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Sample records for 2d dige analysis

  1. 2D DIGE saturation labeling for minute sample amounts.

    PubMed

    Arnold, Georg J; Fröhlich, Thomas

    2012-01-01

    The 2D DIGE technique, based on fluorophores covalently linked to amino acid side chain residues and the concept of an internal standard, has significantly improved reproducibility, sensitivity, and the dynamic range of protein quantification. In saturation DIGE, sulfhydryl groups of cysteines are labeled with cyanine dyes to completion, providing a so far unraveled sensitivity for protein detection and quantification in 2D gel-based proteomic experiments. Only a few micrograms of protein per 2D gel facilitate the analysis of about 2,000 analytes from complex mammalian cell or tissue samples. As a consequence, 2D saturation DIGE is the method of choice when only minute sample amounts are available for quantitative proteome analysis at the level of proteins rather than peptides. Since very low amounts of samples have to be handled in a reproducible manner, saturation DIGE-based proteomic experiments are technically demanding. Moreover, successful saturation DIGE approaches require a strict adherence to adequate reaction conditions at each step. This chapter is dedicated to colleagues already experienced in 2D PAGE protein separation and intends to support the establishment of this ultrasensitive technique in proteomic workgroups. We provide basic guidelines for the experimental design and discuss crucial aspects concerning labeling chemistry, sample preparation, and pitfalls caused by labeling artifacts. A detailed step-by-step protocol comprises all aspects from initial sample preparation to image analysis and statistical evaluation. Furthermore, we describe the generation of preparative saturation DIGE gels necessary for mass spectrometry-based spot identification.

  2. The basics of 2D DIGE.

    PubMed

    Beckett, Phil

    2012-01-01

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

  3. 2D-DIGE proteome analysis on the platelet proteins of patients with major depression

    PubMed Central

    2014-01-01

    Introduction Platelet activation is related to the psychopathology of major depression. We attempted to search and identify protein biomarkers from the platelets of patients with major depression. High resolution two-dimensional Differential Gel Electrophoresis (2D-DIGE), the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), Western blot, and bioinformatic tools were applied to examine the platelet proteins of 10 patients with major depression and 10 healthy controls. Results The levels of 8 proteins were significantly different between the patients with major depression in the acute phase and healthy controls. The levels of protein disulfide-isomerase A3 (PDIA3) and F-actin-capping protein subunit beta (CAPZB) were higher in patients with major depression than in healthy controls. The levels of fibrinogen beta chain (FIBB), fibrinogen gamma chain (FIBG), retinoic acid receptor beta (RARB), glutathione peroxidase 1 (GPX1), SH3 domain-containing protein 19 (SH319), and T-complex protein 1 subunit beta (TCPB) were lower in patients with major depression than in healthy controls. Conclusions Platelet provided valuable information about the pathways and processes of inflammation/immunity, oxidative stress, and neurogenesis, related to major depression. PMID:24383611

  4. Proteomic analysis of heat treated bitter gourd (Momordica charantia L. var. Hong Kong Green) using 2D-DIGE.

    PubMed

    Ng, Zhi Xiang; Chua, Kek Heng; Kuppusamy, Umah Rani

    2014-04-01

    This study aimed to investigate the changes in the proteome of bitter gourd prior to and after subjecting to boiling and microwaving. A comparative analysis of the proteome profiles of raw and thermally treated bitter gourds was performed using 2D-DIGE. The protein content and number of protein spots in raw sample was higher when compared to the cooked samples. Qualitative analysis revealed that 103 (boiled sample) and 110 (microwaved sample) protein spots were up regulated whereas 120 (boiled sample) and 107 (microwaved sample) protein spots were down regulated. Ten protein spots with the highest significant fold change in the cooked samples were involved in carbohydrate/energy metabolisms and stress responses. Small heat shock proteins, superoxide dismutase, quinone oxidoreductase, UDP-glucose pyrophosphorylase and phosphoglycerate kinase play a role in heat-stress-mediated protection of bitter gourd. This study suggests that appropriate heat treatment (cooking methods) can lead to induction of selected proteins in bitter gourd.

  5. 2-D DIGE analysis of UV-C radiation-responsive proteins in globe artichoke leaves.

    PubMed

    Falvo, Sara; Di Carli, Mariasole; Desiderio, Angiola; Benvenuto, Eugenio; Moglia, Andrea; America, Twan; Lanteri, Sergio; Acquadro, Alberto

    2012-02-01

    Plants respond to ultraviolet stress inducing a self-defence through the regulation of specific gene family members. The UV acclimation is the result of biochemical and physiological processes, such as enhancement of the antioxidant enzymatic system and accumulation of UV-absorbing phenolic compounds (e.g. flavonoids). Globe artichoke is an attractive species for studying the protein network involved in UV stress response, being characterized by remarkable levels of inducible antioxidants. Proteomic tools can assist the evaluation of the expression patterns of UV-responsive proteins and we applied the difference in-gel electrophoresis (DIGE) technology for monitoring the globe artichoke proteome variation at four time points following an acute UV-C exposure. A total of 145 UV-C-modulated proteins were observed and 119 were identified by LC-MS/MS using a ∼144,000 customized Compositae protein database, which included about 19,000 globe artichoke unigenes. Proteins were Gene Ontology (GO) categorized, visualized on their pathways and their behaviour was discussed. A predicted protein interaction network was produced and highly connected hub-like proteins were highlighted. Most of the proteins differentially modulated were chloroplast located, involved in photosynthesis, sugar metabolisms, protein folding and abiotic stress. The identification of UV-C-responsive proteins may contribute to shed light on the molecular mechanisms underlying plant responses to UV stress.

  6. Proteome analysis of the large and the small rubber particles of Hevea brasiliensis using 2D-DIGE.

    PubMed

    Xiang, Qiulan; Xia, Kecan; Dai, Longjun; Kang, Guijuan; Li, Yu; Nie, Zhiyi; Duan, Cuifang; Zeng, Rizhong

    2012-11-01

    The rubber particle is a specialized organelle in which natural rubber is synthesised and stored in the laticifers of Hevea brasiliensis (para rubber tree). It has been demonstrated that the small rubber particles (SRPs) has higher rubber biosynthesis ratio than the large rubber particles (LRPs), but the underlying molecular mechanism still remains unknown. In this study, LRPs and SRPs were firstly separated from the fresh latex using differential centrifugation, and two-dimensional difference in-gel electrophoresis (2D-DIGE) combined with MALDI-TOF/TOF was then applied to investigate the proteomic alterations associated with the changed rubber biosynthesis capacity between LRPs and SRPs. A total of 53 spots corresponding to 22 gene products, were significantly altered with the |ratio|≥2.0 and T value ≤0.05, among which 15 proteins were up-regulated and 7 were down-regulated in the SRPs compared with the LRPs. The 15 up-regulated proteins in the SRPs included small rubber particle protein (SRPP), 3-hydroxy-3-methylglutaryl-CoA synthase (HMGCS), phospholipase D alpha (PLD α), ethylene response factor 2, eukaryotic translation initiation factor 5A isoform IV (eIF 5A-4), 70-kDa heat shock cognate protein (HSC 70), several unknown proteins, etc., whereas the 7 up-regulated proteins in the LRPs were rubber elongation factor (REF, 19.6kDa), ASR-like protein 1, REF-like stress-related protein 1, a putative phosphoglyceride transfer family protein, β-1,3-glucanase, a putative retroelement, and a hypothetical protein. Since several proteins related to rubber biosynthesis were differentially expressed between LRPs and SRPs, the comparative proteome data may provide useful insights into understanding the mechanism involved in rubber biosynthesis and latex coagulation in H. brasiliensis.

  7. A combination of metabolic labeling and 2D-DIGE analysis in response to a farnesyltransferase inhibitor facilitates the discovery of new prenylated proteins

    PubMed Central

    Palsuledesai, Charuta C.; Ochocki, Joshua D.; Markowski, Todd W.; Distefano, Mark D.

    2014-01-01

    Protein prenylation is a post-translational modification required for proper cellular localization and activity of many important eukaryotic proteins. Farnesyltransferase inhibitors (FTIs) have been explored extensively for their antitumor activity. To assist in identifying potentially new and more useful markers for therapeutic applications, we developed a strategy that uses a combination of metabolic labeling and 2D DIGE (differential gel electrophoresis) to discover new prenylated proteins whose cellular levels are influenced by FTIs. In this approach, metabolic labeling of prenylated proteins was first carried out with an alkyne-modified isoprenoid analog, C15Alk, in the presence or absence of the FTI L-744,832. The resulting alkyne-tagged proteins were then labeled with Cy3-N3 and Cy5-N3 and subjected to 2D differential gel electrophoresis (DIGE). Multiple spots having altered levels of labeling in presence of the FTI were observed. Mass spectrometric analysis of some of the differentially labeled spots identified several known prenylated proteins, along with HisRS, PACN-3, GNAI-1 and GNAI-2, which are not known to be prenylated. In vitro farnesylation of a C-terminal peptide sequence derived from GNAI-1 and GNAI-2 produced a farnesylated product, suggesting GNAI-1 and GNAI-2 are potential novel farnesylated proteins. These results suggest that this new strategy could be useful for the identification of prenylated proteins whose level of post-translational modification has been modulated by the presence of an FTI. Additionally, this approach, which decreases sample complexity and thereby facilitates analysis, should be applicable to studies of other post-translational modifications as well. PMID:24577581

  8. A combination of metabolic labeling and 2D-DIGE analysis in response to a farnesyltransferase inhibitor facilitates the discovery of new prenylated proteins.

    PubMed

    Palsuledesai, Charuta C; Ochocki, Joshua D; Markowski, Todd W; Distefano, Mark D

    2014-05-01

    Protein prenylation is a post-translational modification required for proper cellular localization and activity of many important eukaryotic proteins. Farnesyltransferase inhibitors (FTIs) have been explored extensively for their antitumor activity. To assist in identifying potentially new and more useful markers for therapeutic applications, we developed a strategy that uses a combination of metabolic labeling and 2D DIGE (differential gel electrophoresis) to discover new prenylated proteins whose cellular levels are influenced by FTIs. In this approach, metabolic labeling of prenylated proteins was first carried out with an alkyne-modified isoprenoid analog, C15Alk, in the presence or absence of the FTI L-744,832. The resulting alkyne-tagged proteins were then labeled with Cy3-N3 and Cy5-N3 and subjected to 2D-DIGE. Multiple spots having altered levels of labeling in presence of the FTI were observed. Mass spectrometric analysis of some of the differentially labeled spots identified several known prenylated proteins, along with HisRS, PACN-3, GNAI-1 and GNAI-2, which are not known to be prenylated. In vitro farnesylation of a C-terminal peptide sequence derived from GNAI-1 and GNAI-2 produced a farnesylated product, suggesting GNAI-1 and GNAI-2 are potential novel farnesylated proteins. These results suggest that this new strategy could be useful for the identification of prenylated proteins whose level of post-translational modification has been modulated by the presence of an FTI. Additionally, this approach, which decreases sample complexity and thereby facilitates analysis, should be applicable to studies of other post-translational modifications as well.

  9. 2D-DIGE analysis of mango (Mangifera indica L.) fruit reveals major proteomic changes associated with ripening.

    PubMed

    Andrade, Jonathan de Magalhães; Toledo, Tatiana Torres; Nogueira, Silvia Beserra; Cordenunsi, Beatriz Rosana; Lajolo, Franco Maria; do Nascimento, João Roberto Oliveira

    2012-06-18

    A comparative proteomic investigation between the pre-climacteric and climacteric mango fruits (cv. Keitt) was performed to identify protein species with variable abundance during ripening. Proteins were phenol-extracted from fruits, cyanine-dye-labeled, and separated on 2D gels at pH 4-7. Total spot count of about 373 proteins spots was detected in each gel and forty-seven were consistently different between pre-climacteric and climacteric fruits and were subjected to LC-MS/MS analysis. Functional classification revealed that protein species involved in carbon fixation and hormone biosynthesis decreased during ripening, whereas those related to catabolism and the stress-response, including oxidative stress and abiotic and pathogen defense factors, accumulated. In relation to fruit quality, protein species putatively involved in color development and pulp softening were also identified. This study on mango proteomics provides an overview of the biological processes that occur during ripening.

  10. Comparative 2D-DIGE proteomic analysis of bovine mammary epithelial cells during lactation reveals protein signatures for lactation persistency and milk yield.

    PubMed

    Janjanam, Jagadeesh; Singh, Surender; Jena, Manoj K; Varshney, Nishant; Kola, Srujana; Kumar, Sudarshan; Kaushik, Jai K; Grover, Sunita; Dang, Ajay K; Mukesh, Manishi; Prakash, B S; Mohanty, Ashok K

    2014-01-01

    Mammary gland is made up of a branching network of ducts that end with alveoli which surrounds the lumen. These alveolar mammary epithelial cells (MEC) reflect the milk producing ability of farm animals. In this study, we have used 2D-DIGE and mass spectrometry to identify the protein changes in MEC during immediate early, peak and late stages of lactation and also compared differentially expressed proteins in MEC isolated from milk of high and low milk producing cows. We have identified 41 differentially expressed proteins during lactation stages and 22 proteins in high and low milk yielding cows. Bioinformatics analysis showed that a majority of the differentially expressed proteins are associated in metabolic process, catalytic and binding activity. The differentially expressed proteins were mapped to the available biological pathways and networks involved in lactation. The proteins up-regulated during late stage of lactation are associated with NF-κB stress induced signaling pathways and whereas Akt, PI3K and p38/MAPK signaling pathways are associated with high milk production mediated through insulin hormone signaling.

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

    PubMed

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

    2011-05-06

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

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

    PubMed

    Feret, Renata; Lilley, Kathryn S

    2014-02-03

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

  13. 2D DIGE analysis of the bursa of Fabricius reveals characteristic proteome profiles for different stages of chicken B-cell development.

    PubMed

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

    2013-01-01

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

  14. Comparative 2D-DIGE proteomic analysis of ovarian carcinoma cells: toward a reorientation of biosynthesis pathways associated with acquired platinum resistance.

    PubMed

    Lincet, Hubert; Guével, Blandine; Pineau, Charles; Allouche, Stéphane; Lemoisson, Edwige; Poulain, Laurent; Gauduchon, Pascal

    2012-02-02

    Ovarian cancer is the fifth most frequent cause of cancer death in women. Emergence of chemoresistance in the course of treatments with platinum drugs is in part responsible for therapeutic failures. In order to improve the understanding of the complex mechanisms involved in acquired platinum chemoresistance, we decided to compare the basal protein expression profile of the platinum-sensitive cell line OAW42 and that of its resistant counterpart OAW42-R by a proteomic approach. Reversed-phase HPLC pre-fractionated extracts from both cell lines were subjected to 2D-DIGE coupled to mass spectrometry (MS). Forty eight differentially expressed proteins were identified, 39 being up-regulated and 19 down-regulated in OAW42-R versus OAW42 cells. From the current knowledge on biological activities of most differentially expressed proteins, it can be inferred that the acquisition of resistance was associated with a global reorganization of biochemical pathways favoring the production of precursors for biosynthesis, and with the mobilization of macromolecule quality control mechanisms, preserving RNA and protein integrity under damage-inducing conditions.

  15. 2-D DIGE analysis of Senegalese sole (Solea senegalensis) testis proteome in wild-caught and hormone-treated F1 fish.

    PubMed

    Forné, Ignasi; Agulleiro, María J; Asensio, Esther; Abián, Joaquín; Cerdà, Joan

    2009-04-01

    In the farmed flatfish Senegalese sole, F1 males reared in captivity often show lower sperm production and fertilization capacity than wild-caught males. To gain insights into the molecular mechanisms that may be altered in the F1 testis, we used 2-D DIGE to compare the protein profiling of the testis of wild-caught males at the spermiation stage with that of F1 males showing different stages of germ cell development after hormone treatment in vivo. The abundance of 58 out of 1014 protein spots was found to differ significantly between the groups. De novo identification of these proteins by MS/MS revealed that proteins implicated in oxidoreductase activity, protein catabolism, formation of the zona pellucida receptor, cytoskeleton organization, and lipid binding and metabolism, were regulated in the F1 testes as germ cell development progressed. However, distinct isoforms or PTMs of some of these proteins, as well as of proteins involved in iron and glucose metabolism and ATP production, were expressed at lower levels in the testes of F1 males than in wild fish regardless of the hormone treatment. These results contribute to identifying proteins associated with spermatogenesis not previously described in teleosts, and suggest potential mechanisms that may be involved in the poor reproductive performance of Senegalese sole F1 males.

  16. Biological versus technical variability in 2-D DIGE experiments with environmental bacteria.

    PubMed

    Zech, Hajo; Echtermeyer, Christoph; Wöhlbrand, Lars; Blasius, Bernd; Rabus, Ralf

    2011-08-01

    Two-dimensional difference gel electrophoresis (2-D DIGE) allows for reliable quantification of global protein abundance changes. The threshold of significance for protein abundance changes depends on the experimental variation (biological and technical). This study estimates biological, technical and total variation inherent to 2-D DIGE analysis of environmental bacteria, using the model organisms "Aromatoleum aromaticum" EbN1 and Phaeobacter gallaeciensis DSM 17395. Of both bacteria the soluble proteomes were analyzed from replicate cultures. For strains EbN1 and DSM 17395, respectively, CV revealed a total variation of below 19 and 15%, an average technical variation of 12 and 7%, and an average biological variation of 18 and 17%. Multivariate analysis of variance confirmed domination of biological over technical variance to be significant in most cases. To visualize variances, the complex protein data have been plotted with a multidimensional scaling technique. Furthermore, comparison of different treatment groups (different substrate conditions) demonstrated that variability within groups is significantly smaller than differences caused by treatment.

  17. Image Pretreatment Tools II: Normalization Techniques for 2-DE and 2-D DIGE.

    PubMed

    Robotti, Elisa; Marengo, Emilio; Quasso, Fabio

    2016-01-01

    Gel electrophoresis is usually applied to identify different protein expression profiles in biological samples (e.g., control vs. pathological, control vs. treated). Information about the effect to be investigated (a pathology, a drug, a ripening effect, etc.) is however generally confounded with experimental variability that is quite large in 2-DE and may arise from small variations in the sample preparation, reagents, sample loading, electrophoretic conditions, staining and image acquisition. Obtaining valid quantitative estimates of protein abundances in each map, before the differential analysis, is therefore fundamental to provide robust candidate biomarkers. Normalization procedures are applied to reduce experimental noise and make the images comparable, improving the accuracy of differential analysis. Certainly, they may deeply influence the final results, and to this respect they have to be applied with care. Here, the most widespread normalization procedures are described both for what regards the applications to 2-DE and 2D Difference Gel-electrophoresis (2-D DIGE) maps.

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

    PubMed

    Guest, Paul C

    2017-01-01

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

  19. The use of 2D-DIGE to understand the regeneration of somatic embryos in avocado.

    PubMed

    Guzmán-García, Eva; Sánchez-Romero, Carolina; Panis, Bart; Carpentier, Sebastien Christian

    2013-12-01

    Avocado embryogenic cell cultures can be classified into two groups based on their morphology when cultured on a medium containing auxin: somatic embryo (SE) and proembryonic masses (PEM) type cultures. The calli of SE-type cell lines are able to go through the maturation process, whereas the calli of PEM cell lines rarely mature. We have investigated four independent avocado cell cultures (two SE and two PEM). The aim of this study was to link the differential regeneration capacity of the four cell cultures to a proteomic pattern and to gain insight into the regeneration capacity. A 2D-DIGE analysis followed by a blind multivariate analysis was able to separate the two SE lines from the PEM lines indicating that the protein profiles of SE and PEM calli are different. Based on the variable importance, that is, the differential protein pattern, we hypothesize that the regeneration capacity in avocado is correlated to the ability to overcome the physicochemical stress stimuli associated with the in vitro culture. Our identical culture conditions do not seem to trigger an appropriate response in PEM lines.

  20. Circadian Profiling of the Arabidopsis Proteome Using 2D-DIGE

    PubMed Central

    Choudhary, Mani K.; Nomura, Yuko; Shi, Hua; Nakagami, Hirofumi; Somers, David E.

    2016-01-01

    Clock-generated biological rhythms provide an adaptive advantage to an organism, resulting in increased fitness and survival. To better elucidate the plant response to the circadian system, we surveyed protein oscillations in Arabidopsis seedlings under constant light. Using large-scale two-dimensional difference in gel electrophoresis (2D-DIGE) the abundance of more than 1000 proteins spots was reproducibly resolved quantified and profiled across a circadian time series. A comparison between phenol-extracted samples and RuBisCO-depleted extracts identified 71 and 40 rhythmically-expressed proteins, respectively, and between 30 and 40% of these derive from non-rhythmic transcripts. These included proteins influencing transcriptional regulation, translation, metabolism, photosynthesis, protein chaperones, and stress-mediated responses. The phasing of maximum expression for the cyclic proteins was similar for both datasets, with a nearly even distribution of peak phases across the time series. STRING clustering analysis identified two interaction networks with a notable number of oscillating proteins: plastid-based and cytosolic chaperones and 10 proteins involved in photosynthesis. The oscillation of the ABA receptor, PYR1/RCAR11, with peak expression near dusk adds to a growing body of evidence that intimately ties ABA signaling to the circadian system. Taken together, this study provides new insights into the importance of post-transcriptional circadian control of plant physiology and metabolism. PMID:27462335

  1. 2D-DIGE and MALDI TOF/TOF MS analysis reveal that small GTPase signaling pathways may play an important role in cadmium-induced colon cell malignant transformation.

    PubMed

    Lu, Jian; Zhou, Zhongping; Zheng, Jianzhou; Zhang, Zhuyi; Lu, Rongzhu; Liu, Hanqing; Shi, Haifeng; Tu, Zhigang

    2015-10-01

    Cadmium is a toxic heavy metal present in the environment and in industrial materials. Cadmium has demonstrated carcinogenic activity that induces cell transformation, but how this occurs is unclear. We used 2D-DIGE and MALDI TOF/TOF MS combined with bioinformatics and immunoblotting to investigate the molecular mechanism of cadmium transformation. We found that small GTPases were critical for transformation. Additionally, proteins involved in mitochondrial transcription, DNA repair, and translation also had altered expression patterns in cadmium treated cells. Collectively, our results suggest that activation of small GTPases contributes to cadmium-induced transformation of colon cells.

  2. Analysis of proteins using DIGE and MALDI mass spectrometry

    EPA Science Inventory

    In this work the sensitivity of the quantitative proteomics approach 2D-DIGE/MS (twoDimensional Difference Gel Electrophoresis / Mass Spectrometry) was tested by detecting decreasing amounts of a specific protein at the low picomole and sub-picomole range. Sensitivity of the 2D-D...

  3. 2D-DIGE as a proteomic biomarker discovery tool in environmental studies with Procambarus clarkii.

    PubMed

    Fernández-Cisnal, Ricardo; García-Sevillano, Miguel A; Gómez-Ariza, José L; Pueyo, Carmen; López-Barea, Juan; Abril, Nieves

    2017-04-15

    A 2D-DIGE/MS approach was used to assess protein abundance differences in the red swamp crayfish Procambarus clarkii from polluted aquatic ecosystems of Doñana National Park and surrounding areas with different pollution loads. Procambarus clarkii accumulated metals in the digestive glands and gills reflecting sediment concentrations. We first stated that, probably related to elements accumulation, pollution increased oxidative damage in P. clarkii tissues, as shown by the thiol oxidation status of proteins and MDA levels. In these animals, the altered redox status might be responsible for the deregulated abundance of proteins involved in cellular responses to oxidative stress including protein folding, mitochondrial imbalance and inflammatory processes. Interestingly, polluted P. clarkii crayfish also displayed a metabolic shift to enhanced aerobic glycolysis, most likely aimed at generating ATP and reduction equivalents in an oxidative stress situation that alters mitochondrial integrity. The deregulated proteins define the physiological processes affected by pollutants in DNP and its surrounding areas and may help us to unravel the molecular mechanisms underlying the toxicity of environmental pollutants. In addition, these proteins might be used as exposure biomarkers in environmental risk assessment. The results obtained might be extrapolated to many other locations all over the world and have the added value of providing information about the molecular responses of this environmentally and economically interesting animal.

  4. Identification and Validation of Potential New Biomarkers for Prostate Cancer Diagnosis and Prognosis Using 2D-DIGE and MS

    PubMed Central

    Geisler, Cordelia; Gaisa, Nadine T.; Pfister, David; Fuessel, Susanne; Kristiansen, Glen; Braunschweig, Till; Gostek, Sonja; Beine, Birte; Diehl, Hanna C.; Jackson, Angela M.; Borchers, Christoph H.; Heidenreich, Axel; Meyer, Helmut E.; Knüchel, Ruth; Henkel, Corinna

    2015-01-01

    This study was designed to identify and validate potential new biomarkers for prostate cancer and to distinguish patients with and without biochemical relapse. Prostate tissue samples analyzed by 2D-DIGE (two-dimensional difference in gel electrophoresis) and mass spectrometry (MS) revealed downregulation of secernin-1 (P < 0.044) in prostate cancer, while vinculin showed significant upregulation (P < 0.001). Secernin-1 overexpression in prostate tissue was validated using Western blot and immunohistochemistry while vinculin expression was validated using immunohistochemistry. These findings indicate that secernin-1 and vinculin are potential new tissue biomarkers for prostate cancer diagnosis and prognosis, respectively. For validation, protein levels in urine were also examined by Western blot analysis. Urinary vinculin levels in prostate cancer patients were significantly higher than in urine from nontumor patients (P = 0.006). Using multiple reaction monitoring-MS (MRM-MS) analysis, prostatic acid phosphatase (PAP) showed significant higher levels in the urine of prostate cancer patients compared to controls (P = 0.012), while galectin-3 showed significant lower levels in the urine of prostate cancer patients with biochemical relapse, compared to those without relapse (P = 0.017). Three proteins were successfully differentiated between patients with and without prostate cancer and patients with and without relapse by using MRM. Thus, this technique shows promise for implementation as a noninvasive clinical diagnostic technique. PMID:25667921

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

    PubMed

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

    2009-12-01

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

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

    PubMed

    Kondo, Tadashi; Hirohashi, Setsuo

    2006-01-01

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

  7. 2D-DIGE-based proteome expression changes in leaves of rice seedlings exposed to low-level gamma radiation at Iitate village, Fukushima.

    PubMed

    Hayashi, Gohei; Moro, Carlo F; Rohila, Jai Singh; Shibato, Junko; Kubo, Akihiro; Imanaka, Tetsuji; Kimura, Shinzo; Ozawa, Shoji; Fukutani, Satoshi; Endo, Satoru; Ichikawa, Katsuki; Agrawal, Ganesh Kumar; Shioda, Seiji; Hori, Motohide; Fukumoto, Manabu; Rakwal, Randeep

    2015-01-01

    The present study continues our previous research on investigating the biological effects of low-level gamma radiation in rice at the heavily contaminated Iitate village in Fukushima, by extending the experiments to unraveling the leaf proteome. 14-days-old plants of Japonica rice (Oryza sativa L. cv. Nipponbare) were subjected to gamma radiation level of upto 4 µSv/h, for 72 h. Following exposure, leaf samples were taken from the around 190 µSv/3 d exposed seedling and total proteins were extracted. The gamma irradiated leaf and control leaf (harvested at the start of the experiment) protein lysates were used in a 2-D differential gel electrophoresis (2D-DIGE) experiment using CyDye labeling in order to asses which spots were differentially represented, a novelty of the study. 2D-DIGE analysis revealed 91 spots with significantly different expression between samples (60 positive, 31 negative). MALDI-TOF and TOF/TOF mass spectrometry analyses revealed those as comprising of 59 different proteins (50 up-accumulated, 9 down-accumulated). The identified proteins were subdivided into 10 categories, according to their biological function, which indicated that the majority of the differentially expressed proteins consisted of the general (non-energy) metabolism and stress response categories. Proteome-wide data point to some effects of low-level gamma radiation exposure on the metabolism of rice leaves.

  8. 2D-DIGE-based proteome expression changes in leaves of rice seedlings exposed to low-level gamma radiation at Iitate village, Fukushima

    PubMed Central

    Hayashi, Gohei; Moro, Carlo F; Rohila, Jai Singh; Shibato, Junko; Kubo, Akihiro; Imanaka, Tetsuji; Kimura, Shinzo; Ozawa, Shoji; Fukutani, Satoshi; Endo, Satoru; Ichikawa, Katsuki; Agrawal, Ganesh Kumar; Shioda, Seiji; Hori, Motohide; Fukumoto, Manabu; Rakwal, Randeep

    2015-01-01

    The present study continues our previous research on investigating the biological effects of low-level gamma radiation in rice at the heavily contaminated Iitate village in Fukushima, by extending the experiments to unraveling the leaf proteome. 14-days-old plants of Japonica rice (Oryza sativa L. cv. Nipponbare) were subjected to gamma radiation level of upto 4 µSv/h, for 72 h. Following exposure, leaf samples were taken from the around 190 µSv/3 d exposed seedling and total proteins were extracted. The gamma irradiated leaf and control leaf (harvested at the start of the experiment) protein lysates were used in a 2-D differential gel electrophoresis (2D-DIGE) experiment using CyDye labeling in order to asses which spots were differentially represented, a novelty of the study. 2D-DIGE analysis revealed 91 spots with significantly different expression between samples (60 positive, 31 negative). MALDI-TOF and TOF/TOF mass spectrometry analyses revealed those as comprising of 59 different proteins (50 up-accumulated, 9 down-accumulated). The identified proteins were subdivided into 10 categories, according to their biological function, which indicated that the majority of the differentially expressed proteins consisted of the general (non-energy) metabolism and stress response categories. Proteome-wide data point to some effects of low-level gamma radiation exposure on the metabolism of rice leaves. PMID:26451896

  9. Proteomic analysis of peach fruit mesocarp softening and chilling injury using difference gel electrophoresis (DIGE)

    PubMed Central

    2010-01-01

    Background Peach fruit undergoes a rapid softening process that involves a number of metabolic changes. Storing fruit at low temperatures has been widely used to extend its postharvest life. However, this leads to undesired changes, such as mealiness and browning, which affect the quality of the fruit. In this study, a 2-D DIGE approach was designed to screen for differentially accumulated proteins in peach fruit during normal softening as well as under conditions that led to fruit chilling injury. Results The analysis allowed us to identify 43 spots -representing about 18% of the total number analyzed- that show statistically significant changes. Thirty-nine of the proteins could be identified by mass spectrometry. Some of the proteins that changed during postharvest had been related to peach fruit ripening and cold stress in the past. However, we identified other proteins that had not been linked to these processes. A graphical display of the relationship between the differentially accumulated proteins was obtained using pairwise average-linkage cluster analysis and principal component analysis. Proteins such as endopolygalacturonase, catalase, NADP-dependent isocitrate dehydrogenase, pectin methylesterase and dehydrins were found to be very important for distinguishing between healthy and chill injured fruit. A categorization of the differentially accumulated proteins was performed using Gene Ontology annotation. The results showed that the 'response to stress', 'cellular homeostasis', 'metabolism of carbohydrates' and 'amino acid metabolism' biological processes were affected the most during the postharvest. Conclusions Using a comparative proteomic approach with 2-D DIGE allowed us to identify proteins that showed stage-specific changes in their accumulation pattern. Several proteins that are related to response to stress, cellular homeostasis, cellular component organization and carbohydrate metabolism were detected as being differentially accumulated

  10. Normalization and expression changes in predefined sets of proteins using 2D gel electrophoresis: A proteomic study of L-DOPA induced dyskinesia in an animal model of Parkinson's disease using DIGE

    PubMed Central

    Kultima, Kim; Scholz, Birger; Alm, Henrik; Sköld, Karl; Svensson, Marcus; Crossman, Alan R; Bezard, Erwan; Andrén, Per E; Lönnstedt, Ingrid

    2006-01-01

    Background Two-Dimensional Difference In Gel Electrophoresis (2D-DIGE) is a powerful tool for measuring differences in protein expression between samples or conditions. However, to remove systematic variability within and between gels the data has to be normalized. In this study we examined the ability of four existing and four novel normalization methods to remove systematic bias in data produced with 2D-DIGE. We also propose a modification of an existing method where the statistical framework determines whether a set of proteins shows an association with the predefined phenotypes of interest. This method was applied to our data generated from a monkey model (Macaca fascicularis) of Parkinson's disease. Results Using 2D-DIGE we analysed the protein content of the striatum from 6 control and 21 MPTP-treated monkeys, with or without de novo or long-term L-DOPA administration. There was an intensity and spatial bias in the data of all the gels examined in this study. Only two of the eight normalization methods evaluated ('2D loess+scale' and 'SC-2D+quantile') successfully removed both the intensity and spatial bias. In 'SC-2D+quantile' we extended the commonly used loess normalization method against dye bias in two-channel microarray systems to suit systems with three or more channels. Further, by using the proposed method, Differential Expression in Predefined Proteins Sets (DEPPS), several sets of proteins associated with the priming effects of L-DOPA in the striatum in parkinsonian animals were identified. Three of these sets are proteins involved in energy metabolism and one set involved proteins which are part of the microtubule cytoskeleton. Conclusion Comparison of the different methods leads to a series of methodological recommendations for the normalization and the analysis of data, depending on the experimental design. Due to the nature of 2D-DIGE data we recommend that the p-values obtained in significance tests should be used as rankings only. Individual

  11. 2-D DIGE reveals changes in wheat xylanase inhibitor protein families due to Fusarium graminearum DeltaTri5 infection and grain development.

    PubMed

    Dornez, Emmie; Croes, Evi; Gebruers, Kurt; Carpentier, Sebastien; Swennen, Rony; Laukens, Kris; Witters, Erwin; Urban, Martin; Delcour, Jan A; Courtin, Christophe M

    2010-06-01

    Wheat contains three different classes of proteinaceous xylanase inhibitors (XIs), i.e. Triticum aestivum xylanase inhibitors (TAXIs) xylanase-inhibiting proteins (XIPs), and thaumatin-like xylanase inhibitors (TLXIs) which are believed to act as a defensive barrier against phytopathogenic attack. In the absence of relevant data in wheat kernels, we here examined the response of the different members of the XI protein population to infection with a DeltaTri5 mutant of Fusarium graminearum, the wild type of which is one of the most important wheat ear pathogens, in early developing wheat grain. Wheat ears were inoculated at anthesis, analyzed using 2-D DIGE and multivariate analysis at 5, 15, and 25 days post anthesis (DPA), and compared with control samples. Distinct abundance patterns could be distinguished for different XI forms in response to infection with F. graminearum DeltaTri5. Some (iso)forms were up-regulated, whereas others were down-regulated. This pathogen-specific regulation of proteins was mostly visible at five DPA and levelled off in the samples situated further from the inoculation point. Furthermore, it was shown that most identified TAXI- and XIP-type XI (iso)forms significantly increased in abundance from the milky (15 DPA) to the soft dough stages (25 DPA) on a per kernel basis, although the extent of increase differed greatly. Non-glycosylated XIP forms increased more strongly than their glycosylated counterparts.

  12. Xanthomonas citri subsp. citri surface proteome by 2D-DIGE: Ferric enterobactin receptor and other outer membrane proteins potentially involved in citric host interaction.

    PubMed

    Carnielli, Carolina Moretto; Artier, Juliana; de Oliveira, Julio Cezar Franco; Novo-Mansur, Maria Teresa Marques

    2017-01-16

    Xanthomonas citri subsp. citri (XAC) is the causative agent of citrus canker, a disease of great economic impact around the world. Understanding the role of proteins on XAC cellular surface can provide new insights on pathogen-plant interaction. Surface proteome was performed in XAC grown in vivo (infectious) and in vitro (non-infectious) conditions, by labeling intact cells followed by cellular lysis and direct 2D-DIGE analysis. Seventy-nine differential spots were analyzed by mass spectrometry. Highest relative abundance for in vivo condition was observed for spots containing DnaK protein, 60kDa chaperonin, conserved hypothetical proteins, malate dehydrogenase, phosphomannose isomerase, and ferric enterobactin receptors. Elongation factor Tu, OmpA-related proteins, Oar proteins and some Ton-B dependent receptors were found in spots decreased in vivo. Some proteins identified on XAC's surface in infectious condition and predicted to be cytoplasmic, such as DnaK and 60KDa chaperonin, have also been previously found at cellular surface in other microorganisms. This is the first study on XAC surface proteome and results point to mediation of molecular chaperones in XAC-citrus interaction. The approach utilized here can be applied to other pathogen-host interaction systems and help to achieve new insights in bacterial pathogenicity toward promising targets of biotechnological interest.

  13. Consensus Brain-derived Protein, Extraction Protocol for the Study of Human and Murine Brain Proteome Using Both 2D-DIGE and Mini 2DE Immunoblotting

    PubMed Central

    Fernandez-Gomez, Francisco-Jose; Jumeau, Fanny; Derisbourg, Maxime; Burnouf, Sylvie; Tran, Hélène; Eddarkaoui, Sabiha; Obriot, Hélène; Dutoit-Lefevre, Virginie; Deramecourt, Vincent; Mitchell, Valérie; Lefranc, Didier; Hamdane, Malika; Blum, David; Buée, Luc; Buée-Scherrer, Valérie; Sergeant, Nicolas

    2014-01-01

    Two-dimensional gel electrophoresis (2DE) is a powerful tool to uncover proteome modifications potentially related to different physiological or pathological conditions. Basically, this technique is based on the separation of proteins according to their isoelectric point in a first step, and secondly according to their molecular weights by SDS polyacrylamide gel electrophoresis (SDS-PAGE). In this report an optimized sample preparation protocol for little amount of human post-mortem and mouse brain tissue is described. This method enables to perform both two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) and mini 2DE immunoblotting. The combination of these approaches allows one to not only find new proteins and/or protein modifications in their expression thanks to its compatibility with mass spectrometry detection, but also a new insight into markers validation. Thus, mini-2DE coupled to western blotting permits to identify and validate post-translational modifications, proteins catabolism and provides a qualitative comparison among different conditions and/or treatments. Herein, we provide a method to study components of protein aggregates found in AD and Lewy body dementia such as the amyloid-beta peptide and the alpha-synuclein. Our method can thus be adapted for the analysis of the proteome and insoluble proteins extract from human brain tissue and mice models too. In parallel, it may provide useful information for the study of molecular and cellular pathways involved in neurodegenerative diseases as well as potential novel biomarkers and therapeutic targets. PMID:24747743

  14. Consensus brain-derived protein, extraction protocol for the study of human and murine brain proteome using both 2D-DIGE and mini 2DE immunoblotting.

    PubMed

    Fernandez-Gomez, Francisco-Jose; Jumeau, Fanny; Derisbourg, Maxime; Burnouf, Sylvie; Tran, Hélène; Eddarkaoui, Sabiha; Obriot, Hélène; Dutoit-Lefevre, Virginie; Deramecourt, Vincent; Mitchell, Valérie; Lefranc, Didier; Hamdane, Malika; Blum, David; Buée, Luc; Buée-Scherrer, Valérie; Sergeant, Nicolas

    2014-04-10

    Two-dimensional gel electrophoresis (2DE) is a powerful tool to uncover proteome modifications potentially related to different physiological or pathological conditions. Basically, this technique is based on the separation of proteins according to their isoelectric point in a first step, and secondly according to their molecular weights by SDS polyacrylamide gel electrophoresis (SDS-PAGE). In this report an optimized sample preparation protocol for little amount of human post-mortem and mouse brain tissue is described. This method enables to perform both two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) and mini 2DE immunoblotting. The combination of these approaches allows one to not only find new proteins and/or protein modifications in their expression thanks to its compatibility with mass spectrometry detection, but also a new insight into markers validation. Thus, mini-2DE coupled to western blotting permits to identify and validate post-translational modifications, proteins catabolism and provides a qualitative comparison among different conditions and/or treatments. Herein, we provide a method to study components of protein aggregates found in AD and Lewy body dementia such as the amyloid-beta peptide and the alpha-synuclein. Our method can thus be adapted for the analysis of the proteome and insoluble proteins extract from human brain tissue and mice models too. In parallel, it may provide useful information for the study of molecular and cellular pathways involved in neurodegenerative diseases as well as potential novel biomarkers and therapeutic targets.

  15. The application of DIGE-based proteomics to renal physiology.

    PubMed

    Hoorn, Ewout J; Hoffert, Jason D; Knepper, Mark A

    2006-01-01

    Proteomics is seeing increasing use as a means of identifying new mechanistic hypotheses in physiology. Proteomics based on two-dimensional electrophoresis (2-DE) has recently been optimized with the development of Difference Gel Electrophoresis (DIGE). In DIGE-based proteomics, the experimental and control samples are derivatized with different fluorophores and are run in the same gel, thereby minimizing technical variation. DIGE is currently one of the few techniques to perform quantitative proteomics, generating a statistical output to differences in protein abundances. In this review, we discuss the principles of DIGE-based proteomics, including sample preparation, 2-DE, statistical analysis of 2D-gels, and mass spectrometry. Strengths and weaknesses of DIGE are discussed, including possible solutions to overcome certain limitations, such as the identification of low abundance and integral membrane proteins. In addition, we provide a brief synopsis of our recent experiments in which DIGE-based proteomics was applied to study vasopressin signaling in the renal collecting duct. Finally, we illustrate how quantification based on the DIGE approach combined with bioinformatics may facilitate the study of systems biology of the kidney.

  16. Difference gel electrophoresis (DIGE) using CyDye DIGE fluor minimal dyes.

    PubMed

    Chakravarti, Bulbul; Gallagher, Sean R; Chakravarti, Deb N

    2005-02-01

    One- and two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (1- and 2-D SDS-PAGE) have been widely used for the separation and quantitative estimation of proteins. Following electrophoresis, the gels are stained appropriately to visualize the proteins. Difference gel electrophoresis (DIGE) is a new technique in which different protein samples, individually labeled with specific CyDyes, are combined together followed by electrophoresis and post electrophoretic co-detection and co-analysis on the same gel. CyDye DIGE fluor minimal dyes, which consist of three different CyDyes with different spectral characteristics, have been widely used for such purposes. The technique is highly sensitive with a wide dynamic range for detection of proteins and compatible with state-of-the-art protein identification techniques using mass spectrometry. Although DIGE is mainly used to compare differential expression of various protein samples using 2-D SDS-PAGE, 1-D DIGE also has important applications in quantitative proteomic studies.

  17. Convolution-deconvolution in DIGES

    SciTech Connect

    Philippacopoulos, A.J.; Simos, N.

    1995-05-01

    Convolution and deconvolution operations is by all means a very important aspect of SSI analysis since it influences the input to the seismic analysis. This paper documents some of the convolution/deconvolution procedures which have been implemented into the DIGES code. The 1-D propagation of shear and dilatational waves in typical layered configurations involving a stack of layers overlying a rock is treated by DIGES in a similar fashion to that of available codes, e.g. CARES, SHAKE. For certain configurations, however, there is no need to perform such analyses since the corresponding solutions can be obtained in analytic form. Typical cases involve deposits which can be modeled by a uniform halfspace or simple layered halfspaces. For such cases DIGES uses closed-form solutions. These solutions are given for one as well as two dimensional deconvolution. The type of waves considered include P, SV and SH waves. The non-vertical incidence is given special attention since deconvolution can be defined differently depending on the problem of interest. For all wave cases considered, corresponding transfer functions are presented in closed-form. Transient solutions are obtained in the frequency domain. Finally, a variety of forms are considered for representing the free field motion both in terms of deterministic as well as probabilistic representations. These include (a) acceleration time histories, (b) response spectra (c) Fourier spectra and (d) cross-spectral densities.

  18. Selective labelling of cell-surface proteins using CyDye DIGE Fluor minimal dyes.

    PubMed

    Hagner-McWhirter, Asa; Winkvist, Maria; Bourin, Stephanie; Marouga, Rita

    2008-11-26

    Surface proteins are central to the cell's ability to react to its environment and to interact with neighboring cells. They are known to be inducers of almost all intracellular signaling. Moreover, they play an important role in environmental adaptation and drug treatment, and are often involved in disease pathogenesis and pathology (1). Protein-protein interactions are intrinsic to signaling pathways, and to gain more insight in these complex biological processes, sensitive and reliable methods are needed for studying cell surface proteins. Two-dimensional (2-D) electrophoresis is used extensively for detection of biomarkers and other targets in complex protein samples to study differential changes. Cell surface proteins, partly due to their low abundance (1 2% of cellular proteins), are difficult to detect in a 2-D gel without fractionation or some other type of enrichment. They are also often poorly represented in 2-D gels due to their hydrophobic nature and high molecular weight (2). In this study, we present a new protocol for intact cells using CyDye DIGE Fluor minimal dyes for specific labeling and detection of this important group of proteins. The results showed specific labeling of a large number of cell surface proteins with minimal labeling of intracellular proteins. This protocol is rapid, simple to use, and all three CyDye DIGE Fluor minimal dyes (Cy 2, Cy 3 and Cy 5) can be used to label cell-surface proteins. These features allow for multiplexing using the 2-D Fluorescence Difference Gel Electrophoresis (2-D DIGE) with Ettan DIGE technology and analysis of protein expression changes using DeCyder 2-D Differential Analysis Software. The level of cell-surface proteins was followed during serum starvation of CHO cells for various lengths of time (see Table 1). Small changes in abundance were detected with high accuracy, and results are supported by defined statistical methods.

  19. Two-dimensional difference gel electrophoresis (DiGE) analysis of plasmas from dengue fever patients.

    PubMed

    Albuquerque, Lidiane M; Trugilho, Monique R O; Chapeaurouge, Alex; Jurgilas, Patrícia B; Bozza, Patrícia T; Bozza, Fernando A; Perales, Jonas; Neves-Ferreira, Ana G C

    2009-12-01

    Dengue fever is the world's most important arthropod-born viral disease affecting humans. To contribute to a better understanding of its pathogenesis, this study aims to identify proteins differentially expressed in plasmas from severe dengue fever patients relative to healthy donors. The use of 2-D Fluorescence Difference Gel Electrophoresis to analyze plasmas depleted of six high-abundance proteins (albumin, IgG, antitrypsin, IgA, transferrin and haptoglobin) allowed for the detection of 73 differentially expressed protein spots (n = 13, p < 0.01), of which 37 could be identified by mass spectrometry. These 37 spots comprised a total of 14 proteins, as follows: 7 had increased expression in plasmas from dengue fever patients (C1 inhibitor, alpha1-antichymotrypsin, vitamin D-binding protein, fibrinogen gamma-chain, alpha1-acid glycoprotein, apolipoprotein J and complement component C3c), while 7 others had decreased expression in the same samples (alpha-2 macroglobulin, prothrombin, histidine-rich glycoprotein, apolipoproteins A-IV and A-I, transthyretin and complement component C3b). The possible involvement of these proteins in the inflammatory process triggered by dengue virus infection and in the repair mechanisms of vascular damage occurring in this pathology is discussed in this study.

  20. Proteomics Studies of Brassinosteroid Signal Transduction Using Prefractionation and Two-dimensional DIGE*

    PubMed Central

    Tang, Wenqiang; Deng, Zhiping; Oses-Prieto, Juan A.; Suzuki, Nagi; Zhu, Shengwei; Zhang, Xin; Burlingame, Alma L.; Wang, Zhi-Yong

    2008-01-01

    Signal transduction involves posttranslational modifications and protein-protein interactions, which can be studied by proteomics. In Arabidopsis, the steroid hormone (brassinosteroid (BR)) binds to the extracellular domain of a receptor kinase (BRI1) to initiate a phosphorylation/dephosphorylation cascade that controls gene expression and plant growth. Here we detected early BR signaling events and identified early response proteins using prefractionation and two-dimensional (2-D) DIGE. Proteomic changes induced rapidly by BR treatments were detected in phosphoprotein and plasma membrane (PM) fractions by 2-D DIGE but not in total protein extracts. LC-MS/MS analysis of gel spots identified 19 BR-regulated PM proteins and six proteins from phosphoprotein fractions. These include the BAK1 receptor kinase and BZR1 transcription factor of the BR signaling pathway. Both proteins showed spot shifts consistent with BR-regulated phosphorylation. In addition, in vivo phosphorylation sites were identified for BZR1, two tetratricopeptide repeat proteins, and a phosphoenolpyruvate carboxykinase (PCK1). Overexpression of a novel BR-induced PM protein (DREPP) partially suppressed the phenotypes of a BR-deficient mutant, demonstrating its important function in BR responses. Our study demonstrates that prefractionation coupled with 2-D DIGE is a powerful approach for studying signal transduction. PMID:18182375

  1. Proteomics studies of brassinosteroid signal transduction using prefractionation and two-dimensional DIGE.

    PubMed

    Tang, Wenqiang; Deng, Zhiping; Oses-Prieto, Juan A; Suzuki, Nagi; Zhu, Shengwei; Zhang, Xin; Burlingame, Alma L; Wang, Zhi-Yong

    2008-04-01

    Signal transduction involves posttranslational modifications and protein-protein interactions, which can be studied by proteomics. In Arabidopsis, the steroid hormone (brassinosteroid (BR)) binds to the extracellular domain of a receptor kinase (BRI1) to initiate a phosphorylation/dephosphorylation cascade that controls gene expression and plant growth. Here we detected early BR signaling events and identified early response proteins using prefractionation and two-dimensional (2-D) DIGE. Proteomic changes induced rapidly by BR treatments were detected in phosphoprotein and plasma membrane (PM) fractions by 2-D DIGE but not in total protein extracts. LC-MS/MS analysis of gel spots identified 19 BR-regulated PM proteins and six proteins from phosphoprotein fractions. These include the BAK1 receptor kinase and BZR1 transcription factor of the BR signaling pathway. Both proteins showed spot shifts consistent with BR-regulated phosphorylation. In addition, in vivo phosphorylation sites were identified for BZR1, two tetratricopeptide repeat proteins, and a phosphoenolpyruvate carboxykinase (PCK1). Overexpression of a novel BR-induced PM protein (DREPP) partially suppressed the phenotypes of a BR-deficient mutant, demonstrating its important function in BR responses. Our study demonstrates that prefractionation coupled with 2-D DIGE is a powerful approach for studying signal transduction.

  2. Noninvasive deep Raman detection with 2D correlation analysis

    NASA Astrophysics Data System (ADS)

    Kim, Hyung Min; Park, Hyo Sun; Cho, Youngho; Jin, Seung Min; Lee, Kang Taek; Jung, Young Mee; Suh, Yung Doug

    2014-07-01

    The detection of poisonous chemicals enclosed in daily necessaries is prerequisite essential for homeland security with the increasing threat of terrorism. For the detection of toxic chemicals, we combined a sensitive deep Raman spectroscopic method with 2D correlation analysis. We obtained the Raman spectra from concealed chemicals employing spatially offset Raman spectroscopy in which incident line-shaped light experiences multiple scatterings before being delivered to inner component and yielding deep Raman signal. Furthermore, we restored the pure Raman spectrum of each component using 2D correlation spectroscopic analysis with chemical inspection. Using this method, we could elucidate subsurface component under thick powder and packed contents in a bottle.

  3. Microscale 2D separation systems for proteomic analysis

    PubMed Central

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

    2012-01-01

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

  4. Meshfree natural vibration analysis of 2D structures

    NASA Astrophysics Data System (ADS)

    Kosta, Tomislav; Tsukanov, Igor

    2014-02-01

    Determination of resonance frequencies and vibration modes of mechanical structures is one of the most important tasks in the product design procedure. The main goal of this paper is to describe a pioneering application of the solution structure method (SSM) to 2D structural natural vibration analysis problems and investigate the numerical properties of the method. SSM is a meshfree method which enables construction of the solutions to the engineering problems that satisfy exactly all prescribed boundary conditions. This method is capable of using spatial meshes that do not conform to the shape of a geometric model. Instead of using the grid nodes to enforce boundary conditions, it employs distance fields to the geometric boundaries and combines them with the basis functions and prescribed boundary conditions at run time. This defines unprecedented geometric flexibility of the SSM as well as the complete automation of the solution procedure. In the paper we will explain the key points of the SSM as well as investigate the accuracy and convergence of the proposed approach by comparing our results with the ones obtained using analytical methods or traditional finite element analysis. Despite in this paper we are dealing with 2D in-plane vibrations, the proposed approach has a straightforward generalization to model vibrations of 3D structures.

  5. A novel improved method for analysis of 2D diffusion relaxation data—2D PARAFAC-Laplace decomposition

    NASA Astrophysics Data System (ADS)

    Tønning, Erik; Polders, Daniel; Callaghan, Paul T.; Engelsen, Søren B.

    2007-09-01

    This paper demonstrates how the multi-linear PARAFAC model can with advantage be used to decompose 2D diffusion-relaxation correlation NMR spectra prior to 2D-Laplace inversion to the T2- D domain. The decomposition is advantageous for better interpretation of the complex correlation maps as well as for the quantification of extracted T2- D components. To demonstrate the new method seventeen mixtures of wheat flour, starch, gluten, oil and water were prepared and measured with a 300 MHz nuclear magnetic resonance (NMR) spectrometer using a pulsed gradient stimulated echo (PGSTE) pulse sequence followed by a Carr-Purcell-Meiboom-Gill (CPMG) pulse echo train. By varying the gradient strength, 2D diffusion-relaxation data were recorded for each sample. From these double exponentially decaying relaxation data the PARAFAC algorithm extracted two unique diffusion-relaxation components, explaining 99.8% of the variation in the data set. These two components were subsequently transformed to the T2- D domain using 2D-inverse Laplace transformation and quantitatively assigned to the oil and water components of the samples. The oil component was one distinct distribution with peak intensity at D = 3 × 10 -12 m 2 s -1 and T2 = 180 ms. The water component consisted of two broad populations of water molecules with diffusion coefficients and relaxation times centered around correlation pairs: D = 10 -9 m 2 s -1, T2 = 10 ms and D = 3 × 10 -13 m 2 s -1, T2 = 13 ms. Small spurious peaks observed in the inverse Laplace transformation of original complex data were effectively filtered by the PARAFAC decomposition and thus considered artefacts from the complex Laplace transformation. The oil-to-water ratio determined by PARAFAC followed by 2D-Laplace inversion was perfectly correlated with known oil-to-water ratio of the samples. The new method of using PARAFAC prior to the 2D-Laplace inversion proved to have superior potential in analysis of diffusion-relaxation spectra, as it

  6. 2-D Finite Element Cable and Box IEMP Analysis

    SciTech Connect

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

    1998-12-17

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

  7. Statistical analysis of quiet stance sway in 2-D.

    PubMed

    Bakshi, Avijit; DiZio, Paul; Lackner, James R

    2014-04-01

    Subjects exposed to a rotating environment that perturbs their postural sway show adaptive changes in their voluntary spatially directed postural motion to restore accurate movement paths but do not exhibit any obvious learning during passive stance. We have found, however, that a variable known to characterize the degree of stochasticity in quiet stance can also reveal subtle learning phenomena in passive stance. We extended Chow and Collins (Phys Rev E 52(1):909-912, 1995) one-dimensional pinned-polymer model (PPM) to two dimensions (2-D) and then evaluated the model's ability to make analytical predictions for 2-D quiet stance. To test the model, we tracked center of mass and centers of foot pressures, and compared and contrasted stance sway for the anterior-posterior versus medio-lateral directions before, during, and after exposure to rotation at 10 rpm. Sway of the body during rotation generated Coriolis forces that acted perpendicular to the direction of sway. We found significant adaptive changes for three characteristic features of the mean square displacement (MSD) function: the exponent of the power law defined at short time scales, the proportionality constant of the power law, and the saturation plateau value defined at longer time scales. The exponent of the power law of MSD at a short time scale lies within the bounds predicted by the 2-D PPM. The change in MSD during exposure to rotation also had a power-law exponent in the range predicted by the theoretical model. We discuss the Coriolis force paradigm for studying postural and movement control and the applicability of the PPM model in 2-D for studying postural adaptation.

  8. Multifractal analysis of 2D gray soil images

    NASA Astrophysics Data System (ADS)

    González-Torres, Ivan; Losada, Juan Carlos; Heck, Richard; Tarquis, Ana M.

    2015-04-01

    Soil structure, understood as the spatial arrangement of soil pores, is one of the key factors in soil modelling processes. Geometric properties of individual and interpretation of the morphological parameters of pores can be estimated from thin sections or 3D Computed Tomography images (Tarquis et al., 2003), but there is no satisfactory method to binarized these images and quantify the complexity of their spatial arrangement (Tarquis et al., 2008, Tarquis et al., 2009; Baveye et al., 2010). The objective of this work was to apply a multifractal technique, their singularities (α) and f(α) spectra, to quantify it without applying any threshold (Gónzalez-Torres, 2014). Intact soil samples were collected from four horizons of an Argisol, formed on the Tertiary Barreiras group of formations in Pernambuco state, Brazil (Itapirema Experimental Station). The natural vegetation of the region is tropical, coastal rainforest. From each horizon, showing different porosities and spatial arrangements, three adjacent samples were taken having a set of twelve samples. The intact soil samples were imaged using an EVS (now GE Medical. London, Canada) MS-8 MicroCT scanner with 45 μm pixel-1 resolution (256x256 pixels). Though some samples required paring to fit the 64 mm diameter imaging tubes, field orientation was maintained. References Baveye, P.C., M. Laba, W. Otten, L. Bouckaert, P. Dello, R.R. Goswami, D. Grinev, A. Houston, Yaoping Hu, Jianli Liu, S. Mooney, R. Pajor, S. Sleutel, A. Tarquis, Wei Wang, Qiao Wei, Mehmet Sezgin. Observer-dependent variability of the thresholding step in the quantitative analysis of soil images and X-ray microtomography data. Geoderma, 157, 51-63, 2010. González-Torres, Iván. Theory and application of multifractal analysis methods in images for the study of soil structure. Master thesis, UPM, 2014. Tarquis, A.M., R.J. Heck, J.B. Grau; J. Fabregat, M.E. Sanchez and J.M. Antón. Influence of Thresholding in Mass and Entropy Dimension of 3-D

  9. Theoretical analysis of the 2D thermal cloaking problem

    NASA Astrophysics Data System (ADS)

    Alekseev, G. V.; Spivak, Yu E.; Yashchenko, E. N.

    2017-01-01

    Coefficient inverse problems for the model of heat scattering with variable coefficients arising when developing technologies of design of thermal cloaking devices are considered. By the optimization method, these problems are reduced to respective control problems. The material parameters (radial and azimuthal conductivities) of the inhomogeneous anisotropic medium, filling the thermal cloak, play the role of control. The model of heat scattering acts as a functional restriction. A unique solvability of direct heat scattering problem in the Sobolev space is proved and the new estimates of solutions are established. Using these results, the solvability of control problem is proved and the optimality system is derived. Based on analysis of optimality system, the stability estimates of optimal solutions are established and efficient numerical algorithm of solving thermal cloaking problems is proposed.

  10. 2-D Acousto-Optic Signal Processors for Simultaneous Spectrum Analysis and Direction Finding

    DTIC Science & Technology

    1990-11-01

    National Dfense Defence nationale 2-D ACOUSTO - OPTIC SIGNAL PROCESSORS FOR SIMULTANEOUS SPECTRUM ANALYSIS 00 AND DIRECTION FINDING (U) by NM Jim P.Y...Wr pdft .1w I0~1111191 3 05089 National DIfense Defence nationale 2-D ACOUSTO - OPTIC SIGNAL PROCESSORS FOR SIMULTANEOUS SPECTRUM ANALYSIS AND DIRECTION...Processing, J.T. Tippet et al., Eds., Chapter 38, pp. 715-748, MIT Press, Cambridge 1965. [6] A.E. Spezio," Acousto - optics for Electronic Warfare

  11. Scientometric analysis and bibliography of digit ratio (2D:4D) research, 1998-2008.

    PubMed

    Voracek, Martin; Loibl, Lisa Mariella

    2009-06-01

    A scientometric analysis of modern research on the second-to-fourth digit ratio (2D:4D), a widely studied putative marker for prenatal androgen action, is presented. In early 2009, this literature totalled more than 300 publications and, since its initiation in 1998, has grown at a rate slightly faster than linear. Key findings included evidence of publication bias and citation bias, incomplete coverage and outdatedness of existing reviews, and a dearth of meta-analyses in this field. 2D:4D research clusters noticeably in terms of researchers, institutions, countries, and journals involved. Although 2D:4D is an anthropometric trait, most of the research has been conducted at psychology departments, not anthropology departments. However, 2D:4D research has not been predominantly published in core and specialized journals of psychology, but rather in more broadly scoped journals of the behavioral sciences, biomedical social sciences, and neurosciences. Total citation numbers of 2D:4D papers for the most part were not larger than their citation counts within 2D:4D research, indicating that until now, only a few 2D:4D studies have attained broader interest outside this specific field. Comparative citation analyses show that 2D:4D research presently is commensurate in size and importance to evolutionary psychological jealousy research, but has grown faster than the latter field. In contrast, it is much smaller and has spread more slowly than research about the Implicit Association Test Fifteen conjectures about anticipated trends in 2D:4D research are outlined, appendixed by a first-time bibliography of the entirety of the published 2D:4D literature.

  12. Aircraft target identification based on 2D ISAR images using multiresolution analysis wavelet

    NASA Astrophysics Data System (ADS)

    Fu, Qiang; Xiao, Huaitie; Hu, Xiangjiang

    2001-09-01

    The formation of 2D ISAR images for radar target identification hold much promise for additional distinguish- ability between targets. Since an image contains important information is a wide range of scales, and this information is often independent from one scale to another, wavelet analysis provides a method of identifying the spatial frequency content of an image and the local regions within the image where those spatial frequencies exist. In this paper, a multiresolution analysis wavelet method based on 2D ISAR images was proposed for use in aircraft radar target identification under the wide band high range resolution radar background. The proposed method was performed in three steps; first, radar backscatter signals were processed in the form of 2D ISAR images, then, Mallat's wavelet algorithm was used in the decomposition of images, finally, a three layer perceptron neural net was used as classifier. The result of experiments demonstrated that the feasibility of using multiresolution analysis wavelet for target identification.

