WorldWideScience

Sample records for single template analysis

  1. Genome-wide analysis of single non-templated nucleotides in plant endogenous siRNAs and miRNAs.

    Science.gov (United States)

    Wang, Feng; Johnson, Nathan R; Coruh, Ceyda; Axtell, Michael J

    2016-09-06

    Plant small RNAs are subject to various modifications. Previous reports revealed widespread 3' modifications (truncations and non-templated tailing) of plant miRNAs when the 2'-O-methyltransferase HEN1 is absent. However, non-templated nucleotides in plant heterochromatic siRNAs have not been deeply studied, especially in wild-type plants. We systematically studied non-templated nucleotide patterns in plant small RNAs by analyzing small RNA sequencing libraries from Arabidopsis, tomato, Medicago, rice, maize and Physcomitrella Elevated rates of non-templated nucleotides were observed at the 3' ends of both miRNAs and endogenous siRNAs from wild-type specimens of all species. 'Off-sized' small RNAs, such as 25 and 23 nt siRNAs arising from loci dominated by 24 nt siRNAs, often had very high rates of 3'-non-templated nucleotides. The same pattern was observed in all species that we studied. Further analysis of 24 nt siRNA clusters in Arabidopsis revealed distinct patterns of 3'-non-templated nucleotides of 23 nt siRNAs arising from heterochromatic siRNA loci. This pattern of non-templated 3' nucleotides on 23 nt siRNAs is not affected by loss of known small RNA 3'-end modifying enzymes, and may result from modifications added to longer heterochromatic siRNA precursors. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. Template analysis for the MAGIC telescopes

    Energy Technology Data Exchange (ETDEWEB)

    Menzel, Uta [Max-Planck-Institut fuer Physik, Muenchen (Germany); Collaboration: MAGIC-Collaboration

    2016-07-01

    The MAGIC telescopes are two 17-m-diameter Imaging Air Cherenkov Telescopes located on the Canary island of La Palma. They record the Cherenkov light from air showers induced by very high energy photons. The current data analysis uses a parametrization of the two shower images (including Hillas parameters) to determine the characteristics of the primary particle. I am implementing an advanced analysis method that compares shower images on a pixel basis with template images based on Monte Carlo simulations. To reduce the simulation effort the templates contain only pure shower images that are convolved with the telescope response later in the analysis. The primary particle parameters are reconstructed by maximizing the likelihood of the template. By using all the information available in the shower images, the performance of MAGIC is expected to improve. In this presentation I will explain the general idea of a template-based analysis and show the first results of the implementation.

  3. Nanoline templates for single atom wires on Si(001)

    Energy Technology Data Exchange (ETDEWEB)

    Koester, Sigrun A.; Owen, James H.G.; Bianco, Francois; Mazur, Daniel; Renner, Chrisoph [Universite de Geneve, Section Physique/DPMC, Geneve (Switzerland); Rodriguez-Prieto, Alvaro; Bowler, David R. [London Centre for Nanotechnology (LCN), University College London (United Kingdom)

    2010-07-01

    Low dimensional structures are of wide scientific and technological interest. The physics of single atom metallic wires is already described in detail by theory, but a more systematic experimental verification is still desirable. The experimental problems are mainly caused by the difficulties of growing electronically isolated wires which is necessary to test the expected properties from existing theories. Here we introduce templates on a Si(001) surface which enable the growth of self-assembled single atom wires on top of them. The main template consists of a Si reconstruction called the Haiku structure which develops underneath self-assembled Bi nanowires. By hydrogenation the Si surface can be passivated and additionally the Bi dimers are stripped off while the underlying reconstruction of the Si surface remains intact. In addition the Bi nanowire by itself can be considered as a template.

  4. Controlled growth of single nanowires within a supported alumina template

    DEFF Research Database (Denmark)

    Vlad, A.; Mátéfi-Tempfli, M.; Faniel, S.

    2006-01-01

    A simple technique for fabricating single nanowires with well-defined position is presented. The process implies the use of a silicon nitride mask for selective electrochemical growth of the nanowires in a porous alumina template. We show that this method allows the realization of complex nanowire...

  5. Fast Template-based Shape Analysis using Diffeomorphic Iterative Centroid

    OpenAIRE

    Cury , Claire; Glaunès , Joan Alexis; Chupin , Marie; Colliot , Olivier

    2014-01-01

    International audience; A common approach for the analysis of anatomical variability relies on the estimation of a representative template of the population, followed by the study of this population based on the parameters of the deformations going from the template to the population. The Large Deformation Diffeomorphic Metric Mapping framework is widely used for shape analysis of anatomical structures, but computing a template with such framework is computationally expensive. In this paper w...

  6. Multi-template tensor-based morphometry: application to analysis of Alzheimer's disease.

    Science.gov (United States)

    Koikkalainen, Juha; Lötjönen, Jyrki; Thurfjell, Lennart; Rueckert, Daniel; Waldemar, Gunhild; Soininen, Hilkka

    2011-06-01

    In this paper methods for using multiple templates in tensor-based morphometry (TBM) are presented and compared to the conventional single-template approach. TBM analysis requires non-rigid registrations which are often subject to registration errors. When using multiple templates and, therefore, multiple registrations, it can be assumed that the registration errors are averaged and eventually compensated. Four different methods are proposed for multi-template TBM. The methods were evaluated using magnetic resonance (MR) images of healthy controls, patients with stable or progressive mild cognitive impairment (MCI), and patients with Alzheimer's disease (AD) from the ADNI database (N=772). The performance of TBM features in classifying images was evaluated both quantitatively and qualitatively. Classification results show that the multi-template methods are statistically significantly better than the single-template method. The overall classification accuracy was 86.0% for the classification of control and AD subjects, and 72.1% for the classification of stable and progressive MCI subjects. The statistical group-level difference maps produced using multi-template TBM were smoother, formed larger continuous regions, and had larger t-values than the maps obtained with single-template TBM. Copyright © 2011 Elsevier Inc. All rights reserved.

  7. Multi-template tensor-based morphometry: application to analysis of Alzheimer's disease

    DEFF Research Database (Denmark)

    Koikkalainen, Juha; Lötjönen, Jyrki; Thurfjell, Lennart

    2011-01-01

    In this paper methods for using multiple templates in tensor-based morphometry (TBM) are presented and compared to the conventional single-template approach. TBM analysis requires non-rigid registrations which are often subject to registration errors. When using multiple templates and, therefore......, multiple registrations, it can be assumed that the registration errors are averaged and eventually compensated. Four different methods are proposed for multi-template TBM. The methods were evaluated using magnetic resonance (MR) images of healthy controls, patients with stable or progressive mild cognitive...... impairment (MCI), and patients with Alzheimer's disease (AD) from the ADNI database (N=772). The performance of TBM features in classifying images was evaluated both quantitatively and qualitatively. Classification results show that the multi-template methods are statistically significantly better than...

  8. Self-templated synthesis of single-crystal and single-domain ferroelectric nanoplates

    KAUST Repository

    Chao, Chunying

    2012-08-15

    Free-standing single-crystal PbTiO 3 nanoplates (see picture) were synthesized by a facile hydrothermal method. A "self-templated" crystal growth is presumed to lead to the formation of the PbTiO 3 nanoplates, which have ferroelectric single-domain structures, whose polarization areas can be manipulated by writing and reading. The nanoplates are also effective catalysts for the oxidation of carbon monoxide. © 2012 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. iTemplate: A template-based eye movement data analysis approach.

    Science.gov (United States)

    Xiao, Naiqi G; Lee, Kang

    2018-02-08

    Current eye movement data analysis methods rely on defining areas of interest (AOIs). Due to the fact that AOIs are created and modified manually, variances in their size, shape, and location are unavoidable. These variances affect not only the consistency of the AOI definitions, but also the validity of the eye movement analyses based on the AOIs. To reduce the variances in AOI creation and modification and achieve a procedure to process eye movement data with high precision and efficiency, we propose a template-based eye movement data analysis method. Using a linear transformation algorithm, this method registers the eye movement data from each individual stimulus to a template. Thus, users only need to create one set of AOIs for the template in order to analyze eye movement data, rather than creating a unique set of AOIs for all individual stimuli. This change greatly reduces the error caused by the variance from manually created AOIs and boosts the efficiency of the data analysis. Furthermore, this method can help researchers prepare eye movement data for some advanced analysis approaches, such as iMap. We have developed software (iTemplate) with a graphic user interface to make this analysis method available to researchers.

  10. Nanolithography based contacting method for electrical measurements on single template synthesized nanowires

    DEFF Research Database (Denmark)

    Fusil, S.; Piraux, L.; Mátéfi-Tempfli, Stefan

    2005-01-01

    A reliable method enabling electrical measurements on single nanowires prepared by electrodeposition in an alumina template is described. This technique is based on electrically controlled nanoindentation of a thin insulating resist deposited on the top face of the template filled by the nanowires....... We show that this method is very flexible, allowing us to electrically address single nanowires of controlled length down to 100 nm and of desired composition. Using this approach, current densities as large as 10 A cm were successfully injected through a point contact on a single magnetic...

  11. DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution

    NARCIS (Netherlands)

    Falconer, Ester; Hills, Mark; Naumann, Ulrike; Poon, Steven S. S.; Chavez, Elizabeth A.; Sanders, Ashley D.; Zhao, Yongjun; Hirst, Martin; Lansdorp, Peter M.

    2012-01-01

    DNA rearrangements such as sister chromatid exchanges (SCEs) are sensitive indicators of genomic stress and instability, but they are typically masked by single-cell sequencing techniques. We developed Strand-seq to independently sequence parental DNA template strands from single cells, making it

  12. One-dimensional Si-in-Si(001) template for single-atom wire growth

    Science.gov (United States)

    Owen, J. H. G.; Bianco, F.; Köster, S. A.; Mazur, D.; Bowler, D. R.; Renner, Ch.

    2010-08-01

    Single atom metallic wires of arbitrary length are of immense technological and scientific interest. We present atomic-resolution scanning tunneling microscope data of a silicon-only template, which modeling predicts to enable the self-organized growth of isolated micrometer long surface and subsurface single-atom chains. It consists of a one-dimensional, defect-free Si reconstruction four dimers wide—the Haiku core—formed by hydrogenation of self-assembled Bi-nanolines on Si(001) terraces, independent of any step edges. We discuss the potential of this Si-in-Si template as an appealing alternative to vicinal surfaces for nanoscale patterning.

  13. A population MRI brain template and analysis tools for the macaque.

    Science.gov (United States)

    Seidlitz, Jakob; Sponheim, Caleb; Glen, Daniel; Ye, Frank Q; Saleem, Kadharbatcha S; Leopold, David A; Ungerleider, Leslie; Messinger, Adam

    2018-04-15

    The use of standard anatomical templates is common in human neuroimaging, as it facilitates data analysis and comparison across subjects and studies. For non-human primates, previous in vivo templates have lacked sufficient contrast to reliably validate known anatomical brain regions and have not provided tools for automated single-subject processing. Here we present the "National Institute of Mental Health Macaque Template", or NMT for short. The NMT is a high-resolution in vivo MRI template of the average macaque brain generated from 31 subjects, as well as a neuroimaging tool for improved data analysis and visualization. From the NMT volume, we generated maps of tissue segmentation and cortical thickness. Surface reconstructions and transformations to previously published digital brain atlases are also provided. We further provide an analysis pipeline using the NMT that automates and standardizes the time-consuming processes of brain extraction, tissue segmentation, and morphometric feature estimation for anatomical scans of individual subjects. The NMT and associated tools thus provide a common platform for precise single-subject data analysis and for characterizations of neuroimaging results across subjects and studies. Copyright © 2017 ElsevierCompany. All rights reserved.

  14. Probing Electron-Induced Bond Cleavage at the Single-Molecule Level Using DNA Origami Templates

    DEFF Research Database (Denmark)

    Keller, Adrian Clemens; Bald, Ilko; Rotaru, Alexandru

    2012-01-01

    specifically designed oligonucleotide targets that are attached to DNA origami templates. In this way, we use a highly selective approach to compare the efficiency of the electron-induced dissociation of a single disulfide bond with the more complex cleavage of the DNA backbone within a TT dinucleotide...

  15. A Template Analysis of Writing Self-Efficacy Measures.

    Science.gov (United States)

    Mitchell, Kim M; Rieger, Kendra L; McMillan, Diana E

    2017-08-01

    This investigation reviews the item content of writing selfefficacy (WSE) measures developed for undergraduate students. Bandura's self-efficacy theory and a writing theory by Flower and Hayes informed the a priori themes used to develop a template of WSE categories critical to the concept. Articles describing WSE measures were identified through Cumulative Index to Nursing and Allied Health Literature (CINAHL), PsycINFO, Education Resources Information Center (ERIC), PubMed, Scopus, and Google Scholar (1984-2015). A template analysis method was used to analyze 182 individual items present on 11 WSE instruments. A nursing perspective was applied. The analysis identified 16 categories influencing WSE as well as gaps in current measurement items. The theoretical examination of WSE is the first step toward the development of a WSE measure specific to the nursing context and contributes to nursing education by advancing the measurement of WSE.

  16. Multi-template analysis of human perirhinal cortex in brain MRI: Explicitly accounting for anatomical variability

    Science.gov (United States)

    Xie, Long; Pluta, John B.; Das, Sandhitsu R.; Wisse, Laura E.M.; Wang, Hongzhi; Mancuso, Lauren; Kliot, Dasha; Avants, Brian B.; Ding, Song-Lin; Manjón, José V.; Wolk, David A.; Yushkevich, Paul A.

    2016-01-01

    Rational The human perirhinal cortex (PRC) plays critical roles in episodic and semantic memory and visual perception. The PRC consists of Brodmann areas 35 and 36 (BA35, BA36). In Alzheimer's disease (AD), BA35 is the first cortical site affected by neurofibrillary tangle pathology, which is closely linked to neural injury in AD. Large anatomical variability, manifested in the form of different cortical folding and branching patterns, makes it difficult to segment the PRC in MRI scans. Pathology studies have found that in ~97% of specimens, the PRC falls into one of three discrete anatomical variants. However, current methods for PRC segmentation and morphometry in MRI are based on single-template approaches, which may not be able to accurately model these discrete variants Methods A multi-template analysis pipeline that explicitly accounts for anatomical variability is used to automatically label the PRC and measure its thickness in T2-weighted MRI scans. The pipeline uses multi-atlas segmentation to automatically label medial temporal lobe cortices including entorhinal cortex, PRC and the parahippocampal cortex. Pairwise registration between label maps and clustering based on residual dissimilarity after registration are used to construct separate templates for the anatomical variants of the PRC. An optimal path of deformations linking these templates is used to establish correspondences between all the subjects. Experimental evaluation focuses on the ability of single-template and multi-template analyses to detect differences in the thickness of medial temporal lobe cortices between patients with amnestic mild cognitive impairment (aMCI, n=41) and age-matched controls (n=44). Results The proposed technique is able to generate templates that recover the three dominant discrete variants of PRC and establish more meaningful correspondences between subjects than a single-template approach. The largest reduction in thickness associated with aMCI, in absolute terms

  17. Template matching method for the analysis of interstellar cloud structure

    OpenAIRE

    Juvela, M.

    2016-01-01

    The structure of interstellar medium can be characterised at large scales in terms of its global statistics (e.g. power spectra) and at small scales by the properties of individual cores. Interest has been increasing in structures at intermediate scales, resulting in a number of methods being developed for the analysis of filamentary structures. We describe the application of the generic template-matching (TM) method to the analysis of maps. Our aim is to show that it provides a fast and stil...

  18. A high throughput system for the preparation of single stranded templates grown in microculture.

    Science.gov (United States)

    Kolner, D E; Guilfoyle, R A; Smith, L M

    1994-01-01

    A high throughput system for the preparation of single stranded M13 sequencing templates is described. Supernatants from clones grown in 48-well plates are treated with a chaotropic agent to dissociate the phage coat protein. Using a semi-automated cell harvester, the free nucleic acid is bound to a glass fiber filter in the presence of chaotrope and then washed with ethanol by aspiration. Individual glass fiber discs are punched out on the cell harvester and dried briefly. The DNA samples are then eluted in water by centrifugation. The processing time from 96 microcultures to sequence quality templates is approximately 1 hr. Assuming the ability to sequence 400 bases per clone, a 0.5 megabase per day genome sequencing facility will require 6250 purified templates a week. Toward accomplishing this goal we have developed a procedure which is a modification of a method that uses a chaotropic agent and glass fiber filter (Kristensen et al., 1987). By exploiting the ability of a cell harvester to uniformly aspirate and wash 96 samples, a rapid system for high quality template preparation has been developed. Other semi-automated systems for template preparation have been developed using commercially available robotic workstations like the Biomek (Mardis and Roe, 1989). Although minimal human intervention is required, processing time is at least twice as long. Custom systems based on paramagnetic beads (Hawkins et al., 1992) produce DNA in insufficient quantity for direct sequencing and therefore require cycle sequencing. These systems require custom programing, have a fairly high initial cost and have not proven to be as fast as the method reported here.

  19. Visual cluster analysis and pattern recognition template and methods

    Science.gov (United States)

    Osbourn, Gordon Cecil; Martinez, Rubel Francisco

    1999-01-01

    A method of clustering using a novel template to define a region of influence. Using neighboring approximation methods, computation times can be significantly reduced. The template and method are applicable and improve pattern recognition techniques.

  20. Visual cluster analysis and pattern recognition template and methods

    Energy Technology Data Exchange (ETDEWEB)

    Osbourn, G.C.; Martinez, R.F.

    1993-12-31

    This invention is comprised of a method of clustering using a novel template to define a region of influence. Using neighboring approximation methods, computation times can be significantly reduced. The template and method are applicable and improve pattern recognition techniques.

  1. Within-subject template estimation for unbiased longitudinal image analysis.

    Science.gov (United States)

    Reuter, Martin; Schmansky, Nicholas J; Rosas, H Diana; Fischl, Bruce

    2012-07-16

    Longitudinal image analysis has become increasingly important in clinical studies of normal aging and neurodegenerative disorders. Furthermore, there is a growing appreciation of the potential utility of longitudinally acquired structural images and reliable image processing to evaluate disease modifying therapies. Challenges have been related to the variability that is inherent in the available cross-sectional processing tools, to the introduction of bias in longitudinal processing and to potential over-regularization. In this paper we introduce a novel longitudinal image processing framework, based on unbiased, robust, within-subject template creation, for automatic surface reconstruction and segmentation of brain MRI of arbitrarily many time points. We demonstrate that it is essential to treat all input images exactly the same as removing only interpolation asymmetries is not sufficient to remove processing bias. We successfully reduce variability and avoid over-regularization by initializing the processing in each time point with common information from the subject template. The presented results show a significant increase in precision and discrimination power while preserving the ability to detect large anatomical deviations; as such they hold great potential in clinical applications, e.g. allowing for smaller sample sizes or shorter trials to establish disease specific biomarkers or to quantify drug effects. Copyright © 2012 Elsevier Inc. All rights reserved.

  2. Synthesis of NaCl Single Crystals with Defined Morphologies as Templates for Fabricating Hollow Nano/micro-structures

    DEFF Research Database (Denmark)

    Wang, B.B.; Jin, P.; Yue, Yuanzheng

    2015-01-01

    Hollow nanostructures have a wide range of applications in nanotechnology. To accurately fabricate such nanostructures, the first and common key step is to synthesize high quality templates with controlled symmetry and geometry, ideally through a green, efficient, and economical approach. However....... These naturally abundant NaCl single crystal templates are water-soluble, environmentally-friendly and uniform in both geometry and size, and hence are ideal for preparing high quality hollow nano/micro structures. The new approach may have the potential to replace the conventional hard or soft template...

  3. Sites of termination of in vitro DNA synthesis on psoralen phototreated single-stranded templates

    International Nuclear Information System (INIS)

    Piette, J.; Hearst, J.

    1985-01-01

    Single-stranded DNA has been photochemically induced to react with 4'-hydroxymethyl-4,5',8-trimethylpsoralen (HMT) and used as substrate for DNA replication with E. coli DNA polymerase I large fragment. By using the dideoxy sequencing procedure, it is possible to map the termination sites on the template photoreacted with HMT. These sites occur at the nucleotides preceding each thymine residue (and a few cytosine residues), emphasizing the fact that in a single-stranded stretch of DNA, HMT reacts with each thymine residue without any specificity regarding the flanking base sequence of the thymine residues. In addition, termination of DNA synthesis due to psoralen-adducted thymine is not influenced by the efficiency of the 3'-5' exonuclease proof-reading activity of the DNA polymerase. (author)

  4. The development of a reliable amateur boxing performance analysis template.

    Science.gov (United States)

    Thomson, Edward; Lamb, Kevin; Nicholas, Ceri

    2013-01-01

    The aim of this study was to devise a valid performance analysis system for the assessment of the movement characteristics associated with competitive amateur boxing and assess its reliability using analysts of varying experience of the sport and performance analysis. Key performance indicators to characterise the demands of an amateur contest (offensive, defensive and feinting) were developed and notated using a computerised notational analysis system. Data were subjected to intra- and inter-observer reliability assessment using median sign tests and calculating the proportion of agreement within predetermined limits of error. For all performance indicators, intra-observer reliability revealed non-significant differences between observations (P > 0.05) and high agreement was established (80-100%) regardless of whether exact or the reference value of ±1 was applied. Inter-observer reliability was less impressive for both analysts (amateur boxer and experienced analyst), with the proportion of agreement ranging from 33-100%. Nonetheless, there was no systematic bias between observations for any indicator (P > 0.05), and the proportion of agreement within the reference range (±1) was 100%. A reliable performance analysis template has been developed for the assessment of amateur boxing performance and is available for use by researchers, coaches and athletes to classify and quantify the movement characteristics of amateur boxing.

  5. Template security analysis of multimodal biometric frameworks based on fingerprint and hand geometry

    Directory of Open Access Journals (Sweden)

    Arvind Selwal

    2016-09-01

    Full Text Available Biometric systems are automatic tools used to provide authentication during various applications of modern computing. In this work, three different design frameworks for multimodal biometric systems based on fingerprint and hand geometry modalities are proposed. An analysis is also presented to diagnose various types of template security issues in the proposed system. Fuzzy analytic hierarchy process (FAHP is applied with five decision parameters on all the designs and framework 1 is found to be better in terms of template data security, templates fusion and computational efficiency. It is noticed that template data security before storage in database is a challenging task. An important observation is that a template may be secured at feature fusion level and an indexing technique may be used to improve the size of secured templates.

  6. Vertical single- and double-walled carbon nanotubes grown from modified porous anodic alumina templates

    International Nuclear Information System (INIS)

    Maschmann, Matthew R; Franklin, Aaron D; Amama, Placidus B; Zakharov, Dmitri N; Stach, Eric A; Sands, Timothy D; Fisher, Timothy S

    2006-01-01

    Vertical single-walled and double-walled carbon nanotube (SWNT and DWNT) arrays have been grown using a catalyst embedded within the pore walls of a porous anodic alumina (PAA) template. The initial film structure consisted of a SiO x adhesion layer, a Ti layer, a bottom Al layer, a Fe layer, and a top Al layer deposited on a Si wafer. The Al and Fe layers were subsequently anodized to create a vertically oriented pore structure through the film stack. CNTs were synthesized from the catalyst layer by plasma-enhanced chemical vapour deposition (PECVD). The resulting structure is expected to form the basis for development of vertically oriented CNT-based electronics and sensors

  7. Highly mesoporous single-crystalline zeolite beta synthesized using a nonsurfactant cationic polymer as a dual-function template

    KAUST Repository

    Zhu, Jie

    2014-02-12

    Mesoporous zeolites are useful solid catalysts for conversion of bulky molecules because they offer fast mass transfer along with size and shape selectivity. We report here the successful synthesis of mesoporous aluminosilicate zeolite Beta from a commercial cationic polymer that acts as a dual-function template to generate zeolitic micropores and mesopores simultaneously. This is the first demonstration of a single nonsurfactant polymer acting as such a template. Using high-resolution electron microscopy and tomography, we discovered that the resulting material (Beta-MS) has abundant and highly interconnected mesopores. More importantly, we demonstrated using a three-dimensional electron diffraction technique that each Beta-MS particle is a single crystal, whereas most previously reported mesoporous zeolites are comprised of nanosized zeolitic grains with random orientations. The use of nonsurfactant templates is essential to gaining single-crystalline mesoporous zeolites. The single-crystalline nature endows Beta-MS with better hydrothermal stability compared with surfactant-derived mesoporous zeolite Beta. Beta-MS also exhibited remarkably higher catalytic activity than did conventional zeolite Beta in acid-catalyzed reactions involving large molecules. © 2014 American Chemical Society.

  8. Content analysis of physical examination templates in electronic health records using SNOMED CT.

    Science.gov (United States)

    Gøeg, Kirstine Rosenbeck; Chen, Rong; Højen, Anne Randorff; Elberg, Pia

    2014-10-01

    Most electronic health record (EHR) systems are built on proprietary information models and terminology, which makes achieving semantic interoperability a challenge. Solving interoperability problems requires well-defined standards. In contrast, the need to support clinical work practice requires a local customization of EHR systems. Consequently, contrasting goals may be evident in EHR template design because customization means that local EHR organizations can define their own templates, whereas standardization implies consensus at some level. To explore the complexity of balancing these two goals, this study analyzes the differences and similarities between templates in use today. A similarity analysis was developed on the basis of SNOMED CT. The analysis was performed on four physical examination templates from Denmark and Sweden. The semantic relationships in SNOMED CT were used to quantify similarities and differences. Moreover, the analysis used these identified similarities to investigate the common content of a physical examination template. The analysis showed that there were both similarities and differences in physical examination templates, and the size of the templates varied from 18 to 49 fields. In the SNOMED CT analysis, exact matches and terminology similarities were represented in all template pairs. The number of exact matches ranged from 7 to 24. Moreover, the number of unrelated fields differed a lot from 1/18 to 22/35. Cross-country comparisons tended to have more unrelated content than within-country comparisons. On the basis of identified similarities, it was possible to define the common content of a physical examination. Nevertheless, a complete view on the physical examination required the inclusion of both exact matches and terminology similarities. This study revealed that a core set of items representing the physical examination templates can be generated when the analysis takes into account not only exact matches but also terminology

  9. Analysis of Permalloy films prepared on anodized alumina templates

    Energy Technology Data Exchange (ETDEWEB)

    Getlawi, Saleh; Koblischka, Michael R.; Hartmann, Uwe [Institute of Experimental Physics, Saarland University, Saarbruecken (Germany)

    2010-07-01

    The magnetic properties of Permalloy (Py) systems have been extensively studied for thick films due to the important role in many technological applications, e.g., in magnetoresistive-based sensors and devices. Nanopatterned magnetic media are important for various current approaches in magnetoelectronics and magnetic recording. Commercially available anodized aluminia templates with pore diameters of 100 mm and 30 mm were employed as substrates for Py thin films. The films were prepared by dc-magnetron sputtering. The film thickness was between 7 nm and 30 nm. The obtained antidot patterns were observed by electron and force microscopy. The resulting magnetic domain structures were characterized by means of magnetic force microscopy performed in externally applied magnetic fields. Additionally, the magnetic parameters were characterized by means of SQUID magnetometry.

  10. A microfluidic approach to fabricate monodisperse hollow or porous poly(HEMA-MMA) microspheres using single emulsions as templates.

    Science.gov (United States)

    Zhang, Hao; Ju, Xiao-Jie; Xie, Rui; Cheng, Chang-Jing; Ren, Ping-Wei; Chu, Liang-Yin

    2009-08-01

    We have successfully developed a novel and simple method to controllably prepare monodisperse poly(hydroxyethyl methacrylate-methyl methacrylate) (poly(HEMA-MMA)) microspheres with two distinct structures using single emulsions as templates. By employing a microfluidic emulsification approach to fabricate monomer-contained oil-in-water (O/W) emulsions as templates, and introducing proper initiators and different types of porogens, poly(HEMA-MMA) microspheres with hollow or porous structure are prepared in a controllable way. The shell thickness of hollow microspheres or the porosity of porous microspheres is controllably achieved by simply adjusting the porogen concentration. The prepared poly(HEMA-MMA) microspheres with controllable hollow or porous structures are favored for various potential applications. Furthermore, by using the simple preparation methodology proposed in this study, fabrication of monodisperse porous microspheres or hollow microcapsules with other materials can also be easily achieved.

  11. The effect of template selection on diffusion tensor voxel-based analysis results.

    Science.gov (United States)

    Van Hecke, Wim; Leemans, Alexander; Sage, Caroline A; Emsell, Louise; Veraart, Jelle; Sijbers, Jan; Sunaert, Stefan; Parizel, Paul M

    2011-03-15

    Diffusion tensor imaging (DTI) is increasingly being used to study white matter (WM) degeneration in patients with psychiatric and neurological disorders. In order to compare diffusion measures across subjects in an automated way, voxel-based analysis (VBA) methods were introduced. In VBA, all DTI data are transformed to a template, after which the diffusion measures of control subjects and patients are compared quantitatively in each voxel. Although VBA has many advantages compared to other post-processing approaches, such as region of interest analysis or tractography, VBA results need to be interpreted cautiously, since it has been demonstrated that they depend on the different parameter settings that are applied in the VBA processing pipeline. In this paper, we examine the effect of the template selection on the VBA results of DTI data. We hypothesized that the choice of template to which all data are transformed would also affect the VBA results. To this end, simulated DTI data sets as well as DTI data from control subjects and multiple sclerosis patients were aligned to (i) a population-specific DTI template, (ii) a subject-based DTI atlas in MNI space, and (iii) the ICBM-81 DTI atlas. Our results suggest that the highest sensitivity and specificity to detect WM abnormalities in a VBA setting was achieved using the population-specific DTI atlas, presumably due to the better spatial image alignment to this template. Copyright © 2010 Elsevier Inc. All rights reserved.

  12. Comparison of template registration methods for multi-site meta-analysis of brain morphometry

    Science.gov (United States)

    Faskowitz, Joshua; de Zubicaray, Greig I.; McMahon, Katie L.; Wright, Margaret J.; Thompson, Paul M.; Jahanshad, Neda

    2016-03-01

    Neuroimaging consortia such as ENIGMA can significantly improve power to discover factors that affect the human brain by pooling statistical inferences across cohorts to draw generalized conclusions from populations around the world. Voxelwise analyses such as tensor-based morphometry also allow an unbiased search for effects throughout the brain. Even so, such consortium-based analyses are limited by a lack of high-powered methods to harmonize voxelwise information across study populations and scanners. While the simplest approach may be to map all images to a single standard space, the benefits of cohort-specific templates have long been established. Here we studied methods to pool voxel-wise data across sites using templates customized for each cohort but providing a meaningful common space across all studies for voxelwise comparisons. As non-linear 3D MRI registrations represent mappings between images at millimeter resolution, we need to consider the reliability of these mappings. To evaluate these mappings, we calculated test-retest statistics on the volumetric maps of expansion and contraction. Further, we created study-specific brain templates for ten T1-weighted MRI datasets, and a common space from four study-specific templates. We evaluated the efficacy of using a two-step registration framework versus a single standard space. We found that the two-step framework more reliably mapped subjects to a common space.

  13. Radiation stability of protein crystals grown by nanostructured templates: synchrotron microfocus analysis

    International Nuclear Information System (INIS)

    Pechkova, Eugenia; Tropiano, Giuseppe; Riekel, Christian; Nicolini, Claudio

    2004-01-01

    X-ray radiation damage of lysozyme single crystals by an intense monochromatic beam from a focussed third-generation synchrotron radiation source has been studied. The preliminary results show a significantly higher resistance to synchrotron radiation of lysozyme microcrystals produced by means of nanotechnology-based template with respect to those prepared by classical methodology. The implications of this finding for protein crystallography are discussed

  14. Applications of the Indicator Template for Measurement and Analysis

    National Research Council Canada - National Science Library

    Goethert, Wolfhart; Siviy, Jeannine

    2004-01-01

    ...) has developed to precisely describe an indicator including its construction, correct interpretation, and how it can be utilized to direct data collection and presentation and measurement and analysis processes...

  15. Dopamine-Imprinted Polymers: Template-Monomer Interactions, Analysis of Template Removal and Application to Solid Phase Extraction

    Directory of Open Access Journals (Sweden)

    Mirosław Szutowski

    2007-11-01

    Full Text Available A dopamine-imprinted polymer (MIP was prepared in aqueous methanolsolution at 60oC by free-radical cross-linking polymerization of methacrylic acid in thepresence of ethylene glycol dimethacrylate as the cross-linker and dopamine hydrochlorideas the template molecule. Its ability to isolate dopamine was evaluated as the basis of asolid phase extraction procedure and compared with that of a non-imprinted polymer(NIP. The binding of dopamine was 84.1% and 29.1% for MIP and NIP, respectively.Various reported post-polymerization treatments to reduce template bleeding wereexamined. In our case the lowest bleeding was achieved after applying a combinedprocedure: continuous extraction in a Soxhlet apparatus (CE, followed by microwave-assisted extraction (ME to a level of 0.061 μg/mL. A simplified model of the template-monomer complexes allowed rationalization of monomer choice based on the heats ofcomplex formation at a PM3 level of theory.

  16. Within-subject template estimation for unbiased longitudinal image analysis

    OpenAIRE

    Reuter, Martin; Schmansky, Nicholas J.; Rosas, H. Diana; Fischl, Bruce

    2012-01-01

    Longitudinal image analysis has become increasingly important in clinical studies of normal aging and neurodegenerative disorders. Furthermore, there is a growing appreciation of the potential utility of longitudinally acquired structural images and reliable image processing to evaluate disease modifying therapies. Challenges have been related to the variability that is inherent in the available cross-sectional processing tools, to the introduction of bias in longitudinal processing and to po...

  17. Constructing of DNA vectors with controlled nanosize and single dispersion by block copolymer coating gold nanoparticles as template assembly

    Energy Technology Data Exchange (ETDEWEB)

    Li, Junbo, E-mail: Lijunbo@haust.edu.cn [Henan University of Science and Technology, School of Chemical Engineering and Pharmaceutics (China); Wu, Wenlan [Henan University of Science and Technology, School of Medicine (China); Gao, Jiayu; Liang, Ju; Zhou, Huiyun; Liang, Lijuan [Henan University of Science and Technology, School of Chemical Engineering and Pharmaceutics (China)

    2017-03-15

    Synthesized vectors with nanoscale size and stable colloid dispersion are highly desirable for improving gene delivery efficiency. Here, a core-shell template particle was constructed with polyethylene glycol-b-poly1-(3-aminopropyl)-3-(2-methacryloyloxy propylimidazolium bromine) (PEG-b-PAMPImB) coating gold nanoparticles (PEG-b-PAMPImB-@-Au NPs) for loading DNA and delivering in vitro. Data from transmission electron microscopy (TEM) and dynamic light scattering (DLS) suggest that these nanoplexes, by forming an electrostatic complex with DNA at the inner PAMPImB shell, offer steric protection for the outer PEG corona leading to single dispersion and small size. Notably, higher colloid stability and lower cytotoxicity were achieved with these nanoplexes when compared with PAMPImB monolayer-coated gold nanoparticles (Au NPs). Confocal laser scanning microscopy and intracellular trafficking TEM further indicate that the nanoplexes can translocate across the cell membrane and partly enter the nucleus for high efficient expression. Thus, template assembly represents a promising approach to control the size and colloid stability of gene vectors and ensure safety and efficiency of DNA delivery.

  18. Single Molecule Atomic Force Microscopy Studies of Photosensitized Singlet Oxygen Behavior on a DNA Origami Template

    DEFF Research Database (Denmark)

    Helmig, Sarah Wendelboe; Rotaru, Alexandru; Arian, Dumitru

    2010-01-01

    DNA origami, the folding of a long single-stranded DNA sequence (scaffold strand) by hundreds of short synthetic oligonucleotides (staple strands) into parallel aligned helices, is a highly efficient method to form advanced self-assembled DNA-architectures. Since molecules and various materials can...... be conjugated to each of the short staple strands, the origami method offers a unique possibility of arranging molecules and materials in well-defined positions on a structured surface. Here we combine the action of light with AFM and DNA nanostructures to study the production of singlet oxygen from a single...

  19. Region Templates: Data Representation and Management for High-Throughput Image Analysis.

    Science.gov (United States)

    Teodoro, George; Pan, Tony; Kurc, Tahsin; Kong, Jun; Cooper, Lee; Klasky, Scott; Saltz, Joel

    2014-12-01

    We introduce a region template abstraction and framework for the efficient storage, management and processing of common data types in analysis of large datasets of high resolution images on clusters of hybrid computing nodes. The region template abstraction provides a generic container template for common data structures, such as points, arrays, regions, and object sets, within a spatial and temporal bounding box. It allows for different data management strategies and I/O implementations, while providing a homogeneous, unified interface to applications for data storage and retrieval. A region template application is represented as a hierarchical dataflow in which each computing stage may be represented as another dataflow of finer-grain tasks. The execution of the application is coordinated by a runtime system that implements optimizations for hybrid machines, including performance-aware scheduling for maximizing the utilization of computing devices and techniques to reduce the impact of data transfers between CPUs and GPUs. An experimental evaluation on a state-of-the-art hybrid cluster using a microscopy imaging application shows that the abstraction adds negligible overhead (about 3%) and achieves good scalability and high data transfer rates. Optimizations in a high speed disk based storage implementation of the abstraction to support asynchronous data transfers and computation result in an application performance gain of about 1.13×. Finally, a processing rate of 11,730 4K×4K tiles per minute was achieved for the microscopy imaging application on a cluster with 100 nodes (300 GPUs and 1,200 CPU cores). This computation rate enables studies with very large datasets.

  20. INTERSTITIAL BRACHYTHERAPY USING TEMPLATE FOR LOCALLY ADVANCED GYNAECOLOGICAL MALIGNANCIES- REVISITING THE FORGOTTEN CLASSICAL ART- A SINGLE INSTITUTE EXPERIENCE

    Directory of Open Access Journals (Sweden)

    Chatharaju Swarna Kumari

    2017-10-01

    Full Text Available BACKGROUND Brachytherapy is an important therapeutic strategy for the treatment of locally advanced gynaecologic (GYN cancers despite evolution of different newer radiotherapy techniques like high-dose-rate and image-guided BT. Despite being used in the management of advanced gynaecological cancer, currently there is a scarcity of studies and data on interstitial BT in Indian context. This is a retrospective analysis on 71 patients with locally advanced gynaecological malignancies treated in the period of 2010 to 2016 to assess the local tumour control, survival, and complications with the template (Syed-Neblett guided interstitial technique. MATERIALS AND METHODS The patients with a median age of 51 years treated from July 2010 to May 2016 were retrospectively reviewed. This study included previously unirradiated 71 patients with advance stage of gynaecological malignancies, not suitable for intracavitary brachytherapy due to distorted anatomy or extensive disease stage. Histologically all patients had squamous cell carcinoma (cervix= 56, vault= 9, vagina= 6 and treated by whole pelvis external beam radiation therapy (EBRT up to a total dose of 50 Gy in 25 fractions. These patients were further treated by high-dose-rate interstitial brachytherapy using SyedNeblett dedicated vaginal plastic template. During treatment all these patients were re-optimised and a dose of 15-21 Gy was delivered in 3 fractions with a minimum gap of 6 hours between fractions using Varisource iX HDR unit. RESULTS Out of 71 patients 5 were lost to followup during study period and they were excluded from the final analysis. The average followup duration ranged between 6-71 months and median followup was 20 months. This study included parameters like local disease control, acute/late complications and distant metastasis. Out of 66 patients, local disease control was seen in 54 (81.81% patients, whereas local recurrence was observed in 12 patients (18.18%. Distant

  1. Kinetic Analysis for Macrocyclizations Involving Anionic Template at the Transition State

    Directory of Open Access Journals (Sweden)

    Vicente Martí-Centelles

    2012-01-01

    competitive oligomerization/polymerization processes yielding undesired oligomeric/polymeric byproducts. The effect of anions has also been included in the kinetic models, as they can act as catalytic templates in the transition state reducing and stabilizing the transition state. The corresponding differential equation systems for each kinetic model can be solved numerically. Through a comprehensive analysis of these results, it is possible to obtain a better understanding of the different parameters that are involved in the macrocyclization reaction mechanism and to develop strategies for the optimization of the desired processes.

  2. ALGORITHM FOR SEMANTIC TEXT ANALYSIS BY MEANS OF BASIC SEMANTIC TEMPLATES WITH DELETION

    Directory of Open Access Journals (Sweden)

    A. V. Mochalova

    2014-09-01

    Full Text Available The systems of automatic text processing have become more and more important due to the constant growth of textual data. One of the main issues arising in such systems is a problem of semantic analysis. The paper deals with an algorithm for finding semantic dependencies by means of basic semantic templates with deletion. While working with the Drools expert system (and PHREAK algorithm for fast pattern matching we have developed and implemented a semantic analyzer for construction of semantic dependencies between parts of a sentence. During the semantic analysis we add some text parts to the priority queue according to the rules described in the semantic templates, and then at each iteration of the sentence being analyzed we drop some segment of the analyzed text which has the highest priority in the queue. To determine the priority in this queue two values are used: the priority of semantic relationship group and word position. The proposed algorithm is implemented in Java. We have prepared 2160 rules using Drools expert system. The software implementation of the proposed algorithm has shown its applicability for the systems of automatic text processing. Testing results have proved that suggested algorithm of semantic analysis without Drools expert system operates 6-8 times slower, on the average. We use proposed semantic analyzer as a composite module to intellectual question-answering system.

  3. Transformation of amorphous calcium carbonate to rod-like single crystal calcite via "copying" collagen template.

    Science.gov (United States)

    Xue, Zhonghui; Hu, Binbin; Dai, Shuxi; Du, Zuliang

    2015-10-01

    Collagen Langmuir films were prepared by spreading the solution of collagen over deionized water, CaCl2 solution and Ca(HCO3)2 solution. Resultant collagen Langmuir monolayers were then compressed to a lateral pressure of 10 mN/m and held there for different duration, allowing the crystallization of CaCO3. The effect of crystallization time on the phase composition and microstructure of CaCO3 was investigated. It was found that amorphous calcium carbonate (ACC) was obtained at a crystallization time of 6 h. The amorphous CaCO3 was transformed to rod-like single crystal calcite crystals at an extended crystallization time of 12 h and 24 h, via "copying" the symmetry and dimensionalities of collagen fibers. Resultant calcite crystallites were well oriented along the longitudinal axis of collagen fibers. The ordered surface structure of collagen fibers and electrostatic interactions played key roles in tuning the oriented nucleation and growth of the calcite crystallites. The mineralized collagen possessing both desired mechanical properties of collagen fiber and good biocompatibility of calcium carbonate may be assembled into an ideal biomaterial for bone implants. Copyright © 2015. Published by Elsevier B.V.

  4. An automatic algorithm for blink-artifact suppression based on iterative template matching: application to single channel recording of cortical auditory evoked potentials

    Science.gov (United States)

    Valderrama, Joaquin T.; de la Torre, Angel; Van Dun, Bram

    2018-02-01

    Objective. Artifact reduction in electroencephalogram (EEG) signals is usually necessary to carry out data analysis appropriately. Despite the large amount of denoising techniques available with a multichannel setup, there is a lack of efficient algorithms that remove (not only detect) blink-artifacts from a single channel EEG, which is of interest in many clinical and research applications. This paper describes and evaluates the iterative template matching and suppression (ITMS), a new method proposed for detecting and suppressing the artifact associated with the blink activity from a single channel EEG. Approach. The approach of ITMS consists of (a) an iterative process in which blink-events are detected and the blink-artifact waveform of the analyzed subject is estimated, (b) generation of a signal modeling the blink-artifact, and (c) suppression of this signal from the raw EEG. The performance of ITMS is compared with the multi-window summation of derivatives within a window (MSDW) technique using both synthesized and real EEG data. Main results. Results suggest that ITMS presents an adequate performance in detecting and suppressing blink-artifacts from a single channel EEG. When applied to the analysis of cortical auditory evoked potentials (CAEPs), ITMS provides a significant quality improvement in the resulting responses, i.e. in a cohort of 30 adults, the mean correlation coefficient improved from 0.37 to 0.65 when the blink-artifacts were detected and suppressed by ITMS. Significance. ITMS is an efficient solution to the problem of denoising blink-artifacts in single-channel EEG applications, both in clinical and research fields. The proposed ITMS algorithm is stable; automatic, since it does not require human intervention; low-invasive, because the EEG segments not contaminated by blink-artifacts remain unaltered; and easy to implement, as can be observed in the Matlab script implemeting the algorithm provided as supporting material.

  5. Development of Design Information Template for Nuclear Power Plants for Electromagnetic Pulse (EMP) Effect Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Minyi; Ryu, Hosan; Ye, Songhae; Lee, Euijong [KNHP CRI, Daejeon (Korea, Republic of)

    2016-10-15

    An electromagnetic pulse (EMP) is a transient electromagnetic shock wave that has powerful electric and magnetic fields that can destroy electronic equipment. It is generally well-known that EMPs can cause the malfunction and disorder of electronic equipment and serious damages to electric power systems and communication networks. Research is being carried out to protect nuclear power plants (NPPs) from EMP threats. Penetration routes of EMPs can be roughly categorized into two groups, radioactivity and conductivity. The radioactive effect refers to an impact transmitted to the ground from high-altitude electromagnetic pulses (HEMP). Such an impact may affect target equipment through the point of entry (POE) of the concrete structure of an NPP. The conductive effect refers to induced voltage or current coupled to the NPPs cable structure. The induced voltage and current affect the target equipment via connected cables. All these factors must be considered when taking into account EMP effect analysis for NPPs. To examine all factors, it is necessary to fully understand the schemes of NPPs. This paper presents a four type design information template that can be used to analyze the EMP effect in operating nuclear power plants. In order to analyze of the effects of EMPs on operating NPPs, we must consider both the conductive and radioactive effects on the target (system, equipment, structure). For these reasons, not only the equipment information, but also the information about the structure and the external penetration will be required. We are developing a design information template for robust nuclear design information acquisition. We expect to develop a block diagram on the basis of the template.

  6. Intrinsic property measurement of surfactant-templated mesoporous silica films using time-resolved single-molecule imaging.

    Science.gov (United States)

    Kennard, Raymond; DeSisto, William J; Giririjan, Thanu Praba; Mason, Michael D

    2008-04-07

    Mesoporous silica membranes fabricated by the surfactant-templated sol-gel process have received attention because of the potential to prepare membranes with a narrow pore size distribution and ordering of the interconnected pores. Potential applications include ultrafiltration, biological separations and drug delivery, and separators in lithium-ion batteries. Despite advancements in synthesis and characterization of these membranes, a quantitative description of the membrane microstructure remains a challenge. Currently the membrane microstructure is characterized by the combination of results from several techniques, i.e., gas permeance testing, x-ray diffraction scanning electron microscopy, transmission electron microscopy, and permporometry. The results from these ensemble methods are then compiled and the data fitted to a particular flow model. Although these methods are very effective in determining membrane performance, general pore size distribution, and defect concentration, they are unable to monitor molecular paths through the membrane and quantitatively measure molecular interactions between the molecular specie and pore network. Single-molecule imaging techniques enable optical measurements that probe materials on nanometer length scales through observation of individual molecules without the influence of averaging. Using single-molecule imaging spectroscopy, we can quantitatively characterize the interaction between the probe molecule and the interior of the pore within mesoporous silica membranes. This approach is radically different from typical membrane characterization methods in that it has the potential to spatially sample the underlying pore structure distribution, the surface energy, and the transport properties. Our hope is that this new fundamental knowledge can be quantitatively linked to both the preparation and the performance of membranes, leading to the advancement of membrane science and technology. Fluorescent molecules, 1

  7. Microfluidics for single cell analysis

    DEFF Research Database (Denmark)

    Jensen, Marie Pødenphant

    Isolation and manipulation of single cells have gained an increasing interest from researchers because of the heterogeneity of cells from the same cell culture. Single cell analysis can ensure a better understanding of differences between individual cells and potentially solve a variety of clinical...... problems. In this thesis lab on a chip systems for rare single cell analysis are investigated. The focus was to develop a commercial, disposable device for circulating tumour cell (CTC) analysis. Such a device must be able to separate rare cells from blood samples and subsequently capture the specific...... cells, and simultaneously be fabricated and operated at low costs and be user-friendly. These challenges were addressed through development of two microfluidic devices, one for rare cell isolation based on pinched flow fractionation (PFF) and one for single cell capture based on hydrodynamic trapping...

  8. Automating Embedded Analysis Capabilities and Managing Software Complexity in Multiphysics Simulation, Part I: Template-Based Generic Programming

    Directory of Open Access Journals (Sweden)

    Roger P. Pawlowski

    2012-01-01

    Full Text Available An approach for incorporating embedded simulation and analysis capabilities in complex simulation codes through template-based generic programming is presented. This approach relies on templating and operator overloading within the C++ language to transform a given calculation into one that can compute a variety of additional quantities that are necessary for many state-of-the-art simulation and analysis algorithms. An approach for incorporating these ideas into complex simulation codes through general graph-based assembly is also presented. These ideas have been implemented within a set of packages in the Trilinos framework and are demonstrated on a simple problem from chemical engineering.

  9. Analysis of single biological cells

    International Nuclear Information System (INIS)

    Watt, Frank

    2002-01-01

    The extraction of elemental information from single cultured cells using nuclear microscopy is an area of great potential because it can provide both quantitative information on the uptake of elements by the cell, and also its elemental response to a wide variety of external stimuli. A recent technique based on nuclear physics technology enables the analysis of single cells down to the parts per million level to be achieved

  10. Report Template

    DEFF Research Database (Denmark)

    Bjørn, Anders; Laurent, Alexis; Owsianiak, Mikołaj

    2017-01-01

    To ensure consistent reporting of life cycle assessment (LCA), we provide a report template. The report includes elements of an LCA study as recommended but the ILCD Handbook. Illustrative case study reported according to this template is presented in Chap. 39 ....

  11. Single Cell Isolation and Analysis

    Directory of Open Access Journals (Sweden)

    Ping Hu

    2016-10-01

    Full Text Available Increasing evidence shows that the heterogeneity of individual cells within a genetically identical population can be critical to their peculiar function and fate. Conventional cell based assays mainly analysis the average responses from a population cells, while the difference within individual cells may often be masked. The cell size, RNA transcripts and protein expression level are quite different within individual cells and these variations are key point to answer the problems in cancer, neurobiology, stem cell biology, immunology and developmental biology. To better understand the cell-to-cell variations, the single cell analysis can provide much more detailed information which may be helpful for therapeutic decisions in an increasingly personalized medicine. In this review, we will focus on the recent development in single cell analysis, including methods used in single cell isolation, analysis and some application examples. The review provides the historical background to single cell analysis, discusses limitations, and current and future possibilities in this exciting field of research.

  12. Photocatalytic segmented nanowires and single-step iron oxide nanotube synthesis: Templated electrodeposition as all-round tool

    NARCIS (Netherlands)

    Maas, M.G.; Rodijk, E.J.B.; Maijenburg, A.W.; ten Elshof, Johan E.; Blank, David H.A.; Nielsch, K.; Fontcuberta i Morral, A.; Holt, J.K.; Thomson, C.V.

    2010-01-01

    Templated electrodeposition was used to synthesize silver-zinc oxide nanowires and iron oxide (Fe2O3) nanotubes in polycarbonate track etched (PCTE) membranes. Metal/oxide segmented nanowires were made to produce hydrogen gas from a water/methanol mixture under ultraviolet irradiation. It was

  13. Template synthesis of two new supramolecular zinc(II) complexes containing pentadentate N3O2 semicarbazone ligand: Nanostructure synthesis, Hirshfeld surface analysis, and DFT studies

    Science.gov (United States)

    Tyula, Yunes Abbasi; Zabardasti, Abedien; Goudarziafshar, Hamid; Roudsari, Majid Sadeghi; Dusek, Michal; Eigner, Vaclav

    2017-12-01

    Two new zinc(II) complexes, [Zn(H2dapsc) (CH3OH)2][ZnBr2Cl2] (1) and [Zn(H2dapsc) (CH3OH)Br]Br.(CH3OH) (2), where H2dapsc is 2,6-diacetylpyridine bis(semicarbazone), were synthesized using a template method in which the pentadentate N3O2 semicarbazone ligand derived from [1 + 2] condensation of 2,6-diacetylpyridine and semicarbazide in the presence of zinc(II) ion as template agent. These compounds were characterized by IR spectroscopy, elemental analysis, and single-crystal X-ray diffraction. Their single crystal X-ray structures showed that in both complex cations, the metal center has a distorted pentagonal-bipyramidal geometry in which the semicarbazone (H2dapsc) ligand occupies the equatorial plane, while the axial positions occupy by two methanol ligands in (1) and two bromo and methanol ligands in (2). Furthermore, the impact of the close intermolecular contacts on the crystal packing of (1) and (2) have been further studied using Hirshfeld surface analysis. Density Functional Theory (DFT) method was applied for the calculation of HOMO-LUMO energy gap, atomic charges and vibrational frequencies of title complexes. Moreover, the nanostructure of zinc complex was synthesized by a sonochemical method and characterized by scanning electron microscopy (SEM), X-ray powder diffraction (XRPD), FT-IR spectroscopy, and elemental analysis.

  14. Review analysis of properties for an ideal secure biometric template scheme

    CSIR Research Space (South Africa)

    Mzila, Phiwa

    2016-02-01

    Full Text Available With new advances in technologies, biometrics is becoming emerging technology for verification and authentication of individuals. However, the storage of biometric templates still needs necessary attention since it poses major threats to user...

  15. Synthesis, structure and topological analysis of glycine templated highly stable cadmium sulfate framework: A New Lewis Acid catalyst

    Science.gov (United States)

    Paul, Avijit Kumar

    2018-04-01

    One new open-framework two-dimensional layer, [Cd(NH3CH2COO)(SO4)], I, has been synthesized using amino acid as templating agent. Single crystal structural analysis shows that the compound crystallizes in monoclinic cell with non-centrosymmetric space group P21, a = 4.9513(1) Å, b = 7.9763(2) Å, c = 8.0967(2) Å, β = 105.917(1)° and V = 307.504(12) Å3. The compound has connectivity between the Cd-centers and the sulfate units forming a two-dimensional layer structure. Sulfate unit is coordinated to metal center with η3, μ4 mode possessing a coordination free oxygen atom. The zwitterionic form of glycine molecule is present in the structure bridging with two metal centers through μ2-mode by carboxylate oxygens. The topological analysis reveals that the two-dimensional network is formed with a novel 4- and 6-connected binodal net of (32,42,52)(34,44,54,63) topology. Although one end of the glycine molecule is free from coordination, the structure is highly stable up to 350 °C. Strong N-H⋯ O hydrogen bonding interactions play an important role in the stabilization and formation of three-dimensional supramolecular structure. The cyanosilylation of imines using the present compounds as heterogeneous catalyst indicates good catalytic behavior. The present study illustrates the usefulness of the amino acid for the structure building in less studied sulfate based framework materials as well as designing of new heterogeneous catalysts for the broad application. The compound has also been characterized through elemental analysis, PXRD, IR, SEM and TG-DT studies.

  16. Human Actions Analysis: Templates Generation, Matching and Visualization Applied to Motion Capture of Highly-Skilled Karate Athletes

    Directory of Open Access Journals (Sweden)

    Tomasz Hachaj

    2017-11-01

    Full Text Available The aim of this paper is to propose and evaluate the novel method of template generation, matching, comparing and visualization applied to motion capture (kinematic analysis. To evaluate our approach, we have used motion capture recordings (MoCap of two highly-skilled black belt karate athletes consisting of 560 recordings of various karate techniques acquired with wearable sensors. We have evaluated the quality of generated templates; we have validated the matching algorithm that calculates similarities and differences between various MoCap data; and we have examined visualizations of important differences and similarities between MoCap data. We have concluded that our algorithms works the best when we are dealing with relatively short (2–4 s actions that might be averaged and aligned with the dynamic time warping framework. In practice, the methodology is designed to optimize the performance of some full body techniques performed in various sport disciplines, for example combat sports and martial arts. We can also use this approach to generate templates or to compare the correct performance of techniques between various top sportsmen in order to generate a knowledge base of reference MoCap videos. The motion template generated by our method can be used for action recognition purposes. We have used the DTW classifier with angle-based features to classify various karate kicks. We have performed leave-one-out action recognition for the Shorin-ryu and Oyama karate master separately. In this case, 100 % actions were correctly classified. In another experiment, we used templates generated from Oyama master recordings to classify Shorin-ryu master recordings and vice versa. In this experiment, the overall recognition rate was 94.2 % , which is a very good result for this type of complex action.

  17. Human Actions Analysis: Templates Generation, Matching and Visualization Applied to Motion Capture of Highly-Skilled Karate Athletes

    Science.gov (United States)

    Piekarczyk, Marcin; Ogiela, Marek R.

    2017-01-01

    The aim of this paper is to propose and evaluate the novel method of template generation, matching, comparing and visualization applied to motion capture (kinematic) analysis. To evaluate our approach, we have used motion capture recordings (MoCap) of two highly-skilled black belt karate athletes consisting of 560 recordings of various karate techniques acquired with wearable sensors. We have evaluated the quality of generated templates; we have validated the matching algorithm that calculates similarities and differences between various MoCap data; and we have examined visualizations of important differences and similarities between MoCap data. We have concluded that our algorithms works the best when we are dealing with relatively short (2–4 s) actions that might be averaged and aligned with the dynamic time warping framework. In practice, the methodology is designed to optimize the performance of some full body techniques performed in various sport disciplines, for example combat sports and martial arts. We can also use this approach to generate templates or to compare the correct performance of techniques between various top sportsmen in order to generate a knowledge base of reference MoCap videos. The motion template generated by our method can be used for action recognition purposes. We have used the DTW classifier with angle-based features to classify various karate kicks. We have performed leave-one-out action recognition for the Shorin-ryu and Oyama karate master separately. In this case, 100% actions were correctly classified. In another experiment, we used templates generated from Oyama master recordings to classify Shorin-ryu master recordings and vice versa. In this experiment, the overall recognition rate was 94.2%, which is a very good result for this type of complex action. PMID:29125560

  18. A template for design personas

    DEFF Research Database (Denmark)

    Nielsen, Lene; Storgaard Nielsen, Kira; Stage, Jan

    2015-01-01

    The persona method is gaining widespread use and support. Many researchers have reported from single cases and from novel domains on how they have used the method. However, the way companies and design groups describe personas has not been the focus of attention. This paper analyses 47 descriptions...... from 13 companies and compares these to an analysis of recommendations from 11 templates from literature. Furthermore, 28 interviews with Danish practitioners with experience in using personas are analyzed for content on persona descriptions. The study finds that a Danish persona style has developed...

  19. Bleeding tendency in dual antiplatelet therapy with aspirin/clopidogrel: rescue of the template bleeding time in a single-center prospective study

    Directory of Open Access Journals (Sweden)

    Altman Raul

    2012-01-01

    Full Text Available Abstract Background Patients with heightened platelet reactivity in response to antiplatelet agents are at an increased risk of recurrent ischemic events. However, there is a lack of diagnostic criteria for increased response to combined aspirin/clopidogrel therapy. The challenge is to identify patients at risk of bleeding. This study sought to characterize bleeding tendency in patients treated with aspirin and clopidogrel. Patients/methods In a single-center prospective study, 100 patients under long-term aspirin/clopidogrel treatment, the effect of therapy was assayed by template bleeding time (BT and the inhibition of platelet aggregation (IPA by light transmission aggregometry (LTA. Arachidonic acid (0.625 mmol/L and adenosine diphosphate (ADP; 2, 4, and 8 μmol/L were used as platelet agonists. Results Bleeding episodes (28 nuisance, 2 hematuria [1 severe], 1 severe proctorrhagia, 1 severe epistaxis were significantly more frequent in patients with longer BT. Template BT ≥ 24 min was associated with bleeding episodes (28 of 32. Risk of bleeding increased 17.4% for each 1 min increase in BT. Correlation was found between BT and IPAmax in response to ADP 2 μmol/L but not to ADP 4 or 8 μmol/L. Conclusion In patients treated with dual aspirin/clopidogrel therapy, nuisance and internal bleeding were significantly associated with template BT and with IPAmax in response to ADP 2 μmol/L but not in response to ADP 4 μmol/L or 8 μmol/L.

  20. Systematic Investigation of Controlled Nanostructuring of Mn 12 Single-Molecule Magnets Templated by Metal–Organic Frameworks

    Energy Technology Data Exchange (ETDEWEB)

    Aulakh, Darpandeep [Department of Chemistry; amp, Biomolecular Science, Clarkson University, Potsdam, New York 13699, United States; Xie, Haomiao [Department of Chemistry, Texas A& amp,M University, College Station, Texas 77845, United States; Shen, Zhe [Department of Chemistry, Texas A& amp,M University, College Station, Texas 77845, United States; Harley, Alexander [Department of Chemistry; amp, Biomolecular Science, Clarkson University, Potsdam, New York 13699, United States; Zhang, Xuan [Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States; Yakovenko, Andrey A. [X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States; Dunbar, Kim R. [Department of Chemistry, Texas A& amp,M University, College Station, Texas 77845, United States; Wriedt, Mario [Department of Chemistry; amp, Biomolecular Science, Clarkson University, Potsdam, New York 13699, United States

    2017-05-25

    This is the first systematic study exploring metal–organic frameworks (MOFs) as platforms for the controlled nanostructuring of molecular magnets. We report the incorporation of seven single-molecule magnets (SMMs) of general composition [Mn12O12(O2CR)16(OH2)4], with R = CF3 (1), (CH3)CCH2 (2), CH2Cl (3), CH2Br (4), CHCl2 (5), CH2But (6), and C6H5 (7), into the hexagonal channel pores of a mesoporous MOF host. The resulting nanostructured composites combine the key SMM properties with the functional properties of the MOF. Synchrotron-based powder diffraction with difference envelope density analysis, physisorption analysis (surface area and pore size distribution), and thermal analyses reveal that the well-ordered hexagonal structure of the host framework is preserved, and magnetic measurements indicate that slow relaxation of the magnetization, characteristic of the corresponding Mn12 derivative guests, occurs inside the MOF pores. Structural host–guest correlations including the bulkiness and polarity of peripheral SMM ligands are discussed as fundamental parameters influencing the global SMM@MOF loading capacities. These results demonstrate that employing MOFs as platforms for the nanostructuration of SMMs is not limited to a particular host–guest system but potentially applicable to a multitude of other molecular magnets. Such fundamental findings will assist in paving the way for the development of novel advanced spintronic devices.

  1. Customized surgical template fabrication under biomechanical consideration by integrating CBCT image, CAD system and finite element analysis.

    Science.gov (United States)

    Yu, Jian-Hong; Wang, Yu-Tzu; Lin, Chun-Li

    2018-01-30

    This study developed a customized surgical template under mechanical consideration for molar intrusion. Two finite element (FE) models were analyzed for the primary stability under 100 gf traction forces with one mini-screw inserted at the buccal side in horizontal and another in palatal side with two optional positions at 60° (P60) or 15° (P15) angles with inclination toward the molar occlusal surface. The surgical template was generated using rapid prototyping (RP) printing for the clinical application based on improved primarily stability model. The surrounding bone strains for models P15 and P60 were far lower than the bone remodeling critical value. Model P60 presented much lower micro-motion in the screw/bone interface and the screw head displacement than those values in model P15. Using FE analysis for biomechanical evaluation and combining with CT image, image superimposed method and CAD technique can fabricate accuracy/security customized surgical template for mini-screws with better primary stability.

  2. Highly Sensitive GMO Detection Using Real-Time PCR with a Large Amount of DNA Template: Single-Laboratory Validation.

    Science.gov (United States)

    Mano, Junichi; Hatano, Shuko; Nagatomi, Yasuaki; Futo, Satoshi; Takabatake, Reona; Kitta, Kazumi

    2018-03-01

    Current genetically modified organism (GMO) detection methods allow for sensitive detection. However, a further increase in sensitivity will enable more efficient testing for large grain samples and reliable testing for processed foods. In this study, we investigated real-time PCR-based GMO detection methods using a large amount of DNA template. We selected target sequences that are commonly introduced into many kinds of GM crops, i.e., 35S promoter and nopaline synthase (NOS) terminator. This makes the newly developed method applicable to a wide range of GMOs, including some unauthorized ones. The estimated LOD of the new method was 0.005% of GM maize events; to the best of our knowledge, this method is the most sensitive among the GM maize detection methods for which the LOD was evaluated in terms of GMO content. A 10-fold increase in the DNA amount as compared with the amount used under common testing conditions gave an approximately 10-fold reduction in the LOD without PCR inhibition. Our method is applicable to various analytical samples, including processed foods. The use of other primers and fluorescence probes would permit highly sensitive detection of various recombinant DNA sequences besides the 35S promoter and NOS terminator.

  3. The Control of Single-color and Multiple-color Visual Search by Attentional Templates in Working Memory and in Long-term Memory.

