    2016-01-01

    In practice, customers can decide whether to buy an extended warranty or not, at the time of item sale or at the end of the basic warranty. In this paper, by taking into account the moments of customers purchasing two-dimensional extended warranty, the optimization of imperfect preventive maintenance for repairable items is investigated from the manufacturer's perspective. A two-dimensional preventive maintenance strategy is proposed, under which the item is preventively maintained according to a specified age interval or usage interval, whichever occurs first. It is highlighted that when the extended warranty is purchased upon the expiration of the basic warranty, the manufacturer faces a two-stage preventive maintenance optimization problem. Moreover, in the second stage, the possibility of reducing the servicing cost over the extended warranty period is explored by classifying customers on the basis of their usage rates and then providing them with customized preventive maintenance programs. Numerical examples show that offering customized preventive maintenance programs can reduce the manufacturer's warranty cost, while a larger saving in warranty cost comes from encouraging customers to buy the extended warranty at the time of item sale. - Highlights: • A two-dimensional PM strategy is investigated. • Imperfect PM strategy is optimized by considering both two-dimensional BW and EW. • Customers are categorized based on their usage rates throughout the BW period. • Servicing cost of the EW is reduced by offering customized PM programs. • Customers buying the EW at the time of sale is preferred for the manufacturer.

  6. Vibrations of thin piezoelectric shallow shells: Two-dimensional ...

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    In this paper we consider the eigenvalue problem for piezoelectric shallow shells and we show that, as the thickness of the shell goes to zero, the eigensolutions of the three-dimensional piezoelectric shells converge to the eigensolutions of a two- dimensional eigenvalue problem. Keywords. Vibrations; piezoelectricity ...

  7. Two-dimensional turbulent flows on a bounded domain

    NARCIS (Netherlands)

    Kramer, W.

    2006-01-01

    Large-scale flows in the oceans and the atmosphere reveal strong similarities with purely two-dimensional flows. One of the most typical features is the cascade of energy from smaller flow scales towards larger scales. This is opposed to three-dimensional turbulence where larger flow structures

  8. In-Depth Characterization of the Phaseolin Protein Diversity of Common Bean (Phaseolus vulgaris L. Based on Two-Dimensional Electrophoresis and Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    María López-Pedrouso

    2012-01-01

    Full Text Available Phaseolin is the major seed storage protein of common bean. It comprises a complex set of glycoproteins heterogeneous in their polypeptide composition that is encoded by a gene family. Analyses of phaseolin banding patterns by one-dimensional electrophoresis (SDS-PAGE have been central to the current understanding of the diversity of wild and cultivated common beans. In this work, we have carried out a detailed description and interpretation of phaseolin diversity in cultivated common beans of different geographic origins (Mesoamerican and Andean gene pools based on the current two-dimensional electrophoresis (2-DE technology and mass spectrometry (MS. High-quality 2-DE gel images revealed very complex phaseolin patterns across the studied cultivars. Specifically, patterns of phaseolin within cultivars were organized in a horizontal string of multiple isospot pairs varying in isoelectric point and molecular mass. The degree of similarity among phaseolin patterns was estimated from the percentage of spots shared between pairs of cultivars. Analyses of proteomic distances between phaseolin types by non-metrical multidimensional scaling revealed that 2-DE phaseolin profiles are more similar among cultivars belonging to the same gene pool. However, higher differentiation was found among cultivars of the Andean gene pool. Analysis of genetic variations of the PCR-based SCAR marker of phaseolin seed protein was in general agreement with 2-DE phaseolin patterns, but provided supplementary information regarding diversity among cultivars. Furthermore, the molecular basis responsible for the complexity of 2-DE phaseolin patterns was investigated. Thus, identification of phaseolin spots from 2-DE gels by MALDI-TOF and MALDI-TOF/TOF MS showed that each single isospot pair contained only one type (α or β of phaseolin polypeptide, but pairs with higher and lower molecular mass corresponded to α- and β-type polypeptides, respectively. In addition, partial

  9. Intrinsic two-dimensional states on the pristine surface of tellurium

    Science.gov (United States)

    Li, Pengke; Appelbaum, Ian

    2018-05-01

    Atomic chains configured in a helical geometry have fascinating properties, including phases hosting localized bound states in their electronic structure. We show how the zero-dimensional state—bound to the edge of a single one-dimensional helical chain of tellurium atoms—evolves into two-dimensional bands on the c -axis surface of the three-dimensional trigonal bulk. We give an effective Hamiltonian description of its dispersion in k space by exploiting confinement to a virtual bilayer, and elaborate on the diminished role of spin-orbit coupling. These intrinsic gap-penetrating surface bands were neglected in the interpretation of seminal experiments, where two-dimensional transport was otherwise attributed to extrinsic accumulation layers.

  10. Determining the static electronic and vibrational energy correlations via two-dimensional electronic-vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Dong, Hui; Lewis, Nicholas H. C.; Oliver, Thomas A. A.; Fleming, Graham R., E-mail: grfleming@lbl.gov [Department of Chemistry, University of California, Berkeley, California 94720 (United States); Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, Californial 94720 (United States); Kavli Energy NanoSciences Institute at Berkeley, Berkeley, California 94720 (United States)

    2015-05-07

    Changes in the electronic structure of pigments in protein environments and of polar molecules in solution inevitably induce a re-adaption of molecular nuclear structure. Both changes of electronic and vibrational energies can be probed with visible or infrared lasers, such as two-dimensional electronic spectroscopy or vibrational spectroscopy. The extent to which the two changes are correlated remains elusive. The recent demonstration of two-dimensional electronic-vibrational (2DEV) spectroscopy potentially enables a direct measurement of this correlation experimentally. However, it has hitherto been unclear how to characterize the correlation from the spectra. In this paper, we present a theoretical formalism to demonstrate the slope of the nodal line between the excited state absorption and ground state bleach peaks in the spectra as a characterization of the correlation between electronic and vibrational transition energies. We also show the dynamics of the nodal line slope is correlated to the vibrational spectral dynamics. Additionally, we demonstrate the fundamental 2DEV spectral line-shape of a monomer with newly developed response functions.

  11. Iterative Two- and One-Dimensional Methods for Three-Dimensional Neutron Diffusion Calculations

    International Nuclear Information System (INIS)

    Lee, Hyun Chul; Lee, Deokjung; Downar, Thomas J.

    2005-01-01

    Two methods are proposed for solving the three-dimensional neutron diffusion equation by iterating between solutions of the two-dimensional (2-D) radial and one-dimensional (1-D) axial solutions. In the first method, the 2-D/1-D equations are coupled using a current correction factor (CCF) with the average fluxes of the lower and upper planes and the axial net currents at the plane interfaces. In the second method, an analytic expression for the axial net currents at the interface of the planes is used for planar coupling. A comparison of the new methods is made with two previously proposed methods, which use interface net currents and partial currents for planar coupling. A Fourier convergence analysis of the four methods was performed, and results indicate that the two new methods have at least three advantages over the previous methods. First, the new methods are unconditionally stable, whereas the net current method diverges for small axial mesh size. Second, the new methods provide better convergence performance than the other methods in the range of practical mesh sizes. Third, the spectral radii of the new methods asymptotically approach zero as the mesh size increases, while the spectral radius of the partial current method approaches a nonzero value as the mesh size increases. Of the two new methods proposed here, the analytic method provides a smaller spectral radius than the CCF method, but the CCF method has several advantages over the analytic method in practical applications

  12. Construction of two-dimensional quantum chromodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Klimek, S.; Kondracki, W.

    1987-12-01

    We present a sketch of the construction of the functional measure for the SU(2) quantum chromodynamics with one generation of fermions in two-dimensional space-time. The method is based on a detailed analysis of Wilson loops.

  13. A two-dimensional Zn coordination polymer with a three-dimensional supra-molecular architecture.

    Science.gov (United States)

    Liu, Fuhong; Ding, Yan; Li, Qiuyu; Zhang, Liping

    2017-10-01

    The title compound, poly[bis-{μ 2 -4,4'-bis-[(1,2,4-triazol-1-yl)meth-yl]biphenyl-κ 2 N 4 : N 4' }bis-(nitrato-κ O )zinc(II)], [Zn(NO 3 ) 2 (C 18 H 16 N 6 ) 2 ] n , is a two-dimensional zinc coordination polymer constructed from 4,4'-bis-[(1 H -1,2,4-triazol-1-yl)meth-yl]-1,1'-biphenyl units. It was synthesized and characterized by elemental analysis and single-crystal X-ray diffraction. The Zn II cation is located on an inversion centre and is coordinated by two O atoms from two symmetry-related nitrate groups and four N atoms from four symmetry-related 4,4'-bis-[(1 H -1,2,4-triazol-1-yl)meth-yl]-1,1'-biphenyl ligands, forming a distorted octa-hedral {ZnN 4 O 2 } coordination geometry. The linear 4,4'-bis-[(1 H -1,2,4-triazol-1-yl)meth-yl]-1,1'-biphenyl ligand links two Zn II cations, generating two-dimensional layers parallel to the crystallographic (132) plane. The parallel layers are connected by C-H⋯O, C-H⋯N, C-H⋯π and π-π stacking inter-actions, resulting in a three-dimensional supra-molecular architecture.

  14. Complacency and Automation Bias in the Use of Imperfect Automation.

    Science.gov (United States)

    Wickens, Christopher D; Clegg, Benjamin A; Vieane, Alex Z; Sebok, Angelia L

    2015-08-01

    We examine the effects of two different kinds of decision-aiding automation errors on human-automation interaction (HAI), occurring at the first failure following repeated exposure to correctly functioning automation. The two errors are incorrect advice, triggering the automation bias, and missing advice, reflecting complacency. Contrasts between analogous automation errors in alerting systems, rather than decision aiding, have revealed that alerting false alarms are more problematic to HAI than alerting misses are. Prior research in decision aiding, although contrasting the two aiding errors (incorrect vs. missing), has confounded error expectancy. Participants performed an environmental process control simulation with and without decision aiding. For those with the aid, automation dependence was created through several trials of perfect aiding performance, and an unexpected automation error was then imposed in which automation was either gone (one group) or wrong (a second group). A control group received no automation support. The correct aid supported faster and more accurate diagnosis and lower workload. The aid failure degraded all three variables, but "automation wrong" had a much greater effect on accuracy, reflecting the automation bias, than did "automation gone," reflecting the impact of complacency. Some complacency was manifested for automation gone, by a longer latency and more modest reduction in accuracy. Automation wrong, creating the automation bias, appears to be a more problematic form of automation error than automation gone, reflecting complacency. Decision-aiding automation should indicate its lower degree of confidence in uncertain environments to avoid the automation bias. © 2015, Human Factors and Ergonomics Society.

  15. Computerized automated remote inspection system

    International Nuclear Information System (INIS)

    The automated inspection system utilizes a computer to control the location of the ultrasonic transducer, the actual inspection process, the display of the data, and the storage of the data on IBM magnetic tape. This automated inspection equipment provides two major advantages. First, it provides a cost savings, because of the reduced inspection time, made possible by the automation of the data acquisition, processing, and storage equipment. This reduced inspection time is also made possible by a computerized data evaluation aid which speeds data interpretation. In addition, the computer control of the transducer location drive allows the exact duplication of a previously located position or flaw. The second major advantage is that the use of automated inspection equipment also allows a higher-quality inspection, because of the automated data acquisition, processing, and storage. This storage of data, in accurate digital form on IBM magnetic tape, for example, facilitates retrieval for comparison with previous inspection data. The equipment provides a multiplicity of scan data which will provide statistical information on any questionable volume or flaw. An automatic alarm for location of all reportable flaws reduces the probability of operator error. This system has the ability to present data on a cathode ray tube as numerical information, a three-dimensional picture, or ''hard-copy'' sheet. One important advantage of this system is the ability to store large amounts of data in compact magnetic tape reels

  16. Two-dimensional effects in nonlinear Kronig-Penney models

    DEFF Research Database (Denmark)

    Gaididei, Yuri Borisovich; Christiansen, Peter Leth; Rasmussen, Kim

    1997-01-01

    An analysis of two-dimensional (2D) effects in the nonlinear Kronig-Penney model is presented. We establish an effective one-dimensional description of the 2D effects, resulting in a set of pseudodifferential equations. The stationary states of the 2D system and their stability is studied...

  17. Noninteracting beams of ballistic two-dimensional electrons

    International Nuclear Information System (INIS)

    Spector, J.; Stormer, H.L.; Baldwin, K.W.; Pfeiffer, L.N.; West, K.W.

    1991-01-01

    We demonstrate that two beams of two-dimensional ballistic electrons in a GaAs-AlGaAs heterostructure can penetrate each other with negligible mutual interaction analogous to the penetration of two optical beams. This allows electrical signal channels to intersect in the same plane with negligible crosstalk between the channels

  18. Automated four-dimensional Monte Carlo workflow using log files and real-time motion monitoring

    International Nuclear Information System (INIS)

    Sibolt, P; Andersen, C E; Cronholm, R O; Heath, E; Behrens, C F

    2017-01-01

    With emerging techniques for tracking and gating methods in radiotherapy of lung cancer patients, there is an increasing need for efficient four-dimensional Monte Carlo (4DMC) based quality assurance (QA). An automated and flexible workflow for 4DMC QA, based on the 4DdefDOSXYZnrc user code, has been developed in python. The workflow has been tested and verified using an in-house developed dosimetry system comprised of a dynamic thorax phantom constructed for plastic scintillator dosimetry. The workflow is directly compatible with any treatment planning system and can also be triggered by the appearance of linac log files. It has minimum user interaction and, with the use of linac log files, it provides a method for verification of the actually delivered dose in the patient geometry. (paper)

  19. Control Operator for the Two-Dimensional Energized Wave Equation

    Directory of Open Access Journals (Sweden)

    Sunday Augustus REJU

    2006-07-01

    Full Text Available This paper studies the analytical model for the construction of the two-dimensional Energized wave equation. The control operator is given in term of space and time t independent variables. The integral quadratic objective cost functional is subject to the constraint of two-dimensional Energized diffusion, Heat and a source. The operator that shall be obtained extends the Conjugate Gradient method (ECGM as developed by Hestenes et al (1952, [1]. The new operator enables the computation of the penalty cost, optimal controls and state trajectories of the two-dimensional energized wave equation when apply to the Conjugate Gradient methods in (Waziri & Reju, LEJPT & LJS, Issues 9, 2006, [2-4] to appear in this series.

  20. Assay of mouse-cell clones for retrovirus p30 protein by use of an automated solid-state radioimmunoassay

    International Nuclear Information System (INIS)

    Kennel, S.J.; Tnnant, R.W.

    1979-01-01

    A solid-state radioimmunoassay system has been developed that is useful for automated analysis of samples in microtiter plates. Assays for interspecies and type-specific antigenic determinants of the C-type retrovirus protein, p30, have been used to identify clones of cells producing this protein. This method allows testing of at least 1000 clones a day, making it useful for studies of frequencies of virus protein induction, defective virus production, and formation of recombinant viruses

  1. Equilibrium: two-dimensional configurations

    International Nuclear Information System (INIS)

    Anon.

    1987-01-01

    In Chapter 6, the problem of toroidal force balance is addressed in the simplest, nontrivial two-dimensional geometry, that of an axisymmetric torus. A derivation is presented of the Grad-Shafranov equation, the basic equation describing axisymmetric toroidal equilibrium. The solutions to equations provide a complete description of ideal MHD equilibria: radial pressure balance, toroidal force balance, equilibrium Beta limits, rotational transform, shear, magnetic wall, etc. A wide number of configurations are accurately modeled by the Grad-Shafranov equation. Among them are all types of tokamaks, the spheromak, the reversed field pinch, and toroidal multipoles. An important aspect of the analysis is the use of asymptotic expansions, with an inverse aspect ratio serving as the expansion parameter. In addition, an equation similar to the Grad-Shafranov equation, but for helically symmetric equilibria, is presented. This equation represents the leading-order description low-Beta and high-Beta stellarators, heliacs, and the Elmo bumpy torus. The solutions all correspond to infinitely long straight helices. Bending such a configuration into a torus requires a full three-dimensional calculation and is discussed in Chapter 7

  2. MIEC-SVM: automated pipeline for protein peptide/ligand interaction prediction.

    Science.gov (United States)

    Li, Nan; Ainsworth, Richard I; Wu, Meixin; Ding, Bo; Wang, Wei

    2016-03-15

    MIEC-SVM is a structure-based method for predicting protein recognition specificity. Here, we present an automated MIEC-SVM pipeline providing an integrated and user-friendly workflow for construction and application of the MIEC-SVM models. This pipeline can handle standard amino acids and those with post-translational modifications (PTMs) or small molecules. Moreover, multi-threading and support to Sun Grid Engine (SGE) are implemented to significantly boost the computational efficiency. The program is available at http://wanglab.ucsd.edu/MIEC-SVM CONTACT: : wei-wang@ucsd.edu Supplementary data available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  3. Automated classification of immunostaining patterns in breast tissue from the human protein atlas.

    Science.gov (United States)

    Swamidoss, Issac Niwas; Kårsnäs, Andreas; Uhlmann, Virginie; Ponnusamy, Palanisamy; Kampf, Caroline; Simonsson, Martin; Wählby, Carolina; Strand, Robin

    2013-01-01

    The Human Protein Atlas (HPA) is an effort to map the location of all human proteins (http://www.proteinatlas.org/). It contains a large number of histological images of sections from human tissue. Tissue micro arrays (TMA) are imaged by a slide scanning microscope, and each image represents a thin slice of a tissue core with a dark brown antibody specific stain and a blue counter stain. When generating antibodies for protein profiling of the human proteome, an important step in the quality control is to compare staining patterns of different antibodies directed towards the same protein. This comparison is an ultimate control that the antibody recognizes the right protein. In this paper, we propose and evaluate different approaches for classifying sub-cellular antibody staining patterns in breast tissue samples. The proposed methods include the computation of various features including gray level co-occurrence matrix (GLCM) features, complex wavelet co-occurrence matrix (CWCM) features, and weighted neighbor distance using compound hierarchy of algorithms representing morphology (WND-CHARM)-inspired features. The extracted features are used into two different multivariate classifiers (support vector machine (SVM) and linear discriminant analysis (LDA) classifier). Before extracting features, we use color deconvolution to separate different tissue components, such as the brownly stained positive regions and the blue cellular regions, in the immuno-stained TMA images of breast tissue. We present classification results based on combinations of feature measurements. The proposed complex wavelet features and the WND-CHARM features have accuracy similar to that of a human expert. Both human experts and the proposed automated methods have difficulties discriminating between nuclear and cytoplasmic staining patterns. This is to a large extent due to mixed staining of nucleus and cytoplasm. Methods for quantification of staining patterns in histopathology have many

  4. Automated classification of immunostaining patterns in breast tissue from the human protein Atlas

    Directory of Open Access Journals (Sweden)

    Issac Niwas Swamidoss

    2013-01-01

    Full Text Available Background: The Human Protein Atlas (HPA is an effort to map the location of all human proteins (http://www.proteinatlas.org/. It contains a large number of histological images of sections from human tissue. Tissue micro arrays (TMA are imaged by a slide scanning microscope, and each image represents a thin slice of a tissue core with a dark brown antibody specific stain and a blue counter stain. When generating antibodies for protein profiling of the human proteome, an important step in the quality control is to compare staining patterns of different antibodies directed towards the same protein. This comparison is an ultimate control that the antibody recognizes the right protein. In this paper, we propose and evaluate different approaches for classifying sub-cellular antibody staining patterns in breast tissue samples. Materials and Methods: The proposed methods include the computation of various features including gray level co-occurrence matrix (GLCM features, complex wavelet co-occurrence matrix (CWCM features, and weighted neighbor distance using compound hierarchy of algorithms representing morphology (WND-CHARM-inspired features. The extracted features are used into two different multivariate classifiers (support vector machine (SVM and linear discriminant analysis (LDA classifier. Before extracting features, we use color deconvolution to separate different tissue components, such as the brownly stained positive regions and the blue cellular regions, in the immuno-stained TMA images of breast tissue. Results: We present classification results based on combinations of feature measurements. The proposed complex wavelet features and the WND-CHARM features have accuracy similar to that of a human expert. Conclusions: Both human experts and the proposed automated methods have difficulties discriminating between nuclear and cytoplasmic staining patterns. This is to a large extent due to mixed staining of nucleus and cytoplasm. Methods for

  5. Extended Polymorphism of Two-Dimensional Material

    NARCIS (Netherlands)

    Yoshida, Masaro; Ye, Jianting; Zhang, Yijin; Imai, Yasuhiko; Kimura, Shigeru; Fujiwara, Akihiko; Nishizaki, Terukazu; Kobayashi, Norio; Nakano, Masaki; Iwasa, Yoshihiro

    When controlling electronic properties of bulk materials, we usually assume that the basic crystal structure is fixed. However, in two-dimensional (2D) materials, atomic structure or to functionalize their properties. Various polymorphs can exist in transition metal dichalcogenides (TMDCs) from

  6. Two-dimensional nonlinear equations of supersymmetric gauge theories

    International Nuclear Information System (INIS)

    Savel'ev, M.V.