  13. CYP2D6 genotype and adjuvant tamoxifen: meta-analysis of heterogeneous study populations.

    PubMed

    Province, M A; Goetz, M P; Brauch, H; Flockhart, D A; Hebert, J M; Whaley, R; Suman, V J; Schroth, W; Winter, S; Zembutsu, H; Mushiroda, T; Newman, W G; Lee, M-T M; Ambrosone, C B; Beckmann, M W; Choi, J-Y; Dieudonné, A-S; Fasching, P A; Ferraldeschi, R; Gong, L; Haschke-Becher, E; Howell, A; Jordan, L B; Hamann, U; Kiyotani, K; Krippl, P; Lambrechts, D; Latif, A; Langsenlehner, U; Lorizio, W; Neven, P; Nguyen, A T; Park, B-W; Purdie, C A; Quinlan, P; Renner, W; Schmidt, M; Schwab, M; Shin, J-G; Stingl, J C; Wegman, P; Wingren, S; Wu, A H B; Ziv, E; Zirpoli, G; Thompson, A M; Jordan, V C; Nakamura, Y; Altman, R B; Ames, M M; Weinshilboum, R M; Eichelbaum, M; Ingle, J N; Klein, T E

    2014-02-01

    The International Tamoxifen Pharmacogenomics Consortium was established to address the controversy regarding cytochrome P450 2D6 (CYP2D6) status and clinical outcomes in tamoxifen therapy. We performed a meta-analysis on data from 4,973 tamoxifen-treated patients (12 globally distributed sites). Using strict eligibility requirements (postmenopausal women with estrogen receptor-positive breast cancer, receiving 20 mg/day tamoxifen for 5 years, criterion 1); CYP2D6 poor metabolizer status was associated with poorer invasive disease-free survival (IDFS: hazard ratio = 1.25; 95% confidence interval = 1.06, 1.47; P = 0.009). However, CYP2D6 status was not statistically significant when tamoxifen duration, menopausal status, and annual follow-up were not specified (criterion 2, n = 2,443; P = 0.25) or when no exclusions were applied (criterion 3, n = 4,935; P = 0.38). Although CYP2D6 is a strong predictor of IDFS using strict inclusion criteria, because the results are not robust to inclusion criteria (these were not defined a priori), prospective studies are necessary to fully establish the value of CYP2D6 genotyping in tamoxifen therapy.

  14. PLAN2D - A PROGRAM FOR ELASTO-PLASTIC ANALYSIS OF PLANAR FRAMES

    NASA Technical Reports Server (NTRS)

    Lawrence, C.

    1994-01-01

    PLAN2D is a FORTRAN computer program for the plastic analysis of planar rigid frame structures. Given a structure and loading pattern as input, PLAN2D calculates the ultimate load that the structure can sustain before collapse. Element moments and plastic hinge rotations are calculated for the ultimate load. The location of hinges required for a collapse mechanism to form are also determined. The program proceeds in an iterative series of linear elastic analyses. After each iteration the resulting elastic moments in each member are compared to the reserve plastic moment capacity of that member. The member or members that have moments closest to their reserve capacity will determine the minimum load factor and the site where the next hinge is to be inserted. Next, hinges are inserted and the structural stiffness matrix is reformulated. This cycle is repeated until the structure becomes unstable. At this point the ultimate collapse load is calculated by accumulating the minimum load factor from each previous iteration and multiplying them by the original input loads. PLAN2D is based on the program STAN, originally written by Dr. E.L. Wilson at U.C. Berkeley. PLAN2D has several limitations: 1) Although PLAN2D will detect unloading of hinges it does not contain the capability to remove hinges; 2) PLAN2D does not allow the user to input different positive and negative moment capacities and 3) PLAN2D does not consider the interaction between axial and plastic moment capacity. Axial yielding and buckling is ignored as is the reduction in moment capacity due to axial load. PLAN2D is written in FORTRAN and is machine independent. It has been tested on an IBM PC and a DEC MicroVAX. The program was developed in 1988.

  15. Proteomic analysis of lung tissue by DIGE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lungs perform an essential physiological function, mediated by a complex series of events that involve the coordination of multiple cell types to support not only gaseous exchange, but homeostasis and protection from infection. Guinea pigs are an important animal disease model for a number of infect...

  16. Ultrasonic tissue characterization via 2-D spectrum analysis: theory and in vitro measurements.

    PubMed

    Liu, Tian; Lizzi, Frederic L; Ketterling, Jeffrey A; Silverman, Ronald H; Kutcher, Gerald J

    2007-03-01

    A theoretical model is described for application in ultrasonic tissue characterization using a calibrated 2-D spectrum analysis method. This model relates 2-D spectra computed from ultrasonic backscatter signals to intrinsic physical properties of tissue microstructures, e.g., size, shape, and acoustic impedance. The model is applicable to most clinical diagnostic ultrasound systems. Two experiments employing two types of tissue architectures, spherical and cylindrical scatterers, are conducted using ultrasound with center frequencies of 10 and 40 MHz, respectively. Measurements of a tissue-mimicking phantom with an internal suspension of microscopic glass beads are used to validate the theoretical model. Results from in vitro muscle fibers are presented to further elucidate the utility of 2-D spectrum analysis in ultrasonic tissue characterization.

  17. New technologies of 2-D and 3-D modeling for analysis and management of natural resources

    NASA Astrophysics Data System (ADS)

    Cheremisina, E. N.; Lyubimova, A. V.; Kirpicheva, E. Yu.

    2016-09-01

    For ensuring technological support of research and administrative activity in the sphere of environmental management a specialized modular program complex was developed. The special attention in developing a program complex is focused to creation of convenient and effective tools for creation and visualization 2d and 3D models providing the solution of tasks of the analysis and management of natural resources.

  18. Elastic shape analysis of cylindrical surfaces for 3D/2D registration in endometrial tissue characterization.

    PubMed

    Samir, Chafik; Kurtek, Sebastian; Srivastava, Anuj; Canis, Michel

    2014-05-01

    We study the problem of joint registration and deformation analysis of endometrial tissue using 3D magnetic resonance imaging (MRI) and 2D trans-vaginal ultrasound (TVUS) measurements. In addition to the different imaging techniques involved in the two modalities, this problem is complicated due to: 1) different patient pose during MRI and TVUS observations, 2) the 3D nature of MRI and 2D nature of TVUS measurements, 3) the unknown intersecting plane for TVUS in MRI volume, and 4) the potential deformation of endometrial tissue during TVUS measurement process. Focusing on the shape of the tissue, we use expert manual segmentation of its boundaries in the two modalities and apply, with modification, recent developments in shape analysis of parametric surfaces to this problem. First, we extend the 2D TVUS curves to generalized cylindrical surfaces through replication, and then we compare them with MRI surfaces using elastic shape analysis. This shape analysis provides a simultaneous registration (optimal reparameterization) and deformation (geodesic) between any two parametrized surfaces. Specifically, it provides optimal curves on MRI surfaces that match with the original TVUS curves. This framework results in an accurate quantification and localization of the deformable endometrial cells for radiologists, and growth characterization for gynecologists and obstetricians. We present experimental results using semi-synthetic data and real data from patients to illustrate these ideas.

  19. Multiple triangulation analysis: application to determine the velocity of 2-D structures

    NASA Astrophysics Data System (ADS)

    Zhou, X.-Z.; Zong, Q.-G.; Wang, J.; Pu, Z. Y.; Zhang, X. G.; Shi, Q. Q.; Cao, J. B.

    2006-11-01

    In order to avoid the ambiguity of the application of the Triangulation Method (multi-spacecraft timing method) to two-dimensional structures, another version of this method, the Multiple Triangulation Analysis (MTA) is used, to calculate the velocities of these structures based on 4-point measurements. We describe the principle of MTA and apply this approach to a real event observed by the Cluster constellation on 2 October 2003. The resulting velocity of the 2-D structure agrees with the ones obtained by some other methods fairly well. So we believe that MTA is a reliable version of the Triangulation Method for 2-D structures, and thus provides us a new way to describe their motion.

  20. Real-time 2D spatially selective MRI experiments: Comparative analysis of optimal control design methods.

    PubMed

    Maximov, Ivan I; Vinding, Mads S; Tse, Desmond H Y; Nielsen, Niels Chr; Shah, N Jon

    2015-05-01

    There is an increasing need for development of advanced radio-frequency (RF) pulse techniques in modern magnetic resonance imaging (MRI) systems driven by recent advancements in ultra-high magnetic field systems, new parallel transmit/receive coil designs, and accessible powerful computational facilities. 2D spatially selective RF pulses are an example of advanced pulses that have many applications of clinical relevance, e.g., reduced field of view imaging, and MR spectroscopy. The 2D spatially selective RF pulses are mostly generated and optimised with numerical methods that can handle vast controls and multiple constraints. With this study we aim at demonstrating that numerical, optimal control (OC) algorithms are efficient for the design of 2D spatially selective MRI experiments, when robustness towards e.g. field inhomogeneity is in focus. We have chosen three popular OC algorithms; two which are gradient-based, concurrent methods using first- and second-order derivatives, respectively; and a third that belongs to the sequential, monotonically convergent family. We used two experimental models: a water phantom, and an in vivo human head. Taking into consideration the challenging experimental setup, our analysis suggests the use of the sequential, monotonic approach and the second-order gradient-based approach as computational speed, experimental robustness, and image quality is key. All algorithms used in this work were implemented in the MATLAB environment and are freely available to the MRI community.

  1. A 2-D diode array and analysis software for verification of intensity modulated radiation therapy delivery.

    PubMed

    Jursinic, Paul A; Nelms, Ben E

    2003-05-01

    An analysis is made of a two-dimensional array of diodes that can be used for measuring dose generated in a plane by a radiation beam. This measuring device is the MapCHECK Model 1175 (Sun Nuclear, Melbourne, FL). This device has 445 N-type diodes in a 22 x 22 cm2 2-D array with variable spacing. The entire array of diodes is easily calibrated to allow for measurements in absolute dose. For IMRT quality assurance, each beam is measured individually with the beam central axis oriented perpendicular to the plane of diodes. Software is available to do the analytical comparison of measurements versus dose distributions calculated by a treatment planning system. Comparison criteria of percent difference and distance-to-agreement are defined by the operator. Data are presented that show the diode array has linear response when beam fluence changes by over 300-fold, which is typical of the level of modulation in intensity modulated radiation therapy, IMRT, beams. A linear dependence is also shown for a 100-fold change in monitors units delivered. Methods for how this device can be used in the clinic for quality assurance of IMRT fields are described. Measurements of typical IMRT beams that are modulated by compensators and MLCs are presented with comparisons to treatment planning system dose calculations. A time analysis is done for typical IMRT quality assurance measurements. The setup, calibration, and analysis time for the 2-D diode array are on the order of 20 min, depending on numbers of fields. This is significantly less time than required to do similar analysis with radiographic film. The 2-D diode array is ideal for per-plan quality assurance after an IMRT system is fully commissioned.

  2. Database of two-dimensional polyacrylamide gel electrophoresis of proteins labeled with CyDye DIGE Fluor saturation dye.

    PubMed

    Fujii, Kazuyasu; Kondo, Tadashi; Yokoo, Hideki; Okano, Tetsuya; Yamada, Masayo; Yamada, Tesshi; Iwatsuki, Keiji; Hirohashi, Setsuo

    2006-03-01

    CyDye DIGE Fluor saturation dye (saturation dye, GE Healthcare Amersham Biosciences) enables highly sensitive 2-D PAGE. As the dye reacts with all reduced cysteine thiols, 2-D PAGE can be performed with a lower amount of protein, compared with CyDye DIGE Fluor minimal dye (GE Healthcare Amersham Biosciences), the sensitivity of which is equivalent to that of silver staining. We constructed a 2-D map of the saturation dye-labeled proteins of a liver cancer cell line (HepG2) and identified by MS 92 proteins corresponding to 123 protein spots. Functional classification revealed that the identified proteins had chaperone, protein binding, nucleotide binding, metal ion binding, isomerase activity, and motor activity. The functional distribution and the cysteine contents of the proteins were similar to those in the most comprehensive 2-D database of hepatoma cells (Seow et al.., Electrophoresis 2000, 21, 1787-1813), where silver staining was used for protein visualization. Hierarchical clustering on the basis of the quantitative expression profiles of the 123 characterized spots labeled with two charge- and mass-matched saturation dyes (Cy3 and Cy5) discriminated between nine hepatocellular carcinoma cell lines and primary cultured hepatocytes from five individuals, suggesting the utility of saturation dye and our database for proteomic studies of liver cancer.

  3. Combining 2D synchrosqueezed wave packet transform with optimization for crystal image analysis

    NASA Astrophysics Data System (ADS)

    Lu, Jianfeng; Wirth, Benedikt; Yang, Haizhao

    2016-04-01

    We develop a variational optimization method for crystal analysis in atomic resolution images, which uses information from a 2D synchrosqueezed transform (SST) as input. The synchrosqueezed transform is applied to extract initial information from atomic crystal images: crystal defects, rotations and the gradient of elastic deformation. The deformation gradient estimate is then improved outside the identified defect region via a variational approach, to obtain more robust results agreeing better with the physical constraints. The variational model is optimized by a nonlinear projected conjugate gradient method. Both examples of images from computer simulations and imaging experiments are analyzed, with results demonstrating the effectiveness of the proposed method.

  4. 2D light scattering static cytometry for label-free single cell analysis with submicron resolution.

    PubMed

    Xie, Linyan; Yang, Yan; Sun, Xuming; Qiao, Xu; Liu, Qiao; Song, Kun; Kong, Beihua; Su, Xuantao

    2015-11-01

    Conventional optical cytometric techniques usually measure fluorescence or scattering signals at fixed angles from flowing cells in a liquid stream. Here we develop a novel cytometer that employs a scanning optical fiber to illuminate single static cells on a glass slide, which requires neither microfluidic fabrication nor flow control. This static cytometric technique measures two dimensional (2D) light scattering patterns via a small numerical aperture (0.25) microscope objective for label-free single cell analysis. Good agreement is obtained between the yeast cell experimental and Mie theory simulated patterns. It is demonstrated that the static cytometer with a microscope objective of a low resolution around 1.30 μm has the potential to perform high resolution analysis on yeast cells with distributed sizes. The capability of the static cytometer for size determination with submicron resolution is validated via measurements on standard microspheres with mean diameters of 3.87 and 4.19 μm. Our 2D light scattering static cytometric technique may provide an easy-to-use, label-free, and flow-free method for single cell diagnostics.

  5. Development of an affordable system for 2D kinematics and dynamics analysis of human gait

    NASA Astrophysics Data System (ADS)

    Mahyuddin, A. I.; Mihradi, S.; Dirgantara, T.; Sukmajaya, A.; Juliyad, N.; Purba, U.

    2009-12-01

    Development of a low-cost, yet reliable, system for 2D gait analysis is presented in this paper. The system consists of a home video camera with speed of 25 fps, LED markers, PC and a technical computing software, which are used for capturing and processing the digital image of markers attached to human body during motion. In the experiments, a person is instructed to walk in a specially arranged measurement area. The recorded images are then digitally processed to detect and track the 2D coordinate of the markers over time. To conduct a dynamics analysis, a mathematical formulation for human motion is constructed where the body is modeled by a system of five rigid bars connected by joints. Finally, a program is developed to plot and calculate the kinematics and dynamics data of human gait, where the markers position data over time, and other variables such as dimensions and weight of the body are used as the input in the program.

  6. Development of an affordable system for 2D kinematics and dynamics analysis of human gait

    NASA Astrophysics Data System (ADS)

    Mahyuddin, A. I.; Mihradi, S.; Dirgantara, T.; Sukmajaya, A.; Juliyad, N.; Purba, U.

    2010-03-01

    Development of a low-cost, yet reliable, system for 2D gait analysis is presented in this paper. The system consists of a home video camera with speed of 25 fps, LED markers, PC and a technical computing software, which are used for capturing and processing the digital image of markers attached to human body during motion. In the experiments, a person is instructed to walk in a specially arranged measurement area. The recorded images are then digitally processed to detect and track the 2D coordinate of the markers over time. To conduct a dynamics analysis, a mathematical formulation for human motion is constructed where the body is modeled by a system of five rigid bars connected by joints. Finally, a program is developed to plot and calculate the kinematics and dynamics data of human gait, where the markers position data over time, and other variables such as dimensions and weight of the body are used as the input in the program.

  7. Lacunarity analysis of raster datasets and 1D, 2D, and 3D point patterns

    NASA Astrophysics Data System (ADS)

    Dong, Pinliang

    2009-10-01

    Spatial scale plays an important role in many fields. As a scale-dependent measure for spatial heterogeneity, lacunarity describes the distribution of gaps within a set at multiple scales. In Earth science, environmental science, and ecology, lacunarity has been increasingly used for multiscale modeling of spatial patterns. This paper presents the development and implementation of a geographic information system (GIS) software extension for lacunarity analysis of raster datasets and 1D, 2D, and 3D point patterns. Depending on the application requirement, lacunarity analysis can be performed in two modes: global mode or local mode. The extension works for: (1) binary (1-bit) and grey-scale datasets in any raster format supported by ArcGIS and (2) 1D, 2D, and 3D point datasets as shapefiles or geodatabase feature classes. For more effective measurement of lacunarity for different patterns or processes in raster datasets, the extension allows users to define an area of interest (AOI) in four different ways, including using a polygon in an existing feature layer. Additionally, directionality can be taken into account when grey-scale datasets are used for local lacunarity analysis. The methodology and graphical user interface (GUI) are described. The application of the extension is demonstrated using both simulated and real datasets, including Brodatz texture images, a Spaceborne Imaging Radar (SIR-C) image, simulated 1D points on a drainage network, and 3D random and clustered point patterns. The options of lacunarity analysis and the effects of polyline arrangement on lacunarity of 1D points are also discussed. Results from sample data suggest that the lacunarity analysis extension can be used for efficient modeling of spatial patterns at multiple scales.

  8. Simultaneous immunoblotting analysis with activity gel electrophoresis and 2-D gel electrophoresis.

    PubMed

    Lee, Der-Yen; Chang, Geen-Dong

    2015-01-01

    Diffusion blotting method can couple immunoblotting analysis with another biochemical technique in a single polyacrylamide gel, however, with lower transfer efficiency as compared to the conventional electroblotting method. Thus, with diffusion blotting, protein blots can be obtained from an SDS polyacrylamide gel for zymography assay, from a native polyacrylamide gel for electrophoretic mobility shift assay (EMSA) or from a 2-D polyacrylamide gel for large-scale screening and identification of a protein marker. Thereafter, a particular signal in zymography, electrophoretic mobility shift assay, and 2-dimensional gel can be confirmed or identified by simultaneous immunoblotting analysis with a corresponding antiserum. These advantages make diffusion blotting desirable when partial loss of transfer efficiency can be tolerated or be compensated by a more sensitive immunodetection reaction using enhanced chemiluminescence detection.

  9. Experimental Analysis of a 2-D Lightcraft in Static and Hypersonic Conditions

    NASA Astrophysics Data System (ADS)

    Salvador, Israel I.; Myrabo, Leik N.; Minucci, Marco A. S.; de Oliveira, Antonio C.; Rego, Israel S.; Toro, Paulo G. P.; Channes, José B.

    2010-05-01

    Aiming at the hypersonic phase of the Earth-to-Orbit trajectory for a laser propelled vehicle, a 2-D Lightcraft model was designed to be tested at the T3 Hypersonic Shock Tunnel at the Henry T. Nagamatsu Laboratory for Aerodynamics and Hypersonics. A high energy laser pulse was supplied by a Lumonics TEA 620 laser system operating in unstable resonator cavity mode. The experiments were performed at quiescent (no flow) conditions and at a nominal Mach number of 9.2. A Schlieren visualization apparatus was used in order to access both the cold hypersonic flowfield structure (without laser deposition) and the time dependent flowfield structure, taking place after the laser induced breakdown inside the absorption chamber. The model was fitted with piezoelectric pressure transducers and surface junction thermocouples in an attempt to measure pressure and heat transfer time dependent distributions at the internal surfaces of the model's absorption chamber. The 2-D model followed a modular design for flexibility on the analysis of geometrical features contribution on the expansion of the laser induced blast wave. Finally, future evolution of the experiments being currently pursued is addressed.

  10. Robust 2D principal component analysis: a structured sparsity regularized approach.

    PubMed

    Yipeng Sun; Xiaoming Tao; Yang Li; Jianhua Lu

    2015-08-01

    Principal component analysis (PCA) is widely used to extract features and reduce dimensionality in various computer vision and image/video processing tasks. Conventional approaches either lack robustness to outliers and corrupted data or are designed for one-dimensional signals. To address this problem, we propose a robust PCA model for two-dimensional images incorporating structured sparse priors, referred to as structured sparse 2D-PCA. This robust model considers the prior of structured and grouped pixel values in two dimensions. As the proposed formulation is jointly nonconvex and nonsmooth, which is difficult to tackle by joint optimization, we develop a two-stage alternating minimization approach to solve the problem. This approach iteratively learns the projection matrices by bidirectional decomposition and utilizes the proximal method to obtain the structured sparse outliers. By considering the structured sparsity prior, the proposed model becomes less sensitive to noisy data and outliers in two dimensions. Moreover, the computational cost indicates that the robust two-dimensional model is capable of processing quarter common intermediate format video in real time, as well as handling large-size images and videos, which is often intractable with other robust PCA approaches that involve image-to-vector conversion. Experimental results on robust face reconstruction, video background subtraction data set, and real-world videos show the effectiveness of the proposed model compared with conventional 2D-PCA and other robust PCA algorithms.

  11. Coherent X-ray beam metrology using 2D high-resolution Fresnel-diffraction analysis.

    PubMed

    Ruiz-Lopez, M; Faenov, A; Pikuz, T; Ozaki, N; Mitrofanov, A; Albertazzi, B; Hartley, N; Matsuoka, T; Ochante, Y; Tange, Y; Yabuuchi, T; Habara, T; Tanaka, K A; Inubushi, Y; Yabashi, M; Nishikino, M; Kawachi, T; Pikuz, S; Ishikawa, T; Kodama, R; Bleiner, D

    2017-01-01

    Direct metrology of coherent short-wavelength beamlines is important for obtaining operational beam characteristics at the experimental site. However, since beam-time limitation imposes fast metrology procedures, a multi-parametric metrology from as low as a single shot is desirable. Here a two-dimensional (2D) procedure based on high-resolution Fresnel diffraction analysis is discussed and applied, which allowed an efficient and detailed beamline characterization at the SACLA XFEL. So far, the potential of Fresnel diffraction for beamline metrology has not been fully exploited because its high-frequency fringes could be only partly resolved with ordinary pixel-limited detectors. Using the high-spatial-frequency imaging capability of an irradiated LiF crystal, 2D information of the coherence degree, beam divergence and beam quality factor M(2) were retrieved from simple diffraction patterns. The developed beam metrology was validated with a laboratory reference laser, and then successfully applied at a beamline facility, in agreement with the source specifications.

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

    NASA Astrophysics Data System (ADS)

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

    2012-10-01

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

  13. Analysis of stochastic phenomena in 2D Hindmarsh-Rose neuron model

    NASA Astrophysics Data System (ADS)

    Bashkirtseva, I.; Ryashko, L.; Slepukhina, E.

    2016-10-01

    In mathematical research of neuronal activity, conceptual models play an important role. We consider 2D Hindmarsh-Rose model, which exhibits the fundamental property of neuron, the excitability. We study how random disturbances affect this property. The effects of noise are analysed in the parametric zone where the deterministic model is characterized by the coexistence of two stable equilibria. We show that under random disturbances, noise-induced transitions between the attractors occur, forming a new complex dynamic regime of stochastic bursting. It is confirmed by changes of distribution of random trajectories and interspike intervals. For the analysis of this noise-induced phenomenon, we apply the stochastic sensitivity technique and confidence domains method. We suggest a method for estimation of threshold noise intensity corresponding to the onset of noise-induced bursting. We show that the obtained values are in a good agreement with direct numerical simulations.

  14. Analysis of the antiferromagnetic phase transitions of the 2D Kondo lattice

    NASA Astrophysics Data System (ADS)

    Jones, Barbara

    2010-03-01

    The Kondo lattice continues to present an interesting and relevant challenge, with its interactions between Kondo, RKKY, and coherent order. We present our study[1] of the antiferromagnetic quantum phase transitions of a 2D Kondo-Heisenberg square lattice. Starting from the nonlinear sigma model as a model of antiferromagnetism, we carry out a renormalization group analysis of the competing Kondo-RKKY interaction to one-loop order in an ɛ-expansion. We find a new quantum critical point (QCP) strongly affected by Kondo fluctuations. Near this QCP, there is a breakdown of hydrodynamic behavior, and the spin waves are logarithmically frozen out. The renormalization group results allow us to propose a new phase diagram near the antiferromagnetic fixed point of this 2D Kondo lattice model. The T=0 phase diagram contains four phases separated by a tetracritical point, the new QCP. For small spin fluctuations, we find a stable local magnetic moment antiferromagnet. For stronger coupling, region II is a metallic quantum disordered paramagnet. We find in region III a paramagnetic phase driven by Kondo interactions, with possible ground states of a heavy fermion liquid or a Kondo driven spin-liquid. The fourth phase is a spiral phase, or a large-Fermi-surface antiferromagnetic phase. We will describe these phases in more detail, including possible experimental confirmation of the spiral phase. The existence of the tetracritical point found here would be expected to affect the phase diagram at finite temperatures as well. In addition, It is hoped that these results, and particularly the Kondo interaction paramagnetic phase, will serve to bridge to solutions starting from the opposite limit, of a Kondo effect leading to a heavy fermion ground state. Work in collaboration with T. Tzen Ong. [4pt] [1] T. Ong and B. A. Jones, Phys. Rev. Lett. 103, 066405 (2009).

  15. 2D map projections for visualization and quantitative analysis of 3D fluorescence micrographs

    PubMed Central

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

    2015-01-01

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

  16. The Design and Analysis of Split Row-Column Addressing Array for 2-D Transducer

    PubMed Central

    Li, Xu; Jia, Yanping; Ding, Mingyue; Yuchi, Ming

    2016-01-01

    For 3-D ultrasound imaging, the row-column addressing (RCA) with 2N connections for an N × N 2-D array makes the fabrication and interconnection simpler than the fully addressing with N2 connections. However, RCA degrades the image quality because of defocusing in signal channel direction in the transmit event. To solve this problem, a split row-column addressing scheme (SRCA) is proposed in this paper. Rather than connecting all the elements in the signal channel direction together, this scheme divides the elements in the signal channel direction into several disconnected blocks, thus enables focusing beam access in both signal channel and switch channel directions. Selecting an appropriate split scheme is the key for SRCA to maintaining a reasonable tradeoff between the image quality and the number of connections. Various split schemes for a 32 × 32 array are fully investigated with point spread function (PSF) analysis and imaging simulation. The result shows the split scheme with five blocks (4, 6, 12, 6, and 4 elements of each block) can provide similar image quality to fully addressing. The splitting schemes for different array sizes from 16 × 16 to 96 × 96 are also discussed. PMID:27690029

  17. Analysis of capacitive sensing for 2D-MEMS scanner laser projection

    NASA Astrophysics Data System (ADS)

    von Wantoch, Thomas; Mallas, Christian; Hofmann, Ulrich; Janes, Joachim; Wagner, Bernhard; Benecke, Wolfgang

    2014-03-01

    Typical applications for resonantly driven vacuum packaged MEMS scanners including laser projection displays require a feedback signal for closed-loop operation as well as high accuracy angle synchronization for data processing. A well known and widely used method is based on determining the angular velocity of the oscillating micromirror by measuring the time derivative of a capacitance. In this work we analyze a capacitive sensing approach that uses integrated vertical comb structures to synchronize the angular motion of a torsional micromirror oscillating in resonance. The investigated measurement method is implemented in a laser display that generates a video projection by scanning a RBG laser beam. As the 2D-micromirror performs sinusoidal oscillations on both perpendicular axes a continuously moving Lissajous pattern is projected. By measuring the displacement current due to an angular deflection of the movable comb structures an appropriate feedback signal for actuation and data synchronization is computed. In order to estimate the angular deflection and velocity a mathematical model of the capacitive sensing system is presented. In particular, the nonlinear characteristic of the capacitance as a function of the angle that is calculated using FEM analysis is approximated using cubic splines. Combining this nonlinear function with a dynamic model of the micromirror oscillation and the analog electronics a mathematical model of the capacitive measurement system is derived. To evaluate the proposed model numerical simulations are realized using MATLAB/Simulink and are compared to experimental measurements.

  18. Performance Analysis of the Microsoft Kinect Sensor for 2D Simultaneous Localization and Mapping (SLAM) Techniques

    PubMed Central

    Kamarudin, Kamarulzaman; Mamduh, Syed Muhammad; Shakaff, Ali Yeon Md; Zakaria, Ammar

    2014-01-01

    This paper presents a performance analysis of two open-source, laser scanner-based Simultaneous Localization and Mapping (SLAM) techniques (i.e., Gmapping and Hector SLAM) using a Microsoft Kinect to replace the laser sensor. Furthermore, the paper proposes a new system integration approach whereby a Linux virtual machine is used to run the open source SLAM algorithms. The experiments were conducted in two different environments; a small room with no features and a typical office corridor with desks and chairs. Using the data logged from real-time experiments, each SLAM technique was simulated and tested with different parameter settings. The results show that the system is able to achieve real time SLAM operation. The system implementation offers a simple and reliable way to compare the performance of Windows-based SLAM algorithm with the algorithms typically implemented in a Robot Operating System (ROS). The results also indicate that certain modifications to the default laser scanner-based parameters are able to improve the map accuracy. However, the limited field of view and range of Kinect's depth sensor often causes the map to be inaccurate, especially in featureless areas, therefore the Kinect sensor is not a direct replacement for a laser scanner, but rather offers a feasible alternative for 2D SLAM tasks. PMID:25490595

  19. 2-D Fourier transform analysis of the gravitational field of Northern Sinai Peninsula

    NASA Astrophysics Data System (ADS)

    Khalil, Mohamed A.; Santos, Fernando M.; Farzamian, Mohammad; El-Kenawy, Abeer

    2015-04-01

    The Sinai Peninsula has fascinated the consideration of many geophysical studies as it is influenced by major tectonic events. Those are (1) the Mesozoic to Early Cenozoic tectonically active opening of Tethys, (2) the Late Cretaceous to Early Tertiary (Laramide) Syrian arc system, due to closing of the Tethys (3) the Oligo-Miocene Gulf of Suez rifted basin, and (4) the Late Miocene to Recent transform Dead Sea-Gulf of Aqaba rift. Moreover, the shear zones inside Sinai have affected intensely the structure development of the northern Sinai area. 2-D fast Fourier transform (FFT) analysis has been applied to transfer the data from space domain to frequency domain, in which basic gradients and derived gradients have been estimated. The frequency domain operations resulted in frequency filtering, first and second degree xyz gradients, horizontal, total (analytical signal) and tilt gradients, maximum horizontal gradient amplitude (total horizontal derivative), and theta map. As a result, the basic and derived gradient maps have succeeded to outline the major structure elements of Northern Sinai Peninsula. Comparisons with some well known surface structures showed a large degree of matching.

  20. Performance analysis of the Microsoft Kinect sensor for 2D Simultaneous Localization and Mapping (SLAM) techniques.

    PubMed

    Kamarudin, Kamarulzaman; Mamduh, Syed Muhammad; Shakaff, Ali Yeon Md; Zakaria, Ammar

    2014-12-05

    This paper presents a performance analysis of two open-source, laser scanner-based Simultaneous Localization and Mapping (SLAM) techniques (i.e., Gmapping and Hector SLAM) using a Microsoft Kinect to replace the laser sensor. Furthermore, the paper proposes a new system integration approach whereby a Linux virtual machine is used to run the open source SLAM algorithms. The experiments were conducted in two different environments; a small room with no features and a typical office corridor with desks and chairs. Using the data logged from real-time experiments, each SLAM technique was simulated and tested with different parameter settings. The results show that the system is able to achieve real time SLAM operation. The system implementation offers a simple and reliable way to compare the performance of Windows-based SLAM algorithm with the algorithms typically implemented in a Robot Operating System (ROS). The results also indicate that certain modifications to the default laser scanner-based parameters are able to improve the map accuracy. However, the limited field of view and range of Kinect's depth sensor often causes the map to be inaccurate, especially in featureless areas, therefore the Kinect sensor is not a direct replacement for a laser scanner, but rather offers a feasible alternative for 2D SLAM tasks.

  1. The Design and Analysis of Split Row-Column Addressing Array for 2-D Transducer.

    PubMed

    Li, Xu; Jia, Yanping; Ding, Mingyue; Yuchi, Ming

    2016-09-27

    For 3-D ultrasound imaging, the row-column addressing (RCA) with 2N connections for an N × N 2-D array makes the fabrication and interconnection simpler than the fully addressing with N² connections. However, RCA degrades the image quality because of defocusing in signal channel direction in the transmit event. To solve this problem, a split row-column addressing scheme (SRCA) is proposed in this paper. Rather than connecting all the elements in the signal channel direction together, this scheme divides the elements in the signal channel direction into several disconnected blocks, thus enables focusing beam access in both signal channel and switch channel directions. Selecting an appropriate split scheme is the key for SRCA to maintaining a reasonable tradeoff between the image quality and the number of connections. Various split schemes for a 32 × 32 array are fully investigated with point spread function (PSF) analysis and imaging simulation. The result shows the split scheme with five blocks (4, 6, 12, 6, and 4 elements of each block) can provide similar image quality to fully addressing. The splitting schemes for different array sizes from 16 × 16 to 96 × 96 are also discussed.

  2. 2-D Stress Accumulation Analysis of the North Anatolian Fault East of the Marmara Sea

    NASA Astrophysics Data System (ADS)

    Karimi, B.; McQuarrie, N.; Harbert, W.; Lin, J.

    2011-12-01

    mesh model. To further validate the results of the simulations, we analyzed lineaments from a digital elevation model (DEM) and a daytime ASTER image. Lineaments were then plotted on a rose diagram to determine the directions of principle stress, which trend SE-NW (sigma-1), and SW-NE (sigma-3). The 2-D geophysical model allows for changes in stress direction and magnitude to be depicted over the entire region, while the lineament analysis is a potential sum of how stress has evolved over time. The map of modeled stress accumulation allows us to evaluate the potential geometry of the faults in this section of the NAF system as well as highlight which faults are host to more stress, and thus predict how that stress may migrate to the east, either north or south of the Marmara Sea. Based on a hundred year record of seismicity in Turkey, it is theorized that a higher magnitude of total stress accumulation will migrate south of the Marmara Sea along the SW-NE trending faults within our region of interest. A greater understanding of the stress field will allow researchers to evaluate the seismic risk within the larger region of Eastern Turkey, as well as understand fault dynamics along the NAF.

  3. Mutation Analysis Identifies GUCY2D as the Major Gene Responsible for Autosomal Dominant Progressive Cone Degeneration

    PubMed Central

    Kitiratschky, Veronique B. D.; Wilke, Robert; Renner, Agnes B.; Kellner, Ulrich; Vadalà, Maria; Birch, David G.; Wissinger, Bernd; Zrenner, Eberhart; Kohl, Susanne

    2017-01-01

    Purpose Heterozygous mutations in the GUCY2D gene, which encodes the membrane-bound retinal guanylyl cyclase-1 protein (RetGC-1), have been shown to cause autosomal dominant inherited cone degeneration and cone–rod degeneration (adCD, adCRD). The present study was a comprehensive screening of the GUCY2D gene in 27 adCD and adCRD unrelated families of these rare disorders. Methods Mutation analysis was performed by direct sequencing as well as PCR and subsequent restriction length polymorphism analysis (PCR/RFLP). Haplotype analysis was performed in selected patients by using microsatellite markers. Results GUCY2D gene mutations were identified in 11 (40%) of 27 patients, and all mutations clustered to codon 838, including two known and one novel missense mutation: p.R838C, p.R838H, and p.R838G. Haplotype analysis showed that among the studied patients only two of the six analyzed p.R838C mutation carriers shared a common haplotype and that none of the p.R838H mutation carriers did. Conclusions GUCY2D is a major gene responsible for progressive autosomal dominant cone degeneration. All identified mutations localize to codon 838. Haplotype analysis indicates that in most cases these mutations arise independently. Thus, codon 838 is likely to be a mutation hotspot in the GUCY2D gene. PMID:18487367

  4. Analysis of 2D hyperbolic metamaterial dispersion by elementary excitation coupling

    NASA Astrophysics Data System (ADS)

    Vaianella, Fabio; Maes, Bjorn

    2016-04-01

    Hyperbolic metamaterials are examined for many applications thanks to the large density of states and extreme confinement of light they provide. For classical hyperbolic metal/dielectric multilayer structures, it was demon- strated that the properties originate from a specific coupling of the surface plasmon polaritons between the metal/dielectric interfaces. We show a similar analysis for 2D hyperbolic arrays of square (or rectangular) silver nanorods in a TiO2 host. In this case the properties derive from a specific coupling of the plasmons carried by the corners of the nanorods. The dispersion can be seen as the coupling of single rods for a through-metal connection of the corners, as the coupling of structures made of four semi-infinite metallic blocks separated by dielectric for a through-dielectric connection, or as the coupling of two semi-infinite rods for a through-metal and through-dielectric situation. For arrays of small square nanorods the elementary structure that explains the dispersion of the array is the single rod, and for arrays of large square nanorods it is four metallic corners. The medium size square nanorod case is more complicated, because the elementary structure can be one of the three basic designs, depending on the frequency and symmetry of the modes. Finally, we show that for arrays of rectangular nanorods the dispersion is explained by coupling of the two coupled rod structure. This work opens the way for a better understanding of a wide class of metamaterials via their elementary excitations.

  5. 2-D nonlinear IIR-filters for image processing - An exploratory analysis

    NASA Technical Reports Server (NTRS)

    Bauer, P. H.; Sartori, M.

    1991-01-01

    A new nonlinear IIR filter structure is introduced and its deterministic properties are analyzed. It is shown to be better suited for image processing applications than its linear shift-invariant counterpart. The new structure is obtained from causality inversion of a 2D quarterplane causal linear filter with respect to the two directions of propagation. It is demonstrated, that by using this design, a nonlinear 2D lowpass filter can be constructed, which is capable of effectively suppressing Gaussian or impulse noise without destroying important image information.

  6. [Applications of 2D and 3D landscape pattern indices in landscape pattern analysis of mountainous area at county level].

    PubMed

    Lu, Chao; Qi, Wei; Li, Le; Sun, Yao; Qin, Tian-Tian; Wang, Na-Na

    2012-05-01

    Landscape pattern indices are the commonly used tools for the quantitative analysis of landscape pattern. However, the traditional 2D landscape pattern indices neglect the effects of terrain on landscape, existing definite limitations in quantitatively describing the landscape patterns in mountains areas. Taking the Qixia City, a typical mountainous and hilly region in Shandong Province of East China, as a case, this paper compared the differences between 2D and 3D landscape pattern indices in quantitatively describing the landscape patterns and their dynamic changes in mountainous areas. On the basis of terrain structure analysis, a set of landscape pattern indices were selected, including area and density (class area and mean patch size), edge and shape (edge density, landscape shape index, and fractal dimension of mean patch), diversity (Shannon's diversity index and evenness index) , and gathering and spread (contagion index). There existed obvious differences between the 3D class area, mean patch area, and edge density and the corresponding 2D indices, but no significant differences between the 3D landscape shape index, fractal dimension of mean patch, and Shannon' s diversity index and evenness index and the corresponding 2D indices. The 3D contagion index and 2D contagion index had no difference. Because the 3D landscape pattern indices were calculated by using patch surface area and surface perimeter whereas the 2D landscape pattern indices were calculated by adopting patch projective area and projective perimeter, the 3D landscape pattern indices could be relative accurate and efficient in describing the landscape area, density and borderline, in mountainous areas. However, there were no distinct differences in describing landscape shape, diversity, and gathering and spread between the 3D and 2D landscape pattern indices. Generally, by introducing 3D landscape pattern indices to topographic pattern, the description of landscape pattern and its dynamic

  7. Applicability extent of 2-D heat equation for numerical analysis of a multiphysics problem

    NASA Astrophysics Data System (ADS)

    Khawaja, H.

    2017-01-01

    This work focuses on thermal problems, solvable using the heat equation. The fundamental question being answered here is: what are the limits of the dimensions that will allow a 3-D thermal problem to be accurately modelled using a 2-D Heat Equation? The presented work solves 2-D and 3-D heat equations using the Finite Difference Method, also known as the Forward-Time Central-Space (FTCS) method, in MATLAB®. For this study, a cuboidal shape domain with a square cross-section is assumed. The boundary conditions are set such that there is a constant temperature at its center and outside its boundaries. The 2-D and 3-D heat equations are solved in a time dimension to develop a steady state temperature profile. The method is tested for its stability using the Courant-Friedrichs-Lewy (CFL) criteria. The results are compared by varying the thickness of the 3-D domain. The maximum error is calculated, and recommendations are given on the applicability of the 2-D heat equation.

  8. Analysis of Korean Students' International Mobility by 2-D Model: Driving Force Factor and Directional Factor

    ERIC Educational Resources Information Center

    Park, Elisa L.

    2009-01-01

    The purpose of this study is to understand the dynamics of Korean students' international mobility to study abroad by using the 2-D Model. The first D, "the driving force factor," explains how and what components of the dissatisfaction with domestic higher education perceived by Korean students drives students' outward mobility to seek…

  9. The Accuracy of Webcams in 2D Motion Analysis: Sources of Error and Their Control

    ERIC Educational Resources Information Center

    Page, A.; Moreno, R.; Candelas, P.; Belmar, F.

    2008-01-01

    In this paper, we show the potential of webcams as precision measuring instruments in a physics laboratory. Various sources of error appearing in 2D coordinate measurements using low-cost commercial webcams are discussed, quantifying their impact on accuracy and precision, and simple procedures to control these sources of error are presented.…

  10. Analysis of vegetation effect on waves using a vertical 2-D RANS model

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A vertical two-dimensional (2-D) model has been applied in the simulation of wave propagation through vegetated water bodies. The model is based on an existing model SOLA-VOF which solves the Reynolds-Averaged Navier-Stokes (RANS) equations with the finite difference method on a staggered rectangula...

  11. Multiple Ising models coupled to 2-d gravity: a CSD analysis

    NASA Astrophysics Data System (ADS)

    Bowick, Mark; Falcioni, Marco; Harris, Geoffrey; Marinari, Enzo

    1994-04-01

    We simulate single and multiple Ising models coupled to 2-d gravity and we measure critical slowing down (CSD) with the standard methods. We find that the Swendsen-Wang and Wolff cluster algorithms do not eliminate CSD. We interpret the result as an effect of the mesh dynamics.

  12. Validation Test Report for the NRL Ocean Surface Flux (NFLUX) Quality Control and 2D Variational Analysis System

    DTIC Science & Technology

    2014-06-11

    Test Report for the NRL Ocean Surface Flux (NFLUX) Quality Control and 2D Variational Analysis System Jackie May Neil VaN de Voorde QinetiQ North...OF RESPONSIBLE PERSON 19b. TELEPHONE NUMBER (include area code) b. ABSTRACT c. THIS PAGE 18. NUMBER OF PAGES 17. LIMITATION OF ABSTRACT Validation Test ...1 2.0 VALIDATION TEST DESIGN

  13. First experiences with 2D-mXRF analysis of gunshot residue on garment, tissue, and cartridge cases

    NASA Astrophysics Data System (ADS)

    Knijnenberg, Alwin; Stamouli, Amalia; Janssen, Martin

    2014-09-01

    The investigation of garment and human tissue originating from a victim of a shooting incident can provide crucial information for the reconstruction of such an incident. The use of 2D-mXRF for such investigations has several advantages over current methods as this new technique can be used to scan large areas, provides simultaneous information on multiple elements, can be applied under ambient conditions and is non-destructive. In this paper we report our experiences and challenges with the implementation of 2D-mXRF in GSR analysis. Currently we mainly focus on the use of 2D-mXRF as a tool for visualizing elemental distributions on various samples.

  14. Multifractal and Singularity Maps of soil surface moisture distribution derived from 2D image analysis.

    NASA Astrophysics Data System (ADS)

    Cumbrera, Ramiro; Millán, Humberto; Martín-Sotoca, Juan Jose; Pérez Soto, Luis; Sanchez, Maria Elena; Tarquis, Ana Maria

    2016-04-01

    methods for mapping geochemical anomalies caused by buried sources and for predicting undiscovered mineral deposits in covered areas. Journal of Geochemical Exploration, 122, 55-70. Cumbrera, R., Ana M. Tarquis, Gabriel Gascó, Humberto Millán (2012) Fractal scaling of apparent soil moisture estimated from vertical planes of Vertisol pit images. Journal of Hydrology (452-453), 205-212. Martin Sotoca; J.J. Antonio Saa-Requejo, Juan Grau and Ana M. Tarquis (2016). Segmentation of singularity maps in the context of soil porosity. Geophysical Research Abstracts, 18, EGU2016-11402. Millán, H., Cumbrera, R. and Ana M. Tarquis (2016) Multifractal and Levy-stable statistics of soil surface moisture distribution derived from 2D image analysis. Applied Mathematical Modelling, 40(3), 2384-2395.

  15. Dynamical Analysis and Big Bang Bifurcations of 1D and 2D Gompertz's Growth Functions

    NASA Astrophysics Data System (ADS)

    Rocha, J. Leonel; Taha, Abdel-Kaddous; Fournier-Prunaret, D.

    In this paper, we study the dynamics and bifurcation properties of a three-parameter family of 1D Gompertz's growth functions, which are defined by the population size functions of the Gompertz logistic growth equation. The dynamical behavior is complex leading to a diversified bifurcation structure, leading to the big bang bifurcations of the so-called “box-within-a-box” fractal type. We provide and discuss sufficient conditions for the existence of these bifurcation cascades for 1D Gompertz's growth functions. Moreover, this work concerns the description of some bifurcation properties of a Hénon's map type embedding: a “continuous” embedding of 1D Gompertz's growth functions into a 2D diffeomorphism. More particularly, properties that characterize the big bang bifurcations are considered in relation with this coupling of two population size functions, varying the embedding parameter. The existence of communication areas of crossroad area type or swallowtails are identified for this 2D diffeomorphism.

  16. A Block-matching based technique for the analysis of 2D gel images.

    PubMed

    Freire, Ana; Seoane, José A; Rodríguez, Alvaro; Ruiz-Romero, Cristina; López-Campos, Guillermo; Dorado, Julián

    2010-01-01

    Research at protein level is a useful practice in personalized medicine. More specifically, 2D gel images obtained after electrophoresis process can lead to an accurate diagnosis. Several computational approaches try to help the clinicians to establish the correspondence between pairs of proteins of multiple 2D gel images. Most of them perform the alignment of a patient image referred to a reference image. In this work, an approach based on block-matching techniques is developed. Its main characteristic is that it does not need to perform the whole alignment between two images considering each protein separately. A comparison with other published methods is presented. It can be concluded that this method works over broad range of proteomic images, although they have a high level of difficulty.

  17. NMR Analysis of Unknowns: An Introduction to 2D NMR Spectroscopy

    ERIC Educational Resources Information Center

    Alonso, David E.; Warren, Steven E.

    2005-01-01

    A study combined 1D (one-dimensional) and 2D (two-dimensional) NMR spectroscopy to solve structural organic problems of three unknowns, which include 2-, 3-, and 4-heptanone. Results showed [to the first power]H NMR and [to the thirteenth power]C NMR signal assignments for 2- and 3-heptanone were more challenging than for 4-heptanone owing to the…

  18. A procedure for the evaluation of 2D radiographic texture analysis to assess 3D bone micro-architecture

    NASA Astrophysics Data System (ADS)

    Apostol, Lian; Peyrin, Francoise; Yot, Sophie; Basset, Olivier; Odet, Christophe; Tabary, Joachim; Dinten, Jean-Marc; Boller, Elodie; Boudousq, Vincent; Kotzki, Pierre-Olivier

    2004-05-01

    Although the diagnosis of osteoporosis is mainly based on Dual X-ray Absorptiometry, it has been shown that trabecular bone micro-architecture is also an important factor in regards of fracture risk, which can be efficiently assessed in vitro using three-dimensional x-ray microtomography (μCT). In vivo, techniques based on high-resolution s-ray radiography associated to texture analysis have been proposed to investigate bone micro-architecture, but their relevance for giving pertinent 3D information is unclear. The purpose of this work was to develop a method for evaluating the relationships betweeen 3D micro-architecture and 2D texture parameters, and optimizing the conditions for radiographic imaging. Bone sample images taken from cortical to cortical were acquired using 3D-synchrotron x-ray μCT at the ESRF. The 3D digital imagees were further used for two purposes: 1) quantification of three-dimensional bone micro-architecture, 2) simulation of realistic x-ray radiographs under different acquisition conditions. Texture analysis was then applied to these 2D radiographs using a large variety of methods (co-occurence, spectrum, fractal...). First results of the statistical analysis between 2D and 3D parameters allowed identfying the most relevant 2D texture parameters.

  19. Parametrics on 2D Navier-Stokes analysis of a Mach 2.68 bifurcated rectangular mixed-compression inlet

    NASA Technical Reports Server (NTRS)

    Mizukami, M.; Saunders, J. D.

    1995-01-01

    The supersonic diffuser of a Mach 2.68 bifurcated, rectangular, mixed-compression inlet was analyzed using a two-dimensional (2D) Navier-Stokes flow solver. Parametric studies were performed on turbulence models, computational grids and bleed models. The computer flowfield was substantially different from the original inviscid design, due to interactions of shocks, boundary layers, and bleed. Good agreement with experimental data was obtained in many aspects. Many of the discrepancies were thought to originate primarily from 3D effects. Therefore, a balance should be struck between expending resources on a high fidelity 2D simulation, and the inherent limitations of 2D analysis. The solutions were fairly insensitive to turbulence models, grids and bleed models. Overall, the k-e turbulence model, and the bleed models based on unchoked bleed hole discharge coefficients or uniform velocity are recommended. The 2D Navier-Stokes methods appear to be a useful tool for the design and analysis of supersonic inlets, by providing a higher fidelity simulation of the inlet flowfield than inviscid methods, in a reasonable turnaround time.

  20. 2D dynamic studies combined with the surface curvature analysis to predict Arias Intensity amplification

    NASA Astrophysics Data System (ADS)

    Torgoev, Almaz; Havenith, Hans-Balder

    2016-07-01

    A 2D elasto-dynamic modelling of the pure topographic seismic response is performed for six models with a total length of around 23.0 km. These models are reconstructed from the real topographic settings of the landslide-prone slopes situated in the Mailuu-Suu River Valley, Southern Kyrgyzstan. The main studied parameter is the Arias Intensity (Ia, m/sec), which is applied in the GIS-based Newmark method to regionally map the seismically-induced landslide susceptibility. This method maps the Ia values via empirical attenuation laws and our studies investigate a potential to include topographic input into them. Numerical studies analyse several signals with varying shape and changing central frequency values. All tests demonstrate that the spectral amplification patterns directly affect the amplification of the Ia values. These results let to link the 2D distribution of the topographically amplified Ia values with the parameter called as smoothed curvature. The amplification values for the low-frequency signals are better correlated with the curvature smoothed over larger spatial extent, while those values for the high-frequency signals are more linked to the curvature with smaller smoothing extent. The best predictions are provided by the curvature smoothed over the extent calculated according to Geli's law. The sample equations predicting the Ia amplification based on the smoothed curvature are presented for the sinusoid-shape input signals. These laws cannot be directly implemented in the regional Newmark method, as 3D amplification of the Ia values addresses more problem complexities which are not studied here. Nevertheless, our 2D results prepare the theoretical framework which can potentially be applied to the 3D domain and, therefore, represent a robust basis for these future research targets.

  1. 2D-CELL: image processing software for extraction and analysis of 2-dimensional cellular structures

    NASA Astrophysics Data System (ADS)

    Righetti, F.; Telley, H.; Leibling, Th. M.; Mocellin, A.

    1992-01-01

    2D-CELL is a software package for the processing and analyzing of photographic images of cellular structures in a largely interactive way. Starting from a binary digitized image, the programs extract the line network (skeleton) of the structure and determine the graph representation that best models it. Provision is made for manually correcting defects such as incorrect node positions or dangling bonds. Then a suitable algorithm retrieves polygonal contours which define individual cells — local boundary curvatures are neglected for simplicity. Using elementary analytical geometry relations, a range of metric and topological parameters describing the population are then computed, organized into statistical distributions and graphically displayed.

  2. Analysis of 2D Phase Contrast MRI in Renal Arteries by Self Organizing Maps

    NASA Astrophysics Data System (ADS)

    Zöllner, Frank G.; Schad, Lothar R.

    We present an approach based on self organizing maps to segment renal arteries from 2D PC Cine MR, images to measure blood velocity and flow. Such information are important in grading renal artery stenosis and support the decision on surgical interventions like percu-tan transluminal angioplasty. Results show that the renal arteries could be extracted automatically. The corresponding velocity profiles show high correlation (r=0.99) compared those from manual delineated vessels. Furthermore, the method could detect possible blood flow patterns within the vessel.

  3. DigesTip: a new device for a rapid and efficient in-solution protein digestion.

    PubMed

    Marangoni, Roberto; Chiarini, Riccardo; Iannone, Giorgio; Salerno, Massimiliano

    2008-06-01

    DigesTip is a new device for in-solution protein digestion, based on a patent pending technology, able to immobilize enzymes (trypsin, in this case) on a solid surface, keeping their activity preserved. DigesTip is a standard pipette tip, usable both by human and by robots. Its main performances are: very short digestion time (1 min) and usability with low protein sample concentrations (5 microg/mL). DigesTip obtains a clear signal in MS measurements and its usage rules out several preparative steps.

  4. Rovibrational analysis of the ethylene isotopologue 13C2D4 by high-resolution Fourier transform infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Tan, T. L.; Gabona, M. G.; Godfrey, Peter D.; McNaughton, Don

    2015-01-01

    The Fourier transform infrared (FTIR) spectrum of the unperturbed a-type ν12 band of 13C2D4 was recorded at an unapodized resolution of 0.0063 cm-1 between 1000 and 1140 cm-1 for a rovibrational analysis. By assigning and fitting a total of 2068 infrared transitions using a Watson's A-reduced and S-reduced Hamiltonians in the Ir representation, rovibrational constants for the upper state (ν12 = 1) up to five quartic centrifugal distortion terms were derived for the first time. The root-mean-square (rms) deviation of the fits was 0.00034 cm-1 both in the A-reduction and S-reduction Hamiltonian. The ground state rovibrational constants of 13C2D4 in the A-reduced and S-reduced Hamiltonians were also determined for the first time by a fit of 985 combination-differences from the present infrared measurements, with rms deviation of 0.00036 cm-1. The ν12 band centre of 13C2D4 was at 1069.970824(17) cm-1 and at 1069.970799(17) cm-1 for the A-reduced and S-reduced Hamiltonians respectively. The ground state constants of 13C2D4 from this experimental work are in close agreement to those derived from theoretical calculations using the B3LYP/cc-pVTZ, MP2/cc-pVTZ, and CSSD(T)/cc-pVTZ levels of theory.

  5. HEAT.PRO - THERMAL IMBALANCE FORCE SIMULATION AND ANALYSIS USING PDE2D

    NASA Technical Reports Server (NTRS)

    Vigue, Y.

    1994-01-01

    HEAT.PRO calculates the thermal imbalance force resulting from satellite surface heating. The heated body of a satellite re-radiates energy at a rate that is proportional to its temperature, losing the energy in the form of photons. By conservation of momentum, this momentum flux out of the body creates a reaction force against the radiation surface, and the net thermal force can be observed as a small perturbation that affects long term orbital behavior of the satellite. HEAT.PRO calculates this thermal imbalance force and then determines its effects on satellite orbits, especially where the Earth's shadowing of an orbiting satellite causes periodic changes in the spacecraft's thermal environment. HEAT.PRO implements a finite element method routine called PDE2D which incorporates material properties to determine the solar panel surface temperatures. The nodal temperatures are computed at specified time steps and are used to determine the magnitude and direction of the thermal force on the spacecraft. These calculations are based on the solar panel orientation and satellite's position with respect to the earth and sun. It is necessary to have accurate, current knowledge of surface emissivity, thermal conductivity, heat capacity, and material density. These parameters, which may change due to degradation of materials in the environment of space, influence the nodal temperatures that are computed and thus the thermal force calculations. HEAT.PRO was written in FORTRAN 77 for Cray series computers running UNICOS. The source code contains directives for and is used as input to the required partial differential equation solver, PDE2D. HEAT.PRO is available on a 9-track 1600 BPI magnetic tape in UNIX tar format (standard distribution medium) or a .25 inch streaming magnetic tape cartridge in UNIX tar format. An electronic copy of the documentation in Macintosh Microsoft Word format is included on the distribution tape. HEAT.PRO was developed in 1991. Cray and UNICOS are

  6. Study on molecular structure and hydration mechanism of Domyoji-ko starch by IR and NIR hetero 2D analysis

    NASA Astrophysics Data System (ADS)

    Katayama, Norihisa; Kondo, Miyuki; Miyazawa, Mitsuhiro

    2010-06-01

    The hydration structure of starch molecule in Domyoji-ko, which is made from gluey rice, was investigated by hetero 2D correlation analysis of IR and NIR spectroscopy. The feature near 1020 cm -1 in the IR spectra of Domyoji-ko is changed by rehydration process, indicating that the molecular structure of amylopectin in the starch has been varied by the hydration without heating. The intensity of a band at 4770 cm -1 in NIR spectra is decreasing with the increasing of either the heating time with water or rehydration time without heating. These results suggest that the hydration of Domyoji-ko has proceeded in similar mechanisms on these processes. The generalized hetero 2D IR-NIR correlation analysis for rehydration of Domyoji-ko has supported the assignments for NIR bands concerning the gelatinization of starch.

  7. Red wine proteins: two dimensional (2-D) electrophoresis and mass spectrometry analysis.

    PubMed

    Mainente, Federica; Zoccatelli, Gianni; Lorenzini, Marilinda; Cecconi, Daniela; Vincenzi, Simone; Rizzi, Corrado; Simonato, Barbara

    2014-12-01

    The aim of the present study was to optimize protein extraction from red wine (cv. Cabernet) in order to obtain a separation by two-dimensional electrophoresis (2-DE) compatible with mass spectrometry identification. Proteins were denatured by sodium dodecyl-sulphate (SDS) and precipitated as potassium salts. The potassium-DS (KDS) protein complexes obtained were treated with different solutions in order to remove the detergent. Proteins were solubilized with different buffers and separated by different electrophoretic approaches [native, urea, acid urea PAGEs and isoelectric focusing (IEF)] as the first-dimension (1-DE). The best 2D separation was achieved by using 10% saccharose in the DS removal step, and 6-cyclohexylhexyl β-d-maltoside detergent in the solubilisation buffer combined with the IEF approach. Several well focalized protein spots were obtained and analyzed through mass-spectrometry.

  8. Analysis of pyruvylated beta-carrageenan by 2D NMR spectroscopy and reductive partial hydrolysis.

    PubMed

    Falshaw, Ruth; Furneaux, Richard H; Wong, Herbert

    2003-06-23

    A polysaccharide rich in 4',6'-O-(1-carboxyethylidene)-substituted (i.e., pyruvylated) beta-carrageenan has been prepared by solvolytic desulfation of a polysaccharide containing predominantly pyruvylated alpha-carrageenan, which was extracted from the red seaweed, Callophycus tridentifer. The 13C and 1H NMR chemical shifts of pyruvylated beta-carrageenan have been fully assigned using 2D NMR spectroscopic techniques. The 4',6'-O-(1-methoxycarbonylethylidene) group, generated during chemical methylation of the polysaccharide, has been shown to survive under the conditions of acidic hydrolysis that cleave the 3,6-anhydro-alpha-D-galactosidic bonds in permethylated samples of both pyruvylated beta- and pyruvylated alpha-carrageenans. As a result, two novel pyruvylated carrabiitol derivatives have been prepared.

  9. Symmetry Analysis and Exact Solutions of the 2D Unsteady Incompressible Boundary-Layer Equations

    NASA Astrophysics Data System (ADS)

    Han, Zhong; Chen, Yong

    2017-01-01

    To find intrinsically different symmetry reductions and inequivalent group invariant solutions of the 2D unsteady incompressible boundary-layer equations, a two-dimensional optimal system is constructed which attributed to the classification of the corresponding Lie subalgebras. The comprehensiveness and inequivalence of the optimal system are shown clearly under different values of invariants. Then by virtue of the optimal system obtained, the boundary-layer equations are directly reduced to a system of ordinary differential equations (ODEs) by only one step. It has been shown that not only do we recover many of the known results but also find some new reductions and explicit solutions, which may be previously unknown. Supported by the Global Change Research Program of China under Grant No. 2015CB953904, National Natural Science Foundation of China under Grant Nos. 11275072, 11435005, 11675054, and Shanghai Collaborative Innovation Center of Trustworthy Software for Internet of Things under Grant No. ZF1213

  10. A 2D correlation Raman spectroscopy analysis of a human cataractous lens

    NASA Astrophysics Data System (ADS)

    Sacharz, Julia; Wesełucha-Birczyńska, Aleksandra; Paluszkiewicz, Czesława; Chaniecki, Piotr; Błażewicz, Marta

    2016-11-01

    This work is a continuation of our study of a cataractous human eye lens removed after phacoemulsification surgery. There are clear differences in the lens colors that allowed for distinguishing two opaque phases in the obtained biological material: the white- and yellow-phase. The Raman spectroscopy and 2D correlation spectroscopy method were used to trace a pathologically altered human cataract lens at a molecular level. Although the Raman spectra of these two phases are relatively similar, taking advantage of 2D correlation, and considering time as an external perturbation, the synchronous and asynchronous spectra were obtained showing completely different patterns. Prominent synchronous auto-peaks appear at 3340, 2920, 1736, 1665 and 1083 cm-1 for the white-, and at 2929 and 1670 cm-1 for the yellow phase. The white phase is characterized by intensive asynchronous peaks at -(2936, 3360), -(1650, 1674) and +(1620,1678). The modifications in the water contained in the white phase structure are ahead of the changes in the protein (CH3-groups), furthermore changes in β-conformation are asynchronous with respect to the α-structure. The yellow phase demonstrates asynchronous peaks: +(2857, 2928), +(1645,1673), +(1663, 1679), and +(1672,1707). These illustrate concomitant modifications in the β- and unordered conformation. Both forms of cataractous human eye lens, white- and yellow-phases, are degenerate forms of the eye lens proteins, both are arranged in a different way. The main differences are observed for the amide I, methyl, methylene and Osbnd H vibrational band region. The effect of Asp, Glu and Tyr amino acids in cataractous lens transformations was observed.

