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Sample records for pickering ngs model

  1. Aging mechanism in model Pickering emulsion

    Science.gov (United States)

    Fouilloux, Sarah; Malloggi, Florent; Daillant, Jean; Thill, Antoine

    We study the stability of a model Pickering emulsion system. A special counter-flow microfluidics set-up was used to prepare monodisperse Pickering emulsions, with oil droplets in water. The wettability of the monodisperse silica nanoparticles (NPs) could be tuned by surface grafting and the surface coverage of the droplets was controlled using the microfluidics setup. A surface coverage as low as 23$\\%$ is enough to stabilize the emulsions and we evidence a new regime of Pickering emulsion stability where the surface coverage of emulsion droplets of constant size increases in time, in coexistence with a large amount of dispersed phase. Our results demonstrate that the previously observed limited coalescence regime where surface coverage tends to control the average size of the final droplets must be put in a broader perspective.

  2. Statistical modelling of spatio-temporal dependencies in NGS data

    NARCIS (Netherlands)

    Ranciati, Saverio

    2016-01-01

    Next-generation sequencing (NGS) heeft zich snel gevestigd als de huidige standaard in de genetische analyse. Deze omschakeling van microarray naar NGS vereist nieuwe statistische strategieën om de onderzoeksvragen aan te pakken. Ten eerste, NGS data bestaat uit discrete waarnemingen, meestal gekenm

  3. Cancer modelling in the NGS era - Part I: Emerging technology and initial modelling.

    Science.gov (United States)

    Rovigatti, Ugo

    2015-11-01

    It is today indisputable that great progresses have been made in our molecular understanding of cancer cells, but an effective implementation of such knowledge into dramatic cancer-cures is still belated and yet desperately needed. This review gives a snapshot at where we stand today in this search for cancer understanding and definitive treatments, how far we have progressed and what are the major obstacles we will have to overcome both technologically and for disease modelling. In the first part, promising 3rd/4th Generation Sequencing Technologies will be summarized (particularly IonTorrent and OxfordNanopore technologies). Cancer modelling will be then reviewed from its origin in XIX Century Germany to today's NGS applications for cancer understanding and therapeutic interventions. Developments after Molecular Biology revolution (1953) are discussed as successions of three phases. The first, PH1, labelled "Clonal Outgrowth" (from 1960s to mid 1980s) was characterized by discoveries in cytogenetics (Nowell, Rowley) and viral oncology (Dulbecco, Bishop, Varmus), which demonstrated clonality. Treatments were consequently dominated by a "cytotoxic eradication" strategy with chemotherapeutic agents. In PH2, (from the mid 1980s to our days) the description of cancer as "Gene Networks" led to targeted-gene-therapies (TGTs). TGTs are the focus of Section 3: in view of their apparent failing (Ephemeral Therapies), alternative strategies will be discussed in review part II (particularly cancer immunotherapy, CIT). Additional Pitfalls impinge on the concepts of tumour heterogeneity (inter/intra; ITH). The described pitfalls set the basis for a new phase, PH3, which is called "NGS Era" and will be also discussed with ten emerging cancer models in the Review 2nd part.

  4. The Use of GOCE/GRACE Information in the Latest NGS xGeoid15 Model for the USA

    Science.gov (United States)

    Holmes, S. A.; Li, X.; Youngman, M.

    2015-12-01

    The U.S. National Geodetic Survey [NGS], through its Gravity for the Redefinition of the American Vertical Datum [GRAV-D] program, is flying airborne gravity surveys over the USA and its territories. By 2022, NGS intends that all orthometric heights in the USA will be determined in the field using a reliable national gravimetric geoid model to transform from geodetic heights obtained from GPS. Towards this end, all available airborne data has been incorporated into a new NGS experimental geoid model - xGEOID15. The xGEOID15 model is the second in a series of annual experimental geoid models that incorporates NGS GRAV-D airborne data. This series provides a useful benchmark for assessing and improving current techniques, to ultimately compute a geoid model that can support a national physical height system by 2022. Here, we focus on the combination of the latest GOCE/GRACE models with the terrestrial gravimetry (land/airborne) that was applied for xGeoid15. Comparisons against existing combination gravitational solutions, such as EGM2008 and EIGEN6C4, as well as recent geoid models, such as xGeoid14 and CGG2013, are interesting for what they reveal about the respective use of the GOCE/GRACE satgrav information.

  5. NgsRelate

    DEFF Research Database (Denmark)

    Korneliussen, Thorfinn Sand; Moltke, Ida

    2015-01-01

    . Using both simulated and real data, we show that NgsRelate provides markedly better estimates for low-depth NGS data than two state-of-the-art genotype-based methods. AVAILABILITY: NgsRelate is implemented in C++ and is available under the GNU license at www.pop gen.dk/software. CONTACT: ida...

  6. NgsRelate

    DEFF Research Database (Denmark)

    Korneliussen, Thorfinn Sand; Moltke, Ida

    2015-01-01

    be called with high certainty. RESULTS: We present a software tool, NgsRelate, for estimating pairwise relatedness from NGS data. It provides maximum likelihood estimates that are based on genotype likelihoods instead of genotypes and thereby takes the inherent uncertainty of the genotypes into account....... Using both simulated and real data, we show that NgsRelate provides markedly better estimates for low-depth NGS data than two state-of-the-art genotype-based methods. AVAILABILITY: NgsRelate is implemented in C++ and is available under the GNU license at www.pop gen.dk/software. CONTACT: ida...

  7. NGS Survey Control Map

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The NGS Survey Control Map provides a map of the US which allows you to find and display geodetic survey control points stored in the database of the National...

  8. NGS Absolute Gravity Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The NGS Absolute Gravity data (78 stations) was received in July 1993. Principal gravity parameters include Gravity Value, Uncertainty, and Vertical Gradient. The...

  9. Multi-body coalescence in Pickering emulsions

    Science.gov (United States)

    Wu, Tong; Wang, Haitao; Jing, Benxin; Liu, Fang; Burns, Peter C.; Na, Chongzheng

    2015-01-01

    Particle-stabilized Pickering emulsions have shown unusual behaviours such as the formation of non-spherical droplets and the sudden halt of coalescence between individual droplets. Here we report another unusual behaviour of Pickering emulsions—the simultaneous coalescence of multiple droplets in a single event. Using latex particles, silica particles and carbon nanotubes as model stabilizers, we show that multi-body coalescence can occur in both water-in-oil and oil-in-water emulsions. The number of droplets involved in the nth coalscence event equals four times the corresponding number of the tetrahedral sequence in close packing. Furthermore, coalescence is promoted by repulsive latex and silica particles but inhibited by attractive carbon nanotubes. The revelation of multi-body coalescence is expected to help better understand Pickering emulsions in natural systems and improve their designs in engineering applications.

