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Sample records for 2-d dige analysis

  1. Allergenicity study of EGFP-transgenic chicken meat by serological and 2D-DIGE analysis.

    PubMed

    Nakamura, Rika; Nakamura, Ryosuke; Nakano, Mikiharu; Arisawa, Kenjiro; Ezaki, Ryo; Horiuchi, Hiroyuki; Teshima, Reiko

    2010-05-01

    Genetically modified (GM) foods must be tested for safety, including by allergenicity tests to ensure that they do not contain new allergens or higher concentrations of known allergens than the same non-GM foods. In this study experimentally developed EGFP-transgenic chickens were used and evaluated the allergenicity of meat from the chicken based on a serological and two-dimensional difference gel electrophoresis (2D-DIGE) analysis. For the serological analysis, a Western blotting with allergen-specific antibodies and a proteomic analysis of chicken meat allergens with patients' sera, a so-called allergenome analysis, were used. The allergenome analysis allowed us to identify five IgE-binding proteins in chicken meat, including a known allergen, chicken serum albumin, and no qualitative difference in their expressions between the GM and non-GM chicken meat was found. Results of the 2D-DIGE analysis showed that none of the IgE-binding proteins in chicken meat were significantly changed in expression levels between non-GM and GM chicken, and only 3 of the 1500 soluble protein spots including green fluorescence protein were markedly different as a result of gene transfer. These above results showed that the combination of serological and 2D-DIGE analysis is a valid method of evaluating quality and quantity of allergens in GM foods.

  2. An overview of 2D DIGE analysis of marine (environmental) bacteria.

    PubMed

    Rabus, Ralf

    2012-01-01

    Microbes are the "unseen majority" of living organisms on Earth and main drivers of the biogeochemical cycles in marine and most other environments. Their significance for an intact biosphere is bringing environmental bacteria increasingly into the focus of genome-based science. Proteomics is playing a prominent role for providing a molecular understanding of how these microbes work and for identifying the key biocatalysts involved in the major biogeochemical processes. This overview describes the major insights obtained from two-dimensional difference gel electrophoresis (2D DIGE) analyses of specific degradation pathways, complex metabolic networks, cellular processes, and regulatory patterns in the marine aerobic heterotrophs Rhodopirellula baltica SH1 (Planctomycetes) and Phaeobacter gallaeciensis DSM 17395 (Roseobacter clade) and the anaerobic aromatic compound degrader Aromatoleum aromaticum EbN1 (Betaproteobacteria). PMID:22311773

  3. 2D-DIGE proteomic analysis of mesenchymal stem cell cultured on the elasticity-tunable hydrogels.

    PubMed

    Kuboki, Thasaneeya; Kantawong, Fahsai; Burchmore, Richard; Dalby, Matthew J; Kidoaki, Satoru

    2012-01-01

    The present study focuses on mechanotransduction in mesenchymal stem cells (MSCs) in response to matrix elasticity. By using photocurable gelatinous gels with tunable stiffness, proteomic profiles of MSCs cultured on tissue culture plastic, soft (3 kPa) and stiff (52 kPa) matrices were deciphered using 2-dimensional differential in-gel analysis (2D-DIGE). The DIGE data, tied to immunofluorescence, indicated abundance and organization changes in the cytoskeletonal proteins as well as differential regulation of important signaling-related proteins, stress-responsing proteins and also proteins involved in collagen synthesis. The major CSK proteins including actin, tubulin and vimentin of the cells cultured on the gels were remarkably changed their expressions. Significant down-regulation of α-tubulin and β-actin can be observed on gel samples in comparison to the rigid tissue culture plates. The expression abundance of vimentin appeared to be highest in the MSCs cultured on hard gels. These results suggested that the substrate stiffness significantly affects expression balances in cytoskeletal proteins of MSCs with some implications to cellular tensegrity. PMID:22971925

  4. Phosphoproteomic analysis of wild-type and antimony-resistant Leishmania braziliensis lines by 2D-DIGE technology.

    PubMed

    Moreira, Douglas de Souza; Pescher, Pascale; Laurent, Christine; Lenormand, Pascal; Späth, Gerald F; Murta, Silvane M F

    2015-09-01

    Protein phosphorylation is one of the most studied post-translational modifications that is involved in different cellular events in Leishmania. In this study, we performed a comparative phosphoproteomics analysis of potassium antimonyl tartrate (SbIII)-resistant and -susceptible lines of Leishmania braziliensis using a 2D-DIGE approach followed by MS. In order to investigate the differential phosphoprotein abundance associated with the drug-induced stress response and SbIII-resistance mechanisms, we compared nontreated and SbIII-treated samples of each line. Pair wise comparisons revealed a total of 116 spots that showed a statistically significant difference in phosphoprotein abundance, including 11 and 34 spots specifically correlated with drug treatment and resistance, respectively. We identified 48 different proteins distributed into seven biological process categories. The category "protein folding/chaperones and stress response" is mainly implicated in response to SbIII treatment, while the categories "antioxidant/detoxification," "metabolic process," "RNA/DNA processing," and "protein biosynthesis" are modulated in the case of antimony resistance. Multiple sequence alignments were performed to validate the conservation of phosphorylated residues in nine proteins identified here. Western blot assays were carried out to validate the quantitative phosphoproteome analysis. The results revealed differential expression level of three phosphoproteins in the lines analyzed. This novel study allowed us to profile the L. braziliensis phosphoproteome, identifying several potential candidates for biochemical or signaling networks associated with antimony resistance phenotype in this parasite.

  5. Monitoring post mortem changes in porcine muscle through 2-D DIGE proteome analysis of Longissimus muscle exudate

    PubMed Central

    2013-01-01

    Background Meat quality is a complex trait influenced by a range of factors with post mortem biochemical processes highly influential in defining ultimate quality. High resolution two-dimensional DIfference Gel Electrophoresis (2-D DIGE) and Western blot were applied to study the influence of post mortem meat ageing on the proteome of pork muscle. Exudate collected from the muscle following centrifugation was analysed at three timepoints representing a seven day meat ageing period. Results The intensity of 136 spots varied significantly (p < 0.05) across this post mortem period and 40 spots were identified using mass spectrometry. The main functional categories represented were metabolic proteins, stress-related proteins, transport and structural proteins. Metabolic and structural proteins were generally observed to increase in abundance post mortem and many likely represent the accumulation of the degradation products of proteolytic enzyme activity. In contrast, stress-related proteins broadly decreased in abundance across the ageing period. Stress response proteins have protective roles in maintaining cellular integrity and a decline in their abundance over time may correlate with a reduction in cellular integrity and the onset of meat ageing. Since cellular conditions alter with muscle ageing, changes in solubility may also contribute to observed abundance profiles. Conclusions Muscle exudate provided valuable information about the pathways and processes underlying the post mortem ageing period, highlighting the importance of post mortem modification of proteins and their interaction for the development of meat quality traits. PMID:23514628

  6. Proteomic analysis of ovomucoid hypersensitivity in mice by two-dimensional difference gel electrophoresis (2D-DIGE).

    PubMed

    Hobson, D J; Rupa, P; Diaz, G J; Zhang, H; Yang, M; Mine, Y; Turner, P V; Kirby, G M

    2007-12-01

    There is a need to develop reliable methods to assess the safety of genetically modified and other novel foods. The aim of this study was to identify protein biomarkers of food allergy in mice exposed to ovomucoid (OVM), a major food allergen found in chicken egg white. BALB/c mice were repeatedly sensitized by gavage with OVM and cholera toxin (CT) and control mice were exposed to a mixture of amino acids with CT. At the endpoint, all mice were challenged intraperitoneally with OVM and alum. Type-1 hypersensitivity was confirmed in OVM-sensitized mice by observation of clinical signs of anaphylaxis and elevated levels of plasma histamine, OVM-specific IgE and OVM-specific IgG by ELISA. Differential protein expression was assessed in albumin-depleted plasma as well as in mesenteric lymph node, liver, spleen, and ileum by two-dimensional difference gel electrophoresis (2D-DIGE). Differentially expressed proteins were identified by liquid chromatography with tandem mass spectrometry. Plasma proteins overexpressed in OVM-sensitized mice included haptoglobin (41-fold), serum amyloid A (19-fold) and peroxiredoxin-2 (1.9-fold). Further validation of these plasma proteins in other animal models of food allergy with different food allergens is required to assess their potential as candidate biomarkers for use in evaluating the allergenicity of novel foods.

  7. 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.

  8. Proteomic analysis of doxorubicin-induced changes in the proteome of HepG2cells combining 2-D DIGE and LC-MS/MS approaches.

    PubMed

    Hammer, Elke; Bien, Sandra; Salazar, Manuela Gesell; Steil, Leif; Scharf, Christian; Hildebrandt, Petra; Schroeder, Henry W S; Kroemer, Heyo K; Völker, Uwe; Ritter, Christoph A

    2010-01-01

    HepG-2 cells are widely used as a cell model to investigate hepatocellular carcinomas and the effect of anticancer drugs such as doxorubicin, an effective antineoplastic agent, which has broad antitumoral activity against many solid and hematological malignancies. To investigate the effect of doxorubicin on the protein pattern, we used complementary proteomic workflows including 2-D gel-based and gel-free methods. The analysis of crude HepG2 cell extracts by 2-D DIGE provided data on 1835 protein spots which was then complemented by MS-centered analysis of stable isotope labeling by amino acids in cell culture-labeled cells. The monitoring of more than 1300 distinct proteins, including proteins of the membrane fraction provides the most comprehensive overview on the proteome of the widely used model cell line HepG2. Of the proteins monitored in total, 155 displayed doxorubicin-induced changes in abundance. Functional analysis revealed major influences of doxorubicin on proteins involved in protein synthesis, DNA damage control, electron transport/mitochondrial function, and tumor growth. The strongest decrease in level was found for proteins involved in DNA replication and protein synthesis, whereas proteins with a function in DNA damage control and oxidative stress management displayed increased levels following treatment with doxorubicin compared with control cells. Furthermore, the doxorubicin-associated increase in levels of multiple forms of keratins 8, 18, and 19 and other structural proteins revealed an influence on the cytoskeleton network.

  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. Distinct metabolic changes between wheat embryo and endosperm during grain development revealed by 2D-DIGE-based integrative proteome analysis.

    PubMed

    Cao, Hui; He, Miao; Zhu, Chong; Yuan, Linlin; Dong, Liwei; Bian, Yanwei; Zhang, Wenying; Yan, Yueming

    2016-05-01

    Two Chinese bread wheat cultivars, Jinghua 9 and Zhongmai 175, distinct in grain weight and dough quality, were used to study proteome changes in the embryo and endosperm during grain development using a two-dimensional difference gel electrophoresis (2D-DIGE)-based proteomics approach. In total, 138 and 127 differentially expressed protein (DEP) spots representing 116 and 113 unique DEPs were identified in the embryo and endosperm, respectively. Among them, 54 (31%) DEPs were commonly present in both organs while 62 (35%) and 59 (34%) DEPs occurred only in the embryo and endosperm, respectively. Embryonic DEPs are primarily stress-related proteins and involved in carbohydrate and lipid metabolism, while those from the endosperm are related primarily to carbohydrate metabolism and storage. Principal component analysis (PCA) indicated that the proteome differences in the endosperm caused by different cultivars were greater than those by development stages, while the differences in the embryo showed the opposite pattern. Protein-protein interaction (PPI) analysis revealed a complex network centered primarily on enzymes involved in carbohydrate and protein metabolism. The transcriptional levels of fourteen important DEPs encoding genes showed high similarity between organs and cultivars. In particular, some key DEPs of the endosperm, such as phosphoglucomutase, ADP-glucose pyrophosphorylase (AGPase), and sucrose synthase (SUS), showed significantly upregulated expression, indicating their key roles in starch biosynthesis and grain yield. Moreover, upregulated expression of some storage proteins in the endosperm could improve wheat bread-making quality.

  11. A 2D-DIGE-based proteomic analysis reveals differences in the platelet releasate composition when comparing thrombin and collagen stimulations

    PubMed Central

    Vélez, Paula; Izquierdo, Irene; Rosa, Isaac; García, Ángel

    2015-01-01

    Upon stimulation, platelets release a high number of proteins (the releasate). There are clear indications that these proteins are involved in the pathogenesis of several diseases, such as atherosclerosis. In the present study we compared the platelet releasate following platelet activation with two major endogenous agonists: thrombin and collagen. Proteome analysis was based on 2D-DIGE and LC-MS/MS. Firstly, we showed the primary role of thrombin and collagen receptors in platelet secretion by these agonists; moreover, we demonstrated that GPVI is the primary responsible for collagen-induced platelet activation/aggregation. Proteomic analysis allowed the detection of 122 protein spots differentially regulated between both conditions. After excluding fibrinogen spots, down-regulated in the releasate of thrombin-activated platelets, 84 differences remained. From those, we successfully identified 42, corresponding to 37 open-reading frames. Many of the differences identified correspond to post-translational modifications, primarily, proteolysis induced by thrombin. Among others, we show vitamin K-dependent protein S, an anticoagulant plasma protein, is up-regulated in thrombin samples. Our results could have pathological implications given that platelets might be playing a differential role in various diseases and biological processes through the secretion of different subsets of granule proteins and microvesicles following a predominant activation of certain receptors. PMID:25645904

  12. Comparative 2D-DIGE Proteomic Analysis of Bovine Mammary Epithelial Cells during Lactation Reveals Protein Signatures for Lactation Persistency and Milk Yield

    PubMed Central

    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. PMID:25111801

  13. High performance CCD camera system for digitalisation of 2D DIGE gels.

    PubMed

    Strijkstra, Annemieke; Trautwein, Kathleen; Roesler, Stefan; Feenders, Christoph; Danzer, Daniel; Riemenschneider, Udo; Blasius, Bernd; Rabus, Ralf

    2016-07-01

    An essential step in 2D DIGE-based analysis of differential proteome profiles is the accurate and sensitive digitalisation of 2D DIGE gels. The performance progress of commercially available charge-coupled device (CCD) camera-based systems combined with light emitting diodes (LED) opens up a new possibility for this type of digitalisation. Here, we assessed the performance of a CCD camera system (Intas Advanced 2D Imager) as alternative to a traditionally employed, high-end laser scanner system (Typhoon 9400) for digitalisation of differential protein profiles from three different environmental bacteria. Overall, the performance of the CCD camera system was comparable to the laser scanner, as evident from very similar protein abundance changes (irrespective of spot position and volume), as well as from linear range and limit of detection.

  14. High performance CCD camera system for digitalisation of 2D DIGE gels.

    PubMed

    Strijkstra, Annemieke; Trautwein, Kathleen; Roesler, Stefan; Feenders, Christoph; Danzer, Daniel; Riemenschneider, Udo; Blasius, Bernd; Rabus, Ralf

    2016-07-01

    An essential step in 2D DIGE-based analysis of differential proteome profiles is the accurate and sensitive digitalisation of 2D DIGE gels. The performance progress of commercially available charge-coupled device (CCD) camera-based systems combined with light emitting diodes (LED) opens up a new possibility for this type of digitalisation. Here, we assessed the performance of a CCD camera system (Intas Advanced 2D Imager) as alternative to a traditionally employed, high-end laser scanner system (Typhoon 9400) for digitalisation of differential protein profiles from three different environmental bacteria. Overall, the performance of the CCD camera system was comparable to the laser scanner, as evident from very similar protein abundance changes (irrespective of spot position and volume), as well as from linear range and limit of detection. PMID:27252121

  15. 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.

  16. 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.

  17. 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

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

    PubMed

    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

  19. 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...

  20. Proteomics Approaches for Identification of Tumor Relevant Protein Targets in Pulmonary Squamous Cell Carcinoma by 2D-DIGE-MS

    PubMed Central

    Yiping, Guo; Yang, Song; Xiaoyu, Qi; Zhuzhu, Guan; Xiaohan, Yang; Xin, Zhou; Liyan, Xue; Shujuan, Shao

    2014-01-01

    Potential markers for progression of pulmonary squamous cell carcinoma (SCC) were identified by examining samples of lung SCC and adjacent normal tissues using a combination of fluorescence two-dimensional difference gel electrophoresis (2D-DIGE), matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS), and electrospray ionization quadrupole-time of flight mass spectrometry (ESI-Q-TOF). The PANTHER System was used for gel image based quantification and statistical analysis. An analysis of proteomic data revealed that 323 protein spots showed significantly different levels of expression (P≤0.05) in lung SCC tissue compared to expression in normal lung tissue. A further analysis of these protein spots by MALDI-TOF-MS identified 81 different proteins. A systems biology approach was used to map these proteins to major pathways involved in numerous cellular processes, including localization, transport, cellular component organization, apoptosis, and reproduction. Additionally, the expression of several proteins in lung SCC and normal tissues was examined using immunohistochemistry and western blot. The functions of individual proteins are being further investigated and validated, and the results might provide new insights into the mechanism of lung SCC progression, potentially leading to the design of novel diagnostic and therapeutic strategies. PMID:24740010

  1. Identification of NaCl Stress-Responsive Apoplastic Proteins in Rice Shoot Stems by 2D-DIGE

    PubMed Central

    Song, Yun; Zhang, Cuijun; Ge, Weina; Zhang, Yafang; Burlingame, Alma L.; Guo, Yi

    2011-01-01

    Plants have evolved sophisticated systems to cope with adverse environmental conditions such as cold, drought, and salinity. Although a number of stress response networks have been proposed, the role of plant apoplast in plant stress response has been ignored. To investigate the role of apoplastic proteins in the salt-stress response, 10-day-old rice plants were treated with 200 mM NaCl for 1, 6 or 12 hours, and the soluble apoplast proteins of rice shoot stems were extracted for differential analysis, compared with untreated controls, by 2-D DIGE saturation labeling techniques. One hundred twenty-two significantly changed spots were identified by LC-MS/MS, and 117 spots representing 69 proteins have been identified. Of these proteins, 37 are apoplastic proteins according to the bioinformatic analysis. These proteins are mainly involved in the processes of carbohydrate metabolism, oxido-reduction, and protein processing and degradation. According to their functional categories and cluster analysis, a stress response model of apoplastic proteins has been proposed. These data indicate that the apoplast is important in plant stress signal reception and response. PMID:21420516

  2. 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

  3. 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.

  4. 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

  5. Revealing oxidative damage to enzymes of carbohydrate metabolism in yeast: An integration of 2D DIGE, quantitative proteomics, and bioinformatics.

    PubMed

    Boone, Cory H T; Grove, Ryan A; Adamcova, Dana; Braga, Camila P; Adamec, Jiri

    2016-07-01

    Clinical usage of lidocaine, a pro-oxidant has been linked with severe, mostly neurological complications. The mechanism(s) causing these complications is independent of the blockade of voltage-gated sodium channels. The budding yeast Saccharomyces cerevisiae lacks voltage-gated sodium channels, thus provides an ideal system to investigate lidocaine-induced protein and pathway alterations. Whole-proteome alterations leading to these complications have not been identified. To address this, S. cerevisiae was grown to stationary phase and exposed to an LC50 dose of lidocaine. The differential proteomes of lidocaine treatment and control were resolved 6 h post exposure using 2D DIGE. Amine reactive dyes and carbonyl reactive dyes were used to assess protein abundance and protein oxidation, respectively. Quantitative analysis of these dyes (⩾ 1.5-fold alteration, p ⩽ 0.05) revealed a total of 33 proteoforms identified by MS differing in abundance and/or oxidation upon lidocaine exposure. Network analysis showed enrichment of apoptotic proteins and cell wall maintenance proteins, while the abundance of proteins central to carbohydrate metabolism, such as triosephosphate isomerase and glyceraldehyde-3-phosphate dehydrogenase, and redox proteins superoxide dismutase and peroxiredoxin were significantly decreased. Enzymes of carbohydrate metabolism, such as phosphoglycerate kinase and enolase, the TCA cycle enzyme aconitase, and multiple ATP synthase subunits were found to be oxidatively modified. Also, the activity of aconitase was found to be decreased. Overall, these data suggest that toxic doses of lidocaine induce significant disruption of glycolytic pathways, energy production, and redox balance, potentially leading to cell malfunction and death. PMID:27193513

  6. Primary style protein expression in the self-incompatible/compatible apricot by the 2D-DIGE technique.

    PubMed

    Cao, Xiaoyan; Feng, Jianrong; Wang, Dajiang; Sun, Junli; Lu, Xiaoyan; Liu, Huaifeng

    2012-07-15

    In order to explore the molecular mechanism underlying self-incompatibility (SI) in the apricot (Prunus armeniaca L.) at the proteome level, we examined the style proteomes at different stages of flower development: small bud, big bud, 24h after self-pollination and 24h after cross-pollination with cultivar Badanshui in the SI apricot cultivar Xinshiji and the self-compatible (SC) apricot cultivar Katy by 2D fluorescence difference gel electrophoresis (2D-DIGE) and mass spectrometry (MS). About 1500 style protein spots were detected; 66 were expressed differently in the four stages in Xinshiji. About 1600 style protein spots were detected; 143 were expressed differently in the four stages of flower development in Katy. In Xinshiji, one protein was expressed specifically, four proteins showed up-regulated expression and twenty-nine proteins showed down-regulated expression in the cross-pollinated style compared to the self-pollinated style. Thirteen proteins were identified unambiguously. In Katy, three proteins were expressed specifically, five proteins showed up-regulated expression and thirteen proteins showed down-regulated expression in the cross-pollinated style compared to self-pollinated style. Seven proteins were identified unambiguously. The different reactions of the style at the proteomic level were triggered in Xinshiji and Katy by self pollen and non-self pollen.

  7. An omics approach to rational feed: Enhancing growth in CHO cultures with NMR metabolomics and 2D-DIGE proteomics.

    PubMed

    Blondeel, Eric J M; Ho, Raymond; Schulze, Steffen; Sokolenko, Stanislav; Guillemette, Simon R; Slivac, Igor; Durocher, Yves; Guillemette, J Guy; McConkey, Brendan J; Chang, David; Aucoin, Marc G

    2016-09-20

    Expression of recombinant proteins exerts stress on cell culture systems, affecting the expression of endogenous proteins, and contributing to the depletion of nutrients and accumulation of waste metabolites. In this work, 2D-DIGE proteomics was employed to analyze differential expression of proteins following stable transfection of a Chinese Hamster Ovary (CHO) cell line to constitutively express a heavy-chain monoclonal antibody. Thirty-four proteins of significant differential expression were identified and cross-referenced with cellular functions and metabolic pathways to identify points of cell stress. Subsequently, 1D-(1)H NMR metabolomics experiments analyzed cultures to observe nutrient depletion and waste metabolite accumulations to further examine these cell stresses and pathways. From among fifty metabolites tracked in time-course, eight were observed to be completely depleted from the production media, including: glucose, glutamine, proline, serine, cystine, asparagine, choline, and hypoxanthine, while twenty-three excreted metabolites were also observed to accumulate. The differentially expressed proteins, as well as the nutrient depletion and accumulation of these metabolites corresponded with upregulated pathways and cell systems related to anaplerotic TCA-replenishment, NADH/NADPH replenishment, tetrahydrofolate cycle C1 cofactor conversions, limitations to lipid synthesis, and redox modulation. A nutrient cocktail was assembled to improve the growth medium and alleviate these cell stresses to achieve a ∼75% improvement to peak cell densities. PMID:27496566

  8. Two-dimensional difference gel electrophoresis (DIGE) analysis of sera from visceral leishmaniasis patients

    PubMed Central

    2011-01-01

    Introduction Visceral leishmaniasis is a parasitic infection caused by Lesihmania donovani complex and transmitted by the bite of the phlebotomine sand fly. It is an endemic disease in many developing countries with more than 90% of the cases occurring in Bangladesh, India, Nepal, Sudan, Ethiopia and Brazil. The disease is fatal if untreated. The disease is conventionally diagnosed by demonstrating the intracellular parasite in bone marrow or splenic aspirates. This study was carried out to discover differentially expressed proteins which could be potential biomarkers. Methods Sera from six visceral leishmaniasis patients and six healthy controls were depleted of high abundant proteins by immunodepletion. The depleted sera were compared by 2-D Difference in gel electrophoresis (DIGE). Differentially expressed proteins were identified the by tandem mass spectrometry. Three of the identified proteins were further validated by western blotting. Results This is the first report of serum proteomics study using quantitative Difference in gel electrophoresis (DIGE) in visceral leishmaniasis. We identified alpha-1-acidglycoprotein and C1 inhibitor as up regulated and transthyretin, retinol binding protein and apolipoprotein A-I as down regulated proteins in visceral leishmaniasis sera in comparison with healthy controls. Western blot validation of C1 inhibitor, transthyretin and apolipoprotein A-I in a larger cohort (n = 29) confirmed significant difference in the expression levels (p < 0.05). Conclusions In conclusion, DIGE based proteomic analysis showed that several proteins are differentially expressed in the sera of visceral leishmaniasis. The five proteins identified here have potential, either independently or in combination, as prognostic biomarkers. PMID:21906353

  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. 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

    2014-01-01

    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

  11. 2D DIGE Does Not Reveal all: A Scotopic Report Suggests Differential Expression of a Single “Calponin Family Member” Protein for Tetany of Sphincters!

    PubMed Central

    Chaudhury, Arun

    2015-01-01

    Using 2D differential gel electrophoresis (DIGE) and mass spectrometry (MS), a recent report by Rattan and Ali (2015) compared proteome expression between tonically contracted sphincteric smooth muscles of the internal anal sphincter (IAS), in comparison to the adjacent rectum [rectal smooth muscles (RSM)] that contracts in a phasic fashion. The study showed the differential expression of a single 23 kDa protein SM22, which was 1.87 fold, overexpressed in RSM in comparison to IAS. Earlier studies have shown differences in expression of different proteins like Rho-associated protein kinase II, myosin light chain kinase, myosin phosphatase, and protein kinase C between IAS and RSM. The currently employed methods, despite its high-throughput potential, failed to identify these well-characterized differences between phasic and tonic muscles. This calls into question the fidelity and validatory potential of the otherwise powerful technology of 2D DIGE/MS. These discrepancies, when redressed in future studies, will evolve this recent report as an important baseline study of “sphincter proteome.” Proteomics techniques are currently underutilized in examining pathophysiology of hypertensive/hypotensive disorders involving gastrointestinal sphincters, including achalasia, gastroesophageal reflux disease (GERD), spastic pylorus, seen during diabetes or chronic chemotherapy, intestinal pseudo-obstruction, and recto-anal incontinence. Global proteome mapping may provide instant snapshot of the complete repertoire of differential proteins, thus expediting to identify the molecular pathology of gastrointestinal motility disorders currently labeled “idiopathic” and facilitating practice of precision medicine. PMID:26151053

  12. Biomarker discovery from the top down: Protein biomarkers for efficient virus transmission by insects (Homoptera: Aphididae) discovered by coupling genetics and 2-D DIGE.

    PubMed

    Cilia, Michelle; Howe, Kevin; Fish, Tara; Smith, Dawn; Mahoney, Jaclyn; Tamborindeguy, Cecilia; Burd, John; Thannhauser, Theodore W; Gray, Stewart

    2011-06-01

    Yellow dwarf viruses cause the most economically important virus diseases of cereal crops worldwide and are vectored by aphids. The identification of vector proteins mediating virus transmission is critical to develop sustainable virus management practices and to understand viral strategies for circulative movement in all insect vectors. Previously, we applied 2-D DIGE to an aphid filial generation 2 population to identify proteins correlated with the transmission phenotype that were stably inherited and expressed in the absence of the virus. In the present study, we examined the expression of the DIGE candidates in previously unstudied, field-collected aphid populations. We hypothesized that the expression of proteins involved in virus transmission could be clinically validated in unrelated, virus transmission-competent, field-collected aphid populations. All putative biomarkers were expressed in the field-collected biotypes, and the expression of nine of these aligned with the virus transmission-competent phenotype. The strong conservation of the expression of the biomarkers in multiple field-collected populations facilitates new and testable hypotheses concerning the genetics and biochemistry of virus transmission. Integration of these biomarkers into current aphid-scouting methodologies will enable rational strategies for vector control aimed at judicious use and development of precision pest control methods that reduce plant virus infection. PMID:21648087

  13. NitroDIGE analysis reveals inhibition of protein S-nitrosylation by epigallocatechin gallates in lipopolysaccharide-stimulated microglial cells

    PubMed Central

    2014-01-01

    Background Nitric oxide (NO) is a signaling molecule regulating numerous cellular functions in development and disease. In the brain, neuronal injury or neuroinflammation can lead to microglial activation, which induces NO production. NO can react with critical cysteine thiols of target proteins forming S-nitroso-proteins. This modification, known as S-nitrosylation, is an evolutionarily conserved redox-based post-translational modification (PTM) of specific proteins analogous to phosphorylation. In this study, we describe a protocol for analyzing S-nitrosylation of proteins using a gel-based proteomic approach and use it to investigate the modes of action of a botanical compound found in green tea, epigallocatechin-3-gallate (EGCG), on protein S-nitrosylation after microglial activation. Methods/Results To globally and quantitatively analyze NO-induced protein S-nitrosylation, the sensitive gel-based proteomic method, termed NitroDIGE, was developed by combining two-dimensional differential in-gel electrophoresis (2-D DIGE) with the modified biotin switch technique (BST) using fluorescence-tagged CyDye™ thiol reactive agents to label S-nitrosothiols. The NitroDIGE method showed high specificity and sensitivity in detecting S-nitrosylated proteins (SNO-proteins). Using this approach, we identified a subset of SNO-proteins ex vivo by exposing immortalized murine BV-2 microglial cells to a physiological NO donor, or in vivo by exposing BV-2 cells to endotoxin lipopolysaccharides (LPS) to induce a proinflammatory response. Moreover, EGCG was shown to attenuate S-nitrosylation of proteins after LPS-induced activation of microglial cells primarily by modulation of the nuclear factor erythroid 2-related factor 2 (Nrf2)-mediated oxidative stress response. Conclusions These results demonstrate that NitroDIGE is an effective proteomic strategy for “top-down” quantitative analysis of protein S-nitrosylation in multi-group samples in response to nitrosative stress due

  14. 2D-DIGE screening of high-productive CHO cells under glucose limitation--basic changes in the proteome equipment and hints for epigenetic effects.

    PubMed

    Wingens, Marc; Gätgens, Jochem; Schmidt, Anica; Albaum, Stefan P; Büntemeyer, Heino; Noll, Thomas; Hoffrogge, Raimund

    2015-05-10

    CHO derivates (Chinese hamster ovary) belong to the most important mammalian cells for industrial recombinant protein production. Many efforts have been made to improve productivity and stability of CHO cells in bioreactor processes. Here, we followed up one barely understood phenomenon observed with process optimizations: a significantly increased cell-specific productivity in late phases of glucose-limited perfusion cultivations, when glucose (and lactate) reserves are exhausted. Our aim was to elucidate the cellular activities connected to the metabolic shift from glucose surplus to glucose limitation phase. With 2D-DIGE, we compared three stages in a perfusion culture of CHO cells: the initial growth with high glucose concentration and low lactate production, the second phase with glucose going to limitation and high lactate level, and finally the state of glucose limitation and also low lactate concentration but increased cell-specific productivity. With our proteomic approach we were able to demonstrate consequences of glucose limitation for the protein expression machinery which also could play a role for a higher recombinant protein production. Most interestingly, we detected epigenetic effects on the level of proteins involved in histone modification (HDAC1/-2, SET, RBBP7, DDX5). Together with shifts in the protein inventory of energy metabolism, cytoskeleton and protein expression, a picture emerges of basic changes in the cellular equipment under long-term glucose limitation of CHO cells.

  15. Identification of novel biomarkers of abdominal aortic aneurysms by 2D-DIGE and MALDI-MS from AAA-thrombus-conditioned media.

    PubMed

    Martinez-Pinna, Roxana; Lopez, Juan Antonio; Ramos-Mozo, Priscila; Blanco-Colio, Luis M; Camafeita, Emilio; Calvo, Enrique; Meilhac, Olivier; Michel, Jean Baptiste; Egido, Jesús; Martin-Ventura, José Luis

    2013-01-01

    In the search for novel biomarkers, noncandidate-based proteomic strategies open up new opportunities to gain a deeper insight into disease processes regarding their molecular mechanisms, the risk factors involved, and the monitoring of disease progression. To carry out these complex analyses, the combined use of gel electrophoresis with mass spectrometry (MS) represents a powerful choice. In addition, the introduction of protein dye labeling has notably improved the reliability of differential expression studies by increasing the statistical significance of the protein candidates. Here, we describe a strategy where different layers (luminal/abluminal) from the intraluminal thrombus (ILT) of human abdominal aortic aneurysm (AAA) patients were incubated in protein-free medium. Then, the levels of the proteins released were compared by two-dimensional differential in-gel electrophoresis (2D-DIGE) and the proteins of interest identified by MS. We consider that the use of tissue-conditioned media could offer a substantial advantage in the analytical study of biological fluids, as they provide a source of proteins to be released to the bloodstream, which could serve as potential circulating biomarkers.

  16. Protein expression profiles of human lymph and plasma mapped by 2D-DIGE and 1D SDS–PAGE coupled with nanoLC–ESI–MS/MS bottom-up proteomics

    PubMed Central

    Clement, Cristina C.; Aphkhazava, David; Nieves, Edward; Callaway, Myrasol; Olszewski, Waldemar; Rotzschke, Olaf; Santambrogio, Laura

    2013-01-01

    In this study a proteomic approach was used to define the protein content of matched samples of afferent prenodal lymph and plasma derived from healthy volunteers. The analysis was performed using two analytical methodologies coupled with nanoliquid chromatography-tandem mass spectrometry: one-dimensional gel electrophoresis (1DEF nanoLC Orbitrap–ESI–MS/MS), and two-dimensional fluorescence difference-in-gel electrophoresis (2D-DIGE nanoLC–ESI–MS/MS). The 253 significantly identified proteins (p<0.05), obtained from the tandem mass spectrometry data, were further analyzed with pathway analysis (IPA) to define the functional signature of prenodal lymph and matched plasma. The 1DEF coupled with nanoLC–MS–MS revealed that the common proteome between the two biological fluids (144 out of 253 proteins) was dominated by complement activation and blood coagulation components, transporters and protease inhibitors. The enriched proteome of human lymph (72 proteins) consisted of products derived from the extracellular matrix, apoptosis and cellular catabolism. In contrast, the enriched proteome of human plasma (37 proteins) consisted of soluble molecules of the coagulation system and cell–cell signaling factors. The functional networks associated with both common and source-distinctive proteomes highlight the principal biological activity of these immunologically relevant body fluids. PMID:23202415

  17. Proteomic analysis of beta-catenin activation in mouse liver by DIGE analysis identifies glucose metabolism as a new target of the Wnt pathway.

    PubMed

    Chafey, Philippe; Finzi, Laetitia; Boisgard, Raphael; Caüzac, Michèle; Clary, Guillem; Broussard, Cédric; Pégorier, Jean-Paul; Guillonneau, François; Mayeux, Patrick; Camoin, Luc; Tavitian, Bertrand; Colnot, Sabine; Perret, Christine

    2009-08-01

    The Wnt/beta-catenin signaling pathway has been increasingly implicated in liver development and physiology. Aberrant activation of this pathway is one of the major genetic events observed during the process of human HCC development. To gain insight into the mechanism underlying beta-catenin action in the liver, we conducted a quantitative differential proteomic analysis using 2-D DIGE combined with MS, in mice with liver-specific deletion of Apc resulting in acute activation of beta-catenin signaling (Apc(KOliv) mice). We identified 94 protein spots showing differential expression between mutant Apc(KOliv) and control mice, corresponding to 56 individual proteins. Most of the proteins identified were associated with metabolic pathways, such as ammonia and glucose metabolism. Our analysis showed an increase in lactate dehydrogenase activity together with a downregulation of two mitochondrial ATPase subunits (ATP5a1 and ATP5b). These observations indicate that beta-catenin signaling may induce a shift in the glucose metabolism from oxidative phosphorylation to glycolysis, known as the "Warburg effect". Imaging with (18)F-fluoro-2-deoxy-D-glucose-positron emission tomography suggests that the specific metabolic reprogramming induced by beta-catenin in the liver does not imply the first step of glycolysis. This observation may explain why some HCCs are difficult to assess by fluoro-2-deoxy-D-glucose-positron emission tomography imaging.

  18. 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.

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

    PubMed

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

    2008-01-01

    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.

  20. 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.

  1. 2D proteome analysis initiates new Insights on the Salmonella Typhimurium LuxS protein

    PubMed Central

    2009-01-01

    Background Quorum sensing is a term describing a bacterial communication system mediated by the production and recognition of small signaling molecules. The LuxS enzyme, catalyzing the synthesis of AI-2, is conserved in a wide diversity of bacteria. AI-2 has therefore been suggested as an interspecies quorum sensing signal. To investigate the role of endogenous AI-2 in protein expression of the Gram-negative pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium), we performed a 2D-DIGE proteomics experiment comparing total protein extract of wildtype S. Typhimurium with that of a luxS mutant, unable to produce AI-2. Results Differential proteome analysis of wildtype S. Typhimurium versus a luxS mutant revealed relatively few changes beyond the known effect on phase 2 flagellin. However, two highly differentially expressed protein spots with similar molecular weight but differing isoelectric point, were identified as LuxS whereas the S. Typhimurium genome contains only one luxS gene. This observation was further explored and we show that the S. Typhimurium LuxS protein can undergo posttranslational modification at a catalytic cysteine residue. Additionally, by constructing LuxS-βla and LuxS-PhoA fusion proteins, we demonstrate that S. Typhimurium LuxS can substitute the cognate signal peptide sequences of β-lactamase and alkaline phosphatase for translocation across the cytoplasmic membrane in S. Typhimurium. This was further confirmed by fractionation of S. Typhimurium protein extracts, followed by Western blot analysis. Conclusion 2D-DIGE analysis of a luxS mutant vs. wildtype Salmonella Typhimurium did not reveal new insights into the role of AI-2/LuxS in Salmonella as only a small amount of proteins were differentially expressed. However, subsequent in depth analysis of the LuxS protein itself revealed two interesting features: posttranslational modification and potential translocation across the cytoplasmic membrane. As the S. Typhimurium Lux

  2. DIGE Proteome Analysis Reveals Suitability of Ischemic Cardiac In Vitro Model for Studying Cellular Response to Acute Ischemia and Regeneration

    PubMed Central

    Haas, Sina; Jahnke, Heinz-Georg; Moerbt, Nora; von Bergen, Martin; Aharinejad, Seyedhossein; Andrukhova, Olena; Robitzki, Andrea A.