  11. Computational Study and Analysis of Structural Imperfections in 1D and 2D Photonic Crystals

    SciTech Connect

    Maskaly, Karlene Rosera

    2005-06-01

    Dielectric reflectors that are periodic in one or two dimensions, also known as 1D and 2D photonic crystals, have been widely studied for many potential applications due to the presence of wavelength-tunable photonic bandgaps. However, the unique optical behavior of photonic crystals is based on theoretical models of perfect analogues. Little is known about the practical effects of dielectric imperfections on their technologically useful optical properties. In order to address this issue, a finite-difference time-domain (FDTD) code is employed to study the effect of three specific dielectric imperfections in 1D and 2D photonic crystals. The first imperfection investigated is dielectric interfacial roughness in quarter-wave tuned 1D photonic crystals at normal incidence. This study reveals that the reflectivity of some roughened photonic crystal configurations can change up to 50% at the center of the bandgap for RMS roughness values around 20% of the characteristic periodicity of the crystal. However, this reflectivity change can be mitigated by increasing the index contrast and/or the number of bilayers in the crystal. In order to explain these results, the homogenization approximation, which is usually applied to single rough surfaces, is applied to the quarter-wave stacks. The results of the homogenization approximation match the FDTD results extremely well, suggesting that the main role of the roughness features is to grade the refractive index profile of the interfaces in the photonic crystal rather than diffusely scatter the incoming light. This result also implies that the amount of incoherent reflection from the roughened quarterwave stacks is extremely small. This is confirmed through direct extraction of the amount of incoherent power from the FDTD calculations. Further FDTD studies are done on the entire normal incidence bandgap of roughened 1D photonic crystals. These results reveal a narrowing and red-shifting of the normal incidence bandgap with

  12. 2D correlation analysis of the magnetic excitations in Raman spectra of HoMnO3

    NASA Astrophysics Data System (ADS)

    Nguyen, Thi Huyen; Nguyen, Thi Minh Hien; Chen, Xiang-Bai; Yang, In-Sang; Park, Yeonju; Jung, Young Mee

    2014-07-01

    2D correlation analysis is performed on the temperature-dependent Raman spectra of HoMnO3 thin films. As the temperature of the HoMnO3 thin films decrease, the depletion of the spectral weight at 336, 656, and 1304 cm-1 occurs at higher temperatures than the increase of the intensity at 508, 766, and 945 cm-1 below ∼70 K, the Néel temperature. The power spectrum asserts that all the changes in the spectral weight are strongly correlated. Most of the temperature-induced spectral changes of HoMnO3 occur at lower temperature than 70 K, while there is slight depletion of the spectral weight at 336, 656, and 1304 cm-1 even at higher temperature than 70 K. PCA scores and loading vectors plots also support these 2D correlation results. Our 2D correlation analysis supports the existence of the short range spin correlations between Mn sites in HoMnO3 even above the Néel temperature.

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

    PubMed Central

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

    2016-01-01

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

  14. 2D CFD Analysis of an Airfoil with Active Continuous Trailing Edge Flap

    NASA Astrophysics Data System (ADS)

    Jaksich, Dylan; Shen, Jinwei

    2014-11-01

    Efficient and quieter helicopter rotors can be achieved through on-blade control devices, such as active Continuous Trailing-Edge Flaps driven by embedded piezoelectric material. This project aims to develop a CFD simulation tool to predict the aerodynamic characteristics of an airfoil with CTEF using open source code: OpenFOAM. Airfoil meshes used by OpenFOAM are obtained with MATLAB scripts. Once created it is possible to rotate the airfoil to various angles of attack. When the airfoil is properly set up various OpenFOAM properties, such as kinematic viscosity and flow velocity, are altered to achieve the desired testing conditions. Upon completion of a simulation, the program gives the lift, drag, and moment coefficients as well as the pressure and velocity around the airfoil. The simulation is then repeated across multiple angles of attack to give full lift and drag curves. The results are then compared to previous test data and other CFD predictions. This research will lead to further work involving quasi-steady 2D simulations incorporating NASTRAN to model aeroelastic deformation and eventually to 3D aeroelastic simulations. NSF ECE Grant #1358991 supported the first author as an REU student.

  15. Usability analysis of 2D graphics software for designing technical clothing.

    PubMed

    Teodoroski, Rita de Cassia Clark; Espíndola, Edilene Zilma; Silva, Enéias; Moro, Antônio Renato Pereira; Pereira, Vera Lucia D V

    2012-01-01

    With the advent of technology, the computer became a working tool increasingly present in companies. Its purpose is to increase production and reduce the inherent errors in manual production. The aim of this study was to analyze the usability of 2D graphics software in creating clothing designs by a professional during his work. The movements of the mouse, keyboard and graphical tools were monitored in real time by software Camtasia 7® installed on the user's computer. To register the use of mouse and keyboard we used auxiliary software called MouseMeter®, which quantifies the number of times they pressed the right, middle and left mouse's buttons, the keyboard and also the distance traveled in meters by the cursor on the screen. Data was collected in periods of 15 minutes, 1 hour and 8 hours, consecutively. The results showed that the job is considered repetitive and high demands physical efforts, which can lead to the appearance of repetitive strain injuries. Thus, the goal of minimizing operator efforts and thereby enhance the usability of the examined tool, becomes imperative to replace the mouse by a device called tablet, which also offers an electronic pen and a drawing platform for design development.

  16. Rifaximin-mediated changes to the epithelial cell proteome: 2-D gel analysis.

    PubMed

    Schrodt, Caroline; McHugh, Erin E; Gawinowicz, Mary Ann; Dupont, Herbert L; Brown, Eric L

    2013-01-01

    Rifaximin is a semi-synthetic rifamycin derivative that is used to treat different conditions including bacterial diarrhea and hepatic encephalopathy. Rifaximin is of particular interest because it is poorly adsorbed in the intestines and has minimal effect on colonic microflora. We previously demonstrated that rifaximin affected epithelial cell physiology by altering infectivity by enteric pathogens and baseline inflammation suggesting that rifaximin conferred cytoprotection against colonization and infection. Effects of rifaximin on epithelial cells were further examined by comparing the protein expression profile of cells pretreated with rifaximin, rifampin (control antibiotic), or media (untreated). Two-dimensional (2-D) gel electrophoresis identified 36 protein spots that were up- or down-regulated by over 1.7-fold in rifaximin treated cells compared to controls. 15 of these spots were down-regulated, including annexin A5, intestinal-type alkaline phosphatase, histone H4, and histone-binding protein RbbP4. 21 spots were up-regulated, including heat shock protein (HSP) 90α and fascin. Many of the identified proteins are associated with cell structure and cytoskeleton, transcription and translation, and cellular metabolism. These data suggested that in addition to its antimicrobial properties, rifaximin may alter host cell physiology that provides cytoprotective effects against bacterial pathogens.

  17. Simulation and analysis of solute transport in 2D fracture/pipe networks: the SOLFRAC program.

    PubMed

    Bodin, Jacques; Porel, Gilles; Delay, Fred; Ubertosi, Fabrice; Bernard, Stéphane; de Dreuzy, Jean-Raynald

    2007-01-05

    The Time Domain Random Walk (TDRW) method has been recently developed by Delay and Bodin [Delay, F. and Bodin, J., 2001. Time domain random walk method to simulate transport by advection-dispersion and matrix diffusion in fracture networks. Geophys. Res. Lett., 28(21): 4051-4054.] and Bodin et al. [Bodin, J., Porel, G. and Delay, F., 2003c. Simulation of solute transport in discrete fracture networks using the time domain random walk method. Earth Planet. Sci. Lett., 6566: 1-8.] for simulating solute transport in discrete fracture networks. It is assumed that the fracture network can reasonably be represented by a network of interconnected one-dimensional pipes (i.e. flow channels). Processes accounted for are: (1) advection and hydrodynamic dispersion in the channels, (2) matrix diffusion, (3) diffusion into stagnant zones within the fracture planes, (4) sorption reactions onto the fracture walls and in the matrix, (5) linear decay, and (6) mass sharing at fracture intersections. The TDRW method is handy and very efficient in terms of computation costs since it allows for the one-step calculation of the particle residence time in each bond of the network. This method has been programmed in C++, and efforts have been made to develop an efficient and user-friendly software, called SOLFRAC. This program is freely downloadable at the URL (labo.univ-poitiers.fr/hydrasa/intranet/telechargement.htm). It calculates solute transport into 2D pipe networks, while considering different types of injections and different concepts of local dispersion within each flow channel. Post-simulation analyses are also available, such as the mean velocity or the macroscopic dispersion at the scale of the entire network. The program may be used to evaluate how a given transport mechanism influences the macroscopic transport behaviour of fracture networks. It may also be used, as is the case, e.g., with analytical solutions, to interpret laboratory or field tracer test experiments performed

  18. A detailed postprocess analysis of an argon gas puff Z-pinch plasma using SPEC2D

    NASA Astrophysics Data System (ADS)

    Chong, Y. K.; Kammash, T.; Davis, J.

    1997-05-01

    A postprocess analysis of a single time frame hydrodynamic profile from the PRISM two-dimensional MHD simulation of an argon gas puff Z-pinch plasma experiment on Double-Eagle generator at Physics Internationals, Co. is presented. In addition, spatially resolved emission spectra and filtered (K- and L-shell radiation) x-ray pinhole images, generated using the SPEC2D code, are examined toward the understanding of the emission characteristics of the hot spots and the formation of the Rayleigh-Taylor instability in the plasma.

  19. Analysis of high Reynolds numbers effects on a wind turbine airfoil using 2D wind tunnel test data

    NASA Astrophysics Data System (ADS)

    Pires, O.; Munduate, X.; Ceyhan, O.; Jacobs, M.; Snel, H.

    2016-09-01

    The aerodynamic behaviour of a wind turbine airfoil has been measured in a dedicated 2D wind tunnel test at the DNW High Pressure Wind Tunnel in Gottingen (HDG), Germany. The tests have been performed on the DU00W212 airfoil at different Reynolds numbers: 3, 6, 9, 12 and 15 million, and at low Mach numbers (below 0.1). Both clean and tripped conditions of the airfoil have been measured. An analysis of the impact of a wide Reynolds number variation over the aerodynamic characteristics of this airfoil has been performed.

  20. Global 2D stability analysis of the cross lid-driven cavity flow with a streamfunction-vorticity approach

    NASA Astrophysics Data System (ADS)

    Gogoi, Bidyut B.

    2016-07-01

    We have recently analyzed the global two-dimensional (2D) stability of the staggered lid-driven cavity (LDC) flow with a higher order compact (HOC) approach. In the analysis, critical parameters are determined for both the parallel and anti-parallel motion of the lids and a detailed analysis has been carried out on either side of the critical values. In this article, we carry out an investigation of flow stabilities inside a two-sided cross lid-driven cavity with a pair of opposite lids moving in both parallel and anti-parallel directions. On discretization, the governing 2D Navier-Stokes (N-S) equations describing the steady flow and flow perturbations results in a generalized eigenvalue problem which is solved for determining the critical parameters on four different grids. Elaborate computation is performed for a wide range of Reynolds numbers (Re) on either side of the critical values in the range 200 ⩽ Re ⩽ 10000. For flows below the critical Reynolds number Rec, our numerical results are compared with established steady-state results and excellent agreement is obtained in all the cases. For Reynolds numbers above Rec, phase plane and spectral density analysis confirmed the existence of periodic, quasi-periodic, and stable flow patterns.

  1. Application of 2D-HPLC/taste dilution analysis on taste compounds in aniseed (Pimpinella anisum L.).

    PubMed

    Pickrahn, Stephen; Sebald, Karin; Hofmann, Thomas

    2014-09-24

    This is the first application of fully automated, preparative, two-dimensional HPLC combined with sensory analysis for taste compound discovery using a sweet and licorice-like bitter-tasting aniseed extract as an example. Compared to the traditional iterative fractionation of food extracts by sensory-guided sequential application of separation techniques, the fully automated 2D-HPLC allowed the comprehensive separation of the aniseed extract into 256 subfractions and reduced the fractionation time from about 1 week to <1day. Using a smart sensory strategy to locate high-impact fractions, e.g., by evaluating first-dimension fractions by reconstituting them from second-dimension subfractions, followed by straightforward application of the taste dilution analysis on the individual second-dimension subfractions revealed the sweet-tasting trans-anethole and the bitter-tasting trans-pseudoisoeugenol 2-methylbutyrate, showing recognition thresholds of 70 and 68 μmol/L, respectively, as the primary orosensory active compounds in aniseed. 2D-HPLC combined with smart sensory analysis seems to be a promising strategy to speed the discovery of the key players imparting the attractive taste of foods.

  2. Conditional independence mapping of DIGE data reveals PDIA3 protein species as key nodes associated with muscle aerobic capacity

    PubMed Central

    Burniston, Jatin G.; Kenyani, Jenna; Gray, Donna; Guadagnin, Eleonora; Jarman, Ian H.; Cobley, James N.; Cuthbertson, Daniel J.; Chen, Yi-Wen; Wastling, Jonathan M.; Lisboa, Paulo J.; Koch, Lauren G.; Britton, Steven L.

    2014-01-01

    Profiling of protein species is important because gene polymorphisms, splice variations and post-translational modifications may combine and give rise to multiple protein species that have different effects on cellular function. Two-dimensional gel electrophoresis is one of the most robust methods for differential analysis of protein species, but bioinformatic interrogation is challenging because the consequences of changes in the abundance of individual protein species on cell function are unknown and cannot be predicted. We conducted DIGE of soleus muscle from male and female rats artificially selected as either high- or low-capacity runners (HCR and LCR, respectively). In total 696 protein species were resolved and LC–MS/MS identified proteins in 337 spots. Forty protein species were differentially (P < 0.05, FDR < 10%) expressed between HCR and LCR and conditional independence mapping found distinct networks within these data, which brought insight beyond that achieved by functional annotation. Protein disulphide isomerase A3 emerged as a key node segregating with differences in aerobic capacity and unsupervised bibliometric analysis highlighted further links to signal transducer and activator of transcription 3, which were confirmed by western blotting. Thus, conditional independence mapping is a useful technique for interrogating DIGE data that is capable of highlighting latent features. PMID:24769234

  3. Multichannel response analysis on 2D projection views for detection of clustered microcalcifications in digital breast tomosynthesis

    SciTech Connect

    Wei, Jun Chan, Heang-Ping; Hadjiiski, Lubomir M.; Helvie, Mark A.; Lu, Yao; Zhou, Chuan; Samala, Ravi

    2014-04-15

    Purpose: To investigate the feasibility of a new two-dimensional (2D) multichannel response (MCR) analysis approach for the detection of clustered microcalcifications (MCs) in digital breast tomosynthesis (DBT). Methods: With IRB approval and informed consent, a data set of two-view DBTs from 42 breasts containing biopsy-proven MC clusters was collected in this study. The authors developed a 2D approach for MC detection using projection view (PV) images rather than the reconstructed three-dimensional (3D) DBT volume. Signal-to-noise ratio (SNR) enhancement processing was first applied to each PV to enhance the potential MCs. The locations of MC candidates were then identified with iterative thresholding. The individual MCs were decomposed with Hermite–Gaussian (HG) and Laguerre–Gaussian (LG) basis functions and the channelized Hotelling model was trained to produce the MCRs for each MC on the 2D images. The MCRs from the PVs were fused in 3D by a coincidence counting method that backprojects the MC candidates on the PVs and traces the coincidence of their ray paths in 3D. The 3D MCR was used to differentiate the true MCs from false positives (FPs). Finally a dynamic clustering method was used to identify the potential MC clusters in the DBT volume based on the fact that true MCs of clinical significance appear in clusters. Using two-fold cross validation, the performance of the 3D MCR for classification of true and false MCs was estimated by the area under the receiver operating characteristic (ROC) curve and the overall performance of the MCR approach for detection of clustered MCs was assessed by free response receiver operating characteristic (FROC) analysis. Results: When the HG basis function was used for MCR analysis, the detection of MC cluster achieved case-based test sensitivities of 80% and 90% at the average FP rates of 0.65 and 1.55 FPs per DBT volume, respectively. With LG basis function, the average FP rates were 0.62 and 1.57 per DBT volume at

  4. The 2dF Galaxy Redshift Survey: power-spectrum analysis of the final data set and cosmological implications

    NASA Astrophysics Data System (ADS)

    Cole, Shaun; Percival, Will J.; Peacock, John A.; Norberg, Peder; Baugh, Carlton M.; Frenk, Carlos S.; Baldry, Ivan; Bland-Hawthorn, Joss; Bridges, Terry; Cannon, Russell; Colless, Matthew; Collins, Chris; Couch, Warrick; Cross, Nicholas J. G.; Dalton, Gavin; Eke, Vincent R.; De Propris, Roberto; Driver, Simon P.; Efstathiou, George; Ellis, Richard S.; Glazebrook, Karl; Jackson, Carole; Jenkins, Adrian; Lahav, Ofer; Lewis, Ian; Lumsden, Stuart; Maddox, Steve; Madgwick, Darren; Peterson, Bruce A.; Sutherland, Will; Taylor, Keith

    2005-09-01

    We present a power-spectrum analysis of the final 2dF Galaxy Redshift Survey (2dFGRS), employing a direct Fourier method. The sample used comprises 221414 galaxies with measured redshifts. We investigate in detail the modelling of the sample selection, improving on previous treatments in a number of respects. A new angular mask is derived, based on revisions to the photometric calibration. The redshift selection function is determined by dividing the survey according to rest-frame colour, and deducing a self-consistent treatment of k-corrections and evolution for each population. The covariance matrix for the power-spectrum estimates is determined using two different approaches to the construction of mock surveys, which are used to demonstrate that the input cosmological model can be correctly recovered. We discuss in detail the possible differences between the galaxy and mass power spectra, and treat these using simulations, analytic models and a hybrid empirical approach. Based on these investigations, we are confident that the 2dFGRS power spectrum can be used to infer the matter content of the universe. On large scales, our estimated power spectrum shows evidence for the `baryon oscillations' that are predicted in cold dark matter (CDM) models. Fitting to a CDM model, assuming a primordial ns= 1 spectrum, h= 0.72 and negligible neutrino mass, the preferred parameters are Ωmh= 0.168 +/- 0.016 and a baryon fraction Ωb/Ωm= 0.185 +/- 0.046 (1σ errors). The value of Ωmh is 1σ lower than the 0.20 +/- 0.03 in our 2001 analysis of the partially complete 2dFGRS. This shift is largely due to the signal from the newly sampled regions of space, rather than the refinements in the treatment of observational selection. This analysis therefore implies a density significantly below the standard Ωm= 0.3: in combination with cosmic microwave background (CMB) data from the Wilkinson Microwave Anisotropy Probe (WMAP), we infer Ωm= 0.231 +/- 0.021.

  5. 2D pair distribution function analysis of anisotropic small-angle scattering patterns from elongated nano-composite hydrogels.

    PubMed

    Nishi, Kengo; Shibayama, Mitsuhiro

    2017-03-01

    Small angle scattering (SAS) on polymer nanocomposites under elongation or shear flow is an important experimental method to investigate the reinforcement effects of the mechanical properties by fillers. However, the anisotropic scattering patterns that appear in SAS are very complicated and difficult to interpret. A representative example is a four-spot scattering pattern observed in the case of polymer materials containing silica nanoparticles, the origin of which is still in debate because of the lack of quantitative analysis. The difficulties in the interpretation of anisotropic scattering patterns mainly arise from the abstract nature of the reciprocal space. Here, we focus on the 2D pair distribution function (PDF) directly evaluated from anisotropic scattering patterns. We applied this method to elongated poly(N,N-dimethylacrylamide) gels containing silica nanoparticles (PDAM-NP gel), which show a four-spot scattering pattern under elongation. From 2D PDFs, we obtained detailed and concrete structural information about the elongated PDAM-NP gel, such as affine and non-affine displacements of directly attached and homogeneously dispersed silica nanoparticles, respectively. We proposed that nanoparticles homogeneously dispersed in the perpendicular direction are not displaced due to the collision of the adsorbed polymer layer during elongation, while those in the parallel direction are displaced in an affine way. We assumed that this suppression of the lateral compression is the origin of the four-spot pattern in this study. These results strongly indicate that our 2D PDF analysis will provide deep insight into the internal structure of polymer nanocomposites hidden in the anisotropic scattering patterns.

  6. A 2-D oscillating flow analysis in Stirling engine heat exchangers

    NASA Technical Reports Server (NTRS)

    Ahn, Kyung H.; Ibrahim, Mounir B.

    1991-01-01

    A two dimensional oscillating flow analysis was conducted, simulating the gas flow inside Stirling heat exchangers. Both laminar and turbulent oscillating pipe flow were investigated numerically for Re(max) = 1920 (Va = 80), 10800 (Va = 272), 19300 (Va = 272), and 60800 (Va = 126). The results are compared with experimental results of previous investigators. Also, predictions of the flow regime on present oscillating flow conditions were checked by comparing velocity amplitudes and phase differences with those from laminar theory and quasi-steady profile. A high Reynolds number k-epsilon turbulence model was used for turbulent oscillating pipe flow. Finally, performance evaluation of the K-epsilon model was made to explore the applicability of quasi-steady turbulent models to unsteady oscillating flow analysis.

  7. Feasibility of radial and circumferential strain analysis using 2D speckle tracking echocardiography in cats

    PubMed Central

    TAKANO, Hiroshi; ISOGAI, Tomomi; AOKI, Takuma; WAKAO, Yoshito; FUJII, Yoko

    2014-01-01

    The purpose of the present study is to investigate the feasibility of strain analysis using speckle tracking echocardiography (STE) in cats and to evaluate STE variables in cats with hypertrophic cardiomyopathy (HCM). Sixteen clinically healthy cats and 17 cats with HCM were used. Radial and circumferential strain and strain rate variables in healthy cats were measured using STE to assess the feasibility. Comparisons of global strain and strain variables between healthy cats and cats with HCM were performed. Segmental assessments of left ventricle (LV) wall for strain and strain rate variables in cats with HCM were also performed. As a result, technically adequate images were obtained in 97.6% of the segments for STE analysis. Sedation using buprenorphine and acepromazine did not affect any global strain nor strain rate variable. In LV segments of cats with HCM, reduced segmental radial strain and strain rate variables had significantly related with segmental LV hypertrophy. It is concluded that STE analysis using short axis images of LV appeared to be clinically feasible in cats, having the possibility to be useful for detecting myocardial dysfunctions in cats with diseased heart. PMID:25373881

  8. Feasibility of radial and circumferential strain analysis using 2D speckle tracking echocardiography in cats.

    PubMed

    Takano, Hiroshi; Isogai, Tomomi; Aoki, Takuma; Wakao, Yoshito; Fujii, Yoko

    2015-02-01

    The purpose of the present study is to investigate the feasibility of strain analysis using speckle tracking echocardiography (STE) in cats and to evaluate STE variables in cats with hypertrophic cardiomyopathy (HCM). Sixteen clinically healthy cats and 17 cats with HCM were used. Radial and circumferential strain and strain rate variables in healthy cats were measured using STE to assess the feasibility. Comparisons of global strain and strain variables between healthy cats and cats with HCM were performed. Segmental assessments of left ventricle (LV) wall for strain and strain rate variables in cats with HCM were also performed. As a result, technically adequate images were obtained in 97.6% of the segments for STE analysis. Sedation using buprenorphine and acepromazine did not affect any global strain nor strain rate variable. In LV segments of cats with HCM, reduced segmental radial strain and strain rate variables had significantly related with segmental LV hypertrophy. It is concluded that STE analysis using short axis images of LV appeared to be clinically feasible in cats, having the possibility to be useful for detecting myocardial dysfunctions in cats with diseased heart.

  9. Analysis of simple 2-D and 3-D metal structures subjected to fragment impact

    NASA Technical Reports Server (NTRS)

    Witmer, E. A.; Stagliano, T. R.; Spilker, R. L.; Rodal, J. J. A.

    1977-01-01

    Theoretical methods were developed for predicting the large-deflection elastic-plastic transient structural responses of metal containment or deflector (C/D) structures to cope with rotor burst fragment impact attack. For two-dimensional C/D structures both, finite element and finite difference analysis methods were employed to analyze structural response produced by either prescribed transient loads or fragment impact. For the latter category, two time-wise step-by-step analysis procedures were devised to predict the structural responses resulting from a succession of fragment impacts: the collision force method (CFM) which utilizes an approximate prediction of the force applied to the attacked structure during fragment impact, and the collision imparted velocity method (CIVM) in which the impact-induced velocity increment acquired by a region of the impacted structure near the impact point is computed. The merits and limitations of these approaches are discussed. For the analysis of 3-d responses of C/D structures, only the CIVM approach was investigated.

  10. Modeling of 2D diffusion processes based on microscopy data: parameter estimation and practical identifiability analysis

    PubMed Central

    2013-01-01

    Background Diffusion is a key component of many biological processes such as chemotaxis, developmental differentiation and tissue morphogenesis. Since recently, the spatial gradients caused by diffusion can be assessed in-vitro and in-vivo using microscopy based imaging techniques. The resulting time-series of two dimensional, high-resolutions images in combination with mechanistic models enable the quantitative analysis of the underlying mechanisms. However, such a model-based analysis is still challenging due to measurement noise and sparse observations, which result in uncertainties of the model parameters. Methods We introduce a likelihood function for image-based measurements with log-normal distributed noise. Based upon this likelihood function we formulate the maximum likelihood estimation problem, which is solved using PDE-constrained optimization methods. To assess the uncertainty and practical identifiability of the parameters we introduce profile likelihoods for diffusion processes. Results and conclusion As proof of concept, we model certain aspects of the guidance of dendritic cells towards lymphatic vessels, an example for haptotaxis. Using a realistic set of artificial measurement data, we estimate the five kinetic parameters of this model and compute profile likelihoods. Our novel approach for the estimation of model parameters from image data as well as the proposed identifiability analysis approach is widely applicable to diffusion processes. The profile likelihood based method provides more rigorous uncertainty bounds in contrast to local approximation methods. PMID:24267545

  11. An Asymptotic Analysis of a 2-D Model of Dynamically Active Compartments Coupled by Bulk Diffusion

    NASA Astrophysics Data System (ADS)

    Gou, J.; Ward, M. J.

    2016-08-01

    A class of coupled cell-bulk ODE-PDE models is formulated and analyzed in a two-dimensional domain, which is relevant to studying quorum-sensing behavior on thin substrates. In this model, spatially segregated dynamically active signaling cells of a common small radius ɛ ≪ 1 are coupled through a passive bulk diffusion field. For this coupled system, the method of matched asymptotic expansions is used to construct steady-state solutions and to formulate a spectral problem that characterizes the linear stability properties of the steady-state solutions, with the aim of predicting whether temporal oscillations can be triggered by the cell-bulk coupling. Phase diagrams in parameter space where such collective oscillations can occur, as obtained from our linear stability analysis, are illustrated for two specific choices of the intracellular kinetics. In the limit of very large bulk diffusion, it is shown that solutions to the ODE-PDE cell-bulk system can be approximated by a finite-dimensional dynamical system. This limiting system is studied both analytically, using a linear stability analysis and, globally, using numerical bifurcation software. For one illustrative example of the theory, it is shown that when the number of cells exceeds some critical number, i.e., when a quorum is attained, the passive bulk diffusion field can trigger oscillations through a Hopf bifurcation that would otherwise not occur without the coupling. Moreover, for two specific models for the intracellular dynamics, we show that there are rather wide regions in parameter space where these triggered oscillations are synchronous in nature. Unless the bulk diffusivity is asymptotically large, it is shown that a diffusion-sensing behavior is possible whereby more clustered spatial configurations of cells inside the domain lead to larger regions in parameter space where synchronous collective oscillations between the small cells can occur. Finally, the linear stability analysis for these cell

  12. Uncertainty Estimation for 2D PIV: An In-Depth Comparative Analysis

    NASA Astrophysics Data System (ADS)

    Boomsma, Aaron; Bhattacharya, Syantan; Troolin, Dan; Vlachos, Pavlos; Pothos, Stamatios

    2016-11-01

    Uncertainty quantification methods have recently made great strides in accurately predicting uncertainties for planar PIV, and several different approaches are now documented. In the present study, we provide an analysis of these methods across different experiments and different PIV processing codes. To assess the performance of said methods, we follow the approach of Sciacchitano et al. (2015) and utilize two PIV measurement systems with overlapping fields of view-one acting as a reference (which is validated using simultaneous LDV measurements) and the other as a measurement system, paying close attention to the effects of interrogation window overlap and bias errors on the analysis. A total of three experiments were performed: a jet flow and a cylinder in cross flow at two Reynolds numbers. In brief, the standard coverages (68% confidence interval) ranged from approximately 65%-77% for PPR and MI methods, 40%-50% for image matching methods. We present an in-depth survey of both global (e.g., coverage and error histograms) and local (e.g., spatially varying statistics) parameters to examine the strengths and weaknesses of each method in monitor their responses to different regions of the experimental flows.

  13. Multiscale quantification of morphodynamics: MorphoLeaf software for 2D shape analysis.

    PubMed

    Biot, Eric; Cortizo, Millán; Burguet, Jasmine; Kiss, Annamaria; Oughou, Mohamed; Maugarny-Calès, Aude; Gonçalves, Beatriz; Adroher, Bernard; Andrey, Philippe; Boudaoud, Arezki; Laufs, Patrick

    2016-09-15

    A major challenge in morphometrics is to analyse complex biological shapes formed by structures at different scales. Leaves exemplify this challenge as they combine differences in their overall shape with smaller shape variations at their margin, leading to lobes or teeth. Current methods based on contour or on landmark analysis are successful in quantifying either overall leaf shape or leaf margin dissection, but fail in combining the two. Here, we present a comprehensive strategy and its associated freely available platform for the quantitative, multiscale analysis of the morphology of leaves with different architectures. For this, biologically relevant landmarks are automatically extracted and hierarchised, and used to guide the reconstruction of accurate average contours that properly represent both global and local features. Using this method, we establish a quantitative framework of the developmental trajectory of Arabidopsis leaves of different ranks and retrace the origin of leaf heteroblasty. When applied to different mutant forms, our method can contribute to a better understanding of gene function, as we show here for the role of CUC2 during Arabidopsis leaf serration. Finally, we illustrate the wider applicability of our tool by analysing hand morphometrics.

  14. Multi-level model for 2D human motion analysis and description

    NASA Astrophysics Data System (ADS)

    Foures, Thomas; Joly, Philippe

    2003-01-01

    This paper deals with the proposition of a model for human motion analysis in a video. Its main caracteristic is to adapt itself automatically to the current resolution, the actual quality of the picture, or the level of precision required by a given application, due to its possible decomposition into several hierarchical levels. The model is region-based to address some analysis processing needs. The top level of the model is only defined with 5 ribbons, which can be cut into sub-ribbons regarding to a given (or an expected) level of details. Matching process between model and current picture consists in the comparison of extracted subject shape with a graphical rendering of the model built on the base of some computed parameters. The comparison is processed by using a chamfer matching algorithm. In our developments, we intend to realize a platform of interaction between a dancer and tools synthetizing abstract motion pictures and music in the conditions of a real-time dialogue between a human and a computer. In consequence, we use this model in a perspective of motion description instead of motion recognition: no a priori gestures are supposed to be recognized as far as no a priori application is specially targeted. The resulting description will be made following a Description Scheme compliant with the movement notation called "Labanotation".

  15. Comparison of new and existing algorithms for the analysis of 2D radioxenon beta gamma spectra

    DOE PAGES

    Deshmukh, Nikhil; Prinke, Amanda; Miller, Brian; ...

    2017-01-13

    The aim of this study is to compare radioxenon beta–gamma analysis algorithms using simulated spectra with experimentally measured background, where the ground truth of the signal is known. We believe that this is among the largest efforts to date in terms of the number of synthetic spectra generated and number of algorithms compared using identical spectra. We generate an estimate for the minimum detectable counts for each isotope using each algorithm. The paper also points out a conceptual model to put the various algorithms into a continuum. Finally, our results show that existing algorithms can be improved and some newermore » algorithms can be better than the ones currently used.« less

  16. UCF WASTE PACKAGE SHIELDING ANALYSIS/2-D DORT (SCPB: N/A)

    SciTech Connect

    D.J. Skulina

    1996-01-18

    This analysis is prepared by the Mined Geologic Disposal System (MGDS) Waste Package Development Department (WPDD) to determine the dose rates from the UCF waste packages to be used by the EBS and other repository systems to incorporate ALARA practices in the overall repository design in compliance with the goals of the Waste Package Implementation Plan for conceptual design. These design calculations are performed in sufficient detail to provide a comprehensive comparison base with other design alternatives. The objectives of this evaluation are (1) to show the dose rate as a function of distance from the waste package surface and (2) to provide the shielding thicknesses required for the waste package transporter to meet a 10 mr/hr target dose rate at 2 meters from the transporter surface.

  17. High pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis

    SciTech Connect

    Yang, Feng; Shen, Yufeng; Camp, David G.; Smith, Richard D.

    2012-04-01

    Orthogonal high-resolution separations are critical for attaining improved analytical dynamic ranges of proteome measurements. Concatenated high pH reversed phase liquid chromatography affords better separations than the strong cation exchange conventionally applied for two-dimensional shotgun proteomic analysis. For example, concatenated high pH reversed phase liquid chromatography increased identification coverage for peptides (e.g., by 1.8-fold) and proteins (e.g., by 1.6-fold) in shotgun proteomics analyses of a digested human protein sample. Additional advantages of concatenated high pH RPLC include improved protein sequence coverage, simplified sample processing, and reduced sample losses, making this an attractive first dimension separation strategy for two-dimensional proteomics analyses.

  18. 2D analysis of polydisperse core-shell nanoparticles using analytical ultracentrifugation.

    PubMed

    Walter, Johannes; Gorbet, Gary; Akdas, Tugce; Segets, Doris; Demeler, Borries; Peukert, Wolfgang

    2016-12-19

    Accurate knowledge of the size, density and composition of nanoparticles (NPs) is of major importance for their applications. In this work the hydrodynamic characterization of polydisperse core-shell NPs by means of analytical ultracentrifugation (AUC) is addressed. AUC is one of the most accurate techniques for the characterization of NPs in the liquid phase because it can resolve particle size distributions (PSDs) with unrivaled resolution and detail. Small NPs have to be considered as core-shell systems when dispersed in a liquid since a solvation layer and a stabilizer shell will significantly contribute to the particle's hydrodynamic diameter and effective density. AUC measures the sedimentation and diffusion transport of the analytes, which are affected by the core-shell compositional properties. This work demonstrates that polydisperse and thus widely distributed NPs pose significant challenges for current state-of-the-art data evaluation methods. The existing methods either have insufficient resolution or do not correctly reproduce the core-shell properties. First, we investigate the performance of different data evaluation models by means of simulated data. Then, we propose a new methodology to address the core-shell properties of NPs. This method is based on the parametrically constrained spectrum analysis and offers complete access to the size and effective density of polydisperse NPs. Our study is complemented using experimental data derived for ZnO and CuInS2 NPs, which do not have a monodisperse PSD. For the first time, the size and effective density of such structures could be resolved with high resolution by means of a two-dimensional AUC analysis approach.

  19. A 2-D Interface Element for Coupled Analysis of Independently Modeled 3-D Finite Element Subdomains

    NASA Technical Reports Server (NTRS)

    Kandil, Osama A.

    1998-01-01

    Over the past few years, the development of the interface technology has provided an analysis framework for embedding detailed finite element models within finite element models which are less refined. This development has enabled the use of cascading substructure domains without the constraint of coincident nodes along substructure boundaries. The approach used for the interface element is based on an alternate variational principle often used in deriving hybrid finite elements. The resulting system of equations exhibits a high degree of sparsity but gives rise to a non-positive definite system which causes difficulties with many of the equation solvers in general-purpose finite element codes. Hence the global system of equations is generally solved using, a decomposition procedure with pivoting. The research reported to-date for the interface element includes the one-dimensional line interface element and two-dimensional surface interface element. Several large-scale simulations, including geometrically nonlinear problems, have been reported using the one-dimensional interface element technology; however, only limited applications are available for the surface interface element. In the applications reported to-date, the geometry of the interfaced domains exactly match each other even though the spatial discretization within each domain may be different. As such, the spatial modeling of each domain, the interface elements and the assembled system is still laborious. The present research is focused on developing a rapid modeling procedure based on a parametric interface representation of independently defined subdomains which are also independently discretized.

  20. Analysis of 2D periodic nanostructures with an oxide overlayer via spectroscopic ellipsometry.

    PubMed

    Ghong, T H; Byun, J S; Han, S-H; Chung, J-M; Kim, Y D

    2011-07-01

    The accurate nondestructive determination of the shapes or critical dimensions of periodic nanostructures is essential to the current integrated-circuits technology. Optical critical dimension (OCD) metrology is fast, nondestructive, and can be used in air, allows higher sampling rates compared to the non-optical methods such as scanning electron microscopy (SEM) or atomic-force microscopy (AFM), and does not damage the sample. The data are typically analyzed via rigorous coupled-wave analysis (RCWA), where the sample is modeled as a series of layers whose dimensional parameters are determined by a least-squares fit. The layers are typically approximated as a combination of core material and ambient. Oxide overlayers and surface roughness are common, however, and call into question two-phase approximation. In this study, a structure that is periodic in two dimensions and that is coated with a thin (3 nm) oxide was studied, and an extension of the RCWA method that allows structural information to be extracted from optical data even in the presence of oxide overlayers or surface roughness was developed.

  1. A Complete 2D Stability Analysis of Fast MHD Shocks in an Ideal Gas

    NASA Astrophysics Data System (ADS)

    Trakhinin, Yuri

    An algorithm of numerical testing of the uniform Lopatinski condition for linearized stability problems for 1-shocks is suggested. The algorithm is used for finding the domains of uniform stability, neutral stability, and instability of planar fast MHD shocks. A complete stability analysis of fast MHD shock waves is first carried out in two space dimensions for the case of an ideal gas. Main results are given for the adiabatic constant γ=5/3 (mono-atomic gas), that is most natural for the MHD model. The cases γ=7/5 (two-atomic gas) and γ>5/3 are briefly discussed. Not only the domains of instability and linear (in the usual sense) stability, but also the domains of uniform stability, for which a corresponding linearized stability problem satisfies the uniform Lopatinski condition, are numerically found for different given angles of inclination of the magnetic field behind the shock to the planar shock front. As is known, uniform linearized stability implies the nonlinear stability, that is local existence of discontinuous shock front solutions of a quasilinear system of hyperbolic conservation laws.

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  3. Micropolar dissipative models for the analysis of 2D dispersive waves in periodic lattices

    NASA Astrophysics Data System (ADS)

    Reda, H.; Ganghoffer, J. F.; Lakiss, H.

    2017-03-01

    The computation of the dispersion relations for dissipative periodic lattices having the attributes of metamaterials is an actual research topic raising the interest of researchers in the field of acoustics and wave propagation phenomena. We analyze in this contribution the impact of wave damping on the dispersion features of periodic lattices, which are modeled as beam-lattices. The band diagram structure and damping ratio are computed for different repetitive lattices, based on the homogenized continuum response of the initially discrete lattice architecture, modeled as Kelvin-Voigt viscoelastic beams. Three of these lattices (reentrant hexagonal, chiral diamond, hexachiral lattice) are auxetic metamaterials, since they show negative Poisson's ratio. The effective viscoelastic anisotropic continuum behavior of the lattices is first computed in terms of the homogenized stiffness and viscosity matrices, based on the discrete homogenization technique. The dynamical equations of motion are obtained for an equivalent homogenized micropolar continuum evaluated based on the homogenized properties, and the dispersion relation and damping ratio are obtained by inserting an harmonic plane waves Ansatz into these equations. The comparison of the acoustic properties obtained in the low frequency range for the four considered lattices shows that auxetic lattices attenuate waves at lower frequencies compared to the classical hexagonal lattice. The diamond chiral lattice shows the best attenuation properties of harmonic waves over the entire Brillouin zone, and the hexachiral lattice presents better acoustic properties than the reentrant hexagonal lattice. The range of validity of the effective continuum obtained by the discrete homogenization has been assessed by comparing the frequency band structure of this continuum with that obtained by a Floquet-Bloch analysis.

  4. Stress analysis of a rectangular implant in laminated composites using 2-D and 3-D finite elements

    NASA Technical Reports Server (NTRS)

    Chow, Wai T.; Graves, Michael J.

    1992-01-01

    An analysis method using the FEM based on the Hellinger-Reissner variation principle has been developed to determine the 3-D stresses and displacements near a rectangular implant inside a laminated composite material. Three-dimensional elements are employed in regions where the interlaminar stress is considered to be significant; 2-D elements are used in other areas. Uniaxially loaded graphite-epoxy laminates have been analyzed; the implant was modeled as four plies of 3501/6 epoxy located in the middle of the laminate. It is shown that the interlaminar stresses are an order of magnitude lower than the stress representing the applied far-field load. The stress concentration factors of both the interlaminar and in-plane stresses depend on the stacking sequence of the laminate.

  5. Relevance of 2D radiographic texture analysis for the assessment of 3D bone micro-architecture

    SciTech Connect

    Apostol, Lian; Boudousq, Vincent; Basset, Oliver; Odet, Christophe; Yot, Sophie; Tabary, Joachim; Dinten, Jean-Marc; Boller, Elodie; Kotzki, Pierre-Olivier; Peyrin, Francoise

    2006-09-15

    Although the diagnosis of osteoporosis is mainly based on dual x-ray absorptiometry, it has been shown that trabecular bone micro-architecture is also an important factor in regard to fracture risk. In vivo, techniques based on high-resolution x-ray radiography associated to texture analysis have been proposed to investigate bone micro-architecture, but their relevance for giving pertinent 3D information is unclear. Thirty-three calcaneus and femoral neck bone samples including the cortical shells (diameter: 14 mm, height: 30-40 mm) were imaged using 3D-synchrotron x-ray micro-CT at the ESRF. The 3D reconstructed images with a cubic voxel size of 15 {mu}m were further used for two purposes: (1) quantification of three-dimensional trabecular bone micro-architecture (2) simulation of realistic x-ray radiographs under different acquisition conditions. The simulated x-ray radiographs were then analyzed using a large variety of texture analysis methods (co-occurrence, spectral density, fractal, morphology, etc.). The range of micro-architecture parameters was in agreement with previous studies and rather large, suggesting that the population was representative. More than 350 texture parameters were tested. A small number of them were selected based on their correlation to micro-architectural morphometric parameters. Using this subset of texture parameters, multiple regression allowed one to predict up to 93% of the variance of micro-architecture parameters using three texture features. 2D texture features predicting 3D micro-architecture parameters other than BV/TV were identified. The methodology proposed for evaluating the relationships between 3D micro-architecture and 2D texture parameters may also be used for optimizing the conditions for radiographic imaging. Further work will include the application of the method to physical radiographs. In the future, this approach could be used in combination with DXA to refine osteoporosis diagnosis.

  6. WASI-2D: A software tool for regionally optimized analysis of imaging spectrometer data from deep and shallow waters

    NASA Astrophysics Data System (ADS)

    Gege, Peter

    2014-01-01

    An image processing software has been developed which allows quantitative analysis of multi- and hyperspectral data from oceanic, coastal and inland waters. It has been implemented into the Water Colour Simulator WASI, which is a tool for the simulation and analysis of optical properties and light field parameters of deep and shallow waters. The new module WASI-2D can import atmospherically corrected images from airborne sensors and satellite instruments in various data formats and units like remote sensing reflectance or radiance. It can be easily adapted by the user to different sensors and to optical properties of the studied area. Data analysis is done by inverse modelling using established analytical models. The bio-optical model of the water column accounts for gelbstoff (coloured dissolved organic matter, CDOM), detritus, and mixtures of up to 6 phytoplankton classes and 2 spectrally different types of suspended matter. The reflectance of the sea floor is treated as sum of up to 6 substrate types. An analytic model of downwelling irradiance allows wavelength dependent modelling of sun glint and sky glint at the water surface. The provided database covers the spectral range from 350 to 1000 nm in 1 nm intervals. It can be exchanged easily to represent the optical properties of water constituents, bottom types and the atmosphere of the studied area.

  7. Proteomic analysis of the mouse brain after repetitive exposure to hypoxia.

    PubMed

    Cui, Can; Zhou, Tao; Li, Jingyi; Wang, Hong; Li, Xiaorong; Xiong, Jie; Xu, Pingxiang; Xue, Ming

    2015-07-05

    Hypoxic preconditioning (HPC) is known to have a protective effect against hypoxic damage; however, the precise mechanisms involved remain unknown. In this study, an acute and repetitive hypoxia mouse model, two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) coupled with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/TOF-MS), and Western blot experiments were used to identify the differential expression of key proteins in the mouse brain during HPC. Approximately 2100 2D-DIGE spots were observed following gel imaging and spot detection. Significant differences (p < 0.05) in the expression of 66 proteins were observed between the 3× HPC treatment group and the control group, 45 proteins were observed between the 6× HPC treatment group and the control group, and 70 proteins were observed between the 3× HPC treatment group and the 6× HPC group. Consistent results among Western blot, 2D-DIGE and MS methods were observed for the proteins, ATP synthase subunit alpha, malate dehydrogenase, guanine nucleotide-binding protein subunit beta-1 and proteasome subunit alpha type-2. The proteins associated with ATP synthesis and the citric acid cycle were down-regulated, while those linked to glycolysis and oxygen-binding were up-regulated. This proteomic analysis of the mouse brain after HPC furthers understanding of the molecular pathways involved in the protective effect of HPC and these findings provide new insight into the mechanisms of hypoxia and HPC.

  8. 2D wavelet-analysis-based calibration technique for flat-panel imaging detectors: application in cone beam volume CT

    NASA Astrophysics Data System (ADS)

    Tang, Xiangyang; Ning, Ruola; Yu, Rongfeng; Conover, David L.

    1999-05-01

    The application of the newly developed flat panel x-ray imaging detector in cone beam volume CT has attracted increasing interest recently. Due to an imperfect solid state array manufacturing process, however, defective elements, gain non-uniformity and offset image unavoidably exist in all kinds of flat panel x-ray imaging detectors, which will cause severe streak and ring artifacts in a cone beam reconstruction image and severely degrade image quality. A calibration technique, in which the artifacts resulting from the defective elements, gain non-uniformity and offset image can be reduced significantly, is presented in this paper. The detection of defective elements is distinctively based upon two-dimensional (2D) wavelet analysis. Because of its inherent localizability in recognizing singularities or discontinuities, wavelet analysis possesses the capability of detecting defective elements over a rather large x-ray exposure range, e.g., 20% to approximately 60% of the dynamic range of the detector used. Three-dimensional (3D) images of a low-contrast CT phantom have been reconstructed from projection images acquired by a flat panel x-ray imaging detector with and without calibration process applied. The artifacts caused individually by defective elements, gain non-uniformity and offset image have been separated and investigated in detail, and the correlation with each other have also been exposed explicitly. The investigation is enforced by quantitative analysis of the signal to noise ratio (SNR) and the image uniformity of the cone beam reconstruction image. It has been demonstrated that the ring and streak artifacts resulting from the imperfect performance of a flat panel x-ray imaging detector can be reduced dramatically, and then the image qualities of a cone beam reconstruction image, such as contrast resolution and image uniformity are improved significantly. Furthermore, with little modification, the calibration technique presented here is also applicable

  9. Anisotropic multi-resolution analysis in 2D, application to long-range correlations in cloud mm-radar fields

    SciTech Connect

    Davis, A.B.; Clothiaux, E.

    1999-03-01

    Because of Earth`s gravitational field, its atmosphere is strongly anisotropic with respect to the vertical; the effect of the Earth`s rotation on synoptic wind patterns also causes a more subtle form of anisotropy in the horizontal plane. The authors survey various approaches to statistically robust anisotropy from a wavelet perspective and present a new one adapted to strongly non-isotropic fields that are sampled on a rectangular grid with a large aspect ratio. This novel technique uses an anisotropic version of Multi-Resolution Analysis (MRA) in image analysis; the authors form a tensor product of the standard dyadic Haar basis, where the dividing ratio is {lambda}{sub z} = 2, and a nonstandard triadic counterpart, where the dividing ratio is {lambda}{sub x} = 3. The natural support of the field is therefore 2{sup n} pixels (vertically) by 3{sup n} pixels (horizontally) where n is the number of levels in the MRA. The natural triadic basis includes the French top-hat wavelet which resonates with bumps in the field whereas the Haar wavelet responds to ramps or steps. The complete 2D basis has one scaling function and five wavelets. The resulting anisotropic MRA is designed for application to the liquid water content (LWC) field in boundary-layer clouds, as the prevailing wind advects them by a vertically pointing mm-radar system. Spatial correlations are notoriously long-range in cloud structure and the authors use the wavelet coefficients from the new MRA to characterize these correlations in a multifractal analysis scheme. In the present study, the MRA is used (in synthesis mode) to generate fields that mimic cloud structure quite realistically although only a few parameters are used to control the randomness of the LWC`s wavelet coefficients.

  10. Integral equation analysis and optimization of 2D layered nanolithography masks by complex images Green's function technique in TM polarization.

    PubMed

    Haghtalab, Mohammad; Faraji-Dana, Reza

    2012-05-01

    Analysis and optimization of diffraction effects in nanolithography through multilayered media with a fast and accurate field-theoretical approach is presented. The scattered field through an arbitrary two-dimensional (2D) mask pattern in multilayered media illuminated by a TM-polarized incident wave is determined by using an electric field integral equation formulation. In this formulation the electric field is represented in terms of complex images Green's functions. The method of moments is then employed to solve the resulting integral equation. In this way an accurate and computationally efficient approximate method is achieved. The accuracy of the proposed method is vindicated through comparison with direct numerical integration results. Moreover, the comparison is made between the results obtained by the proposed method and those obtained by the full-wave finite-element method. The ray tracing method is combined with the proposed method to describe the imaging process in the lithography. The simulated annealing algorithm is then employed to solve the inverse problem, i.e., to design an optimized mask pattern to improve the resolution. Two binary mask patterns under normal incident coherent illumination are designed by this method, where it is shown that the subresolution features improve the critical dimension significantly.

  11. Interaction Between Tropical Convection and its Embedding Environment: An Energetics Analysis of a 2-D Cloud Resolving Simulation

    NASA Technical Reports Server (NTRS)

    Li, Xiaofan; Sui, C.-H.; Lau, K.-M.

    1999-01-01

    The phase relation between the perturbation kinetic energy (K') associated with the tropical convection and the horizontal-mean moist available potential energy (bar-P) associated with environmental conditions is investigated by an energetics analysis of a numerical experiment. This experiment is performed using a 2-D cloud resolving model forced by the TOGA-COARE derived vertical velocity. The imposed upward motion leads to a decrease of bar-P directly through the associated vertical advective cooling, and to an increase of K' directly through cloud related processes, feeding the convection. The maximum K' and its maximum growth rate lags and leads, respectively, the maximum imposed large-scale upward motion by about 1-2 hours, indicating that convection is phase locked with large-scale forcing. The dominant life cycle of the simulated convection is about 9 hours, whereas the time scales of the imposed large-scale forcing are longer than the diurnal cycle. In the convective events, maximum growth of K' leads maximum decay of the perturbation moist available potential energy (P') by about 3 hours through vertical heat transport by perturbation circulation, and perturbation cloud heating. Maximum decay of P' leads maximum decay of bar-P by about one hour through the perturbation radiative, processes, the horizontal-mean cloud heating, and the large-scale vertical advective cooling. Therefore, maximum gain of K' occurs about 4-5 hours before maximum decay of bar-P.

  12. 2D fluid model analysis for the effect of 3D gas flow on a capacitively coupled plasma deposition reactor

    NASA Astrophysics Data System (ADS)

    Kim, Ho Jun; Lee, Hae June

    2016-06-01

    The wide applicability of capacitively coupled plasma (CCP) deposition has increased the interest in developing comprehensive numerical models, but CCP imposes a tremendous computational cost when conducting a transient analysis in a three-dimensional (3D) model which reflects the real geometry of reactors. In particular, the detailed flow features of reactive gases induced by 3D geometric effects need to be considered for the precise calculation of radical distribution of reactive species. Thus, an alternative inclusive method for the numerical simulation of CCP deposition is proposed to simulate a two-dimensional (2D) CCP model based on the 3D gas flow results by simulating flow, temperature, and species fields in a 3D space at first without calculating the plasma chemistry. A numerical study of a cylindrical showerhead-electrode CCP reactor was conducted for particular cases of SiH4/NH3/N2/He gas mixture to deposit a hydrogenated silicon nitride (SiN x H y ) film. The proposed methodology produces numerical results for a 300 mm wafer deposition reactor which agree very well with the deposition rate profile measured experimentally along the wafer radius.

  13. Monitoring guanidinium-induced structural changes in ribonuclease proteins using Raman spectroscopy and 2D correlation analysis.

    PubMed

    Brewster, Victoria L; Ashton, Lorna; Goodacre, Royston

    2013-04-02

    Assessing the stability of proteins by comparing their unfolding profiles is a very important characterization and quality control step for any biopharmaceutical, and this is usually measured by fluorescence spectroscopy. In this paper we propose Raman spectroscopy as a rapid, noninvasive alternative analytical method and we shall show this has enhanced sensitivity and can therefore reveal very subtle protein conformational changes that are not observed with fluorescence measurements. Raman spectroscopy is a powerful nondestructive method that has a strong history of applications in protein characterization. In this work we describe how Raman microscopy can be used as a fast and reliable method of tracking protein unfolding in the presence of a chemical denaturant. We have compared Raman spectroscopic data to the equivalent samples analyzed using fluorescence spectroscopy in order to validate the Raman approach. Calculations from both Raman and fluorescence unfolding curves of [D]50 values and Gibbs free energy correlate well with each other and more importantly agree with the values found in the literature for these proteins. In addition, 2D correlation analysis has been performed on both Raman and fluorescence data sets in order to allow further comparisons of the unfolding behavior indicated by each method. As many biopharmaceuticals are glycosylated in order to be functional, we compare the unfolding profiles of a protein (RNase A) and a glycoprotein (RNase B) as measured by Raman spectroscopy and discuss the implications that glycosylation has on the stability of the protein.

  14. Experimental analysis of natural convection in square cavities heated from below with 2D-PIV and holographic interferometry techniques

    SciTech Connect

    Corvaro, F.; Paroncini, M.

    2007-07-15

    A numerical and experimental analysis was performed to study the natural convection heat transfer in a square cavity heated from below and cooled by the sidewalls. The enclosure was filled with air (Pr = 0.71) and a discrete heater was mounted on its lower surface; the effect of three different positions was evaluated. The air temperature distribution and the Nusselt numbers at different Rayleigh numbers on the heated strip were measured by an holographic interferometry thanks to the real-time and the double-exposure technique. The double-exposure technique was performed at steady-state and it was used to obtain the isothermal lines in the cavity at different Rayleigh numbers; while the real-time technique was used to control the presence of the plume oscillations and to determinate the achievement of the steady-state. A 2D particle image velocimetry (PIV) was utilized to measure the velocity fields at the same Rayleigh numbers. In particular we analysed the distribution of the velocity vectors and their modulus inside the cavity. The convective phenomenon was studied and the Nusselt numbers were presented as well as the Rayleigh numbers analysed. Moreover experimental and numerical correlations were determined for each position analysed to connect the Rayleigh numbers with the Nusselt numbers. Measured quantities were compared with the numerical results which were obtained with the finite volume code Fluent 6.2.16. (author)

  15. Digit ratio (2D:4D) and male facial attractiveness: new data and a meta-analysis.

    PubMed

    Hönekopp, Johannes

    2013-10-01

    Digit ratio (2D:4D) appears to correlate negatively with prenatal testosterone (T) effects in humans. As T probably increases facial masculinity, which in turn might be positively related to male facial attractiveness, a number of studies have looked into the relationship between 2D:4D and male facial attractiveness, showing equivocal results. Here, I present the largest and third largest samples so far, which investigate the relationship between 2D:4D and male facial attractiveness in adolescents (n = 115) and young men (n = 80). I then present random-effects meta-analyses of the available data (seven to eight samples, overall n = 362 to 469). These showed small (r ≈ -.09), statistically non-significant relationships between 2D:4D measures and male facial attractiveness. Thus, 2D:4D studies offer no convincing evidence at present that prenatal T has a positive effect on male facial attractiveness. However, a consideration of confidence intervals shows that, at present, a theoretically meaningful relationship between 2D:4D and male facial attractiveness cannot be ruled out either.

  16. Allosteric pathway identification through network analysis: from molecular dynamics simulations to interactive 2D and 3D graphs.

    PubMed

    Allain, Ariane; Chauvot de Beauchêne, Isaure; Langenfeld, Florent; Guarracino, Yann; Laine, Elodie; Tchertanov, Luba

    2014-01-01

    Allostery is a universal phenomenon that couples the information induced by a local perturbation (effector) in a protein to spatially distant regulated sites. Such an event can be described in terms of a large scale transmission of information (communication) through a dynamic coupling between structurally rigid (minimally frustrated) and plastic (locally frustrated) clusters of residues. To elaborate a rational description of allosteric coupling, we propose an original approach - MOdular NETwork Analysis (MONETA) - based on the analysis of inter-residue dynamical correlations to localize the propagation of both structural and dynamical effects of a perturbation throughout a protein structure. MONETA uses inter-residue cross-correlations and commute times computed from molecular dynamics simulations and a topological description of a protein to build a modular network representation composed of clusters of residues (dynamic segments) linked together by chains of residues (communication pathways). MONETA provides a brand new direct and simple visualization of protein allosteric communication. A GEPHI module implemented in the MONETA package allows the generation of 2D graphs of the communication network. An interactive PyMOL plugin permits drawing of the communication pathways between chosen protein fragments or residues on a 3D representation. MONETA is a powerful tool for on-the-fly display of communication networks in proteins. We applied MONETA for the analysis of communication pathways (i) between the main regulatory fragments of receptors tyrosine kinases (RTKs), KIT and CSF-1R, in the native and mutated states and (ii) in proteins STAT5 (STAT5a and STAT5b) in the phosphorylated and the unphosphorylated forms. The description of the physical support for allosteric coupling by MONETA allowed a comparison of the mechanisms of (a) constitutive activation induced by equivalent mutations in two RTKs and (b) allosteric regulation in the activated and non

  17. FDTD analysis of 2D triangular-lattice photonic crystals with arbitrary-shape inclusions based on unit cell transformation

    NASA Astrophysics Data System (ADS)

    Ma, Zetao; Ogusu, Kazuhiko

    2009-04-01

    A finite-difference time-domain method based on Yee's orthogonal cell is utilized to calculate the band structures of 2D triangular-lattice-based photonic crystals through a simple modification to properly shifting the boundaries of the original unit cell. A strategy is proposed for transforming the triangular unit cell into an orthogonal one, which can be used to calculate the band structures of 2D PhCs with various shapes of inclusions, such as triangular, quadrangular, and hexagonal shapes, to overcome the shortage of plane-wave expansion method for circular one. The band structures of 2D triangular-lattice-based PhCs with hexagonal air-holes are calculated and discussed for different values of its radius and rotation angle. The obtained results provide an insight to manipulate the band structures of PhCs.

  18. Time evolution analysis of a 2D solid gas equilibrium: a model system for molecular adsorption and diffusion

    NASA Astrophysics Data System (ADS)

    Berner, S.; Brunner, M.; Ramoino, L.; Suzuki, H.; Güntherodt, H.-J.; Jung, T. A.

    2001-11-01

    The adsorption of sub-phthalocyanine molecules on Ag(1 1 1) has been studied by means of scanning tunneling microscopy (STM). The molecules are observed in different two-dimensional (2D) phases of adsorption which coexist in thermodynamic equilibrium. In the condensed phase the molecules form well-ordered islands with a honeycomb pattern. In the gas phase single molecules can be discriminated in single scan lines by characteristic tip excursions which occur randomly. The energy barrier for surface diffusion as well as the condensation energy to form 2D islands is estimated and discussed.

  19. Key genes and proteins involved in CTCM-reducing microvascular endothelial cell permeability induced by SLT-IIv using gene chips and DIGE.

    PubMed

    Yi, Pengfei; Guo, Yang; Wang, Xin; Mu, Xiang; Wei, Xubin

    2010-01-01

    An Affymetrix mouse genome array and differential in-gel electrophoresis (DIGE) techniques were used to investigate the pharmacological mechanisms of a mixture of herbs, designated CTCM, a compound of traditional Chinese medicine, for the treatment of increased permeability in mouse intestinal microvascular endothelial cells (MIMECs) induced by the Shiga-like toxin type II variant (SLT-IIv). MIMECs were challenged with 10microg/ml SLT-IIv for 12h and then treated with CTCM at a concentration of 200microg/ml for 12h. Total RNA and proteins from each treatment group were extracted from cultured MIMECs for analysis by the Affymetrix GeneChip Mouse Genome 430 2.0 microarray and DIGE. The results obtained demonstrated that there were one genes downregulated and one genes upregulated, one protein downregulated and four proteins upregulated in the SLT-IIv group compared to the control group. In the CTCM group, four genes were upregulated, three genes were downregulated, a single protein was downregulated and a single protein was upregulated when compared to the control group. When the CTCM-treated group was compared to the SLT-IIv group, expression of one gene was found to be increased, and all other genes were decreased, with five proteins downregulated. Analysis of the data suggested that CTCM specifically and effectively reduced microvascular endothelial cell permeability to SLT-IIv in the treatment of pig edema disease. In the CTCM-treated group, hspa9 expression was increased in both gene chip and DIGE analysis, so it may be a key protein in reducing cell permeability and utilized in medical treatments.

  20. Molecular analysis and modeling of inactivation of human CYP2D6 by four mechanism based inactivators.

    PubMed

    Livezey, Mara; Nagy, Leslie D; Diffenderfer, Laura E; Arthur, Evan J; Hsi, David J; Holton, Jeffrey M; Furge, Laura Lowe

    2012-03-01

    Human cytochrome P450 2D6 (CYP2D6) is involved in metabolism of approximately 25% of pharmaceutical drugs. Inactivation of CYP2D6 can lead to adverse drug interactions. Four inactivators of CYP2D6 have previously been identified: 5-Fluoro-2-[4-[(2-phenyl-1H-imidazol-5-yl)methyl]-1-piperazinyl]pyrimidine(SCH66712), (1-[(2-ethyl- 4-methyl-1H-imidazol-5-yl)-methyl]-4-[4-(trifluoromethyl)-2-pyridinyl]piperazine(EMTPP), paroxetine, and 3,4- methylenedioxymethamphetamine (MDMA). All four contain planar, aromatic groups as well as basic nitrogens common to CYP2D6 substrates. SCH66712 and EMTPP also contain piperazine groups and substituted imidazole rings that are common in pharmaceutical agents, though neither of these compounds is clinically relevant. Paroxetine and MDMA contain methylenedioxyphenyls. SCH66712 and EMTPP are both known protein adductors while paroxetine and MDMA are probable heme modifiers. The current study shows that each inactivator displays Type I binding with Ks values that vary by 2-orders of magnitude with lower Ks values associated with greater inactivation. Comparison of KI, kinact, and partition ratio values shows SCH66712 is the most potent inactivator. Molecular modeling experiments using AutoDock identify Phe120 as a key interaction for all four inactivators with face-to-face and edge-to-face pi interactions apparent. Distance between the ligand and heme iron correlates with potency of inhibition. Ligand conformations were scored according to their binding energies as calculated by AutoDock and correlation was observed between molecular models and Ks values.

  1. 2D Hydrodynamic Based Logic Modeling Tool for River Restoration Decision Analysis: A Quantitative Approach to Project Prioritization

    NASA Astrophysics Data System (ADS)

    Bandrowski, D.; Lai, Y.; Bradley, N.; Gaeuman, D. A.; Murauskas, J.; Som, N. A.; Martin, A.; Goodman, D.; Alvarez, J.