    1985-01-01

    Supersymmetric generalization of two-dimensional nonlinear dynamical equations of gauge theories is presented. The nontrivial dynamics of a physical system in the supersymmetry and supergravity theories for (2+2)-dimensions is described by the integrable embeddings of Vsub(2/2) superspace into the flat enveloping superspace Rsub(N/M), supplied with the structure of a Lie superalgebra. An equation is derived which describes a supersymmetric generalization of the two-dimensional Toda lattice. It contains both super-Liouville and Sinh-Gordon equations

  7. Semi-Automated Hydrophobic Interaction Chromatography Column Scouting Used in the Two-Step Purification of Recombinant Green Fluorescent Protein

    Science.gov (United States)

    Murphy, Patrick J. M.

    2014-01-01

    Background Hydrophobic interaction chromatography (HIC) most commonly requires experimental determination (i.e., scouting) in order to select an optimal chromatographic medium for purifying a given target protein. Neither a two-step purification of untagged green fluorescent protein (GFP) from crude bacterial lysate using sequential HIC and size exclusion chromatography (SEC), nor HIC column scouting elution profiles of GFP, have been previously reported. Methods and Results Bacterial lysate expressing recombinant GFP was sequentially adsorbed to commercially available HIC columns containing butyl, octyl, and phenyl-based HIC ligands coupled to matrices of varying bead size. The lysate was fractionated using a linear ammonium phosphate salt gradient at constant pH. Collected HIC eluate fractions containing retained GFP were then pooled and further purified using high-resolution preparative SEC. Significant differences in presumptive GFP elution profiles were observed using in-line absorption spectrophotometry (A395) and post-run fluorimetry. SDS-PAGE and western blot demonstrated that fluorometric detection was the more accurate indicator of GFP elution in both HIC and SEC purification steps. Comparison of composite HIC column scouting data indicated that a phenyl ligand coupled to a 34 µm matrix produced the highest degree of target protein capture and separation. Conclusions Conducting two-step protein purification using the preferred HIC medium followed by SEC resulted in a final, concentrated product with >98% protein purity. In-line absorbance spectrophotometry was not as precise of an indicator of GFP elution as post-run fluorimetry. These findings demonstrate the importance of utilizing a combination of detection methods when evaluating purification strategies. GFP is a well-characterized model protein, used heavily in educational settings and by researchers with limited protein purification experience, and the data and strategies presented here may aid in

  8. Superintegrability on the two dimensional hyperboloid

    International Nuclear Information System (INIS)

    Akopyan, E.; Pogosyan, G.S.; Kalnins, E.G.; Miller, W. Jr

    1998-01-01

    This work is devoted to the investigation of the quantum mechanical systems on the two dimensional hyperboloid which admit separation of variables in at least two coordinate systems. Here we consider two potentials introduced in a paper of C.P.Boyer, E.G.Kalnins and P.Winternitz, which haven't been studied yet. An example of an interbasis expansion is given and the structure of the quadratic algebra generated by the integrals of motion is carried out

  9. Few helium atoms in quasi two-dimensional space

    International Nuclear Information System (INIS)

    Kilic, Srecko; Vranjes, Leandra

    2003-01-01

    Two, three and four 3 He and 4 He atoms in quasi two-dimensional space above graphite and cesium surfaces and in 'harmonic' potential perpendicular to the surface have been studied. Using some previously examined variational wave functions and the Diffusion Monte Carlo procedure, it has been shown that all molecules: dimers, trimers and tetramers, are bound more strongly than in pure two- and three-dimensional space. The enhancement of binding with respect to unrestricted space is more pronounced on cesium than on graphite. Furthermore, for 3 He 3 ( 3 He 4 ) on all studied surfaces, there is an indication that the configuration of a dimer and a 'free' particle (two dimers) may be equivalently established

  10. Two-dimensional versus three-dimensional CT angiography in analysis of anatomical suitability for stentgraft repair of abdominal aortic aneurysms

    International Nuclear Information System (INIS)

    Pitoulias, Georgios A.; Aslanidou, Eleni A.; Papadimitriou, Dimitrios K.; Donas, Konstantinos P.; Schulte, Stefan

    2011-01-01

    Background The morphological analysis prior to endovascular abdominal aneurysm repair (EVAR) plays an important role in long-term outcomes. Post-imaging analysis of computed tomographic angiography (CTA) by three-dimensional reconstruction with central lumen line detection (CLL 3D-CTA) enables measurements to be made in orthogonal slices. This might be more precise than equal post-imaging analysis in axial slices by two-dimensional computed tomographic angiography (2D-CTA). Purpose To evaluate the intra- and interobserver variability of CLL 3D-CTA and 2D-CTA post-imaging analysis methods and the agreement between them in pre-EVAR suitability analysis of patients with abdominal aortic aneurysm (AAA). Material and Methods Anonymized CTA data-sets from 70 patients with AAA were analyzed retrospectively. Length measurements included proximal and distal aortic neck lengths and total distance from the lower renal artery to the higher iliac bifurcation. Width measurements included proximal and distal neck diameters, maximum AAA diameter and common iliac diameters just above the iliac bifurcations. The measurements were performed in random order by two vascular surgeons, twice per method with 1-month interval between readings. In the CLL 3D-CTA method we used semi-automated CLL detection by software and manual measurements on CTA slices perpendicular to CLL. The equal measurements in 2D-CTA were performed manually on axial CTA slices using a DICOM viewer workstation. The intra- and interobserver variability, as well as the agreement between the two methods were assessed by Bland-Altman test and bivariate correlation analysis. Results The intraobserver variability was significantly higher in 2D-CTA measurements for both readers. The interobserver variability was significant in 2D-CTA measurements of proximal neck dimensions while the agreement in CLL 3D-CTA analysis between the two readers was excellent in all studied parameters. The agreement between the two suitability

  11. Electronic transport on the spatial structure of the protein: Three-dimensional lattice model

    International Nuclear Information System (INIS)

    Sarmento, R.G.; Frazão, N.F.; Macedo-Filho, A.

    2017-01-01

    Highlights: • The electronic transport on the structure of the three-dimensional lattice model of the protein is studied. • The signing of the current–voltage is directly affected by permutations of the weak bonds in the structure. • Semiconductor behave of the proteins suggest a potential application in the development of novel biosensors. - Abstract: We report a numerical analysis of the electronic transport in protein chain consisting of thirty-six standard amino acids. The protein chains studied have three-dimensional structure, which can present itself in three distinct conformations and the difference consist in the presence or absence of thirteen hydrogen-bondings. Our theoretical method uses an electronic tight-binding Hamiltonian model, appropriate to describe the protein segments modeled by the amino acid chain. We note that the presence and the permutations between weak bonds in the structure of proteins are directly related to the signing of the current–voltage. Furthermore, the electronic transport depends on the effect of temperature. In addition, we have found a semiconductor behave in the models investigated and it suggest a potential application in the development of novel biosensors for molecular diagnostics.

  12. Electronic transport on the spatial structure of the protein: Three-dimensional lattice model

    Energy Technology Data Exchange (ETDEWEB)

    Sarmento, R.G. [Departamento de Ciências Biológicas, Universidade Federal do Piauí, 64800-000 Floriano, PI (Brazil); Frazão, N.F. [Centro de Educação e Saúde, Universidade Federal de Campina Grande, 581750-000 Cuité, PB (Brazil); Macedo-Filho, A., E-mail: amfilho@gmail.com [Campus Prof. Antonio Geovanne Alves de Sousa, Universidade Estadual do Piauí, 64260-000 Piripiri, PI (Brazil)

    2017-01-30

    Highlights: • The electronic transport on the structure of the three-dimensional lattice model of the protein is studied. • The signing of the current–voltage is directly affected by permutations of the weak bonds in the structure. • Semiconductor behave of the proteins suggest a potential application in the development of novel biosensors. - Abstract: We report a numerical analysis of the electronic transport in protein chain consisting of thirty-six standard amino acids. The protein chains studied have three-dimensional structure, which can present itself in three distinct conformations and the difference consist in the presence or absence of thirteen hydrogen-bondings. Our theoretical method uses an electronic tight-binding Hamiltonian model, appropriate to describe the protein segments modeled by the amino acid chain. We note that the presence and the permutations between weak bonds in the structure of proteins are directly related to the signing of the current–voltage. Furthermore, the electronic transport depends on the effect of temperature. In addition, we have found a semiconductor behave in the models investigated and it suggest a potential application in the development of novel biosensors for molecular diagnostics.

  13. Dynamic three-dimensional display of common congenital cardiac defects from reconstruction of two-dimensional echocardiographic images.

    Science.gov (United States)

    Hsieh, K S; Lin, C C; Liu, W S; Chen, F L

    1996-01-01

    Two-dimensional echocardiography had long been a standard diagnostic modality for congenital heart disease. Further attempts of three-dimensional reconstruction using two-dimensional echocardiographic images to visualize stereotypic structure of cardiac lesions have been successful only recently. So far only very few studies have been done to display three-dimensional anatomy of the heart through two-dimensional image acquisition because such complex procedures were involved. This study introduced a recently developed image acquisition and processing system for dynamic three-dimensional visualization of various congenital cardiac lesions. From December 1994 to April 1995, 35 cases were selected in the Echo Laboratory here from about 3000 Echo examinations completed. Each image was acquired on-line with specially designed high resolution image grazmber with EKG and respiratory gating technique. Off-line image processing using a window-architectured interactive software package includes construction of 2-D ehcocardiographic pixel to 3-D "voxel" with conversion of orthogonal to rotatory axial system, interpolation, extraction of region of interest, segmentation, shading and, finally, 3D rendering. Three-dimensional anatomy of various congenital cardiac defects was shown, including four cases with ventricular septal defects, two cases with atrial septal defects, and two cases with aortic stenosis. Dynamic reconstruction of a "beating heart" is recorded as vedio tape with video interface. The potential application of 3D display of the reconstruction from 2D echocardiographic images for the diagnosis of various congenital heart defects has been shown. The 3D display was able to improve the diagnostic ability of echocardiography, and clear-cut display of the various congenital cardiac defects and vavular stenosis could be demonstrated. Reinforcement of current techniques will expand future application of 3D display of conventional 2D images.

  14. Exploring two-dimensional electron gases with two-dimensional Fourier transform spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Paul, J.; Dey, P.; Karaiskaj, D., E-mail: karaiskaj@usf.edu [Department of Physics, University of South Florida, 4202 East Fowler Ave., Tampa, Florida 33620 (United States); Tokumoto, T.; Hilton, D. J. [Department of Physics, University of Alabama at Birmingham, Birmingham, Alabama 35294 (United States); Reno, J. L. [CINT, Sandia National Laboratories, Albuquerque, New Mexico 87185 (United States)

    2014-10-07

    The dephasing of the Fermi edge singularity excitations in two modulation doped single quantum wells of 12 nm and 18 nm thickness and in-well carrier concentration of ∼4 × 10{sup 11} cm{sup −2} was carefully measured using spectrally resolved four-wave mixing (FWM) and two-dimensional Fourier transform (2DFT) spectroscopy. Although the absorption at the Fermi edge is broad at this doping level, the spectrally resolved FWM shows narrow resonances. Two peaks are observed separated by the heavy hole/light hole energy splitting. Temperature dependent “rephasing” (S{sub 1}) 2DFT spectra show a rapid linear increase of the homogeneous linewidth with temperature. The dephasing rate increases faster with temperature in the narrower 12 nm quantum well, likely due to an increased carrier-phonon scattering rate. The S{sub 1} 2DFT spectra were measured using co-linear, cross-linear, and co-circular polarizations. Distinct 2DFT lineshapes were observed for co-linear and cross-linear polarizations, suggesting the existence of polarization dependent contributions. The “two-quantum coherence” (S{sub 3}) 2DFT spectra for the 12 nm quantum well show a single peak for both co-linear and co-circular polarizations.

  15. An automated method for the layup of fiberglass fabric

    Science.gov (United States)

    Zhu, Siqi

    This dissertation presents an automated composite fabric layup solution based on a new method to deform fiberglass fabric referred to as shifting. A layup system was designed and implemented using a large robotic gantry and custom end-effector for shifting. Layup tests proved that the system can deposit fabric onto two-dimensional and three-dimensional tooling surfaces accurately and repeatedly while avoiding out-of-plane deformation. A process planning method was developed to generate tool paths for the layup system based on a geometric model of the tooling surface. The approach is analogous to Computer Numerical Controlled (CNC) machining, where Numerical Control (NC) code from a Computer-Aided Design (CAD) model is generated to drive the milling machine. Layup experiments utilizing the proposed method were conducted to validate the performance. The results show that the process planning software requires minimal time or human intervention and can generate tool paths leading to accurate composite fabric layups. Fiberglass fabric samples processed with shifting deformation were observed for meso-scale deformation. Tow thinning, bending and spacing was observed and measured. Overall, shifting did not create flaws in amounts that would disqualify the method from use in industry. This suggests that shifting is a viable method for use in automated manufacturing. The work of this dissertation provides a new method for the automated layup of broad width composite fabric that is not possible with any available composite automation systems to date.

  16. Two-dimensional time dependent Riemann solvers for neutron transport

    International Nuclear Information System (INIS)

    Brunner, Thomas A.; Holloway, James Paul

    2005-01-01

    A two-dimensional Riemann solver is developed for the spherical harmonics approximation to the time dependent neutron transport equation. The eigenstructure of the resulting equations is explored, giving insight into both the spherical harmonics approximation and the Riemann solver. The classic Roe-type Riemann solver used here was developed for one-dimensional problems, but can be used in multidimensional problems by treating each face of a two-dimensional computation cell in a locally one-dimensional way. Several test problems are used to explore the capabilities of both the Riemann solver and the spherical harmonics approximation. The numerical solution for a simple line source problem is compared to the analytic solution to both the P 1 equation and the full transport solution. A lattice problem is used to test the method on a more challenging problem

  17. On the ground state of the two-dimensional non-ideal Bose gas

    International Nuclear Information System (INIS)

    Lozovik, Yu.E.; Yudson, V.I.

    1978-01-01

    The theory of the ground state of the two-dimensional non-ideal Bose gas is presented. The conditions for the validity of the ladder and the Bogolubov approximations are derived. These conditions ensure the existence of a Bose condensate in the ground state of two-dimensional systems. These conditions are different from the corresponding conditions for the three-dimensional case. The connection between the effective interaction and the two-dimensional scattering amplitude at some characteristic energy kappa 2 /2m (not equal to 0) is obtained (f(kappa = 0) = infinity in the two-dimensional case). (Auth.)

  18. Method for coupling two-dimensional to three-dimensional discrete ordinates calculations

    International Nuclear Information System (INIS)

    Thompson, J.L.; Emmett, M.B.; Rhoades, W.A.; Dodds, H.L. Jr.

    1985-01-01

    A three-dimensional (3-D) discrete ordinates transport code, TORT, has been developed at the Oak Ridge National Laboratory for radiation penetration studies. It is not feasible to solve some 3-D penetration problems with TORT, such as a building located a large distance from a point source, because (a) the discretized 3-D problem is simply too big to fit on the computer or (b) the computing time (and corresponding cost) is prohibitive. Fortunately, such problems can be solved with a hybrid approach by coupling a two-dimensional (2-D) description of the point source, which is assumed to be azimuthally symmetric, to a 3-D description of the building, the region of interest. The purpose of this paper is to describe this hybrid methodology along with its implementation and evaluation in the DOTTOR (Discrete Ordinates to Three-dimensional Oak Ridge Transport) code

  19. Automated Analysis of Protein Expression and Gene Amplification within the Same Cells of Paraffin-Embedded Tumour Tissue

    Directory of Open Access Journals (Sweden)

    Timo Gaiser

    2010-01-01

    Full Text Available Background: The simultaneous detection of protein expression and gene copy number changes in patient samples, like paraffin-embedded tissue sections, is challenging since the procedures of immunohistochemistry (IHC and Fluorescence in situ Hybridization (FISH negatively influence each other which often results in suboptimal staining. Therefore, we developed a novel automated algorithm based on relocation which allows subsequent detection of protein content and gene copy number changes within the same cell.

  20. Warranty menu design for a two-dimensional warranty

    International Nuclear Information System (INIS)

    Ye, Zhi-Sheng; Murthy, D.N. Pra

    2016-01-01

    Fierce competitions in the commercial product market have forced manufacturers to provide customer-friendly warranties with a view to achieving higher customer satisfaction and increasing the market share. This study proposes a strategy that offers customers a two-dimensional warranty menu with a number of warranty choices, called a flexible warranty policy. We investigate the design of a flexible two-dimensional warranty policy that contains a number of rectangular regions. This warranty policy is obtained by dividing customers into several groups according to their use rates and providing each group a germane warranty region. Consumers choose a favorable one from the menu according to their usage behaviors. Evidently, this flexible warranty policy is attractive to users of different usage behaviors, and thus, it gives the manufacturer a good position in advertising the product. When consumers are unaware about their use rates upon purchase, we consider a fixed two-dimensional warranty policy with a stair-case warranty region and show that it is equivalent to the flexible policy. Such an equivalence reveals the inherent relationship between the rectangular warranty policy, the L-shape warranty policy, the step-stair warranty policy and the iso-probability of failure warranty policy that were extensively discussed in the literature. - Highlights: • We design a two-dimensional warranty menu with a number of warranty choices. • Consumers can choose a favorable one from the menu as per their usage behavior. • We further consider a fixed 2D warranty policy with a stair-case warranty region. • We show the equivalence of the two warranty policies.

  1. Two-dimensional gel proteome reference map of human small intestine

    Directory of Open Access Journals (Sweden)

    Canzonieri Vincenzo

    2009-03-01

    Full Text Available Abstract Background The small intestine is an important human organ that plays a central role in many physiological functions including digestion, absorption, secretion and defense. Duodenal pathologies include, for instance, the ulcer associated to Helicobacter Pylori infection, adenoma and, in genetically predisposed individuals, celiac disease. Alterations in the bowel reduce its capability to absorb nutrients, minerals and fat-soluble vitamins. Anemia and osteopenia or osteoporosis may develop as a consequence of vitamins malabsorption. Adenoma is a benign tumor that has the potential to become cancerous. Adult celiac disease patients present an overall risk of cancer that is almost twice than that found in the general population. These disease processes are not completely known. To date, a two dimensional (2D reference map of proteins expressed in human duodenal tissue is not yet available: the aim of our study was to characterize the 2D protein map, and to identify proteins of duodenal mucosa of adult individuals without duodenal illness, to create a protein database. This approach, may be useful for comparing similar protein samples in different laboratories and for the molecular characterization of intestinal pathologies without recurring to the use of surgical material. Results The enrolled population comprised five selected samples (3 males and 2 females, aged 19 to 42, taken from 20 adult subjects, on their first visit at the gastroenterology unit for a suspected celiac disease, who did not turn to be affected by any duodenal pathology after gastrointestinal and histological evaluations. Proteins extracted from the five duodenal mucosal specimens were singly separated by 2D gel electrophoresis. After image analysis of each 2D gel, 179 protein spots, representing 145 unique proteins, from 218 spots tested, were successfully identified by MALDI-TOF ms analysis. Normalized volumes, for each protein, have been reported for every gel

  2. Two-dimensional condensation of physi-sorbed methane on layer-like halides

    International Nuclear Information System (INIS)

    Nardon, Yves

    1972-01-01

    Two-dimensional condensation of methane in physi-sorbed layers has been studied from sets of stepped isotherms of methane on the cleavage plane of layer-like halides (FeCl 2 , CdCl 2 , NiBr 2 , CdBr 2 , FeI 2 , CaI 2 , CaI 2 and PbI 2 ) in most cases prepared by sublimation in a rapid current of inert gas. The vertical parts of the steps of adsorption isotherms correspond to the formation of successive monomolecular layers by two-dimensional condensation. Thermodynamic analysis of experimental results, has mainly emphasized the important effect of the potential relief of adsorbent surfaces, on both the structure of the physi-sorbed layers and the two-dimensional critical temperature. From its entropy, we conclude that the first layer is a (111) plane of f.c.c.: methane which becomes more loosely packed as the dimensional compatibility of the lattices of the adsorbent and adsorbate becomes poorer. Experimental values of the two-dimensional critical temperatures in the first, second and third layers have been determined, and interpreted on the following basis. An expansion of the layer induces a lowering of the two-dimensional critical temperature by decreasing the lateral interaction energy, while a localisation of the adsorbed molecules in potential wells, when possible, induces a rise of the two-dimensional critical temperature. (author) [fr

  3. Assessing the accuracy and reliability of ultrasonographic three-dimensional parathyroid volume measurement in a patient with secondary hyperparathyroidism: a comparison with the two-dimensional conventional method

    Directory of Open Access Journals (Sweden)

    Sung-Hye You

    2017-01-01

    Full Text Available Purpose The purpose of this study was to investigate the accuracy and reliability of the semi-automated ultrasonographic volume measurement tool, virtual organ computer-aided analysis (VOCAL, for measuring the volume of parathyroid glands. Methods Volume measurements for 40 parathyroid glands were performed in patients with secondary hyperparathyroidism caused by chronic renal failure. The volume of the parathyroid glands was measured twice by experienced radiologists by two-dimensional (2D and three-dimensional (3D methods using conventional sonograms and the VOCAL with 30°angle increments before parathyroidectomy. The specimen volume was also measured postoperatively. Intraclass correlation coefficients (ICCs and the absolute percentage error were used for estimating the reproducibility and accuracy of the two different methods. Results The ICC value between two measurements of the 2D method and the 3D method was 0.956 and 0.999, respectively. The mean absolute percentage error of the 2D method and the 3D VOCAL technique was 29.56% and 5.78%, respectively. For accuracy and reliability, the plots of the 3D method showed a more compact distribution than those of the 2D method on the Bland-Altman graph. Conclusion The rotational VOCAL method for measuring the parathyroid gland is more accurate and reliable than the conventional 2D measurement. This VOCAL method could be used as a more reliable follow-up imaging modality in a patient with hyperparathyroidism.