    Science.gov (United States)

    Grubert, Anna; Carlisle, Nancy B; Eimer, Martin

    2016-12-01

    The question whether target selection in visual search can be effectively controlled by simultaneous attentional templates for multiple features is still under dispute. We investigated whether multiple-color attentional guidance is possible when target colors remain constant and can thus be represented in long-term memory but not when they change frequently and have to be held in working memory. Participants searched for one, two, or three possible target colors that were specified by cue displays at the start of each trial. In constant-color blocks, the same colors remained task-relevant throughout. In variable-color blocks, target colors changed between trials. The contralateral delay activity (CDA) to cue displays increased in amplitude as a function of color memory load in variable-color blocks, which indicates that cued target colors were held in working memory. In constant-color blocks, the CDA was much smaller, suggesting that color representations were primarily stored in long-term memory. N2pc components to targets were measured as a marker of attentional target selection. Target N2pcs were attenuated and delayed during multiple-color search, demonstrating less efficient attentional deployment to color-defined target objects relative to single-color search. Importantly, these costs were the same in constant-color and variable-color blocks. These results demonstrate that attentional guidance by multiple-feature as compared with single-feature templates is less efficient both when target features remain constant and can be represented in long-term memory and when they change across trials and therefore have to be maintained in working memory.

  4. Comparison of MRI based and PET template based approaches in the quantitative analysis of amyloid imaging with PIB-PET.

    Science.gov (United States)

    Edison, P; Carter, S F; Rinne, J O; Gelosa, G; Herholz, K; Nordberg, A; Brooks, D J; Hinz, R

    2013-04-15

    [(11)C]Pittsburgh compound-B (PIB) has been the most widely used positron emission tomography (PET) imaging agent for brain amyloid. Several longitudinal studies evaluating the progression of Alzheimer's disease (AD), and numerous therapeutic intervention studies are underway using [(11)C]PIB PET as an AD biomarker. Quantitative analysis of [(11)C]PIB data requires the definition of regional volumes of interest. This investigation systematically compared two data analysis routes both using a probabilistic brain atlas with 11 bilateral regions. Route 1 used individually segmented structural magnetic resonance images (MRI) for each subject while Route 2 used a standardised [(11)C]PIB PET template. A total of 54 subjects, 20 with probable Alzheimer's disease (AD), 14 with amnestic Mild Cognitive Impairment (MCI) and 20 age-matched healthy controls, were scanned at two imaging centres either in London (UK) or in Turku (Finland). For all subjects structural volumetric MRI and [(11)C]PIB PET scans were acquired. Target-to-cerebellum ratios 40 min to 60 min post injection were used as outcome measures. Regional read outs for grey matter target regions were generated for both routes. Based on a composite neocortical, frontal, posterior cingulate, combined posterior cingulate and frontal cortical regions, scans were categorised into either 'PIB negative' (PIB-) or 'PIB positive' (PIB+) using previously reported cut-off target-to-cerebellar ratios of 1.41, 1.5 and 1.6, respectively. Target-to-cerebellum ratios were greater when defined with a [(11)C]PIB PET template than with individual MRIs for all cortical regions regardless of diagnosis. This difference was highly significant for controls (pPIB PET template (Route 2) is adequate for clinical diagnostic purposes, while MRI based analysis (Route 1) remains more appropriate for clinical research. Copyright © 2012 Elsevier Inc. All rights reserved.

  5. A Template Analysis of Intimate Partner Violence Survivors' Experiences of Animal Maltreatment: Implications for Safety Planning and Intervention.

    Science.gov (United States)

    Collins, Elizabeth A; Cody, Anna M; McDonald, Shelby Elaine; Nicotera, Nicole; Ascione, Frank R; Williams, James Herbert

    2018-03-01

    This study explores the intersection of intimate partner violence (IPV) and animal cruelty in an ethnically diverse sample of 103 pet-owning IPV survivors recruited from community-based domestic violence programs. Template analysis revealed five themes: (a) Animal Maltreatment by Partner as a Tactic of Coercive Power and Control, (b) Animal Maltreatment by Partner as Discipline or Punishment of Pet, (c) Animal Maltreatment by Children, (d) Emotional and Psychological Impact of Animal Maltreatment Exposure, and (e) Pets as an Obstacle to Effective Safety Planning. Results demonstrate the potential impact of animal maltreatment exposure on women and child IPV survivors' health and safety.

  6. Fabrication and thermal analysis of submicron silver tubes prepared from electrospun fiber templates.

    Science.gov (United States)

    Ochanda, Frederick; Jones, Wayne E

    2007-01-16

    Submicron silver tubes have been synthesized by a polymer-based template approach. Two different approaches to metallization, electroless deposition and exchange plating, were evaluated within the template approach. Silver films with average thickness approximately 50-100 nm were deposited on polycarbonate fibers approximately 400 nm in diameter by each technique, resulting in tubes with a diameter between 450 and 500 nm after thermal degradation of core fibers. These nanomaterials were characterized by scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), and scanning thermal microscopy. The thermal conductivity of the silver submicron tubes was found to differ depending on the method of preparation, with tubes from electroless plating possessing relative thermal conductivity values that were 1 order of magnitude higher than that from exchange plating, 3000 W/m x K and 660 W/m x K, respectively. Interestingly, these results indicate that silver submicron tubes possess higher thermal conductivity than the bulk metal. This observation is discussed in the context of the continuous conduction path of the tubes and their high surface area-to-volume ratio.

  7. Single-Cell Genomic Analysis in Plants

    Directory of Open Access Journals (Sweden)

    Yuxuan Yuan

    2018-01-01

    Full Text Available Individual cells in an organism are variable, which strongly impacts cellular processes. Advances in sequencing technologies have enabled single-cell genomic analysis to become widespread, addressing shortcomings of analyses conducted on populations of bulk cells. While the field of single-cell plant genomics is in its infancy, there is great potential to gain insights into cell lineage and functional cell types to help understand complex cellular interactions in plants. In this review, we discuss current approaches for single-cell plant genomic analysis, with a focus on single-cell isolation, DNA amplification, next-generation sequencing, and bioinformatics analysis. We outline the technical challenges of analysing material from a single plant cell, and then examine applications of single-cell genomics and the integration of this approach with genome editing. Finally, we indicate future directions we expect in the rapidly developing field of plant single-cell genomic analysis.

  8. Retrospective analysis of role of interstitial brachytherapy using template (MUPIT in locally advanced gynecological malignancies

    Directory of Open Access Journals (Sweden)

    Nandwani Pooja

    2007-01-01

    Full Text Available Aim : The aim of this retrospective study was to assess treatment outcomes for patients with locally advanced gynecological malignancies being treated with interstitial brachytherapy using Martinez universal perineal interstitial template (MUPIT and to study the acute and late sequelae and survival after treatment by this technique. Materials and Methods : Ninety seven patients untreated with histopathological confirmation of carcinoma of cervix (37 vault (40 and vagina (20 were treated by combination of external beam RT (EBRT using megavoltage irradiation to pelvis to dose of 4000-5000 cGy followed by interstitial brachytherapy using MUPIT between September 2001 to March 2005. Median age was 46 years. Only those patients who were found unsuitable for conventional brachytherapy or in whom intracavitatory radiotherapy was found to be unlikely to encompass a proper dose distribution were treated by interstitial template brachytherapy using MUPIT application and were enrolled in this study. The dose of MUPIT was 1600-2400 cGy in 4-6# with 400 cGy /# and two fractions a day with minimum gap of six hours in between two fractions on micro-HDR. Criteria for inclusion of patients were as follows: Hb minimum 10 gm/dl, performance status - 70% or more (Karnofsy scale, histopathological confirmation FIGO stage IIB-IIIB (excluding frozen pelvis. Results : Among the 97 patients studied, 12 patients lost to follow-up and hence they were excluded from the study. Follow-up of rest of the patients was then done up to September 2006. The duration of follow-up was in the range of 20-60 months. Parameters studied were local control rate, complication rate, mortality rate and number of patients developing systemic metastasis. Local control was achieved in 56/85 (64.7% and complication rate was 15/85 (17.6%. Local control was better for nonbulky tumors compared bulky tumors irrespective of stage of disease. Local control was better in patients with good regression of

  9. Monitoring the Retention of Human Proliferating Cell Nuclear Antigen at Primer/Template Junctions by Proteins That Bind Single-Stranded DNA.

    Science.gov (United States)

    Hedglin, Mark; Aitha, Mahesh; Benkovic, Stephen J

    2017-07-11

    In humans, proliferating cell nuclear antigen (PCNA) sliding clamps encircling DNA coordinate various aspects of DNA metabolism throughout the cell cycle. A critical aspect of this is restricting PCNA to the vicinity of its DNA target site. For example, PCNA must be maintained at or near primer/template (P/T) junctions during DNA synthesis. With a diverse array of cellular factors implicated, many of which interact with PCNA, DNA, or both, it is unknown how this critical feat is achieved. Furthermore, current biochemical assays that examine the retention of PCNA near P/T junctions are inefficient, discontinuous, and qualitative and significantly deviate from physiologically relevant conditions. To overcome these challenges and limitations, we recently developed a novel and convenient Förster resonance energy transfer (FRET) assay that directly and continuously monitors the retention of human PCNA at a P/T junction. Here we describe in detail the design, methodology, interpretation, and limitations of this quantitative FRET assay using the single-stranded DNA-binding protein, SSB, from Escherichia coli as an example. This powerful tool is broadly applicable to any single-stranded DNA-binding protein and may be utilized and/or expanded upon to dissect DNA metabolic pathways that are dependent upon PCNA.

  10. Virus templated metallic nanoparticles

    Science.gov (United States)

    Aljabali, Alaa A. A.; Barclay, J. Elaine; Lomonossoff, George P.; Evans, David J.

    2010-12-01

    Plant viruses are considered as nanobuilding blocks that can be used as synthons or templates for novel materials. Cowpea mosaic virus (CPMV) particles have been shown to template the fabrication of metallic nanoparticles by an electroless deposition metallization process. Palladium ions were electrostatically bound to the virus capsid and, when reduced, acted as nucleation sites for the subsequent metal deposition from solution. The method, although simple, produced highly monodisperse metallic nanoparticles with a diameter of ca. used as synthons or templates for novel materials. Cowpea mosaic virus (CPMV) particles have been shown to template the fabrication of metallic nanoparticles by an electroless deposition metallization process. Palladium ions were electrostatically bound to the virus capsid and, when reduced, acted as nucleation sites for the subsequent metal deposition from solution. The method, although simple, produced highly monodisperse metallic nanoparticles with a diameter of ca. agarose gel electrophoresis results, energy dispersive X-ray spectra, ζ-potential measurements, dynamic light scattering data, nanoparticle tracking analysis and an atomic force microscopy image of Ni-CPMV. See DOI: 10.1039/c0nr00525h

  11. Perl Template Toolkit

    CERN Document Server

    Chamberlain, Darren; Cross, David; Torkington, Nathan; Diaz, tatiana Apandi

    2004-01-01

    Among the many different approaches to "templating" with Perl--such as Embperl, Mason, HTML::Template, and hundreds of other lesser known systems--the Template Toolkit is widely recognized as one of the most versatile. Like other templating systems, the Template Toolkit allows programmers to embed Perl code and custom macros into HTML documents in order to create customized documents on the fly. But unlike the others, the Template Toolkit is as facile at producing HTML as it is at producing XML, PDF, or any other output format. And because it has its own simple templating language, templates

  12. The interplay of primer-template DNA phosphorylation status and single-stranded DNA binding proteins in directing clamp loaders to the appropriate polarity of DNA.

    Science.gov (United States)

    Hayner, Jaclyn N; Douma, Lauren G; Bloom, Linda B

    2014-01-01

    Sliding clamps are loaded onto DNA by clamp loaders to serve the critical role of coordinating various enzymes on DNA. Clamp loaders must quickly and efficiently load clamps at primer/template (p/t) junctions containing a duplex region with a free 3'OH (3'DNA), but it is unclear how clamp loaders target these sites. To measure the Escherichia coli and Saccharomyces cerevisiae clamp loader specificity toward 3'DNA, fluorescent β and PCNA clamps were used to measure clamp closing triggered by DNA substrates of differing polarity, testing the role of both the 5'phosphate (5'P) and the presence of single-stranded binding proteins (SSBs). SSBs inhibit clamp loading by both clamp loaders on the incorrect polarity of DNA (5'DNA). The 5'P groups contribute selectivity to differing degrees for the two clamp loaders, suggesting variations in the mechanism by which clamp loaders target 3'DNA. Interestingly, the χ subunit of the E. coli clamp loader is not required for SSB to inhibit clamp loading on phosphorylated 5'DNA, showing that χ·SSB interactions are dispensable. These studies highlight a common role for SSBs in directing clamp loaders to 3'DNA, as well as uncover nuances in the mechanisms by which SSBs perform this vital role. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Single-Level and Multilevel Mediation Analysis

    Science.gov (United States)

    Tofighi, Davood; Thoemmes, Felix

    2014-01-01

    Mediation analysis is a statistical approach used to examine how the effect of an independent variable on an outcome is transmitted through an intervening variable (mediator). In this article, we provide a gentle introduction to single-level and multilevel mediation analyses. Using single-level data, we demonstrate an application of structural…

  14. Code Generation with Templates

    CERN Document Server

    Arnoldus, Jeroen; Serebrenik, A

    2012-01-01

    Templates are used to generate all kinds of text, including computer code. The last decade, the use of templates gained a lot of popularity due to the increase of dynamic web applications. Templates are a tool for programmers, and implementations of template engines are most times based on practical experience rather than based on a theoretical background. This book reveals the mathematical background of templates and shows interesting findings for improving the practical use of templates. First, a framework to determine the necessary computational power for the template metalanguage is presen

  15. Synthesis of mesoporous zeolite catalysts by in situ formation of carbon template over nickel nanoparticles

    DEFF Research Database (Denmark)

    Abildstrøm, Jacob Oskar; Kegnæs, Marina; Hytoft, Glen

    2016-01-01

    A novel synthesis procedure for the preparation of the hierarchical zeolite materials with MFI structure based on the carbon templating method with in situ generated carbon template is presented in this study. Through chemical vapour deposition of coke on nickel nanoparticles supported on silica...... oxide, a carbon-silica composite is obtained and exploited as a combined carbon template/silica source for zeolite synthesis. This approach has several advantages in comparison with conventional carbon templating methods, where relatively complicated preparative strategies involving multistep...... impregnation procedures and rather expensive chemicals are used. Removal of the carbon template by combustion results in zeolite single crystals with intracrystalline pore volumes between 0.28 and 0.48 cm3/g. The prepared zeolites are characterized by XRD, SEM, TEM and physisorption analysis. The isomerization...

  16. Parallel single-cell analysis microfluidic platform

    NARCIS (Netherlands)

    van den Brink, Floris Teunis Gerardus; Gool, Elmar; Frimat, Jean-Philippe; Bomer, Johan G.; van den Berg, Albert; le Gac, Severine

    2011-01-01

    We report a PDMS microfluidic platform for parallel single-cell analysis (PaSCAl) as a powerful tool to decipher the heterogeneity found in cell populations. Cells are trapped individually in dedicated pockets, and thereafter, a number of invasive or non-invasive analysis schemes are performed.

  17. The need of appropriate brain SPECT templates for SPM comparisons

    International Nuclear Information System (INIS)

    Morbelli, S.; Altrinetti, V.; Piccardo, A.; Rodriguez, G.; Brugnolo, A.; Nobili, F.; Mignone, A.; Pupi, A.; Koulibaly, P.M.

    2008-01-01

    Statistical parametric mapping (SPM) is used worldwide to compare brain perfusion single photon emission computed tomography (SPECT) data. The default template within the SPM package used for SPECT image normalization includes images of a group of healthy subjects studied with 99m TcHMPAO. Since [ 99m Tc] HMPAO and [ 99m Tc] ECD have shown to distribute differently in SPECT studies, we formulated the hypothesis that comparing set of [ 99m Tc]ECD data normalized by means of a [ 99m Tc]HMPAO template may lead to incorrect results. A customized [ 99m Tc]ECD template was built with SPECT and magnetic resonance imaging (MRI) images of 22 neurologically healthy women. Then, two sets of subjects, i.e. a group of patients with very early Alzheimer's disease (eAD) and a matched control group, studied by means of [ 99m Tc]ECD SPECT, were chosen for comparisons. The same statistical approach (t-test between eAD patients and controls and correlation analysis between brain SPECT and a cognitive score) was applied twice, i.e. after normalization with either the default [ 99m Tc]HMPAO template or the customized [ 99m Tc]ECD template. In the comparison between eAD and controls, a cluster of difference in the posterior-cingulate gyrus of both hemispheres was only highlighted when using the customized [ 99m Tc]ECD template, but was missed when using the default [ 99m Tc]HMPAO template. In the correlation between brain perfusion and a cognitive score, the significant cluster was more significant and far more extended, also including the right superior temporal gyrus, using the customized [ 99m Tc]ECD template than using the default [ 99m Tc]HMPAO template. These data suggest the need of customized, radiopharmaceutical-matched SPECT templates to be used within the SPM package. The present customized [ 99m Tc]ECD template is now freely available on the web. (authors)

  18. RJS Templates for Rails

    CERN Document Server

    Fauser, Cody

    2006-01-01

    RJS templates are an exciting and powerful new type of template added to Rails 1.1. Unlike conventional Rails templates that generate HTML or XML, RJS templates generate JavaScript code that is executed when it is returned to the browser. This JavaScript generation allows you to perform multiple page updates in-place without a page reload using Ajax. All the JavaScript you need is generated from simple templates written in Ruby. This document helps you get acquainted with how RJS templates fit into the Rails framework and gets you started with a few easy-to-follow examples.

  19. Methanol conversion to light olefins over nanostructured CeAPSO-34 catalyst: Thermodynamic analysis of overall reactions and effect of template type on catalytic properties and performance

    International Nuclear Information System (INIS)

    Aghamohammadi, Sogand; Haghighi, Mohammad; Charghand, Mojtaba

    2014-01-01

    Graphical abstract: In this research nanostructured CeAPSO-34 was synthesized to explore the effect of TEAOH and morpholine on its physiochemical properties and MTO performance. Prepared catalysts were characterized with XRD, FESEM, BET, FTIR and NH3-TPD techniques. The results indicated that the nature of the template determines the physiochemical properties of CeAPSO-34 due to different rate of crystal growth. The catalyst obtained by using morpholine showed longer life time as well as sustaining light olefins selectivity at higher values. Furthermore, a comprehensive thermodynamic analysis of overall reactions network was carried out to address the major channels of methanol to olefins conversion. - Highlights: • Introduction of Ce into SAPO-34 framework. • Comparison of CeAPSO-34 synthesized using morpholine and TEAOH. • The nature of the template determines the physiochemical properties of CeAPSO-34. • Morpholine enhances catalyst lifetime in MTO process. • Presenting a complete reaction network for MTO process. - Abstract: TEAOH and morpholine were employed in synthesis of nanostructured CeAPSO-34 molecular sieve and used in methanol to olefins conversion. Prepared samples were characterized by XRD, FESEM, EDX, BET, FTIR and NH 3 -TPD techniques. XRD patterns reflected the higher crystallinity of the catalyst synthesized with morpholine. The FESEM results indicated that the nature of the template determines the morphology of nanostructured CeAPSO-34 due to different rate of crystal growth. There was a meaningful difference in the strength of both strong and weak acid sites for CeAPSO-34 catalysts synthesized with TEAOH and morpholine templates. The catalyst synthesized with morpholine showed higher desorption temperature of both weak and strong acid sites evidenced by NH 3 -TPD characterization. The catalyst obtained using morpholine template had the longer lifetime and sustained desired light olefins at higher values. A comprehensive thermodynamic

  20. Barbell-shaped stir bar sorptive extraction using dummy template molecularly imprinted polymer coatings for analysis of bisphenol A in water.

    Science.gov (United States)

    Liu, Ruimei; Feng, Feng; Chen, Guolin; Liu, Zhimin; Xu, Zhigang

    2016-07-01

    This study reports the development of a novel dummy template molecularly imprinted polymer (MIP)-coated barbell-shaped stir bar. The MIP stir bar coatings were prepared by using 2,2-bis(4-hydroxyphenyl)butane (BPB), 4,4'-dihydroxydiphenylmethane (BPF), 4-tert-butylphenol (PTBP), and tetrabromobisphenol A (TBBA) as dummy templates using a capillary in situ polymerization method. Uniform coatings can be prepared controllably. The method is simple, easy, and reproducible. The barbell-shaped stir bar was developed by using medical silicone tubes as wheels. The wheels could be removed and reinstalled when necessary; therefore, the barbell-shaped stir bar was easy to disassemble and reassemble. The novel MIP-coated stir bar showed good selectivity for the target analyte, bisphenol A (BPA). The established method is selective and sensitive with a lower detection limit for BPA of 0.003 μg/L. The dummy template MIP-coated stir bar is suitable for trace BPA analysis in real environmental water samples without template leakage. The novel stir bar can be used at least 100 times.

  1. Rock physics template (RPT) analysis of well logs and seismic data for lithology and fluid classification in Cambay Basin

    Science.gov (United States)

    Datta Gupta, Saurabh; Chatterjee, Rima; Farooqui, M. Y.

    2012-07-01

    The Cambay Basin is 450-km-long north-south-trending graben with an average width of 50 km, having maximum depth of about 7 km. The origin of the Cambay and other Basins on the western margin of India are related to the break up of the Gondwana super-continent in the Late-Triassic to Early-Jurassic (215 ma). The structural disposition of the Pre-Cambrian basement—a complex of igneous and metamorphic rocks exposed in the vicinity of the Cambay Basin—controls its architecture. The principal lineaments in the Basin are aligned towards NE-SE, ENE-WSW and NNW-SSE, respectively. Rock physics templates (RPTs) are charts and graphs generated by using rock physics models, constrained by local geology, that serve as tools for lithology and fluid differentiation. RPT can act as a powerful tool in validating hydrocarbon anomalies in undrilled areas and assist in seismic interpretation and prospect evaluation. However, the success of RPT analysis depends on the availability of the local geological information and the use of the proper model. RPT analysis has been performed on well logs and seismic data of a particular study area in mid Cambay Basin. Rock physics diagnostic approach is adopted in the study area placed at mid Cambay Basin to estimate the volume in the reservoir sands from 6 wells (namely; A, B, C, D, E and F) where oil was already encountered in one well, D. In the study area, hydrocarbon prospective zone has been marked through compressional (P wave) and shear wave (S wave) impedance only. In the RPT analysis, we have plotted different kinds of graphical responses of Lame's parameters, which are the function of P-wave velocity, S-wave velocity and density. The discrete thin sand reservoirs have been delineated through the RPT analysis. The reservoir pay sand thickness map of the study area has also been derived from RPT analysis and fluid characterization. Through this fluid characterization, oil-bearing thin sand layers have been found in well E including

  2. Templating mesoporous zeolites

    DEFF Research Database (Denmark)

    Egeblad, Kresten; Christensen, Christina Hviid; Kustova, Marina

    2008-01-01

    The application of templating methods to produce zeolite materials with hierarchical bi- or trimodal pore size distributions is reviewed with emphasis on mesoporous materials. Hierarchical zeolite materials are categorized into three distinctly different types of materials: hierarchical zeolite...... originates almost exclusively from the support material. The methods for introducing mesopores into zeolite materials are discussed and categorized. In general, mesopores can be templated in zeolite materials by use of solid templating, supramolecular templating, or indirect templating....... In this categorization of templating methods, the nature of the interface between the zeolite crystal and the mesopore exactly when the mesopore starts to form is emphasized. In solid templating, the zeolite crystal is in intimate contact with a solid material that is being removed to produce the mesoporosity. Similarly...

  3. The control of single-colour and multiple-colour visual search by attentional templates in working memory and in long-term memory

    OpenAIRE

    Grubert, Anna; Carlisle, N.; Eimer, Martin

    2016-01-01

    The question whether target selection in visual search can be effectively controlled by simultaneous attentional templates for multiple features is still under dispute. We investigated whether multiple-colour attentional guidance is possible when target colours remain constant and can thus be represented in long-term memory but not when they change frequently and have to be held in working memory. Participants searched for one, two, or three possible target colours that were specified by cue ...

  4. A Deformable Template Model, with Special Reference to Elliptical Templates

    DEFF Research Database (Denmark)

    Hobolth, Asger; Pedersen, Jan; Jensen, Eva Bjørn Vedel

    2002-01-01

    , is allowed to be non-stationary. Stationarity is obtained by a time change. A parametric model for the residual process is suggested and straightforward parameter estimation techniques are developed. The deformable template model makes it possible to detect pathologies as demonstrated by an analysis...

  5. Optimization of genetic analysis for single cell

    Directory of Open Access Journals (Sweden)

    hussein mouawia

    2012-03-01

    Full Text Available The molecular genetic analysis of microdissected cells by laser, a method for selecting a starting material of pure DNA or RNA uncontaminated. Our study focuses on technical pre-PCR (polymerase chain reaction for the amplification of DNA from a single cell (leukocyte isolated from human blood after laser microdissection and aims to optimize the yield of DNA extracted of this cell to be amplified without errors and provide reliable genetic analyzes. This study has allowed us to reduce the duration of cell lysis in order to perform the step of expanding genomic PEP (primer extension preamplification directly after lysis the same day and the quality of genomic amplification and eliminate purification step of the product PEP, step with a risk of contamination and risk of loss of genetic material related to manipulation. This approach has shown that the combination of at least 3 STR (short tandem repeat markers for genetic analysis of single cell improves the efficiency and accuracy of PCR and minimizes the loss of allele (allele drop out; ADO. This protocol can be applied to large scale and an effective means suitable for genetic testing for molecular diagnostic from isolated single cell (cancerous - fetal.

  6. A Functional Monomer Is Not Enough: Principal Component Analysis of the Influence of Template Complexation in Pre-Polymerization Mixtures on Imprinted Polymer Recognition and Morphology

    Directory of Open Access Journals (Sweden)

    Kerstin Golker

    2014-11-01

    Full Text Available In this report, principal component analysis (PCA has been used to explore the influence of template complexation in the pre-polymerization phase on template molecularly imprinted polymer (MIP recognition and polymer morphology. A series of 16 bupivacaine MIPs were studied. The ethylene glycol dimethacrylate (EGDMA-crosslinked polymers had either methacrylic acid (MAA or methyl methacrylate (MMA as the functional monomer, and the stoichiometry between template, functional monomer and crosslinker was varied. The polymers were characterized using radioligand equilibrium binding experiments, gas sorption measurements, swelling studies and data extracted from molecular dynamics (MD simulations of all-component pre-polymerization mixtures. The molar fraction of the functional monomer in the MAA-polymers contributed to describing both the binding, surface area and pore volume. Interestingly, weak positive correlations between the swelling behavior and the rebinding characteristics of the MAA-MIPs were exposed. Polymers prepared with MMA as a functional monomer and a polymer prepared with only EGDMA were found to share the same characteristics, such as poor rebinding capacities, as well as similar surface area and pore volume, independent of the molar fraction MMA used in synthesis. The use of PCA for interpreting relationships between MD-derived descriptions of events in the pre-polymerization mixture, recognition properties and morphologies of the corresponding polymers illustrates the potential of PCA as a tool for better understanding these complex materials and for their rational design.

  7. A functional monomer is not enough: principal component analysis of the influence of template complexation in pre-polymerization mixtures on imprinted polymer recognition and morphology.

    Science.gov (United States)

    Golker, Kerstin; Karlsson, Björn C G; Rosengren, Annika M; Nicholls, Ian A

    2014-11-10

    In this report, principal component analysis (PCA) has been used to explore the influence of template complexation in the pre-polymerization phase on template molecularly imprinted polymer (MIP) recognition and polymer morphology. A series of 16 bupivacaine MIPs were studied. The ethylene glycol dimethacrylate (EGDMA)-crosslinked polymers had either methacrylic acid (MAA) or methyl methacrylate (MMA) as the functional monomer, and the stoichiometry between template, functional monomer and crosslinker was varied. The polymers were characterized using radioligand equilibrium binding experiments, gas sorption measurements, swelling studies and data extracted from molecular dynamics (MD) simulations of all-component pre-polymerization mixtures. The molar fraction of the functional monomer in the MAA-polymers contributed to describing both the binding, surface area and pore volume. Interestingly, weak positive correlations between the swelling behavior and the rebinding characteristics of the MAA-MIPs were exposed. Polymers prepared with MMA as a functional monomer and a polymer prepared with only EGDMA were found to share the same characteristics, such as poor rebinding capacities, as well as similar surface area and pore volume, independent of the molar fraction MMA used in synthesis. The use of PCA for interpreting relationships between MD-derived descriptions of events in the pre-polymerization mixture, recognition properties and morphologies of the corresponding polymers illustrates the potential of PCA as a tool for better understanding these complex materials and for their rational design.

  8. Pre-steady state kinetic analysis of HIV-1 reverse transcriptase for non-canonical ribonucleoside triphosphate incorporation and DNA synthesis from ribonucleoside-containing DNA template.

    Science.gov (United States)

    Nguyen, Laura A; Domaoal, Robert A; Kennedy, Edward M; Kim, Dong-Hyun; Schinazi, Raymond F; Kim, Baek

    2015-03-01

    Non-dividing macrophages maintain extremely low cellular deoxyribonucleotide triphosphate (dNTP) levels, but high ribonucleotide triphosphate (rNTP) concentrations. The disparate nucleotide pools kinetically forces Human Immunodeficiency Virus 1 (HIV-1) reverse transcriptase (RT) to incorporate non-canonical rNTPs during reverse transcription. HIV-1 RT pauses near ribonucleoside monophosphates (rNMPs) embedded in the template DNA, which has previously been shown to enhance mismatch extension. Here, pre-steady state kinetic analysis shows rNTP binding affinity (Kd) of HIV-1 RT for non-canonical rNTPs was 1.4- to 43-fold lower, and the rNTP rate of incorporation (kpol) was 15- to 1551-fold slower than for dNTPs. This suggests that RT is more selective for incorporation of dNTPs rather than rNTPs. HIV-1 RT selectivity for dNTP versus rNTP is the lowest for ATP, implying that HIV-1 RT preferentially incorporates ATP when dATP concentration is limited. We observed that incorporation of a dNTP occurring one nucleotide before an embedded rNMP in the template had a 29-fold greater Kd and a 20-fold slower kpol as compared to the same template containing dNMP. This reduced the overall dNTP incorporation efficiency of HIV-1 RT by 581-fold. Finally, the RT mutant Y115F displayed lower discrimination against rNTPs due to its increase in binding affinity for non-canonical rNTPs. Overall, these kinetic results demonstrate that HIV-1 RT utilizes both substrate binding and a conformational change during: (1) enzymatic discrimination of non-canonical rNTPs from dNTPs and (2) during dNTP primer extension with DNA templates containing embedded rNMP. Copyright © 2014 Elsevier B.V. All rights reserved.

  9. Template characterization and correlation algorithm created from segmentation for the iris biometric authentication based on analysis of textures implemented on a FPGA

    International Nuclear Information System (INIS)

    Giacometto, F J; Vilardy, J M; Torres, C O; Mattos, L

    2011-01-01

    Among the most used biometric signals to set personal security permissions, taker increasingly importance biometric iris recognition based on their textures and images of blood vessels due to the rich in these two unique characteristics that are unique to each individual. This paper presents an implementation of an algorithm characterization and correlation of templates created for biometric authentication based on iris texture analysis programmed on a FPGA (Field Programmable Gate Array), authentication is based on processes like characterization methods based on frequency analysis of the sample, and frequency correlation to obtain the expected results of authentication.

  10. Templates, Numbers & Watercolors.

    Science.gov (United States)

    Clemesha, David J.

    1990-01-01

    Describes how a second-grade class used large templates to draw and paint five-digit numbers. The lesson integrated artistic knowledge and vocabulary with their mathematics lesson in place value. Students learned how draftspeople use templates, and they studied number paintings by Charles Demuth and Jasper Johns. (KM)

  11. Optimizing preventive maintenance with maintenance templates

    International Nuclear Information System (INIS)

    Dozier, I.J.

    1996-01-01

    Rising operating costs has caused maintenance professionals to rethink their strategy for preventive maintenance (PM) programs. Maintenance Templates are pre-engineered PM task recommendations for a component type based on application of the component. Development of the maintenance template considers the dominant failure cause of the component and the type of preventive maintenance that can predict or prevent the failure from occurring. Maintenance template development also attempts to replace fixed frequency tasks with condition monitoring tasks such as vibration analysis or thermography. For those components that have fixed frequency PM intervals, consideration is given to the maintenance drivers such as criticality, environment and usage. This helps to maximize the PM frequency intervals and maximize the component availability. Maintenance Templates have been used at PECO Energy's Limerick Generating Station during the Reliability Centered Maintenance (RCM) Process to optimize their PM program. This paper describes the development and uses of the maintenance templates

  12. Single Molecule Analysis of Resection Tracks.

    Science.gov (United States)

    Huertas, Pablo; Cruz-García, Andrés

    2018-01-01

    Homologous recombination is initiated by the so-called DNA end resection, the 5'-3' nucleolytic degradation of a single strand of the DNA at each side of the break. The presence of resected DNA is an obligatory step for homologous recombination. Moreover, the amount of resected DNA modulates the prevalence of different recombination pathways. In different model organisms, there are several published ways to visualize and measure with more or less detail the amount of DNA resected. In human cells, however, technical constraints hampered the study of resection at high resolution. Some information might be gathered from the study of endonuclease-created DSBs, in which the resection of breaks at known sites can be followed by PCR or ChIP. In this chapter, we describe in detail a novel assay to study DNA end resection in breaks located on unknown positions. Here, we use ionizing radiation to induce double-strand breaks, but the same approach can be used to monitor resection induced by different DNA damaging agents. By modifying the DNA-combing technique, used for high-resolution replication analyses, we can measure resection progression at the level of individual DNA fibers. Thus, we named the method Single Molecule Analysis of Resection Tracks (SMART). We use human cells in culture as a model system, but in principle the same approach would be feasible to any model organism adjusting accordingly the DNA isolation part of the protocol.

  13. Well log and seismic data analysis for complex pore-structure carbonate reservoir using 3D rock physics templates

    Science.gov (United States)

    Li, Hongbing; Zhang, Jiajia

    2018-04-01

    The pore structure in heterogeneous carbonate rock is usually very complex. This complex pore system makes the relationship between the velocity and porosity of the rock highly scattered, so that for the classical two-dimensional rock physics template (2D RPT) it is not enough to accurately describe the quantitative relationship between the rock elastic parameters of this kind of reservoir and its porosity and water saturation. Therefore it is possible to attribute the effect of pore type to that of the porosity or water saturation, and leads to great deviations when applying such a 2D RPT to predict the porosity and water saturation in seismic reservoir prediction and hydrocarbon detection. This paper first presents a method to establish a new three-dimensional rock physics template (3D RPT) by integrating the Gassmann equations and the porous rock physics model, and use it to characterize the quantitative relation between rock elastic properties and the reservoir parameters including the pore aspect ratio, porosity and water saturation, and to predict these parameters from the known elastic properties. The test results on the real logging and seismic inversion data show that the 3D RPT can accurately describe the variations of elastic properties with the porosity, water saturation and pore-structure parameters, and effectively improve the accuracy of reservoir parameters prediction.

  14. Rapid analysis of ractopamine in pig tissues by dummy-template imprinted solid-phase extraction coupling with surface-enhanced Raman spectroscopy.

    Science.gov (United States)

    Xiao, Xiaohua; Yan, Kuanglin; Xu, Xianfang; Li, Gongke

    2015-06-01

    Ritodrine has similar skeleton structure to ractopamine and it was selected as the dummy-template molecule to synthesize the molecular imprinted polymers (MIPs). The MIPs exhibited better selectivity to ractopamine than to the dummy-template molecule: the imprint factor for ractopamine was 8.9, while 7.6 for ritodrine. The MIPs were used as sorbents in solid-phase extraction for selective enrichment of ractopamine, and some key parameters were optimized. After that, a rapid surface-enhanced Raman spectroscopy method was developed for analysis of ractopamine and isoxuprine in pig tissue samples. Under the optimal conditions, good linearity was achieved in the range of 20.0-200.0 μg/L for ractopamine and isoxsuprine at 842 cm(-1) and 993 cm(-1), respectively. The limits of detection were 3.1-4.3 μg/L, which were lower than the maximum allowed by U. S. Food and Drug Administration. The recoveries of ractopamine and isoxsuprine were 72.4-79.7% and 71.0-78.2% for the spiked pork and pig liver, respectively, while the relative standard deviations ranging from 7.4% to 13.0%. The results suggest that the proposed method is sensitive and selective, and it has good potential on the quantitative analysis of trace amounts of β-agonists in complex samples. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. images_template

    Data.gov (United States)

    National Aeronautics and Space Administration — Images for the website template go here. It will not change their names or locations, but will hopefully help to organize them. Oh, but for a directory structure...

  16. Reliability and accuracy of digital templating for the humeral component of total shoulder arthroplasty.

    Science.gov (United States)

    Lee, Christopher S; Davis, Shane M; Lane, Christianne J; Koonce, Ryan C; Hartman, Andrew P; Ball, Kenneth; Esch, James C

    2015-01-01

    This experimental study evaluated the interobserver reliability and accuracy of pre-operative digital templating for humeral head size, stem size and neck angle for total shoulder arthroplasty. Twenty-five patients underwent a total shoulder arthroplasty with a single prosthesis. Four independent, blinded surgeons (two experienced shoulder surgeons and two PGY-6 fellows) used pre-operative radiographs and templating software to generate templates of the humeral head, stem and neck for each patient. Interobserver reliability was calculated using weighted kappa (κ) analysis. Accuracy was assessed by comparing templates to actual implant sizes. Interobserver reliability was fair to substantial (κ = 0.26 to 0.71) for head size, fair to substantial (κ = 0.39 to 0.72) for stem size and slight to fair (κ = 0.16 to 0.34) for neck angle. Templated head size, stem size and neck angle had accuracies of 53%, 77% and 68% within one size variation, respectively. Experience did not affect accuracy (p = 0.11 to 0.48). Digital templating is not a useful guide for pre-operative surgical planning and should not be used to select a prosthesis.

  17. Single particle raster image analysis of diffusion.

    Science.gov (United States)

    Longfils, M; Schuster, E; Lorén, N; Särkkä, A; Rudemo, M

    2017-04-01

    As a complement to the standard RICS method of analysing Raster Image Correlation Spectroscopy images with estimation of the image correlation function, we introduce the method SPRIA, Single Particle Raster Image Analysis. Here, we start by identifying individual particles and estimate the diffusion coefficient for each particle by a maximum likelihood method. Averaging over the particles gives a diffusion coefficient estimate for the whole image. In examples both with simulated and experimental data, we show that the new method gives accurate estimates. It also gives directly standard error estimates. The method should be possible to extend to study heterogeneous materials and systems of particles with varying diffusion coefficient, as demonstrated in a simple simulation example. A requirement for applying the SPRIA method is that the particle concentration is low enough so that we can identify the individual particles. We also describe a bootstrap method for estimating the standard error of standard RICS. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

  18. Micro-PIXE for single cell analysis

    International Nuclear Information System (INIS)

    Ortega, Richard

    2012-01-01

    The knowledge of the intracellular distribution of biological relevant metals is important to understand their mechanisms of action in cells, either for physiological, toxicological or pathological processes. However, the direct detection of trace metals in single cells is a challenging task that requires sophisticated analytical developments. The combination of micro-PIXE with RBS and STIM (Scanning Transmission Ion Microscopy) allows the quantitative determination of trace metal content within sub-cellular compartments. The application of STIM analysis provides high spatial resolution imaging (< 200 nm) and excellent mass sensitivity (< 0.1 ng). Application of the STIM-PIXE-RBS methodology is absolutely needed when organic mass loss appears during PIXE-RBS irradiation. This combination of STIM-PIXE-RBS provides fully quantitative determination of trace element content, expressed in μg/g, which is a quite unique capability for micro-PIXE compared to other micro-analytical methods such as the electron and synchrotron x-ray fluorescence. Examples of micro-PIXE studies for sub-cellular imaging of trace elements in various fields of interest will be presented: in patho-physiology of trace elements involved in neurodegenerative diseases such as Parkinson's disease, and in toxicology of metals such as cobalt. (author)

  19. Stress analysis of a single osteon

    Science.gov (United States)

    Ismail, A. A.; Daud, R.; Amin, N. A. M.; Majid, M. S. Abdul; Basaruddin, K. S.; Junoh, A. K.

    2017-09-01

    Cortical boneis considered as a composite material as it was made up of different phases such as osteon, interstitial bone and cement line. Bone is known for its function to give supports in vertebrae. The bone also has a special feature that was enable it to resist the fracture under certain condition. Many researchers are interested in understanding the fracture mechanic of the bone because of its special micro-structure. The objective of this study was to develop numericalmodelof a single osteon using Finite Element Method to determine stress distribution and predict the location of microcrack initiation.A finite element stress and strain analysis has been carried out for an osteon under radial loading. With radial loading, high values of stresses were predicted at the innermost lamellar of osteon. These findings suggest that stress was accumulated in the lamella near the Haversian canal. The microcrack in osteon may start in the lamella near to the canal, correlates with the data in literature.

  20. Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method

    Directory of Open Access Journals (Sweden)

    Zou Fei

    2010-10-01

    Full Text Available Abstract Background The primer and amplicon length have been found to affect PCR based estimates of microbial diversity by pyrosequencing, while other PCR conditions have not been addressed using any deep sequencing method. The present study determined the effects of polymerase, template dilution and PCR cycle number using the Solexa platform. Results The PfuUltra II Fusion HS DNA Polymerase (Stratagene with higher fidelity showed lower amount of PCR artifacts and determined lower taxa richness than the Ex Taq (Takara. More importantly, the two polymerases showed different efficiencies for amplifying some of very abundant sequences, and determined significantly different community structures. As expected, the dilution of the DNA template resulted in a reduced estimation of taxa richness, particularly at the 200 fold dilution level, but the community structures were similar for all dilution levels. The 30 cycle group increased the PCR artifacts while comparing to the 25 cycle group, but the determined taxa richness was lower than that of the 25 cycle group. The PCR cycle number did not changed the microbial community structure significantly. Conclusions These results highlight the PCR conditions, particularly the polymerase, have significant effect on the analysis of microbial diversity with next generation sequencing methods.

  1. Single-Molecule Luminescence and High Efficiency Photovoltaic Cells Based on Percolated Conducting Carbon Nanotubes Scaffolds Templated with Light-Harvesting Conjugated Polymers and Nanohybrids

    National Research Council Canada - National Science Library

    Yang, Arnold C

    2009-01-01

    .... Nanocomposites constructed by surface-grafted multiwall carbon nanotubes (CNTs) with conjugated polymers dispersed in a polymer matrix were synthesized to form novel optoelectronic materials that exploit single-molecule effects...

  2. Semiconductor nanowires and templates for electronic applications

    Energy Technology Data Exchange (ETDEWEB)

    Ying, Xiang

    2009-07-15

    This thesis starts by developing a platform for the organized growth of nanowires directly on a planar substrate. For this, a method to fabricate horizontal porous alumina membranes is studied. The second part of the thesis focuses on the study of nanowires. It starts by the understanding of the growth mechanisms of germanium nanowires and follows by the structural and electrical properties at the single nanowire level. Horizontally aligned porous anodic alumina (PAA) was used as a template for the nanowire synthesis. Three PAA arrangements were studied: - high density membranes - micron-sized fingers - multi-contacts Membranes formed by a high density of nanopores were obtained by anodizing aluminum thin films. Metallic and semiconducting nanowires were synthesized into the PAA structures via DC deposition, pulsed electro-depostion and CVD growth. The presence of gold, copper, indium, nickel, tellurium, and silicon nanowires inside PAA templates was verified by SEM and EDX analysis. Further, room-temperature transport measurements showed that the pores are completely filled till the bottom of the pores. In this dissertation, single crystalline and core-shell germanium nanowires are synthesized using indium and bismuth as catalyst in a chemical vapor deposition procedure with germane (GeH{sub 4}) as growth precursor. A systematic growth study has been performed to obtain high aspect-ratio germanium nanowires. The influence of the growth conditions on the final morphology and the crystalline structure has been determined via scanning electron microscopy (SEM) and high-resolution transmission electron microscopy (HRTEM). In the case of indium catalyzed germanium nanowires, two different structures were identified: single crystalline and crystalline core-amorphous shell. The preferential growth axis of both kinds of nanowires is along the [110] direction. The occurrence of the two morphologies was found to only depend on the nanowire dimension. In the case of bismuth

  3. Biometric Template Security

    Directory of Open Access Journals (Sweden)

    Abhishek Nagar

    2008-03-01

    Full Text Available Biometric recognition offers a reliable solution to the problem of user authentication in identity management systems. With the widespread deployment of biometric systems in various applications, there are increasing concerns about the security and privacy of biometric technology. Public acceptance of biometrics technology will depend on the ability of system designers to demonstrate that these systems are robust, have low error rates, and are tamper proof. We present a high-level categorization of the various vulnerabilities of a biometric system and discuss countermeasures that have been proposed to address these vulnerabilities. In particular, we focus on biometric template security which is an important issue because, unlike passwords and tokens, compromised biometric templates cannot be revoked and reissued. Protecting the template is a challenging task due to intrauser variability in the acquired biometric traits. We present an overview of various biometric template protection schemes and discuss their advantages and limitations in terms of security, revocability, and impact on matching accuracy. A template protection scheme with provable security and acceptable recognition performance has thus far remained elusive. Development of such a scheme is crucial as biometric systems are beginning to proliferate into the core physical and information infrastructure of our society.

  4. New NIR light-curve templates for classical Cepheids

    NARCIS (Netherlands)

    Inno, L.; Matsunaga, N.; Romaniello, M.; Bono, G.; Monson, A.; Ferraro, I.; Iannicola, G.; Persson, E.; Buonanno, R.; Freedman, W.; Gieren, W.; Groenewegen, M.A.T.; Ita, Y.; Laney, C.D.; Lemasle, B.; Madore, B.F.; Nagayama, T.; Nakada, Y.; Nonino, M.; Pietrzyński, G.; Primas, F.; Scowcroft, V.; Soszyński, I.; Tanabé, T.; Udalski, A.

    2015-01-01

    Aims. We present new near-infrared (NIR) light-curve templates for fundamental (FU, J, H, KS) and first overtone (FO, J) classical Cepheids. The new templates together with period-luminosity and period-Wesenheit (PW) relations provide Cepheid distances from single-epoch observations with a precision

  5. Joomla! 3 template essentials

    CERN Document Server

    Frankowski, Pawel

    2013-01-01

    Using this hands-on, step-by step tutorial filled with practical examples, the readers will be able to create beautiful templates and themes for your websites that will make them stand out from others.This book is written for all of you who wish to create your own unique templates for Joomla! 3.x. This book can be used by Joomla! administrators or visual designers (with no programming experience) or those of you who are used to working with common web developer tools like HTML/CSS editors for coding purposes. You would need basic knowledge of Joomla! and some knowledge of CSS and HTML.

  6. Initial Single-Shell Tank Retrieval System mission analysis report

    International Nuclear Information System (INIS)

    Hertzel, J.S.

    1996-03-01

    This document provides the mission analysis for the Initial Single-Shell Tank Retrieval System task, which supports the Single-Shell Tank Waste Retrieval Program in its commitment to remove waste from single-shell tanks for treatment and final closure

  7. A dual-template imprinted polymer-modified carbon ceramic electrode for ultra trace simultaneous analysis of ascorbic acid and dopamine.

    Science.gov (United States)

    Bali Prasad, Bhim; Jauhari, Darshika; Tiwari, Mahavir Prasad

    2013-12-15

    A dual-template imprinted polymer film containing dispersed multiwalled carbon nanotubes was exploited in the fabrication of a typical, reproducible, and rugged carbon ceramic electrode, adopting "surface grafting from" approach for the growth of a nanometer thin coating on its surface. For this, chloro groups were first introduced at the exterior surface of silica-carbon composite electrode through sol-gel modification using (3-chloropropyl)-trimethoxysilane, followed by an iniferter (sodium diethyl dithiocarbamate) initiated photopolymerization of functional monomer (2,4,6-trisacrylamido-1,3,5-triazine), mixed templates (ascorbic acid and dopamine), and cross-linker (ethylene glycol dimethacrylate), in the presence of multiwalled carbon nanotubes. The modified sensor was validated for the simultaneous analysis of ascorbic acid and dopamine in aqueous, blood serum, cerebrospinal fluid, and pharmaceutical samples, using differential pulse anodic stripping voltammetric technique. The oxidation peak potentials for both analytes were found to be well apart approximately by 300 mV, which was large enough to allow selective and sensitive analysis of one in the presence of other, without any cross reactivity, interferences and false-positives. The detection limits realized by the proposed sensor, under optimized conditions, were found to be as low as 2.24 ng mL(-1) for ascorbic acid and 0.21 ng mL(-1) for dopamine (S/N=3). Such stringent limits could be considered suitable for the primitive diagnosis of several chronic diseases, in clinical settings. Copyright © 2013 Elsevier B.V. All rights reserved.

  8. Computing layouts with deformable templates

    KAUST Repository

    Peng, Chi-Han

    2014-07-22

    In this paper, we tackle the problem of tiling a domain with a set of deformable templates. A valid solution to this problem completely covers the domain with templates such that the templates do not overlap. We generalize existing specialized solutions and formulate a general layout problem by modeling important constraints and admissible template deformations. Our main idea is to break the layout algorithm into two steps: a discrete step to lay out the approximate template positions and a continuous step to refine the template shapes. Our approach is suitable for a large class of applications, including floorplans, urban layouts, and arts and design. Copyright © ACM.

  9. Multi-template polymerase chain reaction

    Directory of Open Access Journals (Sweden)

    Elena Kalle

    2014-12-01

    Full Text Available PCR is a formidable and potent technology that serves as an indispensable tool in a wide range of biological disciplines. However, due to the ease of use and often lack of rigorous standards many PCR applications can lead to highly variable, inaccurate, and ultimately meaningless results. Thus, rigorous method validation must precede its broad adoption to any new application. Multi-template samples possess particular features, which make their PCR analysis prone to artifacts and biases: multiple homologous templates present in copy numbers that vary within several orders of magnitude. Such conditions are a breeding ground for chimeras and heteroduplexes. Differences in template amplification efficiencies and template competition for reaction compounds undermine correct preservation of the original template ratio. In addition, the presence of inhibitors aggravates all of the above-mentioned problems. Inhibitors might also have ambivalent effects on the different templates within the same sample. Yet, no standard approaches exist for monitoring inhibitory effects in multitemplate PCR, which is crucial for establishing compatibility between samples.

  10. Autonomous Gait Event Detection with Portable Single-Camera Gait Kinematics Analysis System

    Directory of Open Access Journals (Sweden)

    Cheng Yang

    2016-01-01

    Full Text Available Laboratory-based nonwearable motion analysis systems have significantly advanced with robust objective measurement of the limb motion, resulting in quantified, standardized, and reliable outcome measures compared with traditional, semisubjective, observational gait analysis. However, the requirement for large laboratory space and operational expertise makes these systems impractical for gait analysis at local clinics and homes. In this paper, we focus on autonomous gait event detection with our bespoke, relatively inexpensive, and portable, single-camera gait kinematics analysis system. Our proposed system includes video acquisition with camera calibration, Kalman filter + Structural-Similarity-based marker tracking, autonomous knee angle calculation, video-frame-identification-based autonomous gait event detection, and result visualization. The only operational effort required is the marker-template selection for tracking initialization, aided by an easy-to-use graphic user interface. The knee angle validation on 10 stroke patients and 5 healthy volunteers against a gold standard optical motion analysis system indicates very good agreement. The autonomous gait event detection shows high detection rates for all gait events. Experimental results demonstrate that the proposed system can automatically measure the knee angle and detect gait events with good accuracy and thus offer an alternative, cost-effective, and convenient solution for clinical gait kinematics analysis.

  11. gel template method

    Indian Academy of Sciences (India)

    TiO2 nanotubes have been synthesized by sol–gel template method using alumina membrane. Scanning electron microscopy (SEM), transmission electron microscopy (TEM), Raman spectroscopy, UV absorption spectrum and X-ray diffraction techniques have been used to investigate the structure, morphology and optical ...

  12. Template Composite Dark Matter

    DEFF Research Database (Denmark)

    Drach, Vincent; Hietanen, Ari; Pica, Claudio

    2015-01-01

    We present a non perturbative study of SU(2) gauge theory with two fundamental Dirac flavours. We discuss how the model can be used as a template for composite Dark Matter (DM). We estimate one particular interaction of the DM candidate with the Standard Model : the interaction through photon...

  13. Comparing methods for single paragraph similarity analysis.

    Science.gov (United States)

    Stone, Benjamin; Dennis, Simon; Kwantes, Peter J

    2011-01-01

    The focus of this paper is two-fold. First, similarities generated from six semantic models were compared to human ratings of paragraph similarity on two datasets-23 World Entertainment News Network paragraphs and 50 ABC newswire paragraphs. Contrary to findings on smaller textual units such as word associations (Griffiths, Tenenbaum, & Steyvers, 2007), our results suggest that when single paragraphs are compared, simple nonreductive models (word overlap and vector space) can provide better similarity estimates than more complex models (LSA, Topic Model, SpNMF, and CSM). Second, various methods of corpus creation were explored to facilitate the semantic models' similarity estimates. Removing numeric and single characters, and also truncating document length improved performance. Automated construction of smaller Wikipedia-based corpora proved to be very effective, even improving upon the performance of corpora that had been chosen for the domain. Model performance was further improved by augmenting corpora with dataset paragraphs. Copyright © 2010 Cognitive Science Society, Inc.

  14. Silver nanowires - unique templates for functional nanostructures

    Science.gov (United States)

    Sun, Yugang

    2010-09-01

    This feature article reviews the synthesis and application of silver nanowires with the focus on a polyol process that is capable of producing high quality silver nanowires with high yield. The as-synthesized silver nanowires can be used as both physical templates for the synthesis of metal/dielectric core/shell nanowires and chemical templates for the synthesis of metal nanotubes as well as semiconductor nanowires. Typical examples including Ag/SiO2 coaxial nanocables, single- and multiple-walled nanotubes made of Au-Ag alloy, AgCl nanowires and AgCl/Au core/shell nanowires are discussed in detail to illustrate the versatility of nanostructures derived from silver nanowire templates. Novel properties associated with these one-dimensional nanostructures are also briefly discussed to shed the light on their potential applications in electronics, photonics, optoelectronics, catalysis, and medicine.

  15. Analysis of Single Event Evoked Potentials.

    Science.gov (United States)

    1979-11-01

    stimuli is available in the literature, and since this study deals with single responses, an assumption had to be made before the information in the...Figue 4 Repon e mocekroadpten.trp atrsadt ln 0m10 4 4 22 A S10 2D 3 40 5 64 10 i 13 10 II0 Visul wo (miautes) of side of dck Figure 5. The effect of unit...differences in their average evoked responses. These responses will also lend themselves to detection based on information from multiple electrodes because

  16. Multiplex single particle analysis in microfluidics.

    Science.gov (United States)

    Dannhauser, D; Romeo, G; Causa, F; De Santo, I; Netti, P A

    2014-10-21

    A straightforward way to measure separated micrometric sized particles in microfluidic flow is reported. The light scattering profile (LSP) of each single particle is fully characterized by using a CMOS-camera based small angle light scattering (SALS) apparatus, ranging from 2° up to 30°. To ensure controlled particle passage through the incident laser, a viscoelastic 3D alignment effect by viscoelastic induced particle migration has been implemented in a simple and cost-effective microfluidic device. Different polystyrene particle sizes are measured in microfluidic flows and the obtained scattering signatures are matched with the Lorenz-Mie based scattering theory. The results confirm the possibility of using this apparatus for real multiplex particle analyses in microfluidic particle flows.

  17. Efficient cleavage of single and clustered AP site lesions within mono-nucleosome templates by CHO-K1 nuclear extract contrasts with retardation of incision by purified APE1

    Science.gov (United States)

    Eccles, Laura J.; Menoni, Hervé; Angelov, Dimitar; Lomax, Martine E.; O’Neill, Peter

    2015-01-01

    Clustered DNA damage is a unique characteristic of radiation-induced DNA damage and the formation of these sites poses a serious challenge to the cell’s repair machinery. Within a cell DNA is compacted, with nucleosomes being the first order of higher level structure. However, few data are reported on the efficiency of clustered-lesion processing within nucleosomal DNA templates. Here, we show retardation of cleavage of a single AP site by purified APE1 when contained in nucleosomal DNA, compared to cleavage of an AP site in non-nucleosomal DNA. This retardation seen in nucleosomal DNA was alleviated by incubation with CHO-K1 nuclear extract. When clustered DNA damage sites containing bistranded AP sites were present in nucleosomal DNA, efficient cleavage of the AP sites was observed after treatment with nuclear extract. The resultant DSB formation led to DNA dissociating from the histone core and nucleosomal dispersion. Clustered damaged sites containing bistranded AP site/8-oxoG residues showed no retardation of cleavage of the AP site but retardation of 8-oxoG excision, compared to isolated lesions, thus DSB formation was not seen. An increased understanding of processing of clustered DNA damage in a nucleosomal environment may lead to new strategies to enhance the cytotoxic effects of radiotherapeutics. PMID:26439176

  18. Manufacturing ontology through templates

    Directory of Open Access Journals (Sweden)

    Diciuc Vlad

    2017-01-01

    Full Text Available The manufacturing industry contains a high volume of knowhow and of high value, much of it being held by key persons in the company. The passing of this know-how is the basis of manufacturing ontology. Among other methods like advanced filtering and algorithm based decision making, one way of handling the manufacturing ontology is via templates. The current paper tackles this approach and highlights the advantages concluding with some recommendations.

  19. Single cell array impedance analysis in a microfluidic device

    Science.gov (United States)

    Altinagac, Emre; Taskin, Selen; Kizil, Huseyin

    2016-10-01

    Impedance analysis of single cells is presented in this paper. Following the separation of a target cell type by dielectrophoresis in our previous work, this paper focuses on capturing the cells as a single array and performing impedance analysis to point out the signature difference between each cell type. Lab-on-a-chip devices having a titanium interdigitated electrode layer on a glass substrate and a PDMS microchannel are fabricated to capture each cell in a single form and perform impedance analysis. HCT116 (homosapiens colon colorectal carcin) and HEK293 (human embryonic kidney) cells are used in our experiments.

  20. Templates for integrated nanofiber growth

    DEFF Research Database (Denmark)

    Oliveira Hansen, Roana Melina de

    interface circuitry such as metal electrodes for electrical connection continues to be a significant hindrance toward their large-scale implementation. In-situ growth constitutes a very promising strategy for integrating functional nanostructures into device platforms due to the possibility of parallel......-crystalline substrates, such as muscovite mica, on which long, mutually parallel nanofibers are self-assembled upon vapor deposition of the organic material under high vacuum conditions. However, the lack of ability to further process these substrates and for integration of such fragile nanostructures with the necessary......, high-volume integration. Besides such single-crystalline templates, the nanofibers can also be grown on non-crystalline gold surfaces, on which the orientation of the nanofibers can be manipulated by structuring the gold surface prior to p6P deposition. In this work, a novel method for in-situ growth...

  1. Single-shell tank interim stabilization risk analysis

    International Nuclear Information System (INIS)

    Basche, A.D.

    1998-01-01

    The purpose of the Single-Shell Tank (SST) Interim Stabilization Risk Analysis is to provide a cost and schedule risk analysis of HNF-2358, Rev. 1, Single-Shell Tank Interim Stabilization Project Plan (Project Plan) (Ross et al. 1998). The analysis compares the required cost profile by fiscal year (Section 4.2) and revised schedule completion date (Section 4.5) to the Project Plan. The analysis also evaluates the executability of the Project Plan and recommends a path forward for risk mitigation

  2. A template for writing radiotherapy protocols.

    Science.gov (United States)

    Nilsson, Per; Ceberg, Crister; Kjellén, Elisabeth; Gagliardi, Giovanna; Blomgren, Klas; Nilsson, Sten; Johansson, Mikael; Glimelius, Bengt

    2015-02-01

    Well-specified and unambiguous treatment protocols are essential both for current practice and for the future development of radiation therapy. In order to provide assistance for writing good protocols, irrespective of treatment intention and complexity, up-to-date guidelines are highly desirable. We have analysed the radiotherapy work-flow, including clinical and physical aspects, such as preparatory imaging, treatment planning, delivery and evaluation, with the aim to outline a consistent framework covering the entire radiotherapy process. Based on the analysis, a recipe-style template for specifying the description of the radiotherapy process has been designed. The template is written in a general format, which allows for modified phrasing, and should be customised for the specific clinical situation and diagnosis, as well as facility resources. The template can be used as a tool to ensure a consistent and comprehensive description of the radiotherapy section of clinical guidelines, care programmes and clinical trial protocols.

  3. Microstructural analysis in the depth direction of a heteroepitaxial AlN thick film grown on a trench-patterned template by nanobeam X-ray diffraction

    Science.gov (United States)

    Shida, K.; Takeuchi, S.; Tohei, T.; Miyake, H.; Hiramatsu, K.; Sumitani, K.; Imai, Y.; Kimura, S.; Sakai, A.

    2018-04-01

    This work quantitatively assessed the three-dimensional distribution of crystal lattice distortions in an epitaxial AlN thick film grown on a trench-patterned template, using nanobeam X-ray diffraction. Position-dependent ω-2θ-φ mapping clearly demonstrated local tilting, spacing and twisting of lattice planes as well as fluctuations in these phenomena on a sub-micrometer scale comparable to the pitch of the trench-and-terrace patterning. Analysis of the crystal lattice distortion in the depth direction was performed using a newly developed method in which the X-ray nanobeam diffracted from the sample surface to specific depths can be selectively detected by employing a Pt wire profiler. This technique generated depth-resolved ω-2θ-φ maps confirming that fluctuations in lattice plane tilting and spacing greatly depend on the dislocation distribution and the history of the AlN epitaxial growth on the trench-patterned structure. It was also found that both fluctuations were reduced on approaching the AlN surface and, in particular, were sharply reduced at specific depths in the terrace regions. These sharp reductions are attributed to the formation of sacrificial zones with degraded crystal quality around the trenches and possibly lead to raising the crystal quality near the surface of the AlN film.

  4. Bioinformatics approaches to single-cell analysis in developmental biology.

    Science.gov (United States)

    Yalcin, Dicle; Hakguder, Zeynep M; Otu, Hasan H

    2016-03-01

    Individual cells within the same population show various degrees of heterogeneity, which may be better handled with single-cell analysis to address biological and clinical questions. Single-cell analysis is especially important in developmental biology as subtle spatial and temporal differences in cells have significant associations with cell fate decisions during differentiation and with the description of a particular state of a cell exhibiting an aberrant phenotype. Biotechnological advances, especially in the area of microfluidics, have led to a robust, massively parallel and multi-dimensional capturing, sorting, and lysis of single-cells and amplification of related macromolecules, which have enabled the use of imaging and omics techniques on single cells. There have been improvements in computational single-cell image analysis in developmental biology regarding feature extraction, segmentation, image enhancement and machine learning, handling limitations of optical resolution to gain new perspectives from the raw microscopy images. Omics approaches, such as transcriptomics, genomics and epigenomics, targeting gene and small RNA expression, single nucleotide and structural variations and methylation and histone modifications, rely heavily on high-throughput sequencing technologies. Although there are well-established bioinformatics methods for analysis of sequence data, there are limited bioinformatics approaches which address experimental design, sample size considerations, amplification bias, normalization, differential expression, coverage, clustering and classification issues, specifically applied at the single-cell level. In this review, we summarize biological and technological advancements, discuss challenges faced in the aforementioned data acquisition and analysis issues and present future prospects for application of single-cell analyses to developmental biology. © The Author 2015. Published by Oxford University Press on behalf of the European

  5. Single-shell tank retrieval program mission analysis report

    Energy Technology Data Exchange (ETDEWEB)

    Stokes, W.J.

    1998-08-11

    This Mission Analysis Report was prepared to provide the foundation for the Single-Shell Tank (SST) Retrieval Program, a new program responsible for waste removal for the SSTS. The SST Retrieval Program is integrated with other Tank Waste Remediation System activities that provide the management, technical, and operations elements associated with planning and execution of SST and SST Farm retrieval and closure. This Mission Analysis Report provides the basis and strategy for developing a program plan for SST retrieval. This Mission Analysis Report responds to a US Department of Energy request for an alternative single-shell tank retrieval approach (Taylor 1997).

  6. Single-shell tank retrieval program mission analysis report

    International Nuclear Information System (INIS)

    Stokes, W.J.

    1998-01-01

    This Mission Analysis Report was prepared to provide the foundation for the Single-Shell Tank (SST) Retrieval Program, a new program responsible for waste removal for the SSTS. The SST Retrieval Program is integrated with other Tank Waste Remediation System activities that provide the management, technical, and operations elements associated with planning and execution of SST and SST Farm retrieval and closure. This Mission Analysis Report provides the basis and strategy for developing a program plan for SST retrieval. This Mission Analysis Report responds to a US Department of Energy request for an alternative single-shell tank retrieval approach (Taylor 1997)

  7. A single-chip computer analysis system for liquid fluorescence

    International Nuclear Information System (INIS)

    Zhang Yongming; Wu Ruisheng; Li Bin

    1998-01-01

    The single-chip computer analysis system for liquid fluorescence is an intelligent analytic instrument, which is based on the principle that the liquid containing hydrocarbons can give out several characteristic fluorescences when irradiated by strong light. Besides a single-chip computer, the system makes use of the keyboard and the calculation and printing functions of a CASIO printing calculator. It combines optics, mechanism and electronics into one, and is small, light and practical, so it can be used for surface water sample analysis in oil field and impurity analysis of other materials

  8. A model-based telecoupling analysis for the Patagonian shelf: a new suggested template on how to study global seabirds-fisheries interactions for sustainability

    Science.gov (United States)

    Huettmann, F.; Raya Rey, A.