    2012-01-01

    Proteomic analysis of myocardial tissue from patient population is suited to yield insights into cellular and molecular mechanisms taking place in cardiovascular diseases. However, it has been limited by small sized biopsies and complicated by high variances between patients. Therefore, there is a high demand for suitable model systems with the capability to simulate ischemic and cardiotoxic effects in vitro, under defined conditions. In this context, we established an in vitro ischemia/reperfusion cardiac disease model based on the contractile HL-1 cell line. To identify pathways involved in the cellular alterations induced by ischemia and thereby defining disease-specific biomarkers and potential target structures for new drug candidates we used fluorescence 2D-difference gel electrophoresis. By comparing spot density changes in ischemic and reperfusion samples we detected several protein spots that were differentially abundant. Using MALDI-TOF/TOF-MS and ESI-MS the proteins were identified and subsequently grouped by functionality. Most prominent were changes in apoptosis signalling, cell structure and energy-metabolism. Alterations were confirmed by analysis of human biopsies from patients with ischemic cardiomyopathy. With the establishment of our in vitro disease model for ischemia injury target identification via proteomic research becomes independent from rare human material and will create new possibilities in cardiac research. PMID:22384053

  3. 2D Wavefront Sensor Analysis and Control

    1996-02-19

    This software is designed for data acquisition and analysis of two dimensional wavefront sensors. The software includes data acquisition and control functions for an EPIX frame grabber to acquire data from a computer and all the appropriate analysis functions necessary to produce and display intensity and phase information. This software is written in Visual Basic for windows.

  4. 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.

  5. Finite Element Analysis of 2-D Elastic Contacts Involving FGMs

    NASA Astrophysics Data System (ADS)

    Abhilash, M. N.; Murthy, H.

    2014-05-01

    The response of elastic indenters in contact with Functionally Graded Material (FGM) coated homogeneous elastic half space has been presented in the current paper. Finite element analysis has been used due to its ability to handle complex geometry, material, and boundary conditions. Indenters of different typical surface profiles have been considered and the problem has been idealized as a two-dimensional (2D) plane strain problem considering only normal loads. Initially, indenters were considered to be rigid and the results were validated with the solutions presented in the literature. The analysis has then been extended to the case of elastic indenters on FGM-coated half spaces and the results are discussed.

  6. Syndrome identification based on 2D analysis software.

    PubMed

    Boehringer, Stefan; Vollmar, Tobias; Tasse, Christiane; Wurtz, Rolf P; Gillessen-Kaesbach, Gabriele; Horsthemke, Bernhard; Wieczorek, Dagmar

    2006-10-01

    Clinical evaluation of children with developmental delay continues to present a challenge to the clinicians. In many cases, the face provides important information to diagnose a condition. However, database support with respect to facial traits is limited at present. Computer-based analyses of 2D and 3D representations of faces have been developed, but it is unclear how well a larger number of conditions can be handled by such systems. We have therefore analysed 2D pictures of patients each being affected with one of 10 syndromes (fragile X syndrome; Cornelia de Lange syndrome; Williams-Beuren syndrome; Prader-Willi syndrome; Mucopolysaccharidosis type III; Cri-du-chat syndrome; Smith-Lemli-Opitz syndrome; Sotos syndrome; Microdeletion 22q11.2; Noonan syndrome). We can show that a classification accuracy of >75% can be achieved for a computer-based diagnosis among the 10 syndromes, which is about the same accuracy achieved for five syndromes in a previous study. Pairwise discrimination of syndromes ranges from 80 to 99%. Furthermore, we can demonstrate that the criteria used by the computer decisions match clinical observations in many cases. These findings indicate that computer-based picture analysis might be a helpful addition to existing database systems, which are meant to assist in syndrome diagnosis, especially as data acquisition is straightforward and involves off-the-shelf digital camera equipment. PMID:16773127

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

    PubMed

    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 T(2)-D domain. The decomposition is advantageous for better interpretation of the complex correlation maps as well as for the quantification of extracted T(2)-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 T(2)-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 x 10(-12) m(2) s(-1) and T(2)=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), T(2)=10 ms and D=3 x 10(-13) m(2) s(-1), T(2)=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

  8. 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

  9. In search of secreted protein biomarkers for the anti-inflammatory effect of beta2-adrenergic receptor agonists: application of DIGE technology in combination with multivariate and univariate data analysis tools.

    PubMed

    Verhoeckx, Kitty C M; Gaspari, Marco; Bijlsma, Sabina; van der Greef, Jan; Witkamp, Renger F; Doornbos, Robert P; Rodenburg, Richard J T

    2005-01-01

    Two-dimensional difference gel electrophoresis (DIGE) in combination with univariate (Student's t-test) and multivariate data analysis, principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were used to study the anti-inflammatory effects of the beta(2)-adrenergic receptor (beta(2)-AR) agonist zilpaterol. U937 macrophages were exposed to the endotoxin lipopolysaccharide (LPS) to induce an inflammatory reaction, which was inhibited by the addition of zilpaterol (LZ). This inhibition was counteracted by addition of the beta(2)-AR antagonist propranolol (LZP). The extracellular proteome of the U937 cells induced by the three treatments were examined by DIGE. PCA was used as an explorative tool to investigate the clustering of the proteome dataset. Using this tool, the dataset obtained from cells treated with LPS and LZP were separated from those obtained from LZ treated cells. PLS-DA, a multivariate data analysis tool that also takes correlations between protein spots and class assignment into account, correctly classified the different extracellular proteomes and showed that many proteins were differentially expressed between the proteome of inflamed cells (LPS and LZP) and cells in which the inflammatory response was inhibited (LZ). The Student's t-test revealed 8 potential protein biomarkers, each of which was expressed at a similar level in the LPS and LZP treated cells, but differently expressed in the LZ treated cells. Two of the identified proteins, macrophage inflammatory protein-1beta (MIP-1beta) and macrophage inflammatory protein-1alpha (MIP-1alpha) are known secreted proteins. The inhibition of MIP-1beta by zilpaterol and the involvement of the beta(2)-AR and cAMP were confirmed using a specific immunoassay.

  10. PARCEQ2D heat transfer grid sensitivity analysis

    SciTech Connect

    Saladino, A.J.; Praharaj, S.C.; Collins, F.G. Tennessee Univ., Tullahoma )

    1991-01-01

    The material presented in this paper is an extension of two-dimensional Aeroassist Flight Experiment (AFE) results shown previously. This study has focused on the heating rate calculations to the AFE obtained from an equilibrium real gas code, with attention placed on the sensitivity of grid dependence and wall temperature. Heat transfer results calculated by the PARCEQ2D code compare well with those computed by other researchers. Temperature convergence in the case of kinetic transport has been accomplished by increasing the wall temperature gradually from 300 K to the wall temperature of 1700 K. 28 refs.

  11. PARCEQ2D heat transfer grid sensitivity analysis

    NASA Technical Reports Server (NTRS)

    Saladino, Anthony J.; Praharaj, Sarat C.; Collins, Frank G.

    1991-01-01

    The material presented in this paper is an extension of two-dimensional Aeroassist Flight Experiment (AFE) results shown previously. This study has focused on the heating rate calculations to the AFE obtained from an equilibrium real gas code, with attention placed on the sensitivity of grid dependence and wall temperature. Heat transfer results calculated by the PARCEQ2D code compare well with those computed by other researchers. Temperature convergence in the case of kinetic transport has been accomplished by increasing the wall temperature gradually from 300 K to the wall temperature of 1700 K.

  12. Estimating 2-D vector velocities using multidimensional spectrum analysis.

    PubMed

    Oddershede, Niels; Løvstakken, Lasse; Torp, Hans; Jensen, Jørgen Arendt

    2008-08-01

    Wilson (1991) presented an ultrasonic wideband estimator for axial blood flow velocity estimation through the use of the 2-D Fourier transform. It was shown how a single velocity component was concentrated along a line in the 2-D Fourier space, where the slope was given by the axial velocity. Later, it was shown that this approach could also be used for finding the lateral velocity component by also including a lateral sampling. A single velocity component would then be concentrated along a plane in the 3-D Fourier space, tilted according to the 2 velocity components. This paper presents 2 new velocity estimators for finding both the axial and lateral velocity components. The estimators essentially search for the plane in the 3- D Fourier space, where the integrated power spectrum is largest. The first uses the 3-D Fourier transform to find the power spectrum, while the second uses a minimum variance approach. Based on this plane, the axial and lateral velocity components are estimated. Several phantom measurements, for flow-to-depth angles of 60, 75, and 90 degrees, were performed. Multiple parallel lines were beamformed simultaneously, and 2 different receive apodization schemes were tried. The 2 estimators were then applied to the data. The axial velocity component was estimated with an average standard deviation below 2.8% of the peak velocity, while the average standard deviation of the lateral velocity estimates was between 2.0% and 16.4%. The 2 estimators were also tested on in vivo data from a transverse scan of the common carotid artery, showing the potential of the vector velocity estimation method under in vivo conditions. PMID:18986918

  13. 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

  14. Lagrangian analysis of vortex shedding behind a 2D airfoil

    NASA Astrophysics Data System (ADS)

    Cardwell, Blake; Mohseni, Kamran

    2007-11-01

    Identifying the coherent structures and their interactions in the mixing zone is a useful means in designing future flow control strategies. To this end, a Lagrangian analysis of two-dimensional vortex shedding over an Eppler 387 airfoil is presented. Stable and unstable material manifolds in the flow are identified. Unstable manifolds such a the shear layer characterize a barrier to fluid mixing and are easily visualized using dye injection in an experiment. On the other hand, stable manifolds are more difficult to visualize in an experiment. Reattachment lines are examples of such manifolds. As such the existence of these structures in the flow, is presented and how these structures are useful in understanding vortex shedding is explored. The manifold structure is also presented in a time averaged view, allowing a comparison with the traditional separation bubble. Furthermore, lobe dynamic calculation are performed and the fluid entrainment into shedded vortices are investigated. Finally, investigation of correlation between the behavior of the material manifolds and more traditional quantities such as skin friction, flow phase portrait, and pressure is presented.

  15. Analysis of activity space by fragment fingerprints, 2D descriptors, and multitarget dependent transformation of 2D descriptors.

    PubMed

    Givehchi, Alireza; Bender, Andreas; Glen, Robert C

    2006-01-01

    The effect of multitarget dependent descriptor transformation on classification performance is explored in this work. To this end decision trees as well as neural net QSAR in combination with PLS were applied to predict the activity class of 5HT3 ligands, angiotensin converting enzyme inhibitors, 3-hydroxyl-3-methyl glutaryl coenzyme A reductase inhibitors, platelet activating factor antagonists, and thromboxane A2 antagonists. Physicochemical descriptors calculated by MOE and fragment-based descriptors (MOLPRINT 2D) were employed to generate descriptor vectors. In a subsequent step the physicochemical descriptor vectors were transformed to a lower dimensional space using multitarget dependent descriptor transformation. Cross-validation of the original physicochemical descriptors in combination with decision trees and neural net QSAR as well as cross-validation of PLS multitarget transformed descriptors with neural net QSAR were performed. For comparison this was repeated using fragment-based descriptors in combination with decision trees.

  16. 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.

  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. T cell triggering: insights from 2D kinetics analysis of molecular interactions

    NASA Astrophysics Data System (ADS)

    Zarnitsyna, Veronika; Zhu, Cheng

    2012-08-01

    Interaction of the T cell receptor (TCR) with pathogen-derived peptide presented by the major histocompatibility complex (pMHC) molecule is central to adaptive immunity as it initiates intracellular signaling to trigger T cell response to infection. Kinetic parameters of this interaction have been under intensive investigation for more than two decades using soluble pMHCs and/or TCRs with at least one of them in the solution (three-dimensional (3D) methods). Recently, several techniques have been developed to enable kinetic analysis on live T cells with pMHCs presented by surrogate antigen presenting cells (APCs) or supported planar lipid bilayers (two-dimensional (2D) methods). Comparison of 2D versus 3D parameters reveals drastic differences with broader ranges of 2D affinities and on-rates and orders of magnitude faster 2D off-rates for functionally distinct pMHCs. Here we review new 2D data and discuss how it may impact previously developed models of T cell discrimination between pMHCs of different potencies.

  19. CAS2D- NONROTATING BLADE-TO-BLADE, STEADY, POTENTIAL TRANSONIC CASCADE FLOW ANALYSIS CODE

    NASA Technical Reports Server (NTRS)

    Dulikravich, D. S.

    1994-01-01

    An exact, full-potential-equation model for the steady, irrotational, homoentropic, and homoenergetic flow of a compressible, inviscid fluid through a two-dimensional planar cascade together with its appropriate boundary conditions has been derived. The CAS2D computer program numerically solves an artificially time-dependent form of the actual full-potential-equation, providing a nonrotating blade-to-blade, steady, potential transonic cascade flow analysis code. Comparisons of results with test data and theoretical solutions indicate very good agreement. In CAS2D, the governing equation is discretized by using type-dependent, rotated finite differencing and the finite area technique. The flow field is discretized by providing a boundary-fitted, nonuniform computational mesh. This mesh is generated by using a sequence of conformal mapping, nonorthogonal coordinate stretching, and local, isoparametric, bilinear mapping functions. The discretized form of the full-potential equation is solved iteratively by using successive line over relaxation. Possible isentropic shocks are captured by the explicit addition of an artificial viscosity in a conservative form. In addition, a four-level, consecutive, mesh refinement feature makes CAS2D a reliable and fast algorithm for the analysis of transonic, two-dimensional cascade flows. The results from CAS2D are not directly applicable to three-dimensional, potential, rotating flows through a cascade of blades because CAS2D does not consider the effects of the Coriolis force that would be present in the three-dimensional case. This program is written in FORTRAN IV for batch execution and has been implemented on an IBM 370 series computer with a central memory requirement of approximately 200K of 8 bit bytes. The CAS2D program was developed in 1980.

  20. The MIPAS2D: 2-D analysis of MIPAS observations of ESA target molecules and minor species

    NASA Astrophysics Data System (ADS)

    Arnone, E.; Brizzi, G.; Carlotti, M.; Dinelli, B. M.; Magnani, L.; Papandrea, E.; Ridolfi, M.

    2008-12-01

    Measurements from the MIPAS instrument onboard the ENVISAT satellite were analyzed with the Geofit Multi- Target Retrieval (GMTR) system to obtain 2-dimensional fields of pressure, temperature and volume mixing ratios of H2O, O3, HNO3, CH4, N2O, and NO2. Secondary target species relevant to stratospheric chemistry were also analysed and robust mixing ratios of N2O5, ClONO2, F11, F12, F14 and F22 were obtained. Other minor species with high uncertainties were not included in the database and will be the object of further studies. The analysis covers the original nominal observation mode from July 2002 to March 2004 and it is currently being extended to the ongoing reduced resolution mission. The GMTR algorithm was operated on a fixed 5 degrees latitudinal grid in order to ease the comparison with model calculations and climatological datasets. The generated database of atmospheric fields can be directly used for analyses based on averaging processes with no need of further interpolation. Samples of the obtained products are presented and discussed. The database of the retrieved quantities is made available to the scientific community.

  1. Image-based RSA: Roentgen stereophotogrammetric analysis based on 2D-3D image registration.

    PubMed

    de Bruin, P W; Kaptein, B L; Stoel, B C; Reiber, J H C; Rozing, P M; Valstar, E R

    2008-01-01

    Image-based Roentgen stereophotogrammetric analysis (IBRSA) integrates 2D-3D image registration and conventional RSA. Instead of radiopaque RSA bone markers, IBRSA uses 3D CT data, from which digitally reconstructed radiographs (DRRs) are generated. Using 2D-3D image registration, the 3D pose of the CT is iteratively adjusted such that the generated DRRs resemble the 2D RSA images as closely as possible, according to an image matching metric. Effectively, by registering all 2D follow-up moments to the same 3D CT, the CT volume functions as common ground. In two experiments, using RSA and using a micromanipulator as gold standard, IBRSA has been validated on cadaveric and sawbone scapula radiographs, and good matching results have been achieved. The accuracy was: |mu |< 0.083 mm for translations and |mu| < 0.023 degrees for rotations. The precision sigma in x-, y-, and z-direction was 0.090, 0.077, and 0.220 mm for translations and 0.155 degrees , 0.243 degrees , and 0.074 degrees for rotations. Our results show that the accuracy and precision of in vitro IBRSA, performed under ideal laboratory conditions, are lower than in vitro standard RSA but higher than in vivo standard RSA. Because IBRSA does not require radiopaque markers, it adds functionality to the RSA method by opening new directions and possibilities for research, such as dynamic analyses using fluoroscopy on subjects without markers and computer navigation applications.

  2. Terahertz Spectroscopy and Global Analysis of the Bending Vibrations of Acetylene 12C2D2

    NASA Astrophysics Data System (ADS)

    Yu, Shanshan; Drouin, Brian J.; Pearson, John C.; Pickett, Herbert M.; Lattanzi, Valerio; Walters, Adam

    2009-06-01

    Two hundred and fifty-one 12C2D2 transitions have been measured in the 0.2-1.6 THz region of its ν5-ν4 difference band and 202 of them were observed for the first time. The accuracy of these measurements is estimated to be ranging from 50 kHz to 100 kHz. The 12C2D2 molecules were generated under room temperature by passing 120-150 mTorr D2O vapor through calcium carbide (CaC2) powder. A multistate analysis was carried out for the bending vibrational modes ν4 and ν5 of 12C2D2, which includes the lines observed in this work and prior microwave, far-infrared and infrared data on the pure bending levels. Significantly improved molecular parameters were obtained for 12C2D2 by adding the new measurements to the old data set, which had only 10 lines with microwave measurement precision. New frequency and intensity predictions have been made based on the obtained molecular parameters. The more precise measurements and new predictions reported here will support the analyses of astronomical observations by the future high-resolution spectroscopy telescopes such as Herschel, SOFIA, and ALMA, which will work in the terahertz spectral region.

  3. Quantitative and functional analysis of CD69(+) NKG2D(+) T regulatory cells in healthy subjects.

    PubMed

    Vitales-Noyola, M; Doníz-Padilla, L; Álvarez-Quiroga, C; Monsiváis-Urenda, A; Portillo-Salazar, H; González-Amaro, R

    2015-07-01

    T regulatory (Treg) cells have a key role in immune homeostasis and the pathogenesis of chronic inflammatory and autoimmune diseases. CD69 is an early leukocyte activation molecule that under steady state conditions is detected in a small proportion of lymphocytes in peripheral blood and lymphoid tissues. Although it has been reported that a subset of CD69(+) T cells behaves as Treg lymphocytes, the possible relationship between CD69(+) Treg cells and CD4(+)NKG2D(+) T lymphocytes, which also exert immunosuppressive activity, has not been explored. In this study, we analyzed the expression of CD69 and NKG2D by T lymphocytes from the peripheral blood of twenty-five healthy subjects by multi-parametric flow cytometry analysis, and their suppressive activity by an assay of inhibition of lymphocyte activation (CD40L expression) and proliferation (carboxyfluorescein partition assay). We found a very small percentage of CD4(+)CD69(+)NKG2D(+) T cells (median 0.002%, Q1-Q3, 0.001-0.004%), which also expressed TGF-β (Latency Associated Peptide or LAP) and IL-10, in all samples analyzed. These cells exerted an important in vitro suppressive effect on both activation and proliferation of T effector cells. Our data suggest that at very small numbers, CD4(+)CD69(+)NKG2D(+) lymphocytes seem to exert a relevant functional immune-regulatory role in healthy subjects.

  4. Human factors flight trial analysis for 2D/3D SVS

    NASA Astrophysics Data System (ADS)

    Schiefele, Jens; Howland, Duncan; Maris, John; Wipplinger, Patrick

    2004-08-01

    The paper describes flight trials performed in Reno, NV. Flight trial were conducted with a Cheyenne 1 from Marinvent. Twelve pilots flew the Cheyenne in seventy-two approaches to the Reno airfield. All pilots flew completely andomized settings. Three different settings (standard displays, 2D moving map, and 2D/3D moving map) were evaluated. They included seamless evaluation for STAR, approach, and taxi operations. The flight trial goal was to evaluate the objective performance of pilots compared among the different settings. As dependent variables, positional and time accuracy were measured. Analysis was conducted by an ANOVA test. In parallel, all pilots answered subjective Cooper-Harper, situation awareness rating technique (SART), situational awareness probe (SAP), and questionnaires.This article describes the human factor analysis from flight trials performed in Reno, NV. Flight trials were conducted with a Cheyenne 1 from Marinvent. Thirteen pilots flew the Cheyenne in seventy-two approaches to the Reno airfield. All pilots flew completely randomized settings. Three different display configurations: Elec. Flight Information System (EFIS), EFIS and 2D moving map, and 3D SVS Primary Flight Display (PFD) and 2D moving map were evaluated. They included normal/abnormal procedure evaluation for: Steep turns and reversals, Unusual attitude recovery, Radar vector guidance towards terrain, Non-precision approaches, En-route alternate for non-IFR rated pilots encountering IMC, and Taxiing on complex taxi-routes. The flight trial goal was to evaluate the objective performance of pilots for the different display configurations. As dependent variables, positional and time data were measured. Analysis was performed by an ANOVA test. In parallel, all pilots answered subjective NASA Task Load Index, Cooper-Harper, Situation Awareness Rating Technique (SART), and questionnaires. The result shows that pilots flying 2D/3D SVS perform no worse than pilots with conventional

  5. 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.

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

    NASA Astrophysics Data System (ADS)

    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.

  7. 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. PMID:25863895

  8. 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.

  9. 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.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-10-01

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

  12. Optical fiber poling by induction: analysis by 2D numerical modeling.

    PubMed

    De Lucia, F; Huang, D; Corbari, C; Healy, N; Sazio, P J A

    2016-04-15

    Since their first demonstration some 25 years ago, thermally poled silica fibers have been used to realize device functions such as electro-optic modulation, switching, polarization-entangled photons, and optical frequency conversion with a number of advantages over bulk free-space components. We have recently developed an innovative induction poling technique that could allow for the development of complex microstructured fiber geometries for highly efficient χ(2)-based device applications. To systematically implement these more advanced poled fiber designs, we report here the development of comprehensive numerical models of the induction poling mechanism itself via two-dimensional (2D) simulations of ion migration and space-charge region formation using finite element analysis. PMID:27082323

  13. Numerical method of crack analysis in 2D finite magnetoelectroelastic media

    NASA Astrophysics Data System (ADS)

    Zhao, Minghao; Xu, Guangtao; Fan, Cuiying

    2010-04-01

    The present paper extends the hybrid extended displacement discontinuity fundamental solution method (HEDD-FSM) (Eng Anal Bound Elem 33:592-600, 2009) to analysis of cracks in 2D finite magnetoelectroelastic media. The solution of the crack is expressed approximately by a linear combination of fundamental solutions of the governing equations, which includes the extended point force fundamental solutions with sources placed at chosen points outside the domain of the problem under consideration, and the extended Crouch fundamental solutions with extended displacement discontinuities placed on the crack. The coefficients of the fundamental solutions are determined by letting the approximated solution satisfy the prescribed boundary conditions on the boundary of the domain and on the crack face. The Crouch fundamental solution for a parabolic element at the crack tip is derived to model the square root variations of near tip fields. The extended stress intensity factors are calculated under different electric and magnetic boundary conditions.

  14. Robust mean traveltime curves: a powerful tool for analysis in 2D transmission tomographic surveys

    NASA Astrophysics Data System (ADS)

    Fernandez Martinez, J.; Pedruelo Gonzalez, L.; Rector, J.

    2008-12-01

    Acoustic tomography methods belong to the class of non destructive inspection techniques and are widely used in engineering applications. One of the main issues for these methods is the direct arrivals, which can be noisy or affected by scattering or other propagation effects. Mean traveltime curves (mean and standard deviation) have been introduced by Fernández Martínez et al (2006), and describe the variation of the main statistical parameters of the traveltime distribution for the different gathering subsets as a function of the gather index. These curves constitute a simple methodology (Fernández Martínez et al., 2008) to analyze before inversion the traveltime quality in 2D acoustic transmission tomography experiments conducted in relatively homogeneous blocks. This analysis can help to discriminate the contribution of picking errors from that of geological heterogeneities. In this contribution we present the so-called robust mean traveltime curves, which refer to the variation of the different p-percentiles and related measures of dispersion (inter-quartile range and minimum absolute deviation) for the above mentioned gathering subsets. Together with the mean curve, the median and upper-quartile traveltime curves are very resistant to the presence of outliers, and thus, are preferred to infer a background velocity model, which is valid at experiment scale and honors the experimental traveltime distribution. This methodology is valid for 2D zonal isotropic or elliptical anisotropic media, explored via any arbitrary acquisition geometry. We show the application to a well-known granitic medium (Febex Project, Nagra, Switzerland). Fernández Martínez et al. 2006. Mathematical Geology:38-3.343-374 Fernández Martínez et al.2008. Computer and Geosciences:34-3,213-225, 2008.

  15. Fully coupled nonlinear thermomechanical analysis including general contact in PALM2D

    SciTech Connect

    Engelmann, B.E.; Whirley, R.G.

    1993-10-07

    Fully coupled thermomechanical analysis solves the thermal problem on the deforming geometry and incorporates thermal loads into the mechanical problem. In contrast, traditional thermal stress analysis is based on an uncoupled approach in which the thermal problem is solved on a fixed geometry, and the resulting temperatures are then used to load a mechanical problem. Thermal contact, in which heat flow paths depend on the mechanical deformations of adjacent surfaces, is a major component of many fully coupled thermomechanical analyses. This paper presents the development of a thermomechanical finite element formulation, including contact. The proposed approach accommodates arbitrarily large relative motions of contact surfaces, fully unstructured meshes, pressure-dependent contact resistance, conduction across small gaps, and approximate models for convection and radiation. The theory described herein has been implemented in the Lawrence Livermore National Laboratory public code PALM2D and has been used to solve a diverse set of thermomechanical problems. Examples illustrating the performance of this code on large deformation thermomechanical problems are presented and discussed.

  16. A comparative analysis of 2D and 3D CAD for calcifications in digital breast tomosynthesis

    NASA Astrophysics Data System (ADS)

    Acciavatti, Raymond J.; Ray, Shonket; Keller, Brad M.; Maidment, Andrew D. A.; Conant, Emily F.

    2015-03-01

    Many medical centers offer digital breast tomosynthesis (DBT) and 2D digital mammography acquired under the same compression (i.e., "Combo" examination) for screening. This paper compares a conventional 2D CAD algorithm (Hologic® ImageChecker® CAD v9.4) for calcification detection against a prototype 3D algorithm (Hologic® ImageChecker® 3D Calc CAD v1.0). Due to the newness of DBT, the development of this 3D CAD algorithm is ongoing, and it is currently not FDA-approved in the United States. For this study, DBT screening cases with suspicious calcifications were identified retrospectively at the University of Pennsylvania. An expert radiologist (E.F.C.) reviewed images with both 2D and DBT CAD marks, and compared the marks to biopsy results. Control cases with one-year negative follow-up were also studied; these cases either possess clearly benign calcifications or lacked calcifications. To allow the user to alter the sensitivity for cancer detection, an operating point is assigned to each CAD mark. As expected from conventional 2D CAD, increasing the operating point in 3D CAD increases sensitivity and reduces specificity. Additionally, we showed that some cancers are occult to 2D CAD at all operating points. By contrast, 3D CAD allows for detection of some cancers that are missed on 2D CAD. We also demonstrated that some non-cancerous CAD marks in 3D are not present at analogous locations in the 2D image. Hence, there are additional marks when using both 2D and 3D CAD in combination, leading to lower specificity than with conventional 2D CAD alone.

  17. Analysis of unsectioned specimens: 2D and tomographic PIXE with STIM

    NASA Astrophysics Data System (ADS)

    Schofield, Robert M. S.; Lefevre, Harlan W.

    1993-05-01

    Two techniques for quantitative analysis of heterogeneous thick specimens are reviewed. First, a measurement of the total zinc content in the abdomen of a fly is reported. The calculation used to determine the uncertainty in this measurement is detailed. STIM measurements at two different angles were used to determine the possible range of the X-ray production cross section and the X-ray attenuation factors. The abdomen content of zinc was determined to be 0.022( + 0.009, -0.006) (μg. Second, a PIXE-STIM mutomographic determination of metal concentrations in the sting of a scorpion is reviewed. STIM tomography was used to determine the X-ray production cross sections and the X-ray attenuation factors for points inside of the specimen. Details of how this information was then used for reconstructions of PIXE tomographic data are given. Finally, 2D PIXE measurements on a thick section of this sting are reported. On this section the measured concentration of zinc reached 22(± 3)% of dry mass, in satisfactory agreement with the results from tomography, 25(± 3)%.

  18. 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.

  19. Numerical analysis using 2D modeling of optical fiber poled by induction

    NASA Astrophysics Data System (ADS)

    Huang, D.; De Lucia, F.; Corbari, C.; Healy, N.; Sazio, P. J. A.

    2016-03-01

    Thermal poling, a technique to introduce effective second-order nonlinearities in silica optical fibers, has found widespread applications in frequency conversion, electro-optic modulation, switching and polarization-entangled photon pair generation. Since its first demonstration around 25 years ago, studies into thermal poling were primarily based on anode-cathode electrode configurations. However, more recently, superior electrode configurations have been investigated that allow for robust and reliable thermally poled fibers with excellent second order nonlinear properties [1, 2]. Very recently, we experimentally demonstrated an electrostatic induction poling technique that creates a stable second-order nonlinearity in a twin-hole fiber without any direct physical contact to internal fiber electrodes whatsoever [3]. This innovative technique lifts a number of restrictions on the use of complex microstructured optical fibers (MOF) for poling, as it is no longer necessary to individually contact internal electrodes and presents a general methodology for selective liquid electrode filling of complex MOF geometries. In order to systematically implement these more advanced device embodiments, it is first necessary to develop comprehensive numerical models of the induction poling mechanism itself. To this end, we have developed two-dimensional (2D) simulations of space-charge region formation using COMSOL finite element analysis, by building on current numerical models [4].

  20. Comparison of a 2D Photochemical Model to Data Using Statistical Trend Analysis

    NASA Technical Reports Server (NTRS)

    Bhartia, P. K. (Technical Monitor); Stolarski, Richard; Jackman, Charles; Fleming, Eric; Frith, Stacey Hollandsworth

    2002-01-01

    We have analyzed our 23-year merged ozone data set for variability and trends with a statistical time-series model. To assist in that analysis, we have analyzed the Goddard 2D photochemical model for the same time period with the same time-series model. Multiple runs of the photochemical model allow us to separate the effects of various terms on ozone, such as solar cycle and volcanic eruptions. We use this to help us separate those signals from each other in the data. We also used a smoothed version of the photochemical model's prediction of global ozone change in place of a simple linear trend. We find a number of interesting results. This particular photochemical model is more sensitive to chlorine perturbations than the atmosphere appears to be. It is less sensitive to solar cycle. It predicts an effect from the Pinatubo eruption that is nearly symmetric in the two hemispheres, but the data appears to have not responded to Pinatubo in the southern mid-latitudes. These results and their uncertainties will be discussed.

  1. 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

    2014-01-01

    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

  2. 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

  3. 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.

  4. Fracture mode analysis and related surface deformation during dyke intrusion: Results from 2D experimental modelling

    NASA Astrophysics Data System (ADS)

    Abdelmalak, M.; Mourgues, R.; Bureau, D.

    2012-04-01

    The analysis of surface deformation in response to approaching intrusion is important for assessing volcanic hazards. In this paper, we present results from 2D scaled models of magma intrusion, in which we discuss the propagation mode and related surface deformation during dyke growth. Our experiments consist in the injection of analogue magma (Golden syrup) into cohesive fine-grained silica powder, simulating the brittle upper crust. Using an optical image correlation technique (Particle Imaging Velocimetry), we were able to follow the surface deformation, the displacements within the country rock and to calculate strains induced by the magma emplacement. We identified two kinds of intrusion morphologies resulting from different interactions between the dyke and plastic deformations occurring in the country rock near the surface. In both morphologies, the dyke is vertical at depth. Our analysis demonstrates that both hydraulic tensile opening and shear-related propagation operate during this first stage of vertical growth. At the same time, the surface lifted up and formed a smooth symmetrical dome. Both types of morphologies differ in the upper part. During a second stage of evolution, the first type of intrusion inclined at a dip between 45 to 65°. This inclination is not caused by shear deformations and is attributed to stress rotation near the tip. Closer to the surface, the growth of the inclined sheet creates shear bands which conduct the fluid toward the surface. The surface uplift becomes asymmetric. The second type of intrusion does not rotate at depth and continues its vertical propagation by catching vertical tensile cracks. The intrusion of magma in these cracks creates horizontal stresses which are responsible for the closure of fractures and the formation of reverse faults. At the surface the dome remains symmetrical. For both intrusions, the surface uplift accelerates during the second stage and it is strongly influenced by the presence or the

  5. 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.

  6. Evaluation of storage phosphor imaging for quantitative analysis of 2-D gels using the Quest II system.

    PubMed

    Patterson, S D; Latter, G I

    1993-12-01

    The advent of storage phosphor technology has been of considerable benefit to the imaging of gel-separated radiolabeled proteins due to the rapid and quantitative nature of the data acquisition process. Previously, times over one month were required to obtain fluorographs of the same gel to yield data of sufficient dynamic range for quantitative analysis of high-resolution two-dimensional (2-D) gels. As we are in the process of building a human 2-D gel protein database, and therefore have a high throughput of 2-D gels both to image and quantitate using the Quest II software, we undertook an evaluation of a storage phosphor imager, including an evaluation of signal fade. The results of this evaluation demonstrate the feasibility of using such a system, and we describe the procedures that allow us to use this technique for quantitative analysis of many complex 2-D gel patterns. These procedures include a useful batch printing program that allows printing of many images in a non-interactive mode. Examples will be presented of how autoradiography, using storage phosphor plates and the Quest II system, have enabled us to begin building a human 2-D gel protein database including posttranslational modification information, without the previous time constraints associated with such a project.

  7. 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 foreign…

  8. 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.…

  9. 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...

  10. Differential Analysis of 2D NMR Spectra: New Natural Products from a Pilot-Scale Fungal Extract Library

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using a newly developed protocol for the differential analysis of arrays of 2D NMR spectra, we were able to rapidly identify two previously unreported indole alkaloids from a library of unfractionated fungal extracts. Differential analyses of NMR spectra thus constitute an effective tool for the non...

  11. Structural and Functional Analysis of JMJD2D Reveals Molecular Basis for Site-Specific Demethylation among JMJD2 Demethylases

    SciTech Connect

    Krishnan, Swathi; Trievel, Raymond C.

    2013-01-08

    We found that JMJD2 lysine demethylases (KDMs) participate in diverse genomic processes. Most JMJD2 homologs display dual selectivity toward H3K9me3 and H3K36me3, with the exception of JMJD2D, which is specific for H3K9me3. Here, we report the crystal structures of the JMJD2D•2-oxoglutarate•H3K9me3 ternary complex and JMJD2D apoenzyme. Utilizing structural alignments with JMJD2A, molecular docking, and kinetic analysis with an array of histone peptide substrates, we elucidate the specific signatures that permit efficient recognition of H3K9me3 by JMJD2A and JMJD2D, and the residues in JMJD2D that occlude H3K36me3 demethylation. Surprisingly, these results reveal that JMJD2A and JMJD2D exhibit subtle yet important differences in H3K9me3 recognition, despite the overall similarity in the substrate-binding conformation. Further, we show that H3T11 phosphorylation abrogates demethylation by JMJD2 KDMs. These studies reveal the molecular basis for JMJD2 site specificity and provide a framework for structure-based design of selective inhibitors of JMJD2 KDMs implicated in disease.

  12. Human 2-D PAGE databases for proteome analysis in health and disease: http://biobase.dk/cgi-bin/celis.

    PubMed

    Celis, J E; Gromov, P; Ostergaard, M; Madsen, P; Honoré, B; Dejgaard, K; Olsen, E; Vorum, H; Kristensen, D B; Gromova, I; Haunsø, A; Van Damme, J; Puype, M; Vandekerckhove, J; Rasmussen, H H

    1996-12-01

    Human 2-D PAGE Databases established at the Danish Centre for Human Genome Research are now available on the World Wide Web (http://biobase.dk/cgi-bin/celis). The databanks, which offer a comprehensive approach to the analysis of the human proteome both in health and disease, contain data on known and unknown proteins recorded in various IEF and NEPHGE 2-D PAGE reference maps (non-cultured keratinocytes, non-cultured transitional cell carcinomas, MRC-5 fibroblasts and urine). One can display names and information on specific protein spots by clicking on the image of the gel representing the 2-D gel map in which one is interested. In addition, the database can be searched by protein name, keywords or organelle or cellular component. The entry files contain links to other databases such as Medline, Swiss-Prot, PIR, PDB, CySPID, OMIM, Methabolic pathways, etc. The on-line information is updated regularly. PMID:8977092

  13. 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.

  14. Advances in fast 2D camera data handling and analysis on NSTX

    SciTech Connect

    Davis, W. M.; Patel, R. I.; Boeglin, W. U.; Roquemore, A. L.; Maqueda, R. J.; Zweben, S. J.

    2010-07-01

    The use of fast 2D cameras on NSTX continues to grow. There are 6 cameras with the capability of taking up to 1–2 gigabytes (GBs) of data apiece during each plasma shot on the National Spherical Torus Experiment (NSTX). Efficient storage and retrieval of this data remains a challenge. Performance comparisons are presented for reading data stored in MDSplus, using both compressed data and segmented records, and direct access I/O with different read sizes. Encouragingly, fast 2D camera data provides considerable insight into plasma complexities, such as small-scale turbulence and particle transport. The last part of this paper is an example of more recent uses: dual cameras looking at the same region of the plasma from different angles, which can provide trajectories of incandescent particles in 3D. A laboratory simulation of the 3D trajectories is presented, as well as corresponding data from NSTX plasma where glowing dust particles can be followed.

  15. Stochastic precision analysis of 2D cardiac strain estimation in vivo

    NASA Astrophysics Data System (ADS)

    Bunting, E. A.; Provost, J.; Konofagou, E. E.