  4. BioXTAS RAW, a software program for high-throughput automated small-angle X-ray scattering data reduction and preliminary analysis

    DEFF Research Database (Denmark)

    Nielsen, S.S.; Toft, K.N.; Snakenborg, Detlef

    2009-01-01

    A fully open source software program for automated two-dimensional and one-dimensional data reduction and preliminary analysis of isotropic small-angle X-ray scattering (SAXS) data is presented. The program is freely distributed, following the open-source philosophy, and does not rely on any...... commercial software packages. BioXTAS RAW is a fully automated program that, via an online feature, reads raw two-dimensional SAXS detector output files and processes and plots data as the data files are created during measurement sessions. The software handles all steps in the data reduction. This includes...... mask creation, radial averaging, error bar calculation, artifact removal, normalization and q calibration. Further data reduction such as background subtraction and absolute intensity scaling is fast and easy via the graphical user interface. BioXTAS RAW also provides preliminary analysis of one...

  5. Conformal invariance and two-dimensional physics

    International Nuclear Information System (INIS)

    Zuber, J.B.

    1993-01-01

    Actually, physicists and mathematicians are very interested in conformal invariance: geometric transformations which keep angles. This symmetry is very important for two-dimensional systems as phase transitions, string theory or node mathematics. In this article, the author presents the conformal invariance and explains its usefulness

  6. Multisoliton formula for completely integrable two-dimensional systems

    International Nuclear Information System (INIS)

    Chudnovsky, D.V.; Chudnovsky, G.V.

    1979-01-01

    For general two-dimensional completely integrable systems, the exact formulae for multisoliton type solutions are given. The formulae are obtained algebrically from solutions of two linear partial differential equations

  7. Application of long-range order to predict unfolding rates of two-state proteins.

    Science.gov (United States)

    Harihar, B; Selvaraj, S

    2011-03-01

    Predicting the experimental unfolding rates of two-state proteins and models describing the unfolding rates of these proteins is quite limited because of the complexity present in the unfolding mechanism and the lack of experimental unfolding data compared with folding data. In this work, 25 two-state proteins characterized by Maxwell et al. (Protein Sci 2005;14:602–616) using a consensus set of experimental conditions were taken, and the parameter long-range order (LRO) derived from their three-dimensional structures were related with their experimental unfolding rates ln(k(u)). From the total data set of 30 proteins used by Maxwell et al. (Protein Sci 2005;14:602–616), five slow-unfolding proteins with very low unfolding rates were considered to be outliers and were not included in our data set. Except all beta structural class, LRO of both the all-alpha and mixed-class proteins showed a strong inverse correlation of r = -0.99 and -0.88, respectively, with experimental ln(k(u)). LRO shows a correlation of -0.62 with experimental ln(k(u)) for all-beta proteins. For predicting the unfolding rates, a simple statistical method has been used and linear regression equations were developed for individual structural classes of proteins using LRO, and the results obtained showed a better agreement with experimental results. Copyright © 2010 Wiley-Liss, Inc.

  8. The blind student’s interpretation of two-dimensional shapes in geometry

    Science.gov (United States)

    Andriyani; Budayasa, I. K.; Juniati, D.

    2018-01-01

    The blind student’s interpretation of two-dimensional shapes represents the blind student’s mental image of two-dimensional shapes that they can’t visualize directly, which is related to illustration of the characteristics and number of edges and angles. The objective of this research is to identify the blind student’s interpretation of two-dimensional shapes. This research was an exploratory study with qualitative approach. A subject of this research is a sixth-grade student who experiencing total blind from the fifth grade of elementary school. Researchers interviewed the subject about his interpretation of two-dimensional shapes according to his thinking.The findings of this study show the uniqueness of blind students, who have been totally blind since school age, in knowing and illustrating the characteristics of edges and angles of two-dimensional shapes by utilizing visual experiences that were previously obtained before the blind. The result can inspire teachers to design further learning for development of blind student geometry concepts.

  9. Critical Behaviour of a Two-Dimensional Random Antiferromagnet

    DEFF Research Database (Denmark)

    Als-Nielsen, Jens Aage; Birgeneau, R. J.; Guggenheim, H. J.

    1976-01-01

    A neutron scattering study of the order parameter, correlation length and staggered susceptibility of the two-dimensional random antiferromagnet Rb2Mn0.5Ni0.5F4 is reported. The system is found to exhibit a well-defined phase transition with critical exponents identical to those of the isomorphou...... pure materials K2NiF4 and K2MnF4. Thus, in these systems, which have the asymptotic critical behaviour of the two-dimensional Ising model, randomness has no measurable effect on the phase-transition behaviour....

  10. [Apply fourier transform infrared spectra coupled with two-dimensional correlation analysis to study the evolution of humic acids during composting].

    Science.gov (United States)

    Bu, Gui-jun; Yu, Jing; Di, Hui-hui; Luo, Shi-jia; Zhou, Da-zhai; Xiao, Qiang

    2015-02-01

    The composition and structure of humic acids formed during composting play an important influence on the quality and mature of compost. In order to explore the composition and evolution mechanism, municipal solid wastes were collected to compost and humic and fulvic acids were obtained from these composted municipal solid wastes. Furthermore, fourier transform infrared spectra and two-dimensional correlation analysis were applied to study the composition and transformation of humic and fulvic acids during composting. The results from fourier transform infrared spectra showed that, the composition of humic acids was complex, and several absorbance peaks were observed at 2917-2924, 2844-2852, 2549, 1662, 1622, 1566, 1454, 1398, 1351, 990-1063, 839 and 711 cm(-1). Compared to humic acids, the composition of fulvci acids was simple, and only three peaks were detected at 1725, 1637 and 990 cm(-1). The appearance of these peaks showed that both humic and fulvic acids comprised the benzene originated from lignin and the polysaccharide. In addition, humic acids comprised a large number of aliphatic and protein which were hardly detected in fulvic acids. Aliphatic, polysaccharide, protein and lignin all were degraded during composting, however, the order of degradation was different between humic and fulvci acids. The result from two-dimensional correlation analysis showed that, organic compounds in humic acids were degraded in the following sequence: aliphatic> protein> polysaccharide and lignin, while that in fulvic acids was as following: protein> polysaccharide and aliphatic. A large number of carboxyl, alcohols and ethers were formed during the degradation process, and the carboxyl was transformed into carbonates. It can be concluded that, fourier transform infrared spectra coupled with two-dimensional correlation analysis not only can analyze the function group composition of humic substances, but also can characterize effectively the degradation sequence of these

  11. Reliability of tunnel angle in ACL reconstruction: two-dimensional versus three-dimensional guide technique.

    Science.gov (United States)

    Leiter, Jeff R S; de Korompay, Nevin; Macdonald, Lindsey; McRae, Sheila; Froese, Warren; Macdonald, Peter B

    2011-08-01

    To compare the reliability of tibial tunnel position and angle produced with a standard ACL guide (two-dimensional guide) or Howell 65° Guide (three-dimensional guide) in the coronal and sagittal planes. In the sagittal plane, the dependent variables were the angle of the tibial tunnel relative to the tibial plateau and the position of the tibial tunnel with respect to the most posterior aspect of the tibia. In the coronal plane, the dependent variables were the angle of the tunnel with respect to the medial joint line of the tibia and the medial and lateral placement of the tibial tunnel relative to the most medial aspect of the tibia. The position and angle of the tibial tunnel in the coronal and sagittal planes were determined from anteroposterior and lateral radiographs, respectively, taken 2-6 months postoperatively. The two-dimensional and three-dimensional guide groups included 28 and 24 sets of radiographs, respectively. Tibial tunnel position was identified, and tunnel angle measurements were completed. Multiple investigators measured the position and angle of the tunnel 3 times, at least 7 days apart. The angle of the tibial tunnel in the coronal plane using a two-dimensional guide (61.3 ± 4.8°) was more horizontal (P guide (64.7 ± 6.2°). The position of the tibial tunnel in the sagittal plane was more anterior (P guide group compared to the three-dimensional guide group (43.3 ± 2.9%). The Howell Tibial Guide allows for reliable placement of the tibial tunnel in the coronal plane at an angle of 65°. Tibial tunnels were within the anatomical footprint of the ACL with either technique. Future studies should investigate the effects of tibial tunnel angle on knee function and patient quality of life. Case-control retrospective comparative study, Level III.

  12. Comparative analysis of excretory-secretory antigens of Trichinella spiralis and Trichinella britovi muscle larvae by two-dimensional difference gel electrophoresis and immunoblotting.

    Science.gov (United States)

    Bien, Justyna; Näreaho, Anu; Varmanen, Pekka; Gozdzik, Katarzyna; Moskwa, Bozena; Cabaj, Wladyslaw; Nyman, Tuula A; Savijoki, Kirsi

    2012-02-11

    Trichinellosis is a zoonotic disease in humans caused by Trichinella spp. The present study was undertaken to discover excretory-secretory (E-S) proteins from T. spiralis and T. britovi muscle larvae (ML) that hold promise for species-specific diagnostics. To that end, the purified E-S proteins were analyzed by fluorescent two-dimensional difference gel electrophoresis (2-D DIGE) coupled with protein identification by liquid chromatography-tandem mass spectrometry (LC-MS/MS). To search for immunoreactive proteins that are specifically recognized by host antibodies the E-S proteins were subjected to two-dimensional (2-DE) immunoblotting with antisera derived from pigs experimentally infected with T. spiralis or T. britovi. According to 2-D DIGE analysis, a total of twenty-two proteins including potentially immunogenic proteins and proteins produced only by one of the two Trichinella species were subjected to LC-MS/MS for protein identification. From these proteins seventeen could be identified, of which many were identified in multiple spots, suggesting that they have undergone post-translational modification, possibly involving glycosylation and/or proteolysis. These proteins included 5'-nucleotidase, serine-type protease/proteinase, and p43 glycoprotein (gp43) as well as 49 kDa E-S protein (p49). Our findings also suggest that some of the commonly identified proteins were post-translationally modified to different extents, which in certain cases seemed to result in species-specific modification. Both commonly and specifically recognized immunoreactive proteins were identified by 2-DE immunoblotting; shared antigens were identified as gp43 and different protease variants, whereas those specific to T. britovi included multiple isoforms of the 5'-nucleotidase. Both 2-D DIGE and 2-DE immunoblotting approaches indicate that T. spiralis and T. britovi produce somewhat distinctive antigen profiles, which contain E-S antigens with potential as species-specific diagnostic

  13. Matching Two-dimensional Gel Electrophoresis' Spots

    DEFF Research Database (Denmark)

    Dos Anjos, António; AL-Tam, Faroq; Shahbazkia, Hamid Reza

    2012-01-01

    This paper describes an approach for matching Two-Dimensional Electrophoresis (2-DE) gels' spots, involving the use of image registration. The number of false positive matches produced by the proposed approach is small, when compared to academic and commercial state-of-the-art approaches. This ar...

  14. Rational solutions to two- and one-dimensional multicomponent Yajima–Oikawa systems

    International Nuclear Information System (INIS)

    Chen, Junchao; Chen, Yong; Feng, Bao-Feng; Maruno, Ken-ichi

    2015-01-01

    Exact explicit rational solutions of two- and one-dimensional multicomponent Yajima–Oikawa (YO) systems, which contain multi-short-wave components and single long-wave one, are presented by using the bilinear method. For two-dimensional system, the fundamental rational solution first describes the localized lumps, which have three different patterns: bright, intermediate and dark states. Then, rogue waves can be obtained under certain parameter conditions and their behaviors are also classified to above three patterns with different definition. It is shown that the simplest (fundamental) rogue waves are line localized waves which arise from the constant background with a line profile and then disappear into the constant background again. In particular, two-dimensional intermediate and dark counterparts of rogue wave are found with the different parameter requirements. We demonstrate that multirogue waves describe the interaction of several fundamental rogue waves, in which interesting curvy wave patterns appear in the intermediate times. Different curvy wave patterns form in the interaction of different types fundamental rogue waves. Higher-order rogue waves exhibit the dynamic behaviors that the wave structures start from lump and then retreat back to it, and this transient wave possesses the patterns such as parabolas. Furthermore, different states of higher-order rogue wave result in completely distinguishing lumps and parabolas. Moreover, one-dimensional rogue wave solutions with three states are constructed through the further reduction. Specifically, higher-order rogue wave in one-dimensional case is derived under the parameter constraints. - Highlights: • Exact explicit rational solutions of two-and one-dimensional multicomponent Yajima–Oikawa systems. • Two-dimensional rogue wave contains three different patterns: bright, intermediate and dark states. • Multi- and higher-order rogue waves exhibit distinct dynamic behaviors in two-dimensional case

  15. Two-dimensional sensitivity calculation code: SENSETWO

    International Nuclear Information System (INIS)

    Yamauchi, Michinori; Nakayama, Mitsuo; Minami, Kazuyoshi; Seki, Yasushi; Iida, Hiromasa.

    1979-05-01

    A SENSETWO code for the calculation of cross section sensitivities with a two-dimensional model has been developed, on the basis of first order perturbation theory. It uses forward neutron and/or gamma-ray fluxes and adjoint fluxes obtained by two-dimensional discrete ordinates code TWOTRAN-II. The data and informations of cross sections, geometry, nuclide density, response functions, etc. are transmitted to SENSETWO by the dump magnetic tape made in TWOTRAN calculations. The required input for SENSETWO calculations is thus very simple. The SENSETWO yields as printed output the cross section sensitivities for each coarse mesh zone and for each energy group, as well as the plotted output of sensitivity profiles specified by the input. A special feature of the code is that it also calculates the reaction rate with the response function used as the adjoint source in TWOTRAN adjoint calculation and the calculated forward flux from the TWOTRAN forward calculation. (author)

  16. Automated microfluidic sample-preparation platform for high-throughput structural investigation of proteins by small-angle X-ray scattering

    DEFF Research Database (Denmark)

    Lafleur, Josiane P.; Snakenborg, Detlef; Nielsen, Søren Skou

    2011-01-01

    A new microfluidic sample-preparation system is presented for the structural investigation of proteins using small-angle X-ray scattering (SAXS) at synchrotrons. The system includes hardware and software features for precise fluidic control, sample mixing by diffusion, automated X-ray exposure...... control, UV absorbance measurements and automated data analysis. As little as 15 l of sample is required to perform a complete analysis cycle, including sample mixing, SAXS measurement, continuous UV absorbance measurements, and cleaning of the channels and X-ray cell with buffer. The complete analysis...

  17. High-velocity two-phase flow two-dimensional modeling

    International Nuclear Information System (INIS)

    Mathes, R.; Alemany, A.; Thilbault, J.P.

    1995-01-01

    The two-phase flow in the nozzle of a LMMHD (liquid metal magnetohydrodynamic) converter has been studied numerically and experimentally. A two-dimensional model for two-phase flow has been developed including the viscous terms (dragging and turbulence) and the interfacial mass, momentum and energy transfer between the phases. The numerical results were obtained by a finite volume method based on the SIMPLE algorithm. They have been verified by an experimental facility using air-water as a simulation pair and a phase Doppler particle analyzer for velocity and droplet size measurement. The numerical simulation of a lithium-cesium high-temperature pair showed that a nearly homogeneous and isothermal expansion of the two phases is possible with small pressure losses and high kinetic efficiencies. In the throat region a careful profiling is necessary to reduce the inertial effects on the liquid velocity field

  18. Establishment of the optimum two-dimensional electrophoresis system of ovine ovarian tissue.

    Science.gov (United States)

    Jia, J L; Zhang, L P; Wu, J P; Wang, J; Ding, Q

    2014-08-26

    Lambing performance of sheep is the most important economic trait and is regarded as a critic factoring affecting the productivity in sheep industry. Ovary plays the most roles in lambing trait. To establish the optimum two-dimensional electrophoresis system (2-DE) of ovine ovarian tissue, the common protein extraction methods of animal tissue (trichloroacetic acid/acetone precipitation and direct schizolysis methods) were used to extract ovine ovarian protein, and 17-cm nonlinear immobilized PH 3-10 gradient strips were used for 2-DE. The sample handling, loading quantity of the protein sample, and isoelectric focusing (IEF) steps were manipulated and optimized in this study. The results indicate that the direct schizolysis III method, a 200-μg loading quantity of the protein sample, and IEF steps II (20°C active hydration, 14 h→500 V, 1 h→1000 V 1 h→1000-9000 V, 6 h→80,000 VH→500 V 24 h) are optimal for 2-DE analysis of ovine ovarian tissue. Therefore, ovine ovarian tissue proteomics 2-DE was preliminarily established by the optimized conditions in this study; meanwhile, the conditions identified herein could provide a reference for ovarian sample preparation and 2-DE using tissues from other animals.

  19. Extinction maps toward the Milky Way bulge: Two-dimensional and three-dimensional tests with apogee

    Energy Technology Data Exchange (ETDEWEB)

    Schultheis, M. [Université de Nice Sophia-Antipolis, CNRS, Observatoire de Côte d' Azur, Laboratoire Lagrange, 06304 Nice Cedex 4 (France); Zasowski, G. [Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD 21218 (United States); Allende Prieto, C. [Instituto de Astrofísica de Canarias, Calle Vía Láctea s/n, E-38205 La Laguna, Tenerife (Spain); Anders, F.; Chiappini, C. [Leibniz-Institut für Astrophysik Potsdam (AIP), D-14482 Potsdam (Germany); Beaton, R. L.; García Pérez, A. E.; Majewski, S. R. [Department of Astronomy, University of Virginia, Charlottesville, VA 22904 (United States); Beers, T. C. [National Optical Astronomy Observatory, Tucson, AZ 85719 (United States); Bizyaev, D. [Apache Point Observatory, Sunspot, NM 88349 (United States); Frinchaboy, P. M. [Department of Physics and Astronomy, Texas Christian University, TCU Box 298840, Fort Worth, TX 76129 (United States); Ge, J. [Astronomy Department, University of Florida, Gainesville, FL 32611 (United States); Hearty, F.; Schneider, D. P. [Department of Astronomy and Astrophysics, The Pennsylvania State University, University Park, PA 16802 (United States); Holtzman, J. [New Mexico State University, Las Cruces, NM 88003 (United States); Muna, D. [Department of Astronomy, The Ohio State University, Columbus, OH 43210 (United States); Nidever, D. [Department of Astronomy, University of Michigan, Ann Arbor, MI 48109 (United States); Shetrone, M., E-mail: mathias.schultheis@oca.eu, E-mail: gail.zasowski@gmail.com [McDonald Observatory, The University of Texas at Austin, Austin, TX 78712 (United States)

    2014-07-01

    Galactic interstellar extinction maps are powerful and necessary tools for Milky Way structure and stellar population analyses, particularly toward the heavily reddened bulge and in the midplane. However, due to the difficulty of obtaining reliable extinction measures and distances for a large number of stars that are independent of these maps, tests of their accuracy and systematics have been limited. Our goal is to assess a variety of photometric stellar extinction estimates, including both two-dimensional and three-dimensional extinction maps, using independent extinction measures based on a large spectroscopic sample of stars toward the Milky Way bulge. We employ stellar atmospheric parameters derived from high-resolution H-band Apache Point Observatory Galactic Evolution Experiment (APOGEE) spectra, combined with theoretical stellar isochrones, to calculate line-of-sight extinction and distances for a sample of more than 2400 giants toward the Milky Way bulge. We compare these extinction values to those predicted by individual near-IR and near+mid-IR stellar colors, two-dimensional bulge extinction maps, and three-dimensional extinction maps. The long baseline, near+mid-IR stellar colors are, on average, the most accurate predictors of the APOGEE extinction estimates, and the two-dimensional and three-dimensional extinction maps derived from different stellar populations along different sightlines show varying degrees of reliability. We present the results of all of the comparisons and discuss reasons for the observed discrepancies. We also demonstrate how the particular stellar atmospheric models adopted can have a strong impact on this type of analysis, and discuss related caveats.