    2016-12-01

    The Southwest Atlantic Ocean, and the extended Patagonian shelf in particular, presents us with a very complex ecosystem of global relevance for food security and global peace. It is a highly productive area and it maintains a great diversity and abundance of seabird species. Fisheries have been identified as a main stressor for the marine ecosystems and as one of the main causes of seabird population declines. Using the framework of telecoupling - a sophisticated description of natural and socioeconomic interactions over large distances - here we present a fresh holistic look at the dynamic fisheries and (endangered) seabird interactions for the Patagonian shelf. While data are sparse, we employ machine learning-based predictions for a more holistic overview. We found that these waters of the Patagonian Shelf are significantly affected by many nations and outside players. We found that the input, output and spill-over of the Patagonian shelf ecosystem are distributed virtually all over the globe. In addition, we also found `losers' (=nations and their citizens that are left out entirely from this global resource and its governance). Our findings are based on best-available public trade and fish harvest analysis for this region, linked with predictive modeling (machine learning and geographic information systems GIS) to generalize for nine seabird species. We conveniently extend this analysis with a perspective from the financial sector and policy that enables the Patagonian fisheries as international investment and development projects. As increasingly recognized elsewhere, we believe that telecoupling can serve as a new but rather sophisticated study template highlighting wider complexities, bottlenecks and sensitivities for a vastly improved conservation research on oceans and global sustainability questions.

  9. DNA analysis by single molecule stretching in nanofluidic biochips

    DEFF Research Database (Denmark)

    Abad, E.; Juarros, A.; Retolaza, A.

    2011-01-01

    Stretching single DNA molecules by confinement in nanofluidic channels has attracted a great interest during the last few years as a DNA analysis tool. We have designed and fabricated a sealed micro/nanofluidic device for DNA stretching applications, based on the use of the high throughput Nano......Imprint Lithography (NIL) technology combined with a conventional anodic bonding of the silicon base and Pyrex cover. Using this chip, we have performed single molecule imaging on a bench-top fluorescent microscope system. Lambda phage DNA was used as a model sample to characterize the chip. Single molecules of λ...... a method to determining DNA size. The results of this work prove that the developed fabrication process is a good alternative for the fabrication of single molecule DNA biochips and it allows developing a variety of innovative bio/chemical sensors based on single-molecule DNA sequencing devices....

  10. Quantitative high-resolution genomic analysis of single cancer cells.

    Directory of Open Access Journals (Sweden)

    Juliane Hannemann

    Full Text Available During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics.

  11. Platforms for Single-Cell Collection and Analysis

    Directory of Open Access Journals (Sweden)

    Lukas Valihrach

    2018-03-01

    Full Text Available Single-cell analysis has become an established method to study cell heterogeneity and for rare cell characterization. Despite the high cost and technical constraints, applications are increasing every year in all fields of biology. Following the trend, there is a tremendous development of tools for single-cell analysis, especially in the RNA sequencing field. Every improvement increases sensitivity and throughput. Collecting a large amount of data also stimulates the development of new approaches for bioinformatic analysis and interpretation. However, the essential requirement for any analysis is the collection of single cells of high quality. The single-cell isolation must be fast, effective, and gentle to maintain the native expression profiles. Classical methods for single-cell isolation are micromanipulation, microdissection, and fluorescence-activated cell sorting (FACS. In the last decade several new and highly efficient approaches have been developed, which not just supplement but may fully replace the traditional ones. These new techniques are based on microfluidic chips, droplets, micro-well plates, and automatic collection of cells using capillaries, magnets, an electric field, or a punching probe. In this review we summarize the current methods and developments in this field. We discuss the advantages of the different commercially available platforms and their applicability, and also provide remarks on future developments.

  12. Single-cell analysis of endothelial morphogenesis in vivo

    Science.gov (United States)

    Yu, Jianxin A.; Castranova, Daniel; Pham, Van N.; Weinstein, Brant M.

    2015-01-01

    Vessel formation has been extensively studied at the tissue level, but the difficulty in imaging the endothelium with cellular resolution has hampered study of the morphogenesis and behavior of endothelial cells (ECs) in vivo. We are using endothelial-specific transgenes and high-resolution imaging to examine single ECs in zebrafish. By generating mosaics with transgenes that simultaneously mark endothelial nuclei and membranes we are able to definitively identify and study the morphology and behavior of individual ECs during vessel sprouting and lumen formation. Using these methods, we show that developing trunk vessels are composed of ECs of varying morphology, and that single-cell analysis can be used to quantitate alterations in morphology and dynamics in ECs that are defective in proper guidance and patterning. Finally, we use single-cell analysis of intersegmental vessels undergoing lumen formation to demonstrate the coexistence of seamless transcellular lumens and single or multicellular enclosed lumens with autocellular or intercellular junctions, suggesting that heterogeneous mechanisms contribute to vascular lumen formation in vivo. The tools that we have developed for single EC analysis should facilitate further rigorous qualitative and quantitative analysis of EC morphology and behavior in vivo. PMID:26253401

  13. Evaluation of Nursing Documentation Completion of Stroke Patients in the Emergency Department: A Pre-Post Analysis Using Flowsheet Templates and Clinical Decision Support.

    Science.gov (United States)

    Richardson, Karen J; Sengstack, Patricia; Doucette, Jeffrey N; Hammond, William E; Schertz, Matthew; Thompson, Julie; Johnson, Constance

    2016-02-01

    The primary aim of this performance improvement project was to determine whether the electronic health record implementation of stroke-specific nursing documentation flowsheet templates and clinical decision support alerts improved the nursing documentation of eligible stroke patients in seven stroke-certified emergency departments. Two system enhancements were introduced into the electronic record in an effort to improve nursing documentation: disease-specific documentation flowsheets and clinical decision support alerts. Using a pre-post design, project measures included six stroke management goals as defined by the National Institute of Neurological Disorders and Stroke and three clinical decision support measures based on entry of orders used to trigger documentation reminders for nursing: (1) the National Institutes of Health's Stroke Scale, (2) neurological checks, and (3) dysphagia screening. Data were reviewed 6 months prior (n = 2293) and 6 months following the intervention (n = 2588). Fisher exact test was used for statistical analysis. Statistical significance was found for documentation of five of the six stroke management goals, although effect sizes were small. Customizing flowsheets to meet the needs of nursing workflow showed improvement in the completion of documentation. The effects of the decision support alerts on the completeness of nursing documentation were not statistically significant (likely due to lack of order entry). For example, an order for the National Institutes of Health Stroke Scale was entered only 10.7% of the time, which meant no alert would fire for nursing in the postintervention group. Future work should focus on decision support alerts that trigger reminders for clinicians to place relevant orders for this population.

  14. A light meson translatable template

    International Nuclear Information System (INIS)

    Allgower, C.E.; Peaslee, D.C.

    2002-01-01

    Recently surveyed (mass)2 values for I = 0, JPC = 2++ light mesons can be assembled into repeating patterns of 4 states, dubbed 'templates'. Within error, both internal and external template spacings approximate simple multiples of Δm2 ≅ 0.35 GeV2. Hopefully, this feature will be useful in predicting the positions of higher isoscalar 2++ states

  15. Template Generation and Selection Algorithms

    NARCIS (Netherlands)

    Guo, Y.; Smit, Gerardus Johannes Maria; Broersma, Haitze J.; Heysters, P.M.; Badaway, W.; Ismail, Y.

    The availability of high-level design entry tooling is crucial for the viability of any reconfigurable SoC architecture. This paper presents a template generation method to extract functional equivalent structures, i.e. templates, from a control data flow graph. By inspecting the graph the algorithm

  16. Comparison of standard PCR/cloning to single genome sequencing for analysis of HIV-1 populations.

    Science.gov (United States)

    Jordan, Michael R; Kearney, Mary; Palmer, Sarah; Shao, Wei; Maldarelli, Frank; Coakley, Eoin P; Chappey, Colombe; Wanke, Christine; Coffin, John M

    2010-09-01

    To compare standard PCR/cloning and single genome sequencing (SGS) in their ability to reflect actual intra-patient polymorphism of HIV-1 populations, a total of 530 HIV-1 pro-pol sequences obtained by both sequencing techniques from a set of 17 ART naïve patient specimens was analyzed. For each specimen, 12 and 15 sequences, on average, were characterized by the two techniques. Using phylogenetic analysis, tests for panmixia and entropy, and Bland-Altman plots, no difference in population structure or genetic diversity was shown in 14 of the 17 subjects. Evidence of sampling bias by the presence of subsets of identical sequences was found by either method. Overall, the study shows that neither method was more biased than the other, and providing that an adequate number of PCR templates is analyzed, and that the bulk sequencing captures the diversity of the viral population, either method is likely to provide a similar measure of population diversity. Copyright 2010 Elsevier B.V. All rights reserved.

  17. Single cell transcriptional analysis reveals novel innate immune cell types

    Directory of Open Access Journals (Sweden)

    Linda E. Kippner

    2014-06-01

    Full Text Available Single-cell analysis has the potential to provide us with a host of new knowledge about biological systems, but it comes with the challenge of correctly interpreting the biological information. While emerging techniques have made it possible to measure inter-cellular variability at the transcriptome level, no consensus yet exists on the most appropriate method of data analysis of such single cell data. Methods for analysis of transcriptional data at the population level are well established but are not well suited to single cell analysis due to their dependence on population averages. In order to address this question, we have systematically tested combinations of methods for primary data analysis on single cell transcription data generated from two types of primary immune cells, neutrophils and T lymphocytes. Cells were obtained from healthy individuals, and single cell transcript expression data was obtained by a combination of single cell sorting and nanoscale quantitative real time PCR (qRT-PCR for markers of cell type, intracellular signaling, and immune functionality. Gene expression analysis was focused on hierarchical clustering to determine the existence of cellular subgroups within the populations. Nine combinations of criteria for data exclusion and normalization were tested and evaluated. Bimodality in gene expression indicated the presence of cellular subgroups which were also revealed by data clustering. We observed evidence for two clearly defined cellular subtypes in the neutrophil populations and at least two in the T lymphocyte populations. When normalizing the data by different methods, we observed varying outcomes with corresponding interpretations of the biological characteristics of the cell populations. Normalization of the data by linear standardization taking into account technical effects such as plate effects, resulted in interpretations that most closely matched biological expectations. Single cell transcription

  18. [Use of diagnostic templates at stages of prosthetics treatment with implant-retained restorations].

    Science.gov (United States)

    Gvetadze, R Sh; Abramyan, S V; Ivanov, A A; Nubaryan, A P

    The comparative analysis of efficiency of various types of diagnostic templates for planning orthopedic treatment of 50 patients with partial or complete absence of teeth was performed. The patients were divided in 3 groups according to template manufacturing technique. All diagnostic templates made in accordance with clinical conditions allowed transfering digital data of the scheduled prosthetic construction for virtual implantation planning. Advantages and pitfalls of each template type are discussed.

  19. Assembling Bare Au Nanoparticles at Positively Charged Templates

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Wenjie; Zhang, Honghu; Kuzmenko, Ivan; Mallapragada, Surya; Vaknin, David

    2016-05-26

    In-situ X-ray reflectivity (XRR) and grazing incidence X-ray small-angle scattering (GISAXS) reveal that unfunctionalized (bare) gold nanoparticles (AuNP) spontaneously adsorb to a cationic lipid template formed by a Langmuir monolayer of DPTAP (1,2-dihexadecanoyl-3-trimethylammonium-propane) at vapor/aqueous interfaces. Analysis of the XRR yields the electron density profile across the chargedinterfaces along the surface normal showing the AuNPs assemble with vertical thickness comparable to the particle size. The GISAXS analysis indicates that the adsorbed mono-particle layer exhibits shortrange in-plane correlations. By contrast, single-stranded DNA-functionalized AuNPs, while attracted to the positively charged surface (more efficiently with the addition of salt to the solution), display less in-plane regular packing compared to bare AuNPs.

  20. Single Particle Tracking: Analysis Techniques for Live Cell Nanoscopy

    Science.gov (United States)

    Relich, Peter Kristopher, II

    Single molecule experiments are a set of experiments designed specifically to study the properties of individual molecules. It has only been in the last three decades where single molecule experiments have been applied to the life sciences; where they have been successfully implemented in systems biology for probing the behaviors of sub-cellular mechanisms. The advent and growth of super-resolution techniques in single molecule experiments has made the fundamental behaviors of light and the associated nano-probes a necessary concern amongst life scientists wishing to advance the state of human knowledge in biology. This dissertation disseminates some of the practices learned in experimental live cell microscopy. The topic of single particle tracking is addressed here in a format that is designed for the physicist who embarks upon single molecule studies. Specifically, the focus is on the necessary procedures to generate single particle tracking analysis techniques that can be implemented to answer biological questions. These analysis techniques range from designing and testing a particle tracking algorithm to inferring model parameters once an image has been processed. The intellectual contributions of the author include the techniques in diffusion estimation, localization filtering, and trajectory associations for tracking which will all be discussed in detail in later chapters. The author of this thesis has also contributed to the software development of automated gain calibration, live cell particle simulations, and various single particle tracking packages. Future work includes further evaluation of this laboratory's single particle tracking software, entropy based approaches towards hypothesis validations, and the uncertainty quantification of gain calibration.

  1. Single cell analysis contemporary research and clinical applications

    CERN Document Server

    Cossarizza, Andrea

    2017-01-01

    This book highlights the current state of the art in single cell analysis, an area that involves many fields of science – from clinical hematology, functional analysis and drug screening, to platelet and microparticle analysis, marine biology and fundamental cancer research. This book brings together an eclectic group of current applications, all of which have a significant impact on our current state of knowledge. The authors of these chapters are all pioneering researchers in the field of single cell analysis. The book will not only appeal to those readers more focused on clinical applications, but also those interested in highly technical aspects of the technologies. All of the technologies identified utilize unique applications of photon detection systems.

  2. Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling.

    Science.gov (United States)

    Meier, Armin; Söding, Johannes

    2015-10-01

    Homology modeling predicts the 3D structure of a query protein based on the sequence alignment with one or more template proteins of known structure. Its great importance for biological research is owed to its speed, simplicity, reliability and wide applicability, covering more than half of the residues in protein sequence space. Although multiple templates have been shown to generally increase model quality over single templates, the information from multiple templates has so far been combined using empirically motivated, heuristic approaches. We present here a rigorous statistical framework for multi-template homology modeling. First, we find that the query proteins' atomic distance restraints can be accurately described by two-component Gaussian mixtures. This insight allowed us to apply the standard laws of probability theory to combine restraints from multiple templates. Second, we derive theoretically optimal weights to correct for the redundancy among related templates. Third, a heuristic template selection strategy is proposed. We improve the average GDT-ha model quality score by 11% over single template modeling and by 6.5% over a conventional multi-template approach on a set of 1000 query proteins. Robustness with respect to wrong constraints is likewise improved. We have integrated our multi-template modeling approach with the popular MODELLER homology modeling software in our free HHpred server http://toolkit.tuebingen.mpg.de/hhpred and also offer open source software for running MODELLER with the new restraints at https://bitbucket.org/soedinglab/hh-suite.

  3. Single base pair mutation analysis by PNA directed PCR clamping

    DEFF Research Database (Denmark)

    Ørum, H.; Nielsen, P.E.; Egholm, M.

    1993-01-01

    A novel method that allows direct analysis of single base mutation by the polymerase chain reaction (PCR) is described. The method utilizes the finding that PNAs (peptide nucleic acids) recognize and bind to their complementary nucleic acid sequences with higher thermal stability and specificity...

  4. Amino acids analysis during lactic acid fermentation by single strain ...

    African Journals Online (AJOL)

    SAM

    2014-07-09

    Jul 9, 2014 ... Amino acids analysis during lactic acid fermentation by single strain cultures of lactobacilli and mixed culture starter made from them. KiBeom Lee1*, Ho-Jin Kim1 and Sang-Kyu Park2. 1Bio Center Technopark, 7-50 Songdo, Yeonsu-Gu, Incheon 406-840, Republic of Korea. 2Nambu University, Chumdan ...

  5. Automatic settlement analysis of single-layer armour layers

    NARCIS (Netherlands)

    Hofland, B.; van gent, Marcel

    2016-01-01

    A method to quantify, analyse, and present the settlement of single-layer concrete armour layers of coastal structures is presented. The use of the image processing technique for settlement analysis is discussed based on various modelling
    studies performed over the years. The accuracy of the

  6. CrazyEgg Reports for Single Page Analysis

    Science.gov (United States)

    CrazyEgg provides an in depth look at visitor behavior on one page. While you can use GA to do trend analysis of your web area, CrazyEgg helps diagnose the design of a single Web page by visually displaying all visitor clicks during a specified time.

  7. Real-time electrocardiogram P-QRS-T detection-delineation algorithm based on quality-supported analysis of characteristic templates.

    Science.gov (United States)

    Karimipour, Atiyeh; Homaeinezhad, Mohammad Reza

    2014-09-01

    The main objective of this study is to introduce a simple, low-latency, and accurate algorithm for real-time detection of P-QRS-T waves in the electrocardiogram (ECG) signal. In the proposed method, real-time signal preprocessing, which includes high frequency noise filtering and baseline wander reduction, is performed by applying discrete wavelet transform (DWT). A method based on signal first-order derivative and adaptive threshold adjustment is employed for real-time detection of the QRS complex. Moreover, detection and delineation of P- and T-waves are achieved by correlation analysis conducted between signal and their templates. Besides, signal quality is investigated online, and if the quality of the analysis window is unacceptable, then the algorithm will guess (estimate) the locations of P- and T-waves. The operating characteristics of the proposed algorithm are evaluated by its implementation to an artificially generated ECG signal whose quality is adjustable from the best (Quality, 100%) to the worst (Quality, ≤40%) cases based on the random-walk noise theory. The algorithm was applied to the MIT-BIH arrhythmia database, QT database, and Physionet/CinC challenge 2011competition database. The obtained results, which were based on the QT database, showed sensitivity and positive predictivity of Se=99.63% and P+=99.83%, Se=99.83% and P+=99.98%, and Se=99.74% and P+=99.89% for the detection of P-, QRS-, and T-waves, respectively, and the obtained results, which were based on the MIT-BIH arrhythmia database, showed Se=99.81% and P+=99.70% for the detection of the QRS complex. Moreover, it will be shown that the results of the proposed method are reliable for a minimum signal quality value of 70%. According to numerical assessments, 8-ms after the occurrence of R-wave, its location will be identified by the computer code of the proposed algorithm. This parameter is 198-ms and 177-ms for P- and T-waves, respectively. Copyright © 2014 Elsevier Ltd. All rights

  8. Image analysis driven single-cell analytics for systems microbiology.

    Science.gov (United States)

    Balomenos, Athanasios D; Tsakanikas, Panagiotis; Aspridou, Zafiro; Tampakaki, Anastasia P; Koutsoumanis, Konstantinos P; Manolakos, Elias S

    2017-04-04

    Time-lapse microscopy is an essential tool for capturing and correlating bacterial morphology and gene expression dynamics at single-cell resolution. However state-of-the-art computational methods are limited in terms of the complexity of cell movies that they can analyze and lack of automation. The proposed Bacterial image analysis driven Single Cell Analytics (BaSCA) computational pipeline addresses these limitations thus enabling high throughput systems microbiology. BaSCA can segment and track multiple bacterial colonies and single-cells, as they grow and divide over time (cell segmentation and lineage tree construction) to give rise to dense communities with thousands of interacting cells in the field of view. It combines advanced image processing and machine learning methods to deliver very accurate bacterial cell segmentation and tracking (F-measure over 95%) even when processing images of imperfect quality with several overcrowded colonies in the field of view. In addition, BaSCA extracts on the fly a plethora of single-cell properties, which get organized into a database summarizing the analysis of the cell movie. We present alternative ways to analyze and visually explore the spatiotemporal evolution of single-cell properties in order to understand trends and epigenetic effects across cell generations. The robustness of BaSCA is demonstrated across different imaging modalities and microscopy types. BaSCA can be used to analyze accurately and efficiently cell movies both at a high resolution (single-cell level) and at a large scale (communities with many dense colonies) as needed to shed light on e.g. how bacterial community effects and epigenetic information transfer play a role on important phenomena for human health, such as biofilm formation, persisters' emergence etc. Moreover, it enables studying the role of single-cell stochasticity without losing sight of community effects that may drive it.

  9. Markov chain analysis of single spin flip Ising simulations

    International Nuclear Information System (INIS)

    Hennecke, M.

    1997-01-01

    The Markov processes defined by random and loop-based schemes for single spin flip attempts in Monte Carlo simulations of the 2D Ising model are investigated, by explicitly constructing their transition matrices. Their analysis reveals that loops over all lattice sites using a Metropolis-type single spin flip probability often do not define ergodic Markov chains, and have distorted dynamical properties even if they are ergodic. The transition matrices also enable a comparison of the dynamics of random versus loop spin selection and Glauber versus Metropolis probabilities

  10. Quantification of brain images using Korean standard templates and structural and cytoarchitectonic probabilistic maps

    International Nuclear Information System (INIS)

    Lee, Jae Sung; Lee, Dong Soo; Kim, Yu Kyeong

    2004-01-01

    Population based structural and functional maps of the brain provide effective tools for the analysis and interpretation of complex and individually variable brain data. Brain MRI and PET standard templates and statistical probabilistic maps based on image data of Korean normal volunteers have been developed and probabilistic maps based on cytoarchitectonic data have been introduced. A quantification method using these data was developed for the objective assessment of regional intensity in the brain images. Age, gender and ethnic specific anatomical and functional brain templates based on MR and PET images of Korean normal volunteers were developed. Korean structural probabilistic maps for 89 brain regions and cytoarchitectonic probabilistic maps for 13 Brodmann areas were transformed onto the standard templates. Brain FDG PET and SPGR MR images of normal volunteers were spatially normalized onto the template of each modality and gender. Regional uptake of radiotracers in PET and gray matter concentration in MR images were then quantified by averaging (or summing) regional intensities weighted using the probabilistic maps of brain regions. Regionally specific effects of aging on glucose metabolism in cingulate cortex were also examined. Quantification program could generate quantification results for single spatially normalized images per 20 seconds. Glucose metabolism change in cingulate gyrus was regionally specific: ratios of glucose metabolism in the rostral anterior cingulate vs. posterior cingulate and the caudal anterior cingulate vs. posterior cingulate were significantly decreased as the age increased. 'Rostral anterior' / 'posterior' was decreased by 3.1% per decade of age (p -11 , r=0.81) and 'caudal anterior' / 'posterior' was decreased by 1.7% (p -8 , r=0.72). Ethnic specific standard templates and probabilistic maps and quantification program developed in this study will be useful for the analysis of brain image of Korean people since the difference

  11. Design and implementation of an algorithm for creating templates for the purpose of iris biometric authentication through the analysis of textures implemented on a FPGA

    Energy Technology Data Exchange (ETDEWEB)

    Giacometto, F J; Vilardy, J M; Torres, C O; Mattos, L, E-mail: franciscogiacometto@unicesar.edu.co [Laboratorio de Optica e Informatica, Universidad Popular del Cesar, Sede balneario Hurtado, Valledupar, Cesar (Colombia)

    2011-01-01

    Currently addressing problems related to security in access control, as a consequence, have been developed applications that work under unique characteristics in individuals, such as biometric features. In the world becomes important working with biometric images such as the liveliness of the iris which are for both the pattern of retinal images as your blood vessels. This paper presents an implementation of an algorithm for creating templates for biometric authentication with ocular features for FPGA, in which the object of study is that the texture pattern of iris is unique to each individual. The authentication will be based in processes such as edge extraction methods, segmentation principle of John Daugman and Libor Masek's, and standardization to obtain necessary templates for the search of matches in a database and then get the expected results of authentication.

  12. Design and implementation of an algorithm for creating templates for the purpose of iris biometric authentication through the analysis of textures implemented on a FPGA

    Science.gov (United States)

    Giacometto, F. J.; Vilardy, J. M.; Torres, C. O.; Mattos, L.

    2011-01-01

    Currently addressing problems related to security in access control, as a consequence, have been developed applications that work under unique characteristics in individuals, such as biometric features. In the world becomes important working with biometric images such as the liveliness of the iris which are for both the pattern of retinal images as your blood vessels. This paper presents an implementation of an algorithm for creating templates for biometric authentication with ocular features for FPGA, in which the object of study is that the texture pattern of iris is unique to each individual. The authentication will be based in processes such as edge extraction methods, segmentation principle of John Daugman and Libor Masek's, and standardization to obtain necessary templates for the search of matches in a database and then get the expected results of authentication.

  13. Dielectrophoretic capture and genetic analysis of single neuroblastoma tumor cells

    Directory of Open Access Journals (Sweden)

    Erica L Carpenter

    2014-07-01

    Full Text Available Our understanding of the diversity of cells that escape the primary tumor and seed micrometastases remains rudimentary, and approaches for studying circulating and disseminated tumor cells have been limited by low throughput and sensitivity, reliance on single parameter sorting, and a focus on enumeration rather than phenotypic and genetic characterization. Here we utilize a highly sensitive microfluidic and dielectrophoretic approach for the isolation and genetic analysis of individual tumor cells. We employed fluorescence labeling to isolate 208 single cells from spiking experiments conducted with 11 cell lines, including 8 neuroblastoma cell lines, and achieved a capture sensitivity of 1 tumor cell per 106 white blood cells. Sample fixation or freezing had no detectable effect on cell capture. Point mutations were accurately detected in the whole genome amplification product of captured single tumor cells but not in negative control white blood cells. We applied this approach to capture 144 single tumor cells from 10 bone marrow samples from patients suffering from neuroblastoma. In this pediatric malignancy, high-risk patients often exhibit wide-spread hematogenous metastasis, but access to primary tumor can be difficult or impossible. Here we used flow-based sorting to pre-enrich samples with tumor involvement below 0.02%. For all patients for whom a mutation in the Anaplastic Lymphoma Kinase gene had already been detected in their primary tumor, the same mutation was detected in single cells from their marrow. These findings demonstrate a novel, non-invasive, and adaptable method for the capture and genetic analysis of single tumor cells from cancer patients.

  14. Optimized variational analysis scheme of single Doppler radar wind data

    Science.gov (United States)

    Sasaki, Yoshi K.; Allen, Steve; Mizuno, Koki; Whitehead, Victor; Wilk, Kenneth E.

    1989-01-01

    A computer scheme for extracting singularities has been developed and applied to single Doppler radar wind data. The scheme is planned for use in real-time wind and singularity analysis and forecasting. The method, known as Doppler Operational Variational Extraction of Singularities is outlined, focusing on the principle of local symmetry. Results are presented from the application of the scheme to a storm-generated gust front in Oklahoma on May 28, 1987.

  15. Thermogravimetric Analysis of Single-Wall Carbon Nanotubes

    Science.gov (United States)

    Arepalli, Sivram; Nikolaev, Pavel; Gorelik, Olga

    2010-01-01

    An improved protocol for thermogravimetric analysis (TGA) of samples of single-wall carbon nanotube (SWCNT) material has been developed to increase the degree of consistency among results so that meaningful comparisons can be made among different samples. This improved TGA protocol is suitable for incorporation into the protocol for characterization of carbon nanotube material. In most cases, TGA of carbon nanotube materials is performed in gas mixtures that contain oxygen at various concentrations. The improved protocol is summarized.

  16. The mining of toxin-like polypeptides from EST database by single residue distribution analysis

    Science.gov (United States)

    2011-01-01

    Background Novel high throughput sequencing technologies require permanent development of bioinformatics data processing methods. Among them, rapid and reliable identification of encoded proteins plays a pivotal role. To search for particular protein families, the amino acid sequence motifs suitable for selective screening of nucleotide sequence databases may be used. In this work, we suggest a novel method for simplified representation of protein amino acid sequences named Single Residue Distribution Analysis, which is applicable both for homology search and database screening. Results Using the procedure developed, a search for amino acid sequence motifs in sea anemone polypeptides was performed, and 14 different motifs with broad and low specificity were discriminated. The adequacy of motifs for mining toxin-like sequences was confirmed by their ability to identify 100% toxin-like anemone polypeptides in the reference polypeptide database. The employment of novel motifs for the search of polypeptide toxins in Anemonia viridis EST dataset allowed us to identify 89 putative toxin precursors. The translated and modified ESTs were scanned using a special algorithm. In addition to direct comparison with the motifs developed, the putative signal peptides were predicted and homology with known structures was examined. Conclusions The suggested method may be used to retrieve structures of interest from the EST databases using simple amino acid sequence motifs as templates. The efficiency of the procedure for directed search of polypeptides is higher than that of most currently used methods. Analysis of 39939 ESTs of sea anemone Anemonia viridis resulted in identification of five protein precursors of earlier described toxins, discovery of 43 novel polypeptide toxins, and prediction of 39 putative polypeptide toxin sequences. In addition, two precursors of novel peptides presumably displaying neuronal function were disclosed. PMID:21281459

  17. Precise analysis of the metal package photomultiplier single photoelectron spectra

    International Nuclear Information System (INIS)

    Chirikov-Zorin, I.E.; Fedorko, I.; Sykora, I.; Tokar, S.; Menzione, A.

    2000-01-01

    A deconvolution method based on a sophisticated photomultiplier response function was used to analyse the compact metal package photomultiplier spectra taken in single photoelectron mode. The spectra taken by Hamamtsu R5600 and R5900 photomultipliers have been analysed. The detailed analysis shows that the method appropriately describes the process of charge multiplication in these photomultipliers in a wide range of working regimes and the deconvoluted parameters are established with about 1% accuracy. The method can be used for a detailed analysis of photomultiplier noise and for calibration purposes

  18. Reduced basis catalogs for gravitational wave templates.

    Science.gov (United States)

    Field, Scott E; Galley, Chad R; Herrmann, Frank; Hesthaven, Jan S; Ochsner, Evan; Tiglio, Manuel

    2011-06-03

    We introduce a reduced basis approach as a new paradigm for modeling, representing and searching for gravitational waves. We construct waveform catalogs for nonspinning compact binary coalescences, and we find that for accuracies of 99% and 99.999% the method generates a factor of about 10-10(5) fewer templates than standard placement methods. The continuum of gravitational waves can be represented by a finite and comparatively compact basis. The method is robust under variations in the noise of detectors, implying that only a single catalog needs to be generated.

  19. Fluid discrimination based on rock physics templates

    International Nuclear Information System (INIS)

    Liu, Qian; Yin, Xingyao; Li, Chao

    2015-01-01

    Reservoir fluid discrimination is an indispensable part of seismic exploration. Reliable fluid discrimination helps to decrease the risk of exploration and to increase the success ratio of drilling. There are many kinds of fluid indicators that are used in fluid discriminations, most of which are single indicators. But single indicators do not always work well under complicated reservoir conditions. Therefore, combined fluid indicators are needed to increase accuracies of discriminations. In this paper, we have proposed an alternative strategy for the combination of fluid indicators. An alternative fluid indicator, the rock physics template-based indicator (RPTI) has been derived to combine the advantages of two single indicators. The RPTI is more sensitive to the contents of fluid than traditional indicators. The combination is implemented based on the characteristic of the fluid trend in the rock physics template, which means few subjective factors are involved. We also propose an inversion method to assure the accuracy of the RPTI input data. The RPTI profile is an intuitionistic interpretation of fluid content. Real data tests demonstrate the applicability and validity. (paper)

  20. A TEMPLATE FOR ONLINE HOMEWORK: FRANKENSTEIN'S MONSTER OR ROBO TA?

    OpenAIRE

    Dahlgran, Roger A.

    2002-01-01

    This paper describes the programming procedures required to implement online homework and evaluates the application of these procedures based on use in the author's course. The description of the procedures utilizes a template showing two representative applications from the author's introductory econometrics course. In one, the students are to collect and record data and in the other, students are to perform econometric analysis on the data. The web address for the template is arec.arizona.e...

  1. Diffeomorphic Iterative Centroid Methods for Template Estimation on Large Datasets

    OpenAIRE

    Cury , Claire; Glaunès , Joan Alexis; Colliot , Olivier

    2014-01-01

    International audience; A common approach for analysis of anatomical variability relies on the stimation of a template representative of the population. The Large Deformation Diffeomorphic Metric Mapping is an attractive framework for that purpose. However, template estimation using LDDMM is computationally expensive, which is a limitation for the study of large datasets. This paper presents an iterative method which quickly provides a centroid of the population in the shape space. This centr...

  2. Signal Integrity Analysis in Single and Bundled Carbon Nanotube Interconnects

    International Nuclear Information System (INIS)

    Majumder, M.K.; Pandya, N.D.; Kaushik, B.K.; Manhas, S.K.

    2013-01-01

    Carbon nanotube (CN T) can be considered as an emerging interconnect material in current nano scale regime. They are more promising than other interconnect materials such as Al or Cu because of their robustness to electromigration. This research paper aims to address the crosstalk-related issues (signal integrity) in interconnect lines. Different analytical models of single- (SWCNT), double- (DWCNT), and multiwalled CNTs (MWCNT) are studied to analyze the crosstalk delay at global interconnect lengths. A capacitively coupled three-line bus architecture employing CMOS driver is used for accurate estimation of crosstalk delay. Each line in bus architecture is represented with the equivalent RLC models of single and bundled SWCNT, DWCNT, and MWCNT interconnects. Crosstalk delay is observed at middle line (victim) when it switches in opposite direction with respect to the other two lines (aggressors). Using the data predicted by ITRS 2012, a comparative analysis on the basis of crosstalk delay is performed for bundled SWCNT/DWCNT and single MWCNT interconnects. It is observed that the overall crosstalk delay is improved by 40.92% and 21.37% for single MWCNT in comparison to bundled SWCNT and bundled DWCNT interconnects, respectively.

  3. Extractables analysis of single-use flexible plastic biocontainers.

    Science.gov (United States)

    Marghitoiu, Liliana; Liu, Jian; Lee, Hans; Perez, Lourdes; Fujimori, Kiyoshi; Ronk, Michael; Hammond, Matthew R; Nunn, Heather; Lower, Asher; Rogers, Gary; Nashed-Samuel, Yasser

    2015-01-01

    Studies of the extractable profiles of bioprocessing components have become an integral part of drug development efforts to minimize possible compromise in process performance, decrease in drug product quality, and potential safety risk to patients due to the possibility of small molecules leaching out from the components. In this study, an effective extraction solvent system was developed to evaluate the organic extractable profiles of single-use bioprocess equipment, which has been gaining increasing popularity in the biopharmaceutical industry because of the many advantages over the traditional stainless steel-based bioreactors and other fluid mixing and storage vessels. The chosen extraction conditions were intended to represent aggressive conditions relative to the application of single-use bags in biopharmaceutical manufacture, in which aqueous based systems are largely utilized. Those extraction conditions, along with a non-targeted analytical strategy, allowed for the generation and identification of an array of extractable compounds; a total of 53 organic compounds were identified from four types of commercially available single-use bags, the majority of which are degradation products of polymer additives. The success of this overall extractables analysis strategy was reflected partially by the effectiveness in the extraction and identification of a compound that was later found to be highly detrimental to mammalian cell growth. The usage of single-use bioreactors has been increasing in biopharmaceutical industry because of the appealing advantages that it promises regarding to the cleaning, sterilization, operational flexibility, and so on, during manufacturing of biologics. However, compared to its conventional counterparts based mainly on stainless steel, single-use bioreactors are more susceptible to potential problems associated with compound leaching into the bioprocessing fluid. As a result, extractable profiling of the single-use system has become

  4. High-throughput templated multisegment synthesis of gold nanowires and nanorods

    International Nuclear Information System (INIS)

    Burdick, Jared; Alonas, Eric; Huang, H-C; Rege, Kaushal; Wang, Joseph

    2009-01-01

    A cost-effective, high-throughput method for generating gold nanowires and/or nanorods based on a multisegment template electrodeposition approach is described. Using this method, multiple nanowires/nanorods can be generated from a single pore of alumina template membranes by alternately depositing segments of desirable (e.g., gold) and non-desirable metals (e.g., silver), followed by dissolution of the template and the non-desirable metal. Critical cost analysis indicates substantial savings in material requirements, processing times, and processing costs compared to the commonly used single-segment method. In addition to solid gold nanowires/nanorods, high yields of porous gold nanowires/nanorods are obtained by depositing alternate segments of gold-silver alloy and silver from the same gold-silver plating solution followed by selective dissolution of the silver from both segments. It is anticipated that this high-throughput method for synthesizing solid and porous gold nanowires and nanorods will accelerate their use in sensing, electronic, and biomedical applications.

  5. Structural Analysis of DFG-in and DFG-out Dual Src-Abl Inhibitors Sharing a Common Vinyl Purine Template

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Tianjun; Commodore, Lois; Huang, Wei-Sheng; Wang, Yihan; Sawyer, Tomi K.; Shakespeare, William C.; Clackson, Tim; Zhu, Xiaotian; Dalgarno, David C. (ARIAD)

    2010-09-30

    Bcr-Abl is the oncogenic protein tyrosine kinase responsible for chronic myeloid leukemia (CML). Treatment of the disease with imatinib (Gleevec) often results in drug resistance via kinase mutations at the advanced phases of the disease, which has necessitated the development of new mutation-resistant inhibitors, notably against the T315I gatekeeper mutation. As part of our efforts to discover such mutation resistant Abl inhibitors, we have focused on optimizing purine template kinase inhibitors, leading to the discovery of potent DFG-in and DFG-out series of Abl inhibitors that are also potent Src inhibitors. Here we present crystal structures of Abl bound by two such inhibitors, based on a common N9-arenyl purine, and that represent both DFG-in and -out binding modes. In each structure the purine template is bound deeply in the adenine pocket and the novel vinyl linker forms a non-classical hydrogen bond to the gatekeeper residue, Thr315. Specific template substitutions promote either a DFG-in or -out binding mode, with the kinase binding site adjusting to optimize molecular recognition. Bcr-Abl T315I mutant kinase is resistant to all currently marketed Abl inhibitors, and is the focus of intense drug discovery efforts. Notably, our DFG-out inhibitor, AP24163, exhibits modest activity against this mutant, illustrating that this kinase mutant can be inhibited by DFG-out class inhibitors. Furthermore our DFG-out inhibitor exhibits dual Src-Abl activity, absent from the prototypical DFG-out inhibitor, imatinib as well as its analog, nilotinib. The data presented here provides structural guidance for the further design of novel potent DFG-out class inhibitors against Src, Abl and Abl T315I mutant kinases.

  6. Reflex test reminders in required cancer synoptic templates decrease order entry error: An analysis of mismatch repair immunohistochemical orders to screen for Lynch syndrome

    Directory of Open Access Journals (Sweden)

    Mark R Kilgore

    2016-01-01

    Full Text Available Background: Endometrial carcinoma (EC is the most common extracolonic malignant neoplasm associated with Lynch syndrome (LS. LS is caused by autosomal dominant germline mutations in DNA mismatch repair (MMR genes. Screening for LS in EC is often evaluated by loss of immunohistochemical (IHC expression of DNA MMR enzymes MLH1, MSH2, MSH6, and PMS2 (MMR IHC. In July 2013, our clinicians asked that we screen all EC in patients ≤60 for loss of MMR IHC expression. Despite this policy, several cases were not screened or screening was delayed. We implemented an informatics-based approach to ensure that all women who met criteria would have timely screening. Subjects and Methods: Reports are created in PowerPath (Sunquest Information Systems, Tucson, AZ with custom synoptic templates. We implemented an algorithm on March 6, 2014 requiring pathologists to address MMR IHC in patients ≤60 with EC before sign out (S/O. Pathologists must answer these questions: is patient ≤60 (yes/no, if yes, follow-up questions (IHC done previously, ordered with addendum to follow, results included in report, N/A, or not ordered, if not ordered, one must explain. We analyzed cases from July 18, 2013 to August 31, 2016 preimplementation (PreImp and postimplementation (PostImp that met criteria. Data analysis was performed using the standard data package included with GraphPad Prism® 7.00 (GraphPad Software, Inc., La Jolla, CA, USA. Results: There were 147 patients who met criteria (29 PreImp and 118 PostImp. IHC was ordered in a more complete and timely fashion PostImp than PreImp. PreImp, 4/29 (13.8% cases did not get any IHC, but PostImp, only 4/118 (3.39% were missed (P = 0.0448. Of cases with IHC ordered, 60.0% (15/25 were ordered before or at S/O PreImp versus 91.2% (104/114 PostImp (P = 0.0004. Relative to day of S/O, the mean days of order delay were longer and more variable PreImp versus PostImp (12.9 ± 40.7 vs. -0.660 ± 1.15; P = 0.0227, with the average

  7. Biological Nanopores: Confined Spaces for Electrochemical Single-Molecule Analysis.

    Science.gov (United States)

    Cao, Chan; Long, Yi-Tao

    2018-02-20

    Nanopore sensing is developing into a powerful single-molecule approach to investigate the features of biomolecules that are not accessible by studying ensemble systems. When a target molecule is transported through a nanopore, the ions occupying the pore are excluded, resulting in an electrical signal from the intermittent ionic blockade event. By statistical analysis of the amplitudes, duration, frequencies, and shapes of the blockade events, many properties of the target molecule can be obtained in real time at the single-molecule level, including its size, conformation, structure, charge, geometry, and interactions with other molecules. With the development of the use of α-hemolysin to characterize individual polynucleotides, nanopore technology has attracted a wide range of research interest in the fields of biology, physics, chemistry, and nanoscience. As a powerful single-molecule analytical method, nanopore technology has been applied for the detection of various biomolecules, including oligonucleotides, peptides, oligosaccharides, organic molecules, and disease-related proteins. In this Account, we highlight recent developments of biological nanopores in DNA-based sensing and in studying the conformational structures of DNA and RNA. Furthermore, we introduce the application of biological nanopores to investigate the conformations of peptides affected by charge, length, and dipole moment and to study disease-related proteins' structures and aggregation transitions influenced by an inhibitor, a promoter, or an applied voltage. To improve the sensing ability of biological nanopores and further extend their application to a wider range of molecular sensing, we focus on exploring novel biological nanopores, such as aerolysin and Stable Protein 1. Aerolysin exhibits an especially high sensitivity for the detection of single oligonucleotides both in current separation and duration. Finally, to facilitate the use of nanopore measurements and statistical analysis

  8. BPFlexTemplate: A Business Process template generation tool based on similarity and flexibility

    Directory of Open Access Journals (Sweden)

    Latifa Ilahi

    2017-01-01

    Full Text Available In large organizations with multiple organizational units, process variants emerge due to many aspects, including local management policies, resources or socio-technical limitations. Organizations then struggle to improve a business process which has no longer a single process model to redesign, implement and adjust. In this paper, we propose an approach to tackle these two challenges: decrease the proliferation of process variants in these organizations, and foresee, at the same time, the need of having flexible business processes that allow for a certain degree of adjustment. To validate our approach, we first conducted case studies where we collected six real-world business process variants from two organizational units of the same healthcare organization. We then proposed an algorithm to derive a template process model from all the variants, which includes common and flexible process elements. We implemented our approach in a software tool called BPFlexTemplate, and tested it with the elicited variants.

  9. Replica Analysis for Portfolio Optimization with Single-Factor Model

    Science.gov (United States)

    Shinzato, Takashi

    2017-06-01

    In this paper, we use replica analysis to investigate the influence of correlation among the return rates of assets on the solution of the portfolio optimization problem. We consider the behavior of an optimal solution for the case where the return rate is described with a single-factor model and compare the findings obtained from our proposed methods with correlated return rates with those obtained with independent return rates. We then analytically assess the increase in the investment risk when correlation is included. Furthermore, we also compare our approach with analytical procedures for minimizing the investment risk from operations research.

  10. Optofluidics for handling and analysis of single living cells

    KAUST Repository

    Perozziello, Gerardo

    2017-12-07

    Optofluidics is a field with important applications in areas such as biotechnology, chemical synthesis and analytical chemistry. Optofluidic devices combine optical elements into microfluidic devices in ways that increase portability and sensitivity of analysis for diagnostic or screening purposes .In fact in these devices fluids give fine adaptability, mobility and accessibility to nanoscale photonic devices which otherwise could not be realized using conventional devices. This review describes several cases inwhich optical or microfluidic approaches are used to trap single cells in proximity of integrated optical sensor for being analysed.

  11. Characterizing single-molecule FRET dynamics with probability distribution analysis.

    Science.gov (United States)

    Santoso, Yusdi; Torella, Joseph P; Kapanidis, Achillefs N

    2010-07-12

    Probability distribution analysis (PDA) is a recently developed statistical tool for predicting the shapes of single-molecule fluorescence resonance energy transfer (smFRET) histograms, which allows the identification of single or multiple static molecular species within a single histogram. We used a generalized PDA method to predict the shapes of FRET histograms for molecules interconverting dynamically between multiple states. This method is tested on a series of model systems, including both static DNA fragments and dynamic DNA hairpins. By fitting the shape of this expected distribution to experimental data, the timescale of hairpin conformational fluctuations can be recovered, in good agreement with earlier published results obtained using different techniques. This method is also applied to studying the conformational fluctuations in the unliganded Klenow fragment (KF) of Escherichia coli DNA polymerase I, which allows both confirmation of the consistency of a simple, two-state kinetic model with the observed smFRET distribution of unliganded KF and extraction of a millisecond fluctuation timescale, in good agreement with rates reported elsewhere. We expect this method to be useful in extracting rates from processes exhibiting dynamic FRET, and in hypothesis-testing models of conformational dynamics against experimental data.

  12. Tetramethylammonium-filled protein nanopore for single-molecule analysis.

    Science.gov (United States)

    Wang, Ying; Yao, Fujun; Kang, Xiao-feng

    2015-10-06

    Nanopore technology, as the simplest and most inexpensive single-molecule tool, is being intensively developed. In nanopore stochastic sensing, KCl and NaCl have traditionally been employed as pore-filled electrolytes for recording the change of ion conductance in nanopores triggered by analyte translocation through the pore. However, some challenges limit its further advance. Here we used tetramethylammonium (TMA) chloride, instead of KCl, as a novel analysis system for nanopores. Some unique nanopore characteristics were observed: (1) The stability of the planar lipid bilayer for embedding the protein pores was elevated at least 6 times. (2) The TMA-Cl system could effectively reduce the noise of single-channel recording. (3) It was easy to control the insertion of protein pores into the lipid bilayer, and the formed single nanopore could last for a sufficiently long time. (4) TMA-Cl could be used as a DNA speed bump in the nanopore to slow DNA translocation speed. (5) The capacity of the nanopore capture of DNA (capture rate) increased significantly and simultaneously increased the translocation time of DNA in the pore. (6) The TMA-filled nanopore could discriminate between various polynucleotides.

  13. Condensing Raman spectrum for single-cell phenotype analysis

    KAUST Repository

    Sun, Shiwei

    2015-12-09

    Background In recent years, high throughput and non-invasive Raman spectrometry technique has matured as an effective approach to identification of individual cells by species, even in complex, mixed populations. Raman profiling is an appealing optical microscopic method to achieve this. To fully utilize Raman proling for single-cell analysis, an extensive understanding of Raman spectra is necessary to answer questions such as which filtering methodologies are effective for pre-processing of Raman spectra, what strains can be distinguished by Raman spectra, and what features serve best as Raman-based biomarkers for single-cells, etc. Results In this work, we have proposed an approach called rDisc to discretize the original Raman spectrum into only a few (usually less than 20) representative peaks (Raman shifts). The approach has advantages in removing noises, and condensing the original spectrum. In particular, effective signal processing procedures were designed to eliminate noise, utilising wavelet transform denoising, baseline correction, and signal normalization. In the discretizing process, representative peaks were selected to signicantly decrease the Raman data size. More importantly, the selected peaks are chosen as suitable to serve as key biological markers to differentiate species and other cellular features. Additionally, the classication performance of discretized spectra was found to be comparable to full spectrum having more than 1000 Raman shifts. Overall, the discretized spectrum needs about 5storage space of a full spectrum and the processing speed is considerably faster. This makes rDisc clearly superior to other methods for single-cell classication.

  14. Making Deformable Template Models Operational

    DEFF Research Database (Denmark)

    Fisker, Rune

    2000-01-01

    for estimation of the model parameters, which applies a combination of a maximum likelihood and minimum distance criterion. Another contribution is a very fast search based initialization algorithm using a filter interpretation of the likelihood model. These two methods can be applied to most deformable template......Deformable template models are a very popular and powerful tool within the field of image processing and computer vision. This thesis treats this type of models extensively with special focus on handling their common difficulties, i.e. model parameter selection, initialization and optimization....... A proper handling of the common difficulties is essential for making the models operational by a non-expert user, which is a requirement for intensifying and commercializing the use of deformable template models. The thesis is organized as a collection of the most important articles, which has been...

  15. Fabrication of cobalt-nickel binary nanowires in a highly ordered alumina template via AC electrodeposition.

    Science.gov (United States)

    Ali, Ghafar; Maqbool, Muhammad

    2013-08-14

    Cobalt-nickel (Co-Ni) binary alloy nanowires of different compositions were co-deposited in the nanopores of highly ordered anodic aluminum oxide (AAO) templates from a single sulfate bath using alternating current (AC) electrodeposition. AC electrodeposition was accomplished without modifying or removing the barrier layer. Field emission scanning electron microscope was used to study the morphology of templates and alloy nanowires. Energy-dispersive X-ray analysis confirmed the deposition of Co-Ni alloy nanowires in the AAO templates. Average diameter of the alloy nanowires was approximately 40 nm which is equal to the diameter of nanopore. X-ray diffraction analysis showed that the alloy nanowires consisted of both hexagonal close-packed and face-centered cubic phases. Magnetic measurements showed that the easy x-axis of magnetization is parallel to the nanowires with coercivity of approximately 706 Oe. AC electrodeposition is very simple, fast, and is useful for the homogenous deposition of various secondary nanostuctured materials into the nanopores of AAO.

  16. Fabrication of cobalt-nickel binary nanowires in a highly ordered alumina template via AC electrodeposition

    Science.gov (United States)

    Ali, Ghafar; Maqbool, Muhammad

    2013-08-01

    Cobalt-nickel (Co-Ni) binary alloy nanowires of different compositions were co-deposited in the nanopores of highly ordered anodic aluminum oxide (AAO) templates from a single sulfate bath using alternating current (AC) electrodeposition. AC electrodeposition was accomplished without modifying or removing the barrier layer. Field emission scanning electron microscope was used to study the morphology of templates and alloy nanowires. Energy-dispersive X-ray analysis confirmed the deposition of Co-Ni alloy nanowires in the AAO templates. Average diameter of the alloy nanowires was approximately 40 nm which is equal to the diameter of nanopore. X-ray diffraction analysis showed that the alloy nanowires consisted of both hexagonal close-packed and face-centered cubic phases. Magnetic measurements showed that the easy x-axis of magnetization is parallel to the nanowires with coercivity of approximately 706 Oe. AC electrodeposition is very simple, fast, and is useful for the homogenous deposition of various secondary nanostuctured materials into the nanopores of AAO.

  17. A template bank to search for gravitational waves from inspiralling compact binaries: II. Phenomenological model

    International Nuclear Information System (INIS)

    Cokelaer, T

    2007-01-01

    Matched filtering is used to search for gravitational waves emitted by inspiralling compact binaries in data from ground-based interferometers. One of the key aspects of the detection process is the deployment of a set of templates, also called a template bank, to cover the astrophysically interesting region of the parameter space. In a companion paper, we described the template bank algorithm used in the analysis of Laser Interferometer Gravitational-Wave Observatory (LIGO) data to search for signals from non-spinning binaries made of neutron star and/or stellar-mass black holes; this template bank is based upon physical template families. In this paper, we describe the phenomenological template bank that was used to search for gravitational waves from non-spinning black hole binaries (from stellar mass formation) in the second, third and fourth LIGO science runs. We briefly explain the design of the bank, whose templates are based on a phenomenological detection template family. We show that this template bank gives matches greater than 95% with the physical template families that are expected to be captured by the phenomenological templates

  18. Surface noise analysis using a single-ion sensor

    Science.gov (United States)

    Daniilidis, N.; Gerber, S.; Bolloten, G.; Ramm, M.; Ransford, A.; Ulin-Avila, E.; Talukdar, I.; Häffner, H.

    2014-06-01

    We use a single-ion electric-field noise sensor in combination with in situ surface treatment and analysis tools, to investigate the relationship between electric-field noise from metal surfaces in vacuum and the composition of the surface. These experiments are performed in a setup that integrates ion trapping capabilities with surface analysis tools. We find that treatment of an aluminum-copper surface with energetic argon ions significantly reduces the level of room-temperature electric-field noise, but the surface does not need to be atomically clean to show noise levels comparable to those of the best cryogenic traps. The noise levels after treatment are low enough to allow fault-tolerant trapped-ion quantum information processing on a microfabricated surface trap at room temperature.

  19. A visual template-matching method for articulation angle measurement

    CSIR Research Space (South Africa)

    De Saxe, C

    2015-09-01

    Full Text Available and proposed sensing methods are limited either in terms of commercial feasibility or measurement accuracy. This paper investigates a vision-based system consisting of a single tractor-mounted camera, a template-matching image processing algorithm...

  20. External and semi-internal controls for PCR amplification of homologous sequences in mixed templates

    DEFF Research Database (Denmark)

    Kalle, Elena; Gulevich, Alexander; Rensing, Christopher Günther T

    2013-01-01

    . The complexity of the external and semi-internal amplification controls must be comparable with the assumed complexity of the samples. We also emphasize that amplification controls should be applied in multi-template PCR regardless of the post-assay method used to analyze products.......In a mixed template, the presence of homologous target DNA sequences creates environments that almost inevitably give rise to artifacts and biases during PCR. Heteroduplexes, chimeras, and skewed template-to-product ratios are the exclusive attributes of mixed template PCR and never occur...... in a single template assay. Yet, multi-template PCR has been used without appropriate attention to quality control and assay validation, in spite of the fact that such practice diminishes the reliability of results. External and internal amplification controls became obligatory elements of good laboratory...

  1. Wide band gap semiconductor templates

    Energy Technology Data Exchange (ETDEWEB)

    Arendt, Paul N. (Los Alamos, NM); Stan, Liliana (Los Alamos, NM); Jia, Quanxi (Los Alamos, NM); DePaula, Raymond F. (Santa Fe, NM); Usov, Igor O. (Los Alamos, NM)

    2010-12-14

    The present invention relates to a thin film structure based on an epitaxial (111)-oriented rare earth-Group IVB oxide on the cubic (001) MgO terminated surface and the ion-beam-assisted deposition ("IBAD") techniques that are amendable to be over coated by semiconductors with hexagonal crystal structures. The IBAD magnesium oxide ("MgO") technology, in conjunction with certain template materials, is used to fabricate the desired thin film array. Similarly, IBAD MgO with appropriate template layers can be used for semiconductors with cubic type crystal structures.

  2. Modal Analysis of a Single-Structure Multiaxis MEMS Gyroscope

    Directory of Open Access Journals (Sweden)

    Muhammad Ali Shah

    2016-01-01

    Full Text Available This paper reports on designing a single-structure triaxes MEMS capacitive gyroscope which is capable of measuring the three angular velocities on a single drive. A Z-shaped beam for the support of folded coupling spring has been applied to suppress the unwanted mode and decrease the stress effect at the spring ends. The unique coupling spring has changed the driving motion, due to which slide film damping in the driving mode has been reduced. This reduction can lead to higher performance of the sensor with less requirements on vacuum level which decreases the cost of fabrication. Simulation analysis has been performed in COMSOL Multiphysics and Matlab Simulink to finalize the design for fabrication. After finite element analysis, the driving, x-sensing, z-sensing, and y-sensing are, respectively, found to be 13.30 KHz, 13.40 KHz, 13.47 KHz, and 13.51 KHz.

  3. Bulk segregant analysis using single nucleotide polymorphism microarrays.

    Directory of Open Access Journals (Sweden)

    Anthony Becker

    2011-01-01

    Full Text Available Bulk segregant analysis (BSA using microarrays, and extreme array mapping (XAM have recently been used to rapidly identify genomic regions associated with phenotypes in multiple species. These experiments, however, require the identification of single feature polymorphisms (SFP between the cross parents for each new combination of genotypes, which raises the cost of experiments. The availability of the genomic polymorphism data in Arabidopsis thaliana, coupled with the efficient designs of Single Nucleotide Polymorphism (SNP genotyping arrays removes the requirement for SFP detection and lowers the per array cost, thereby lowering the overall cost per experiment. To demonstrate that these approaches would be functional on SNP arrays and determine confidence intervals, we analyzed hybridizations of natural accessions to the Arabidopsis ATSNPTILE array and simulated BSA or XAM given a variety of gene models, populations, and bulk selection parameters. Our results show a striking degree of correlation between the genotyping output of both methods, which suggests that the benefit of SFP genotyping in context of BSA can be had with the cheaper, more efficient SNP arrays. As a final proof of concept, we hybridized the DNA from bulks of an F2 mapping population of a Sulfur and Selenium ionomics mutant to both the Arabidopsis ATTILE1R and ATSNPTILE arrays, which produced almost identical results. We have produced R scripts that prompt the user for the required parameters and perform the BSA analysis using the ATSNPTILE1 array and have provided them as supplemental data files.

  4. Author template for journal articles

    African Journals Online (AJOL)

    ThinkPAD

    2012-07-24

    Jul 24, 2012 ... KDML105, and its related varieties as templates, with only O. sativa var. KDML105 being able to be amplified. This amplification is not only rapid, but is also easy to perform. Hence, it is a feasible method for identifying O. sativa var. KDML105 between rice varieties. Key words: Oryza sativa L., varietal ...

  5. Supply-Chain Optimization Template

    Science.gov (United States)

    Quiett, William F.; Sealing, Scott L.

    2009-01-01

    The Supply-Chain Optimization Template (SCOT) is an instructional guide for identifying, evaluating, and optimizing (including re-engineering) aerospace- oriented supply chains. The SCOT was derived from the Supply Chain Council s Supply-Chain Operations Reference (SCC SCOR) Model, which is more generic and more oriented toward achieving a competitive advantage in business.

  6. Single particle analysis with a 3600 light scattering photometer

    International Nuclear Information System (INIS)

    Bartholdi, M.F.

    1979-06-01

    Light scattering by single spherical homogeneous particles in the diameter range 1 to 20 μm and relative refractive index 1.20 is measured. Particle size of narrowly dispersed populations is determined and a multi-modal dispersion of five components is completely analyzed. A 360 0 light scattering photometer for analysis of single particles has been designed and developed. A fluid stream containing single particles intersects a focused laser beam at the primary focal point of an ellipsoidal reflector ring. The light scattered at angles theta = 2.5 0 to 177.5 0 at phi = 0 0 and 180 0 is reflected onto a circular array of photodiodes. The ellipsoidal reflector is situated in a chamber filled with fluid matching that of the stream to minimize refracting and reflecting interfaces. The detector array consists of 60 photodiodes each subtending 3 0 in scattering angle on 6 0 centers around 360 0 . 32 measurements on individual particles can be acquired at rates of 500 particles per second. The intensity and angular distribution of light scattered by spherical particles are indicative of size and relative refractive index. Calculations, using Lorenz--Mie theory, of differential scattering patterns integrated over angle corresponding to the detector geometry determined the instrument response to particle size. From this the expected resolution and experimental procedures are determined.Ultimately, the photometer will be utilized for identification and discrimination of biological cells based on the sensitivity of light scattering to size, shape, refractive index differences, internal granularity, and other internal morphology. This study has demonstrated the utility of the photometer and indicates potential for application to light scattering studies of biological cells

  7. Parallel single cell analysis on an integrated microfluidic platform for cell trapping, lysis and analysis

    NARCIS (Netherlands)

    le Gac, Severine; de Boer, Hans L.; Wijnperle, Daniël; Meuleman, W.; Carlen, Edwin; van den Berg, Albert; Kim, Tae Song; Lee, Yoon-Sik; Chung, Taek-Dong; Jeon, Noo Li; Lee, Sang-Hoon; Suh, Kahp-Yang; Choo, Jaebum; Kim, Yong-Kweon

    2009-01-01

    We report here a novel and easily scalable microfluidic platform for the parallel analysis of hundreds of individual cells, with controlled single cell trapping, followed by their lysis and subsequent retrieval of the cellular content for on-chip analysis. The device consists of a main channel and

  8. Bayesian analysis of inflation: Parameter estimation for single field models

    International Nuclear Information System (INIS)

    Mortonson, Michael J.; Peiris, Hiranya V.; Easther, Richard

    2011-01-01

    Future astrophysical data sets promise to strengthen constraints on models of inflation, and extracting these constraints requires methods and tools commensurate with the quality of the data. In this paper we describe ModeCode, a new, publicly available code that computes the primordial scalar and tensor power spectra for single-field inflationary models. ModeCode solves the inflationary mode equations numerically, avoiding the slow roll approximation. It is interfaced with CAMB and CosmoMC to compute cosmic microwave background angular power spectra and perform likelihood analysis and parameter estimation. ModeCode is easily extendable to additional models of inflation, and future updates will include Bayesian model comparison. Errors from ModeCode contribute negligibly to the error budget for analyses of data from Planck or other next generation experiments. We constrain representative single-field models (φ n with n=2/3, 1, 2, and 4, natural inflation, and 'hilltop' inflation) using current data, and provide forecasts for Planck. From current data, we obtain weak but nontrivial limits on the post-inflationary physics, which is a significant source of uncertainty in the predictions of inflationary models, while we find that Planck will dramatically improve these constraints. In particular, Planck will link the inflationary dynamics with the post-inflationary growth of the horizon, and thus begin to probe the ''primordial dark ages'' between TeV and grand unified theory scale energies.

  9. Size analysis of single-core magnetic nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Ludwig, Frank, E-mail: f.ludwig@tu-bs.de [Institut für Elektrische Messtechnik und Grundlagen der Elektrotechnik, TU Braunschweig, Braunschweig (Germany); Balceris, Christoph; Viereck, Thilo [Institut für Elektrische Messtechnik und Grundlagen der Elektrotechnik, TU Braunschweig, Braunschweig (Germany); Posth, Oliver; Steinhoff, Uwe [Physikalisch-Technische Bundesanstalt, Berlin (Germany); Gavilan, Helena; Costo, Rocio [Instituto de Ciencia de Materiales de Madrid, ICMM/CSIC, Madrid (Spain); Zeng, Lunjie; Olsson, Eva [Department of Applied Physics, Chalmers University of Technology, Göteborg (Sweden); Jonasson, Christian; Johansson, Christer [ACREO Swedish ICT AB, Göteborg (Sweden)

    2017-04-01

    Single-core iron-oxide nanoparticles with nominal core diameters of 14 nm and 19 nm were analyzed with a variety of non-magnetic and magnetic analysis techniques, including transmission electron microscopy (TEM), dynamic light scattering (DLS), static magnetization vs. magnetic field (M-H) measurements, ac susceptibility (ACS) and magnetorelaxometry (MRX). From the experimental data, distributions of core and hydrodynamic sizes are derived. Except for TEM where a number-weighted distribution is directly obtained, models have to be applied in order to determine size distributions from the measurand. It was found that the mean core diameters determined from TEM, M-H, ACS and MRX measurements agree well although they are based on different models (Langevin function, Brownian and Néel relaxation times). Especially for the sample with large cores, particle interaction effects come into play, causing agglomerates which were detected in DLS, ACS and MRX measurements. We observed that the number and size of agglomerates can be minimized by sufficiently strong diluting the suspension. - Highlights: • Investigation of size parameters of single-core magnetic nanoparticles with nominal core diameters of 14 nm and 19 nm utilizing different magnetic and non-magnetic methods • Hydrodynamic size determined from ac susceptibility measurements is consistent with the DLS findings • Core size agrees determined from static magnetization curves, MRX and ACS data agrees with results from TEM although the estimation is based on different models (Langevin function, Brownian and Néel relaxation times).

  10. Renormalisation group analysis of single right-handed neutrino dominance

    International Nuclear Information System (INIS)

    King, S.F.; Nimai Singh, N.