    2014-11-01

    Ultrasonic strain imaging has been applied to echocardiography and carries great potential to be used as a tool in the clinical setting. Two-dimensional (2D) strain estimation may be useful when studying the heart due to the complex, 3D deformation of the cardiac tissue. Increasing the framerate used for motion estimation, i.e. motion estimation rate (MER), has been shown to improve the precision of the strain estimation, although maintaining the spatial resolution necessary to view the entire heart structure in a single heartbeat remains challenging at high MERs. Two previously developed methods, the temporally unequispaced acquisition sequence (TUAS) and the diverging beam sequence (DBS), have been used in the past to successfully estimate in vivo axial strain at high MERs without compromising spatial resolution. In this study, a stochastic assessment of 2D strain estimation precision is performed in vivo for both sequences at varying MERs (65, 272, 544, 815 Hz for TUAS; 250, 500, 1000, 2000 Hz for DBS). 2D incremental strains were estimated during left ventricular contraction in five healthy volunteers using a normalized cross-correlation function and a least-squares strain estimator. Both sequences were shown capable of estimating 2D incremental strains in vivo. The conditional expected value of the elastographic signal-to-noise ratio (E(SNRe|ɛ)) was used to compare strain estimation precision of both sequences at multiple MERs over a wide range of clinical strain values. The results here indicate that axial strain estimation precision is much more dependent on MER than lateral strain estimation, while lateral estimation is more affected by strain magnitude. MER should be increased at least above 544 Hz to avoid suboptimal axial strain estimation. Radial and circumferential strain estimations were influenced by the axial and lateral strain in different ways. Furthermore, the TUAS and DBS were found to be of comparable precision at similar MERs.

  16. Analysis of heat conductivity in a 2D hard disk system

    NASA Astrophysics Data System (ADS)

    Del Pozo, J.; Garrido, P. L.

    2009-01-01

    Using numerical simulations, we study the heat conductivity in a 2d Hard Disk system. We find nonlinear temperature profiles for diferent gradients, and use this profiles to obtain the empirical expresion of heat conductivity κ(T,ρ). We compare our results with predictions based on the Enskog theory, finding good agreement even for large gradients. Also we find that Henderson state equation for Hard Disk stands for our system.

  17. Ion microprobe analysis of bone surface elements: Effects of 1,25(OH)2D3

    SciTech Connect

    Bushinsky, D.A.; Chabala, J.M.; Levi-Setti, R. )

    1989-12-01

    When neonatal mouse calvariae are incubated with 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) there is net calcium efflux from the bone into the medium. The effect of this enhanced cell-mediated Ca efflux on the relative concentrations of mineral 23Na, 39K, and 40Ca has not previously been studied. We used an imaging scanning ion microprobe, utilizing secondary ion mass spectrometry, to compare the relative ion concentrations of Na, K, and Ca on the surface, subsurface, and cross-section of cultured bone incubated in the presence of 1,25(OH)2D3 with the ion concentrations in similar regions of bone incubated in unaltered control medium. Changes in mineral ion concentration were correlated with net fluxes of Na, K, and Ca relative to bone. Calvariae incubated in control medium (24 h at pH approximately 7.40) have abundant surface Na and K relative to Ca (Na/Ca, 85 and K/Ca, 68), whereas the subsurface has less Na/Ca (21) and K/Ca (23), and on cross section the ratios of both Na/Ca (2.0) and K/Ca (1.9) decrease further. After incubation with 10(-8) M 1,25(OH)2D3, there is a significant increase in bone surface Na/Ca (154) and K/Ca (141) without a change in these ratios on the subsurface and a small fall in both ratios on cross section. The linear relationship between Na/Ca and K/Ca across the three regions of bone observed in control calvariae did not change with 1,25(OH)2D3 treatment. As determined by flux measurements there is a net efflux of Ca but not Na or K from bone.

  18. Analysis and comparison of 2D fingerprints: insights into database screening performance using eight fingerprint methods.

    PubMed

    Duan, Jianxin; Dixon, Steven L; Lowrie, Jeffrey F; Sherman, Woody

    2010-09-01

    Virtual screening is a widely used strategy in modern drug discovery and 2D fingerprint similarity is an important tool that has been successfully applied to retrieve active compounds from large datasets. However, it is not always straightforward to select an appropriate fingerprint method and associated settings for a given problem. Here, we applied eight different fingerprint methods, as implemented in the new cheminformatics package Canvas, on a well-validated dataset covering five targets. The fingerprint methods include Linear, Dendritic, Radial, MACCS, MOLPRINT2D, Pairwise, Triplet, and Torsion. We find that most fingerprints have similar retrieval rates on average; however, each has special characteristics that distinguish its performance on different query molecules and ligand sets. For example, some fingerprints exhibit a significant ligand size dependency whereas others are more robust with respect to variations in the query or active compounds. In cases where little information is known about the active ligands, MOLPRINT2D fingerprints produce the highest average retrieval actives. When multiple queries are available, we find that a fingerprint averaged over all query molecules is generally superior to fingerprints derived from single queries. Finally, a complementarity metric is proposed to determine which fingerprint methods can be combined to improve screening results.

  19. [Limits and possibilities of 2D video analysis in evaluating physiological and pathological foot rolling motion in runners].

    PubMed

    Grau, S; Müller, O; Bäurle, W; Beck, M; Krauss, I; Maiwald, C; Baur, H; Mayer, F

    2000-09-01

    Three-dimensional movements of the lower extremities in support phases are usually evaluated with the help of video analysis. This analysis is mainly done two-dimensionally in a frontal and sagittal plane. Usually, the temporal ankle of the achilles tendon respectively rear foot are analysed in the frontal plane, the knee and upper ankle angle in the sagittal plane, because their values are made responsible for different sport injuries. However, so far a correlation between different injuries and biomechanical parameters could not be proven. Often, small changes in 2D video data are discussed without considering the reliability of this method of measurement. It was the aim of this study to evaluate these parameters in 2D video analyses (2D-VA) which characterize the support phases of the foot. A second goal was to find out whether a connection between these angles and chronic achillodynia can then be sensibly proven. 32 male test persons consisting of a control group (KO, n = 14) without injuries and a group with chronic achillodynia (AD, n = 18), have been examined with the test/retest method in weekly intervals. The biomechanical running analysis was done with the help of 2D-VA in the frontal and sagittal plane on a treadmill at a speed of 80% of the individual anaerobic threshold with different shoes. The test/retest variability was for all measuring points not at all satisfying. Both groups showed big mean variations in both shoes and minimal differences in the measured angles. Because of the poor capability of reproduction of the 2D-VA for angles in the frontal plane this measuring method is only usable with restrictions for the evaluation of the support phase.

  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. Initial global 2-D shielding analysis for the Advanced Neutron Source core and reflector

    SciTech Connect

    Bucholz, J.A.

    1995-08-01

    This document describes the initial global 2-D shielding analyses for the Advanced Neutron Source (ANS) reactor, the D{sub 2}O reflector, the reflector vessel, and the first 200 mm of light water beyond the reflector vessel. Flux files generated here will later serve as source terms in subsequent shielding analyses. In addition to reporting fluxes and other data at key points of interest, a major objective of this report was to document how these analyses were performed, the phenomena that were included, and checks that were made to verify that these phenomena were properly modeled. In these shielding analyses, the fixed neutron source distribution in the core was based on the `lifetime-averaged` spatial power distribution. Secondary gamma production cross sections in the fuel were modified so as to account intrinsically for delayed fission gammas in the fuel as well as prompt fission gammas. In and near the fuel, this increased the low-energy gamma fluxes by 50 to 250%, but out near the reflector vessel, these same fluxes changed by only a few percent. Sensitivity studies with respect to mesh size were performed, and a new 2-D mesh distribution developed after some problems were discovered with respect to the use of numerous elongated mesh cells in the reflector. All of the shielding analyses were performed sing the ANSL-V 39n/44g coupled library with 25 thermal neutron groups in order to obtain a rigorous representation of the thermal neutron spectrum throughout the reflector. Because of upscatter in the heavy water, convergence was very slow. Ultimately, the fission cross section in the various materials had to be artificially modified in order to solve this fixed source problem as an eigenvalue problem and invoke the Vondy error-mode extrapolation technique which greatly accelerated convergence in the large 2-D RZ DORT analyses. While this was quite effective, 150 outer iterations (over energy) were still required.

  2. Microphysical Analysis using Airborne 2-D Cloud and Precipitation Imaging Probe Data

    NASA Astrophysics Data System (ADS)

    Guy, N.; Jorgensen, D.; Witte, M.; Chuang, P. Y.; Black, R. A.

    2013-12-01

    The NOAA P-3 instrumented aircraft provided in-situ cloud and precipitation microphysical observations during the DYNAMO (Dynamics of the Madden-Julian Oscillation) field experiment. The Particle Measuring System 2D cloud (2D-C) and precipitation (2D-P) probes collected data for particles between 12.5 μm - 1.55 mm (25 μm resolution) and 100 μm - 6.2 mm (100 μm resolution), respectively. Spectra from each instrument were combined to provide a broad distribution of precipitation particle sizes. The 'method of moments' technique was used to analyze drop size distribution (DSD) spectra, which were modeled by fitting a three-parameter (slope, shape, and intercept) gamma distribution to the spectra. The characteristic shape of the mean spectrum compares to previous maritime measurements. DSD variability will be presented with respect to the temporal evolution of cloud populations during a Madden-Julian Oscillation (MJO) event, as well as in-situ aircraft vertical wind velocity measurements. Using the third and sixth moments, rainfall rate (R) and equivalent radar reflectivity factor (Z), respectively, were computed for each DSD. Linear regression was applied to establish a Z-R relationship for the data for the estimation of precipitation. The study indicated unique characteristics of microphysical processes for this region. These results are important to continue to define the cloud population characteristics in the climatological MJO region. Improved representation of the cloud characteristics on the microphysical scale will serve as a check to model parameterizations, helping to improve numerical simulations.

  3. 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.

  4. 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.

  5. A Numerical Analysis of Sloshing Fluid in 2D Tanks with Baffles

    NASA Astrophysics Data System (ADS)

    Wu, C. H.; Chen, B. F.

    2011-09-01

    A tuned liquid damper (TLD) is one possible damping device of tall buildings under wind and earthquake excitations. A 2D tank with a vertically tank bottom-mounted baffle under horizontal excitation is studied in this work. The combination of time-independent finite difference method [1-3] and one-dimensional ghost cell approach was implemented to solve liquid sloshing in the baffled tank. The correlation between the movement of baffles and flow field due to liquid sloshing might to the clue to investigate the evolution of vortices around the baffle tip. We categorize the interaction process of vortices evolution into three phases: (1) Formation of separated shear layer and generation of vortices; (2) Formation of a vertical jet and shedding of vortices; (3) Interaction between shedding vortices and sloshing flow: the generation of snaky flow.

  6. Quantitative Analysis of Metabolic Mixtures by 2D 13C-Constant-Time TOCSY NMR Spectroscopy

    PubMed Central

    Bingol, Kerem; Zhang, Fengli; Bruschweiler-Li, Lei; Brüschweiler, Rafael

    2013-01-01

    An increasing number of organisms can be fully 13C-labeled, which has the advantage that their metabolomes can be studied by high-resolution 2D NMR 13C–13C constant-time (CT) TOCSY experiments. Individual metabolites can be identified via database searching or, in the case of novel compounds, through the reconstruction of their backbone-carbon topology. Determination of quantitative metabolite concentrations is another key task. Because significant peak overlaps in 1D NMR spectra prevents straightforward quantification through 1D peak integrals, we demonstrate here the direct use of 13C–13C CT-TOCSY spectra for metabolite quantification. This is accomplished through the quantum-mechanical treatment of the TOCSY magnetization transfer at short and long mixing times or by the use of analytical approximations, which are solely based on the knowledge of the carbon-backbone topologies. The methods are demonstrated for carbohydrate and amino-acid mixtures. PMID:23773204

  7. 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.

  8. 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

  9. Analysis of noise properties of a class of exact methods of inverting the 2-D exponential radon transform

    SciTech Connect

    Pan, X.; Metz, C.E.

    1995-12-01

    A general approach that the authors proposed elsewhere reveals the intrinsic relationship among methods for inversion of the 2-D exponential Radon transform described by Bellini et al., by Tretiak and Metz, by Hawkins et al., and by Inouye et al. Moreover, the approach provides an infinite class of linear methods for inverting the 2-D exponential Radon transform. In the work reported here, they systematically investigated the noise characteristics of the methods in this class, obtaining analytical forms for the autocovariance and the variance of the images reconstructed by use of various methods. The noise properties of a new quasi-optimal method were then compared theoretically to those of other methods of the class. The analysis demonstrates that the quasi-optimal method achieves smaller global variance in the reconstructed images than do the other methods of the class. Extensive numerical simulation studies confirm this prediction.

  10. 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

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

    PubMed

    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

  12. Analysis of proteins by direct-scanning infrared-MALDI mass spectrometry after 2D-PAGE separation and electroblotting.

    PubMed

    Eckerskorn, C; Strupat, K; Schleuder, D; Hochstrasser, D; Sanchez, J C; Lottspeich, F; Hillenkamp, F

    1997-08-01

    A novel approach is reported for the analysis and identification of proteins separated by 2D-PAGE with scanning infrared matrix-assisted laser desorption/ionization mass spectrometry (scanning IR-MALDI-MS). The proteins of human blood plasma were separated by 2D-PAGE, electroblotted onto PVDF membranes, incubated in matrix solution, and then scanned by IR-MALDI-MS. Mass contour plots of selected spots were obtained. Protein separation is shown to be conserved by comparison with silver-stained gels. The sensitivity for the protein detection is comparable if not better than that of silver-stained gels. Posttranslational modifications were identified by comparing the measured mass to the one calculated from the known DNA sequence. Adduct formation to unprotected cysteine residues during gel separation is demonstrated for selected proteins. PMID:9253242

  13. 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.

  14. Visual Analysis of time-dependent 2D Uncertainties in Decadal Climate Predictions

    NASA Astrophysics Data System (ADS)

    Böttinger, Michael; Röber, Niklas; Meier-Fleischer, Karin; Pohlmann, Holger

    2016-04-01

    Climate prediction systems used today for investigating the climate predictability on a decadal time scale are based on coupled global climate models. First, ensembles of hindcast experiments are carried out in order to derive the predictive skill of the prediction system. Then, in a second step, the prediction system is initialized with observations and actual future predictions are computed. The ensemble simulation techniques applied enable issuing of probabilistic information along with the quantities predicted. Different aspects of the uncertainty can be derived: The ensemble standard deviation (or ensemble spread) is a measure for the internal variability of the simulation, while the predictive skill is an inverse measure for the uncertainty in the prediction. In this work, we focus on the concurrent visualization of three related time-dependent 2D fields: the forecast variable itself, here the 2m temperature anomaly, along with the corresponding predictive skill and the ensemble spread which is given through the ensemble standard deviation. On the basis of temporally filtered data, animations are used to visualize the mean spatio-temporal development of the three quantities. Furthermore, seasonal analyses are similarly visualized in order to identify seasonal patterns. We show exemplary solutions produced with three different visualization systems: NCL, Avizo Green and ParaView. As example data set, we have used a decadal climate prediction carried out within the German research project "MiKlip - Decadal Predictions" using the MPI-M Earth System Model (MPI-ESM) from the Max Planck Institute for Meteorology in Hamburg.

  15. Bootstrap resampling as a tool for uncertainty analysis in 2-D magnetotelluric inversion modelling

    NASA Astrophysics Data System (ADS)

    Schnaidt, Sebastian; Heinson, Graham

    2015-10-01

    Uncertainty estimation is a vital part of geophysical numerical modelling. There exist a variety of methods aimed at uncertainty estimation, which are often complicated and difficult to implement. We present an inversion technique that produces multiple solutions, based on bootstrap resampling, to create a qualitative uncertainty measure for 2-D magnetotelluric inversion models. The approach is easy to implement, can be used with almost any inversion code, and does not require access to the inversion software's source code. It is capable of detecting the effect of data uncertainties on the model result rather than just analysing the effect of model variations on the model response. To obtain uncertainty estimates for an inversion model, the original data set is resampled repeatedly and alternate data set realizations are created and inverted. This ensemble of solutions is then statistically analysed to determine the variability between the different solutions. The process yields interpretable uncertainty maps for the inversion model and we demonstrate its effectiveness to qualitatively quantify uncertainty in synthetic model tests and a case study.

  16. Carbonate platform-margins and reefs distribution using 2-D seismic analysis, Central Tunisia

    NASA Astrophysics Data System (ADS)

    Harzali, Makrem; Troudi, Habib; Ben Boubaker, Kamel; Ouali, Jamel

    2014-12-01

    The seismic characterization of sedimentary facies in a carbonate platform, comprising different types of reefs constructions, is based using two-dimensional (2-D) seismic and borehole data. Reefs of the Aptian Serdj carbonates are shown as mounds of strong chaotic amplitudes that have a high-amplitude continuous reflection at the top. They are sealed by Albian marl and claystone deposits characterized by mid- to low-amplitude, parallel and discontinuous to weak reflections. These buildups were restricted to the outer platform margin of Central Tunisia. Sea level oscillations associated with master fault rejuvenation governed the growth, the distribution and development of these reefs. Their distribution is largely controlled by deep-seated fault-related folds and the topography of underlying structures, representing local domal uplifts. Falls of sea level led to subaerial exposure and the development of a karstified denudation of the carbonate platform. Subsequently, reefs were partially or totally destroyed and then overlain, during the Albian, by marls and claystones of the Fahdene Formation. Their study indicates that reef buildups have important oil and gas exploration potential, not only onshore, but also in offshore, Central Tunisia.

  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

    2007-01-01

    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. Analysis of the dose calculation accuracy for IMRT in lung: a 2D approach.

    PubMed

    Dvorak, Pavel; Stock, Markus; Kroupa, Bernhard; Bogner, Joachim; Georg, Dietmar

    2007-01-01

    The purpose of this study was to compare the dosimetric accuracy of IMRT plans for targets in lung with the accuracy of standard uniform-intensity conformal radiotherapy for different dose calculation algorithms. Tests were performed utilizing a special phantom manufactured from cork and polystyrene in order to quantify the uncertainty of two commercial TPS for IMRT in the lung. Ionization and film measurements were performed at various measuring points/planes. Additionally, single-beam and uniform-intensity multiple-beam tests were performed, in order to investigate deviations due to other characteristics of IMRT. Helax-TMS V6.1(A) was tested for 6, 10 and 25 MV and BrainSCAN 5.2 for 6 MV photon beams, respectively. Pencil beam (PB) with simple inhomogeneity correction and 'collapsed cone' (CC) algorithms were applied for dose calculations. However, the latter was not incorporated during optimization hence only post-optimization recalculation was tested. Two-dimensional dose distributions were evaluated applying the gamma index concept. Conformal plans showed the same accuracy as IMRT plans. Ionization chamber measurements detected deviations of up to 5% when a PB algorithm was used for IMRT dose calculations. Significant improvement (deviations approximately 2%) was observed when IMRT plans were recalculated with the CC algorithm, especially for the highest nominal energy. All gamma evaluations confirmed substantial improvement with the CC algorithm in 2D. While PB dose distributions showed most discrepancies in lower (<50%) and high (>90%) dose regions, the CC dose distributions deviated mainly in the high dose gradient (20-80%) region. The advantages of IMRT (conformity, intra-target dose control) should be counterbalanced with possible calculation inaccuracies for targets in the lung. Until no superior dose calculation algorithms are involved in the iterative optimization process it should be used with great care. When only PB algorithm with simple

  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. 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. PMID:25186288

  1. 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.

  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

    PubMed Central

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

    2014-01-01

    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. 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

  5. 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.

  6. TSUNAMI analysis of National Ignition Facility 2-D gas dynamics phenomenon

    SciTech Connect

    Chen, X.M.; Peterson, P.F.; Tobin, M.T.

    1994-11-01

    The tests in the chamber of National Ignition Facility will involve complex multi-dimensional dynamics phenomena. Many safety concerns relate to the ablation of the chamber material and the re-condensation of it. The x-ray induced ablation can vaporize surfaces of internal structures. The deposition of the ablated mass to the laser optics can cause significant damage to the laser optics. This study presents a typical analysis of the ablation from the target positioner in the NIF chamber with the TSUNAMI two-dimensional gas dynamics code. Results reveal that the geometry of target positioner has strong influence to the vapor mass amount and distribution over the chamber wall. The analysis done here shows that it is possible to perform parametric study for different NIF chamber design configurations.

  7. 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.

  8. 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.

  9. Coupled 2D-3D finite element method for analysis of a skin panel with a discontinuous stiffener

    NASA Technical Reports Server (NTRS)

    Wang, J. T.; Lotts, C. G.; Davis, D. D., Jr.; Krishnamurthy, T.

    1992-01-01

    This paper describes a computationally efficient analysis method which was used to predict detailed stress states in a typical composite compression panel with a discontinuous hat stiffener. A global-local approach was used. The global model incorporated both 2D shell and 3D brick elements connected by newly developed transition elements. Most of the panel was modeled with 2D elements, while 3D elements were employed to model the stiffener flange and the adjacent skin. Both linear and geometrically nonlinear analyses were performed on the global model. The effect of geometric nonlinearity induced by the eccentric load path due to the discontinuous hat stiffener was significant. The local model used a fine mesh of 3D brick elements to model the region at the end of the stiffener. Boundary conditions of the local 3D model were obtained by spline interpolation of the nodal displacements from the global analysis. Detailed in-plane and through-the-thickness stresses were calculated in the flange-skin interface near the end of the stiffener.

  10. 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

  11. Low-level motion analysis of color and luminance for perception of 2D and 3D motion.

    PubMed

    Shioiri, Satoshi; Yoshizawa, Masanori; Ogiya, Mistuharu; Matsumiya, Kazumichi; Yaguchi, Hirohisa

    2012-01-01

    We investigated the low-level motion mechanisms for color and luminance and their integration process using 2D and 3D motion aftereffects (MAEs). The 2D and 3D MAEs obtained in equiluminant color gratings showed that the visual system has the low-level motion mechanism for color motion as well as for luminance motion. The 3D MAE is an MAE for motion in depth after monocular motion adaptation. Apparent 3D motion can be perceived after prolonged exposure of one eye to lateral motion because the difference in motion signal between the adapted and unadapted eyes generates interocular velocity differences (IOVDs). Since IOVDs cannot be analyzed by the high-level motion mechanism of feature tracking, we conclude that a low-level motion mechanism is responsible for the 3D MAE. Since we found different temporal frequency characteristics between the color and luminance stimuli, MAEs in the equiluminant color stimuli cannot be attributed to a residual luminance component in the color stimulus. Although a similar MAE was found with a luminance and a color test both for 2D and 3D motion judgments after adapting to either color or luminance motion, temporal frequency characteristics were different between the color and luminance adaptation. The visual system must have a low-level motion mechanism for color signals as for luminance ones. We also found that color and luminance motion signals are integrated monocularly before IOVD analysis, showing a cross adaptation effect between color and luminance stimuli. This was supported by an experiment with dichoptic presentations of color and luminance tests. In the experiment, color and luminance tests were presented in the different eyes dichoptically with four different combinations of test and adaptation: color or luminance test in the adapted eye after color or luminance adaptation. Findings of little or no influence of the adaptation/test combinations indicate the integration of color and luminance motion signals prior to the

  12. 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".

  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. PMID:27387872

  14. 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.

  15. 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.

  16. 2-D Time-Dependent Fuel Element, Thermal Analysis Code System.

    2001-09-24

    Version 00 WREM-TOODEE2 is a two dimensional, time-dependent, fuel-element thermal analysis program. Its primary purpose is to evaluate fuel-element thermal response during post-LOCA refill and reflood in a pressurized water reactor (PWR). TOODEE2 calculations are carried out in a two-dimensional mesh region defined in slab or cylindrical geometry by orthogonal grid lines. Coordinates which form order pairs are labeled x-y in slab geometry, and those in cylindrical geometry are labeled r-z for the axisymmetric casemore » and r-theta for the polar case. Conduction and radiation are the only heat transfer mechanisms assumed within the boundaries of the mesh region. Convective and boiling heat transfer mechanisms are assumed at the boundaries. The program numerically solves the two-dimensional, time-dependent, heat conduction equation within the mesh region. KEYWORDS: FUEL MANAGEMENT; HEAT TRANSFER; LOCA; PWR« less

  17. 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.

  18. Polarization analysis for the 2D position-sensitive detector of the HADAS reflectometer in Jülich

    NASA Astrophysics Data System (ADS)

    Rücker, U.; Bergs, W.; Alefeld, B.; Kentzinger, E.; Brückel, Th.

    2001-03-01

    A neutron reflectometer with polarization analysis is being built on the basis of the HADAS spectrometer in the neutron guide hall at the research reactor FRJ-2 (DIDO) in Jülich. The new instrument is optimized for reflectivity and diffuse scattering measurements under grazing incidence on layered magnetic structures with thicknesses in the nm range. In order to measure diffuse scattering with polarization analysis, the 2D position-sensitive detector has been equipped with a polarization analyser that consists of a stack of supermirrors parallel to the scattering plane. First tests have revealed that the resolution of the instrument is not reduced by the polarization analyser. A flipping ratio of 20 has been achieved already during the first experiment.

  19. 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.

  20. 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.

  1. Using 2D Correlation Analysis to Enhance Spectral Information Available from Highly Spatially Resolved AFM-IR Spectra.

    PubMed

    Marcott, Curtis; Lo, Michael; Hu, Qichi; Kjoller, Kevin; Boskey, Adele; Noda, Isao

    2014-07-01

    The recent combination of atomic force microscopy and infrared spectroscopy (AFM-IR) has led to the ability to obtain IR spectra with nanoscale spatial resolution, nearly two orders-of-magnitude better than conventional Fourier transform infrared (FT-IR) microspectroscopy. This advanced methodology can lead to significantly sharper spectral features than are typically seen in conventional IR spectra of inhomogeneous materials, where a wider range of molecular environments are coaveraged by the larger sample cross section being probed. In this work, two-dimensional (2D) correlation analysis is used to examine position sensitive spectral variations in datasets of closely spaced AFM-IR spectra. This analysis can reveal new key insights, providing a better understanding of the new spectral information that was previously hidden under broader overlapped spectral features. Two examples of the utility of this new approach are presented. Two-dimensional correlation analysis of a set of AFM-IR spectra were collected at 200-nm increments along a line through a nucleation site generated by remelting a small spot on a thin film of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate). There are two different crystalline carbonyl band components near 1720 cm(-1) that sequentially disappear before a band at 1740 cm(-1) due to more disordered material appears. In the second example, 2D correlation analysis of a series of AFM-IR spectra spaced every 1 micrometer of a thin cross section of a bone sample measured outward from an osteon center of bone growth. There are many changes in the amide I and phosphate band contours, suggesting changes in the bone structure are occurring as the bone matures.

  2. MIA-QSAR: a simple 2D image-based approach for quantitative structure activity relationship analysis

    NASA Astrophysics Data System (ADS)

    Freitas, Matheus P.; Brown, Steven D.; Martins, José A.

    2005-03-01

    An accessible and quite simple QSAR method, based on 2D image analysis, is reported. A case study is carried out in order to compare this model with a previously reported sophisticated methodology. A well known set of ( S)- N-[(1-ethyl-2-pyrrolidinyl)methyl]-6-methoxybenzamides, compounds with affinity to the dopamine D 2 receptor subtype, was divided in 40 calibration compounds and 18 test compounds and the descriptors were generated from pixels of 2D structures of each compound, which can be drawn with aid of any appropriate program. Bilinear (conventional) PLS was utilized as the regression method and leave-one-out cross-validation was performed using the NIPALS algorithm. The good predicted Q2 value obtained for the series of test compounds (0.58), together with the similar prediction quality obtained to other data sets (nAChR ligands, HIV protease inhibitors, COX-2 inhibitors and anxiolytic agents), suggests that the model is robust and seems to be as applicable as more complex methods.

  3. Scaling Analysis of Ocean Surface Turbulent Heterogeneities from Satellite Remote Sensing: Use of 2D Structure Functions.

    PubMed

    Renosh, P R; Schmitt, Francois G; Loisel, Hubert

    2015-01-01

    Satellite remote sensing observations allow the ocean surface to be sampled synoptically over large spatio-temporal scales. The images provided from visible and thermal infrared satellite observations are widely used in physical, biological, and ecological oceanography. The present work proposes a method to understand the multi-scaling properties of satellite products such as the Chlorophyll-a (Chl-a), and the Sea Surface Temperature (SST), rarely studied. The specific objectives of this study are to show how the small scale heterogeneities of satellite images can be characterised using tools borrowed from the fields of turbulence. For that purpose, we show how the structure function, which is classically used in the frame of scaling time series analysis, can be used also in 2D. The main advantage of this method is that it can be applied to process images which have missing data. Based on both simulated and real images, we demonstrate that coarse-graining (CG) of a gradient modulus transform of the original image does not provide correct scaling exponents. We show, using a fractional Brownian simulation in 2D, that the structure function (SF) can be used with randomly sampled couple of points, and verify that 1 million of couple of points provides enough statistics.

  4. 2D Global Attenuation Model of the Upper Mantle from Combined Analysis of Surface Wave Phase and Amplitude Data

    NASA Astrophysics Data System (ADS)

    Ma, Z.; Masters, G.

    2014-12-01

    We have developed a technique that uses a cluster analysis method to measure Rayleigh wave phase and amplitude anomalies. The measurements are made on the vertical components of all permanent stations recording LHZ data from IRIS. We currently consider earthquakes with Ms>5.5 between 1990 and 2007. Joint inversions for 2D phase velocity and attenuation maps are performed, allowing the coupling through physical dispersion (e.g. Zhou 2009). As demonstrated in Dalton and Ekstrom (2006), correcting the effect of focusing-defocusing is crucial in order to obtain reliable attenuation structures. Ray theory, which has been used to date, may not give reliable predictions of such effects, because it depends strongly on short wavelength velocity structures and so is very sensitive to how the phase velocity maps are smoothed. Instead, we use the 2D finite frequency amplitude kernel (Zhou et al, 2004) to model the focusing-defocusing effect. Attenuation models and evaluations of model error and resolution will be presented.

  5. Combined analysis of 2-D electrical resistivity, seismic refraction and geotechnical investigations for Bukit Bunuh complex crater

    NASA Astrophysics Data System (ADS)

    Azwin, I. N.; Saad, Rosli; Saidin, Mokhtar; Nordiana, M. M.; Anderson Bery, Andy; Hidayah, I. N. E.

    2015-01-01

    Interest in studying impact crater on earth has increased tremendously due to its importance in geologic events, earth inhabitant history as well as economic value. The existences of few shock metamorphism and crater morphology evidences are discovered in Bukit Bunuh, Malaysia thus detailed studies are performed using geophysical and geotechnical methods to verify the type of the crater and characteristics accordingly. This paper presents the combined analysis of 2-D electrical resistivity, seismic refraction, geotechnical SPT N value, moisture content and RQD within the study area. Three stages of data acquisition are made starting with regional study followed by detailed study on West side and East side. Bulk resistivity and p-wave seismic velocity were digitized from 2-D resistivity and seismic sections at specific distance and depth for corresponding boreholes and samples taken. Generally, Bukit Bunuh shows the complex crater characteristics. Standard table of bulk resistivity and p-wave seismic velocity against SPT N value, moisture content and RQD are produce according to geological classifications of impact crater; inside crater, rim/slumped terrace and outside crater.

  6. Scaling Analysis of Ocean Surface Turbulent Heterogeneities from Satellite Remote Sensing: Use of 2D Structure Functions

    PubMed Central

    Renosh, P. R.; Schmitt, Francois G.; Loisel, Hubert

    2015-01-01

    Satellite remote sensing observations allow the ocean surface to be sampled synoptically over large spatio-temporal scales. The images provided from visible and thermal infrared satellite observations are widely used in physical, biological, and ecological oceanography. The present work proposes a method to understand the multi-scaling properties of satellite products such as the Chlorophyll-a (Chl-a), and the Sea Surface Temperature (SST), rarely studied. The specific objectives of this study are to show how the small scale heterogeneities of satellite images can be characterised using tools borrowed from the fields of turbulence. For that purpose, we show how the structure function, which is classically used in the frame of scaling time series analysis, can be used also in 2D. The main advantage of this method is that it can be applied to process images which have missing data. Based on both simulated and real images, we demonstrate that coarse-graining (CG) of a gradient modulus transform of the original image does not provide correct scaling exponents. We show, using a fractional Brownian simulation in 2D, that the structure function (SF) can be used with randomly sampled couple of points, and verify that 1 million of couple of points provides enough statistics. PMID:26017551

  7. High divergent 2D grating

    NASA Astrophysics Data System (ADS)

    Wang, Jin; Ma, Jianyong; Zhou, Changhe

    2014-11-01

    A 3×3 high divergent 2D-grating with period of 3.842μm at wavelength of 850nm under normal incidence is designed and fabricated in this paper. This high divergent 2D-grating is designed by the vector theory. The Rigorous Coupled Wave Analysis (RCWA) in association with the simulated annealing (SA) is adopted to calculate and optimize this 2D-grating.The properties of this grating are also investigated by the RCWA. The diffraction angles are more than 10 degrees in the whole wavelength band, which are bigger than the traditional 2D-grating. In addition, the small period of grating increases the difficulties of fabrication. So we fabricate the 2D-gratings by direct laser writing (DLW) instead of traditional manufacturing method. Then the method of ICP etching is used to obtain the high divergent 2D-grating.

  8. High resolution analysis of C2D4 in the region of 600-1150 cm-1

    NASA Astrophysics Data System (ADS)

    Ulenikov, O. N.; Gromova, O. V.; Bekhtereva, E. S.; Fomchenko, A. L.; Zhang, Fangce; Sydow, C.; Maul, C.; Bauerecker, S.

    2016-10-01

    High-accurate Fourier-transform infrared spectra of C2D4 were recorded and analyzed in the region of 600-1150 cm-1 where the bands ν7(B1u), ν10(B2u), ν12(B3u) are located as well as the ν4(Au) band which is forbidden by the symmetry of the molecule. The ground state rotational structure was re-analyzed by the use of ground state combination differences obtained on the basis of infrared transitions of the ν12 and ν7 absorption bands. This gave us the possibility to considerably improve the rotational and centrifugal parameters of the ground vibrational state. The analysis of the experimental data and the subsequent weighted-fit procedure of the Hamiltonian parameters allowed us to reproduce the initial 4405 "experimental" ro-vibrational energy values with the drms = 2.1 ×10-4cm-1.

  9. 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.

  10. Scaling Analysis of Ocean Surface Turbulent Heterogeneities from Satellite Remote Sensing: Use of 2D Structure Functions, methodology and applications

    NASA Astrophysics Data System (ADS)

    Schmitt, F. G.; Pannimpullath Remanan, R.; Loisel, H.

    2015-12-01

    Satellite remote sensing observations allow the ocean surface to be sampled over large spatio-temporal scales. The images provided from visible and thermal infrared satellite observations are widely used in physical, biological, and ecological oceanography. The present work proposes a method to understand the multi-scaling properties of satellite products such as the Chlorophyll-a (Chl-a), and the Sea Surface Temperature (SST). The specific objectives of this study are to show how the small scale heterogeneities of satellite images can be characterised using tools borrowed from the fields of turbulence. We show how the structure function, which is classically used in the frame of scaling time series analysis, can be used also in 2D. The main advantage of this method is that it can be applied to process images which have missing data. Based on both simulated and real images, we demonstrate that coarse-graining (CG) of a gradient modulus transform of the original image does not provide correct scaling exponents. We show, using a fractional Brownian simulation in 2D, that the structure function (SF) can be used with randomly sampled couple of points, and verify that 1 million of couple of points provides enough statistics. After this methodological study, some applications are presented: the nonlinear moment function ζ(q) is fitted using the lognormal model with 2 parameters, the Hurst index H and the intermittency μ. The values of H and μ are discussed for 4 different parameters (Chl-a, SST, Rrs-443 and Rrs-555) and for different locations, chosen among different contrasted regions of the ocean, characterized by high spatial heterogeneity in Chl-a and SST.

  11. A hybrid wave-mode formulation for the vibro-acoustic analysis of 2D periodic structures

    NASA Astrophysics Data System (ADS)

    Droz, C.; Zhou, C.; Ichchou, M. N.; Lainé, J.-P.

    2016-02-01

    In the framework of vibrational analysis of 2D periodic waveguides, Floquet-Bloch theorem is widely applied for the determination of wave dispersion characteristics. In this context, the Wave Finite Element Method (WFEM) combines Periodic Structure Theory (PST) with standard FE packages, enabling wave dispersion analysis of waveguides involving structurally realistic unit-cells. For such applications, the computational efficiency of the WFEM depends on the choice of the formulation and can lead to numerical issues, worsen by extensive computational cost. This paper presents a coupled wave-mode approach for the determination of wave dispersion characteristics in structurally advanced periodic structures. It combines two scales of model order reduction. At the unit-cell's scale, Component Mode Synthesis (CMS) provides the displacement field associated with local resonances of the periodic structure, while the free wave propagation is considered using a spectral problem projection on a reduced set of shape functions associated with propagating waves, thus providing considerable reduction of the computational cost. An application is provided for a bi-directionally stiffened panel and the influence of reduction parameters is discussed, as well as the robustness of the numerical results.

  12. AMTCLAB: A MATLAB ®-based program for traveltime analysis and velocity tuning in 2D elliptical anisotropic media

    NASA Astrophysics Data System (ADS)

    Fernández Martínez, J. L.; Pedruelo González, L. M.; García Gonzalo, E.

    2009-10-01

    In this paper we present the program AMTCLAB, a MATLAB ®-based computer code that analyzes the traveltime distribution and performs quality analysis at the pre-inversion stage for elliptically anisotropic media explored via 2D transmission experiments. This software generalizes the program MTCLAB presented in the past for the case of layered isotropic media, and makes use of traditional and robust traveltime distribution descriptors (mean, standard deviation, median, lower and upper quartiles, inter-quartile range and minimum absolute deviation), which are valid for all kinds of recording geometries. A guided user interface leads the modeller through the algorithm steps using the same data MTCLAB-structures. This methodology offers better understanding of the data variability prior to inversion, and provides the geophysicist with a macroscopic elliptical anisotropic velocity model, which is valid at the experiment scale, and matches the experimental mean traveltime distribution. To solve the inverse problems involved, program AMTCLAB uses the particle swarm optimisation algorithm, which allows the use of different norms and sampling the region of equivalent anisotropic velocity models in order to perform posterior sample statistics in each individual model parameter. The approximated velocity model issued from this analysis can serve in the traveltime inverse problem as an initial guess, or as a reference model in the subsequent inversion.