  20. Extinction maps toward the Milky Way bulge: Two-dimensional and three-dimensional tests with apogee

    International Nuclear Information System (INIS)

    Schultheis, M.; Zasowski, G.; Allende Prieto, C.; Anders, F.; Chiappini, C.; Beaton, R. L.; García Pérez, A. E.; Majewski, S. R.; Beers, T. C.; Bizyaev, D.; Frinchaboy, P. M.; Ge, J.; Hearty, F.; Schneider, D. P.; Holtzman, J.; Muna, D.; Nidever, D.; Shetrone, M.

    2014-01-01

    Galactic interstellar extinction maps are powerful and necessary tools for Milky Way structure and stellar population analyses, particularly toward the heavily reddened bulge and in the midplane. However, due to the difficulty of obtaining reliable extinction measures and distances for a large number of stars that are independent of these maps, tests of their accuracy and systematics have been limited. Our goal is to assess a variety of photometric stellar extinction estimates, including both two-dimensional and three-dimensional extinction maps, using independent extinction measures based on a large spectroscopic sample of stars toward the Milky Way bulge. We employ stellar atmospheric parameters derived from high-resolution H-band Apache Point Observatory Galactic Evolution Experiment (APOGEE) spectra, combined with theoretical stellar isochrones, to calculate line-of-sight extinction and distances for a sample of more than 2400 giants toward the Milky Way bulge. We compare these extinction values to those predicted by individual near-IR and near+mid-IR stellar colors, two-dimensional bulge extinction maps, and three-dimensional extinction maps. The long baseline, near+mid-IR stellar colors are, on average, the most accurate predictors of the APOGEE extinction estimates, and the two-dimensional and three-dimensional extinction maps derived from different stellar populations along different sightlines show varying degrees of reliability. We present the results of all of the comparisons and discuss reasons for the observed discrepancies. We also demonstrate how the particular stellar atmospheric models adopted can have a strong impact on this type of analysis, and discuss related caveats.

  1. Fully automated synthesis of (phosphopeptide arrays in microtiter plate wells provides efficient access to protein tyrosine kinase characterization

    Directory of Open Access Journals (Sweden)

    Goldstein David J

    2005-01-01

    Full Text Available Abstract Background Synthetic peptides have played a useful role in studies of protein kinase substrates and interaction domains. Synthetic peptide arrays and libraries, in particular, have accelerated the process. Several factors have hindered or limited the applicability of various techniques, such as the need for deconvolution of combinatorial libraries, the inability or impracticality of achieving full automation using two-dimensional or pin solid phases, the lack of convenient interfacing with standard analytical platforms, or the difficulty of compartmentalization of a planar surface when contact between assay components needs to be avoided. This paper describes a process for synthesis of peptides and phosphopeptides on microtiter plate wells that overcomes previous limitations and demonstrates utility in determination of the epitope of an autophosphorylation site phospho-motif antibody and utility in substrate utilization assays of the protein tyrosine kinase, p60c-src. Results The overall reproducibility of phospho-peptide synthesis and multiplexed EGF receptor (EGFR autophosphorylation site (pY1173 antibody ELISA (9H2 was within 5.5 to 8.0%. Mass spectrometric analyses of the released (phosphopeptides showed homogeneous peaks of the expected molecular weights. An overlapping peptide array of the complete EGFR cytoplasmic sequence revealed a high redundancy of 9H2 reactive sites. The eight reactive phospopeptides were structurally related and interestingly, the most conserved antibody reactive peptide motif coincided with a subset of other known EGFR autophosphorylation and SH2 binding motifs and an EGFR optimal substrate motif. Finally, peptides based on known substrate specificities of c-src and related enzymes were synthesized in microtiter plate array format and were phosphorylated by c-Src with the predicted specificities. The level of phosphorylation was proportional to c-Src concentration with sensitivities below 0.1 Units of

  2. Two dimensional unstable scar statistics.

    Energy Technology Data Exchange (ETDEWEB)

    Warne, Larry Kevin; Jorgenson, Roy Eberhardt; Kotulski, Joseph Daniel; Lee, Kelvin S. H. (ITT Industries/AES Los Angeles, CA)

    2006-12-01

    This report examines the localization of time harmonic high frequency modal fields in two dimensional cavities along periodic paths between opposing sides of the cavity. The cases where these orbits lead to unstable localized modes are known as scars. This paper examines the enhancements for these unstable orbits when the opposing mirrors are both convex and concave. In the latter case the construction includes the treatment of interior foci.

  3. Expression of Raf kinase inhibitor protein in human hepatoma tissues by two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight methods.

    Science.gov (United States)

    Tsao, D A; Shiau, Y F; Tseng, C S; Chang, H R

    2016-01-01

    Hepatocellular carcinoma (HCC) is the most common malignant liver tumor. To reduce the mortality and improve the effectiveness of therapy, it is important to search for changes in tumor-specific biomarkers whose function may involve in disease progression and which may be useful as potential therapeutic targets. Materials and Mehtods: In this study, we use two-dimensional polyacrylamide gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to observe proteome alterations of 12 tissue pairs isolated from HCC patients: Normal and tumorous tissue. Comparing the tissue types with each other, 40 protein spots corresponding to fifteen differentially expressed between normal and cancer part of HCC patients. Raf kinase inhibitor protein (RKIP), an inhibitor of Raf-mediated activation of mitogen-activated protein kinase/extracellular signal-regulated kinase, may play an important role in cancer metastasis and cell proliferation and migration of human hepatoma cells. RKIP may be considered as a marker for HCC, because its expression level changes considerably in HCC compared with normal tissue. In addition, we used the methods of Western blotting and real time-polymerase chain reaction to analysis the protein expression and gene expression of RKIP. The result showed RKIP protein and gene expression in tumor part liver tissues of HCC patient is lower than peritumorous non-neoplastic liver tissue of the corresponding HCC samples. These results strongly suggest that RKIP may be considered to be a marker for HCC and RKIP are down-regulated in liver cancer cell.

  4. Sources of variability among replicate samples separated by two-dimensional gel electrophoresis.

    Science.gov (United States)

    Bland, Alison M; Janech, Michael G; Almeida, Jonas S; Arthur, John M

    2010-04-01

    Two-dimensional gel electrophoresis (2DE) offers high-resolution separation for intact proteins. However, variability in the appearance of spots can limit the ability to identify true differences between conditions. Variability can occur at a number of levels. Individual samples can differ because of biological variability. Technical variability can occur during protein extraction, processing, or storage. Another potential source of variability occurs during analysis of the gels and is not a result of any of the causes of variability named above. We performed a study designed to focus only on the variability caused by analysis. We separated three aliquots of rat left ventricle and analyzed differences in protein abundance on the replicate 2D gels. As the samples loaded on each gel were identical, differences in protein abundance are caused by variability in separation or interpretation of the gels. Protein spots were compared across gels by quantile values to determine differences. Fourteen percent of spots had a maximum difference in intensity of 0.4 quantile values or more between replicates. We then looked individually at the spots to determine the cause of differences between the measured intensities. Reasons for differences were: failure to identify a spot (59%), differences in spot boundaries (13%), difference in the peak height (6%), and a combination of these factors (21). This study demonstrates that spot identification and characterization make major contributions to variability seen with 2DE. Methods to highlight why measured protein spot abundance is different could reduce these errors.

  5. Designing a fully automated multi-bioreactor plant for fast DoE optimization of pharmaceutical protein production.

    Science.gov (United States)

    Fricke, Jens; Pohlmann, Kristof; Jonescheit, Nils A; Ellert, Andree; Joksch, Burkhard; Luttmann, Reiner

    2013-06-01

    The identification of optimal expression conditions for state-of-the-art production of pharmaceutical proteins is a very time-consuming and expensive process. In this report a method for rapid and reproducible optimization of protein expression in an in-house designed small-scale BIOSTAT® multi-bioreactor plant is described. A newly developed BioPAT® MFCS/win Design of Experiments (DoE) module (Sartorius Stedim Systems, Germany) connects the process control system MFCS/win and the DoE software MODDE® (Umetrics AB, Sweden) and enables therefore the implementation of fully automated optimization procedures. As a proof of concept, a commercial Pichia pastoris strain KM71H has been transformed for the expression of potential malaria vaccines. This approach has allowed a doubling of intact protein secretion productivity due to the DoE optimization procedure compared to initial cultivation results. In a next step, robustness regarding the sensitivity to process parameter variability has been proven around the determined optimum. Thereby, a pharmaceutical production process that is significantly improved within seven 24-hour cultivation cycles was established. Specifically, regarding the regulatory demands pointed out in the process analytical technology (PAT) initiative of the United States Food and Drug Administration (FDA), the combination of a highly instrumented, fully automated multi-bioreactor platform with proper cultivation strategies and extended DoE software solutions opens up promising benefits and opportunities for pharmaceutical protein production. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Temperature maxima in stable two-dimensional shock waves

    International Nuclear Information System (INIS)

    Kum, O.; Hoover, W.G.; Hoover, C.G.

    1997-01-01

    We use molecular dynamics to study the structure of moderately strong shock waves in dense two-dimensional fluids, using Lucy pair potential. The stationary profiles show relatively broad temperature maxima, for both the longitudinal and the average kinetic temperatures, just as does Mott-Smith model for strong shock waves in dilute three-dimensional gases. copyright 1997 The American Physical Society

  7. Red Blood Cell Count Automation Using Microscopic Hyperspectral Imaging Technology.

    Science.gov (United States)

    Li, Qingli; Zhou, Mei; Liu, Hongying; Wang, Yiting; Guo, Fangmin

    2015-12-01

    Red blood cell counts have been proven to be one of the most frequently performed blood tests and are valuable for early diagnosis of some diseases. This paper describes an automated red blood cell counting method based on microscopic hyperspectral imaging technology. Unlike the light microscopy-based red blood count methods, a combined spatial and spectral algorithm is proposed to identify red blood cells by integrating active contour models and automated two-dimensional k-means with spectral angle mapper algorithm. Experimental results show that the proposed algorithm has better performance than spatial based algorithm because the new algorithm can jointly use the spatial and spectral information of blood cells.

  8. Is automated kinetic measurement superior to end-point for advanced oxidation protein product?

    Science.gov (United States)

    Oguz, Osman; Inal, Berrin Bercik; Emre, Turker; Ozcan, Oguzhan; Altunoglu, Esma; Oguz, Gokce; Topkaya, Cigdem; Guvenen, Guvenc

    2014-01-01

    Advanced oxidation protein product (AOPP) was first described as an oxidative protein marker in chronic uremic patients and measured with a semi-automatic end-point method. Subsequently, the kinetic method was introduced for AOPP assay. We aimed to compare these two methods by adapting them to a chemistry analyzer and to investigate the correlation between AOPP and fibrinogen, the key molecule responsible for human plasma AOPP reactivity, microalbumin, and HbA1c in patients with type II diabetes mellitus (DM II). The effects of EDTA and citrate-anticogulated tubes on these two methods were incorporated into the study. This study included 93 DM II patients (36 women, 57 men) with HbA1c levels > or = 7%, who were admitted to the diabetes and nephrology clinics. The samples were collected in EDTA and in citrate-anticoagulated tubes. Both methods were adapted to a chemistry analyzer and the samples were studied in parallel. In both types of samples, we found a moderate correlation between the kinetic and the endpoint methods (r = 0.611 for citrate-anticoagulated, r = 0.636 for EDTA-anticoagulated, p = 0.0001 for both). We found a moderate correlation between fibrinogen-AOPP and microalbumin-AOPP levels only in the kinetic method (r = 0.644 and 0.520 for citrate-anticoagulated; r = 0.581 and 0.490 for EDTA-anticoagulated, p = 0.0001). We conclude that adaptation of the end-point method to automation is more difficult and it has higher between-run CV% while application of the kinetic method is easier and it may be used in oxidative stress studies.

  9. Resolution of G(s)alpha and G(q)alpha/G(11)alpha proteins in membrane domains by two-dimensional electrophoresis: the effect of long-term agonist stimulation.

    Science.gov (United States)

    Matousek, P; Novotný, J; Svoboda, P

    2004-01-01

    Low-density membrane-domain fractions were prepared from S49 lymphoma cells and clone e2m11 of HEK293 cells expressing a large number of thyrotropin-releasing hormone receptor (TRH-R) and G(11)alpha by flotation on sucrose density gradients. The intact cell structure was broken by detergent-extraction, alkaline-treatment or drastic homogenization. Three types of low-density membranes were resolved by two-dimensional electrophoresis and analyzed for G(s)alpha (S49) or G(q)alpha/G11) (e2m11) content. Four individual immunoblot signals of Gsalpha protein were identified in S49 lymphoma cells indicating complete resolution of the long G(s)alpha L+/-ser and short G(s)alpha S+/-ser variants of G(s)alpha. All these were diminished by prolonged agonist (isoprenaline) stimulation. In e2m11-HEK cells, five different immunoblot signals were detected indicating post-translational modification of G proteins of G(q)alpha/G(11)alpha family. The two major spots corresponding to exogenously (over)expressed G(11)alpha and endogenous G(q)alpha were reduced; the minor spots diminished by hormonal stimulation. Parallel analysis by silver staining of the total protein content indicated that no major changes in protein composition occurred under these conditions. Our data thus indicate that agonist-stimulation of target cells results in down-regulation of all different members of G(s) and G(q)/G(11) families. This agonist-specific effect may be demonstrated in crude membrane as well as domain/raft preparations and it is not accompanied by changes in overall protein composition.

  10. Performance of new automated transthoracic three-dimensional echocardiographic software for left ventricular volumes and function assessment in routine clinical practice: Comparison with 3 Tesla cardiac magnetic resonance.

    Science.gov (United States)

    Levy, Franck; Dan Schouver, Elie; Iacuzio, Laura; Civaia, Filippo; Rusek, Stephane; Dommerc, Carinne; Marechaux, Sylvestre; Dor, Vincent; Tribouilloy, Christophe; Dreyfus, Gilles

    2017-11-01

    Three-dimensional (3D) transthoracic echocardiography (TTE) is superior to two-dimensional Simpson's method for assessment of left ventricular (LV) volumes and LV ejection fraction (LVEF). Nevertheless, 3D TTE is not incorporated into everyday practice, as current LV chamber quantification software products are time-consuming. To evaluate the feasibility, accuracy and reproducibility of new fully automated fast 3D TTE software (HeartModel A.I. ; Philips Healthcare, Andover, MA, USA) for quantification of LV volumes and LVEF in routine practice; to compare the 3D LV volumes and LVEF obtained with a cardiac magnetic resonance (CMR) reference; and to optimize automated default border settings with CMR as reference. Sixty-three consecutive patients, who had comprehensive 3D TTE and CMR examinations within 24hours, were eligible for inclusion. Nine patients (14%) were excluded because of insufficient echogenicity in the 3D TTE. Thus, 54 patients (40 men; mean age 63±13 years) were prospectively included into the study. The inter- and intraobserver reproducibilities of 3D TTE were excellent (coefficient of variation<10%) for end-diastolic volume (EDV), end-systolic volume (ESV) and LVEF. Despite a slight underestimation of EDV using 3D TTE compared with CMR (bias=-22±34mL; P<0.0001), a significant correlation was found between the two measurements (r=0.93; P=0.0001). Enlarging default border detection settings leads to frequent volume overestimation in the general population, but improved agreement with CMR in patients with LVEF≤50%. Correlations between 3D TTE and CMR for ESV and LVEF were excellent (r=0.93 and r=0.91, respectively; P<0.0001). 3D TTE using new-generation fully automated software is a feasible, fast, reproducible and accurate imaging modality for LV volumetric quantification in routine practice. Optimization of border detection settings may increase agreement with CMR for EDV assessment in dilated ventricles. Copyright © 2017 Elsevier Masson

  11. Three-dimensional electron diffraction as a complementary technique to powder X-ray diffraction for phase identification and structure solution of powders

    Directory of Open Access Journals (Sweden)

    Yifeng Yun

    2015-03-01

    Full Text Available Phase identification and structure determination are important and widely used techniques in chemistry, physics and materials science. Recently, two methods for automated three-dimensional electron diffraction (ED data collection, namely automated diffraction tomography (ADT and rotation electron diffraction (RED, have been developed. Compared with X-ray diffraction (XRD and two-dimensional zonal ED, three-dimensional ED methods have many advantages in identifying phases and determining unknown structures. Almost complete three-dimensional ED data can be collected using the ADT and RED methods. Since each ED pattern is usually measured off the zone axes by three-dimensional ED methods, dynamic effects are much reduced compared with zonal ED patterns. Data collection is easy and fast, and can start at any arbitrary orientation of the crystal, which facilitates automation. Three-dimensional ED is a powerful technique for structure identification and structure solution from individual nano- or micron-sized particles, while powder X-ray diffraction (PXRD provides information from all phases present in a sample. ED suffers from dynamic scattering, while PXRD data are kinematic. Three-dimensional ED methods and PXRD are complementary and their combinations are promising for studying multiphase samples and complicated crystal structures. Here, two three-dimensional ED methods, ADT and RED, are described. Examples are given of combinations of three-dimensional ED methods and PXRD for phase identification and structure determination over a large number of different materials, from Ni–Se–O–Cl crystals, zeolites, germanates, metal–organic frameworks and organic compounds to intermetallics with modulated structures. It is shown that three-dimensional ED is now as feasible as X-ray diffraction for phase identification and structure solution, but still needs further development in order to be as accurate as X-ray diffraction. It is expected that three-dimensional

  12. Three-dimensional electron diffraction as a complementary technique to powder X-ray diffraction for phase identification and structure solution of powders.

    Science.gov (United States)

    Yun, Yifeng; Zou, Xiaodong; Hovmöller, Sven; Wan, Wei

    2015-03-01

    Phase identification and structure determination are important and widely used techniques in chemistry, physics and materials science. Recently, two methods for automated three-dimensional electron diffraction (ED) data collection, namely automated diffraction tomography (ADT) and rotation electron diffraction (RED), have been developed. Compared with X-ray diffraction (XRD) and two-dimensional zonal ED, three-dimensional ED methods have many advantages in identifying phases and determining unknown structures. Almost complete three-dimensional ED data can be collected using the ADT and RED methods. Since each ED pattern is usually measured off the zone axes by three-dimensional ED methods, dynamic effects are much reduced compared with zonal ED patterns. Data collection is easy and fast, and can start at any arbitrary orientation of the crystal, which facilitates automation. Three-dimensional ED is a powerful technique for structure identification and structure solution from individual nano- or micron-sized particles, while powder X-ray diffraction (PXRD) provides information from all phases present in a sample. ED suffers from dynamic scattering, while PXRD data are kinematic. Three-dimensional ED methods and PXRD are complementary and their combinations are promising for studying multiphase samples and complicated crystal structures. Here, two three-dimensional ED methods, ADT and RED, are described. Examples are given of combinations of three-dimensional ED methods and PXRD for phase identification and structure determination over a large number of different materials, from Ni-Se-O-Cl crystals, zeolites, germanates, metal-organic frameworks and organic compounds to intermetallics with modulated structures. It is shown that three-dimensional ED is now as feasible as X-ray diffraction for phase identification and structure solution, but still needs further development in order to be as accurate as X-ray diffraction. It is expected that three-dimensional ED methods

  13. Tuning spin transport across two-dimensional organometallic junctions

    Science.gov (United States)

    Liu, Shuanglong; Wang, Yun-Peng; Li, Xiangguo; Fry, James N.; Cheng, Hai-Ping

    2018-01-01

    We study via first-principles modeling and simulation two-dimensional spintronic junctions made of metal-organic frameworks consisting of two Mn-phthalocyanine ferromagnetic metal leads and semiconducting Ni-phthalocyanine channels of various lengths. These systems exhibit a large tunneling magnetoresistance ratio; the transmission functions of such junctions can be tuned using gate voltage by three orders of magnitude. We find that the origin of this drastic change lies in the orbital alignment and hybridization between the leads and the center electronic states. With physical insight into the observed on-off phenomenon, we predict a gate-controlled spin current switch based on two-dimensional crystallines and offer general guidelines for designing spin junctions using 2D materials.