  10. Pickering UDM transportation system

    Energy Technology Data Exchange (ETDEWEB)

    Brennan, P.J.; Vissers, J.J. [GE Canada Nuclear Products, Mechanical Engineering, Peterborough, Ontario (Canada)]. E-mail: patrick.brennan@cdnnuc.ge.com; jeff.vissers@cdnnuc.ge.com; Brown, R. [Ontario Power Generation, Inspection Services Div., Tiverton, Ontario (Canada)

    2003-07-01

    The Universal Delivery Machine (UDM) is a new CANDU reactor maintenance tool that allows safe, timely, and cost-effective inspection and maintenance of fuel channels. The UDM had to be transported through the Pickering nuclear station and installed onto the reactor bridge. This involved lifting the UDM between station levels, navigating it through several challenging airlock and vault areas, and traversing the bridge opening directly in front of the reactor. This paper describes the system used to transport and install the Pickering UDM. (author)

  11. Thermodynamically Stable Pickering Emulsions

    NARCIS (Netherlands)

    Sacanna, S.; Kegel, W.K.; Philipse, A.P.

    2007-01-01

    We show that under appropriate conditions, mixtures of oil, water, and nanoparticles form thermodynamically stable oil-in-water emulsions with monodisperse droplet diameters in the range of 30–150 nm. This observation challenges current wisdom that so-called Pickering emulsions are at most metastabl

  12. Space Telescope and Optical Reverberation Mapping Project. VI. Reverberating Disk Models for NGS 5548

    Science.gov (United States)

    Starkey, D.; Gehrels, Cornelis; Horne, Keith; Fausnaugh, M. M.; Peterson, B. M.; Bentz, M. C.; Kochanek, C. S.; Denney, K. D.; Edelson, R.; Goad, M. R.; hide

    2017-01-01

    We conduct a multi-wavelength continuum variability study of the Seyfert 1 galaxy NGC 5548 to investigate the temperature structure of its accretion disk. The 19 overlapping continuum light curves (1158 Angstrom to 9157 Angstrom) combine simultaneous Hubble Space Telescope, Swift, and ground-based observations over a 180 day period from 2014 January to July. Light-curve variability is interpreted as the reverberation response of the accretion disk to irradiation by a central time-varying point source. Our model yields the disk inclination i = 36deg +/- 10deg, temperature T(sub 1) = (44+/-6) times 10 (exp 3)K at 1 light day from the black hole, and a temperature radius slope (T proportional to r (exp -alpha)) of alpha = 0.99 +/- 0.03. We also infer the driving light curve and find that it correlates poorly with both the hard and soft X-ray light curves, suggesting that the X-rays alone may not drive the ultraviolet and optical variability over the observing period. We also decompose the light curves into bright, faint, and mean accretion-disk spectra. These spectra lie below that expected for a standard blackbody accretion disk accreting at L/L(sub Edd) = 0.1.

  13. Tuneable Rheological Properties of Fluorinated Pickering Emulsions

    Science.gov (United States)

    Chacon Orellana, Laura Andreina; Riechers, Birte; Caen, Ouriel; Baret, Jean-Christophe

    Pickering emulsions are an appealing approach to stabilize liquid-liquid dispersions without surfactants. Recently, amphiphilic silica nanoparticles have been proposed as an alternative to surfactants for droplet microfluidics applications, where aqueous drops are stabilized in fluorinated oils. This system, proved to be effective in preventing the leakage of resorufin, a model dye that was known to leak in surfactant-stabilized drops. The overall capabilities of droplet-based microfluidics technology is highly dependent on the dynamic properties of droplets, interfaces and emulsions. Therefore, fluorinated pickering emulsions dynamic properties need to be characterized, understood and controlled to be used as a substitute of already broadly studied emulsions for droplet microfluidics applications. In this study, fluorinated pickering emulsions have been found to behave as a Herschel Bulkley fluid, representing a challenge for common microfluidic operations as re-injection and sorting of droplets. We found that this behavior is controlled by the interaction between the interfacial properties of the particle-laden interface and the bulk properties of the two phases

  14. Waste Pickers: Why are they there?

    CSIR Research Space (South Africa)

    Oelofse, Suzanna HH

    2011-07-01

    Full Text Available Waste pickers are common on landfills in South Africa, salvaging valuable items in order to earn a living. This presentation provide some insights on the activities of the pickers at landfills....

  15. A New Mathematical Programming Formulation for the Single-Picker Routing Problem in a Single-Block Layout

    OpenAIRE

    Sebastian Henn; André Scholz; Meike Stuhlmann; Gerhard Wäscher

    2015-01-01

    The Single-Picker Routing Problem deals with the determination of sequences according to which items have to be picked in a distribution warehouse and the identification of the corresponding paths which have to be travelled by human operators (order pickers). The Single-Picker Routing Problem represents a special case of the classic Traveling Salesman Problem (TSP) and, therefore, can also be modeled as a TSP. However, the picking area of a warehouse typically possesses a block layout, i.e. t...

  16. Core-shell-structured silica/polyacrylate particles prepared by Pickering emulsion: influence of the nucleation model on particle interfacial organization and emulsion stability.

    Science.gov (United States)

    Ji, Jing; Shu, Shi; Wang, Feng; Li, Zhilin; Liu, Jingjun; Song, Ye; Jia, Yi

    2014-01-01

    This work reports a new evidence of the versatility of silica sol as a stabilizer for Pickering emulsions. The organization of silica particles at the oil-water interface is a function of the nucleation model. The present results show that nucleation model, together with monomer hydrophobicity, can be used as a trigger to modify the packing density of silica particles at the oil-water interface: Less hydrophobic methylmethacrylate, more wettable with silica particles, favors the formation of core-shell-structured composite when the composite particles are prepared by miniemulsion polymerization in which monomers are fed in batch (droplet nucleation). By contrast, hydrophobic butylacrylate promotes the encapsulating efficiency of silica when monomers are fed dropwise (homogeneous nucleation). The morphologies of polyacrylate-nano-SiO2 composites prepared from different feed ratio of methylmethacrylate/butylacrylate (with different hydrophobicity) and by different feed processes are characterized by transmission electron microscopy (TEM) and scanning electron microscopy (SEM) techniques. The results from SEM and TEM show that the morphologies of the as-prepared polyacrylate/nano-SiO2 composite can be a core-shell structure or a bare acrylic sphere. The stability of resulting emulsions composed of these composite particles is strongly dependent on the surface coverage of silica particles. The emulsion stability is improved by densely silica-packed composite particles.

  17. Spindle picker harvest speed effects

    Science.gov (United States)

    The gear drive of a modern John Deere Pro 16 picker unit was modified so that spindle speed was reduced without changing the drum speed. Three 1-row picking units were used in the study, one with the standard drive speeds, one with 25% reduction in spindle drive speed, and one with 50% reduction in...

  18. Open cherry picker simulation results

    Science.gov (United States)

    Nathan, C. A.

    1982-01-01

    The simulation program associated with a key piece of support equipment to be used to service satellites directly from the Shuttle is assessed. The Open Cherry Picker (OCP) is a manned platform mounted at the end of the remote manipulator system (RMS) and is used to enhance extra vehicular activities (EVA). The results of simulations performed on the Grumman Large Amplitude Space Simulator (LASS) and at the JSC Water Immersion Facility are summarized.