  13. New aQTL SNPs for the CYP2D6 Identified by a Novel Mediation Analysis of Genome-Wide SNP Arrays, Gene Expression Arrays, and CYP2D6 Activity

    PubMed Central

    Wang, Zhiping; Boustani, Malaz; Liu, Yunlong; Skaar, Todd; Li, Lang

    2013-01-01

    Background. The genome-wide association studies (GWAS) have been successful during the last few years. A key challenge is that the interpretation of the results is not straightforward, especially for transacting SNPs. Integration of transcriptome data into GWAS may provide clues elucidating the mechanisms by which a genetic variant leads to a disease. Methods. Here, we developed a novel mediation analysis approach to identify new expression quantitative trait loci (eQTL) driving CYP2D6 activity by combining genotype, gene expression, and enzyme activity data. Results. 389,573 and 1,214,416 SNP-transcript-CYP2D6 activity trios are found strongly associated (P < 10−5, FDR = 16.6% and 11.7%) for two different genotype platforms, namely, Affymetrix and Illumina, respectively. The majority of eQTLs are trans-SNPs. A single polymorphism leads to widespread downstream changes in the expression of distant genes by affecting major regulators or transcription factors (TFs), which would be visible as an eQTL hotspot and can lead to large and consistent biological effects. Overlapped eQTL hotspots with the mediators lead to the discovery of 64 TFs. Conclusions. Our mediation analysis is a powerful approach in identifying the trans-QTL-phenotype associations. It improves our understanding of the functional genetic variations for the liver metabolism mechanisms. PMID:24232670

  14. 2D Cross Sectional Analysis and Associated Electrochemistry of Composite Electrodes Containing Dispersed Agglomerates of Nanocrystalline Magnetite, Fe₃O₄.

    PubMed

    Bock, David C; Kirshenbaum, Kevin C; Wang, Jiajun; Zhang, Wei; Wang, Feng; Wang, Jun; Marschilok, Amy C; Takeuchi, Kenneth J; Takeuchi, Esther S

    2015-06-24

    When electroactive nanomaterials are fully incorporated into an electrode structure, characterization of the crystallite sizes, agglomerate sizes, and dispersion of the electroactive materials can lend insight into the complex electrochemistry associated with composite electrodes. In this study, composite magnetite electrodes were sectioned using ultramicrotome techniques, which facilitated the direct observation of crystallites and agglomerates of magnetite (Fe3O4) as well as their dispersal patterns in large representative sections of electrode, via 2D cross sectional analysis by Transmission Electron Microscopy (TEM). Further, the electrochemistry of these electrodes were recorded, and Transmission X-ray Microscopy (TXM) was used to determine the distribution of oxidation states of the reduced magnetite. Unexpectedly, while two crystallite sizes of magnetite were employed in the production of the composite electrodes, the magnetite agglomerate sizes and degrees of dispersion in the two composite electrodes were similar to each other. This observation illustrates the necessity for careful characterization of composite electrodes, in order to understand the effects of crystallite size, agglomerate size, and level of dispersion on electrochemistry. PMID:26024206

  15. 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.

  16. 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.

  17. Proteomic analysis of a decellularized human vocal fold mucosa scaffold using 2D electrophoresis and high-resolution mass spectrometry

    PubMed Central

    Welham, Nathan V.; Chang, Zhen; Smith, Lloyd M.; Frey, Brian L.

    2012-01-01

    Natural biologic scaffolds for tissue engineering are commonly generated by decellularization of tissues and organs. Despite some preclinical and clinical success, in vivo scaffold remodeling and functional outcomes remain variable, presumably due to the influence of unidentified bioactive molecules on the scaffold-host interaction. Here, we used 2D electrophoresis and high-resolution mass spectrometry-based proteomic analyses to evaluate decellularization effectiveness and identify potentially bioactive protein remnants in a human vocal fold mucosa model. We noted proteome, phosphoproteome and O-glycoproteome depletion post-decellularization, and identified >200 unique protein species within the decellularized scaffold. Gene ontology-based enrichment analysis revealed a dominant set of functionally-related ontology terms associated with extracellular matrix assembly, organization, morphology and patterning, consistent with preservation of a tissue-specific niche for later cell seeding and infiltration. We further identified a subset of ontology terms associated with bioactive (some of which are antigenic) cellular proteins, despite histological and immunohistochemical data indicating complete decellularization. These findings demonstrate the value of mass spectrometry-based proteomics in identifying agents potentially responsible for variation in host response to engineered tissues derived from decellularized scaffolds. This work has implications for the manufacturing of biologic scaffolds from any tissue or organ, as well as for prediction and monitoring of the scaffold-host interaction in vivo. PMID:23102991

  18. 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

    2015-07-01

    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. PMID:25937538

  19. DNS of hydrodynamically interacting droplets in turbulent clouds: Parallel implementation and scalability analysis using 2D domain decomposition

    NASA Astrophysics Data System (ADS)

    Ayala, Orlando; Parishani, Hossein; Chen, Liu; Rosa, Bogdan; Wang, Lian-Ping

    2014-12-01

    The study of turbulent collision of cloud droplets requires simultaneous considerations of the transport by background air turbulence (i.e., geometric collision rate) and influence of droplet disturbance flows (i.e., collision efficiency). In recent years, this multiscale problem has been addressed through a hybrid direct numerical simulation (HDNS) approach (Ayala et al., 2007). This approach, while currently is the only viable tool to quantify the effects of air turbulence on collision statistics, is computationally expensive. In order to extend the HDNS approach to higher flow Reynolds numbers, here we developed a highly scalable implementation of the approach using 2D domain decomposition. The scalability of the parallel implementation was studied using several parallel computers, at 5123 and 10243 grid resolutions with O(106)-O(107) droplets. It was found that the execution time scaled with number of processors almost linearly until it saturates and deteriorates due to communication latency issues. To better understand the scalability, we developed a complexity analysis by partitioning the execution tasks into computation, communication, and data copy. Using this complexity analysis, we were able to predict the scalability performance of our parallel code. Furthermore, the theory was used to estimate the maximum number of processors below which the approximately linear scalability is sustained. We theoretically showed that we could efficiently solved problems of up to 81923 with O(100,000) processors. The complexity analysis revealed that the pseudo-spectral simulation of background turbulent flow for a dilute droplet suspension typical of cloud conditions typically takes about 80% of the total execution time, except when the droplets are small (less than 5 μm in a flow with energy dissipation rate of 400 cm2/s3 and liquid water content of 1 g/m3), for which case the particle-particle hydrodynamic interactions become the bottleneck. The complexity analysis

  20. Holistic differential analysis of embryo-induced alterations in the proteome of bovine endometrium in the preattachment period.

    PubMed

    Berendt, Frank J; Fröhlich, Thomas; Schmidt, Susanne E M; Reichenbach, Horst-Dieter; Wolf, Eckhard; Arnold, Georg J

    2005-07-01

    During the peri-implantation period, molecular signaling between embryo and endometrium (layer of tissue lining the uterus lumen) is supposed to be crucial for the maintenance of pregnancy. To investigate embryo-induced alterations in the proteome of bovine endometrium in the preattachment period (day 18), we used monozygotic cattle twins (generated by embryo splitting) as a model eliminating genetic variability as a source for proteome differences. One of the twins was pregnant after the transfer of two in vitro produced blastocysts, while the corresponding twin received a sham-transfer and served as a nonpregnant control. The two-dimensional fluorescence difference gel electrophoresis (2-D DIGE) analysis of the endometrium samples of three twin pairs (pregnant/nonpregnant) revealed four proteins with significantly higher abundance (p < 10(-9)) in each sample derived from the pregnant animals: Rho GDP dissociation inhibitor beta; 20 alpha-hydroxysteroid dehydrogenase (20 alpha-HSD); soluble NADP(+)-dependent isocitrate dehydrogenase 1; and acyl-CoA-binding protein. To verify the accuracy of the 2-D DIGE quantification, the abundances of 20 alpha-HSD were quantified by a targeted cleavable isotope-coded affinity tag (ICAT) approach. The mass spectrometry-based ICAT quantification matched perfectly the results obtained by 2-D DIGE quantification, demonstrating the accuracy of our data. These results demonstrate that our model (monozygotic twins) in combination with the appropriate analytical tools is particularly suitable for the detection of the proteins involved in the embryo-maternal interactions.

  1. Comparison and Characterization of Proteomes in the ThreeDomains of Life Using 2D Correlation Analysis

    NASA Astrophysics Data System (ADS)

    Fujishima, K.; Komasa, M.; Kitamura, S.; Tomita, M.; Kanai, A.

    Proteins are a major regulatory component in complex biological systems.Among them, DNA/RNA-binding proteins, the key components of the central dogma of molecular biology, and membrane proteins, which are necessary for both signal transduction and metabolite transport, are suggested to be the most important protein families that arose in the early stage of life. In this study, we computationally analyzed the whole proteome data of six model species to overview the protein diversity in the three domains of life (Bacteria, Archaea and Eukaryota), especially focusing on the above two protein families. To compare the protein distribution among the six model species, we calculated various protein profiles: hydropathy, molecular weight, amino acid composition and periodicity for each protein. We found a domain-specific distribution of the proteome based on 2D correlation analysis of hydropathy and molecular weight. Further, the merged protein distribution of Archaea and other do mains revealed many membrane proteins localized in Bacteria-specific regions with a high ratio of hydropathy and many DNA/RNA-binding proteins localized in Eukaryota-specific regions with a low ratio of hydropathy. Since about half of the proteins encoded in the genome are still functionally unknown, we further conducted Support Vector Machine (SVM)-based functional prediction using amino acid composition (CO score) and periodicity (PD score) as feature vectors to predict the overall number of DNA/RNA-binding proteins and membrane proteins in the proteome. Our estimation indicated that two functional categories occupy approximately 60% to 80% of the proteome, and further, the proportion of the two categories varied among the three domains of life, suggesting that the proteome has gone through different selective pressure during evolution.

  2. Rainfall/runoff simulation with 2D full shallow water equations: Sensitivity analysis and calibration of infiltration parameters

    NASA Astrophysics Data System (ADS)

    Fernández-Pato, Javier; Caviedes-Voullième, Daniel; García-Navarro, Pilar

    2016-05-01

    One of the most difficult issues in the development of hydrologic models is to find a rigorous source of data and specific parameters to a given problem, on a given location that enable reliable calibration. In this paper, a distributed and physically based model (2D Shallow Water Equations) is used for surface flow and runoff calculations in combination with two infiltration laws (Horton and Green-Ampt) for estimating infiltration in a watershed. This technique offers the capability of assigning a local and time-dependent infiltration rate to each computational cell depending on the available surface water, soil type or vegetation. We investigate how the calibration of parameters is affected by transient distributed Shallow Water model and the complexity of the problem. In the first part of this work, we calibrate the infiltration parameters for both Horton and Green-Ampt models under flat ponded soil conditions. Then, by means of synthetic test cases, we perform a space-distributed sensitivity analysis in order to show that this calibration can be significantly affected by the introduction of topography or rainfall. In the second part, parameter calibration for a real catchment is addressed by comparing the numerical simulations with two different sets of experimental data, corresponding to very different events in terms of the rainfall volume. We show that the initial conditions of the catchment and the rainfall pattern have a special relevance in the quality of the adjustment. Hence, it is shown that the topography of the catchment and the storm characteristics affect the calibration of infiltration parameters.

  3. 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

  4. Combining random forest and 2D correlation analysis to identify serum spectral signatures for neuro-oncology.

    PubMed

    Smith, Benjamin R; Ashton, Katherine M; Brodbelt, Andrew; Dawson, Timothy; Jenkinson, Michael D; Hunt, Neil T; Palmer, David S; Baker, Matthew J

    2016-06-01

    Fourier transform infrared (FTIR) spectroscopy has long been established as an analytical technique for the measurement of vibrational modes of molecular systems. More recently, FTIR has been used for the analysis of biofluids with the aim of becoming a tool to aid diagnosis. For the clinician, this represents a convenient, fast, non-subjective option for the study of biofluids and the diagnosis of disease states. The patient also benefits from this method, as the procedure for the collection of serum is much less invasive and stressful than traditional biopsy. This is especially true of patients in whom brain cancer is suspected. A brain biopsy is very unpleasant for the patient, potentially dangerous and can occasionally be inconclusive. We therefore present a method for the diagnosis of brain cancer from serum samples using FTIR and machine learning techniques. The scope of the study involved 433 patients from whom were collected 9 spectra each in the range 600-4000 cm(-1). To begin the development of the novel method, various pre-processing steps were investigated and ranked in terms of final accuracy of the diagnosis. Random forest machine learning was utilised as a classifier to separate patients into cancer or non-cancer categories based upon the intensities of wavenumbers present in their spectra. Generalised 2D correlational analysis was then employed to further augment the machine learning, and also to establish spectral features important for the distinction between cancer and non-cancer serum samples. Using these methods, sensitivities of up to 92.8% and specificities of up to 91.5% were possible. Furthermore, ratiometrics were also investigated in order to establish any correlations present in the dataset. We show a rapid, computationally light, accurate, statistically robust methodology for the identification of spectral features present in differing disease states. With current advances in IR technology, such as the development of rapid discrete

  5. 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

  6. Generalized two-dimensional (2D) linear system analysis metrics (GMTF, GDQE) for digital radiography systems including the effect of focal spot, magnification, scatter, and detector characteristics

    PubMed Central

    Kuhls-Gilcrist, Andrew T.; Gupta, Sandesh K.; Bednarek, Daniel R.; Rudin, Stephen

    2010-01-01

    The MTF, NNPS, and DQE are standard linear system metrics used to characterize intrinsic detector performance. To evaluate total system performance for actual clinical conditions, generalized linear system metrics (GMTF, GNNPS and GDQE) that include the effect of the focal spot distribution, scattered radiation, and geometric unsharpness are more meaningful and appropriate. In this study, a two-dimensional (2D) generalized linear system analysis was carried out for a standard flat panel detector (FPD) (194-micron pixel pitch and 600-micron thick CsI) and a newly-developed, high-resolution, micro-angiographic fluoroscope (MAF) (35-micron pixel pitch and 300-micron thick CsI). Realistic clinical parameters and x-ray spectra were used. The 2D detector MTFs were calculated using the new Noise Response method and slanted edge method and 2D focal spot distribution measurements were done using a pin-hole assembly. The scatter fraction, generated for a uniform head equivalent phantom, was measured and the scatter MTF was simulated with a theoretical model. Different magnifications and scatter fractions were used to estimate the 2D GMTF, GNNPS and GDQE for both detectors. Results show spatial non-isotropy for the 2D generalized metrics which provide a quantitative description of the performance of the complete imaging system for both detectors. This generalized analysis demonstrated that the MAF and FPD have similar capabilities at lower spatial frequencies, but that the MAF has superior performance over the FPD at higher frequencies even when considering focal spot blurring and scatter. This 2D generalized performance analysis is a valuable tool to evaluate total system capabilities and to enable optimized design for specific imaging tasks. PMID:21243038

  7. 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...

  8. 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.

  9. Source rock potential analysis using rock physics approach and 2D seismic data inversion: case study of Great Australian Bight

    NASA Astrophysics Data System (ADS)

    Shulakova, V.

    2015-12-01

    The quantity of total organic carbon (TOC) and its type determine the ability of source rocks to generate hydrocarbons. Thus, the quantification of TOC content is an essential part of any reservoir characterisation project. Traditionally TOC is estimated from geochemical analysis of core samples. In this case the results are limited spatially by a well location as well as vertically by a number of tested samples. At the same time TOC vertical variability might be very high, changing every 1-3 m. The several methods have been deployed to estimate TOC from well-log data which provides continuous vertical profile estimations. The basin wide information might be provided by the utilization of seismic surveys. The methodology of mapping source rocks based on seismic data has been lately reported to be successful for the thick source rocks (>20 m) with relatively high TOC values up to 3-4% (Løseth et al., 2011). We employ the described approach and demonstrate our findings for a case study from Ceduna Basin (Great Australian Bight, Australia). The reported TOC values estimated from the cores go up to only 1.3%. The organic matter is contained in thin layers of claystones interlayered with sandstones. The workflow included TOC estimation from the well-log data and then seismic data inversion performed in JasonTM software. The inverted acoustic impedance decreases nonlinearly with increasing TOC content. The obtained results comprises 2D section of TOC distribution. The calculated TOC values are in a good agreement with the results of laboratory measurements. The results of this study show that TOC can be successfully estimated from seismic data inversion even in the case of low organic matter values. Further work has to be done to understand whether this approach works for different types of organic matter and stages of its maturation. Løseth H., Wensaas L., Gading M., Duffaut K., Springer M. 2001. Can hydrocarbon source rocks be identified on seismic data? Geology 39/12.

  10. 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

  11. Digit Ratios (2D:4D) Determined by Computer-Assisted Analysis are More Reliable than Those Using Physical Measurements, Photocopies, and Printed Scans

    PubMed Central

    ALLAWAY, HEATHER C.; BLOSKI, TERRI G.; PIERSON, ROGER A.; LUJAN, MARLA E.

    2010-01-01

    Prenatal androgens influence the second to fourth digit ratio (2D:4D) of hands with men having lower ratios than women. Numerous methods are used to assess 2D:4D including, physical measurements with calipers, and measurements made from photocopies, scanned images, digital photographs, radiographs, and scaled tubes. Although each method appears relatively reliable, agreement upon a gold standard is necessary to better explore the putative effects of prenatal androgens. Our objective was to assess the level of intra and interobserver reliability when evaluating 2D:4D using four techniques: (1) physical measurements, (2) photocopies, (3) printed scanned images, and (4) computer-assisted image analysis. Physical measurements, photocopies, and printed scanned images were measured with Vernier calipers. Scanned images were also measured with computer-based calipers. Measurements were made in 30 men and 30 women at two different time points, by three experienced observers. Intraclass correlation coefficients were used to assess the level of reliability. Intraobserver reliability was best for computer-assisted (0.957), followed by photocopies (0.939), physical measurements (0.925), and printed scans (0.842; P = 0.015). Interobserver reliability was also greatest for computer-assisted (0.892), followed by photocopies (0.858), physical measurements (0.795), and printed scans (0.761; P = 0.001). Mean 2D:4D from physical measurements were higher than all other techniques (P < 0.0001). Digit ratios determined from computer-assisted, physical measurements, and printed scans were more reliable in men than women (P = 0.009, P = 0.017, and P = 0.012, respectively). In summary, 2D:4D determined from computer-assisted analysis yielded the most accurate and consistent measurements among observers. Investigations of 2D:4D should use computer-assisted measurements over alternate methods whenever possible. PMID:19263413

  12. VARSAT2D: Finite-element analysis of variably saturated two-dimensional flow. Information circular/1994

    SciTech Connect

    Nieber, J.L.; Friedel, M.J.; Munir, H.M.

    1994-01-01

    This information circular describes a computer program called VARSAT2D, a comprehensive unsaturated fluid flow simulator developed by the U.S. Bureau of Mines. VARSAT2D solves for either a vertical or horizontal, transient or steady-state solution in variably saturated, heterogeneous, anisotropic porous media using the Galerkin finite-element approach. Simplex triangular elements are used. Moisture retention characteristics are described by specifying either the Brooks and Corey, Brutsaert, or Van Genuchten power functions, with hysteresis described using the Maulem independent domain model. Boundary conditions may include any combination of time-varying seepage, pressure along solution domain boundaries and/or at internal node points, unit hydraulic gradient at the lower boundary, and a uniform source and/or sink. The program should be a welcome addition for mining and environmental hydrologists, researchers, and engineers interested in modeling unsaturated fluid flow.

  13. 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. PMID:24110125

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Proteomic Profiling of Macrophages by 2D Electrophoresis

    PubMed Central

    Bouvet, Marion; Turkieh, Annie; Acosta-Martin, Adelina E.; Chwastyniak, Maggy; Beseme, Olivia; Amouyel, Philippe; Pinet, Florence

    2014-01-01

    The goal of the two-dimensional (2D) electrophoresis protocol described here is to show how to analyse the phenotype of human cultured macrophages. The key role of macrophages has been shown in various pathological disorders such as inflammatory, immunological, and infectious diseases. In this protocol, we use primary cultures of human monocyte-derived macrophages that can be differentiated into the M1 (pro-inflammatory) or the M2 (anti-inflammatory) phenotype. This in vitro model is reliable for studying the biological activities of M1 and M2 macrophages and also for a proteomic approach. Proteomic techniques are useful for comparing the phenotype and behaviour of M1 and M2 macrophages during host pathogenicity. 2D gel electrophoresis is a powerful proteomic technique for mapping large numbers of proteins or polypeptides simultaneously. We describe the protocol of 2D electrophoresis using fluorescent dyes, named 2D Differential Gel Electrophoresis (DIGE). The M1 and M2 macrophages proteins are labelled with cyanine dyes before separation by isoelectric focusing, according to their isoelectric point in the first dimension, and their molecular mass, in the second dimension. Separated protein or polypeptidic spots are then used to detect differences in protein or polypeptide expression levels. The proteomic approaches described here allows the investigation of the macrophage protein changes associated with various disorders like host pathogenicity or microbial toxins. PMID:25408153

  20. 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

  1. A meshfree local RBF collocation method for anti-plane transverse elastic wave propagation analysis in 2D phononic crystals

    NASA Astrophysics Data System (ADS)

    Zheng, Hui; Zhang, Chuanzeng; Wang, Yuesheng; Sladek, Jan; Sladek, Vladimir

    2016-01-01

    In this paper, a meshfree or meshless local radial basis function (RBF) collocation method is proposed to calculate the band structures of two-dimensional (2D) anti-plane transverse elastic waves in phononic crystals. Three new techniques are developed for calculating the normal derivative of the field quantity required by the treatment of the boundary conditions, which improve the stability of the local RBF collocation method significantly. The general form of the local RBF collocation method for a unit-cell with periodic boundary conditions is proposed, where the continuity conditions on the interface between the matrix and the scatterer are taken into account. The band structures or dispersion relations can be obtained by solving the eigenvalue problem and sweeping the boundary of the irreducible first Brillouin zone. The proposed local RBF collocation method is verified by using the corresponding results obtained with the finite element method. For different acoustic impedance ratios, various scatterer shapes, scatterer arrangements (lattice forms) and material properties, numerical examples are presented and discussed to show the performance and the efficiency of the developed local RBF collocation method compared to the FEM for computing the band structures of 2D phononic crystals.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. CYP2D6*4 Allele Polymorphism Increases the Risk of Parkinson’s Disease: Evidence from Meta-Analysis

    PubMed Central

    Chen, Siyuan; Xie, Yantong; Peng, Qiliu; He, Yu; Deng, Yan; Wang, Jian; Xie, Li; Zeng, Jie; Li, Shan; Qin, Xue

    2013-01-01

    Background Many epidemiological studies have been conducted to explore the association between a single CYP2D6 gene polymorphism and Parkinson’s disease (PD) susceptibility. However, the results remain controversial. Objectives To clarify the effects of a single CYP2D6 gene polymorphism on the risk of PD, a meta-analysis of all available studies relating to CYP2D6*4 polymorphism and the risk of PD was conducted. Methods A comprehensive literature search of PubMed, EMBASE, and the China National Knowledge Infrastructure (CNKI) up to September 1, 2013 was conducted. Data were extracted by two independent authors and pooled odds ratio (OR) with 95% confidence interval (CI) were calculated. Meta-regression, Galbraith plots, subgroup analysis, sensitivity analysis, and publication bias analysis were also performed. Results Twenty-two separate comparisons consisting of 2,629 patients and 3,601 controls were included in our meta-analysis. The pooled analyses showed a significant association between CYP2D6*4G/A polymorphism and PD risk in all of the comparisons (A vs. G allele: OR = 1.28, 95% CI = 1.14–1.43, P = 0.001; AA vs. GG: OR = 1.43, 95% CI = 1.06–1.93, P = 0.018; AG vs. GG: OR = 1.22, 95% CI = 1.06–1.40, P = 0.006; AG+AA vs. GG: OR = 1.26, 95% CI = 1.10–1.44, P = 0.001; AA vs. AG+GG: OR = 1.37, 95% CI = 1.02–1.83, P = 0.036). In subgroup analysis stratified by ethnicity, significant associations were also demonstrated in Caucasians but not in Asians. No significant association was found in subgroup analysis stratified by age of onset or disease form. Conclusions We concluded that the CYP2D6*4G/A polymorphism denotes an increased genetic susceptibility to PD in the overall population, especially in Caucasians. Further large and well-designed studies are needed to confirm this association. PMID:24376807

  7. Single-Step Syngas-to-Distillates (S2D) Process Based on Biomass-Derived Syngas – A Techno-Economic Analysis

    SciTech Connect

    Zhu, Yunhua; Jones, Susanne B.; Biddy, Mary J.; Dagle, Robert A.; Palo, Daniel R.

    2012-08-01

    This study reports the comparison of biomass gasification based syngas-to-distillate (S2D) systems using techno-economic analysis (TEA). Three cases, state of technology (SOT) case, goal case, and conventional case, were compared in terms of performance and cost. The SOT case and goal case represent technology being developed at Pacific Northwest National Laboratory for a process starting with syngas using a single-step dual-catalyst reactor for distillate generation (S2D process). The conventional case mirrors the two-step S2D process previously utilized and reported by Mobil using natural gas feedstock and consisting of separate syngas-to-methanol and methanol-to-gasoline (MTG) processes. Analysis of the three cases revealed that the goal case could indeed reduce fuel production cost over the conventional case, but that the SOT was still more expensive than the conventional. The SOT case suffers from low one-pass yield and high selectivity to light hydrocarbons, both of which drive up production cost. Sensitivity analysis indicated that light hydrocarbon yield, single pass conversion efficiency, and reactor space velocity are the key factors driving the high cost for the SOT case.

  8. 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.

  9. A unified analysis of exact methods of inverting the 2-D exponential radon transform, with implications for noise control in SPECT

    SciTech Connect

    Metz, C.E.; Pan, X.

    1995-12-01

    Exact methods of inverting the two-dimensional (2-D) exponential Radon transform have been proposed by Bellini et al. and by Inouye et al., both of whom worked in the spatial-frequency domain to estimate the 2-D Fourier transform of the unattenuated sinogram; by Hawkins et al., who worked with circularly harmonic Bessel transforms; and by Tretiak and Metz, who followed filtering of appropriately-modified projections by exponentially-weighted backprojection. With perfect sampling, all four of these methods are exact in the absence of projection-data noise, but empirical studies have shown that they propagate noise differently, and no underlying theoretical relationship among the methods has been evident. In this paper, an analysis of the 2-D Fourier transform of the modified sinogram reveals that all previously-proposed linear methods can be interpreted as special cases of a broad class of methods, and that each method in the class can be implemented, in principle, by any one of four distinct techniques. Moreover, the analysis suggests a new member of the class that is predicted to have noise properties better than those of previously proposed members.

  10. Single-Step Syngas-to-Distillates (S2D) Process Based on Biomass-Derived Syngas - A Techno-Economic Analysis

    SciTech Connect

    Zhu, Y.; Jones, S. B.; Biddy, M. J.; Dagle, R. A.; Palo, D. R.

    2012-08-01

    This study compared biomass gasification based syngas-to-distillate (S2D) systems using techno-economic analysis (TEA). Three cases, state of technology (SOT), goal, and conventional, were compared in terms of performance and cost. The SOT case represented the best available experimental results for a process starting with syngas using a single-step dual-catalyst reactor for distillate generation. The conventional case mirrored a conventional two-step S2D process consisting of separate syngas-to-methanol and methanol-to-gasoline (MTG) processes. The goal case assumed the same performance as the conventional, but with a single-step S2D technology. TEA results revealed that the SOT was more expensive than the conventional and goal cases. The SOT case suffers from low one-pass yield and high selectivity to light hydrocarbons, both of which drive up production cost. Sensitivity analysis indicated that light hydrocarbon yield and single pass conversion efficiency were the key factors driving the high cost for the SOT case.

  11. 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.

  12. A Rapid and Efficient 2D/3D Nuclear Segmentation Method for Analysis of Early Mouse Embryo and Stem Cell Image Data

    PubMed Central

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

    2014-01-01

    Summary 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. PMID:24672759

  13. Aniso2D

    2005-07-01

    Aniso2d is a two-dimensional seismic forward modeling code. The earth is parameterized by an X-Z plane in which the seismic properties Can have monoclinic with x-z plane symmetry. The program uses a user define time-domain wavelet to produce synthetic seismograms anrwhere within the two-dimensional media.

  14. Towards 2D nanocomposites

    NASA Astrophysics Data System (ADS)

    Jang, Hyun-Sook; Yu, Changqian; Hayes, Robert; Granick, Steve

    2015-03-01

    Polymer vesicles (``polymersomes'') are an intriguing class of soft materials, commonly used to encapsulate small molecules or particles. Here we reveal they can also effectively incorporate nanoparticles inside their polymer membrane, leading to novel ``2D nanocomposites.'' The embedded nanoparticles alter the capacity of the polymersomes to bend and to stretch upon external stimuli.

  15. 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.

  16. Real-time texture analysis for identifying optimum microbubble concentration in 2-D ultrasonic particle image velocimetry.

    PubMed

    Niu, Lili; Qian, Ming; Yan, Liang; Yu, Wentao; Jiang, Bo; Jin, Qiaofeng; Wang, Yanping; Shandas, Robin; Liu, Xin; Zheng, Hairong

    2011-08-01

    Many recent studies on ultrasonic particle image velocimetry (Echo PIV) showed that the accuracy of two-dimensional (2-D) flow velocity measured depends largely on the concentration of ultrasound contrast agents (UCAs) during imaging. This article presents a texture-based method for identifying the optimum microbubble concentration for Echo PIV measurements in real-time. The texture features, standard deviation of gray level, and contrast, energy and homogeneity of gray level co-occurrence matrix were extracted from ultrasound contrast images of rotational and pulsatile flow (10 MHz) in vitro and in vivo mouse common carotid arterial flow (40 MHz) with UCAs at various concentrations. The results showed that, at concentration of 0.8∼2 × 10³ bubbles/mL in vitro and 1∼5 × 10⁵ bubbles/mL in vivo, image texture features had a peak value or trough value, and velocity vectors with high accuracy can be obtained. Otherwise, poor quality velocity vectors were obtained. When the texture features were used as a feature set, the accuracy of K-nearest neighbor classifier can reach 86.4% in vitro and 87.5% in vivo, respectively. The texture-based method is shown to be able to quickly identify the optimum microbubble concentration and improve the accuracy for Echo PIV imaging.

  17. Hetero Diels-Alder Reaction with Aqueous Glyoxylic Acid: An Experiment in Organic Synthesis and 2-D NMR Analysis for Advanced Undergraduate Students

    NASA Astrophysics Data System (ADS)

    Augé, Jacques; Lubin-Germain, Nadège

    1998-10-01

    As an application of the use of water as solvent in organic synthesis, a convenient synthesis of a-hydroxy-g-lactones from an aqueous solution of glyoxylic acid is described. The mechanism of the reaction leading to the lactones goes through cycloadducts which rearrange in situ. The NMR analysis of the diastereomeric lactones is particularly interesting; such an analysis illustrates the importance of modern techniques including 2-D NMR spectroscopy. Complete assignments of the signals are mentioned and NOESY spectra are enclosed. The full experiment is addressed to advanced undergraduate students who are trained in organic synthesis and NMR spectroscopy.

  18. Terahertz Spectroscopy and Global Analysis of the Bending Vibrations of ^{12}C_2H_2 and ^{12}C_2D_2

    NASA Astrophysics Data System (ADS)

    Yu, Shanshan; Drouin, Brian J.; Pearson, John C.; Pickett, Herbert M.; Lattanzi, Valerio; Walters, Adam

    2009-06-01

    Symmetric molecules have no permanent dipole moment and are undetectable by rotational spectroscopy. Their interstellar observations have previously been limited to mid-infrared vibration-rotation spectroscopy. Although relatively weak, vibrational difference bands provide a means for detection of non polar molecules by terahertz techniques with microwave precision. Herschel, SOFIA, and ALMA have the potential to identify a number of difference bands of light symmetric species, e.g., C_2H_2, CH_4 and C_3. This paper reports the results of the laboratory study on ^{12}C_2H_2 and ^{12}C_2D_2. The symmetric isotopomers of acetylene have two bending modes, the trans bending ν_4 (^1{π}_g), and the cis bending ν_5 (^1{π}_u). For ^{12}C_2H_2, the two bending modes occur at 612 and 729 cm^{-1}, respectively. For ^{12}C_2D_2, the two bending modes occur at 511 and 538 cm^{-1}. The ν_5-ν_4 difference bands are allowed and occur in the microwave, terahertz, and far-infrared wavelengths, with band origins at 117 cm^{-1} (3500 GHz) for ^{12}C_2H_2 and 27 cm^{-1} (900 GHz) for ^{12}C_2D_2. Two hundred and fifty-one ^{12}C_2D_2 transitions, which are from ν_5-ν_4, (ν_5+ν_4)-2ν_4 and 2ν_5-(ν_5+ν_4) bands, have been measured in the 0.2-1.6 THz region, and 202 of them were observed for the first time. The precision of these measurements is estimated to be from 50 kHz to 100 kHz. A multistate analysis was carried out for the bending vibrational modes ν_4 and ν_5 of ^{12}C_2D_2, which includes the lines observed in this work and prior microwave, far-infrared and infrared data on the pure bending levels. Significantly improved molecular parameters were obtained for ^{12}C_2D_2 by adding the new measurements to the old data set which had only 10 lines with microwave measurement precision. The experiments on ^{12}C_2H_2 are in progress and ten P branch lines have been observed. We will present the ^{12}C_2H_2 results to date.

  19. 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.

  20. Fast and high-resolution stereochemical analysis by nonuniform sampling and covariance processing of anisotropic natural abundance 2D 2H NMR datasets.

    PubMed

    Lafon, Olivier; Hu, Bingwen; Amoureux, Jean-Paul; Lesot, Philippe

    2011-06-01

    Natural abundance deuterium (NAD) 2D NMR spectroscopy using chiral or achiral liquid crystals is an efficient analytical tool for the stereochemical analysis of enantio- or diastereomers by the virtue of proton-to-deuterium substitution. In particular, it allows the measurement of enantiopurity of organic synthetic molecules or the determination of the natural isotopic (1)H/(2)H fractionation in biological molecules, such as fatty acid methyl esters (FAME). So far, the NAD 2D spectra of solutes were acquired by using uniform sampling (US) and processed by conventional 2D Fourier transform (FT), which could result in long measurement times for medium-sized analytes or low solute concentrations. Herein, we demonstrate that this conventional approach can be advantageously replaced by nonuniform sampling (NUS) processed by covariance (Cov) transform. This original spectral reconstruction provides a significant enhancement of spectral resolution, as well as a reduction of measurement times. The application of Cov to NUS data has required the introduction of a regularization procedure in the time domain for the indirect dimension. The analytical potential of combining Cov and NUS is demonstrated by measuring the enantiomeric excess of a scalemic mixture of 2-ethyloxirane and by determining the diastereomeric excess of methyl vernoleate, a natural FAME. These two organic compounds were aligned in a polypeptide (poly(γ-benzyl-L-glutamate)) mesophase. In the case of NAD 2D NMR spectroscopy, we show that Cov and NUS methods allow a decrease in measurement time by a factor of two compared with Cov applied to US data and a factor of four compared with FT applied to US data.

  1. Mesh2d

    2011-12-31

    Mesh2d is a Fortran90 program designed to generate two-dimensional structured grids of the form [x(i),y(i,j)] where [x,y] are grid coordinates identified by indices (i,j). The x(i) coordinates alone can be used to specify a one-dimensional grid. Because the x-coordinates vary only with the i index, a two-dimensional grid is composed in part of straight vertical lines. However, the nominally horizontal y(i,j0) coordinates along index i are permitted to undulate or otherwise vary. Mesh2d also assignsmore » an integer material type to each grid cell, mtyp(i,j), in a user-specified manner. The complete grid is specified through three separate input files defining the x(i), y(i,j), and mtyp(i,j) variations.« less

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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

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

    PubMed

    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

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

    PubMed

    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.

  11. NOTE: A software tool for 2D/3D visualization and analysis of phase-space data generated by Monte Carlo modelling of medical linear accelerators

    NASA Astrophysics Data System (ADS)

    Neicu, Toni; Aljarrah, Khaled M.; Jiang, Steve B.

    2005-10-01

    A computer program has been developed for novel 2D/3D visualization and analysis of the phase-space parameters of Monte Carlo simulations of medical accelerator radiation beams. The software is written in the IDL language and reads the phase-space data generated in the BEAMnrc/BEAM Monte Carlo code format. Contour and colour-wash plots of the fluence, mean energy, energy fluence, mean angle, spectra distribution, energy fluence distribution, angular distribution, and slices and projections of the 3D ZLAST distribution can be calculated and displayed. Based on our experience of using it at Massachusetts General Hospital, the software has proven to be a useful tool for analysis and verification of the Monte Carlo generated phase-space files. The software is in the public domain.

  12. 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

  13. Diagnostic Accuracy of 2D-Shear Wave Elastography for Liver Fibrosis Severity: A Meta-Analysis

    PubMed Central

    Jiang, Tian’an; Tian, Guo; Zhao, Qiyu; Kong, Dexing; Cheng, Chao; Zhong, Liyun; Li, Lanjuan

    2016-01-01

    Purpose To evaluate the accuracy of shear wave elastography (SWE) in the quantitative diagnosis of liver fibrosis severity. Methods The published literatures were systematically retrieved from PubMed, Embase, Web of science and Scopus up to May 13th, 2016. Included studies reported the pooled sensitivity, specificity, positive and negative predictive values, as well as the diagnostic odds ratio of SWE in populations with liver fibrosis. A bivariate mixed-effects regression model was used, which was estimated by the I2 statistics. The quality of articles was evaluated by quality assessment of diagnostic accuracy studies (QUADAS). Results Thirteen articles including 2303 patients were qualified for the study. The pooled sensitivity and specificity of SWE for the diagnosis of liver fibrosis are as follows: ≥F1 0.76 (p<0.001, 95% CI, 0.71–0.81, I2 = 75.33%), 0.92 (p<0.001, 95% CI, 0.80–0.97, I2 = 79.36%); ≥F2 0.84 (p = 0.35, 95% CI, 0.81–0.86, I2 = 9.55%), 0.83 (p<0.001, 95% CI, 0.77–0.88, I2 = 86.56%); ≥F3 0.89 (p = 0.56, 95% CI, 0.86–0.92, I2 = 0%), 0.86 (p<0.001, 95% CI, 0.82–0.90, I2 = 75.73%); F4 0.89 (p = 0.24, 95% CI, 0.84–0.92, I2 = 20.56%), 0.88 (p<0.001, 95% CI, 0.84–0.92, I2 = 82.75%), respectively. Sensitivity analysis showed no significant changes if any one of the studies was excluded. Publication bias was not detected in this meta-analysis. Conclusions Our study suggests that SWE is a helpful method to appraise liver fibrosis severity. Future studies that validate these findings would be appropriate. PMID:27300569

  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. 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.