    2000-01-01

    We perform a renormalisation group (RG) analysis of neutrino masses and mixing angles in the see-saw mechanism in the minimal supersymmetric standard model with three right-handed neutrinos, including the effects of the heavy neutrino thresholds. We focus on the case that one of the right-handed neutrinos provides the dominant contribution to the 23 block of the light Majorana matrix, causing its determinant to approximately vanish and giving an automatic neutrino mass hierarchy, so-called single right-handed neutrino dominance which may arise from a U(1) family symmetry. In these models radiative corrections can increase atmospheric and solar neutrino mixing by up to about 10% and 5%, respectively, and may help to achieve bi-maximal mixing. Significantly we find that the radiative corrections over the heavy neutrino threshold region are at least as important as those usually considered from the lightest right-handed neutrino down to low energies

  11. Robust stability analysis of adaptation algorithms for single perceptron.

    Science.gov (United States)

    Hui, S; Zak, S H

    1991-01-01

    The problem of robust stability and convergence of learning parameters of adaptation algorithms in a noisy environment for the single preceptron is addressed. The case in which the same input pattern is presented in the adaptation cycle is analyzed. The algorithm proposed is of the Widrow-Hoff type. It is concluded that this algorithm is robust. However, the weight vectors do not necessarily converge in the presence of measurement noise. A modified version of this algorithm in which the reduction factors are allowed to vary with time is proposed, and it is shown that this algorithm is robust and that the weight vectors converge in the presence of bounded noise. Only deterministic-type arguments are used in the analysis. An ultimate bound on the error in terms of a convex combination of the initial error and the bound on the noise is obtained.

  12. Single-cell phospho-protein analysis by flow cytometry.

    Science.gov (United States)

    Schulz, Kenneth R; Danna, Erika A; Krutzik, Peter O; Nolan, Garry P

    2012-02-01

    This protocol describes methods for monitoring intracellular phosphorylation-dependent signaling events on a single-cell basis. This approach measures cell signaling by treating cells with exogenous stimuli, fixing cells with formaldehyde, permeabilizing with methanol, and then staining with phospho-specific antibodies. Thus, cell signaling states can be determined as a measure of how cells interact with their environment. This method has applications in clinical research as well as mechanistic studies of basic biology. In clinical research, diagnostic or drug efficacy information can be retrieved by discovering how a disease affects the ability of cells to respond to growth factors. Basic scientists can use this technique to analyze signaling events in cell lines and human or murine primary cells, including rare populations, like B1 cells or stem cells. This technique has broad applications bringing standard biochemical analysis into primary cells in order to garner valuable information about signaling events in physiologic settings. © 2012 by John Wiley & Sons, Inc.

  13. Organic-inorganic templates in biomineralization of shells, bone, teeth, and bacterial biofilms

    Science.gov (United States)

    de Stasio, Gelsomina Pupa

    2005-03-01

    Recent experiments with the Spectromicroscope for PHotoelectron Imaging of Nanostructure with X-rays (SPHINX)[1] on the biofilm formed by Fe-oxidizing bacteria in fresh, ground water, demonstrated that microbially extruded polysaccharide filaments provide the precipitation site for amorphous FeOOH filaments [2]. Upon aging the mineralized filaments crystallize to ferrihydrite (2-line FeOOH), with one curved pseudo-single crystal of akaganeite β-FeOOH), at the core of each filament. The crystals are only 2 nm wide and up to 10 micron long (aspect ratio 1:1000:1), and their structure and morphology is unprecedented. Furthermore, akaganeite should not form in fresh water, therefore a templation mechanism was hypothesized, and supported by SPHINX analysis of carbon XANES. The results indicate that after formation of the crystal fiber, the polysaccharide structure is also altered, and C1s spectra suggest that the COO^- group is involved in the templation mechanism. This was the first successful attempt to understand the organic-inorganic chemical interface in a biomineralized system. Many more templated biomineral systems can and will now be analyzed with this new approach. *Ultramicroscopy 99, 87-94 (2004). *Science 303, 1656-1658 (2004).

  14. DNA templated magnetic nanoparticles

    Science.gov (United States)

    Kinsella, Joseph M.

    Recent discoveries in nanoscience are predicted to potentially revolutionize future technologies in an extensive number of fields. These developments are contingent upon discovering new and often unconventional methods to synthesize and control nanoscale components. Nature provides several examples of working nanotechnology such as the use of programmed self assembly to build and deconstruct complex molecular systems. We have adopted a method to control the one dimensional assembly of magnetic nanoparticles using DNA as a scaffold molecule. With this method we have demonstrated the ability to organize 5 nm particles into chains that stretch up to ˜20 mum in length. One advantage of using DNA compared is the ability of the molecule to interact with other biomolecules. After assembling particles onto DNA we have been able to cleave the molecule into smaller fragments using restriction enzymes. Using ligase enzymes we have re-connected these fragments, coated with either gold or iron oxide, to form long one-dimensional arrangements of the two different types of nanoparticles on a single molecular guide. We have also created a sensitive magnetic field sensor by incorporating magnetic nanoparticle coated DNA strands with microfabricated electrodes. The IV characteristics of the aligned nanoparticles are dependant on the magnitude of an externally applied magnetic field. This transport phenomenon known as tunneling magnetoresistance (TMR) shows room temperature resistance of our devices over 80% for cobalt ferrite coated DNA when a field of 20 kOe is applied. In comparison, studies using two dimensional nanoparticle films of irox oxides xii only exhibit a 35% MR effect. Confinement into one dimension using the DNA guide produces a TMR mechanism which produces significant increases in magnetoresistance. This property can be utilized for applications in magnetic field sensing, data storage, and logic elements.

  15. Low aspect ratio micropores for single-particle and single-cell analysis.

    Science.gov (United States)

    Goyal, Gaurav; Mulero, Rafael; Ali, Jamel; Darvish, Armin; Kim, Min Jun

    2015-05-01

    This paper describes microparticle and bacterial translocation studies using low aspect ratio solid-state micropores. Micropores, 5 μm in diameter, were fabricated in 200 nm thick free-standing silicon nitride membranes, resulting in pores with an extremely low aspect ratio, nominally 0.04. For microparticle translocation experiments, sulfonated polystyrene microparticles and magnetic microbeads in size range of 1-4 μm were used. Using the microparticle translocation characteristics, we find that particle translocations result in a change only in the pore's geometrical resistance while the access resistance remains constant. Furthermore, we demonstrate the ability of our micropore to probe high-resolution shape information of translocating analytes using concatenated magnetic microspheres. Distinct current drop peaks were observed for each microsphere of the multibead architecture. For bacterial translocation experiments, nonflagellated Escherichia coli (strain HCB 5) and wild type flagellated Salmonella typhimurium (strain SJW1103) were used. Distinct current signatures for the two bacteria were obtained and this difference in translocation behavior was attributed to different surface protein distributions on the bacteria. Our findings may help in developing low aspect ratio pores for high-resolution microparticle characterization and single-cell analysis. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. A Validated Task Analysis of the Single Pilot Operations Concept

    Science.gov (United States)

    Wolter, Cynthia A.; Gore, Brian F.

    2015-01-01

    The current day flight deck operational environment consists of a two-person Captain/First Officer crew. A concept of operations (ConOps) to reduce the commercial cockpit to a single pilot from the current two pilot crew is termed Single Pilot Operations (SPO). This concept has been under study by researchers in the Flight Deck Display Research Laboratory (FDDRL) at the National Aeronautics and Space Administration's (NASA) Ames (Johnson, Comerford, Lachter, Battiste, Feary, and Mogford, 2012) and researchers from Langley Research Centers (Schutte et al., 2007). Transitioning from a two pilot crew to a single pilot crew will undoubtedly require changes in operational procedures, crew coordination, use of automation, and in how the roles and responsibilities of the flight deck and ATC are conceptualized in order to maintain the high levels of safety expected of the US National Airspace System. These modifications will affect the roles and the subsequent tasks that are required of the various operators in the NextGen environment. The current report outlines the process taken to identify and document the tasks required by the crew according to a number of operational scenarios studied by the FDDRL between the years 2012-2014. A baseline task decomposition has been refined to represent the tasks consistent with a new set of entities, tasks, roles, and responsibilities being explored by the FDDRL as the move is made towards SPO. Information from Subject Matter Expert interviews, participation in FDDRL experimental design meetings, and study observation was used to populate and refine task sets that were developed as part of the SPO task analyses. The task analysis is based upon the proposed ConOps for the third FDDRL SPO study. This experiment possessed nine different entities operating in six scenarios using a variety of SPO-related automation and procedural activities required to guide safe and efficient aircraft operations. The task analysis presents the roles and

  17. Ferritin-Templated Quantum-Dots for Quantum Logic Gates

    Science.gov (United States)

    Choi, Sang H.; Kim, Jae-Woo; Chu, Sang-Hyon; Park, Yeonjoon; King, Glen C.; Lillehei, Peter T.; Kim, Seon-Jeong; Elliott, James R.

    2005-01-01

    Quantum logic gates (QLGs) or other logic systems are based on quantum-dots (QD) with a stringent requirement of size uniformity. The QD are widely known building units for QLGs. The size control of QD is a critical issue in quantum-dot fabrication. The work presented here offers a new method to develop quantum-dots using a bio-template, called ferritin, that ensures QD production in uniform size of nano-scale proportion. The bio-template for uniform yield of QD is based on a ferritin protein that allows reconstitution of core material through the reduction and chelation processes. One of the biggest challenges for developing QLG is the requirement of ordered and uniform size of QD for arrays on a substrate with nanometer precision. The QD development by bio-template includes the electrochemical/chemical reconsitution of ferritins with different core materials, such as iron, cobalt, manganese, platinum, and nickel. The other bio-template method used in our laboratory is dendrimers, precisely defined chemical structures. With ferritin-templated QD, we fabricated the heptagonshaped patterned array via direct nano manipulation of the ferritin molecules with a tip of atomic force microscope (AFM). We also designed various nanofabrication methods of QD arrays using a wide range manipulation techniques. The precise control of the ferritin-templated QD for a patterned arrangement are offered by various methods, such as a site-specific immobilization of thiolated ferritins through local oxidation using the AFM tip, ferritin arrays induced by gold nanoparticle manipulation, thiolated ferritin positioning by shaving method, etc. In the signal measurements, the current-voltage curve is obtained by measuring the current through the ferritin, between the tip and the substrate for potential sweeping or at constant potential. The measured resistance near zero bias was 1.8 teraohm for single holoferritin and 5.7 teraohm for single apoferritin, respectively.

  18. Kinetic analysis of single molecule FRET transitions without trajectories

    Science.gov (United States)

    Schrangl, Lukas; Göhring, Janett; Schütz, Gerhard J.

    2018-03-01

    Single molecule Förster resonance energy transfer (smFRET) is a popular tool to study biological systems that undergo topological transitions on the nanometer scale. smFRET experiments typically require recording of long smFRET trajectories and subsequent statistical analysis to extract parameters such as the states' lifetimes. Alternatively, analysis of probability distributions exploits the shapes of smFRET distributions at well chosen exposure times and hence works without the acquisition of time traces. Here, we describe a variant that utilizes statistical tests to compare experimental datasets with Monte Carlo simulations. For a given model, parameters are varied to cover the full realistic parameter space. As output, the method yields p-values which quantify the likelihood for each parameter setting to be consistent with the experimental data. The method provides suitable results even if the actual lifetimes differ by an order of magnitude. We also demonstrated the robustness of the method to inaccurately determine input parameters. As proof of concept, the new method was applied to the determination of transition rate constants for Holliday junctions.

  19. How to Test Mandatory Text Templates: The European Patient Information Leaflet.

    Directory of Open Access Journals (Sweden)

    Henk Pander Maat

    Full Text Available The structure of patient information leaflets (PILs supplied with medicines in the European Union is largely determined by a regulatory template, requiring a fixed sequence of pre-formulated headings and sub-headings. The template has been criticized on various occasions, but it has never been tested with users. This paper proposes an alternative template, informed by templates used in the USA and Australia, and by previous user testing.The main research question is whether the revision better enables users to find relevant information. Besides, the paper proposes a methodology for testing templates. Testing document templates is complex, as they are "empty". For both the current and the alternative template, we produced a document with bogus text and real headings (reflecting the empty template and a real-life document with readable text (reflecting the "filled" template. The documents were tested both in Dutch and in English, with 64 British and 64 Dutch users. The test used a set of scenario questions that covers the full range of template (subtopics; users needed to indicate the text locations where they expected each question to be answered. The revised template improved findability of information; this effect was strongest for the "filled" template with readable text. When participants were shown both filled templates, there was a clear preference for the revised template. A closer analysis of the findability data revealed question-specific effects of topic grouping, topic ordering, subtopic granularity and wording of headings. Most of these favoured the revised template, but our revision led to adverse effects as well, for instance in the new heading Check with your doctor. Language-specific effects showed that the wording of the headings is a delicate task. Generally, we conclude that document template designs can be analyzed in terms of the four parameters grouping, ordering, granularity and wording. Furthermore, they need to be tested

  20. Single-cell analysis of targeted transcriptome predicts drug sensitivity of single cells within human myeloma tumors.

    Science.gov (United States)

    Mitra, A K; Mukherjee, U K; Harding, T; Jang, J S; Stessman, H; Li, Y; Abyzov, A; Jen, J; Kumar, S; Rajkumar, V; Van Ness, B

    2016-05-01

    Multiple myeloma (MM) is characterized by significant genetic diversity at subclonal levels that have a defining role in the heterogeneity of tumor progression, clinical aggressiveness and drug sensitivity. Although genome profiling studies have demonstrated heterogeneity in subclonal architecture that may ultimately lead to relapse, a gene expression-based prediction program that can identify, distinguish and quantify drug response in sub-populations within a bulk population of myeloma cells is lacking. In this study, we performed targeted transcriptome analysis on 528 pre-treatment single cells from 11 myeloma cell lines and 418 single cells from 8 drug-naïve MM patients, followed by intensive bioinformatics and statistical analysis for prediction of proteasome inhibitor sensitivity in individual cells. Using our previously reported drug response gene expression profile signature at the single-cell level, we developed an R Statistical analysis package available at https://github.com/bvnlabSCATTome, SCATTome (single-cell analysis of targeted transcriptome), that restructures the data obtained from Fluidigm single-cell quantitative real-time-PCR analysis run, filters missing data, performs scaling of filtered data, builds classification models and predicts drug response of individual cells based on targeted transcriptome using an assortment of machine learning methods. Application of SCATT should contribute to clinically relevant analysis of intratumor heterogeneity, and better inform drug choices based on subclonal cellular responses.

  1. Design reflowable digital book template

    Science.gov (United States)

    Prasetya, Didik Dwi; Widiyaningtyas, Triyanna; Arifin, M. Zainal; Wahyu Sakti G., I.

    2017-09-01

    Electronic books (e-books or digital books) increasingly in demand and continue to grow in the form of future books. One of the standard format electronic books that potential is EPUB (electronic publication) published by the International Digital Publishing Forum (IDPF). This digital book has major advantages are able to provide interactive and reflowable content, which are not found in another book format, such as PDF. Reflowable content allows the book can be accessed through a variety of reader device, like desktop and mobile with a fit and comfort view. However, because the generating process of an EPUB digital book is not as easy a PDF, so this format is less popular. Therefore, in order to help overcome the existing problems, this paper develops digital reflowable text book templates to support electronic learning, especially in Indonesia. This template can be used by anyone to produce a standard digital book quickly and easily without requiring additional specialized knowledge.

  2. Modelling Template for the Development of the Process Flowsheet

    DEFF Research Database (Denmark)

    Fedorova, Marina; Gani, Rafiqul

    2015-01-01

    provides building blocks for the templates (generic models previously developed); 3) computer aided methods and tools, that include procedures to perform model translation, model analysis, model verification/validation, model solution and model documentation. In this work, the integrated use of all three......Models are playing important roles in design and analysis of chemicals/bio-chemicals based products and the processes that manufacture them. Model-based methods and tools have the potential to decrease the number of experiments, which can be expensive and time consuming, and point to candidates......, where the experimental effort could be focused.In this contribution a general modelling framework for systematic model building through modelling templates, which supports the reuse of existing models via its tools integration and model import and export capabilities, is presented. Modelling templates...

  3. Random template banks and relaxed lattice coverings

    International Nuclear Information System (INIS)

    Messenger, C.; Prix, R.; Papa, M. A.

    2009-01-01

    Template-based searches for gravitational waves are often limited by the computational cost associated with searching large parameter spaces. The study of efficient template banks, in the sense of using the smallest number of templates, is therefore of great practical interest. The traditional approach to template-bank construction requires every point in parameter space to be covered by at least one template, which rapidly becomes inefficient at higher dimensions. Here we study an alternative approach, where any point in parameter space is covered only with a given probability η n and A n * lattices), which similarly cover any signal location only with probability η. The relaxed A n * lattice is found to yield the most efficient template banks at low dimensions (n < or approx. 10), while random template banks increasingly outperform any other method at higher dimensions.

  4. Single particle raster image analysis of diffusion for particle mixtures.

    Science.gov (United States)

    Longfils, M; Röding, M; Altskär, A; Schuster, E; Lorén, N; Särkkä, A; Rudemo, M

    2018-03-01

    Recently we complemented the raster image correlation spectroscopy (RICS) method of analysing raster images via estimation of the image correlation function with the method single particle raster image analysis (SPRIA). In SPRIA, individual particles are identified and the diffusion coefficient of each particle is estimated by a maximum likelihood method. In this paper, we extend the SPRIA method to analyse mixtures of particles with a finite set of diffusion coefficients in a homogeneous medium. In examples with simulated and experimental data with two and three different diffusion coefficients, we show that SPRIA gives accurate estimates of the diffusion coefficients and their proportions. A simple technique for finding the number of different diffusion coefficients is also suggested. Further, we study the use of RICS for mixtures with two different diffusion coefficents and investigate, by plotting level curves of the correlation function, how large the quotient between diffusion coefficients needs to be in order to allow discrimination between models with one and two diffusion coefficients. We also describe a minor correction (compared to published papers) of the RICS autocorrelation function. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

  5. Analysis of the Single Toggle Jaw Crusher Force Transmission Characteristics

    Directory of Open Access Journals (Sweden)

    Moses Frank Oduori

    2016-01-01

    Full Text Available This paper sets out to perform a static force analysis of the single toggle jaw crusher mechanism and to obtain the force transmission characteristics of the mechanism. In order to obtain force transmission metrics that are characteristic of the structure of the mechanism, such influences as friction, dead weight, and inertia are considered to be extraneous and neglected. Equations are obtained by considering the balance of forces at the moving joints and appropriately relating these to the input torque and the output torque. A mechanical advantage, the corresponding transmitted torque, and the variations thereof, during the cycle of motion of the mechanism, are obtained. The mechanical advantage that characterizes the mechanism is calculated as the mean value over the active crushing stroke of the mechanism. The force transmission characteristics can be used as criteria for the comparison of different jaw crusher mechanism designs in order to select the most suitable design for a given application. The equations obtained can also be used in estimating the forces sustained by the components of the mechanism.

  6. Watching mesoporous metal films grow during templated electrodeposition with in situ SAXS.

    Science.gov (United States)

    Richardson, S J; Burton, M R; Luo, X; Staniec, P A; Nandhakumar, I S; Terrill, N J; Elliott, J M; Squires, A M

    2017-07-27

    In this paper, we monitor the real-time growth of mesoporous platinum during electrodeposition using small-angle X-ray scattering (SAXS). Previously, we have demonstrated that platinum films featuring the 'single diamond' (Fd3m) morphology can be produced from 'double diamond' (Pn3m) lipid cubic phase templates; the difference in symmetry provides additional scattering signals unique to the metal. Taking advantage of this, we present simultaneous in situ SAXS/electrochemical measurement as the platinum nanostructures grow within the lipid template. This measurement allows us to correlate the nanostructure appearance with the deposition current density and to monitor the evolution of the orientational and lateral ordering of the lipid and platinum during deposition and after template removal. In other periodic metal nanomaterials deposited within any of the normal topology liquid crystal, mesoporous silica or block copolymer templates previously published, the template and emerging metal have the same symmetry, so such a study has not been possible previously.

  7. Design and Analysis of Single-Cell Sequencing Experiments

    NARCIS (Netherlands)

    Grün, Dominic; van Oudenaarden, Alexander

    2015-01-01

    Recent advances in single-cell sequencing hold great potential for exploring biological systems with unprecedented resolution. Sequencing the genome of individual cells can reveal somatic mutations and allows the investigation of clonal dynamics. Single-cell transcriptome sequencing can elucidate

  8. Macroporous inorganic solids from a biomineral template

    Science.gov (United States)

    Yue, Wenbo; Park, Robert J.; Kulak, Alex N.; Meldrum, Fiona C.

    2006-08-01

    A range of macroporous inorganic solids, with unique, sponge-like structures were synthesised by templating sea urchin skeletal plates. Although composed of a single crystal of calcite, a sea urchin plate exhibits a bicontinuous morphology with pores of diameter 10-15 μm. As both the solid and porous fractions of the plate exhibit identical form and dimensions, filling the porous network with an alternative material and dissolving away the CaCO 3 generates a cast with identical morphology to the original plate. The versatility of this approach is demonstrated in this paper, which provides both a review of previously published work, and a description of the application to a number of new systems. Macroporous metals, including gold and nickel were synthesised either from pre-prepared particles or via electroless deposition, while silica and titania were generated by sol-gel techniques. Sponge-like polymer membranes, formed as casts of the sea urchin plates, were also used as an environment in which to precipitate a range of single crystals with complex morphologies: CaCO 3, SrSO 4, PbSO 4, PbCO 3, NaCl and CuSO 4·5H 2O. These experiments demonstrate that single crystals with intricate forms are not restricted to the realms of biology, but that shape constraint provides an extremely general route for morphological control.

  9. Automatic script identification from images using cluster-based templates

    Energy Technology Data Exchange (ETDEWEB)

    Hochberg, J.; Kerns, L.; Kelly, P.; Thomas, T.

    1995-02-01

    We have developed a technique for automatically identifying the script used to generate a document that is stored electronically in bit image form. Our approach differs from previous work in that the distinctions among scripts are discovered by an automatic learning procedure, without any handson analysis. We first develop a set of representative symbols (templates) for each script in our database (Cyrillic, Roman, etc.). We do this by identifying all textual symbols in a set of training documents, scaling each symbol to a fixed size, clustering similar symbols, pruning minor clusters, and finding each cluster`s centroid. To identify a new document`s script, we identify and scale a subset of symbols from the document and compare them to the templates for each script. We choose the script whose templates provide the best match. Our current system distinguishes among the Armenian, Burmese, Chinese, Cyrillic, Ethiopic, Greek, Hebrew, Japanese, Korean, Roman, and Thai scripts with over 90% accuracy.

  10. Single aflatoxin contaminated corn kernel analysis with fluorescence hyperspectral image

    Science.gov (United States)

    Yao, Haibo; Hruska, Zuzana; Kincaid, Russell; Ononye, Ambrose; Brown, Robert L.; Cleveland, Thomas E.

    2010-04-01

    Aflatoxins are toxic secondary metabolites of the fungi Aspergillus flavus and Aspergillus parasiticus, among others. Aflatoxin contaminated corn is toxic to domestic animals when ingested in feed and is a known carcinogen associated with liver and lung cancer in humans. Consequently, aflatoxin levels in food and feed are regulated by the Food and Drug Administration (FDA) in the US, allowing 20 ppb (parts per billion) limits in food and 100 ppb in feed for interstate commerce. Currently, aflatoxin detection and quantification methods are based on analytical tests including thin-layer chromatography (TCL) and high performance liquid chromatography (HPLC). These analytical tests require the destruction of samples, and are costly and time consuming. Thus, the ability to detect aflatoxin in a rapid, nondestructive way is crucial to the grain industry, particularly to corn industry. Hyperspectral imaging technology offers a non-invasive approach toward screening for food safety inspection and quality control based on its spectral signature. The focus of this paper is to classify aflatoxin contaminated single corn kernels using fluorescence hyperspectral imagery. Field inoculated corn kernels were used in the study. Contaminated and control kernels under long wavelength ultraviolet excitation were imaged using a visible near-infrared (VNIR) hyperspectral camera. The imaged kernels were chemically analyzed to provide reference information for image analysis. This paper describes a procedure to process corn kernels located in different images for statistical training and classification. Two classification algorithms, Maximum Likelihood and Binary Encoding, were used to classify each corn kernel into "control" or "contaminated" through pixel classification. The Binary Encoding approach had a slightly better performance with accuracy equals to 87% or 88% when 20 ppb or 100 ppb was used as classification threshold, respectively.

  11. Robust structural identification via polyhedral template matching

    DEFF Research Database (Denmark)

    Larsen, Peter Mahler; Schmidt, Søren; Schiøtz, Jakob

    2016-01-01

    thresholds thereof) to classify atomic structure. As a consequence they are sensitive to strain and thermal displacements, and preprocessing such as quenching or temporal averaging of the atomic positions is necessary to provide reliable identifications. We propose a new method, polyhedral template matching......Successful scientific applications of large-scale molecular dynamics often rely on automated methods for identifying the local crystalline structure of condensed phases. Many existing methods for structural identification, such as common neighbour analysis, rely on interatomic distances (or...... (PTM), which classifies structures according to the topology of the local atomic environment, without any ambiguity in the classification, and with greater reliability than e.g. common neighbour analysis in the presence of thermal fluctuations. We demonstrate that the method can reliably be used...

  12. Quantification of brain images using Korean standard templates and structural and cytoarchitectonic probabilistic maps

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jae Sung; Lee, Dong Soo; Kim, Yu Kyeong [College of Medicine, Seoul National Univ., Seoul (Korea, Republic of)] [and others

    2004-06-01

    Population based structural and functional maps of the brain provide effective tools for the analysis and interpretation of complex and individually variable brain data. Brain MRI and PET standard templates and statistical probabilistic maps based on image data of Korean normal volunteers have been developed and probabilistic maps based on cytoarchitectonic data have been introduced. A quantification method using these data was developed for the objective assessment of regional intensity in the brain images. Age, gender and ethnic specific anatomical and functional brain templates based on MR and PET images of Korean normal volunteers were developed. Korean structural probabilistic maps for 89 brain regions and cytoarchitectonic probabilistic maps for 13 Brodmann areas were transformed onto the standard templates. Brain FDG PET and SPGR MR images of normal volunteers were spatially normalized onto the template of each modality and gender. Regional uptake of radiotracers in PET and gray matter concentration in MR images were then quantified by averaging (or summing) regional intensities weighted using the probabilistic maps of brain regions. Regionally specific effects of aging on glucose metabolism in cingulate cortex were also examined. Quantification program could generate quantification results for single spatially normalized images per 20 seconds. Glucose metabolism change in cingulate gyrus was regionally specific: ratios of glucose metabolism in the rostral anterior cingulate vs. posterior cingulate and the caudal anterior cingulate vs. posterior cingulate were significantly decreased as the age increased. 'Rostral anterior' / 'posterior' was decreased by 3.1% per decade of age (p<10{sup -11}, r=0.81) and 'caudal anterior' / 'posterior' was decreased by 1.7% (p<10{sup -8}, r=0.72). Ethnic specific standard templates and probabilistic maps and quantification program developed in this study will be useful for the analysis

  13. Reducing Individual Variation for fMRI Studies in Children by Minimizing Template Related Errors.

    Directory of Open Access Journals (Sweden)

    Jian Weng

    Full Text Available Spatial normalization is an essential process for group comparisons in functional MRI studies. In practice, there is a risk of normalization errors particularly in studies involving children, seniors or diseased populations and in regions with high individual variation. One way to minimize normalization errors is to create a study-specific template based on a large sample size. However, studies with a large sample size are not always feasible, particularly for children studies. The performance of templates with a small sample size has not been evaluated in fMRI studies in children. In the current study, this issue was encountered in a working memory task with 29 children in two groups. We compared the performance of different templates: a study-specific template created by the experimental population, a Chinese children template and the widely used adult MNI template. We observed distinct differences in the right orbitofrontal region among the three templates in between-group comparisons. The study-specific template and the Chinese children template were more sensitive for the detection of between-group differences in the orbitofrontal cortex than the MNI template. Proper templates could effectively reduce individual variation. Further analysis revealed a correlation between the BOLD contrast size and the norm index of the affine transformation matrix, i.e., the SFN, which characterizes the difference between a template and a native image and differs significantly across subjects. Thereby, we proposed and tested another method to reduce individual variation that included the SFN as a covariate in group-wise statistics. This correction exhibits outstanding performance in enhancing detection power in group-level tests. A training effect of abacus-based mental calculation was also demonstrated, with significantly elevated activation in the right orbitofrontal region that correlated with behavioral response time across subjects in the trained group.

  14. Reducing Individual Variation for fMRI Studies in Children by Minimizing Template Related Errors.

    Science.gov (United States)

    Weng, Jian; Dong, Shanshan; He, Hongjian; Chen, Feiyan; Peng, Xiaogang

    2015-01-01

    Spatial normalization is an essential process for group comparisons in functional MRI studies. In practice, there is a risk of normalization errors particularly in studies involving children, seniors or diseased populations and in regions with high individual variation. One way to minimize normalization errors is to create a study-specific template based on a large sample size. However, studies with a large sample size are not always feasible, particularly for children studies. The performance of templates with a small sample size has not been evaluated in fMRI studies in children. In the current study, this issue was encountered in a working memory task with 29 children in two groups. We compared the performance of different templates: a study-specific template created by the experimental population, a Chinese children template and the widely used adult MNI template. We observed distinct differences in the right orbitofrontal region among the three templates in between-group comparisons. The study-specific template and the Chinese children template were more sensitive for the detection of between-group differences in the orbitofrontal cortex than the MNI template. Proper templates could effectively reduce individual variation. Further analysis revealed a correlation between the BOLD contrast size and the norm index of the affine transformation matrix, i.e., the SFN, which characterizes the difference between a template and a native image and differs significantly across subjects. Thereby, we proposed and tested another method to reduce individual variation that included the SFN as a covariate in group-wise statistics. This correction exhibits outstanding performance in enhancing detection power in group-level tests. A training effect of abacus-based mental calculation was also demonstrated, with significantly elevated activation in the right orbitofrontal region that correlated with behavioral response time across subjects in the trained group.

  15. I - Template Metaprogramming for Massively Parallel Scientific Computing - Expression Templates

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    Large scale scientific computing raises questions on different levels ranging from the fomulation of the problems to the choice of the best algorithms and their implementation for a specific platform. There are similarities in these different topics that can be exploited by modern-style C++ template metaprogramming techniques to produce readable, maintainable and generic code. Traditional low-level code tend to be fast but platform-dependent, and it obfuscates the meaning of the algorithm. On the other hand, object-oriented approach is nice to read, but may come with an inherent performance penalty. These lectures aim to present he basics of the Expression Template (ET) idiom which allows us to keep the object-oriented approach without sacrificing performance. We will in particular show to to enhance ET to include SIMD vectorization. We will then introduce techniques for abstracting iteration, and introduce thread-level parallelism for use in heavy data-centric loads. We will show to to apply these methods i...

  16. Template-assisted materials engineering

    Science.gov (United States)

    Song, Jung Hun (Kevin)

    Recent developments in colloidal assembly have led to novel fabrication techniques for nano- and microscopic materials of interest to many fields of science and engineering. The design of more complex processes and applications requires a greater variety of versatile preparation techniques. In this thesis, we present the application of Template-Assisted Materials Engineering (TAME) to obtain porous polymeric materials using various types of colloids and explore potential applications of the resulting porous materials. TAME is used to fabricate three-dimensional (3D) colloidal assemblies within geometric confinement. Further, we show that TAME can be used as a secondary template to form porous polymeric materials retaining the shape of the templating confinement. Advantages of utilizing TAME in colloidal assembly are the precise positioning and sizing of colloidal assemblies. For porous materials, advantages include control over pore size and distribution, porosity, shape, and materials. Building on these advantages, the TAME technique is employed to fabricate multi-sectional porous polymeric fibers with controlled sections of varying pore structure and is subsequently extended to synthesizing a multi-stage catalytic membrane reactor using catalyst-coated, surface-anisotropic colloids. Further, the versatility of the TAME approach is illustrated by applying it to the fabrication of macroscopic, porous materials using a biodegradable polymer and PDMS. Last but not least, TAME is applied to assemble 3D colloidal crystals for the study of photonic properties using fluorescently tagged and novel, magnetically enhanced colloids. Overall, TAME is shown to be a versatile, yet precise fabrication technique that can be employed in the preparation of materials for a wide range of applications. In addition, the intrinsic control over the colloidal assembly and the resulting porous materials make TAME an effective and efficient method for obtaining functional 3D materials.

  17. Power budget analysis of dual/single feeder fiber WDMPON

    Science.gov (United States)

    Imtiaz, Waqas A.; Khan, Yousaf; Qamar, Affaq; Khan, Jehanzeb; Khan, Noaman Ahmed

    2014-03-01

    This paper investigates how to reduce the cost of wavelength division multiplexing passive optical network (WDMPON) by comparing the transmission performance of bidirectional single feeder fiber and dual feeder fiber. Comparison is performed on the basis of power budgeting and cost of both arrangements. Simulation results using Optisystem show that the performance of a single feeder fiber is almost equivalent to that of a dual feeder fiber. Therefore, the single feeder fiber WDM-PON can efficiently replace the dual feeder fiber WDM-PON with the minimum deterioration in system performance and reduction in cost.

  18. Single channel analysis of membrane proteins in artificial bilayer membranes.

    Science.gov (United States)

    Bartsch, Philipp; Harsman, Anke; Wagner, Richard

    2013-01-01

    The planar lipid bilayer technique is a powerful experimental approach for electrical single channel recordings of pore-forming membrane proteins in a chemically well-defined and easily modifiable environment. Here we provide a general survey of the basic materials and procedures required to set up a robust bilayer system and perform electrophysiological single channel recordings of reconstituted proteins suitable for the in-depth characterization of their functional properties.

  19. Shot Noise Thermometry for Thermal Characterization of Templated Carbon Nanotubes

    OpenAIRE

    Sayer, Robert A; Kim, Sunkook; Franklin, Aaron D; Mohammadi, Saeed; Fisher, Timothy

    2010-01-01

    A carbon nanotube (CNT) thermometer that operates on the principles of electrical shot noise is reported. Shot noise thermometry is a self-calibrating measurement technique that relates statistical fluctuations in dc current across a device to temperature. A structure consisting of vertical, top, and bottom-contacted single-walled carbon nanotubes in a porous anodic alumina template was fabricated and used to measure shot noise. Frequencies between 60 and 100 kHz were observed to preclude sig...

  20. Template-Directed Olefin Cross Metathesis

    OpenAIRE

    Cantrill, Stuart J.; Grubbs, Robert H.; Lanari, Daniela; Leung, Ken C.-F.; Nelson, Alshakim; Poulin-Kerstien, Katherine G.; Smidt, Sebastian P.; Stoddart, J. Fraser; Tirrell, David A.

    2005-01-01

    A template containing two secondary dialkylammonium ion recognition sites for encirclement by olefin-bearing dibenzo[24]crown-8 derivatives has been used to promote olefin cross metatheses with ruthenium-alkylidene catalysts. For monoolefin monomers, the rates of metatheses and yields of the dimers are both amplified in the presence of the template. Likewise, for a diolefin monomer, the yield of the dimer is enhanced in the presence of the template under conditions where higher oligomers are ...

  1. Vertical Carbon Nanotube Device in Nanoporous Templates

    Science.gov (United States)

    Maschmann, Matthew Ralph (Inventor); Fisher, Timothy Scott (Inventor); Sands, Timothy (Inventor); Bashir, Rashid (Inventor)

    2014-01-01

    A modified porous anodic alumina template (PAA) containing a thin CNT catalyst layer directly embedded into the pore walls. CNT synthesis using the template selectively catalyzes SWNTs and DWNTs from the embedded catalyst layer to the top PAA surface, creating a vertical CNT channel within the pores. Subsequent processing allows for easy contact metallization and adaptable functionalization of the CNTs and template for a myriad of applications.

  2. DNA-templated assembly of nanoscale architectures

    Science.gov (United States)

    Stanca, Sarmiza Elena; Ongaro, Andrea; Eritja, Ramon; Fitzmaurice, Donald

    2005-09-01

    The assembly and detailed structural characterization of a Y-shaped DNA template incorporating a central biotin moiety is reported. Also reported is the use of this template to assemble a model protein-functionalized three-electrode architecture. Of particular significance is the finding that a biotin-modified nanoparticle will recognize and selectively bind the central biotin moiety, once functionalized by the protein streptavidin. Potential applications of the above and related DNA templates in the emerging field of nanoelectronics are considered.

  3. Single-site robotic cholecystectomy: efficiency and cost analysis.

    Science.gov (United States)

    Buzad, Francis A; Corne, Louis M; Brown, Thomas C; Fagin, Randy S; Hebert, April E; Kaczmarek, Charles A; Pack, Angie N; Payne, Thomas N

    2013-09-01

    Single-incision surgery has gained in popularity, and the recent development of specialized robotic and laparoscopic instruments may remove some of the ergonomic and technical difficulties associated with this approach. However, questions of cost and efficiency remain. We prospectively collected perioperative outcome and efficiency (operative time, case volume) data for our single-site robotic cholecystectomy cases and retrospectively reviewed data for our single-incision laparoscopic cholecystectomy cases. There were no differences in patient characteristics or perioperative outcomes between the robotic (n = 20) and laparoscopic (n = 10) groups; operative times were equivalent (84.6 vs 85.5 min; p = 0.8737) and blood loss and complications were minimal. There was a higher robotic case volume, with an average of two robotic cases (range 1-4)/day vs one/day for laparoscopic cases (range 1-1; p = 0.0306). Streamlined instrument costs were essentially equivalent. Robotic single-site cholecystectomy is a safe, cost-effective alternative to single-incision laparoscopic cholecystectomy in a robot-existing model. Copyright © 2013 John Wiley & Sons, Ltd.

  4. Templated Dry Printing of Conductive Metal Nanoparticles

    Science.gov (United States)

    Rolfe, David Alexander

    Printed electronics can lower the cost and increase the ubiquity of electrical components such as batteries, sensors, and telemetry systems. Unfortunately, the advance of printed electronics has been held back by the limited minimum resolution, aspect ratio, and feature fidelity of present printing techniques such as gravure, screen printing and inkjet printing. Templated dry printing offers a solution to these problems by patterning nanoparticle inks into templates before drying. This dissertation shows advancements in two varieties of templated dry nanoprinting. The first, advective micromolding in vapor-permeable templates (AMPT) is a microfluidic approach that uses evaporation-driven mold filling to create submicron features with a 1:1 aspect ratio. We will discuss submicron surface acoustic wave (SAW) resonators made through this process, and the refinement process in the template manufacturing process necessary to make these devices. We also present modeling techniques that can be applied to future AMPT templates. We conclude with a modified templated dry printing that improves throughput and isolated feature patterning by transferring dry-templated features with laser ablation. This method utilizes surface energy-defined templates to pattern features via doctor blade coating. Patterned and dried features can be transferred to a polymer substrate with an Nd:YAG MOPA fiber laser, and printed features can be smaller than the laser beam width.

  5. Influence of template fill in graphoepitaxy DSA

    Science.gov (United States)

    Doise, Jan; Bekaert, Joost; Chan, Boon Teik; Hong, SungEun; Lin, Guanyang; Gronheid, Roel

    2016-03-01

    Directed self-assembly (DSA) of block copolymers (BCP) is considered a promising patterning approach for the 7 nm node and beyond. Specifically, a grapho-epitaxy process using a cylindrical phase BCP may offer an efficient solution for patterning randomly distributed contact holes with sub-resolution pitches, such as found in via and cut mask levels. In any grapho-epitaxy process, the pattern density impacts the template fill (local BCP thickness inside the template) and may cause defects due to respectively over- or underfilling of the template. In order to tackle this issue thoroughly, the parameters that determine template fill and the influence of template fill on the resulting pattern should be investigated. In this work, using three process flow variations (with different template surface energy), template fill is experimentally characterized as a function of pattern density and film thickness. The impact of these parameters on template fill is highly dependent on the process flow, and thus pre-pattern surface energy. Template fill has a considerable effect on the pattern transfer of the DSA contact holes into the underlying layer. Higher fill levels give rise to smaller contact holes and worse critical dimension uniformity. These results are important towards DSA-aware design and show that fill is a crucial parameter in grapho-epitaxy DSA.

  6. Mesoporous carbon prepared from carbohydrate as hard template for hierarchical zeolites

    DEFF Research Database (Denmark)

    Egeblad, Kresten; Christensen, Claus H.

    2007-01-01

    treatment of a mixture of sucrose and ammonia followed by carbonization of the mixture in N-2 at high temperatures. The porous carbon produced by this method was subsequently applied as a hard template in the synthesis of mesoporous silicalite-1 and removed by combustion after synthesis. X-ray diffraction......A mesoporous carbon prepared from sucrose was successfully employed as a hard template to produce hierarchical silicalite-1, thus providing a very simple and inexpensive route to desirable zeolite catalysts from widely available raw materials. The porous carbon was prepared by hydrothermal...... the porous carbon template as well as the mesoporous zeolite single-crystal material....

  7. Colloid-templated multisectional porous polymeric fibers.

    Science.gov (United States)

    Song, Jung Hun; Kretzschmar, Ilona

    2008-10-07

    A fabrication method for porous polymeric fibers (PPFs) is reported. We show that a multisectional colloidal crystal can be assembled within a microcapillary by alternating dipping into colloidal solutions of varying size. Subsequent infiltration with curable polymer and washing with suitable solvents results in porous fibers with a cylindrical cross section. Along the length of the fiber, alternating sections of controlled length, pore size, and pore size distribution exist. These fibers present interesting materials for neural scaffolding, catalysis, and possibly photonics if produced with a high degree of crystallinity. The surface pores and bulk porosity of the fibers are characterized by variable-pressure scanning electron microscopy (vp-SEM). Careful analysis shows that the surface pores vary with the colloidal template diameter and polymer infiltration time.

  8. Single-sweep spectral analysis of contact heat evoked potentials

    DEFF Research Database (Denmark)

    Hansen, Tine M; Graversen, Carina; Frøkjaer, Jens B

    2015-01-01

    AIMS: The cortical response to nociceptive thermal stimuli recorded as contact heat evoked potentials (CHEPs) may be altered by morphine. However, previous studies have averaged CHEPs over multiple stimuli, which are confounded by jitter between sweeps. Thus, the aim was to assess single-sweep ch...

  9. Simulation and analysis of single-ribosome translation

    International Nuclear Information System (INIS)

    Tinoco, Ignacio Jr; Wen, Jin-Der

    2009-01-01

    In the cell, proteins are synthesized by ribosomes in a multi-step process called translation. The ribosome translocates along the messenger RNA to read the codons that encode the amino acid sequence of a protein. Elongation factors, including EF-G and EF-Tu, are used to catalyze the process. Recently, we have shown that translation can be followed at the single-molecule level using optical tweezers; this technique allows us to study the kinetics of translation by measuring the lifetime the ribosome spends at each codon. Here, we analyze the data from single-molecule experiments and fit the data with simple kinetic models. We also simulate the translation kinetics based on a multi-step mechanism from ensemble kinetic measurements. The mean lifetimes from the simulation were consistent with our experimental single-molecule measurements. We found that the calculated lifetime distributions were fit in general by equations with up to five rate-determining steps. Two rate-determining steps were only obtained at low concentrations of elongation factors. These analyses can be used to design new single-molecule experiments to better understand the kinetics and mechanism of translation

  10. Discrete dislocation plasticity analysis of single slip tension

    NARCIS (Netherlands)

    Deshpande, VS; Needleman, A; Van der Giessen, E

    2005-01-01

    The effect of loading conditions on the tensile stress versus strain response of micron-sized planar crystals with a single active slip system is investigated via finite and small deformation discrete dislocation plasticity analyses. When rotation of the tensile axis is prevented, lattice curvature

  11. Biomechanical analysis of the single-leg decline squat

    NARCIS (Netherlands)

    Zwerver, J.; Bredeweg, S. W.; Hof, A. L.

    Background: The single-leg squat on a 25 decline board has been described as a clinical assessment tool and as a rehabilitation exercise for patients with patellar tendinopathy. Several assumptions have been made about its working mechanism on patellar load and patellofemoral forces, but these are

  12. Single-cell Analysis of Lambda Immunity Regulation

    DEFF Research Database (Denmark)

    Bæk, Kristoffer Torbjørn; Svenningsen, Sine Lo; Eisen, Harvey

    2003-01-01

    We have examined expression of the ¿cI operon in single cells via a rexgfp substitution. Although average fluorescence agreed with expectations for expression of ¿-repressor, fluorescence fluctuated greatly from cell-to-cell. Fluctuations in repressor concentration are not predicted by previous m...

  13. Comparison between the standard SPM2 template and Korean-standard template in FDG-PET

    International Nuclear Information System (INIS)

    Kim, Jung Hee; Lee, Byeong Il; Song, Ho Chun; Min, Jung Joon; Bom, Hee Seung; Lee, Jae Sung

    2005-01-01

    The preprocessing step of statistical parametric mapping (SPM) requires the procedure of spatial normalization that consists of applying the nonlinear deformations needed to force every particular PET scan to match a reference template. The purpose of this study is to asses the statistic influence of using 2 different templates (the standard SPM2-PET template and Korean-standard PET template) in the normalization. We compared the regional metabolic patterns on 18F-FDG (fluorodeoxyglucose) images obtained from 4 patients with Alzheimers disease (AD) and 16 normal subjects. The statistical outcome of between- group comparison was analyzed with SPM2 and was applied into two levels of thresholds (an uncorrected P value of P <0.001, a corrected P value of P < 0.05). As a result, the most significant hypometabolic region was commonly found in the left temporal gyrus regardless of template type or thresholds. However, inconsistent results including different extent and the t-score statistics representing metabolic changes could be also observed between two templates. While the standard SPM2 template showed hypometabolic regions corresponding to Brodman area (BA) 7 and 9, Korean-standard template was not observed these regions. In addition, hypometabolic regions corresponding to BA 38 and 46 indicated not the standard SPM2 template but Korean-standard template. Statistic result showed that the standard SPM2 template effectively reflects the dorsal region of the brain while Korean-standard template is more sensitive to the medial region of the brain

  14. Computational resources to filter gravitational wave data with P-approximant templates

    International Nuclear Information System (INIS)

    Porter, Edward K

    2002-01-01

    The prior knowledge of the gravitational waveform from compact binary systems makes matched filtering an attractive detection strategy. This detection method involves the filtering of the detector output with a set of theoretical waveforms or templates. One of the most important factors in this strategy is knowing how many templates are needed in order to reduce the loss of possible signals. In this study, we calculate the number of templates and computational power needed for a one-step search for gravitational waves from inspiralling binary systems. We build on previous works by first expanding the post-Newtonian waveforms to 2.5-PN order and second, for the first time, calculating the number of templates needed when using P-approximant waveforms. The analysis is carried out for the four main first-generation interferometers, LIGO, GEO600, VIRGO and TAMA. As well as template number, we also calculate the computational cost of generating banks of templates for filtering GW data. We carry out the calculations for two initial conditions. In the first case we assume a minimum individual mass of 1 M o-dot and in the second, we assume a minimum individual mass of 5 M o-dot . We find that, in general, we need more P-approximant templates to carry out a search than if we use standard PN templates. This increase varies according to the order of PN-approximation, but can be as high as a factor of 3 and is explained by the smaller span of the P-approximant templates as we go to higher masses. The promising outcome is that for 2-PN templates, the increase is small and is outweighed by the known robustness of the 2-PN P-approximant templates

  15. A new route of synthesizing perovskite nanotubes by templating approach

    Science.gov (United States)

    Habiballah, Anisah Shafiqah; Osman, Nafisah; Jani, Abdul Mutalib Md

    2017-09-01

    A perovskite oxide for example Ba0.5Sr0.5Co0.8Fe0.2O3-δ (BSCF) has attracted growing attention due to its high catalytic activity and mixed ionic/electronic conductivity. Recent research of BSCF is more comprehensively based on a remarkable trajectory of innovation, in particular with regards to the synthesis of perovskite structures in one-dimensional (1-D) nanometric scales as they promote not only to increase an active electrode area for the oxygen reduction reaction, but also allow the tailoring of electrode's architecture. Nevertheless, achieving the desired 1-D structure by a conventional method such as hydrothermal, solvothermal, or sonochemical are far from satisfactory. Herein, the aim of this work is to synthesize the BSCF perovskite nanotubes via soft templating approach, particularly using anodic aluminium oxide (AAO) as a template, focusing on the morphology, composition and structural properties were demonstrated. After the AAO template was anodized at 80 V, the fabricated template was clamped between apair of spectroscopic cells containing BSCF sol and deionized water (with a hole of both sides) for 24 hours. After that, the sample was removed from the cells followed by heat treatment process. The FESEM images showed that BSCF nanotubes were successfully achieved, with the diameter of the nanotubes' approximately 80 nm. The EDX result also confirmed the nominal stoichiometry of Ba0.5Sr0.5Co0.8Fe0.2O3-δ. Meanwhile, the XRD pattern confirmed a single crystalline phase of BSCF nanotubes was successfully obtained and congruent to a cubic perovskite structure of BSCF. Possible formation mechanism,as well as the schematic illustration of BSCF nanotubes inside the template was also discussed in this paper.

  16. Single particle and molecular assembly analysis of polyribosomes by single- and double-tilt cryo electron tomography

    Energy Technology Data Exchange (ETDEWEB)

    Myasnikov, Alexander G. [IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Department of Integrative Structural Biology, Centre National de la Recherche Scientifique (CNRS) UMR 7104/ Institut National de la Santé de la Recherche Médicale INSERM U964/ Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch (France); Afonina, Zhanna A. [Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region (Russian Federation); Klaholz, Bruno P., E-mail: klaholz@igbmc.fr [IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Department of Integrative Structural Biology, Centre National de la Recherche Scientifique (CNRS) UMR 7104/ Institut National de la Santé de la Recherche Médicale INSERM U964/ Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch (France)

    2013-03-15

    Cryo electron tomography (cryo-ET) can provide cellular and molecular structural information on various biological samples. However, the detailed interpretation of tomograms reconstructed from single-tilt data tends to suffer from low signal-to-noise ratio and artefacts caused by some systematically missing angular views. While these can be overcome by sub-tomogram averaging, they remain limiting for the analysis of unique structures. Double-tilt ET can improve the tomogram quality by acquiring a second tilt series after an in-plane rotation, but its usage is not widespread yet because it is considered technically demanding and it is rarely used under cryo conditions. Here we show that double-tilt cryo-ET improves the quality of 3D reconstructions so significantly that even single particle analysis can be envisaged despite of the intrinsically low image contrast obtained from frozen-hydrated specimens. This is illustrated by the analysis of eukaryotic polyribosomes in which individual ribosomes were reconstructed using single-tilt, partial and full double-tilt geometries. The improved tomograms favour the faster convergence of iterative sub-tomogram averaging and allow a better 3D classification using multivariate statistical analysis. Our study of single particles and molecular assemblies within polysomes illustrates that the dual-axis approach is particularly useful for cryo applications of ET, both for unique objects and for structures that can be classified and averaged. - Highlights: ► Double-tilt cryo-ET improves 3D reconstructions thus making single particle analysis possible. ► Dual-axis cryo-ET data favour a faster convergence of iterative sub-tomogram averaging. ► Individual ribosomes were reconstructed from single-tilt, partial/ full double-tilt geometries. ► Double-tilt cryo-ET facilitates analysis of larger molecular assemblies such as in cell sections. ► Dual-axis cryo-ET is applicable to unique objects and to structures that can be

  17. Intersection tests for single marker QTL analysis can be more powerful than two marker QTL analysis

    Directory of Open Access Journals (Sweden)

    Doerge RW

    2003-06-01

    Full Text Available Abstract Background It has been reported in the quantitative trait locus (QTL literature that when testing for QTL location and effect, the statistical power supporting methodologies based on two markers and their estimated genetic map is higher than for the genetic map independent methodologies known as single marker analyses. Close examination of these reports reveals that the two marker approaches are more powerful than single marker analyses only in certain cases. Simulation studies are a commonly used tool to determine the behavior of test statistics under known conditions. We conducted a simulation study to assess the general behavior of an intersection test and a two marker test under a variety of conditions. The study was designed to reveal whether two marker tests are always more powerful than intersection tests, or whether there are cases when an intersection test may outperform the two marker approach. We present a reanalysis of a data set from a QTL study of ovariole number in Drosophila melanogaster. Results Our simulation study results show that there are situations where the single marker intersection test equals or outperforms the two marker test. The intersection test and the two marker test identify overlapping regions in the reanalysis of the Drosophila melanogaster data. The region identified is consistent with a regression based interval mapping analysis. Conclusion We find that the intersection test is appropriate for analysis of QTL data. This approach has the advantage of simplicity and for certain situations supplies equivalent or more powerful results than a comparable two marker test.

  18. Polymeric Bicontinuous Microemulsions as Templates for Nanostructured Materials

    Science.gov (United States)

    Jones, Brad Howard

    nanoporous materials with well-defined pore structures prepared from a single PE template. They are anticipated to have potential application in diverse technological areas, including catalysis, separations, sensors, and electronic devices.

  19. Raman analysis of gold on WSe2 single crystal film

    International Nuclear Information System (INIS)

    Mukherjee, Bablu; Sun Leong, Wei; Li, Yida; Thong, John T L; Gong, Hao; Sun, Linfeng; Xiang Shen, Ze; Simsek, Ergun

    2015-01-01

    Synthesis and characterization of high-quality single-crystal tungsten diselenide (WSe 2 ) films on a highly insulating substrate is presented. We demonstrate for the first time that the presence of gold (Au) nanoparticles in the basal plane of a WSe 2 film can enhance its Raman scattering intensity. The experimentally observed enhancement ratio in the Raman signal correlates well with the simulated electric field intensity using both three-dimensional electromagnetic software and theoretical calculation considering layered medium coupled-dipole approximation (LM-CDA). This work serves as a guideline for the use of Au nanoparticles on WSe 2 single-crystal thin films for surface enhanced Raman scattering (SERS) applications in the future. (paper)

  20. Glycan family analysis for deducing N-glycan topology from single MS

    OpenAIRE

    Goldberg, David; Bern, Marshall; North, Simon J.; Haslam, Stuart M.; Dell, Anne

    2008-01-01

    Motivation: In the past few years, mass spectrometry (MS) has emerged as the premier tool for identification and quantification of biological molecules such as peptides and glycans. There are two basic strategies: single-MS, which uses a single round of mass analysis, and MS/MS (or higher order MSn), which adds one or more additional rounds of mass analysis, interspersed with fragmentation steps. Single-MS offers higher throughput, broader mass coverage and more direct quantitation, but gener...

  1. Applications of heavy ion microprobe for single event effects analysis

    International Nuclear Information System (INIS)

    Reed, Robert A.; Vizkelethy, Gyorgy; Pellish, Jonathan A.; Sierawski, Brian; Warren, Kevin M.; Porter, Mark; Wilkinson, Jeff; Marshall, Paul W.; Niu, Guofu; Cressler, John D.; Schrimpf, Ronald D.; Tipton, Alan; Weller, Robert A.

    2007-01-01

    The motion of ionizing-radiation-induced rogue charge carriers in a semiconductor can create unwanted voltage and current conditions within a microelectronic circuit. If sufficient unwanted charge or current occurs on a sensitive node, a variety of single event effects (SEEs) can occur with consequences ranging from trivial to catastrophic. This paper describes the application of heavy ion microprobes to assist with calibration and validation of SEE modeling approaches

  2. Surgical Templates for Dental Implant Positioning; Current ...

    African Journals Online (AJOL)

    also dictates to the surgeon about the implant body placement that offers the best ... surgical template. The requirements are more relevant than the. Surgical Templates for Dental Implant Positioning;. Current Knowledge and Clinical Perspectives. Mohammed Zaheer Kola ..... A risk of damage to vital anatomical structures.

  3. Surgical Templates for Dental Implant Positioning; Current ...

    African Journals Online (AJOL)

    to the surgeon the implant body placement that offers the best combination of (1) support for the repetitive forces of occlusion, (2) esthetics, (3) hygiene requirements.[2,3]. Literature evidenced various methods of fabrication for the surgical template. The requirements are more relevant than the. Surgical Templates for Dental ...

  4. Screening for templates that promote crystallization

    NARCIS (Netherlands)

    Urbanus, J.; Roelands, C.P.M.; Horst, J.H. ter; Verdoes, D.; Jansens, P.J.

    2008-01-01

    In Situ Product Recovery (ISPR) applied in fermentation processes leads to improved yield and productivity of these processes. In principle, ISPR can be achieved using Template Induced Crystallization (TIC), which is one possible ISPR technique. With TIC, templates are added to the solution as a

  5. Template-less surfactant-free hydrothermal synthesis NiO nanoflowers and their photoelectrochemical hydrogen production

    KAUST Repository

    Qurashi, Ahsanulhaq

    2015-12-01

    A facile direct surfactant-free template-less hydrothermal method is employed for the growth of high surface-area NiO nanoflowers made up of complex and assembled nanosheets network.Field emission scanning electron microscopy revealed that each nanosheet is about 50-60nm thick. Detailed structural analysis reveals single-crystalline nature of NiO nanoflowers with cubic crystal structure. The optical absorption bands in the wavelength range of 350-800nm illustrated in terms of ligand field theory. The photoelectrochemical (PEC), water splitting performance on the NiO nanoflowers were also investigated. © 2015 Hydrogen Energy Publications, LLC.

  6. [Low template DNA profiling and its application in forensic science].

    Science.gov (United States)

    Ma, Yan; Kuang, Jin-zhi; Hou, Yi-ping

    2010-04-01

    Low template DNA (LTDNA) has been widely applied in the field of forensic science in recent years. However, the application of low copy number(LCN) analysis is still controversial in certain forensic. This paper focus on the definition of LCN and LTDNA, casework because of its inherent limiting factors. the validity and application of LCN in forensic science, methods of typing, quality control, replicate analysis, detection thresholds and then reviews the latest development of LCN in forensic science.

  7. 2D vector-cyclic deformable templates

    DEFF Research Database (Denmark)

    Schultz, Nette; Conradsen, Knut

    1998-01-01

    In this paper the theory of deformable templates is a vector cycle in 2D is described. The deformable template model originated in (Grenander, 1983) and was further investigated in (Grenander et al., 1991). A template vector distribution is induced by parameter distribution from transformation...... matrices applied to the vector cycle. An approximation in the parameter distribution is introduced. The main advantage by using the deformable template model is the ability to simulate a wide range of objects trained by e.g. their biological variations, and thereby improve restoration, segmentation...... and probabillity measurement. The case study concerns estimation of meat percent in pork carcasses. Given two cross-sectional images - one at the front and one near the ham of the carcass - the areas of lean and fat and a muscle in the lean area are measured automatically by the deformable templates....

  8. [The template principle: paradigm of modern genetics].

    Science.gov (United States)

    Inge-Vechtomov, S G

    2013-01-01

    The idea of continuity in living systems, which was initially developed in mid-19th century, reached its peak in 1928 thanks to N.K. Koltsov, who proposed the template principle in chromosome reproduction. The determination of genetic functions of nucleic acids and the advent of molecular genetics led to F. Crick's statement of the central dogma of molecular biology in 1958. This dogma became a contemporary version of the template principle (templates of the first order). The discovery of "protein inheritance" underlay the notion of steric or conformational templates (second order) for reproducing conformation in a number of proteins. The template principle supplemented by this notion claims to be the main paradigm of modern genetics.

  9. Template Assembly for Detailed Urban Reconstruction

    KAUST Repository

    Nan, Liangliang

    2015-05-04

    We propose a new framework to reconstruct building details by automatically assembling 3D templates on coarse textured building models. In a preprocessing step, we generate an initial coarse model to approximate a point cloud computed using Structure from Motion and Multi View Stereo, and we model a set of 3D templates of facade details. Next, we optimize the initial coarse model to enforce consistency between geometry and appearance (texture images). Then, building details are reconstructed by assembling templates on the textured faces of the coarse model. The 3D templates are automatically chosen and located by our optimization-based template assembly algorithm that balances image matching and structural regularity. In the results, we demonstrate how our framework can enrich the details of coarse models using various data sets.

  10. Chinese license plate character segmentation using multiscale template matching

    Science.gov (United States)

    Tian, Jiangmin; Wang, Guoyou; Liu, Jianguo; Xia, Yuanchun

    2016-09-01

    Character segmentation (CS) plays an important role in automatic license plate recognition and has been studied for decades. A method using multiscale template matching is proposed to settle the problem of CS for Chinese license plates. It is carried out on a binary image integrated from maximally stable extremal region detection and Otsu thresholding. Afterward, a uniform harrow-shaped template with variable length is designed, by virtue of which a three-dimensional matching space is constructed for searching of candidate segmentations. These segmentations are detected at matches with local minimum responses. Finally, the vertical boundaries of each single character are located for subsequent recognition. Experiments on a data set including 2349 license plate images of different quality levels show that the proposed method can achieve a higher accuracy at comparable time cost and is robust to images in poor conditions.

  11. DNA-Templated Introduction of an Aldehyde Handle in Proteins

    DEFF Research Database (Denmark)

    Kodal, Anne Louise Bank; Rosen, Christian Bech; Mortensen, Michael Rosholm

    2016-01-01

    Many medical and biotechnological applications rely on labeling of proteins, but one key challenge is the production of homogeneous and site-specific conjugates. This can rarely be achieved by mere residue-specific random labeling, but requires genetic engineering. Using site-selective DNA......-templated reductive amination we create DNA-protein conjugates with control over labeling stoichiometry without genetic engineering. A guiding DNA strand with a metal-binding functionality facilitates site-selectivity by directing coupling of a second reactive DNA strand to the vicinity of a protein metal......-binding site. Here, we demonstrate DNA-templated reductive amination for His6-tagged proteins and native metal-binding proteins, including IgG1 antibodies. We also use a cleavable linker between the DNA and the protein to remove the DNA and introduce a single aldehyde to proteins. This functions as a handle...

  12. Highly tailorable thiol-ene based emulsion-templated monoliths

    DEFF Research Database (Denmark)

    Lafleur, J. P.; Kutter, J. P.

    2014-01-01

    The attractive surface properties of thiol-ene polymers combined with their ease of processing make them ideal substrates in many bioanalytical applications. We report the synthesis of highly tailorable emulsion-templated porous polymers and beads in microfluidic devices based on off-stoichiometr......The attractive surface properties of thiol-ene polymers combined with their ease of processing make them ideal substrates in many bioanalytical applications. We report the synthesis of highly tailorable emulsion-templated porous polymers and beads in microfluidic devices based on off......-stoichiometry thiolene chemistry. The method allows monolith synthesis and anchoring inside thiol-ene microchannels in a single step. Variations in the monomer stoichiometric ratios and/or amount of porogen used allow for the creation of extremely varied polymer morphologies, from foam-like materials to dense networks...

  13. Tailoring the porosity of hierarchical zeolites by carbon-templating

    DEFF Research Database (Denmark)

    Zhu, Kake; Egeblad, Kresten; Christensen, Claus H.

    2008-01-01

    We report the synthesis and characterization of a series of hierarchical porous zeolite single crystal materials with a range of porosities made available by carbon-templating using differently-sized carbon particles as templates for the additional non-micropore porosity. The materials were...... prepared by adsorption of the required zeolite synthesis gel components onto various commercially available carbon black powders followed by crystallization of the zeolite crystals in the presence of the inert carbon matrix and subsequent removal of the carbon particles embedded in the zeolite crystals...... by combustion. It is shown that the additional porosity of the hierarchical zeolites can be tailored by encapsulation of the differently-sized carbon particles during crystallization....

  14. A SCHEME FOR TEMPLATE SECURITY AT FEATURE FUSION LEVEL IN MULTIMODAL BIOMETRIC SYSTEM

    Directory of Open Access Journals (Sweden)

    Arvind Selwal

    2016-09-01

    Full Text Available Biometric is the science of human recognition based upon using their biological, chemical or behavioural traits. These systems are used in many real life applications simply from biometric based attendance system to providing security at very sophisticated level. A biometric system deals with raw data captured using a sensor and feature template extracted from raw image. One of the challenges being faced by designers of these systems is to secure template data extracted from the biometric modalities of the user and protect the raw images. To minimize spoof attacks on biometric systems by unauthorised users one of the solutions is to use multi-biometric systems. Multi-modal biometric system works by using fusion technique to merge feature templates generated from different modalities of the human. In this work a new scheme is proposed to secure template during feature fusion level. Scheme is based on union operation of fuzzy relations of templates of modalities during fusion process of multimodal biometric systems. This approach serves dual purpose of feature fusion as well as transformation of templates into a single secured non invertible template. The proposed technique is cancelable and experimentally tested on a bimodal biometric system comprising of fingerprint and hand geometry. Developed scheme removes the problem of an attacker learning the original minutia position in fingerprint and various measurements of hand geometry. Given scheme provides improved performance of the system with reduction in false accept rate and improvement in genuine accept rate.

  15. The role of the geophysical template and environmental regimes in controlling stream-living trout populations

    Science.gov (United States)

    Penaluna, Brooke E.; Railsback, Steve F.; Dunham, Jason B.; Johnson, S.; Bilby, Richard E.; Skaugset, Arne E.

    2015-01-01

    The importance of multiple processes and instream factors to aquatic biota has been explored extensively, but questions remain about how local spatiotemporal variability of aquatic biota is tied to environmental regimes and the geophysical template of streams. We used an individual-based trout model to explore the relative role of the geophysical template versus environmental regimes on biomass of trout (Oncorhynchus clarkii clarkii). We parameterized the model with observed data from each of the four headwater streams (their local geophysical template and environmental regime) and then ran 12 simulations where we replaced environmental regimes (stream temperature, flow, turbidity) of a given stream with values from each neighboring stream while keeping the geophysical template fixed. We also performed single-parameter sensitivity analyses on the model results from each of the four streams. Although our modeled findings show that trout biomass is most responsive to changes in the geophysical template of streams, they also reveal that biomass is restricted by available habitat during seasonal low flow, which is a product of both the stream’s geophysical template and flow regime. Our modeled results suggest that differences in the geophysical template among streams render trout more or less sensitive to environmental change, emphasizing the importance of local fish–habitat relationships in streams.