  14. CORPORATE VALUATION USING TWO-DIMENSIONAL MONTE CARLO SIMULATION

    Directory of Open Access Journals (Sweden)

    Toth Reka

    2010-12-01

    Full Text Available In this paper, we have presented a corporate valuation model. The model combine several valuation methods in order to get more accurate results. To determine the corporate asset value we have used the Gordon-like two-stage asset valuation model based on the calculation of the free cash flow to the firm. We have used the free cash flow to the firm to determine the corporate market value, which was calculated with use of the Black-Scholes option pricing model in frame of the two-dimensional Monte Carlo simulation method. The combined model and the use of the two-dimensional simulation model provides a better opportunity for the corporate value estimation.

  15. Laser sheet dropsizing based on two-dimensional Raman and Mie scattering.

    Science.gov (United States)

    Malarski, Anna; Schürer, Benedikt; Schmitz, Ingo; Zigan, Lars; Flügel, Alexandre; Leipertz, Alfred

    2009-04-01

    The imaging and quantification of droplet sizes in sprays is a challenging task for optical scientists and engineers. Laser sheet dropsizing (LSDS) combines the two-dimensional information of two different optical processes, one that is proportional to the droplet volume and one that depends on the droplet surface, e.g., Mie scattering. Besides Mie scattering, here we use two-dimensional Raman scattering as the volume-dependent measurement technique. Two different calibration strategies are presented and discussed. Two-dimensional droplet size distributions in a spray have been validated in comparison with the results of point-resolved phase Doppler anemometry (PDA) measurements.

  16. Laser sheet dropsizing based on two-dimensional Raman and Mie scattering

    International Nuclear Information System (INIS)

    Malarski, Anna; Schuerer, Benedikt; Schmitz, Ingo; Zigan, Lars; Fluegel, Alexandre; Leipertz, Alfred

    2009-01-01

    The imaging and quantification of droplet sizes in sprays is a challenging task for optical scientists and engineers. Laser sheet dropsizing (LSDS) combines the two-dimensional information of two different optical processes, one that is proportional to the droplet volume and one that depends on the droplet surface, e.g., Mie scattering. Besides Mie scattering, here we use two-dimensional Raman scattering as the volume-dependent measurement technique. Two different calibration strategies are presented and discussed. Two-dimensional droplet size distributions in a spray have been validated in comparison with the results of point-resolved phase Doppler anemometry (PDA) measurements

  17. Two dimensional solid state NMR

    International Nuclear Information System (INIS)

    Kentgens, A.P.M.

    1987-01-01

    This thesis illustrates, by discussing some existing and newly developed 2D solid state experiments, that two-dimensional NMR of solids is a useful and important extension of NMR techniques. Chapter 1 gives an overview of spin interactions and averaging techniques important in solid state NMR. As 2D NMR is already an established technique in solutions, only the basics of two dimensional NMR are presented in chapter 2, with an emphasis on the aspects important for solid spectra. The following chapters discuss the theoretical background and applications of specific 2D solid state experiments. An application of 2D-J resolved NMR, analogous to J-resolved spectroscopy in solutions, to natural rubber is given in chapter 3. In chapter 4 the anisotropic chemical shift is mapped out against the heteronuclear dipolar interaction to obtain information about the orientation of the shielding tensor in poly-(oxymethylene). Chapter 5 concentrates on the study of super-slow molecular motions in polymers using a variant of the 2D exchange experiment developed by us. Finally chapter 6 discusses a new experiment, 2D nutation NMR, which makes it possible to study the quadrupole interaction of half-integer spins. 230 refs.; 48 figs.; 8 tabs

  18. Sums of two-dimensional spectral triples

    DEFF Research Database (Denmark)

    Christensen, Erik; Ivan, Cristina

    2007-01-01

    construct a sum of two dimensional modules which reflects some aspects of the topological dimensions of the compact metric space, but this will only give the metric back approximately. At the end we make an explicit computation of the last module for the unit interval in. The metric is recovered exactly...

  19. New hybrid lead iodides: From one-dimensional chain to two-dimensional layered perovskite structure

    International Nuclear Information System (INIS)

    Xiong, Kecai; Liu, Wei; Teat, Simon J.; An, Litao; Wang, Hao; Emge, Thomas J.; Li, Jing

    2015-01-01

    Two new hybrid lead halides (H 2 BDA)[PbI 4 ] (1) (H 2 BDA=1,4-butanediammonium dication) and (HNPEIM)[PbI 3 ] (2) (HNPEIM=N-​phenyl-ethanimidamidine cation) have been synthesized and structurally characterized. X-ray diffraction analyses reveal that compound 1 features a two-dimensional corner-sharing perovskite layer whereas compound 2 contains one-dimensional edge-sharing double chains. The N-​phenyl-ethanimidamidine cation within compound 2 was generated in-situ under solvothermal conditions. The optical absorption spectra collected at room temperature suggest that both compounds are semiconductors having direct band gaps, with estimated values of 2.64 and 2.73 eV for 1 and 2, respectively. Results from the density functional theory (DFT) calculations are consistent with the experimental data. Density of states (DOS) analysis reveals that in both compounds 1 and 2, the energy states in the valence band maximum region are iodine 5p atomic orbitals with a small contribution from lead 6s, while in the region of conduction band minimum, the major contributions are from the inorganic (Pb 6p atomic orbitals) and organic components (C and N 2p atomic orbitals) in compound 1 and 2, respectively. - Graphical abstract: Two new hybrid lead halides built on one-dimensional edge-sharing double chains and two-dimensional corner-sharing perovskite layers are synthesized and their structural and electronic properties are analyzed. - Highlights: • Two new hybrid lead iodides are designed, synthesized, and characterized. • They are closely related to, but different from, perovskite structures. • The electronic properties of both compounds are analyzed by DFT calculations

  20. New hybrid lead iodides: From one-dimensional chain to two-dimensional layered perovskite structure

    Energy Technology Data Exchange (ETDEWEB)

    Xiong, Kecai; Liu, Wei [Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854 (United States); Teat, Simon J. [Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); An, Litao; Wang, Hao; Emge, Thomas J. [Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854 (United States); Li, Jing, E-mail: jingli@rutgers.edu [Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854 (United States)

    2015-10-15

    Two new hybrid lead halides (H{sub 2}BDA)[PbI{sub 4}] (1) (H{sub 2}BDA=1,4-butanediammonium dication) and (HNPEIM)[PbI{sub 3}] (2) (HNPEIM=N-​phenyl-ethanimidamidine cation) have been synthesized and structurally characterized. X-ray diffraction analyses reveal that compound 1 features a two-dimensional corner-sharing perovskite layer whereas compound 2 contains one-dimensional edge-sharing double chains. The N-​phenyl-ethanimidamidine cation within compound 2 was generated in-situ under solvothermal conditions. The optical absorption spectra collected at room temperature suggest that both compounds are semiconductors having direct band gaps, with estimated values of 2.64 and 2.73 eV for 1 and 2, respectively. Results from the density functional theory (DFT) calculations are consistent with the experimental data. Density of states (DOS) analysis reveals that in both compounds 1 and 2, the energy states in the valence band maximum region are iodine 5p atomic orbitals with a small contribution from lead 6s, while in the region of conduction band minimum, the major contributions are from the inorganic (Pb 6p atomic orbitals) and organic components (C and N 2p atomic orbitals) in compound 1 and 2, respectively. - Graphical abstract: Two new hybrid lead halides built on one-dimensional edge-sharing double chains and two-dimensional corner-sharing perovskite layers are synthesized and their structural and electronic properties are analyzed. - Highlights: • Two new hybrid lead iodides are designed, synthesized, and characterized. • They are closely related to, but different from, perovskite structures. • The electronic properties of both compounds are analyzed by DFT calculations.

  1. Pair Interaction of Dislocations in Two-Dimensional Crystals

    Science.gov (United States)

    Eisenmann, C.; Gasser, U.; Keim, P.; Maret, G.; von Grünberg, H. H.

    2005-10-01

    The pair interaction between crystal dislocations is systematically explored by analyzing particle trajectories of two-dimensional colloidal crystals measured by video microscopy. The resulting pair energies are compared to Monte Carlo data and to predictions derived from the standard Hamiltonian of the elastic theory of dislocations. Good agreement is found with respect to the distance and temperature dependence of the interaction potential, but not regarding the angle dependence where discrete lattice effects become important. Our results on the whole confirm that the dislocation Hamiltonian allows a quantitative understanding of the formation and interaction energies of dislocations in two-dimensional crystals.

  2. Three-dimensional versus two-dimensional vision in laparoscopy

    DEFF Research Database (Denmark)

    Sørensen, Stine D; Savran, Mona Meral; Konge, Lars

    2016-01-01

    were cohort size and characteristics, skill trained or operation performed, instrument used, outcome measures, and conclusions. Two independent authors performed the search and data extraction. RESULTS: Three hundred and forty articles were screened for eligibility, and 31 RCTs were included...... through a two-dimensional (2D) projection on a monitor, which results in loss of depth perception. To counter this problem, 3D imaging for laparoscopy was developed. A systematic review of the literature was performed to assess the effect of 3D laparoscopy. METHODS: A systematic search of the literature...... in the review. Three trials were carried out in a clinical setting, and 28 trials used a simulated setting. Time was used as an outcome measure in all of the trials, and number of errors was used in 19 out of 31 trials. Twenty-two out of 31 trials (71 %) showed a reduction in performance time, and 12 out of 19...

  3. Self-focusing instability of two-dimensional solitons and vortices

    DEFF Research Database (Denmark)

    Kuznetsov, E.A.; Juul Rasmussen, J.

    1995-01-01

    The instability of two-dimensional solitons and vortices is demonstrated in the framework of the three-dimensional nonlinear Schrodinger equation (NLSE). The instability can be regarded as the analog of the Kadomtsev-Petviashvili instability [B. B. Kadomtsev and V. I. Petviashvili, Sov. Phys. Dokl...

  4. Three-dimensional protein structure prediction: Methods and computational strategies.

    Science.gov (United States)

    Dorn, Márcio; E Silva, Mariel Barbachan; Buriol, Luciana S; Lamb, Luis C

    2014-10-12

    A long standing problem in structural bioinformatics is to determine the three-dimensional (3-D) structure of a protein when only a sequence of amino acid residues is given. Many computational methodologies and algorithms have been proposed as a solution to the 3-D Protein Structure Prediction (3-D-PSP) problem. These methods can be divided in four main classes: (a) first principle methods without database information; (b) first principle methods with database information; (c) fold recognition and threading methods; and (d) comparative modeling methods and sequence alignment strategies. Deterministic computational techniques, optimization techniques, data mining and machine learning approaches are typically used in the construction of computational solutions for the PSP problem. Our main goal with this work is to review the methods and computational strategies that are currently used in 3-D protein prediction. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Alpha1-acid glycoprotein post-translational modifications: a comparative two dimensional electrophoresis based analysis

    Directory of Open Access Journals (Sweden)

    P. Roncada

    2010-04-01

    Full Text Available Alpha1-acid glycoprotein (AGP is an immunomodulatory protein expressed by hepatocytes in response to the systemic reaction that follows tissue damage caused by inflammation, infection or trauma. A proteomic approach based on two dimensional electrophoresis, immunoblotting and staining of 2DE gels with dyes specific for post-translational modifications (PTMs such as glycosylation and phosphorylation has been used to evaluate the differential interspecific protein expression of AGP purified from human, bovine and ovine sera. By means of these techniques, several isoforms have been identified in the investigated species: they have been found to change both with regard to the number of isoforms expressed under physiological condition and with regard to the quality of PTMs (i.e. different oligosaccharidic chains, presence/absence of phosphorilations. In particular, it is suggested that bovine serum AGP may have one of the most complex pattern of PTMs among serum proteins of mammals studied so far.

  6. Automated de novo phasing and model building of coiled-coil proteins.

    Science.gov (United States)

    Rämisch, Sebastian; Lizatović, Robert; André, Ingemar

    2015-03-01

    Models generated by de novo structure prediction can be very useful starting points for molecular replacement for systems where suitable structural homologues cannot be readily identified. Protein-protein complexes and de novo-designed proteins are examples of systems that can be challenging to phase. In this study, the potential of de novo models of protein complexes for use as starting points for molecular replacement is investigated. The approach is demonstrated using homomeric coiled-coil proteins, which are excellent model systems for oligomeric systems. Despite the stereotypical fold of coiled coils, initial phase estimation can be difficult and many structures have to be solved with experimental phasing. A method was developed for automatic structure determination of homomeric coiled coils from X-ray diffraction data. In a benchmark set of 24 coiled coils, ranging from dimers to pentamers with resolutions down to 2.5 Å, 22 systems were automatically solved, 11 of which had previously been solved by experimental phasing. The generated models contained 71-103% of the residues present in the deposited structures, had the correct sequence and had free R values that deviated on average by 0.01 from those of the respective reference structures. The electron-density maps were of sufficient quality that only minor manual editing was necessary to produce final structures. The method, named CCsolve, combines methods for de novo structure prediction, initial phase estimation and automated model building into one pipeline. CCsolve is robust against errors in the initial models and can readily be modified to make use of alternative crystallographic software. The results demonstrate the feasibility of de novo phasing of protein-protein complexes, an approach that could also be employed for other small systems beyond coiled coils.

  7. Quasi-two-dimensional thermoelectricity in SnSe

    Science.gov (United States)

    Tayari, V.; Senkovskiy, B. V.; Rybkovskiy, D.; Ehlen, N.; Fedorov, A.; Chen, C.-Y.; Avila, J.; Asensio, M.; Perucchi, A.; di Pietro, P.; Yashina, L.; Fakih, I.; Hemsworth, N.; Petrescu, M.; Gervais, G.; Grüneis, A.; Szkopek, T.

    2018-01-01

    Stannous selenide is a layered semiconductor that is a polar analog of black phosphorus and of great interest as a thermoelectric material. Unusually, hole doped SnSe supports a large Seebeck coefficient at high conductivity, which has not been explained to date. Angle-resolved photoemission spectroscopy, optical reflection spectroscopy, and magnetotransport measurements reveal a multiple-valley valence-band structure and a quasi-two-dimensional dispersion, realizing a Hicks-Dresselhaus thermoelectric contributing to the high Seebeck coefficient at high carrier density. We further demonstrate that the hole accumulation layer in exfoliated SnSe transistors exhibits a field effect mobility of up to 250 cm2/V s at T =1.3 K . SnSe is thus found to be a high-quality quasi-two-dimensional semiconductor ideal for thermoelectric applications.

  8. Acoustic phonon emission by two dimensional plasmons

    International Nuclear Information System (INIS)

    Mishonov, T.M.

    1990-06-01

    Acoustic wave emission of the two dimensional plasmons in a semiconductor or superconductor microstructure is investigated by using the phenomenological deformation potential within the jellium model. The plasmons are excited by the external electromagnetic (e.m.) field. The power conversion coefficient of e.m. energy into acoustic wave energy is also estimated. It is shown, the coherent transformation has a sharp resonance at the plasmon frequency of the two dimensional electron gas (2DEG). The incoherent transformation of the e.m. energy is generated by ohmic dissipation of 2DEG. The method proposed for coherent phonon beam generation can be very effective for high mobility 2DEG and for thin superconducting layers if the plasmon frequency ω is smaller than the superconducting gap 2Δ. (author). 21 refs, 1 fig

  9. Two- and three-dimensional CT evaluation of sacral and pelvic anomalies

    International Nuclear Information System (INIS)

    Kuhlman, J.E.; Fishman, E.K.; Magid, D.

    1988-01-01

    Pelvic anomalies are difficult to evaluate with standard techniques. Detailed knowledge of the existing pelvic structures and musculature is essential for successful repair. The authors evaluated 12 patients with complex malformations of the pelvis using two- and three-dimensional imaging. The anomalies included bladder exstrophy (n = 4), cloacal exstrophy (n = 1), duplicated and absent sacrum (n = 3), myelomeningoceles (n = 2), and diastrophic dwarfism (n = 2). The two-dimensional images consisted of sequential coronal and sagittal reconstructions that could be reviewed dynamically on screen. Three-dimensional images were generated on the Pixar imaging computer with use of volumetric rendering. Two- and three-dimensional CT proved complementary in the evaluation of pelvic anomalies, providing optimal information from transaxial CT data

  10. Two-dimensional Lorentz-Weyl anomaly and gravitational Chern-Simons theory

    International Nuclear Information System (INIS)

    Chamseddine, A.H.; Froehlich, J.

    1992-01-01

    Two-dimensional chiral fermions and bosons, more generally conformal blocks of two-dimensional conformal field theories, exhibit Weyl-, Lorentz- and mixed Lorentz-Weyl anomalies. A novel way of computing these anomalies for a system of chiral bosons of arbitrary conformal spin j is sketched. It is shown that the Lorentz- and mixed Lorentz-Weyl anomalies of these theories can be cancelled by the anomalies of a three-dimensional classical Chern-Simons action for the spin connection, expressed in terms of the dreibein field. Some tentative applications of this result to string theory are indicated. (orig.)

  11. Bayesian approach for peak detection in two-dimensional chromatography

    NARCIS (Netherlands)

    Vivó-Truyols, G.

    2012-01-01

    A new method for peak detection in two-dimensional chromatography is presented. In a first step, the method starts with a conventional one-dimensional peak detection algorithm to detect modulated peaks. In a second step, a sophisticated algorithm is constructed to decide which of the individual

  12. Energy Spectra of Vortex Distributions in Two-Dimensional Quantum Turbulence

    Directory of Open Access Journals (Sweden)

    Ashton S. Bradley

    2012-10-01

    Full Text Available We theoretically explore key concepts of two-dimensional turbulence in a homogeneous compressible superfluid described by a dissipative two-dimensional Gross-Pitaeveskii equation. Such a fluid supports quantized vortices that have a size characterized by the healing length ξ. We show that, for the divergence-free portion of the superfluid velocity field, the kinetic-energy spectrum over wave number k may be decomposed into an ultraviolet regime (k≫ξ^{-1} having a universal k^{-3} scaling arising from the vortex core structure, and an infrared regime (k≪ξ^{-1} with a spectrum that arises purely from the configuration of the vortices. The Novikov power-law distribution of intervortex distances with exponent -1/3 for vortices of the same sign of circulation leads to an infrared kinetic-energy spectrum with a Kolmogorov k^{-5/3} power law, which is consistent with the existence of an inertial range. The presence of these k^{-3} and k^{-5/3} power laws, together with the constraint of continuity at the smallest configurational scale k≈ξ^{-1}, allows us to derive a new analytical expression for the Kolmogorov constant that we test against a numerical simulation of a forced homogeneous, compressible, two-dimensional superfluid. The numerical simulation corroborates our analysis of the spectral features of the kinetic-energy distribution, once we introduce the concept of a clustered fraction consisting of the fraction of vortices that have the same sign of circulation as their nearest neighboring vortices. Our analysis presents a new approach to understanding two-dimensional quantum turbulence and interpreting similarities and differences with classical two-dimensional turbulence, and suggests new methods to characterize vortex turbulence in two-dimensional quantum fluids via vortex position and circulation measurements.

  13. Dynamics of vortex interactions in two-dimensional flows

    DEFF Research Database (Denmark)

    Juul Rasmussen, J.; Nielsen, A.H.; Naulin, V.

    2002-01-01

    The dynamics and interaction of like-signed vortex structures in two dimensional flows are investigated by means of direct numerical solutions of the two-dimensional Navier-Stokes equations. Two vortices with distributed vorticity merge when their distance relative to their radius, d/R-0l. is below...... a critical value, a(c). Using the Weiss-field, a(c) is estimated for vortex patches. Introducing an effective radius for vortices with distributed vorticity, we find that 3.3 ... is effectively producing small scale structures and the relation to the enstrophy "cascade" in developed 2D turbulence is discussed. The influence of finite viscosity on the merging is also investigated. Additionally, we examine vortex interactions on a finite domain, and discuss the results in connection...