  16. Near-infrared (NIR) imaging analysis of polylactic acid (PLA) nanocomposite by multiple-perturbation two-dimensional (2D) correlation spectroscopy

    NASA Astrophysics Data System (ADS)

    Shinzawa, Hideyuki; Murakami, Takurou N.; Nishida, Masakazu; Kanematsu, Wataru; Noda, Isao

    2014-07-01

    Multiple-perturbation two-dimensional (2D) correlation spectroscopy was applied to sets of near-infrared (NIR) imaging data of polylactic acid (PLA) nanocomposite samples undergoing UV degradation. Incorporation of clay nanoparticles substantially lowers the surface free energy barrier for the nucleation of PLA and eventually increases the frequency of the spontaneous nucleation of PLA crystals. Thus, when exposed to external stimuli such as UV light, PLA nanocomposite may show different structure alternation depending on the clay dispersion. Multiple-perturbation 2D correlation analysis of the PLA nanocomposite samples revealed different spatial variation between crystalline and amorphous structure of PLA, and the phenomenon especially becomes acute in the region where the clay particles are coagulated. The incorporation of the clay leads to the cleavage-induced crystallization of PLA when the sample is subjected to the UV light. The additional development of the ordered crystalline structure then works favorably to restrict the initial degradation of the polymer, providing the delay in the weight loss of the PLA.

  17. [Analysis and identification of Poria cocos peels harvested from different producing areas by FTIR and 2D-IR correlation spectroscopy].

    PubMed

    Ma, Fang; Zhang, Fang; Tang, Jin; Chen, Ping; Chen, Jian-Bo; Zhou, Qun; Sun, Su-Qin

    2014-02-01

    Different geographical regions of traditional Chinese medicine (TCM), its chemical composition is different, the accumulation of drug and medicinal properties is different. The accurate identification and analysis of different production area of medicinal herbs is critical for the quality control and pharmacological research of TCM. In this paper, a tri-step infrared spectroscopy (Fourier transform infrared spectroscopy (FTIR) combined with second derivative spectra and two-dimensional correlation infrared spectroscopy (2D-COS) were employed to identify and analyze the main components of Hubei (HB), Anhui (AH), Yun-nan (YN) genuine Poria Cocos peels. The emergence of several characteristic absorption peaks of carbohydrates including 1149, 1079 1036 cm(-1), peaks around 1619, 1315, 780 cm(-1) belonged to calcium oxalate suggested that HB and AH Poria Cocos peels contained calcium oxalate, but peaks around 797, 779, 537, 470 cm(-1) belonged to kaoline suggested that YN Poria Cocos peels contained kaoline. Their carbohydrates were different by comparing the second derivative infrared spectra in the range of 1640-450 cm(-1) and Yongping come from YN contains both calcium oxalate and kaoline. Furthermore, the above differences were visually validated by two-dimensional correlation spectroscopy (2D-COS). It was demonstrated that the Tri-step infrared spectroscopy were successfully applied to fast analyze and identify Poria Cocos peels from different geographical regions and subsequently would be applicable to explain the relevance of geographical regions and medicinal properties for the TCM.

  18. 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.

  19. 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. PMID:17499878

  20. 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.

  1. 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.

  2. 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.

  3. A quantitative analysis of 2-D gels identifies proteins in which labeling is increased following long-term sensitization in Aplysia

    SciTech Connect

    Castellucci, V.F.; Kennedy, T.E.; Kandel, E.R.; Goelet, P. )

    1988-06-01

    Long-term memory for sensitization of the gill- and siphon-withdrawal reflex in Aplysia, produced by 4 days of training, is associated with increased synaptic efficacy of the connection between the sensory and motor neurons. This training is also accompanied by neuronal growth; there is an increase in the number of synaptic varicosities per sensory neuron and in the number of active zones. Such structural changes may be due to changes in the rates of synthesis of certain proteins. We have searched for proteins in which the rates of ({sup 35}S)methionine labeling are altered during the maintenance phase of long-term memory for sensitization by using computer-assisted quantitative 2-D gel analysis. This method has allowed us to detect 4 proteins in which labeling is altered after 4 days of sensitization training.

  4. 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).

  5. 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

  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 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

  8. 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

  9. 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

  10. Internal Photoemission Spectroscopy of 2-D Materials

    NASA Astrophysics Data System (ADS)

    Nguyen, Nhan; Li, Mingda; Vishwanath, Suresh; Yan, Rusen; Xiao, Shudong; Xing, Huili; Cheng, Guangjun; Hight Walker, Angela; Zhang, Qin

    Recent research has shown the great benefits of using 2-D materials in the tunnel field-effect transistor (TFET), which is considered a promising candidate for the beyond-CMOS technology. The on-state current of TFET can be enhanced by engineering the band alignment of different 2D-2D or 2D-3D heterostructures. Here we present the internal photoemission spectroscopy (IPE) approach to determine the band alignments of various 2-D materials, in particular SnSe2 and WSe2, which have been proposed for new TFET designs. The metal-oxide-2-D semiconductor test structures are fabricated and characterized by IPE, where the band offsets from the 2-D semiconductor to the oxide conduction band minimum are determined by the threshold of the cube root of IPE yields as a function of photon energy. In particular, we find that SnSe2 has a larger electron affinity than most semiconductors and can be combined with other semiconductors to form near broken-gap heterojunctions with low barrier heights which can produce a higher on-state current. The details of data analysis of IPE and the results from Raman spectroscopy and spectroscopic ellipsometry measurements will also be presented and discussed.

  11. PCaAnalyser: a 2D-image analysis based module for effective determination of prostate cancer progression in 3D culture.

    PubMed

    Hoque, Md Tamjidul; Windus, Louisa C E; 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.

  12. Ontology analysis of global gene expression differences of human bone marrow stromal cells cultured on 3D scaffolds or 2D films.

    PubMed

    Baker, Bryan A; Pine, P Scott; Chatterjee, Kaushik; Kumar, Girish; Lin, Nancy J; McDaniel, Jennifer H; Salit, Marc L; Simon, Carl G

    2014-08-01

    Differences in gene expression of human bone marrow stromal cells (hBMSCs) during culture in three-dimensional (3D) nanofiber scaffolds or on two-dimensional (2D) films were investigated via pathway analysis of microarray mRNA expression profiles. Previous work has shown that hBMSC culture in nanofiber scaffolds can induce osteogenic differentiation in the absence of osteogenic supplements (OS). Analysis using ontology databases revealed that nanofibers and OS regulated similar pathways and that both were enriched for TGF-β and cell-adhesion/ECM-receptor pathways. The most notable difference between the two was that nanofibers had stronger enrichment for cell-adhesion/ECM-receptor pathways. Comparison of nanofibers scaffolds with flat films yielded stronger differences in gene expression than comparison of nanofibers made from different polymers, suggesting that substrate structure had stronger effects on cell function than substrate polymer composition. These results demonstrate that physical (nanofibers) and biochemical (OS) signals regulate similar ontological pathways, suggesting that these cues use similar molecular mechanisms to control hBMSC differentiation. PMID:24840613

  13. 2D FTLE in 3D Flows: The accuracy of using two-dimensional data for Lagrangian analysis in a three-dimensional turbulent channel simulation

    NASA Astrophysics Data System (ADS)

    Rockwood, Matthew; Green, Melissa

    2012-11-01

    In experimental, three-dimensional vortex-dominated flows, common particle image velocimetry (PIV) data is often collected in only the plane of interest due to equipment constraints. For flows with significant out of plane velocities or velocity gradients, this can create large discrepancies in Lagrangian analyses that require accurate particle trajectories. A Finite Time Lyapunov Exponent (FTLE) analysis is one such example, and has been shown to be very powerful at examining vortex dynamics and interactions in a variety of aperiodic flows. In this work, FTLE analysis of a turbulent channel simulation was conducted using both full three-dimensional velocity data and modified planar data extracted from the same computational domain. When the out of plane velocity component is neglected the difference in FTLE fields is non-trivial. A quantitative comparison and computation of error is presented for several planes across the width of the channel to determine the efficacy of using 2D analyses on the inherently 3D flows.

  14. 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.

  15. 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.

  16. 2-d Finite Element Code Postprocessor

    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 forcesmore » 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.« less

  17. A novel phosphoprotein analysis scheme for assessing changes in premalignant and malignant breast cell lines using 2D liquid separations, protein microarrays and tandem mass spectrometry

    PubMed Central

    Patwa, Tasneem H.; Wang, Yanfei; Miller, Fred R.; Goodison, Steve; Pennathur, Subramaniam; Barder, Timothy J.; Lubman, David M.

    2008-01-01

    An analysis of phosphorylation changes that occur during cancer progression would provide insights into the molecular pathways responsible for a malignant phenotype. In this study we employed a novel coupling of 2D-liquid separations and protein microarray technology to reveal changes in phosphoprotein status between premalignant (AT1) and malignant (CA1a) cell lines derived from the human MCF10A breast cell lines. Intact proteins were first separated according to their isoelectric point and hydrophobicities, then arrayed on SuperAmine glass slides. Phosphoproteins were detected using the universal, inorganic phospho-sensor dye, ProQ Diamond. Using this dye, out of 140 spots that were positive for phosphorylation, a total of 85 differentially expressed spots were detected over a pH range of 7.2 to 4.0. Proteins were identified and their peptides sequenced by mass spectrometry. The strategy enabled the identification of 75 differentially expressed phosphoproteins, from which 51 phosphorylation sites in 27 unique proteins were confirmed. Interestingly, the majority of differentially expressed phosphorylated proteins observed were nuclear proteins. Three regulators of apoptosis, Bad, Bax and Acinus, were also differentially phosphorylated in the two cell lines. Further development of this strategy will facilitate an understanding of the mechanisms involved in malignancy progression and other disease-related phenotypes. PMID:19194518

  18. Analysis of NAD 2D-NMR spectra of saturated fatty acids in polypeptide aligning media by experimental and modeling approaches.

    PubMed

    Serhan, Zeinab; Borgogno, Andrea; Billault, Isabelle; Ferrarini, Alberta; Lesot, Philippe

    2012-01-01

    The overall and detailed elucidation (including the stereochemical aspects) of enzymatic mechanisms requires the access to all reliable information related to the natural isotopic fractionation of both precursors and products. Natural abundance deuterium (NAD) 2D-NMR experiments in polypeptide liquid-crystalline solutions are a new, suitable tool for analyzing site-specific deuterium isotopic distribution profiles. Here this method is utilized for analyzing saturated C14 to C18 fatty acid methyl esters (FAMEs), which are challenging because of the crowding of signals in a narrow spectral region. Experiments in achiral and chiral oriented solutions were performed. The spectral analysis is supplemented by the theoretical prediction of quadrupolar splittings as a function of the geometry and flexibility of FAMEs, based on a novel computational methodology. This allows us to confirm the spectral assignments, while providing insights into the mechanism of solute ordering in liquid-crystalline polypeptide solutions. This is found to be dominated by steric repulsions between FAMEs and polypeptides.

  19. 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.

  20. 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. PMID:26209290

  1. Interaction network and mass spectrometry data of Xanthomonas citri subsp. citri surface proteins from differential proteomic analysis of infectious and non-infectious cells.

    PubMed

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

    2016-09-01

    Here we provide the mass-spectrometry and in silico interaction network dataset of proteins identified on our research article on surface proteomic analysis from Xanthomonas citri subsp. citri (XAC) cells grown in vivo (infectious) and in vitro (non-infectious, control) by 2D-DIGE approach. Fluorescence labeling of proteins were performed on intact cells followed by cellular lysis and labeled spots from 2D gel differing in abundance between the two conditions (ANOVA, p-value<0.05) were analyzed by a nano-electrospray tandem mass spectrometry Q-Tof Ultima API mass spectrometer (MicroMass/Waters) (LC-ESI-MS/MS). This article contains raw data of proteins detected in the 79 spots analyzed by LC-ESI-MS/MS approach and also an enrichment analysis on the resulting protein-protein interaction network performed with the Integrated Interactome System (IIS) platform and Cytoscape software. The data are supplementary to our original research article, "Xanthomonas citri subsp. citri surface proteome by 2D-DIGE: ferric enterobactin receptor and other outer membrane proteins potentially involved in citric host interaction" (Carnielli et al., 2016) [1], and raw data are available via Peptide Atlas (ftp://PASS00850:ZJ7425v@ftp.peptideatlas.org/). PMID:27595129

  2. Basement and Basin Structures of the Northwest Paraná Basin, Brazil: Illuminated by Matched-Filter Analysis and 2D Modeling of Gravity and Magnetic Data

    NASA Astrophysics Data System (ADS)

    Curto, J. B.; Blakely, R. J.; Vidotti, R. M.; Fuck, R. A.

    2015-12-01

    The South American Platform includes two major geological components with common structural roots: the Transbrasiliano Lineament (LTB) and the Paraná Basin. Important relationships between the two components occur within the northwest Paraná Basin and concealed beneath sedimentary cover. We integrated all available airborne magnetic and gravity surveys and ground-based gravity data to produce consistent, digital magnetic and Bouguer anomaly maps. Data-processing and modeling techniques then were used in order to reveal principal crustal compartments and basin-basement structures at various depths. Three large magnetic discontinuities delineate crustal compartments in the area with N30°E, N60°E, and N70°E strike, from east to west, respectively. These magnetic lineaments bound regions with distinct gravity anomaly character. Robust matched-filter analysis applied to magnetic and gravity data yielded important depth estimates: (i) 2.5 km to the top of the Paraná Basin Neoproterozoic basement; (ii) 4-6 km to the top of a second group of basement units; (iii) 20 km, possibly associated with the upper-lower crust interface; and (iv) 33-39 and 43 km related to crustal thicknesses west and southeast of a major N30°E trending lineament, respectively. The 2D joint modeling of gravity and magnetic data sheds light on the asymmetric geometry of the basement beneath the Paraná basin, with at least three half-grabens formed by LTB reactivated structures. The central region of the study area is characterized by thinner crust and higher crustal weakness, where important structures have developed in the Mesozoic, including NW trending reactivations, linked to crustal uplift and evolution of small NE-aligned Cretaceous basins. Important depocenters occur to the north and east of the study area, with N70ºE and N30°E - NS strike, respectively.

  3. Ultrafast 2D IR microscopy

    PubMed Central

    Baiz, Carlos R.; Schach, Denise; Tokmakoff, Andrei

    2014-01-01

    We describe a microscope for measuring two-dimensional infrared (2D IR) spectra of heterogeneous samples with μm-scale spatial resolution, sub-picosecond time resolution, and the molecular structure information of 2D IR, enabling the measurement of vibrational dynamics through correlations in frequency, time, and space. The setup is based on a fully collinear “one beam” geometry in which all pulses propagate along the same optics. Polarization, chopping, and phase cycling are used to isolate the 2D IR signals of interest. In addition, we demonstrate the use of vibrational lifetime as a contrast agent for imaging microscopic variations in molecular environments. PMID:25089490

  4. Analysis of genetic variations in CYP2C9, CYP2C19, CYP2D6 and CYP3A5 genes using oligonucleotide microarray

    PubMed Central

    Dong, Yuanyuan; Xiao, Huasheng; Wang, Qi; Zhang, Chunxiu; Liu, Xiuming; Yao, Na; Sheng, Haihui; Li, Haiyan

    2015-01-01

    The cytochrome P450 enzymes play a critical role in the metabolism of many commonly prescribed drugs. Among them, the most important enzymes are highly polymorphic CYP2C9, CYP2C19, CYP2D6 and CYP3A5, which are responsible for about 40% of the metabolism of clinical used drugs. Here we developed a novel CYP450 oligonucleotide microarray that allow for detection of 32 known variations of CYP genes from a single multiplex reaction, including 19 polymorphisms of CYP2D6 gene, 8 polymorphisms of CYP2C9 gene, 4 polymorphisms of CYP2C19 gene and 1 polymorphism of CYP3A5 gene. 229 genomic DNA samples from unrelated Han subjects were analyzed. The microarray results showed to have high call rate and accuracy according to concordance with genotypes identified by independent bidirectional sequencing. Furthermore, we found that the major CYP2C9, CYP2C19, CYP2D6 and CYP3A5 alleles in Chinese Han population were CYP2C9*3 (allelic frequency of 10.7%), CYP2C9*2 (20.31%), CYP2C19*2 (5.68%), CYP2D6*10 (58.52%), CYP2D6*2 (13.76) and CYP3A5*3 (70.69%). With flexible DNA preparation, the microarray can significantly facilitates the process of detecting genetics variations in CYP2C9, CYP2C19, CYP2D6 and CYP3A5 gene and provide safe and effective therapy for individual patients. PMID:26770516

  5. 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

  6. 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

  7. 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

  8. AnisWave 2D

    2004-08-01

    AnisWave2D is a 2D finite-difference code for a simulating seismic wave propagation in fully anisotropic materials. The code is implemented to run in parallel over multiple processors and is fully portable. A mesh refinement algorithm has been utilized to allow the grid-spacing to be tailored to the velocity model, avoiding the over-sampling of high-velocity materials that usually occurs in fixed-grid schemes.

  9. 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...

  10. 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

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. Morphologic Analysis of the Temporomandibular Joint Between Patients With Facial Asymmetry and Asymptomatic Subjects by 2D and 3D Evaluation: A Preliminary Study.

    PubMed

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

    2016-03-01

    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

  16. Modal analysis of delaminated composite plates using the finite element method and damage detection via combined Ritz/2D-wavelet analysis

    NASA Astrophysics Data System (ADS)

    Gallego, A.; Moreno-García, P.; Casanova, Cesar F.

    2013-06-01

    Structural studies to find defects (in particular delaminations) in composite plates have been very prevalent in the Structural Health Monitoring field. The present work develops a new method to detect delaminations in CFRP (Carbon Fiber Reinforced Polymer) plates. In this paper the method is validated with numerical simulations, which come to support its adequacy for use with real acquisition data. This is done firstly through the implementation of a delaminated plate finite element. Using the classical lamination plate theory, delamination is considered in the kinematic equations through jump functions and additional degrees of freedom. The element allows the introduction of nd delaminations through its thickness. Classical QMITC (Quadrilateral Mixed Interpolation Tensorial Components) and DKQ (Discrete Kirchhoff Quadrilateral) elements are used for the membrane and bending FEM (Finite Element Method) formulation. Second, using the vibration modes obtained with the FEM, a damage location technique based on the variational Ritz method and Wavelet Analysis is proposed. The approach has the advantage of requiring only damaged modes and not the healthy ones. Both FEM simulations and Ritz/Wavelet damage detection schemes are applied in an orthotropic CFRP plate with the stacking sequence [0/90]3S. In addition, the influence of delamination thickness position, boundary conditions and added noise (in order to simulate experimental measures) was studied.

  17. 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.

  18. DYNA2D96. Explicit 2-D Hydrodynamic FEM Program

    SciTech Connect

    Whirley, R.G.

    1992-04-01

    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.

  19. Analysis of bell-shape negative giant-magnetoresistance in high mobility GaAs/AlGaAs 2D electron systems using multi-conduction model

    NASA Astrophysics Data System (ADS)

    Samaraweera, Rasanga; Liu, Han-Chun; Wegscheider, Werner; Mani, Ramesh

    Recent advancements in the growth techniques of the GaAs/AlGaAs two dimensional electron system (2DES) routinely yield high quality heterostructures with enhanced physical and electrical properties, including devices with 2D electron mobilities well above 107 cm2/Vs. These improvements have opened new pathways to study interesting physical phenomena associated with the 2D electron system. Negative giant-magnetoresistance (GMR) is one such phenomenon which can observed in the high mobility 2DES. However, the negative GMR in the GaAs/AlGaAs 2DES is still not fully understood. In this contribution, we present an experimental study of the bell-shape negative GMR in high mobility GaAs/AlGaAs devices and quantitatively analyze the results utilizing the multi-conduction model. The multi-conduction model includes interesting physical characteristics such as negative diagonal conductivity, non-vanishing off-diagonal conductivity, etc. The aim of the study is to examine GMR over a wider experimental parameter space and determine whether the multi-conduction model serves to describe the experimental results.

  20. MOSS2D V1

    2001-01-31

    This software reduces the data from two-dimensional kSA MOS program, k-Space Associates, Ann Arbor, MI. Initial MOS data is recorded without headers in 38 columns, with one row of data per acquisition per lase beam tracked. The final MOSS 2d data file is reduced, graphed, and saved in a tab-delimited column format with headers that can be plotted in any graphing software.

  1. 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

  2. 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

  3. A systematic analysis of the effects of increasing degrees of serum immunodepletion in terms of depth of coverage and other key aspects in top-down and bottom-up proteomic analyses

    PubMed Central

    Smith, Matthew P Welberry; Wood, Steven L; Zougman, Alexandre; Ho, Jenny T C; Peng, Jianhe; Jackson, David; Cairns, David A; Lewington, Andrew J P; Selby, Peter J; Banks, Rosamonde E

    2011-01-01

    Immunodepletion of clinical fluids to overcome the dominance by a few very abundant proteins has been explored but studies are few, commonly examining only limited aspects with one analytical platform. We have systematically compared immunodepletion of 6, 14, or 20 proteins using serum from renal transplant patients, analysing reproducibility, depth of coverage, efficiency, and specificity using 2-D DIGE (‘top-down’) and LC-MS/MS (‘bottom-up’). A progressive increase in protein number (≥2 unique peptides) was found from 159 in unfractionated serum to 301 following 20 protein depletion using a relatively high-throughput 1-D-LC-MS/MS approach, including known biomarkers and moderate–lower abundance proteins such as NGAL and cytokine/growth factor receptors. On the contrary, readout by 2-D DIGE demonstrated good reproducibility of immunodepletion, but additional proteins seen tended to be isoforms of existing proteins. Depletion of 14 or 20 proteins followed by LC-MS/MS showed excellent reproducibility of proteins detected and a significant overlap between columns. Using label-free analysis, greater run-to-run variability was seen with the Prot20 column compared with the MARS14 column (median %CVs of 30.9 versus 18.2%, respectively) and a corresponding wider precision profile for the Prot20. These results illustrate the potential of immunodepletion followed by 1-D nano-LC-LTQ Orbitrap Velos analysis in a moderate through-put biomarker discovery process. PMID:21548096

  4. 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

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

    PubMed

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

    2016-05-13

    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

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

    PubMed

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

    2016-05-13

    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.

  7. WFR-2D: an analytical model for PWAS-generated 2D ultrasonic guided wave propagation

    NASA Astrophysics Data System (ADS)

    Shen, Yanfeng; Giurgiutiu, Victor

    2014-03-01

    This paper presents WaveFormRevealer 2-D (WFR-2D), an analytical predictive tool for the simulation of 2-D ultrasonic guided wave propagation and interaction with damage. The design of structural health monitoring (SHM) systems and self-aware smart structures requires the exploration of a wide range of parameters to achieve best detection and quantification of certain types of damage. Such need for parameter exploration on sensor dimension, location, guided wave characteristics (mode type, frequency, wavelength, etc.) can be best satisfied with analytical models which are fast and efficient. The analytical model was constructed based on the exact 2-D Lamb wave solution using Bessel and Hankel functions. Damage effects were inserted in the model by considering the damage as a secondary wave source with complex-valued directivity scattering coefficients containing both amplitude and phase information from wave-damage interaction. The analytical procedure was coded with MATLAB, and a predictive simulation tool called WaveFormRevealer 2-D was developed. The wave-damage interaction coefficients (WDICs) were extracted from harmonic analysis of local finite element model (FEM) with artificial non-reflective boundaries (NRB). The WFR-2D analytical simulation results were compared and verified with full scale multiphysics finite element models and experiments with scanning laser vibrometer. First, Lamb wave propagation in a pristine aluminum plate was simulated with WFR-2D, compared with finite element results, and verified by experiments. Then, an inhomogeneity was machined into the plate to represent damage. Analytical modeling was carried out, and verified by finite element simulation and experiments. This paper finishes with conclusions and suggestions for future work.

  8. Static & Dynamic Response of 2D Solids

    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 surfacemore » 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.« less

  9. 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.

  10. Form finding and analysis of extensible membranes attached to 2-D and 3-D frames intended for micro air vehicles via experimentally validated finite element methods

    NASA Astrophysics Data System (ADS)

    Abudaram, Yaakov Jack

    This work is concerned with a new method to apply consistent and known pretension to silicone rubber membranes intended for micro air vehicles as well as an understanding in the science of developed pre-tension in membranes constrained by 2- D and 3-D frames and structures. Pre-tension has a marked effect on the static and dynamic response of membrane wings and controls the overall deflections, as such control and measurement of the membrane pre-tension is important. Two different 2-D frame geometries were fabricated to evaluate the technique. For open-cell frames, the pretension was not uniform, whereas it was for closed-cell frames. Results show developed full-field stress and strain fields as a function of membrane attachment temperature and frame geometry along with experimental iterations to prove repeatability. The membranes can be stretched to a specific pretension according to the temperature at which it adheres to frames. Strain fields in membranes attached to 3-D frames at various temperatures are modeled through FEA utilizing Abaqus to be able to predict the developed membrane deformations, stresses, and strains. Rigid frames with various curvatures are built via appropriate molds and then adhered to silicone rubber membranes and elevated to various temperatures to achieve different pre-strains for experimental validation. Additional experiments are conducted for more complex frame geometries involving both convex and concave topologies embedded within frames. Results are then compared with the Abaqus outputs to validate the accuracy of the FEA model. Highly compliant wings have been used for MAV platforms, where the wing structure is determined by some combination of carbon fiber composites and a membrane skin, adhered in between the layers of composite material. Another new technique of attaching membranes firmly on wing structures is introduced, which involves the application of a technology known as corona treatment coupled with another method of

  11. Probabilistic hazard analysis of dense Pyroclastic Density Currents at Vesuvius (Italy) via parametric uncertainty characterization of TITAN2D numerical simulator

    NASA Astrophysics Data System (ADS)

    Tierz, Pablo; Ramona Stefanescu, Elena; Sandri, Laura; Patra, Abani; Marzocchi, Warner; Sulpizio, Roberto

    2014-05-01

    Probabilistic hazard assessments of Pyroclastic Density Currents (PDCs) are of great interest for decision-making purposes. However, there is a limited number of published works available on this topic. Recent advances in computation and statistical methods are offering new opportunities beyond the classical Monte Carlo (MC) sampling which is known as a simple and robust method but it usually turns out to be slow and computationally intractable. In this work, Titan2D numerical simulator has been coupled to Polynomial Chaos Quadrature (PCQ) to propagate the simulator parametric uncertainty and compute VEI-based probabilistic hazard maps of dense PDCs formed as a result of column collapse at Vesuvius volcano, Italy. Due to the lack of knowledge about the exact conditions under which these PDCs will form, Probability Distribution Functions (PDFs) are assigned to the simulator input parameters (Bed Friction Angle and Volume) according to three VEI sizes. Uniform distributions were used for both parameters since there is insufficient information to assume that any value in the range is more likely that any other value. Reasonable (and compatible) ranges for both variables were constrained according to past eruptions at Vesuvius volcanic system. On the basis of reasoning above a number of quadrature points were taken within those ranges, which resulted in one execution of the TITAN2D code at each quadrature point. With a computational cost several orders of magnitude smaller than MC, exceedance probabilities for a given threshold of flow depth (and conditional to the occurrence of VEI3, VEI4 and VEI5 eruptions) were calculated using PCQ. Moreover, PCQ can be run at different threshold values of the same output variable (flow depth, speed, kinetic energy, …) and, therefore, it can serve to compute Exceedance Probability curves (aka hazard curves) at singular points inside the hazard domain, representing the most important and useful scientific input to quantitative risk

  12. 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.

  13. Kinematic Analysis of Healthy Hips during Weight-Bearing Activities by 3D-to-2D Model-to-Image Registration Technique

    PubMed Central

    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. PMID:25506056

  14. 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.

  15. MAGNUM-2D computer code: user's guide

    SciTech Connect

    England, R.L.; Kline, N.W.; Ekblad, K.J.; Baca, R.G.

    1985-01-01

    Information relevant to the general use of the MAGNUM-2D computer code is presented. This computer code was developed for the purpose of modeling (i.e., simulating) the thermal and hydraulic conditions in the vicinity of a waste package emplaced in a deep geologic repository. The MAGNUM-2D computer computes (1) the temperature field surrounding the waste package as a function of the heat generation rate of the nuclear waste and thermal properties of the basalt and (2) the hydraulic head distribution and associated groundwater flow fields as a function of the temperature gradients and hydraulic properties of the basalt. MAGNUM-2D is a two-dimensional numerical model for transient or steady-state analysis of coupled heat transfer and groundwater flow in a fractured porous medium. The governing equations consist of a set of coupled, quasi-linear partial differential equations that are solved using a Galerkin finite-element technique. A Newton-Raphson algorithm is embedded in the Galerkin functional to formulate the problem in terms of the incremental changes in the dependent variables. Both triangular and quadrilateral finite elements are used to represent the continuum portions of the spatial domain. Line elements may be used to represent discrete conduits. 18 refs., 4 figs., 1 tab.

  16. Identification of differentially expressed proteins in blood plasma of control and cigarette smoke-exposed mice by 2D differential in-gel electrophoresis/MS

    PubMed Central

    Tewari, Arun K.; Popova-Butler, Alexandra; El-Mahdy, Mohamed A.; Zweier, Jay L.

    2014-01-01

    Cigarette smoke exposure is known to induce obstructive lung disease and several cardiovascular disease states in humans and also in animal models. Smoking leads to oxidative stress and inflammation that are important in triggering pulmonary and cardiovascular disease. The objective of the current study was to quantify differences in expression levels of plasma proteins of cigarette smoke exposed and control mice, at the time of disease onset, and identify these proteins for use as potential biomarkers of the onset of smoking-induced disease. We utilized two dimensional difference in-gel electrophoresis/ mass spectroscopy (2D-DIGE/MS) to characterize these proteomic changes. 2D-DIGE of plasma samples identified 11 differentially expressed proteins in cigarette smoke exposed mice. From these 11 proteins, 9 were down-regulated and two were up-regulated. The proteins identified are involved in vascular function, coagulation, metabolism, and immune function. Among these, the alterations in fibrinogen (2.2 fold decrease), alpha-1-antitrypsin (1.8 fold increase) and arginase (4.5 fold decrease) are of particular interest since these have been directly linked to cardiovascular and lung pathology. Differences in expression levels of these proteins were also confirmed by immunoblotting. Thus, we observe that chronic cigarette smoke exposure in mice leads to prominent changes in the protein expression profile of blood plasma and these changes in turn can potentially serve as markers predictive of the onset and progression of cardiovascular and pulmonary disease. PMID:21500341

  17. 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.

  18. 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

  19. CYP2D6: novel genomic structures and alleles

    PubMed Central

    Kramer, Whitney E.; Walker, Denise L.; O’Kane, Dennis J.; Mrazek, David A.; Fisher, Pamela K.; Dukek, Brian A.; Bruflat, Jamie K.; Black, John L.

    2010-01-01

    Objective CYP2D6 is a polymorphic gene. It has been observed to be deleted, to be duplicated and to undergo recombination events involving the CYP2D7 pseudogene and surrounding sequences. The objective of this study was to discover the genomic structure of CYP2D6 recombinants that interfere with clinical genotyping platforms that are available today. Methods Clinical samples containing rare homozygous CYP2D6 alleles, ambiguous readouts, and those with duplication signals and two different alleles were analyzed by long-range PCR amplification of individual genes, PCR fragment analysis, allele-specific primer extension assay, and DNA sequencing to characterize alleles and genomic structure. Results Novel alleles, genomic structures, and the DNA sequence of these structures are described. Interestingly, in 49 of 50 DNA samples that had CYP2D6 gene duplications or multiplications where two alleles were detected, the chromosome containing the duplication or multiplication had identical tandem alleles. Conclusion Several new CYP2D6 alleles and genomic structures are described which will be useful for CYP2D6 genotyping. The findings suggest that the recombination events responsible for CYP2D6 duplications and multiplications are because of mechanisms other than interchromosomal crossover during meiosis. PMID:19741566

  20. 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

  1. Two new Cu(ii) and La(iii) 2D coordination polymers, synthesis and in situ structural analysis by X-ray diffraction.

    PubMed

    Lundvall, F; Wragg, D S; Dietzel, P D C; Fjellvåg, H

    2016-08-01

    Two new coordination polymers were synthesized solvothermally using 4,4'-dimethoxy-3,3'-biphenyldicarboxylic acid (H2dmbpdc), and di- and trivalent metal salts (Cu(NO3)2·2.5H2O and La(NO3)3·6H2O). Their structures were determined by single-crystal X-ray diffraction analysis, and their thermal stability was evaluated by thermogravimetric analysis. The copper compound Cu(dmbpdc)(DMF; N,N-dimethylformamide), CPO-71-Cu, is based on the well known copper acetate paddlewheel secondary building unit. The asymmetric unit comprises one copper cation with one DMF molecule and one linker molecule coordinated. The lanthanum compound La2(dmbpdc)3(DMF)(H2O)3, CPO-72-La, is formed from a dimer of nine-coordinate, edge sharing lanthanum cations. To this dimer, three water molecules and one DMF molecule are coordinated in an ordered fashion. In addition, the asymmetric unit contains three crystallographically unique linker molecules. Both CPO-71-Cu and CPO-72-La form two-dimensional layered structures, and topological analyses reveal sql topologies with point symbol 4(4)·6(2) and vertex symbol 4·4·4·4·6(2)·6(2). The thermal behavior of CPO-71-Cu was investigated in an in situ structural analysis by variable temperature powder- and single-crystal X-ray diffraction. PMID:27469613

  2. 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.

  3. A contact-area model for rail-pads connections in 2-D simulations: sensitivity analysis of train-induced vibrations

    NASA Astrophysics Data System (ADS)

    Ferrara, R.; Leonardi, G.; Jourdan, F.

    2013-09-01

    A numerical model to predict train-induced vibrations is presented. The dynamic computation considers mutual interactions in vehicle/track coupled systems by means of a finite and discrete elements method. The rail defects and the case of out-of-round wheels are considered. The dynamic interaction between the wheel-sets and the rail is accomplished by using the non-linear Hertzian model with hysteresis damping. A sensitivity analysis is done to evaluate the variables affecting more the maintenance costs. The rail-sleeper contact is assumed extended to an area-defined contact zone, rather than a single-point assumption which fits better real case studies. Experimental validations show how prediction fits well experimental data.

  4. Label free cell-tracking and division detection based on 2D time-lapse images for lineage analysis of early embryo development.

    PubMed

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

    2014-08-01

    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; and (5) statistical analysis of various timing distributions obtained from those examples. PMID:24873887

  5. 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

  6. 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

  7. 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. PMID:26201050

  8. Comparative Proteomics Profile of Lipid-Cumulating Oleaginous Yeast: An iTRAQ-Coupled 2-D LC-MS/MS Analysis

    PubMed Central

    Shi, Jiahua; Feng, Huixing; Lee, Jaslyn; Ning Chen, Wei

    2013-01-01

    Accumulation of intracellular lipid in oleaginous yeast cells has been studied for providing an alternative supply for energy, biofuel. Numerous studies have been conducted on increasing lipid content in oleaginous yeasts. However, few explore the mechanism of the high lipid accumulation ability of oleaginous yeast strains at the proteomics level. In this study, a time-course comparative proteomics analysis was introduced to compare the non-oleaginous yeast Saccharomyces cerevisiae, with two oleaginous yeast strains, Cryptococcus albidus and Rhodosporidium toruloides at different lipid accumulation stages. Two dimensional LC-MS/MS approach has been applied for protein profiling together with isobaric tag for relative and absolute quantitation (iTRAQ) labelling method. 132 proteins were identified when three yeast strains were all at early lipid accumulation stage; 122 and 116 proteins were found respectively within cells of three strains collected at middle and late lipid accumulation stages. Significantly up-regulation or down-regulation of proteins were experienced among comparison. Essential proteins correlated to lipid synthesis and regulation were detected. Our approach provides valuable indication and better understanding for lipid accumulation mechanism from proteomics level and would further contribute to genetic engineering of oleaginous yeasts. PMID:24386479

  9. Comparative proteomics profile of lipid-cumulating oleaginous yeast: an iTRAQ-coupled 2-D LC-MS/MS analysis.

    PubMed

    Shi, Jiahua; Feng, Huixing; Lee, Jaslyn; Ning Chen, Wei

    2013-01-01

    Accumulation of intracellular lipid in oleaginous yeast cells has been studied for providing an alternative supply for energy, biofuel. Numerous studies have been conducted on increasing lipid content in oleaginous yeasts. However, few explore the mechanism of the high lipid accumulation ability of oleaginous yeast strains at the proteomics level. In this study, a time-course comparative proteomics analysis was introduced to compare the non-oleaginous yeast Saccharomyces cerevisiae, with two oleaginous yeast strains, Cryptococcus albidus and Rhodosporidium toruloides at different lipid accumulation stages. Two dimensional LC-MS/MS approach has been applied for protein profiling together with isobaric tag for relative and absolute quantitation (iTRAQ) labelling method. 132 proteins were identified when three yeast strains were all at early lipid accumulation stage; 122 and 116 proteins were found respectively within cells of three strains collected at middle and late lipid accumulation stages. Significantly up-regulation or down-regulation of proteins were experienced among comparison. Essential proteins correlated to lipid synthesis and regulation were detected. Our approach provides valuable indication and better understanding for lipid accumulation mechanism from proteomics level and would further contribute to genetic engineering of oleaginous yeasts.

  10. Structural studies of an arabinan from the stems of Ephedra sinica by methylation analysis and 1D and 2D NMR spectroscopy.