    2014-12-01

    In the field of river restoration sciences there is a growing need for analytical modeling tools and quantitative processes to help identify and prioritize project sites. 2D hydraulic models have become more common in recent years and with the availability of robust data sets and computing technology, it is now possible to evaluate large river systems at the reach scale. The Trinity River Restoration Program is now analyzing a 40 mile segment of the Trinity River to determine priority and implementation sequencing for its Phase II rehabilitation projects. A comprehensive approach and quantitative tool has recently been developed to analyze this complex river system referred to as: 2D-Hydrodynamic Based Logic Modeling (2D-HBLM). This tool utilizes various hydraulic output parameters combined with biological, ecological, and physical metrics at user-defined spatial scales. These metrics and their associated algorithms are the underpinnings of the 2D-HBLM habitat module used to evaluate geomorphic characteristics, riverine processes, and habitat complexity. The habitat metrics are further integrated into a comprehensive Logic Model framework to perform statistical analyses to assess project prioritization. The Logic Model will analyze various potential project sites by evaluating connectivity using principal component methods. The 2D-HBLM tool will help inform management and decision makers by using a quantitative process to optimize desired response variables with balancing important limiting factors in determining the highest priority locations within the river corridor to implement restoration projects. Effective river restoration prioritization starts with well-crafted goals that identify the biological objectives, address underlying causes of habitat change, and recognizes that social, economic, and land use limiting factors may constrain restoration options (Bechie et. al. 2008). Applying natural resources management actions, like restoration prioritization, is

  2. MOLECULAR ANALYSIS AND MODELING OF INACTIVATION OF HUMAN CYP2D6 BY FOUR MECHANISM BASED INACTIVATORS

    PubMed Central

    Livezey, Mara; Nagy, Leslie D.; Diffenderfer, Laura E.; Arthur, Evan J.; Hsi, David J.; Holton, Jeffrey M.; Furge, Laura Lowe

    2014-01-01

    Human cytochrome P450 2D6 (CYP2D6) is involved in metabolism of approximately 25% of pharmaceutical drugs. Inactivation of CYP2D6 can lead to adverse drug interactions. Four inactivators of CYP2D6 have previously been identified: 5-Fluoro-2-[4-[(2-phenyl-1H-imidazol-5-yl)methyl]-1-piperazinyl]pyrimidine (SCH66712), (1-[(2-ethyl-4-methyl-1H(-EMTPP-imidazol-5-yl)-methyl]-4-[4-(trifluoromethyl)-2-pyridinyl]piperazine (EMTPP), paroxetine, and 3,4-methylenedioxymethamphetamine (MDMA). All four contain planar, aromatic groups as well as basic nitrogens common to CYP2D6 substrates. SCH66712 and EMTPP also contain piperazine groups and substituted imidazole rings that are common in pharmaceutical agents, though neither of these compounds is clinically relevant. Paroxetine and MDMA contain methylenedioxyphenyls. SCH66712 and EMTPP are both known protein adductors while paroxetine and MDMA are probable heme modifiers. The current study shows that each inactivator displays Type I binding with Ks values that vary by 2-orders of magnitude with lower Ks values associated with greater inactivation. Comparison of KI, kinact, and partition ratio values shows SCH66712 is the most potent inactivator. Molecular modeling experiments using AutoDock identify Phe120 as a key interaction for all four inactivators with face-to-face and edge-to-face pi interactions apparent. Distance between the ligand and heme iron correlates with potency of inhibition. Ligand conformations were scored according to their binding energies as calculated by AutoDock and correlation was observed between molecular models and Ks values. PMID:22372551

  3. Analysis of the terrestrial ion foreshock: 2D Full-Particle simulation of a curved supercritical shock

    NASA Astrophysics Data System (ADS)

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

    2013-05-01

    Two distinct ion populations backstreaming into the solar wind have been clearly evidenced by various space missions within the quasi-perpendicular region of the ion foreshock located upstream of the Earth's Bow shock (i.e. for 45° ≤ Theta_Bn ≤ 90°, where Theta_Bn is the angle between the shock normal and the upstream magnetostatic field): (i) field-aligned ion beams (« FAB ») characterized by a gyrotropic distribution, and (ii) gyro-phase bunched ions («GPB »), characterized by a NON gyrotropic distribution. The origin of these backstreaming ions has not been clearly identified and is presently analyzed with the help of 2D PIC simulation of a curved shock, where full curvature effects, time of flight effects and both electrons and ions dynamics are fully described within a self consistent approach. Present simulations evidence that these two populations can be effectively created directly by the shock front without invoking microinstabilities. The analysis of both individual and statistical ion trajectories evidences that: (i) two new parameters, namely the interaction time DT_inter and distance of penetration L_depth into the shock wave, play a key role and allow to discriminate these two populations. "GPB" population is characterized by a very short interaction time (DT_inter = 1 to 2 Tci) in comparison to the "FAB" population (DT_inter = 2 Tci to 10 Tci) which moves back and forth between the upstream edge of the shock front and the overshoot, where tci is the upstream ion gyroperiod. (ii) the importance of the injection angle (i.e. the angle between the normal of the shock front and the gyration velocity when ions reach the shock) to understand how the reflection process takes place. (iii) "FAB" population drifts along the curved shock front scanning a large Theta_Bn range from 90°. (iv) "GPB" population is embedded within the "FAB" population near the shock front which explains the difficulty to identify such a population in the experimental

  4. Modeling and Analysis of Granite Matrix Pore Structure and Hydraulic Characteristics in 2D and 3D Networks

    NASA Astrophysics Data System (ADS)

    Gvozdik, L.; Polak, M.; Zaruba, J.; Vanecek, M.

    2010-12-01

    A geological environment labeled as a Granite massif represents in terms of groundwater flow and transport a distinct hydrogeological environment from that of sedimentary basins, the characterisation of which is generally more complex and uncertain. Massifs are composed of hard crystalline rocks with the very low effective porosity. Due to their rheological properties such rocks are predisposed to brittle deformation resulting from changes in stress conditions. Our specific research project (Research on the influence of intergrangular porosity on deep geological disposal: geological formations, methodology and the development of measurement apparatus) is focussed on the problem of permeable zones within apparently undisturbed granitic rock matrix. The project including the both laboratory and in-situ tracer tests study migration along and through mineral grains in fresh and altered granite. The objective of the project is to assess whether intergranular porosity is a general characteristic of the granitic rock matrix or subject to significant evolution resulting from geochemical and/or hydrogeochemical processes, geotechnical and/or mechanical processes. Moreover, the research is focussed on evaluating methods quantifying intergranular porosity by both physical testing and mathematical modelling using verified standard hydrological software tools. Groundwater flow in microfractures and intergranular pores in granite rock matrix were simulated in three standard hydrogeological modeling programs with completely different conceptual approaches: MODFLOW (Equivalent Continuum concept), FEFLOW (Discrete Fracture and Equivalent Continuum concepts) and NAPSAC (Discrete Fracture Network concept). Specialized random fracture generators were used for creation of several 2D and 3D models in each of the chosen program. Percolation characteristics of these models were tested and analyzed. Several scenarios of laboratory tests of the rock samples permeability made in triaxial

  5. A BENCHMARKING ANALYSIS FOR FIVE RADIONUCLIDE VADOSE ZONE MODELS (CHAIN, MULTIMED_DP, FECTUZ, HYDRUS, AND CHAIN 2D) IN SOIL SCREENING LEVEL CALCULATIONS

    EPA Science Inventory

    Five radionuclide vadose zone models with different degrees of complexity (CHAIN, MULTIMED_DP, FECTUZ, HYDRUS, and CHAIN 2D) were selected for use in soil screening level (SSL) calculations. A benchmarking analysis between the models was conducted for a radionuclide (99Tc) rele...

  6. User's Guide for ECAP2D: an Euler Unsteady Aerodynamic and Aeroelastic Analysis Program for Two Dimensional Oscillating Cascades, Version 1.0

    NASA Technical Reports Server (NTRS)

    Reddy, T. S. R.

    1995-01-01

    This guide describes the input data required for using ECAP2D (Euler Cascade Aeroelastic Program-Two Dimensional). ECAP2D can be used for steady or unsteady aerodynamic and aeroelastic analysis of two dimensional cascades. Euler equations are used to obtain aerodynamic forces. The structural dynamic equations are written for a rigid typical section undergoing pitching (torsion) and plunging (bending) motion. The solution methods include harmonic oscillation method, influence coefficient method, pulse response method, and time integration method. For harmonic oscillation method, example inputs and outputs are provided for pitching motion and plunging motion. For the rest of the methods, input and output for pitching motion only are given.

  7. Localization of the CYP2D gene locus to human chromosome 22q13. 1 by polymerase chain reaction, in situ hybridization, and linkage analysis

    SciTech Connect

    Gouch, A.C.; Howell, S.M.; Bryant, S.P.; Spurr, N.K. ); Smith, C.A.D.; Wolf, C.R. )

    1993-02-01

    Using a combination of somatic cell hybrids, in situ hybridization, and linkage mapping, we have been able to localize the cytochrome P450 CYP2D6 gene to chromosome 22 in the region q13.1. Linkage analysis, using locus-specific primers, showed a maximum sex-average lod score of 8.12 ([theta] = 0.00) between the marker pH130 (D22S64) and CYPsD6, of 6.92 ([theta] - 0.00) between the marker KI839 (D22S95) and CYP2D6, and 4.80 ([theta] = 0.036) between the platelet-derived growth factor [beta] subunit gene (PDGFB) and CYP2D6. 16 refs., 2 figs.

  8. A New Family of 2-D Optical Orthogonal Codes and Analysis of Its Performance in Optical CDMA Access Networks

    NASA Astrophysics Data System (ADS)

    Shurong, Sun; Yin, Hongxi; Wang, Ziyu; Xu, Anshi

    2006-04-01

    A new family of two-dimensional optical orthogonal code (2-D OOC), one-coincidence frequency hop code (OCFHC)/OOC, which employs OCFHC and OOC as wavelengthhopping and time-spreading patterns, respectively, is proposed in this paper. In contrary to previously constructed 2-D OOCs, OCFHC/OOC provides more choices on the number of available wavelengths and its cardinality achieves the upper bound in theory without sacrificing good auto-and-cross correlation properties, i.e., the correlation properties of the code is still ideal. Meanwhile, we utilize a new method, called effective normalized throughput, to compare the performance of diverse codes applicable to optical code division multiple access (OCDMA) systems besides conventional measure bit error rate, and the results indicate that our code performs better than obtained OCDMA codes and is truly applicable to OCDMA networks as multiaccess codes and will greatly facilitate the implementation of OCDMA access networks.

  9. Quantification and geometric analysis of coiling patterns in gastropod shells based on 3D and 2D image data.

    PubMed

    Noshita, Koji

    2014-12-21

    The morphology of gastropod shells has been a focus of analyses in ecology and evolution. It has recently emerged as an important issue in developmental biology, thanks to recent advancements in molecular biological techniques. The growing tube model is a theoretical morphological model for describing various coiling patterns of molluscan shells, and it is a useful theoretical tool to relate local tissue growth with global shell morphology. However, the growing tube model has rarely been adopted in empirical research owing to the difficulty in estimating the parameters of the model from morphological data. In this article, I solve this problem by developing methods of parameter estimation when (1) 3D Computed Tomography (CT) data are available and (2) only 2D image data (such as photographs) are available. When 3D CT data are available, the parameters can be estimated by fitting an analytical solution of the growing tube model to the data. When only 2D image data are available, we first fit Raup׳s model to the 2D image data and then convert the parameters of Raup׳s model to those of the growing tube model. To illustrate the use of these methods, I apply them to data generated by a computer simulation of the model. Both methods work well, except when shells grow without coiling. I also demonstrate the effectiveness of the methods by applying the model to actual 3D CT data and 2D image data of land snails. I conclude that the method proposed in this article can reconstruct the coiling pattern from observed data.

  10. A simple method to produce 2D and 3D microfluidic paper-based analytical devices for clinical analysis.

    PubMed

    de Oliveira, Ricardo A G; Camargo, Fiamma; Pesquero, Naira C; Faria, Ronaldo Censi

    2017-03-08

    This paper describes the fabrication of 2D and 3D microfluidic paper-based analytical devices (μPADs) for monitoring glucose, total protein, and nitrite in blood serum and artificial urine. A new method of cutting and sealing filter paper to construct μPADs was demonstrated. Using an inexpensive home cutter printer soft cellulose-based filter paper was easily and precisely cut to produce pattern hydrophilic microchannels. 2D and 3D μPADs were designed with three detection zones each for the colorimetric detection of the analytes. A small volume of samples was added to the μPADs, which was photographed after 15 min using a digital camera. Both μPADs presented an excellent analytical performance for all analytes. The 2D device was applied in artificial urine samples and reached limits of detection (LODs) of 0.54 mM, 5.19 μM, and 2.34 μM for glucose, protein, and nitrite, respectively. The corresponding LODs of the 3D device applied for detecting the same analytes in artificial blood serum were 0.44 mM, 1.26 μM, and 4.35 μM.

  11. Analysis of EEG signals regularity in adults during video game play in 2D and 3D.

    PubMed

    Khairuddin, Hamizah R; Malik, Aamir S; Mumtaz, Wajid; Kamel, Nidal; Xia, Likun

    2013-01-01

    Video games have long been part of the entertainment industry. Nonetheless, it is not well known how video games can affect us with the advancement of 3D technology. The purpose of this study is to investigate the EEG signals regularity when playing video games in 2D and 3D modes. A total of 29 healthy subjects (24 male, 5 female) with mean age of 21.79 (1.63) years participated. Subjects were asked to play a car racing video game in three different modes (2D, 3D passive and 3D active). In 3D passive mode, subjects needed to wear a passive polarized glasses (cinema type) while for 3D active, an active shutter glasses was used. Scalp EEG data was recorded during game play using 19-channel EEG machine and linked ear was used as reference. After data were pre-processed, the signal irregularity for all conditions was computed. Two parameters were used to measure signal complexity for time series data: i) Hjorth-Complexity and ii) Composite Permutation Entropy Index (CPEI). Based on these two parameters, our results showed that the complexity level increased from eyes closed to eyes open condition; and further increased in the case of 3D as compared to 2D game play.

  12. SU-E-T-77: Comparison of 2D and 3D Gamma Analysis in Patient-Specific QA for Prostate VMAT Plans

    SciTech Connect

    Clemente, F; Perez, C

    2014-06-01

    Purpose: Patient-specific QA procedures for IMRT and VMAT are traditionally performed by comparing TPS calculations with measured single point values and plane dose distributions by means of gamma analysis. New QA devices permit us to calculate 3D dose distributions on patient anatomy as redundant secondary check and reconstruct it from measurements taken with 2D and 3D detector arrays. 3D dose calculations allow us to perform DVH-based comparisons with clinical relevance, as well as 3D gamma analysis. One of these systems (Compass, IBA Dosimetry) combines traditional 2D with new anatomical-based 3D gamma analysis. This work shows the ability of this system by comparing 2D and 3D gamma analysis in pre-treatment QA for several VMAT prostate plans. Methods: Compass is capable of calculating dose as secondary check from DICOM TPS data and reconstructing it from measurements taken by a 2D ion chamber array (MatriXX Evolution, IBA Dosimetry). Both 2D and 3D gamma tests are available to compare calculated and reconstructed dose in Compass with TPS RT Dose. Results: 15 VMAT prostate plans have been measured with Compass. Dose is reconstructed with Compass for these plans. 2D gamma comparisons can be done for any plane from dose matrix. Mean gamma passing rates for isocenter planes (axial, coronal, sagittal) are (99.7±0.2)%, (99.9±0.1)%, (99.9±0.1)% for reconstructed dose planes. 3D mean gamma passing rates are (98.5±1.7)% for PTVs, (99.1±1.5)% for rectum, (100.0±0.0)% for bladder, (99.6±0.7)% for femoral heads and (98.1±4.1)% for penile bulb. Conclusion: Compass is a powerful tool to perform a complete pre-treatment QA analysis, from 2D techniques to 3D DVH-based techniques with clinical relevance. All reported values for VMAT prostate plans are in good agreement with TPS values. This system permits us to ensure the accuracy in the delivery of VMAT treatments completing a full patient-specific QA program.

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

    NASA Astrophysics Data System (ADS)

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

    2003-07-01

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

  14. Sensitivity and specificity of 3-D texture analysis of lung parenchyma is better than 2-D for discrimination of lung pathology in stage 0 COPD

    NASA Astrophysics Data System (ADS)

    Xu, Ye; Sonka, Milan; McLennan, Geoffrey; Guo, Junfeng; Hoffman, Eric

    2005-04-01

    Lung parenchyma evaluation via multidetector-row CT (MDCT), has significantly altered clinical practice in the early detection of lung disease. Our goal is to enhance our texture-based tissue classification ability to differentiate early pathologic processes by extending our 2-D Adaptive Multiple Feature Method (AMFM) to 3-D AMFM. We performed MDCT on 34 human volunteers in five categories: emphysema in severe Chronic Obstructive Pulmonary Disease (COPD) as EC, emphysema in mild COPD (MC), normal appearing lung in COPD (NC), non-smokers with normal lung function (NN), smokers with normal function (NS). We volumetrically excluded the airway and vessel regions, calculated 24 volumetric texture features for each Volume of Interest (VOI); and used Bayesian rules for discrimination. Leave-one-out and half-half methods were used for testing. Sensitivity, specificity and accuracy were calculated. The accuracy of the leave-one-out method for the four-class classification in the form of 3-D/2-D is: EC: 84.9%/70.7%, MC: 89.8%/82.7%; NC: 87.5.0%/49.6%; NN: 100.0%/60.0%. The accuracy of the leave-one-out method for the two-class classification in the form of 3-D/2-D is: NN: 99.3%/71.6%; NS: 99.7%/74.5%. We conclude that 3-D AMFM analysis of the lung parenchyma improves discrimination compared to 2-D analysis of the same images.

  15. User's Guide for MSAP2D: A Program for Unsteady Aerodynamic and Aeroelastic (Flutter and Forced Response) Analysis of Multistage Compressors and Turbines. 1.0

    NASA Technical Reports Server (NTRS)

    Reddy, T. S. R.; Srivastava, R.

    1996-01-01

    This guide describes the input data required for using MSAP2D (Multi Stage Aeroelastic analysis Program - Two Dimensional) computer code. MSAP2D can be used for steady, unsteady aerodynamic, and aeroelastic (flutter and forced response) analysis of bladed disks arranged in multiple blade rows such as those found in compressors, turbines, counter rotating propellers or propfans. The code can also be run for single blade row. MSAP2D code is an extension of the original NPHASE code for multiblade row aerodynamic and aeroelastic analysis. Euler equations are used to obtain aerodynamic forces. The structural dynamic equations are written for a rigid typical section undergoing pitching (torsion) and plunging (bending) motion. The aeroelastic equations are solved in time domain. For single blade row analysis, frequency domain analysis is also provided to obtain unsteady aerodynamic coefficients required in an eigen analysis for flutter. In this manual, sample input and output are provided for a single blade row example, two blade row example with equal and unequal number of blades in the blade rows.

  16. Importance of the Correlation between Width and Length in the Shape Analysis of Nanorods: Use of a 2D Size Plot To Probe Such a Correlation.

    PubMed

    Zhao, Zhihua; Zheng, Zhiqin; Roux, Clément; Delmas, Céline; Marty, Jean-Daniel; Kahn, Myrtil L; Mingotaud, Christophe

    2016-08-22

    Analysis of nanoparticle size through a simple 2D plot is proposed in order to extract the correlation between length and width in a collection or a mixture of anisotropic particles. Compared to the usual statistics on the length associated with a second and independent statistical analysis of the width, this simple plot easily points out the various types of nanoparticles and their (an)isotropy. For each class of nano-objects, the relationship between width and length (i.e., the strong or weak correlations between these two parameters) may suggest information concerning the nucleation/growth processes. It allows one to follow the effect on the shape and size distribution of physical or chemical processes such as simple ripening. Various electron microscopy pictures from the literature or from the authors' own syntheses are used as examples to demonstrate the efficiency and simplicity of the proposed 2D plot combined with a multivariate analysis.

  17. A Comparative Analysis for Verification of IMRT and VMAT Treatment Plans using a 2-D and 3-D Diode Array

    NASA Astrophysics Data System (ADS)

    Dance, Michael J.

    With the added complexity of current radiation treatment dose delivery modalities such as IMRT (Intensity Modulated Radiation Therapy) and VMAT (Volumetric Modulated Arc Therapy), quality assurance (QA) of these plans become multifaceted and labor intensive. To simplify the patient specific quality assurance process, 2D or 3D diode arrays are used to measure the radiation fluence for IMRT and VMAT treatments which can then be quickly and easily compared against the planned dose distribution. Because the arrays that can be used for IMRT and VMAT patient-specific quality assurance are of different geometry (planar vs. cylindrical), the same IMRT or VMAT treatment plan measured by two different arrays could lead to different measured radiation fluences, regardless of the output and performance of linear accelerator. Thus, the purpose of this study is to compare patient specific QA results as measured by the MapCHECK 2 and ArcCHECK diode arrays for the same IMRT and VMAT treatment plans to see if one diode array consistently provides a closer comparison to reference data. Six prostate and three thoracic spine IMRT treatment plans as well as three prostate and three thoracic spine VMAT treatment plans were produced. Radiotherapy plans for this study were generated using the Pinnacle TPS v9.6 (Philips Radiation Oncology Systems, Fitchburg, WI) using 6 MV, 6 MV FFF, and 10 MV x-ray beams from a Varian TrueBeam linear accelerator (Varian Medical Systems, Palo Alto, CA) with a 120-millenium multi-leaf collimator (MLC). Each IMRT and VMAT therapy plan was measured on Sun Nuclear's MapCHECK 2 and ArcCHECK diode arrays. IMRT measured data was compared with planned dose distribution using Sun Nuclear's 3DVH quality assurance software program using gamma analysis and dose-volume histograms for target volumes and critical structures comparison. VMAT arc plans measured on the MapCHECK 2 and ArcCHECK were compared using beam-by-beam analysis with the gamma evaluation method with

  18. Parasitic extraction and magnetic analysis for transformers, inductors and igbt bridge busbar with maxwell 2d and maxwell 3d simulation

    NASA Astrophysics Data System (ADS)

    Zhang, Ning

    This thesis presents the parasitic extraction and magnetic analysis for transformers, inductors, and IGBT bridge busbars with Maxwell 2D and Maxwell 3D simulation. In the first chapter, the magnetic field of a transformer in Maxwell 2D is analyzed. The parasitic capacitance between each winding of the transformer are extracted by Maxwell 2D. According to the actual dimensions, the parasitic capacitances are calculated. The results are verified by comparing with the measurement results from 4395A impedance analyzer. In the second chapter, two CM inductors are simulated in Maxwell 3D. One is the conventional winding inductor, the other one is the proposed one. The magnetic field distributions of different winding directions are analyzed. The analysis is verified by the simulation result. The last chapter introduces a technique to analyze, extract, and measure the parasitic inductance of planar busbars. With this technique, the relationship between self-inductance and mutual-inductance is analyzed. Secondly, a total inductance is calculated based on the developed technique. Thirdly, the current paths and the inductance on a planar busbar are investigated with DC-link capacitors. Furthermore, the analysis of the inductance is addressed. Ansys Q3D simulation and analysis are presented. Finally, the experimental verification is shown by the S-parameter measurement.

  19. Differential Gel Electrophoresis (DIGE) Evaluation of Naphthoimidazoles Mode of Action: A Study in Trypanosoma cruzi Bloodstream Trypomastigotes

    PubMed Central

    Brunoro, Giselle Villa Flor; Faça, Vitor Marcel; Caminha, Marcelle Almeida; Ferreira, André Teixeira da Silva; Trugilho, Monique; de Moura, Kelly Cristina Gallan; Perales, Jonas; Valente, Richard Hemmi; Menna-Barreto, Rubem Figueiredo Sadok

    2016-01-01

    Background The obligate intracellular protozoan Trypanosoma cruzi is the causative agent of Chagas disease, a neglected illness affecting millions of people in Latin America that recently entered non-endemic countries through immigration, as a consequence of globalization. The chemotherapy for this disease is based mainly on benznidazole and nifurtimox, which are very efficient nitroderivatives against the acute stage but present limited efficacy during the chronic phase. Our group has been studying the trypanocidal effects of naturally occurring quinones and their derivatives, and naphthoimidazoles derived from β-lapachone N1, N2 and N3 were the most active. To assess the molecular mechanisms of action of these compounds, we applied proteomic techniques to analyze treated bloodstream trypomastigotes, which are the clinically relevant stage of the parasite. Methodology/Principal Findings The approach consisted of quantification by 2D-DIGE followed by MALDI-TOF/TOF protein identification. A total of 61 differentially abundant protein spots were detected when comparing the control with each N1, N2 or N3 treatment, for 34 identified spots. Among the differentially abundant proteins were activated protein kinase C receptor, tubulin isoforms, asparagine synthetase, arginine kinase, elongation factor 2, enolase, guanine deaminase, heat shock proteins, hypothetical proteins, paraflagellar rod components, RAB GDP dissociation inhibitor, succinyl-CoA ligase, ATP synthase subunit B and methionine sulfoxide reductase. Conclusion/Significance Our results point to different modes of action for N1, N2 and N3, which indicate a great variety of metabolic pathways involved and allow for novel perspectives on the development of trypanocidal agents. PMID:27551855

  20. Users manual for AUTOMESH-2D: A program of automatic mesh generation for two-dimensional scattering analysis by the finite element method

    NASA Technical Reports Server (NTRS)

    Hua, Chongyu; Volakis, John L.

    1990-01-01

    AUTOMESH-2D is a computer program specifically designed as a preprocessor for the scattering analysis of two dimensional bodies by the finite element method. This program was developed due to a need for reproducing the effort required to define and check the geometry data, element topology, and material properties. There are six modules in the program: (1) Parameter Specification; (2) Data Input; (3) Node Generation; (4) Element Generation; (5) Mesh Smoothing; and (5) Data File Generation.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  2. Analysis of Highly-Resolved Simulations of 2-D Humps Toward Improvement of Second-Moment Closures

    NASA Technical Reports Server (NTRS)

    Jeyapaul, Elbert; Rumsey Christopher

    2013-01-01

    Fully resolved simulation data of flow separation over 2-D humps has been used to analyze the modeling terms in second-moment closures of the Reynolds-averaged Navier- Stokes equations. Existing models for the pressure-strain and dissipation terms have been analyzed using a priori calculations. All pressure-strain models are incorrect in the high-strain region near separation, although a better match is observed downstream, well into the separated-flow region. Near-wall inhomogeneity causes pressure-strain models to predict incorrect signs for the normal components close to the wall. In a posteriori computations, full Reynolds stress and explicit algebraic Reynolds stress models predict the separation point with varying degrees of success. However, as with one- and two-equation models, the separation bubble size is invariably over-predicted.

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

    PubMed

    Zhang, Zepeng; Hu, Qian; Zhao, Yong

    2017-01-01

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

  4. Computer-aided 2D and 3D quantification of human stem cell fate from in vitro samples using Volocity high performance image analysis software.

    PubMed

    Piltti, Katja M; Haus, Daniel L; Do, Eileen; Perez, Harvey; Anderson, A J; Cummings, B J

    2011-11-01

    Accurate automated cell fate analysis of immunostained human stem cells from 2- and 3-dimensional (2D-3D) images would improve efficiency in the field of stem cell research. Development of an accurate and precise tool that reduces variability and the time needed for human stem cell fate analysis will improve productivity and interpretability of the data across research groups. In this study, we have created protocols for high performance image analysis software Volocity® to classify and quantify cytoplasmic and nuclear cell fate markers from 2D-3D images of human neural stem cells after in vitro differentiation. To enhance 3D image capture efficiency, we optimized the image acquisition settings of an Olympus FV10i® confocal laser scanning microscope to match our quantification protocols and improve cell fate classification. The methods developed in this study will allow for a more time efficient and accurate software based, operator validated, stem cell fate classification and quantification from 2D and 3D images, and yield the highest ≥94.4% correspondence with human recognized objects.

  5. Comparative Variable Temperature Studies of Polyamide II with a Benchtop Fourier Transform and a Miniature Handheld Near-Infrared Spectrometer Using 2D-COS and PCMW-2D Analysis.

    PubMed

    Unger, Miriam; Pfeifer, Frank; Siesler, Heinz W

    2016-07-01

    The main objective of this communication is to compare the performance of a miniaturized handheld near-infrared (NIR) spectrometer with a benchtop Fourier transform near-infrared (FT-NIR) spectrometer. Generally, NIR spectroscopy is an extremely powerful analytical tool to study hydrogen-bonding changes of amide functionalities in solid and liquid materials and therefore variable temperature NIR measurements of polyamide II (PAII) have been selected as a case study. The information content of the measurement data has been further enhanced by exploiting the potential of two-dimensional correlation spectroscopy (2D-COS) and the perturbation correlation moving window two-dimensional (PCMW2D) evaluation technique. The data provide valuable insights not only into the changes of the hydrogen-bonding structure and the recrystallization of the hydrocarbon segments of the investigated PAII but also in their sequential order. Furthermore, it has been demonstrated that the 2D-COS and PCMW2D results derived from the spectra measured with the miniaturized NIR instrument are equivalent to the information extracted from the data obtained with the high-performance FT-NIR instrument.

  6. Atom Probe Tomography Analysis of Ag Doping in 2D Layered Material (PbSe)5(Bi2Se3)3.

    PubMed

    Ren, Xiaochen; Singh, Arunima K; Fang, Lei; Kanatzidis, Mercouri G; Tavazza, Francesca; Davydov, Albert V; Lauhon, Lincoln J

    2016-10-12

    Impurity doping in two-dimensional (2D) materials can provide a route to tuning electronic properties, so it is important to be able to determine the distribution of dopant atoms within and between layers. Here we report the tomographic mapping of dopants in layered 2D materials with atomic sensitivity and subnanometer spatial resolution using atom probe tomography (APT). APT analysis shows that Ag dopes both Bi2Se3 and PbSe layers in (PbSe)5(Bi2Se3)3, and correlations in the position of Ag atoms suggest a pairing across neighboring Bi2Se3 and PbSe layers. Density functional theory (DFT) calculations confirm the favorability of substitutional doping for both Pb and Bi and provide insights into the observed spatial correlations in dopant locations.

  7. 2-D zymographic analysis of Broccoli (Brassica oleracea L. var. Italica) florets proteases: follow up of cysteine protease isotypes in the course of post-harvest senescence.

    PubMed

    Rossano, Rocco; Larocca, Marilena; Riccio, Paolo

    2011-09-01

    Zymographic analysis of Broccoli florets (Brassica oleracea L. var. Italica) revealed the presence of acidic metallo-proteases, serine proteases and cysteine proteases. Under conditions which were denaturing for the other proteases, the study was restricted to cysteine proteases. 2-D zymography, a technique that combines IEF and zymography was used to show the presence of 11 different cysteine protease spots with molecular mass of 44 and 47-48kDa and pIs ranging between 4.1 and 4.7. pI differences could be ascribed to different degrees of phosphorylation that partly disappeared in the presence of alkaline phosphatase. Post-harvest senescence of Broccoli florets was characterized by decrease in protein and chlorophyll contents and increase of protease activity. In particular, as determined by 2-D zymography, the presence of cysteine protease clearly increased during senescence, a finding that may represent a useful tool for the control of the aging process.

  8. A rapid and efficient 2D/3D nuclear segmentation method for analysis of early mouse embryo and stem cell image data.

    PubMed

    Lou, Xinghua; Kang, Minjung; Xenopoulos, Panagiotis; Muñoz-Descalzo, Silvia; Hadjantonakis, Anna-Katerina

    2014-03-11

    Segmentation is a fundamental problem that dominates the success of microscopic image analysis. In almost 25 years of cell detection software development, there is still no single piece of commercial software that works well in practice when applied to early mouse embryo or stem cell image data. To address this need, we developed MINS (modular interactive nuclear segmentation) as a MATLAB/C++-based segmentation tool tailored for counting cells and fluorescent intensity measurements of 2D and 3D image data. Our aim was to develop a tool that is accurate and efficient yet straightforward and user friendly. The MINS pipeline comprises three major cascaded modules: detection, segmentation, and cell position classification. An extensive evaluation of MINS on both 2D and 3D images, and comparison to related tools, reveals improvements in segmentation accuracy and usability. Thus, its accuracy and ease of use will allow MINS to be implemented for routine single-cell-level image analyses.

  9. Analysis of 2D Torus and Hub Topologies of 100Mb/s Ethernet for the Whitney Commodity Computing Testbed

    NASA Technical Reports Server (NTRS)

    Pedretti, Kevin T.; Fineberg, Samuel A.; Kutler, Paul (Technical Monitor)

    1997-01-01

    A variety of different network technologies and topologies are currently being evaluated as part of the Whitney Project. This paper reports on the implementation and performance of a Fast Ethernet network configured in a 4x4 2D torus topology in a testbed cluster of 'commodity' Pentium Pro PCs. Several benchmarks were used for performance evaluation: an MPI point to point message passing benchmark, an MPI collective communication benchmark, and the NAS Parallel Benchmarks version 2.2 (NPB2). Our results show that for point to point communication on an unloaded network, the hub and 1 hop routes on the torus have about the same bandwidth and latency. However, the bandwidth decreases and the latency increases on the torus for each additional route hop. Collective communication benchmarks show that the torus provides roughly four times more aggregate bandwidth and eight times faster MPI barrier synchronizations than a hub based network for 16 processor systems. Finally, the SOAPBOX benchmarks, which simulate real-world CFD applications, generally demonstrated substantially better performance on the torus than on the hub. In the few cases the hub was faster, the difference was negligible. In total, our experimental results lead to the conclusion that for Fast Ethernet networks, the torus topology has better performance and scales better than a hub based network.

  10. Analysis of amorphous solid dispersions using 2D solid-state NMR and (1)H T(1) relaxation measurements.

    PubMed

    Pham, Tran N; Watson, Simon A; Edwards, Andrew J; Chavda, Manisha; Clawson, Jacalyn S; Strohmeier, Mark; Vogt, Frederick G

    2010-10-04

    Solid-state NMR (SSNMR) can provide detailed structural information about amorphous solid dispersions of pharmaceutical small molecules. In this study, the ability of SSNMR experiments based on dipolar correlation, spin diffusion, and relaxation measurements to characterize the structure of solid dispersions is explored. Observation of spin diffusion effects using the 2D (1)H-(13)C cross-polarization heteronuclear correlation (CP-HETCOR) experiment is shown to be a useful probe of association between the amorphous drug and polymer that is capable of directly proving glass solution formation. Dispersions of acetaminophen and indomethacin in different polymers are examined using this approach, as well as (1)H double-quantum correlation experiments to probe additional structural features. (1)H-(19)F CP-HETCOR serves a similar role for fluorinated drug molecules such as diflunisal in dispersions, providing a rapid means to prove the formation of a glass solution. Phase separation is detected using (13)C, (19)F, and (23)Na-detected (1)H T(1) experiments in crystalline and amorphous solid dispersions that contain small domains. (1)H T(1) measurements of amorphous nanosuspensions of trehalose and dextran illustrate the ability of SSNMR to detect domain size effects in dispersions that are not glass solutions via spin diffusion effects. Two previously unreported amorphous solid dispersions involving up to three components and containing voriconazole and telithromycin are analyzed using these experiments to demonstrate the general applicability of the approach.

  11. [Identification and analysis of genuine and false Flos Rosae Rugosae by FTIR and 2D correlation IR spectroscopy].

    PubMed

    Cai, Fang; Sun, Su-qin; Yan, Wen-rong; Niu, Shi-jie; Li, Xian-en

    2009-09-01

    The genuine and false Flos Rosae Rugosae (Flos Rosae Chinensis and Flos Rosa multiflora) were examined in terms of their differences by using Fourier transform infrared spectroscopy (FTIR) combined with two-dimensional (2D) correlation IR spectroscopy. The three species were shown very similar in FTIR spectra. The peak of 1318 cm(-1) of genuine Flos Rosae Rugosae is not obvious but this peak could be found sharp in Flos Rosae Chinensis and Flos Rosa multiflora. Generally, the second derivative IR spectrum can clearly enhance the spectral resolution. Flos Rosae Rugosae and Flos rosae Chinensis have aromatic compounds distinct fingerprint characteristics at 1 617 and 1 618 cm(-1), respectively. Nevertheless, FlosRosa multiflora has the peak at 1612 cm(-1). There is a discrepancy of 5 to 6 cm(-1). FlosRosa multiflora has glucide's distinct fingerprint characteristics at 1 044 cm(-1), but Flos Rosae Rugosae and Flos Rosae Chinensis don't. The second derivative infrared spectra indicated different fingerprint characteristics. Three of them showed aromatic compounds with autopeaks at 1620, 1560 and 1460 cm(-1). Flos Rosae Chinensis and Flos Rosa multiflora have the shoulder peak at 1660 cm(-1). In the range of 850-1250 cm(-1), three of them are distinct different, Flos Rosae Rugosae has the strongest autopeak, Flos Rosae Chinensis has the feeble autopeak and Flos Rosa multiflora has no autopeak at 1050 cm(-1). In third-step identification, the different contents of aromatic compounds and glucide in Flos Rosae Rugosae, Flos Rosae Chinensis and Flos Rosa multiflora were revealed. It is proved that the method is fast and effective for distinguishing and analyzing genuine Flos Rosae Rugosae and false Flos Rosae Rugosae (Flos Rosae Chinensis and Flos Rosa multiflora).

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

    NASA Astrophysics Data System (ADS)

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

    2008-06-01

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

  13. Vertical 2D Heterostructures

    NASA Astrophysics Data System (ADS)

    Lotsch, Bettina V.

    2015-07-01

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

  14. A Fast One Step Extraction and UPLC-MS/MS Analysis for E2/D2 Series Prostaglandins and Isoprostanes

    PubMed Central

    Brose, Stephen A.; Baker, Andrew G.; Golovko, Mikhail Y.

    2013-01-01

    Prostaglandins (PG) and isoprostanes (iso-PG) may be derived through cyclooxygenase or free radical pathways and are important signaling molecules that are also robust biomarkers of oxidative stress. Their quantification is important for understanding many biological processes where PG, iso-PG, or oxidative stress are involved. One of the common methods for PG and iso-PG quantifications is LC-MS/MS that allows a highly selective, sensitive, simultaneous analysis for prostanoids without derivatization. However, the currently used LC-MS/MS methods require a multi-step extraction and a long (within an hour) LC separation to achieve simultaneous separation and analysis of the major iso-PG. The developed and validated for brain tissue analysis one-step extraction protocol and UPLC-MS/MS method significantly increases the recovery of the PG extraction up to 95%, and allows for a much faster (within 4 min) major iso-PGE2 and -PGD2 separation with 5 times narrower chromatographic peaks as compared to previously used methods. In addition, it decreases the time and cost of analysis due to one-step extraction approach performed in disposable centrifuge tubes. All together, this significantly increases the sensitivity, and the time and cost efficiency of the PG and iso-PG analysis. PMID:23400687

  15. RixsToolBox: software for the analysis of soft X-ray RIXS data acquired with 2D detectors.

    PubMed

    Kummer, K; Tamborrino, A; Amorese, A; Minola, M; Braicovich, L; Brookes, N B; Ghiringhelli, G

    2017-03-01

    A software with a graphical user interface has been developed with the aim of facilitating the data analysis for users of a new resonant inelastic X-ray scattering (RIXS) spectrometer installed at the ESRF beamline ID32. The software is organized in modules covering all relevant steps in the data reduction from a stack of several hundred two-dimensional CCD images to a single RIXS spectrum. It utilizes both full charge integration and single-photon centroiding to cope with high-flux and high-resolution requirements. Additional modules for further data analysis and the extraction of instrumental parameters are available. The software has been in routine use for about a year now and in that time many additional features have been incorporated. It now meets the users' need for an easy-to-use data analysis tool that allows looking at and understanding data as it is acquired and thus steering users' experiments more efficiently.

  16. 2D semiconductor optoelectronics

    NASA Astrophysics Data System (ADS)

    Novoselov, Kostya

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

  17. Hydrophobic cluster analysis: procedures to derive structural and functional information from 2-D-representation of protein sequences.

    PubMed

    Lemesle-Varloot, L; Henrissat, B; Gaboriaud, C; Bissery, V; Morgat, A; Mornon, J P

    1990-08-01

    Hydrophobic cluster analysis (HCA) [15] is a very efficient method to analyse and compare protein sequences. Despite its effectiveness, this method is not widely used because it relies in part on the experience and training of the user. In this article, detailed guidelines as to the use of HCA are presented and include discussions on: the definition of the hydrophobic clusters and their relationships with secondary and tertiary structures; the length of the clusters; the amino acid classification used for HCA; the HCA plot programs; and the working strategies. Various procedures for the analysis of a single sequence are presented: structural segmentation, structural domains and secondary structure evaluation. Like most sequence analysis methods, HCA is more efficient when several homologous sequences are compared. Procedures for the detection and alignment of distantly related proteins by HCA are described through several published examples along with 2 previously unreported cases: the beta-glucosidase from Ruminococcus albus is clearly related to the beta-glucosidases from Clostridum thermocellum and Hansenula anomala although they display a reverse organization of their constitutive domains; the alignment of the sequence of human GTPase activating protein with that of the Crk oncogene is presented. Finally, the pertinence of HCA in the identification of important residues for structure/function as well as in the preparation of homology modelling is discussed.

  18. High-throughput morphometric analysis of pulmonary airways in MSCT via a mixed 3D/2D approach

    NASA Astrophysics Data System (ADS)

    Ortner, Margarete; Fetita, Catalin; Brillet, Pierre-Yves; Pr"teux, Françoise; Grenier, Philippe

    2011-03-01

    Asthma and COPD are complex airway diseases with an increased incidence estimated for the next decade. Today, the mechanisms and relationships between airway structure/physiology and the clinical phenotype and genotype are not completely understood. We thus lack the tools to predict disease progression or therapeutic responses. One of the main causes is our limited ability to assess the complexity of airway diseases in large populations of patients with appropriate controls. Multi-slice computed tomography (MSCT) imaging opened the way to the non-invasive assessment of airway physiology and structure, but the use of such technology in large cohorts requires a high degree of automation of the measurements. This paper develops an investigation framework and the associated image quantification tools for high-throughput analysis of airways in MSCT. A mixed approach is proposed, combining 3D and cross-section measurements of the airway tree where the user-interaction is limited to the choice of the desired analysis patterns. Such approach relies on the fully-automated segmentation of the 3D airway tree, caliber estimation and visualization based on morphologic granulometry, central axis computation and tree segment selection, cross-section morphometry of airway lumen and wall, and bronchus longitudinal shape analysis for stenosis/bronciectasis detection and measure validation. The developed methodology has been successfully applied to a cohort of 96 patients from a multi-center clinical study of asthma control in moderate and persistent asthma.

  19. The chemical composition of animal cells reconstructed from 2D and 3D ToF-SIMS analysis

    NASA Astrophysics Data System (ADS)

    Breitenstein, D.; Rommel, C. E.; Stolwijk, J.; Wegener, J.; Hagenhoff, B.

    2008-12-01

    This paper gives an overview on the progress achieved in our lab within the last two years in the analysis of single cells and tissue-like cell layers by time-of-flight secondary ion mass spectrometry (ToF-SIMS). Basically two types of investigations were performed: on the one hand a two-dimensional imaging and on the other hand a three-dimensional microarea analysis. In both cases chemical fixation in combination with slow air-drying were used as easy sample preparation method. It was the goal of both approaches to identify the distribution of natural components as well as the localisation of xenobiotic fluorophors. In our experimental set-ups the distribution of phophatidylcholine and amino-acid signals were in line with the expectation. In contrast, the distribution of the fluorophor ethidiumhomodimer could only be detected within the two-dimensional imaging, whereas it was not detected in the three-dimensional analysis. Also four other fluorophors failed in the latter approach. Thus, in our hands the three-dimensional detection is to date limited to certain molecules with a comparably low mass and/or an intrinsical charge.

  20. 2-D difference gel electrophoresis approach to assess protein expression profiles in Bathymodiolus azoricus from Mid-Atlantic Ridge hydrothermal vents.

    PubMed

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

    2011-11-18

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

  1. Data of the recombination loss mechanisms analysis on Al2O3 PERC cell using PC1D and PC2D simulations.

    PubMed

    Huang, Haibing; Lv, Jun; Bao, Yameng; Xuan, Rongwei; Sun, Shenghua; Sneck, Sami; Li, Shuo; Modanese, Chiara; Savin, Hele; Wang, Aihua; Zhao, Jianhua

    2017-04-01

    This data article is related to our recently published article ('20.8% industrial PERC solar cell: ALD Al2O3 rear surface passivation, efficiency loss mechanisms analysis and roadmap to 24%', Huang et al., 2017 [1]) where we have presented a systematic evaluation of the overall cell processing and a cost-efficient industrial roadmap for PERC cells. Aside from the information already presented in Huang et al., 2017 [1], here we provide data related to Sectin 3 in Huang et al., 2017 [1] concerning the analysis of the recombination losses׳ mechanisms by PC1D V5.9 and PC2D simulations (Clugston and Basore, 1997, Basore and Cabanas-Holmen, 2011, Cabanas-Holmen and Basore, 2012 and Cabanas-Holmen and Basore, 2012.) [2], [3], [4], [5] on our current industrial Al2O3 PERC cell. The data include: i) PC2D simulations on J02, ii) the calculation of series resistance and back surface recombination velocity (BSRV) on the rear side metallization of PERC cell for the case of a point contact, and iii) the PC1D simulation on the cumulative photo-generation and recombination along the distance from the front surface. Finally, the roadmap of the solar cell efficiency for an industrial PERC technology up to 24% is presented, with the aim of providing a potential guideline for industrial researchers.

  2. A Model Based Cost-Effectiveness Analysis of Routine Genotyping for CYP2D6 among Older, Depressed Inpatients Starting Nortriptyline Pharmacotherapy

    PubMed Central

    Luttjeboer, Jos; Wilffert, Bob; Postma, Maarten J.

    2016-01-01

    Objective Genotyping for CYP2D6 has the potential to predict differences in metabolism of nortriptyline. This information could optimize pharmacotherapy. We determined the costs and effects of routine genotyping for old aged Dutch depressed inpatients. Methods With a decision-tree, we modelled the first 12 weeks of nortriptyline therapy. Direct costs of genotyping, hospitalization, therapeutic drug monitoring and drugs were included. Based on genotype, patients could be correctly, sub-, or supratherapeutically dosed. Improvement from sub- or supratherapeutically dosed patients to correctly dosed patients was simulated, assuming that genotyping would prevent under- or overdosing of patients. In the base case, this improvement was assumed to be 35%. A probabilistic sensitivity analysis (PSA) was performed to determine uncertainty around the incremental cost-effectiveness ratio (ICER). Results In the base case analysis, costs for genotyping were assumed €200 per test with a corresponding ICER at €1 333 000 per QALY. To reach a €50 000 per QALY cut-off, genotyping costs should be decreased towards €40 per test. At genotyping test costs < €35 per test, genotyping was dominant. At test costs of €17 per test there was a 95% probability that genotyping was cost-effective at €50 000 per QALY. Conclusions CYP2D6 genotyping was not cost-effective at current genotyping costs at a €50 000 per QALY threshold, however at test costs below €40, genotyping could be costs-effective. PMID:28033366

  3. Evaluation of Accuracy for 2D Elastic-Plastic Analysis by Embedded Force Doublet Model Combined with Automated Delaunay Tessellation

    NASA Astrophysics Data System (ADS)

    Ino, Takuichiro; Hasib, M. D. Abdul; Takase, Toru; Saimoto, Akihide

    2015-03-01

    An embedded force doublet (EFD) model is proposed to express the presence of permanent strain in body force method (BFM). BFM is known as a boundary type method for elastic stress analysis based on the principle of superposition. In EFD model, the permanent strain is replaced by distributed force doublets. In an actual elastic-plastic analysis, the plastic region whose shape is not clear a priori, have to be discretized into elements where the magnitude of embedded force doublets is unknown to be determined numerically. In general, the determination process of magnitude of EFD is considerably difficult due to nonlinear nature of yield criterion and plastic constitutive relations. In this study, by introducing the automated Delaunay tessellation scheme for discretizing the prospective plastic region, appreciable reduction in input data was realized. Adding to this, in order to improve the computational efficiency, influence coefficients used for determining the magnitude of EFD are stored in a database. The effectiveness of these two inventions was examined by computing the elastic-plastic problem of an infinite medium with circular hole subjected to uniform internal pressure. The numerical solution was compared with Nadai’s closed form solution and found a good agreement.

  4. Comparison of 2D Finite Element Modeling Assumptions with Results From 3D Analysis for Composite Skin-Stiffener Debonding

    NASA Technical Reports Server (NTRS)

    Krueger, Ronald; Paris, Isbelle L.; OBrien, T. Kevin; Minguet, Pierre J.

    2004-01-01

    The influence of two-dimensional finite element modeling assumptions on the debonding prediction for skin-stiffener specimens was investigated. Geometrically nonlinear finite element analyses using two-dimensional plane-stress and plane-strain elements as well as three different generalized plane strain type approaches were performed. The computed skin and flange strains, transverse tensile stresses and energy release rates were compared to results obtained from three-dimensional simulations. The study showed that for strains and energy release rate computations the generalized plane strain assumptions yielded results closest to the full three-dimensional analysis. For computed transverse tensile stresses the plane stress assumption gave the best agreement. Based on this study it is recommended that results from plane stress and plane strain models be used as upper and lower bounds. The results from generalized plane strain models fall between the results obtained from plane stress and plane strain models. Two-dimensional models may also be used to qualitatively evaluate the stress distribution in a ply and the variation of energy release rates and mixed mode ratios with delamination length. For more accurate predictions, however, a three-dimensional analysis is required.

  5. Comprehensive Analysis of the Membrane Phosphoproteome Regulated by Oligogalacturonides in Arabidopsis thaliana

    PubMed Central

    Mattei, Benedetta; Spinelli, Francesco; Pontiggia, Daniela; De Lorenzo, Giulia

    2016-01-01

    Early changes in the Arabidopsis thaliana membrane phosphoproteome in response to oligogalacturonides (OGs), a class of plant damage-associated molecular patterns (DAMPs), were analyzed by two complementary proteomic approaches. Differentially phosphorylated sites were determined through phosphopeptide enrichment followed by LC-MS/MS using label-free quantification; differentially phosphorylated proteins were identified by 2D-DIGE combined with phospho-specific fluorescent staining (phospho-DIGE). This large-scale phosphoproteome analysis of early OG-signaling enabled us to determine 100 regulated phosphosites using LC-MS/MS and 46 differential spots corresponding to 34 pdhosphoproteins using phospho-DIGE. Functional classification showed that the OG-responsive phosphoproteins include kinases, phosphatases and receptor-like kinases, heat shock proteins (HSPs), reactive oxygen species (ROS) scavenging enzymes, proteins related to cellular trafficking, transport, defense and signaling as well as novel candidates for a role in immunity, for which elicitor-induced phosphorylation changes have not been shown before. A comparison with previously identified elicitor-regulated phosphosites shows only a very limited overlap, uncovering the immune-related regulation of 70 phosphorylation sites and revealing novel potential players in the regulation of elicitor-dependent immunity. PMID:27532006

  6. Characterization of the isomeric configuration and impurities of (Z)-endoxifen by 2D NMR, high resolution LC⬜MS, and quantitative HPLC analysis.

    PubMed

    Elkins, Phyllis; Coleman, Donna; Burgess, Jason; Gardner, Michael; Hines, John; Scott, Brendan; Kroenke, Michelle; Larson, Jami; Lightner, Melissa; Turner, Gregory; White, Jonathan; Liu, Paul

    2014-01-01

    (Z)-Endoxifen (4-hydroxy-N-desmethyltamoxifen), an active metabolite generated via actions of CYP3A4/5 and CYP2D6, is a more potent selective estrogen receptor modulator (SERM) than tamoxifen. In the MCF-7 human mammary tumor xenograft model with female athymic mice, (Z)-endoxifen, at an oral dose of 4⬜8 mg/kg, significantly inhibits tumor growth. (Z)-Endoxifen's potential as an alternative therapeutic agent independent of CYP2D6 activities, which can vary widely in ER+ breast cancer patients, is being actively evaluated. This paper describes confirmation of the configuration of the active (Z)-isomer through 2D NMR experiments, including NOE (ROESY) to establish spatial proton⬜proton correlations, and identification of the major impurity as the (E)-isomer in endoxifen drug substance by HPLC/HRMS (HPLC/MS-TOF). Stability of NMR solutions was confirmed by HPLC/UV analysis. For pre-clinical studies, a reverse-phase HPLC⬜UV method, with methanol/water mobile phases containing 10 mM ammonium formate at pH 4.3, was developed and validated for the accurate quantitation and impurity profiling of drug substance and drug product. Validation included demonstration of linearity, method precision, accuracy, and specificity in the presence of impurities, excipients (for the drug product), and degradation products. Ruggedness and reproducibility of the method were confirmed by collaborative studies between two independent laboratories. The method is being applied for quality control of the API and oral drug product. Kinetic parameters of Z- to E-isomerization were also delineated in drug substance and in aqueous formulation, showing conversion at temperatures above 25 °C.

  7. Characterization of the isomeric configuration and impurities of (Z)-endoxifen by 2D NMR, high resolution LC–MS, and quantitative HPLC analysis

    PubMed Central

    Elkins, Phyllis; Coleman, Donna; Burgess, Jason; Gardner, Michael; Hines, John; Scott, Brendan; Kroenke, Michelle; Larson, Jami; Lightner, Melissa; Turner, Gregory; White, Jonathan; Liu, Paul

    2014-01-01

    (Z)-Endoxifen (4-hydroxy-N-desmethyltamoxifen), an active metabolite generated via actions of CYP3A4/5 and CYP2D6, is a more potent selective estrogen receptor modulator (SERM) than tamoxifen. In the MCF-7 human mammary tumor xenograft model with female athymic mice, (Z)-endoxifen, at an oral dose of 4– 8 mg/kg, significantly inhibits tumor growth. (Z)-Endoxifen's potential as an alternative therapeutic agent independent of CYP2D6 activities, which can vary widely in ER+ breast cancer patients, is being actively evaluated. This paper describes confirmation of the configuration of the active (Z)-isomer through 2D NMR experiments, including NOE (ROESY) to establish spatial proton–proton correlations, and identification of the major impurity as the (E)-isomer in endoxifen drug substance by HPLC/HRMS (HPLC/MS-TOF). Stability of NMR solutions was confirmed by HPLC/UV analysis. For pre-clinical studies, a reverse-phase HPLC–UV method, with methanol/water mobile phases containing 10 mM ammonium formate at pH 4.3, was developed and validated for the accurate quantitation and impurity profiling of drug substance and drug product. Validation included demonstration of linearity, method precision, accuracy, and specificity in the presence of impurities, excipients (for the drug product), and degradation products. Ruggedness and reproducibility of the method were confirmed by collaborative studies between two independent laboratories. The method is being applied for quality control of the API and oral drug product. Kinetic parameters of Z- to E-isomerization were also delineated in drug substance and in aqueous formulation, showing conversion at temperatures above 25 °C. PMID:24055701

  8. Extended multiscale finite element method for elasto-plastic analysis of 2D periodic lattice truss materials

    NASA Astrophysics Data System (ADS)

    Zhang, H. W.; Wu, J. K.; Fu, Z. D.

    2010-05-01

    An extended multiscale finite element method is developed for small-deformation elasto-plastic analysis of periodic truss materials. The base functions constructed numerically are employed to establish the relationship between the macroscopic displacement and the microscopic stress and strain. The unbalanced nodal forces in the micro-scale of unit cells are treated as the combined effects of macroscopic equivalent forces and microscopic perturbed forces, in which macroscopic equivalent forces are used to solve the macroscopic displacement field and microscopic perturbed forces are used to obtain the stress and strain in the micro-scale to make sure the correctness of the results obtained by the downscale computation in the elastic-plastic problems. Numerical examples are carried out and the results verify the validity and efficiency of the developed method by comparing it with the conventional finite element method.

  9. Self-diffusion of polycrystalline ice Ih under confining pressure: Hydrogen isotope analysis using 2-D Raman imaging

    NASA Astrophysics Data System (ADS)

    Noguchi, Naoki; Kubo, Tomoaki; Durham, William B.; Kagi, Hiroyuki; Shimizu, Ichiko

    2016-08-01

    We have developed a high-resolution technique based on micro Raman spectroscopy to measure hydrogen isotope diffusion profiles in ice Ih. The calibration curve for quantitative analysis of deuterium in ice Ih was constructed using micro Raman spectroscopy. Diffusion experiments using diffusion couples composed of dense polycrystalline H2O and D2O ice were carried out under a gas confining pressure of 100 MPa (to suppress micro-fracturing and pore formation) at temperatures from 235 K to 245 K and diffusion times from 0.2 to 94 hours. Two-dimensional deuterium profiles across the diffusion couples were determined by Raman imaging. The location of small spots of frost from room air could be detected from the shapes of the Raman bands of OH and OD stretching modes, which change because of the effect of the molar ratio of deuterium on the molecular coupling interaction. We emphasize the validity for screening the impurities utilizing the coupling interaction. Some recrystallization and grain boundary migration occurred in recovered diffusion couples, but analysis of two-dimensional diffusion profiles of regions not affected by grain boundary migration allowed us to measure a volume diffusivity for ice at 100 MPa of (2.8 ± 0.4) ×10-3exp[ -57.0 ± 15.4kJ /mol/RT ] m2 /s (R is the gas constant, T is temperature). Based on ambient pressure diffusivity measurements by others, this value indicates a high (negative) activation volume for volume diffusivity of -29.5 cm3/mol or more. We can also constrain the value of grain boundary diffusivity in ice at 100 MPa to be <104 that of volume diffusivity.

  10. Quantitative 2D liquid-state NMR.

    PubMed

    Giraudeau, Patrick

    2014-06-01

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

  11. Hyporheic Exchange: Analysis of Aquifer Heterogeneity, Channel Morphology and Bedforms- 2D and 3D Simulations Using MODFLOW and MODPATH

    NASA Astrophysics Data System (ADS)

    Matos, J. R.; Welty, C.; Packman, A.

    2005-12-01

    The main purpose of the simulations in this research is the analysis of three-dimensional surface-groundwater interchange in heterogeneous systems. The effects of channel pattern, bed forms and aquifer heterogeneity on flow interactions between stream and groundwater systems are examined in order to contribute for a better understanding of the hyporheic process. A two-dimensional approach was also adopted to allow comparisons with the three-dimensional results. The grid was designed using the correlation scales of the heterogeneous fields and the scale of the stream meanders. MODFLOW and MODPATH were used to evaluate magnitude, direction and spatial distribution of the exchange flow. PMWIN and PMPATH were used as pre and post-processors during the construction of the models and analysis of results. Gaining and losing streams as well as parallel flow and flow across streams were simulated as idealized cases intended to describe how properties of the streambed and aquifer in low-gradient lowland streams contribute to hyporheic exchange. At first a straight river was analyzed then meandering streams were created with a sine curve and variations on wavelength and amplitude. Bed forms were simulated assuming a sinusoidal distribution of pressure head in the bed surface. Aspects of the influence of bedforms on mechanisms such as "pumping" and "turnover" are expected to be addressed with simulations. Flow velocities between 20 and 40 cm/s in the channel were tested with the objective of showing the influence of river morphology and natural bed forms on the flow exchange in the hyporheic zone. Several meander cycles and four levels of hydraulic conductivity variance were analyzed. Results of flow variances along the cross-sections and wetted perimeter show the increasing on hyporheic exchange as the degree of heterogeneity increases. Particle tracking was performed to define hyporheic residence time distributions. When comparing the homogeneous fields with all degrees of

  12. ZORNOC: a 1 1/2-D tokamak data analysis code for studying noncircular high beta plasmas

    SciTech Connect

    Zurro, B.; Wieland, R.M.; Murakami, M.; Swain, D.W.

    1980-03-01

    A new tokamak data analysis code, ZORNOC, was developed to study noncircular, high beta plasmas in the Impurity Study Experiment (ISX-B). These plasmas exhibit significant flux surface shifts and elongation in both ohmically heated and beam-heated discharges. The MHD equilibrium flux surface geometry is determined by solving the Grad-Shafranov equation based on: (1) the shape of the outermost flux surface, deduced from the magnetic loop probes; (2) a pressure profile, deduced by means of Thomson scattering data (electrons), charge exchange data (ions), and a Fokker-Planck model (fast ions); and (3) a safety factor profile, determined from the experimental data using a simple model (Z/sub eff/ = const) that is self-consistently altered while the plasma equilibrium is iterated. For beam-heated discharches the beam deposition profile is determined by means of a Monte Carlo scheme and the slowing down of the fast ions by means of an analytical solution of the Fokker-Planck equation. The code also carries out an electron power balance and calculates various confinement parameters. The code is described and examples of its operation are given.

  13. Semi-automated 2D Bruch's membrane shape analysis in papilledema using spectral-domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Wang, Jui-Kai; Sibony, Patrick A.; Kardon, Randy H.; Kupersmith, Mark J.; Garvin, Mona K.

    2015-03-01

    Recent studies have shown that the Bruch's membrane (BM) and retinal pigment epithelium (RPE), visualized on spectral-domain optical coherence tomography (SD-OCT), is deformed anteriorly towards the vitreous in patients with intracranial hypertension and papilledema. The BM/RPE shape has been quantified using a statistical-shape-model approach; however, to date, the approach has involved the tedious and time-consuming manual placement of landmarks and correspondingly, only the shape (and shape changes) of a limited number of patients has been studied. In this work, we first present a semi-automated approach for the extraction of 20 landmarks along the BM from an optic-nerve-head (ONH) centered OCT slice from each patient. In the approach, after the manual placement of the two Bruch's membrane opening (BMO) points, the remaining 18 landmarks are automatically determined using a graph-based segmentation approach. We apply the approach to the OCT scans of 116 patients (at baseline) enrolled in the Idiopathic Intracranial Hypertension Treatment Trial and generate a statistical shape model using principal components analysis. Using the resulting shape model, the coefficient (shape measure) corresponding to the second principal component (eigenvector) for each set of landmarks indicates the degree of the BM/RPE is oriented away from the vitreous. Using a subset of 20 patients, we compare the shape measure computed using this semi-automated approach with the resulting shape measure when (1) all landmarks are specified manually (Experiment I); and (2) a different expert specifies the two BMO points (Experiment II). In each case, a correlation coefficient >= 0.99 is obtained.