  19. Airborne Gravity Data Enhances NGS Experimental Gravimetric Geoid in Alaska

    Science.gov (United States)

    Holmes, S. A.; Childers, V. A.; Li, X.; Roman, D. R.

    2014-12-01

    The U.S. National Geodetic Survey [NGS], through their Gravity for the Redefinition of the American Vertical Datum [GRAV-D] program, continues to update its gravimetry holdings by flying new airborne gravity surveys over a large fraction of the USA and its territories. By 2022, NGS intends that all orthometric heights in the USA will be determined in the field by using a reliable national gravimetric geoid model to transform from geodetic heights obtained from GPS. Several airborne campaigns have already been flown over Alaska and its coastline. Some of this Alaskan coastal data have been incorporated into a new NGS experimental geoid model - xGEOID14. The xGEOID14 model is the first in a series of annual experimental geoid models that will incorporate NGS GRAV-D airborne data. This series provides a useful benchmark for assessing and improving current techniques by which the airborne and land-survey data are filtered and cleaned, and then combined with satellite gravity models, elevation data (etc.) with the ultimate aim of computing a geoid model that can support a national physical height system by 2022. Here we will examine the NGS GRAV-D airborne data in Alaska, and assess its contribution to xGEOID14. Future prospects for xGEOID15 will also be considered.

  20. A dynamic retreat model for the North Sea Lobe of the British and Irish Ice sheet from the Vale of Pickering, UK

    Science.gov (United States)

    Eddey, Laura; Bateman, Mark D.; Livingstone, Stephen J.; Lee, Jonathan R.

    2017-04-01

    During the Last Glaciation, a large proglacial lake occupied the Vale of Pickering in North Yorkshire, UK. The lake was bounded to the east by ice in the North Sea and to the west by ice in the Vale of York. Until recently, the duration, extent and evolution of Glacial Lake Pickering in response to changes in ice sheet dynamics was uncertain (e.g. Livingstone et al 2012). New research using glacial geomorphological mapping from high-resolution LiDAR and NextMap data combined with luminescence dating has shown that ice may have extended into the Vale of Pickering much earlier and in several advance/retreat stages, leaving a series of subtle moraines. This is also supported through several stages of lake development, reflected in historical and recently recovered boreholes. These results indicate a much earlier onset of glaciation of the North Sea Lobe of the British and Irish Ice Sheet in the region and a longer and more dynamic history. As such this work has important implications for understanding the wider glacial and deglacial history of the North Sea Basin. Livingstone, S.J., Evans, D.J.A., Cofaigh, C.O. et al. (6 more authors) (2012) Glaciodynamics of the central sector of the last British-Irish Ice Sheet in Northern England. Earth Science Reviews, 111 (1-2). 25 - 55.

  1. Pickering emulsions for skin decontamination.

    Science.gov (United States)

    Salerno, Alicia; Bolzinger, Marie-Alexandrine; Rolland, Pauline; Chevalier, Yves; Josse, Denis; Briançon, Stéphanie

    2016-08-01

    This study aimed at developing innovative systems for skin decontamination. Pickering emulsions, i.e. solid-stabilized emulsions, containing silica (S-PE) or Fuller's earth (FE-PE) were formulated. Their efficiency for skin decontamination was evaluated, in vitro, 45min after an exposure to VX, one of the most highly toxic chemical warfare agents. Pickering emulsions were compared to FE (FE-W) and silica (S-W) aqueous suspensions. PE containing an oil with a similar hydrophobicity to VX should promote its extraction. All the formulations reduced significantly the amount of VX quantified on and into the skin compared to the control. Wiping the skin surface with a pad already allowed removing more than half of VX. FE-W was the less efficient (85% of VX removed). The other formulations (FE-PE, S-PE and S-W) resulted in more than 90% of the quantity of VX removed. The charge of particles was the most influential factor. The low pH of formulations containing silica favored electrostatic interactions of VX with particles explaining the better elimination from the skin surface. Formulations containing FE had basic pH, and weak interactions with VX did not improve the skin decontamination. However, these low interactions between VX and FE promote the transfer of VX into the oil droplets in the FE-PE.

  2. NGS-based deep bisulfite sequencing.

    Science.gov (United States)

    Lee, Suman; Kim, Joomyeong

    2016-01-01

    We have developed an NGS-based deep bisulfite sequencing protocol for the DNA methylation analysis of genomes. This approach allows the rapid and efficient construction of NGS-ready libraries with a large number of PCR products that have been individually amplified from bisulfite-converted DNA. This approach also employs a bioinformatics strategy to sort the raw sequence reads generated from NGS platforms and subsequently to derive DNA methylation levels for individual loci. The results demonstrated that this NGS-based deep bisulfite sequencing approach provide not only DNA methylation levels but also informative DNA methylation patterns that have not been seen through other existing methods.•This protocol provides an efficient method generating NGS-ready libraries from individually amplified PCR products.•This protocol provides a bioinformatics strategy sorting NGS-derived raw sequence reads.•This protocol provides deep bisulfite sequencing results that can measure DNA methylation levels and patterns of individual loci.

  3. Pickering miniemulsion polymerization using Laponite clay as a stabilizer.

    Science.gov (United States)

    Bon, Stefan A F; Colver, Patrick J

    2007-07-31

    Solid-stabilized, or Pickering, miniemulsion polymerizations using Laponite clay discs as stabilizer are investigated. Free radical polymerizations are carried out using a variety of hydrophobic monomers (i.e., styrene, lauryl (meth)acrylate, butyl (meth)acrylate, octyl acrylate, and 2-ethyl hexyl acrylate). Armored latexes, of which the surfaces of the particles are covered with clay discs, are obtained, as confirmed by scanning electron microscopy (FE-SEM) and atomic force microscopy (AFM). Overall polymerization kinetics of the Pickering miniemulsion polymerizations of styrene were investigated via gravimetry. Comparison with the bulk polymerization analogue clearly shows compartmentalization. Moreover, retardation effects up to intermediate monomer conversions are observed; they are more prominent for the smaller particles and are ascribed to the Laponite clay. A model is presented that allows for the prediction of the average particle size of the latexes produced as a function of the amounts of monomer and Pickering stabilizers used. It shows that under specific generic conditions the number of clay discs used correlates in a linear fashion with the total surface area of the latex particles. This is a direct result of the reversibility of the Laponite clay disc adhesion process under the emulsification conditions (i.e., sonication) used.

  4. Toward Better Oversight of NGS Tests.

    Science.gov (United States)

    2016-09-01

    The FDA has published two draft guidance documents aimed at streamlining its oversight of tests based on next-generation sequencing (NGS). One contains preliminary recommendations addressing the analytic validity of NGS-based tests for hereditary diseases; the other explains how test developers can obtain official recognition of their genetic variant databases, potentially speeding marketing clearance or approval.