    PubMed

    Xia, Yong-Gang; Liang, Jun; Yang, Bing-You; Wang, Qiu-Hong; Kuang, Hai-Xue

    2015-05-01

    Plant arabinan has important biological activity. In this study, a water-soluble arabinan (Mw∼6.15kDa) isolated from the stems of Ephedra sinica was found to consist of (1→5)-Araƒ, (1→3,5)-Araƒ, T-Araƒ, (1→3)-Araƒ and (1→2,5)-Araƒ residues at proportions of 10:2:3:2:1. A tentative structure was proposed by methylation analysis, nuclear magnetic resonance (NMR) spectroscopy ((1)H NMR, (13)C NMR, DEPT-135, (1)H-(1)H COSY, HSQC, HMBC and ROESY) and literature. The structure proposed includes a branched (1→5)-α-Araf backbone where branching occurs at the O-2 and O-3 positions of the residues with 7.7% and 15.4% of the 1,5-linked α-Araf substituted at the O-2 and O-3 positions. The presence of a branched structure was further observed by atomic force microscopy. This polymer was characterized as having a much longer linear (1→5)-α-Araf backbone as a repeating unit. In particular, the presence of α-Araf→3)-α-Araf-(1→3)-α-Araf-(1→ attached at the O-2 is a new finding. This study may facilitate a deeper understanding of structure-activity relationships of biological polysaccharides from the stems of E. sinica.

  11. Can anti-migratory drugs be screened in vitro? A review of 2D and 3D assays for the quantitative analysis of cell migration.

    PubMed

    Decaestecker, Christine; Debeir, Olivier; Van Ham, Philippe; Kiss, Robert

    2007-03-01

    The aim of the present review is to detail and analyze the pros and cons of in vitro tests available to quantify the anti-migratory effects of anti-cancer drugs for their eventual use in combating the dispersal of tumor cells, a clinical need which currently remains unsatisfied. We therefore briefly sum up why anti-migratory drugs constitute a promising approach in oncology while at the same time emphasizing that migrating cancer cells are resistant to apoptosis. To analyze the pros and cons of the various in vitro tests under review we also briefly sum up the molecular and cellular stages of cancer cell migration, an approach that enables us to argue both that no single in vitro test is sufficient to characterize the anti-migratory potential of a drug and that standardization is needed for the efficient quantitative analysis of cell locomotion in a 3D environment. Before concluding our review we devote the final two parts (i) to the description of new prototypes which, in the near future, could enter the screening process with a view to identifying novel anti-migratory compounds, and (ii) to the anti-migratory compounds currently developed against cancer, with particular emphasis on how these compounds were selected before entering the clinical trial phase.

  12. 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

    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.

  13. 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

  14. 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.

  15. 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.

  16. Practical Algorithm For Computing The 2-D Arithmetic Fourier Transform

    NASA Astrophysics Data System (ADS)

    Reed, Irving S.; Choi, Y. Y.; Yu, Xiaoli

    1989-05-01

    Recently, Tufts and Sadasiv [10] exposed a method for computing the coefficients of a Fourier series of a periodic function using the Mobius inversion of series. They called this method of analysis the Arithmetic Fourier Transform(AFT). The advantage of the AFT over the FN 1' is that this method of Fourier analysis needs only addition operations except for multiplications by scale factors at one stage of the computation. The disadvantage of the AFT as they expressed it originally is that it could be used effectively only to compute finite Fourier coefficients of a real even function. To remedy this the AFT developed in [10] is extended in [11] to compute the Fourier coefficients of both the even and odd components of a periodic function. In this paper, the improved AFT [11] is extended to a two-dimensional(2-D) Arithmetic Fourier Transform for calculating the Fourier Transform of two-dimensional discrete signals. This new algorithm is based on both the number-theoretic method of Mobius inversion of double series and the complex conjugate property of Fourier coefficients. The advantage of this algorithm over the conventional 2-D FFT is that the corner-turning problem needed in a conventional 2-D Discrete Fourier Transform(DFT) can be avoided. Therefore, this new 2-D algorithm is readily suitable for VLSI implementation as a parallel architecture. Comparing the operations of 2-D AFT of a MxM 2-D data array with the conventional 2-D FFT, the number of multiplications is significantly reduced from (2log2M)M2 to (9/4)M2. Hence, this new algorithm is faster than the FFT algorithm. Finally, two simulation results of this new 2-D AFT algorithm for 2-D artificial and real images are given in this paper.

  17. On-line 1D and 2D porous layer open tubular/LC-ESI-MS using 10-microm-i.d. poly(styrene-divinylbenzene) columns for ultrasensitive proteomic analysis.

    PubMed

    Luo, Quanzhou; Yue, Guihua; Valaskovic, Gary A; Gu, Ye; Wu, Shiaw-Lin; Karger, Barry L

    2007-08-15

    Following on our recent work, on-line one-dimensional (1D) and two-dimensional (2D) porous layer open tubular/liquid chromatography-electrospray ionization-mass spectrometry (PLOT/LC-ESI-MS) platforms using 3.2 mx10 microm i.d. poly(styrene-divinylbenzene) (PS-DVB) PLOT columns have been developed to provide robust, high-performance, and ultrasensitive proteomic analysis. With the use of a PicoClear tee, the dead volume connection between a 50 microm i.d. PS-DVB monolithic micro-SPE column and the PLOT column was minimized. The micro-SPE/PLOT column assembly provided a separation performance similar to that obtained with direct injection onto the PLOT column at a mobile phase flow rate of 20 nL/min. The trace analysis potential of the platform was evaluated using an in-gel tryptic digest sample of a gel fraction (15-40 kDa) of a cervical cancer (SiHa) cell line. As an example of the sensitivity of the system, approximately 2.5 ng of protein in 2 microL of solution, an amount corresponding to 20 SiHa cells, was subjected to on-line micro-SPE-PLOT/LC-ESI-MS/MS analysis using a linear ion trap MS. A total of 237 peptides associated with 163 unique proteins were identified from a single analysis when using stringent criteria associated with a false positive rate of less than 1%. The number of identified peptides and proteins increased to 638 and 343, respectively, as the injection amount was raised to approximately 45 ng of protein, an amount corresponding to 350 SiHa cells. In comparison, only 338 peptides and 231 unique proteins were identified (false positive rate again less than 1%) from 750 ng of protein from the identical gel fraction, an amount corresponding to 6000 SiHa cells, using a typical 15 cmx75 microm i.d. packed capillary column. The greater sensitivity, higher recovery, and higher resolving power of the PLOT column resulted in the increased number of identifications from only approximately 5% of the injected sample amount. The resolving power of the

  18. 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

  19. Analysis of membrane-protein complexes of the marine sulfate reducer Desulfobacula toluolica Tol2 by 1D blue native-PAGE complexome profiling and 2D blue native-/SDS-PAGE.

    PubMed

    Wöhlbrand, Lars; Ruppersberg, Hanna S; Feenders, Christoph; Blasius, Bernd; Braun, Hans-Peter; Rabus, Ralf

    2016-03-01

    Sulfate-reducing bacteria (SRB) obtain energy from cytoplasmic reduction of sulfate to sulfide involving APS-reductase (AprAB) and dissimilatory sulfite reductase (DsrAB). These enzymes are predicted to obtain electrons from membrane redox complexes, i.e. the quinone-interacting membrane-bound oxidoreductase (QmoABC) and DsrMKJOP complexes. In addition to these conserved complexes, the genomes of SRB encode a large number of other (predicted) membrane redox complexes, the function and actual formation of which is unknown. This study reports the establishment of 1D Blue Native-PAGE complexome profiling and 2D BN-/SDS-PAGE for analysis of the membrane protein complexome of the marine sulfate reducer Desulfobacula toluolica Tol2. Analysis of normalized score profiles of >800 proteins in combination with hierarchical clustering and identification of 2D BN-/SDS-PAGE separated spots demonstrated separation of membrane complexes in their native form, e.g. ATP synthase. In addition to the QmoABC and DsrMKJOP complexes, other complexes were detected that constitute the basic membrane complexome of D. toluolica Tol2, e.g. transport proteins (e.g. sodium/sulfate symporters) or redox complexes involved in Na(+) -based bioenergetics (RnfABCDEG). Notably, size estimation indicates dimer and quadruple formation of the DsrMKJOP complex in vivo. Furthermore, cluster analysis suggests interaction of this complex with a rhodanese-like protein (Tol2_C05230) possibly representing a periplasmic electron transfer partner for DsrMKJOP. PMID:26792001

  20. 2D Electrostatic Actuation of Microshutter Arrays

    NASA Technical Reports Server (NTRS)

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

    2015-01-01

    Electrostatically actuated microshutter arrays 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 microshutters 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.

  1. 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.

  2. 'Brukin2D': a 2D visualization and comparison tool for LC-MS data

    PubMed Central

    Tsagkrasoulis, Dimosthenis; Zerefos, Panagiotis; Loudos, George; Vlahou, Antonia; Baumann, Marc; Kossida, Sophia

    2009-01-01

    Background Liquid Chromatography-Mass Spectrometry (LC-MS) is a commonly used technique to resolve complex protein mixtures. Visualization of large data sets produced from LC-MS, namely the chromatogram and the mass spectra that correspond to its compounds is the focus of this work. Results The in-house developed 'Brukin2D' software, built in Matlab 7.4, which is presented here, uses the compound data that are exported from the Bruker 'DataAnalysis' program, and depicts the mean mass spectra of all the chromatogram compounds from one LC-MS run, in one 2D contour/density plot. Two contour plots from different chromatograph runs can then be viewed in the same window and automatically compared, in order to find their similarities and differences. The results of the comparison can be examined through detailed mass quantification tables, while chromatogram compound statistics are also calculated during the procedure. Conclusion 'Brukin2D' provides a user-friendly platform for quick, easy and integrated view of complex LC-MS data. The software is available at . PMID:19534737

  3. Combination Analysis in Genetic Polymorphisms of Drug-Metabolizing Enzymes CYP1A2, CYP2C9, CYP2C19, CYP2D6 and CYP3A5 in the Japanese Population

    PubMed Central

    Ota, Tomoko; Kamada, Yuka; Hayashida, Mariko; Iwao-Koizumi, Kyoko; Murata, Shigenori; Kinoshita, Kenji

    2015-01-01

    The Cytochrome P450 is the major enzyme involved in drug metabolism. CYP enzymes are responsible for the metabolism of most clinically used drugs. Individual variability in CYP activity is one important factor that contributes to drug therapy failure. We have developed a new straightforward TaqMan PCR genotyping assay to investigate the prevalence of the most common allelic variants of polymorphic CYP enzymes CYP1A2, CYP2C9, CYP2C19, CYP2D6 and CYP3A5 in the Japanese population. Moreover, we focused on the combination of each genotype for clinical treatment. The genotype analysis identified a total of 139 out of 483 genotype combinations of five genes in the 1,003 Japanese subjects. According to our results, most of subjects seemed to require dose modification during clinical treatment. In the near future, modifications should be considered based on the individual patient genotype of each treatment. PMID:25552922

  4. Perspectives for spintronics in 2D materials

    NASA Astrophysics Data System (ADS)

    Han, Wei

    2016-03-01

    The past decade has been especially creative for spintronics since the (re)discovery of various two dimensional (2D) materials. Due to the unusual physical characteristics, 2D materials have provided new platforms to probe the spin interaction with other degrees of freedom for electrons, as well as to be used for novel spintronics applications. This review briefly presents the most important recent and ongoing research for spintronics in 2D materials.

  5. 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.

  6. Detection of phosphorylation patterns in rat cortical neurons by combining phosphatase treatment and DIGE technology.

    PubMed

    Raggiaschi, Roberto; Lorenzetto, Chiara; Diodato, Enrica; Caricasole, Andrea; Gotta, Stefano; Terstappen, Georg C

    2006-02-01

    Although protein phosphorylation is probably the most studied post-translational modification occurring in cells, the number of proteins, which are the target of this modification, is still largely unknown. Increasing the coverage of the phosphoproteome as well as the detection of variation at the phosphorylation level would be very helpful for understanding the mechanisms of cell life and the modifications of the cell state leading to pathological conditions such as neurodegeneration. In order to further investigate variations occurring at the phosphorylation level, we have initiated the creation of a reference map of phosphorylated proteins in rat cortical neurons, employing a combination of phosphatase treatment and 2-DE/differential in gel electrophoresis technology. About 131 spots were recognized as phosphorylated proteins as they showed different migration behaviour after phosphatase treatment. The analysis of 42 selected spots was carried out by LC/MS/MS technology resulting in the identification of two new phosphoproteins.

  7. 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.

  8. Simulating MEMS Chevron Actuator for Strain Engineering 2D Materials

    NASA Astrophysics Data System (ADS)

    Vutukuru, Mounika; Christopher, Jason; Bishop, David; Swan, Anna

    2D materials pose an exciting paradigm shift in the world of electronics. These crystalline materials have demonstrated high electric and thermal conductivities and tensile strength, showing great potential as the new building blocks of basic electronic circuits. However, strain engineering 2D materials for novel devices remains a difficult experimental feat. We propose the integration of 2D materials with MEMS devices to investigate the strain dependence on material properties such as electrical and thermal conductivity, refractive index, mechanical elasticity, and band gap. MEMS Chevron actuators, provides the most accessible framework to study strain in 2D materials due to their high output force displacements for low input power. Here, we simulate Chevron actuators on COMSOL to optimize actuator design parameters and accurately capture the behavior of the devices while under the external force of a 2D material. Through stationary state analysis, we analyze the response of the device through IV characteristics, displacement and temperature curves. We conclude that the simulation precisely models the real-world device through experimental confirmation, proving that the integration of 2D materials with MEMS is a viable option for constructing novel strain engineered devices. The authors acknowledge support from NSF DMR1411008.

  9. 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

  10. 2D materials for nanophotonic devices

    NASA Astrophysics Data System (ADS)

    Xu, Renjing; Yang, Jiong; Zhang, Shuang; Pei, Jiajie; Lu, Yuerui

    2015-12-01

    Two-dimensional (2D) materials have become very important building blocks for electronic, photonic, and phononic devices. The 2D material family has four key members, including the metallic graphene, transition metal dichalcogenide (TMD) layered semiconductors, semiconducting black phosphorous, and the insulating h-BN. Owing to the strong quantum confinements and defect-free surfaces, these atomically thin layers have offered us perfect platforms to investigate the interactions among photons, electrons and phonons. The unique interactions in these 2D materials are very important for both scientific research and application engineering. In this talk, I would like to briefly summarize and highlight the key findings, opportunities and challenges in this field. Next, I will introduce/highlight our recent achievements. We demonstrated atomically thin micro-lens and gratings using 2D MoS2, which is the thinnest optical component around the world. These devices are based on our discovery that the elastic light-matter interactions in highindex 2D materials is very strong. Also, I would like to introduce a new two-dimensional material phosphorene. Phosphorene has strongly anisotropic optical response, which creates 1D excitons in a 2D system. The strong confinement in phosphorene also enables the ultra-high trion (charged exciton) binding energies, which have been successfully measured in our experiments. Finally, I will briefly talk about the potential applications of 2D materials in energy harvesting.

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

    PubMed Central

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

    2014-01-01

    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. PMID:26693303

  12. 2D materials: to graphene and beyond.

    PubMed

    Mas-Ballesté, Rubén; Gómez-Navarro, Cristina; Gómez-Herrero, Julio; Zamora, Félix

    2011-01-01

    This review is an attempt to illustrate the different alternatives in the field of 2D materials. Graphene seems to be just the tip of the iceberg and we show how the discovery of alternative 2D materials is starting to show the rest of this iceberg. The review comprises the current state-of-the-art of the vast literature in concepts and methods already known for isolation and characterization of graphene, and rationalizes the quite disperse literature in other 2D materials such as metal oxides, hydroxides and chalcogenides, and metal-organic frameworks.

  13. 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.

  14. 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.

  15. 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.

  16. 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. PMID:27478083

  17. 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.

  18. Glitter in a 2D monolayer.

    PubMed

    Yang, Li-Ming; Dornfeld, Matthew; Frauenheim, Thomas; Ganz, Eric

    2015-10-21

    We predict a highly stable and robust atomically thin gold monolayer with a hexagonal close packed lattice stabilized by metallic bonding with contributions from strong relativistic effects and aurophilic interactions. We have shown that the framework of the Au monolayer can survive 10 ps MD annealing simulations up to 1400 K. The framework is also able to survive large motions out of the plane. Due to the smaller number of bonds per atom in the 2D layer compared to the 3D bulk we observe significantly enhanced energy per bond (0.94 vs. 0.52 eV per bond). This is similar to the increase in bond strength going from 3D diamond to 2D graphene. It is a non-magnetic metal, and was found to be the global minima in the 2D space. Phonon dispersion calculations demonstrate high kinetic stability with no negative modes. This 2D gold monolayer corresponds to the top monolayer of the bulk Au(111) face-centered cubic lattice. The close-packed lattice maximizes the aurophilic interactions. We find that the electrons are completely delocalized in the plane and behave as 2D nearly free electron gas. We hope that the present work can inspire the experimental fabrication of novel free standing 2D metal systems.

  19. 2d index and surface operators

    NASA Astrophysics Data System (ADS)

    Gadde, Abhijit; Gukov, Sergei

    2014-03-01

    In this paper we compute the superconformal index of 2d (2, 2) supersymmetric gauge theories. The 2d superconformal index, a.k.a. flavored elliptic genus, is computed by a unitary matrix integral much like the matrix integral that computes the 4d superconformal index. We compute the 2d index explicitly for a number of examples. In the case of abelian gauge theories we see that the index is invariant under flop transition and under CY-LG correspondence. The index also provides a powerful check of the Seiberg-type duality for non-abelian gauge theories discovered by Hori and Tong. In the later half of the paper, we study half-BPS surface operators in = 2 super-conformal gauge theories. They are engineered by coupling the 2d (2, 2) supersymmetric gauge theory living on the support of the surface operator to the 4d = 2 theory, so that different realizations of the same surface operator with a given Levi type are related by a 2d analogue of the Seiberg duality. The index of this coupled system is computed by using the tools developed in the first half of the paper. The superconformal index in the presence of surface defect is expected to be invariant under generalized S-duality. We demonstrate that it is indeed the case. In doing so the Seiberg-type duality of the 2d theory plays an important role.

  20. 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…

  1. 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.

  2. Finite temperature corrections in 2d integrable models

    NASA Astrophysics Data System (ADS)

    Caselle, M.; Hasenbusch, M.

    2002-09-01

    We study the finite size corrections for the magnetization and the internal energy of the 2d Ising model in a magnetic field by using transfer matrix techniques. We compare these corrections with the functional form recently proposed by Delfino and LeClair-Mussardo for the finite temperature behaviour of one-point functions in integrable 2d quantum field theories. We find a perfect agreement between theoretical expectations and numerical results. Assuming the proposed functional form as an input in our analysis we obtain a relevant improvement in the precision of the continuum limit estimates of both quantities.

  3. FPCAS2D user's guide, version 1.0

    NASA Astrophysics Data System (ADS)

    Bakhle, Milind A.

    1994-12-01

    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.

  4. 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.

  5. 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

  6. 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.

  7. Optical modulators with 2D layered materials

    NASA Astrophysics Data System (ADS)

    Sun, Zhipei; Martinez, Amos; Wang, Feng

    2016-04-01

    Light modulation is an essential operation in photonics and optoelectronics. With existing and emerging technologies increasingly demanding compact, efficient, fast and broadband optical modulators, high-performance light modulation solutions are becoming indispensable. The recent realization that 2D layered materials could modulate light with superior performance has prompted intense research and significant advances, paving the way for realistic applications. In this Review, we cover the state of the art of optical modulators based on 2D materials, including graphene, transition metal dichalcogenides and black phosphorus. We discuss recent advances employing hybrid structures, such as 2D heterostructures, plasmonic structures, and silicon and fibre integrated structures. We also take a look at the future perspectives and discuss the potential of yet relatively unexplored mechanisms, such as magneto-optic and acousto-optic modulation.

  8. Accurate coronary modeling procedure using 2D calibrated projections based on 2D centerline points on a single projection

    NASA Astrophysics Data System (ADS)

    Movassaghi, Babak; Rasche, Volker; Viergever, Max A.; Niessen, Wiro J.

    2004-05-01

    For the diagnosis of ischemic heart disease, accurate quantitative analysis of the coronary arteries is important. In coronary angiography, a number of projections is acquired from which 3D models of the coronaries can be reconstructed. A signifcant limitation of the current 3D modeling procedures is the required user interaction for defining the centerlines of the vessel structures in the 2D projections. Currently, the 3D centerlines of the coronary tree structure are calculated based on the interactively determined centerlines in two projections. For every interactively selected centerline point in a first projection the corresponding point in a second projection has to be determined interactively by the user. The correspondence is obtained based on the epipolar-geometry. In this paper a method is proposed to retrieve all the information required for the modeling procedure, by the interactive determination of the 2D centerline-points in only one projection. For every determined 2D centerline-point the corresponding 3D centerline-point is calculated by the analysis of the 1D gray value functions of the corresponding epipolarlines in space for all available 2D projections. This information is then used to build a 3D representation of the coronary arteries using coronary modeling techniques. The approach is illustrated on the analysis of calibrated phantom and calibrated coronary projection data.

  9. Proteomic analysis of human bladder epithelial cells by 2D blue native SDS-PAGE reveals TCDD-induced alterations of calcium and iron homeostasis possibly mediated by nitric oxide.

    PubMed

    Verma, Nisha; Pink, Mario; Petrat, Frank; Rettenmeier, Albert W; Schmitz-Spanke, Simone

    2015-01-01

    A proteomic analysis of the interaction among multiprotein complexes involved in 2,3,7,8-dibenzo-p-dioxin (TCDD)-mediated toxicity in urinary bladder epithelial RT4 cells was performed using two-dimensional blue native SDS-PAGE (2D BN/SDS-PAGE). To enrich the protein complexes, unexposed and TCDD-exposed cells were fractionated. BN/SDS-PAGE of the resulting fractions led to an effective separation of proteins and protein complexes of various origins, including cell membrane, mitochondria, and other intracellular compartments. Major differences between the proteome of control and exposed cells involved the alteration of many calcium-regulated proteins (calmodulin, protein S100-A2, annexin A5, annexin A10, gelsolin isoform b) and iron-regulated proteins (ferritin, heme-binding protein 2, transferrin). On the basis of these findings, the intracellular calcium concentration was determined, revealing a significant increase after 24 h of exposure to TCDD. Moreover, the concentration of the labile iron pool (LIP) was also significantly elevated in TCDD-exposed cells. This increase was strongly inhibited by the calmodulin (CaM) antagonist W-7, which pointed toward a possible interaction between iron and calcium signaling. Because nitric oxide (NO) production was significantly enhanced in TCDD-exposed cells and was also inhibited by W-7, we hypothesize that alterations in calcium and iron homeostasis upon exposure to TCDD may be linked through NO generated by CaM-activated nitric oxide synthase. In our model, we propose that NO produced upon TCDD exposure interacts with the iron centers of iron-regulatory proteins (IRPs) that modulate the alteration of ferritin and transferrin, resulting in an augmented cellular LIP and, hence, increased toxicity.

  10. The NH2D hyperfine structure revealed by astrophysical observations

    NASA Astrophysics Data System (ADS)

    Daniel, F.; Coudert, L. H.; Punanova, A.; Harju, J.; Faure, A.; Roueff, E.; Sipilä, O.; Caselli, P.; Güsten, R.; Pon, A.; Pineda, J. E.

    2016-02-01

    Context. The 111-101 lines of ortho- and para-NH2D (o/p-NH2D) at 86 and 110 GHz, respectively, are commonly observed to provide constraints on the deuterium fractionation in the interstellar medium. In cold regions, the hyperfine structure that is due to the nitrogen (14N) nucleus is resolved. To date, this splitting is the only one that is taken into account in the NH2D column density estimates. Aims: We investigate how including the hyperfine splitting caused by the deuterium (D) nucleus affects the analysis of the rotational lines of NH2D. Methods: We present 30 m IRAM observations of the above mentioned lines and APEX o/p-NH2D observations of the 101-000 lines at 333 GHz. The hyperfine patterns of the observed lines were calculated taking into account the splitting induced by the D nucleus. The analysis then relies on line lists that either neglect or include the splitting induced by the D nucleus. Results: The hyperfine spectra are first analyzed with a line list that only includes the hyperfine splitting that is due to the 14N nucleus. We find inconsistencies between the line widths of the 101-000 and 111-101 lines, the latter being larger by a factor of ~1.6 ± 0.3. Such a large difference is unexpected because the two sets of lines probably originate from the same region. We next employed a newly computed line list for the o/p-NH2D transitions where the hyperfine structure induced by both nitrogen and deuterium nuclei was included. With this new line list, the analysis of the previous spectra leads to compatible line widths. Conclusions: Neglecting the hyperfine structure caused by D leads to overestimating the line widths of the o/p-NH2D lines at 3 mm. The error for a cold molecular core is about 50%. This error propagates directly to the column density estimate. We therefore recommend to take the hyperfine splittings caused by both the 14N and D nuclei into account in any analysis that relies on these lines. Based on observations carried out with the IRAM

  11. 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. PMID:25169938

  12. 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.

  13. Parallel stitching of 2D materials

    DOE PAGES

    Ling, Xi; Wu, Lijun; Lin, Yuxuan; Ma, Qiong; Wang, Ziqiang; Song, Yi; Yu, Lili; Huang, Shengxi; Fang, Wenjing; Zhang, Xu; et al

    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.

  14. 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.

  15. Correlated Electron Phenomena in 2D Materials

    NASA Astrophysics Data System (ADS)

    Lambert, Joseph G.

    In this thesis, I present experimental results on coherent electron phenomena in layered two-dimensional materials: single layer graphene and van der Waals coupled 2D TiSe2. Graphene is a two-dimensional single-atom thick sheet of carbon atoms first derived from bulk graphite by the mechanical exfoliation technique in 2004. Low-energy charge carriers in graphene behave like massless Dirac fermions, and their density can be easily tuned between electron-rich and hole-rich quasiparticles with electrostatic gating techniques. The sharp interfaces between regions of different carrier densities form barriers with selective transmission, making them behave as partially reflecting mirrors. When two of these interfaces are set at a separation distance within the phase coherence length of the carriers, they form an electronic version of a Fabry-Perot cavity. I present measurements and analysis of multiple Fabry-Perot modes in graphene with parallel electrodes spaced a few hundred nanometers apart. Transition metal dichalcogenide (TMD) TiSe2 is part of the family of materials that coined the term "materials beyond graphene". It contains van der Waals coupled trilayer stacks of Se-Ti-Se. Many TMD materials exhibit a host of interesting correlated electronic phases. In particular, TiSe2 exhibits chiral charge density waves (CDW) below TCDW ˜ 200 K. Upon doping with copper, the CDW state gets suppressed with Cu concentration, and CuxTiSe2 becomes superconducting with critical temperature of T c = 4.15 K. There is still much debate over the mechanisms governing the coexistence of the two correlated electronic phases---CDW and superconductivity. I will present some of the first conductance spectroscopy measurements of proximity coupled superconductor-CDW systems. Measurements reveal a proximity-induced critical current at the Nb-TiSe2 interfaces, suggesting pair correlations in the pure TiSe2. The results indicate that superconducting order is present concurrently with CDW in

  16. 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

  17. 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

  18. 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

    2016-01-01

    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.

  19. 77 FR 72291 - Approval and Promulgation of Implementation Plans; Region 4 States; Section 110(a)(2)(D)(i)(II...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-05

    ... address under sections 110(a)(2)(D)? III. What is EPA's analysis of how region 4 states addressed element... section 110(a)(2)(D)(i). III. What is EPA's analysis of how region 4 states addressed element (D)(i)(II...)(2)(D)(i)(II) Infrastructure Requirement for the 1997 and 2006 Fine Particulate Matter...

  20. A Better 2-D Mechanical Energy Conservation Experiment

    NASA Astrophysics Data System (ADS)

    Paesler, Michael

    2012-02-01

    A variety of simple classical mechanics energy conservation experiments are used in teaching laboratories. Typical one-dimensional (1-D) setups may involve falling balls or oscillating springs. Many of these can be quite satisfying in that students can confirm—within a few percent—that mechanical energy is conserved. Students generally have little trouble identifying discrepancies such as the loss of a few percent of the gravitational potential energy due to air friction encountered by a falling ball. Two-dimensional (2-D) systems can require more sophisticated analysis for higher level laboratories, but such systems often incorporate complicating components that can make the exercise academically incomplete and experimentally less accurate. The following describes a simple 2-D energy conservation experiment based on the popular "Newton's Cradle" toy that allows students to account for nearly all of the mechanical energy in the system in an academically complete analysis.

  1. Improving VERITAS sensitivity by fitting 2D Gaussian image parameters

    NASA Astrophysics Data System (ADS)

    Christiansen, Jodi; VERITAS Collaboration

    2012-12-01

    Our goal is to improve the acceptance and angular resolution of VERITAS by implementing a camera image-fitting algorithm. Elliptical image parameters are extracted from 2D Gaussian distribution fits using a χ2 minimization instead of the standard technique based on the principle moments of an island of pixels above threshold. We optimize the analysis cuts and then characterize the improvements using simulations. We find an improvement of 20% less observing time to reach 5-sigma for weak point sources.

  2. 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

  3. Stochastic Inversion of 2D Magnetotelluric Data

    SciTech Connect

    Chen, Jinsong

    2010-07-01

    The algorithm is developed to invert 2D magnetotelluric (MT) data based on sharp boundary parametrization using a Bayesian framework. Within the algorithm, we consider the locations and the resistivity of regions formed by the interfaces are as unknowns. We use a parallel, adaptive finite-element algorithm to forward simulate frequency-domain MT responses of 2D conductivity structure. Those unknown parameters are spatially correlated and are described by a geostatistical model. The joint posterior probability distribution function is explored by Markov Chain Monte Carlo (MCMC) sampling methods. The developed stochastic model is effective for estimating the interface locations and resistivity. Most importantly, it provides details uncertainty information on each unknown parameter. Hardware requirements: PC, Supercomputer, Multi-platform, Workstation; Software requirements C and Fortan; Operation Systems/version is Linux/Unix or Windows

  4. Explicit 2-D Hydrodynamic FEM Program

    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. Themore » 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.« less

  5. Stochastic Inversion of 2D Magnetotelluric Data

    2010-07-01

    The algorithm is developed to invert 2D magnetotelluric (MT) data based on sharp boundary parametrization using a Bayesian framework. Within the algorithm, we consider the locations and the resistivity of regions formed by the interfaces are as unknowns. We use a parallel, adaptive finite-element algorithm to forward simulate frequency-domain MT responses of 2D conductivity structure. Those unknown parameters are spatially correlated and are described by a geostatistical model. The joint posterior probability distribution function ismore » explored by Markov Chain Monte Carlo (MCMC) sampling methods. The developed stochastic model is effective for estimating the interface locations and resistivity. Most importantly, it provides details uncertainty information on each unknown parameter. Hardware requirements: PC, Supercomputer, Multi-platform, Workstation; Software requirements C and Fortan; Operation Systems/version is Linux/Unix or Windows« less

  6. 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.

  7. 2D photonic-crystal optomechanical nanoresonator.

    PubMed

    Makles, K; Antoni, T; Kuhn, A G; Deléglise, S; Briant, T; Cohadon, P-F; Braive, R; Beaudoin, G; Pinard, L; Michel, C; Dolique, V; Flaminio, R; Cagnoli, G; Robert-Philip, I; Heidmann, A

    2015-01-15

    We present the optical optimization of an optomechanical device based on a suspended InP membrane patterned with a 2D near-wavelength grating (NWG) based on a 2D photonic-crystal geometry. We first identify by numerical simulation a set of geometrical parameters providing a reflectivity higher than 99.8% over a 50-nm span. We then study the limitations induced by the finite value of the optical waist and lateral size of the NWG pattern using different numerical approaches. The NWG grating, pierced in a suspended InP 265-nm thick membrane, is used to form a compact microcavity involving the suspended nanomembrane as an end mirror. The resulting cavity has a waist size smaller than 10 μm and a finesse in the 200 range. It is used to probe the Brownian motion of the mechanical modes of the nanomembrane. PMID:25679837

  8. 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. PMID:21890007

  9. 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.

  10. 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.

  11. 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. PMID:27541575

  12. 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.

  13. 2D materials: Graphene and others

    NASA Astrophysics Data System (ADS)

    Bansal, Suneev Anil; Singh, Amrinder Pal; Kumar, Suresh

    2016-05-01

    Present report reviews the recent advancements in new atomically thick 2D materials. Materials covered in this review are Graphene, Silicene, Germanene, Boron Nitride (BN) and Transition metal chalcogenides (TMC). These materials show extraordinary mechanical, electronic and optical properties which make them suitable candidates for future applications. Apart from unique properties, tune-ability of highly desirable properties of these materials is also an important area to be emphasized on.

  14. Layer Engineering of 2D Semiconductor Junctions.

    PubMed

    He, Yongmin; Sobhani, Ali; Lei, Sidong; Zhang, Zhuhua; Gong, Yongji; Jin, Zehua; Zhou, Wu; Yang, Yingchao; Zhang, Yuan; Wang, Xifan; Yakobson, Boris; Vajtai, Robert; Halas, Naomi J; Li, Bo; Xie, Erqing; Ajayan, Pulickel

    2016-07-01

    A new concept for junction fabrication by connecting multiple regions with varying layer thicknesses, based on the thickness dependence, is demonstrated. This type of junction is only possible in super-thin-layered 2D materials, and exhibits similar characteristics as p-n junctions. Rectification and photovoltaic effects are observed in chemically homogeneous MoSe2 junctions between domains of different thicknesses. PMID:27136275

  15. Realistic and efficient 2D crack simulation

    NASA Astrophysics Data System (ADS)

    Yadegar, Jacob; Liu, Xiaoqing; Singh, Abhishek

    2010-04-01

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

  16. 2D Spinodal Decomposition in Forced Turbulence

    NASA Astrophysics Data System (ADS)

    Fan, Xiang; Diamond, Patrick; Chacon, Luis; Li, Hui

    2015-11-01

    Spinodal decomposition is a second order phase transition for binary fluid mixture, from one thermodynamic phase to form two coexisting phases. The governing equation for this coarsening process below critical temperature, Cahn-Hilliard Equation, is very similar to 2D MHD Equation, especially the conserved quantities have a close correspondence between each other, so theories for MHD turbulence are used to study spinodal decomposition in forced turbulence. Domain size is increased with time along with the inverse cascade, and the length scale can be arrested by a forced turbulence with direct cascade. The two competing mechanisms lead to a stabilized domain size length scale, which can be characterized by Hinze Scale. The 2D spinodal decomposition in forced turbulence is studied by both theory and simulation with ``pixie2d.'' This work focuses on the relation between Hinze scale and spectra and cascades. Similarities and differences between spinodal decomposition and MHD are investigated. Also some transport properties are studied following MHD theories. This work is supported by the Department of Energy under Award Number DE-FG02-04ER54738.

  17. 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.

  18. Genetic mechanisms for duplication and multiduplication of the human CYP2D6 gene and methods for detection of duplicated CYP2D6 genes.

    PubMed

    Lundqvist, E; Johansson, I; Ingelman-Sundberg, M

    1999-01-21

    The polymorphic CYP2D6 gene determines the rates at which several different classes of clinically important drugs are metabolized in vivo. A specific phenotype whereby a subject metabolizes drugs very rapidly (ultrarapid metabolizer, UM) has been shown to be caused by the presence of multiple active CYP2D6 genes on one allele. Hitherto, individuals with 1, 2, 3, 4, 5, or 13 CYP2D6 genes in tandem have been described for various ethnic groups. In the present investigation, we present results from restriction mapping of the CYP2D loci of individuals with two or more consecutive CYP2D6 genes, along with sequence analysis of this gene (CYP2D6*2). Our results indicate that alleles with duplicated or multiduplicated genes have occurred through unequal crossover at a specific breakpoint in the 3'-flanking region of the CYP2D6*2B allele with a specific repetitive sequence. In contrast, alleles with 13 copies of the gene are proposed to have been formed by unequal segregation and extrachromosomal replication of the acentric DNA. We present a rapid and efficient PCR-based allele-specific method for the detection of duplicated, multiduplicated, or amplified CYP2D6 genes.

  19. Interpretation of Magnetic Phase Anomalies over 2D Tabular Bodies

    NASA Astrophysics Data System (ADS)

    Subrahmanyam, M.

    2016-05-01

    In this study, phase angle (inverse tangent of the ratio of the horizontal to vertical gradients of magnetic anomalies) profile over two-dimensional tabular bodies has been subjected to detailed analysis for determining the source parameters. Distances between certain characteristic positions on this phase curve are related to the parameters of two-dimensional tabular magnetic sources. In this paper, I have derived the mathematical expressions for these relations. It has been demonstrated here that for locating the origin of the 2D tabular source, knowledge on the type of the model (contact, sheet, dyke, and fault) is not necessary. A procedure is evolved to determine the location, depth, width and magnetization angle of the 2D sources from the mathematical expressions. The method is tested on real field data. The effect of the overlapping bodies is also discussed with two synthetic examples. The interpretation technique is developed for contact, sheet, dike and inclined fault bodies.

  20. Visualization of 2-D and 3-D Tensor Fields

    NASA Technical Reports Server (NTRS)

    Hesselink, Lambertus

    1997-01-01

    In previous work we have developed a novel approach to visualizing second order symmetric 2-D tensor fields based on degenerate point analysis. At degenerate points the eigenvalues are either zero or equal to each other, and the hyper-streamlines about these points give rise to tri-sector or wedge points. These singularities and their connecting hyper-streamlines determine the topology of the tensor field. In this study we are developing new methods for analyzing and displaying 3-D tensor fields. This problem is considerably more difficult than the 2-D one, as the richness of the data set is much larger. Here we report on our progress and a novel method to find , analyze and display 3-D degenerate points. First we discuss the theory, then an application involving a 3-D tensor field, the Boussinesq problem with two forces.