  14. A model of adsorption of albumin on the implant surface titanium and titanium modified carbon coatings (MWCNT-EPD). 2D correlation analysis

    NASA Astrophysics Data System (ADS)

    Wesełucha-Birczyńska, Aleksandra; Stodolak-Zych, Ewa; Piś, Wojciech; Długoń, Elżbieta; Benko, Aleksandra; Błażewicz, Marta

    2016-11-01

    Common materials used as orthopedic implants are titanium and its alloys. To improve its compatibility with the environment of a living organism titanium implant surfaces are covered with bioactive layers of MWCNT. During the insertion into a living organism such material is exposed to direct contact with the patient's blood, which includes proteins - eg. albumin. The adsorption of albumin may constitute one of the early stages of implant surface modification serving cell adhesion. An analysis of this phenomenon in terms of the kinetics of deposition of protein on the surface of the implant confirms its biocompatibility in vivo. The proposed working model of the adsorption of albumin allows for choosing the best of time for the protein to form a stable connection with the surface of the titanium implant. Traditional methods of materials engineering and chemistry allow for the obtaining of information about the presence of a protein on the surface (UV-Vis, the wettability). The application of 2D correlation analysis, in turn, gains insight into the dynamics of the changes associated with the deposition of protein (the formation of a uniform layer, the change in conformation). This analysis has allowed for the selection of an optimal time of protein adsorption to the surface of the implant. Better compatibility with the body of the implant provides its modification by introducing layers that accelerate the material-tissue interactions. Such a composition is a layer of carbon nanotubes (MWCNTs) deposited on titanium by the electrophoretic (EPD) method. Using Raman spectroscopy and analyzing the spectra with the 2D correlation method it is possible to gain insight into the molecular structure of this layer. Our studies indicate that albumin in contact with the surface of titanium has obtained stable conformation after 30 min (confirmed by: UV-Vis, Raman). Shifts of the CH2, CH3 stretching bands position as well as an analysis of the amide I band confirms this

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  16. Analysis of tissue proteomes of the Gulf killifish, Fundulus grandis, by 2D electrophoresis and MALDI-TOF/TOF mass spectrometry.

    PubMed

    Abbaraju, Naga V; Boutaghou, Mohamed Nazim; Townley, Ian K; Zhang, Qiang; Wang, Guangdi; Cole, Richard B; Rees, Bernard B

    2012-11-01

    The Gulf killifish, Fundulus grandis, is a small teleost fish that inhabits marshes of the Gulf of Mexico and demonstrates high tolerance of environmental variation, making it an excellent subject for the study of physiological and molecular adaptations to environmental stress. In the present study, two-dimensional (2D) gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry were used to resolve and identify proteins from five tissues: skeletal muscle, liver, brain, heart, and gill. Of 864 protein features excised from 2D gels, 424 proteins were identified, corresponding to a 49% identification rate. For any given tissue, several protein features were identified as the same protein, resulting in a total of 254 nonredundant proteins. These nonredundant proteins were categorized into a total of 11 molecular functions, including catalytic activity, structural molecule, binding, and transport. In all tissues, catalytic activity and binding were the most highly represented molecular functions. Comparing across the tissues, proteome coverage was lowest in skeletal muscle, due to a combination of a low number of gel spots excised for analysis and a high redundancy of identifications among these spots. Nevertheless, the identification of a substantial number of proteins with high statistical confidence from other tissues suggests that F. grandis may serve as a model fish for future studies of environmental proteomics and ultimately help to elucidate proteomic responses of fish and other vertebrates to environmental stress.

  17. Application of rank-ordered multifractal analysis (ROMA) to intermittent fluctuations in 3D turbulent flows, 2D MHD simulation and solar wind data

    NASA Astrophysics Data System (ADS)

    Wu, C.; Chang, T.

    2010-12-01

    A new method in describing the multifractal characteristics of intermittent events was introduced by Cheng and Wu [Chang T. and Wu C.C., Physical Rev, E77, 045401(R), 2008]. The procedure provides a natural connection between the rank-ordered spectrum and the idea of one-parameter scaling for monofractals. This technique has been demonstrated using results obtained from a 2D MHD simulation. It has also been successfully applied to in-situ solar wind observations [Chang T., Wu, C.C. and Podesta, J., AIP Conf Proc. 1039, 75, 2008], and the broadband electric field oscillations from the auroral zone [Tam, S.W.Y. et al., Physical Rev, E81, 036414, 2010]. We take the next step in this procedure. By using the ROMA spectra and the scaled probability distribution functions (PDFs), raw PDFs can be calculated, which can be compared directly with PDFs from observations or simulation results. In addition to 2D MHD simulation results and in-situ solar wind observation, we show clearly using the ROMA analysis the multifractal character of the 3D fluid simulation data obtained from the JHU turbulence database cluster at http://turbulence.pha.jhu.edu. In particular, we show the scaling of the non-symmetrical PDF for the parallel-velocity fluctuations of this 3D fluid data.

  18. Hip2Norm: an object-oriented cross-platform program for 3D analysis of hip joint morphology using 2D pelvic radiographs.

    PubMed

    Zheng, G; Tannast, M; Anderegg, C; Siebenrock, K A; Langlotz, F

    2007-07-01

    We developed an object-oriented cross-platform program to perform three-dimensional (3D) analysis of hip joint morphology using two-dimensional (2D) anteroposterior (AP) pelvic radiographs. Landmarks extracted from 2D AP pelvic radiographs and optionally an additional lateral pelvic X-ray were combined with a cone beam projection model to reconstruct 3D hip joints. Since individual pelvic orientation can vary considerably, a method for standardizing pelvic orientation was implemented to determine the absolute tilt/rotation. The evaluation of anatomically morphologic differences was achieved by reconstructing the projected acetabular rim and the measured hip parameters as if obtained in a standardized neutral orientation. The program had been successfully used to interactively objectify acetabular version in hips with femoro-acetabular impingement or developmental dysplasia. Hip(2)Norm is written in object-oriented programming language C++ using cross-platform software Qt (TrollTech, Oslo, Norway) for graphical user interface (GUI) and is transportable to any platform.

  19. An analysis of electrochemical energy storage using electrodes fabricated from atomically thin 2D structures of MoS2, graphene and MoS2/graphene composites

    NASA Astrophysics Data System (ADS)

    Huffstutler, Jacob D.

    The behavior of 2D materials has become of great interest in the wake of development of electrochemical double-layer capacitors (EDLCs) and the discovery of monolayer graphene by Geim and Novoselov. This study aims to analyze the response variance of 2D electrode materials for EDLCs prepared through the liquid-phase exfoliation method when subjected to differing conditions. Once exfoliated, samples are tested with a series of structural characterization methods, including tunneling electron microscopy, atomic force microscopy, Raman spectroscopy, and x-ray photoelectron spectroscopy. A new ionic liquid for EDLC use, 1-butyl-1-methylpyrrolidinium tris(pentafluoroethyl)trifluorophosphate is compared in performance to 6M potassium hydroxide aqueous electrolyte. Devices composed of liquid-phase exfoliated graphene / MoS2 composites are analyzed by concentration for ideal performance. Device performance under cold extreme temperatures for the ionic fluid is presented as well. A brief overview of by-layer analysis of graphene electrode materials is presented as-is. All samples were tested with cyclic voltammetry, galvanostatic charge-discharge, and electrochemical impedance spectroscopy, with good capacitive results. The evolution of electrochemical behavior through the altered parameters is tracked as well.

  20. Performance analysis of junctionless double gate VeSFET considering the effects of thermal variation - An explicit 2D analytical model

    NASA Astrophysics Data System (ADS)

    Chaudhary, Tarun; Khanna, Gargi

    2017-03-01

    The purpose of this paper is to explore junctionless double gate vertical slit field effect transistor (JLDG VeSFET) with reduced short channel effects and to develop an analytical threshold voltage model for the device considering the impact of thermal variations for the very first time. The model has been derived by solving 2D Poisson's equation and the effects of variation in temperature on various electrical parameters of the device such as Rout, drain current, mobility, subthreshold slope and DIBL has been studied and described in the paper. The model provides a deep physical insight of the device behavior and is also very helpful in contributing to the design space exploration for JLDG VeSFET. The proposed model is verified with simulative analysis at different radii of the device and it has been observed that there is a good agreement between the analytical model and simulation results.

  1. Serum Proteome Analysis for Profiling Predictive Protein Markers Associated with the Severity of Skin Lesions Induced by Ionizing Radiation

    PubMed Central

    Chaze, Thibault; Hornez, Louis; Chambon, Christophe; Haddad, Iman; Vinh, Joelle; Peyrat, Jean-Philippe; Benderitter, Marc; Guipaud, Olivier

    2013-01-01

    The finding of new diagnostic and prognostic markers of local radiation injury, and particularly of the cutaneous radiation syndrome, is crucial for its medical management, in the case of both accidental exposure and radiotherapy side effects. Especially, a fast high-throughput method is still needed for triage of people accidentally exposed to ionizing radiation. In this study, we investigated the impact of localized irradiation of the skin on the early alteration of the serum proteome of mice in an effort to discover markers associated with the exposure and severity of impending damage. Using two different large-scale quantitative proteomic approaches, 2D-DIGE-MS and SELDI-TOF-MS, we performed global analyses of serum proteins collected in the clinical latency phase (days 3 and 7) from non-irradiated and locally irradiated mice exposed to high doses of 20, 40 and 80 Gy which will develop respectively erythema, moist desquamation and necrosis. Unsupervised and supervised multivariate statistical analyses (principal component analysis, partial-least square discriminant analysis and Random Forest analysis) using 2D-DIGE quantitative protein data allowed us to discriminate early between non-irradiated and irradiated animals, and between uninjured/slightly injured animals and animals that will develop severe lesions. On the other hand, despite a high number of animal replicates, PLS-DA and Random Forest analyses of SELDI-TOF-MS data failed to reveal sets of MS peaks able to discriminate between the different groups of animals. Our results show that, unlike SELDI-TOF-MS, the 2D-DIGE approach remains a powerful and promising method for the discovery of sets of proteins that could be used for the development of clinical tests for triage and the prognosis of the severity of radiation-induced skin lesions. We propose a list of 15 proteins which constitutes a set of candidate proteins for triage and prognosis of skin lesion outcomes. PMID:28250398

  2. Subclinical hypothyroidism and the risk of chronic kidney disease in T2D subjects: A case-control and dose-response analysis.

    PubMed

    Zhou, Jian-Bo; Li, Hong-Bing; Zhu, Xiao-Rong; Song, Hai-Lin; Zhao, Ying-Ying; Yang, Jin-Kui

    2017-04-01

    Evidence indicated a positive association between subclinical hypothyroidism (SCH) and cardiovascular diseases. But the relationship between SCH and chronic kidney diseases (CKD) remains unclear. A case-control study was performed to ascertain this relationship followed by a meta-analysis. In this hospital-based, case-control study, we recruited 3270 type 2 diabetic patients with euthyroidism and 545 type 2 diabetic patients with SCH. All English studies were searched upon the relationship between SCH and CKD up to October 2016. Meta-analysis was performed using STATA 13.0 software. Our case-control study indicated an association between SCH and CKD in patients with type 2 diabetes [OR (95% CI): 1.22 (1.09-1.36)]. Five observational studies reporting risk of CKD in SCH individuals were enrolled. A significant relationship between SCH and CKD was shown [pooled OR 1.80, (95% CI) 1.38-2.35]. Among normal TSH range, individuals with TSH ≥3.0 μIU/ml had a significantly higher rate of CKD (Fisher exact test, P = 0.027). Dose-response linear increase of CKD events was explored [pooled OR 1.09 (95% CI): 1.03-1.16 per1 mIU/L increase of TSH]. The present evidence suggests that SCH is probably a significant risk factor of CKD in T2D. Linear trend is shown between TSH elevation and CKD in T2D. This relationship between serum TSH and renal impairment in type 2 diabetic patients needs further studies to investigate.

  3. Analysis and Visualization of 2D and 3D Grain and Pore Size ofFontainebleau Sandstone Using Digital Rock Physics

    NASA Astrophysics Data System (ADS)

    Latief, FDE

    2016-08-01

    Fontainebleau sandstone is sandstone found in one of the cities in France. This sandstone has unique characteristics, which is a clean-fme sandstone, composed of 99% quartz, virtually devoid of clay, with the grain size of about 200 μm. Fontainebleau sandstone is widely used as a reference in the study of rock microstructure analysis and modelling. In this work analysis regarding the grain and pore size of Fontainebleau is presented. Calculation of 2D pore size and grain size distribution were done on the 299 slice of digital image of the Fontainebleau sandstone using Feret's diameters, equivalent diameters (d = 4A/P), and by means of local thickness/separation using plate model. For the 3D grain and pore size distribution, calculation of local thickness and local separation of the structure were used. Two dimensional analysis by means of Feret's diameter and equivalent diameter reveal that both grain and pore size distributions are in the form of reverse-J shaped (right skewed) while the local thickness/separation approach produces almost similar to symmetric Gaussian distribution. Three dimensional analysis produces fairly symmetric Gaussian distribution for both the grain and pore size. Further image processing were conducted and were succeed in producing three dimensional visual of the colour coded structure thickness (grain related) and structure separation (pore related).

  4. Performance Analysis of Error Probabilities for Arbitrary 2-D Signaling with I/Q Unbalances over Nakagami-m Fading Channels

    NASA Astrophysics Data System (ADS)

    Lee, Jaeyoon; Yoon, Dongweon; Park, Sang Kyu

    Recently, we provided closed-form expressions involving two-dimensional (2-D) joint Gaussian Q-function for the symbol error rate (SER) and bit error rate (BER) of an arbitrary 2-D signal with I/Q unbalances over an additive white Gaussian noise (AWGN) channel [1]. In this letter, we extend the expressions to Nakagami-m fading channels. Using Craig representation of the 2-D joint Gaussian Q-function, we derive an exact and general expression for the error probabilities of arbitrary 2-D signaling with I/Q phase and amplitude unbalances over Nakagami-m fading channels.

  5. A Comparative Analysis of 2D and 3D Tasks for Virtual Reality Therapies Based on Robotic-Assisted Neurorehabilitation for Post-stroke Patients

    PubMed Central

    Lledó, Luis D.; Díez, Jorge A.; Bertomeu-Motos, Arturo; Ezquerro, Santiago; Badesa, Francisco J.; Sabater-Navarro, José M.; García-Aracil, Nicolás

    2016-01-01

    Post-stroke neurorehabilitation based on virtual therapies are performed completing repetitive exercises shown in visual electronic devices, whose content represents imaginary or daily life tasks. Currently, there are two ways of visualization of these task. 3D virtual environments are used to get a three dimensional space that represents the real world with a high level of detail, whose realism is determinated by the resolucion and fidelity of the objects of the task. Furthermore, 2D virtual environments are used to represent the tasks with a low degree of realism using techniques of bidimensional graphics. However, the type of visualization can influence the quality of perception of the task, affecting the patient's sensorimotor performance. The purpose of this paper was to evaluate if there were differences in patterns of kinematic movements when post-stroke patients performed a reach task viewing a virtual therapeutic game with two different type of visualization of virtual environment: 2D and 3D. Nine post-stroke patients have participated in the study receiving a virtual therapy assisted by PUPArm rehabilitation robot. Horizontal movements of the upper limb were performed to complete the aim of the tasks, which consist in reaching peripheral or perspective targets depending on the virtual environment shown. Various parameter types such as the maximum speed, reaction time, path length, or initial movement are analyzed from the data acquired objectively by the robotic device to evaluate the influence of the task visualization. At the end of the study, a usability survey was provided to each patient to analysis his/her satisfaction level. For all patients, the movement trajectories were enhanced when they completed the therapy. This fact suggests that patient's motor recovery was increased. Despite of the similarity in majority of the kinematic parameters, differences in reaction time and path length were higher using the 3D task. Regarding the success rates

  6. A Comparative Analysis of 2D and 3D Tasks for Virtual Reality Therapies Based on Robotic-Assisted Neurorehabilitation for Post-stroke Patients.

    PubMed

    Lledó, Luis D; Díez, Jorge A; Bertomeu-Motos, Arturo; Ezquerro, Santiago; Badesa, Francisco J; Sabater-Navarro, José M; García-Aracil, Nicolás

    2016-01-01

    Post-stroke neurorehabilitation based on virtual therapies are performed completing repetitive exercises shown in visual electronic devices, whose content represents imaginary or daily life tasks. Currently, there are two ways of visualization of these task. 3D virtual environments are used to get a three dimensional space that represents the real world with a high level of detail, whose realism is determinated by the resolucion and fidelity of the objects of the task. Furthermore, 2D virtual environments are used to represent the tasks with a low degree of realism using techniques of bidimensional graphics. However, the type of visualization can influence the quality of perception of the task, affecting the patient's sensorimotor performance. The purpose of this paper was to evaluate if there were differences in patterns of kinematic movements when post-stroke patients performed a reach task viewing a virtual therapeutic game with two different type of visualization of virtual environment: 2D and 3D. Nine post-stroke patients have participated in the study receiving a virtual therapy assisted by PUPArm rehabilitation robot. Horizontal movements of the upper limb were performed to complete the aim of the tasks, which consist in reaching peripheral or perspective targets depending on the virtual environment shown. Various parameter types such as the maximum speed, reaction time, path length, or initial movement are analyzed from the data acquired objectively by the robotic device to evaluate the influence of the task visualization. At the end of the study, a usability survey was provided to each patient to analysis his/her satisfaction level. For all patients, the movement trajectories were enhanced when they completed the therapy. This fact suggests that patient's motor recovery was increased. Despite of the similarity in majority of the kinematic parameters, differences in reaction time and path length were higher using the 3D task. Regarding the success rates

  7. A Benchmarking Analysis for Five Radionuclide Vadose Zone Models (Chain, Multimed{_}DP, Fectuz, Hydrus, and Chain 2D) in Soil Screening Level Calculations

    SciTech Connect

    Chen, J-S.; Drake, R.; Lin, Z.; Jewett, D. G.

    2002-02-26

    Five vadose zone models with different degrees of complexity (CHAIN, MULTIMED{_}DP, FECTUZ, HYDRUS, and CHAIN 2D) were selected for use in radionuclide soil screening level (SSL) calculations. A benchmarking analysis between the models was conducted for a radionuclide ({sup 99}Tc) release scenario at the Las Cruces Trench Site in New Mexico. Sensitivity of three model outputs to the input parameters were evaluated and compared among the models. The three outputs were peak contaminant concentrations, time to peak concentrations at the water table, and time to exceed the contaminants maximum critical level at a representative receptor well. Model parameters investigated include soil properties such as bulk density, water content, soil water retention parameters and hydraulic conductivity. Chemical properties examined include distribution coefficient, radionuclide half-life, dispersion coefficient, and molecular diffusion. Other soil characteristics, such as recharge rate, also were examined. Model sensitivity was quantified in the form of sensitivity and relative sensitivity coefficients. Relative sensitivities were used to compare the sensitivities of different parameters. The analysis indicates that soil water content, recharge rate, saturated soil water content, and soil retention parameter, {beta}, have a great influence on model outputs. In general, the results of sensitivities and relative sensitivities using five models are similar for a specific scenario. Slight differences were observed in predicted peak contaminant concentrations due to different mathematical treatment among models. The results of benchmarking and sensitivity analysis would facilitate the model selection and application of the model in SSL calculations.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

    Direct quantitative chemical analysis with high lateral and vertical resolution of solid materials is of prime importance for the development of a wide variety of research fields, including e.g., astrobiology, archeology, mineralogy, electronics, among many others. Nowadays, studies carried out by complementary state-of-the-art analytical techniques such as Auger Electron Spectroscopy (AES), X-ray Photoelectron Spectroscopy (XPS), Secondary Ion Mass Spectrometry (SIMS), Glow Discharge Time-of-Flight Mass Spectrometry (GD-TOF-MS) or Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) provide extensive insight into the chemical composition and allow for a deep understanding of processes that might have fashioned the outmost layers of an analyte due to its interaction with the surrounding environment. Nonetheless, these investigations typically employ equipment that is not suitable for implementation on spacecraft, where requirements concerning weight, size and power consumption are very strict. In recent years Laser Ablation/Ionization Mass Spectrometry (LIMS) has re-emerged as a powerful analytical technique suitable not only for laboratory but also for space applications.[1-3] Its improved performance and measurement capabilities result from the use of cutting edge ultra-short femtosecond laser sources, improved vacuum technology and fast electronics. Because of its ultimate compactness, simplicity and robustness it has already proven to be a very suitable analytical tool for elemental and isotope investigations in space research.[4] In this contribution we demonstrate extended capabilities of our LMS instrument by means of three case studies: i) 2D chemical imaging performed on an Allende meteorite sample,[5] ii) depth profiling with unprecedented sub-nm vertical resolution on Cu electrodeposited interconnects[6,7] and iii) preliminary molecular desorption of polymers without assistance of matrix or functionalized substrates.[8] On the whole

  9. PCaAnalyser: A 2D-Image Analysis Based Module for Effective Determination of Prostate Cancer Progression in 3D Culture

    PubMed Central

    Lovitt, Carrie J.; Avery, Vicky M.

    2013-01-01

    Three-dimensional (3D) in vitro cell based assays for Prostate Cancer (PCa) research are rapidly becoming the preferred alternative to that of conventional 2D monolayer cultures. 3D assays more precisely mimic the microenvironment found in vivo, and thus are ideally suited to evaluate compounds and their suitability for progression in the drug discovery pipeline. To achieve the desired high throughput needed for most screening programs, automated quantification of 3D cultures is required. Towards this end, this paper reports on the development of a prototype analysis module for an automated high-content-analysis (HCA) system, which allows for accurate and fast investigation of in vitro 3D cell culture models for PCa. The Java based program, which we have named PCaAnalyser, uses novel algorithms that allow accurate and rapid quantitation of protein expression in 3D cell culture. As currently configured, the PCaAnalyser can quantify a range of biological parameters including: nuclei-count, nuclei-spheroid membership prediction, various function based classification of peripheral and non-peripheral areas to measure expression of biomarkers and protein constituents known to be associated with PCa progression, as well as defining segregate cellular-objects effectively for a range of signal-to-noise ratios. In addition, PCaAnalyser architecture is highly flexible, operating as a single independent analysis, as well as in batch mode; essential for High-Throughput-Screening (HTS). Utilising the PCaAnalyser, accurate and rapid analysis in an automated high throughput manner is provided, and reproducible analysis of the distribution and intensity of well-established markers associated with PCa progression in a range of metastatic PCa cell-lines (DU145 and PC3) in a 3D model demonstrated. PMID:24278197

  10. VIBA-Lab 3.0: Computer program for simulation and semi-quantitative analysis of PIXE and RBS spectra and 2D elemental maps

    NASA Astrophysics Data System (ADS)

    Orlić, Ivica; Mekterović, Darko; Mekterović, Igor; Ivošević, Tatjana

    2015-11-01

    VIBA-Lab is a computer program originally developed by the author and co-workers at the National University of Singapore (NUS) as an interactive software package for simulation of Particle Induced X-ray Emission and Rutherford Backscattering Spectra. The original program is redeveloped to a VIBA-Lab 3.0 in which the user can perform semi-quantitative analysis by comparing simulated and measured spectra as well as simulate 2D elemental maps for a given 3D sample composition. The latest version has a new and more versatile user interface. It also has the latest data set of fundamental parameters such as Coster-Kronig transition rates, fluorescence yields, mass absorption coefficients and ionization cross sections for K and L lines in a wider energy range than the original program. Our short-term plan is to introduce routine for quantitative analysis for multiple PIXE and XRF excitations. VIBA-Lab is an excellent teaching tool for students and researchers in using PIXE and RBS techniques. At the same time the program helps when planning an experiment and when optimizing experimental parameters such as incident ions, their energy, detector specifications, filters, geometry, etc. By "running" a virtual experiment the user can test various scenarios until the optimal PIXE and BS spectra are obtained and in this way save a lot of expensive machine time.

  11. Novel TOPP descriptors in 3D-QSAR analysis of apoptosis inducing 4-aryl-4H-chromenes: comparison versus other 2D- and 3D-descriptors.

    PubMed

    Sciabola, Simone; Carosati, Emanuele; Cucurull-Sanchez, Lourdes; Baroni, Massimo; Mannhold, Raimund

    2007-10-01

    Novel 3D-descriptors using Triplets Of Pharmacophoric Points (TOPP) were evaluated in QSAR-studies on 80 apoptosis-inducing 4-aryl-4H-chromenes. A predictive QSAR model was obtained using PLS, confirmed by means of internal and external validations. Performance of the TOPP approach was compared with that of other 2D- and 3D-descriptors; statistical analysis indicates that TOPP descriptors perform best. A ranking of TOPP>GRIND>BCI 4096=ECFP>FCFP>GRID-GOLPE>DRAGON>MDL 166 was achieved. Finally, in a 'consensus' analysis predictions obtained using the single methods were compared with an average approach using six out of eight methods. The use of the average is statistically superior to the single methods. Beyond it, the use of several methods can help to easily investigate the presence/absence of outliers according to the 'consensus' of the predicted values: agreement among all the methods indicates a precise prediction, whereas large differences between predicted values (for the same compounds by different methods) would demand caution when using such predictions.

  12. Structural requirements of 3-carboxyl-4(1H)-quinolones as potential antimalarials from 2D and 3D QSAR analysis.

    PubMed

    Li, Jiazhong; Li, Shuyan; Bai, Chongliang; Liu, Huanxiang; Gramatica, Paola

    2013-07-01

    Malaria is a fatal tropical and subtropical disease caused by the protozoal species Plasmodium. Many commonly available antimalarial drugs and therapies are becoming ineffective because of the emergence of multidrug resistant Plasmodium falciparum, which drives the need for the development of new antimalarial drugs. Recently, a series of 3-carboxyl-4(1H)-quinolone analogs, derived from the famous compound endochin, were reported as promising candidates for orally efficacious antimalarials. In this study, to analyze the structure-activity relationships (SAR) of these quinolones and investigate the structural requirements for antimalarial activity, the 2D multiple linear regressions (MLR) method and 3D comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods are employed to evolve different QSAR models. All these models give satisfactory results with highly accurate fitting and strong external predictive abilities for chemicals not used in model development. Furthermore, the contour maps from 3D models can provide an intuitive understanding of the key structure features responsible for the antimalarial activities. In conclusion, we summarize the detailed position-specific structural requirements of these derivatives accordingly. All these results are helpful for the rational design of new compounds with higher antimalarial bioactivities.

  13. Comparative proteomics profile of osteoblasts cultured on dissimilar hydroxyapatite biomaterials: an iTRAQ-coupled 2-D LC-MS/MS analysis.

    PubMed

    Xu, Jinling; Khor, Khiam Aik; Sui, Jianjun; Zhang, Jianhua; Tan, Tuan Lin; Chen, Wei Ning

    2008-10-01

    Hydroxyapatite (HA) and its derived bioceramic materials have been widely used for skeletal implants and/or bone repair scaffolds. It has been reported that carbon nanotube (CNT) is able to enhance the brittle ceramic matrix without detrimental to the bioactivity. However, interaction between osteoblasts and these bioceramics, as well as the underlying mechanism of osteoblast proliferation on these bioceramic surfaces remain to be determined. Using iTRAQ-coupled 2-D LC-MS/MS analysis, we report the first comparative proteomics profiling of human osteoblast cells cultured on plane HA and CNT reinforced HA, respectively. Cytoskeletal proteins, metabolic enzymes, signaling, and cell growth proteins previous associated with cell adhesion and proliferation were found to be differentially expressed on these two surfaces. The level of these proteins was generally higher in cells adhered to HA surface, indicating a higher level of cellular proliferation in these cells. The significance of these findings was further assessed by Western blot analysis. The differential protein profile in HA and CNT strengthened HA established in our study should be valuable for future design of biocompatible ceramics.

  14. Enhanced dietary formulation to mitigate winter thermal stress in gilthead sea bream (Sparus aurata): a 2D-DIGE plasma proteome study.

    PubMed

    Schrama, Denise; Richard, Nadège; Silva, Tomé S; Figueiredo, Filipe A; Conceição, Luís E C; Burchmore, Richard; Eckersall, David; Rodrigues, Pedro M L

    2016-11-24

    Low water temperatures during winter are common in farming of gilthead sea bream in the Mediterranean. This causes metabolic disorders that in extreme cases can lead to a syndrome called "winter disease." An improved immunostimulatory nutritional status might mitigate the effects of this thermal metabolic stress. A trial was set up to assess the effects of two different diets on gilthead sea bream physiology and nutritional state through plasma proteome and metabolites. Four groups of 25 adult gilthead sea bream were reared during winter months, being fed either with a control diet (CTRL) or with a diet called "winter feed" (WF). Proteome results show a slightly higher number of proteins upregulated in plasma of fish fed the WF. These proteins are mostly involved in the immune system and cell protection mechanisms. Lipid metabolism was also affected, as shown both by plasma proteome and by the cholesterol plasma levels. Overall, the winter feed diet tested seems to have positive effects in terms of fish condition and nutritional status, reducing the metabolic effects of thermal stress.

  15. MTCLAB: A MATLAB ®-based program for traveltime quality analysis and pre-inversion velocity tuning in 2D transmission tomography

    NASA Astrophysics Data System (ADS)

    Fernández-Martínez, J. L.; Fernández-Alvarez, J. P.; Pedruelo-González, L. M.

    2008-03-01

    A MATLAB ®-based computer code that analyses the traveltime distribution and performs quality analysis at the pre-inversion stage for 2D transmission experiments is presented. The core tools of this approach are the so-called mean traveltime curves. For any general recording geometry, the user may select any pair of subsets of contiguous sources and receivers. The portion of the domain swept by the implied rays defines a zone of analysis, and for each source (receiver) the outcoming (incoming) ray fan is named a source (receiver) gather. The empirical mean traveltime curves are constructed, for each zone, by assigning the average and the standard deviation of the traveltimes in the gathers to the positions of the sources (receivers). The theoretical expressions assume isotropic homogeneous velocity inside each zone. The empirical counterparts use the observed traveltimes and make no assumptions. Isotropic velocity in each zone is inferred by least-squares fitting of the empirical mean traveltime curves. The user may refine the analysis considering different zones (multi-zone analysis). Initially the whole domain is modelled as a single zone. The procedure compares empirical versus theoretical curves. In addition, residuals can be plotted using source-receiver positions as plane coordinates. The results are used to unravel the possible presence of anomalous gathers, heterogeneities, anisotropies, etc. Depending on the kind of anomalies, velocity estimation and mean time residuals are different in the source and receiver gather curves. This software helps to grasp a better understanding of the data variability before the inversion and provides to the geophysicist an approximate zonal isotropic model and a range of velocity variation that can be used in the inverse problem as a priori information (regularization term). Its use is described through tutorial examples. A guided user interface leads the user through the algorithm steps.

  16. Simultaneous extraction of nucleic acids and proteins from tissue specimens by ultracentrifugation: A protocol using the high-salt protein fraction for quantitative proteome analysis.

    PubMed

    Grzendowski, Michael; Riemenschneider, Markus J; Hawranke, Eva; Stefanski, Anja; Meyer, Helmut E; Reifenberger, Guido; Stühler, Kai

    2009-11-01

    Comprehensive molecular profiling of human tumor tissue specimens at the DNA, mRNA and protein level is often obstructed by a limited amount of available material. Homogenization of frozen tissue samples in guanidine isothiocyanate followed by ultracentrifugation over cesium chloride allows the simultaneous extraction of high-molecular weight DNA and RNA. Here, we present a protocol for quantitative proteome analysis using the high-salt protein fraction obtained as supernatant after ultracentrifugation for nucleic acid extraction. We applied this method to extracts from primary human brain tumors and demonstrate its successful application for protein expression profiling in these tumors using 2-D DIGE, MS and Western blotting.

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

    DTIC Science & Technology

    2015-12-01

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

  18. 2-d Finite Element Code Postprocessor

    SciTech Connect

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

    1996-07-15

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

  19. MO-F-CAMPUS-J-05: Using 2D Relative Gamma Analysis From EPID Image as a Predictor of Plan Deterioration Due to Anatomical Changes

    SciTech Connect

    Piron, O; Varfalvy, N; Archambault, L

    2015-06-15

    Purpose: One of the side effects of radiotherapy for head and neck (H&N) cancer is the patient’s anatomical changes. The changes can strongly affect the planned dose distribution. In this work, our goal is to demonstrate that relative analysis of EPID images is a fast and simple method to detect anatomical changes that can have a strong dosimetric impact on the treatment plan for H&N patients. Methods: EPID images were recorded at every beam and all fractions for 50 H&N patients. Of these, five patients that showed important anatomical changes were selected to evaluate dosimetric impacts of these changes and to correlate them with a 2D relative gamma analysis of EPID images. The planning CT and original contours were deformed onto CBCTs (one mid treatment and one at the end of treatment). By using deformable image registration, it was possible to map accurate CT numbers from the planning CT to the anatomy of the day obtained with CBCTs. Clinical treatment plan were then copied on the deformed dataset and dose was re-computed. In parallel, EPID images were analysed using the gamma index (3%3mm) relative to the first image. Results: It was possible to divide patients in two distinct, statistically different (p<0.001) categories using an average gamma index of 0.5 as a threshold. Below this threshold no significant dosimetric degradation of the plan are observed. Above this threshold two types of plan deterioration were seen: (1) target dose increases, but coverage remains adequate while dose to at least one OAR increases beyond tolerances; (2) the OAR doses remain low, but the target dose is reduced and coverage becomes inadequate. Conclusion: Relative analysis gamma of EPID images could indeed be a fast and simple method to detect anatomical changes that can potentially deteriorates treatment plan for H&N patients. This work was supported in part by Varian Medical System.

  20. Automated screening of 2D crystallization trials using transmission electron microscopy: a high-throughput tool-chain for sample preparation and microscopic analysis.

    PubMed

    Coudray, Nicolas; Hermann, Gilles; Caujolle-Bert, Daniel; Karathanou, Argyro; Erne-Brand, Françoise; Buessler, Jean-Luc; Daum, Pamela; Plitzko, Juergen M; Chami, Mohamed; Mueller, Urs; Kihl, Hubert; Urban, Jean-Philippe; Engel, Andreas; Rémigy, Hervé-W

    2011-02-01

    We have built and extensively tested a tool-chain to prepare and screen two-dimensional crystals of membrane proteins by transmission electron microscopy (TEM) at room temperature. This automated process is an extension of a new procedure described recently that allows membrane protein 2D crystallization in parallel (Iacovache et al., 2010). The system includes a gantry robot that transfers and prepares the crystalline solutions on grids suitable for TEM analysis and an entirely automated microscope that can analyze 96 grids at once without human interference. The operation of the system at the user level is solely controlled within the MATLAB environment: the commands to perform sample handling (loading/unloading in the microscope), microscope steering (magnification, focus, image acquisition, etc.) as well as automatic crystal detection have been implemented. Different types of thin samples can efficiently be screened provided that the particular detection algorithm is adapted to the specific task. Hence, operating time can be shared between multiple users. This is a major step towards the integration of transmission electron microscopy into a high throughput work-flow.

  1. A 2-D hydro-morphodynamic modelling approach for predicting suspended sediment propagation and related heavy metal contamination in floodplain: a sensitivity analysis

    NASA Astrophysics Data System (ADS)

    Hostache, R.; Hissler, C.; Matgen, P.; Guignard, C.; Bates, P.

    2014-02-01

    Fine sediments represent an important vector of pollutant diffusion in rivers. When deposited in floodplains and riverbeds they can be responsible for soil pollution. In this context, this paper proposes a hydro-morphodynamic modelling exercise aiming at predicting transport and diffusion of fine sediments and dissolved pollutants. The model is based upon the Telemac hydro-informatic system (dynamical coupling Telemac-2D-Sysiphe). As empirical and semi-empirical parameters need to be calibrated for such a modelling exercise, a sensitivity analysis is proposed. In parallel to the modelling exercise, an extensive hydrological/geochemical database has been set up during two flood events. The main sensitive parameters were found to be the hydraulic friction coefficient and the sediment particle settling velocity in water. Using the two monitored hydrological events as calibration and validation, it was found that the model is able to satisfyingly predict suspended sediment and dissolve pollutant transport in the river channel. In addition, a qualitative comparison between simulated sediment deposition in the floodplain and a soil contamination map shows that the preferential zones for deposition identified by the model are realistic.

  2. Large-scale flooding analysis in the suburbs of Tokyo Metropolis caused by levee breach of the Tone River using a 2D hydrodynamic model.

    PubMed

    Hai, Pham T; Magome, J; Yorozuya, A; Inomata, H; Fukami, K; Takeuchi, K

    2010-01-01

    In order to assess the effects of climate change on flood disasters in urban areas, we applied a two dimensional finite element hydrodynamic model (2D-FEM) to simulate flood processes for the case analysis of levee breach caused by Kathleen Typhoon on 16 September 1947 in Kurihashi reach of Tone River, upstream of Tokyo area. The purpose is to use the model to simulate flood inundation processes under the present topography and land-use conditions with impending extreme flood scenarios due to climate change for mega-urban areas like Tokyo. Simulation used 100 m resolution topographic data (in PWRI), which was derived from original LiDAR (Light Detection and Ranging) data, and levee breach hydrographic data in 1947. In this paper, we will describe the application of the model with calibration approach and techniques when applying for such fine spatial resolution in urban environments. The fine unstructured triangular FEM mesh of the model appeared to be the most capable of introducing of constructions like roads/levees in simulations. Model results can be used to generate flood mapping, subsequently uploaded to Google Earth interface, making the modeling and presentation process much comprehensible to the general public.

  3. Inversion of TEM data and analysis of the 2D induced magnetic field applied to the aquifers characterization in the Paraná basin, Brazil

    NASA Astrophysics Data System (ADS)

    Realpe Campaña, Julian David; Porsani, Jorge Luís; Bortolozo, Cassiano Antonio; Serejo de Oliveira, Gabriela; Monteiro dos Santos, Fernando Acácio

    2017-03-01

    Results of a TEM profile by using the fixed-loop array and an analysis of the induced magnetic field are presented in this work performed in the northwest region of São Paulo State, Brazil, Paraná Basin. The objectives of this research were to map the sedimentary and crystalline aquifers in the area and analyzing the behavior of the magnetic field by observation of magnetic profiles. TEM measurements in the three spatial components were taken to create magnetic profiles of the induced (secondary) magnetic field. The TEM data were acquired using a fixed transmitter loop of 200 m × 200 m and a 3D coil receiver moving along a profile line of 1000 m. Magnetic profiles of dBz, dBx and dBy components showed symmetrical spatial behavior related with loop geometry. z-component showed a behavior probably related to superparamagnetic effect (SPM). dBz data was used to perform individual 1D inversion for each position and to generate an interpolated pseudo-2D geoelectric profile. The results showed two low resistivity zones: the first shallow, between 10 m and 70 m deep, probably related to the Adamantina Formation (sedimentary aquifer). The second between 200 m and 300 m depth, probably related to a fractured zone filled with water or clay inside the basalt layer of the Serra Geral Formation (crystalline aquifer). These results agree with the well logs information available in the studied region.

  4. Effects of coffee bean aroma on the rat brain stressed by sleep deprivation: a selected transcript- and 2D gel-based proteome analysis.

    PubMed

    Seo, Han-Seok; Hirano, Misato; Shibato, Junko; Rakwal, Randeep; Hwang, In Kyeong; Masuo, Yoshinori

    2008-06-25

    The aim of this study was 2-fold: (i) to demonstrate influences of roasted coffee bean aroma on rat brain functions by using the transcriptomics and proteomics approaches and (ii) to evaluate the impact of roasted coffee bean aroma on stress induced by sleep deprivation. The aroma of the roasted coffee beans was administered to four groups of adult male Wistar rats: 1, control group; 2, 24 h sleep deprivation-induced stress group (the stress group); 3, coffee aroma-exposed group without stress (the coffee group); and 4, the stress with coffee aroma group (the stress with coffee group). Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of some known genes responsive to aroma or stress was performed using total RNA from these four groups. A total of 17 selected genes of the coffee were differently expressed over the control. Additionally, the expression levels of 13 genes were different between the stress group and the stress with coffee group: Up-regulation was found for 11 genes, and down-regulation was seen for two genes in the stress with coffee group. We also looked to changes in protein profiles in these four samples using two-dimensional (2D) gel electrophoresis; 25 differently expressed gel spots were detected on 2D gels stained by silver nitrate. Out of these, a total of nine proteins were identified by mass spectrometry. Identified proteins belonged to five functional categories: antioxidant; protein fate; cell rescue, defense, and virulence; cellular communication/signal transduction mechanism; and energy metabolism. Among the differentially expressed genes and proteins between the stress and the stress with coffee group, NGFR, trkC, GIR, thiol-specific antioxidant protein, and heat shock 70 kDa protein 5 are known to have antioxidant or antistress functions. In conclusion, the roasted coffee bean aroma changes the mRNA and protein expression levels of the rat brain, providing for the first time clues to the potential antioxidant or stress

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

    PubMed

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

    2015-11-01

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

  6. Influences of CYP2D6*10 polymorphisms on the pharmacokinetics of iloperidone and its metabolites in Chinese patients with schizophrenia: a population pharmacokinetic analysis

    PubMed Central

    Pei, Qi; Huang, Lu; Huang, Jie; Gu, Jing-kai; Kuang, Yun; Zuo, Xiao-cong; Ding, Jun-jie; Tan, Hong-yi; Guo, Cheng-xian; Liu, Shi-kun; Yang, Guo-ping

    2016-01-01

    Aim: Iloperidone is an atypical antipsychotic drug that is mainly metabolized by CYP2D6, CYP3A4, and cytosolic enzymes. Previous studies show that extensive and poor metabolizers of CYP2D6 exhibit different plasma concentrations of iloperidone and its metabolites. The aim of this study was to develop a parent-metabolite population pharmacokinetic (PPK) model to quantify the effects of CYP2D6*10 allele on the pharmacokinetics of iloperidone and its metabolites in Chinese schizophrenia patients. Methods: Seventy Chinese schizophrenia patients were enrolled, from whom limited blood samples were collected on d 15 (0 h) and d 28 (0, 4 and 12 h after drug administration). The plasma concentrations of iloperidone and its metabolites M1 (P-88) and M2 (P-95) were simultaneously detected using a validated HPLC-MS assay. CYP2D6*10 (rs1065852) genotyping was performed. A PPK model was developed based on data from the patients using the NONMEM software (version 7.2). A one-compartment model with first-order absorption and elimination was used to describe the pharmacokinetic data related to iloperidone and its metabolites. Results: Patients with the CYP2D6*10 T/T genotype had significantly higher concentrations of iloperidone and M1, and lower concentrations of M2 than the patients with C/C or C/T genotypes. The CYP2D6*10 genotype affected the elimination constants for transformation of iloperidone to the metabolites M1 (K23) and M2 (K24). The K23 value of the patients with T/T genotype was 1.34-fold as great as that of the patients with C/C or C/T genotype. The K24 value of the patients with C/T and T/T genotypes was 0.693- and 0.492-fold, respectively, as low as that of the patients with C/C genotype. Conclusion: CYP2D6*10 mutations affect the pharmacokinetics of iloperidone and its metabolites in Chinese schizophrenia patients, suggesting that the clinical doses of iloperidone for patients with CYP2D6*10 mutations need to be optimized. PMID:27665849

  7. 2D design rule and layout analysis using novel large-area first-principles-based simulation flow incorporating lithographic and stress effects

    NASA Astrophysics Data System (ADS)

    Prins, Steven L.; Blatchford, James; Olubuyide, Oluwamuyiwa; Riley, Deborah; Chang, Simon; Hong, Qi-Zhong; Kim, T. S.; Borges, Ricardo; Lin, Li

    2009-03-01

    As design rules and corresponding logic standard cell layouts continue to shrink node-on-node in accordance with Moore's law, complex 2D interactions, both intra-cell and between cells, become much more prominent. For example, in lithography, lack of scaling of λ/NA implies aggressive use of resolution enhancement techniques to meet logic scaling requirements-resulting in adverse effects such as 'forbidden pitches'-and also implies an increasing range of optical influence relative to cell size. These adverse effects are therefore expected to extend well beyond the cell boundary, leading to lithographic marginalities that occur only when a given cell is placed "in context" with other neighboring cells in a variable design environment [1]. This context dependence is greatly exacerbated by increased use of strain engineering techniques such as SiGe and dual-stress liners (DSL) to enhance transistor performance, both of which also have interaction lengths on the order of microns. The use of these techniques also breaks the formerly straightforward connection between lithographic 'shapes' and end-of-line electrical performance, thus making the formulation of design rules that are robust to process variations and complex 2D interactions more difficult. To address these issues, we have developed a first-principles-based simulation flow to study contextdependent electrical effects in layout, arising not only from lithography, but also from stress and interconnect parasitic effects. This flow is novel in that it can be applied to relatively large layout clips- required for context-dependent analysis-without relying on semi-empirical or 'black-box' models for the fundamental electrical effects. The first-principles-based approach is ideal for understanding contextdependent effects early in the design phase, so that they can be mitigated through restrictive design rules. The lithographic simulations have been discussed elsewhere [1] and will not be presented in detail. The

  8. Comparative analysis of excretory-secretory antigens of Trichinella spiralis and Trichinella britovi muscle larvae by two-dimensional difference gel electrophoresis and immunoblotting

    PubMed Central

    2012-01-01

    Background 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. Results 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. Conclusions 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

  9. The effect of excitation and preparation pulses on nonslice selective 2D UTE bicomponent analysis of bound and free water in cortical bone at 3T

    SciTech Connect

    Li, Shihong; Chang, Eric Y.; Chung, Christine B.; Bae, Won C.; Du, Jiang; Hua, Yanqing; Zhou, Yi

    2014-02-15

    Purpose: The purpose of this study was to investigate the effect of excitation, fat saturation, long T2 saturation, and adiabatic inversion pulses on ultrashort echo time (UTE) imaging with bicomponent analysis of bound and free water in cortical bone for potential applications in osteoporosis. Methods: Six bovine cortical bones and six human tibial midshaft samples were harvested for this study. Each bone sample was imaged with eight sequences using 2D UTE imaging at 3T with half and hard excitation pulses, without and with fat saturation, long T2 saturation, and adiabatic inversion recovery (IR) preparation pulses. Single- and bicomponent signal models were utilized to calculate the T2{sup *}s and/or relative fractions of short and long T2{sup *}s. Results: For all bone samples UTE T2{sup *} signal decay showed bicomponent behavior. A higher short T2{sup *} fraction was observed on UTE images with hard pulse excitation compared with half pulse excitation (75.6% vs 68.8% in bovine bone, 79.9% vs 73.2% in human bone). Fat saturation pulses slightly reduced the short T2{sup *} fraction relative to regular UTE sequences (5.0% and 2.0% reduction, respectively, with half and hard excitation pulses for bovine bone, 6.3% and 8.2% reduction, respectively, with half and hard excitation pulses for human bone). Long T2 saturation pulses significantly reduced the long T2{sup *} fraction relative to regular UTE sequence (18.9% and 17.2% reduction, respectively, with half and hard excitation pulses for bovine bone, 26.4% and 27.7% reduction, respectively, with half and hard excitation pulses for human bone). With IR-UTE preparation the long T2{sup *} components were significantly reduced relative to regular UTE sequence (75.3% and 66.4% reduction, respectively, with half and hard excitation pulses for bovine bone, 87.7% and 90.3% reduction, respectively, with half and hard excitation pulses for human bone). Conclusions: Bound and free water T2{sup *}s and relative fractions can

  10. Proteomic Analysis of Various Rat Ocular Tissues after Ischemia–Reperfusion Injury and Possible Relevance to Acute Glaucoma

    PubMed Central

    Chen, Hsin-Yi; Chou, Hsiu-Chuan; Chang, Shing-Jyh; Liao, En-Chi; Tsai, Yi-Ting; Wei, Yu-Shan; Li, Ji-Min; Lin, Li-Hsun; Lin, Meng-Wei; Chen, Ying-Jen; Chen, Yu-Sheng; Lin, Chih-Chun; Wang, Yi-Shiuan; Ko, Mei-Lan; Chan, Hong-Lin

    2017-01-01

    Glaucoma is a group of eye diseases that can cause vision loss and optical nerve damage. To investigate the protein expression alterations in various intraocular tissues (i.e., the cornea, conjunctiva, uvea, retina, and sclera) during ischemia–reperfusion (IR) injury, this study performed a proteomic analysis to qualitatively investigate such alterations resulting from acute glaucoma. The IR injury model combined with the proteomic analysis approach of two-dimensional difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used to monitor the protein expression alterations in two groups of specimens (an IR injury group and a control group). The analysis results revealed 221 unique differentially expressed proteins of a total of 1481 proteins in the cornea between the two groups. In addition, 97 of 1206 conjunctival proteins, 90 of 1354 uveal proteins, 61 of 1180 scleral proteins, and 37 of 1204 retinal proteins were differentially expressed. These findings imply that different ocular tissues have different tolerances against IR injury. To sum up, this study utilized the acute glaucoma model combined with 2D-DIGE and MALDI-TOF MS to investigate the IR injury affected protein expression on various ocular tissues, and based on the ratio of protein expression alterations, the alterations in the ocular tissues were in the following order: the cornea, conjunctiva, uvea, sclera, and retina. PMID:28165428

  11. NEW SCX PEPTIDE ELUTION SCORE FOR PH/SALT-GRADIENT SCX CHROMATOGRAPHY IN 2D-NANO-LC/MSMS ANALYSIS OF PROTEIN DIGESTS

    EPA Science Inventory

    A new automated 2D-(SCX/RP)-nano-LC/MSMS method was developed. Separation of the peptides in the first LC dimension was the main focus of this work, and it was optimized using human serum albumin (HSA) and human lung cell lysate tryptic digests. Samples were reduced and alkylated...

  12. VERA2D-84: a computer program for two-dimensional analysis of flow, heat, and mass transfer in evaporative cooling towers. Volume 2. User's manual. Final report

    SciTech Connect

    Majumdar, A.K.; Agrawal, N.K.; Keeton, L.W.; Singhal, A.K.

    1985-07-01

    Cooling towers that do not meet design performance standards can add millions of dollars to the long-term operating costs of generating plants. The VERA2D-84 code offers a reliable method for predicting the performance of natural-draft and mechanical-draft towers on the basis of physical design information.

  13. 2D discrete Fourier transform on sliding windows.

    PubMed

    Park, Chun-Su

    2015-03-01

    Discrete Fourier transform (DFT) is the most widely used method for determining the frequency spectra of digital signals. In this paper, a 2D sliding DFT (2D SDFT) algorithm is proposed for fast implementation of the DFT on 2D sliding windows. The proposed 2D SDFT algorithm directly computes the DFT bins of the current window using the precalculated bins of the previous window. Since the proposed algorithm is designed to accelerate the sliding transform process of a 2D input signal, it can be directly applied to computer vision and image processing applications. The theoretical analysis shows that the computational requirement of the proposed 2D SDFT algorithm is the lowest among existing 2D DFT algorithms. Moreover, the output of the 2D SDFT is mathematically equivalent to that of the traditional DFT at all pixel positions.

  14. A 2D hydro-morphodynamic modelling approach for predicting suspended sediment propagation and related heavy metal contamination in floodplains: a sensitivity analysis

    NASA Astrophysics Data System (ADS)

    Hostache, Renaud; Hissler, Christophe; Matgen, Patrick; Guignard, Cédric; Bates, Paul

    2014-05-01

    Recent years have seen a growing awareness for the central role that fine sediment loads play in transport and diffusion of pollutants by rivers and streams. Suspended sediment can potentially carry important amounts of nutrients and contaminants, such as trace metals among which some are recognized as Potential Harmful Elements (PHE). These threaten water quality in rivers and wetlands and soil quality in floodplains. Currently, many studies focusing on sediment transport modelling deal with marine and estuarine areas. Some studies evaluate sediment transport at basin scales and often evaluate yearly sediment fluxes using hydrologic and simplified hydraulic models. Some more theoretical studies develop and improve numerical models on the basis of physical model experiments. As a matter of fact, sediment transport modelling in small rivers at reach/floodplain scale is a rather new research field. In this study, we aim at simulating sediment transport at the floodplain scale and the single flood event scale in order to predict sediment spreading on alluvial soils. This simulation will help for the estimation of the potential pollution of soils due to the transport of PHEs by suspended sediments. The model is based upon the Telemac hydro-informatic system (i.e. dynamical coupling of Telemac-2D and Sysiphe). As empirical and semi-empirical parameters need to be calibrated for such a modelling exercise, a sensitivity analysis is proposed. In parallel to the modelling exercise, an extensive hydrological/geochemical database has been set up for two flood events. The most sensitive parameters were found to be the hydraulic friction coefficient and the sediment particle settling velocity in water. Using the two monitored hydrological events for calibration and validation, it was found that the model is able to satisfyingly predict suspended sediment and dissolved pollutant transport in the river channel. In addition, a qualitative comparison between simulated sediment

  15. The Curvelet Transform in the analysis of 2-D GPR data: Signal enhancement and extraction of orientation-and-scale-dependent information

    NASA Astrophysics Data System (ADS)

    Tzanis, Andreas

    2013-04-01

    processing GPR data is its capability to describe wavefronts. The roots of the CT are traced to the field of Harmonic Analysis, where curvelets were introduced as expansions for asymptotic solutions of wave equations (Smith, 1998; Candès, 1999). In consequence, curvelets can be viewed as primitive and prototype waveforms - they are local in both space and spatial frequency and correspond to a partitioning of the 2D Fourier plane by highly anisotropic elements (for the high frequencies) that obey the parabolic scaling principle, that their width is proportional to the square of their length (Smith, 1998). The GPR data essentially comprise recordings of the amplitudes of transient waves generated and recorded by source and receiver antennae, with each source/receiver pair generating a data trace that is a function of time. An ensemble of traces collected sequentially along a scan line, i.e. a GPR section or B-scan, provides a spatio-temporal sampling of the wavefield which contains different arrivals that correspond to different interactions with wave scatterers (inhomogeneities) in the subsurface. All these arrivals represent wavefronts that are relatively smooth in their longitudinal direction and oscillatory in their transverse direction. The connection between Harmonic Analysis and curvelets has resulted in important nonlinear approximations of functions with intermittent regularity (Candès and Donoho, 2004). Such functions are assumed to be piecewise smooth with singularities, i.e. regions where the derivative diverges. In the subsurface, these singularities correspond to geological inhomogeneities, at the boundaries of which waves reflect. In GPR data, these singularities correspond to wavefronts. Owing to their anisotropic shape, curvelets are well adapted to detect wavefronts at different angles and scales because aligned curvelets of a given scale, locally correlate with wavefronts of the same scale. The CT can also be viewed as a higher dimensional extension of the

  16. Optoelectronics with 2D semiconductors

    NASA Astrophysics Data System (ADS)

    Mueller, Thomas

    2015-03-01

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

  17. High-resolution FTIR spectroscopic analysis of the ν11 and ν2 + ν7 bands of 13C2D4

    NASA Astrophysics Data System (ADS)

    Gabona, M. G.; Tan, T. L.

    2016-06-01

    The FTIR spectrum of the ν11 band of 13C2D4 was recorded at a resolution of 0.0063 cm-1 in the 2130-2250 cm-1 region. This band was perturbed by the unobserved ν2 + ν7 band. By fitting 862 infrared transitions for the ν11 band with a rms deviation of 0.0024 cm-1 using a Watson's A-reduced Hamiltonian in the Ir representation including a Coriolis coupling constant, the rovibrational constants for the ν11 = 1 state and three rotational constants for the ν2 = ν7 = 1 state of 13C2D4 were derived for the first time. The band centers of ν11 and ν2 + ν7 were determined to be 2193.75982(25) cm-1 and 2184.613(11) cm-1 respectively.

  18. 2D THD and 3D TEHD analysis of large spindle supported thrust bearings with pins and double layer system used in the three gorges hydroelectric generators

    NASA Astrophysics Data System (ADS)

    Huang, B.; Wu, Z. D.; Wu, J. L.; Wang, L. Q.

    2012-11-01

    A 2D THD model and a 3DTEHD model for large spindle supported thrust bearings were set up and used to analyze the lubrication performance of the Three Gorges test thrust beating withpins and double layer system developed by Alstom Power. The finite difference method was employed to solve the THD model, and the thermal-elasticdeformations in the pad and runner were obtained by the finite element software ANSYS11.0. The data transfer between the THD model and ANSYS11.0 was carried out automatically by an interface program.A detailed comparison between the experimental results and numerical predictions by the two different modelsset up in this paper was carried out. Poor agreement has been found between the theoretical results obtained by 2D THD model and experimental data, while 3D TEHD provides fairly good agreement, confirming the importance of thermal effects and thermal-elastic deformations in both pad and runner.

  19. Theoretical analysis on the measurement errors of local 2D DIC: Part I temporal and spatial uncertainty quantification of displacement measurements

    SciTech Connect

    Wang, Yueqi; Lava, Pascal; Reu, Phillip; Debruyne, Dimitri; Van Houtte, Paul

    2015-12-23

    This study presents a theoretical uncertainty quantification of displacement measurements by subset-based 2D-digital image correlation. A generalized solution to estimate the random error of displacement measurement is presented. The obtained solution suggests that the random error of displacement measurements is determined by the image noise, the summation of the intensity gradient in a subset, the subpixel part of displacement, and the interpolation scheme. The proposed method is validated with virtual digital image correlation tests.

  20. Proteomic analysis of the porcine platelet proteome and alterations induced by thrombin activation.

    PubMed

    Esteso, Gloria; Mora, María Isabel; Garrido, Juan José; Corrales, Fernando; Moreno, Angela

    2008-12-02

    Platelets are enucleated cells derived from bone marrow megakaryocytes and defects in platelet functions could be involved in many cardiovascular diseases. Proteomics can be used to provide a new insight in the study of these platelet functions and can help to identify the biochemical events underlying platelet activation. In this study, we have obtained a reference 2-DE map of porcine platelet proteins. A large number of cytoskeletal and metabolic proteins were found as well as some proteins related to cell mobility and immunological functions. Other proteins implicated in the cell signalling process, transport or apoptosis were also identified. Moreover, we have analysed, by 2D-DIGE methodology, quantitative modifications of platelet proteins following their activation by thrombin. 26 spots exhibited statistically significant differences, and a total of 16 spots corresponding to 13 different proteins were successfully identified. Using Ingenuity Pathway Analysis, the association of the deregulated proteins with canonical pathways highlighted two major pathways; coagulation system and integrin signalling. These results confirm that this proteomic approach (based on 2D-DIGE, mass spectrometry and bioinformatic and pathway databases) has proved to be a powerful tool when applied to studying signalling pathways that could play a relevant role in the activation of platelets.

  1. Morphologic Analysis of the Temporomandibular Joint Between Patients With Facial Asymmetry and Asymptomatic Subjects by 2D and 3D Evaluation

    PubMed Central

    Zhang, Yuan-Li; Song, Jin-Lin; Xu, Xian-Chao; Zheng, Lei-Lei; Wang, Qing-Yuan; Fan, Yu-Bo; Liu, Zhan

    2016-01-01

    Abstract Signs and symptoms of temporomandibular joint (TMJ) dysfunction are commonly found in patients with facial asymmetry. Previous studies on the TMJ position have been limited to 2-dimensional (2D) radiographs, computed tomography (CT), or cone-beam computed tomography (CBCT). The purpose of this study was to compare the differences of TMJ position by using 2D CBCT and 3D model measurement methods. In addition, the differences of TMJ positions between patients with facial asymmetry and asymptomatic subjects were investigated. We prospectively recruited 5 patients (cases, mean age, 24.8 ± 2.9 years) diagnosed with facial asymmetry and 5 asymptomatic subjects (controls, mean age, 26 ± 1.2 years). The TMJ spaces, condylar and ramus angles were assessed by using 2D and 3D methods. The 3D models of mandible, maxilla, and teeth were reconstructed with the 3D image software. The variables in each group were assessed by t-test and the level of significance was 0.05. There was a significant difference in the horizontal condylar angle (HCA), coronal condylar angle (CCA), sagittal ramus angle (SRA), medial joint space (MJS), lateral joint space (LJS), superior joint space (SJS), and anterior joint space (AJS) measured in the 2D CBCT and in the 3D models (P < 0.05). The case group had significantly smaller SJS compared to the controls on both nondeviation side (P = 0.009) and deviation side (P = 0.004). In the case group, the nondeviation SRA was significantly larger than the deviation side (P = 0.009). There was no significant difference in the coronal condylar width (CCW) in either group. In addition, the anterior disc displacement (ADD) was more likely to occur on the deviated side in the case group. In conclusion, the 3D measurement method is more accurate and effective for clinicians to investigate the morphology of TMJ than the 2D method. PMID:27043669

  2. Highly crystalline 2D superconductors

    NASA Astrophysics Data System (ADS)

    Saito, Yu; Nojima, Tsutomu; Iwasa, Yoshihiro

    2016-12-01

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

  3. Extensions of 2D gravity

    SciTech Connect

    Sevrin, A.

    1993-06-01

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

  4. Comparison and analysis of 2-D simulation results with two implosion radiation experiments on the Los Alamos Pegasus I and Pegasus II capacitor banks

    SciTech Connect

    Peterson, D.L.; Bowers, R.L.; Lebeda, C.F.; Matuska, W.; Benage, J.; Idzorek, G.; Oona, H.; Stokes, J.; Roderick, N.F.

    1995-09-01

    Two experiments, PegI-41, conducted on the Los Alamos Pegasus I capacitor bank, and PegII-25, on the Pegasus II bank, consisted of the implosions of 13 mg (nominal), 5 cm radius, 2 cm high thin cylindrical aluminum foils resulting in soft x-ray radiation pulses from the plasma thermalization on axis. The implosions were conducted in direct-drive (no intermediate switching) mode with peak currents of about 4 MA and 5 MA respectively, and implosion times of about 2.5 {micro}s and 2.0 {micro}s. A radiation yield of about 250 kJ was measured for PegII-25. The purpose of these experiments was to examine the physics of the implosion and relate this physics to the production of the radiation pulse and to provide detailed experimental data which could be compared with 2-D radiation-magnetohydrodynamic (RMHD) simulations. Included in the experimental diagnostic suites were faraday rotation and dB/dt current measurements, a visible framing camera, an x-ray stripline camera, time-dependent spectroscopy, bolometers and XRD`S. A comparison of the results from these experiments shows agreement with 2-D simulation results in the instability development, current, and radiation pulse data, including the pulsewidth, shape, peak power and total radiation yield as measured by bolometry. Instabilities dominate the behavior of the implosion and largely determine the properties of the resulting radiation pulse. The 2-D simulations can be seen to be an important tool in understanding the implosion physics.

  5. Comparison of Analysis Results Between 2D/1D Synthesis and RAPTOR-M3G in the Korea Standard Nuclear Plant (KSNP)

    NASA Astrophysics Data System (ADS)

    Joung Lim, Mi; Maeng, Young Jae; Fero, Arnold H.; Anderson, Stanwood L.