  16. Tools for Genomic and Transcriptomic Analysis of Microbes at Single-Cell Level

    Directory of Open Access Journals (Sweden)

    Zixi Chen

    2017-09-01

    Full Text Available Microbiologists traditionally study population rather than individual cells, as it is generally assumed that the status of individual cells will be similar to that observed in the population. However, the recent studies have shown that the individual behavior of each single cell could be quite different from that of the whole population, suggesting the importance of extending traditional microbiology studies to single-cell level. With recent technological advances, such as flow cytometry, next-generation sequencing (NGS, and microspectroscopy, single-cell microbiology has greatly enhanced the understanding of individuality and heterogeneity of microbes in many biological systems. Notably, the application of multiple ‘omics’ in single-cell analysis has shed light on how individual cells perceive, respond, and adapt to the environment, how heterogeneity arises under external stress and finally determines the fate of the whole population, and how microbes survive under natural conditions. As single-cell analysis involves no axenic cultivation of target microorganism, it has also been demonstrated as a valuable tool for dissecting the microbial ‘dark matter.’ In this review, current state-of-the-art tools and methods for genomic and transcriptomic analysis of microbes at single-cell level were critically summarized, including single-cell isolation methods and experimental strategies of single-cell analysis with NGS. In addition, perspectives on the future trends of technology development in the field of single-cell analysis was also presented.

  17. Chip based single cell analysis for nanotoxicity assessment.

    Science.gov (United States)

    Shah, Pratikkumar; Kaushik, Ajeet; Zhu, Xuena; Zhang, Chengxiao; Li, Chen-Zhong

    2014-05-07

    Nanomaterials, because of their tunable properties and performances, have been utilized extensively in everyday life related consumable products and technology. On exposure, beyond the physiological range, nanomaterials cause health risks via affecting the function of organisms, genomic systems, and even the central nervous system. Thus, new analytical approaches for nanotoxicity assessment to verify the feasibility of nanomaterials for future use are in demand. The conventional analytical techniques, such as spectrophotometric assay-based techniques, usually require a lengthy and time-consuming process and often produce false positives, and often cannot be implemented at a single cell level measurement for studying cell behavior without interference from its surrounding environment. Hence, there is a demand for a precise, accurate, sensitive assessment for toxicity using single cells. Recently, due to the advantages of automation of fluids and minimization of human errors, the integration of a cell-on-a-chip (CoC) with a microfluidic system is in practice for nanotoxicity assessments. This review explains nanotoxicity and its assessment approaches with advantages/limitations and new approaches to overcome the confines of traditional techniques. Recent advances in nanotoxicity assessment using a CoC integrated with a microfluidic system are also discussed in this review, which may be of use for nanotoxicity assessment and diagnostics.

  18. Single-crystal neutron diffraction analysis in chemistry

    International Nuclear Information System (INIS)

    Hosoya, Takaaki; Ohhara, Takashi

    2010-01-01

    Single-crystal neutron diffraction technique is a powerful method to analyze the reaction mechanism whose hydrogen atom or proton has a key role in the reaction. Especially hydrogen atom or proton transfer(HT/PT) is one of the most elemental phenomena and often observed in many organic, inorganic, enzymatic and catalytic reactions. We describe several applications in chemistry. At first, hydrogen atom in metal hydride complexes, which is quite difficult to do using X-ray diffraction because of the great cloud of electrons of central metal atom. Secondary, hydrogen atom in hydrogen-bonding network, e.g., low-barrier hydrogen bond(LBHB) system. Neutron diffraction can refine the thermal motion of hydrogen atom. Finally, our results, photo-induced HT/PTs using 'deuterium atom labeling' technique and 'crystalline-state reaction' technique, which are currently developing applications. Despite the success illustrated by the many studies presented here or many other studies, we have many problems in using single-crystal neutron diffraction technique. For example, extremely limited flux and the requirement for mm-size sample crystals. Now, these limitations are being solved by the operation of powerful instruments at a new generation of pulsed neutron sources, including iBIX diffractometer running at Japan Proton Accelerator Research Complex(J-PARC) in Japan. (author)

  19. Template Interfaces for Agile Parallel Data-Intensive Science

    Energy Technology Data Exchange (ETDEWEB)

    2017-04-28

    Tigres provides a programming library to compose and execute large-scale data-intensive scientific workflows from desktops to supercomputers. DOE User Facilities and large science collaborations are increasingly generating large enough data sets that it is no longer practical to download them to a desktop to operate on them. They are instead stored at centralized compute and storage resources such as high performance computing (HPC) centers. Analysis of this data requires an ability to run on these facilities, but with current technologies, scaling an analysis to an HPC center and to a large data set is difficult even for experts. Tigres is addressing the challenge of enabling collaborative analysis of DOE Science data through a new concept of reusable "templates" that enable scientists to easily compose, run and manage collaborative computational tasks. These templates define common computation patterns used in analyzing a data set.

  20. Single-case research design in pediatric psychology: considerations regarding data analysis.

    Science.gov (United States)

    Cohen, Lindsey L; Feinstein, Amanda; Masuda, Akihiko; Vowles, Kevin E

    2014-03-01

    Single-case research allows for an examination of behavior and can demonstrate the functional relation between intervention and outcome in pediatric psychology. This review highlights key assumptions, methodological and design considerations, and options for data analysis. Single-case methodology and guidelines are reviewed with an in-depth focus on visual and statistical analyses. Guidelines allow for the careful evaluation of design quality and visual analysis. A number of statistical techniques have been introduced to supplement visual analysis, but to date, there is no consensus on their recommended use in single-case research design. Single-case methodology is invaluable for advancing pediatric psychology science and practice, and guidelines have been introduced to enhance the consistency, validity, and reliability of these studies. Experts generally agree that visual inspection is the optimal method of analysis in single-case design; however, statistical approaches are becoming increasingly evaluated and used to augment data interpretation.

  1. Analysis and meta-analysis of single-case designs: an introduction.

    Science.gov (United States)

    Shadish, William R

    2014-04-01

    The last 10 years have seen great progress in the analysis and meta-analysis of single-case designs (SCDs). This special issue includes five articles that provide an overview of current work on that topic, including standardized mean difference statistics, multilevel models, Bayesian statistics, and generalized additive models. Each article analyzes a common example across articles and presents syntax or macros for how to do them. These articles are followed by commentaries from single-case design researchers and journal editors. This introduction briefly describes each article and then discusses several issues that must be addressed before we can know what analyses will eventually be best to use in SCD research. These issues include modeling trend, modeling error covariances, computing standardized effect size estimates, assessing statistical power, incorporating more accurate models of outcome distributions, exploring whether Bayesian statistics can improve estimation given the small samples common in SCDs, and the need for annotated syntax and graphical user interfaces that make complex statistics accessible to SCD researchers. The article then discusses reasons why SCD researchers are likely to incorporate statistical analyses into their research more often in the future, including changing expectations and contingencies regarding SCD research from outside SCD communities, changes and diversity within SCD communities, corrections of erroneous beliefs about the relationship between SCD research and statistics, and demonstrations of how statistics can help SCD researchers better meet their goals. Copyright © 2013 Society for the Study of School Psychology. Published by Elsevier Ltd. All rights reserved.

  2. Classification using diffraction patterns for single-particle analysis

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Hongli; Zhang, Kaiming [Department of Biophysics, the Health Science Centre, Peking University, Beijing 100191 (China); Meng, Xing, E-mail: xmeng101@gmail.com [Wadsworth Centre, New York State Department of Health, Albany, New York 12201 (United States)

    2016-05-15

    An alternative method has been assessed; diffraction patterns derived from the single particle data set were used to perform the first round of classification in creating the initial averages for proteins data with symmetrical morphology. The test protein set was a collection of Caenorhabditis elegans small heat shock protein 17 obtained by Cryo EM, which has a tetrahedral (12-fold) symmetry. It is demonstrated that the initial classification on diffraction patterns is workable as well as the real-space classification that is based on the phase contrast. The test results show that the information from diffraction patterns has the enough details to make the initial model faithful. The potential advantage using the alternative method is twofold, the ability to handle the sets with poor signal/noise or/and that break the symmetry properties. - Highlights: • New classification method. • Create the accurate initial model. • Better in handling noisy data.

  3. Classification using diffraction patterns for single-particle analysis

    International Nuclear Information System (INIS)

    Hu, Hongli; Zhang, Kaiming; Meng, Xing

    2016-01-01

    An alternative method has been assessed; diffraction patterns derived from the single particle data set were used to perform the first round of classification in creating the initial averages for proteins data with symmetrical morphology. The test protein set was a collection of Caenorhabditis elegans small heat shock protein 17 obtained by Cryo EM, which has a tetrahedral (12-fold) symmetry. It is demonstrated that the initial classification on diffraction patterns is workable as well as the real-space classification that is based on the phase contrast. The test results show that the information from diffraction patterns has the enough details to make the initial model faithful. The potential advantage using the alternative method is twofold, the ability to handle the sets with poor signal/noise or/and that break the symmetry properties. - Highlights: • New classification method. • Create the accurate initial model. • Better in handling noisy data.

  4. The Analysis of Forming Forces in Single Point Incremental Forming

    Directory of Open Access Journals (Sweden)

    Koh Kyung Hee

    2016-01-01

    Full Text Available Incremental forming is a process to produce sheet metal parts in quick. Because there is no need for dedicated dies and molds, this process is less cost and time spent. The purpose of this study is to investigate forming forces in single point incremental forming. Producing a cone frustum of aluminum is tested for forming forces. A dynamometer is used to collect forming forces and analyze them. These forces are compared with cutting forces upon producing same geometrical shapes of experimental parts. The forming forces in Z direction are 40 times larger than the machining forces. A spindle and its axis of a forming machine should be designed enough to withstand the forming forces.

  5. Single-cell analysis of G-protein signal transduction.

    Science.gov (United States)

    Clister, Terri; Mehta, Sohum; Zhang, Jin

    2015-03-13

    The growing use of fluorescent biosensors to directly probe the spatiotemporal dynamics of biochemical processes in living cells has revolutionized the study of intracellular signaling. In this review, we summarize recent developments in the use of biosensors to illuminate the molecular details of G-protein-coupled receptor (GPCR) signaling pathways, which have long served as the model for our understanding of signal transduction, while also offering our perspectives on the future of this exciting field. Specifically, we highlight several ways in which biosensor-based single-cell analyses are being used to unravel many of the enduring mysteries that surround these diverse signaling pathways. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. BioAssay templates for the semantic web

    Directory of Open Access Journals (Sweden)

    Alex M. Clark

    2016-05-01

    Full Text Available Annotation of bioassay protocols using semantic web vocabulary is a way to make experiment descriptions machine-readable. Protocols are communicated using concise scientific English, which precludes most kinds of analysis by software algorithms. Given the availability of a sufficiently expressive ontology, some or all of the pertinent information can be captured by asserting a series of facts, expressed as semantic web triples (subject, predicate, object. With appropriate annotation, assays can be searched, clustered, tagged and evaluated in a multitude of ways, analogous to other segments of drug discovery informatics. The BioAssay Ontology (BAO has been previously designed for this express purpose, and provides a layered hierarchy of meaningful terms which can be linked to. Currently the biggest challenge is the issue of content creation: scientists cannot be expected to use the BAO effectively without having access to software tools that make it straightforward to use the vocabulary in a canonical way. We have sought to remove this barrier by: (1 defining a BioAssay Template (BAT data model; (2 creating a software tool for experts to create or modify templates to suit their needs; and (3 designing a common assay template (CAT to leverage the most value from the BAO terms. The CAT was carefully assembled by biologists in order to find a balance between the maximum amount of information captured vs. low degrees of freedom in order to keep the user experience as simple as possible. The data format that we use for describing templates and corresponding annotations is the native format of the semantic web (RDF triples, and we demonstrate some of the ways that generated content can be meaningfully queried using the SPARQL language. We have made all of these materials available as open source (http://github.com/cdd/bioassay-template, in order to encourage community input and use within diverse projects, including but not limited to our own

  7. The Digital Single Market and Legal Certainty : A Critical Analysis

    NARCIS (Netherlands)

    Castermans, A.G.; Graaff, de R.; Haentjens, M.; Colombi, Ciacchi A.

    2016-01-01

    This chapter critically examines the CESL from the viewpoint of its capability to provide legal certainty for commercial actors. This chapter’s analysis focuses on three important stages in the life cycle of a contract, seen from a business perspective: the scope rules that determine whether the

  8. Numerical Analysis of Hydrodynamic Flow in Microfluidic Biochip for Single-Cell Trapping Application

    Directory of Open Access Journals (Sweden)

    Amelia Ahmad Khalili

    2015-11-01

    Full Text Available Single-cell analysis has become the interest of a wide range of biological and biomedical engineering research. It could provide precise information on individual cells, leading to important knowledge regarding human diseases. To perform single-cell analysis, it is crucial to isolate the individual cells before further manipulation is carried out. Recently, microfluidic biochips have been widely used for cell trapping and single cell analysis, such as mechanical and electrical detection. This work focuses on developing a finite element simulation model of single-cell trapping system for any types of cells or particles based on the hydrodynamic flow resistance (Rh manipulations in the main channel and trap channel to achieve successful trapping. Analysis is carried out using finite element ABAQUS-FEA™ software. A guideline to design and optimize single-cell trapping model is proposed and the example of a thorough optimization analysis is carried out using a yeast cell model. The results show the finite element model is able to trap a single cell inside the fluidic environment. Fluid’s velocity profile and streamline plots for successful and unsuccessful single yeast cell trapping are presented according to the hydrodynamic concept. The single-cell trapping model can be a significant important guideline in designing a new chip for biomedical applications.

  9. Nanowires and nanostructures fabrication using template methods

    DEFF Research Database (Denmark)

    Mátéfi-Tempfli, Stefan; Mátéfi-Tempfli, M.; Vlad, A.

    2009-01-01

    One of the great challenges of today is to find reliable techniques for the fabrication of nanomaterials and nanostructures. Methods based on template synthesis and on self organization are the most promising due to their easiness and low cost. This paper focuses on the electrochemical synthesis...... of nanowires and nanostructures using nanoporous host materials such as supported anodic aluminum considering it as a key template for nanowires based devices. New ways are opened for applications by combining such template synthesis methods with nanolithographic techniques....

  10. Single Nucleotide Polymorphism Analysis of Protamine Genes in Infertile Men

    Directory of Open Access Journals (Sweden)

    Ahamad Salamian

    2008-01-01

    Full Text Available Background: Single nucleotide polymorphism (SNPs are considered as one of the underlyingcauses of male infertility. Proper sperm chromatin packaging which involves replacement ofhistones with protamines has profound effect on male fertility. Over 20 SNPs have been reportedfor the protamine 1 and 2.Materials and Methods: The aim of this study was to evaluate the frequency of two previouslyreported SNPs using polymerase chain reaction (PCR-restriction fragment length polymorphism(RFLP approach in 35, 96 and 177 normal, oligozoospermic and azoospermic individuals. TheseSNPs are: 1. A base pair substitution (G at position 197 instead of T in protamine type 1 Openreading frame (ORF including untranslated region, which causes an Arg residue change to Serresidue in a highly conserved region. 2. cytidine nucleotide change to thymidine in position of 248of protamine type 2 ORF which caused a nonsense point mutation.Results: The two mentioned SNPs were not present in the studied population, thus concluding thatthese SNPs can not serves as molecular markers for male infertility diagnosis.Conclusion: The results of our study reveal that in a selected Iranian population, the SNP G197Tand C248T are completely absent and are not associated with male infertility and therefore theseSNPs may not represent a molecular marker for genetic diagnosis of male infertility.

  11. Analysis of ripple formation in single crystal spot welds

    Energy Technology Data Exchange (ETDEWEB)

    Rappaz, M. [Ecole Polytechnique Federale de Lausanne (Switzerland). Lab de Metallurgie Physique; Corrigan, D.; Boatner, L.A. [Oak Ridge National Lab., TN (United States). Solid State Div.

    1997-10-01

    Stationary spot welds have been made at the (001) surface of Fe-l5%Ni-15%Cr single crystals using a Gas Tungsten Arc (GTA). On the top surface of the spot welds, very regular and concentric ripples were observed after solidification by differential interference color microscopy. Their height (typically 1--5 {micro}m) and spacing (typically {approximately} 60 {micro}m) decreased with the radius of the pool. These ripples were successfully accounted for in terms of capillary-wave theory using the fundamental mode frequency f{sub 0} given by the first zero of the zero-order Bessel function. The spacing d between the ripples was then equated to v{sub s}/f{sub 0}, where v{sub s} is the solidification rate. From the measured ripple spacing, the velocity of the pool was deduced as a function of the radius, and this velocity was in good agreement with the results of a heat-flow simulation.

  12. Exploring aphasic grammar. 1: A single case analysis of conversation.

    Science.gov (United States)

    Beeke, Suzanne; Wilkinson, Ray; Maxim, Jane

    2003-03-01

    This paper uses the methodology and analytical findings of conversation analysis to investigate the notion that aphasic grammar may be understood at least partly in the context of the demands of turns at talk in conversation. An investigation of the conversation of an English-speaking person with aphasia reveals two distinct grammatical phenomena, and it is suggested that their use may be interactionally motivated by the need to take a relatively unproblematic turn at talk despite the constraints of non-fluent aphasia. The grammatical patterns that are revealed by this analysis look considerably different from those elicited by standard methods of data sampling. The possibility that interactional grammatical phenomena are not visible in the language data elicited by clinical assessments is raised. This question is addressed via an in-depth comparison of the same speaker's interactional and elicited grammar in a linked article. It is suggested that the tool of conversation analysis provides researchers with a new and fruitful approach to the study of grammatical abilities in aphasia.

  13. Single-block rockfall dynamics inferred from seismic signal analysis

    Directory of Open Access Journals (Sweden)

    C. Hibert

    2017-05-01

    Full Text Available Seismic monitoring of mass movements can significantly help to mitigate the associated hazards; however, the link between event dynamics and the seismic signals generated is not completely understood. To better understand these relationships, we conducted controlled releases of single blocks within a soft-rock (black marls gully of the Rioux-Bourdoux torrent (French Alps. A total of 28 blocks, with masses ranging from 76 to 472 kg, were used for the experiment. An instrumentation combining video cameras and seismometers was deployed along the travelled path. The video cameras allow reconstructing the trajectories of the blocks and estimating their velocities at the time of the different impacts with the slope. These data are compared to the recorded seismic signals. As the distance between the falling block and the seismic sensors at the time of each impact is known, we were able to determine the associated seismic signal amplitude corrected for propagation and attenuation effects. We compared the velocity, the potential energy lost, the kinetic energy and the momentum of the block at each impact to the true amplitude and the radiated seismic energy. Our results suggest that the amplitude of the seismic signal is correlated to the momentum of the block at the impact. We also found relationships between the potential energy lost, the kinetic energy and the seismic energy radiated by the impacts. Thanks to these relationships, we were able to retrieve the mass and the velocity before impact of each block directly from the seismic signal. Despite high uncertainties, the values found are close to the true values of the masses and the velocities of the blocks. These relationships allow for gaining a better understanding of the physical processes that control the source of high-frequency seismic signals generated by rockfalls.

  14. X-ray diffraction analysis of some single crystals with special properties

    Energy Technology Data Exchange (ETDEWEB)

    Antipin, M.Yu. [Russian Academy of Sciences, Moscow (Russian Federation). Inst. of Organoelement Compounds

    1996-12-31

    New possibilities of the X-ray diffraction method for studies of some single crystals with special physical properties are analyzed. It is demonstrated that wide range temperature diffraction data, special single crystals experiments under strong electric fields, and charge density analysis in crystals might enrich the knowledge on the nature of the crystal properties.

  15. Quantitative Synthesis and Component Analysis of Single-Participant Studies on the Picture Exchange Communication System

    Science.gov (United States)

    Tincani, Matt; Devis, Kathryn

    2011-01-01

    The "Picture Exchange Communication System" (PECS) has emerged as the augmentative communication intervention of choice for individuals with autism spectrum disorder (ASD), with a supporting body of single-participant studies. This report describes a meta-analysis of 16 single-participant studies on PECS with percentage of nonoverlapping data…

  16. Toward Single Enzyme Analysis in a Droplet-based Micro and Nanofluidic Systems

    NARCIS (Netherlands)

    Arayanarakool, Rerngchai

    2012-01-01

    In this thesis, we demonstrate the application of a micro- and nanofluidic device for the single-enzyme analysis by encapsulating single enzymes into the generated aqueous droplets in oil. This thesis consists of the introduction (chapter 1), a review of the generation and manipulation of droplets

  17. Template for safety reports with descriptive example

    International Nuclear Information System (INIS)

    1995-12-01

    This report provides a template for future safety reports on long-term safety in support of important decisions and permit applications in connection with the construction of a deep repository system. The template aims at providing a uniform structure for describing long-term safety, after the repository has been closed and sealed. The availability of such a structure will simplify both preparation and review of the safety reports, and make it possible to follow how safety assessments are influenced by the progressively more detailed body of data that emerges. A separate section containing 'descriptive examples' has been appended to the template. This section illustrates what the different chapters of the template should contain. 279 refs

  18. Template for safety reports with descriptive example

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-12-01

    This report provides a template for future safety reports on long-term safety in support of important decisions and permit applications in connection with the construction of a deep repository system. The template aims at providing a uniform structure for describing long-term safety, after the repository has been closed and sealed. The availability of such a structure will simplify both preparation and review of the safety reports, and make it possible to follow how safety assessments are influenced by the progressively more detailed body of data that emerges. A separate section containing `descriptive examples` has been appended to the template. This section illustrates what the different chapters of the template should contain. 279 refs.

  19. Dazomet Fumigant Management Plan Phase 2 Templates

    Science.gov (United States)

    These templates provide a framework for reporting application block information, buffer zones, emergency response plan, tarp plan, soil conditions, air monitoring, and more for pesticide products containing the active ingredient dazomet, such as Basamid G.

  20. Template Approach for Adaptive Learning Strategies

    NARCIS (Netherlands)

    Abbing, Jana; Koidl, Kevin

    2006-01-01

    Please, cite this publication as: Abbing, J. & Koidl, K. (2006). Template Approach for Adaptive Learning Strategies. Proceedings of Adaptive Hypermedia. June, Dublin, Ireland. Retrieved June 30th, 2006, from http://dspace.learningnetworks.org

  1. Nucleic Acid Templated Reactions for Chemical Biology.

    Science.gov (United States)

    Di Pisa, Margherita; Seitz, Oliver

    2017-06-21

    Nucleic acid directed bioorthogonal reactions offer the fascinating opportunity to unveil and redirect a plethora of intracellular mechanisms. Nano- to picomolar amounts of specific RNA molecules serve as templates and catalyze the selective formation of molecules that 1) exert biological effects, or 2) provide measurable signals for RNA detection. Turnover of reactants on the template is a valuable asset when concentrations of RNA templates are low. The idea is to use RNA-templated reactions to fully control the biodistribution of drugs and to push the detection limits of DNA or RNA analytes to extraordinary sensitivities. Herein we review recent and instructive examples of conditional synthesis or release of compounds for in cellulo protein interference and intracellular nucleic acid imaging. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  2. Technical Support for the Active Templates Program

    National Research Council Canada - National Science Library

    Lafferty, Lawrence G; Lizza, Carl S

    2005-01-01

    The DARPA Active Templates (AcT) program was established to develop a scalable, simple, distributed software infrastructure for mission planning and execution, in essence, a kind of "spreadsheet" for planning, information monitoring...

  3. Essentials of single-cell analysis concepts, applications and future prospects

    CERN Document Server

    Santra, Tuhin

    2016-01-01

    This book provides an overview of single-cell isolation, separation, injection, lysis and dynamics analysis as well as a study of their heterogeneity using different miniaturized devices. As an important part of single-cell analysis, different techniques including electroporation, microinjection, optical trapping, optoporation, rapid electrokinetic patterning and optoelectronic tweezers are described in detail. It presents different fluidic systems (e.g. continuous micro/nano-fluidic devices, microfluidic cytometry) and their integration with sensor technology, optical and hydrodynamic stretchers etc., and demonstrates the applications of single-cell analysis in systems biology, proteomics, genomics, epigenomics, cancer transcriptomics, metabolomics, biomedicine and drug delivery systems. It also discusses the future challenges for single-cell analysis, including the advantages and limitations. This book is enjoyable reading material while at the same time providing essential information to scientists in acad...

  4. Preparation of silver nanopatterns on DNA templates

    OpenAIRE

    Dai, Shuxi; Zhang, Xingtang; Li, Tianfeng; Du, Zuliang; Dang, Hongxin

    2010-01-01

    Patterns of silver metal were prepared on DNA networks by a template-directed selective deposition and subsequent metallization process. Scanning force microscopic observations and XPS investigations demonstrated that uniform networks of nanosized silver metal clusters formed after incubation of DNA LB films with silver ions and subsequent chemical reduction of silver ions/DNA films samples. The results showed that this template-directed metallization on DNA LB films provided a simple and eff...

  5. Conformational analysis of single perfluoroalkyl chains by single-molecule real-time transmission electron microscopic imaging.

    Science.gov (United States)

    Harano, Koji; Takenaga, Shinya; Okada, Satoshi; Niimi, Yoshiko; Yoshikai, Naohiko; Isobe, Hiroyuki; Suenaga, Kazu; Kataura, Hiromichi; Koshino, Masanori; Nakamura, Eiichi

    2014-01-08

    Whereas a statistical average of molecular ensembles has been the conventional source of information on molecular structures, atomic resolution movies of single organic molecules obtained by single-molecule real-time transmission electron microscopy have recently emerged as a new tool to study the time evolution of the structures of individual molecules. The present work describes a proof-of-principle study of the determination of the conformation of each C-C bond in single perfluoroalkyl fullerene molecules encapsulated in a single-walled carbon nanotube (CNT) as well as those attached to the outer surface of a carbon nanohorn (CNH). Analysis of 82 individual molecules in CNTs under a 120 kV electron beam indicated that 6% of the CF2-CF2 bonds and about 20% of the CH2-CH2 bonds in the corresponding hydrocarbon analogue are in the gauche conformation. This comparison qualitatively matches the known conformational data based on time- and molecular-average as determined for ensembles. The transmission electron microscopy images also showed that the molecules entered the CNTs predominantly in one orientation. The molecules attached on a CNH surface moved more freely and exhibited more diverse conformation than those in a CNT, suggesting the potential applicability of this method for the determination of the dynamic shape of flexible molecules and of detailed conformations. We observed little sign of any decomposition of the specimen molecules, at least up to 10(7) e·nm(-2) (electrons/nm(2)) at 120 kV acceleration voltage. Decomposition of CNHs under irradiation with a 300 kV electron beam was suppressed by cooling to 77 K, suggesting that the decomposition is a chemical process. Several lines of evidence suggest that the graphitic substrate and the attached molecules are very cold.

  6. Clival chordoma: a single-centre outcome analysis.

    Science.gov (United States)

    Jägersberg, Max; El Rahal, Amir; Dammann, Philipp; Merkler, Doron; Weber, Damien Charles; Schaller, Karl

    2017-10-01

    The treatment of clival chordomas remains challenging. Total tumour resection is often impossible without hampering adjacent anatomical structures and causing functional sequelae. On the other hand, chordomas show limited response to non-surgical treatment modalities. Up to now, no well-established interdisciplinary treatment algorithms for clival chordomas exist. In this regard, we analysed the data from all patients that underwent interdisciplinary treatment for clival chordoma in our institution over the last 10 years. Retrospective report of all patients treated at the authors' institution from 2005 to 2015. Thirteen patients underwent 24 surgeries, of which 2 (8%) were gross total resections and 22 (92%) incomplete resections. Neurological deterioration, endocrinological disturbances and other surgical complications were observed in six (25%), three (13%) and nine (38%) cases, respectively. Three surgeries (13%) led to an improvement of the initial preoperative neurological condition. All patients were discussed on the interdisciplinary tumour board and all underwent one type of radiotherapy following initial surgery: proton beam in 11 cases (85%) and photon beam in two (15%) cases. In the course of their recurrent disease, three patients (23%) received systemic therapy (imatinib, pazopanib and nivolumab). One patient received a personalised cellular immunotherapy. One patient (8%) was lost to follow-up. Of the remaining 12 patients, four patients (33%) died in the period of analysis; all deaths were chordoma-related. The 5-year cumulative survival rate was 83% (52-97%, CI 95%), 5-year progression-free survival rate was 53% (26-79%, CI 95%). The eight patients (66%) still alive had favourable outcome (KPS, 90 ± 10.7%). SF36 analysis among the survivors revealed 43 points for the Physical Component Summary (12% above, 38% at and 50% below the general population norm) and 47 points for the Mental Component Summary (25% above, 38% at and 38% below). Our

  7. Retrospective analysis of paediatric achalasia in India: Single centre experience

    Directory of Open Access Journals (Sweden)

    Sunita Singh

    2012-01-01

    Full Text Available Background: Developing countries at tertiary referral centre. The aim of this study was to share our experience of paediatric achalasia in Indian scenario. Materials and Methods: This was a retrospective analysis of children <16 years, operated for achalasia at our centre, from December 1998 to December 2011. Results: Total 40 patients (mean age 39 ± 4.29 months, including 1 patient of megaesophagus were operated over 13 years of period; 17 patients (associated congenital H-type tracheoesophageal fistula in one patient, non- responders/ lost follow-up for minimum of 3 years in 16 patients were excluded from the study. The response rate of parents in follow-up was 60.0%. Mean symptoms duration was 27.88 ± 2 months. Most common symptoms were regurgitation and failure to thrive (78.2%. Mean symptom scoring in follow-up after 3 year was 1 ± 0.7 compared to 5 ± 0.51 at the time of admission (P < 0.012. One infant expired (mediastenitis, one developed adhesive intestinal obstruction and one needed posterior re-myotomy (for megaesophagus. There were no treatment failures in mean follow-up of 40.2 ± 5.07 months. Conclusions: Cardiomyotomy with partial fundoplication is the best modality of treatment for paediatric achalasia cardia, even from parents′ perspective.

  8. ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis.

    Science.gov (United States)

    Pierson, Emma; Yau, Christopher

    2015-11-02

    Single-cell RNA-seq data allows insight into normal cellular function and various disease states through molecular characterization of gene expression on the single cell level. Dimensionality reduction of such high-dimensional data sets is essential for visualization and analysis, but single-cell RNA-seq data are challenging for classical dimensionality-reduction methods because of the prevalence of dropout events, which lead to zero-inflated data. Here, we develop a dimensionality-reduction method, (Z)ero (I)nflated (F)actor (A)nalysis (ZIFA), which explicitly models the dropout characteristics, and show that it improves modeling accuracy on simulated and biological data sets.

  9. Characterization of nickel nanocones routed by electrodeposition without any template.

    Science.gov (United States)

    Hang, Tao; Li, Ming; Fei, Qin; Mao, Dali

    2008-01-23

    This work reports the synthesis of Ni nanocones by a one-step electrodeposition method without any template. With the addition of ethylenediamine dihydrochloride (EDA·2HCl) in the nickel plating solution, the novel Ni conical structure can be easily deposited onto different metal surfaces. The as-prepared nickel nanocones grow preferentially along [Formula: see text] directions with very sharp tips. The conical structures are single crystalline without any disruption of the lattice planes. In addition, the Ni nanocone structure is demonstrated to show magnetocrystalline anisotropy and enhance the magnetic properties when compared with other Ni nanostructures.

  10. DNA origami as a nanoscale template for protein assembly

    International Nuclear Information System (INIS)

    Kuzyk, Anton; Laitinen, Kimmo T; Toermae, Paeivi

    2009-01-01

    We describe two general approaches to the utilization of DNA origami structures for the assembly of materials. In one approach, DNA origami is used as a prefabricated template for subsequent assembly of materials. In the other, materials are assembled simultaneously with the DNA origami, i.e. the DNA origami technique is used to drive the assembly of materials. Fabrication of complex protein structures is demonstrated by these two approaches. The latter approach has the potential to be extended to the assembly of multiple materials with single attachment chemistry.

  11. Fluidic Logic Used in a Systems Approach to Enable Integrated Single-cell Functional Analysis

    Directory of Open Access Journals (Sweden)

    Naveen Ramalingam

    2016-09-01

    Full Text Available The study of single cells has evolved over the past several years to include expression and genomic analysis of an increasing number of single cells. Several studies have demonstrated wide-spread variation and heterogeneity within cell populations of similar phenotype. While the characterization of these populations will likely set the foundation for our understanding of genomic- and expression-based diversity, it will not be able to link the functional differences of a single cell to its underlying genomic structure and activity. Currently, it is difficult to perturb single cells in a controlled environment, monitor and measure the response due to perturbation, and link these response measurements to downstream genomic and transcriptomic analysis. In order to address this challenge, we developed a platform to integrate and miniaturize many of the experimental steps required to study single-cell function. The heart of this platform is an elastomer-based Integrated Fluidic Circuit (IFC that uses fluidic logic to select and sequester specific single cells based on a phenotypic trait for downstream experimentation. Experiments with sequestered cells that have been performed include on-chip culture, exposure to a variety of stimulants, and post-exposure image-based response analysis, followed by preparation of the mRNA transcriptome for massively parallel sequencing analysis. The flexible system embodies experimental design and execution that enable routine functional studies of single cells.

  12. Rapid earthquake detection through GPU-Based template matching

    Science.gov (United States)

    Mu, Dawei; Lee, En-Jui; Chen, Po

    2017-12-01

    The template-matching algorithm (TMA) has been widely adopted for improving the reliability of earthquake detection. The TMA is based on calculating the normalized cross-correlation coefficient (NCC) between a collection of selected template waveforms and the continuous waveform recordings of seismic instruments. In realistic applications, the computational cost of the TMA is much higher than that of traditional techniques. In this study, we provide an analysis of the TMA and show how the GPU architecture provides an almost ideal environment for accelerating the TMA and NCC-based pattern recognition algorithms in general. So far, our best-performing GPU code has achieved a speedup factor of more than 800 with respect to a common sequential CPU code. We demonstrate the performance of our GPU code using seismic waveform recordings from the ML 6.6 Meinong earthquake sequence in Taiwan.

  13. A PBOM configuration and management method based on templates

    Science.gov (United States)

    Guo, Kai; Qiao, Lihong; Qie, Yifan

    2018-03-01

    The design of Process Bill of Materials (PBOM) holds a hinge position in the process of product development. The requirements of PBOM configuration design and management for complex products are analysed in this paper, which include the reuse technique of configuration procedure and urgent management need of huge quantity of product family PBOM data. Based on the analysis, the function framework of PBOM configuration and management has been established. Configuration templates and modules are defined in the framework to support the customization and the reuse of configuration process. The configuration process of a detection sensor PBOM is shown as an illustration case in the end. The rapid and agile PBOM configuration and management can be achieved utilizing template-based method, which has a vital significance to improve the development efficiency for complex products.

  14. Cancelable remote quantum fingerprint templates protection scheme

    International Nuclear Information System (INIS)

    Liao Qin; Guo Ying; Huang Duan

    2017-01-01

    With the increasing popularity of fingerprint identification technology, its security and privacy have been paid much attention. Only the security and privacy of biological information are insured, the biological technology can be better accepted and used by the public. In this paper, we propose a novel quantum bit (qbit)-based scheme to solve the security and privacy problem existing in the traditional fingerprint identification system. By exploiting the properties of quantm mechanics, our proposed scheme, cancelable remote quantum fingerprint templates protection scheme, can achieve the unconditional security guaranteed in an information-theoretical sense. Moreover, this novel quantum scheme can invalidate most of the attacks aimed at the fingerprint identification system. In addition, the proposed scheme is applicable to the requirement of remote communication with no need to worry about its security and privacy during the transmission. This is an absolute advantage when comparing with other traditional methods. Security analysis shows that the proposed scheme can effectively ensure the communication security and the privacy of users’ information for the fingerprint identification. (paper)

  15. Synthesis and catalytic activity of polysaccharide templated nanocrystalline sulfated zirconia

    Science.gov (United States)

    Sherly, K. B.; Rakesh, K.

    2014-01-01

    Nanoscaled materials are of great interest due to their unique enhanced optical, electrical and magnetic properties. Sulfate-promoted zirconia has been shown to exhibit super acidic behavior and high activity for acid catalyzed reactions. Nanocrystalline zirconia was prepared in the presence of polysaccharide template by interaction between ZrOCl2ṡ8H2O and chitosan template. The interaction was carried out in aqueous phase, followed by the removal of templates by calcination at optimum temperature and sulfation. The structural and textural features were characterized by powder XRD, TG, SEM and TEM. XRD patterns showed the peaks of the diffractogram were in agreement with the theoretical data of zirconia with the catalytically active tetragonal phase and average crystalline size of the particles was found to be 9 nm, which was confirmed by TEM. TPD using ammonia as probe, FTIR and BET surface area analysis were used for analyzing surface features like acidity and porosity. The BET surface area analysis showed the sample had moderately high surface area. FTIR was used to find the type species attached to the surface of zirconia. UV-DRS found the band gap of the zirconia was found to be 2.8 eV. The benzylation of o-xylene was carried out batchwise in atmospheric pressure and 433K temperature using sulfated zirconia as catalyst.

  16. Synthesis and catalytic activity of polysaccharide templated nanocrystalline sulfated zirconia

    Energy Technology Data Exchange (ETDEWEB)

    Sherly, K. B.; Rakesh, K. [Mahatma Gandhi University Regional Research Center in Chemistry, Department of Chemistry, Mar Athanasius College, Kothamangalam-686666, Kerala (India)

    2014-01-28

    Nanoscaled materials are of great interest due to their unique enhanced optical, electrical and magnetic properties. Sulfate-promoted zirconia has been shown to exhibit super acidic behavior and high activity for acid catalyzed reactions. Nanocrystalline zirconia was prepared in the presence of polysaccharide template by interaction between ZrOCl{sub 2}⋅8H{sub 2}O and chitosan template. The interaction was carried out in aqueous phase, followed by the removal of templates by calcination at optimum temperature and sulfation. The structural and textural features were characterized by powder XRD, TG, SEM and TEM. XRD patterns showed the peaks of the diffractogram were in agreement with the theoretical data of zirconia with the catalytically active tetragonal phase and average crystalline size of the particles was found to be 9 nm, which was confirmed by TEM. TPD using ammonia as probe, FTIR and BET surface area analysis were used for analyzing surface features like acidity and porosity. The BET surface area analysis showed the sample had moderately high surface area. FTIR was used to find the type species attached to the surface of zirconia. UV-DRS found the band gap of the zirconia was found to be 2.8 eV. The benzylation of o-xylene was carried out batchwise in atmospheric pressure and 433K temperature using sulfated zirconia as catalyst.

  17. Comparison of five-axis milling and rapid prototyping for implant surgical templates.

    Science.gov (United States)

    Park, Ji-Man; Yi, Tae-Kyoung; Koak, Jai-Young; Kim, Seong-Kyoon; Park, Eun-Jin; Heo, Seong-Joo

    2014-01-01

    This study aims to compare and evaluate the accuracy of surgical templates fabricated using coordinate synchronization processing with five-axis milling and design-related processing with rapid prototyping (RP). Master phantoms with 10 embedded gutta-percha cylinders hidden under artificial gingiva were fabricated and imaged using cone beam computed tomography. Vectors of the hidden cylinders were extracted and transferred to those of the planned implants through reverse engineering using virtual planning software. An RP-produced template was fabricated by stereolithography in photopolymer at the RP center according to planned data. Metal sleeves were bonded after holes were bored (group RP). For the milled template, milling coordinates were synchronized using the conversion process for the coordinate synchronization platform located on the model's bottom. Metal bushings were set on holes milled on the five-axis milling machine, on which the model was fixed through the coordinate synchronization plate, and the framework was constructed on the model using orthodontic resin (group CS). A computed tomography image was taken with templates firmly fixed on models using anchor pins (RP) or anchor screws (CS). The accuracy was analyzed via reverse engineering. Differences between the two groups were compared by repeated measures two-factor analysis. From the reverse-engineered image of the template on the experimental model, RP-produced templates showed significantly larger deviations than did milled surgical guides. Maximum deviations of the group RP were 1.58 mm (horizontal), 1.68 mm (vertical), and 8.51 degrees (angular); those of the group CS were 0.68 mm (horizontal), 0.41 mm (vertical), and 3.23 degrees (angular). A comparison of milling and RP template production methods showed that a vector-milled surgical guide had significantly smaller deviations than did an RP-produced template. The accuracy of computer-guided milled surgical templates was within the safety

  18. QSpec: online control and data analysis system for single-cell Raman spectroscopy

    Directory of Open Access Journals (Sweden)

    Lihui Ren

    2014-06-01

    Full Text Available Single-cell phenotyping is critical to the success of biological reductionism. Raman-activated cell sorting (RACS has shown promise in resolving the dynamics of living cells at the individual level and to uncover population heterogeneities in comparison to established approaches such as fluorescence-activated cell sorting (FACS. Given that the number of single-cells would be massive in any experiment, the power of Raman profiling technique for single-cell analysis would be fully utilized only when coupled with a high-throughput and intelligent process control and data analysis system. In this work, we established QSpec, an automatic system that supports high-throughput Raman-based single-cell phenotyping. Additionally, a single-cell Raman profile database has been established upon which data-mining could be applied to discover the heterogeneity among single-cells under different conditions. To test the effectiveness of this control and data analysis system, a sub-system was also developed to simulate the phenotypes of single-cells as well as the device features.

  19. SmashCell: A software framework for the analysis of single-cell amplified genome sequences

    DEFF Research Database (Denmark)

    Harrington, Eoghan D; Arumugam, Manimozhiyan; Raes, Jeroen

    2010-01-01

    SUMMARY: Recent advances in single-cell manipulation technology, whole genome amplification and high-throughput sequencing have now made it possible to sequence the genome of an individual cell. The bioinformatic analysis of these genomes however is far more complicated than the analysis of those...

  20. Infrared analysis of urinary calculi by a single reflection accessory and a neural network interpretation algorithm

    NARCIS (Netherlands)

    Volmer, M; de Vries, JCM; Goldschmidt, HMJ

    Background: Preparation of KBr tablets, used for Fourier transform infrared (FT-IR) analysis of urinary calculus composition, is time-consuming and often hampered by pellet breakage. We developed a new F:T-IR method for urinary calculus analysis. This method makes use of a Golden Gate Single

  1. Analysis of Single-cell Gene Transcription by RNA Fluorescent In Situ Hybridization (FISH)

    DEFF Research Database (Denmark)

    Ronander, Elena; Bengtsson, Dominique C; Joergensen, Louise

    2012-01-01

    fluorescent in situ hybridization (FISH) analysis of var gene transcription by the parasite in individual nuclei of P. falciparum IE(1). Here, we present a detailed protocol for carrying out the RNA-FISH methodology for analysis of var gene transcription in single-nuclei of P. falciparum infected human...

  2. Radial artery pseudoaneurysm: A rare complication after a single arterial puncture for blood-gas analysis.

    Science.gov (United States)

    Patel, Kajal Nitin; Gandhi, Shruti P; Sutariya, Harsh C

    2016-10-01

    With a reported incidence of 0.048%, radial artery pseudoaneurysm (PA) is a rare but serious complication of arterial cannulation. We report a case of PA developing after a single puncture of the right radial artery for arterial blood-gas analysis diagnosed by Doppler ultrasound in young male patient. The development of PA after puncture of radial artery for continuous blood pressure monitoring and serial blood-gas analysis has been reported in the past; however, to the best of our knowledge, there is only one case report of development of PA after a single arterial puncture for blood-gas analysis is reported in the past.

  3. Conversion of Radiology Reporting Templates to the MRRT Standard.

    Science.gov (United States)

    Kahn, Charles E; Genereaux, Brad; Langlotz, Curtis P

    2015-10-01

    In 2013, the Integrating the Healthcare Enterprise (IHE) Radiology workgroup developed the Management of Radiology Report Templates (MRRT) profile, which defines both the format of radiology reporting templates using an extension of Hypertext Markup Language version 5 (HTML5), and the transportation mechanism to query, retrieve, and store these templates. Of 200 English-language report templates published by the Radiological Society of North America (RSNA), initially encoded as text and in an XML schema language, 168 have been converted successfully into MRRT using a combination of automated processes and manual editing; conversion of the remaining 32 templates is in progress. The automated conversion process applied Extensible Stylesheet Language Transformation (XSLT) scripts, an XML parsing engine, and a Java servlet. The templates were validated for proper HTML5 and MRRT syntax using web-based services. The MRRT templates allow radiologists to share best-practice templates across organizations and have been uploaded to the template library to supersede the prior XML-format templates. By using MRRT transactions and MRRT-format templates, radiologists will be able to directly import and apply templates from the RSNA Report Template Library in their own MRRT-compatible vendor systems. The availability of MRRT-format reporting templates will stimulate adoption of the MRRT standard and is expected to advance the sharing and use of templates to improve the quality of radiology reports.

  4. Improved PCR Amplification of Broad Spectrum GC DNA Templates.

    Science.gov (United States)

    Guido, Nicholas; Starostina, Elena; Leake, Devin; Saaem, Ishtiaq

    2016-01-01

    Many applications in molecular biology can benefit from improved PCR amplification of DNA segments containing a wide range of GC content. Conventional PCR amplification of DNA sequences with regions of GC less than 30%, or higher than 70%, is complex due to secondary structures that block the DNA polymerase as well as mispriming and mis-annealing of the DNA. This complexity will often generate incomplete or nonspecific products that hamper downstream applications. In this study, we address multiplexed PCR amplification of DNA segments containing a wide range of GC content. In order to mitigate amplification complications due to high or low GC regions, we tested a combination of different PCR cycling conditions and chemical additives. To assess the fate of specific oligonucleotide (oligo) species with varying GC content in a multiplexed PCR, we developed a novel method of sequence analysis. Here we show that subcycling during the amplification process significantly improved amplification of short template pools (~200 bp), particularly when the template contained a low percent of GC. Furthermore, the combination of subcycling and 7-deaza-dGTP achieved efficient amplification of short templates ranging from 10-90% GC composition. Moreover, we found that 7-deaza-dGTP improved the amplification of longer products (~1000 bp). These methods provide an updated approach for PCR amplification of DNA segments containing a broad range of GC content.

  5. Single cell analysis: the new frontier in 'Omics'

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Daojing; Bodovitz, Steven

    2010-01-14

    Cellular heterogeneity arising from stochastic expression of genes, proteins, and metabolites is a fundamental principle of cell biology, but single cell analysis has been beyond the capabilities of 'Omics' technologies. This is rapidly changing with the recent examples of single cell genomics, transcriptomics, proteomics, and metabolomics. The rate of change is expected to accelerate owing to emerging technologies that range from micro/nanofluidics to microfabricated interfaces for mass spectrometry to third- and fourth-generation automated DNA sequencers. As described in this review, single cell analysis is the new frontier in Omics, and single cell Omics has the potential to transform systems biology through new discoveries derived from cellular heterogeneity.

  6. Synthesis and characterization of diblock copolymer templated iron oxide nanoparticles

    Science.gov (United States)

    Akcora, Pinar

    2005-07-01

    Templating ordered assemblies of magnetic oxide nanoparticles within self-assembled diblock copolymers of varying morphologies is an important problem with a wide applicability such as in electromagnetics, optical devices, metal catalysts, medicine and biology. In this thesis, the effects of different polymer structures on particle ordering and resultant magnetic properties have been investigated using various microstructure and magnetic characterization tools. Ring-opening metathesis polymerization (ROMP) of norbornene and functionalized norbornene monomers has been used to synthesize diblock copolymers of narrow polydispersities using Grubbs' catalyst. These block copolymers can be used as templates to form inorganic nanoparticles. In this research, the structural and physical understanding of the inorganic-copolymer system was studied by small-angle neutron and x-ray scattering techniques and transmission electron microscopy. Synthesis of gamma-Fe2O3 nanoparticles has been achieved within novel block copolymers of (norbornene)-b-(deuterated norbornene dicarboxylic) acid and (norbornene methanol-(norbornene dicarboxylic acid). The polymer morphologies were controlled by varying the volume fractions of the constituent blocks. The pure norbornene based diblock copolymer morphologies were demonstrated by electron microscopy for the first tune. Spherical, cylindrical and lamellar morphologies of these novel diblock copolymers were reported. The block ratios of the synthesized polymers were determined using gel permeation chromatography-light scattering, elemental analysis and UV-VIS spectroscopy. Solution phase doping and submersion of thin films in metal salt solutions were employed as metal doping methods and the observed nanoparticle structures were compared to those of the undoped copolymer morphologies. This project reports on the types of templating structures and dispersion of the nanoparticles. The effects of particle, interactions on the microphase

  7. Standardized ultrasound templates for diagnosing appendicitis reduce annual imaging costs.

    Science.gov (United States)

    Nordin, Andrew B; Sales, Stephen; Nielsen, Jason W; Adler, Brent; Bates, David Gregory; Kenney, Brian

    2018-01-01

    Ultrasound is preferred over computed tomography (CT) for diagnosing appendicitis in children to avoid undue radiation exposure. We previously reported our experience in instituting a standardized appendicitis ultrasound template, which decreased CT rates by 67.3%. In this analysis, we demonstrate the ongoing cost savings associated with using this template. Retrospective chart review for the time period preceding template implementation (June 2012-September 2012) was combined with prospective review through December 2015 for all patients in the emergency department receiving diagnostic imaging for appendicitis. The type of imaging was recorded, and imaging rates and ultrasound test statistics were calculated. Estimated annual imaging costs based on pretemplate ultrasound and CT utilization rates were compared with post-template annual costs to calculate annual and cumulative savings. In the pretemplate period, ultrasound and CT rates were 80.2% and 44.3%, respectively, resulting in a combined annual cost of $300,527.70. Similar calculations were performed for each succeeding year, accounting for changes in patient volume. Using pretemplate rates, our projected 2015 imaging cost was $371,402.86; however, our ultrasound rate had increased to 98.3%, whereas the CT rate declined to 9.6%, yielding an annual estimated cost of $224,853.00 and a savings of $146,549.86. Since implementation, annual savings have steadily increased for a cumulative cost savings of $336,683.83. Standardizing ultrasound reports for appendicitis not only reduces the use of CT scans and the associated radiation exposure but also decreases annual imaging costs despite increased numbers of imaging studies. Continued cost reduction may be possible by using diagnostic algorithms. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Incorporating nonoverlap indices with visual analysis for quantifying intervention effectiveness in single-case experimental designs.

    Science.gov (United States)

    Brossart, Daniel F; Vannest, Kimberly J; Davis, John L; Patience, Marc A

    2014-01-01

    The field of neuropsychological rehabilitation frequently employs single case experimental designs (SCED) in research, but few if any, of the published studies use the effect sizes recommended by the American Psychological Association. Among the available methods for analysing single case designs, this paper focuses on nonoverlap methods. This paper provides examples and suggestions for integrating visual and statistical analysis, pointing out where contradictions may occur and how to be a critical consumer.

  9. Analysis of Installed Measures and Energy Savings for Single-Family Residential Better Buildings Projects

    Energy Technology Data Exchange (ETDEWEB)

    Heaney, M. [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Polly, B. [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2015-04-30

    This report presents an analysis of data for residential single-family projects reported by 37 organizations that were awarded federal financial assistance (cooperative agreements or grants) by the U.S. Department of Energy’s Better Buildings Neighborhood Program.1 The report characterizes the energy-efficiency measures installed for single-family residential projects and analyzes energy savings and savings prediction accuracy for measures installed in a subset of those projects.

  10. RT-qPCR work-flow for single-cell data analysis

    Czech Academy of Sciences Publication Activity Database

    Stahlberg, A.; Rusňáková, Vendula; Forootan, A.; Anděrová, Miroslava; Kubista, Mikael

    2013-01-01

    Roč. 59, č. 1 (2013), s. 80-88 ISSN 1046-2023 R&D Projects: GA MŠk(CZ) ME10052; GA ČR GAP303/10/1338 Institutional research plan: CEZ:AV0Z50520701 Institutional support: RVO:68378041 Keywords : RT-qPCR * Single-cell biology * Single-cell data analysis Subject RIV: EB - Genetics ; Molecular Biology; FH - Neurology (UEM-P) Impact factor: 3.221, year: 2013

  11. Single crystal growth and X-ray structure analysis of non-peripheral octahexyl phthalocyanine

    Science.gov (United States)

    Ohmori, Masashi; Nakano, Chika; Higashi, Takuya; Miyano, Tetsuya; Tohnai, Norimitsu; Fujii, Akihiko; Ozaki, Masanori

    2016-07-01

    The single-crystal structure of metal-free non-peripheral octahexyl-substituted phthalocyanine (C6PcH2) has been investigated by single-crystal X-ray structure analysis. Two types of C6PcH2 single crystal, bulk and needle crystals, were separately grown by controlling the recrystallization conditions. The structures of the two types of crystal were determined, and were found to be completely different, that is, C6PcH2 exhibits structural polymorphism. It has been clarified that the C6PcH2 microcrystals in thin films used in previously reported electronic devices have the needle structure.

  12. New insights into human primordial germ cells and early embryonic development from single-cell analysis.

    Science.gov (United States)

    Otte, Jörg; Wruck, Wasco; Adjaye, James

    2017-08-01

    Human preimplantation developmental studies are difficult to accomplish due to associated ethical and moral issues. Preimplantation cells are rare and exist only in transient cell states. From a single cell, it is very challenging to analyse the origination of the heterogeneity and complexity inherent to the human body. However, recent advances in single-cell technology and data analysis have provided new insights into the process of early human development and germ cell specification. In this Review, we examine the latest single-cell datasets of human preimplantation embryos and germ cell development, compare them to bulk cell analyses, and interpret their biological implications. © 2017 Federation of European Biochemical Societies.

  13. ergm.userterms: A Template Package for Extending statnet.

    Science.gov (United States)

    Hunter, David R; Goodreau, Steven M; Handcock, Mark S

    2013-02-01

    Exponential-family random graph models (ERGMs) represent a powerful and flexible class of models for the statistical analysis of networks. statnet is a suite of software packages that implement these models. This paper details how the capabilities for ERGM modeling can be expanded and customized by programming additional network statistics that may be included in ERGMs. We describe a template R package called ergm.userterms that can be modified for this purpose. It is designed to make this process as straightforward as possible. We also explain some of the internal workings of statnet that will help users develop their own network analysis capabilities.

  14. Learning probabilistic document template models via interaction

    Science.gov (United States)

    Ahmadullin, Ildus; Damera-Venkata, Niranjan

    2013-03-01

    Document aesthetics measures are key to automated document composition. Recently we presented a probabilistic document model (PDM) which is a micro-model for document aesthetics based on a probabilistic modeling of designer choice in document design. The PDM model comes with efficient layout synthesis algorithms once the aesthetic model is defined. A key element of this approach is an aesthetic prior on the parameters of a template encoding aesthetic preferences for template parameters. Parameters of the prior were required to be chosen empirically by designers. In this work we show how probabilistic template models (and hence the PDM cost function) can be learnt directly by observing a designer making design choices in composing sample documents. From such training data our learning approach can learn a quality measure that can mimic some of the design tradeoffs a designer makes in practice.

  15. A Hybrid Approach to Protect Palmprint Templates

    Directory of Open Access Journals (Sweden)

    Hailun Liu

    2014-01-01

    Full Text Available Biometric template protection is indispensable to protect personal privacy in large-scale deployment of biometric systems. Accuracy, changeability, and security are three critical requirements for template protection algorithms. However, existing template protection algorithms cannot satisfy all these requirements well. In this paper, we propose a hybrid approach that combines random projection and fuzzy vault to improve the performances at these three points. Heterogeneous space is designed for combining random projection and fuzzy vault properly in the hybrid scheme. New chaff point generation method is also proposed to enhance the security of the heterogeneous vault. Theoretical analyses of proposed hybrid approach in terms of accuracy, changeability, and security are given in this paper. Palmprint database based experimental results well support the theoretical analyses and demonstrate the effectiveness of proposed hybrid approach.

  16. Thermal-Hydraulics analysis of pressurized water reactor core by using single heated channel model

    Directory of Open Access Journals (Sweden)

    Reza Akbari

    2017-08-01

    Full Text Available Thermal hydraulics of nuclear reactor as a basis of reactor safety has a very important role in reactor design and control. The thermal-hydraulic analysis provides input data to the reactor-physics analysis, whereas the latter gives information about the distribution of heat sources, which is needed to perform the thermal-hydraulic analysis. In this study single heated channel model as a very fast model for predicting thermal hydraulics behavior of pressurized water reactor core has been developed. For verifying the results of this model, we used RELAP5 code as US nuclear regulatory approved thermal hydraulics code. The results of developed single heated channel model have been checked with RELAP5 results for WWER-1000. This comparison shows the capability of single heated channel model for predicting thermal hydraulics behavior of reactor core.

  17. Hydrogen bond templated 1:1 macrocyclization through an olefin metathesis/hydrogenation sequence.

    Science.gov (United States)

    Trita, Andrada Stefania; Roisnel, Thierry; Mongin, Florence; Chevallier, Floris

    2013-07-19

    The construction of pyridine-containing macrocyclic architectures using a nonmetallic template is described. 4,6-Dichlororesorcinol was used as an exotemplate to self-organize two aza-heterocyclic units by OH···N hydrogen bonds. Subsequent sequential double olefin metathesis/hydrogenation reactions employing a single ruthenium-alkylidene precatalyst open access to macrocyclic molecules.

  18. Affordance Templates for Shared Robot Control

    Science.gov (United States)

    Hart, Stephen; Dinh, Paul; Hambuchen, Kim

    2014-01-01

    This paper introduces the Affordance Template framework used to supervise task behaviors on the NASA-JSC Valkyrie robot at the 2013 DARPA Robotics Challenge (DRC) Trials. This framework provides graphical interfaces to human supervisors that are adjustable based on the run-time environmental context (e.g., size, location, and shape of objects that the robot must interact with, etc.). Additional improvements, described below, inject degrees of autonomy into instantiations of affordance templates at run-time in order to enable efficient human supervision of the robot for accomplishing tasks.

  19. Preparation of porous lanthanum phosphate with templates

    Energy Technology Data Exchange (ETDEWEB)

    Onoda, Hiroaki, E-mail: onoda@kpu.ac.jp [Department of Informatics and Environmental Sciences, Faculty of Life and Environmental Sciences, Kyoto Prefectural University, 1-5, Shimogamo Nakaragi-cyo, Sakyo-ku, Kyoto 606-8522 (Japan); Ishima, Yuya [Department of Applied Chemistry, Faculty of Life Sciences, Ritsumeikan University, 1-1-1, Nojihigashi, Kusatsu, Shiga 525-8577 (Japan); Takenaka, Atsushi [Department of Materials Science, Yonago National College of Technology, 4448, Hikona-cho, Yonago, Tottori 683-8502 (Japan); Tanaka, Isao [Department of Materials Science and Engineering, Faculty of Engineering, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501 (Japan)

    2009-08-05

    Malonic acid, propionic acid, glycine, n-butylamine, and urea were added to the preparation of lanthanum phosphate from lanthanum nitrate and phosphoric acid solutions. All additives were taken into lanthanum phosphate particles. The additives that have a basic site were easy to contain in precipitates. The addition of templates improved the specific surface area of lanthanum phosphate. The amount of pore, with radius smaller than 4 nm, increased with the addition of templates. The remained additives had influence on the acidic properties of lanthanum phosphate.

  20. RoboSCell: An automated single cell arraying and analysis instrument

    KAUST Repository

    Sakaki, Kelly

    2009-09-09

    Single cell research has the potential to revolutionize experimental methods in biomedical sciences and contribute to clinical practices. Recent studies suggest analysis of single cells reveals novel features of intracellular processes, cell-to-cell interactions and cell structure. The methods of single cell analysis require mechanical resolution and accuracy that is not possible using conventional techniques. Robotic instruments and novel microdevices can achieve higher throughput and repeatability; however, the development of such instrumentation is a formidable task. A void exists in the state-of-the-art for automated analysis of single cells. With the increase in interest in single cell analyses in stem cell and cancer research the ability to facilitate higher throughput and repeatable procedures is necessary. In this paper, a high-throughput, single cell microarray-based robotic instrument, called the RoboSCell, is described. The proposed instrument employs a partially transparent single cell microarray (SCM) integrated with a robotic biomanipulator for in vitro analyses of live single cells trapped at the array sites. Cells, labeled with immunomagnetic particles, are captured at the array sites by channeling magnetic fields through encapsulated permalloy channels in the SCM. The RoboSCell is capable of systematically scanning the captured cells temporarily immobilized at the array sites and using optical methods to repeatedly measure extracellular and intracellular characteristics over time. The instrument\\'s capabilities are demonstrated by arraying human T lymphocytes and measuring the uptake dynamics of calcein acetoxymethylester-all in a fully automated fashion. © 2009 Springer Science+Business Media, LLC.

  1. Glycan family analysis for deducing N-glycan topology from single MS.

    Science.gov (United States)

    Goldberg, David; Bern, Marshall; North, Simon J; Haslam, Stuart M; Dell, Anne

    2009-02-01

    In the past few years, mass spectrometry (MS) has emerged as the premier tool for identification and quantification of biological molecules such as peptides and glycans. There are two basic strategies: single-MS, which uses a single round of mass analysis, and MS/MS (or higher order MS(n)), which adds one or more additional rounds of mass analysis, interspersed with fragmentation steps. Single-MS offers higher throughput, broader mass coverage and more direct quantitation, but generally much weaker identification. Single-MS, however, does work fairly well for the case of N-glycan identification, which are more constrained than other biological polymers. We previously demonstrated single-MS identification of N-glycans to the level of 'cartoons' (monosaccharide composition and topology) by a system that incorporates an expert's detailed knowledge of the biological sample. In this article, we explore the possibility of ab initio single-MS N-glycan identification, with the goal of extending single-MS, or primarily-single-MS, identification to non-expert users, novel conditions and unstudied tissues. We propose and test three cartoon-assignment algorithms that make inferences informed by biological knowledge about glycan synthesis. To test the algorithms, we used 71 single-MS spectra from a variety of tissues and organisms, containing more than 2800 manually annotated peaks. The most successful of the algorithms computes the most richly connected subgraph within a 'cartoon graph'. This algorithm uniquely assigns the correct cartoon to more than half of the peaks in 41 out of the 71 spectra.

  2. Synthesis and single crystal X-ray analysis of two griseofulvin metabolites

    DEFF Research Database (Denmark)

    Rønnest, Mads Holger; Harris, Pernille; Gotfredsen, Charlotte Held

    2010-01-01

    The two phenols, 6-O-desmethyl griseofulvin and 4-O-desmethyl griseofulvin are metabolites of the antifungal drug griseofulvin. Herein, we present an improved synthesis of the 6-phenol derivative, and an unequivocal proof of both structures by single-crystal X-ray analysis.......The two phenols, 6-O-desmethyl griseofulvin and 4-O-desmethyl griseofulvin are metabolites of the antifungal drug griseofulvin. Herein, we present an improved synthesis of the 6-phenol derivative, and an unequivocal proof of both structures by single-crystal X-ray analysis....

  3. Single-phase power distribution system power flow and fault analysis

    Science.gov (United States)

    Halpin, S. M.; Grigsby, L. L.

    1992-01-01

    Alternative methods for power flow and fault analysis of single-phase distribution systems are presented. The algorithms for both power flow and fault analysis utilize a generalized approach to network modeling. The generalized admittance matrix, formed using elements of linear graph theory, is an accurate network model for all possible single-phase network configurations. Unlike the standard nodal admittance matrix formulation algorithms, the generalized approach uses generalized component models for the transmission line and transformer. The standard assumption of a common node voltage reference point is not required to construct the generalized admittance matrix. Therefore, truly accurate simulation results can be obtained for networks that cannot be modeled using traditional techniques.

  4. The Applied Behavior Analysis Research Paradigm and Single-Subject Designs in Adapted Physical Activity Research.

    Science.gov (United States)

    Haegele, Justin A; Hodge, Samuel Russell

    2015-10-01

    There are basic philosophical and paradigmatic assumptions that guide scholarly research endeavors, including the methods used and the types of questions asked. Through this article, kinesiology faculty and students with interests in adapted physical activity are encouraged to understand the basic assumptions of applied behavior analysis (ABA) methodology for conducting, analyzing, and presenting research of high quality in this paradigm. The purposes of this viewpoint paper are to present information fundamental to understanding the assumptions undergirding research methodology in ABA, describe key aspects of single-subject research designs, and discuss common research designs and data-analysis strategies used in single-subject studies.