  1. Visualization of 2-D and 3-D Tensor Fields

    NASA Technical Reports Server (NTRS)

    Hesselink, Lambertus

    1995-01-01

    In previous work we have developed a novel approach to visualizing second order symmetric 2-D tensor fields based on degenerate point analysis. At degenerate points the eigenvalues are either zero or equal to each other, and the hyperstreamlines about these points give rise to trisector or wedge points. These singularities and their connecting hyperstreamlines determine the topology of the tensor field. In this study we are developing new methods for analyzing and displaying 3-D tensor fields. This problem is considerably more difficult than the 2-D one, as the richness of the data set is much larger. Here we report on our progress and a novel method to find, analyze and display 3-D degenerate points. First we discuss the theory, then an application involving a 3-D tensor field, the Boussinesq problem with two forces.

  2. 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.

  3. 2D FEM Heat Transfer & E&M Field Code

    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.more » 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.« less

  4. GBL-2D Version 1.0: a 2D geometry boolean library.

    SciTech Connect

    McBride, Cory L. (Elemental Technologies, American Fort, UT); Schmidt, Rodney Cannon; Yarberry, Victor R.; Meyers, Ray J.

    2006-11-01

    This report describes version 1.0 of GBL-2D, a geometric Boolean library for 2D objects. The library is written in C++ and consists of a set of classes and routines. The classes primarily represent geometric data and relationships. Classes are provided for 2D points, lines, arcs, edge uses, loops, surfaces and mask sets. The routines contain algorithms for geometric Boolean operations and utility functions. Routines are provided that incorporate the Boolean operations: Union(OR), XOR, Intersection and Difference. A variety of additional analytical geometry routines and routines for importing and exporting the data in various file formats are also provided. The GBL-2D library was originally developed as a geometric modeling engine for use with a separate software tool, called SummitView [1], that manipulates the 2D mask sets created by designers of Micro-Electro-Mechanical Systems (MEMS). However, many other practical applications for this type of software can be envisioned because the need to perform 2D Boolean operations can arise in many contexts.

  5. Linkage studies for T2D in Chop and C/EBPbeta chromosomal regions in Italians.

    PubMed

    Gragnoli, Claudia; Pierpaoli, Laura; Piumelli, Nunzia; Chiaramonte, Francesco

    2007-11-01

    The genes causing type 2 diabetes (T2D), a complex heterogeneous disorder, differ and/or overlap in various populations. Among others there are two loci in linkage to T2D, the chromosomes 20q12-13.1 and 12q15. These two regions harbor two genes, C/EBPbeta and CHOP, which are excellent candidate genes for T2D. In fact, C/EBPbeta protein cooperates with HNF4alpha (MODY1, monogenic form of diabetes) and 1alpha (MODY3, monogenic form of diabetes). C/EBPbeta mediates suppression of insulin gene transcription in hyperglycemia and may contribute to insulin-resistance. It interacts in a complex pathway with the CHOP protein. CHOP may play a role in altered beta-cell glucose metabolism, in beta-cell apoptosis, and in lack of beta-cell replication. Thus, both C/EBPbeta and CHOP genes may independently and interactively contribute to T2D. The chromosomal regions targeting C/EBPbeta and CHOP genes have never been previously explored in T2D. We planned to identify their potential contribution to T2D in Italians. We have genotyped a group of affected siblings/families with both late- and early-onset T2D around the C/EBPbeta and the CHOP genes. We have performed non-parametric linkage analysis in the total T2D group, in the late-onset and the early-onset group, separately. We have identified a suggestive linkage to T2D in the CHOP gene locus in the early-onset T2D group (P = 0.04). We identified the linkage to T2D in the chromosome 12q15 region in the early-onset T2D families and specifically target the CHOP gene. Our next step will be the identification of CHOP gene variants, which may contribute to the linkage to T2D in Italians. PMID:17620318

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Multienzyme Inkjet Printed 2D Arrays.

    PubMed

    Gdor, Efrat; Shemesh, Shay; Magdassi, Shlomo; Mandler, Daniel

    2015-08-19

    The use of printing to produce 2D arrays is well established, and should be relatively facile to adapt for the purpose of printing biomaterials; however, very few studies have been published using enzyme solutions as inks. Among the printing technologies, inkjet printing is highly suitable for printing biomaterials and specifically enzymes, as it offers many advantages. Formulation of the inkjet inks is relatively simple and can be adjusted to a variety of biomaterials, while providing nonharmful environment to the enzymes. Here we demonstrate the applicability of inkjet printing for patterning multiple enzymes in a predefined array in a very straightforward, noncontact method. Specifically, various arrays of the enzymes glucose oxidase (GOx), invertase (INV) and horseradish peroxidase (HP) were printed on aminated glass surfaces, followed by immobilization using glutardialdehyde after printing. Scanning electrochemical microscopy (SECM) was used for imaging the printed patterns and to ascertain the enzyme activity. The successful formation of 2D arrays consisting of enzymes was explored as a means of developing the first surface confined enzyme based logic gates. Principally, XOR and AND gates, each consisting of two enzymes as the Boolean operators, were assembled, and their operation was studied by SECM. PMID:26214072

  11. Dopamine D2/D3 receptor availability and venturesomeness.

    PubMed

    Bernow, Nina; Yakushev, Igor; Landvogt, Christian; Buchholz, Hans-Georg; Smolka, Michael N; Bartenstein, Peter; Lieb, Klaus; Gründer, Gerhard; Vernaleken, Ingo; Schreckenberger, Mathias; Fehr, Christoph

    2011-08-30

    The construct of impulsivity is considered as a major trait of personality. There is growing evidence that the mesolimbic dopamine system plays an important role in the modulation of impulsivity and venturesomeness, the two key components within the impulsivity-construct. The aim of the present study was to explore an association between trait impulsivity measured with self-assessment and the dopaminergic neurotransmission as measured by positron emission tomography (PET) in a cohort of healthy male subjects. In vivo D2/D3 receptor availability was determined with [(18)F]fallypride PET in 18 non-smoking healthy subjects. The character trait impulsivity was measured using the Impulsiveness-Venturesomeness-Empathy questionnaire (I7). Image processing and statistical analysis was performed on a voxel-by-voxel basis using statistical parametric mapping (SPM) software. The I7 subscale venturesomeness correlated positively with the D2/D3 receptor availability within the left temporal cortex and the thalamus. Measures on the I7 subscale impulsiveness and empathy did not correlate with the D2/D3 receptor availability in any brain region investigated. Our results suggest the involvement of extrastriatal dopaminergic neurotransmission in venturesomeness, a component of impulsivity. PMID:21689908

  12. 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

  13. 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

  14. TOPAZ2D heat transfer code users manual and thermal property data base

    NASA Astrophysics Data System (ADS)

    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.

  15. 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.

  16. 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.

  17. 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).

  18. 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

  19. 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.

  20. CYP2D6*36 gene arrangements within the cyp2d6 locus: association of CYP2D6*36 with poor metabolizer status.

    PubMed

    Gaedigk, Andrea; Bradford, L Dianne; Alander, Sarah W; Leeder, J Steven

    2006-04-01

    Unexplained cases of CYP2D6 genotype/phenotype discordance continue to be discovered. In previous studies, several African Americans with a poor metabolizer phenotype carried the reduced function CYP2D6*10 allele in combination with a nonfunctional allele. We pursued the possibility that these alleles harbor either a known sequence variation (i.e., CYP2D6*36 carrying a gene conversion in exon 9 along the CYP2D6*10-defining 100C>T single-nucleotide polymorphism) or novel sequences variation(s). Discordant cases were evaluated by long-range polymerase chain reaction (PCR) to test for gene rearrangement events, and a 6.6-kilobase pair PCR product encompassing the CYP2D6 gene was cloned and entirely sequenced. Thereafter, allele frequencies were determined in different study populations comprising whites, African Americans, and Asians. Analyses covering the CYP2D7 to 2D6 gene region established that CYP2D6*36 did not only exist as a gene duplication (CYP2D6*36x2) or in tandem with *10 (CYP2D6*36+*10), as previously reported, but also by itself. This "single" CYP2D6*36 allele was found in nine African Americans and one Asian, but was absent in the whites tested. Ultimately, the presence of CYP2D6*36 resolved genotype/phenotype discordance in three cases. We also discovered an exon 9 conversion-positive CYP2D6*4 gene in a duplication arrangement (CYP2D6*4Nx2) and a CYP2D6*4 allele lacking 100C>T (CYP2D6*4M) in two white subjects. The discovery of an allele that carries only one CYP2D6*36 gene copy provides unequivocal evidence that both CYP2D6*36 and *36x2 are associated with a poor metabolizer phenotype. Given a combined frequency of between 0.5 and 3% in African Americans and Asians, genotyping for CYP2D6*36 should improve the accuracy of genotype-based phenotype prediction in these populations.

  1. Protein kinase A represses skeletal myogenesis by targeting myocyte enhancer factor 2D.

    PubMed

    Du, Min; Perry, Robert L S; Nowacki, Nathaniel B; Gordon, Joseph W; Salma, Jahan; Zhao, Jianzhong; Aziz, Arif; Chan, Joseph; Siu, K W Michael; McDermott, John C

    2008-05-01

    Activation of protein kinase A (PKA) by elevation of the intracellular cyclic AMP (cAMP) level inhibits skeletal myogenesis. Previously, an indirect modulation of the myogenic regulatory factors (MRFs) was implicated as the mechanism. Because myocyte enhancer factor 2 (MEF2) proteins are key regulators of myogenesis and obligatory partners for the MRFs, here we assessed whether these proteins could be involved in PKA-mediated myogenic repression. Initially, in silico analysis revealed several consensus PKA phosphoacceptor sites on MEF2, and subsequent analysis by in vitro kinase assays indicated that PKA directly and efficiently phosphorylates MEF2D. Using mass spectrometric determination of phosphorylated residues, we document that MEF2D serine 121 and serine 190 are targeted by PKA. Transcriptional reporter gene assays to assess MEF2D function revealed that PKA potently represses the transactivation properties of MEF2D. Furthermore, engineered mutation of MEF2D PKA phosphoacceptor sites (serines 121 and 190 to alanine) rendered a PKA-resistant MEF2D protein, which efficiently rescues myogenesis from PKA-mediated repression. Concomitantly, increased intracellular cAMP-mediated PKA activation also resulted in an enhanced nuclear accumulation of histone deacetylase 4 (HDAC4) and a subsequent increase in the MEF2D-HDAC4 repressor complex. Collectively, these data identify MEF2D as a primary target of PKA signaling in myoblasts that leads to inhibition of the skeletal muscle differentiation program.

  2. 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.

  3. Simulation of 2D Fields of Raindrop Size Distributions

    NASA Astrophysics Data System (ADS)

    Berne, A.; Schleiss, M.; Uijlenhoet, R.

    2008-12-01

    The raindrop size distribution (DSD hereafter) is of primary importance for quantitative applications of weather radar measurements. The radar reflectivity~Z (directly measured by radar) is related to the power backscattered by the ensemble of hydrometeors within the radar sampling volume. However, the rain rate~R (the flux of water to the surface) is the variable of interest for many applications (hydrology, weather forecasting, air traffic for example). Usually, radar reflectivity is converted into rain rate using a power law such as Z=aRb. The coefficients a and b of the Z-R relationship depend on the DSD. The variability of the DSD in space and time has to be taken into account to improve radar rain rate estimates. Therefore, the ability to generate a large number of 2D fields of DSD which are statistically homogeneous provides a very useful simulation framework that nicely complements experimental approaches based on DSD data, in order to investigate radar beam propagation through rain as well as radar retrieval techniques. The proposed approach is based on geostatistics for structural analysis and stochastic simulation. First, the DSD is assumed to follow a gamma distribution. Hence a 2D field of DSDs can be adequately described as a 2D field of a multivariate random function consisting of the three DSD parameters. Such fields are simulated by combining a Gaussian anamorphosis and a multivariate Gaussian random field simulation algorithm. Using the (cross-)variogram models fitted on data guaranties that the spatial structure of the simulated fields is consistent with the observed one. To assess its validity, the proposed method is applied to data collected during intense Mediterranean rainfall. As only time series are available, Taylor's hypothesis is assumed to convert time series in 1D range profile. Moreover, DSD fields are assumed to be isotropic so that the 1D structure can be used to simulate 2D fields. A large number of 2D fields of DSD parameters are

  4. A new inversion method for (T2, D) 2D NMR logging and fluid typing

    NASA Astrophysics Data System (ADS)

    Tan, Maojin; Zou, Youlong; Zhou, Cancan

    2013-02-01

    One-dimensional nuclear magnetic resonance (1D NMR) logging technology has some significant limitations in fluid typing. However, not only can two-dimensional nuclear magnetic resonance (2D NMR) provide some accurate porosity parameters, but it can also identify fluids more accurately than 1D NMR. In this paper, based on the relaxation mechanism of (T2, D) 2D NMR in a gradient magnetic field, a hybrid inversion method that combines least-squares-based QR decomposition (LSQR) and truncated singular value decomposition (TSVD) is examined in the 2D NMR inversion of various fluid models. The forward modeling and inversion tests are performed in detail with different acquisition parameters, such as magnetic field gradients (G) and echo spacing (TE) groups. The simulated results are discussed and described in detail, the influence of the above-mentioned observation parameters on the inversion accuracy is investigated and analyzed, and the observation parameters in multi-TE activation are optimized. Furthermore, the hybrid inversion can be applied to quantitatively determine the fluid saturation. To study the effects of noise level on the hybrid method and inversion results, the numerical simulation experiments are performed using different signal-to-noise-ratios (SNRs), and the effect of different SNRs on fluid typing using three fluid models are discussed and analyzed in detail.

  5. 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.

  6. RADON and DIRPOWER: Projection software for 2-D Fourier power spectra

    NASA Astrophysics Data System (ADS)

    Prince, Christopher M.

    1993-07-01

    Two-dimensional (2-D) Fourier analysis provides a method for spatial analysis of rock fabrics in thin section. RADON and DIRPOWER are analytical aids designed to create projections of 2-D real-valued functions, including 2-D Fourier power spectra. RADON is used to create parallel projections, projecting the power spectrum towards a line oriented at any angle relative to the spectrum. It provides an "edge-on" view of the power spectrum. DIRPOWER is used to create a Mean Directional Power Spectrum (MDPS), a circular projection used to assess the direction and degree of orientation within rock fabrics.

  7. 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.

  8. Proteomic Analysis of Alzheimer’s Disease Cerebrospinal Fluid from Neuropathologically Diagnosed Subjects

    PubMed Central

    Maarouf, Chera L.; Andacht, Tracy M.; Kokjohn, Tyler A.; Castaño, Eduardo M.; Sue, Lucia I.; Beach, Thomas G.; Roher, Alex E.

    2010-01-01

    A crucial need exists for reliable Alzheimer’s disease (AD) diagnostic and prognostic tests. Given its intimate communication with the brain, the cerebrospinal fluid (CSF) has been surveyed intensively for reliable AD biomarkers. The heterogeneity of AD pathology and the unavoidable difficulties associated with the clinical diagnosis and differentiation of this dementia from other pathologies have confounded biomarker studies in antemortem CSF samples. Using postmortem ventricular CSF (V-CSF) pools, two-dimensional difference gel electrophoresis (2D DIGE) analyses revealed a set of proteins that showed significant differences between neuropathologically-diagnosed AD and elderly non-demented controls (NDC), as well as subjects with non-AD dementias. The 2D DIGE system identified a set of 21 different protein biomarkers. This panel of proteins probably reflects fundamental pathological changes that are divergent from both normal aging and non-AD dementias. PMID:19689240

  9. 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.

  10. 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

  11. Phase Engineering of 2D Tin Sulfides.

    PubMed

    Mutlu, Zafer; Wu, Ryan J; Wickramaratne, Darshana; Shahrezaei, Sina; Liu, Chueh; Temiz, Selcuk; Patalano, Andrew; Ozkan, Mihrimah; Lake, Roger K; Mkhoyan, K A; Ozkan, Cengiz S

    2016-06-01

    Tin sulfides can exist in a variety of phases and polytypes due to the different oxidation states of Sn. A subset of these phases and polytypes take the form of layered 2D structures that give rise to a wide host of electronic and optical properties. Hence, achieving control over the phase, polytype, and thickness of tin sulfides is necessary to utilize this wide range of properties exhibited by the compound. This study reports on phase-selective growth of both hexagonal tin (IV) sulfide SnS2 and orthorhombic tin (II) sulfide SnS crystals with diameters of over tens of microns on SiO2 substrates through atmospheric pressure vapor-phase method in a conventional horizontal quartz tube furnace with SnO2 and S powders as the source materials. Detailed characterization of each phase of tin sulfide crystals is performed using various microscopy and spectroscopy methods, and the results are corroborated by ab initio density functional theory calculations. PMID:27099950

  12. Phase Engineering of 2D Tin Sulfides.

    PubMed

    Mutlu, Zafer; Wu, Ryan J; Wickramaratne, Darshana; Shahrezaei, Sina; Liu, Chueh; Temiz, Selcuk; Patalano, Andrew; Ozkan, Mihrimah; Lake, Roger K; Mkhoyan, K A; Ozkan, Cengiz S

    2016-06-01

    Tin sulfides can exist in a variety of phases and polytypes due to the different oxidation states of Sn. A subset of these phases and polytypes take the form of layered 2D structures that give rise to a wide host of electronic and optical properties. Hence, achieving control over the phase, polytype, and thickness of tin sulfides is necessary to utilize this wide range of properties exhibited by the compound. This study reports on phase-selective growth of both hexagonal tin (IV) sulfide SnS2 and orthorhombic tin (II) sulfide SnS crystals with diameters of over tens of microns on SiO2 substrates through atmospheric pressure vapor-phase method in a conventional horizontal quartz tube furnace with SnO2 and S powders as the source materials. Detailed characterization of each phase of tin sulfide crystals is performed using various microscopy and spectroscopy methods, and the results are corroborated by ab initio density functional theory calculations.

  13. 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.

  14. 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

  15. 2-D Animation's Not Just for Mickey Mouse.

    ERIC Educational Resources Information Center

    Weinman, Lynda

    1995-01-01

    Discusses characteristics of two-dimensional (2-D) animation; highlights include character animation, painting issues, and motion graphics. Sidebars present Silicon Graphics animations tools and 2-D animation programs for the desktop computer. (DGM)

  16. 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.

  17. 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.

  18. 2d PDE Linear Symmetric Matrix Solver

    1983-10-01

    ICCG2 (Incomplete Cholesky factorized Conjugate Gradient algorithm for 2d symmetric problems) was developed to solve a linear symmetric matrix system arising from a 9-point discretization of two-dimensional elliptic and parabolic partial differential equations found in plasma physics applications, such as resistive MHD, spatial diffusive transport, and phase space transport (Fokker-Planck equation) problems. These problems share the common feature of being stiff and requiring implicit solution techniques. When these parabolic or elliptic PDE''s are discretized withmore » finite-difference or finite-element methods,the resulting matrix system is frequently of block-tridiagonal form. To use ICCG2, the discretization of the two-dimensional partial differential equation and its boundary conditions must result in a block-tridiagonal supermatrix composed of elementary tridiagonal matrices. The incomplete Cholesky conjugate gradient algorithm is used to solve the linear symmetric matrix equation. Loops are arranged to vectorize on the Cray1 with the CFT compiler, wherever possible. Recursive loops, which cannot be vectorized, are written for optimum scalar speed. For matrices lacking symmetry, ILUCG2 should be used. Similar methods in three dimensions are available in ICCG3 and ILUCG3. A general source containing extensions and macros, which must be processed by a pre-compiler to obtain the standard FORTRAN source, is provided along with the standard FORTRAN source because it is believed to be more readable. The pre-compiler is not included, but pre-compilation may be performed by a text editor as described in the UCRL-88746 Preprint.« less

  19. 2d PDE Linear Asymmetric Matrix Solver

    1983-10-01

    ILUCG2 (Incomplete LU factorized Conjugate Gradient algorithm for 2d problems) was developed to solve a linear asymmetric matrix system arising from a 9-point discretization of two-dimensional elliptic and parabolic partial differential equations found in plasma physics applications, such as plasma diffusion, equilibria, and phase space transport (Fokker-Planck equation) problems. These equations share the common feature of being stiff and requiring implicit solution techniques. When these parabolic or elliptic PDE''s are discretized with finite-difference or finite-elementmore » methods, the resulting matrix system is frequently of block-tridiagonal form. To use ILUCG2, the discretization of the two-dimensional partial differential equation and its boundary conditions must result in a block-tridiagonal supermatrix composed of elementary tridiagonal matrices. A generalization of the incomplete Cholesky conjugate gradient algorithm is used to solve the matrix equation. Loops are arranged to vectorize on the Cray1 with the CFT compiler, wherever possible. Recursive loops, which cannot be vectorized, are written for optimum scalar speed. For problems having a symmetric matrix ICCG2 should be used since it runs up to four times faster and uses approximately 30% less storage. Similar methods in three dimensions are available in ICCG3 and ILUCG3. A general source, containing extensions and macros, which must be processed by a pre-compiler to obtain the standard FORTRAN source, is provided along with the standard FORTRAN source because it is believed to be more readable. The pre-compiler is not included, but pre-compilation may be performed by a text editor as described in the UCRL-88746 Preprint.« less

  20. Position control using 2D-to-2D feature correspondences in vision guided cell micromanipulation.

    PubMed

    Zhang, Yanliang; Han, Mingli; Shee, Cheng Yap; Ang, Wei Tech

    2007-01-01

    Conventional camera calibration that utilizes the extrinsic and intrinsic parameters of the camera and the objects has certain limitations for micro-level cell operations due to the presence of hardware deviations and external disturbances during the experimental process, thereby invalidating the extrinsic parameters. This invalidation is often neglected in macro-world visual servoing and affects the visual image processing quality, causing deviation from the desired position in micro-level cell operations. To increase the success rate of vision guided biological micromanipulations, a novel algorithm monitoring the changing image pattern of the manipulators including the injection micropipette and cell holder is designed and implemented based on 2 dimensional (2D)-to 2D feature correspondences and can adjust the manipulator and perform position control simultaneously. When any deviation is found, the manipulator is retracted to the initial focusing plane before continuing the operation.

  1. A Planar Quantum Transistor Based on 2D-2D Tunneling in Double Quantum Well Heterostructures

    SciTech Connect

    Baca, W.E.; Blount, M.A.; Hafich, M.J.; Lyo, S.K.; Moon, J.S.; Reno, J.L.; Simmons, J.A.; Wendt, J.R.

    1998-12-14

    We report on our work on the double electron layer tunneling transistor (DELTT), based on the gate-control of two-dimensional -- two-dimensional (2D-2D) tunneling in a double quantum well heterostructure. While previous quantum transistors have typically required tiny laterally-defined features, by contrast the DELTT is entirely planar and can be reliably fabricated in large numbers. We use a novel epoxy-bond-and-stop-etch (EBASE) flip-chip process, whereby submicron gating on opposite sides of semiconductor epitaxial layers as thin as 0.24 microns can be achieved. Because both electron layers in the DELTT are 2D, the resonant tunneling features are unusually sharp, and can be easily modulated with one or more surface gates. We demonstrate DELTTs with peak-to-valley ratios in the source-drain I-V curve of order 20:1 below 1 K. Both the height and position of the resonant current peak can be controlled by gate voltage over a wide range. DELTTs with larger subband energy offsets ({approximately} 21 meV) exhibit characteristics that are nearly as good at 77 K, in good agreement with our theoretical calculations. Using these devices, we also demonstrate bistable memories operating at 77 K. Finally, we briefly discuss the prospects for room temperature operation, increases in gain, and high-speed.

  2. Inhibition of human cytochrome P450 2D6 (CYP2D6) by methadone.

    PubMed Central

    Wu, D; Otton, S V; Sproule, B A; Busto, U; Inaba, T; Kalow, W; Sellers, E M

    1993-01-01

    1. In microsomes prepared from three human livers, methadone competitively inhibited the O-demethylation of dextromethorphan, a marker substrate for CYP2D6. The apparent Ki value of methadone ranged from 2.5 to 5 microM. 2. Two hundred and fifty-two (252) white Caucasians, including 210 unrelated healthy volunteers and 42 opiate abusers undergoing treatment with methadone were phenotyped using dextromethorphan as the marker drug. Although the frequency of poor metabolizers was similar in both groups, the extensive metabolizers among the opiate abusers tended to have higher O-demethylation metabolic ratios and to excrete less of the dose as dextromethorphan metabolites than control extensive metabolizer subjects. These data suggest inhibition of CYP2D6 by methadone in vivo as well. 3. Because methadone is widely used in the treatment of opiate abuse, inhibition of CYP2D6 activity in these patients might contribute to exaggerated response or unexpected toxicity from drugs that are substrates of this enzyme. PMID:8448065

  3. Proteome analysis of Physcomitrella patens exposed to progressive dehydration and rehydration.

    PubMed

    Cui, Suxia; Hu, Jia; Guo, Shilei; Wang, Jie; Cheng, Yali; Dang, Xinxing; Wu, Lili; He, Yikun

    2012-01-01

    Physcomitrella patens is an extremely dehydration-tolerant moss. However, the molecular basis of its responses to loss of cellular water remains unclear. A comprehensive proteomic analysis of dehydration- and rehydration-responsive proteins has been conducted using quantitative two-dimensional difference in-gel electrophoresis (2D-DIGE), and traditional 2-D gel electrophoresis (2-DE) combined with MALDI TOF/TOF MS. Of the 216 differentially-expressed protein spots, 112 and 104 were dehydration- and rehydration-responsive proteins, respectively. The functional categories of the most differentially-expressed proteins were seed maturation, defence, protein synthesis and quality control, and energy production. Strikingly, most of the late embryogenesis abundant (LEA) proteins were expressed at a basal level under control conditions and their synthesis was strongly enhanced by dehydration, a pattern that was confirmed by RT-PCR. Actinoporins, phosphatidylethanolamine-binding protein, arabinogalactan protein, and phospholipase are the likely dominant players in the defence system. In addition, 24 proteins of unknown function were identified as novel dehydration- or rehydration-responsive proteins. Our data indicate that Physcomitrella adopts a rapid protein response mechanism to cope with dehydration in its leafy-shoot and basal expression levels of desiccation-tolerant proteins are rapidly upgraded at high levels under stress. This mechanism appears similar to that seen in angiosperm seeds.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. 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

  11. ORMDIN. 2-D Nonlinear Inverse Heat Conduction

    SciTech Connect

    Bass, B.R.

    1990-05-01

    ORMDIN is a finite-element program developed for two-dimensional nonlinear inverse heat conduction analysis as part of the Oak Ridge National Laboratory Pressurized Water Reactor Blowdown Heat Transfer (BDHT) program. One of the primary objectives of the program was to determine the transient surface temperature and surface heat flux of fuel pin simulators from internal thermocouple signals obtained during a loss-of-coolant accident experiment in the Thermal-Hydraulic Test Facility (THTF). ORMDIN was designed primarily to perform a transient two-dimensional nonlinear inverse heat conduction analysis of the THTF bundle 3 heater rod; however, it can be applied to other cylindrical geometries for which the thermophysical properties are prescribed functions of temperature. The program assumes that discretized temperature histories are provided at three thermocouple locations in the interior of the cylinder. Concurrent with the two-dimensional analysis, ORMDIN also generates one-dimensional solutions for each of the three thermocouple radial planes.

  12. 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.

  13. 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.

  14. areaDetector: Software for 2-D Detectors in EPICS

    SciTech Connect

    Rivers, Mark L.

    2010-06-23

    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.

  15. Experimental identification of diffusive coupling using 2D NMR.

    PubMed

    Song, Y-Q; Carneiro, G; Schwartz, L M; Johnson, D L

    2014-12-01

    Spin relaxation based nuclear magnetic resonance (NMR) methods have been used extensively to determine pore size distributions in a variety of materials. This approach is based on the assumption that each pore is in the fast diffusion limit but that diffusion between pores can be neglected. However, in complex materials these assumptions may be violated and the relaxation time distribution is not easily interpreted. We present a 2D NMR technique and an associated data analysis that allow us to work directly with the time dependent experimental data without Laplace inversion to identify the signature of diffusive coupling between different pores. Measurements on microporous glass beads and numerical simulations are used to illustrate the technique. PMID:25526135

  16. 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.

  17. 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. PMID:25329392

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization.

    PubMed

    Lasala, R; Coudray, N; Abdine, A; Zhang, Z; Lopez-Redondo, M; Kirshenbaum, R; Alexopoulos, J; Zolnai, Z; Stokes, D L; Ubarretxena-Belandia, I

    2015-02-01

    Electron crystallography is well suited for studying the structure of membrane proteins in their native lipid bilayer environment. This technique relies on electron cryomicroscopy of two-dimensional (2D) crystals, grown generally by reconstitution of purified membrane proteins into proteoliposomes under conditions favoring the formation of well-ordered lattices. Growing these crystals presents one of the major hurdles in the application of this technique. To identify conditions favoring crystallization a wide range of factors that can lead to a vast matrix of possible reagent combinations must be screened. However, in 2D crystallization these factors have traditionally been surveyed in a relatively limited fashion. To address this problem we carried out a detailed analysis of published 2D crystallization conditions for 12 β-barrel and 138 α-helical membrane proteins. From this analysis we identified the most successful conditions and applied them in the design of new sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. Using these matrices we have run 19 crystallization screens for 16 different membrane proteins totaling over 1300 individual crystallization conditions. Six membrane proteins have yielded diffracting 2D crystals suitable for structure determination, indicating that these new matrices show promise to accelerate the success rate of membrane protein 2D crystallization.

  3. Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization

    PubMed Central

    Lasala, R.; Coudray, N.; Abdine, A.; Zhang, Z.; Lopez-Redondo, M.; Kirshenbaum, R.; Alexopoulos, J.; Zolnai, Z.; Stokes, D.L.; Ubarretxena-Belandia, I.

    2014-01-01

    Electron crystallography is well suited for studying the structure of membrane proteins in their native lipid bilayer environment. This technique relies on electron cryomicroscopy of two-dimensional (2D) crystals, grown generally by reconstitution of purified membrane proteins into proteoliposomes under conditions favoring the formation of well-ordered lattices. Growing these crystals presents one of the major hurdles in the application of this technique. To identify conditions favoring crystallization a wide range of factors that can lead to a vast matrix of possible reagent combinations must be screened. However, in 2D crystallization these factors have traditionally been surveyed in a relatively limited fashion. To address this problem we carried out a detailed analysis of published 2D crystallization conditions for 12 β-barrel and 138 α-helical membrane proteins. From this analysis we identified the most successful conditions and applied them in the design of new sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. Using these matrices we have run 19 crystallization screens for 16 different membrane proteins totaling over 1,300 individual crystallization conditions. Six membrane proteins have yielded diffracting 2D crystals suitable for structure determination, indicating that these new matrices show promise to accelerate the success rate of membrane protein 2D crystallization. PMID:25478971

  4. Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization.

    PubMed

    Lasala, R; Coudray, N; Abdine, A; Zhang, Z; Lopez-Redondo, M; Kirshenbaum, R; Alexopoulos, J; Zolnai, Z; Stokes, D L; Ubarretxena-Belandia, I

    2015-02-01

    Electron crystallography is well suited for studying the structure of membrane proteins in their native lipid bilayer environment. This technique relies on electron cryomicroscopy of two-dimensional (2D) crystals, grown generally by reconstitution of purified membrane proteins into proteoliposomes under conditions favoring the formation of well-ordered lattices. Growing these crystals presents one of the major hurdles in the application of this technique. To identify conditions favoring crystallization a wide range of factors that can lead to a vast matrix of possible reagent combinations must be screened. However, in 2D crystallization these factors have traditionally been surveyed in a relatively limited fashion. To address this problem we carried out a detailed analysis of published 2D crystallization conditions for 12 β-barrel and 138 α-helical membrane proteins. From this analysis we identified the most successful conditions and applied them in the design of new sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. Using these matrices we have run 19 crystallization screens for 16 different membrane proteins totaling over 1300 individual crystallization conditions. Six membrane proteins have yielded diffracting 2D crystals suitable for structure determination, indicating that these new matrices show promise to accelerate the success rate of membrane protein 2D crystallization. PMID:25478971

  5. L-plastin is involved in NKG2D recruitment into lipid rafts and NKG2D-mediated NK cell migration.

    PubMed

    Serrano-Pertierra, Esther; Cernuda-Morollón, Eva; Brdička, Tomáš; Hoøejši, Václav; López-Larrea, Carlos

    2014-09-01

    Membrane rafts are microdomains of the plasma membrane that have multiple biological functions. The involvement of these structures in the biology of T cells, namely in signal transduction by the TCR, has been widely studied. However, the role of membrane rafts in immunoreceptor signaling in NK cells is less well known. We studied the distribution of the activating NKG2D receptor in lipid rafts by isolating DRMs in a sucrose density gradient or by raft fractionation by β-OG-selective solubility in the NKL cell line. We found that the NKG2D-DAP10 complex and pVav are recruited into rafts upon receptor stimulation. Qualitative proteomic analysis of these fractions showed that the actin cytoskeleton is involved in this process. In particular, we found that the actin-bundling protein L-plastin plays an important role in the clustering of NKG2D into lipid rafts. Moreover, coengagement of the inhibitory receptor NKG2A partially disrupted NKG2D recruitment into rafts. Furthermore, we demonstrated that L-plastin participates in NKG2D-mediated inhibition of NK cell chemotaxis.

  6. A Geometric Boolean Library for 2D Objects

    2006-01-05

    The 2D Boolean Library is a collection of C++ classes -- which primarily represent 2D geometric data and relationships, and routines -- which contain algorithms for 2D geometric Boolean operations and utility functions. Classes are provided for 2D points, lines, arcs, edgeuses, loops, surfaces and mask sets. Routines are provided that incorporate the Boolean operations Union(OR), XOR, Intersection and Difference. Various analytical geometry routines and routines for importing and exporting the data in various filemore » formats, are also provided in the library.« less

  7. Synthesis, characterization and anti-microbial evaluation of Cu(II), Ni(II), Pt(II) and Pd(II) sulfonylhydrazone complexes; 2D-QSAR analysis of Ni(II) complexes of sulfonylhydrazone derivatives

    NASA Astrophysics Data System (ADS)

    Özbek, Neslihan; Alyar, Saliha; Alyar, Hamit; Şahin, Ertan; Karacan, Nurcan

    2013-05-01

    Copper(II), nickel(II), platinum(II) and palladium(II) complexes with 2-hydroxy-1-naphthaldehyde-N-methylpropanesulfonylhydrazone (nafpsmh) derived from propanesulfonic acid-1-methylhydrazide (psmh) were synthesized, their structure were identified, and antimicrobial activity of the compounds was screened against three Gram-positive and three Gram-negative bacteria. The results of antimicrobial studies indicate that Pt(II) and Pd(II) complexes showed the most activity against all bacteria. The crystal structure of 2-hydroxy-1-naphthaldehyde-N-methylpropanesulfonylhydrazone (nafpsmh) was also investigated by X-ray analysis. A series of Ni(II) sulfonyl hydrazone complexes (1-33) was synthesized and tested in vitro against Escherichia coli and Staphylococcus aureus. Their antimicrobial activities were used in the QSAR analysis. Four-parameter QSAR models revealed that nucleophilic reaction index for Ni and O atoms, and HOMO-LUMO energy gap play key roles in the antimicrobial activity.

  8. VizieR Online Data Catalog: The 2dF Galaxy Redshift Survey (2dFGRS) (2dFGRS Team, 1998-2003)

    NASA Astrophysics Data System (ADS)

    Colless, M.; Dalton, G.; Maddox, S.; Sutherland, W.; Norberg, P.; Cole, S.; Bland-Hawthorn, J.; Bridges, T.; Cannon, R.; Collins, C.; Couch, W.; Cross, N.; Deeley, K.; de Propris, R.; Driver, S. P.; Efstathiou, G.; Ellis, R. S.; Frenk, C. S.; Glazebrook, K.; Jackson, C.; Lahav, O.; Lewis, I.; Lumsden, S.; Madgwick, D.; Peacock, J. A.; Peterson, B. A.; Price, I.; Seaborne, M.; Taylor, K.

    2007-11-01

    The 2dF Galaxy Redshift Survey (2dFGRS) is a major spectroscopic survey taking full advantage of the unique capabilities of the 2dF facility built by the Anglo-Australian Observatory. The 2dFGRS is integrated with the 2dF QSO survey (2QZ, Cat. VII/241). The 2dFGRS obtained spectra for 245591 objects, mainly galaxies, brighter than a nominal extinction-corrected magnitude limit of bJ=19.45. Reliable (quality>=3) redshifts were obtained for 221414 galaxies. The galaxies cover an area of approximately 1500 square degrees selected from the extended APM Galaxy Survey in three regions: a North Galactic Pole (NGP) strip, a South Galactic Pole (SGP) strip, and random fields scattered around the SGP strip. Redshifts are measured from spectra covering 3600-8000 Angstroms at a two-pixel resolution of 9.0 Angstrom and a median S/N of 13 per pixel. All redshift identifications are visually checked and assigned a quality parameter Q in the range 1-5; Q>=3 redshifts are 98.4% reliable and have an rms uncertainty of 85 km/s. The overall redshift completeness for Q>=3 redshifts is 91.8% but this varies with magnitude from 99% for the brightest galaxies to 90% for objects at the survey limit. The 2dFGRS data base is available on the World Wide Web at http://www.mso.anu.edu.au/2dFGRS/. (6 data files).