    2016-02-01

    The 2D/1D synthesis methodology has been used to calculate the fast neutron (E > 1.0 MeV) exposure to the beltline region of the reactor pressure vessel. This method uses the DORT 3.1 discrete ordinates code and the BUGLE-96 cross-section library based on ENDF/B-VI. RAPTOR-M3G (RApid Parallel Transport Of Radiation-Multiple 3D Geometries) which performs full 3D calculations was developed and is based on domain decomposition algorithms, where the spatial and angular domains are allocated and processed on multi-processor computer architecture. As compared to traditional single-processor applications, this approach reduces the computational load as well as the memory requirement per processor. Both methods are applied to surveillance test results for the Korea Standard Nuclear Plant (KSNP)-OPR (Optimized Power Reactor) 1000 MW. The objective of this paper is to compare the results of the KSNP surveillance program between 2D/1D synthesis and RAPTOR-M3G. Each operating KSNP has a reactor vessel surveillance program consisting of six surveillance capsules located between the core and the reactor vessel in the downcomer region near the reactor vessel wall. In addition to the In-Vessel surveillance program, an Ex-Vessel Neutron Dosimetry (EVND) program has been implemented. In order to estimate surveillance test results, cycle-specific forward transport calculations were performed by 2D/1D synthesis and by RAPTOR-M3G. The ratio between measured and calculated (M/C) reaction rates will be discussed. The current plan is to install an EVND system in all of the Korea PWRs including the new reactor type, APR (Advanced Power Reactor) 1400 MW. This work will play an important role in establishing a KSNP-specific database of surveillance test results and will employ RAPTOR-M3G for surveillance dosimetry location as well as positions in the KSNP reactor vessel.

  6. Enantioselective analysis of citalopram and escitalopram in postmortem blood together with genotyping for CYP2D6 and CYP2C19.

    PubMed

    Carlsson, Björn; Holmgren, Anita; Ahlner, Johan; Bengtsson, Finn

    2009-03-01

    Citalopram is marketed as a racemate (50:50) mixture of the S(+)-enantiomer and R(-)-enantiomer and the active S(+)-enantiomer (escitalopram) that possess inhibitory effects. Citalopram was introduced in Sweden in 1992 and is the most frequently used antidepressant to date in Sweden. In 2002, escitalopram was introduced onto the Swedish market for treatment of depression and anxiety disorders. The main objective of this study was to investigate S(+)-citalopram [i.e., the racemic drug (citalopram) or the enantiomer (escitalopram)] present in forensic autopsy cases positive for the presence of citalopram in routine screening using a non-enantioselective bioanalytical method. Fifty out of the 270 samples found positive by gas chromatography-nitrogen-phosphorus detection were further analyzed using enantioselective high-performance liquid chromatography. The 50 cases were genotyped for CYP2D6 and CYP2C19, as these isoenzymes are implicated in the metabolism of citalopram and escitalopram. In samples positive for racemic citalopram using the screening method for forensic autopsy cases, up to 20% would have been misinterpreted in the absence of an enantioselective method. An enantioselective method is thus necessary for correct interpretation of autopsy cases, after the enantiomer has been introduced onto the market. The percentage of poor metabolizers was 6% for CYP2D6 and 8% for CYP2C19.

  7. Quantum chemical analysis of thermodynamics of 2D cluster formation of alkanes at the water/vapor interface in the presence of aliphatic alcohols.

    PubMed

    Vysotsky, Yu B; Kartashynska, E S; Belyaeva, E A; Fainerman, V B; Vollhardt, D; Miller, R

    2015-11-21

    Using the quantum chemical semi-empirical PM3 method it is shown that aliphatic alcohols favor the spontaneous clusterization of vaporous alkanes at the water surface due to the change of adsorption from the barrier to non-barrier mechanism. A theoretical model of the non-barrier mechanism for monolayer formation is developed. In the framework of this model alcohols (or any other surfactants) act as 'floats', which interact with alkane molecules of the vapor phase using their hydrophobic part, whereas the hydrophilic part is immersed into the water phase. This results in a significant increase of contact effectiveness of alkanes with the interface during the adsorption and film formation. The obtained results are in good agreement with the existing experimental data. To test the model the thermodynamic and structural parameters of formation and clusterization are calculated for vaporous alkanes C(n)H(2n+2) (n(CH3) = 6-16) at the water surface in the presence of aliphatic alcohols C(n)H(2n+1)OH (n(OH) = 8-16) at 298 K. It is shown that the values of clusterization enthalpy, entropy and Gibbs' energy per one monomer of the cluster depend on the chain lengths of corresponding alcohols and alkanes, the alcohol molar fraction in the monolayers formed, and the shift of the alkane molecules with respect to the alcohol molecules Δn. Two possible competitive structures of mixed 2D film alkane-alcohol are considered: 2D films 1 with single alcohol molecules enclosed by alkane molecules (the alcohols do not form domains) and 2D films 2 that contain alcohol domains enclosed by alkane molecules. The formation of the alkane films of the first type is nearly independent of the surfactant type present at the interface, but depends on their molar fraction in the monolayer formed and the chain length of the compounds participating in the clusterization, whereas for the formation of the films of the second type the interaction between the hydrophilic parts of the surfactant is

  8. A 2D Microphysical Analysis of Aerosol Nucleation in the Polar Winter Stratosphere: Implications for H2SO4 Photolysis and Nucleation Mechanisms

    NASA Technical Reports Server (NTRS)

    Mills, Michael J.; Toon, Owen B.; Mills, Michael J.; Solomon, Susan

    1997-01-01

    Each spring a layer of small particles forms between 20 and 30 km in the polar regions. Results are presented from a 2D microphysical model of sulfate aerosol, which provide the first self-consistent explanation of the observed "CN layer." Photochemical conversion of sulfuric acid to SO2 in the upper stratosphere and mesosphere is necessary for this layer to form. Recent laboratory measurements of H2SO4 and SO3 photolysis rates are consistent with such conversion, though an additional source of SO2 may be required. Nucleation throughout the polar winter extends the top of the aerosol layer to higher altitudes, despite strong downward transport of ambient air. This finding may be important to heterogeneous chemistry at the top of the aerosol layer in polar winter and spring.

  9. Strategies of statistical image analysis of 2D immunoblots: the case of IgG response in experimental Taenia crassiceps cysticercosis.

    PubMed

    Ostoa-Saloma, Pedro; Esquivel-Velázquez, Marcela; Ostoa-Jacobo, Pedro; Larralde, Carlos

    2009-12-31

    A procedure is described to measure the diversity and enrich the meaning and usefulness of the information contained in 2D immunoblot images of the reaction between a complex mixture of parasite antigens and the complex set of antibodies usually present in the sera of infected individual hosts. The procedure and results are illustrated by the experimental infection of 30 mice (three strains, both sexes, 5 mice in each strain x sex combination) with Taenia crassiceps cysticerci, thirty days after the challenge. The exercise revealed a significant positive correlation of parasite loads with the hosts' IgG response, in association with their genetic background and less clearly with their sex, all in the midst of a remarkable diversity of both response variables among individual mice. After superimposing a 10 x 10 grid upon the 2D immunoblots some 10% of the positive grid-cells (those who had at least one spot) were positively correlated, suggesting shared epitopes between different antigen spots and/or similar factors controlling different antibody-producing cell clones. Also, a significant correlation was found between many of the positive grid-cells with high values of [Sigma]parasites, but none with low. Thus, the procedure provided many clues for the selection of antigen spots useful to improve immunodiagnosis of cysticercosis and weakened the inclusion of any as vaccine candidate(s). However, some 16 antigen spots were shared almost exclusively by the resistant strains and could relate to protection. The procedure here illustrated may be used in other infections to assess and identify the relevance of antibodies in diagnosis and prevention, as well as provides a measurement of the expected diversity in the hosts' antibody response to the pathogen and of the possible relations between the individual responses towards different antigens contained in the mixture.

  10. 2D X-ray and FTIR micro-analysis of the degradation of cadmium yellow pigment in paintings of Henri Matisse

    NASA Astrophysics Data System (ADS)

    Pouyet, E.; Cotte, M.; Fayard, B.; Salomé, M.; Meirer, F.; Mehta, A.; Uffelman, E. S.; Hull, A.; Vanmeert, F.; Kieffer, J.; Burghammer, M.; Janssens, K.; Sette, F.; Mass, J.

    2015-11-01

    The chemical and physical alterations of cadmium yellow (CdS) paints in Henri Matisse's The Joy of Life (1905-1906, The Barnes Foundation) have been recognized since 2006, when a survey by portable X-ray fluorescence identified this pigment in all altered regions of the monumental painting. This alteration is visible as fading, discoloration, chalking, flaking, and spalling of several regions of light to medium yellow paint. Since that time, synchrotron radiation-based techniques including elemental and spectroscopic imaging, as well as X-ray scattering have been employed to locate and identify the alteration products observed in this and related works by Henri Matisse. This information is necessary to formulate one or multiple mechanisms for degradation of Matisse's paints from this period, and thus ensure proper environmental conditions for the storage and the display of his works. This paper focuses on 2D full-field X-ray Near Edge Structure imaging, 2D micro-X-ray Diffraction, X-ray Fluorescence, and Fourier Transform Infra-red imaging of the altered paint layers to address one of the long-standing questions about cadmium yellow alteration—the roles of cadmium carbonates and cadmium sulphates found in the altered paint layers. These compounds have often been assumed to be photo-oxidation products, but could also be residual starting reagents from an indirect wet process synthesis of CdS. The data presented here allow identifying and mapping the location of cadmium carbonates, cadmium chlorides, cadmium oxalates, cadmium sulphates, and cadmium sulphides in thin sections of altered cadmium yellow paints from The Joy of Life and Matisse's Flower Piece (1906, The Barnes Foundation). Distribution of various cadmium compounds confirms that cadmium carbonates and sulphates are photo-degradation products in The Joy of Life, whereas in Flower Piece, cadmium carbonates appear to have been a [(partially) unreacted] starting reagent for the yellow paint, a role

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

    PubMed Central

    Jia, Yan-Long; Chen, Hui; Zhang, Chong; Gao, Li-Jie; Wang, Xi-Cheng; Qiu, Le-Le; Wu, Jun-Fang

    2016-01-01

    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. PMID:27192131

  12. Static & Dynamic Response of 2D Solids

    SciTech Connect

    Lin, Jerry

    1996-07-15

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

  13. Single nucleotide polymorphism analysis of the NKG2D ligand cluster on the long arm of chromosome 6: Extensive polymorphisms and evidence of diversity between human populations.

    PubMed

    Antoun, Ayman; Jobson, Shirley; Cook, Mark; O'Callaghan, Chris A; Moss, Paul; Briggs, David C

    2010-06-01

    NKG2D is an important activating receptor on NK cells and T-cells and has a diverse panel of ligands (NKG2DL) which include the ULBP and RAET1 proteins. Several NKG2DL exhibit a considerable degree of genetic polymorphism, and although the functional significance of such allelic variation remains unclear, genetic variants have been implicated in susceptibility to infection and auto-immune disease. We used sequence-specific primer polymerase chain reaction to determine the frequency of 25 single nucleotide polymorphisms (SNPs) in the promoter and coding regions of genes of the RAET1/ULBP cluster in 223 Euro-Caucasoid, 60 Afro-Caribbean, and 52 Indo-Asian individuals to determine NKG2DL allele and haplotype frequencies within these populations. We show marked differences in the frequency of NKG2DL SNPs and haplotypes among the three ethnic groups, and certain haplotypes were observed almost exclusively in Afro-Caribbean compared with the Euro-Caucasoid and Indo-Asian populations. Interestingly, variation was focused within the RAET1E (ULBP4), RAET1L, and ULBP3 genes, whereas the ULBP1, ULBP2 and RAET1G (ULBP5) genes were highly conserved. These findings suggest that individual NKG2DL alleles have been subject to divergent selective pressures during the migration of Homo sapiens. This information will be of importance in understanding the biology and clinical significance of NKG2DL polymorphism.

  14. Rotational Analysis of Bands in the High-Resolution Infrared Spectra of cis,cis- and trans,trans-1,4-difluorobutadiene-2-d1

    SciTech Connect

    Craig, Norman C.; Easterday, Clay C.; Nemchick, Deacon J.; Williamson, Drew; Sams, Robert L.

    2012-02-01

    Pure samples of cis,cis- and trans,trans-1,4-difluorobutadiene-2-d1 have been synthesized, and high-resolution (0.0015 cm-1) infrared spectra have been recorded for these nonpolar molecules in the gas phase. For the cis,cis isomer, the rotational structure in two C-type bands at 775 and 666 cm-1 and one A-type band at 866 cm-1 has been analyzed to yield a combined set of 2020 ground state combination differences (GSCDs). Ground state rotational constants fit to these GSCDs are A0 = 0.4195790(4), B0 = 0.0536508(8), and C0 = 0.0475802(9) cm-1. For the trans,trans isomer, three Ctype bands at 856, 839, and 709 cm-1 have been investigated to give a combined set of 1624 GSCDs. Resulting ground state rotational constants for this isomer are A0 = 0.9390117(8), B0 = 0.0389225(4), and C0 = 0.0373778(3) cm-1. Small inertial defects confirm the planarity of both isomers in the ground state. Upper state rotational constants have been determined for most of the transitions. The ground state rotational constants for the two isotopologues will contribute to the data set needed for determining semiexperimental equilibrium structures for the nonpolar isomers of 1,4- difluorobutadiene.

  15. High resolution infrared synchrotron study of CH2D81Br: ground state constants and analysis of the ν5, ν6 and ν9 fundamentals

    NASA Astrophysics Data System (ADS)

    Baldacci, A.; Stoppa, P.; Visinoni, R.; Wugt Larsen, R.

    2012-09-01

    The high resolution infrared absorption spectrum of CH2D81Br has been recorded by Fourier transform spectroscopy in the range 550-1075 cm-1, with an unapodized resolution of 0.0025 cm-1, employing a synchrotron radiation source. This spectral region is characterized by the ν6 (593.872 cm-1), ν5 (768.710 cm-1) and ν9 (930.295 cm-1) fundamental bands. The ground state constants up to sextic centrifugal distortion terms have been obtained for the first time by ground-state combination differences from the three bands and subsequently employed for the evaluation of the excited state parameters. Watson's A-reduced Hamiltonian in the Ir representation has been used in the calculations. The ν 6 = 1 level is essentially free from perturbation whereas the ν 5 = 1 and ν 9 = 1 states are mutually interacting through a-type Coriolis coupling. Accurate spectroscopic parameters of the three excited vibrational states and a high-order coupling constant which takes into account the interaction between ν5 and ν9 have been determined.

  16. Kinematic analysis of healthy hips during weight-bearing activities by 3D-to-2D model-to-image registration technique.

    PubMed

    Hara, Daisuke; Nakashima, Yasuharu; Hamai, Satoshi; Higaki, Hidehiko; Ikebe, Satoru; Shimoto, Takeshi; Hirata, Masanobu; Kanazawa, Masayuki; Kohno, Yusuke; Iwamoto, Yukihide

    2014-01-01

    Dynamic hip kinematics during weight-bearing activities were analyzed for six healthy subjects. Continuous X-ray images of gait, chair-rising, squatting, and twisting were taken using a flat panel X-ray detector. Digitally reconstructed radiographic images were used for 3D-to-2D model-to-image registration technique. The root-mean-square errors associated with tracking the pelvis and femur were less than 0.3 mm and 0.3° for translations and rotations. For gait, chair-rising, and squatting, the maximum hip flexion angles averaged 29.6°, 81.3°, and 102.4°, respectively. The pelvis was tilted anteriorly around 4.4° on average during full gait cycle. For chair-rising and squatting, the maximum absolute value of anterior/posterior pelvic tilt averaged 12.4°/11.7° and 10.7°/10.8°, respectively. Hip flexion peaked on the way of movement due to further anterior pelvic tilt during both chair-rising and squatting. For twisting, the maximum absolute value of hip internal/external rotation averaged 29.2°/30.7°. This study revealed activity dependent kinematics of healthy hip joints with coordinated pelvic and femoral dynamic movements. Kinematics' data during activities of daily living may provide important insight as to the evaluating kinematics of pathological and reconstructed hips.

  17. 2D quasiperiodic plasmonic crystals

    PubMed Central

    Bauer, Christina; Kobiela, Georg; Giessen, Harald

    2012-01-01

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

  18. Valleytronics in 2D materials

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  19. Unparticle example in 2D.

    PubMed

    Georgi, Howard; Kats, Yevgeny

    2008-09-26

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

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

    PubMed Central

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

    2017-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

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

    PubMed

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

    2017-03-10

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

  3. The Curvelet Transform in the analysis of 2-D GPR data: Signal enhancement and extraction of orientation-and-scale-dependent information

    NASA Astrophysics Data System (ADS)

    Tzanis, Andreas

    2015-04-01

    The Ground Probing Radar (GPR) is a valuable tool for near surface geological, geotechnical, engineering, environmental, archaeological and other work. GPR images of the subsurface frequently contain geometric information (constant or variable-dip reflections) from various structures such as bedding, cracks, fractures etc. Such features are frequently the target of the survey; however, they are usually not good reflectors and they are highly localized in time and in space. Their scale is therefore a factor significantly affecting their detectability. At the same time, the GPR method is very sensitive to broadband noise from buried small objects, electromagnetic anthropogenic activity and systemic factors, which frequently blurs the reflections from such targets. The purpose of this paper is to investigate the Curvelet Transform (CT) as a means of S/N enhancement and information retrieval from 2-D GPR sections, with particular emphasis on the recovery of features associated with specific temporal or spatial scales and geometry (orientation/dip). The CT is a multiscale and multidirectional expansion that formulates an optimally sparse representation of bivariate functions with singularities on twice-differentiable (C2-continuous) curves (e.g. edges) and allows for the optimal, whole or partial reconstruction of such objects. The CT can be viewed as a higher dimensional extension of the wavelet transform: whereas discrete wavelets are isotropic and provide sparse representations of functions with point singularities, curvelets are highly anisotropic and provide sparse representations of functions with singularities on curves. A GPR section essentially comprises a spatio-temporal sampling of the transient wavefield which contains different arrivals that correspond to different interactions with wave scatterers in the subsurface (wavefronts). These are generally longitudinally piecewise smooth and transversely oscillatory, i.e. they comprise edges. Curvelets can detect

  4. Statistical Characterization of Altitude Matrices by Computer. Report 2. Calibration Tests on the Rayner-McCalden Program for 2-D Spectral Analysis.

    DTIC Science & Technology

    1974-01-01

    igurecs for th e %oT t o t al ’a iac rC i n domain show how mucl , variance is sacrificod In rm;nni ,’-sir.., S1.ClOdS I the case of C’amclon the...analysis; Te-’- 1- 4C S 3 (𔃼 I. .- 2 TOBLER, W.R. 1969, An analysis of a digitalizd sUr ac; 2xs 2~ (Ed.) A Study of the Land T1’r-e (U.S. Army "Reseal’ch Qfc,~ru North Carolina, Contract DA-31-12-4-ARG-D)-453, z;9-6~

  5. Linear-Elastic 2D and 3D Finite Element Contact Analysis of a Hole Containing a Circular Insert in a Fatigue Test Coupon

    DTIC Science & Technology

    2015-07-01

    circular hole in an aluminium plate fitted with a titanium fastener that were computed using two-dimensional finite element contact analysis. By...used to validate the contact stress distributions associated with a circular hole in an aluminium plate fitted with a titanium fastener that were...fatigue life and aircraft structural integrity management of RAAF airframes. An aluminium coupon has been previously designed in support of the

  6. Comparison of 2D and 3D gamma analyses

    SciTech Connect

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

    2014-02-15

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

  7. Proteome analysis of responses to ascochlorin in a human osteosarcoma cell line by 2-D gel electrophoresis and MALDI-TOF MS.

    PubMed

    Kang, Jeong Han; Park, Kwan-Kyu; Lee, In-Seon; Magae, Junji; Ando, Kunio; Kim, Cheorl-Ho; Chang, Young-Chae

    2006-10-01

    Ascochlorin is a prenyl-phenol compound that was isolated from the fungus Ascochyta viciae. Ascochlorin reduces serum cholesterol and triglyceride levels, suppresses hypertension and tumor development, and ameliorates type I and II diabetes. Here, to better understand the mechanisms by which ascochlorin regulates physiological or pathological events and induces responses in the pharmacological treatment of cancer, we performed differential analysis of the proteome of the human osteosarcoma cells U2OS in response to ascochlorin. In addition, we established the first two-dimensional map of the U2OS proteome. The U2OS cell proteomes with and without treatment with ascochlorin were compared using two-dimensional electrophoresis, matrix-assisted laser desorption/ionization mass spectrometry and bioinformatics. The largest differences in expression were observed for the epidermal growth factor receptor (4-fold decrease), ribulose-5-phosphate-epimerase (13-fold decrease), ATP-dependent RNA helicase (8-fold decrease), and kelch-like ECH-associated protein 1 (6-fold decrease). The abundance of heterogeneous nuclear ribonucleoprotein L and minichromosome maintenance protein 7 increased 12- and 8.2-fold, respectively. In addition, Erk 2 was increased 3-fold in U2OS cells treated with ascochlorin. The expression of some selected proteins was confirmed by western blotting, zymography and RT-PCR analysis.

  8. Megaflood analysis through channel networks of the Athabasca Valles, Mars based on multi-resolution stereo DTMs and 2D hydrodynamic modeling

    NASA Astrophysics Data System (ADS)

    Kim, Jung-Rack; Schumann, Guy; Neal, Jeffrey C.; Lin, Shih-Yuan

    2014-09-01

    Stereo analysis of in-orbital imagery provides valuable topographic data for scientific research over planetary surfaces especially for the interpretation of potential fluvial activity. The focus of research into planetary fluvial activity has been shifting toward quantitative modeling with various spatial resolution DTMs from visual interpretation with ortho images. Thus in this study, we tested the application of hydraulic analysis with multi resolution Martian DTMs, which were constructed following the approaches of Kim and Muller (2009). Planet. Space Sci. 57 (14), 2095. Subsequently, a two-dimensional hydraulic model was introduced to conduct flow simulation using the extracted 1.2-150 m resolution DTMs. As a result, it was found that the simulated water flows coincided with what might be water eroded geomorphic features over target areas. Moreover, the information acquired from the modeling, such as water depth along the time line, flow direction and travel time, is proving of great value for the interpretation of surface characteristics. Results highlighted the importance of DTM quality for simulating fluvial channel hydraulics across planetary surfaces.

  9. Proteome analysis of Sorangium cellulosum employing 2D-HPLC-MS/MS and improved database searching strategies for CID and ETD fragment spectra.

    PubMed

    Leinenbach, Andreas; Hartmer, Ralf; Lubeck, Markus; Kneissl, Benny; Elnakady, Yasser A; Baessmann, Carsten; Müller, Rolf; Huber, Christian G

    2009-09-01

    Shotgun proteome analysis of the myxobacterial model strain for secondary metabolite biosynthesis Sorangium cellulosum was performed employing off-line two-dimensional high-pH reversed-phase HPLC x low-pH ion-pair reversed-phase HPLC and dual tandem mass spectrometry with collision-induced dissociation (CID) and electron transfer dissociation (ETD) as complementary fragmentation techniques. Peptide identification using database searching was optimized for ETD fragment spectra to obtain the maximum number of identifications at equivalent false discovery rates (1.0%) in the evaluation of both fragmentation techniques. In the database search of the CID MS/MS data, the mass tolerance was set to the well-established 0.3 Da window, whereas for ETD data, it was widened to 1.1 Da to account for hydrogen-rearrangement in the radical-intermediate of the peptide precursor ion. To achieve a false discovery rate comparable to the CID results, we increased the significance threshold for peptide identification to 0.001 for the ETD data. The ETD based analysis yielded about 74% of all peptides and about 78% of all proteins compared to the CID-method. In the combined data set, 952 proteins of S. cellulosum were confidently identified by at least two peptides per protein, facilitating the study of the function of regulatory proteins in the social myxobacteria and their role in secondary metabolism.

  10. Structure and Metabolic-Flow Analysis of Molecular Complexity in a (13) C-Labeled Tree by 2D and 3D NMR.

    PubMed

    Komatsu, Takanori; Ohishi, Risa; Shino, Amiu; Kikuchi, Jun

    2016-05-10

    Improved signal identification for biological small molecules (BSMs) in a mixture was demonstrated by using multidimensional NMR on samples from (13) C-enriched Rhododendron japonicum (59.5 atom%) cultivated in air containing (13) C-labeled carbon dioxide for 14 weeks. The resonance assignment of 386 carbon atoms and 380 hydrogen atoms in the mixture was achieved. 42 BSMs, including eight that were unlisted in the spectral databases, were identified. Comparisons between the experimental values and the (13) C chemical shift values calculated by density functional theory supported the identifications of unlisted BSMs. Tracing the (13) C/(12) C ratio by multidimensional NMR spectra revealed faster and slower turnover ratios of BSMs involved in central metabolism and those categorized as secondary metabolites, respectively. The identification of BSMs and subsequent flow analysis provided insight into the metabolic systems of the plant.

  11. Label Free Cell-Tracking and Division Detection Based on 2D Time-Lapse Images For Lineage Analysis of Early Embryo Development

    PubMed Central

    Cicconet, Marcelo; Gutwein, Michelle; Gunsalus, Kristin C; Geiger, Davi

    2014-01-01

    In this paper we report a database and a series of techniques related to the problem of tracking cells, and detecting their divisions, in time-lapse movies of mammalian embryos. Our contributions are: (1) a method for counting embryos in a well, and cropping each individual embryo across frames, to create individual movies for cell tracking; (2) a semi-automated method for cell tracking that works up to the 8-cell stage, along with a software implementation available to the public (this software was used to build the reported database); (3) an algorithm for automatic tracking up to the 4-cell stage, based on histograms of mirror symmetry coefficients captured using wavelets; (4) a cell-tracking database containing 100 annotated examples of mammalian embryos up to the 8-cell stage; (5) statistical analysis of various timing distributions obtained from those examples. PMID:24873887

  12. The Langley Stability and Transition Analysis Code (LASTRAC) : LST, Linear and Nonlinear PSE for 2-D, Axisymmetric, and Infinite Swept Wing Boundary Layers

    NASA Technical Reports Server (NTRS)

    Chang, Chau-Lyan

    2003-01-01

    During the past two decades, our understanding of laminar-turbulent transition flow physics has advanced significantly owing to, in a large part, the NASA program support such as the National Aerospace Plane (NASP), High-speed Civil Transport (HSCT), and Advanced Subsonic Technology (AST). Experimental, theoretical, as well as computational efforts on various issues such as receptivity and linear and nonlinear evolution of instability waves take part in broadening our knowledge base for this intricate flow phenomenon. Despite all these advances, transition prediction remains a nontrivial task for engineers due to the lack of a widely available, robust, and efficient prediction tool. The design and development of the LASTRAC code is aimed at providing one such engineering tool that is easy to use and yet capable of dealing with a broad range of transition related issues. LASTRAC was written from scratch based on the state-of-the-art numerical methods for stability analysis and modem software technologies. At low fidelity, it allows users to perform linear stability analysis and N-factor transition correlation for a broad range of flow regimes and configurations by using either the linear stability theory (LST) or linear parabolized stability equations (LPSE) method. At high fidelity, users may use nonlinear PSE to track finite-amplitude disturbances until the skin friction rise. Coupled with the built-in receptivity model that is currently under development, the nonlinear PSE method offers a synergistic approach to predict transition onset for a given disturbance environment based on first principles. This paper describes the governing equations, numerical methods, code development, and case studies for the current release of LASTRAC. Practical applications of LASTRAC are demonstrated for linear stability calculations, N-factor transition correlation, non-linear breakdown simulations, and controls of stationary crossflow instability in supersonic swept wing boundary

  13. Validation of a computer analysis to determine 3-D rotations and translations of the rib cage in upright posture from three 2-D digital images

    PubMed Central

    Harrison, Deed E.; Janik, Tadeusz J.; Cailliet, Rene; Normand, Martin C.; Perron, Denise L.; Ferrantelli, Joseph R

    2006-01-01

    Since thoracic cage posture affects lumbar spine coupling and loads on the spinal tissues and extremities, a scientific analysis of upright posture is needed. Common posture analyzers measure human posture as displacements from a plumb line, while the PosturePrint™ claims to measure head, rib cage, and pelvic postures as rotations and translations. In this study, it was decided to evaluate the validity of the PosturePrint™ Internet computer system’s analysis of thoracic cage postures. In a university biomechanics laboratory, photographs of a mannequin thoracic cage were obtained in different postures on a stand in front of a digital camera. For each mannequin posture, three photographs were obtained (left lateral, right lateral, and AP). The mannequin thoracic cage was placed in 68 different single and combined postures (requiring 204 photographs) in five degrees of freedom: lateral translation (Tx), lateral flexion (Rz), axial rotation (Ry), flexion–extension (Rx), and anterior–posterior translation (Tz). The PosturePrint™ system requires 13 reflective markers to be placed on the subject (mannequin) during photography and 16 additional “click-on” markers via computer mouse before a set of three photographs is analyzed by the PosturePrint™ computer system over the Internet. Errors were the differences between the positioned mannequin and the calculated positions from the computer system. Average absolute value errors were obtained by comparing the exact inputted posture to the PosturePrint™’s computed values. Mean and standard deviation of computational errors for sagittal displacements of the thoracic cage were Rx=0.3±0.1°, Tz=1.6±0.7 mm, and for frontal view displacements were Ry=1.2±1.0°, Rz=0.6±0.4°, and Tx=1.5±0.6 mm. The PosturePrint™ system is sufficiently accurate in measuring thoracic cage postures in five degrees of freedom on a mannequin indicating the need for a further study on human subjects. PMID:16547756

  14. Identification of Serine Conformers by Matrix-Isolation IR Spectroscopy Aided by Near-Infrared Laser-Induced Conformational Change, 2D Correlation Analysis, and Quantum Mechanical Anharmonic Computations.

    PubMed

    Najbauer, Eszter E; Bazsó, Gábor; Apóstolo, Rui; Fausto, Rui; Biczysko, Malgorzata; Barone, Vincenzo; Tarczay, György

    2015-08-20

    The conformers of α-serine were investigated by matrix-isolation IR spectroscopy combined with NIR laser irradiation. This method, aided by 2D correlation analysis, enabled unambiguously grouping the spectral lines to individual conformers. On the basis of comparison of at least nine experimentally observed vibrational transitions of each conformer with empirically scaled (SQM) and anharmonic (GVPT2) computed IR spectra, six conformers were identified. In addition, the presence of at least one more conformer in Ar matrix was proved, and a short-lived conformer with a half-life of (3.7 ± 0.5) × 10(3) s in N2 matrix was generated by NIR irradiation. The analysis of the NIR laser-induced conversions revealed that the excitation of the stretching overtone of both the side chain and the carboxylic OH groups can effectively promote conformational changes, but remarkably different paths were observed for the two kinds of excitations.

  15. Application of the order-of-magnitude analysis to a fourth-order RANS closure for simulating a 2D boundary layer

    NASA Astrophysics Data System (ADS)

    Poroseva, Svetlana V.

    2013-11-01

    Simulations of turbulent boundary-layer flows are usually conducted using a set of the simplified Reynolds-Averaged Navier-Stokes (RANS) equations obtained by order-of-magnitude analysis (OMA) of the original RANS equations. The resultant equations for the mean-velocity components are closed using the Boussinesq approximation for the Reynolds stresses. In this study OMA is applied to the fourth-order RANS (FORANS) set of equations. The FORANS equations are chosen as they can be closed on the level of the 5th-order correlations without using unknown model coefficients, i.e. no turbulent diffusion modeling is required. New models for the 2nd-, 3rd- and 4th-order velocity-pressure gradient correlations are derived for the current FORANS equations. This set of FORANS equations and models are analyzed for the case of two-dimensional mean flow. The equations include familiar transport terms for the mean-velocity components along with algebraic expressions for velocity correlations of different orders specific to the FORANS approach. Flat plate DNS data (Spalart, 1988) are used to verify these expressions and the areas of the OMA applicability within the boundary layer. The material is based upon work supported by NASA under award NNX12AJ61A.

  16. Qualitative and quantitative analysis of the unsaponifiable fraction of vegetable oils by using comprehensive 2D GC with dual MS/FID detection.

    PubMed

    Tranchida, Peter Q; Salivo, Simona; Franchina, Flavio A; Bonaccorsi, Ivana; Dugo, Paola; Mondello, Luigi

    2013-05-01

    The present investigation is focused on the development of a comprehensive two-dimensional GC (GC × GC) method, with dual MS/FID detection, for the qualitative and quantitative analysis of the entire unsaponifiable fraction of vegetable oils. The unsaponifiable fraction forms a minor, highly specific part of a vegetable oil, and can be used as an indicator of genuineness. The column set used consisted of a low-polarity first dimension, and a medium-polarity secondary one, both characterized by a high thermal stability. The use of dual detection enabled the attainment of both mass spectral information and relative % FID data. The complexity of the fingerprint, generated by the unsaponifiable fraction, fully justified the employment of the two-dimensional GC technology. Furthermore, two other GC × GC benefits contributed greatly to the attainment of promising results, namely sensitivity enhancement and the formation of group-type patterns. The method herein proposed could potentially open a new opportunity for the more in-depth knowledge of the unsaponifiable fraction of vegetable oils.

  17. Origin of the Ion Foreshock in a Quasi-perpendicular Curved Collisionless Shock: Particles Trajectory Analysis in 2D PIC Simulations

    NASA Astrophysics Data System (ADS)

    Savoini, P.; Lembege, B.

    2015-12-01

    The ion foreshock located upstream of the Earth's shock wave is populated with ions having interacted with the shock, and then, reflected back with an high energy gain. Spacecrafts have clearly established the existence of two distinct populations in the quasi-perpendicular shock region (i.e. for 45° ≤ ΘBn ≤ 90°, where ΘBn is the angle between the shock normal and the upstream magnetic field) : (i) field-aligned ion beams or « FAB » characterized by a gyrotropic distribution, and (ii) gyro-phase bunched ions or « GPB » characterized by a NON gyrotropic distribution. One of the important unresolved problem is the exact origin of the particles contributing to these two populations. To our knowledge, it was the first time that full-particle simulations have been performed including self-consistently the shock front curvature and nonstationarity, and the time-of-flight effects. Our analysis evidences that these two backstreaming populations may be reflected by the front itself and can be differentiated both in terms of interaction time and trajectory within the shock front. In particular, simulations evidence that "GPB" population is characterized by a short interaction time (ΔTinter = 1 to 2 τci) while the "FAB" population corresponds to a much larger time range (from 1 τci to 10 τci), where tci is the upstream ion gyroperiod. Present individual ion trajectories evidence that "FAB" population shows a strong perpendicular drift at the shock front (i.e. strong dependence of the pitch angle to the perpendicular velocity) whereas the "GPB" population shows no perpendicular drift (i.e. its pitch angle is mainly driven by the parallel velocity). Such differences explain why the "FAB" population loses their gyro-phase coherency and become gyrotropic which is not the case for the "GPB". This important result was not expected and greatly simplifies the question of their origin.

  18. 2D spatiotemporal visualization system of expired gaseous ethanol after oral administration for real-time illustrated analysis of alcohol metabolism.

    PubMed

    Wang, Xin; Ando, Eri; Takahashi, Daishi; Arakawa, Takahiro; Kudo, Hiroyuki; Saito, Hirokazu; Mitsubayashi, Kohji

    2010-08-15

    A novel 2-dimensional spatiotemporal visualization system of expired gaseous ethanol after oral administration for real-time illustrated analysis of alcohol metabolism has been developed, which employed a low level light CCD camera to detect chemiluminescence (CL) generated by catalytic reactions of standard gaseous ethanol and expired gaseous ethanol after oral administration. First, the optimization of the substrates for visualization and the concentration of luminol solution for CL were investigated. The cotton mesh and 5.0 mmol L(-1) luminol solution were selected for further investigations and this system is useful for 0.1-20.0 mmol L(-1) of H(2)O(2) solution. Then, the effect of pH condition of Tris-HCl buffer solution was also evaluated with CL intensity and under the Tris-HCl buffer solution pH 10.1, a wide calibration range of standard gaseous ethanol (30-400 ppm) was obtained. Finally, expired air of 5 healthy volunteers after oral administration was measured at 15, 30, 45, 60, 75, 90, 105 and 120 min after oral administration, and this system showed a good sensitivity on expired gaseous ethanol for alcohol metabolism. The peaks of expired gaseous ethanol concentration appeared within 30 min after oral administration. During the 30 min after oral administration, the time variation profile based on mean values showed the absorption and distribution function, and the values onward showed the elimination function. The absorption and distribution of expired gaseous ethanol in 5 healthy volunteers following first-order absorption process were faster than the elimination process, which proves efficacious of this system for described alcohol metabolism in healthy volunteers. This system is expected to be used as a non-invasive method to detect VOCs as well as several other drugs in expired air for clinical purpose.

  19. NKG2D ligands as therapeutic targets

    PubMed Central

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

    2013-01-01

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

  20. Prediction of p38 map kinase inhibitory activity of 3, 4-dihydropyrido [3, 2-d] pyrimidone derivatives using an expert system based on principal component analysis and least square support vector machine

    PubMed Central

    Shahlaei, M.; Saghaie, L.

    2014-01-01

    A quantitative structure–activity relationship (QSAR) study is suggested for the prediction of biological activity (pIC50) of 3, 4-dihydropyrido [3,2-d] pyrimidone derivatives as p38 inhibitors. Modeling of the biological activities of compounds of interest as a function of molecular structures was established by means of principal component analysis (PCA) and least square support vector machine (LS-SVM) methods. The results showed that the pIC50 values calculated by LS-SVM are in good agreement with the experimental data, and the performance of the LS-SVM regression model is superior to the PCA-based model. The developed LS-SVM model was applied for the prediction of the biological activities of pyrimidone derivatives, which were not in the modeling procedure. The resulted model showed high prediction ability with root mean square error of prediction of 0.460 for LS-SVM. The study provided a novel and effective approach for predicting biological activities of 3, 4-dihydropyrido [3,2-d] pyrimidone derivatives as p38 inhibitors and disclosed that LS-SVM can be used as a powerful chemometrics tool for QSAR studies. PMID:26339262

  1. NIKE2D96. Static & Dynamic Response of 2D Solids

    SciTech Connect

    Raboin, P.; Engelmann, B.; Halquist, J.O.

    1992-01-24

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

  2. Concrete resource analysis of the quantum linear-system algorithm used to compute the electromagnetic scattering cross section of a 2D target

    NASA Astrophysics Data System (ADS)

    Scherer, Artur; Valiron, Benoît; Mau, Siun-Chuon; Alexander, Scott; van den Berg, Eric; Chapuran, Thomas E.

    2017-03-01

    We provide a detailed estimate for the logical resource requirements of the quantum linear-system algorithm (Harrow et al. in Phys Rev Lett 103:150502, 2009) including the recently described elaborations and application to computing the electromagnetic scattering cross section of a metallic target (Clader et al. in Phys Rev Lett 110:250504, 2013). Our resource estimates are based on the standard quantum-circuit model of quantum computation; they comprise circuit width (related to parallelism), circuit depth (total number of steps), the number of qubits and ancilla qubits employed, and the overall number of elementary quantum gate operations as well as more specific gate counts for each elementary fault-tolerant gate from the standard set { X, Y, Z, H, S, T, { CNOT } }. In order to perform these estimates, we used an approach that combines manual analysis with automated estimates generated via the Quipper quantum programming language and compiler. Our estimates pertain to the explicit example problem size N=332{,}020{,}680 beyond which, according to a crude big-O complexity comparison, the quantum linear-system algorithm is expected to run faster than the best known classical linear-system solving algorithm. For this problem size, a desired calculation accuracy ɛ =0.01 requires an approximate circuit width 340 and circuit depth of order 10^{25} if oracle costs are excluded, and a circuit width and circuit depth of order 10^8 and 10^{29}, respectively, if the resource requirements of oracles are included, indicating that the commonly ignored oracle resources are considerable. In addition to providing detailed logical resource estimates, it is also the purpose of this paper to demonstrate explicitly (using a fine-grained approach rather than relying on coarse big-O asymptotic approximations) how these impressively large numbers arise with an actual circuit implementation of a quantum algorithm. While our estimates may prove to be conservative as more efficient

  3. First evidence of overlaps between HIV-Associated Dementia (HAD) and non-viral neurodegenerative diseases: proteomic analysis of the frontal cortex from HIV+ patients with and without dementia

    PubMed Central

    2010-01-01

    Background The pathogenesis of HIV-associated dementia (HAD) is poorly understood. To date, detailed proteomic fingerprinting directly from autopsied brain tissues of HAD and HIV non-dementia patients has not been performed. Result Here, we have analyzed total proteins from the frontal cortex of 9 HAD and 5 HIV non-dementia patients. Using 2-Dimensional differential in-gel electrophoresis (2-DIGE) to analyze the brain tissue proteome, 76 differentially expressed proteins (p < 0.05; fold change>1.25) were identified between HAD and HIV non-dementia patients, of which 36 protein spots (based on 3D appearance of spots on the images) were chosen for the mass spectrometry analysis. The large majority of identified proteins were represented in the energy metabolic (mitochondria) and signal transduction pathways. Furthermore, over 90% of the protein candidates are common to both HAD and other non-viral neurodegenerative disease, such as Alzheimer's disease. The data was further validated using specific antibodies to 4 proteins (CA2, GS, CKMT and CRMP2) by western blot (WB) in the same samples used for 2D-DIGE, with additional confirmation by immunohistochemitsry (IHC) using frontal lobe tissue from different HAD and HIV+ non-dementia patients. The validation for all 4 antibodies by WB and IHC was in concordance with the DIGE results, lending further credence to the current findings. Conclusion These results suggest not only convergent pathogenetic pathways for the two diseases but also the possibility of increased Alzheimer's disease (AD) susceptibility in HAD patients whose life expectancy has been significantly increased by highly active antiretroviral therapy. PMID:20573273

  4. 2-D Versus 3-D Magnetotelluric Data Interpretation

    NASA Astrophysics Data System (ADS)

    Ledo, Juanjo

    2005-09-01

    In recent years, the number of publications dealing with the mathematical and physical 3-D aspects of the magnetotelluric method has increased drastically. However, field experiments on a grid are often impractical and surveys are frequently restricted to single or widely separated profiles. So, in many cases we find ourselves with the following question: is the applicability of the 2-D hypothesis valid to extract geoelectric and geological information from real 3-D environments? The aim of this paper is to explore a few instructive but general situations to understand the basics of a 2-D interpretation of 3-D magnetotelluric data and to determine which data subset (TE-mode or TM-mode) is best for obtaining the electrical conductivity distribution of the subsurface using 2-D techniques. A review of the mathematical and physical fundamentals of the electromagnetic fields generated by a simple 3-D structure allows us to prioritise the choice of modes in a 2-D interpretation of responses influenced by 3-D structures. This analysis is corroborated by numerical results from synthetic models and by real data acquired by other authors. One important result of this analysis is that the mode most unaffected by 3-D effects depends on the position of the 3-D structure with respect to the regional 2-D strike direction. When the 3-D body is normal to the regional strike, the TE-mode is affected mainly by galvanic effects, while the TM-mode is affected by galvanic and inductive effects. In this case, a 2-D interpretation of the TM-mode is prone to error. When the 3-D body is parallel to the regional 2-D strike the TE-mode is affected by galvanic and inductive effects and the TM-mode is affected mainly by galvanic effects, making it more suitable for 2-D interpretation. In general, a wise 2-D interpretation of 3-D magnetotelluric data can be a guide to a reasonable geological interpretation.

  5. 2D Electrostatic Actuation of Microshutter Arrays

    NASA Technical Reports Server (NTRS)

    Burns, Devin E.; Oh, Lance H.; Li, Mary J.; Jones, Justin S.; Kelly, Daniel P.; Zheng, Yun; Kutyrev, Alexander S.; Moseley, Samuel H.

    2015-01-01

    An electrostatically actuated microshutter array consisting of rotational microshutters (shutters that rotate about a torsion bar) were designed and fabricated through the use of models and experiments. Design iterations focused on minimizing the torsional stiffness of the microshutters, while maintaining their structural integrity. Mechanical and electromechanical test systems were constructed to measure the static and dynamic behavior of the microshutters. The torsional stiffness was reduced by a factor of four over initial designs without sacrificing durability. Analysis of the resonant behavior of the microshutter arrays demonstrates that the first resonant mode is a torsional mode occurring around 3000 Hz. At low vacuum pressures, this resonant mode can be used to significantly reduce the drive voltage necessary for actuation requiring as little as 25V. 2D electrostatic latching and addressing was demonstrated using both a resonant and pulsed addressing scheme.

  6. Frequency of undetected CYP2D6 hybrid genes in clinical samples: impact on phenotype prediction.

    PubMed

    Black, John Logan; Walker, Denise L; O'Kane, Dennis J; Harmandayan, Maria

    2012-01-01

    Cytochrome P450 2D6 (CYP2D6) is highly polymorphic. CYP2D6-2D7 hybrid genes can be present in samples containing CYP2D6*4 and CYP2D6*10 alleles. CYP2D7-2D6 hybrid genes can be present in samples with duplication signals and in samples with homozygous genotyping results. The frequency of hybrid genes in clinical samples is unknown. We evaluated 1390 samples for undetected hybrid genes by polymerase chain reaction (PCR) amplification, PCR fragment analysis, TaqMan copy number assays, DNA sequencing, and allele-specific primer extension assay. Of 508 CYP2D6*4-containing samples, 109 (21.5%) harbored CYP2D6*68 + *4-like, whereas 9 (1.8%) harbored CYP2D6*4N + *4-like. Of 209 CYP2D6*10-containing samples, 44 (21.1%) were found to have CYP2D6*36 + *10. Of 332 homozygous samples, 4 (1.2%) harbored a single CYP2D7-2D6 hybrid, and of 341 samples with duplication signals, 25 (7.3%) harbored an undetected CYP2D7-2D6 hybrid. Phenotype before and after accurate genotyping was predicted using a method in clinical use. The presence of hybrid genes had no effect on the phenotype prediction of CYP2D6*4- and CYP2D6*10-containing samples. Four of four (100%) homozygous samples containing a CYP2D7-2D6 gene had a change in predicted phenotype, and 23 of 25 (92%) samples with a duplication signal and a CYP2D7-2D6 gene had a change in predicted phenotype. Four novel genes were identified (CYP2D6*13A1 variants 1 and 2, CYP2D6*13G1, and CYP2D6*13G2), and two novel hybrid tandem structures consisting of CYP2D6*13B + *68×2 + *4-like and CYP2D6*13A1 variant 2 + *1×N were observed.

  7. 2D shear wave velocity mapping of the Hartoušov CO2 degassing area in the Cheb Basin, NW Bohemia (Czech Republic), using Multichannel Analysis of Surface Waves

    NASA Astrophysics Data System (ADS)

    Flores Estrella, H.; Henke, M.

    2015-12-01

    For the characterization of the subsurface of the Hartoušov CO2 degassing area in the Cheb Basin, NW Bohemia, Czech Republic several different approaches have been made. However, no active seismic characterization has been presented, nor published. The Multi­channel Analysis of Surface Waves (MASW) offers an useful tool to estimate vertical and horizontal velocity changes of the shallow subsurface. This can correlate to variations on rock elastic properties and/or fluid content, and represents the subsurface-layering.Surface waves were stimulated using a sledgehammer as source, and were measured with 48 vertical geophones with spacing of 1 m and the roll along method with a setup dis­placement of 2 m. Two source offsets, 10 m and 30 m, were used to increase the data quality and the resolution.The analysis of propagation velocities leads to dispersion curves from which 1D shear wave velocity profiles can be inverted. Those will be interpolated to create a 2D ground stiffness map. The measurements were taken in the NW area of the main degassing zone and are partially in the same spot of former investigations, i.e. CO2 concentration and gas flux measurements, electric and gravimetric surveys and continuous seismic noise mea­surements.Changes in the structure of the 2D velocity maps can be explained potentially with the oc­currence of fluid paths and their diffusion in the subsurface or the existence of the Počatky-Plesná fault zone, which position is not fully understood yet or both features in combination.

  8. ORION96. 2-d Finite Element Code Postprocessor

    SciTech Connect

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

    1992-02-02

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

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

    PubMed

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

    2013-02-21

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

  10. Assessment of bone microarchitecture in chronic kidney disease: a comparison of 2D bone texture analysis and high-resolution peripheral quantitative computed tomography at the radius and tibia.

    PubMed

    Bacchetta, Justine; Boutroy, Stéphanie; Vilayphiou, Nicolas; Fouque-Aubert, Anne; Delmas, Pierre D; Lespessailles, Eric; Fouque, Denis; Chapurlat, Roland

    2010-11-01

    Bone microarchitecture can be studied noninvasively using high-resolution peripheral quantitative computed tomography (HR-pQCT). However, this technique is not widely available, so more simple techniques may be useful. BMA is a new 2D high-resolution digital X-ray device, allowing for bone texture analysis with a fractal parameter (H(mean)). The aims of this study were (1) to evaluate the reproducibility of BMA at two novel sites (radius and tibia) in addition to the conventional site (calcaneus), (2) to compare the results obtained with BMA at all of those sites, and (3) to study the relationship between H(mean) and trabecular microarchitecture measured with an in vivo 3D device (HR-pQCT) at the distal tibia and radius. BMA measurements were performed at three sites (calcaneus, distal tibia, and radius) in 14 healthy volunteers to measure the short-term reproducibility and in a group of 77 patients with chronic kidney disease to compare BMA results to HR-pQCT results. The coefficient of variation of H(mean) was 1.2, 2.1, and 4.7% at the calcaneus, radius, and tibia, respectively. We found significant associations between trabecular volumetric bone mineral density and microarchitectural variables measured by HR-pQCT and H(mean) at the three sites (e.g., Pearson correlation between radial trabecular number and radial H(mean) r = 0.472, P < 0.001). This study demonstrated a significant but moderate relationship between 2D bone texture and 3D trabecular microarchitecture. BMA is a new reproducible technique with few technical constraints. Thus, it may represent an interesting tool for evaluating bone structure, in association with biological parameters and DXA.

  11. Annotated Bibliography of EDGE2D Use

    SciTech Connect

    J.D. Strachan and G. Corrigan

    2005-06-24

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

  12. Staring 2-D hadamard transform spectral imager

    DOEpatents

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

    2006-02-07

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

  13. Regulation of NKG2D ligand gene expression.

    PubMed

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

    2006-03-01

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

  14. Quantitative analysis of proteome extracted from barley crowns grown under different drought conditions.

    PubMed

    Vítámvás, Pavel; Urban, Milan O; Škodáček, Zbynek; Kosová, Klára; Pitelková, Iva; Vítámvás, Jan; Renaut, Jenny; Prášil, Ilja T

    2015-01-01

    Barley cultivar Amulet was used to study the quantitative proteome changes through different drought conditions utilizing two-dimensional difference gel electrophoresis (2D-DIGE). Plants were cultivated for 10 days under different drought conditions. To obtain control and differentially drought-treated plants, the soil water content was kept at 65, 35, and 30% of soil water capacity (SWC), respectively. Osmotic potential, water saturation deficit, (13)C discrimination, and dehydrin accumulation were monitored during sampling of the crowns for proteome analysis. Analysis of the 2D-DIGE gels revealed 105 differentially abundant spots; most were differentially abundant between the controls and drought-treated plants, and 25 spots displayed changes between both drought conditions. Seventy-six protein spots were successfully identified by tandem mass spectrometry. The most frequent functional categories of the identified proteins can be put into the groups of: stress-associated proteins, amino acid metabolism, carbohydrate metabolism, as well as DNA and RNA regulation and processing. Their possible role in the response of barley to drought stress is discussed. Our study has shown that under drought conditions barley cv. Amulet decreased its growth and developmental rates, displayed a shift from aerobic to anaerobic metabolism, and exhibited increased levels of several protective proteins. Comparison of the two drought treatments revealed plant acclimation to milder drought (35% SWC); but plant damage under more severe drought treatment (30% SWC). The results obtained revealed that cv. Amulet is sensitive to drought stress. Additionally, four spots revealing a continuous and significant increase with decreasing SWC (UDP-glucose 6-dehydrogenase, glutathione peroxidase, and two non-identified) could be good candidates for testing of their protein phenotyping capacity together with proteins that were significantly distinguished in both drought treatments.

  15. Quantitative analysis of proteome extracted from barley crowns grown under different drought conditions

    PubMed Central

    Vítámvás, Pavel; Urban, Milan O.; Škodáček, Zbynek; Kosová, Klára; Pitelková, Iva; Vítámvás, Jan; Renaut, Jenny; Prášil, Ilja T.

    2015-01-01

    Barley cultivar Amulet was used to study the quantitative proteome changes through different drought conditions utilizing two-dimensional difference gel electrophoresis (2D-DIGE). Plants were cultivated for 10 days under different drought conditions. To obtain control and differentially drought-treated plants, the soil water content was kept at 65, 35, and 30% of soil water capacity (SWC), respectively. Osmotic potential, water saturation deficit, 13C discrimination, and dehydrin accumulation were monitored during sampling of the crowns for proteome analysis. Analysis of the 2D-DIGE gels revealed 105 differentially abundant spots; most were differentially abundant between the controls and drought-treated plants, and 25 spots displayed changes between both drought conditions. Seventy-six protein spots were successfully identified by tandem mass spectrometry. The most frequent functional categories of the identified proteins can be put into the groups of: stress-associated proteins, amino acid metabolism, carbohydrate metabolism, as well as DNA and RNA regulation and processing. Their possible role in the response of barley to drought stress is discussed. Our study has shown that under drought conditions barley cv. Amulet decreased its growth and developmental rates, displayed a shift from aerobic to anaerobic metabolism, and exhibited increased levels of several protective proteins. Comparison of the two drought treatments revealed plant acclimation to milder drought (35% SWC); but plant damage under more severe drought treatment (30% SWC). The results obtained revealed that cv. Amulet is sensitive to drought stress. Additionally, four spots revealing a continuous and significant increase with decreasing SWC (UDP-glucose 6-dehydrogenase, glutathione peroxidase, and two non-identified) could be good candidates for testing of their protein phenotyping capacity together with proteins that were significantly distinguished in both drought treatments. PMID:26175745

  16. Differences in atrial fibrillation-associated proteins between the left and right atrial appendages from patients with rheumatic mitral valve disease: A comparative proteomic analysis

    PubMed Central

    Liu, Hai; Chen, Guangxian; Zheng, Hongsheng; Qin, Han; Liang, Mengya; Feng, Kangni; Wu, Zhongkai

    2016-01-01

    The majority of proteomic studies have focused on identifying atrial fibrillation (AF)-associated proteins in the right atrium (RA), thus potential differences in AF-associated proteins between the RA and left atrium (LA) remain unknown. The aim of the present study was to perform proteomic analysis to compare the potential differences in AF-associated proteins between the right atrial appendage (RAA) and left atrial appendage (LAA) in patients with rheumatic mitral valve disease (RMVD). RAA and LAA tissues were obtained from 18 patients with RMVD (10 with AF) during mitral valve replacement surgery. Two-dimensional fluorescence difference gel electrophoresis (2-D DIGE) proteomics analysis was performed using these tissues to identify AF-associated proteins in RAA and LAA. Subsequently, the proteomics data was validated using western blot analysis of nine selected proteins. In RAA, 32 AF-associated proteins were significantly dysregulated (15 upregulated and 17 downregulated). In LAA, 31 AF-associated proteins were significantly dysregulated (13 upregulated and 18 downregulated). Among these AF-associated proteins, 17 were AF-associated in both RAA and LAA, 15 were AF-associated only in RAA, and 14 were AF-associated only in LAA. Amongst the differentially expressed proteins, western blot analysis validated the results for 6 AF-associated proteins, and demonstrated similar distributions in RAA and LAA compared with the 2-D DIGE results. Of these proteins, 2 proteins were AF-associated in both RAA and LAA, 2 were AF-associated only in RAA, and 2 were AF-associated only in LAA. Additionally, the different distributions of AF-associated proteins in the RAA and LAA of patients with RMVD was analyzed, which may reflect the different regulatory mechanisms of the RA and LA in AF. These findings may provide new insights into the underlying molecular mechanisms of AF in patients with RMVD. PMID:27667121

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

    PubMed

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

    2014-12-01

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

  18. 2-D Clinostat for Simulated Microgravity Experiments with Arabidopsis Seedlings

    NASA Astrophysics Data System (ADS)

    Wang, Hui; Li, Xugang; Krause, Lars; Görög, Mark; Schüler, Oliver; Hauslage, Jens; Hemmersbach, Ruth; Kircher, Stefan; Lasok, Hanna; Haser, Thomas; Rapp, Katja; Schmidt, Jürgen; Yu, Xin; Pasternak, Taras; Aubry-Hivet, Dorothée; Tietz, Olaf; Dovzhenko, Alexander; Palme, Klaus; Ditengou, Franck Anicet

    2016-04-01

    Ground-based simulators of microgravity such as fast rotating 2-D clinostats are valuable tools to study gravity related processes. We describe here a versatile g-value-adjustable 2-D clinostat that is suitable for plant analysis. To avoid seedling adaptation to 1 g after clinorotation, we designed chambers that allow rapid fixation. A detailed protocol for fixation, RNA isolation and the analysis of selected genes is described. Using this clinostat we show that mRNA levels of LONG HYPOCOTYL 5 (HY5), MIZU-KUSSEI 1 (MIZ1) and microRNA MIR163 are down-regulated in 5-day-old Arabidopsis thaliana roots after 3 min and 6 min of clinorotation using a maximal reduced g-force of 0.02 g, hence demonstrating that this 2-D clinostat enables the characterization of early transcriptomic events during root response to microgravity. We further show that this 2-D clinostat is able to compensate the action of gravitational force as both gravitropic-dependent statolith sedimentation and subsequent auxin redistribution (monitoring D R5 r e v :: G F P reporter) are abolished when plants are clinorotated. Our results demonstrate that 2-D clinostats equipped with interchangeable growth chambers and tunable rotation velocity are suitable for studying how plants perceive and respond to simulated microgravity.

  19. Matrix models of 2d gravity

    SciTech Connect

    Ginsparg, P.

    1991-01-01

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

  20. Matrix models of 2d gravity

    SciTech Connect

    Ginsparg, P.

    1991-12-31

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

  1. Brittle damage models in DYNA2D

    SciTech Connect

    Faux, D.R.

    1997-09-01

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

  2. 2D/3D switchable displays

    NASA Astrophysics Data System (ADS)

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

    2006-02-01

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

  3. Chemical Approaches to 2D Materials.

    PubMed

    Samorì, Paolo; Palermo, Vincenzo; Feng, Xinliang

    2016-08-01

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

  4. Discrepant Results in a 2-D Marble Collision

    ERIC Educational Resources Information Center

    Kalajian, Peter

    2013-01-01

    Video analysis of 2-D collisions is an excellent way to investigate conservation of linear momentum. The often-desired experimental design goal is to minimize the momentum loss in order to demonstrate the conservation law. An air table with colliding pucks is an ideal medium for this experiment, but such equipment is beyond the budget of many…

  5. 2D signature for detection and identification of drugs

    NASA Astrophysics Data System (ADS)

    Trofimov, Vyacheslav A.; Varentsova, Svetlana A.; Shen, Jingling; Zhang, Cunlin; Zhou, Qingli; Shi, Yulei

    2011-06-01

    The method of spectral dynamics analysis (SDA-method) is used for obtaining the2D THz signature of drugs. This signature is used for the detection and identification of drugs with similar Fourier spectra by transmitted THz signal. We discuss the efficiency of SDA method for the identification problem of pure methamphetamine (MA), methylenedioxyamphetamine (MDA), 3, 4-methylenedioxymethamphetamine (MDMA) and Ketamine.

  6. FPCAS2D user's guide, version 1.0

    NASA Technical Reports Server (NTRS)

    Bakhle, Milind A.

    1994-01-01

    The FPCAS2D computer code has been developed for aeroelastic stability analysis of bladed disks such as those in fans, compressors, turbines, propellers, or propfans. The aerodynamic analysis used in this code is based on the unsteady two-dimensional full potential equation which is solved for a cascade of blades. The structural analysis is based on a two degree-of-freedom rigid typical section model for each blade. Detailed explanations of the aerodynamic analysis, the numerical algorithms, and the aeroelastic analysis are not given in this report. This guide can be used to assist in the preparation of the input data required by the FPCAS2D code. A complete description of the input data is provided in this report. In addition, four test cases, including inputs and outputs, are provided.

  7. Available information in 2D motional Stark effect imaging.

    PubMed

    Creese, Mathew; Howard, John

    2010-10-01

    Recent advances in imaging techniques have allowed the extension of the standard polarimetric 1D motional Stark effect (MSE) diagnostic to 2D imaging of the internal magnetic field of fusion devices [J. Howard, Plasma Phys. Controlled Fusion 50, 125003 (2008)]. This development is met with the challenge of identifying and extracting the new information, which can then be used to increase the accuracy of plasma equilibrium and current density profile determinations. This paper develops a 2D analysis of the projected MSE polarization orientation and Doppler phase shift. It is found that, for a standard viewing position, the 2D MSE imaging system captures sufficient information to allow imaging of the internal vertical magnetic field component B(Z)(r,z) in a tokamak.

  8. Immunoproteomic and two-dimensional difference gel electrophoresis analysis of Arabidopsis dehydration response element-binding protein 1A (DREB1A)-transgenic potato.

    PubMed

    Nakamura, Rika; Satoh, Rie; Nakamura, Ryosuke; Shimazaki, Takayoshi; Kasuga, Mie; Yamaguchi-Shinozaki, Kazuko; Kikuchi, Akira; Watanabe, Kazuo N; Teshima, Reiko

    2010-01-01

    To produce crops that are more tolerant to stresses such as heat, cold, and salt, transgenic plants have been produced those express stress-associated proteins. In this study, we used immunoproteomic and two-dimensional difference gel electrophoresis (2D-DIGE) methods to investigate the allergenicity of transgenic potatoes expressing Arabidopsis DREB1A (dehydration responsive element-binding protein 1A), driven by the rd29A promoter or the 35S promoter. Immunoproteomic analysis using sera from potato-allergic patients revealed several immunoglobulin E (IgE)-binding protein spots. The patterns of protein binding were almost the same between transgenic and non-transgenic potatoes. The IgE-binding proteins in potato were identified as patatin precursors, a segment of serine protease inhibitor 2, and proteinase inhibitor II by matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) MS/MS. 2D-DIGE analysis revealed several differences in protein expression between non-transgenic potato and transgenic potato; those showing increased expression in transgenic potatoes were identified as precursors of patatin, a major potato allergen, and those showing decreased expression in transgenic potatoes were identified as lipoxygenase and glycogen (starch) synthase. These results suggested that transgenic potatoes may express slightly higher levels of allergens, but their IgE-binding patterns were almost the same as those of control potatoes. Further research on changes in protein expressions in response to environmental factors is required to confirm whether the differences observed in this study are due to gene transfection, rather than environmental factors.

  9. Identification of native Escherichia coli BL21 (DE3) proteins that bind to immobilized metal affinity chromatography under high imidazole conditions and use of 2D-DIGE to evaluate contamination pools with respect to recombinant protein expression level.

    PubMed

    Bartlow, Patrick; Uechi, Guy T; Cardamone, John J; Sultana, Tamanna; Fruchtl, McKinzie; Beitle, Robert R; Ataai, Mohammad M

    2011-08-01

    Immobilized metal affinity chromatography (IMAC) is a widely used purification tool for the production of active, soluble recombinant proteins. Escherichia coli proteins that routinely contaminate IMAC purifications have been characterized to date. The work presented here narrows that focus to the most problematic host proteins, those retaining nickel affinity under elevated imidazole conditions, using a single bind-and-elute step. Two-dimensional difference gel electrophoresis, a favored technique for resolving complex protein mixtures and evaluating their expression, here discerns variation in the soluble extract pools that are loaded in IMAC and the remaining contaminants with respect to varied levels of recombinant protein expression. Peptidyl-prolyl isomerase SlyD and catabolite activator protein (CAP) are here shown to be the most persistent contaminants and have greater prevalence at low target protein expression.