  5. Normal and compound poisson approximations for pattern occurrences in NGS reads.

    Science.gov (United States)

    Zhai, Zhiyuan; Reinert, Gesine; Song, Kai; Waterman, Michael S; Luan, Yihui; Sun, Fengzhu

    2012-06-01

    Next generation sequencing (NGS) technologies are now widely used in many biological studies. In NGS, sequence reads are randomly sampled from the genome sequence of interest. Most computational approaches for NGS data first map the reads to the genome and then analyze the data based on the mapped reads. Since many organisms have unknown genome sequences and many reads cannot be uniquely mapped to the genomes even if the genome sequences are known, alternative analytical methods are needed for the study of NGS data. Here we suggest using word patterns to analyze NGS data. Word pattern counting (the study of the probabilistic distribution of the number of occurrences of word patterns in one or multiple long sequences) has played an important role in molecular sequence analysis. However, no studies are available on the distribution of the number of occurrences of word patterns in NGS reads. In this article, we build probabilistic models for the background sequence and the sampling process of the sequence reads from the genome. Based on the models, we provide normal and compound Poisson approximations for the number of occurrences of word patterns from the sequence reads, with bounds on the approximation error. The main challenge is to consider the randomness in generating the long background sequence, as well as in the sampling of the reads using NGS. We show the accuracy of these approximations under a variety of conditions for different patterns with various characteristics. Under realistic assumptions, the compound Poisson approximation seems to outperform the normal approximation in most situations. These approximate distributions can be used to evaluate the statistical significance of the occurrence of patterns from NGS data. The theory and the computational algorithm for calculating the approximate distributions are then used to analyze ChIP-Seq data using transcription factor GABP. Software is available online (www-rcf.usc.edu/∼fsun/Programs/NGS_motif_power/NGS

  6. Arresting relaxation in Pickering Emulsions

    Science.gov (United States)

    Atherton, Tim; Burke, Chris

    2015-03-01

    Pickering emulsions consist of droplets of one fluid dispersed in a host fluid and stabilized by colloidal particles absorbed at the fluid-fluid interface. Everyday materials such as crude oil and food products like salad dressing are examples of these materials. Particles can stabilize non spherical droplet shapes in these emulsions through the following sequence: first, an isolated droplet is deformed, e.g. by an electric field, increasing the surface area above the equilibrium value; additional particles are then adsorbed to the interface reducing the surface tension. The droplet is then allowed to relax toward a sphere. If more particles were adsorbed than can be accommodated by the surface area of the spherical ground state, relaxation of the droplet is arrested at some non-spherical shape. Because the energetic cost of removing adsorbed colloids exceeds the interfacial driving force, these configurations can remain stable over long timescales. In this presentation, we present a computational study of the ordering present in anisotropic droplets produced through the mechanism of arrested relaxation and discuss the interplay between the geometry of the droplet, the dynamical process that produced it, and the structure of the defects observed.

  7. Tuning Amphiphilicity of Particles for Controllable Pickering Emulsion

    OpenAIRE

    Zhen Wang; Yapei Wang

    2016-01-01

    Pickering emulsions with the use of particles as emulsifiers have been extensively used in scientific research and industrial production due to their edge in biocompatibility and stability compared with traditional emulsions. The control over Pickering emulsion stability and type plays a significant role in these applications. Among the present methods to build controllable Pickering emulsions, tuning the amphiphilicity of particles is comparatively effective and has attracted enormous attent...

  8. Estimating inbreeding coefficients from NGS data

    DEFF Research Database (Denmark)

    Vieira, Filipe Garrett; Fumagalli, Matteo; Albrechtsen, Anders;

    2013-01-01

    Most methods for Next-Generation Sequencing (NGS) data analyses incorporate information regarding allele frequencies using the assumption of Hardy-Weinberg Equilibrium (HWE) as a prior. However, many organisms including domesticated, partially selfing or with asexual life cycles show strong...... deviations from HWE. For such species, and specially for low coverage data, it is necessary to obtain estimates of inbreeding coefficients (F) for each individual beforecalling genotypes. Here, we present two methods for estimating inbreeding coefficients from NGS data based on an Expectation...

  9. Nano-encapsulated PCM via Pickering Emulsification

    Science.gov (United States)

    Wang, Xuezhen; Zhang, Lecheng; Yu, Yi-Hsien; Jia, Lisi; Sam Mannan, M.; Chen, Ying; Cheng, Zhengdong

    2015-08-01

    We designed a two-step Pickering emulsification procedure to create nano-encapsulated phase changing materials (NEPCMs) using a method whose simplicity and low energy consumption suggest promise for scale-up and mass production. Surface-modified amphiphilic zirconium phosphate (ZrP) platelets were fabricated as the Pickering emulsifiers, nonadecane was chosen as the core phase change material (PCM), and polystyrene, the shell material. The resultant capsules were submicron in size with remarkable uniformity in size distribution, which has rarely been reported. Differential scanning calorimetry (DSC) characterization showed that the capsulation efficiency of NEPCMs, and they were found to be thermal stable, as characterized by the DSC data for the sample after 200 thermal cycles. NEPCMs exhibit superior mechanical stability and mobility when compared with the well-developed micro-encapsulated phase change materials (MEPCMs). NEPCMs find useful applications in thermal management, including micro-channel coolants; solar energy storage media; building temperature regulators; and thermal transfer fabrics.

  10. Dynamics of Pickering Emulsions in the Presence of an Interfacial Reaction: A Simulation Study.

    Science.gov (United States)

    Zhao, Shuangliang; Zhan, Bicai; Hu, Yaofeng; Fan, Zhaoyu; Pera-Titus, Marc; Liu, Honglai

    2016-12-13

    Pickering emulsions combining surface-active and catalytic properties offer a promising platform for conducting interfacial reactions between immiscible reagents. Despite the significant progress in the design of Pickering interfacial catalysts for a broad panel of reactions, the dynamics of Pickering emulsions under reaction conditions is still poorly understood. Herein, using benzene hydroxylation with aqueous H2O2 as a model system, we explored the dynamics of benzene/water Pickering emulsions during reaction by dissipative particle dynamics. Our study points out that the surface wettability of the silica nanoparticles is affected to a higher extent by the degree of polymer grafting rather than an increase of the chain length of hydrophobic polymer moieties. A remarkable decline of the oil-in-water (O/W) interfacial tension was observed when increasing the yield of the reaction product (phenol), affecting the emulsion stability. However, phenol did not alter to an important extent the distribution of immiscible reagents around the nanoparticles sitting at the benzene/water interface. A synergistic effect between phenol and silica nanoparticles on the O/W interfacial tension of the biphasic system could be ascertained.