  14. Two-dimensional atom localization via Raman-driven coherence

    Energy Technology Data Exchange (ETDEWEB)

    Rahmatullah,; Qamar, Sajid, E-mail: sajid_qamar@comsats.edu.pk

    2014-02-07

    A scheme for two-dimensional (2D) atom localization via Raman-driven coherence in a four-level diamond-configuration system is suggested. The atom interacts with two orthogonal standing-wave fields where each standing-wave field is constructed from the superposition of the two-standing wave fields along the corresponding directions. Due to the position-dependent atom–field interaction, the frequency of the spontaneously emitted photon carries the position information about the atom. We investigate the effect of the detunings and phase shifts associated with standing-wave fields. Unique position information of the single atom is obtained by properly adjusting the system parameters. This is an extension of our previous proposal for one-dimensional atom localization via Raman-driven coherence.

  15. Efficient processing of two-dimensional arrays with C or C++

    Science.gov (United States)

    Donato, David I.

    2017-07-20

    Because fast and efficient serial processing of raster-graphic images and other two-dimensional arrays is a requirement in land-change modeling and other applications, the effects of 10 factors on the runtimes for processing two-dimensional arrays with C and C++ are evaluated in a comparative factorial study. This study’s factors include the choice among three C or C++ source-code techniques for array processing; the choice of Microsoft Windows 7 or a Linux operating system; the choice of 4-byte or 8-byte array elements and indexes; and the choice of 32-bit or 64-bit memory addressing. This study demonstrates how programmer choices can reduce runtimes by 75 percent or more, even after compiler optimizations. Ten points of practical advice for faster processing of two-dimensional arrays are offered to C and C++ programmers. Further study and the development of a C and C++ software test suite are recommended.Key words: array processing, C, C++, compiler, computational speed, land-change modeling, raster-graphic image, two-dimensional array, software efficiency

  16. Dynamical class of a two-dimensional plasmonic Dirac system.

    Science.gov (United States)

    Silva, Érica de Mello

    2015-10-01

    A current goal in plasmonic science and technology is to figure out how to manage the relaxational dynamics of surface plasmons in graphene since its damping constitutes a hinder for the realization of graphene-based plasmonic devices. In this sense we believe it might be of interest to enlarge the knowledge on the dynamical class of two-dimensional plasmonic Dirac systems. According to the recurrence relations method, different systems are said to be dynamically equivalent if they have identical relaxation functions at all times, and such commonality may lead to deep connections between seemingly unrelated physical systems. We employ the recurrence relations approach to obtain relaxation and memory functions of density fluctuations and show that a two-dimensional plasmonic Dirac system at long wavelength and zero temperature belongs to the same dynamical class of standard two-dimensional electron gas and classical harmonic oscillator chain with an impurity mass.

  17. Two-dimensional microstrip detector for neutrons

    Energy Technology Data Exchange (ETDEWEB)

    Oed, A [Institut Max von Laue - Paul Langevin (ILL), 38 - Grenoble (France)

    1997-04-01

    Because of their robust design, gas microstrip detectors, which were developed at ILL, can be assembled relatively quickly, provided the prefabricated components are available. At the beginning of 1996, orders were received for the construction of three two-dimensional neutron detectors. These detectors have been completed. The detectors are outlined below. (author). 2 refs.

  18. Robotic Automation of In Vivo Two-Photon Targeted Whole-Cell Patch-Clamp Electrophysiology.

    Science.gov (United States)

    Annecchino, Luca A; Morris, Alexander R; Copeland, Caroline S; Agabi, Oshiorenoya E; Chadderton, Paul; Schultz, Simon R

    2017-08-30

    Whole-cell patch-clamp electrophysiological recording is a powerful technique for studying cellular function. While in vivo patch-clamp recording has recently benefited from automation, it is normally performed "blind," meaning that throughput for sampling some genetically or morphologically defined cell types is unacceptably low. One solution to this problem is to use two-photon microscopy to target fluorescently labeled neurons. Combining this with robotic automation is difficult, however, as micropipette penetration induces tissue deformation, moving target cells from their initial location. Here we describe a platform for automated two-photon targeted patch-clamp recording, which solves this problem by making use of a closed loop visual servo algorithm. Our system keeps the target cell in focus while iteratively adjusting the pipette approach trajectory to compensate for tissue motion. We demonstrate platform validation with patch-clamp recordings from a variety of cells in the mouse neocortex and cerebellum. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  19. Two-dimensional transport of tokamak plasmas

    International Nuclear Information System (INIS)

    Hirshman, S.P.; Jardin, S.C.

    1979-01-01

    A reduced set of two-fluid transport equations is obtained from the conservation equations describing the time evolution of the differential particle number, entropy, and magnetic fluxes in an axisymmetric toroidal plasma with nested magnetic surfaces. Expanding in the small ratio of perpendicular to parallel mobilities and thermal conductivities yields as solubility constraints one-dimensional equations for the surface-averaged thermodynamic variables and magnetic fluxes. Since Ohm's law E +u x B =R', where R' accounts for any nonideal effects, only determines the particle flow relative to the diffusing magnetic surfaces, it is necessary to solve a single two-dimensional generalized differential equation, (partial/partialt) delpsi. (delp - J x B) =0, to find the absolute velocity of a magnetic surface enclosing a fixed toroidal flux. This equation is linear but nonstandard in that it involves flux surface averages of the unknown velocity. Specification of R' and the cross-field ion and electron heat fluxes provides a closed system of equations. A time-dependent coordinate transformation is used to describe the diffusion of plasma quantities through magnetic surfaces of changing shape

  20. Decoherence in two-dimensional quantum walks

    International Nuclear Information System (INIS)

    Oliveira, A. C.; Portugal, R.; Donangelo, R.

    2006-01-01

    We analyze the decoherence in quantum walks in two-dimensional lattices generated by broken-link-type noise. In this type of decoherence, the links of the lattice are randomly broken with some given constant probability. We obtain the evolution equation for a quantum walker moving on two-dimensional (2D) lattices subject to this noise, and we point out how to generalize for lattices in more dimensions. In the nonsymmetric case, when the probability of breaking links in one direction is different from the probability in the perpendicular direction, we have obtained a nontrivial result. If one fixes the link-breaking probability in one direction, and gradually increases the probability in the other direction from 0 to 1, the decoherence initially increases until it reaches a maximum value, and then it decreases. This means that, in some cases, one can increase the noise level and still obtain more coherence. Physically, this can be explained as a transition from a decoherent 2D walk to a coherent 1D walk

  1. An automated three-dimensional detection and segmentation method for touching cells by integrating concave points clustering and random walker algorithm.

    Directory of Open Access Journals (Sweden)

    Yong He

    Full Text Available Characterizing cytoarchitecture is crucial for understanding brain functions and neural diseases. In neuroanatomy, it is an important task to accurately extract cell populations' centroids and contours. Recent advances have permitted imaging at single cell resolution for an entire mouse brain using the Nissl staining method. However, it is difficult to precisely segment numerous cells, especially those cells touching each other. As presented herein, we have developed an automated three-dimensional detection and segmentation method applied to the Nissl staining data, with the following two key steps: 1 concave points clustering to determine the seed points of touching cells; and 2 random walker segmentation to obtain cell contours. Also, we have evaluated the performance of our proposed method with several mouse brain datasets, which were captured with the micro-optical sectioning tomography imaging system, and the datasets include closely touching cells. Comparing with traditional detection and segmentation methods, our approach shows promising detection accuracy and high robustness.

  2. Two- and three-dimensional evaluation of the acetabulum in the pediatric patient

    International Nuclear Information System (INIS)

    Magid, D.; Fishman, E.K.; Sponseller, P.D.

    1987-01-01

    Complex anatomic structures such as the hip and acetabulum are best evaluated with the use of two- and three-dimensional reconstruction techniques and standard transaxial CT data. CT scans of children with various hip pathologies, including congenital hip dislocation, slipped capital femoral epiphyses, hip dysplasias, dwarfism, and acetabular fractures, were reviewed to determine the value of two- and three-dimensional imaging. The advantages of two-dimensional imaging techniques (sequential coronal/sagittal reconstruction) and three-dimensional valumetric imaging techniques (using real-time video display) are illustrated with specific examples

  3. Equivalency of two-dimensional algebras

    International Nuclear Information System (INIS)

    Santos, Gildemar Carneiro dos; Pomponet Filho, Balbino Jose S.

    2011-01-01

    Full text: Let us consider a vector z = xi + yj over the field of real numbers, whose basis (i,j) satisfy a given algebra. Any property of this algebra will be reflected in any function of z, so we can state that the knowledge of the properties of an algebra leads to more general conclusions than the knowledge of the properties of a function. However structural properties of an algebra do not change when this algebra suffers a linear transformation, though the structural constants defining this algebra do change. We say that two algebras are equivalent to each other whenever they are related by a linear transformation. In this case, we have found that some relations between the structural constants are sufficient to recognize whether or not an algebra is equivalent to another. In spite that the basis transform linearly, the structural constants change like a third order tensor, but some combinations of these tensors result in a linear transformation, allowing to write the entries of the transformation matrix as function of the structural constants. Eventually, a systematic way to find the transformation matrix between these equivalent algebras is obtained. In this sense, we have performed the thorough classification of associative commutative two-dimensional algebras, and find that even non-division algebra may be helpful in solving non-linear dynamic systems. The Mandelbrot set was used to have a pictorial view of each algebra, since equivalent algebras result in the same pattern. Presently we have succeeded in classifying some non-associative two-dimensional algebras, a task more difficult than for associative one. (author)

  4. Histogram deconvolution - An aid to automated classifiers

    Science.gov (United States)

    Lorre, J. J.

    1983-01-01

    It is shown that N-dimensional histograms are convolved by the addition of noise in the picture domain. Three methods are described which provide the ability to deconvolve such noise-affected histograms. The purpose of the deconvolution is to provide automated classifiers with a higher quality N-dimensional histogram from which to obtain classification statistics.

  5. Two-dimensional inverse planning and delivery with a preclinical image guided microirradiator

    International Nuclear Information System (INIS)

    Stewart, James M. P.; Lindsay, Patricia E.; Jaffray, David A.

    2013-01-01

    Purpose: Recent advances in preclinical radiotherapy systems have provided the foundation for scaling many of the elements of clinical radiation therapy practice to the dimensions and energy demanded in small animal studies. Such systems support the technical capabilities to accurately deliver highly complex dose distributions, but methods to optimize and deliver such distributions remain in their infancy. This study developed an optimization method based on empirically measured two-dimensional dose kernel measurements to deliver arbitrary planar dose distributions on a recently developed small animal radiotherapy platform.Methods: A two-dimensional dose kernel was measured with repeated radiochromic film measurements for the circular 1 mm diameter fixed collimator of the small animal radiotherapy system at 1 cm depth in a solid water phantom. This kernel was utilized in a sequential quadratic programming optimization framework to determine optimal beam positions and weights to deliver an arbitrary desired dose distribution. The positions and weights were then translated to a set of stage motions to automatically deliver the optimized dose distribution. End-to-end efficacy of the framework was quantified through five repeated deliveries of two dosimetric challenges: (1) a 5 mm radius bullseye distribution, and (2) a “sock” distribution contained within a 9 × 13 mm bounding box incorporating rectangular, semicircular, and exponentially decaying geometric constructs and a rectangular linear dose gradient region. These two challenges were designed to gauge targeting, geometric, and dosimetric fidelity.Results: Optimization of the bullseye and sock distributions required 2.1 and 5.9 min and utilized 50 and 77 individual beams for delivery, respectively. Automated delivery of the resulting optimized distributions, validated using radiochromic film measurements, revealed an average targeting accuracy of 0.32 mm, and a dosimetric delivery error along four line

  6. Comparison of two three-dimensional cephalometric analysis computer software.

    Science.gov (United States)

    Sawchuk, Dena; Alhadlaq, Adel; Alkhadra, Thamer; Carlyle, Terry D; Kusnoto, Budi; El-Bialy, Tarek

    2014-10-01

    Three-dimensional cephalometric analyses are getting more attraction in orthodontics. The aim of this study was to compare two softwares to evaluate three-dimensional cephalometric analyses of orthodontic treatment outcomes. Twenty cone beam computed tomography images were obtained using i-CAT(®) imaging system from patient's records as part of their regular orthodontic records. The images were analyzed using InVivoDental5.0 (Anatomage Inc.) and 3DCeph™ (University of Illinois at Chicago, Chicago, IL, USA) software. Before and after orthodontic treatments data were analyzed using t-test. Reliability test using interclass correlation coefficient was stronger for InVivoDental5.0 (0.83-0.98) compared with 3DCeph™ (0.51-0.90). Paired t-test comparison of the two softwares shows no statistical significant difference in the measurements made in the two softwares. InVivoDental5.0 measurements are more reproducible and user friendly when compared to 3DCeph™. No statistical difference between the two softwares in linear or angular measurements. 3DCeph™ is more time-consuming in performing three-dimensional analysis compared with InVivoDental5.0.

  7. Chimera patterns in two-dimensional networks of coupled neurons

    Science.gov (United States)

    Schmidt, Alexander; Kasimatis, Theodoros; Hizanidis, Johanne; Provata, Astero; Hövel, Philipp

    2017-03-01

    We discuss synchronization patterns in networks of FitzHugh-Nagumo and leaky integrate-and-fire oscillators coupled in a two-dimensional toroidal geometry. A common feature between the two models is the presence of fast and slow dynamics, a typical characteristic of neurons. Earlier studies have demonstrated that both models when coupled nonlocally in one-dimensional ring networks produce chimera states for a large range of parameter values. In this study, we give evidence of a plethora of two-dimensional chimera patterns of various shapes, including spots, rings, stripes, and grids, observed in both models, as well as additional patterns found mainly in the FitzHugh-Nagumo system. Both systems exhibit multistability: For the same parameter values, different initial conditions give rise to different dynamical states. Transitions occur between various patterns when the parameters (coupling range, coupling strength, refractory period, and coupling phase) are varied. Many patterns observed in the two models follow similar rules. For example, the diameter of the rings grows linearly with the coupling radius.

  8. Design of a rotational three-dimensional nonimaging device by a compensated two-dimensional design process.

    Science.gov (United States)

    Yang, Yi; Qian, Ke-Yuan; Luo, Yi

    2006-07-20

    A compensation process has been developed to design rotational three-dimensional (3D) nonimaging devices. By compensating the desired light distribution during a two-dimensional (2D) design process for an extended Lambertian source using a compensation coefficient, the meridian plane of a 3D device with good performance can be obtained. This method is suitable in many cases with fast calculation speed. Solutions to two kinds of optical design problems have been proposed, and the limitation of this compensated 2D design method is discussed.

  9. Study on two-dimensional induced signal readout of MRPC

    International Nuclear Information System (INIS)

    Wu Yucheng; Yue Qian; Li Yuanjing; Ye Jin; Cheng Jianping; Wang Yi; Li Jin

    2012-01-01

    A kind of two-dimensional readout electrode structure for the induced signal readout of MRPC has been studied in both simulation and experiments. Several MRPC prototypes are produced and a series of test experiments have been done to compare with the result of simulation, in order to verify the simulation model. The experiment results are in good agreement with those of simulation. This method will be used to design the two-dimensional signal readout mode of MRPC in the future work.

  10. Two-dimensional electronic femtosecond stimulated Raman spectroscopy

    Directory of Open Access Journals (Sweden)

    Ogilvie J.P.

    2013-03-01

    Full Text Available We report two-dimensional electronic spectroscopy with a femtosecond stimulated Raman scattering probe. The method reveals correlations between excitation energy and excited state vibrational structure following photoexcitation. We demonstrate the method in rhodamine 6G.

  11. Remotely Piloted Aircraft Systems Panel (RPASP) Working Paper: Autonomy and Automation

    Science.gov (United States)

    Shively, Jay

    2017-01-01

    A significant level of debate and confusion has surrounded the meaning of the terms "autonomy" and "automation". Automation is a multi-dimensional concept, and we propose that RPAS automation should be described with reference to the specific system and task that has been automated, the context in which the automation functions, and other relevant dimensions. In this paper, we present a definition of "automation". We recommend that autonomy and autonomous operations are out of the scope of the RPAS panel. WG7 proposes to develop, in consultation with other workgroups, a taxonomy of "Levels of Automation" for RPAS.

  12. Stability of two-dimensional vorticity filaments

    International Nuclear Information System (INIS)

    Elhmaidi, D.; Provenzale, A.; Lili, T.; Babiano, A.

    2004-01-01

    We discuss the results of a numerical study on the stability of two-dimensional vorticity filaments around a circular vortex. We illustrate how the stability of the filaments depends on the balance between the strain associated with the far field of the vortex and the local vorticity of the filament, and we discuss an empirical criterion for filament stability

  13. The Stanford Automated Mounter: Enabling High-Throughput Protein Crystal Screening at SSRL

    International Nuclear Information System (INIS)

    Smith, C.A.; Cohen, A.E.

    2009-01-01

    The macromolecular crystallography experiment lends itself perfectly to high-throughput technologies. The initial steps including the expression, purification, and crystallization of protein crystals, along with some of the later steps involving data processing and structure determination have all been automated to the point where some of the last remaining bottlenecks in the process have been crystal mounting, crystal screening, and data collection. At the Stanford Synchrotron Radiation Laboratory, a National User Facility that provides extremely brilliant X-ray photon beams for use in materials science, environmental science, and structural biology research, the incorporation of advanced robotics has enabled crystals to be screened in a true high-throughput fashion, thus dramatically accelerating the final steps. Up to 288 frozen crystals can be mounted by the beamline robot (the Stanford Auto-Mounting System) and screened for diffraction quality in a matter of hours without intervention. The best quality crystals can then be remounted for the collection of complete X-ray diffraction data sets. Furthermore, the entire screening and data collection experiment can be controlled from the experimenter's home laboratory by means of advanced software tools that enable network-based control of the highly automated beamlines.

  14. Identification of DNA-binding proteins that interact with the 5'-flanking region of the human D-amino acid oxidase gene by pull-down assay coupled with two-dimensional gel electrophoresis and mass spectrometry.

    Science.gov (United States)

    Tran, Diem Hong; Shishido, Yuji; Chung, Seong Pil; Trinh, Huong Thi Thanh; Yorita, Kazuko; Sakai, Takashi; Fukui, Kiyoshi

    2015-12-10

    D-Amino acid oxidase (DAO) is a flavoenzyme that metabolizes D-amino acids and is expected to be a promising therapeutic target of schizophrenia and glioblastoma. The study of DNA-binding proteins has yielded much information in the regulation of transcription and other biological processes. However, proteins interacting with DAO gene have not been elucidated. Our assessment of human DAO promoter activity using luciferase reporter system indicated the 5'-flanking region of this gene (-4289 bp from transcription initiation site) has a regulatory sequence for gene expression, which is regulated by multi-protein complexes interacting with this region. By using pull-down assay coupled with two-dimensional gel electrophoresis and mass spectrometry, we identified six proteins binding to the 5'-flanking region of the human DAO gene (zinc finger C2HC domain-containing protein 1A; histidine-tRNA ligase, cytoplasmic; molybdenum cofactor biosynthesis protein; 60S ribosomal protein L37; calponin-1; calmodulin binding protein and heterogeneous nuclear ribonucleoprotein A2/B1). These preliminary results will contribute to the advance in the understanding of the potential factors associated with the regulatory mechanism of DAO expression. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Micropatterning of bacteria on two-dimensional lattice protein surface observed by atomic force microscopy

    International Nuclear Information System (INIS)

    Oh, Y.J.; Jo, W.; Lim, J.; Park, S.; Kim, Y.S.; Kim, Y.