  5. Microfluidic device for continuous single cells analysis via Raman spectroscopy enhanced by integrated plasmonic nanodimers

    DEFF Research Database (Denmark)

    Perozziello, Gerardo; Candeloro, Patrizio; De Grazia, Antonio

    2016-01-01

    In this work a Raman flow cytometer is presented. It consists of a microfluidic device that takes advantages of the basic principles of Raman spectroscopy and flow cytometry. The microfluidic device integrates calibrated microfluidic channels-where the cells can flow one-by-one -, allowing single...... cell Raman analysis. The microfluidic channel integrates plasmonic nanodimers in a fluidic trapping region. In this way it is possible to perform Enhanced Raman Spectroscopy on single cell. These allow a label-free analysis, providing information about the biochemical content of membrane and cytoplasm...

  6. Stability boundary analysis in single-phase grid-connected inverters with PLL by LTP theory

    OpenAIRE

    Salis, Valerio; Costabeber, Alessando; Cox, Stephen M.; Zanchetta, Pericle; Formentini, Andrea

    2017-01-01

    Stability analysis of power converters in AC net¬works is complex due to the non-linear nature of the conversion systems. Whereas interactions of converters in DC networks can be studied by linearising about the operating point, the extension of the same approach to AC systems poses serious challenges, especially for single-phase or unbalanced three-phase systems. A general method for stability analysis of power converters suitable for single-phase or unbalanced AC networks is presented in th...

  7. Polydimethylsiloxane (PDMS Sub-Micron Traps for Single-Cell Analysis of Bacteria

    Directory of Open Access Journals (Sweden)

    Dietrich Kohlheyer

    2013-10-01

    Full Text Available Microfluidics has become an essential tool in single-cell analysis assays for gaining more accurate insights into cell behavior. Various microfluidics methods have been introduced facilitating single-cell analysis of a broad range of cell types. However, the study of prokaryotic cells such as Escherichia coli and others still faces the challenge of achieving proper single-cell immobilization simply due to their small size and often fast growth rates. Recently, new approaches were presented to investigate bacteria growing in monolayers and single-cell tracks under environmental control. This allows for high-resolution time-lapse observation of cell proliferation, cell morphology and fluorescence-coupled bioreporters. Inside microcolonies, interactions between nearby cells are likely and may cause interference during perturbation studies. In this paper, we present a microfluidic device containing hundred sub-micron sized trapping barrier structures for single E. coli cells. Descendant cells are rapidly washed away as well as components secreted by growing cells. Experiments show excellent growth rates, indicating high cell viability. Analyses of elongation and growth rates as well as morphology were successfully performed. This device will find application in prokaryotic single-cell studies under constant environment where by-product interference is undesired.

  8. Less accurate but more efficient family of search templates for detection of gravitational waves from inspiraling compact binaries

    International Nuclear Information System (INIS)

    Chronopoulos, Andreas E.; Apostolatos, Theocharis A.

    2001-01-01

    for detecting gravitational waves from inspiraling, compact, nonspinning, binaries. Apart from this useful quantitative result, this study constitutes an application of the template-numbering technique, introduced by Owen, for families of templates that are not described by the same mathematical expression as the assumed signals. For example, this analysis will be very useful when constructing sufficiently simple templates for detecting precessing spinning binaries

  9. Less accurate but more efficient family of search templates for detection of gravitational waves from inspiraling compact binaries

    Energy Technology Data Exchange (ETDEWEB)

    Chronopoulos, Andreas E.; Apostolatos, Theocharis A.

    2001-08-15

    templates more favorable for detecting gravitational waves from inspiraling, compact, nonspinning, binaries. Apart from this useful quantitative result, this study constitutes an application of the template-numbering technique, introduced by Owen, for families of templates that are not described by the same mathematical expression as the assumed signals. For example, this analysis will be very useful when constructing sufficiently simple templates for detecting precessing spinning binaries.

  10. [Clinical application of individualized three-dimensional printing implant template in multi-tooth dental implantation].

    Science.gov (United States)

    Wang, Lie; Chen, Zhi-Yuan; Liu, Rong; Zeng, Hao

    2017-08-01

    To study the value and satisfaction of three-dimensional printing implant template and conventional implant template in multi-tooth dental implantation. Thirty cases (83 teeth) with missing teeth needing to be implanted were randomly divided into conventional implant template group (CIT group, 15 cases, 42 teeth) and 3D printing implant template group (TDPIT group, 15 cases, 41 teeth). Patients in CIT group were operated by using conventional implant template, while patients in TDPIT group were operated by using three-dimensional printing implant template. The differences of implant neck and tip deviation, implant angle deviation and angle satisfaction between the two groups were compared. The difference of probing depth and bone resorption of implant were compared 1 year after operation between the two groups. The difference of success rate and satisfaction of dental implantation were compared 1 year after operation between the two groups. SPSS19.0 software package was used for statistical analysis. The deviation direction of the neck and the tip in disto-mesial, bucco-palatal, vertical direction and angle of implants in disto-mesial and bucco-palatal direction in TDPIT group were significantly lower than in CIT group (P0.05). The difference of the cumulative success rate in dental implantation at 3 months and 6 months between the two groups were not significant (P>0.05), but the cumulative success rate of TDPIT group was significantly higher than CIT group at 9 months and 1 year (90.48% vs 100%,P=0.043). The patients' satisfaction rate of dental implantation in TDPIT group was significantly higher than in CIT group (86.67% vs 53.33%, P=0.046). Using three-dimensional printing implant template can obtain better accuracy of implant, higher implant success rate and better patients' satisfaction than using conventional implant template. It is suitable for clinical application.

  11. Engineering of DNA templated tri-functional nano-chain of Fecore–Aushell and a preliminary study for cancer cell labeling and treatment

    Directory of Open Access Journals (Sweden)

    Madhuri Mandal

    2012-10-01

    Full Text Available Here DNA has been used as templating and self-assembling reagent to grow the chain like nanostructure. We have designed the composite in such a fashion that we obtained optical and magnetic properties together in a single biological material. Optical properties characterized by UV–visible absorption, Circular Dichroism (CD and their analysis show no denaturization of DNA. Transmission electron micrographs (TEM indicate formation of chain like structure of the nanoparticles. Particles were functionalized with folic acid for labeling and treatment of cancer cell.

  12. Electrochemical synthesis of magnetic nanostructures using anodic aluminum oxide templates

    Science.gov (United States)

    Gong, Jie

    In this dissertation, template electrodeposition was employed to fabricate high quality magnetic nanostructures suited for the reliable investigation of novel spintronics phenomena such as CIMS, BMR, and CPP-GMR. Several critical aspects/steps relating to the synthesis process were investigated in this work. In order to obtain high quality magnetic nanostructures, free-standing and Si-supported anodic aluminum oxide templates with closely controlled pore diameters, lengths, as well as constriction sizes, were synthesized by anodization, followed by appropriate post-processing. The pore opening size on the barrier layer can be controlled down to 5 nm by ion beam etching. After optimization of the compositional, structural, and magnetic properties of homogeneous FeCoNiCu layers electrodeposited under different conditions, the pulsed deposition process of FeCoNI/Cu multilayers on n-Si was studied. The influence of Cu deposition potential and Fe2+ concentration on microstructure, chemical and electrochemical properties, magnetic properties, and hence magnetotransport properties were assessed. The dissolution of the FM layer during potential transition was minimized in order to control interface sharpness. Combined with the systematic sublayer thickness and FM layer composition optimization, unprecedented GMR sensitivity of 0.11%/Oe at 5-15 Oe was obtained. Growth of multilayer nanowires was performed, and contact to a single wire was attempted using an electrochemical technique. We succeeded in addressing a small number of nanowires and measured a CPP-GMR of 17%. Template electrodeposition thus provides a promising way to repeatably fabricate prototypes for spin dependent transport studies.

  13. Microwave assisted template synthesis of silver nanoparticles

    Indian Academy of Sciences (India)

    Administrator

    Various methods for synthesis, such as conventional temperature as- sisted process, controlled reaction at elevated temperatures, and microwave assisted process have been evalu- ated for the kind of silver nanoparticles synthesized. Starch has been employed as a template and reducing agent. Electron microscopy ...

  14. Binary palmprint representation for feature template protection

    NARCIS (Netherlands)

    Mu, Meiru; Ruan, Qiuqi; Shao, X.; Spreeuwers, Lieuwe Jan; Veldhuis, Raymond N.J.

    2012-01-01

    The major challenge of biometric template protection comes from the intraclass variations of biometric data. The helper data scheme aims to solve this problem by employing the Error Correction Codes (ECC). However, many reported biometric binary features from the same user reach bit error rate (BER)

  15. Iris Template Protection Based on Local Ranking

    Directory of Open Access Journals (Sweden)

    Dongdong Zhao

    2018-01-01

    Full Text Available Biometrics have been widely studied in recent years, and they are increasingly employed in real-world applications. Meanwhile, a number of potential threats to the privacy of biometric data arise. Iris template protection demands that the privacy of iris data should be protected when performing iris recognition. According to the international standard ISO/IEC 24745, iris template protection should satisfy the irreversibility, revocability, and unlinkability. However, existing works about iris template protection demonstrate that it is difficult to satisfy the three privacy requirements simultaneously while supporting effective iris recognition. In this paper, we propose an iris template protection method based on local ranking. Specifically, the iris data are first XORed (Exclusive OR operation with an application-specific string; next, we divide the results into blocks and then partition the blocks into groups. The blocks in each group are ranked according to their decimal values, and original blocks are transformed to their rank values for storage. We also extend the basic method to support the shifting strategy and masking strategy, which are two important strategies for iris recognition. We demonstrate that the proposed method satisfies the irreversibility, revocability, and unlinkability. Experimental results on typical iris datasets (i.e., CASIA-IrisV3-Interval, CASIA-IrisV4-Lamp, UBIRIS-V1-S1, and MMU-V1 show that the proposed method could maintain the recognition performance while protecting the privacy of iris data.

  16. Organic or organometallic template mediated clay synthesis

    Science.gov (United States)

    Gregar, K.C.; Winans, R.E.; Botto, R.E.

    1994-05-03

    A method is described for incorporating diverse varieties of intercalates or templates directly during hydrothermal synthesis of clays such as hectorite or montmorillonite-type layer-silicate clays. For a hectorite layer-silicate clay, refluxing a gel of silica sol, magnesium hydroxide sol and lithium fluoride for two days in the presence of an organic or organometallic intercalate or template results in crystalline products containing either (a) organic dye molecules such as ethyl violet and methyl green, (b) dye molecules such as alcian blue that are based on a Cu(II)-phthalocyannine complex, or (c) transition metal complexes such as Ru(II)phenanthroline and Co(III)sepulchrate or (d) water-soluble porphyrins and metalloporphyrins. Montmorillonite-type clays are made by the method taught by U.S. Pat. No. 3,887,454 issued to Hickson, Jun. 13, 1975; however, a variety of intercalates or templates may be introduced. The intercalates or templates should have (i) water-solubility, (ii) positive charge, and (iii) thermal stability under moderately basic (pH 9-10) aqueous reflux conditions or hydrothermal pressurized conditions for the montmorillonite-type clays. 22 figures.

  17. Author template for journal articles

    African Journals Online (AJOL)

    SONY

    2013-02-06

    Feb 6, 2013 ... an in vitro propagation technique for 'Virupakshi' through ... analysis, and were converted back to percentages for presentation. ..... dessert banana cv. Grande Nain (Musa spp. Cavendish sub-group. AAA) via somatic embryogenesis. Plant Cell Rep. 2:482-488. Becker DK, Dugdale B, Smith MK, Harding ...

  18. The on-line analysis of aerosol-delivered pharmaceuticals via single particle aerosol mass spectrometry.

    Science.gov (United States)

    Morrical, Bradley D; Balaxi, Maria; Fergenson, David

    2015-07-15

    The use of single particle aerosol mass spectrometry (SPAMS) was evaluated for the analysis of inhaled pharmaceuticals to determine the mass distribution of the individual active pharmaceutical ingredients (API) in both single ingredient and combination drug products. SPAMS is an analytical technique where the individual aerodynamic diameters and chemical compositions of many aerosol particles are determined in real-time. The analysis was performed using a Livermore Instruments SPAMS 3.0, which allowed the efficient analysis of aerosol particles with broad size distributions and can acquire data even under a very large particle load. Data similar to what would normally require roughly three days of experimentation and analysis was collected in a five minute period and analyzed automatically. The results were computed to be comparable to those returned by a typical Next Generation Impactor (NGI) particle size distribution experiment. Copyright © 2015. Published by Elsevier B.V.

  19. Vibrational Analysis of Curved Single-Walled Carbon Nanotube on a Pasternak Elastic Foundation

    DEFF Research Database (Denmark)

    Mehdipour, I.; Barari, Amin; Kimiaeifar, Amin

    2012-01-01

    Continuum mechanics and an elastic beam model were employed in the nonlinear force vibrational analysis of an embedded, curved, single-walled carbon nanotube. The analysis considered the effects of the curvature or waviness and midplane stretching of the nanotube on the nonlinear frequency....... By utilizing He’s Energy Balance Method (HEBM), the relationships of the nonlinear amplitude and frequency were expressed for a curved, single-walled carbon nanotube. The amplitude frequency response curves of the nonlinear free vibration were obtained for a curved, single-walled carbon nanotube embedded...... in a Pasternak elastic foundation. Finally, the influence of the amplitude of the waviness, midplane stretching nonlinearity, shear foundation modulus, surrounding elastic medium, radius, and length of the curved carbon nanotube on the amplitude frequency response characteristics are discussed. As a result...

  20. A Single Centre Analysis of Clinical Characteristics and Treatment of Endocrine Pancreatic Tumours

    OpenAIRE

    Adil, M. T.; Nagaraja, R.; Varma, V.; Mehta, N.; Kumaran, V.; Nundy, S.

    2015-01-01

    Background. Endocrine Pancreatic Tumours (PENs) are rare and can be nonfunctioning or functioning. They carry a good prognosis overall though high grade lesions show a relatively shorter survival. The aim of the current study is to describe a single centre analysis of the clinical characteristics and surgical treatment of PENs. Patients and Methods. This is a cohort analysis of 40 patients of PENs who underwent surgery at Sir Ganga Ram Hospital, New Delhi, India, from 1995 to 2013. Patient pa...

  1. A single mode method for the analysis and identification of nonlinear MDOF systems

    Science.gov (United States)

    Huang, Liping; Iwan, W. D.

    In order to apply mode approach to describe a nonlinear system, the concept of modal response of nonlinear systems is examined, and an amplitude-dependent modal model is presented based on an analysis of a single mode of response. The effectiveness of this model is examined under different types and various levels of excitation. A corresponding identification procedure for cubic systems is proposed and applied to the analysis of a 3DOF soltening nonlinear system.

  2. Social antecedents of children's eyewtness testimony a single-subject experimental analysis.

    Science.gov (United States)

    Doepke, Karla J; Henderson, Angela L; Critchfield, Thomas S

    2003-01-01

    In a laboratory simulation, a single-subject design was used to examine the effects of two types of social influence on children's eyewitness testimony, which has not been the subject of systematic behavioral analyses. This study replicates and extends findings from group-comparison studies, and shows that a topic of pressing social importance is amenable to analysis at the individual level, and therefore, potentially, to a behavioral analysis.

  3. Phylogenetic and functional analysis of the bacteriophage P1 single-stranded DNA-binding protein

    DEFF Research Database (Denmark)

    Bendtsen, Jannick Dyrløv; Nilsson, A.S.; Lehnherr, H.

    2002-01-01

    Bacteriophage P1 encodes a single-stranded DNA-binding protein (SSB-P1), which shows 66% amino acid sequence identity to the SSB protein of the host bacterium Escherichia coli. A phylogenetic analysis indicated that the P1 ssb gene coexists with its E. coli counterpart as an independent unit...

  4. Analysis of U and Pu resin bead samples with a single stage mass spectrometer

    International Nuclear Information System (INIS)

    Smith, D.H.; Walker, R.L.; Bertram, L.K.; Carter, J.A.

    1979-01-01

    Resin bead sampling enables the shipment of nanogram U and Pu quantities for analysis. Application of this sampling technique to safeguards was investigated with a single-stage mass spectrometer. Standards gave results in good agreement with NBS certified values. External precisions of +-0.5% were obtained on isotopic ratios of approx. 0.01; precisions on quantitative measurements are +-1.0%

  5. Optimization and Modeling of Quadrupole Orbitrap Parameters for Sensitive Analysis toward Single-Cell Proteomics.

    Science.gov (United States)

    Sun, Bingyun; Kovatch, Jessica Rae; Badiong, Albert; Merbouh, Nabyl

    2017-10-06

    Single-cell proteomics represents a field of extremely sensitive proteomic analysis, owing to the minute amount of yet complex proteins in a single cell. Without amplification potential as of nucleic acids, single-cell mass spectrometry (MS) analysis demands special instrumentation running with optimized parameters to maximize the sensitivity and throughput for comprehensive proteomic discovery. To facilitate such analysis, we here investigated two factors critical to peptide sequencing and protein detection in shotgun proteomics, i.e. precursor ion isolation window (IW) and maximum precursor ion injection time (ITmax), on an ultrahigh-field quadrupole Orbitrap (Q-Exactive HF). Counterintuitive to the frequently used proteomic parameters for bulk samples (>100 ng), our experimental data and subsequent modeling suggested a universally optimal IW of 4.0 Th for sample quantity ranging from 100 ng to 1 ng, and a sample-quantity dependent ITmax of more than 250 ms for 1-ng samples. Compared with the benchmark condition of IW = 2.0 Th and ITmax = 50 ms, our optimization generated up to 300% increase to the detected protein groups for 1-ng samples. The additionally identified proteins allowed deeper penetration of proteome for better revealing crucial cellular functions such as signaling and cell adhesion. We hope this effort can prompt single-cell and trace proteomic analysis and enable a rational selection of MS parameters.

  6. Composite Beam Cross-Section Analysis by a Single High-Order Element Layer

    DEFF Research Database (Denmark)

    Couturier, Philippe; Krenk, Steen

    2015-01-01

    An analysis procedure of general cross-section properties is presented. The formulation is based on the stress-strain states in the classic six equilibrium modes of a beam by considering a finite thickness slice modelled by a single layer of 3D finite elements. The theory is illustrated by applic...

  7. Improving Treatment Plan Implementation in Schools: A Meta-Analysis of Single Subject Design Studies

    Science.gov (United States)

    Noell, George H.; Gansle, Kristin A.; Mevers, Joanna Lomas; Knox, R. Maria; Mintz, Joslyn Cynkus; Dahir, Amanda

    2014-01-01

    Twenty-nine peer-reviewed journal articles that analyzed intervention implementation in schools using single-case experimental designs were meta-analyzed. These studies reported 171 separate data paths and provided 3,991 data points. The meta-analysis was accomplished by fitting data extracted from graphs in mixed linear growth models. This…

  8. Recent advances in the development of single cell analysis-A review

    Czech Academy of Sciences Publication Activity Database

    Klepárník, Karel; Foret, František

    2013-01-01

    Roč. 800, OCT (2013), s. 12-21 ISSN 0003-2670 R&D Projects: GA MŠk(CZ) EE2.3.20.0182; GA ČR GAP206/11/2377 Institutional support: RVO:68081715 Keywords : single cell analysis * capillary electrophoresis * electrochemistry * microfluidic devices Subject RIV: CB - Analytical Chemistry , Separation Impact factor: 4.517, year: 2013

  9. Phenylketonuria in The Netherlands : 93% of the mutations are detected by single-strand conformation analysis

    NARCIS (Netherlands)

    vanderSijsBos, CJM; Diepstraten, CM; Juyn, JA; Plaisier, M; Giltay, JC; vanSpronsen, FJ; Smit, GPA; Berger, R; Smeitink, JAM; PollThe, BT; vanAmstel, JKP

    1996-01-01

    Single-strand conformational analysis was used to screen for genetic defects in all thirteen exons of the phenylalanine hydroxylase gene (PAH) in phenylketonuria and hyperphenylalaninemia patients in the Netherlands. Exons that showed a bandshift were sequenced directly, In this way, we were able to

  10. Analysis of Kinetic Intermediates in Single-Particle Dwell-Time Distributions

    NARCIS (Netherlands)

    Floyd, Daniel L.; Harrison, Stephen C.; Oijen, Antoine M. van

    2010-01-01

    Many biological and chemical processes proceed through one or more intermediate steps. Statistical analysis of dwell-time distributions from single molecule trajectories enables the study of intermediate steps that are not directly observable. Here, we discuss the application of the randomness

  11. Iterative method of analysis of single queue, multi-server with limited ...

    African Journals Online (AJOL)

    In this paper, analysis of single queue, multi-server with limited system capacity under first come first served discipline was carried out using iterative method. The arrivals of customers and service times of customers are assumed poisson and exponential distributions respectively. This queuing model is an extension of ...

  12. Synthesis and Single Crystal X-Ray Crystallographic Analysis of 2 ...

    African Journals Online (AJOL)

    dihydropyrimidin-1-ium) tetrachlorocobaltate(II) [H2pymo]2[CoCl4]. The compound was re-crystallized in diethyl ether to obtain a suitable single crystal for X-ray diffraction analysis which revealed a molecule crystallizes in the orthorhombic ...

  13. Recent advances in the development of single cell analysis-A review

    Czech Academy of Sciences Publication Activity Database

    Klepárník, Karel; Foret, František

    2013-01-01

    Roč. 800, OCT (2013), s. 12-21 ISSN 0003-2670 R&D Projects: GA MŠk(CZ) EE2.3.20.0182; GA ČR GAP206/11/2377 Institutional support: RVO:68081715 Keywords : single cell analysis * capillary electrophoresis * electrochemistry * microfluidic devices Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 4.517, year: 2013

  14. Analysis of multiple single nucleotide polymorphisms (SNP) on DNA traces from plasma and dried blood samples

    NARCIS (Netherlands)

    Catsburg, Arnold; van der Zwet, Wil C.; Morre, Servaas A.; Ouburg, Sander; Vandenbroucke-Grauls, Christina M. J. E.; Savelkoul, Paul H. M.

    2007-01-01

    Reliable analysis of single nucleotide polymorphisms (SNPs) in DNA derived from samples containing low numbers of cells or from suboptimal sources can be difficult. A new procedure to characterize multiple SNPs in traces of DNA from plasma and old dried blood samples was developed. Six SNPs in the

  15. Atrophy-specific MRI brain template for Alzheimer's disease and mild cognitive impairment

    DEFF Research Database (Denmark)

    Fonov, Vladimir; Coupe, Pierrick; Eskildsen, Simon Fristed

    and MCI makes use of a single disease-specific template challenging. We propose a novel approach to generate a continuous four-dimensional template, where the 4th dimension is a surrogate measure of overall brain atrophy. Methods We used MRI scans obtained from the ADNI database (www...... of the brain and the contrast between different tissue types for the given level of atrophy. Figure 1 shows images through 6 example values of increasing RLVV. Conclusions The proposed method and resulting template will be useful tools for the development of robust automatic image processing methods targeted.......loni.ucla.edu/ADNI). Automated methods to estimate intracranial capacity (ICC) and lateral ventricles volume (LVV) [2] was applied to all available datasets at base line. The ratio between LVV and ICC (RLVV) was used as a surrogate measure of overall brain atrophy with mean(standard deviation) value of 2.46(0.87)%. Subsets from...

  16. Anion Exchange in II-VI Semiconducting Nanostructures via Atomic Templating

    Science.gov (United States)

    Agarwal, Rahul; Krook, Nadia M.; Ren, Ming-Liang; Tan, Liang Z.; Liu, Wenjing; Rappe, Andrew M.; Agarwal, Ritesh

    2018-03-01

    Controlled chemical transformation of nanostructures is a promising technique to obtain precisely designed novel materials which are difficult to synthesize otherwise. We report high-temperature vapor phase anion exchange reactions to chemically transform II-VI semiconductor nanostructures (100-300 nm length scale) while retaining the single crystallinity, crystal structure, morphology and even defect distribution of the parent material via atomic templating. The concept of atomic templating is employed to obtain kinetically controlled, thermodynamically metastable structural phases such as zincblende CdSe and CdS from zincblende CdTe upon complete chemical replacement of Te with Se or S. The underlying transformation mechanisms are explained through first-principles density functional theory calculations. Atomic templating is a unique path to independently tune materials phase and composition at the nanoscale allowing synthesis of novel materials.

  17. Insights into the Determination of the Templating Nucleotide at the Initiation of φ29 DNA Replication.

    Science.gov (United States)

    del Prado, Alicia; Lázaro, José M; Longás, Elisa; Villar, Laurentino; de Vega, Miguel; Salas, Margarita

    2015-11-06

    Bacteriophage φ29 from Bacillus subtilis starts replication of its terminal protein (TP)-DNA by a protein-priming mechanism. To start replication, the DNA polymerase forms a heterodimer with a free TP that recognizes the replication origins, placed at both 5' ends of the linear chromosome, and initiates replication using as primer the OH-group of Ser-232 of the TP. The initiation of φ29 TP-DNA replication mainly occurs opposite the second nucleotide at the 3' end of the template. Earlier analyses of the template position that directs the initiation reaction were performed using single-stranded and double-stranded oligonucleotides containing the replication origin sequence without the parental TP. Here, we show that the parental TP has no influence in the determination of the nucleotide used as template in the initiation reaction. Previous studies showed that the priming domain of the primer TP determines the template position used for initiation. The results obtained here using mutant TPs at the priming loop where Ser-232 is located indicate that the aromatic residue Phe-230 is one of the determinants that allows the positioning of the penultimate nucleotide at the polymerization active site to direct insertion of the initiator dAMP during the initiation reaction. The role of Phe-230 in limiting the internalization of the template strand in the polymerization active site is discussed. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  18. Photometric redshifts for the next generation of deep radio continuum surveys - I. Template fitting

    Science.gov (United States)

    Duncan, Kenneth J.; Brown, Michael J. I.; Williams, Wendy L.; Best, Philip N.; Buat, Veronique; Burgarella, Denis; Jarvis, Matt J.; Małek, Katarzyna; Oliver, S. J.; Röttgering, Huub J. A.; Smith, Daniel J. B.

    2018-01-01

    We present a study of photometric redshift performance for galaxies and active galactic nuclei detected in deep radio continuum surveys. Using two multiwavelength data sets, over the NOAO Deep Wide Field Survey Boötes and COSMOS fields, we assess photometric redshift (photo-z) performance for a sample of ∼4500 radio continuum sources with spectroscopic redshifts relative to those of ∼63 000 non-radio-detected sources in the same fields. We investigate the performance of three photometric redshift template sets as a function of redshift, radio luminosity and infrared/X-ray properties. We find that no single template library is able to provide the best performance across all subsets of the radio-detected population, with variation in the optimum template set both between subsets and between fields. Through a hierarchical Bayesian combination of the photo-z estimates from all three template sets, we are able to produce a consensus photo-z estimate that equals or improves upon the performance of any individual template set.

  19. Computational templates for introductory nuclear science using mathcad

    Science.gov (United States)

    Sarantites, D. G.; Sobotka, L. G.

    2013-01-01

    Computational templates used to teach an introductory course in nuclear chemistry and physics at Washington University in St. Louis are presented in brief. The templates cover both basic and applied topics.

  20. Emergency department documentation templates: variability in template selection and association with physical examination and test ordering in dizziness presentations

    Directory of Open Access Journals (Sweden)

    Meurer William J

    2011-03-01

    Full Text Available Abstract Background Clinical documentation systems, such as templates, have been associated with process utilization. The T-System emergency department (ED templates are widely used but lacking are analyses of the templates association with processes. This system is also unique because of the many different template options available, and thus the selection of the template may also be important. We aimed to describe the selection of templates in ED dizziness presentations and to investigate the association between items on templates and process utilization. Methods Dizziness visits were captured from a population-based study of EDs that use documentation templates. Two relevant process outcomes were assessed: head computerized tomography (CT scan and nystagmus examination. Multivariable logistic regression was used to estimate the probability of each outcome for patients who did or did not receive a relevant-item template. Propensity scores were also used to adjust for selection effects. Results The final cohort was 1,485 visits. Thirty-one different templates were used. Use of a template with a head CT item was associated with an increase in the adjusted probability of head CT utilization from 12.2% (95% CI, 8.9%-16.6% to 29.3% (95% CI, 26.0%-32.9%. The adjusted probability of documentation of a nystagmus assessment increased from 12.0% (95%CI, 8.8%-16.2% when a nystagmus-item template was not used to 95.0% (95% CI, 92.8%-96.6% when a nystagmus-item template was used. The associations remained significant after propensity score adjustments. Conclusions Providers use many different templates in dizziness presentations. Important differences exist in the various templates and the template that is used likely impacts process utilization, even though selection may be arbitrary. The optimal design and selection of templates may offer a feasible and effective opportunity to improve care delivery.

  1. DNA template dependent accuracy variation of nucleotide selection in transcription.

    Directory of Open Access Journals (Sweden)

    Harriet Mellenius

    Full Text Available It has been commonly assumed that the effect of erroneous transcription of DNA genes into messenger RNAs on peptide sequence errors are masked by much more frequent errors of mRNA translation to protein. We present a theoretical model of transcriptional accuracy. It uses experimentally estimated standard free energies of double-stranded DNA and RNA/DNA hybrids and predicts a DNA template dependent transcriptional accuracy variation spanning several orders of magnitude. The model also identifies high-error as well a high-accuracy transcription motifs. The source of the large accuracy span is the context dependent variation of the stacking free energy of pairs of correct and incorrect base pairs in the ever moving transcription bubble. Our model predictions have direct experimental support from recent single molecule based identifications of transcriptional errors in the C. elegans transcriptome. Our conclusions challenge the general view that amino acid substitution errors in proteins are mainly caused by translational errors. It suggests instead that transcriptional error hotspots are the dominating source of peptide sequence errors in some DNA template contexts, while mRNA translation is the major cause of protein errors in other contexts.

  2. Insight and Evidence Motivating the Simplification of Dual-Analysis Hybrid Systems into Single-Analysis Hybrid Systems

    Science.gov (United States)

    Todling, Ricardo; Diniz, F. L. R.; Takacs, L. L.; Suarez, M. J.

    2018-01-01

    Many hybrid data assimilation systems currently used for NWP employ some form of dual-analysis system approach. Typically a hybrid variational analysis is responsible for creating initial conditions for high-resolution forecasts, and an ensemble analysis system is responsible for creating sample perturbations used to form the flow-dependent part of the background error covariance required in the hybrid analysis component. In many of these, the two analysis components employ different methodologies, e.g., variational and ensemble Kalman filter. In such cases, it is not uncommon to have observations treated rather differently between the two analyses components; recentering of the ensemble analysis around the hybrid analysis is used to compensated for such differences. Furthermore, in many cases, the hybrid variational high-resolution system implements some type of four-dimensional approach, whereas the underlying ensemble system relies on a three-dimensional approach, which again introduces discrepancies in the overall system. Connected to these is the expectation that one can reliably estimate observation impact on forecasts issued from hybrid analyses by using an ensemble approach based on the underlying ensemble strategy of dual-analysis systems. Just the realization that the ensemble analysis makes substantially different use of observations as compared to their hybrid counterpart should serve as enough evidence of the implausibility of such expectation. This presentation assembles numerous anecdotal evidence to illustrate the fact that hybrid dual-analysis systems must, at the very minimum, strive for consistent use of the observations in both analysis sub-components. Simpler than that, this work suggests that hybrid systems can reliably be constructed without the need to employ a dual-analysis approach. In practice, the idea of relying on a single analysis system is appealing from a cost-maintenance perspective. More generally, single-analysis systems avoid

  3. Outcomes with single-coil versus dual-coil implantable cardioverter defibrillators: a meta-analysis.

    Science.gov (United States)

    Sunderland, Nicholas; Kaura, Amit; Murgatroyd, Francis; Dhillon, Para; Scott, Paul A

    2018-03-01

    Dual-coil implantable cardioverter defibrillator (ICD) leads have traditionally been used over single-coil leads due to concerns regarding high defibrillation thresholds (DFT) and consequent poor shock efficacy. However, accumulating evidence suggests that this position may be unfounded and that dual-coil leads may also be associated with higher complication rates during lead extraction. This meta-analysis collates data comparing dual- and single-coil ICD leads. Electronic databases were systematically searched for randomized controlled trials (RCT) and non-randomized studies comparing single-coil and dual-coil leads. The mean differences in DFT and summary estimates of the odds-ratio (OR) for first-shock efficacy and the hazard-ratio (HR) for all-cause mortality were calculated using random effects models. Eighteen studies including a total of 138,124 patients were identified. Dual-coil leads were associated with a lower DFT compared to single coil leads (mean difference -0.83J; 95% confidence interval [CI] -1.39--0.27; P = 0.004). There was no difference in the first-shock success rate with dual-coil compared to single-coil leads (OR 0.74; 95%CI 0.45-1.21; P=0.22). There was a significantly lower risk of all-cause mortality associated with single-coil leads (HR 0.91; 95%CI 0.86-0.95; P dual-coil leads. The mortality benefit with single-coil leads most likely represents patient selection bias. Given the increased risk and complexity of extracting dual-coil leads, centres should strongly consider single-coil ICD leads as the lead of choice for routine new left-sided ICD implants. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2017. For permissions, please email: journals.permissions@oup.com.

  4. Approach to analysis of single nucleotide polymorphisms by automated constant denaturant capillary electrophoresis

    International Nuclear Information System (INIS)

    Bjoerheim, Jens; Abrahamsen, Torveig Weum; Kristensen, Annette Torgunrud; Gaudernack, Gustav; Ekstroem, Per O.

    2003-01-01

    Melting gel techniques have proven to be amenable and powerful tools in point mutation and single nucleotide polymorphism (SNP) analysis. With the introduction of commercially available capillary electrophoresis instruments, a partly automated platform for denaturant capillary electrophoresis with potential for routine screening of selected target sequences has been established. The aim of this article is to demonstrate the use of automated constant denaturant capillary electrophoresis (ACDCE) in single nucleotide polymorphism analysis of various target sequences. Optimal analysis conditions for different single nucleotide polymorphisms on ACDCE are evaluated with the Poland algorithm. Laboratory procedures include only PCR and electrophoresis. For direct genotyping of individual SNPs, the samples are analyzed with an internal standard and the alleles are identified by co-migration of sample and standard peaks. In conclusion, SNPs suitable for melting gel analysis based on theoretical thermodynamics were separated by ACDCE under appropriate conditions. With this instrumentation (ABI 310 Genetic Analyzer), 48 samples could be analyzed without any intervention. Several institutions have capillary instrumentation in-house, thus making this SNP analysis method accessible to large groups of researchers without any need for instrument modification

  5. Single Particle ICP-MS: Advances toward routine analysis of nanomaterials.

    Science.gov (United States)

    Montaño, Manuel D; Olesik, John W; Barber, Angela G; Challis, Katie; Ranville, James F

    2016-07-01

    From its early beginnings in characterizing aerosol particles to its recent applications for investigating natural waters and waste streams, single particle inductively coupled plasma-mass spectrometry (spICP-MS) has proven to be a powerful technique for the detection and characterization of aqueous dispersions of metal-containing nanomaterials. Combining the high-throughput of an ensemble technique with the specificity of a single particle counting technique and the elemental specificity of ICP-MS, spICP-MS is capable of rapidly providing researchers with information pertaining to size, size distribution, particle number concentration, and major elemental composition with minimal sample perturbation. Recently, advances in data acquisition, signal processing, and the implementation of alternative mass analyzers (e.g., time-of-flight) has resulted in a wider breadth of particle analyses and made significant progress toward overcoming many of the challenges in the quantitative analysis of nanoparticles. This review provides an overview of spICP-MS development from a niche technique to application for routine analysis, a discussion of the key issues for quantitative analysis, and examples of its further advancement for analysis of increasingly complex environmental and biological samples. Graphical Abstract Single particle ICP-MS workflow for the analysis of suspended nanoparticles.

  6. Deconstructing stem cell population heterogeneity: Single-cell analysis and modeling approaches

    Science.gov (United States)

    Wu, Jincheng; Tzanakakis, Emmanuel S.

    2014-01-01

    Isogenic stem cell populations display cell-to-cell variations in a multitude of attributes including gene or protein expression, epigenetic state, morphology, proliferation and proclivity for differentiation. The origins of the observed heterogeneity and its roles in the maintenance of pluripotency and the lineage specification of stem cells remain unclear. Addressing pertinent questions will require the employment of single-cell analysis methods as traditional cell biochemical and biomolecular assays yield mostly population-average data. In addition to time-lapse microscopy and flow cytometry, recent advances in single-cell genomic, transcriptomic and proteomic profiling are reviewed. The application of multiple displacement amplification, next generation sequencing, mass cytometry and spectrometry to stem cell systems is expected to provide a wealth of information affording unprecedented levels of multiparametric characterization of cell ensembles under defined conditions promoting pluripotency or commitment. Establishing connections between single-cell analysis information and the observed phenotypes will also require suitable mathematical models. Stem cell self-renewal and differentiation are orchestrated by the coordinated regulation of subcellular, intercellular and niche-wide processes spanning multiple time scales. Here, we discuss different modeling approaches and challenges arising from their application to stem cell populations. Integrating single-cell analysis with computational methods will fill gaps in our knowledge about the functions of heterogeneity in stem cell physiology. This combination will also aid the rational design of efficient differentiation and reprogramming strategies as well as bioprocesses for the production of clinically valuable stem cell derivatives. PMID:24035899

  7. Using the Image Analysis Method for Describing Soil Detachment by a Single Water Drop Impact

    Directory of Open Access Journals (Sweden)

    Magdalena Ryżak

    2012-08-01

    Full Text Available The aim of the present work was to develop a method based on image analysis for describing soil detachment caused by the impact of a single water drop. The method consisted of recording tracks made by splashed particles on blotting paper under an optical microscope. The analysis facilitated division of the recorded particle tracks on the paper into drops, “comets” and single particles. Additionally, the following relationships were determined: (i the distances of splash; (ii the surface areas of splash tracks into relation to distance; (iii the surface areas of the solid phase transported over a given distance; and (iv the ratio of the solid phase to the splash track area in relation to distance. Furthermore, the proposed method allowed estimation of the weight of soil transported by a single water drop splash in relation to the distance of the water drop impact. It was concluded that the method of image analysis of splashed particles facilitated analysing the results at very low water drop energy and generated by single water drops.

  8. Single cells for forensic DNA analysis--from evidence material to test tube.

    Science.gov (United States)

    Brück, Simon; Evers, Heidrun; Heidorn, Frank; Müller, Ute; Kilper, Roland; Verhoff, Marcel A

    2011-01-01

    The purpose of this project was to develop a method that, while providing morphological quality control, allows single cells to be obtained from the surfaces of various evidence materials and be made available for DNA analysis in cases where only small amounts of cell material are present or where only mixed traces are found. With the SteREO Lumar.V12 stereomicroscope and UV unit from Zeiss, it was possible to detect and assess single epithelial cells on the surfaces of various objects (e.g., glass, plastic, metal). A digitally operated micromanipulator developed by aura optik was used to lift a single cell from the surface of evidence material and to transfer it to a conventional PCR tube or to an AmpliGrid(®) from Advalytix. The actual lifting of the cells was performed with microglobes that acted as carriers. The microglobes were held with microtweezers and were transferred to the DNA analysis receptacles along with the adhering cells. In a next step, the PCR can be carried out in this receptacle without removing the microglobe. Our method allows a single cell to be isolated directly from evidence material and be made available for forensic DNA analysis. © 2010 American Academy of Forensic Sciences.

  9. Regulatory compliance analysis for the closure of single-shell tanks

    International Nuclear Information System (INIS)

    Smith, E.H.; Boomer, K.D.; Letourneau, M.; Oakes, L.; Lorang, R.

    1991-08-01

    This document provides a regulatory compliance analysis of the baseline environmental protection requirements for the closure of single-shell tanks. In preparing this document, the Westinghouse Hanford Company has analyzed the regulatory pathways and decisions points that have been identified to data through systems engineering and related studies as they relate to environmental protection. This regulatory compliance analysis has resulted in several conclusions that will aid the US Department of Energy in managing the single-shell tank waste and in developing strategies for the closure of these tanks. These conclusions include likely outcomes of current strategies, regulatory rulings that are required for future actions, variances and exemptions to be pursued, where appropriate, and potential rulings that may affect systems engineering and other portions of the single-shell tank closure effort. The conclusions and recommendations presented here are based on analysis of current regulations, regulatory exemptions and variances, and federal facility agreements. Because the remediation of the single-shell tanks will span 30 years, regulations that have yet to be promulgated and future interpretations of existing laws and regulations may impact the recommendations and conclusions presented here. 50 refs., 22 figs

  10. Cu(I)/Cu(II) templated functional pseudorotaxanes and rotaxanes

    Indian Academy of Sciences (India)

    we focus on the synthetic strategies developed to construct pseudorotaxanes and rotaxanes using Cu(I)/Cu(II) ions as template. Further, brief discussions ... the metal templated synthesis of interlocked molecules. In the absence of a metal template, .... hindering 2,2 -bipyridine derivative (figure 6). An elec- trochemical signal ...

  11. Templated electrodeposition of functional nanostructures: nanowires, nanotubes and nanocubes

    NARCIS (Netherlands)

    Maijenburg, A.W.

    2014-01-01

    This thesis is entitled “Templated electrodeposition of functional nanostructures: nanowires, nanotubes and nanocubes”. Templated electrodeposition is the synthesis technique that was used throughout this thesis, and it comprises the use of a template with specific shape and dimensions for the

  12. FDG-PET template MNI152 1mm

    DEFF Research Database (Denmark)

    2013-01-01

    A FDG-PET template in MNI space aligned to the MNI152 atlas This PET-FDG template is provided as is free of charge for all purposes, provided that the following paper is cited......(to appear) when ever the template is used. The authors cannot, under any circumstances, be held responsible for any...

  13. Finite Element Analysis of a Copper Single Crystal Shape Memory Alloy-Based Endodontic Instruments

    Science.gov (United States)

    Vincent, Marin; Thiebaud, Frédéric; Bel Haj Khalifa, Saifeddine; Engels-Deutsch, Marc; Ben Zineb, Tarak

    2015-10-01

    The aim of the present paper is the development of endodontic Cu-based single crystal Shape Memory Alloy (SMA) instruments in order to eliminate the antimicrobial and mechanical deficiencies observed with the conventional Nickel-Titane (NiTi) SMA files. A thermomechanical constitutive law, already developed and implemented in a finite element code by our research group, is adopted for the simulation of the single crystal SMA behavior. The corresponding material parameters were identified starting from experimental results for a tensile test at room temperature. A computer-aided design geometry has been achieved and considered for a finite element structural analysis of the endodontic Cu-based single crystal SMA files. They are meshed with tetrahedral continuum elements to improve the computation time and the accuracy of results. The geometric parameters tested in this study are the length of the active blade, the rod length, the pitch, the taper, the tip diameter, and the rod diameter. For each set of adopted parameters, a finite element model is built and tested in a combined bending-torsion loading in accordance with ISO 3630-1 norm. The numerical analysis based on finite element procedure allowed purposing an optimal geometry suitable for Cu-based single crystal SMA endodontic files. The same analysis was carried out for the classical NiTi SMA files and a comparison was made between the two kinds of files. It showed that Cu-based single crystal SMA files are less stiff than the NiTi files. The Cu-based endodontic files could be used to improve the root canal treatments. However, the finite element analysis brought out the need for further investigation based on experiments.

  14. PAM50: Unbiased multimodal template of the brainstem and spinal cord aligned with the ICBM152 space.

    Science.gov (United States)

    De Leener, Benjamin; Fonov, Vladimir S; Collins, D Louis; Callot, Virginie; Stikov, Nikola; Cohen-Adad, Julien

    2018-01-15

    Template-based analysis of multi-parametric MRI data of the spinal cord sets the foundation for standardization and reproducibility, thereby helping the discovery of new biomarkers of spinal-related diseases. While MRI templates of the spinal cord have been recently introduced, none of them cover the entire spinal cord. In this study, we introduced an unbiased multimodal MRI template of the spinal cord and the brainstem, called PAM50, which is anatomically compatible with the ICBM152 brain template and uses the same coordinate system. The PAM50 template is based on 50 healthy subjects, covers the full spinal cord (C1 to L2 vertebral levels) and the brainstem, is available for T1-, T2-and T2*-weighted MRI contrasts and includes a probabilistic atlas of the gray matter and white matter tracts. Template creation accuracy was assessed by computing the mean and maximum distance error between each individual spinal cord centerline and the PAM50 centerline, after registration to the template. Results showed high accuracy for both T1- (mean = 0.37 ± 0.06 mm; max = 1.39 ± 0.58 mm) and T2-weighted (mean = 0.11 ± 0.03 mm; max = 0.71 ± 0.27 mm) contrasts. Additionally, the preservation of the spinal cord topology during the template creation process was verified by comparing the cross-sectional area (CSA) profile, averaged over all subjects, and the CSA profile of the PAM50 template. The fusion of the PAM50 and ICBM152 templates will facilitate group and multi-center studies of combined brain and spinal cord MRI, and enable the use of existing atlases of the brainstem compatible with the ICBM space. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Analysis of InP-based single photon avalanche diodes based on a single recess-etching process

    Science.gov (United States)

    Lee, Kiwon

    2018-04-01

    Effects of the different etching techniques have been investigated by analyzing electrical and optical characteristics of two-types of single-diffused single photon avalanche diodes (SPADs). The fabricated two-types of SPADs have no diffusion depth variation by using a single diffusion process at the same time. The dry-etched SPADs show higher temperature dependence of a breakdown voltage, larger dark-count-rate (DCR), and lower photon-detection-efficiency (PDE) than those of the wet-etched SPADs due to plasma-induced damage of dry-etching process. The results show that the dry etching damages can more significantly affect the performance of the SPADs based on a single recess-etching process.

  16. In situ preparation of magnetic nanocomposites of goethite in a styrene-maleimide copolymer template

    International Nuclear Information System (INIS)

    Sepulveda-Guzman, S.; Perez-Camacho, O.; Rodriguez-Fernandez, O.; Garcia-Zamora, M.

    2005-01-01

    Magnetic composites were prepared by in situ precipitation of α-FeOOH (goethite) using a new styrene-co-N-4 carboxybutylmaleimide cross-linked copolymer as template. Thermogravimetric analysis showed iron oxide content in the composites up to 45%. The iron oxide phase was identified as goethite by X-ray diffraction analysis. Transmission electron microscopy revealed that the crosslinking extent of polymeric templates affected both the shape and dimension of the goethite particles, and consequently, the magnetic behavior of the polymer/iron oxide composites

  17. Chemical approaches to the elucidation of template biosynthesis: study of replication and reverse transcription

    Science.gov (United States)

    Knorre, Dmitrii G.; Kudryashova, Natal'ya V.; Lavrik, Ol'ga I.

    1998-05-01

    Chemical approaches to the elucidation of DNA template biosynthesis using DNA polymerases and reverse transcriptases, predominantly DNA polymerase I from E. coli and reverse transcriptase from HIV-1, are considered. Special attention is paid to the comparison of chemical modification and X-ray structural analysis data as well as to quantitative aspects of the interaction of DNA polymerases with templates, primers, and nucleoside 5'-triphosphates. New versions of a catalytically competent labelling method developed in the course of investigation of these enzymes are described. The data obtained in the analysis of replication complexes using primer analogues with photoreactive groups are presented. The bibliography includes 98 references.

  18. Chemical approaches to the elucidation of template biosynthesis: study of replication and reverse transcription

    International Nuclear Information System (INIS)

    Knorre, Dmitrii G; Kudryashova, Natal'ya V; Lavrik, Ol'ga I

    1998-01-01

    Chemical approaches to the elucidation of DNA template biosynthesis using DNA polymerases and reverse transcriptases, predominantly DNA polymerase I from E. coli and reverse transcriptase from HIV-1, are considered. Special attention is paid to the comparison of chemical modification and X-ray structural analysis data as well as to quantitative aspects of the interaction of DNA polymerases with templates, primers, and nucleoside 5'-triphosphates. New versions of a catalytically competent labelling method developed in the course of investigation of these enzymes are described. The data obtained in the analysis of replication complexes using primer analogues with photoreactive groups are presented. The bibliography includes 98 references.

  19. Failure analysis of high strength pipeline with single and multiple corrosions

    International Nuclear Information System (INIS)

    Chen, Yanfei; Zhang, Hong; Zhang, Juan; Li, Xin; Zhou, Jing

    2015-01-01

    Highlights: • We study failure of high strength pipelines with single corrosion. • We give regression equations for failure pressure prediction. • We propose assessment procedure for pipelines with multiple corrosions. - Abstract: Corrosion will compromise safety operation of oil and gas pipelines, accurate determination of failure pressure finds importance in residual strength assessment and corrosion allowance design of onshore and offshore pipelines. This paper investigates failure pressure of high strength pipeline with single and multiple corrosions using nonlinear finite element analysis. On the basis of developed regression equations for failure pressure prediction of high strength pipeline with single corrosion, the paper proposes an assessment procedure for predicting failure pressure of high strength pipeline with multiple corrosions. Furthermore, failure pressures predicted by proposed solutions are compared with experimental results and various assessment methods available in literature, where accuracy and versatility are demonstrated

  20. Zeolite-templated microporous carbon as a superior adsorbent for removal of monoaromatic compounds from aqueous solution.

    Science.gov (United States)

    Ji, Liangliang; Liu, Fengling; Xu, Zhaoyi; Zheng, Shourong; Zhu, Dongqiang

    2009-10-15

    A microporous carbon with very high specific surface area and narrow pore size distribution was synthesized using Y zeolite as a template. The structural, porosity, and surface characteristics of the material were investigated by elemental analysis, N2 adsorption, powder X-ray diffraction, and Raman spectroscopy. The batch adsorption technique was performed to assess adsorption of three monoaromatic compounds, phenol, 1,3-dichlorobenzene, and 1,3-dinitrobenzene, on the synthesized carbon. Nonporous graphite, single-walled carbon nanotubes, and two commercial microporous activated carbons were also included as comparative adsorbents. The synthesized microporous carbon showed extraordinarily high adsorption affinity (comparable or higher than activated carbons and carbon nanotubes) for the three adsorbates, and very fast adsorption/ desorption kinetics (equilibrium reached less than 3 h) and complete adsorption reversibility for phenol. These adsorption properties were attributed to the large hydrophobic surface area and the regular-shaped, open and interconnected three-dimensional pore structure of the synthesized microporous carbon. Additionally, with normalization of adsorbent surface area adsorption of a bulky solute, 1,2,4,5-tetrachlorobenzene, was prominently higher on the synthesized carbon than on the activated carbons, due to alleviated size exclusion effect. Findings of the present work highlight the potential of using zeolite-templated carbons as effective adsorbents for removal of hydrophobic organic contaminants in water treatment.

  1. Recent advances in the development of single cell analysis--a review.

    Science.gov (United States)

    Klepárník, Karel; Foret, František

    2013-10-24

    Development of techniques for the analysis of the content of individual cells represents an important direction in modern bioanalytical chemistry. While the analysis of chromosomes, organelles, or location of selected proteins has been traditionally the domain of microscopic techniques, the advances in miniaturized analytical systems bring new possibilities for separations and detections of molecules inside the individual cells including smaller molecules such as hormones or metabolites. It should be stressed that the field of single cell analysis is very broad, covering advanced optical, electrochemical and mass spectrometry instrumentation, sensor technology and separation techniques. The number of papers published on single cell analysis has reached several hundred in recent years. Thus a complete literature coverage is beyond the limits of a journal article. The following text provides a critical overview of some of the latest developments with the main focus on mass spectrometry, microseparation methods, electrophoresis in capillaries and microfluidic devices and respective detection techniques for performing single cell analyses. Copyright © 2013 Elsevier B.V. All rights reserved.

  2. Spider silk as a template for obtaining magnesium oxide and magnesium hydroxide fibers

    Directory of Open Access Journals (Sweden)

    Dmitrović Svetlana

    2018-01-01

    Full Text Available Spider silk fibers, collected from Pholcus Phalangioides spider were used as a template for obtaining magnesium oxide (MgO, periclase as well as magnesium hydroxide (Mg(OH2, brucite fibers. Magnesium oxide fibers were obtained in a simple manner by heat induced decomposition of magnesium salt (MgCl2 in the presence of the spider silk fibers, while magnesium hydroxide fibers were synthesized by hydration of MgO fibers at 50, 70 and 90 C, for 48 and 96 h. According to Scanning electron microscopy (SEM, dimensions of spider silk fibers determined the dimension of synthesized MgO fibers, while for Mg(OH2 fibers, the average diameter was increased with prolonging the hydration period. The surface of Mg(OH2 fibers was noticed to be covered with brucite in a form of plates. X-Ray diffraction (XRD analysis showed that MgO fibers were single-phased (the pure magnesium oxide fibers were obtained, while Mg(OH2 fibers were two- or single-phased brucite depending on incubation period, and/or incubation temperature. [Project of the Serbian Ministry of Education, Science and Technological Development, Grant no. 45012

  3. Physical synthesis of quantum circuits using templates

    Science.gov (United States)

    Mirkhani, Zahra; Mohammadzadeh, Naser

    2016-10-01

    Similar to traditional CMOS circuits, quantum circuit design flow is divided into two main processes: logic synthesis and physical design. Addressing the limitations imposed on optimization of the quantum circuit metrics because of no information sharing between logic synthesis and physical design processes, the concept of " physical synthesis" was introduced for quantum circuit flow, and a few techniques were proposed for it. Following that concept, in this paper a new approach for physical synthesis inspired by template matching idea in quantum logic synthesis is proposed to improve the latency of quantum circuits. Experiments show that by using template matching as a physical synthesis approach, the latency of quantum circuits can be improved by more than 23.55 % on average.

  4. Multibiometric Systems: Fusion Strategies and Template Security

    Science.gov (United States)

    2008-01-01

    same user corresponding to the individual biometric sources. Template security is an important issue in biomet - ric systems because unlike passwords...FTER and FTCR in a biometric system. • Inter-user similarity: Inter-user similarity refers to the overlap of the biomet - ric samples from two different...and right index fingers of a person) and multiple biomet - ric traits (e.g., fingerprint and iris). Towards this end, we have developed a fully

  5. Initiating Knowledge Management in Colleges and Universities: A template

    Directory of Open Access Journals (Sweden)

    Naresh Kumar Agarwal

    2014-12-01

    Full Text Available Knowledge Management (KM is a collaborative and integrated approach adopted at various levels to ensure that an organization’s knowledge assets are best utilized to increase organizational performance. While KM has been adopted in a large number of sectors and organizations, colleges and universities, and the higher education sector in general, is yet to take full advantage of the possibilities offered by KM. Also, while past research has sought to highlight the importance of implementing KM in higher education, there is a lack of a single, clear template for KM implementation that universities leaders and administrators can adopt. The contribution of the paper is a practical, actionable, step-by-step plan, as well as a diagrammatic, theoretical framework for initiating KM successfully in colleges and universities.

  6. TRANSPA: a code for transient thermal analysis of a single fuel pin

    International Nuclear Information System (INIS)

    Prenger, F.C.

    1985-02-01

    An analytical model (TRANSPA) for the transient thermal analysis of a single uranium carbide fuel pin was developed. This model uses thermal boundary conditions obtained from COBRA-WC output and calculates the transient thermal response of a single fuel pin to changes in internal power generation, coolant flowrate, or fuel pin physical configuration. The model uses the MITAS finite difference thermal analyzer. MITAS provides the means to input separate conductance models through the use of a user subroutine input capability. The model is a lumped-mass representation of the fuel pin using 26 nodes and 42 conductors. Run time for each transient analysis is approximately one minute of central processor time on the NOS operating system

  7. FEM analysis of an single stator dual PM rotors axial synchronous machine

    Science.gov (United States)

    Tutelea, L. N.; Deaconu, S. I.; Popa, G. N.

    2017-01-01

    The actual e - continuously variable transmission (e-CVT) solution for the parallel Hybrid Electric Vehicle (HEV) requires two electric machines, two inverters, and a planetary gear. A distinct electric generator and a propulsion electric motor, both with full power converters, are typical for a series HEV. In an effort to simplify the planetary-geared e-CVT for the parallel HEV or the series HEV we hereby propose to replace the basically two electric machines and their two power converters by a single, axial-air-gap, electric machine central stator, fed from a single PWM converter with dual frequency voltage output and two independent PM rotors. The proposed topologies, the magneto-motive force analysis and quasi 3D-FEM analysis are the core of the paper.

  8. Microfluidic device for continuous single cells analysis via Raman spectroscopy enhanced by integrated plasmonic nanodimers

    KAUST Repository

    Perozziello, Gerardo

    2015-12-11

    In this work a Raman flow cytometer is presented. It consists of a microfluidic device that takes advantages of the basic principles of Raman spectroscopy and flow cytometry. The microfluidic device integrates calibrated microfluidic channels- where the cells can flow one-by-one -, allowing single cell Raman analysis. The microfluidic channel integrates plasmonic nanodimers in a fluidic trapping region. In this way it is possible to perform Enhanced Raman Spectroscopy on single cell. These allow a label-free analysis, providing information about the biochemical content of membrane and cytoplasm of the each cell. Experiments are performed on red blood cells (RBCs), peripheral blood lymphocytes (PBLs) and myelogenous leukemia tumor cells (K562). © 2015 Optical Society of America.

  9. Fast Step Transition and State Identification (STaSI) for Discrete Single-Molecule Data Analysis.

    Science.gov (United States)

    Shuang, Bo; Cooper, David; Taylor, J Nick; Kisley, Lydia; Chen, Jixin; Wang, Wenxiao; Li, Chun Biu; Komatsuzaki, Tamiki; Landes, Christy F

    2014-09-18

    We introduce a step transition and state identification (STaSI) method for piecewise constant single-molecule data with a newly derived minimum description length equation as the objective function. We detect the step transitions using the Student's t test and group the segments into states by hierarchical clustering. The optimum number of states is determined based on the minimum description length equation. This method provides comprehensive, objective analysis of multiple traces requiring few user inputs about the underlying physical models and is faster and more precise in determining the number of states than established and cutting-edge methods for single-molecule data analysis. Perhaps most importantly, the method does not require either time-tagged photon counting or photon counting in general and thus can be applied to a broad range of experimental setups and analytes.

  10. Structural analysis of a composite continuous girder with a single rectangular web opening

    Directory of Open Access Journals (Sweden)

    Mohamed A. ElShaer

    2017-08-01

    In this paper, a non-linear finite element analysis has been done to analyze the deflection in the steel section and internal stresses in the concrete slab for continuous composite girders with a single rectangular opening in the steel web. ANSYS computer program (version 15 has been used to analyze the three-dimensional model. The reliability of the model was demonstrated by comparison with experimental results of continuous composite beams without an opening in the steel web carried out by another author. The parametric analysis was executed to investigate the width, height, and position of the opening in one span on the behavior of a composite girder under vertical load. The results indicated that when the width of opening is less than 0.05 of length of a single span and the height is less than 0.15 of the steel web, the deflection and internal stresses increased less than 10% comparing to continuous composite girders without an opening.

  11. Single-Use Sensor Strips for Reliable Field Analysis of Gunshot Residue

    Science.gov (United States)

    2013-10-13

    determined in a single GSR assay. Wearable textile -based printed electrodes were also examined towards a ’Lab-on-Sleeve’ forensic field analysis. New...Example of the different cyclic square-wave stripping voltammetric signals obtained with “swiping” samples at a bare SPCE electrode . Score plot of the...A) The Forensic Finger exhibiting the three electrode surface screen-printed onto a flexible nitrile finger cot (bottom left inset), as well as a

  12. Analysis of the paired TCR α- and β-chains of single human T cells.

    Directory of Open Access Journals (Sweden)

    Song-Min Kim

    Full Text Available Analysis of the paired i.e. matching TCR α- and β-chain rearrangements of single human T cells is required for a precise investigation of clonal diversity, tissue distribution and specificity of protective and pathologic T-cell mediated immune responses. Here we describe a multiplex RT-PCR based technology, which for the first time allows for an unbiased analysis of the complete sequences of both α- and β-chains of TCR from single T cells. We validated our technology by the analysis of the pathologic T-cell infiltrates from tissue lesions of two T-cell mediated autoimmune diseases, psoriasis vulgaris (PV and multiple sclerosis (MS. In both disorders we could detect various T cell clones as defined by multiple T cells with identical α- and β-chain rearrangements distributed across the tissue lesions. In PV, single cell TCR analysis of lesional T cells identified clonal CD8(+ T cell expansions that predominated in the epidermis of psoriatic plaques. An MS brain lesion contained two dominant CD8(+ T-cell clones that extended over the white and grey matter and meninges. In both diseases several clonally expanded T cells carried dual TCRs composed of one Vβ and two different Vα-chain rearrangements. These results show that our technology is an efficient instrument to analyse αβ-T cell responses with single cell resolution in man. It should facilitate essential new insights into the mechanisms of protective and pathologic immunity in many human T-cell mediated conditions and allow for resurrecting functional TCRs from any αβ-T cell of choice that can be used for investigating their specificity.

  13. Single-Molecule Analysis of Pre-mRNA Splicing with Colocalization Single-Molecule Spectroscopy (CoSMoS).

    Science.gov (United States)

    Braun, Joerg E; Serebrov, Victor

    2017-01-01

    Recent development of single-molecule techniques to study pre-mRNA splicing has provided insights into the dynamic nature of the spliceosome. Colocalization single-molecule spectroscopy (CoSMoS) allows following spliceosome assembly in real time at single-molecule resolution in the full complexity of cellular extracts. A detailed protocol of CoSMoS has been published previously (Anderson and Hoskins, Methods Mol Biol 1126:217-241, 2014). Here, we provide an update on the technical advances since the first CoSMoS studies including slide surface treatment, data processing, and representation. We describe various labeling strategies to generate RNA reporters with multiple dyes (or other moieties) at specific locations.

  14. Measurement of the Top Quark Mass at CDF Using the Template Method in the Lepton + Jets Channel

    Energy Technology Data Exchange (ETDEWEB)

    Adelman, Jahred A. [Univ. of Chicago, IL (United States)

    2008-06-01

    A measurement of the top quark mass in p$\\bar{p}$ collisions at √s = 1.96 TeV is presented. The analysis uses a template method, in which the overconstrained kinematics of the Lepton+Jets channel of the t$\\bar{t}$ system are used to measure a single quantity, the reconstructed top quark mass, that is strongly correlated with the true top quark mass. in addition, the dijet mass of the hadronically decaying W boson is used to constrain in situ the uncertain jet energy scale in the CDF detector. Two-dimensional probability density functions are derived using a kernel density estimate-based machinery. Using 1.9 fb-1 of data, the top quark mass is measured to be 171.8$+1.9\\atop{-1.9}$(stat.) ± 1.0(syst.)GeV/c2.

  15. Quantitative studies of rhubarb using quantitative analysis of multicomponents by single marker and response surface methodology.

    Science.gov (United States)

    Sun, Jiachen; Wu, Yueting; Dong, Shengjie; Li, Xia; Gao, Wenyuan

    2017-10-01

    In this work, we developed a novel approach to evaluate the contents of bioactive components in rhubarb. The present method was based on the quantitative analysis of multicomponents by a single-marker and response surface methodology approaches. The quantitative analysis of multicomponents by a single-marker method based on high-performance liquid chromatography coupled with photodiode array detection was developed and applied to determine the contents of 12 bioactive components in rhubarb. No significant differences were found in the results from the quantitative analysis of multicomponents by a single-marker and the external standard method. In order to maximize the extraction of 12 bioactive compounds in rhubarb, the ultrasonic-assisted extraction conditions were obtained by the response surface methodology coupled with Box-Behnken design. According to the obtained results, we showed that the optimal conditions would be as follows: proportion of ethanol/water 74.39%, solvent-to-solid ratio 24.07:1 v/w, extraction time 51.13 min, and extraction temperature 63.61°C. The analytical scheme established in this research should be a reliable, convenient, and appropriate method for quantitative determination of bioactive compounds in rhubarb. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Accounting for technical noise in differential expression analysis of single-cell RNA sequencing data.

    Science.gov (United States)

    Jia, Cheng; Hu, Yu; Kelly, Derek; Kim, Junhyong; Li, Mingyao; Zhang, Nancy R

    2017-11-02

    Recent technological breakthroughs have made it possible to measure RNA expression at the single-cell level, thus paving the way for exploring expression heterogeneity among individual cells. Current single-cell RNA sequencing (scRNA-seq) protocols are complex and introduce technical biases that vary across cells, which can bias downstream analysis without proper adjustment. To account for cell-to-cell technical differences, we propose a statistical framework, TASC (Toolkit for Analysis of Single Cell RNA-seq), an empirical Bayes approach to reliably model the cell-specific dropout rates and amplification bias by use of external RNA spike-ins. TASC incorporates the technical parameters, which reflect cell-to-cell batch effects, into a hierarchical mixture model to estimate the biological variance of a gene and detect differentially expressed genes. More importantly, TASC is able to adjust for covariates to further eliminate confounding that may originate from cell size and cell cycle differences. In simulation and real scRNA-seq data, TASC achieves accurate Type I error control and displays competitive sensitivity and improved robustness to batch effects in differential expression analysis, compared to existing methods. TASC is programmed to be computationally efficient, taking advantage of multi-threaded parallelization. We believe that TASC will provide a robust platform for researchers to leverage the power of scRNA-seq. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. Single-Cell Phosphospecific Flow Cytometric Analysis of Canine and Murine Adipose-Derived Stem Cells

    Directory of Open Access Journals (Sweden)

    Harumichi Itoh

    2017-01-01

    Full Text Available This study aimed to demonstrate single-cell phosphospecific flow cytometric analysis of canine and murine adipose-derived stem/stromal cells (ADSCs. ADSCs were obtained from clinically healthy laboratory beagles and C57BL/6 mice. Cell differentiation into adipocytes, osteocytes, and chondrocytes was observed for the cultured canine ADSCs (cADSCs and murine ADSCs (mADSCs to determine their multipotency. We also performed single-cell phosphospecific flow cytometric analysis related to cell differentiation and stemness. Cultured cADSCs and mADSCs exhibited the potential to differentiate into adipocytes, osteocytes, and chondrocytes. In addition, single-cell phosphospecific flow cytometric analysis revealed similar β-catenin and Akt phosphorylation between mADSCs and cADSCs. On the other hand, it showed the phosphorylation of different Stat proteins. It was determined that cADSCs and mADSCs show the potential to differentiate into adipocytes, osteocytes, and chondrocytes. Furthermore, a difference in protein phosphorylation between undifferentiated cADSCs and mADSCs was identified.