  11. Surfactant-enhanced cellulose nanocrystal Pickering emulsions.

    Science.gov (United States)

    Hu, Zhen; Ballinger, Sarah; Pelton, Robert; Cranston, Emily D

    2015-02-01

    The effect of surfactants on the properties of Pickering emulsions stabilized by cellulose nanocrystals (CNCs) was investigated. Electrophoretic mobility, interfacial tension, confocal microscopy and three-phase contact angle measurements were used to elucidate the interactions between anionic CNCs and cationic alkyl ammonium surfactants didecyldimethylammonium bromide (DMAB) and cetyltrimethylammonium bromide (CTAB). Both surfactants were found to adsorb onto CNCs with concentration-dependent morphology. At low concentrations, individual surfactant molecules adsorbed with alkyl tails pointing outward leading to hydrophobic CNCs. At higher concentrations, above the surfactant's apparent critical micelle concentration, surfactant aggregate morphologies on CNCs were inferred and the hydrophobicity of CNCs decreased. DMAB, which has two alkyl tails, rendered the CNCs more hydrophobic than CTAB which has only a single alkyl tail, at all surfactant concentrations. The change in CNC wettability from surfactant adsorption was directly linked to emulsion properties; adding surfactant increased the emulsion stability, decreased the droplet size, and controlled the internal phase of CNC Pickering emulsions. More specifically, a double transitional phase inversion, from oil-in-water to water-in-oil and back to oil-in-water, was observed for emulsions with CNCs and increasing amounts of DMAB (the more hydrophobic surfactant). With CNCs and CTAB, no phase inversion was induced. This work represents the first report of CNC Pickering emulsions with surfactants as well as the first CNC Pickering emulsions that can be phase inverted. The ability to surface modify CNCs in situ and tailor emulsions by adding surfactants may extend the potential of CNCs to new liquid formulations and extruded/spray-dried materials.

  12. Fungal infections in corn picker hand injury

    Directory of Open Access Journals (Sweden)

    Obradović-Tomašev Milana

    2016-01-01

    Full Text Available Introduction. Hand injuries caused by corn pickers are relatively rare but in most cases extensive, with massive tissue destruction. Severe wounds sustained during agricultural work are contaminated, with high incidence of infection. Objective. The aim of the study was to determine the frequency and type of fungal infection in corn picker injuries and their impact on the course and outcome of treatment. Methods. Corn picker hand injuries for the period 2006-2012 were analyzed. After setting up clinical suspicion, direct examination of repeated swabs and histopathological analysis of biopsy material were done in order to detect fungi. Results. From the total number of 60 patients, there was a fungal infection in nine of them (which makes 15% of the total number of patients. Aspergillus spp. was isolated in seven patients, Candida spp. in three, and Mucor spp. in one patient. None of the patients had increased risk factors for developing a fungal infection. In most cases, there was loss of graft and tissue necrosis in previously normally looking wound, after seven or more days. All patients were treated with repeated surgical debridement and concomitant parenteral and topical application of appropriate antifungal agents. There was no need for reamputation in any patient. Conclusion. A high degree of suspicion and a multidisciplinary approach are needed for early diagnosis of fungal infection. Confirmation of diagnosis and the initiation of surgical and appropriate antifungal therapy are essential for a successful outcome.

  13. VA contracts give unfair advantage to Picker--study.

    Science.gov (United States)

    Wagner, M

    1991-08-19

    Service contracts for computed tomography scanners in Dept. of Veterans Affairs hospitals have given an unfair advantage to Picker International, according to a study by the VA's inspector general's office. The report is the latest round in a controversy that has pitted Picker against at least two independent service organizations and enmeshed it in a $1.65 billion lawsuit.

  14. Data-driven warehouse optimization : Deploying skills of order pickers

    NARCIS (Netherlands)

    M. Matusiak (Marek); M.B.M. de Koster (René); J. Saarinen (Jari)

    2015-01-01

    textabstractBatching orders and routing order pickers is a commonly studied problem in many picker-to-parts warehouses. The impact of individual differences in picking skills on performance has received little attention. In this paper, we show that taking into account differences in the skills of in

  15. Data-driven warehouse optimization : Deploying skills of order pickers

    NARCIS (Netherlands)

    M. Matusiak (Marek); M.B.M. de Koster (René); J. Saarinen (Jari)

    2015-01-01

    textabstractBatching orders and routing order pickers is a commonly studied problem in many picker-to-parts warehouses. The impact of individual differences in picking skills on performance has received little attention. In this paper, we show that taking into account differences in the skills of

  16. From bijels to Pickering emulsions: A lattice Boltzmann study

    Science.gov (United States)

    Jansen, Fabian; Harting, Jens

    2011-04-01

    Particle stabilized emulsions are ubiquitous in the food and cosmetics industry, but our understanding of the influence of microscopic fluid-particle and particle-particle interactions on the macroscopic rheology is still limited. In this paper we present a simulation algorithm based on a multicomponent lattice Boltzmann model to describe the solvents combined with a molecular dynamics solver for the description of the solved particles. It is shown that the model allows a wide variation of fluid properties and arbitrary contact angles on the particle surfaces. We demonstrate its applicability by studying the transition from a “bicontinuous interfacially jammed emulsion gel” (bijel) to a “Pickering emulsion” in dependence on the contact angle, the particle concentration, and the ratio of the solvents.

  17. 基于"货到人"拣选模式的储位分配模型与算法%Study on Storage Space Allocation Model and Algorithm Based on Rack-to-picker Mode

    Institute of Scientific and Technical Information of China (English)

    周方圆; 李珍萍

    2015-01-01

    研究了基于"货到人"拣选模式的储位分配问题,建立了以总拣选成本最小化为目标的储位分配问题数学模型,针对"货到人"拣选模式的特点,利用复杂二分网络社团结构划分的基本思想,设计了求解储位分配问题的快速有效算法.进一步通过模拟实验分析了利用本文算法分配储位与利用传统分类存储方法分配储位对应的货架搬运次数和搬运成本,结果显示,与传统的储位分配方法相比,根据本文算法分配储位可以使订单拣选过程中的货架搬运次数和总搬运成本平均减少约40%.%In this paper, we studied the storage space allocation problem in the rack-to-picker mode, built the corresponding mathematical model with the minimal total picking cost as the objective, and then in view of the characteristics of the picking mode and following the basic principle in partitioning the structure of complex bipartite network organizations, designed a quick and effective solution to the storage space allocation problem. Next through a simulation test, we further compared the number of rack movements and the total handling cost entailed by the algorithm proposed here and by the traditional classification and storage processes.

  18. The potential of whole genome NGS for infectious disease diagnosis.

    Science.gov (United States)

    Lecuit, Marc; Eloit, Marc

    2015-01-01

    Non-targeted identification of microbes is now possible directly in biological samples, based on whole-genome-NGS (WG-NGS) techniques that allow deep sequencing of nucleic acids, data mining and sorting out of sequences of pathogens without any a priori hypothesis. WG-NGS was first only used as a research tool due to its cost, complexity and lack of standardization. Recent improvements in sample preparation and bioinformatics pipelines and decrease in cost now allow actionable diagnostics in patients. The potency and limits of WG-NGS and possible future indications are discussed here. WG-NGS will likely soon become a standard procedure in microbiological diagnosis.