    2008-01-01

    In this study, we characterized the two-dimensional lattice of bovine serum albumin (BSA) as a chemical and physical barrier against bacterial adhesion, using fluorescence microscopy and atomic force microscopy (AFM). The lattice of BSA on glass surface was fabricated by micro-contact printing (μCP), which is a useful way to pattern a wide range of molecules into microscale features on different types of substrates. The contact-mode AFM measurements showed that the average height of the printed BSA monolayer was 5-6 nm. Escherichia coli adhered rapidly on bare glass slide, while the bacterial adhesion was minimized on the lattices in the range of 1-3 μm 2 . Especially, the bacterial adhesion was completely inhibited on a 1 μm 2 lattice. The results suggest that the anti-adhesion effects are due by the steric repulsion forces exerted by BSA

  16. Strain-engineered growth of two-dimensional materials.

    Science.gov (United States)

    Ahn, Geun Ho; Amani, Matin; Rasool, Haider; Lien, Der-Hsien; Mastandrea, James P; Ager Iii, Joel W; Dubey, Madan; Chrzan, Daryl C; Minor, Andrew M; Javey, Ali

    2017-09-20

    The application of strain to semiconductors allows for controlled modification of their band structure. This principle is employed for the manufacturing of devices ranging from high-performance transistors to solid-state lasers. Traditionally, strain is typically achieved via growth on lattice-mismatched substrates. For two-dimensional (2D) semiconductors, this is not feasible as they typically do not interact epitaxially with the substrate. Here, we demonstrate controlled strain engineering of 2D semiconductors during synthesis by utilizing the thermal coefficient of expansion mismatch between the substrate and semiconductor. Using WSe 2 as a model system, we demonstrate stable built-in strains ranging from 1% tensile to 0.2% compressive on substrates with different thermal coefficient of expansion. Consequently, we observe a dramatic modulation of the band structure, manifested by a strain-driven indirect-to-direct bandgap transition and brightening of the dark exciton in bilayer and monolayer WSe 2 , respectively. The growth method developed here should enable flexibility in design of more sophisticated devices based on 2D materials.Strain engineering is an essential tool for modifying local electronic properties in silicon-based electronics. Here, Ahn et al. demonstrate control of biaxial strain in two-dimensional materials based on the growth substrate, enabling more complex low-dimensional electronics.

  17. Two-dimensional heat flow apparatus

    Science.gov (United States)

    McDougall, Patrick; Ayars, Eric

    2014-06-01

    We have created an apparatus to quantitatively measure two-dimensional heat flow in a metal plate using a grid of temperature sensors read by a microcontroller. Real-time temperature data are collected from the microcontroller by a computer for comparison with a computational model of the heat equation. The microcontroller-based sensor array allows previously unavailable levels of precision at very low cost, and the combination of measurement and modeling makes for an excellent apparatus for the advanced undergraduate laboratory course.

  18. Two-Dimensional Extreme Learning Machine

    Directory of Open Access Journals (Sweden)

    Bo Jia

    2015-01-01

    (BP networks. However, like many other methods, ELM is originally proposed to handle vector pattern while nonvector patterns in real applications need to be explored, such as image data. We propose the two-dimensional extreme learning machine (2DELM based on the very natural idea to deal with matrix data directly. Unlike original ELM which handles vectors, 2DELM take the matrices as input features without vectorization. Empirical studies on several real image datasets show the efficiency and effectiveness of the algorithm.

  19. Two-dimensional Semiconductor-Superconductor Hybrids

    DEFF Research Database (Denmark)

    Suominen, Henri Juhani

    This thesis investigates hybrid two-dimensional semiconductor-superconductor (Sm-S) devices and presents a new material platform exhibiting intimate Sm-S coupling straight out of the box. Starting with the conventional approach, we investigate coupling superconductors to buried quantum well....... To overcome these issues we integrate the superconductor directly into the semiconducting material growth stack, depositing it in-situ in a molecular beam epitaxy system under high vacuum. We present a number of experiments on these hybrid heterostructures, demonstrating near unity interface transparency...

  20. Two-Dimensional Tellurene as Excellent Thermoelectric Material

    KAUST Repository

    Sharma, Sitansh; Singh, Nirpendra; Schwingenschlö gl, Udo

    2018-01-01

    We study the thermoelectric properties of two-dimensional tellurene by first-principles calculations and semiclassical Boltzmann transport theory. The HSE06 hybrid functional results in a moderate direct band gap of 1.48 eV at the Γ point. A high

  1. Automated high-throughput protein purification using an ÄKTApurifier and a CETAC autosampler.

    Science.gov (United States)

    Yoo, Daniel; Provchy, Justin; Park, Cynthia; Schulz, Craig; Walker, Kenneth

    2014-05-30

    As the pace of drug discovery accelerates there is an increased focus on screening larger numbers of protein therapeutic candidates to identify those that are functionally superior and to assess manufacturability earlier in the process. Although there have been advances toward high throughput (HT) cloning and expression, protein purification is still an area where improvements can be made to conventional techniques. Current methodologies for purification often involve a tradeoff between HT automation or capacity and quality. We present an ÄKTA combined with an autosampler, the ÄKTA-AS, which has the capability of purifying up to 240 samples in two chromatographic dimensions without the need for user intervention. The ÄKTA-AS has been shown to be reliable with sample volumes between 0.5 mL and 100 mL, and the innovative use of a uniquely configured loading valve ensures reliability by efficiently removing air from the system as well as preventing sample cross contamination. Incorporation of a sample pump flush minimizes sample loss and enables recoveries ranging from the low tens of micrograms to milligram quantities of protein. In addition, when used in an affinity capture-buffer exchange format the final samples are formulated in a buffer compatible with most assays without requirement of additional downstream processing. The system is designed to capture samples in 96-well microplate format allowing for seamless integration of downstream HT analytic processes such as microfluidic or HPLC analysis. Most notably, there is minimal operator intervention to operate this system, thereby increasing efficiency, sample consistency and reducing the risk of human error. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. RPE cell surface proteins in normal and dystrophic rats

    International Nuclear Information System (INIS)

    Clark, V.M.; Hall, M.O.

    1986-01-01

    Membrane-bound proteins in plasma membrane enriched fractions from cultured rat RPE were analyzed by two-dimensional gel electrophoresis. Membrane proteins were characterized on three increasingly specific levels. Total protein was visualized by silver staining. A maximum of 102 separate proteins were counted in silver-stained gels. Glycoproteins were labeled with 3H-glucosamine or 3H-fucose and detected by autoradiography. Thirty-eight fucose-labeled and 61-71 glucosamine-labeled proteins were identified. All of the fucose-labeled proteins were labeled with glucosamine-derived radioactivity. Proteins exposed at the cell surface were labeled by lactoperoxidase-catalyzed radioiodination prior to preparation of membranes for two-dimensional analysis. Forty separate 125I-labeled surface proteins were resolved by two-dimensional electrophoresis/autoradiography. Comparison with the glycoprotein map showed that a number of these surface labeled proteins were glycoproteins. Two-dimensional maps of total protein, fucose-labeled, and glucosamine-labeled glycoproteins, and 125I-labeled surface proteins of membranes from dystrophic (RCS rdy-p+) and normal (Long Evans or RCS rdy+p+) RPE were compared. No differences in the total protein or surface-labeled proteins were observed. However, the results suggest that a 183K glycoprotein is more heavily glycosylated with glucosamine and fucose in normal RPE membranes as compared to membranes from dystrophic RPE

  3. Laser bistatic two-dimensional scattering imaging simulation of lambert cone

    Science.gov (United States)

    Gong, Yanjun; Zhu, Chongyue; Wang, Mingjun; Gong, Lei

    2015-11-01

    This paper deals with the laser bistatic two-dimensional scattering imaging simulation of lambert cone. Two-dimensional imaging is called as planar imaging. It can reflect the shape of the target and material properties. Two-dimensional imaging has important significance for target recognition. The expression of bistatic laser scattering intensity of lambert cone is obtained based on laser radar eauqtion. The scattering intensity of a micro-element on the target could be obtained. The intensity is related to local angle of incidence, local angle of scattering and the infinitesimal area on the cone. According to the incident direction of laser, scattering direction and normal of infinitesimal area, the local incidence angle and scattering angle can be calculated. Through surface integration and the introduction of the rectangular function, we can get the intensity of imaging unit on the imaging surface, and then get Lambert cone bistatic laser two-dimensional scattering imaging simulation model. We analyze the effect of distinguishability, incident direction, observed direction and target size on the imaging. From the results, we can see that the scattering imaging simulation results of the lambert cone bistatic laser is correct.

  4. Bayesian approach for peak detection in two-dimensional chromatography.

    Science.gov (United States)

    Vivó-Truyols, Gabriel

    2012-03-20

    A new method for peak detection in two-dimensional chromatography is presented. In a first step, the method starts with a conventional one-dimensional peak detection algorithm to detect modulated peaks. In a second step, a sophisticated algorithm is constructed to decide which of the individual one-dimensional peaks have been originated from the same compound and should then be arranged in a two-dimensional peak. The merging algorithm is based on Bayesian inference. The user sets prior information about certain parameters (e.g., second-dimension retention time variability, first-dimension band broadening, chromatographic noise). On the basis of these priors, the algorithm calculates the probability of myriads of peak arrangements (i.e., ways of merging one-dimensional peaks), finding which of them holds the highest value. Uncertainty in each parameter can be accounted by adapting conveniently its probability distribution function, which in turn may change the final decision of the most probable peak arrangement. It has been demonstrated that the Bayesian approach presented in this paper follows the chromatographers' intuition. The algorithm has been applied and tested with LC × LC and GC × GC data and takes around 1 min to process chromatograms with several thousands of peaks.

  5. Linkage analysis by two-dimensional DNA typing

    NARCIS (Netherlands)

    te Meerman, G J; Mullaart, E; Meulen ,van der Martin; den Daas, J H; Morolli, B; Uitterlinden, A G; Vijg, J

    1993-01-01

    In two-dimensional (2-D) DNA typing, genomic DNA fragments are separated, first according to size by electrophoresis in a neutral polyacrylamide gel and second according to sequence by denaturing gradient gel electrophoresis, followed by hybridization analysis using micro- and minisatellite core

  6. Device for measuring the two-dimensional distribution of a radioactive substance on a surface

    International Nuclear Information System (INIS)

    Anon.

    1986-01-01

    A device is described by which, using a one-dimensional measuring proportional counter tube depending on position, one can measure the two-dimensionally distributed radioactivity of a surface and can plot this to scale two-dimensionally, after computer processing, or can show it two-dimensionally on a monitor. (orig.) [de

  7. Two-dimensional PCA-based human gait identification

    Science.gov (United States)

    Chen, Jinyan; Wu, Rongteng

    2012-11-01

    It is very necessary to recognize person through visual surveillance automatically for public security reason. Human gait based identification focus on recognizing human by his walking video automatically using computer vision and image processing approaches. As a potential biometric measure, human gait identification has attracted more and more researchers. Current human gait identification methods can be divided into two categories: model-based methods and motion-based methods. In this paper a two-Dimensional Principal Component Analysis and temporal-space analysis based human gait identification method is proposed. Using background estimation and image subtraction we can get a binary images sequence from the surveillance video. By comparing the difference of two adjacent images in the gait images sequence, we can get a difference binary images sequence. Every binary difference image indicates the body moving mode during a person walking. We use the following steps to extract the temporal-space features from the difference binary images sequence: Projecting one difference image to Y axis or X axis we can get two vectors. Project every difference image in the difference binary images sequence to Y axis or X axis difference binary images sequence we can get two matrixes. These two matrixes indicate the styles of one walking. Then Two-Dimensional Principal Component Analysis(2DPCA) is used to transform these two matrixes to two vectors while at the same time keep the maximum separability. Finally the similarity of two human gait images is calculated by the Euclidean distance of the two vectors. The performance of our methods is illustrated using the CASIA Gait Database.

  8. A two-dimensional lattice equation as an extension of the Heideman-Hogan recurrence

    Science.gov (United States)

    Kamiya, Ryo; Kanki, Masataka; Mase, Takafumi; Tokihiro, Tetsuji

    2018-03-01

    We consider a two dimensional extension of the so-called linearizable mappings. In particular, we start from the Heideman-Hogan recurrence, which is known as one of the linearizable Somos-like recurrences, and introduce one of its two dimensional extensions. The two dimensional lattice equation we present is linearizable in both directions, and has the Laurent and the coprimeness properties. Moreover, its reduction produces a generalized family of the Heideman-Hogan recurrence. Higher order examples of two dimensional linearizable lattice equations related to the Dana Scott recurrence are also discussed.

  9. Two-dimensional QCD as a model for strong interaction

    International Nuclear Information System (INIS)

    Ellis, J.

    1977-01-01

    After an introduction to the formalism of two-dimensional QCD, its applications to various strong interaction processes are reviewed. Among the topics discussed are spectroscopy, deep inelastic cross-sections, ''hard'' processes involving hadrons, ''Regge'' behaviour, the existence of the Pomeron, and inclusive hadron cross-sections. Attempts are made to abstracts features useful for four-dimensional QCD phenomenology. (author)

  10. Two-dimensional nuclear magnetic resonance of quadrupolar systems

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Shuanhu [Univ. of California, Berkeley, CA (United States)

    1997-09-01

    This dissertation describes two-dimensional nuclear magnetic resonance theory and experiments which have been developed to study quadruples in the solid state. The technique of multiple-quantum magic-angle spinning (MQMAS) is extensively reviewed and expanded upon in this thesis. Specifically, MQMAS is first compared with another technique, dynamic-angle spinning (DAS). The similarity between the two techniques allows us to extend much of the DAS work to the MQMAS case. Application of MQMAS to a series of aluminum containing materials is then presented. The superior resolution enhancement through MQMAS is exploited to detect the five- and six-coordinated aluminum in many aluminosilicate glasses. Combining the MQMAS method with other experiments, such as HETCOR, greatly expands the possibility of the use of MQMAS to study a large range of problems and is demonstrated in Chapter 5. Finally, the technique switching-angle spinning (SAS) is applied to quadrupolar nuclei to fully characterize a quadrupolar spin system in which all of the 8 NMR parameters are accurately determined. This dissertation is meant to demonstrate that with the combination of two-dimensional NMR concepts and new advanced spinning technologies, a series of multiple-dimensional NMR techniques can be designed to allow a detailed study of quadrupolar nuclei in the solid state.

  11. Two dimensional infinite conformal symmetry

    International Nuclear Information System (INIS)

    Mohanta, N.N.; Tripathy, K.C.

    1993-01-01

    The invariant discontinuous (discrete) conformal transformation groups, namely the Kleinian and Fuchsian groups Gamma (with an arbitrary signature) of H (the Poincare upper half-plane l) and the unit disc Delta are explicitly constructed from the fundamental domain D. The Riemann surface with signatures of Gamma and conformally invariant automorphic forms (functions) with Peterson scalar product are discussed. The functor, where the category of complex Hilbert spaces spanned by the space of cusp forms constitutes the two dimensional conformal field theory. (Author) 7 refs

  12. Stabilizing local boundary conditions for two-dimensional shallow water equations

    KAUST Repository

    Dia, Ben Mansour; Oppelstrup, Jesper

    2018-01-01

    In this article, we present a sub-critical two-dimensional shallow water flow regulation. From the energy estimate of a set of one-dimensional boundary stabilization problems, we obtain a set of polynomial equations with respect to the boundary

  13. Logarithmic Superdiffusion in Two Dimensional Driven Lattice Gases

    Science.gov (United States)

    Krug, J.; Neiss, R. A.; Schadschneider, A.; Schmidt, J.

    2018-03-01

    The spreading of density fluctuations in two-dimensional driven diffusive systems is marginally anomalous. Mode coupling theory predicts that the diffusivity in the direction of the drive diverges with time as (ln t)^{2/3} with a prefactor depending on the macroscopic current-density relation and the diffusion tensor of the fluctuating hydrodynamic field equation. Here we present the first numerical verification of this behavior for a particular version of the two-dimensional asymmetric exclusion process. Particles jump strictly asymmetrically along one of the lattice directions and symmetrically along the other, and an anisotropy parameter p governs the ratio between the two rates. Using a novel massively parallel coupling algorithm that strongly reduces the fluctuations in the numerical estimate of the two-point correlation function, we are able to accurately determine the exponent of the logarithmic correction. In addition, the variation of the prefactor with p provides a stringent test of mode coupling theory.

  14. Waterlike anomalies in a two-dimensional core-softened potential

    Science.gov (United States)

    Bordin, José Rafael; Barbosa, Marcia C.

    2018-02-01

    We investigate the structural, thermodynamic, and dynamic behavior of a two-dimensional (2D) core-corona system using Langevin dynamics simulations. The particles are modeled by employing a core-softened potential which exhibits waterlike anomalies in three dimensions. In previous studies in a quasi-2D system a new region in the pressure versus temperature phase diagram of structural anomalies was observed. Here we show that for the two-dimensional case two regions in the pressure versus temperature phase diagram with structural, density, and diffusion anomalies are observed. Our findings indicate that, while the anomalous region at lower densities is due the competition between the two length scales in the potential at higher densities, the anomalous region is related to the reentrance of the melting line.

  15. Automated 3D ultrasound measurement of the angle of progression in labor.

    Science.gov (United States)

    Montaguti, Elisa; Rizzo, Nicola; Pilu, Gianluigi; Youssef, Aly

    2018-01-01

    To assess the feasibility and reliability of an automated technique for the assessment of the angle of progression (AoP) in labor by using three-dimensional (3D) ultrasound. AoP was assessed by using 3D transperineal ultrasound by two operators in 52 women in active labor to evaluate intra- and interobserver reproducibility. Furthermore, intermethod agreement between automated and manual techniques on 3D images, and between automated technique on 3D vs 2D images were evaluated. Automated measurements were feasible in all cases. Automated measurements were considered acceptable in 141 (90.4%) out of the 156 on the first assessments and in all 156 after repeating measurements for unacceptable evaluations. The automated technique on 3D images demonstrated good intra- and interobserver reproducibility. The 3D-automated technique showed a very good agreement with the 3D manual technique. Notably, AoP calculated with the 3D automated technique were significantly wider in comparison with those measured manually on 3D images (133 ± 17° vs 118 ± 21°, p = 0.013). The assessment of the angle of progression through 3D ultrasound is highly reproducible. However, automated software leads to a systematic overestimation of AoP in comparison with the standard manual technique thus hindering its use in clinical practice in its present form.

  16. On the confinement of a Dirac particle to a two-dimensional ring

    International Nuclear Information System (INIS)

    Bakke, K.; Furtado, C.

    2012-01-01

    In this contribution, we propose a new model for studying the confinement of a spin-half particle to a two-dimensional quantum ring for systems described by the Dirac equation by introducing a new coupling into the Dirac equation. We show that the introduction of this new coupling into the Dirac equation yields a generalization of the two-dimensional quantum ring model proposed by Tan and Inkson [W.-C. Tan, J.C. Inkson, Semicond. Sci. Technol. 11 (1996) 1635] for relativistic spin-half quantum particles. -- Highlights: ► Two-dimensional ring model for condensed matter systems described by the Dirac equation. ► Exact solutions of the Dirac equation. ► Persistent currents for Dirac-like systems confined to a two-dimensional quantum ring.

  17. Mode selection in two-dimensional Bragg resonators based on planar dielectric waveguides

    International Nuclear Information System (INIS)

    Baryshev, V R; Ginzburg, N S; Zaslavskii, V Yu; Malkin, A M; Sergeev, A S; Thumm, M

    2009-01-01

    Two-dimensional Bragg resonators based on planar dielectric waveguides are analysed. It is shown that the doubly periodic corrugation deposited on the dielectric surface in the form of two gratings with translational vectors directed perpendicular to each other ensures effective selection of modes along two coordinates at large Fresnel parameters. This result is obtained both by the method of coupled waves (geometrical optics approximation) and by the direct numerical simulations. Two-dimensional Bragg resonators make it possible to fabricate two-dimensional distributed feedback lasers and to provide generation of spatially coherent radiation in large-volume active media. (waveguides)

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

    Science.gov (United States)

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

    2015-09-01

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

  19. Theories to support method development in comprehensive two-dimensional liquid chromatography - A review

    NARCIS (Netherlands)

    Bedani, F.; Schoenmakers, P.J.; Janssen, H.-G.

    2012-01-01

    On-line comprehensive two-dimensional liquid chromatography techniques promise to resolve samples that current one-dimensional liquid chromatography methods cannot adequately deal with. To make full use of the potential of two-dimensional liquid chromatography, optimization is required. Optimization

  20. Two-dimensional gel electrophoresis data for proteomic profiling of Sporothrix yeast cells

    Directory of Open Access Journals (Sweden)

    Anderson Messias Rodrigues

    2015-03-01

    Full Text Available Sporotrichosis is a chronic infection of the skin and subcutaneous tissues of human and other mammals caused by a complex of cryptic dimorphic fungi in the plant-associated order Ophiostomatales. With major differences between routes of transmission, Sporothrix infections are emerging as new threat in tropical and subtropical areas, particularly in form of outbreaks. The mechanisms underlying the pathogenesis and invasion of Sporothrix spp. are still poorly understood and many virulence factors remain unidentified. In this scenario, a global analysis of proteins expressed by clinical Sporothrix species combined with the identification of seroreactive proteins is overdue. Optimization of sample preparation and electrophoresis conditions are key steps toward reproducibility of gel-based proteomics assays. We provide the data generated using an efficient protocol of protein extraction for rapid and large-scale proteome analysis using two-dimensional gel electrophoresis. The protocol was established and optimized for pathogenic and non-pathogenic Sporothrix spp. including Sporothrix brasiliensis (CBS 132990, Sporothrix schenckii sensu stricto (CBS 132974, Sporothrix globosa (CBS 132922, and Sporothrix mexicana (CBS 120341. The data, supplied in this article, are related to the research article entitled “Immunoproteomic analysis reveals a convergent humoral response signature in the Sporothrix schenckii complex” (Rodrigues et al., 2014 [1].