  18. Extracting Surveillance Data from Templated Sections of an Electronic Medical Note: Challenges and Opportunities

    Science.gov (United States)

    Gundlapalli, Adi; Divita, Guy; Carter, Marjorie; Shen, Shuying; Palmer, Miland; Forbush, Tyler; South, Brett; Redd, Andrew; Sauer, Brian; Samore, Matthew

    2013-01-01

    documents as determined by human review. The NLP algorithm successfully extracted concepts from these documents. The H set had an average of 8 concepts related to homelessness per document (median 8, range 1 to 34). The NH set had an average 2 concepts (median 1, range 1 to 13)”. Thirteen template patterns were identified in this set of documents. The three most common were check boxes with square brackets, Yes/No and free text answer after a question. Several positively and negatively asserted concepts were noted to be in the responses to templated questions such as “Are you currently homeless: Yes or No”; “How many times have you been homeless in the past 3 years: (free text response)”; “Have you ever been in jail? [Y] or [N]”; Are you in need of substance abuse services? Yes or No”. Human review of a random sample of documents at the concept level indicated that the NLP algorithm generated 28% false positives in extracting concepts related to homelessness when templates were ignored among the H documents. When the algorithm was refined to include templates, the false positive rate declined to 22%. For the NH documents, the corresponding false positive rates were 56% and 21%. Conclusions To our knowledge, this is one of the first attempts to address the problem of information extraction from templates or templated sections of the EMR. A key challenge of templates is that they will most likely lead to poor performance of NLP algorithms and cause bottlenecks in processing if they are not considered. Acknowledging the presence of templates and refining NLP algorithms to handle them improves information extraction from free text medical notes, thus creating an opportunity for improved surveillance using the EMR. Algorithms will likely need to be customized to the electronic medical record and the surveillance domain of interest. A more detailed analysis of the templated sections is underway.

  19. PCR-based analysis of disease in tomato singly or mixed inoculated with Fusarium oxysporum f. sp. lycopersici races 1 and 2

    Directory of Open Access Journals (Sweden)

    OLUSEGUN SAMUEL BALOGUN

    2008-07-01

    Full Text Available The pathogenic response of two tomato cultivars to races of Fusarium oxysporum f. sp.. lycopersici (cv. Momotaro, insensitive to race 1 of the pathogen, and cv. Ponderosa sensitive to race 1, was studied in greenhouse and laboratory experiments by inoculating the cultivars singly with race 1 or race 2, and in mixed inoculation with the two races of the pathogen. A pre-symptom PCR assay two weeks after inoculation showed that a fragment of the intergenic spacer region (IGS of ribosomal DNA was amplifi ed by DNA templates from leaf samples of cv. Momotaro tomato plants inoculated with only race 2, or with race 1+2, but in the cv. Ponderosa the fragment was amplifi ed only in plants inoculated with race 1+2. Race-specifi c analysis using the sp13 and sp23 primers confi rmed that the amplifi ed fragment was from race 2 in cv. Momotaro and from races 1+2 in cv. Ponderosa. Later wilt symptoms mirrored the pre-symptom and post-symptom molecular analytical results: cv. Momotaro plants inoculated with only race 1 remained symptomless, while the ‘Momotaro’ plants inoculated with both races (1+2 did not manifest more severe wilt symptoms than plants inoculated with race 2 alone; cv. Ponderosa plants that were mixed-inoculated with race 1+2 manifested more severe symptoms, and at an earlier date than plants inoculated with only race 2. Growth parameters such as number of leaves and plant height showed the race 1+2 infected cv. Ponderosa were significantly retarded in growth, suggesting that significant synergism between the fungal races in tomato pathosystem can occur only when the host cultivar is sensitive to both races. An additional important finding is that pre-symptom leaf sampling of apparently healthy plants is useful in PCR diagnostic analysis to predict impending fusarial wilt outbreaks in tomato especially in infested soil.

  20. Spatiotemporal analysis of single-trial EEG of emotional pictures based on independent component analysis and source location

    Science.gov (United States)

    Liu, Jiangang; Tian, Jie

    2007-03-01

    The present study combined the Independent Component Analysis (ICA) and low-resolution brain electromagnetic tomography (LORETA) algorithms to identify the spatial distribution and time course of single-trial EEG record differences between neural responses to emotional stimuli vs. the neutral. Single-trial multichannel (129-sensor) EEG records were collected from 21 healthy, right-handed subjects viewing the emotion emotional (pleasant/unpleasant) and neutral pictures selected from International Affective Picture System (IAPS). For each subject, the single-trial EEG records of each emotional pictures were concatenated with the neutral, and a three-step analysis was applied to each of them in the same way. First, the ICA was performed to decompose each concatenated single-trial EEG records into temporally independent and spatially fixed components, namely independent components (ICs). The IC associated with artifacts were isolated. Second, the clustering analysis classified, across subjects, the temporally and spatially similar ICs into the same clusters, in which nonparametric permutation test for Global Field Power (GFP) of IC projection scalp maps identified significantly different temporal segments of each emotional condition vs. neutral. Third, the brain regions accounted for those significant segments were localized spatially with LORETA analysis. In each cluster, a voxel-by-voxel randomization test identified significantly different brain regions between each emotional condition vs. the neutral. Compared to the neutral, both emotional pictures elicited activation in the visual, temporal, ventromedial and dorsomedial prefrontal cortex and anterior cingulated gyrus. In addition, the pleasant pictures activated the left middle prefrontal cortex and the posterior precuneus, while the unpleasant pictures activated the right orbitofrontal cortex, posterior cingulated gyrus and somatosensory region. Our results were well consistent with other functional imaging

  1. A Computer Program for Flow-Log Analysis of Single Holes (FLASH)

    Science.gov (United States)

    Day-Lewis, F. D.; Johnson, C.D.; Paillet, Frederick L.; Halford, K.J.

    2011-01-01

    A new computer program, FLASH (Flow-Log Analysis of Single Holes), is presented for the analysis of borehole vertical flow logs. The code is based on an analytical solution for steady-state multilayer radial flow to a borehole. The code includes options for (1) discrete fractures and (2) multilayer aquifers. Given vertical flow profiles collected under both ambient and stressed (pumping or injection) conditions, the user can estimate fracture (or layer) transmissivities and far-field hydraulic heads. FLASH is coded in Microsoft Excel with Visual Basic for Applications routines. The code supports manual and automated model calibration. ?? 2011, The Author(s). Ground Water ?? 2011, National Ground Water Association.

  2. Development of Total Knee Replacement Digital Templating Software

    Science.gov (United States)

    Yusof, Siti Fairuz; Sulaiman, Riza; Thian Seng, Lee; Mohd. Kassim, Abdul Yazid; Abdullah, Suhail; Yusof, Shahril; Omar, Masbah; Abdul Hamid, Hamzaini

    In this study, by taking full advantage of digital X-ray and computer technology, we have developed a semi-automated procedure to template knee implants, by making use of digital templating method. Using this approach, a software system called OrthoKneeTMhas been designed and developed. The system is to be utilities as a study in the Department of Orthopaedic and Traumatology in medical faculty, UKM (FPUKM). OrthoKneeTMtemplating process employs uses a technique similar to those used by many surgeons, using acetate templates over X-ray films. Using template technique makes it easy to template various implant from every Implant manufacturers who have with a comprehensive database of templates. The templating functionality includes, template (knee) and manufactures templates (Smith & Nephew; and Zimmer). From an image of patient x-ray OrthoKneeTMtemplates help in quickly and easily reads to the approximate template size needed. The visual templating features then allow us quickly review multiple template sizes against the X-ray and thus obtain the nearly precise view of the implant size required. The system can assist by templating on one patient image and will generate reports that can accompany patient notes. The software system was implemented in Visual basic 6.0 Pro using the object-oriented techniques to manage the graphics and objects. The approaches for image scaling will be discussed. Several of measurement in orthopedic diagnosis process have been studied and added in this software as measurement tools features using mathematic theorem and equations. The study compared the results of the semi-automated (using digital templating) method to the conventional method to demonstrate the accuracy of the system.

  3. Multi-Unit Initiating Event Analysis for a Single-Unit Internal Events Level 1 PSA

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Dong San; Park, Jin Hee; Lim, Ho Gon [KAERI, Daejeon (Korea, Republic of)

    2016-05-15

    The Fukushima nuclear accident in 2011 highlighted the importance of considering the risks from multi-unit accidents at a site. The ASME/ANS probabilistic risk assessment (PRA) standard also includes some requirements related to multi-unit aspects, one of which (IE-B5) is as follows: 'For multi-unit sites with shared systems, DO NOT SUBSUME multi-unit initiating events if they impact mitigation capability [1].' However, the existing single-unit PSA models do not explicitly consider multi-unit initiating events and hence systems shared by multiple units (e.g., alternate AC diesel generator) are fully credited for the single unit and ignores the need for the shared systems by other units at the same site [2]. This paper describes the results of the multi-unit initiating event (IE) analysis performed as a part of the at-power internal events Level 1 probabilistic safety assessment (PSA) for an OPR1000 single unit ('reference unit'). In this study, a multi-unit initiating event analysis for a single-unit PSA was performed, and using the results, dual-unit LOOP initiating event was added to the existing PSA model for the reference unit (OPR1000 type). Event trees were developed for dual-unit LOOP and dual-unit SBO which can be transferred from dual- unit LOOP. Moreover, CCF basic events for 5 diesel generators were modelled. In case of simultaneous SBO occurrences in both units, this study compared two different assumptions on the availability of the AAC D/G. As a result, when dual-unit LOOP initiating event was added to the existing single-unit PSA model, the total CDF increased by 1∼ 2% depending on the probability that the AAC D/G is available to a specific unit in case of simultaneous SBO in both units.

  4. [Comparative study of prenatal diagnosis with single nucleotide polymorphism array and karyotype analysis].

    Science.gov (United States)

    Chang, Ling; Zhao, Nan; Wei, Yuan; Zhong, Su; Liu, Ping; Qiao, Jie

    2014-10-18

    To compare the roles of single nucleotide polymorphism array (SNP array) and karyotype analysis in high-risk pregnant women prenatal diagnosis. From July 2012 to December 2013, a total of 141 pregnant women with high-risk in prenatal diagnosis were selected as the object of study in Department of Obstetrics and Gynecology, Peking University Third Hospital, 78 cases of umbilical cord puncture and 63 of amnion cavity puncture , both taking SNP array detection and karyotype analysis. The abnormality karyotype rate was 6.4%, the abnormal rate of SNP array result was 11.3%, and the abnormal rate of the combined two methods for detecting was 12.1%. There were significant differences between the SNP array and karyotype analysis (P=0.039). There were obvious differences between the two techniques. It is an effective way to determine genetic disease by integrating SNP array and karyotype analysis in prenatal diagnosis.

  5. Single particle transfer for quantitative analysis with total-reflection X-ray fluorescence spectrometry

    International Nuclear Information System (INIS)

    Esaka, Fumitaka; Esaka, Konomi T.; Magara, Masaaki; Sakurai, Satoshi; Usuda, Shigekazu; Watanabe, Kazuo

    2006-01-01

    The technique of single particle transfer was applied to quantitative analysis with total-reflection X-ray fluorescence (TXRF) spectrometry. The technique was evaluated by performing quantitative analysis of individual Cu particles with diameters between 3.9 and 13.2 μm. The direct quantitative analysis of the Cu particle transferred onto a Si carrier gave a discrepancy between measured and calculated Cu amounts due to the absorption effects of incident and fluorescent X-rays within the particle. By the correction for the absorption effects, the Cu amounts in individual particles could be determined with the deviation within 10.5%. When the Cu particles were dissolved with HNO 3 solution prior to the TXRF analysis, the deviation was improved to be within 3.8%. In this case, no correction for the absorption effects was needed for quantification

  6. Visual analysis in single case experimental design studies: brief review and guidelines.

    Science.gov (United States)

    Lane, Justin D; Gast, David L

    2014-01-01

    Visual analysis of graphic displays of data is a cornerstone of studies using a single case experimental design (SCED). Data are graphed for each participant during a study with trend, level, and stability of data assessed within and between conditions. Reliable interpretations of effects of an intervention are dependent on researchers' understanding and use of systematic procedures. The purpose of this paper is to provide readers with a rationale for visual analysis of data when using a SCED, a step-by-step guide for conducting a visual analysis of graphed data, as well as to highlight considerations for persons interested in using visual analysis to evaluate an intervention, especially the importance of collecting reliability data for dependent measures and fidelity of implementation of study procedures.

  7. Alkali metal ion templated transition metal formate framework materials: synthesis, crystal structures, ion migration, and magnetism.

    Science.gov (United States)

    Eikeland, Espen; Lock, Nina; Filsø, Mette; Stingaciu, Marian; Shen, Yanbin; Overgaard, Jacob; Iversen, Bo Brummerstedt

    2014-10-06

    Four transition metal formate coordination polymers with anionic frameworks, namely, Na[Mn(HCOO)3], K[Mn(HCOO)3], Na2[Cu3(HCOO)8], and K2[Cu5(HCOO)12], were synthesized using a mild solution chemistry approach. Multitemperature single-crystal (100-300 K) and powder X-ray diffraction studies of the compounds reveal structures of large diversity ranging from cubic chiral Na-Mn formate to triclinic Na-Cu formate. The structural variety is caused by the nature of the transition metals, the alkali metal ion templation, and the versatility of the formate group, which offers metal-metal coordination through three different O-C-O bridging modes (syn-syn, syn-anti, anti-anti) in addition to metal-metal bridging via a single oxygen atom. The two manganese(II) compounds contain mononuclear, octahedrally coordinated moieties, but the three-dimensional connectivity between the manganese octahedra is very different in the two structures. The two copper frameworks, in contrast, consist of binuclear and mononuclear moieties (Na-Cu formate) and trinuclear and mononuclear moieties (K-Cu formate), respectively. Procrystal electron density analysis of the compounds indicates one-dimensional K(+)-ion conductivity in K-Mn and K-Cu, and the nature of the proposed potassium ion migration is compared with results from similar analysis on known Na(+) and K(+) ion conductors. K-Mn and Na-Mn were tested as cathode materials, but this resulted in poor reversibility due to low conductivity or structural collapse. The magnetic properties of the compounds were studied by vibrating sample magnetometric measurements, and their thermal stabilities were determined by thermogravimetric analysis and differential thermal analysis. Despite structural differences, the metal formates that contain the same transition metal have similar magnetic properties and thermal decomposition pathways, that is, the nature of the transition metal controls the compound properties.

  8. Computer templates in chronic disease management: ethnographic case study in general practice.

    Science.gov (United States)

    Swinglehurst, Deborah; Greenhalgh, Trisha; Roberts, Celia

    2012-01-01

    To investigate how electronic templates shape, enable and constrain consultations about chronic diseases. Ethnographic case study, combining field notes, video-recording, screen capture with a microanalysis of talk, body language and data entry-an approach called linguistic ethnography. Two general practices in England. Ethnographic observation of administrative areas and 36 nurse-led consultations was done. Twenty-four consultations were directly observed and 12 consultations were video-recorded alongside computer screen capture. Consultations were transcribed using conversation analysis conventions, with notes on body language and the electronic record. The analysis involved repeated rounds of viewing video, annotating field notes, transcription and microanalysis to identify themes. The data was interpreted using discourse analysis, with attention to the sociotechnical theory. Consultations centred explicitly or implicitly on evidence-based protocols inscribed in templates. Templates did not simply identify tasks for completion, but contributed to defining what chronic diseases were, how care was being delivered and what it meant to be a patient or professional in this context. Patients' stories morphed into data bytes; the particular became generalised; the complex was made discrete, simple and manageable; and uncertainty became categorised and contained. Many consultations resembled bureaucratic encounters, primarily oriented to completing data fields. We identified a tension, sharpened by the template, between different framings of the patient-as 'individual' or as 'one of a population'. Some clinicians overcame this tension, responding creatively to prompts within a dialogue constructed around the patient's narrative. Despite their widespread implementation, little previous research has examined how templates are actually used in practice. Templates do not simply document the tasks of chronic disease management but profoundly change the nature of this work

  9. Solvothermal removal of the organic template from L 3 ("sponge") templated silica monoliths

    Science.gov (United States)

    Dabbs, Daniel M.; Mulders, Norbert; Aksay, Ilhan A.

    2006-10-01

    We compare the methods of continuous solvent (Soxhlet) and supercritical solvent extractions for the removal of the organic template from nanostructured silica monoliths. Our monoliths are formed by templating the L 3 liquid crystal phase of cetylpyridinium chloride in aqueous solutions with tetramethoxy silane. The monoliths that result from both Soxhlet and supercritical extraction methods are mechanically robust, optically clear, and free of cracks. The Soxhlet method compares favorably with supercritical solvent extraction in that equivalent L 3-templated silica can be synthesized without the use of specialized reactor hardware or higher temperatures and high pressures, while avoiding noxious byproducts. The comparative effectiveness of various solvents in the Soxhlet process is related to the Hildebrand solubility parameter, determined by the effective surface area of the extracted silica.

  10. Immigrant Sexual Citizenship: Intersectional Templates among Mexican Gay Immigrants to the United States

    Science.gov (United States)

    Epstein, Steven; Carrillo, Héctor

    2014-01-01

    Existing literature on sexual citizenship has emphasized the sexuality-related claims of de jure citizens of nation-states, generally ignoring immigrants. Conversely, the literature on immigration rarely attends to the salience of sexual issues in understanding the social incorporation of migrants. This article seeks to fill the gap by theorizing and analyzing immigrant sexual citizenship. While some scholars of sexual citizenship have focused on the rights and recognition granted formally by the nation-state and others have stressed more diffuse, cultural perceptions of community and local belonging, we argue that the lived experiences of immigrant sexual citizenship call for multiscalar scrutiny of templates and practices of citizenship that bridge national policies with local connections. Analysis of ethnographic data from a study of 76 Mexican gay and bisexual male immigrants to San Diego, California reveals the specific citizenship templates that these men encounter as they negotiate their intersecting social statuses as gay/bisexual and as immigrants (legal or undocumented); these include an “asylum” template, a “rights” template, and a “local attachments” template. However, the complications of their intersecting identities constrain their capacity to claim immigrant sexual citizenship. The study underscores the importance of both intersectional and multiscalar approaches in research on citizenship as social practice. PMID:25013360

  11. Immigrant Sexual Citizenship: Intersectional Templates among Mexican Gay Immigrants to the United States.

    Science.gov (United States)

    Epstein, Steven; Carrillo, Héctor

    2014-01-01

    Existing literature on sexual citizenship has emphasized the sexuality-related claims of de jure citizens of nation-states, generally ignoring immigrants. Conversely, the literature on immigration rarely attends to the salience of sexual issues in understanding the social incorporation of migrants. This article seeks to fill the gap by theorizing and analyzing immigrant sexual citizenship . While some scholars of sexual citizenship have focused on the rights and recognition granted formally by the nation-state and others have stressed more diffuse, cultural perceptions of community and local belonging, we argue that the lived experiences of immigrant sexual citizenship call for multiscalar scrutiny of templates and practices of citizenship that bridge national policies with local connections. Analysis of ethnographic data from a study of 76 Mexican gay and bisexual male immigrants to San Diego, California reveals the specific citizenship templates that these men encounter as they negotiate their intersecting social statuses as gay/bisexual and as immigrants (legal or undocumented); these include an "asylum" template, a "rights" template, and a "local attachments" template. However, the complications of their intersecting identities constrain their capacity to claim immigrant sexual citizenship. The study underscores the importance of both intersectional and multiscalar approaches in research on citizenship as social practice.

  12. Subtle Distinctions: How Attentional Templates Influence EEG Parameters of Cognitive Control in a Spatial Cuing Paradigm

    Directory of Open Access Journals (Sweden)

    Christine Mertes

    2018-03-01

    Full Text Available Using event-related potentials (ERPs of the electroencephalogram, we investigated how cognitive control is altered by the scope of an attentional template currently activated in visual working memory. Participants performed a spatial cuing task where an irrelevant color singleton cue was presented prior to a target array. Blockwise, the target was either a red circle or a gray square and had to be searched within homogenous (gray circles or heterogeneous non-targets (differently colored circles or various shapes. Thereby we aimed to trigger the adoption of different attentional templates: a broader singleton or a narrower, more specific feature template. ERP markers of attentional selection and inhibitory control showed that the amount of cognitive control was overall enhanced when participants searched on the basis of a feature-specific template: the analysis revealed reduced selection (N2pc, frontal P2 and pronounced inhibition (negative shift of frontal N2 of the irrelevant color cue when participants searched for a feature target. On behavioral level attentional capture was most pronounced in the color condition with no differentiation between the task-induced scopes of the attentional template.

  13. Bio-fabrication and physiological self-release of tissue equivalents using smart peptide amphiphile templates.

    Science.gov (United States)

    Gouveia, Ricardo M; Hamley, Ian W; Connon, Che J

    2015-10-01

    In this study we applied a smart biomaterial formed from a self-assembling, multi-functional synthetic peptide amphiphile (PA) to coat substrates with various surface chemistries. The combination of PA coating and alignment-inducing functionalised substrates provided a template to instruct human corneal stromal fibroblasts to adhere, become aligned and then bio-fabricate a highly-ordered, multi-layered, three-dimensional tissue by depositing an aligned, native-like extracellular matrix. The newly-formed corneal tissue equivalent was subsequently able to eliminate the adhesive properties of the template and govern its own complete release via the action of endogenous proteases. Tissues recovered through this method were structurally stable, easily handled, and carrier-free. Furthermore, topographical and mechanical analysis by atomic force microscopy showed that tissue equivalents formed on the alignment-inducing PA template had highly-ordered, compact collagen deposition, with a two-fold higher elastic modulus compared to the less compact tissues produced on the non-alignment template, the PA-coated glass. We suggest that this technology represents a new paradigm in tissue engineering and regenerative medicine, whereby all processes for the bio-fabrication and subsequent self-release of natural, bio-prosthetic human tissues depend solely on simple template-tissue feedback interactions.

  14. Gause's principle and the effect of resource partitioning on the dynamical coexistence of replicating templates.

    Science.gov (United States)

    Szilágyi, András; Zachar, István; Szathmáry, Eörs

    2013-01-01

    Models of competitive template replication, although basic for replicator dynamics and primordial evolution, have not yet taken different sequences explicitly into account, neither have they analyzed the effect of resource partitioning (feeding on different resources) on coexistence. Here we show by analytical and numerical calculations that Gause's principle of competitive exclusion holds for template replicators if resources (nucleotides) affect growth linearly and coexistence is at fixed point attractors. Cases of complementary or homologous pairing between building blocks with parallel or antiparallel strands show no deviation from the rule that the nucleotide compositions of stably coexisting species must be different and there cannot be more coexisting replicator species than nucleotide types. Besides this overlooked mechanism of template coexistence we show also that interesting sequence effects prevail as parts of sequences that are copied earlier affect coexistence more strongly due to the higher concentration of the corresponding replication intermediates. Template and copy always count as one species due their constraint of strict stoichiometric coupling. Stability of fixed-point coexistence tends to decrease with the length of sequences, although this effect is unlikely to be detrimental for sequences below 100 nucleotides. In sum, resource partitioning (niche differentiation) is the default form of competitive coexistence for replicating templates feeding on a cocktail of different nucleotides, as it may have been the case in the RNA world. Our analysis of different pairing and strand orientation schemes is relevant for artificial and potentially astrobiological genetics.

  15. Photon-by-Photon Hidden Markov Model Analysis for Microsecond Single-Molecule FRET Kinetics.

    Science.gov (United States)

    Pirchi, Menahem; Tsukanov, Roman; Khamis, Rashid; Tomov, Toma E; Berger, Yaron; Khara, Dinesh C; Volkov, Hadas; Haran, Gilad; Nir, Eyal

    2016-12-29

    The function of biological macromolecules involves large-scale conformational dynamics spanning multiple time scales, from microseconds to seconds. Such conformational motions, which may involve whole domains or subunits of a protein, play a key role in allosteric regulation. There is an urgent need for experimental methods to probe the fastest of these motions. Single-molecule fluorescence experiments can in principle be used for observing such dynamics, but there is a lack of analysis methods that can extract the maximum amount of information from the data, down to the microsecond time scale. To address this issue, we introduce H 2 MM, a maximum likelihood estimation algorithm for photon-by-photon analysis of single-molecule fluorescence resonance energy transfer (FRET) experiments. H 2 MM is based on analytical estimators for model parameters, derived using the Baum-Welch algorithm. An efficient and effective method for the calculation of these estimators is introduced. H 2 MM is shown to accurately retrieve the reaction times from ∼1 s to ∼10 μs and even faster when applied to simulations of freely diffusing molecules. We further apply this algorithm to single-molecule FRET data collected from Holliday junction molecules and show that at low magnesium concentrations their kinetics are as fast as ∼10 4 s -1 . The new algorithm is particularly suitable for experiments on freely diffusing individual molecules and is readily incorporated into existing analysis packages. It paves the way for the broad application of single-molecule fluorescence to study ultrafast functional dynamics of biomolecules.

  16. Single-cell analysis of growth and cell division of the anaerobe Desulfovibrio vulgaris Hildenborough

    Directory of Open Access Journals (Sweden)

    Anouchka eFievet

    2015-12-01

    Full Text Available Recent years have seen significant progress in understanding basic bacterial cell cycle properties such as cell growth and cell division. While characterization and regulation of bacterial cell cycle is quite well documented in the case of fast growing aerobic model organisms, no data has been so far reported for anaerobic bacteria. This lack of information in anaerobic microorganisms can mainly be explained by the absence of molecular and cellular tools such as single cell microscopy and fluorescent probes usable for anaerobes and essential to study cellular events and/or subcellular localization of the actors involved in cell cycle.In this study, single-cell microscopy has been adapted to study for the first time, in real time, the cell cycle of a bacterial anaerobe, Desulfovibrio vulgaris Hildenborough (DvH. This single-cell analysis provides mechanistic insights into the cell division cycle of DvH, which seems to be governed by the recently discussed so-called incremental model that generates remarkably homogeneous cell sizes. Furthermore, cell division was reversibly blocked during oxygen exposure. This may constitute a strategy for anaerobic cells to cope with transient exposure to oxygen that they may encounter in their natural environment, thereby contributing to their aerotolerance. This study lays the foundation for the first molecular, single-cell assay that will address factors that cannot otherwise be resolved in bulk assays and that will allow visualization of a wide range of molecular mechanisms within living anaerobic cells.

  17. Microscopic and magnetic properties of template assisted electrodeposited iron nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Irshad, M. I., E-mail: imrancssp@gmail.com; Mohamed, N. M., E-mail: noranimuti-mohamed@petronas.com.my; Yar, A., E-mail: asfandyarhargan@gmail.com [Department of Fundamental & Applied Sciences, Universiti Teknologi PETRONAS, 31750 PERAK (Malaysia); Ahmad, F., E-mail: faizahmad@petronas.com.my; Abdullah, M. Z., E-mail: zaki-abdullah@petronas.com.my [Department of Mechanical Engineering, Universiti Teknologi PETRONAS, 31750 PERAK (Malaysia)

    2015-07-22

    Nanowires of magnetic materials such as Iron, nickel, cobalt, and alloys of them are one of the most widely investigated structures because of their possible applications in high density magnetic recording media, sensor elements, and building blocks in biological transport systems. In this work, Iron nanowires have been prepared by electrodeposition technique using Anodized Aluminium Oxide (AAO) templates. The electrolyte used consisted of FeSO{sub 4.}6H{sub 2}O buffered with H{sub 3}BO{sub 3} and acidized by dilute H{sub 2}SO{sub 4}. FESEM analysis shows that the asdeposited nanowires are parallel to one another and have high aspect ratio with a reasonably high pore-filing factor. To fabricate the working electrode, a thin film of copper (∼ 220 nm thick) was coated on back side of AAO template by e-beam evaporation system to create electrical contact with the external circuit. The TEM results show that electrodeposited nanowires have diameter around 100 nm and are polycrystalline in structure. Magnetic properties show the existence of anisotropy for in and out of plane configuration. These nanowires have potential applications in magnetic data storage, catalysis and magnetic sensor applications.

  18. Biosynthesis of amorphous mesoporous aluminophosphates using yeast cells as templates

    Energy Technology Data Exchange (ETDEWEB)

    Sifontes, Ángela B., E-mail: asifonte@ivic.gob.ve [Centro de Química, Instituto Venezolano de Investigaciones Científicas, Apartado 20632, Caracas 1020-A (Venezuela, Bolivarian Republic of); González, Gema [Centro de Ingeniería de Materiales y Nanotecnología, Instituto Venezolano de Investigaciones Científicas, Apartado 20632, Caracas 1020-A (Venezuela, Bolivarian Republic of); Tovar, Leidy M.; Méndez, Franklin J. [Centro de Química, Instituto Venezolano de Investigaciones Científicas, Apartado 20632, Caracas 1020-A (Venezuela, Bolivarian Republic of); Gomes, Maria E. [Centro de Ingeniería de Materiales y Nanotecnología, Instituto Venezolano de Investigaciones Científicas, Apartado 20632, Caracas 1020-A (Venezuela, Bolivarian Republic of); Cañizales, Edgar [Área de Análisis Químico Inorgánico, PDVSA, INTEVEP, Los Teques 1070-A (Venezuela, Bolivarian Republic of); Niño-Vega, Gustavo; Villalobos, Hector [Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Apartado 20632, Caracas 1020-A (Venezuela, Bolivarian Republic of); Brito, Joaquin L. [Centro de Química, Instituto Venezolano de Investigaciones Científicas, Apartado 20632, Caracas 1020-A (Venezuela, Bolivarian Republic of)

    2013-02-15

    Graphical abstract: Display Omitted Highlights: ► Amorphous aluminophosphates can take place using yeast as template. ► A mesoporous material was obtained. ► The specific surface area after calcinations ranged between 176 and 214 m{sup 2} g{sup −1}. -- Abstract: In this study aluminophosphates have been synthesized from aluminum isopropoxide and phosphoric acid solutions using yeast cells as template. The physicochemical characterization was carried out by thermogravimetric analysis; X-ray diffraction; Fourier transform infrared; N{sub 2} adsorption–desorption isotherms; scanning electron microscopy; transmission electron microscopy and potentiometric titration with N-butylamine for determination of: thermal stability; crystalline structure; textural properties; morphology and surface acidity, respectively. The calcined powders consisted of an intimate mixture of amorphous and crystallized AlPO particles with sizes between 23 and 30 nm. The average pore size observed is 13–16 nm and the specific surface area after calcinations (at 650 °C) ranged between 176 and 214 m{sup 2} g{sup −1}.

  19. Fire Protection Engineering Design Brief Template. Hydrogen Refueling Station.

    Energy Technology Data Exchange (ETDEWEB)

    LaFleur, Angela Christine [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Muna, Alice Baca [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Groth, Katrina M. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)

    2015-08-01

    Building a hydrogen infrastructure system is critical to supporting the development of alternate- fuel vehicles. This report provides a methodology for implementing a performance-based design of an outdoor hydrogen refueling station that does not meet specific prescriptive requirements in NFPA 2, The Hydrogen Technologies Code . Performance-based designs are a code-compliant alternative to meeting prescriptive requirements. Compliance is demonstrated by comparing a prescriptive-based fueling station design with a performance-based design approach using Quantitative Risk Assessment (QRA) methods and hydrogen risk assessment tools. This template utilizes the Sandia-developed QRA tool, Hydrogen Risk Analysis Models (HyRAM), which combines reduced-order deterministic models that characterize hydrogen release and flame behavior with probabilistic risk models to quantify risk values. Each project is unique and this template is not intended to account for site-specific characteristics. Instead, example content and a methodology are provided for a representative hydrogen refueling site which can be built upon for new hydrogen applications.

  20. Biosynthesis of amorphous mesoporous aluminophosphates using yeast cells as templates

    International Nuclear Information System (INIS)

    Sifontes, Ángela B.; González, Gema; Tovar, Leidy M.; Méndez, Franklin J.; Gomes, Maria E.; Cañizales, Edgar; Niño-Vega, Gustavo; Villalobos, Hector; Brito, Joaquin L.

    2013-01-01

    Graphical abstract: Display Omitted Highlights: ► Amorphous aluminophosphates can take place using yeast as template. ► A mesoporous material was obtained. ► The specific surface area after calcinations ranged between 176 and 214 m 2 g −1 . -- Abstract: In this study aluminophosphates have been synthesized from aluminum isopropoxide and phosphoric acid solutions using yeast cells as template. The physicochemical characterization was carried out by thermogravimetric analysis; X-ray diffraction; Fourier transform infrared; N 2 adsorption–desorption isotherms; scanning electron microscopy; transmission electron microscopy and potentiometric titration with N-butylamine for determination of: thermal stability; crystalline structure; textural properties; morphology and surface acidity, respectively. The calcined powders consisted of an intimate mixture of amorphous and crystallized AlPO particles with sizes between 23 and 30 nm. The average pore size observed is 13–16 nm and the specific surface area after calcinations (at 650 °C) ranged between 176 and 214 m 2 g −1 .

  1. In-situ preparation of functionalized molecular sieve material and a methodology to remove template.

    Science.gov (United States)

    Yadav, Rekha; Ahmed, Maqsood; Singh, Arvind Kumar; Sakthivel, Ayyamperumal

    2016-03-10

    A series of diaminosilane-functionalized silicoaluminophosphate molecular sieve (SAPO-37) was prepared by in-situ synthesis, and a novel method was developed for the selective removal of structure directing agent (SDA)/template from the functionalized SAPO-37.The complete removal of the SDA was evident according to FT-IR, TGA, (13)C MAS-NMR and elemental analysis. The developed method was found to be efficient for removal of template from microporous molecular sieve viz., SAPO-37 and can be applied for other microporous molecular sieves such as SAPO-5, SAPO-40, etc. The powder XRD pattern of the template-removed samples showed a highly crystalline SAPO-37 phase. Argentometric titration revealed that more than 90% of diamine functionality exposed on the surface was accessible for catalytic applications. The resultant materials showed promising activity for ring opening of epoxide with aniline to yield β-amino-alcohol.

  2. In-situ preparation of functionalized molecular sieve material and a methodology to remove template

    Science.gov (United States)

    Yadav, Rekha; Ahmed, Maqsood; Singh, Arvind Kumar; Sakthivel, Ayyamperumal

    2016-01-01

    A series of diaminosilane-functionalized silicoaluminophosphate molecular sieve (SAPO-37) was prepared by in-situ synthesis, and a novel method was developed for the selective removal of structure directing agent (SDA)/template from the functionalized SAPO-37.The complete removal of the SDA was evident according to FT-IR, TGA, 13C MAS-NMR and elemental analysis. The developed method was found to be efficient for removal of template from microporous molecular sieve viz., SAPO-37 and can be applied for other microporous molecular sieves such as SAPO-5, SAPO-40, etc. The powder XRD pattern of the template-removed samples showed a highly crystalline SAPO-37 phase. Argentometric titration revealed that more than 90% of diamine functionality exposed on the surface was accessible for catalytic applications. The resultant materials showed promising activity for ring opening of epoxide with aniline to yield β-amino-alcohol. PMID:26960707

  3. Enhanced Template Matching Using Dynamic Positional Warping for Identification of Specific Patterns in Electroencephalogram

    Directory of Open Access Journals (Sweden)

    Won-Du Chang

    2014-01-01

    Full Text Available Template matching is an approach for signal pattern recognition, often used for biomedical signals including electroencephalogram (EEG. Since EEG is often severely contaminated by various physiological or pathological artifacts, identification and rejection of these artifacts with improved template matching algorithms would enhance the overall quality of EEG signals. In this paper, we propose a novel approach to improve the accuracy of conventional template matching methods by adopting the dynamic positional warping (DPW technique, developed recently for handwriting pattern analysis. To validate the feasibility and superiority of the proposed method, eye-blink artifacts in the EEG signals were detected, and the results were then compared to those from conventional methods. DPW was found to outperform the conventional methods in terms of artifact detection accuracy, demonstrating the power of DPW in identifying specific one-dimensional data patterns.

  4. Evaluation of template-based models in CASP8 with standard measures

    KAUST Repository

    Cozzetto, Domenico

    2009-01-01

    The strategy for evaluating template-based models submitted to CASP has continuously evolved from CASP1 to CASP5, leading to a standard procedure that has been used in all subsequent editions. The established approach includes methods for calculating the quality of each individual model, for assigning scores based on the distribution of the results for each target and for computing the statistical significance of the differences in scores between prediction methods. These data are made available to the assessor of the template-based modeling category, who uses them as a starting point for further evaluations and analyses. This article describes the detailed workflow of the procedure, provides justifications for a number of choices that are customarily made for CASP data evaluation, and reports the results of the analysis of template-based predictions at CASP8.

  5. Recognition and separation of single particles with size variation by statistical analysis of their images.

    Science.gov (United States)

    White, Helen E; Saibil, Helen R; Ignatiou, Athanasios; Orlova, Elena V

    2004-02-13

    Macromolecules may occupy conformations with structural differences that cannot be resolved biochemically. The separation of mixed molecular populations is a pressing problem in single-particle analysis. Until recently, the task of distinguishing small structural variations was intractable, but developments in cryo-electron microscopy hardware and software now make it possible to address this problem. We have developed a general strategy for recognizing and separating structures of variable size from cryo-electron micrographs of single particles. The method uses a combination of statistical analysis and projection matching to multiple models. Identification of size variations by multivariate statistical analysis was used to do an initial separation of the data and generate starting models by angular reconstitution. Refinement was performed using alternate projection matching to models and angular reconstitution of the separated subsets. The approach has been successful at intermediate resolution, taking it within range of resolving secondary structure elements of proteins. Analysis of simulated and real data sets is used to illustrate the problems encountered and possible solutions. The strategy developed was used to resolve the structures of two forms of a small heat shock protein (Hsp26) that vary slightly in diameter and subunit packing.

  6. A Single Electrochemical Probe Used for Analysis of Multiple Nucleic Acid Sequences

    Science.gov (United States)

    Mills, Dawn M.; Calvo-Marzal, Percy; Pinzon, Jeffer M.; Armas, Stephanie; Kolpashchikov, Dmitry M.; Chumbimuni-Torres, Karin Y.

    2017-01-01

    Electrochemical hybridization sensors have been explored extensively for analysis of specific nucleic acids. However, commercialization of the platform is hindered by the need for attachment of separate oligonucleotide probes complementary to a RNA or DNA target to an electrode’s surface. Here we demonstrate that a single probe can be used to analyze several nucleic acid targets with high selectivity and low cost. The universal electrochemical four-way junction (4J)-forming (UE4J) sensor consists of a universal DNA stem-loop (USL) probe attached to the electrode’s surface and two adaptor strands (m and f) which hybridize to the USL probe and the analyte to form a 4J associate. The m adaptor strand was conjugated with a methylene blue redox marker for signal ON sensing and monitored using square wave voltammetry. We demonstrated that a single sensor can be used for detection of several different DNA/RNA sequences and can be regenerated in 30 seconds by a simple water rinse. The UE4J sensor enables a high selectivity by recognition of a single base substitution, even at room temperature. The UE4J sensor opens a venue for a re-useable universal platform that can be adopted at low cost for the analysis of DNA or RNA targets. PMID:29371782

  7. Mapping cellular hierarchy by single-cell analysis of the cell surface repertoire.

    Science.gov (United States)

    Guo, Guoji; Luc, Sidinh; Marco, Eugenio; Lin, Ta-Wei; Peng, Cong; Kerenyi, Marc A; Beyaz, Semir; Kim, Woojin; Xu, Jian; Das, Partha Pratim; Neff, Tobias; Zou, Keyong; Yuan, Guo-Cheng; Orkin, Stuart H

    2013-10-03

    Stem cell differentiation pathways are most often studied at the population level, whereas critical decisions are executed at the level of single cells. We have established a highly multiplexed, quantitative PCR assay to profile in an unbiased manner a panel of all commonly used cell surface markers (280 genes) from individual cells. With this method, we analyzed over 1,500 single cells throughout the mouse hematopoietic system and illustrate its utility for revealing important biological insights. The comprehensive single cell data set permits mapping of the mouse hematopoietic stem cell differentiation hierarchy by computational lineage progression analysis. Further profiling of 180 intracellular regulators enabled construction of a genetic network to assign the earliest differentiation event during hematopoietic lineage specification. Analysis of acute myeloid leukemia elicited by MLL-AF9 uncovered a distinct cellular hierarchy containing two independent self-renewing lineages with different clonal activities. The strategy has broad applicability in other cellular systems. Copyright © 2013 Elsevier Inc. All rights reserved.

  8. Modeling and analysis of variable speed single phase induction motors with iron loss

    International Nuclear Information System (INIS)

    Vaez-Zadeh, S.; Zahedi, B.

    2009-01-01

    Despite their usual low power ratings of single phase induction motors, they consume a considerable part of total motors energy consumption due to their large and ever-increasing quantity. The recent rising of oil prices and environmental crises has fortified the idea of energy saving practices in all applications; particularly in single phase induction motors due to their typical low efficiency. An essential requirement for this practice is the modeling and analysis of machine electrical losses under variable frequency operation. In this paper an improved steady state model of single phase induction motors is derived to investigate major motor characteristics like torque-speed, input power, output power, etc. A special emphasis is placed on accurately representing core losses at variable frequency. The winding currents phase difference is reintroduced as a fundamental motor variable to determine motor performances including losses and efficiency. An advanced computerized motor test setup is designed and built for on-line measurement of motor characteristics at different supply and operating conditions. The extensive experimental results, in good agreement with the simulation results based on the mentioned analysis, confirm the validity of the proposed model.

  9. Disentangling subpopulations in single-molecule FRET and ALEX experiments with photon distribution analysis.

    Science.gov (United States)

    Tomov, Toma E; Tsukanov, Roman; Masoud, Rula; Liber, Miran; Plavner, Noa; Nir, Eyal

    2012-03-07

    Among the advantages of the single-molecule approach when used to study biomolecular structural dynamics and interaction is its ability to distinguish between and independently observe minor subpopulations. In a single-molecule Förster resonance energy transfer (FRET) and alternating laser excitation diffusion experiment, the various populations are apparent in the resultant histograms. However, because histograms are calculated based on the per-burst mean FRET and stoichiometry ratio and not on the internal photon distribution, much of the acquired information is lost, thereby reducing the capabilities of the method. Here we suggest what to our knowledge is a novel statistical analysis tool that significantly enhances these capabilities, and we use it to identify and isolate static and dynamic subpopulations. Based on a kernel density estimator and a proper photon distribution analysis, for each individual burst, we calculate scores that reflect properties of interest. Specifically, we determine the FRET efficiency and brightness ratio distributions and use them to reveal 1), the underlying structure of a two-state DNA-hairpin and a DNA hairpin that is bound to DNA origami; 2), a minor doubly labeled dsDNA subpopulation concealed in a larger singly labeled dsDNA; and 3), functioning DNA origami motors concealed within a larger subpopulation of defective motors. Altogether, these findings demonstrate the usefulness of the proposed approach. The method was developed and tested using simulations, its rationality is described, and a computer algorithm is provided. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  10. Single molecule force spectroscopy at high data acquisition: A Bayesian nonparametric analysis

    Science.gov (United States)

    Sgouralis, Ioannis; Whitmore, Miles; Lapidus, Lisa; Comstock, Matthew J.; Pressé, Steve

    2018-03-01

    Bayesian nonparametrics (BNPs) are poised to have a deep impact in the analysis of single molecule data as they provide posterior probabilities over entire models consistent with the supplied data, not just model parameters of one preferred model. Thus they provide an elegant and rigorous solution to the difficult problem encountered when selecting an appropriate candidate model. Nevertheless, BNPs' flexibility to learn models and their associated parameters from experimental data is a double-edged sword. Most importantly, BNPs are prone to increasing the complexity of the estimated models due to artifactual features present in time traces. Thus, because of experimental challenges unique to single molecule methods, naive application of available BNP tools is not possible. Here we consider traces with time correlations and, as a specific example, we deal with force spectroscopy traces collected at high acquisition rates. While high acquisition rates are required in order to capture dwells in short-lived molecular states, in this setup, a slow response of the optical trap instrumentation (i.e., trapped beads, ambient fluid, and tethering handles) distorts the molecular signals introducing time correlations into the data that may be misinterpreted as true states by naive BNPs. Our adaptation of BNP tools explicitly takes into consideration these response dynamics, in addition to drift and noise, and makes unsupervised time series analysis of correlated single molecule force spectroscopy measurements possible, even at acquisition rates similar to or below the trap's response times.

  11. Single-Trial Linear Correlation Analysis: Application to characterization of stimulus modality effects

    Directory of Open Access Journals (Sweden)

    Christoforos eChristoforou

    2013-03-01

    Full Text Available A key objective in systems and cognitive neuroscience is to establish associations between behavioral measures and concurrent neuronal activity. Single-trial analysis has been proposed as a novel method for characterizing such correlates by first extracting neural components that maximally discriminate trials on a categorical variable, (e.g., hard vs. easy, correct vs. incorrect etc., and then correlate those components to a continues dependent variable of interest , e.g. reaction time, difficulty Index, etc. However, often times in experiment design it is difficult to either define meaningful categorical variables, or to record enough trials for the method to extract the discriminant components. Experiments designed for the study of the effects of stimulus presentation modality in working memory provide such a scenario, as will be exemplified. In this paper, we proposed a new approach to single-trial analysis in which we directly extract neural activity that maximally correlates to single-trial manual response times; eliminating the need to define an arbitrary categorical variable. We demonstrate our method on real EEG data recordings from the study of stimulus presentation modality effect.

  12. Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution.

    Science.gov (United States)

    Cabili, Moran N; Dunagin, Margaret C; McClanahan, Patrick D; Biaesch, Andrew; Padovan-Merhar, Olivia; Regev, Aviv; Rinn, John L; Raj, Arjun

    2015-01-29

    Long non-coding RNAs (lncRNAs) have been implicated in diverse biological processes. In contrast to extensive genomic annotation of lncRNA transcripts, far fewer have been characterized for subcellular localization and cell-to-cell variability. Addressing this requires systematic, direct visualization of lncRNAs in single cells at single-molecule resolution. We use single-molecule RNA-FISH to systematically quantify and categorize the subcellular localization patterns of a representative set of 61 lncRNAs in three different cell types. Our survey yields high-resolution quantification and stringent validation of the number and spatial positions of these lncRNA, with an mRNA set for comparison. Using this highly quantitative image-based dataset, we observe a variety of subcellular localization patterns, ranging from bright sub-nuclear foci to almost exclusively cytoplasmic localization. We also find that the low abundance of lncRNAs observed from cell population measurements cannot be explained by high expression in a small subset of 'jackpot' cells. Additionally, nuclear lncRNA foci dissolve during mitosis and become widely dispersed, suggesting these lncRNAs are not mitotic bookmarking factors. Moreover, we see that divergently transcribed lncRNAs do not always correlate with their cognate mRNA, nor do they have a characteristic localization pattern. Our systematic, high-resolution survey of lncRNA localization reveals aspects of lncRNAs that are similar to mRNAs, such as cell-to-cell variability, but also several distinct properties. These characteristics may correspond to particular functional roles. Our study also provides a quantitative description of lncRNAs at the single-cell level and a universally applicable framework for future study and validation of lncRNAs.

  13. Phase field simulation of template growth process in textured ceramics

    Science.gov (United States)

    Zhang, Yongmei; Liu, Liangliang

    2018-01-01

    The microstructure evolution of a template particle in a polycrystalline matrix during the templated grain growth process was simulated by a phase field approach. An initial microstructure including a rectangle (representing the template particle) and many circles (representing the matrix particles) was established with MATLAB software. The effects of the size and aspect ratio of the template particle on the development of microstructure were investigated by setting different areas and perimeters of the rectangle, respectively. When the aspect ratio >1, it was found that the template particle grew preferentially in the perpendicular direction rather than in the lateral direction along the casting plane. This could be attributed to the greater interface area between the large template and small matrix particles in the perpendicular direction. The results of the calculations indicated that there was a growth advantage for the template particle when its size was 3.46 times than that of the matrix particles in the two-dimensional system. The growth rate mainly depended on the aspect ratio of the template particle rather than on the template size. The simulation results gave a guiding principle for optimizing the process parameters, such as initial size and aspect ratio of template particle, when preparing highly textured ceramics.

  14. Pseudo-template synthesis of gold nanoparticles based on polyhydrosilanes

    International Nuclear Information System (INIS)

    Sacarescu, Liviu; Simionescu, Mihaela; Sacarescu, Gabriela

    2011-01-01

    Highly stable colloidal gold nanoparticles are obtained in a pseudo-template system using a specific polyhydrosilane copolymeric structure. This process takes place in situ by microwaves activation of the polymer solution in a non-polar solvent followed by stirring with solid HAuCl 4 in natural light. The experimental procedure is very simple and the resulted colloidal gold solution is indefinitely stable. The specific surface plasmon resonance absorption band of the gold nanoparticles is strongly red shifted and is strictly related to their size. AFM correlated with DLS analysis showed flattened round shaped colloidal polymer-gold nanoparticles with large diameters. SEM-EDX combined analysis reveals that the polysilane-gold nanoparticles show a natural tendency to auto-assemble in close packed structures which form large areas over the polymer film surface.

  15. Method for exploratory cluster analysis and visualisation of single-trial ERP ensembles.

    Science.gov (United States)

    Williams, N J; Nasuto, S J; Saddy, J D

    2015-07-30

    The validity of ensemble averaging on event-related potential (ERP) data has been questioned, due to its assumption that the ERP is identical across trials. Thus, there is a need for preliminary testing for cluster structure in the data. We propose a complete pipeline for the cluster analysis of ERP data. To increase the signal-to-noise (SNR) ratio of the raw single-trials, we used a denoising method based on Empirical Mode Decomposition (EMD). Next, we used a bootstrap-based method to determine the number of clusters, through a measure called the Stability Index (SI). We then used a clustering algorithm based on a Genetic Algorithm (GA) to define initial cluster centroids for subsequent k-means clustering. Finally, we visualised the clustering results through a scheme based on Principal Component Analysis (PCA). After validating the pipeline on simulated data, we tested it on data from two experiments - a P300 speller paradigm on a single subject and a language processing study on 25 subjects. Results revealed evidence for the existence of 6 clusters in one experimental condition from the language processing study. Further, a two-way chi-square test revealed an influence of subject on cluster membership. Our analysis operates on denoised single-trials, the number of clusters are determined in a principled manner and the results are presented through an intuitive visualisation. Given the cluster structure in some experimental conditions, we suggest application of cluster analysis as a preliminary step before ensemble averaging. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. A Single-Molecule Barcoding System using Nanoslits for DNA Analysis

    Science.gov (United States)

    Jo, Kyubong; Schramm, Timothy M.; Schwartz, David C.

    Single DNA molecule approaches are playing an increasingly central role in the analytical genomic sciences because single molecule techniques intrinsically provide individualized measurements of selected molecules, free from the constraints of bulk techniques, which blindly average noise and mask the presence of minor analyte components. Accordingly, a principal challenge that must be addressed by all single molecule approaches aimed at genome analysis is how to immobilize and manipulate DNA molecules for measurements that foster construction of large, biologically relevant data sets. For meeting this challenge, this chapter discusses an integrated approach for microfabricated and nanofabricated devices for the manipulation of elongated DNA molecules within nanoscale geometries. Ideally, large DNA coils stretch via nanoconfinement when channel dimensions are within tens of nanometers. Importantly, stretched, often immobilized, DNA molecules spanning hundreds of kilobase pairs are required by all analytical platforms working with large genomic substrates because imaging techniques acquire sequence information from molecules that normally exist in free solution as unrevealing random coils resembling floppy balls of yarn. However, nanoscale devices fabricated with sufficiently small dimensions fostering molecular stretching make these devices impractical because of the requirement of exotic fabrication technologies, costly materials, and poor operational efficiencies. In this chapter, such problems are addressed by discussion of a new approach to DNA presentation and analysis that establishes scaleable nanoconfinement conditions through reduction of ionic strength; stiffening DNA molecules thus enabling their arraying for analysis using easily fabricated devices that can also be mass produced. This new approach to DNA nanoconfinement is complemented by the development of a novel labeling scheme for reliable marking of individual molecules with fluorochrome labels

  17. Operation analysis of a Chebyshev-Pantograph leg mechanism for a single DOF biped robot

    Science.gov (United States)

    Liang, Conghui; Ceccarelli, Marco; Takeda, Yukio

    2012-12-01

    In this paper, operation analysis of a Chebyshev-Pantograph leg mechanism is presented for a single degree of freedom (DOF) biped robot. The proposed leg mechanism is composed of a Chebyshev four-bar linkage and a pantograph mechanism. In contrast to general fully actuated anthropomorphic leg mechanisms, the proposed leg mechanism has peculiar features like compactness, low-cost, and easy-operation. Kinematic equations of the proposed leg mechanism are formulated for a computer oriented simulation. Simulation results show the operation performance of the proposed leg mechanism with suitable characteristics. A parametric study has been carried out to evaluate the operation performance as function of design parameters. A prototype of a single DOF biped robot equipped with two proposed leg mechanisms has been built at LARM (Laboratory of Robotics and Mechatronics). Experimental test shows practical feasible walking ability of the prototype, as well as drawbacks are discussed for the mechanical design.

  18. Finite Element Analysis of Doorframe Structure of Single Oblique Pole Type in Container Crane

    Science.gov (United States)

    Cheng, X. F.; Wu, F. Q.; Tang, G.; Hu, X.

    2017-07-01

    Compared with the composite type, the single oblique pole type has more advantages, such as simple structure, thrift steel and high safe overhead clearance. The finite element model of the single oblique pole type is established in nodes by ANSYS, and more details are considered when the model is simplified, such as the section of Girder and Boom, torque in Girder and Boom occurred by Machinery house and Trolley, density according to the way of simplification etc. The stress and deformation of ten observation points are compared and analyzed, when the trolley is in nine dangerous positions. Based on the result of analysis, six dangerous points are selected to provide reference for the detection and evaluation of container crane.

  19. Stress relaxation analysis of single chondrocytes using porohyperelastic model based on AFM experiments

    Directory of Open Access Journals (Sweden)

    Trung Dung Nguyen

    2014-01-01

    Full Text Available Based on atomic force microscopytechnique, we found that the chondrocytes exhibits stress relaxation behavior. We explored the mechanism of this stress relaxation behavior and concluded that the intracellular fluid exuding out from the cells during deformation plays the most important role in the stress relaxation. We applied the inverse finite element analysis technique to determine necessary material parameters for porohyperelastic (PHE model to simulate stress relaxation behavior as this model is proven capable of capturing the non-linear behavior and the fluid-solid interaction during the stress relaxation of the single chondrocytes. It is observed that PHE model can precisely capture the stress relaxation behavior of single chondrocytes and would be a suitable model for cell biomechanics.

  20. Scaling analysis for the ocean motions in single phase natural circulation

    International Nuclear Information System (INIS)

    Yan, B.H.; Wen, Q.L.

    2015-01-01

    Highlights: • The scaling criteria for ocean motions are obtained. • The optimization and selection of the scaling criteria is also analyzed. • The oscillating period in experiments is determined by the time scale. - Abstract: The effects of ocean motions should be analyzed properly in order to guarantee the safety margin of facilities in the engineering design of floating nuclear reactor system. The scaling analysis for the ocean motions in single phase natural circulation is performed. The scaling criteria for both single ocean motions and compound ocean motions are obtained. The selection and optimization of scaling criteria is also analyzed. The oscillating amplitude in experiments should be kept to be identical to that in actual ocean motions. The oscillating period is determined by the time scale. The length scale, oscillating period and experimental power should be taken into consideration synthetically to obtain a reasonable experimental period

  1. A uHPLC-MS mathematical modeling approach to dry powder inhaler single agglomerate analysis.

    Science.gov (United States)

    Pennington, Justin; Lena, John; Medendorp, Joseph; Ewing, Gary

    2011-10-01

    Demonstration of content uniformity (CU) is critical toward the successful development of dry powder inhalers (DPIs). Methods for unit dose CU determination for DPI products are well-established within the field of respiratory science. Recent advances in the area include a uHPLC-MS method for high-throughput uniformity analysis, which allows for a greater understanding of blending operations as the industry transitions to a quality-by-design approach to development. Further enhancements to this uHPLC-MS method now enable it to determine CU and sample weight at the single agglomerate level, which is roughly 50× smaller than a unit dose. When coupled with optical microscopy-based agglomerate sizing, the enhanced uHPLC-MS method can also predict the density and porosity of individual agglomerates. Expanding analytical capabilities to the single agglomerate level provides greater insights and confidence in the DPI manufacturing process.

  2. A comprehensive strategy for the analysis of acoustic compressibility and optical deformability on single cells

    Science.gov (United States)

    Yang, Tie; Bragheri, Francesca; Nava, Giovanni; Chiodi, Ilaria; Mondello, Chiara; Osellame, Roberto; Berg-Sørensen, Kirstine; Cristiani, Ilaria; Minzioni, Paolo

    2016-04-01

    We realized an integrated microfluidic chip that allows measuring both optical deformability and acoustic compressibility on single cells, by optical stretching and acoustophoresis experiments respectively. Additionally, we propose a measurement protocol that allows evaluating the experimental apparatus parameters before performing the cell-characterization experiments, including a non-destructive method to characterize the optical force distribution inside the microchannel. The chip was used to study important cell-mechanics parameters in two human breast cancer cell lines, MCF7 and MDA-MB231. Results indicate that MDA-MB231 has both higher acoustic compressibility and higher optical deformability than MCF7, but statistical analysis shows that optical deformability and acoustic compressibility are not correlated parameters. This result suggests the possibility to use them to analyze the response of different cellular structures. We also demonstrate that it is possible to perform both measurements on a single cell, and that the order of the two experiments does not affect the retrieved values.

  3. Dataset for the quantitative proteomics analysis of the primary hepatocellular carcinoma with single and multiple lesions

    Directory of Open Access Journals (Sweden)

    Xiaohua Xing

    2015-12-01

    Full Text Available Hepatocellular Carcinoma (HCC is one of the most common malignant tumor, which is causing the second leading cancer-related death worldwide. The tumor tissues and the adjacent noncancerous tissues obtained from HCC patients with single and multiple lesions were quantified using iTRAQ. A total of 5513 proteins (FDR of 1% were identified which correspond to roughly 27% of the total liver proteome. And 107 and 330 proteins were dysregulated in HCC tissue with multiple lesions (MC group and HCC tissue with a single lesion (SC group, compared with their noncancerous tissue (MN and SN group respectively. Bioinformatics analysis (GO, KEGG and IPA allowed these data to be organized into distinct categories. The data accompanying the manuscript on this approach (Xing et al., J. Proteomics (2015, http://dx.doi.org/10.1016/j.jprot.2015.08.007 [1] have been deposited to the iProX with identifier IPX00037601.

  4. Synthesis and photocatalytic properties of graphitic carbon nitride nanofibers using porous anodic alumina templates

    Science.gov (United States)

    Suchitra, S. M.; Udayashankar, N. K.

    2017-12-01

    In the present study, we describe an effective method for the synthesis of Graphitic carbon nitride (GCN) nanostructures using porous anodic alumina (AAO) membrane as template by simple thermal condensation of cyanamide. Synthesized nanostructure was fully analysed by various techniques to detect its crystalline nature, morphology, luminescent properties followed by the evaluation of its photocatalytic activity in the degradation of Methylene blue dye. Structural analysis of synthesized GCNNF was systematically carried out using x-ray powder diffraction (XRD) and scanning electron microscope (SEM), and. The results confirmed the growth of GCN inside the nanochannels of anodic alumina templates. Luminescent properties of GCNNF were studied using photoluminescence (PL) spectroscopy. PL analysis showed the presence of a strong emission peak in the wavelength range of 350–600 nm in blue region. GCNNF displays higher photocatalytic performance in the photodegradation of methylene blue compare to the bulk GCN. Highlights 1. In the present paper, we report the synthesis of graphitic carbon nitride nanofibers (GCNNF) using porous anodic aluminium oxide membranes as templates through thermal condensation of cyanamide at 500 °C. 2. The synthesis of Graphitic carbon nitride nanofibers using porous andic alumina template is the efficient approach for increasing crystallinity and surface area. 3. The high surface area of graphitic carbon nitride nanofibers has a good impact on novel optical and photocatalytic properties of the bulkGCN. 4. AAO templating of GCN is one of the versatile method to produce tailorable GCN nanostructures with higher surface area and less number of structural defects. 5. Towards photocatalytic degradation of dyes, the tuning of physical properties is very essential thing hence we are succeeded in achieving better catalytic performance of GCN nanostructures by making use of AAO templates.

  5. Sampling and single particle analysis for the chemical characterisation of fine atmospheric particulates: A review.

    Science.gov (United States)

    Elmes, Michele; Gasparon, Massimo

    2017-11-01

    To better understand the potential environmental and human health impacts of fine airborne particulate matter (APM), detailed physical and chemical characterisation is required. The only means to accurately distinguish between the multiple compositions in APM is by single particle analysis. A variety of methods and instruments are available, which range from filter-based sample collection for off-line laboratory analysis to on-line instruments that detect the airborne particles and generate size distribution and chemical data in real time. There are many reasons for sampling particulates in the ambient atmosphere and as a consequence, different measurement strategies and sampling devices are used depending on the scientific objectives and subsequent analytical techniques. This review is designed as a guide to some of the techniques available for the sampling and subsequent chemical analysis of individual inorganic particles. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Combustion Analysis and Knock Detection in Single Cylinder DI-Diesel Engine Using Vibration Signature Analysis

    OpenAIRE

    Y.V.V.SatyanarayanaMurthy

    2011-01-01

    The purpose of this paper is to detect the “knock” in Diesel engines which deteriorate the engine performance adversely. The methodology introduced in the present work suggests a newly developed approach towards analyzing the vibration analysis of diesel engines. The method is based on fundamental relationship between the engine vibration pattern and the relative characteristics of the combustion process in each or different cylinders. Knock in diesel engine is detected by measuring the vibra...

  7. Nanostructured gold deposited in gelatin template applied for electrochemical assay of glucose in serum

    Czech Academy of Sciences Publication Activity Database

    Juřík, T.; Podešva, Pavel; Farka, Z.; Kovář, D.; Skládal, P.; Foret, František

    2016-01-01

    Roč. 188, JAN (2016), s. 277-285 ISSN 0013-4686 R&D Projects: GA ČR(CZ) GA15-15479S Institutional support: RVO:68081715 Keywords : gold nanostructures * gelatin template * glucose electrooxidation * blood analysis * non-enzymatic sensor Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 4.798, year: 2016

  8. Porous copper template from partially spark plasma-sintered Cu–Zn ...

    Indian Academy of Sciences (India)

    Administrator

    Dezincification and pore formation are conducted on sintered 0∙5 mm thick 12 mm diameter disc samples. The size, distribution and nature of pores in porous templates of Cu are then investigated using optical microscopy and SEM–EDS analysis. Keywords. Metal; corrosion; porous structure; sintering; powder metallurgy. 1.

  9. COPASAAR – A database for proteomic analysis of single amino acid repeats

    Directory of Open Access Journals (Sweden)

    Dalby Andrew R

    2005-08-01

    Full Text Available Abstract Background Single amino acid repeats make up a significant proportion in all of the proteomes that have currently been determined. They have been shown to be functionally and medically significant, and are associated with cancers and neuro-degenerative diseases such as Huntington's Chorea, where a poly-glutamine repeat is responsible for causing the disease. The COPASAAR database is a new tool to facilitate the rapid analysis of single amino acid repeats at a proteome level. The database aims to simplify the comparison of repeat distributions between proteomes in order to provide a better understanding of their function and evolution. Results A comparative analysis of all proteomes in the database (currently 244 shows that single amino acid repeats account for about 12–14% of the proteome of any given species. They are more common in eukaryotes (14% than in either archaea or bacteria (both 13%. Individual analyses of proteomes show that long single amino acid repeats (6+ residues are much more common in the Eukaryotes and that longer repeats are usually made up of hydrophilic amino acids such as glutamine, glutamic acid, asparagine, aspartic acid and serine. Conclusion COPASAAR is a useful tool for comparative proteomics that provides rapid access to amino acid repeat data that can be readily data-mined. The COPASAAR database can be queried at the kingdom, proteome or individual protein level. As the amount of available proteome data increases this will be increasingly important in order to automate proteome comparison. The insights gained from these studies will give a better insight into the evolution of protein sequence and function.