  19. The number of pickers and stock-keeping unit arrangement on a uni-directional picking line

    Directory of Open Access Journals (Sweden)

    Hagspihl, Robert

    2014-10-01

    Full Text Available The order picking process is often the single largest expense in a distribution centre (DC. The DC considered in this paper uses a picking line configuration to perform order picking. The number of pickers in a picking line, and the initial arrangement of stock-keeping units (SKUs, are two important factors that affect the total completion time of the picking lines. In this paper, the picking line configuration is simulated with an agent-based approach to describe the behaviour of an individual picker. The simulation is then used to analyse the effect of the number of pickers and the SKU arrangement. Verification and validation of this model shows that the model represents the real-world picking line to a satisfactory degree. Marginal analysis (MA was chosen to determine a ‘good’ number of pickers by means of the simulation model. A look-up table is presented to provide decision support for the choice of a ‘good’ number of pickers to improve completion times of the picking line, for the properties of a specific picking line. The initial SKU arrangement on a picking line is shown to be a factor that can affect the level of picker congestion and the total completion time. The greedy ranking and partitioning (GRP and organ pipe arrangement (OPA techniques from the literature, as well as the historical SKU arrangements used by the retailer under consideration, were compared with the proposed classroom discipline heuristic (CDH for SKU arrangement. It was found that the CDH provides an more even spread of SKUs that are picked most frequently, thus decreasing congestion and total completion time.

  20. The CERN Neutrino beam to Gran Sasso (NGS)

    CERN Document Server

    Bailey, R; Ball, A E; Bonnal, P; Buhler-Broglin, Manfred; Détraz, C; Elsener, Konrad; Ereditato, A; Faugeras, Paul E; Ferrari, A; Fortuna, G; Grant, A L; Guglielmi, A M; Hilaire, A; Hübner, Kurt; Jonker, M; Kissler, Karl Heinz; López-Hernandez, L A; Maugain, J M; Migliozzi, P; Palladino, Vittorio; Pietropaolo, F; Revol, Jean Pierre Charles; Sala, P R; Sanelli, C; Stevenson, Graham Roger; Vassilopoulos, N; Vincke, H H; Weisse, E; Wilhemsson, M

    1999-01-01

    The conceptual technical design of the NGS (CERN neutrino beam to Gran Sasso) facility has been presented in the report CERN 98-02 / INFN-AE/98-05. Additional information, in particular an update on various neutrino beam options for the NGS facility, has been provided in a memorandum to the CERN-SPSC Committee (CERN-SPSC/98-35). In the present report, further improvements on the NGS design and performance, in particular new scenarios for SPS proton cycles for NGS operation and a new version of the NGS "high energy" neutrino beam for nt appearance experiments, are described. This new NGS reference beam is estimated to provide three times more nt events per year than the beam presented in the 1998 report. The radiological aspects of the NGS facility have been re-examined with the new beam design. An updated version of the construction schedule is also presented.

  1. Non-aqueous Isorefractive Pickering Emulsions

    OpenAIRE

    Thompson, K. L.; Lane, J.A.; Derry, M.J.; Armes, S. P.

    2015-01-01

    Non-aqueous Pickering emulsions of 16–240 μm diameter have been prepared using diblock copolymer worms with ethylene glycol as the droplet phase and an n-alkane as the continuous phase. Initial studies using n-dodecane resulted in stable emulsions that were significantly less turbid than conventional water-in-oil emulsions. This is attributed to the rather similar refractive indices of the latter two phases. By utilizing n-tetradecane as an alternative oil that almost precisely matches the re...

  2. Tuning Amphiphilicity of Particles for Controllable Pickering Emulsion

    Directory of Open Access Journals (Sweden)

    Zhen Wang

    2016-11-01

    Full Text Available Pickering emulsions with the use of particles as emulsifiers have been extensively used in scientific research and industrial production due to their edge in biocompatibility and stability compared with traditional emulsions. The control over Pickering emulsion stability and type plays a significant role in these applications. Among the present methods to build controllable Pickering emulsions, tuning the amphiphilicity of particles is comparatively effective and has attracted enormous attention. In this review, we highlight some recent advances in tuning the amphiphilicity of particles for controlling the stability and type of Pickering emulsions. The amphiphilicity of three types of particles including rigid particles, soft particles, and Janus particles are tailored by means of different mechanisms and discussed here in detail. The stabilization-destabilization interconversion and phase inversion of Pickering emulsions have been successfully achieved by changing the surface properties of these particles. This article provides a comprehensive review of controllable Pickering emulsions, which is expected to stimulate inspiration for designing and preparing novel Pickering emulsions, and ultimately directing the preparation of functional materials.

  3. The ICR142 NGS validation series: a resource for orthogonal assessment of NGS analysis.

    Science.gov (United States)

    Ruark, Elise; Renwick, Anthony; Clarke, Matthew; Snape, Katie; Ramsay, Emma; Elliott, Anna; Hanks, Sandra; Strydom, Ann; Seal, Sheila; Rahman, Nazneen

    2016-01-01

    To provide a useful community resource for orthogonal assessment of NGS analysis software, we present the ICR142 NGS validation series. The dataset includes high-quality exome sequence data from 142 samples together with Sanger sequence data at 730 sites; 409 sites with variants and 321 sites at which variants were called by an NGS analysis tool, but no variant is present in the corresponding Sanger sequence. The dataset includes 286 indel variants and 275 negative indel sites, and thus the ICR142 validation dataset is of particular utility in evaluating indel calling performance. The FASTQ files and Sanger sequence results can be accessed in the European Genome-phenome Archive under the accession number EGAS00001001332.

  4. Toxocariasis in waste pickers: a case control seroprevalence study.

    Directory of Open Access Journals (Sweden)

    Cosme Alvarado-Esquivel

    Full Text Available BACKGROUND: The epidemiology of Toxocara infection in humans in Mexico has been poorly explored. There is a lack of information about Toxocara infection in waste pickers. AIMS: Determine the seroepidemiology of Toxocara infection in waste pickers. METHODS: Through a case control study design, the presence of anti-Toxocara IgG antibodies was determined in 90 waste pickers and 90 age- and gender-matched controls using an enzyme-linked immunoassay. Associations of Toxocara exposure with socio-demographic, work, clinical, and behavioral data of the waste pickers were also evaluated. RESULTS: The seroprevalence of anti-Toxocara IgG antibodies was significantly higher in waste pickers (12/90: 13% than in control subjects (1/90: 1% (OR = 14; 95% CI: 2-288. The seroprevalence was not influenced by socio-demographic or work characteristics. In contrast, increased seroprevalence was found in waste pickers suffering from gastritis, and reflex and visual impairments. Multivariate analysis showed that Toxocara exposure was associated with a low frequency of eating out of home (OR = 26; 95% CI: 2-363 and negatively associated with consumption of chicken meat (OR = 0.03; 95% CI: 0.003-0.59. Other behavioral characteristics such as animal contacts or exposure to soil were not associated with Toxocara seropositivity. CONCLUSIONS: 1 Waste pickers are a risk group for Toxocara infection. 2 Toxocara is impacting the health of waste pickers. This is the first report of Toxocara exposure in waste pickers and of associations of gastritis and reflex impairment with Toxocara seropositivity. Results warrant for further research.