  1. Quantitative optical mapping of two-dimensional materials

    DEFF Research Database (Denmark)

    Jessen, Bjarke S.; Whelan, Patrick R.; Mackenzie, David M. A.

    2018-01-01

    The pace of two-dimensional materials (2DM) research has been greatly accelerated by the ability to identify exfoliated thicknesses down to a monolayer from their optical contrast. Since this process requires time-consuming and error-prone manual assignment to avoid false-positives from image...

  2. The accuracy of a designed software for automated localization of craniofacial landmarks on CBCT images

    International Nuclear Information System (INIS)

    Shahidi, Shoaleh; Bahrampour, Ehsan; Soltanimehr, Elham; Zamani, Ali; Oshagh, Morteza; Moattari, Marzieh; Mehdizadeh, Alireza

    2014-01-01

    Two-dimensional projection radiographs have been traditionally considered the modality of choice for cephalometric analysis. To overcome the shortcomings of two-dimensional images, three-dimensional computed tomography (CT) has been used to evaluate craniofacial structures. However, manual landmark detection depends on medical expertise, and the process is time-consuming. The present study was designed to produce software capable of automated localization of craniofacial landmarks on cone beam (CB) CT images based on image registration and to evaluate its accuracy. The software was designed using MATLAB programming language. The technique was a combination of feature-based (principal axes registration) and voxel similarity-based methods for image registration. A total of 8 CBCT images were selected as our reference images for creating a head atlas. Then, 20 CBCT images were randomly selected as the test images for evaluating the method. Three experts twice located 14 landmarks in all 28 CBCT images during two examinations set 6 weeks apart. The differences in the distances of coordinates of each landmark on each image between manual and automated detection methods were calculated and reported as mean errors. The combined intraclass correlation coefficient for intraobserver reliability was 0.89 and for interobserver reliability 0.87 (95% confidence interval, 0.82 to 0.93). The mean errors of all 14 landmarks were <4 mm. Additionally, 63.57% of landmarks had a mean error of <3 mm compared with manual detection (gold standard method). The accuracy of our approach for automated localization of craniofacial landmarks, which was based on combining feature-based and voxel similarity-based methods for image registration, was acceptable. Nevertheless we recommend repetition of this study using other techniques, such as intensity-based methods

  3. Two dimensional gel electrophoresis using narrow pH 3-5.6 immobilised pH gradient strips identifies potential novel disease biomarkers in plasma or serum

    OpenAIRE

    sprotocols

    2015-01-01

    Authors: Bevin Gangadharan & Nicole Zitzmann ### Abstract Two-dimensional gel electrophoresis (2-DE) is a protein separation technique often used to separate plasma or serum proteins in an attempt to identify novel biomarkers. This protocol describes how to run 2-DE gels using narrow pH 3-5.6 immobilised pH gradient strips to separate 2 mg of serum proteins. pH 3-6 ampholytes are used to enhance the solubility of proteins in this pH range before the serum proteins are separated in the...

  4. Improvement of an automated protein crystal exchange system PAM for high-throughput data collection

    International Nuclear Information System (INIS)

    Hiraki, Masahiko; Yamada, Yusuke; Chavas, Leonard M. G.; Wakatsuki, Soichi; Matsugaki, Naohiro

    2013-01-01

    A special liquid-nitrogen Dewar with double capacity for the sample-exchange robot has been created at AR-NE3A at the Photon Factory, allowing continuous fully automated data collection. In this work, this new system is described and the stability of its calibration is discussed. Photon Factory Automated Mounting system (PAM) protein crystal exchange systems are available at the following Photon Factory macromolecular beamlines: BL-1A, BL-5A, BL-17A, AR-NW12A and AR-NE3A. The beamline AR-NE3A has been constructed for high-throughput macromolecular crystallography and is dedicated to structure-based drug design. The PAM liquid-nitrogen Dewar can store a maximum of three SSRL cassettes. Therefore, users have to interrupt their experiments and replace the cassettes when using four or more of them during their beam time. As a result of investigation, four or more cassettes were used in AR-NE3A alone. For continuous automated data collection, the size of the liquid-nitrogen Dewar for the AR-NE3A PAM was increased, doubling the capacity. In order to check the calibration with the new Dewar and the cassette stand, calibration experiments were repeatedly performed. Compared with the current system, the parameters of the novel system are shown to be stable

  5. Improvement of an automated protein crystal exchange system PAM for high-throughput data collection

    Energy Technology Data Exchange (ETDEWEB)

    Hiraki, Masahiko, E-mail: masahiko.hiraki@kek.jp; Yamada, Yusuke; Chavas, Leonard M. G. [High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Wakatsuki, Soichi [High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); SLAC National Accelerator Laboratory, 2575 Sand Hill Road, MS 69, Menlo Park, CA 94025-7015 (United States); Stanford University, Beckman Center B105, Stanford, CA 94305-5126 (United States); Matsugaki, Naohiro [High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan)

    2013-11-01

    A special liquid-nitrogen Dewar with double capacity for the sample-exchange robot has been created at AR-NE3A at the Photon Factory, allowing continuous fully automated data collection. In this work, this new system is described and the stability of its calibration is discussed. Photon Factory Automated Mounting system (PAM) protein crystal exchange systems are available at the following Photon Factory macromolecular beamlines: BL-1A, BL-5A, BL-17A, AR-NW12A and AR-NE3A. The beamline AR-NE3A has been constructed for high-throughput macromolecular crystallography and is dedicated to structure-based drug design. The PAM liquid-nitrogen Dewar can store a maximum of three SSRL cassettes. Therefore, users have to interrupt their experiments and replace the cassettes when using four or more of them during their beam time. As a result of investigation, four or more cassettes were used in AR-NE3A alone. For continuous automated data collection, the size of the liquid-nitrogen Dewar for the AR-NE3A PAM was increased, doubling the capacity. In order to check the calibration with the new Dewar and the cassette stand, calibration experiments were repeatedly performed. Compared with the current system, the parameters of the novel system are shown to be stable.

  6. Two-dimensional analysis of metabolically and cell surface radiolabeled proteins of some human lymphoid and myeloid leukemia cell lines. II. Glycosylated and phosphorylated proteins

    Energy Technology Data Exchange (ETDEWEB)

    Chorvath, B; Duraj, J; Sedlak, J; Pleskova, I

    1986-01-01

    Cell surface glycoproteins, radiolabelled by the sodium metaperiodate/tritiated borohydride technique, and cell phosphoproteins, metabolically radiolabelled with /sup 32/P-orthophosphate were analyzed by two-dimensional electrophoretic analysis in some myeloid and lymphoid leukemia cell lines. Some markedly expressed major glycoproteins were predominant in some of the cell lines (such as 95k and 100k glycoproteins with marked charge heterogeneity in non-T, non-B acute lymphoblastic leukemia cell lines NALM 6 and NALM 16), but markedly quantitatively reduced in other examined cell lines, such as lymphoblastoid cell line UHKT 34/2. /sup 32/P-orthophosphate radiolabelled phosphoprotein two-dimensional patterns of the examined lymphoid leukemia cell lines were essentially similar, with some minor differences, in examined lymphoid and myeloid leukemia cell lines, such as marked expression of a series of large phosphoproteins in the molecular weight range 80-100k in lymphoid cell lines and almost complete absence of these phosphoproteins on the examined myeloid leukemia cell lines. Another configuration of acidic phosphoproteins (30-35k) exhibited individual cell line variability and differences between both individual myeloid leukemia cell lines and between the lymphoid and myeloid cell lines examined. (author) 2 figs., 15 refs.

  7. Experimental two-dimensional quantum walk on a photonic chip.

    Science.gov (United States)

    Tang, Hao; Lin, Xiao-Feng; Feng, Zhen; Chen, Jing-Yuan; Gao, Jun; Sun, Ke; Wang, Chao-Yue; Lai, Peng-Cheng; Xu, Xiao-Yun; Wang, Yao; Qiao, Lu-Feng; Yang, Ai-Lin; Jin, Xian-Min

    2018-05-01

    Quantum walks, in virtue of the coherent superposition and quantum interference, have exponential superiority over their classical counterpart in applications of quantum searching and quantum simulation. The quantum-enhanced power is highly related to the state space of quantum walks, which can be expanded by enlarging the photon number and/or the dimensions of the evolution network, but the former is considerably challenging due to probabilistic generation of single photons and multiplicative loss. We demonstrate a two-dimensional continuous-time quantum walk by using the external geometry of photonic waveguide arrays, rather than the inner degree of freedoms of photons. Using femtosecond laser direct writing, we construct a large-scale three-dimensional structure that forms a two-dimensional lattice with up to 49 × 49 nodes on a photonic chip. We demonstrate spatial two-dimensional quantum walks using heralded single photons and single photon-level imaging. We analyze the quantum transport properties via observing the ballistic evolution pattern and the variance profile, which agree well with simulation results. We further reveal the transient nature that is the unique feature for quantum walks of beyond one dimension. An architecture that allows a quantum walk to freely evolve in all directions and at a large scale, combining with defect and disorder control, may bring up powerful and versatile quantum walk machines for classically intractable problems.

  8. Altering user' acceptance of automation through prior automation exposure.

    Science.gov (United States)

    Bekier, Marek; Molesworth, Brett R C

    2017-06-01

    Air navigation service providers worldwide see increased use of automation as one solution to overcome the capacity constraints imbedded in the present air traffic management (ATM) system. However, increased use of automation within any system is dependent on user acceptance. The present research sought to determine if the point at which an individual is no longer willing to accept or cooperate with automation can be manipulated. Forty participants underwent training on a computer-based air traffic control programme, followed by two ATM exercises (order counterbalanced), one with and one without the aid of automation. Results revealed after exposure to a task with automation assistance, user acceptance of high(er) levels of automation ('tipping point') decreased; suggesting it is indeed possible to alter automation acceptance. Practitioner Summary: This paper investigates whether the point at which a user of automation rejects automation (i.e. 'tipping point') is constant or can be manipulated. The results revealed after exposure to a task with automation assistance, user acceptance of high(er) levels of automation decreased; suggesting it is possible to alter automation acceptance.

  9. Two-dimensional filtering of SPECT images using the Metz and Wiener filters

    International Nuclear Information System (INIS)

    King, M.A.; Schwinger, R.B.; Penney, B.C.; Doherty, P.W.

    1984-01-01

    Presently, single photon emission computed tomographic (SPECT) images are usually reconstructed by arbitrarily selecting a one-dimensional ''window'' function for use in reconstruction. A better method would be to automatically choose among a family of two-dimensional image restoration filters in such a way as to produce ''optimum'' image quality. Two-dimensional image processing techniques offer the advantages of a larger statistical sampling of the data for better noise reduction, and two-dimensional image deconvolution to correct for blurring during acquisition. An investigation of two such ''optimal'' digital image restoration techniques (the count-dependent Metz filter and the Wiener filter) was made. They were applied both as two-dimensional ''window'' functions for preprocessing SPECT images, and for filtering reconstructed images. Their performance was compared by measuring image contrast and per cent fractional standard deviation (% FSD) in multiple-acquisitions of the Jaszczak SPECT phantom at two different count levels. A statistically significant increase in image contrast and decrease in % FSD was observed with these techniques when compared to the results of reconstruction with a ramp filter. The adaptability of the techniques was manifested in a lesser % reduction in % FSD at the high count level coupled with a greater enhancement in image contrast. Using an array processor, processing time was 0.2 sec per image for the Metz filter and 3 sec for the Wiener filter. It is concluded that two-dimensional digital image restoration with these techniques can produce a significant increase in SPECT image quality

  10. Vector (two-dimensional) magnetic phenomena

    International Nuclear Information System (INIS)

    Enokizono, Masato

    2002-01-01

    In this paper, some interesting phenomena were described from the viewpoint of two-dimensional magnetic property, which is reworded with the vector magnetic property. It shows imperfection of conventional magnetic property and some interested phenomena were discovered, too. We found magnetic materials had the strong nonlinearity both magnitude and spatial phase due to the relationship between the magnetic field strength H-vector and the magnetic flux density B-vector. Therefore, magnetic properties should be defined as the vector relationship. Furthermore, the new Barukhausen signal was observed under rotating flux. (Author)

  11. Mass relations for two-dimensional classical configurations

    International Nuclear Information System (INIS)

    Tataru-Mihai, P.

    1980-01-01

    Using the two-dimensional sigma-nonlinear models as a framework mass relations for classical configurations of instanton/soliton type are derived. Our results suggest an interesting differential-geometric interpretation of the mass of a classical configuration in terms of the topological characteristics of an associated manifold. (orig.)

  12. Analytical simulation of two dimensional advection dispersion ...

    African Journals Online (AJOL)

    The study was designed to investigate the analytical simulation of two dimensional advection dispersion equation of contaminant transport. The steady state flow condition of the contaminant transport where inorganic contaminants in aqueous waste solutions are disposed of at the land surface where it would migrate ...

  13. Analytical Simulation of Two Dimensional Advection Dispersion ...

    African Journals Online (AJOL)

    ADOWIE PERE

    ABSTRACT: The study was designed to investigate the analytical simulation of two dimensional advection dispersion equation of contaminant transport. The steady state flow condition of the contaminant transport where inorganic contaminants in aqueous waste solutions are disposed of at the land surface where it would ...

  14. Nonlinear dynamic characterization of two-dimensional materials

    NARCIS (Netherlands)

    Davidovikj, D.; Alijani, F.; Cartamil Bueno, S.J.; van der Zant, H.S.J.; Amabili, M.; Steeneken, P.G.

    2017-01-01

    Owing to their atomic-scale thickness, the resonances of two-dimensional (2D) material membranes show signatures of nonlinearities at forces of only a few picoNewtons. Although the linear dynamics of membranes is well understood, the exact relation between the nonlinear response and the resonator's

  15. Linear negative magnetoresistance in two-dimensional Lorentz gases

    Science.gov (United States)

    Schluck, J.; Hund, M.; Heckenthaler, T.; Heinzel, T.; Siboni, N. H.; Horbach, J.; Pierz, K.; Schumacher, H. W.; Kazazis, D.; Gennser, U.; Mailly, D.

    2018-03-01

    Two-dimensional Lorentz gases formed by obstacles in the shape of circles, squares, and retroreflectors are reported to show a pronounced linear negative magnetoresistance at small magnetic fields. For circular obstacles at low number densities, our results agree with the predictions of a model based on classical retroreflection. In extension to the existing theoretical models, we find that the normalized magnetoresistance slope depends on the obstacle shape and increases as the number density of the obstacles is increased. The peaks are furthermore suppressed by in-plane magnetic fields as well as by elevated temperatures. These results suggest that classical retroreflection can form a significant contribution to the magnetoresistivity of two-dimensional Lorentz gases, while contributions from weak localization cannot be excluded, in particular for large obstacle densities.

  16. Automated analysis of two-dimensional positions and body lengths of earthworms (Oligochaeta); MimizuTrack.

    Science.gov (United States)

    Kodama, Naomi; Kimura, Toshifumi; Yonemura, Seiichiro; Kaneda, Satoshi; Ohashi, Mizue; Ikeno, Hidetoshi

    2014-01-01

    Earthworms are important soil macrofauna inhabiting almost all ecosystems. Their biomass is large and their burrowing and ingestion of soils alters soil physicochemical properties. Because of their large biomass, earthworms are regarded as an indicator of "soil heath". However, primarily because the difficulties in quantifying their behavior, the extent of their impact on soil material flow dynamics and soil health is poorly understood. Image data, with the aid of image processing tools, are a powerful tool in quantifying the movements of objects. Image data sets are often very large and time-consuming to analyze, especially when continuously recorded and manually processed. We aimed to develop a system to quantify earthworm movement from video recordings. Our newly developed program successfully tracked the two-dimensional positions of three separate parts of the earthworm and simultaneously output the change in its body length. From the output data, we calculated the velocity of the earthworm's movement. Our program processed the image data three times faster than the manual tracking system. To date, there are no existing systems to quantify earthworm activity from continuously recorded image data. The system developed in this study will reduce input time by a factor of three compared with manual data entry and will reduce errors involved in quantifying large data sets. Furthermore, it will provide more reliable measured values, although the program is still a prototype that needs further testing and improvement. Combined with other techniques, such as measuring metabolic gas emissions from earthworm bodies, this program could provide continuous observations of earthworm behavior in response to environmental variables under laboratory conditions. In the future, this standardized method will be applied to other animals, and the quantified earthworm movement will be incorporated into models of soil material flow dynamics or behavior in response to chemical

  17. Effects of sharp vorticity gradients in two-dimensional hydrodynamic turbulence

    DEFF Research Database (Denmark)

    Kuznetsov, E.A.; Naulin, Volker; Nielsen, Anders Henry

    2007-01-01

    The appearance of sharp vorticity gradients in two-dimensional hydrodynamic turbulence and their influence on the turbulent spectra are considered. We have developed the analog of the vortex line representation as a transformation to the curvilinear system of coordinates moving together with the ......The appearance of sharp vorticity gradients in two-dimensional hydrodynamic turbulence and their influence on the turbulent spectra are considered. We have developed the analog of the vortex line representation as a transformation to the curvilinear system of coordinates moving together...... with the divorticity lines. Compressibility of this mapping can be considered as the main reason for the formation of the sharp vorticity gradients at high Reynolds numbers. For two-dimensional turbulence in the case of strong anisotropy the sharp vorticity gradients can generate spectra which fall off as k−3 at large...

  18. Magnetic anisotropy of two-dimensional nanostructures: Transition-metal triangular stripes

    International Nuclear Information System (INIS)

    Dorantes-Davila, J.; Villasenor-Gonzalez, P.; Pastor, G.M.

    2005-01-01

    The magnetic anisotropy energy (MAE) of one-dimensional stripes having infinite length and triangular lateral structure are investigated in the framework of a self-consistent tight-binding method. One observes discontinuous changes in the easy magnetization direction along the crossover from one to two dimensions. The MAE oscillates as a function of stripe width and depends strongly on the considered transition metal (TM). The MAE of the two-leg ladder is strongly reduced as compared to that of the monoatomic chain and the convergence to the two-dimensional limit is rather slow

  19. Reduction of multi-dimensional laboratory data to a two-dimensional plot: a novel technique for the identification of laboratory error.

    Science.gov (United States)

    Kazmierczak, Steven C; Leen, Todd K; Erdogmus, Deniz; Carreira-Perpinan, Miguel A

    2007-01-01

    The clinical laboratory generates large amounts of patient-specific data. Detection of errors that arise during pre-analytical, analytical, and post-analytical processes is difficult. We performed a pilot study, utilizing a multidimensional data reduction technique, to assess the utility of this method for identifying errors in laboratory data. We evaluated 13,670 individual patient records collected over a 2-month period from hospital inpatients and outpatients. We utilized those patient records that contained a complete set of 14 different biochemical analytes. We used two-dimensional generative topographic mapping to project the 14-dimensional record to a two-dimensional space. The use of a two-dimensional generative topographic mapping technique to plot multi-analyte patient data as a two-dimensional graph allows for the rapid identification of potentially anomalous data. Although we performed a retrospective analysis, this technique has the benefit of being able to assess laboratory-generated data in real time, allowing for the rapid identification and correction of anomalous data before they are released to the physician. In addition, serial laboratory multi-analyte data for an individual patient can also be plotted as a two-dimensional plot. This tool might also be useful for assessing patient wellbeing and prognosis.

  20. On the size distribution of one-, two- and three-dimensional Voronoi cells

    International Nuclear Information System (INIS)

    Marthinsen, K.

    1994-03-01

    The present report gives a presentation of the different cell size distribution obtained by computer simulations of random Voronoi cell structures in one-, two- and three-dimensional space. The random Voronoi cells are constructed from cell centroids randomly distributed along a string, in the plane and in three-dimensional space, respectively. The size distributions are based on 2-3 · 10 4 cells. For the spacial polyhedra both the distribution of volumes, areas and radii are presented, and the two latter quantities are compared to the distributions of areas and radii from a planar section through the three-dimensional structure as well as to the corresponding distributions obtained from a pure two-dimensional cell structure. 11 refs., 11 figs