  9. Proteomic analysis identifies interleukin 11 regulated plasma membrane proteins in human endometrial epithelial cells in vitro

    PubMed Central

    2011-01-01

    Background During the peri-implantation period, the embryo adheres to an adequately prepared or receptive endometrial surface epithelium. Abnormal embryo adhesion to the endometrium results in embryo implantation failure and infertility. Endometrial epithelial cell plasma membrane proteins critical in regulating adhesion may potentially be infertility biomarkers or targets for treating infertility. Interleukin (IL) 11 regulates human endometrial epithelial cells (hEEC) adhesion. Its production is abnormal in women with infertility. The objective of the study was to identify IL11 regulated plasma membrane proteins in hEEC in vitro using a proteomic approach. Methods Using a 2D-differential in-gel electrophoresis (DIGE) electrophoresis combined with LCMS/MS mass spectrometry approach, we identified 20 unique plasma membrane proteins differentially regulated by IL11 in ECC-1 cells, a hEEC derived cell line. Two IL11 regulated proteins with known roles in cell adhesion, annexin A2 (ANXA2) and flotillin-1 (FLOT1), were validated by Western blot and immunocytochemistry in hEEC lines (ECC-1 and an additional cell line, Ishikawa) and primary hEEC. Flotilin-1 was further validated by immunohistochemistry in human endometrium throughout the menstrual cycle (n = 6-8/cycle). Results 2D-DIGE analysis identified 4 spots that were significantly different between control and IL11 treated group. Of these 4 spots, there were 20 proteins that were identified with LCMS/MS. Two proteins; ANXA2 and FLOT1 were chosen for further analyses and have found to be significantly up-regulated following IL11 treatment. Western blot analysis showed a 2-fold and a 2.5-fold increase of ANXA2 in hEEC membrane fraction of ECC-1 and Ishikawa cells respectively. Similarly, a 1.8-fold and a 2.3/2.4-fold increase was also observed for FLOT1 in hEEC membrane fraction of ECC-1 and Ishikawa cells respectively. In vitro, IL11 induced stronger ANXA2 expression on cell surface of primary hEEC and ECC-1 whilst

  10. 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

  11. Nonlinear Heat Transfer 2d Structure

    1987-09-01

    DOT-BPMD is a general-purpose, finite-element, heat-transfer program used to predict thermal environments. The code considers linear and nonlinear transient or steady-state heat conduction in two-dimensional planar or axisymmetric representations of structures. Capabilities are provided for modeling anisotropic heterogeneous materials with temperature-dependent thermal properties and time-dependent temperature, heat flux, convection and radiation boundary conditions, together with time-dependent internal heat generation. DOT-BPMD may be used in the evaluation of steady-state geothermal gradients as well as in themore » transient heat conduction analysis of repository and waste package subsystems. Strengths of DOT-BPMD include its ability to account for a wide range of possible boundary conditions, nonlinear material properties, and its efficient equation solution algorithm. Limitations include the lack of a three-dimensional analysis capability, no radiative or convective internal heat transfer, and the need to maintain a constant time-step in each program execution.« less

  12. Klassifikation von Standardebenen in der 2D-Echokardiographie mittels 2D-3D-Bildregistrierung

    NASA Astrophysics Data System (ADS)

    Bergmeir, Christoph; Subramanian, Navneeth

    Zum Zweck der Entwicklung eines Systems, das einen unerfahrenen Anwender von Ultraschall (US) zur Aufnahme relevanter anatomischer Strukturen leitet, untersuchen wir die Machbarkeit von 2D-US zu 3D-CT Registrierung. Wir verwenden US-Aufnahmen von Standardebenen des Herzens, welche zu einem 3D-CT-Modell registriert werden. Unser Algorithmus unterzieht sowohl die US-Bilder als auch den CT-Datensatz Vorverarbeitungsschritten, welche die Daten durch Segmentierung auf wesentliche Informationen in Form von Labein für Muskel und Blut reduzieren. Anschließend werden diese Label zur Registrierung mittels der Match-Cardinality-Metrik genutzt. Durch mehrmaliges Registrieren mit verschiedenen Initialisierungen ermitteln wir die im US-Bild sichtbare Standardebene. Wir evaluierten die Methode auf sieben US-Bildern von Standardebenen. Fünf davon wurden korrekt zugeordnet.

  13. 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

    2016-09-01

    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. PMID:27537619

  14. CVMAC 2D Program: A method of converting 3D to 2D

    SciTech Connect

    Lown, J.

    1990-06-20

    This paper presents the user with a method of converting a three- dimensional wire frame model into a technical illustration, detail, or assembly drawing. By using the 2D Program, entities can be mapped from three-dimensional model space into two-dimensional model space, as if they are being traced. Selected entities to be mapped can include circles, arcs, lines, and points. This program prompts the user to digitize the view to be mapped, specify the layers in which the new two-dimensional entities will reside, and select the entities, either by digitizing or windowing. The new two-dimensional entities are displayed in a small view which the program creates in the lower left corner of the drawing. 9 figs.

  15. 2-D and 3-D numerical simulation of a supersonic inlet flowfield

    NASA Astrophysics Data System (ADS)

    Enomoto, Shunji; Arakawa, Chuichi

    The 2-D and 3-D steady, Reynolds-averaged Navier-Stokes equations were numerically solved for the flowfields in an experimentally tested inlet model with bleed through a cavity. In the 2-D analysis, a normal shock was located at diffuser inlet instead of the position below the cavity. The normal shock in the middle of the diffuser caused a massive separation of the boundary layer and a large total pressure loss. In the 3-D analysis, the shock wave was distorted by the side wall boundary layer separation, and the complex flow structure was established. The result of the 3-D analysis agreed well with the experiment.

  16. 2D Four-Channel Perfect Reconstruction Filter Bank Realized with the 2D Lattice Filter Structure

    NASA Astrophysics Data System (ADS)

    Sezen, S.; Ertüzün, A.

    2006-12-01

    A novel orthogonal 2D lattice structure is incorporated into the design of a nonseparable 2D four-channel perfect reconstruction filter bank. The proposed filter bank is obtained by using the polyphase decomposition technique which requires the design of an orthogonal 2D lattice filter. Due to constraint of perfect reconstruction, each stage of this lattice filter bank is simply parameterized by two coefficients. The perfect reconstruction property is satisfied regardless of the actual values of these parameters and of the number of the lattice stages. It is also shown that a separable 2D four-channel perfect reconstruction lattice filter bank can be constructed from the 1D lattice filter and that this is a special case of the proposed 2D lattice filter bank under certain conditions. The perfect reconstruction property of the proposed 2D lattice filter approach is verified by computer simulations.

  17. FluoRender: An Application of 2D Image Space Methods for 3D and 4D Confocal Microscopy Data Visualization in Neurobiology Research

    PubMed Central

    Wan, Yong; Otsuna, Hideo; Chien, Chi-Bin; Hansen, Charles

    2013-01-01

    2D image space methods are processing methods applied after the volumetric data are projected and rendered into the 2D image space, such as 2D filtering, tone mapping and compositing. In the application domain of volume visualization, most 2D image space methods can be carried out more efficiently than their 3D counterparts. Most importantly, 2D image space methods can be used to enhance volume visualization quality when applied together with volume rendering methods. In this paper, we present and discuss the applications of a series of 2D image space methods as enhancements to confocal microscopy visualizations, including 2D tone mapping, 2D compositing, and 2D color mapping. These methods are easily integrated with our existing confocal visualization tool, FluoRender, and the outcome is a full-featured visualization system that meets neurobiologists’ demands for qualitative analysis of confocal microscopy data. PMID:23584131

  18. FluoRender: An Application of 2D Image Space Methods for 3D and 4D Confocal Microscopy Data Visualization in Neurobiology Research.

    PubMed

    Wan, Yong; Otsuna, Hideo; Chien, Chi-Bin; Hansen, Charles

    2012-01-01

    2D image space methods are processing methods applied after the volumetric data are projected and rendered into the 2D image space, such as 2D filtering, tone mapping and compositing. In the application domain of volume visualization, most 2D image space methods can be carried out more efficiently than their 3D counterparts. Most importantly, 2D image space methods can be used to enhance volume visualization quality when applied together with volume rendering methods. In this paper, we present and discuss the applications of a series of 2D image space methods as enhancements to confocal microscopy visualizations, including 2D tone mapping, 2D compositing, and 2D color mapping. These methods are easily integrated with our existing confocal visualization tool, FluoRender, and the outcome is a full-featured visualization system that meets neurobiologists' demands for qualitative analysis of confocal microscopy data.

  19. 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

  20. Functional characterization of CYP2D6 enhancer polymorphisms

    PubMed Central

    Wang, Danxin; Papp, Audrey C.; Sun, Xiaochun

    2015-01-01

    CYP2D6 metabolizes nearly 25% of clinically used drugs. Genetic polymorphisms cause large inter-individual variability in CYP2D6 enzyme activity and are currently used as biomarker to predict CYP2D6 metabolizer phenotype. Previously, we had identified a region 115 kb downstream of CYP2D6 as enhancer for CYP2D6, containing two completely linked single nucleotide polymorphisms (SNPs), rs133333 and rs5758550, associated with enhanced transcription. However, the enhancer effect on CYP2D6 expression, and the causative variant, remained to be ascertained. To characterize the CYP2D6 enhancer element, we applied chromatin conformation capture combined with the next-generation sequencing (4C assays) and chromatin immunoprecipitation with P300 antibody, in HepG2 and human primary culture hepatocytes. The results confirmed the role of the previously identified enhancer region in CYP2D6 expression, expanding the number of candidate variants to three highly linked SNPs (rs133333, rs5758550 and rs4822082). Among these, only rs5758550 demonstrated regulating enhancer activity in a reporter gene assay. Use of clustered regularly interspaced short palindromic repeats mediated genome editing in HepG2 cells targeting suspected enhancer regions decreased CYP2D6 mRNA expression by 70%, only upon deletion of the rs5758550 region. These results demonstrate robust effects of both the enhancer element and SNP rs5758550 on CYP2D6 expression, supporting consideration of rs5758550 for CYP2D6 genotyping panels to yield more accurate phenotype prediction. PMID:25381333

  1. An Incompressible 2D Didactic Model with Singularity and Explicit Solutions of the 2D Boussinesq Equations

    NASA Astrophysics Data System (ADS)

    Chae, Dongho; Constantin, Peter; Wu, Jiahong

    2014-09-01

    We give an example of a well posed, finite energy, 2D incompressible active scalar equation with the same scaling as the surface quasi-geostrophic equation and prove that it can produce finite time singularities. In spite of its simplicity, this seems to be the first such example. Further, we construct explicit solutions of the 2D Boussinesq equations whose gradients grow exponentially in time for all time. In addition, we introduce a variant of the 2D Boussinesq equations which is perhaps a more faithful companion of the 3D axisymmetric Euler equations than the usual 2D Boussinesq equations.

  2. 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.

  3. 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).

  4. 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…

  5. 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. PMID:27334788

  6. 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.

  7. Glutamate dependent NMDA receptor 2D is a novel angiogenic tumour endothelial marker in colorectal cancer

    PubMed Central

    Ward, Stephen; Heath, Victoria L.; Ismail, Tariq; Bicknell, Roy

    2016-01-01

    Current vascular-targeted therapies in colorectal cancer (CRC) have shown limited benefit. The lack of novel, specific treatment in CRC has been hampered by a dearth of specific endothelial markers. Microarray comparison of endothelial gene expression in patient-matched CRC and normal colon identified a panel of putative colorectal tumour endothelial markers. Of these the glutamate dependent NMDA receptor GRIN2D emerged as the most interesting target. GRIN2D expression was shown to be specific to colorectal cancer vessels by RTqPCR and IHC analysis. Its expression was additionally shown be predictive of improved survival in CRC. Targeted knockdown studies in vitro demonstrated a role for GRIN2D in endothelial function and angiogenesis. This effect was also shown in vivo as vaccination against the extracellular region of GRIN2D resulted in reduced vascularisation in the subcutaneous sponge angiogenesis assay. The utility of immunologically targeting GRIN2D in CRC was demonstrated by the vaccination approach inhibiting murine CRC tumour growth and vascularisation. GRIN2D represents a promising target for the future treatment of CRC. PMID:26943033

  8. 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.

  9. 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.

  10. Van der Waals stacked 2D layered materials for optoelectronics

    NASA Astrophysics Data System (ADS)

    Zhang, Wenjing; Wang, Qixing; Chen, Yu; Wang, Zhuo; Wee, Andrew T. S.

    2016-06-01

    The band gaps of many atomically thin 2D layered materials such as graphene, black phosphorus, monolayer semiconducting transition metal dichalcogenides and hBN range from 0 to 6 eV. These isolated atomic planes can be reassembled into hybrid heterostructures made layer by layer in a precisely chosen sequence. Thus, the electronic properties of 2D materials can be engineered by van der Waals stacking, and the interlayer coupling can be tuned, which opens up avenues for creating new material systems with rich functionalities and novel physical properties. Early studies suggest that van der Waals stacked 2D materials work exceptionally well, dramatically enriching the optoelectronics applications of 2D materials. Here we review recent progress in van der Waals stacked 2D materials, and discuss their potential applications in optoelectronics.

  11. Presence of activatable Shiga toxin genotype (stx(2d)) in Shiga toxigenic Escherichia coli from livestock sources.

    PubMed

    Gobius, Kari S; Higgs, Glen M; Desmarchelier, Patricia M

    2003-08-01

    Stx2d is a recently described Shiga toxin whose cytotoxicity is activated 10- to 1000-fold by the elastase present in mouse or human intestinal mucus. We examined Shiga toxigenic Escherichia coli (STEC) strains isolated from food and livestock sources for the presence of activatable stx(2d). The stx(2) operons of STEC were first analyzed by PCR-restriction fragment length polymorphism (RFLP) analysis and categorized as stx(2), stx(2c vha), stx(2c vhb), or stx(2d EH250). Subsequently, the stx(2c vha) and stx(2c vhb) operons were screened for the absence of a PstI site in the stx(2A) subunit gene, a restriction site polymorphism which is a predictive indicator for the stx(2d) (activatable) genotype. Twelve STEC isolates carrying putative stx(2d) operons were identified, and nucleotide sequencing was used to confirm the identification of these operons as stx(2d). The complete nucleotide sequences of seven representative stx(2d) operons were determined. Shiga toxin expression in stx(2d) isolates was confirmed by immunoblotting. stx(2d) isolates were induced for the production of bacteriophages carrying stx. Two isolates were able to produce bacteriophages phi1662a and phi1720a carrying the stx(2d) operons. RFLP analysis of bacteriophage genomic DNA revealed that phi1662a and phi1720a were highly related to each other; however, the DNA sequences of these two stx(2d) operons were distinct. The STEC strains carrying these operons were isolated from retail ground beef. Surveillance for STEC strains expressing activatable Stx2d Shiga toxin among clinical cases may indicate the significance of this toxin subtype to human health.

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

    PubMed Central

    Pan, Xian

    2015-01-01

    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. PMID:25943116

  13. The Mammalian Orthologs of Drosophila Lgd, CC2D1A and CC2D1B, Function in the Endocytic Pathway, but Their Individual Loss of Function Does Not Affect Notch Signalling

    PubMed Central

    Drusenheimer, Nadja; Migdal, Bernhard; Jäckel, Sandra; Tveriakhina, Lena; Scheider, Kristina; Schulz, Katharina; Gröper, Jieny; Köhrer, Karl; Klein, Thomas

    2015-01-01

    CC2D1A and CC2D1B belong to the evolutionary conserved Lgd protein family with members in all multi-cellular animals. Several functions such as centrosomal cleavage, involvement in signalling pathways, immune response and synapse maturation have been described for CC2D1A. Moreover, the Drosophila melanogaster ortholog Lgd was shown to be involved in the endosomal trafficking of the Notch receptor and other transmembrane receptors and physically interacts with the ESCRT-III component Shrub/CHMP4. To determine if this function is conserved in mammals we generated and characterized Cc2d1a and Cc2d1b conditional knockout mice. While Cc2d1b deficient mice displayed no obvious phenotype, we found that Cc2d1a deficient mice as well as conditional mutants that lack CC2D1A only in the nervous system die shortly after birth due to respiratory distress. This finding confirms the suspicion that the breathing defect is caused by the central nervous system. However, an involvement in centrosomal function could not be confirmed in Cc2d1a deficient MEF cells. To analyse an influence on Notch signalling, we generated intestine specific Cc2d1a mutant mice. These mice did not display any alterations in goblet cell number, proliferating cell number or expression of the Notch reporter Hes1-emGFP, suggesting that CC2D1A is not required for Notch signalling. However, our EM analysis revealed that the average size of endosomes of Cc2d1a mutant cells, but not Cc2d1b mutant cells, is increased, indicating a defect in endosomal morphogenesis. We could show that CC2D1A and its interaction partner CHMP4B are localised on endosomes in MEF cells, when the activity of the endosomal protein VPS4 is reduced. This indicates that CC2D1A cycles between the cytosol and the endosomal membrane. Additionally, in rescue experiments in D. melanogaster, CC2D1A and CC2D1B were able to functionally replace Lgd. Altogether our data suggest a functional conservation of the Lgd protein family in the ESCRT

  14. Two-dimensional (2D) correlation coefficient analyses of heavily overlapped near-infrared spectra.

    PubMed

    Sasić, Slobodan; Sato, Harumi; Shimoyama, Masahiko; Ozaki, Yukihiro

    2005-05-01

    Two-dimensional (2D) correlation coefficient analysis is employed to classify and characterize spectral variations among heavily overlapped near-infrared spectra of pellets and films of three kinds of polyethylene (PE), high-density (HD), low density (LD), and linear low-density (LLD) polyethylene, and five kinds of ivory signature seals. The sample-sample (SS) 2D correlation maps are used for classification while the wavenumber-wavenumber (WW) 2D correlation maps are used for determining spectral variation among the above materials. Both correlation maps are obtained by multiplying the original data with themselves. It is found that the NIR spectra of pellets and films of HD PE are clearly different from those of LD PE and LLD PE, while the NIR spectra of five kinds of ivory seals yield easily discernable squares in the SS correlation maps. The background variation is thought to be behind the differentiation of the PE samples because the WW correlation maps do not indicate appearance of new bands. The correlation results are compared with those of principal component analysis (PCA). This study is a novel application of 2D correlation coefficient analysis which reveals that a comprehensive description of demanding spectral systems is achievable by utterly simple mathematical means because 2D correlation maps are obtained via a single mathematical operation.

  15. 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

  16. Measuring (13)C-(2)D dipolar couplings with a universal REDOR dephasing curve

    PubMed

    Gullion

    2000-09-01

    A (13)C-observe REDOR experiment is described which allows (13)C-(2)D dipolar couplings to be obtained by a universal dipolar dephasing curve. Previous (13)C-observe REDOR experiments on (13)C-(2)D spin pairs generally relied on numerical simulations to obtain the dipolar coupling. The REDOR experiment described in this article is based on a deuterium composite pulse, and the data analysis eliminates the need for numerical simulations and is the same as the traditional REDOR analysis performed on pairs of spin-12 nuclei. Copyright 2000 Academic Press. PMID:10968975

  17. 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

    2016-08-01

    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.

  18. [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.

  19. [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. PMID:27220253

  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. FRANC2D: A two-dimensional crack propagation simulator. Version 2.7: User's guide

    NASA Technical Reports Server (NTRS)

    Wawrzynek, Paul; Ingraffea, Anthony

    1994-01-01

    FRANC 2D (FRacture ANalysis Code, 2 Dimensions) is a menu driven, interactive finite element computer code that performs fracture mechanics analyses of 2-D structures. The code has an automatic mesh generator for triangular and quadrilateral elements. FRANC2D calculates the stress intensity factor using linear elastic fracture mechanics and evaluates crack extension using several methods that may be selected by the user. The code features a mesh refinement and adaptive mesh generation capability that is automatically developed according to the predicted crack extension direction and length. The code also has unique features that permit the analysis of layered structure with load transfer through simulated mechanical fasteners or bonded joints. The code was written for UNIX workstations with X-windows graphics and may be executed on the following computers: DEC DecStation 3000 and 5000 series, IBM RS/6000 series, Hewlitt-Packard 9000/700 series, SUN Sparc stations, and most Silicon Graphics models.

  2. Installed Transonic 2D Nozzle Nacelle Boattail Drag Study

    NASA Technical Reports Server (NTRS)

    Malone, Michael B.; Peavey, Charles C.

    1999-01-01

    The Transonic Nozzle Boattail Drag Study was initiated in 1995 to develop an understanding of how external nozzle transonic aerodynamics effect airplane performance and how strongly those effects are dependent on nozzle configuration (2D vs. axisymmetric). MDC analyzed the axisymmetric nozzle. Boeing subcontracted Northrop-Grumman to analyze the 2D nozzle. AU participants analyzed the AGARD nozzle as a check-out and validation case. Once the codes were checked out and the gridding resolution necessary for modeling the separated flow in this region determined, the analysis moved to the installed wing/body/nacelle/diverter cases. The boat tail drag validation case was the AGARD B.4 rectangular nozzle. This test case offered both test data and previous CFD analyses for comparison. Results were obtained for test cases B.4.1 (M=0.6) and B.4.2 (M=0.938) and compared very well with the experimental data. Once the validation was complete a CFD grid was constructed for the full Ref. H configuration (wing/body/nacelle/diverter) using a combination of patched and overlapped (Chimera) grids. This was done to ensure that the grid topologies and density would be adequate for the full model. The use of overlapped grids allowed the same grids from the full configuration model to be used for the wing/body alone cases, thus eliminating the risk of grid differences affecting the determination of the installation effects. Once the full configuration model was run and deemed to be suitable the nacelle/diverter grids were removed and the wing/body analysis performed. Reference H wing/body results were completed for M=0.9 (a=0.0, 2.0, 4.0, 6.0 and 8.0), M=1.1 (a=4.0 and 6.0) and M=2.4 (a=0.0, 2.0, 4.4, 6.0 and 8.0). Comparisons of the M=0.9 and M=2.4 cases were made with available wind tunnel data and overall comparisons were good. The axi-inlet/2D nozzle nacelle was analyzed isolated. The isolated nacelle data coupled with the wing/body result enabled the interference effects of the

  3. Long-Read Single Molecule Real-Time Full Gene Sequencing of Cytochrome P450-2D6.

    PubMed

    Qiao, Wanqiong; Yang, Yao; Sebra, Robert; Mendiratta, Geetu; Gaedigk, Andrea; Desnick, Robert J; Scott, Stuart A

    2016-03-01

    The cytochrome P450-2D6 (CYP2D6) enzyme metabolizes ∼25% of common medications, yet homologous pseudogenes and copy number variants (CNVs) make interrogating the polymorphic CYP2D6 gene with short-read sequencing challenging. Therefore, we developed a novel long-read, full gene CYP2D6 single molecule real-time (SMRT) sequencing method using the Pacific Biosciences platform. Long-range PCR and CYP2D6 SMRT sequencing of 10 previously genotyped controls identified expected star (*) alleles, but also enabled suballele resolution, diplotype refinement, and discovery of novel alleles. Coupled with an optimized variant-calling pipeline, CYP2D6 SMRT sequencing was highly reproducible as triplicate intra- and inter-run nonreference genotype results were completely concordant. Importantly, targeted SMRT sequencing of upstream and downstream CYP2D6 gene copies characterized the duplicated allele in 15 control samples with CYP2D6 CNVs. The utility of CYP2D6 SMRT sequencing was further underscored by identifying the diplotypes of 14 samples with discordant or unclear CYP2D6 configurations from previous targeted genotyping, which again included suballele resolution, duplicated allele characterization, and discovery of a novel allele and tandem arrangement. Taken together, long-read CYP2D6 SMRT sequencing is an innovative, reproducible, and validated method for full-gene characterization, duplication allele-specific analysis, and novel allele discovery, which will likely improve CYP2D6 metabolizer phenotype prediction for both research and clinical testing applications.

  4. 2D electron cyclotron emission imaging at ASDEX Upgrade (invited)

    SciTech Connect

    Classen, I. G. J.; Boom, J. E.; Vries, P. C. de; Suttrop, W.; Schmid, E.; Garcia-Munoz, M.; Schneider, P. A.; Tobias, B.; Domier, C. W.; Luhmann, N. C. Jr.; Donne, A. J. H.; Jaspers, R. J. E.; Park, H. K.; Munsat, T.

    2010-10-15

    The newly installed electron cyclotron emission imaging diagnostic on ASDEX Upgrade provides measurements of the 2D electron temperature dynamics with high spatial and temporal resolution. An overview of the technical and experimental properties of the system is presented. These properties are illustrated by the measurements of the edge localized mode and the reversed shear Alfven eigenmode, showing both the advantage of having a two-dimensional (2D) measurement, as well as some of the limitations of electron cyclotron emission measurements. Furthermore, the application of singular value decomposition as a powerful tool for analyzing and filtering 2D data is presented.

  5. Recent advances in 2D materials for photocatalysis.

    PubMed

    Luo, Bin; Liu, Gang; Wang, Lianzhou

    2016-04-01

    Two-dimensional (2D) materials have attracted increasing attention for photocatalytic applications because of their unique thickness dependent physical and chemical properties. This review gives a brief overview of the recent developments concerning the chemical synthesis and structural design of 2D materials at the nanoscale and their applications in photocatalytic areas. In particular, recent progress on the emerging strategies for tailoring 2D material-based photocatalysts to improve their photo-activity including elemental doping, heterostructure design and functional architecture assembly is discussed.

  6. The infrared spectrum of the Ne-C2D2 complex.

    PubMed

    Moazzen-Ahmadi, N; McKellar, A R W; Fernández, Berta; Farrelly, David

    2015-11-28

    Infrared spectra of Ne-C2D2 are observed in the region of the ν3 fundamental band (asymmetric C-D stretch, ≈2440 cm(-1)) using a tunable optical parametric oscillator to probe a pulsed supersonic slit jet expansion from a cooled nozzle. Like helium-acetylene, this system lies close to the free rotor limit, making analysis tricky because stronger transitions tend to pile up close to monomer (C2D2) rotation-vibration transitions. Assignments are aided by predicted rotational energies calculated from a published ab initio intermolecular potential energy surface. The analysis extends up to the j = 3←2 band, where j labels C2D2 rotation within the dimer, and is much more complete than the limited infrared assignments previously reported for Ne-C2H2 and Ne-C2HD. Two previous microwave transitions within the j = 1 state of Ne-C2D2 are reassigned. Coriolis model fits to the theoretical levels and to the spectrum are compared. Since the variations observed as a function of C2D2 vibrational excitation are comparable to those noted between theory and experiment, it is evident that more detailed testing of theory will require vibrational averaging over the acetylene intramolecular modes.

  7. FLAC/SPECFEM2D coupled numerical simulation of wavefields near excavation boundaries in underground mines

    NASA Astrophysics Data System (ADS)

    Wang, X.; Cai, M.

    2016-11-01

    A nonlinear velocity model that considers the influence of confinement and rock mass failure on wave velocity is developed. A numerical method, which couples FLAC and SPECFEM2D, is developed for ground motion modeling near excavation boundaries in underground mines. The motivation of developing the FLAC/SPECFEM2D coupled approach is to take merits of each code, such as the stress analysis capability in FLAC and the powerful wave propagation analysis capability in SPECFEM2D. Because stress redistribution and failure of the rock mass around an excavation are considered, realistic non-uniform velocity fields for the SPECFEM2D model can be obtained, and this is a notable feature of this study. Very large differences in wavefields and ground motion are observed between the results from the non-uniform and the uniform velocity models. If the non-uniform velocity model is used, the ground motion around a stope can be amplified up to five times larger than that given by the design scaling law. If a uniform velocity model is used, the amplification factor is only about three. Using the FLAC/SPECFEM2D coupled modeling approach, accurate velocity models can be constructed and this in turn will assist in predicting ground motions accurately around underground excavations.

  8. Synthesis, structural elucidation and spectroscopic analysis of 3a,8b-dihydroxy-4-oxo-1H,2H,3H,3aH,4H,8bH-indeno[1,2-d]imidazolidin-2-iminium chloride

    NASA Astrophysics Data System (ADS)

    Uma Devi, T.; Priya, S.; Selvanayagam, S.; Ravikumar, K.; Anitha, K.

    2012-11-01

    Ninhydrin guanidinium chloride (3a,8b-dihydroxy-4-oxo-1H,2H,3H,3aH,4H,8bH-indeno [1,2-d]imidazolidin-2-iminium chloride) a semiorganic crystal was synthesized. The structure was determined using X-ray single crystal technique. Comparisons between the FT-IR spectrum of ninhydrin guanidinium chloride with ninhydrin were made. Melting point was found using thermal measurements. The molecular geometry, vibrational frequencies and Mulliken charges of the compound in the ground state have been calculated by the density functional theory (DFT) method with 3-21G(d,p) basis set and theoretical frequencies were compared with the experimental FT-IR spectrum. Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis, natural bond orbitals (NBO) and thermodynamic properties at various temperatures of the compound were investigated by theoretical calculations.

  9. Spot Weld Analysis With 2D Ultrasonic Arrays

    PubMed Central

    Denisov, A. A.; Shakarji, C. M.; Lawford, B. B.; Maev, R. Gr.; Paille, J. M.

    2004-01-01

    This paper describes a threefold method of testing the performance of an array-based ultrasonic tool for nondestructive testing of spot welds. The tool is described in its capabilities, use, and advantages over existing counterparts. Performance testing for and the results from carrying out the testing are described. The three performance testing methods include 1) the use of calibrated samples, 2) comparisons with actual spot-welds, and 3) a performance evaluation of the embedded fitting software. The test of the fitting software was carried out by a comparison of results with reference fits supplied by the National Institute of Standards and Technology. PMID:27366607

  10. Analysis Strategy of Powder Diffraction Data with 2-D Detector

    SciTech Connect

    Kumar, Abhik; /SLAC, SSRL

    2006-01-25

    To gain a clearer understanding of orientation and grain deformation of crystalline materials, x-ray powder diffraction has played an integral role in extracting three-dimensional structural information from one-dimensional diffraction patterns. Powder diffraction models identical geometry to the intersection of a normal right cone with a plane. The purpose of this paper is to develop a general expression defining the conic sections based on the geometry of a powder diffraction experiment. Applying the derived formulation of a diffraction arc to experimental data will give insight to the molecular and structural properties of the sample in question. Instead of using complex three-dimensional Euclidian geometry, we define the problem solving technique with a simpler two-dimensional transformation approach to arrive at the final equation describing the conic sections. Using the diffraction geometry parameters, we can use this equation to calibrate the diffractometer from the diffraction pattern of a known reference material, or to determine the crystalline lattice structure of the compound.

  11. Scaling analysis of 2D fractal cellular structures

    NASA Astrophysics Data System (ADS)

    Schliecker, Gudrun

    2001-01-01

    The correlations between topological and metric properties of fractal tessellations are analysed. To this end, Sierpinski cellular structures are constructed for different geometries related to Sierpinski gaskets and to the Apollonian packing of discs. For these geometries, the properties of the distribution of the cells' areas and topologies can be derived analytically. In all cases, an algebraic increase of the cell's average area with its number of neighbours is obtained. This property, unknown from natural cellular structures, confirms previous observations in numerical studies of Voronoi tessellations generated by fractal point sets. In addition, a simple rigorous scaling resp. multiscaling properties relating the shapes and the sizes of the cells are found.

  12. NATRAN2. Fluid Hammer Analysis 1D & 2D Systems

    SciTech Connect

    Shin, Y.W.; Valentin, R.A.

    1992-03-03

    NATRAN2 analyzes short-term pressure-pulse transients in a closed hydraulic system consisting of a two-dimensional axisymmetric domain connected to a one-dimensional piping network. The one-dimensional network may consist of series or parallel piping, pipe junctions, diameter discontinuities, junctions of three to six branches, closed ends, surge tanks, far ends, dummy junctions, acoustic impedance discontinuities, and rupture disks. By default, the working fluid is assumed to be liquid sodium without cavitation; but another working fluid can be specified in terms of its density, sonic speed, and viscosity. The source pressure pulse can arise from one of the following: a pressure-time function specified at some point in the two-dimensional domain, a pressure-time function or a sodium-water reaction specified at some point in the one-dimensional domain. The pressure pulse from a sodium-water reaction is assumed to be generated according to the dynamic model of Zaker and Salmon.

  13. 2D/3D registration algorithm for lung brachytherapy

    SciTech Connect

    Zvonarev, P. S.; Farrell, T. J.; Hunter, R.; Wierzbicki, M.; Hayward, J. E.; Sur, R. K.

    2013-02-15

    Purpose: A 2D/3D registration algorithm is proposed for registering orthogonal x-ray images with a diagnostic CT volume for high dose rate (HDR) lung brachytherapy. Methods: The algorithm utilizes a rigid registration model based on a pixel/voxel intensity matching approach. To achieve accurate registration, a robust similarity measure combining normalized mutual information, image gradient, and intensity difference was developed. The algorithm was validated using a simple body and anthropomorphic phantoms. Transfer catheters were placed inside the phantoms to simulate the unique image features observed during treatment. The algorithm sensitivity to various degrees of initial misregistration and to the presence of foreign objects, such as ECG leads, was evaluated. Results: The mean registration error was 2.2 and 1.9 mm for the simple body and anthropomorphic phantoms, respectively. The error was comparable to the interoperator catheter digitization error of 1.6 mm. Preliminary analysis of data acquired from four patients indicated a mean registration error of 4.2 mm. Conclusions: Results obtained using the proposed algorithm are clinically acceptable especially considering the complications normally encountered when imaging during lung HDR brachytherapy.

  14. An Investigation of 2D Electrostatic Dust Levitation about Bennu

    NASA Astrophysics Data System (ADS)

    Hartzell, Christine; Zimmerman, Michael

    2015-11-01

    Electrostatic dust levitation has been hypothesized to occur near the surface of asteroids, due to the interaction of the solar wind plasma and UV radiation with the asteroids’ surfaces and their near-zero surficial gravity. Dust levitation could provide a mechanism to move regolith across the surface of an asteroid. Our preliminary investigations have identified grains sizes and the altitudes at which grains may levitate considering a semi-analytical 1D plasma model. However, our initial semi-analytical plasma model was not well-suited to the complex terminator region, where the surface transitions between positive (dominated by photoemission) and negative (in the plasma wake) potentials. In this analysis, we use a new 2D treecode-based plasma simulation to more accurately model the plasma environment about a simplified circular cross-section of the asteroid Bennu. We investigate the altitudes and grain sizes where electrostatic levitation could occur at Bennu. The improved plasma model will allow more accurate predictions of dust levitation and deposition, particularly in the terminator and wake regions that could not be characterized be earlier plasma models.

  15. Quasi 2D Materials: Raman Nanometrology and Thermal Management Applications

    NASA Astrophysics Data System (ADS)

    Shahil, Khan Mohammad Farhan

    Quasi two-dimensional (2D) materials obtained by the "graphene-like" exfoliation attracted tremendous attention. Such materials revealed unique electronic, thermal and optical properties, which can be potentially used in electronics, thermal management and energy conversion. This dissertation research addresses two separate but synergetic problems: (i) preparation and optical characterization of quasi-2D films of the bismuth-telluride (Bi 2Te3) family of materials, which demonstrate both thermoelectric and topological insulator properties; and (ii) investigation of thermal properties of composite materials prepared with graphene and few-layer graphene (FLG). The first part of dissertation reports properties of the exfoliated few-quintuple layers of Bi2Te3, Bi2Se3 and Sb 2Te3. Both non-resonant and resonant Raman scattering spectra have been investigated. It was found that the crystal symmetry breaking in few-quintuple films results in appearance of A1u-symmetry Raman peaks, which are not active in the bulk crystals. The scattering spectra measured under the 633-nm wavelength excitation reveals a number of resonant features, which could be used for analysis of the electronic and phonon processes in these materials. The obtained results help to understand the physical mechanisms of Raman scattering in the few-quintuple-thick films and can be used for nanometrology of topological insulator films on various substrates. The second part of the dissertation is dedicated to investigation of properties of composite materials prepared with graphene and FLG. It was found that the optimized mixture of graphene and multilayer graphene---produced by the high-yield inexpensive liquid-phase-exfoliation technique---can lead to an extremely strong enhancement of the cross-plane thermal conductivity K of the composite. The "laser flash" measurements revealed a record-high enhancement of K by 2300 % in the graphene-based polymer at the filler loading fraction f =10 vol. %. It was

  16. Alloyed 2D Metal-Semiconductor Atomic Layer Junctions.

    PubMed

    Kim, Ah Ra; Kim, Yonghun; Nam, Jaewook; Chung, Hee-Suk; Kim, Dong Jae; Kwon, Jung-Dae; Park, Sang Won; Park, Jucheol; Choi, Sun Young; Lee, Byoung Hun; Park, Ji Hyeon; Lee, Kyu Hwan; Kim, Dong-Ho; Choi, Sung Mook; Ajayan, Pulickel M; Hahm, Myung Gwan; Cho, Byungjin

    2016-03-01

    Heterostructures of compositionally and electronically variant two-dimensional (2D) atomic layers are viable building blocks for ultrathin optoelectronic devices. We show that the composition of interfacial transition region between semiconducting WSe2 atomic layer channels and metallic NbSe2 contact layers can be engineered through interfacial doping with Nb atoms. WxNb1-xSe2 interfacial regions considerably lower the potential barrier height of the junction, significantly improving the performance of the corresponding WSe2-based field-effect transistor devices. The creation of such alloyed 2D junctions between dissimilar atomic layer domains could be the most important factor in controlling the electronic properties of 2D junctions and the design and fabrication of 2D atomic layer devices.

  17. Emerging and potential opportunities for 2D flexible nanoelectronics

    NASA Astrophysics Data System (ADS)

    Zhu, Weinan; Park, Saungeun; Akinwande, Deji

    2016-05-01

    The last 10 years have seen the emergence of two-dimensional (2D) nanomaterials such as graphene, transition metal dichalcogenides (TMDs), and black phosphorus (BP) among the growing portfolio of layered van der Waals thin films. Graphene, the prototypical 2D material has advanced rapidly in device, circuit and system studies that has resulted in commercial large-area applications. In this work, we provide a perspective of the emerging and potential translational applications of 2D materials including semiconductors, semimetals, and insulators that comprise the basic material set for diverse nanosystems. Applications include RF transceivers, smart systems, the so-called internet of things, and neurotechnology. We will review the DC and RF electronic performance of graphene and BP thin film transistors. 2D materials at sub-um channel length have so far enabled cut-off frequencies from baseband to 100GHz suitable for low-power RF and sub-THz concepts.

  18. 2D hexagonal quaternion Fourier transform in color image processing

    NASA Astrophysics Data System (ADS)

    Grigoryan, Artyom M.; Agaian, Sos S.

    2016-05-01

    In this paper, we present a novel concept of the quaternion discrete Fourier transform on the two-dimensional hexagonal lattice, which we call the two-dimensional hexagonal quaternion discrete Fourier transform (2-D HQDFT). The concept of the right-side 2D HQDFT is described and the left-side 2-D HQDFT is similarly considered. To calculate the transform, the image on the hexagonal lattice is described in the tensor representation when the image is presented by a set of 1-D signals, or splitting-signals which can be separately processed in the frequency domain. The 2-D HQDFT can be calculated by a set of 1-D quaternion discrete Fourier transforms (QDFT) of the splitting-signals.

  19. Technical Review of the UNET2D Hydraulic Model

    SciTech Connect

    Perkins, William A.; Richmond, Marshall C.

    2009-05-18

    The Kansas City District of the US Army Corps of Engineers is engaged in a broad range of river management projects that require knowled