  5. Genetic Architecture of Milk, Fat, Protein, Mastitis and Fertility Studied using NGS Data in Holstein Cattle

    DEFF Research Database (Denmark)

    Sahana, Goutam; Janss, Luc; Guldbrandtsen, Bernt;

    cattle using NGS variants. The analysis was done using a linear mixed model (LMM) and a Bayesian mixture model (BMM). The top 10 QTL identified by LMM analyses explained 22.61, 23.86, 10.88, 18.58 and 14.83% of the total genetic variance for these traits respectively. Trait-specific sets of 4,964 SNPs...... from NGS variants (most ‘associated’ SNP for each 0.5 Mbp bin) explained 81.0, 81.6, 85.0, 60.4 and 70.9% of total genetic variance for milk, fat, protein, mastitis and fertility indices when analyzed simultaneously by BMM...

  6. Simulation Analysis of Level Spindle-Type Cotton Picker Roller Based on ADAMS%基于ADAMS的水平摘锭式采棉机采棉滚筒运动仿真分析

    Institute of Scientific and Technical Information of China (English)

    何磊; 周亚立; 刘向新; 赵岩

    2013-01-01

    采棉滚筒是水平摘锭式采棉机的核心工作部件,其工作的可靠性直接影响着采棉机的采摘质量和业效率.以约翰·迪尔7760型采棉机为例,介绍了采棉滚筒的结构及工作原理,利用ADAMS软件建立了采棉滚筒的三维模型并进行运动仿真,分析了运动规律,为采棉滚筒的设计和研究提供了理论依据和参考.%Cotton picker roller is key part of the level spindle-type cotton picker as its reliability affects the quality and operational efficiency of cotton picker directly.Taking John Deere 7760 cotton picker as an example,the structure and working principle of cotton picker roller was introduced.Meanwhile,three-dimensional model of the cotton picker rollers was established using ADAMS software and applied for motion simulation.The law of motion was analyzed to provide theoretical basis and reference for design and research of cotton picker roller.

  7. Comparison of Pickering and network stabilization in water-in-oil emulsions.

    Science.gov (United States)

    Ghosh, Supratim; Tran, Tu; Rousseau, Dérick

    2011-06-07

    We compared the efficacy of Pickering crystals, a continuous phase crystal network, and a combination thereof against sedimentation and dispersed phase coalescence in water-in-oil (W/O) emulsions. Using 20 wt % water-in-canola oil emulsions as our model, glycerol monostearate (GMS) permitted Pickering-type stabilization, whereas simultaneous usage of hydrogenated canola oil (HCO) and glycerol monooleate (GMO) primarily led to network-stabilized emulsions. A minimum of 4 wt % GMS or 10 wt % HCO was required for long-term sedimentation stability. Although there were no significant differences between the two in mean droplet size with time, the free water content of the network-stabilized emulsions was higher than Pickering-stabilized emulsions, suggesting higher instability. Microscopy revealed the presence of crystal shells around the dispersed phase in the GMS-stabilized emulsions, whereas in the HCO-stabilized emulsion, spherulitic growth in the continuous phase and on the droplet surface occurred. The displacement energy (E(disp)) to detach crystals from the oil-water interface was ∼10(4) kT, and was highest for GMS crystals. Thermal cycling to induce dispersed phase coalescence of the emulsions resulted in desorption of both GMS and GMO from the interface, which we ascribed to solute-solvent hydrogen bonding between the emulsifier molecules and the solvent oil, based on IR spectra. Overall, Pickering crystals were more effective than network crystals for emulsion stabilization. However, the thermal stability of all emulsions was hampered by the diffusion of the molten emulsifiers from the interface.

  8. ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence

    Directory of Open Access Journals (Sweden)

    Cañizares Joaquin

    2011-06-01

    Full Text Available Abstract Background The possibilities offered by next generation sequencing (NGS platforms are revolutionizing biotechnological laboratories. Moreover, the combination of NGS sequencing and affordable high-throughput genotyping technologies is facilitating the rapid discovery and use of SNPs in non-model species. However, this abundance of sequences and polymorphisms creates new software needs. To fulfill these needs, we have developed a powerful, yet easy-to-use application. Results The ngs_backbone software is a parallel pipeline capable of analyzing Sanger, 454, Illumina and SOLiD (Sequencing by Oligonucleotide Ligation and Detection sequence reads. Its main supported analyses are: read cleaning, transcriptome assembly and annotation, read mapping and single nucleotide polymorphism (SNP calling and selection. In order to build a truly useful tool, the software development was paired with a laboratory experiment. All public tomato Sanger EST reads plus 14.2 million Illumina reads were employed to test the tool and predict polymorphism in tomato. The cleaned reads were mapped to the SGN tomato transcriptome obtaining a coverage of 4.2 for Sanger and 8.5 for Illumina. 23,360 single nucleotide variations (SNVs were predicted. A total of 76 SNVs were experimentally validated, and 85% were found to be real. Conclusions ngs_backbone is a new software package capable of analyzing sequences produced by NGS technologies and predicting SNVs with great accuracy. In our tomato example, we created a highly polymorphic collection of SNVs that will be a useful resource for tomato researchers and breeders. The software developed along with its documentation is freely available under the AGPL license and can be downloaded from http://bioinf.comav.upv.es/ngs_backbone/ or http://github.com/JoseBlanca/franklin.

  9. An Assessment of Airborn Gravimetry Collected under the NGS GRAV-D Project

    Science.gov (United States)

    Holmes, S. A.

    2009-12-01

    In the United States, the National Geodetic Survey [NGS] holds the official charter to maintain the vertical datum for the USA and its territories. This includes the responsibility to maintain a current geoid model for transforming between orthometric (H) and geodetic (h) heights. The latest (2009) NGS geoid model incorporates the latest GRACE-based satellite-only geopotential solutions, very-high-resolution digital elevation models [DEMs] derived from the Shuttle Radar Topography Mission [SRTM], and other additional data and processing improvements. This recent geoid model also benefited greatly from the prior release of the National Geospatial-Intelligence Agency’s [NGA] Earth Gravitational Model 2008 [EGM2008], which served as a computational reference field for the new geoid, but was also particularly useful for identifying and removing corrupted data from the NGS gravimetry database. Looking forwards, NGS intends to increase its efforts to refine and improve its future national geoid models. To this end, their ambitious "Gravity for the Re-definition of the American Datum” [GRAV-D] project aims to update the NGS gravimetry holdings by flying new airborn gravity surveys over a large fraction of the USA and it territories. Concurrent efforts will focus on developing new processing techniques for optimally incorporating improved gravimetry into the final geoid solution. To this end, the GRAV-D team has already flown several surveys in the Gulf of Mexico, Puerto Rico, US Virgin Islands, and Alaska. Testing and analysis aimed at calibrating and validating the preliminary survey data is already underway. The latest assessment of these recent efforts, including the extent to which this new data can be expected to contribute to an improved gravimetric geoid model, is presented here.