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

    PubMed Central

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

    2016-01-01

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

  11. Orthotropic Piezoelectricity in 2D Nanocellulose

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  12. Orthotropic Piezoelectricity in 2D Nanocellulose

    PubMed Central

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

    2016-01-01

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

  13. Orthotropic Piezoelectricity in 2D Nanocellulose.

    PubMed

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

    2016-10-06

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

  14. 2D microwave imaging reflectometer electronics

    SciTech Connect

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

    2014-11-15

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

  15. Large Area Synthesis of 2D Materials

    NASA Astrophysics Data System (ADS)

    Vogel, Eric

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

  16. 2D microwave imaging reflectometer electronics.

    PubMed

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

    2014-11-01

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

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

    PubMed

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

    2016-12-08

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

  18. Marmoset cytochrome P450 2D8 in livers and small intestines metabolizes typical human P450 2D6 substrates, metoprolol, bufuralol and dextromethorphan.

    PubMed

    Uehara, Shotaro; Uno, Yasuhiro; Hagihira, Yuya; Murayama, Norie; Shimizu, Makiko; Inoue, Takashi; Sasaki, Erika; Yamazaki, Hiroshi

    2015-01-01

    1. Although the New World non-human primate, the common marmoset (Callithrix jacchus), is a potentially useful animal model, comprehensive understanding of drug metabolizing enzymes is insufficient. 2. A cDNA encoding a novel cytochrome P450 (P450) 2D8 was identified in marmosets. The amino acid sequence deduced from P450 2D8 cDNA showed a high sequence identity (83-86%) with other primate P450 2Ds. Phylogenetic analysis showed that marmoset P450 2D8 was closely clustered with human P450 2D6, unlike P450 2Ds of miniature pig, dog, rabbit, guinea pig, mouse or rat. 3. Marmoset P450 2D8 mRNA was predominantly expressed in the liver and small intestine among the tissues types analyzed, whereas marmoset P450 2D6 mRNA was expressed predominantly in the liver where P450 2D protein was detected by immunoblotting. 4. By metabolic assays using marmoset P450 2D8 protein heterologously expressed in Escherichia coli, although P450 2D8 exhibits lower catalytic efficiency compared to marmoset and human P450 2D6 enzymes, P450 2D8 mediated O-demethylations of metoprolol and dextromethorphan and bufuralol 1'-hydroxylation. 5. These results suggest that marmoset P450 2D8 (also expressed in the extrahepatic tissues) has potential roles in drug metabolism in a similar manner to those of human and marmoset P450 2D6.

  19. 2D Distributed Sensing Via TDR

    DTIC Science & Technology

    2007-11-02

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

  20. Inkjet printing of 2D layered materials.

    PubMed

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

    2014-11-10

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

  1. Parallel Stitching of 2D Materials.

    PubMed

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

    2016-03-23

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

  2. Parallel stitching of 2D materials

    DOE PAGES

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

    2016-01-27

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

  3. 2d-LCA - an alternative to x-wires

    NASA Astrophysics Data System (ADS)

    Puczylowski, Jaroslaw; Hölling, Michael; Peinke, Joachim

    2014-11-01

    The 2d-Laser Cantilever Anemometer (2d-LCA) is an innovative sensor for two-dimensional velocity measurements in fluids. It uses a micostructured cantilever made of silicon and SU-8 as a sensing element and is capable of performing mesurements with extremly high temporal resolutions up to 150 kHz. The size of the cantilever defines its spatial resolution, which is in the order of 150 μm only. Another big feature is a large angular range of 180° in total. The 2d-LCA has been developed as an alternative measurement method to x-wires with the motivation to create a sensor that can operate in areas where the use of hot-wire anemometry is difficult. These areas include measurements in liquids and in near-wall or particle-laden flows. Unlike hot-wires, the resolution power of the 2d-LCA does not decrease with increasing flow velocity, making it particularly suitable for measurements in high speed flows. Comparative measurements with the 2d-LCA and hot-wires have been carried out in order to assess the performance of the new anemometer. The data of both measurement techniques were analyzed using the same stochastic methods including a spectral analysis as well as an inspection of increment statistics and structure functions. Furthermore, key parameters, such as mean values of both velocity components, angles of attack and the characteristic length scales were determined from both data sets. The analysis reveals a great agreement between both anemometers and thus confirms the new approach.

  4. Development of a MEMS 2D separations device

    NASA Astrophysics Data System (ADS)

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

    2004-12-01

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

  5. 2D nanomaterials based electrochemical biosensors for cancer diagnosis.

    PubMed

    Wang, Lu; Xiong, Qirong; Xiao, Fei; Duan, Hongwei

    2017-03-15

    Cancer is a leading cause of death in the world. Increasing evidence has demonstrated that early diagnosis holds the key towards effective treatment outcome. Cancer biomarkers are extensively used in oncology for cancer diagnosis and prognosis. Electrochemical sensors play key roles in current laboratory and clinical analysis of diverse chemical and biological targets. Recent development of functional nanomaterials offers new possibilities of improving the performance of electrochemical sensors. In particular, 2D nanomaterials have stimulated intense research due to their unique array of structural and chemical properties. The 2D materials of interest cover broadly across graphene, graphene derivatives (i.e., graphene oxide and reduced graphene oxide), and graphene-like nanomaterials (i.e., 2D layered transition metal dichalcogenides, graphite carbon nitride and boron nitride nanomaterials). In this review, we summarize recent advances in the synthesis of 2D nanomaterials and their applications in electrochemical biosensing of cancer biomarkers (nucleic acids, proteins and some small molecules), and present a personal perspective on the future direction of this area.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-02-06

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

  8. 2D FT-IR Study of Compositional and Structural Change in Developing Cotton Fibers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two-dimensional (2D) correlation analysis was applied to characterize the ATR spectral intensity fluctuations of immature and mature cotton fibers. Prior to 2D analysis, the spectra were leveled to zero at the peak intensity of 1800 cm-1 and then were normalized at the peak intensity of 660 cm-1 to ...

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

    PubMed

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

    2016-01-01

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

  10. Effects of Clostridium difficile Toxin A on the proteome of colonocytes studied by differential 2D electrophoresis.

    PubMed

    Zeiser, Johannes J; Klodmann, Jennifer; Braun, Hans-Peter; Gerhard, Ralf; Just, Ingo; Pich, Andreas

    2011-12-21

    Clostridium difficile is a spore-forming anaerobic pathogen, commonly associated with severe diarrhea or life-threatening pseudomembraneous colitis. Its main virulence factors are the single-chain, multi-domain toxin A (TcdA) and B (TcdB). Their glucosyltransferase domain selectively inactivates Rho proteins leading to a reorganization of the cytoskeleton. To study exclusively glucosyltransferase-dependent molecular effects of TcdA, human colonic cells (Caco-2) were treated with recombinant wild type TcdA and the glucosyltransferase deficient variant of the toxin, TcdA(gd) for 24h. Changes in the protein pattern of the colonic cells were investigated by 2-D DIGE and LCMS/MS methodology combined with detailed proteome mapping. gdTcdA did not induce any detectable significant changes in the protein pattern. Comparing TcdA-treated cells with a control group revealed seven spots of higher and two of lower intensity (p<0.05). Three proteins are involved in the assembly of the cytoskeleton (β-actin, ezrin, and DPYL2) and four are involved in metabolism and/or oxidative stress response (ubiquitin, DHE3, MCCB, FABPL) and two in regulatory processes (FUBP1, AL1A1). These findings correlate well to known effects of TcdA like the reorganization of the cytoskeleton and stress the importance of Rho protein glucosylation for the pathogenic effects of TcdA.

  11. Pharmacogenetics in American Indian Populations: Analysis of CYP2D6, CYP3A4, CYP3A5, and CYP2C9 in the Confederated Salish and Kootenai Tribes

    PubMed Central

    Fohner, Alison; Muzquiz, LeeAnna I.; Austin, Melissa A.; Gaedigk, Andrea; Gordon, Adam; Thornton, Timothy; Rieder, Mark J.; Pershouse, Mark A.; Putnam, Elizabeth A.; Howlett, Kevin; Beatty, Patrick; Thummel, Kenneth E.; Woodahl, Erica L.

    2014-01-01

    Objectives Cytochrome P450 enzymes play a dominant role in drug elimination and variation in these genes is a major source of interindividual differences in drug response. Little is known, however, about pharmacogenetic variation in American Indian and Alaska Native (AI/AN) populations. We have developed a partnership with the Confederated Salish and Kootenai Tribes (CSKT) in northwestern Montana to address this knowledge gap. Methods We resequenced CYP2D6 in 187 CSKT subjects and CYP3A4, CYP3A5, and CYP2C9 in 94 CSKT subjects. Results We identified 67 variants in CYP2D6, 15 in CYP3A4, 10 in CYP3A5, and 41 in CYP2C9. The most common CYP2D6 alleles were CYP2D6*4 and *41 (20.86 and 11.23%, respectively). CYP2D6*3, *5, *6, *9, *10, *17, *28, *33, *35, *49, *1xN, *2xN, and *4xN frequencies were less than 2%. CYP3A5*3, CYP3A4*1G, and *1B were detected with frequencies of 92.47, 26.81, and 2.20%, respectively. Allelic variation in CYP2C9 was low: CYP2C9*2 (5.17%) and *3 (2.69%). In general, allele frequencies in CYP2D6, CYP2C9 and CYP3A5 were similar to those observed in European Americans. There was, however, a marked divergence in CYP3A4 for the CYP3A4*1G allele. We also observed low levels of linkage between CYP3A4*1G and CYP3A5*1 in the CSKT. The combination of nonfunctional CYP3A5*3 and putative reduced function CYP3A4*1G alleles may predict diminished clearance of CYP3A substrates. Conclusions These results highlight the importance of conducting pharmacogenomic research in AI/AN populations and demonstrate that extrapolation from other populations is not appropriate. This information could help to optimize drug therapy for the CSKT population. PMID:23778323

  12. Compatible embedding for 2D shape animation.

    PubMed

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

    2009-01-01

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

  13. Schottky diodes from 2D germanane

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  14. Extrinsic Cation Selectivity of 2D Membranes

    PubMed Central

    2017-01-01

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

  15. Explicit 2-D Hydrodynamic FEM Program

    SciTech Connect

    Lin, Jerry

    1996-08-07

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

  16. Cytochrome P-450 2D6 (CYP2D6) Genotype and Breast Cancer Recurrence in Tamoxifen-Treated Patients: Evaluating the Importance of Loss of Heterozygosity.

    PubMed

    Ahern, Thomas P; Hertz, Daniel L; Damkier, Per; Ejlertsen, Bent; Hamilton-Dutoit, Stephen J; Rae, James M; Regan, Meredith M; Thompson, Alastair M; Lash, Timothy L; Cronin-Fenton, Deirdre P

    2017-01-15

    Tamoxifen therapy for estrogen receptor-positive breast cancer reduces the risk of recurrence by approximately one-half. Cytochrome P-450 2D6, encoded by the polymorphic cytochrome P-450 2D6 gene (CYP2D6), oxidizes tamoxifen to its most active metabolites. Steady-state concentrations of endoxifen (4-hydroxy-N-desmethyltamoxifen), the most potent antiestrogenic metabolite, are reduced in women whose CYP2D6 genotypes confer poor enzyme function. Thirty-one studies of the association of CYP2D6 genotype with breast cancer survival have yielded heterogeneous results. Some influential studies genotyped DNA from tumor-infiltrated tissues, and their results may have been susceptible to germline genotype misclassification from loss of heterozygosity at the CYP2D6 locus. We systematically reviewed 6 studies of concordance between genotypes obtained from paired nonneoplastic and breast tumor-infiltrated tissues, all of which showed excellent CYP2D6 genotype agreement. We applied these concordance data to a quantitative bias analysis of the subset of the 31 studies that were based on genotypes from tumor-infiltrated tissue to examine whether genotyping errors substantially biased estimates of association. The bias analysis showed negligible bias by discordant genotypes. Summary estimates of association, with or without bias adjustment, indicated no clinically important association between CYP2D6 genotype and breast cancer survival in tamoxifen-treated women.

  17. Quasiparticle interference in unconventional 2D systems

    NASA Astrophysics Data System (ADS)

    Chen, Lan; Cheng, Peng; Wu, Kehui

    2017-03-01

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

  18. Compact 2-D graphical representation of DNA

    NASA Astrophysics Data System (ADS)

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

    2003-05-01

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

  19. 2D Metals by Repeated Size Reduction.

    PubMed

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

    2016-10-01

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

  20. Realistic and efficient 2D crack simulation

    NASA Astrophysics Data System (ADS)

    Yadegar, Jacob; Liu, Xiaoqing; Singh, Abhishek

    2010-04-01

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

  1. Engineering light outcoupling in 2D materials.

    PubMed

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

    2015-02-11

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

  2. Irreversibility-inversions in 2D turbulence

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  3. Half-metallicity in 2D organometallic honeycomb frameworks.

    PubMed

    Sun, Hao; Li, Bin; Zhao, Jin

    2016-10-26

    Half-metallic materials with a high Curie temperature (T C) have many potential applications in spintronics. Magnetic metal free two-dimensional (2D) half-metallic materials with a honeycomb structure contain graphene-like Dirac bands with π orbitals and show excellent aspects in transport properties. In this article, by investigating a series of 2D organometallic frameworks with a honeycomb structure using first principles calculations, we study the origin of forming half-metallicity in this kind of 2D organometallic framework. Our analysis shows that charge transfer and covalent bonding are two crucial factors in the formation of half-metallicity in organometallic frameworks. (i) Sufficient charge transfer from metal atoms to the molecules is essential to form the magnetic centers. (ii) These magnetic centers need to be connected through covalent bonding, which guarantee the strong ferromagnetic (FM) coupling. As examples, the organometallic frameworks composed by (1,3,5)-benzenetricarbonitrile (TCB) molecules with noble metals (Au, Ag, Cu) show half-metallic properties with T C as high as 325 K. In these organometallic frameworks, the strong electronegative cyano-groups (CN groups) drive the charge transfer from metal atoms to the TCB molecules, forming the local magnetic centers. These magnetic centers experience strong FM coupling through the d-p covalent bonding. We propose that most of the 2D organometallic frameworks composed by molecule-CN-noble metal honeycomb structures contain similar half metallicity. This is verified by replacing TCB molecules with other organic molecules. Although the TCB-noble metal organometallic framework has not yet been synthesized, we believe the development of synthesizing techniques and facility will enable the realization of them. Our study provides new insight into the 2D half-metallic material design for the potential applications in nanotechnology.

  4. 2D/3D Image Registration using Regression Learning

    PubMed Central

    Chou, Chen-Rui; Frederick, Brandon; Mageras, Gig; Chang, Sha; Pizer, Stephen

    2013-01-01

    In computer vision and image analysis, image registration between 2D projections and a 3D image that achieves high accuracy and near real-time computation is challenging. In this paper, we propose a novel method that can rapidly detect an object’s 3D rigid motion or deformation from a 2D projection image or a small set thereof. The method is called CLARET (Correction via Limited-Angle Residues in External Beam Therapy) and consists of two stages: registration preceded by shape space and regression learning. In the registration stage, linear operators are used to iteratively estimate the motion/deformation parameters based on the current intensity residue between the target projec-tion(s) and the digitally reconstructed radiograph(s) (DRRs) of the estimated 3D image. The method determines the linear operators via a two-step learning process. First, it builds a low-order parametric model of the image region’s motion/deformation shape space from its prior 3D images. Second, using learning-time samples produced from the 3D images, it formulates the relationships between the model parameters and the co-varying 2D projection intensity residues by multi-scale linear regressions. The calculated multi-scale regression matrices yield the coarse-to-fine linear operators used in estimating the model parameters from the 2D projection intensity residues in the registration. The method’s application to Image-guided Radiation Therapy (IGRT) requires only a few seconds and yields good results in localizing a tumor under rigid motion in the head and neck and under respiratory deformation in the lung, using one treatment-time imaging 2D projection or a small set thereof. PMID:24058278

  5. Half-metallicity in 2D organometallic honeycomb frameworks

    NASA Astrophysics Data System (ADS)

    Sun, Hao; Li, Bin; Zhao, Jin

    2016-10-01

    Half-metallic materials with a high Curie temperature (T C) have many potential applications in spintronics. Magnetic metal free two-dimensional (2D) half-metallic materials with a honeycomb structure contain graphene-like Dirac bands with π orbitals and show excellent aspects in transport properties. In this article, by investigating a series of 2D organometallic frameworks with a honeycomb structure using first principles calculations, we study the origin of forming half-metallicity in this kind of 2D organometallic framework. Our analysis shows that charge transfer and covalent bonding are two crucial factors in the formation of half-metallicity in organometallic frameworks. (i) Sufficient charge transfer from metal atoms to the molecules is essential to form the magnetic centers. (ii) These magnetic centers need to be connected through covalent bonding, which guarantee the strong ferromagnetic (FM) coupling. As examples, the organometallic frameworks composed by (1,3,5)-benzenetricarbonitrile (TCB) molecules with noble metals (Au, Ag, Cu) show half-metallic properties with T C as high as 325 K. In these organometallic frameworks, the strong electronegative cyano-groups (CN groups) drive the charge transfer from metal atoms to the TCB molecules, forming the local magnetic centers. These magnetic centers experience strong FM coupling through the d-p covalent bonding. We propose that most of the 2D organometallic frameworks composed by molecule—CN—noble metal honeycomb structures contain similar half metallicity. This is verified by replacing TCB molecules with other organic molecules. Although the TCB-noble metal organometallic framework has not yet been synthesized, we believe the development of synthesizing techniques and facility will enable the realization of them. Our study provides new insight into the 2D half-metallic material design for the potential applications in nanotechnology.

  6. Two-dimensional difference gel electrophoresis applied for analytical proteomics: fundamentals and applications to the study of plant proteomics.

    PubMed

    Arruda, Sandra Cristina Capaldi; Barbosa, Herbert de Sousa; Azevedo, Ricardo Antunes; Arruda, Marco Aurélio Zezzi

    2011-10-21

    The present review reports the principles, fundamentals and some applications of two-dimensional difference gel electrophoresis for analytical proteomics based on plant proteome analysis, also emphasizing some advantages of 2-D DIGE over 2-D PAGE techniques. Some fluorescent protein labeling reagents, methods of protein labeling, models of 2-D DIGE experiments, and some limitations of this technique are presented and discussed in terms of 2-D DIGE plant proteomes. Finally, some practical applications of this technique are pointed out, emphasizing its potentialities in plant proteomics.

  7. Three-dimensional textural analysis of products from the Vulcanian explosions of Soufrière Hills Volcano, Montserrat, 1997, using X-ray computed microtomography: comparison with 2D data and implications for vesiculation processes

    NASA Astrophysics Data System (ADS)

    Giachetti, T.; Burgisser, A.; Druitt, T. H.

    2009-12-01

    X-ray computed microtomography is a powerful, non-destructive method for imaging textures and for quantifying vesicle spatial relationships and size distributions. It was applied to one breadcrust bomb and three pumices from the 1997 Vulcanian explosions of the Soufrière Hills Volcano, Montserrat. A detailed 2D textural study of these same samples, including high-resolution vesicle size distributions, has already been carried out. In order to cover the wide range of vesicle and crystal sizes (few µm to a few hundreds of µm), we acquired tomographic images at three magnifications (0.37, 4.0 and 17.4 µm/voxel) on each sample. Each magnification covers only part of the whole vesicle size range, but with large overlaps. Vesicle walls were reconstructed using ImageJ and 3DMA_Rock softwares, and a Matlab code was written to combine the data from the three stacks and to calculate vesicle size and sphericity distributions for the whole sample. Comparison with the 2D results show only minor differences in the vesicle size distributions. Cumulative vesicle number densities obtained by the two methods are of the same order of magnitude (~1015 m-3 of glass). Three vesicle populations are recognized in the samples, the same three recognized in 2D, although minor shifts in modes are observed. As in 2D, vesicle sphericity decreases with size, vesicle shape being progressively more complicated as the vesicle grows and coalesces with neighbours. Coalescence in all samples appears to occur between neighbouring vesicles of any sizes, but, as intuitively expected, the larger the vesicle, the more connected it is. Our results show that coalescence affected indifferently pre- and syn-eruptive bubbles. This suggests that the syn-eruptive gas was rapidly connected to large-scale pathways through which it could escape. Depending on clast permeability, this mechanism has the potential to double the amount of gas available for propulsion of the Vulcanian jet.

  8. 2D superconductivity by ionic gating

    NASA Astrophysics Data System (ADS)

    Iwasa, Yoshi

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

  9. Krüppel-like factor 9 promotes hepatic cytochrome P450 2D6 expression during pregnancy in CYP2D6-humanized mice.

    PubMed

    Koh, Kwi Hye; Pan, Xian; Zhang, Wei; McLachlan, Alan; Urrutia, Raul; Jeong, Hyunyoung

    2014-12-01

    Cytochrome P450 2D6 (CYP2D6), a major drug-metabolizing enzyme, is responsible for metabolism of approximately 25% of marketed drugs. Clinical evidence indicates that metabolism of CYP2D6 substrates is increased during pregnancy, but the underlying mechanisms remain unclear. To identify transcription factors potentially responsible for CYP2D6 induction during pregnancy, a panel of genes differentially expressed in the livers of pregnant versus nonpregnant CYP2D6-humanized (tg-CYP2D6) mice was compiled via microarray experiments followed by real-time quantitative reverse-transcription polymerase chain reaction(qRT-PCR) verification. As a result, seven transcription factors-activating transcription factor 5 (ATF5), early growth response 1 (EGR1), forkhead box protein A3 (FOXA3), JUNB, Krüppel-like factor 9 (KLF9), KLF10, and REV-ERBα-were found to be up-regulated in liver during pregnancy. Results from transient transfection and promoter reporter gene assays indicate that KLF9 itself is a weak transactivator of CYP2D6 promoter but significantly enhances CYP2D6 promoter transactivation by hepatocyte nuclear factor 4 (HNF4α), a known transcriptional activator of CYP2D6 expression. The results from deletion and mutation analysis of CYP2D6 promoter activity identified a KLF9 putative binding motif at -22/-14 region to be critical in the potentiation of HNF4α-induced transactivation of CYP2D6. Electrophoretic mobility shift assays revealed a direct binding of KLF9 to the putative KLF binding motif. Results from chromatin immunoprecipitation assay showed increased recruitment of KLF9 to CYP2D6 promoter in the livers of tg-CYP2D6 mice during pregnancy. Taken together, our data suggest that increased KLF9 expression is in part responsible for CYP2D6 induction during pregnancy via the potentiation of HNF4α transactivation of CYP2D6.

  10. Extreme Growth of Enstrophy on 2D Bounded Domains

    NASA Astrophysics Data System (ADS)

    Protas, Bartosz; Sliwiak, Adam

    2016-11-01

    We study the vortex states responsible for the largest instantaneous growth of enstrophy possible in viscous incompressible flow on 2D bounded domain. The goal is to compare these results with estimates obtained using mathematical analysis. This problem is closely related to analogous questions recently considered in the periodic setting on 1D, 2D and 3D domains. In addition to systematically characterizing the most extreme behavior, these problems are also closely related to the open question of the finite-time singularity formation in the 3D Navier-Stokes system. We demonstrate how such extreme vortex states can be found as solutions of constrained variational optimization problems which in the limit of small enstrophy reduce to eigenvalue problems. Computational results will be presented for circular and square domains emphasizing the effect of geometric singularities (corners of the domain) on the structure of the extreme vortex states. Supported by an NSERC (Canada) Discovery Grant.

  11. 2D FEM Heat Transfer & E&M Field Code

    SciTech Connect

    1992-04-02

    TOPAZ and TOPAZ2D are two-dimensional implicit finite element computer codes for heat transfer analysis. TOPAZ2D can also be used to solve electrostatic and magnetostatic problems. The programs solve for the steady-state or transient temperature or electrostatic and magnetostatic potential field on two-dimensional planar or axisymmetric geometries. Material properties may be temperature or potential-dependent and either isotropic or orthotropic. A variety of time and temperature-dependent boundary conditions can be specified including temperature, flux, convection, and radiation. By implementing the user subroutine feature, users can model chemical reaction kinetics and allow for any type of functional representation of boundary conditions and internal heat generation. The programs can solve problems of diffuse and specular band radiation in an enclosure coupled with conduction in the material surrounding the enclosure. Additional features include thermal contact resistance across an interface, bulk fluids, phase change, and energy balances.

  12. Periodically sheared 2D Yukawa systems

    SciTech Connect

    Kovács, Anikó Zsuzsa; Hartmann, Peter; Donkó, Zoltán

    2015-10-15

    We present non-equilibrium molecular dynamics simulation studies on the dynamic (complex) shear viscosity of a 2D Yukawa system. We have identified a non-monotonic frequency dependence of the viscosity at high frequencies and shear rates, an energy absorption maximum (local resonance) at the Einstein frequency of the system at medium shear rates, an enhanced collective wave activity, when the excitation is near the plateau frequency of the longitudinal wave dispersion, and the emergence of significant configurational anisotropy at small frequencies and high shear rates.

  13. ENERGY LANDSCAPE OF 2D FLUID FORMS

    SciTech Connect

    Y. JIANG; ET AL

    2000-04-01

    The equilibrium states of 2D non-coarsening fluid foams, which consist of bubbles with fixed areas, correspond to local minima of the total perimeter. (1) The authors find an approximate value of the global minimum, and determine directly from an image how far a foam is from its ground state. (2) For (small) area disorder, small bubbles tend to sort inwards and large bubbles outwards. (3) Topological charges of the same sign repel while charges of opposite sign attract. (4) They discuss boundary conditions and the uniqueness of the pattern for fixed topology.

  14. Codon Constraints on Closed 2D Shapes,

    DTIC Science & Technology

    2014-09-26

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

  15. Fracture surfaces of heterogeneous materials: A 2D solvable model

    NASA Astrophysics Data System (ADS)

    Katzav, E.; Adda-Bedia, M.; Derrida, B.

    2007-05-01

    Using an elastostatic description of crack growth based on the Griffith criterion and the principle of local symmetry, we present a stochastic model describing the propagation of a crack tip in a 2D heterogeneous brittle material. The model ensures the stability of straight cracks and allows for the study of the roughening of fracture surfaces. When neglecting the effect of the nonsingular stress, the problem becomes exactly solvable and yields analytic predictions for the power spectrum of the paths. This result suggests an alternative to the conventional power law analysis often used in the analysis of experimental data.

  16. A comparative 2D QSAR study on a series of hydroxamic acid-based histone deacetylase inhibitors vis-à-vis comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA).

    PubMed

    Bajpai, Anubha; Agarwal, Neeraj; Gupta, Satya P

    2014-06-01

    A quantitative structure-activity relationship (QSAR) study was performed on a series of indole amide analogues reported by Dai et al. [Bioorg Med Chem Lett (2003), 13, 1897-1901] to act as histone deacetylase (HDAC) inhibitors. The multiple regression analysis (MRA) revealed a model showing the significant dependence of the activity on molar refractivity (MR) and global topological charge index (GTCI) of the compounds, suggesting that inhibition of the HDAC by this series of compounds might involve the dispersion interaction with the receptor, where charge transfer between pairs of atoms might greatly help to polarize the molecule. The MRA results were then compared with those obtained by Guo et al. [Bioorg Med Chem (2005), 13, 5424-5434] by comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). It was found that MRA gave as good results and had as good predictive ability as CoMFA and CoMSIA. Besides, MRA was also able to throw the light on the physicochemical properties of the molecules that were involved in drug-receptor interactions, while CoMFA and CoMSIA could not. The dispersion interaction between the molecule and the active site of the receptor is suggested to be the main interaction.

  17. 2D NMR analysis of highly restricted internal rotation in 2-methylthio-3H-4- p-bromophenyl)-7-[( ortho- and para-substituted)-phenylthio]-1,5-benzodiazepines

    NASA Astrophysics Data System (ADS)

    Cortes C., E.; Becerra L., M. I.; Osornio P., Y. M.; Díaz T., E.; Jankowski, K.

    2000-08-01

    The complete assignments of twelve 4-ary1-7-thioary1-1,5-benzodiazepines 1H and 13C spectra, performed with the use of high resolution variable solvent and temperature 1D and 2D techniques (e.g. HOMOCOSY, NOESY, HMQC and HMBC), lead to the determination of conformational equilibria between two rotamers having the aromatic ring of the thioaryl oriented in a perpendicular or helical orientation toward the benzodiazepine ring. The restricted rotation was evaluated from the population of these conformers.

  18. Implications for Extraterrestrial Hydrocarbon Chemistry: Analysis of Ethylene (C2H4) and D4-Ethylene (C2D4) Ices Exposed to Ionizing Radiation via Combined Infrared Spectroscopy and Reflectron Time-of-flight Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Abplanalp, Matthew J.; Kaiser, Ralf I.

    2017-02-01

    The processing of the hydrocarbon ice, ethylene (C2H4/C2D4), via energetic electrons, thus simulating the processes in the track of galactic cosmic-ray particles, was carried out in an ultrahigh vacuum apparatus. The chemical evolution of the ices was monitored online and in situ utilizing Fourier transform infrared spectroscopy (FTIR) and during temperature programmed desorption, via a quadrupole mass spectrometer utilizing electron impact ionization (EI-QMS) and a reflectron time-of-flight mass spectrometer utilizing a photoionization source (PI-ReTOF-MS). Several previous in situ studies of ethylene ice irradiation using FTIR were substantiated with the detection of six products: [CH4 (CD4)], acetylene [C2H2 (C2D2)], the ethyl radical [C2H5 (C2D5)], ethane [C2H6 (C2D6)], 1-butene [C4H8 (C4D8)], and n-butane [C4H10 (C4D10)]. Contrary to previous gas phase studies, the PI-ReTOF-MS detected several groups of hydrocarbon with varying degrees of saturation: C n H2n+2 (n = 4–10), C n H2n (n = 2–12, 14, 16), C n H2n‑2 (n = 3–12, 14, 16), C n H2n‑4 (n = 4–12, 14, 16), C n H2n‑6 (n = 4–10, 12), C n H2n‑8 (n = 6–10), and C n H2n‑10 (n = 6–10). Multiple laboratory studies have shown the facile production of ethylene from methane, which is a known ice constituent in the interstellar medium. Various astrophysically interesting molecules can be associated with the groups detected here, such as allene/methylacetylene (C3H4) or 1, 3-butadiene (C4H6) and its isomers, which have been shown to lead to polycyclic aromatic hydrocarbons. Finally, several hydrocarbon groups detected here are unique to ethylene ice versus ethane ice and may provide understanding of how complex hydrocarbons form in astrophysical environments.

  19. Remarks on thermalization in 2D CFT

    NASA Astrophysics Data System (ADS)

    de Boer, Jan; Engelhardt, Dalit

    2016-12-01

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

  20. Microwave Assisted 2D Materials Exfoliation

    NASA Astrophysics Data System (ADS)

    Wang, Yanbin

    Two-dimensional materials have emerged as extremely important materials with applications ranging from energy and environmental science to electronics and biology. Here we report our discovery of a universal, ultrafast, green, solvo-thermal technology for producing excellent-quality, few-layered nanosheets in liquid phase from well-known 2D materials such as such hexagonal boron nitride (h-BN), graphite, and MoS2. We start by mixing the uniform bulk-layered material with a common organic solvent that matches its surface energy to reduce the van der Waals attractive interactions between the layers; next, the solutions are heated in a commercial microwave oven to overcome the energy barrier between bulk and few-layers states. We discovered the minutes-long rapid exfoliation process is highly temperature dependent, which requires precise thermal management to obtain high-quality inks. We hypothesize a possible mechanism of this proposed solvo-thermal process; our theory confirms the basis of this novel technique for exfoliation of high-quality, layered 2D materials by using an as yet unknown role of the solvent.

  1. 2-D or not 2-D, that is the question: A Northern California test

    SciTech Connect

    Mayeda, K; Malagnini, L; Phillips, W S; Walter, W R; Dreger, D

    2005-06-06

    Reliable estimates of the seismic source spectrum are necessary for accurate magnitude, yield, and energy estimation. In particular, how seismic radiated energy scales with increasing earthquake size has been the focus of recent debate within the community and has direct implications on earthquake source physics studies as well as hazard mitigation. The 1-D coda methodology of Mayeda et al. has provided the lowest variance estimate of the source spectrum when compared against traditional approaches that use direct S-waves, thus making it ideal for networks that have sparse station distribution. The 1-D coda methodology has been mostly confined to regions of approximately uniform complexity. For larger, more geophysically complicated regions, 2-D path corrections may be required. The complicated tectonics of the northern California region coupled with high quality broadband seismic data provides for an ideal ''apples-to-apples'' test of 1-D and 2-D path assumptions on direct waves and their coda. Using the same station and event distribution, we compared 1-D and 2-D path corrections and observed the following results: (1) 1-D coda results reduced the amplitude variance relative to direct S-waves by roughly a factor of 8 (800%); (2) Applying a 2-D correction to the coda resulted in up to 40% variance reduction from the 1-D coda results; (3) 2-D direct S-wave results, though better than 1-D direct waves, were significantly worse than the 1-D coda. We found that coda-based moment-rate source spectra derived from the 2-D approach were essentially identical to those from the 1-D approach for frequencies less than {approx}0.7-Hz, however for the high frequencies (0.7{le} f {le} 8.0-Hz), the 2-D approach resulted in inter-station scatter that was generally 10-30% smaller. For complex regions where data are plentiful, a 2-D approach can significantly improve upon the simple 1-D assumption. In regions where only 1-D coda correction is available it is still preferable over 2

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

    NASA Technical Reports Server (NTRS)

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

    2002-01-01

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

  3. Parallel-pipeline 2-D DCT/IDCT processor chip

    NASA Astrophysics Data System (ADS)

    Ruiz, G. A.; Michell, J. A.; Buron, A.

    2005-06-01

    This paper describes the architecture of an 8x8 2-D DCT/IDCT processor with high throughput and a cost-effective architecture. The 2D DCT/IDCT is calculated using the separability property, so that its architecture is made up of two 1-D processors and a transpose buffer (TB) as intermediate memory. This transpose buffer presents a regular structure based on D-type flip-flops with a double serial input/output data-flow very adequate for pipeline architectures. The processor has been designed with parallel and pipeline architecture to attain high throughput, reduced hardware and maximum efficiency in all arithmetic elements. This architecture allows that the processing elements and arithmetic units work in parallel at half the frequency of the data input rate, except for normalization of transform which it is done in a multiplier operating at maximum frequency. Moreover, it has been verified that the precision analysis of the proposed processor meets the demands of IEEE Std. 1180-1990 used in video codecs ITU-T H.261 and ITU-T H.263. This processor has been conceived using a standard cell design methodology and manufactured in a 0.35-μm CMOS CSD 3M/2P 3.3V process. It has an area of 6.25 mm2 (the core is 3mm2) and contains a total of 11.7k gates, of which 5.8k gates are flip-flops. A data input rate frequency of 300MHz has been established with a latency of 172 cycles for the 2-D DCT and 178 cycles for the 2-D IDCT. The computing time of a block is close to 580ns. Its performances in computing speed as well as hardware complexity indicate that the proposed design is suitable for HDTV applications.

  4. Transition to turbulence: 2D directed percolation

    NASA Astrophysics Data System (ADS)

    Chantry, Matthew; Tuckerman, Laurette; Barkley, Dwight

    2016-11-01

    The transition to turbulence in simple shear flows has been studied for well over a century, yet in the last few years has seen major leaps forward. In pipe flow, this transition shows the hallmarks of (1 + 1) D directed percolation, a universality class of continuous phase transitions. In spanwisely confined Taylor-Couette flow the same class is found, suggesting the phenomenon is generic to shear flows. However in plane Couette flow the largest simulations and experiments to-date find evidence for a discrete transition. Here we study a planar shear flow, called Waleffe flow, devoid of walls yet showing the fundamentals of planar transition to turbulence. Working with a quasi-2D yet Navier-Stokes derived model of this flow we are able to attack the (2 + 1) D transition problem. Going beyond the system sizes previously possible we find all of the required scalings of directed percolation and thus establish planar shears flow in this class.

  5. 2D quantum gravity from quantum entanglement.

    PubMed

    Gliozzi, F

    2011-01-21

    In quantum systems with many degrees of freedom the replica method is a useful tool to study the entanglement of arbitrary spatial regions. We apply it in a way that allows them to backreact. As a consequence, they become dynamical subsystems whose position, form, and extension are determined by their interaction with the whole system. We analyze, in particular, quantum spin chains described at criticality by a conformal field theory. Its coupling to the Gibbs' ensemble of all possible subsystems is relevant and drives the system into a new fixed point which is argued to be that of the 2D quantum gravity coupled to this system. Numerical experiments on the critical Ising model show that the new critical exponents agree with those predicted by the formula of Knizhnik, Polyakov, and Zamolodchikov.

  6. Simulation of Yeast Cooperation in 2D.

    PubMed

    Wang, M; Huang, Y; Wu, Z

    2016-03-01

    Evolution of cooperation has been an active research area in evolutionary biology in decades. An important type of cooperation is developed from group selection, when individuals form spatial groups to prevent them from foreign invasions. In this paper, we study the evolution of cooperation in a mixed population of cooperating and cheating yeast strains in 2D with the interactions among the yeast cells restricted to their small neighborhoods. We conduct a computer simulation based on a game theoretic model and show that cooperation is increased when the interactions are spatially restricted, whether the game is of a prisoner's dilemma, snow drifting, or mutual benefit type. We study the evolution of homogeneous groups of cooperators or cheaters and describe the conditions for them to sustain or expand in an opponent population. We show that under certain spatial restrictions, cooperator groups are able to sustain and expand as group sizes become large, while cheater groups fail to expand and keep them from collapse.

  7. Graphene suspensions for 2D printing

    NASA Astrophysics Data System (ADS)

    Soots, R. A.; Yakimchuk, E. A.; Nebogatikova, N. A.; Kotin, I. A.; Antonova, I. V.

    2016-04-01

    It is shown that, by processing a graphite suspension in ethanol or water by ultrasound and centrifuging, it is possible to obtain particles with thicknesses within 1-6 nm and, in the most interesting cases, 1-1.5 nm. Analogous treatment of a graphite suspension in organic solvent yields eventually thicker particles (up to 6-10 nm thick) even upon long-term treatment. Using the proposed ink based on graphene and aqueous ethanol with ethylcellulose and terpineol additives for 2D printing, thin (~5 nm thick) films with sheet resistance upon annealing ~30 MΩ/□ were obtained. With the ink based on aqueous graphene suspension, the sheet resistance was ~5-12 kΩ/□ for 6- to 15-nm-thick layers with a carrier mobility of ~30-50 cm2/(V s).

  8. Canard configured aircraft with 2-D nozzle

    NASA Technical Reports Server (NTRS)

    Child, R. D.; Henderson, W. P.

    1978-01-01

    A closely-coupled canard fighter with vectorable two-dimensional nozzle was designed for enhanced transonic maneuvering. The HiMAT maneuver goal of a sustained 8g turn at a free-stream Mach number of 0.9 and 30,000 feet was the primary design consideration. The aerodynamic design process was initiated with a linear theory optimization minimizing the zero percent suction drag including jet effects and refined with three-dimensional nonlinear potential flow techniques. Allowances were made for mutual interference and viscous effects. The design process to arrive at the resultant configuration is described, and the design of a powered 2-D nozzle model to be tested in the LRC 16-foot Propulsion Wind Tunnel is shown.

  9. Numerical Evaluation of 2D Ground States

    NASA Astrophysics Data System (ADS)

    Kolkovska, Natalia

    2016-02-01

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

  10. Flexible and Scalable Full‐Length CYP2D6 Long Amplicon PacBio Sequencing

    PubMed Central

    Vossen, Rolf H.A.M.; Anvar, Seyed Yahya; Allard, William G.; Guchelaar, Henk‐Jan; White, Stefan J.; den Dunnen, Johan T.; Swen, Jesse J.; van der Straaten, Tahar

    2017-01-01

    ABSTRACT Cytochrome P450 2D6 (CYP2D6) is among the most important genes involved in drug metabolism. Specific variants are associated with changes in the enzyme's amount and activity. Multiple technologies exist to determine these variants, like the AmpliChip CYP450 test, Taqman qPCR, or Second‐Generation Sequencing, however, sequence homology between cytochrome P450 genes and pseudogene CYP2D7 impairs reliable CYP2D6 genotyping, and variant phasing cannot accurately be determined using these assays. To circumvent this, we sequenced CYP2D6 using the Pacific Biosciences RSII and obtained high‐quality, full‐length, phased CYP2D6 sequences, enabling accurate variant calling and haplotyping of the entire gene‐locus including exonic, intronic, and upstream and downstream regions. Unphased diplotypes (Roche AmpliChip CYP450 test) were confirmed for 24 of the 25 samples, including gene duplications. Cases with gene deletions required additional specific assays to resolve. In total, 61 unique variants were detected, including variants that had not previously been associated with specific haplotypes. To further aid genomic analysis using standard reference sequences, we have established an LOVD‐powered CYP2D6 gene‐variant database, and added all reference haplotypes and data reported here. We conclude that our CYP2D6 genotyping approach produces reliable CYP2D6 diplotypes and reveals information about additional variants, including phasing and copy‐number variation. PMID:28044414

  11. Differential patterns of 2D location versus depth decoding along the visual hierarchy.

    PubMed

    Finlayson, Nonie J; Zhang, Xiaoli; Golomb, Julie D

    2017-02-15

    Visual information is initially represented as 2D images on the retina, but our brains are able to transform this input to perceive our rich 3D environment. While many studies have explored 2D spatial representations or depth perception in isolation, it remains unknown if or how these processes interact in human visual cortex. Here we used functional MRI and multi-voxel pattern analysis to investigate the relationship between 2D location and position-in-depth information. We stimulated different 3D locations in a blocked design: each location was defined by horizontal, vertical, and depth position. Participants remained fixated at the center of the screen while passively viewing the peripheral stimuli with red/green anaglyph glasses. Our results revealed a widespread, systematic transition throughout visual cortex. As expected, 2D location information (horizontal and vertical) could be strongly decoded in early visual areas, with reduced decoding higher along the visual hierarchy, consistent with known changes in receptive field sizes. Critically, we found that the decoding of position-in-depth information tracked inversely with the 2D location pattern, with the magnitude of depth decoding gradually increasing from intermediate to higher visual and category regions. Representations of 2D location information became increasingly location-tolerant in later areas, where depth information was also tolerant to changes in 2D location. We propose that spatial representations gradually transition from 2D-dominant to balanced 3D (2D and depth) along the visual hierarchy.

  12. Metrology for graphene and 2D materials

    NASA Astrophysics Data System (ADS)

    Pollard, Andrew J.

    2016-09-01

    The application of graphene, a one atom-thick honeycomb lattice of carbon atoms with superlative properties, such as electrical conductivity, thermal conductivity and strength, has already shown that it can be used to benefit metrology itself as a new quantum standard for resistance. However, there are many application areas where graphene and other 2D materials, such as molybdenum disulphide (MoS2) and hexagonal boron nitride (h-BN), may be disruptive, areas such as flexible electronics, nanocomposites, sensing and energy storage. Applying metrology to the area of graphene is now critical to enable the new, emerging global graphene commercial world and bridge the gap between academia and industry. Measurement capabilities and expertise in a wide range of scientific areas are required to address this challenge. The combined and complementary approach of varied characterisation methods for structural, chemical, electrical and other properties, will allow the real-world issues of commercialising graphene and other 2D materials to be addressed. Here, examples of metrology challenges that have been overcome through a multi-technique or new approach are discussed. Firstly, the structural characterisation of defects in both graphene and MoS2 via Raman spectroscopy is described, and how nanoscale mapping of vacancy defects in graphene is also possible using tip-enhanced Raman spectroscopy (TERS). Furthermore, the chemical characterisation and removal of polymer residue on chemical vapour deposition (CVD) grown graphene via secondary ion mass spectrometry (SIMS) is detailed, as well as the chemical characterisation of iron films used to grow large domain single-layer h-BN through CVD growth, revealing how contamination of the substrate itself plays a role in the resulting h-BN layer. In addition, the role of international standardisation in this area is described, outlining the current work ongoing in both the International Organization of Standardization (ISO) and the

  13. Design and characterization of low-loss 2D grating couplers for silicon photonics integrated circuits

    NASA Astrophysics Data System (ADS)

    Lacava, C.; Carrol, L.; Bozzola, A.; Marchetti, R.; Minzioni, P.; Cristiani, I.; Fournier, M.; Bernabe, S.; Gerace, D.; Andreani, L. C.

    2016-03-01

    We present the characterization of Silicon-on-insulator (SOI) photonic-crystal based 2D grating-couplers (2D-GCs) fabricated by CEA-Leti in the frame of the FP7 Fabulous project, which is dedicated to the realization of devices and systems for low-cost and high-performance passives-optical-networks. On the analyzed samples different test structures are present, including 2D-GC connected to another 2D-GC by different waveguides (in a Mach-Zehnder like configuration), and 2D-GC connected to two separate 2D-GCs, so as to allow a complete assessment of different parameters. Measurements were carried out using a tunable laser source operating in the extended telecom bandwidth and a fiber-based polarization controlling system at the input of device-under-test. The measured data yielded an overall fiber-to-fiber loss of 7.5 dB for the structure composed by an input 2D-GC connected to two identical 2D-GCs. This value was obtained at the peak wavelength of the grating, and the 3-dB bandwidth of the 2D-GC was assessed to be 43 nm. Assuming that the waveguide losses are negligible, so as to make a worst-case analysis, the coupling efficiency of the single 2D-GC results to be equal to -3.75 dB, constituting, to the best of our knowledge, the lowest value ever reported for a fully CMOS compatible 2D-GC. It is worth noting that both the obtained values are in good agreement with those expected by the numerical simulations performed using full 3D analysis by Lumerical FDTD-solutions.

  14. Quantifying Therapeutic and Diagnostic Efficacy in 2D Microvascular Images

    NASA Technical Reports Server (NTRS)

    Parsons-Wingerter, Patricia; Vickerman, Mary B.; Keith, Patricia A.

    2009-01-01

    VESGEN is a newly automated, user-interactive program that maps and quantifies the effects of vascular therapeutics and regulators on microvascular form and function. VESGEN analyzes two-dimensional, black and white vascular images by measuring important vessel morphology parameters. This software guides the user through each required step of the analysis process via a concise graphical user interface (GUI). Primary applications of the VESGEN code are 2D vascular images acquired as clinical diagnostic images of the human retina and as experimental studies of the effects of vascular regulators and therapeutics on vessel remodeling.

  15. Peak width issues with generalised 2D correlation NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Kirwan, Gemma M.; Adams, Michael J.

    2008-12-01

    Two-dimensional spectral correlation analysis is shown to be sensitive to fluctuations in spectral peak width as a function of perturbation variable. This is particularly significant where peak width fluctuations are of similar order of magnitude as the peak width values themselves and where changes in peak width are not random but are, for example, proportional to intensity. In such cases these trends appear in the asynchronous matrix as false peaks that serve to interfere with interpretation of the data. Complex, narrow band spectra such as provided by 1H NMR spectroscopy are demonstrated to be prone to such interference. 2D correlation analysis was applied to a series of NMR spectra corresponding to a commercial wine fermentation, in which the samples collected over a period of several days exhibit dramatic changes in concentration of minor and major components. The interference due to changing peak width effects is eliminated by synthesizing the recorded spectra using a constant peak width value prior to performing 2D correlation analysis.

  16. Human erythrocytes analyzed by generalized 2D Raman correlation spectroscopy

    NASA Astrophysics Data System (ADS)

    Wesełucha-Birczyńska, Aleksandra; Kozicki, Mateusz; Czepiel, Jacek; Łabanowska, Maria; Nowak, Piotr; Kowalczyk, Grzegorz; Kurdziel, Magdalena; Birczyńska, Malwina; Biesiada, Grażyna; Mach, Tomasz; Garlicki, Aleksander

    2014-07-01

    The most numerous elements of the blood cells, erythrocytes, consist mainly of two components: homogeneous interior filled with hemoglobin and closure which is the cell membrane. To gain insight into their specific properties we studied the process of disintegration, considering these two constituents, and comparing the natural aging process of human healthy blood cells. MicroRaman spectra of hemoglobin within the single RBC were recorded using 514.5, and 785 nm laser lines. The generalized 2D correlation method was applied to analyze the collected spectra. The time passed from blood donation was regarded as an external perturbation. The time was no more than 40 days according to the current storage limit of blood banks, although, the average RBC life span is 120 days. An analysis of the prominent synchronous and asynchronous cross peaks allow us to get insight into the mechanism of hemoglobin decomposition. Appearing asynchronous cross-peaks point towards globin and heme separation from each other, while synchronous shows already broken globin into individual amino acids. Raman scattering analysis of hemoglobin "wrapping", i.e. healthy erythrocyte ghosts, allows for the following peculiarity of their behavior. The increasing power of the excitation laser induced alterations in the assemblage of membrane lipids. 2D correlation maps, obtained with increasing laser power recognized as an external perturbation, allows for the consideration of alterations in the erythrocyte membrane structure and composition, which occurs first in the proteins. Cross-peaks were observed indicating an asynchronous correlation between the senescent-cell antigen (SCA) and heme or proteins vibrations. The EPR spectra of the whole blood was analyzed regarding time as an external stimulus. The 2D correlation spectra points towards participation of the selected metal ion centers in the disintegration process.

  17. Quantitation of protein in samples prepared for 2-D electrophoresis.

    PubMed

    Berkelman, Tom

    2008-01-01

    The concentration of protein in a sample prepared for two dimensional (2-D) electrophoretic analysis is usually determined by protein assay. Reasons for this include the following. (1) Protein quantitation ensures that the amount of protein to be separated is appropriate for the gel size and visualization method. (2) Protein quantitation facilitates comparison among similar samples, as image-based analysis is simplified when equivalent quantities of proteins have been loaded on the gels to be compared. (3) Quantitation is necessary in cases where the protein sample is labeled with dye before separation (1,2). The labeling chemistry is affected by the dye to protein ratio so it is essential to know the protein concentration before setting up the labeling reaction.A primary consideration with quantitating protein in samples prepared for 2-D electrophoresis is interference by nonprotein substances that may be present in the sample. These samples generally contain chaotropic solubilizing agents, detergents, reductants, buffers or carrier ampholytes, all of which potentially interfere with protein quantitation. The most commonly used protein assays in proteomics research are colorimetric assays in which the presence of protein causes a color change that can be measured spectrophotometrically (3). All protein assays utilize standards, a dilution series of a known concentration of a known protein, to create a standard curve. Two methods will be considered that circumvent some of the problems associated with interfering substances and are well suited for samples prepared for 2-D electrophoresis. The first method (4.1.1) relies on a color change that occurs upon binding of a dye to protein and the second (4.1.2) relies on binding and reduction of cupric ion (Cu2+) ion to cuprous ion (Cu+) by proteins.

  18. Global regularity and uniqueness of weak solution for the 2-D liquid crystal flows

    NASA Astrophysics Data System (ADS)

    Xu, Xiang; Zhang, Zhifei

    We prove the global existence and regularity of weak solution for the 2-D liquid crystal flows with the large initial velocity. The uniqueness of weak solution is also proved by using the Littlewood-Paley analysis.

  19. Persistence Measures for 2d Soap Froth

    NASA Astrophysics Data System (ADS)

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

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

  20. SEM signal emulation for 2D patterns

    NASA Astrophysics Data System (ADS)

    Sukhov, Evgenii; Muelders, Thomas; Klostermann, Ulrich; Gao, Weimin; Braylovska, Mariya

    2016-03-01

    The application of accurate and predictive physical resist simulation is seen as one important use model for fast and efficient exploration of new patterning technology options, especially if fully qualified OPC models are not yet available at an early pre-production stage. The methodology of using a top-down CD-SEM metrology to extract the 3D resist profile information, such as the critical dimension (CD) at various resist heights, has to be associated with a series of presumptions which may introduce such small, but systematic CD errors. Ideally, the metrology effects should be carefully minimized during measurement process, or if possible be taken into account through proper metrology modeling. In this paper we discuss the application of a fast SEM signal emulation describing the SEM image formation. The algorithm is applied to simulated resist 3D profiles and produces emulated SEM image results for 1D and 2D patterns. It allows estimating resist simulation quality by comparing CDs which were extracted from the emulated and from the measured SEM images. Moreover, SEM emulation is applied for resist model calibration to capture subtle error signatures through dose and defocus. Finally, it should be noted that our SEM emulation methodology is based on the approximation of physical phenomena which are taking place in real SEM image formation. This approximation allows achieving better speed performance compared to a fully physical model.

  1. Competing coexisting phases in 2D water

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  2. Competing coexisting phases in 2D water

    PubMed Central

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

    2016-01-01

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

  3. Radiofrequency Spectroscopy and Thermodynamics of Fermi Gases in the 2D to Quasi-2D Dimensional Crossover

    NASA Astrophysics Data System (ADS)

    Cheng, Chingyun; Kangara, Jayampathi; Arakelyan, Ilya; Thomas, John

    2016-05-01

    We tune the dimensionality of a strongly interacting degenerate 6 Li Fermi gas from 2D to quasi-2D, by adjusting the radial confinement of pancake-shaped clouds to control the radial chemical potential. In the 2D regime with weak radial confinement, the measured pair binding energies are in agreement with 2D-BCS mean field theory, which predicts dimer pairing energies in the many-body regime. In the qausi-2D regime obtained with increased radial confinement, the measured pairing energy deviates significantly from 2D-BCS theory. In contrast to the pairing energy, the measured radii of the cloud profiles are not fit by 2D-BCS theory in either the 2D or quasi-2D regimes, but are fit in both regimes by a beyond mean field polaron-model of the free energy. Supported by DOE, ARO, NSF, and AFOSR.

  4. Triglyceride High-Density Lipoprotein Ratios Predict Glycemia-Lowering in Response to Insulin Sensitizing Drugs in Type 2 Diabetes: A Post Hoc Analysis of the BARI 2D

    PubMed Central

    Zonszein, Joel; Lombardero, Manuel; Ismail-Beigi, Faramarz; Palumbo, Pasquale; Foucher, Suzy; Groenewoud, Yolanda; Cushing, Gary; Wajchenberg, Bernardo; Genuth, Saul; BARI 2D Study Group

    2015-01-01

    Glycemic management is central in prevention of small vessel and cardiovascular complications in type 2 diabetes. With the plethora of newer medications and recommendations for a patient centered approach, more information is necessary to match the proper drug to each patient. We showed that BARI 2D, a five-year trial designed to compare two different glycemic treatment strategies, was suitable for assessing different responses according to different phenotypic characteristics. Treatment with insulin sensitizing medications such as thiazolidinediones and metformin was more effective in improving glycemic control, particularly in the more insulin resistant patient, when compared to the insulin provision strategy using insulin and or sulfonylureas. Triglyceride and high density lipoprotein ratio (TG/HDL-cholesterol ratio) was found to be a readily available and practical biomarker that helps to identify the insulin resistant patient. These results support the concept that not all medications for glycemic control work the same in all patients. Thus, tailored therapy can be done using phenotypic characteristics rather than a “one-size-fits-all approach.” PMID:26106623

  5. MAGNUM2D. Radionuclide Transport Porous Media

    SciTech Connect

    Langford, D.W.; Baca, R.G.

    1989-03-01

    MAGNUM2D was developed to analyze thermally driven fluid motion in the deep basalts below the Paco Basin at the Westinghouse Hanford Site. Has been used in the Basalt Waste Isolation Project to simulate nonisothermal groundwater flow in a heterogeneous anisotropic medium and heat transport in a water/rock system near a high level nuclear waste repository. Allows three representations of the hydrogeologic system: an equivalent porous continuum, a system of discrete, unfilled, and interconnecting fractures separated by impervious rock mass, and a low permeability porous continuum with several discrete, unfilled fractures traversing the medium. The calculations assume local thermodynamic equilibrium between the rock and groundwater, nonisothermal Darcian flow in the continuum portions of the rock, and nonisothermal Poiseuille flow in discrete unfilled fractures. In addition, the code accounts for thermal loading within the elements, zero normal gradient and fixed boundary conditions for both temperature and hydraulic head, and simulation of the temperature and flow independently. The Q2DGEOM preprocessor was developed to generate, modify, plot and verify quadratic two dimensional finite element geometries. The BCGEN preprocessor generates the boundary conditions for head and temperature and ICGEN generates the initial conditions. The GRIDDER postprocessor interpolates nonregularly spaced nodal flow and temperature data onto a regular rectangular grid. CONTOUR plots and labels contour lines for a function of two variables and PARAM plots cross sections and time histories for a function of time and one or two spatial variables. NPRINT generates data tables that display the data along horizontal or vertical cross sections. VELPLT differentiates the hydraulic head and buoyancy data and plots the velocity vectors. The PATH postprocessor plots flow paths and computes the corresponding travel times.

  6. MAGNUM2D. Radionuclide Transport Porous Media

    SciTech Connect

    Langford, D.W.; Baca, R.G.

    1988-08-01

    MAGNUM2D was developed to analyze thermally driven fluid motion in the deep basalts below the Paco Basin at the Westinghouse Hanford Site. Has been used in the Basalt Waste Isolation Project to simulate nonisothermal groundwater flow in a heterogeneous anisotropic medium and heat transport in a water/rock system near a high level nuclear waste repository. Allows three representations of the hydrogeologic system: an equivalent porous continuum, a system of discrete, unfilled, and interconnecting fractures separated by impervious rock mass, and a low permeability porous continuum with several discrete, unfilled fractures traversing the medium. The calculation assumes local thermodynamic equilibrium between the rock and groundwater, nonisothermal Darcian flow in the continuum portions of the rock, and nonisothermal Poiseuille flow in discrete unfilled fractures. In addition, the code accounts for thermal loading within the elements, zero normal gradient and fixed boundary conditions for both temperature and hydraulic head, and simulation of the temperature and flow independently. The Q2DGEOM preprocessor was developed to generate, modify, plot and verify quadratic two dimensional finite element geometries. The BCGEN preprocessor generates the boundary conditions for head and temperature and ICGEN generates the initial conditions. The GRIDDER postprocessor interpolates nonregularly spaced nodal flow and temperature data onto a regular rectangular grid. CONTOUR plots and labels contour lines for a function of two variables and PARAM plots cross sections and time histories for a function of time and one or two spatial variables. NPRINT generates data tables that display the data along horizontal or vertical cross sections. VELPLT differentiates the hydraulic head and buoyancy data and plots the velocity vectors. The PATH postprocessor plots flow paths and computes the corresponding travel times.

  7. Generates 2D Input for DYNA NIKE & TOPAZ

    SciTech Connect

    Hallquist, J. O.; Sanford, Larry

    1996-07-15

    MAZE is an interactive program that serves as an input and two-dimensional mesh generator for DYNA2D, NIKE2D, TOPAZ2D, and CHEMICAL TOPAZ2D. MAZE also generates a basic template for ISLAND input. MAZE has been applied to the generation of input data to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

  8. MAZE96. Generates 2D Input for DYNA NIKE & TOPAZ

    SciTech Connect

    Sanford, L.; Hallquist, J.O.

    1992-02-24

    MAZE is an interactive program that serves as an input and two-dimensional mesh generator for DYNA2D, NIKE2D, TOPAZ2D, and CHEMICAL TOPAZ2D. MAZE also generates a basic template for ISLAND input. MAZE has been applied to the generation of input data to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

  9. Discrepant Results in a 2-D Marble Collision

    NASA Astrophysics Data System (ADS)

    Kalajian, Peter

    2013-03-01

    Video analysis of 2-D collisions is an excellent way to investigate conservation of linear momentum. The often-desired experimental design goal is to minimize the momentum loss in order to demonstrate the conservation law. An air table with colliding pucks is an ideal medium for this experiment, but such equipment is beyond the budget of many schools. Substituting marbles on a table for air pucks introduces angular momentum and sliding friction so that simple video analysis will demonstrate that linear momentum is not conserved.1,2 Nevertheless, these labs offer students insights into the real-world application of physics. During a recent classroom trial, an unexpected result forced my students to think creatively and critically about what happened in the experiment.

  10. Device and methods for "gold standard" registration of clinical 3D and 2D cerebral angiograms

    NASA Astrophysics Data System (ADS)

    Madan, Hennadii; Likar, Boštjan; Pernuš, Franjo; Å piclin, Žiga

    2015-03-01

    Translation of any novel and existing 3D-2D image registration methods into clinical image-guidance systems is limited due to lack of their objective validation on clinical image datasets. The main reason is that, besides the calibration of the 2D imaging system, a reference or "gold standard" registration is very difficult to obtain on clinical image datasets. In the context of cerebral endovascular image-guided interventions (EIGIs), we present a calibration device in the form of a headband with integrated fiducial markers and, secondly, propose an automated pipeline comprising 3D and 2D image processing, analysis and annotation steps, the result of which is a retrospective calibration of the 2D imaging system and an optimal, i.e., "gold standard" registration of 3D and 2D images. The device and methods were used to create the "gold standard" on 15 datasets of 3D and 2D cerebral angiograms, whereas each dataset was acquired on a patient undergoing EIGI for either aneurysm coiling or embolization of arteriovenous malformation. The use of the device integrated seamlessly in the clinical workflow of EIGI. While the automated pipeline eliminated all manual input or interactive image processing, analysis or annotation. In this way, the time to obtain the "gold standard" was reduced from 30 to less than one minute and the "gold standard" of 3D-2D registration on all 15 datasets of cerebral angiograms was obtained with a sub-0.1 mm accuracy.

  11. TOPAZ2D heat transfer code users manual and thermal property data base

    SciTech Connect

    Shapiro, A.B.; Edwards, A.L.

    1990-05-01

    TOPAZ2D is a two dimensional implicit finite element computer code for heat transfer analysis. This user's manual provides information on the structure of a TOPAZ2D input file. Also included is a material thermal property data base. This manual is supplemented with The TOPAZ2D Theoretical Manual and the TOPAZ2D Verification Manual. TOPAZ2D has been implemented on the CRAY, SUN, and VAX computers. TOPAZ2D can be used to solve for the steady state or transient temperature field on two dimensional planar or axisymmetric geometries. Material properties may be temperature dependent and either isotropic or orthotropic. A variety of time and temperature dependent boundary conditions can be specified including temperature, flux, convection, and radiation. Time or temperature dependent internal heat generation can be defined locally be element or globally by material. TOPAZ2D can solve problems of diffuse and specular band radiation in an enclosure coupled with conduction in material surrounding the enclosure. Additional features include thermally controlled reactive chemical mixtures, thermal contact resistance across an interface, bulk fluid flow, phase change, and energy balances. Thermal stresses can be calculated using the solid mechanics code NIKE2D which reads the temperature state data calculated by TOPAZ2D. A three dimensional version of the code, TOPAZ3D is available. The material thermal property data base, Chapter 4, included in this manual was originally published in 1969 by Art Edwards for use with his TRUMP finite difference heat transfer code. The format of the data has been altered to be compatible with TOPAZ2D. Bob Bailey is responsible for adding the high explosive thermal property data.