  10. A pharmacoeconomic analysis of the use of single MMC instillation in low risk NMIBC in Italy

    Directory of Open Access Journals (Sweden)

    Renzo Colombo

    2013-03-01

    Full Text Available BACKGROUND: Bladder cancer accounts for 5-10% of all cancers in Europe and up to 85% patients presents a noninvasive tumor, whose treatment of choice is the transurethral bladder resection (TURB paired with adjuvant intravesical chemotherapy or immunotherapy. Despite several clinical trials showed that this treatment is safe and decreases recurrences by 17% to 44% this practice is limited for many reasons. The study objective is to analyze the economical advantages of the single immediate post operative Mitomycin C instillation in Non Muscle-invasive Bladder Cancer (NMIBC low-risk patients.METHODS: A cost-benefit analysis was performed evaluating the economical gain that would raised from a scenario with a single immediate post operative mitomycin C instillation in each low-risk NMIBC patient who underwent to TURB. Net present value and cost-benefit ratio were calculated and sensitivity analyses were performed. Base case analysis was performed considering tumor recurrence rate reduction of 11.7% and a TURB costs of 2,167.0 €, while sensitivity analyses were performed using a recurrence rate reduction of 19.2% and 15.0% and a TURB cost of 2,472.93 €. The discount rate was 2%.RESULTS: The single immediate post operative instillation of mitomycin C resulted to be cost-beneficial with a cost-benefit ratio that goes from 0.48 to 0.79 when compared to TURB alone raising a Net Present Value that goes from 660,284.39 € to 2,650,530.79 €.CONCLUSION: This study demonstrates that even assuming conservative parameters for recurrence rates reduction, a single immediate post operative mitomycin C instillation in low risk NMIBC patients would lower not only the recurrence rate but also the caring cost for bladder cancer.

  11. Microbial single-cell analysis in picoliter-sized batch cultivation chambers.

    Science.gov (United States)

    Kaganovitch, Eugen; Steurer, Xenia; Dogan, Deniz; Probst, Christopher; Wiechert, Wolfgang; Kohlheyer, Dietrich

    2018-03-14

    Microfluidics has enabled various research projects in the field of microbial single-cell analysis. In particular, single-use microfluidic cultivation devices combined with automated time-lapse imaging provide powerful approaches for analyzing microbial phenomena at the single-cell level. High spatiotemporal resolution facilitates individual cell identification and tracking, delivering detailed insights into areas like phenotypic population heterogeneity, which can be highly relevant to the fate of a microbial population and may negatively impact the efficiency of biotechnological fermentations. New tools need to be developed to access the origin of population heterogeneity and understand its functional role. In this study, we present a microfluidic device for batch cultivations inside picoliter-sized cultivation chambers that can be reversibly isolated from continuous medium supply. Therefore, the cultivation broth is simply replaced by a continuous flow of humidified air, removing any medium residue along the supply channels but preserving five picoliters of cultivation medium inside the cultivation chambers in a highly parallel manner. Living cells can grow inside our microfabricated batch chambers, which can accommodate up to several hundred cells. The chamber height approximately matches the diameter of a single cell, facilitating cell growth in monolayers that are ideal for image-based cell analysis. We successfully demonstrated the growth of Escherichia coli during continuous medium perfusion and batch cultivation conditions. As expected, the cells grew exponentially under continuous medium influx until the maximum chamber capacity was reached, but when they were cultivated under batch conditions, cellular growth underwent an exponential phase, followed by a stationary phase with obvious morphological changes. Copyright © 2018 Elsevier B.V. All rights reserved.

  12. Progress of UV-NIL template making

    Science.gov (United States)

    Hiraka, Takaaki; Mizuochi, Jun; Nakanishi, Yuko; Yusa, Satoshi; Sasaki, Shiho; Morikawa, Yasutaka; Mohri, Hiroshi; Hayashi, Naoya

    2009-04-01

    Nano-imprint lithography (NIL) has been counted as one of the lithography candidates for hp32nm node and beyond and has showed excellent resolution capability with remarkable low line edge roughness that is attracting many researchers in the industry who were searching for the finest patterning technology. Therefore, recently we have been focusing on the resolution improvement on the NIL templates with the 100keV acceleration voltage spot beam (SB) EB writer and the 50keV acceleration voltage variable shaped beam (VSB) EB writer. The 100keV SB writers have high resolution capability, but they show fatally low throughput if we need full chip writing. Usually templates for resolution pioneers needed just a small field (several hundred microns square or so), but recently requirements for full chip templates are increasing. For full chip writing, we have also started the resolution improvement with the 50keV VSB writers used in current 4X photomask manufacturing. The 50keV VSB writers could generate full chip pattern in a reasonable time though resolution limits are inferior to that with the 100keV SB writers. In this paper, we will show latest results with both the 100keV SB and the 50keV VSB EB writers. With the 100keV SB EB writer, we have achieved down to hp15nm resolution for line and space pattern, but found that to achieve further improvement, an innovation in pattern generation method or material would be inevitable. With the 50keV VSB EB writer, we have achieved down to hp22nm resolution for line and space pattern. Though NIL has excellent resolution capability, solutions for defect inspection and repair are not clearly shown yet. In this paper, we will show preliminary inspection results with an EB inspection tool. We tested an EB inspection tool by Hermes Microvision, Inc. (HMI), which was originally developed for and are currently used as a wafer inspection tool, and now have been started to seek the application for mask use, using a programmed defect

  13. Consensus on Exercise Reporting Template (CERT)

    DEFF Research Database (Denmark)

    Slade, Susan C; Dionne, Clermont E; Underwood, Martin

    2016-01-01

    trials: the Consensus on Exercise Reporting Template (CERT). DESIGN AND METHODS: Using the EQUATOR Network's methodological framework, 137 exercise experts were invited to participate in a Delphi consensus study. A list of 41 items was identified from a meta-epidemiologic study of 73 systematic reviews......BACKGROUND: Exercise interventions are often incompletely described in reports of clinical trials, hampering evaluation of results and replication and implementation into practice. OBJECTIVE: The aim of this study was to develop a standardized method for reporting exercise programs in clinical...

  14. The Contextualization of Archetypes: Clinical Template Governance.

    Science.gov (United States)

    Pedersen, Rune; Ulriksen, Gro-Hilde; Ellingsen, Gunnar

    2015-01-01

    This paper is a status report from a large-scale openEHR-based EPR project from the North Norway Regional Health Authority. It concerns the standardization of a regional ICT portfolio and the ongoing development of a new process oriented EPR systems encouraged by the unfolding of a national repository for openEHR archetypes. Subject of interest; the contextualization of clinical templates is governed over multiple national boundaries which is complex due to the dependency of clinical resources. From the outset of this, we are interested in how local, regional, and national organizers maneuver to standardize while applying OpenEHR technology.

  15. Elliptical tiling method to generate a 2-dimensional set of templates for gravitational wave search

    International Nuclear Information System (INIS)

    Arnaud, Nicolas; Barsuglia, Matteo; Bizouard, Marie-Anne; Brisson, Violette; Cavalier, Fabien; Davier, Michel; Hello, Patrice; Kreckelbergh, Stephane; Porter, Edward K.

    2003-01-01

    Searching for a signal depending on unknown parameters in a noisy background with matched filtering techniques always requires an analysis of the data with several templates in parallel in order to ensure a proper match between the filter and the real waveform. The key feature of such an implementation is the design of the filter bank which must be small to limit the computational cost while keeping the detection efficiency as high as possible. This paper presents a geometrical method that allows one to cover the corresponding physical parameter space by a set of ellipses, each of them being associated with a given template. After the description of the main characteristics of the algorithm, the method is applied in the field of gravitational wave (GW) data analysis, for the search of damped sine signals. Such waveforms are expected to be produced during the deexcitation phase of black holes - the so-called 'ringdown' signals - and are also encountered in some numerically computed supernova signals. First, the number of templates N computed by the method is similar to its analytical estimation, despite the overlaps between neighbor templates and the border effects. Moreover, N is small enough to test for the first time the performances of the set of templates for different choices of the minimal match MM, the parameter used to define the maximal allowed loss of signal-to-noise ratio (SNR) due to the mismatch between real signals and templates. The main result of this analysis is that the fraction of SNR recovered is on average much higher than MM, which dramatically decreases the mean percentage of false dismissals. Indeed, it goes well below its estimated value of 1-MM 3 used as input of the algorithm. Thus, as this feature should be common to any tiling algorithm, it seems possible to reduce the constraint on the value of MM - and indeed the number of templates and the computing power - without losing as many events as expected on average. This should be of great

  16. Nanofluidic single-molecule sorting of DNA: a new concept in separation and analysis of biomolecules towards ultimate level performance

    International Nuclear Information System (INIS)

    Yamamoto, Takatoki; Fujii, Teruo

    2010-01-01

    Separation and separation-based analysis of biomolecules are fundamentally important techniques in the field of biotechnology. These techniques, however, depend on stochastic processes that intrinsically involve uncertainty, and thus it is not possible to achieve 100% separation accuracy. Theoretically, the ultimate resolution and sensitivity should be realized in a single-molecule system because of the deterministic nature of single-molecule manipulation. Here, we have proposed and experimentally demonstrated the concept of a 'single-molecule sorter' that detects and correctly identifies individual single molecules, realizing the ultimate level of resolution and sensitivity for any separation-based technology. The single-molecule sorter was created using a nanofluidic network consisting of a single inlet channel that branches off into multiple outlet channels. It includes two major functional elements, namely a single-molecule detection and identification element and a flow path switching element to accurately separate single molecules. With this system we have successfully demonstrated the world's first single-molecule sorting using DNA as a sample molecule. In the future, we hope to expand the application of such devices to comprehensive sorting of single-proteins from a single cell. We also believe that in addition to the single-molecule sorting method reported here, other types of single-molecule based processes will emerge and find use in a wide variety of applications.

  17. Automated patterning and probing with multiple nanoscale tools for single-cell analysis.

    Science.gov (United States)

    Li, Jiayao; Kim, Yeonuk; Liu, Boyin; Qin, Ruwen; Li, Jian; Fu, Jing

    2017-10-01

    The nano-manipulation approach that combines Focused Ion Beam (FIB) milling and various imaging and probing techniques enables researchers to investigate the cellular structures in three dimensions. Such fusion approach, however, requires extensive effort on locating and examining randomly-distributed targets due to limited Field of View (FOV) when high magnification is desired. In the present study, we present the development that automates 'pattern and probe' particularly for single-cell analysis, achieved by computer aided tools including feature recognition and geometric planning algorithms. Scheduling of serial FOVs for imaging and probing of multiple cells was considered as a rectangle covering problem, and optimal or near-optimal solutions were obtained with the heuristics developed. FIB milling was then employed automatically followed by downstream analysis using Atomic Force Microscopy (AFM) to probe the cellular interior. Our strategy was applied to examine bacterial cells (Klebsiella pneumoniae) and achieved high efficiency with limited human interference. The developed algorithms can be easily adapted and integrated with different imaging platforms towards high-throughput imaging analysis of single cells. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Accuracy of computer-assisted implant placement with insertion templates

    Science.gov (United States)

    Naziri, Eleni; Schramm, Alexander; Wilde, Frank

    2016-01-01

    Objectives: The purpose of this study was to assess the accuracy of computer-assisted implant insertion based on computed tomography and template-guided implant placement. Material and methods: A total of 246 implants were placed with the aid of 3D-based transfer templates in 181 consecutive partially edentulous patients. Five groups were formed on the basis of different implant systems, surgical protocols and guide sleeves. After virtual implant planning with the CoDiagnostiX Software, surgical guides were fabricated in a dental laboratory. After implant insertion, the actual implant position was registered intraoperatively and transferred to a model cast. Deviations between the preoperative plan and postoperative implant position were measured in a follow-up computed tomography of the patient’s model casts and image fusion with the preoperative computed tomography. Results: The median deviation between preoperative plan and postoperative implant position was 1.0 mm at the implant shoulder and 1.4 mm at the implant apex. The median angular deviation was 3.6º. There were significantly smaller angular deviations (P=0.000) and significantly lower deviations at the apex (P=0.008) in implants placed for a single-tooth restoration than in those placed at a free-end dental arch. The location of the implant, whether in the upper or lower jaw, did not significantly affect deviations. Increasing implant length had a significant negative influence on deviations from the planned implant position. There was only one significant difference between two out of the five implant systems used. Conclusion: The data of this clinical study demonstrate the accuracy and predictable implant placement when using laboratory-fabricated surgical guides based on computed tomography. PMID:27274440

  19. BOBA FRET: bootstrap-based analysis of single-molecule FRET data.

    Directory of Open Access Journals (Sweden)

    Sebastian L B König

    Full Text Available Time-binned single-molecule Förster resonance energy transfer (smFRET experiments with surface-tethered nucleic acids or proteins permit to follow folding and catalysis of single molecules in real-time. Due to the intrinsically low signal-to-noise ratio (SNR in smFRET time traces, research over the past years has focused on the development of new methods to extract discrete states (conformations from noisy data. However, limited observation time typically leads to pronounced cross-sample variability, i.e., single molecules display differences in the relative population of states and the corresponding conversion rates. Quantification of cross-sample variability is necessary to perform statistical testing in order to assess whether changes observed in response to an experimental parameter (metal ion concentration, the presence of a ligand, etc. are significant. However, such hypothesis testing has been disregarded to date, precluding robust biological interpretation. Here, we address this problem by a bootstrap-based approach to estimate the experimental variability. Simulated time traces are presented to assess the robustness of the algorithm in conjunction with approaches commonly used in thermodynamic and kinetic analysis of time-binned smFRET data. Furthermore, a pair of functionally important sequences derived from the self-cleaving group II intron Sc.ai5γ (d3'EBS1/IBS1 is used as a model system. Through statistical hypothesis testing, divalent metal ions are shown to have a statistically significant effect on both thermodynamic and kinetic aspects of their interaction. The Matlab source code used for analysis (bootstrap-based analysis of smFRET data, BOBA FRET, as well as a graphical user interface, is available via http://www.aci.uzh.ch/rna/.

  20. Survivorship Analysis of Clinical Adjacent-Segment Pathology After Single-Level Cervical Fusion.

    Science.gov (United States)

    Kong, Lingde; Ma, Qinghua; Yu, Kunlun; Cao, Junming; Wang, Linfeng; Shen, Yong

    2017-10-25

    BACKGROUND Clinical adjacent-segment pathology (CASP) is an important problem after anterior cervical surgery. The purpose of this study was to predict prevalence of CASP and determine the possible risk factors for CASP after single-level anterior cervical discectomy and fusion surgery. MATERIAL AND METHODS We retrospectively reviewed a series of patients who underwent single-level cervical discectomy and fusion surgery (ACDF). Both basic and radiographic data of patients were collected. Life-table method and Kaplan-Meier analysis were used to calculate prevalence of CASP and disease-free survival rate. Cox analysis was performed to determine the predictive factors for it. RESULTS A total of 256 patients were included in this study. The mean length of follow-up was 70.64 months. Among them, 31 patients were diagnosed as having CASP during follow-up. Nineteen of them were at the cephalad adjacent segment, and the other 12 were at the caudal segment. After ACDF procedures, 10.01% of patients developed new symptoms of CASP within 5 years, and the incidence increased to 23.89% after 10 years. The incidence rate of CASP was an average of 2.46% per year. Multivariate Cox regression analysis showed that congenital stenosis (hazard ratio [HR], 3.250; 95% confidence interval [CI], 1.538-6.867) and degeneration of adjacent segment (HR, 2.681; 95% CI, 1.259-5.709) were correlated with the incidence of CASP. CONCLUSIONS Patients with congenital stenosis and pre-existing degenerative changes of adjacent segments had a higher risk of developing CASP after single-level anterior cervical discectomy and fusion.

  1. Micromagnetic Cancer Cell Immobilization and Release for Real-Time Single Cell Analysis

    Science.gov (United States)

    Jaiswal, Devina; Rad, Armin Tahmasbi; Nieh, Mu-Ping; Claffey, Kevin P.; Hoshino, Kazunori

    2017-04-01

    Understanding the interaction of live cells with macromolecules is crucial for designing efficient therapies. Considering the functional heterogeneity found in cancer cells, real-time single cell analysis is necessary to characterize responses. In this study, we have designed and fabricated a microfluidic channel with patterned micromagnets which can temporarily immobilize the cells during analysis and release them after measurements. The microchannel is composed of plain coverslip top and bottom panels to facilitate easy microscopic observation and undisturbed application of analytes to the cells. Cells labeled with functionalized magnetic beads were immobilized in the device with an efficiency of 90.8±3.6%. Since the micromagnets are made of soft magnetic material (Ni), they released cells when external magnetic field was turned off from the channel. This allows the reuse of the channel for a new sample. As a model drug analysis, the immobilized breast cancer cells (MCF7) were exposed to fluorescent lipid nanoparticles and association and dissociation were measured through fluorescence analysis. Two concentrations of nanoparticles, 0.06 μg/ml and 0.08 μg/ml were tested and time lapse images were recorded and analyzed. The microfluidic device was able to provide a microenvironment for sample analysis, making it an efficient platform for real-time analysis.

  2. Micromagnetic Cancer Cell Immobilization and Release for Real-Time Single Cell Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Jaiswal, Devina; Rad, Armin Tahmasbi [Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269 (United States); Nieh, Mu-Ping [Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269 (United States); Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269 (United States); Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT 06269 (United States); Claffey, Kevin P. [Department of Cell Biology, University of Connecticut Health Center, Farmington, CT 06030 (United States); Hoshino, Kazunori, E-mail: hoshino@engr.uconn.edu [Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269 (United States)

    2017-04-01

    Understanding the interaction of live cells with macromolecules is crucial for designing efficient therapies. Considering the functional heterogeneity found in cancer cells, real-time single cell analysis is necessary to characterize responses. In this study, we have designed and fabricated a microfluidic channel with patterned micromagnets which can temporarily immobilize the cells during analysis and release them after measurements. The microchannel is composed of plain coverslip top and bottom panels to facilitate easy microscopic observation and undisturbed application of analytes to the cells. Cells labeled with functionalized magnetic beads were immobilized in the device with an efficiency of 90.8±3.6%. Since the micromagnets are made of soft magnetic material (Ni), they released cells when external magnetic field was turned off from the channel. This allows the reuse of the channel for a new sample. As a model drug analysis, the immobilized breast cancer cells (MCF7) were exposed to fluorescent lipid nanoparticles and association and dissociation were measured through fluorescence analysis. Two concentrations of nanoparticles, 0.06 µg/ml and 0.08 µg/ml were tested and time lapse images were recorded and analyzed. The microfluidic device was able to provide a microenvironment for sample analysis, making it an efficient platform for real-time analysis.

  3. Gamma Radiation-Induced Template Polymerization Technique

    International Nuclear Information System (INIS)

    Siyam, T.

    2005-01-01

    Gamma radiation induced copolymerization of acrylamide sodiumacrylate (AM-AANa) in the presence and absence of the polymer additive was studied at low monomer concentration(1.4M/l). The results showed that the exponents of the dose rate for the polymerization rate was found to be 1.3 and 1.4 in the absence and in the presence of the polymer additive respectively. The molecular weight of the formed polymer increased by addition of the polymer to the system. In the presence of the polymer the comonomers polymerize on the added polymer. In the absence of the added polymer the comonomers polymerize according to the copolymerization process at the initial stage of the copolymerization. While at high conversion the residual comonomers polymerize on the formed macromolecular chains of the produced polymer. These studies showed that the copolymerization in the presence of added polymer is completely template copolymerization while in the absence of the polymer the copolymerization process is only template process with a high conversion

  4. Random template placement and prior information

    International Nuclear Information System (INIS)

    Roever, Christian

    2010-01-01

    In signal detection problems, one is usually faced with the task of searching a parameter space for peaks in the likelihood function which indicate the presence of a signal. Random searches have proven to be very efficient as well as easy to implement, compared e.g. to searches along regular grids in parameter space. Knowledge of the parameterised shape of the signal searched for adds structure to the parameter space, i.e., there are usually regions requiring to be densely searched while in other regions a coarser search is sufficient. On the other hand, prior information identifies the regions in which a search will actually be promising or may likely be in vain. Defining specific figures of merit allows one to combine both template metric and prior distribution and devise optimal sampling schemes over the parameter space. We show an example related to the gravitational wave signal from a binary inspiral event. Here the template metric and prior information are particularly contradictory, since signals from low-mass systems tolerate the least mismatch in parameter space while high-mass systems are far more likely, as they imply a greater signal-to-noise ratio (SNR) and hence are detectable to greater distances. The derived sampling strategy is implemented in a Markov chain Monte Carlo (MCMC) algorithm where it improves convergence.

  5. Biocompatibility of Soft-Templated Mesoporous Carbons

    Energy Technology Data Exchange (ETDEWEB)

    Gencoglu, Maria F. [Michigan Technological Univ., Houghton, MI (United States). Dept. of Chemical Engineering; Spurri, Amanda [Widener Univ., Chester, PA (United States). Dept. of Chemical Engineering; Franko, Mitchell [Widener Univ., Chester, PA (United States). Dept. of Chemical Engineering; Chen, Jihua [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Science (CNMS); Hensley, Dale K. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Science (CNMS); Heldt, Caryn L. [Michigan Technological Univ., Houghton, MI (United States). Dept. of Chemical Engineering; Saha, Dipendu [Widener Univ., Chester, PA (United States). Dept. of Chemical Engineering

    2014-08-21

    We report that soft-templated mesoporous carbon is morphologically a non-nano type of carbon. It is a relatively newer variety of biomaterial, which has already demonstrated its successful role in drug delivery applications. To investigate the toxicity and biocompatibility, we introduced three types of mesoporous carbons with varying synthesis conditions and pore textural properties. We compared the Brunauer–Emmett–Teller (BET) surface area and pore width and performed cytotoxicity experiments with HeLa cells, cell viability studies with fibroblast cells and hemocomapatibility studies. Cytotoxicity tests reveal that two of the carbons are not cytotoxic, with cell survival over 90%. The mesoporous carbon with the highest surface area showed slight toxicity (~70% cell survival) at the highest carbon concentration of 500 μg/mL. Fibroblast cell viability assays suggested high and constant viability of over 98% after 3 days with no apparent relation with materials property and good visible cell-carbon compatibility. No hemolysis (<1%) was confirmed for all the carbon materials. Protein adsorption experiments with bovine serum albumin (BSA) and fibrinogen revealed a lower protein binding capacity of 0.2–0.6 mg/m2 and 2–4 mg/m2 for BSA and fibrinogen, respectively, with lower binding associated with an increase in surface area. The results of this study confirm the biocompatibility of soft-templated mesoporous carbons.

  6. Psychometric functions of uncertain template matching observers.

    Science.gov (United States)

    Geisler, Wilson S

    2018-02-01

    This theoretical note describes a simple equation that closely approximates the psychometric functions of template-matching observers with arbitrary levels of position and orientation uncertainty. We show that the approximation is accurate for detection of targets in white noise, 1/f noise, and natural backgrounds. In its simplest form, this equation, which we call the uncertain normal integral (UNI) function, has two parameters: one that varies only with the level of uncertainty and one that varies only with the other properties of the stimuli. The UNI function is useful for understanding and generating predictions of uncertain template matching (UTM) observers. For example, we use the UNI function to derive a closed-form expression for the detectability (d') of UTM observers in 1/f noise, as a function of target amplitude, background contrast, and position uncertainty. As a descriptive function, the UNI function is just as flexible and simple as other common descriptive functions, such as the Weibull function, and it avoids some of their undesirable properties. In addition, the estimated parameters have a clear interpretation within the family of UTM observers. Thus, the UNI function may be the better default descriptive formula for psychometric functions in detection and discrimination tasks.

  7. Periodic titania nanostructures using block copolymer templates.

    Science.gov (United States)

    Chinthamanipeta, Pavan S; Lou, Qin; Shipp, Devon A

    2011-01-25

    The deposition of periodic titania nanostructures, templated by a polystyrene-block-poly(4-vinylpyridine) (PS-b-P4VP) block copolymer, is reported. When cast as a thin film (30-50 nm thick), the PS-b-P4VP forms a morphology that consists of P4VP cylinders that are orientated perpendicular to the substrate. The P4VP phase was lightly cross-linked by exposing the film to diiodobutane. When the block copolymer film was exposed to the sol-gel titania precursor, titanium(IV) bis(ammonium lactate) dihydroxide (TALH), titania was formed in the P4VP phase. The resulting titania structures were identical in size to the P4VP cylinders and only formed (under the deposition conditions used in this study) when the block copolymer film was present on the substrate, thus providing evidence that the block copolymer indeed acts as a template. The process works for both silicon and indium tin oxide substrates.

  8. Templated electrodeposition of functional nanostructures: nanowires, nanotubes and nanocubes

    OpenAIRE

    Maijenburg, A.W.

    2014-01-01

    This thesis is entitled “Templated electrodeposition of functional nanostructures: nanowires, nanotubes and nanocubes”. Templated electrodeposition is the synthesis technique that was used throughout this thesis, and it comprises the use of a template with specific shape and dimensions for the formation of different types of nanostructures. Throughout this thesis, three different nanostructures were made: nanowires (Chapters 2 to 6), nanotubes (Chapters 2 and 5) and nanocubes (Chapters 7 and ...

  9. Modal analysis based equivalent circuit model and its verification for a single cMUT cell

    International Nuclear Information System (INIS)

    Mao, S P; Rottenberg, X; Rochus, V; Czarnecki, P; Helin, P; Severi, S; Tilmans, H A C; Nauwelaers, B

    2017-01-01

    This paper presents the lumped equivalent circuit model and its verification of both transmission and reception properties of a single cell capacitive micromachined ultrasonic transducer (cMUT), which is operating in a non-collapse small signal region. The derivation of this equivalent circuit model is based on the modal analysis techniques, harmonic modes are included by using the mode superposition method; and thus a wide frequency range response of the cMUT cell can be simulated by our equivalent circuit model. The importance of the cross modal coupling between different eigenmodes of a cMUT cell is discussed by us for the first time. In this paper the development of this model is only illustrated by a single circular cMUT cell under a uniform excitation. Extension of this model and corresponding results under a more generalized excitation will be presented in our upcoming publication (Mao et al 2016 Proc. IEEE Int. Ultrasonics Symp .). This model is verified by both finite element method (FEM) simulation and experimental characterizations. Results predicted by our model are in a good agreement with the FEM simulation results, and this works for a single cMUT cell operated in either transmission or reception. Results obtained from the model also rather match the experimental results of the cMUT cell. This equivalent circuit model provides an easy and precise way to rapidly predict the behaviors of cMUT cells. (paper)

  10. Modal analysis based equivalent circuit model and its verification for a single cMUT cell

    Science.gov (United States)

    Mao, S. P.; Rottenberg, X.; Rochus, V.; Czarnecki, P.; Helin, P.; Severi, S.; Nauwelaers, B.; Tilmans, H. A. C.

    2017-03-01

    This paper presents the lumped equivalent circuit model and its verification of both transmission and reception properties of a single cell capacitive micromachined ultrasonic transducer (cMUT), which is operating in a non-collapse small signal region. The derivation of this equivalent circuit model is based on the modal analysis techniques, harmonic modes are included by using the mode superposition method; and thus a wide frequency range response of the cMUT cell can be simulated by our equivalent circuit model. The importance of the cross modal coupling between different eigenmodes of a cMUT cell is discussed by us for the first time. In this paper the development of this model is only illustrated by a single circular cMUT cell under a uniform excitation. Extension of this model and corresponding results under a more generalized excitation will be presented in our upcoming publication (Mao et al 2016 Proc. IEEE Int. Ultrasonics Symp.). This model is verified by both finite element method (FEM) simulation and experimental characterizations. Results predicted by our model are in a good agreement with the FEM simulation results, and this works for a single cMUT cell operated in either transmission or reception. Results obtained from the model also rather match the experimental results of the cMUT cell. This equivalent circuit model provides an easy and precise way to rapidly predict the behaviors of cMUT cells.

  11. Expression analysis of multiple myeloma CD138 negative progenitor cells using single molecule microarray readout

    Science.gov (United States)

    Jacak, Jaroslaw; Schnidar, Harald; Muresan, Leila; Regl, Gerhard; Frischauf, Annemarie; Aberger, Fritz; Schütz, Gerhard J.; Hesse, Jan

    2013-01-01

    We present a highly sensitive bioanalytical microarray assay that enables the analysis of small genomic sample material. By combining an optimized cDNA purification step with single molecule cDNA detection on the microarray, the platform has improved sensitivity compared to conventional systems, allowing amplification-free determination of expression profiles with as little as 600 ng total RNA. Total RNA from cells was reverse transcribed into fluorescently labeled cDNA and purified employing a precipitation method that minimizes loss of cDNA material. The microarray was scanned on a fluorescence chip-reader with single molecule sensitivity. Using the newly developed platform we were able to analyze the RNA expression profile of a subpopulation of rare multiple myeloma CD138 negative progenitor (MM CD138neg) cells. The high-sensitivity microarray approach led to the identification of a set of 20 genes differentially expressed in MM CD138neg cells. Our work demonstrates the applicability of a straight-forward single-molecule DNA array technology to current topics of molecular and cellular cancer research, which are otherwise difficult to address due to the limited amount of sample material. PMID:23416329

  12. Single-incision versus conventional laparoscopic appendectomy in 688 patients: a retrospective comparative analysis

    Science.gov (United States)

    Liang, Hung-Hua; Hung, Chin-Sheng; Wang, Weu; Tam, Ka-Wai; Chang, Chun-Chao; Liu, Hui-Hsiung; Yen, Ko-Li; Wei, Po-Li

    2014-01-01

    Background Laparoscopic surgery has become the standard for treating appendicitis. The cosmetic benefits of using single-incision laparoscopy are well known, but its duration, complications and time to recovery have not been well documented. We compared 2 laparoscopic approaches for treating appendicitis and evaluated postoperative pain, complications and time to full recovery. Methods We retrospectively reviewed the cases of consecutive patients with appendicitis and compared those who underwent conventional laparoscopic appendectomy (CLA) performed using 3 incisions and those who underwent single-incision laparoscopic appendectomy (SILA). During SILA, the single port was prepared to increase visibility of the operative site. Results Our analysis included 688 consecutive patients: 618 who underwent CLA and 70 who underwent SILA. Postsurgical complications occurred more frequently in the CLA than the SILA group (18.1% v. 7.1%, p = 0.018). Patients who underwent SILA returned to oral feeding sooner than those who underwent CLA (median 12 h v. 22 h, p cosmetic advantages, SILA led to rapid recovery and no increase in postsurgical pain or complications. PMID:24869622

  13. Automatic CTF correction for single particles based upon multivariate statistical analysis of individual power spectra.

    Science.gov (United States)

    Sander, B; Golas, M M; Stark, H

    2003-06-01

    Three-dimensional electron cryomicroscopy of randomly oriented single particles is a method that is suitable for the determination of three-dimensional structures of macromolecular complexes at molecular resolution. However, the electron-microscopical projection images are modulated by a contrast transfer function (CTF) that prevents the calculation of three-dimensional reconstructions of biological complexes at high resolution from uncorrected images. We describe here an automated method for the accurate determination and correction of the CTF parameters defocus, twofold astigmatism and amplitude-contrast proportion from single-particle images. At the same time, the method allows the frequency-dependent signal decrease (B factor) and the non-convoluted background signal to be estimated. The method involves the classification of the power spectra of single-particle images into groups with similar CTF parameters; this is done by multivariate statistical analysis (MSA) and hierarchically ascending classification (HAC). Averaging over several power spectra generates class averages with enhanced signal-to-noise ratios. The correct CTF parameters can be deduced from these class averages by applying an iterative correlation procedure with theoretical CTF functions; they are then used to correct the raw images. Furthermore, the method enables the tilt axis of the sample holder to be determined and allows the elimination of individual poor-quality images that show high drift or charging effects.

  14. Analysis of ergosterol in single kernel and ground grain by gas chromatography-mass spectrometry.

    Science.gov (United States)

    Dong, Yanhong; Steffenson, Brian J; Mirocha, Chester J

    2006-06-14

    A method for analyzing ergosterol in a single kernel and ground barley and wheat was developed using gas chromatography-mass spectrometry (GC-MS). Samples were saponified in methanolic KOH. Ergosterol was extracted by "one step" hexane extraction and subsequently silylated by N-trimethylsilylimidazole/trimethylchlorosilane (TMSI/TMCS) reagent at room temperature. The recoveries of ergosterol from ground barley were 96.6, 97.1, 97.1, 88.5, and 90.3% at the levels of 0.2, 1, 5, 10, and 20 microg/g (ppm), respectively. The recoveries from a single kernel were between 93.0 and 95.9%. The precision (coefficient of variance) of the method was in the range 0.8-12.3%. The method detection limit (MDL) and the method quantification limit (MQL) were 18.5 and 55.6 ng/g (ppb), respectively. The ergosterol analysis method developed can be used to handle 80 samples daily by one person, making it suitable for screening cereal cultivars for resistance to fungal infection. The ability for detecting low levels of ergosterol in a single kernel provides a tool to investigate early fungal invasion and to study mechanisms of resistance to fungal diseases.

  15. Preparing Viable Single Cells from Human Tissue and Tumors for Cytomic Analysis.

    Science.gov (United States)

    Leelatian, Nalin; Doxie, Deon B; Greenplate, Allison R; Sinnaeve, Justine; Ihrie, Rebecca A; Irish, Jonathan M

    2017-04-03

    Mass cytometry is a single-cell biology technique that samples >500 cells per second, measures >35 features per cell, and is sensitive across a dynamic range of >10 4 relative intensity units per feature. This combination of technical assets has powered a series of recent cytomic studies where investigators used mass cytometry to measure protein and phospho-protein expression in millions of cells, characterize rare cell types in healthy and diseased tissues, and reveal novel, unexpected cells. However, these advances largely occurred in studies of blood, lymphoid tissues, and bone marrow, since the cells in these tissues are readily obtained in single-cell suspensions. This unit establishes a primer for single-cell analysis of solid tumors and tissues, and has been tested with mass cytometry. The cells obtained from these protocols can be fixed for study, cryopreserved for long-term storage, or perturbed ex vivo to dissect responses to stimuli and inhibitors. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  16. Spatial-Temporal Feature Analysis on Single-Trial Event Related Potential for Rapid Face Identification

    Directory of Open Access Journals (Sweden)

    Lei Jiang

    2017-11-01

    Full Text Available The event-related potential (ERP is the brain response measured in electroencephalography (EEG, which reflects the process of human cognitive activity. ERP has been introduced into brain computer interfaces (BCIs to communicate the computer with the subject's intention. Due to the low signal-to-noise ratio of EEG, most ERP studies are based on grand-averaging over many trials. Recently single-trial ERP detection attracts more attention, which enables real time processing tasks as rapid face identification. All the targets needed to be retrieved may appear only once, and there is no knowledge of target label for averaging. More interestingly, how the features contribute temporally and spatially to single-trial ERP detection has not been fully investigated. In this paper, we propose to implement a local-learning-based (LLB feature extraction method to investigate the importance of spatial-temporal components of ERP in a task of rapid face identification using single-trial detection. Comparing to previous methods, LLB method preserves the nonlinear structure of EEG signal distribution, and analyze the importance of original spatial-temporal components via optimization in feature space. As a data-driven methods, the weighting of the spatial-temporal component does not depend on the ERP detection method. The importance weights are optimized by making the targets more different from non-targets in feature space, and regularization penalty is introduced in optimization for sparse weights. This spatial-temporal feature extraction method is evaluated on the EEG data of 15 participants in performing a face identification task using rapid serial visual presentation paradigm. Comparing with other methods, the proposed spatial-temporal analysis method uses sparser (only 10% of the total features, and could achieve comparable performance (98% of single-trial ERP detection as the whole features across different detection methods. The interesting finding is

  17. A generic process template for continuous pharmaceutical production

    DEFF Research Database (Denmark)

    Singh, Ravendra; Rozada-Sanches, Raquel; Dean, William

    2012-01-01

    In the work reported here, a conceptual generic continuous process template for pharmaceutical production is presented. The template is demonstrated on a nitro reduction case study that should in principle be generic such that it can handle a series of substrates with similar molecular functional......In the work reported here, a conceptual generic continuous process template for pharmaceutical production is presented. The template is demonstrated on a nitro reduction case study that should in principle be generic such that it can handle a series of substrates with similar molecular...

  18. Directed self-assembly graphoepitaxy template generation with immersion lithography

    Science.gov (United States)

    Ma, Yuansheng; Lei, Junjiang; Andres Torres, J.; Hong, Le; Word, James; Fenger, Germain; Tritchkov, Alexander; Lippincott, George; Gupta, Rachit; Lafferty, Neal; He, Yuan; Bekaert, Joost; Vanderberghe, Geert

    2015-07-01

    We present an optimization methodology for the template designs of subresolution contacts using directed self-assembly (DSA) with graphoepitaxy and immersion lithography. We demonstrate the flow using a 60-nm-pitch contact design in doublet with Monte Carlo simulations for DSA. We introduce the notion of template error enhancement factor (TEEF) to gauge the sensitivity of DSA printing infidelity to template printing infidelity and evaluate optimized template designs with TEEF metrics. Our data show that source mask optimization and inverse lithography technology are critical to achieve sub-80 nm non-L0 pitches for DSA patterns using 193i.

  19. Short template switch events explain mutation clusters in the human genome.

    Science.gov (United States)

    Löytynoja, Ari; Goldman, Nick

    2017-06-01

    Resequencing efforts are uncovering the extent of genetic variation in humans and provide data to study the evolutionary processes shaping our genome. One recurring puzzle in both intra- and inter-species studies is the high frequency of complex mutations comprising multiple nearby base substitutions or insertion-deletions. We devised a generalized mutation model of template switching during replication that extends existing models of genome rearrangement and used this to study the role of template switch events in the origin of short mutation clusters. Applied to the human genome, our model detects thousands of template switch events during the evolution of human and chimp from their common ancestor and hundreds of events between two independently sequenced human genomes. Although many of these are consistent with a template switch mechanism previously proposed for bacteria, our model also identifies new types of mutations that create short inversions, some flanked by paired inverted repeats. The local template switch process can create numerous complex mutation patterns, including hairpin loop structures, and explains multinucleotide mutations and compensatory substitutions without invoking positive selection, speculative mechanisms, or implausible coincidence. Clustered sequence differences are challenging for current mapping and variant calling methods, and we show that many erroneous variant annotations exist in human reference data. Local template switch events may have been neglected as an explanation for complex mutations because of biases in commonly used analyses. Incorporation of our model into reference-based analysis pipelines and comparisons of de novo assembled genomes will lead to improved understanding of genome variation and evolution. © 2017 Löytynoja and Goldman; Published by Cold Spring Harbor Laboratory Press.

  20. Analysis of the Working Cable System of Single-span Circulating Ropeway

    Directory of Open Access Journals (Sweden)

    Qin Jian

    2017-01-01

    Full Text Available Based on the analysis of the mutual interaction between bearing cable and traction cable of single-span circulating ropeway, the calculation method is proposed for working cables of ropeway with arbitrary loads. The 5 sets nonlinear equations are set up for the working cables according to the equal spans and altitude differences of the bearing cable and the traction cable, the constant of the load running space and the bearing cable length, and the tension balance of bearing cable and traction cable beside load. The resolving method is proposed based on the Newton iterative method. The correctness and feasibility of the method are proved by the results of engineering test. From the solution, the tension and coordinate of working cables can be obtained accurately, which is meaningful for the design and analysis of the freight ropeway.

  1. Combustion Property Analysis and Control System for the Dynamics of a Single Cylinder Diesel Engine

    Directory of Open Access Journals (Sweden)

    Bambang Wahono

    2013-12-01

    Full Text Available Corresponding to global environment problems in recent year, the technology for reducing fuel consumption and exhaust gas emission of engine was needed. Simulation of transient engine response is needed to predict engine performance that frequently experience rapid changes of speed. The aim of this research is to develop a non-linear dynamic control model for direct injection single cylinder diesel engine which can simulate engine performance under transient conditions. In this paper, the combustion model with multistage injection and conducted experiments in the transient conditions to clarify the combustion characteristics was proposed. In order to perform the analysis of acceleration operation characteristics, it was built a Model Predictive Control (MPC to reproduce the characteristic values of the exhaust gas and fuel consumption from the control parameters in particular. Finally, MPC is an effective method to perform the analysis of characteristic in diesel engine under transient conditions.

  2. Moving scanning emitter tracking by a single observer using time of interception: Observability analysis and algorithm

    Directory of Open Access Journals (Sweden)

    Yifei ZHANG

    2017-06-01

    Full Text Available The target motion analysis (TMA for a moving scanning emitter with known fixed scan rate by a single observer using the time of interception (TOI measurements only is investigated in this paper. By transforming the TOI of multiple scan cycles into the direction difference of arrival (DDOA model, the observability analysis for the TMA problem is performed. Some necessary conditions for uniquely identifying the scanning emitter trajectory are obtained. This paper also proposes a weighted instrumental variable (WIV estimator for the scanning emitter TMA, which does not require any initial solution guess and is closed-form and computationally attractive. More importantly, simulations show that the proposed algorithm can provide estimation mean square error close to the Cramer-Rao lower bound (CRLB at moderate noise levels with significantly lower estimation bias than the conventional pseudo-linear least square (PLS estimator.

  3. Series solution for continuous population models for single and interacting species by the homotopy analysis method

    Directory of Open Access Journals (Sweden)

    Magdy A. El-Tawil

    2012-07-01

    Full Text Available The homotopy analysis method (HAM is used to find approximate analytical solutions of continuous population models for single and interacting species. The homotopy analysis method contains the auxiliary parameter $hbar,$ which provides us with a simple way to adjust and control the convergence region of series solution. the solutions are compared with the numerical results obtained using NDSolve, an ordinary differential equation solver found in the Mathematica package and a good agreement is found. Also the solutions are compared with the available analytic results obtained by other methods and more accurate and convergent series solution found. The convergence region is also computed which shows the validity of the HAM solution. This method is reliable and manageable.

  4. Synthesis, structure, and photoluminescence properties of an organically-templated uranyl selenite

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Dong-Sheng; Kuang, Han-Mao; Chen, Wen-Tong; Luo, Qiu-Yan; Sui, Yan [Institute of Applied Chemistry, School of Chemistry and Chemical Engineering, Jinggangshan University, Ji' an, Jiangxi 343009 (China)

    2015-09-15

    The organically-templated uranyl selenite, (H{sub 2}en)[(UO{sub 2})(SeO{sub 3})(HSeO{sub 3})](NO{sub 3}).0.5H{sub 2}O (1) (en = 1,2-ethylenediamine) was synthesized and characterized by elemental analyses, IR spectroscopy, TG, and single-crystal X-ray diffraction. Compound 1 crystallizes in the orthorhombic system, space group Pbca, with a = 13.170(3) Aa, b = 11.055(2) Aa, c = 18.009(4) Aa, V = 2621.8(9) Aa{sup 3}, M = 1316.19, Z = 4, D{sub cal} = 3.334 g.cm{sup -3}, μ(Mo-K{sub α}) = 17.998 mm{sup -1}, GOF = 1.059, R{sub 1} = 0.0263, wR{sub 2} = 0.0532 [I>2σ(I)]. The X-ray diffraction analysis reveals that compound 1 has a three-dimensional (3D) supramolecular structure. It contains negatively charged [UO{sub 2}(HSeO{sub 3})(SeO{sub 3})]{sup -} inorganic anion layers and is balanced by [H{sub 2}en]{sup 2+} cations and NO{sub 3}{sup -} anions located in the interlayers. Furthermore, the photoluminescence properties of 1 were investigated. (Copyright copyright 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  5. Synthesis, structure, and photoluminescence properties of an organically-templated uranyl selenite

    International Nuclear Information System (INIS)

    Liu, Dong-Sheng; Kuang, Han-Mao; Chen, Wen-Tong; Luo, Qiu-Yan; Sui, Yan

    2015-01-01

    The organically-templated uranyl selenite, (H 2 en)[(UO 2 )(SeO 3 )(HSeO 3 )](NO 3 ).0.5H 2 O (1) (en = 1,2-ethylenediamine) was synthesized and characterized by elemental analyses, IR spectroscopy, TG, and single-crystal X-ray diffraction. Compound 1 crystallizes in the orthorhombic system, space group Pbca, with a = 13.170(3) Aa, b = 11.055(2) Aa, c = 18.009(4) Aa, V = 2621.8(9) Aa 3 , M = 1316.19, Z = 4, D cal = 3.334 g.cm -3 , μ(Mo-K α ) = 17.998 mm -1 , GOF = 1.059, R 1 = 0.0263, wR 2 = 0.0532 [I>2σ(I)]. The X-ray diffraction analysis reveals that compound 1 has a three-dimensional (3D) supramolecular structure. It contains negatively charged [UO 2 (HSeO 3 )(SeO 3 )] - inorganic anion layers and is balanced by [H 2 en] 2+ cations and NO 3 - anions located in the interlayers. Furthermore, the photoluminescence properties of 1 were investigated. (Copyright copyright 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  6. Synthesis of MnO2 Microfiber with Secondary Nanostructure by Cotton Template

    Directory of Open Access Journals (Sweden)

    Huan-qin Wang

    2010-01-01

    Full Text Available Hierarchical MnO2 microfibers were prepared by using cotton as the template and KMnO4 as the precursor via an ultrasonic assistance route. The results of scanning electron microscope characterization showed that the concentration of KMnO4 had a significant effect on the morphology of MnO2 microfiber. At low concentration of KMnO4, the microfiber was composed of MnO2 nanorods with single crystal structure. With increasing the concentration of KMnO4, the secondary nanostructure of MnO2 microfibers had a transformation from nanorod to nanoparticle. The results of N2 adsorption-desorption analysis indicated that MnO2 microfibers had BET surface area of about 25 m2/g. This synthesis provides a new way to control the secondary nanostructure of MnO2 microfiber by adjusting the concentration of precursor. Furthermore, the mechanism for the replication was proposed and discussed.

  7. Genetic analysis of glucosinolate variability in broccoli florets using genome-anchored single nucleotide polymorphisms.

    Science.gov (United States)

    Brown, Allan F; Yousef, Gad G; Reid, Robert W; Chebrolu, Kranthi K; Thomas, Aswathy; Krueger, Christopher; Jeffery, Elizabeth; Jackson, Eric; Juvik, John A

    2015-07-01

    The identification of genetic factors influencing the accumulation of individual glucosinolates in broccoli florets provides novel insight into the regulation of glucosinolate levels in Brassica vegetables and will accelerate the development of vegetables with glucosinolate profiles tailored to promote human health. Quantitative trait loci analysis of glucosinolate (GSL) variability was conducted with a B. oleracea (broccoli) mapping population, saturated with single nucleotide polymorphism markers from a high-density array designed for rapeseed (Brassica napus). In 4 years of analysis, 14 QTLs were associated with the accumulation of aliphatic, indolic, or aromatic GSLs in floret tissue. The accumulation of 3-carbon aliphatic GSLs (2-propenyl and 3-methylsulfinylpropyl) was primarily associated with a single QTL on C05, but common regulation of 4-carbon aliphatic GSLs was not observed. A single locus on C09, associated with up to 40 % of the phenotypic variability of 2-hydroxy-3-butenyl GSL over multiple years, was not associated with the variability of precursor compounds. Similarly, QTLs on C02, C04, and C09 were associated with 4-methylsulfinylbutyl GSL concentration over multiple years but were not significantly associated with downstream compounds. Genome-specific SNP markers were used to identify candidate genes that co-localized to marker intervals and previously sequenced Brassica oleracea BAC clones containing known GSL genes (GSL-ALK, GSL-PRO, and GSL-ELONG) were aligned to the genomic sequence, providing support that at least three of our 14 QTLs likely correspond to previously identified GSL loci. The results demonstrate that previously identified loci do not fully explain GSL variation in broccoli. The identification of additional genetic factors influencing the accumulation of GSL in broccoli florets provides novel insight into the regulation of GSL levels in Brassicaceae and will accelerate development of vegetables with modified or enhanced GSL

  8. Single trial time-frequency domain analysis of error processing in post-traumatic stress disorder.

    Science.gov (United States)

    Clemans, Zachary A; El-Baz, Ayman S; Hollifield, Michael; Sokhadze, Estate M

    2012-09-13

    Error processing studies in psychology and psychiatry are relatively common. Event-related potentials (ERPs) are often used as measures of error processing, two such response-locked ERPs being the error-related negativity (ERN) and the error-related positivity (Pe). The ERN and Pe occur following committed error in reaction time tasks as low frequency (4-8 Hz) electroencephalographic (EEG) oscillations registered at the midline fronto-central sites. We created an alternative method for analyzing error processing using time-frequency analysis in the form of a wavelet transform. A study was conducted in which subjects with PTSD and healthy control completed a forced-choice task. Single trial EEG data from errors in the task were processed using a continuous wavelet transform. Coefficients from the transform that corresponded to the theta range were averaged to isolate a theta waveform in the time-frequency domain. Measures called the time-frequency ERN and Pe were obtained from these waveforms for five different channels and then averaged to obtain a single time-frequency ERN and Pe for each error trial. A comparison of the amplitude and latency for the time-frequency ERN and Pe between the PTSD and control group was performed. A significant group effect was found on the amplitude of both measures. These results indicate that the developed single trial time-frequency error analysis method is suitable for examining error processing in PTSD and possibly other psychiatric disorders. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  9. A single-operator learning curve analysis for the endoscopic sleeve gastroplasty.

    Science.gov (United States)

    Saumoy, Monica; Schneider, Yecheskel; Zhou, Xi Kathy; Shukla, Alpana; Kahaleh, Michel; Aronne, Louis; Sharaiha, Reem Z

    2018-02-01

    Endoscopic sleeve gastroplasty (ESG) is a novel, incisionless technique for gastric volume reduction to promote weight loss. Our aim was to describe the learning curve for performing ESG using a prospective case series. Using a prospective case series design, we analyzed the first 128 consecutive patients at a tertiary care academic medical center who underwent ESG performed by a single operator from August 2013 to December 2016. Efficiency (refining performance to decrease procedure time) and mastery (absence of outliers) for performing ESG was evaluated by using a penalized basis-spline regression and cumulative sum analysis. Efficiency for ESG was attained after 38 ESGs, with mastery after 55 procedures. At 12 months, the mean percent total body weight loss was 15.8% (standard deviation, 9.47%). A total of 71.7% of patients achieved successful weight loss. When using multiple linear regression analysis, both number of sutures and baseline weight were significantly associated with procedure time. Other patient characteristics, such as age, sex, and race, did not significantly affect procedure time. In addition, number of sutures, baseline weight, and endoscopist achieving efficiency were not correlated with successful weight loss at 12 months. Mastery of ESG by a single operator is suggested after sufficient endoscopic experience and may help guide widespread clinical adaptability. Copyright © 2018. Published by Elsevier Inc.

  10. Single Molecule Cluster Analysis Identifies Signature Dynamic Conformations along the Splicing Pathway

    Science.gov (United States)

    Blanco, Mario R.; Martin, Joshua S.; Kahlscheuer, Matthew L.; Krishnan, Ramya; Abelson, John; Laederach, Alain; Walter, Nils G.

    2016-01-01

    The spliceosome is the dynamic RNA-protein machine responsible for faithfully splicing introns from precursor messenger RNAs (pre-mRNAs). Many of the dynamic processes required for the proper assembly, catalytic activation, and disassembly of the spliceosome as it acts on its pre-mRNA substrate remain poorly understood, a challenge that persists for many biomolecular machines. Here, we developed a fluorescence-based Single Molecule Cluster Analysis (SiMCAn) tool to dissect the manifold conformational dynamics of a pre-mRNA through the splicing cycle. By clustering common dynamic behaviors derived from selectively blocked splicing reactions, SiMCAn was able to identify signature conformations and dynamic behaviors of multiple ATP-dependent intermediates. In addition, it identified a conformation adopted late in splicing by a 3′ splice site mutant, invoking a mechanism for substrate proofreading. SiMCAn presents a novel framework for interpreting complex single molecule behaviors that should prove widely useful for the comprehensive analysis of a plethora of dynamic cellular machines. PMID:26414013

  11. Laser microdissection of the alveolar duct enables single-cell genomic analysis

    Directory of Open Access Journals (Sweden)

    Robert eBennett

    2014-09-01

    Full Text Available Complex tissues such as the lung are composed of structural hierarchies such as alveoli, alveolar ducts and lobules. Some structural units, such as the alveolar duct, appear to selectively participate in tissue regeneration. Here, we demonstrate an approach to conduct laser microdissection of the lung alveolar duct for single-cell PCR analysis. Our approach involved three steps. 1 The initial preparation used mechanical sectioning of the lung tissue with sufficient thickness to encompass the structure of interest. In the case of the alveolar duct, the precision-cut lung slices were 200um thick; the slices were processed using near-physiologic conditions to preserve the state of viable cells. 2 The lung slices were examined by transmission light microscopy to target the alveolar duct. The air-filled lung was sufficiently accessible by light microscopy that counterstains or fluorescent labels were unnecessary to identify the alveolar duct. 3 The enzymatic and microfluidic isolation of single cells allowed for the harvest of as few as several thousand cells for PCR analysis. Microfluidics based arrays were used to measure the expression of selected marker genes in individual cells to characterize different cell populations. Preliminary work suggests the unique value of this approach to understanding the intra- and intercellular interactions within the regenerating alveolar duct.

  12. Zooplankton diversity analysis through single-gene sequencing of a community sample

    Directory of Open Access Journals (Sweden)

    Nishida Mutsumi

    2009-09-01

    Full Text Available Abstract Background Oceans cover more than 70% of the earth's surface and are critical for the homeostasis of the environment. Among the components of the ocean ecosystem, zooplankton play vital roles in energy and matter transfer through the system. Despite their importance, understanding of zooplankton biodiversity is limited because of their fragile nature, small body size, and the large number of species from various taxonomic phyla. Here we present the results of single-gene zooplankton community analysis using a method that determines a large number of mitochondrial COI gene sequences from a bulk zooplankton sample. This approach will enable us to estimate the species richness of almost the entire zooplankton community. Results A sample was collected from a depth of 721 m to the surface in the western equatorial Pacific off Pohnpei Island, Micronesia, with a plankton net equipped with a 2-m2 mouth opening. A total of 1,336 mitochondrial COI gene sequences were determined from the cDNA library made from the sample. From the determined sequences, the occurrence of 189 species of zooplankton was estimated. BLASTN search results showed high degrees of similarity (>98% between the query and database for 10 species, including holozooplankton and merozooplankton. Conclusion In conjunction with the Census of Marine Zooplankton and Barcode of Life projects, single-gene zooplankton community analysis will be a powerful tool for estimating the species richness of zooplankton communities.

  13. Simplified thermal-hydraulic analysis of single phase natural circulation circuit with two heat exchangers

    Energy Technology Data Exchange (ETDEWEB)

    Pinheiro, Larissa Cunha; Su, Jian, E-mail: larissa@lasme.coppe.ufrj.br, E-mail: sujian@lasme.coppe.ufrj.br [Coordenacao dos Programas de Pos-Graduacao em Engenharia (COPPE/UFRJ), Rio de Janeiro, RJ (Brazil). Programa de Engenhraria Nuclear; Cotta, Renato Machado, E-mail: cotta@mecanica.coppe.ufrj.br [Coordenacao dos Programas de Pos-Graduacao em Engenharia (POLI/COPPE/UFRJ), Rio de Janeiro, RJ (Brazil). Dept. de Engenharia Mecanica

    2015-07-01

    Single phase natural circulation circuits composed of two convective heat exchangers and connecting tubes are important for the passive heat removal from spent fuel pools (SFP). To keep the structural integrity of the stored spent fuel assemblies, continuously cooling has to be provided in order to avoid increase at the pool temperature and subsequent uncovering of the fuel and enhanced reaction between water and metal releasing hydrogen. Decay heat can achieve considerably high amounts of energy e.g. in the AP1000, considering the emergency fuel assemblies, the maximum heat decay will reach 13 MW in the 15th day (Westinghouse Electric Company, 2010). A highly efficient alternative to do so is by means of natural circulation, which is cost-effective compared to active cooling systems and is inherently safer since presents less associated devices and no external work is required. Many researchers have investigated safety and stability aspects of natural circulation loops (NCL). However, there is a lack of literature concerning the improvement of NCL through a standard unified methodology, especially for natural circulation circuits with two heat exchangers. In the present study, a simplified thermal-hydraulic analysis of single phase natural circulation circuit with two heat exchanges is presented. Relevant dimensionless key groups were proposed to for the design and safety analysis of a scaled NCL for the cooling of spent fuel storage pool with convective cooling and heating. (author)

  14. Robust model-based analysis of single-particle tracking experiments with Spot-On.

    Science.gov (United States)

    Hansen, Anders S; Woringer, Maxime; Grimm, Jonathan B; Lavis, Luke D; Tjian, Robert; Darzacq, Xavier

    2018-01-04

    Single-particle tracking (SPT) has become an important method to bridge biochemistry and cell biology since it allows direct observation of protein binding and diffusion dynamics in live cells. However, accurately inferring information from SPT studies is challenging due to biases in both data analysis and experimental design. To address analysis bias, we introduce 'Spot-On', an intuitive web-interface. Spot-On implements a kinetic modeling framework that accounts for known biases, including molecules moving out-of-focus, and robustly infers diffusion constants and subpopulations from pooled single-molecule trajectories. To minimize inherent experimental biases, we implement and validate stroboscopic photo-activation SPT (spaSPT), which minimizes motion-blur bias and tracking errors. We validate Spot-On using experimentally realistic simulations and show that Spot-On outperforms other methods. We then apply Spot-On to spaSPT data from live mammalian cells spanning a wide range of nuclear dynamics and demonstrate that Spot-On consistently and robustly infers subpopulation fractions and diffusion constants. © 2018, Hansen et al.

  15. The impact of ordinate scaling on the visual analysis of single-case data.

    Science.gov (United States)

    Dart, Evan H; Radley, Keith C

    2017-08-01

    Visual analysis is the primary method for detecting the presence of treatment effects in graphically displayed single-case data and it is often referred to as the "gold standard." Although researchers have developed standards for the application of visual analysis (e.g., Horner et al., 2005), over- and underestimation of effect size magnitude is not uncommon among analysts. Several characteristics have been identified as potential contributors to these errors; however, researchers have largely focused on characteristics of the data itself (e.g., autocorrelation), paying less attention to characteristics of the graphic display which are largely in control of the analyst (e.g., ordinate scaling). The current study investigated the impact that differences in ordinate scaling, a graphic display characteristic, had on experts' accuracy in judgments regarding the magnitude of effect present in single-case percentage data. 32 participants were asked to evaluate eight ABAB data sets (2 each presenting null, small, moderate, and large effects) along with three iterations of each (32 graphs in total) in which only the ordinate scale was manipulated. Results suggest that raters are less accurate in their detection of treatment effects as the ordinate scale is constricted. Additionally, raters were more likely to overestimate the size of a treatment effect when the ordinate scale was constricted. Copyright © 2017 Society for the Study of School Psychology. Published by Elsevier Ltd. All rights reserved.

  16. Copper removal and microbial community analysis in single-chamber microbial fuel cell.

    Science.gov (United States)

    Wu, Yining; Zhao, Xin; Jin, Min; Li, Yan; Li, Shuai; Kong, Fanying; Nan, Jun; Wang, Aijie

    2018-04-01

    In this study, copper removal and electricity generation were investigated in a single-chamber microbial fuel cell (MFC). Result showed that copper was efficiently removed in the membrane-less MFC with removal efficiency of 98.3% at the tolerable Cu 2+ concentration of 12.5 mg L -1 , the corresponding open circuit voltage and maximum power density were 0.78 V and 10.2 W m -3 , respectively. The mechanism analysis demonstrated that microbial electrochemical reduction contributed to the copper removal with the products of Cu and Cu 2 O deposited at biocathode. Moreover, the microbial community analysis indicated that microbial communities changed with different copper concentrations. The dominant phyla were Proteobacteria and Bacteroidetes which could play key roles in electricity generation, while Actinobacteria and Acidobacteria were also observed which were responsible for Cu-resistant and copper removal. It will be of important guiding significance for the recovery of copper from low concentration wastewater through single-chamber MFC with simultaneous energy recovery. Copyright © 2018 Elsevier Ltd. All rights reserved.

  17. Can a single pain rating replace a multiple pain rating in third molar surgery studies? Analysis of 220 patients

    NARCIS (Netherlands)

    Martin, W.J.J.M.; Heymans, M.W.; Skorpil, N.E.; Forouzanfar, T.

    2012-01-01

    This study describes the comparison of multiple and single pain ratings in patients after surgical removal of the third molar. Correlation and agreement analysis were performed between the average pain intensity measured three times a day over a period of 7 days and one single pain rating

  18. Single particle tracking-based reaction progress kinetic analysis reveals a series of molecular mechanisms of cetuximab-induced EGFR processes in a single living cell.

    Science.gov (United States)

    Kim, Do-Hyeon; Kim, Dong-Kyun; Zhou, Kai; Park, Soyeon; Kwon, Yonghoon; Jeong, Min Gyu; Lee, Nam Ki; Ryu, Sung Ho

    2017-07-01

    Cellular processes occur through the orchestration of multi-step molecular reactions. Reaction progress kinetic analysis (RPKA) can provide the mechanistic details to elucidate the multi-step molecular reactions. However, current tools have limited ability to simultaneously monitor dynamic variations in multiple complex states at the single molecule level to apply RPKA in living cells. In this research, a single particle tracking-based reaction progress kinetic analysis (sptRPKA) was developed to simultaneously determine the kinetics of multiple states of protein complexes in the membrane of a single living cell. The subpopulation ratios of different states were quantitatively (and statistically) reliably extracted from the diffusion coefficient distribution rapidly acquired by single particle tracking at constant and high density over a long period of time using super-resolution microscopy. Using sptRPKA, a series of molecular mechanisms of epidermal growth factor receptor (EGFR) cellular processing induced by cetuximab were investigated. By comprehensively measuring the rate constants and cooperativity of the molecular reactions involving four EGFR complex states, a previously unknown intermediate state was identified that represents the rate limiting step responsible for the selectivity of cetuximab-induced EGFR endocytosis to cancer cells.

  19. Precise Coating of a Wide Range of DNA Templates by a Protein Polymer with a DNA Binding Domain

    NARCIS (Netherlands)

    Hernandez-Garcia, Armando; Estrich, Nicole A.; Werten, Marc W.T.; Maarel, van der Johan R.C.; Labean, Thomas H.; Wolf, de Frits A.; Cohen Stuart, Martien A.; Vries, de Renko

    2017-01-01

    Emerging DNA-based nanotechnologies would benefit from the ability to modulate the properties (e.g., solubility, melting temperature, chemical stability) of diverse DNA templates (single molecules or origami nanostructures) through controlled, self-assembling coatings. We here introduce a DNA

  20. SDR grafting of a murine antibody using multiple human germline templates to minimize its immunogenicity.

    Science.gov (United States)

    Gonzales, Noreen R; Padlan, Eduardo A; De Pascalis, Roberto; Schuck, Peter; Schlom, Jeffrey; Kashmiri, Syed V S

    2004-07-01

    The humanization of mAbs by complementarity-determining region (CDR)-grafting has become a standard procedure to improve the clinical utility of xenogeneic Abs by reducing human anti-murine Ab (HAMA) responses elicited in patients. However, CDR-grafted humanized Abs may still evoke anti-V region responses when administered in patients. To minimize anti-V region responses, the Ab may be humanized by grafting onto the human templates only the specificity-determining residues (SDRs), the residues that are essential for the surface complementarity of the Ab and its ligand. Typically, humanization of an Ab, whether by CDR or SDR grafting, involves the use of a single human template for the entire VL or VH domain of an Ab. We hypothesized, however, that the homology between the human template sequences and mAb to be humanized may be maximized by using templates from multiple human germline sequences corresponding to the different segments of the variable domain. This could be more advantageous in reducing the potential immunogenicity of the humanized Ab. This report describes the SDR grafting of the murine anti-carcinoembryonic antigen (CEA) mAb COL-1 using three different human germline V-kappa sequences as templates for the VL CDRs and another human template for the VL frameworks. In competition RIAs, the SDR-grafted COL-1 (HuCOL-1SDR) completely inhibited the binding of radiolabeled murine COL-1 (mCOL-1) to CEA, and showed that its binding affinity is comparable to that of the CDR-grafted Ab (HuCOL-1). The HuCOL-1SDR showed similar binding reactivity to the CEA expressed on the surface of a tumor cell line as the HuCOL-1. More importantly, compared to HuCOL-1 and the "abbreviated" CDR-grafted Ab, HuCOL-1SDR showed lower reactivity to patients' sera carrying anti-V region Abs to mCOL-1. HuCOL-1SDR, which shows a lower sera reactivity than that of the parental Abs while retaining its Ag-binding property, is a potentially useful clinical reagent. To the best of our