  12. Reconstruction of a 2D seismic wavefield by seismic gradiometry

    NASA Astrophysics Data System (ADS)

    Maeda, Takuto; Nishida, Kiwamu; Takagi, Ryota; Obara, Kazushige

    2016-12-01

    We reconstructed a 2D seismic wavefield and obtained its propagation properties by using the seismic gradiometry method together with dense observations of the Hi-net seismograph network in Japan. The seismic gradiometry method estimates the wave amplitude and its spatial derivative coefficients at any location from a discrete station record by using a Taylor series approximation. From the spatial derivatives in horizontal directions, the properties of a propagating wave packet, including the arrival direction, slowness, geometrical spreading, and radiation pattern can be obtained. In addition, by using spatial derivatives together with free-surface boundary conditions, the 2D vector elastic wavefield can be decomposed into divergence and rotation components. First, as a feasibility test, we performed an analysis with a synthetic seismogram dataset computed by a numerical simulation for a realistic 3D medium and the actual Hi-net station layout. We confirmed that the wave amplitude and its spatial derivatives were very well-reproduced for period bands longer than 25 s. Applications to a real large earthquake showed that the amplitude and phase of the wavefield were well reconstructed, along with slowness vector. The slowness of the reconstructed wavefield showed a clear contrast between body and surface waves and regional non-great-circle-path wave propagation, possibly owing to scattering. Slowness vectors together with divergence and rotation decomposition are expected to be useful for determining constituents of observed wavefields in inhomogeneous media.

  13. 2D Hilbert transform for phase retrieval of speckle fields

    NASA Astrophysics Data System (ADS)

    Gorsky, M. P.; Ryabyi, P. A.; Ivanskyi, D. I.

    2016-09-01

    The paper presents principal approaches to diagnosing the structure forming skeleton of the complex optical field. An analysis of optical field singularity algorithms depending on intensity discretization and image resolution has been carried out. An optimal approach is chosen, which allows to bring much closer the solution of the phase problem of localization speckle-field special points. The use of a "window" 2D Hilbert transform for reconstruction of the phase distribution of the intensity of a speckle field is proposed. It is shown that the advantage of this approach consists in the invariance of a phase map to a change of the position of the kernel of transformation and in a possibility to reconstruct the structure-forming elements of the skeleton of an optical field, including singular points and saddle points. We demonstrate the possibility to reconstruct the equi-phase lines within a narrow confidence interval, and introduce an additional algorithm for solving the phase problem for random 2D intensity distributions.

  14. Influence of Elevation Data Source on 2D Hydraulic Modelling

    NASA Astrophysics Data System (ADS)

    Bakuła, Krzysztof; StĘpnik, Mateusz; Kurczyński, Zdzisław

    2016-08-01

    The aim of this paper is to analyse the influence of the source of various elevation data on hydraulic modelling in open channels. In the research, digital terrain models from different datasets were evaluated and used in two-dimensional hydraulic models. The following aerial and satellite elevation data were used to create the representation of terrain-digital terrain model: airborne laser scanning, image matching, elevation data collected in the LPIS, EuroDEM, and ASTER GDEM. From the results of five 2D hydrodynamic models with different input elevation data, the maximum depth and flow velocity of water were derived and compared with the results of the most accurate ALS data. For such an analysis a statistical evaluation and differences between hydraulic modelling results were prepared. The presented research proved the importance of the quality of elevation data in hydraulic modelling and showed that only ALS and photogrammetric data can be the most reliable elevation data source in accurate 2D hydraulic modelling.

  15. Application Perspective of 2D+SCALE Dimension

    NASA Astrophysics Data System (ADS)

    Karim, H.; Rahman, A. Abdul

    2016-09-01

    Different applications or users need different abstraction of spatial models, dimensionalities and specification of their datasets due to variations of required analysis and output. Various approaches, data models and data structures are now available to support most current application models in Geographic Information System (GIS). One of the focuses trend in GIS multi-dimensional research community is the implementation of scale dimension with spatial datasets to suit various scale application needs. In this paper, 2D spatial datasets that been scaled up as the third dimension are addressed as 2D+scale (or 3D-scale) dimension. Nowadays, various data structures, data models, approaches, schemas, and formats have been proposed as the best approaches to support variety of applications and dimensionality in 3D topology. However, only a few of them considers the element of scale as their targeted dimension. As the scale dimension is concerned, the implementation approach can be either multi-scale or vario-scale (with any available data structures and formats) depending on application requirements (topology, semantic and function). This paper attempts to discuss on the current and new potential applications which positively could be integrated upon 3D-scale dimension approach. The previous and current works on scale dimension as well as the requirements to be preserved for any given applications, implementation issues and future potential applications forms the major discussion of this paper.

  16. CYP2D7 Sequence Variation Interferes with TaqMan CYP2D6*15 and *35 Genotyping

    PubMed Central

    Riffel, Amanda K.; Dehghani, Mehdi; Hartshorne, Toinette; Floyd, Kristen C.; Leeder, J. Steven; Rosenblatt, Kevin P.; Gaedigk, Andrea

    2016-01-01

    TaqMan™ genotyping assays are widely used to genotype CYP2D6, which encodes a major drug metabolizing enzyme. Assay design for CYP2D6 can be challenging owing to the presence of two pseudogenes, CYP2D7 and CYP2D8, structural and copy number variation and numerous single nucleotide polymorphisms (SNPs) some of which reflect the wild-type sequence of the CYP2D7 pseudogene. The aim of this study was to identify the mechanism causing false-positive CYP2D6*15 calls and remediate those by redesigning and validating alternative TaqMan genotype assays. Among 13,866 DNA samples genotyped by the CompanionDx® lab on the OpenArray platform, 70 samples were identified as heterozygotes for 137Tins, the key SNP of CYP2D6*15. However, only 15 samples were confirmed when tested with the Luminex xTAG CYP2D6 Kit and sequencing of CYP2D6-specific long range (XL)-PCR products. Genotype and gene resequencing of CYP2D6 and CYP2D7-specific XL-PCR products revealed a CC>GT dinucleotide SNP in exon 1 of CYP2D7 that reverts the sequence to CYP2D6 and allows a TaqMan assay PCR primer to bind. Because CYP2D7 also carries a Tins, a false-positive mutation signal is generated. This CYP2D7 SNP was also responsible for generating false-positive signals for rs769258 (CYP2D6*35) which is also located in exon 1. Although alternative CYP2D6*15 and *35 assays resolved the issue, we discovered a novel CYP2D6*15 subvariant in one sample that carries additional SNPs preventing detection with the alternate assay. The frequency of CYP2D6*15 was 0.1% in this ethnically diverse U.S. population sample. In addition, we also discovered linkage between the CYP2D7 CC>GT dinucleotide SNP and the 77G>A (rs28371696) SNP of CYP2D6*43. The frequency of this tentatively functional allele was 0.2%. Taken together, these findings emphasize that regardless of how careful genotyping assays are designed and evaluated before being commercially marketed, rare or unknown SNPs underneath primer and/or probe regions can impact

  17. CYP2D7 Sequence Variation Interferes with TaqMan CYP2D6 (*) 15 and (*) 35 Genotyping.

    PubMed

    Riffel, Amanda K; Dehghani, Mehdi; Hartshorne, Toinette; Floyd, Kristen C; Leeder, J Steven; Rosenblatt, Kevin P; Gaedigk, Andrea

    2015-01-01

    TaqMan™ genotyping assays are widely used to genotype CYP2D6, which encodes a major drug metabolizing enzyme. Assay design for CYP2D6 can be challenging owing to the presence of two pseudogenes, CYP2D7 and CYP2D8, structural and copy number variation and numerous single nucleotide polymorphisms (SNPs) some of which reflect the wild-type sequence of the CYP2D7 pseudogene. The aim of this study was to identify the mechanism causing false-positive CYP2D6 (*) 15 calls and remediate those by redesigning and validating alternative TaqMan genotype assays. Among 13,866 DNA samples genotyped by the CompanionDx® lab on the OpenArray platform, 70 samples were identified as heterozygotes for 137Tins, the key SNP of CYP2D6 (*) 15. However, only 15 samples were confirmed when tested with the Luminex xTAG CYP2D6 Kit and sequencing of CYP2D6-specific long range (XL)-PCR products. Genotype and gene resequencing of CYP2D6 and CYP2D7-specific XL-PCR products revealed a CC>GT dinucleotide SNP in exon 1 of CYP2D7 that reverts the sequence to CYP2D6 and allows a TaqMan assay PCR primer to bind. Because CYP2D7 also carries a Tins, a false-positive mutation signal is generated. This CYP2D7 SNP was also responsible for generating false-positive signals for rs769258 (CYP2D6 (*) 35) which is also located in exon 1. Although alternative CYP2D6 (*) 15 and (*) 35 assays resolved the issue, we discovered a novel CYP2D6 (*) 15 subvariant in one sample that carries additional SNPs preventing detection with the alternate assay. The frequency of CYP2D6 (*) 15 was 0.1% in this ethnically diverse U.S. population sample. In addition, we also discovered linkage between the CYP2D7 CC>GT dinucleotide SNP and the 77G>A (rs28371696) SNP of CYP2D6 (*) 43. The frequency of this tentatively functional allele was 0.2%. Taken together, these findings emphasize that regardless of how careful genotyping assays are designed and evaluated before being commercially marketed, rare or unknown SNPs underneath primer

  18. Enhanced sampling of 2D interference patterns.

    PubMed

    Schwartz, Eyal; Ribak, Erez N

    2017-03-01

    We propose a simple analysis to improve the resolution of interference patterns which consist of straight fringes. As the pattern is rotated with respect to the detector, each row or column in the camera perceives it in a slightly shifted manner. We support this proposed method by analyzing both simulated and experimental interference patterns, and verify it using an interferogram obtained from a spectrally complex light source. The results imply that this technique could be implemented in different aspects of image analysis common in many fields in physics.

  19. Residual lens effects in 2D mode of auto-stereoscopic lenticular-based switchable 2D/3D displays

    NASA Astrophysics Data System (ADS)

    Sluijter, M.; IJzerman, W. L.; de Boer, D. K. G.; de Zwart, S. T.

    2006-04-01

    We discuss residual lens effects in multi-view switchable auto-stereoscopic lenticular-based 2D/3D displays. With the introduction of a switchable lenticular, it is possible to switch between a 2D mode and a 3D mode. The 2D mode displays conventional content, whereas the 3D mode provides the sensation of depth to the viewer. The uniformity of a display in the 2D mode is quantified by the quality parameter modulation depth. In order to reduce the modulation depth in the 2D mode, birefringent lens plates are investigated analytically and numerically, by ray tracing. We can conclude that the modulation depth in the 2D mode can be substantially decreased by using birefringent lens plates with a perfect index match between lens material and lens plate. Birefringent lens plates do not disturb the 3D performance of a switchable 2D/3D display.

  20. The IDOL–UBE2D complex mediates sterol-dependent degradation of the LDL receptor

    PubMed Central

    Zhang, Li; Fairall, Louise; Goult, Benjamin T.; Calkin, Anna C.; Hong, Cynthia; Millard, Christopher J.; Tontonoz, Peter; Schwabe, John W.R.

    2011-01-01

    We previously identified the E3 ubiquitin ligase IDOL as a sterol-dependent regulator of the LDL receptor (LDLR). The molecular pathway underlying IDOL action, however, remains to be determined. Here we report the identification and biochemical and structural characterization of an E2–E3 ubiquitin ligase complex for LDLR degradation. We identified the UBE2D family (UBE2D1–4) as E2 partners for IDOL that support both autoubiquitination and IDOL-dependent ubiquitination of the LDLR in a cell-free system. NMR chemical shift mapping and a 2.1 Å crystal structure of the IDOL RING domain–UBE2D1 complex revealed key interactions between the dimeric IDOL protein and the E2 enzyme. Analysis of the IDOL–UBE2D1 interface also defined the stereochemical basis for the selectivity of IDOL for UBE2Ds over other E2 ligases. Structure-based mutations that inhibit IDOL dimerization or IDOL–UBE2D interaction block IDOL-dependent LDLR ubiquitination and degradation. Furthermore, expression of a dominant-negative UBE2D enzyme inhibits the ability of IDOL to degrade the LDLR in cells. These results identify the IDOL–UBE2D complex as an important determinant of LDLR activity, and provide insight into molecular mechanisms underlying the regulation of cholesterol uptake. PMID:21685362

  1. A novel method for measuring the 2D information of burst strong flashing object in space

    NASA Astrophysics Data System (ADS)

    Zhong, P.; Jin, Ye

    2009-11-01

    The burst strongly flashing event taking place in space such as strong explosion in low air is very random in time and position, and its duration time is very short. In this paper, a photoelectric measuring device, namely, 2D angle localizer for measuring 2D angle of a burst strongly flashing object appearing in place randomly has been presented. It mainly includes detecting head with narrow slot, cylinder silicon photoelectric receiver, absolute photoelectric encoder and computer. It can complete the measurement of 2D information, namely, the azimuth angle and pitching angle of the center position of a spatial flashing object. The principle of measuring angle and basic structure of measuring angle device are introduced. The critical parts of the device are briefly described. A contrast experiment of measuring the sun's 2D angle by 2D angle localizer and theodolite was made. The measuring results and accuracy analysis have been given. Due to being equipped with variable gain amplifiers and three silicon photoelectric accepters with cylinder surface, the 2D angle localizer has the characteristics of Wide dynamic measurement range and omnidirectional angle measurement. The measuring accuracy of 2D angle localizer is more than 2mil and the act of measuring can be finished in 0.5s.

  2. Differential CYP 2D6 metabolism alters primaquine pharmacokinetics.

    PubMed

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

    2015-04-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

  4. Effective Hamiltonians of 2D Spin Glass Clusters

    NASA Astrophysics Data System (ADS)

    Clement, Colin; Liarte, Danilo; Middleton, Alan; Sethna, James

    2015-03-01

    We have a method for directly identifying the clusters which are thought to dominate the dynamics of spin glasses. We also have a method for generating an effective Hamiltonian treating each cluster as an individual spin. We used these methods on a 2D Ising spin glass with Gaussian bonds. We study these systems by generating samples and correlation functions using a combination of Monte Carlo and high-performance numerically exact Pfaffian methods. With effective cluster Hamiltonians we can calculate the free energy asymmetry of the original clusters and perform a scaling analysis. The scaling exponents found are consistent with Domain-Wall Renormalization Group methods, and probe all length scales. We can also study the flow of these effective Hamiltonians by clustering the clustered spins, and we find that our hard spin Hamiltonians at high temperature retain accurate low-temperature fluctuations when compared to their parent models.

  5. Adaptive superplastic forming using NIKE2D with ISLAND

    SciTech Connect

    Engelmann, B.E.; Whirley, R.G.; Raboin, P.J.

    1992-07-30

    Superplastic forming has emerged as an important manufacturing process for producing near-net-shape parts. The design of a superplastic forming process is more difficult than conventional manufacturing operations, and is less amenable to trial and error approaches. This paper describes a superplastic forming process design capability incorporating nonlinear finite element analysis. The material constraints to allow superplastic behavior are integrated into an external constraint equation which is solved concurrently with the nonlinear finite element equations. The implementation of this approach using the ISLAND solution control language with the nonlinear finite element code NIKE2D is discussed in detail. Superplastic forming process design problems with one and two control parameters are presented as examples.

  6. areaDetector: Software for 2-D Detectors in EPICS

    SciTech Connect

    Rivers, M.

    2011-09-23

    areaDetector is a new EPICS module designed to support 2-D detectors. It is modular C++ code that greatly simplifies the task of writing support for a new detector. It also supports plugins, which receive detector data from the driver and process it in some way. Existing plugins perform Region-Of-Interest extraction and analysis, file saving (in netCDF, HDF, TIFF and JPEG formats), color conversion, and export to EPICS records for image display in clients like ImageJ and IDL. Drivers have now been written for many of the detectors commonly used at synchrotron beamlines, including CCDs, pixel array and amorphous silicon detectors, and online image plates.

  7. TOPAZ2D validation status report, August 1990

    SciTech Connect

    Davis, B.

    1990-08-01

    Analytic solutions to two heat transfer problems were used to partially evaluate the performance TOPAZ, and LLNL finite element heat transfer code. The two benchmark analytic solutions were for: 2D steady state slab, with constant properties, constant uniform temperature boundary conditions on three sides, and constant temperature distribution according to a sine function on the fourth side; 1D transient non-linear, with temperature dependent conductivity and specific heat (varying such that the thermal diffusivity remained constant), constant heat flux on the front face and adiabatic conditions on the other face. The TOPAZ solution converged to the analytic solution in both the transient and the steady state problem. Consistent mass matrix type of analysis yielded best performance for the transient problem, in the late-time response; but notable unnatural anomalies were observed in the early-time temperature response at nodal locations near the front face. 5 refs., 22 figs.

  8. Development of wide-angle 2D light scattering static cytometry

    NASA Astrophysics Data System (ADS)

    Xie, Linyan; Liu, Qiao; Shao, Changshun; Su, Xuantao

    2016-10-01

    We have recently developed a 2D light scattering static cytometer for cellular analysis in a label-free manner, which measures side scatter (SSC) light in the polar angular range from 79 to 101 degrees. Compared with conventional flow cytometry, our cytometric technique requires no fluorescent labeling of the cells, and static cytometry measurements can be performed without flow control. In this paper we present an improved label-free static cytometer that can obtain 2D light scattering patterns in a wider angular range. By illuminating the static microspheres on chip with a scanning optical fiber, wide-angle 2D light scattering patterns of single standard microspheres with a mean diameter of 3.87 μm are obtained. The 2D patterns of 3.87 μm microspheres contain both large-angle forward scatter (FSC) and SSC light in the polar angular range from 40 to 100 degrees, approximately. Experimental 2D patterns of 3.87 μm microspheres are in good agreement with Mie theory simulated ones. The wide-angle light scattering measurements may provide a better resolution for particle analysis as compared with the SSC measurements. Two dimensional light scattering patterns of HL-60 human acute leukemia cells are obtained by using our static cytometer. Compared with SSC 2D light scattering patterns, wide-angle 2D patterns contain richer information of the HL-60 cells. The obtaining of 2D light scattering patterns in a wide angular range could help to enhance the capabilities of our label-free static cytometry for cell analysis.

  9. Distribution of CYP2D6 alleles and phenotypes in the Brazilian population.

    PubMed

    Friedrich, Deise C; Genro, Júlia P; Sortica, Vinicius A; Suarez-Kurtz, Guilherme; de Moraes, Maria Elizabete; Pena, Sergio D J; dos Santos, Andrea K Ribeiro; Romano-Silva, Marco A; Hutz, Mara H

    2014-01-01

    The CYP2D6 enzyme is one of the most important members of the cytochrome P450 superfamily. This enzyme metabolizes approximately 25% of currently prescribed medications. The CYP2D6 gene presents a high allele heterogeneity that determines great inter-individual variation. The aim of this study was to evaluate the variability of CYP2D6 alleles, genotypes and predicted phenotypes in Brazilians. Eleven single nucleotide polymorphisms and CYP2D6 duplications/multiplications were genotyped by TaqMan assays in 1020 individuals from North, Northeast, South, and Southeast Brazil. Eighteen CYP2D6 alleles were identified in the Brazilian population. The CYP2D6*1 and CYP2D6*2 alleles were the most frequent and widely distributed in different geographical regions of Brazil. The highest number of CYPD6 alleles observed was six and the frequency of individuals with more than two copies ranged from 6.3% (in Southern Brazil) to 10.2% (Northern Brazil). The analysis of molecular variance showed that CYP2D6 is homogeneously distributed across different Brazilian regions and most of the differences can be attributed to inter-individual differences. The most frequent predicted metabolic status was EM (83.5%). Overall 2.5% and 3.7% of Brazilians were PMs and UMs respectively. Genomic ancestry proportions differ only in the prevalence of intermediate metabolizers. The IM predicted phenotype is associated with a higher proportion of African ancestry and a lower proportion of European ancestry in Brazilians. PM and UM classes did not vary among regions and/or ancestry proportions therefore unique CYP2D6 testing guidelines for Brazilians are possible and could potentially avoid ineffective or adverse events outcomes due to drug prescriptions.

  10. Distribution of CYP2D6 Alleles and Phenotypes in the Brazilian Population

    PubMed Central

    Sortica, Vinicius A.; Suarez-Kurtz, Guilherme; de Moraes, Maria Elizabete; Pena, Sergio D. J.; dos Santos, Ândrea K. Ribeiro; Romano-Silva, Marco A.; Hutz, Mara H.

    2014-01-01

    Abstract The CYP2D6 enzyme is one of the most important members of the cytochrome P450 superfamily. This enzyme metabolizes approximately 25% of currently prescribed medications. The CYP2D6 gene presents a high allele heterogeneity that determines great inter-individual variation. The aim of this study was to evaluate the variability of CYP2D6 alleles, genotypes and predicted phenotypes in Brazilians. Eleven single nucleotide polymorphisms and CYP2D6 duplications/multiplications were genotyped by TaqMan assays in 1020 individuals from North, Northeast, South, and Southeast Brazil. Eighteen CYP2D6 alleles were identified in the Brazilian population. The CYP2D6*1 and CYP2D6*2 alleles were the most frequent and widely distributed in different geographical regions of Brazil. The highest number of CYPD6 alleles observed was six and the frequency of individuals with more than two copies ranged from 6.3% (in Southern Brazil) to 10.2% (Northern Brazil). The analysis of molecular variance showed that CYP2D6 is homogeneously distributed across different Brazilian regions and most of the differences can be attributed to inter-individual differences. The most frequent predicted metabolic status was EM (83.5%). Overall 2.5% and 3.7% of Brazilians were PMs and UMs respectively. Genomic ancestry proportions differ only in the prevalence of intermediate metabolizers. The IM predicted phenotype is associated with a higher proportion of African ancestry and a lower proportion of European ancestry in Brazilians. PM and UM classes did not vary among regions and/or ancestry proportions therefore unique CYP2D6 testing guidelines for Brazilians are possible and could potentially avoid ineffective or adverse events outcomes due to drug prescriptions. PMID:25329392

  11. Computational Screening of 2D Materials for Photocatalysis.

    PubMed

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

    2015-03-19

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

  12. Synthetic Covalent and Non-Covalent 2D Materials.

    PubMed

    Boott, Charlotte E; Nazemi, Ali; Manners, Ian

    2015-11-16

    The creation of synthetic 2D materials represents an attractive challenge that is ultimately driven by their prospective uses in, for example, electronics, biomedicine, catalysis, sensing, and as membranes for separation and filtration. This Review illustrates some recent advances in this diverse field with a focus on covalent and non-covalent 2D polymers and frameworks, and self-assembled 2D materials derived from nanoparticles, homopolymers, and block copolymers.

  13. Proteomic Analysis of Kveim Reagent Identifies Targets of Cellular Immunity in Sarcoidosis

    PubMed Central

    Parker, Robert; Siddiqui, Nazneen; Potiphar, Lee; Goldin, Rob; Timms, John F.; Wells, Athol U.; Kon, Onn M.; Wickremasinghe, Melissa; Mitchell, Donald; Weeks, Mark E.; Lalvani, Ajit

    2017-01-01

    Background Kveim-reagent (Kv) skin testing was a historical method of diagnosing sarcoidosis. Intradermal injection of treated sarcoidosis spleen tissue resulted in a granuloma response at injection site by 4–6 weeks. Previous work indicates proteins as the possible trigger of this reaction. We aimed to identify Kv-specific proteins and characterise the ex vivo response of Peripheral Blood Mononuclear Cells (PBMCs) from sarcoidosis, tuberculosis and healthy control patients when stimulated with both Kv and selected Kv-specific proteins. Methods Kv extracts were separated by 1D-SDS-PAGE and 2D-DIGE and then underwent mass spectrometric analysis for protein identification. Sarcoidosis and control PBMCs were first stimulated with Kv and then with three selected recombinant protein candidates which were identified from the proteomic analysis. PBMC secreted cytokines were subsequently measured by Multiplex Cytokine Assay. Results We observed significantly increased IFN-γ and TNF-α secretion from Kv-stimulated PBMCs of sarcoidosis patients vs. PBMCs from healthy volunteers (IFN-γ: 207.2 pg/mL vs. 3.86 pg/mL, p = 0.0018; TNF-α: 2375 pg/mL vs. 42.82 pg/mL, p = 0.0003). Through proteomic approaches we then identified 74 sarcoidosis tissue-specific proteins. Of these, 3 proteins (vimentin, tubulin and alpha-actinin-4) were identified using both 1D-SDS-PAGE and 2D-DIGE. Data are available via ProteomeXchange with identifier PXD005150. Increased cytokine secretion was subsequently observed with vimentin stimulation of sarcoidosis PBMCs vs. tuberculosis PBMCs (IFN-γ: 396.6 pg/mL vs 0.1 pg/mL, p = 0.0009; TNF-α: 1139 pg/mL vs 0.1 pg/mL, p<0.0001). This finding was also observed in vimentin stimulation of sarcoidosis PBMCs compared to PBMCs from healthy controls (IFN-γ: 396.6 pg/mL vs. 0.1 pg/mL, p = 0.014; TNF-α: 1139 pg/mL vs 42.29 pg/mL, p = 0.027). No difference was found in cytokine secretion between sarcoidosis and control PBMCs when stimulated with either tubulin

  14. Epitaxial 2D SnSe2/ 2D WSe2 van der Waals Heterostructures.

    PubMed

    Aretouli, Kleopatra Emmanouil; Tsoutsou, Dimitra; Tsipas, Polychronis; Marquez-Velasco, Jose; Aminalragia Giamini, Sigiava; Kelaidis, Nicolaos; Psycharis, Vassilis; Dimoulas, Athanasios

    2016-09-07

    van der Waals heterostructures of 2D semiconductor materials can be used to realize a number of (opto)electronic devices including tunneling field effect devices (TFETs). It is shown in this work that high quality SnSe2/WSe2 vdW heterostructure can be grown by molecular beam epitaxy on AlN(0001)/Si(111) substrates using a Bi2Se3 buffer layer. A valence band offset of 0.8 eV matches the energy gap of SnSe2 in such a way that the VB edge of WSe2 and the CB edge of SnSe2 are lined up, making this materials combination suitable for (nearly) broken gap TFETs.

  15. Mechanical loading and the synthesis of 1,25(OH)2D in primary human osteoblasts.

    PubMed

    van der Meijden, K; Bakker, A D; van Essen, H W; Heijboer, A C; Schulten, E A J M; Lips, P; Bravenboer, N

    2016-02-01

    The metabolite 1,25-dihydroxyvitamin D (1,25(OH)2D) is synthesized from its precursor 25-hydroxyvitamin D (25(OH)D) by human osteoblasts leading to stimulation of osteoblast differentiation in an autocrine or paracrine way. Osteoblast differentiation is also stimulated by mechanical loading through activation of various responses in bone cells such as nitric oxide signaling. Whether mechanical loading affects osteoblast differentiation through an enhanced synthesis of 1,25(OH)2D by human osteoblasts is still unknown. We hypothesized that mechanical loading stimulates the synthesis of 1,25(OH)2D from 25(OH)D in primary human osteoblasts. Since the responsiveness of bone to mechanical stimuli can be altered by various endocrine factors, we also investigated whether 1,25(OH)2D or 25(OH)D affect the response of primary human osteoblasts to mechanical loading. Primary human osteoblasts were pre-incubated in medium with/without 25(OH)D3 (400 nM) or 1,25(OH)2D3 (100 nM) for 24h and subjected to mechanical loading by pulsatile fluid flow (PFF). The response of osteoblasts to PFF was quantified by measuring nitric oxide, and by PCR analysis. The effect of PFF on the synthesis of 1,25(OH)2D3 was determined by subjecting osteoblasts to PFF followed by 24h post-incubation in medium with/without 25(OH)D3 (400 nM). We showed that 1,25(OH)2D3 reduced the PFF-induced NO response in primary human osteoblasts. 25(OH)D3 did not significantly alter the NO response of primary human osteoblasts to PFF, but 25(OH)D3 increased osteocalcin and RANKL mRNA levels, similar to 1,25(OH)2D3. PFF did not increase 1,25(OH)2D3 amounts in our model, even though PFF did increase CYP27B1 mRNA levels and reduced VDR mRNA levels. CYP24 mRNA levels were not affected by PFF, but were strongly increased by both 25(OH)D3 and 1,25(OH)2D3. In conclusion, 1,25(OH)2D3 may affect the response of primary human osteoblasts to mechanical stimuli, at least with respect to NO production. Mechanical stimuli may affect

  16. A method for the direct injection and analysis of small volume human blood spots and plasma extracts containing high concentrations of organic solvents using revered-phase 2D UPLC/MS.

    PubMed

    Rainville, Paul D; Simeone, Jennifer L; Root, Dan S; Mallet, Claude R; Wilson, Ian D; Plumb, Robert S

    2015-03-21

    The emergence of micro sampling techniques holds great potential to improve pharmacokinetic data quality, reduce animal usage, and save costs in safety assessment studies. The analysis of these samples presents new challenges for bioanalytical scientists, both in terms of sample processing and analytical sensitivity. The use of two dimensional LC/MS with, at-column-dilution for the direct analysis of highly organic extracts prepared from biological fluids such as dried blood spots and plasma is demonstrated. This technique negated the need to dry down and reconstitute, or dilute samples with water/aqueous buffer solutions, prior to injection onto a reversed-phase LC system. A mixture of model drugs, including bromhexine, triprolidine, enrofloxacin, and procaine were used to test the feasibility of the method. Finally an LC/MS assay for the probe pharmaceutical rosuvastatin was developed from dried blood spots and protein-precipitated plasma. The assays showed acceptable recovery, accuracy and precision according to US FDA guidelines. The resulting analytical method showed an increase in assay sensitivity of up to forty fold as compared to conventional methods by maximizing the amount loaded onto the system and the MS response for the probe pharmaceutical rosuvastatin from small volume samples.

  17. Circular photogalvanic effect caused by the transitions between edge and 2D states in a 2D topological insulator

    NASA Astrophysics Data System (ADS)

    Magarill, L. I.; Entin, M. V.

    2016-12-01

    The electron absorption and the edge photocurrent of a 2D topological insulator are studied for transitions between edge states to 2D states. The circular polarized light is found to produce the edge photocurrent, the direction of which is determined by light polarization and edge orientation. It is shown that the edge-state current is found to exceed the 2D current owing to the topological protection of the edge states.

  18. Detection of Leptomeningeal Metastasis by Contrast-Enhanced 3D T1-SPACE: Comparison with 2D FLAIR and Contrast-Enhanced 2D T1-Weighted Images

    PubMed Central

    Gil, Bomi; Hwang, Eo-Jin; Lee, Song; Jang, Jinhee; Jung, So-Lyung; Ahn, Kook-Jin; Kim, Bum-soo

    2016-01-01

    Introduction To compare the diagnostic accuracy of contrast-enhanced 3D(dimensional) T1-weighted sampling perfection with application-optimized contrasts by using different flip angle evolutions (T1-SPACE), 2D fluid attenuated inversion recovery (FLAIR) images and 2D contrast-enhanced T1-weighted image in detection of leptomeningeal metastasis except for invasive procedures such as a CSF tapping. Materials and Methods Three groups of patients were included retrospectively for 9 months (from 2013-04-01 to 2013-12-31). Group 1 patients with positive malignant cells in CSF cytology (n = 22); group 2, stroke patients with steno-occlusion in ICA or MCA (n = 16); and group 3, patients with negative results on MRI, whose symptom were dizziness or headache (n = 25). A total of 63 sets of MR images are separately collected and randomly arranged: (1) CE 3D T1-SPACE; (2) 2D FLAIR; and (3) CE T1-GRE using a 3-Tesla MR system. A faculty neuroradiologist with 8-year-experience and another 2nd grade trainee in radiology reviewed each MR image- blinded by the results of CSF cytology and coded their observations as positives or negatives of leptomeningeal metastasis. The CSF cytology result was considered as a gold standard. Sensitivity and specificity of each MR images were calculated. Diagnostic accuracy was compared using a McNemar’s test. A Cohen's kappa analysis was performed to assess inter-observer agreements. Results Diagnostic accuracy was not different between 3D T1-SPACE and CSF cytology by both raters. However, the accuracy test of 2D FLAIR and 2D contrast-enhanced T1-weighted GRE was inconsistent by the two raters. The Kappa statistic results were 0.657 (3D T1-SPACE), 0.420 (2D FLAIR), and 0.160 (2D contrast-enhanced T1-weighted GRE). The 3D T1-SPACE images showed the highest inter-observer agreements between the raters. Conclusions Compared to 2D FLAIR and 2D contrast-enhanced T1-weighted GRE, contrast-enhanced 3D T1 SPACE showed a better detection rate of

  19. Multichannel Analysis of Surface Waves and Down-Hole Tests in the Archeological "Palatine Hill" Area (Rome, Italy): Evaluation and Influence of 2D Effects on the Shear Wave Velocity

    NASA Astrophysics Data System (ADS)

    Di Fiore, V.; Cavuoto, G.; Tarallo, D.; Punzo, M.; Evangelista, L.

    2016-05-01

    A joint analysis of down-hole (DH) and multichannel analysis of surface waves (MASW) measurements offers a complete evaluation of shear wave velocity profiles, especially for sites where a strong lateral variability is expected, such as archeological sites. In this complex stratigraphic setting, the high "subsoil anisotropy" (i.e., sharp lithological changes due to the presence of anthropogenic backfill deposits and/or buried man-made structures) implies a different role for DH and MASW tests. This paper discusses some results of a broad experimental program conducted on the Palatine Hill, one of the most ancient areas of the city of Rome (Italy). The experiments were part of a project on seismic microzoning and consisted of 20 MASW and 11 DH tests. The main objective of this study was to examine the difficulties related to the interpretation of the DH and MASW tests and the reliability limits inherent in the application of the noninvasive method in complex stratigraphic settings. As is well known, DH tests provide good determinations of shear wave velocities (Vs) for different lithologies and man-made materials, whereas MASW tests provide average values for the subsoil volume investigated. The data obtained from each method with blind tests were compared and were correlated to site-specific subsurface conditions, including lateral variability. Differences between punctual (DH) and global (MASW) Vs measurements are discussed, quantifying the errors by synthetic comparison and by site response analyses. This study demonstrates that, for archeological sites, VS profiles obtained from the DH and MASW methods differ by more than 15 %. However, the local site effect showed comparable results in terms of natural frequencies, whereas the resolution of the inverted shear wave velocity was influenced by the fundamental mode of propagation.

  20. Lagrangian statistics in laboratory 2D turbulence

    NASA Astrophysics Data System (ADS)

    Xia, Hua; Francois, Nicolas; Punzmann, Horst; Shats, Michael

    2014-05-01

    Turbulent mixing in liquids and gases is ubiquitous in nature and industrial flows. Understanding statistical properties of Lagrangian trajectories in turbulence is crucial for a range of problems such as spreading of plankton in the ocean, transport of pollutants, etc. Oceanic data on trajectories of the free-drifting instruments, indicate that the trajectory statistics can often be described by a Lagrangian integral scale. Turbulence however is a state of a flow dominated by a hierarchy of scales, and it is not clear which of these scales mostly affect particle dispersion. Moreover, coherent structures often coexist with turbulence in laboratory experiments [1]. The effect of coherent structures on particle dispersion in turbulent flows is not well understood. Recent progress in scientific imaging and computational power made it possible to tackle this problem experimentally. In this talk, we report the analysis of the higher order Lagrangian statistics in laboratory two-dimensional turbulence. Our results show that fluid particle dispersion is diffusive and it is determined by a single measurable Lagrangian scale related to the forcing scale [2]. Higher order moments of the particle dispersion show strong self-similarity in fully developed turbulence [3]. Here we introduce a new dispersion law that describes single particle dispersion during the turbulence development [4]. These results offer a new way of predicting dispersion in turbulent flows in which one of the low energy scales are persistent. It may help better understanding of drifter Lagrangian statistics in the regions of the ocean where small scale coherent eddies are present [5]. Reference: 1. H. Xia, H. Punzmann, G. Falkovich and M. Shats, Physical Review Letters, 101, 194504 (2008) 2. H. Xia, N. Francois, H. Punzmann, and M. Shats, Nature Communications, 4, 2013 (2013) 3. R. Ferrari, A.J. Manfroi , W.R. Young, Physica D 154 111 (2001) 4. H. Xia, N. Francois, H. Punzmann and M. Shats, submitted (2014

  1. Energy Efficiency of D2D Multi-User Cooperation.

    PubMed

    Zhang, Zufan; Wang, Lu; Zhang, Jie

    2017-03-28

    The Device-to-Device (D2D) communication system is an important part of heterogeneous networks. It has great potential to improve spectrum efficiency, throughput and energy efficiency cooperation of multiple D2D users with the advantage of direct communication. When cooperating, D2D users expend extraordinary energy to relay data to other D2D users. Hence, the remaining energy of D2D users determines the life of the system. This paper proposes a cooperation scheme for multiple D2D users who reuse the orthogonal spectrum and are interested in the same data by aiming to solve the energy problem of D2D users. Considering both energy availability and the Signal to Noise Ratio (SNR) of each D2D user, the Kuhn-Munkres algorithm is introduced in the cooperation scheme to solve relay selection problems. Thus, the cooperation issue is transformed into a maximum weighted matching (MWM) problem. In order to enhance energy efficiency without the deterioration of Quality of Service (QoS), the link outage probability is derived according to the Shannon Equation by considering the data rate and delay. The simulation studies the relationships among the number of cooperative users, the length of shared data, the number of data packets and energy efficiency.

  2. Integrating Mobile Multimedia into Textbooks: 2D Barcodes

    ERIC Educational Resources Information Center

    Uluyol, Celebi; Agca, R. Kagan

    2012-01-01

    The major goal of this study was to empirically compare text-plus-mobile phone learning using an integrated 2D barcode tag in a printed text with three other conditions described in multimedia learning theory. The method examined in the study involved modifications of the instructional material such that: a 2D barcode was used near the text, the…

  3. Efficient Visible Quasi-2D Perovskite Light-Emitting Diodes.

    PubMed

    Byun, Jinwoo; Cho, Himchan; Wolf, Christoph; Jang, Mi; Sadhanala, Aditya; Friend, Richard H; Yang, Hoichang; Lee, Tae-Woo

    2016-09-01

    Efficient quasi-2D-structure perovskite light-emitting diodes (4.90 cd A(-1) ) are demonstrated by mixing a 3D-structured perovskite material (methyl ammonium lead bromide) and a 2D-structured perovskite material (phenylethyl ammonium lead bromide), which can be ascribed to better film uniformity, enhanced exciton confinement, and reduced trap density.

  4. Adaptation algorithms for 2-D feedforward neural networks.

    PubMed

    Kaczorek, T

    1995-01-01

    The generalized weight adaptation algorithms presented by J.G. Kuschewski et al. (1993) and by S.H. Zak and H.J. Sira-Ramirez (1990) are extended for 2-D madaline and 2-D two-layer feedforward neural nets (FNNs).

  5. Synthesis and structural analysis using 2-D NMR of Sialyl Lewis X (SLe{sup x}) and Lewis X (Le{sup x}) oligosaccharides: Ligands related to E-selectin [ELAM-1] binding

    SciTech Connect

    Ball, G.E.; Nagy, J.O.; Brown, E.G.

    1992-06-17

    The sialyl Lewis X (SLe{sup x}) determinant (NeuAc-{alpha}-2,3-Gal-{beta}-1,4-[Fuc-{alpha}-1,3]-GlcNAc), compound 1, is a ligand for E-selectin (endothelial leucocyte adhesion molecule 1, or ELAM-1), a member of the selectin family of cell adhesion molecules. Interactions between E-selectin and leucocyte-bound SLe{sup x} or closely related oligosaccharides are thought to be important early events in the inflammation process. Binding analysis has shown that the sialic acid (NeuAc) and the fucose (Fuc) moieties are essential for high affinity. The related desialylated trisaccharide Le{sup x} (Gas-{beta}-1,4-[Fuc-{alpha}-1,3]-GlcNAc), for example, is not a high-affinity ligand for E-selectin. In this communication, the authors describe the syntheses of SLe{sup x} 1 and the {beta}-O-allyl glycoside of Le{sup x} 2 using a cloned fucosyltransferase and their complete NMR spectral assignments including ROESY and NOESY experiments in order to investigate the conformation of these compounds in solution. 25 refs., 2 figs.

  6. A 2D-QSAR and Grid-Independent Molecular Descriptor (GRIND) Analysis of Quinoline-Type Inhibitors of Akt2: Exploration of the Binding Mode in the Pleckstrin Homology (PH) Domain

    PubMed Central

    Akhtar, Noreen; Jabeen, Ishrat

    2016-01-01

    Protein kinase B-β (PKBβ/Akt2) is a serine/threonine-specific protein kinase that has emerged as one of the most important regulators of cell growth, differentiation, and division. Upregulation of Akt2 in various human carcinomas, including ovarian, breast, and pancreatic, is a well-known tumorigenesis phenomenon. Early on, the concept of the simultaneous administration of anticancer drugs with inhibitors of Akt2 was advocated to overcome cell proliferation in the chemotherapeutic treatment of cancer. However, clinical studies have not lived up to the high expectations, and several phase II and phase III clinical studies have been terminated prematurely because of severe side effects related to the non-selective isomeric inhibition of Akt2. The notion that the sequence identity of pleckstrin homology (PH) domains within Akt-isoforms is less than 30% might indicate the possibility of the development of selective antagonists against the Akt2 PH domain. Therefore, in this study, various in silico tools were utilized to explore the hypothesis that quinoline-type inhibitors bind in the Akt2 PH domain. A Grid-Independent Molecular Descriptor (GRIND) analysis indicated that two hydrogen bond acceptors, two hydrogen bond donors and one hydrophobic feature at a certain distance from each other were important for the selective inhibition of Akt2. Our docking results delineated the importance of Lys30 as an anchor point for mapping the distances of important amino acid residues in the binding pocket, including Lys14, Glu17, Arg25, Asn53, Asn54 and Arg86. The binding regions identified complement the GRIND-based pharmacophoric features. PMID:28036396

  7. Regulation of ligands for the NKG2D activating receptor

    PubMed Central

    Raulet, David H.; Gasser, Stephan; Gowen, Benjamin G.; Deng, Weiwen; Jung, Heiyoun

    2014-01-01

    NKG2D is an activating receptor expressed by all NK cells and subsets of T cells. It serves as a major recognition receptor for detection and elimination of transformed and infected cells and participates in the genesis of several inflammatory diseases. The ligands for NKG2D are self-proteins that are induced by pathways that are active in certain pathophysiological states. NKG2D ligands are regulated transcriptionally, at the level of mRNA and protein stability, and by cleavage from the cell surface. In some cases, ligand induction can be attributed to pathways that are activated specifically in cancer cells or infected cells. We review the numerous pathways that have been implicated in the regulation of NKG2D ligands, discuss the pathologic states in which those pathways are likely to act, and attempt to synthesize the findings into general schemes of NKG2D ligand regulation in NK cell responses to cancer and infection. PMID:23298206

  8. 2D materials and van der Waals heterostructures.

    PubMed

    Novoselov, K S; Mishchenko, A; Carvalho, A; Castro Neto, A H

    2016-07-29

    The physics of two-dimensional (2D) materials and heterostructures based on such crystals has been developing extremely fast. With these new materials, truly 2D physics has begun to appear (for instance, the absence of long-range order, 2D excitons, commensurate-incommensurate transition, etc.). Novel heterostructure devices--such as tunneling transistors, resonant tunneling diodes, and light-emitting diodes--are also starting to emerge. Composed from individual 2D crystals, such devices use the properties of those materials to create functionalities that are not accessible in other heterostructures. Here we review the properties of novel 2D crystals and examine how their properties are used in new heterostructure devices.

  9. New generation transistor technologies enabled by 2D crystals

    NASA Astrophysics Data System (ADS)

    Jena, D.

    2013-05-01

    The discovery of graphene opened the door to 2D crystal materials. The lack of a bandgap in 2D graphene makes it unsuitable for electronic switching transistors in the conventional field-effect sense, though possible techniques exploiting the unique bandstructure and nanostructures are being explored. The transition metal dichalcogenides have 2D crystal semiconductors, which are well-suited for electronic switching. We experimentally demonstrate field effect transistors with current saturation and carrier inversion made from layered 2D crystal semiconductors such as MoS2, WS2, and the related family. We also evaluate the feasibility of such semiconducting 2D crystals for tunneling field effect transistors for low-power digital logic. The article summarizes the current state of new generation transistor technologies either proposed, or demonstrated, with a commentary on the challenges and prospects moving forward.

  10. Proteomic analysis of hippocampal proteins of F344 rats exposed to 1-bromopropane

    SciTech Connect

    Huang, Zhenlie; Ichihara, Sahoko; Oikawa, Shinji; Chang, Jie; Zhang, Lingyi; Takahashi, Masahide; Subramanian, Kaviarasan; Mohideen, Sahabudeen Sheik; Wang, Yun; Ichihara, Gaku

    2011-11-15

    1-Bromopropane (1-BP) is a compound used as an alternative to ozone-depleting solvents and is neurotoxic both in experimental animals and human. However, the molecular mechanisms of the neurotoxic effects of 1-BP are not well known. To identify the molecular mechanisms of 1-BP-induced neurotoxicity, we analyzed quantitatively changes in protein expression in the hippocampus of rats exposed to 1-BP. Male F344 rats were exposed to 1-BP at 0, 400, or 1000 ppm for 8 h/day for 1 or 4 weeks by inhalation. Two-dimensional difference in gel electrophoresis (2D-DIGE) combined with matrix-assisted laser-desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) were conducted to detect and identify protein modification. Changes in selected proteins were further confirmed by western blot. 2D-DIGE identified 26 proteins with consistently altered model (increase or decrease after both 1- and 4-week 1-BP exposures) and significant changes in their levels (p < 0.05; fold change {>=} {+-} 1.2) at least at one exposure level or more compared with the corresponding controls. Of these proteins, 19 were identified by MALDI-TOF-TOF/MS. Linear regression analysis of 1-BP exposure level identified 8 differentially expressed proteins altered in a dose-dependent manner both in 1- and 4-week exposure experiments. The identified proteins could be categorized into diverse functional classes such as nucleocytoplasmic transport, immunity and defense, energy metabolism, ubiquitination-proteasome pathway, neurotransmitter and purine metabolism. Overall, the results suggest that 1-BP-induced hippocampal damage involves oxidative stress, loss of ATP production, neurotransmitter dysfunction and inhibition of ubiquitination-proteasome system. -- Highlights: Black-Right-Pointing-Pointer 1-BP modified hippocampal proteome in rat and 19 altered proteins were identified. Black-Right-Pointing-Pointer Expression of Ran, TPI, HSP60, PSMA1, ECH1, TPI, B-CK and DJ-1 was changed by 1-BP. Black

  11. SNP genotyping using TaqMan technology: the CYP2D6*17 assay conundrum.

    PubMed

    Gaedigk, Andrea; Freeman, Natalie; Hartshorne, Toinette; Riffel, Amanda K; Irwin, David; Bishop, Jeffrey R; Stein, Mark A; Newcorn, Jeffrey H; Jaime, Lazara Karelia Montané; Cherner, Mariana; Leeder, J Steven

    2015-03-19

    CYP2D6 contributes to the metabolism of many clinically used drugs and is increasingly tested to individualize drug therapy. The CYP2D6 gene is challenging to genotype due to the highly complex nature of its gene locus. TaqMan technology is widely used in the clinical and research settings for genotype analysis due to assay reliability, low cost, and the availability of commercially available assays. The assay identifying 1023C>T (rs28371706) defining a reduced function (CYP2D6*17) and several nonfunctional alleles, produced a small number of unexpected diplotype calls in three independent sets of samples, i.e. calls suggested the presence of a CYP2D6*4 subvariant containing 1023C>T. Gene resequencing did not reveal any unknown SNPs in the primer or probe binding sites in any of the samples, but all affected samples featured a trio of SNPs on their CYP2D6*4 allele between one of the PCR primer and probe binding sites. While the phenomenon was ultimately overcome by an alternate assay utilizing a PCR primer excluding the SNP trio, the mechanism causing this phenomenon remains elusive. This rare and unexpected event underscores the importance of assay validation in samples representing a variety of genotypes, but also vigilance of assay performance in highly polymorphic genes such as CYP2D6.

  12. Investigation of the partially coherent effects in a 2D Talbot interferometer.

    PubMed

    Ge, Xin; Wang, Zhili; Gao, Kun; Zhang, Kai; Hong, Youli; Wang, Dajiang; Zhu, Zhongzhu; Zhu, Peiping; Wu, Ziyu

    2011-08-01

    The recent use of a one-dimensional (1D) X-ray Talbot interferometer has triggered great interest in X-ray differential phase contrast imaging. As an improved version of a 1D interferometer, the development of two-dimensional (2D) grating interferometry strongly stimulated applications of grating-based imaging. In the framework of Fresnel diffraction theory, we investigated the self-image of 2D-phase gratings under partially coherent illumination. The fringe visibility of the self-image has been analyzed as a function of the spatial coherence length. From the viewpoint of self-image visibility, it is possible to find the optimal 2D grid for 2D X-ray grating interferometer imaging. Numerical simulations have been also carried out for quantitative evaluation. Results, in good agreement with theoretical analysis, indicate the spatial coherence requirements of the radiation illuminating a 2D grating interferometer. Moreover, our results can be used to optimize performances of a 2D grating interferometer and for further theoretical and experimental research on grating-based imaging systems.

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

    PubMed

    Pan, Xian; Jeong, Hyunyoung

    2015-07-01

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

  14. Evidence for polymorphism in the cytochrome P450 2D50 gene in horses.

    PubMed

    Corado, C R; McKemie, D S; Young, A; Knych, H K

    2016-06-01

    Metabolism is an essential factor in the clearance of many drugs and as such plays a major role in the establishment of dosage regimens and withdrawal times. CYP2D6, the human orthologue to equine CYP2D50, is a drug-metabolizing enzyme that is highly polymorphic in humans leading to widely differing levels of metabolic activity. As CYP2D6 is highly polymorphic, in this study it was hypothesized that the gene coding for the equine orthologue, CYP2D50, may also be prone to polymorphism. Blood samples were collected from 150 horses, the CYP2D50 gene was cloned and sequenced; and full-length sequences were analyzed for single nucleotide polymorphisms (SNPs), deletions, or insertions. Pharmacokinetic data were collected from a subset of horses following the administration of a single oral dose of tramadol and probit analysis used to calculate metabolic ratios. Prior to drug administration, the ability of recombinant CYP2D50 to metabolize tramadol to O-desmethyltramadol was confirmed. Sequencing of CYP2D50 identified 126 exonic SNPs, with 31 of those appearing in multiple horses. Oral administration of tramadol to a subset of these horses revealed variable metabolic ratios (tramadol: O-desmethyltramadol) in individual horses and separation into three metabolic groups. While a limited number of horses of primarily a single breed were studied, the variability in tramadol metabolism to O-desmethyltramadol between horses and preliminary evidence of what appears to be poor, extensive, and ultra-rapid metabolizers supports further study of the potential for genetic polymorphisms in the CYP2D50 gene in horses.

  15. Stability of two-dimensional (2D) natural convection flows in air-filled differentially heated cavities: 2D/3D disturbances

    NASA Astrophysics Data System (ADS)

    Xin, Shihe; Le Quéré, Patrick

    2012-06-01

    Following our previous two-dimensional (2D) studies of flows in differentially heated cavities filled with air, we studied the stability of 2D natural convection flows in these cavities with respect to 3D periodic perturbations. The basis of the numerical methods is a time-stepping code using the Chebyshev spectral collocation method and the direct Uzawa method for velocity-pressure coupling. Newton's iteration, Arnoldi's method and the continuation method have been used in order to, respectively, compute the 2D steady-state base solution, estimate the leading eigenmodes of the Jacobian and perform linear stability analysis. Differentially heated air-filled cavities of aspect ratios from 1 to 7 were investigated. Neutral curves (Rayleigh number versus wave number) have been obtained. It turned out that only for aspect ratio 7, 3D stationary instability occurs at slightly higher Rayleigh numbers than the onset of 2D time-dependent flow and that for other aspect ratios 3D instability always takes place before 2D time-dependent flows. 3D unstable modes are stationary and anti-centro-symmetric. 3D nonlinear simulations revealed that the corresponding pitchfork bifurcations are supercritical and that 3D instability leads only to weak flow in the third direction. Further 3D computations are also performed at higher Rayleigh number in order to understand the effects of the weak 3D fluid motion on the onset of time-dependent flow. 3D flow structures are responsible for the onset of time-dependent flow for aspect ratios 1, 2 and 3, while for larger aspect ratios they do not alter the transition scenario, which was observed in the 2D cases and that vertical boundary layers become unstable to traveling waves.

  16. [FUNCTIONAL DIFFERENTIATION IN BRYOZOAN COLONY: A PROTEOMIC ANALYSIS].

    PubMed

    Kutyumov, V A; Maltseva, A L; Kotenko, N; Ostrovsky, A N

    2016-01-01

    Bryozoans are typical modular organisms. They consist of repetitive structural units, the zooids. Bryozoan colonies grow by zooidal budding, with the distribution pattern of the budding loci underlying the diversity of colony forms. Budding is usually restricted to the zooids at the periphery of the colony, which form a "growing edge" or local terminal growth zones. Non-budding parts of the colony can be functionally subdivided, too. In many species colonies consists of regular, often repetitive zones of feeding and non-feeding modules, associated with a periodical degeneration and regeneration of the polypide, retractile tentacle crown with a gut and the accompanying musculature. So, there is functional differentiation in bryozoan colonies but its mechanisms are unknown. Presumably, budding and/or polypide recycling in different colony parts are induced or inhibited by certain determinants of functional specialization. An effective tool of their identification is the comparison of proteomes of functionally different zones. Here we report the results of proteomic analysis of three bryozoan species from the White Sea, which have a different colony form: Flustrellidra hispida, Terminoflustra membranaceotruncata and Securiflustra securifrons. Using differential two-dimensional electrophoresis (2D-DIGE), we compared proteomes of the growing edge and the zones consisting of feeding and non-feeding zooids in these species. We estimated the overall proteome variability, revealed proteins whose relative abundance gradually changed along the proximal-distal colony axis and suggested that they might be involved in the functional differentiation of the colony.

  17. Proteomic analysis of early seed development in Pinus massoniana L.

    PubMed

    Zhen, Yan; Zhao, Zhen-Zhou; Zheng, Ren-Hua; Shi, Jisen

    2012-05-01

    Understanding seed development is important for large-scale propagation and germplasm conservation for the Masson pine. We undertook a proteomic analysis of Masson pine seeds during the early stages of embryogenesis. Two-dimensional difference gel electrophoresis (2D DIGE) was used to quantify the differences in protein expression during early seed development. Using electrospray ionization mass spectrometry/mass spectrometry, we identified proteins from 43 gel spots that had been excised from preparative "pick" gels. Proteins involved in carbon metabolism were identified and were predominantly expressed at higher levels during the cleavage polyembryony and columnar embryo stages. Functional annotation of one seed protein revealed it involvement in programmed cell death and translation of selective mRNAs, which may play an important role in subordinate embryo elimination and suspensor degeneration in polyembryonic seed gymnosperms. Other identified proteins were associated with protein folding, nitrogen metabolism, disease/defense response, and protein storage, synthesis and stabilization. The comprehensive protein expression profiles generated by this study will provide new insights into the complex developmental process of seed development in Masson pine.

  18. Cytochrome P450 2D6 variants in a Caucasian population: Allele frequencies and phenotypic consequences

    SciTech Connect

    Sachse, C.; Brockmoeller, J.; Bauer, S.; Roots, I.

    1997-02-01

    Cytochrome P450 2D6 (CYP2D6) metabolizes many important drugs. CYP2D6 activity ranges from complete deficiency to ultrafast metabolism, depending on at least 16 different known alleles. Their frequencies were determined in 589 unrelated German volunteers and correlated with enzyme activity measured by phenotyping with dextromethorphan or debrisoquine. For genotyping, nested PCR-RFLP tests from a PCR amplificate of the entire CYP2D6 gene were developed. The frequency of the CYP2D6*1 allele coding for extensive metabolizer (EM) phenotype was .364. The alleles coding for slightly (CYP2D6*2) or moderately (*9 and *10) reduced activity (intermediate metabolizer phenotype [IM]) showed frequencies of .324, .018, and .015, respectively. By use of novel PCR tests for discrimination, CYP2D6 gene duplication alleles were found with frequencies of.005 (*1 x 2), .013 (* 2 x 2), and .001 (*4 x 2). Frequencies of alleles with complete deficiency (poor metabolizer phenotype [PM]) were .207 (*4), .020 (*3 and *5), .009 (*6), and .001 (*7, *15, and *16). The defective CYP2D6 alleles *8, *11, *12, *13, and *14 were not found. All 41 PMs (7.0%) in this sample were explained by five mutations detected by four PCR-RFLP tests, which may suffice, together with the gene duplication test, for clinical prediction of CYP2D6 capacity. Three novel variants of known CYP2D6 alleles were discovered: *1C (T{sub 1957}C), *2B (additional C{sub 2558}T), and *4E (additional C{sub 2938}T). Analysis of variance showed significant differences in enzymatic activity measured by the dextromethorphan metabolic ratio (MR) between carriers of EN/PM (mean MR = .006) and IM/PM (mean MR = .014) alleles and between carriers of one (mean MR = .009) and two (mean MR = .003) functional alleles. The results of this study provide a solid basis for prediction of CYP2D6 capacity, as required in drug research and routine drug treatment. 35 refs., 4 figs., 5 tabs.

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

    PubMed

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

    2016-08-04

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

  20. Efficient 2D MRI relaxometry using compressed sensing

    NASA Astrophysics Data System (ADS)

    Bai, Ruiliang; Cloninger, Alexander; Czaja, Wojciech; Basser, Peter J.

    2015-06-01

    Potential applications of 2D relaxation spectrum NMR and MRI to characterize complex water dynamics (e.g., compartmental exchange) in biology and other disciplines have increased in recent years. However, the large amount of data and long MR acquisition times required for conventional 2D MR relaxometry limits its applicability for in vivo preclinical and clinical MRI. We present a new MR pipeline for 2D relaxometry that incorporates compressed sensing (CS) as a means to vastly reduce the amount of 2D relaxation data needed for material and tissue characterization without compromising data quality. Unlike the conventional CS reconstruction in the Fourier space (k-space), the proposed CS algorithm is directly applied onto the Laplace space (the joint 2D relaxation data) without compressing k-space to reduce the amount of data required for 2D relaxation spectra. This framework is validated using synthetic data, with NMR data acquired in a well-characterized urea/water phantom, and on fixed porcine spinal cord tissue. The quality of the CS-reconstructed spectra was comparable to that of the conventional 2D relaxation spectra, as assessed using global correlation, local contrast between peaks, peak amplitude and relaxation parameters, etc. This result brings this important type of contrast closer to being realized in preclinical, clinical, and other applications.

  1. 2D vs. 3D mammography observer study

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

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

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

    PubMed

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

    2017-04-01

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

  3. Cell Counting in Human Endobronchial Biopsies - Disagreement of 2D versus 3D Morphometry

    PubMed Central

    Bratu, Vlad A.; Erpenbeck, Veit J.; Fehrenbach, Antonia; Rausch, Tanja; Rittinghausen, Susanne; Krug, Norbert; Hohlfeld, Jens M.; Fehrenbach, Heinz

    2014-01-01

    Question Inflammatory cell numbers are important endpoints in clinical studies relying on endobronchial biopsies. Assumption-based bidimensional (2D) counting methods are widely used, although theoretically design-based stereologic three-dimensional (3D) methods alone offer an unbiased quantitative tool. We assessed the method agreement between 2D and 3D counting designs in practice when applied to identical samples in parallel. Materials and Methods Biopsies from segmental bronchi were collected from healthy non-smokers (n = 7) and smokers (n = 7), embedded and sectioned exhaustively. Systematic uniform random samples were immunohistochemically stained for macrophages (CD68) and T-lymphocytes (CD3), respectively. In identical fields of view, cell numbers per volume unit (NV) were assessed using the physical disector (3D), and profiles per area unit (NA) were counted (2D). For CD68+ cells, profiles with and without nucleus were separately recorded. In order to enable a direct comparison of the two methods, the zero-dimensional CD68+/CD3+-ratio was calculated for each approach. Method agreement was tested by Bland-Altmann analysis. Results In both groups, mean CD68+/CD3+ ratios for NV and NA were significantly different (non-smokers: 0.39 and 0.68, p<0.05; smokers: 0.49 and 1.68, p<0.05). When counting only nucleated CD68+ profiles, mean ratios obtained by 2D and 3D counting were similar, but the regression-based Bland-Altmann analysis indicated a bias of the 2D ratios proportional to their magnitude. This magnitude dependent deviation differed between the two groups. Conclusions 2D counts of cell and nuclear profiles introduce a variable size-dependent bias throughout the measurement range. Because the deviation between the 3D and 2D data was different in the two groups, it precludes establishing a ‘universal conversion formula’. PMID:24663339

  4. NKG2D receptor and its ligands in host defense

    PubMed Central

    Lanier, Lewis L.

    2015-01-01

    NKG2D is an activating receptor expressed on the surface of natural killer (NK) cells, CD8+ T cells, and subsets of CD4+ T cells, iNKT cells, and γδ T cells. In humans NKG2D transmits signals by its association with the DAP10 adapter subunit and in mice alternatively spliced isoforms transmit signals either using DAP10 or DAP12 adapter subunits. Although NKG2D is encoded by a highly conserved gene (KLRK1) with limited polymorphism, the receptor recognizes an extensive repertoire of ligands, encoded by at least 8 genes in humans (MICA, MICB, RAET1E, RAET1G, RAET1H, RAET1I, RAET1L, and RAET1N), some with extensive allelic polymorphism. Expression of the NKG2D ligands is tightly regulated at the level of transcription, translation, and post-translation. In general healthy adult tissues do not express NKG2D glycoproteins on the cell surface, but these ligands can be induced by hyper-proliferation and transformation, as well as when cells are infected by pathogens. Thus, the NKG2D pathway serves a mechanism for the immune system to detect and eliminate cells that have undergone “stress”. Viruses and tumor cells have devised numerous strategies to evade detection by the NKG2D surveillance system and diversification of the NKG2D ligand genes likely has been driven by selective pressures imposed by pathogens. NKG2D provides an attractive target for therapeutics in the treatment of infectious diseases, cancer, and autoimmune diseases. PMID:26041808