  10. Repulsive van der Waals forces enable Pickering emulsions with non-touching colloids

    NARCIS (Netherlands)

    Elbers, Nina; van der Hoeven, Jessi; de Winter, D.A.M.; Schneijdenberg, C.T.W.M.; van der Linden, M.N.; Filion, L.C.; van Blaaderen, A.

    2016-01-01

    Emulsions stabilized by solid particles, called Pickering emulsions, offer promising applications in drug delivery, cosmetics, food science and the manufacturing of porous materials. This potential stems from their high stability against coalescence and ‘surfactant-free’ nature. Generally, Pickering

  11. Estimating cancer risk in relation to tritium exposure from routine operation of a nuclear-generating station in Pickering, Ontario.

    Science.gov (United States)

    Wanigaratne, S; Holowaty, E; Jiang, H; Norwood, T A; Pietrusiak, M A; Brown, P

    2013-09-01

    Evidence suggests that current levels of tritium emissions from CANDU reactors in Canada are not related to adverse health effects. However, these studies lack tritium-specific dose data and have small numbers of cases. The purpose of our study was to determine whether tritium emitted from a nuclear-generating station during routine operation is associated with risk of cancer in Pickering, Ontario. A retrospective cohort was formed through linkage of Pickering and north Oshawa residents (1985) to incident cancer cases (1985-2005). We examined all sites combined, leukemia, lung, thyroid and childhood cancers (6-19 years) for males and females as well as female breast cancer. Tritium estimates were based on an atmospheric dispersion model, incorporating characteristics of annual tritium emissions and meteorology. Tritium concentration estimates were assigned to each cohort member based on exact location of residence. Person-years analysis was used to determine whether observed cancer cases were higher than expected. Cox proportional hazards regression was used to determine whether tritium was associated with radiation-sensitive cancers in Pickering. Person-years analysis showed female childhood cancer cases to be significantly higher than expected (standardized incidence ratio [SIR] = 1.99, 95% confidence interval [CI]: 1.08-3.38). The issue of multiple comparisons is the most likely explanation for this finding. Cox models revealed that female lung cancer was significantly higher in Pickering versus north Oshawa (HR = 2.34, 95% CI: 1.23-4.46) and that tritium was not associated with increased risk. The improved methodology used in this study adds to our understanding of cancer risks associated with low-dose tritium exposure. Tritium estimates were not associated with increased risk of radiationsensitive cancers in Pickering.

  12. NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL.

    Science.gov (United States)

    May, Ali; Abeln, Sanne; Buijs, Mark J; Heringa, Jaap; Crielaard, Wim; Brandt, Bernd W

    2015-07-01

    Massively parallel sequencing of microbial genetic markers (MGMs) is used to uncover the species composition in a multitude of ecological niches. These sequencing runs often contain a sample with known composition that can be used to evaluate the sequencing quality or to detect novel sequence variants. With NGS-eval, the reads from such (mock) samples can be used to (i) explore the differences between the reads and their references and to (ii) estimate the sequencing error rate. This tool maps these reads to references and calculates as well as visualizes the different types of sequencing errors. Clearly, sequencing errors can only be accurately calculated if the reference sequences are correct. However, even with known strains, it is not straightforward to select the correct references from databases. We previously analysed a pyrosequencing dataset from a mock sample to estimate sequencing error rates and detected sequence variants in our mock community, allowing us to obtain an accurate error estimation. Here, we demonstrate the variant detection and error analysis capability of NGS-eval with Illumina MiSeq reads from the same mock community. While tailored towards the field of metagenomics, this server can be used for any type of MGM-based reads. NGS-eval is available at http://www.ibi.vu.nl/programs/ngsevalwww/.

  13. System dynamics applied to closed loop supply chains of desktops and laptops in Brazil: A perspective for social inclusion of waste pickers.

    Science.gov (United States)

    Ghisolfi, Verônica; Diniz Chaves, Gisele de Lorena; Ribeiro Siman, Renato; Xavier, Lúcia Helena

    2017-02-01

    The structure of reverse logistics for waste electrical and electronic equipment (WEEE) is essential to minimize the impacts of their improper disposal. In this context, the Brazilian Solid Waste Policy (BSWP) was a regulatory milestone in Brazil, submitting WEEE to the mandatory implementation of reverse logistics systems, involving the integration of waste pickers on the shared responsibility for the life cycle of products. This article aims to measure the impact of such legal incentives and the bargaining power obtained by the volume of collected waste on the effective formalization of waste pickers. The proposed model evaluates the sustainability of supply chains in terms of the use of raw materials due to disposal fees, collection, recycling and return of some materials from desktops and laptops using system dynamics methodology. The results show that even in the absence of bargaining power, the formalization of waste pickers occurs due to legal incentives. It is important to ensure the waste pickers cooperatives access to a minimum amount, which requires a level of protection against unfair competition with companies. Regarding the optimal level of environmental policies, even though the formalization time is long, it is still not enough to guarantee the formalization of waste picker cooperatives, which is dependent on their bargaining power. Steel is the material with the largest decrease in acquisition rate of raw material.

  14. Partitioning of Laponite Clay Platelets in Pickering Emulsion Polymerization.

    Science.gov (United States)

    Brunier, Barthélémy; Sheibat-Othman, Nida; Chevalier, Yves; Bourgeat-Lami, Elodie

    2016-01-12

    Partitioning of laponite disklike clay platelets between polymer particles and bulk aqueous phase was investigated in Pickering surfactant-free emulsion polymerization of styrene. Adsorption of laponite clay platelets plays an important role in the stabilization of this system, influencing the particle size and the number of particles, and, hence, the reaction rate. Adsorption isotherms show that, while the laponite clay platelets are almost fully exfoliated in water, they form multilayers on the surface of the polymer particles by the end of polymerization, as confirmed by transmission electron microscopy (TEM). This observation is supported by quartz crystal microbalance, conductivity, and TEM measurements, which reveal interactions between the clay and polystyrene, as a function of the ionic strength. The strong adsorption of clay platelets leaves a low residual concentration in the aqueous phase that cannot cause further nucleation of polymer particles, as demonstrated during seeded emulsion polymerization experiments in the presence of a high excess of clay. A Brunauer-Emmett-Teller (BET)-type model for laponite adsorption on polystyrene particles matches the adsorption isotherms.

  15. Edge-modified amphiphilic Laponite nano-discs for stabilizing Pickering emulsions.

    Science.gov (United States)

    Yang, Ying; Liu, Zhi; Wu, Dayong; Wu, Man; Tian, Ye; Niu, Zhongwei; Huang, Yong

    2013-11-15

    We investigated the effect of amphiphilic Laponite nano-discs, which were edge-modified by hydrophobic chains, on the properties of Pickering emulsions and Pickering emulsions polymerization. Comparing to unmodified Laponites, these amphiphilic nano-discs can greatly reduce the surface tension, resulting in very stable Pickering emulsions. These particles uniquely combine the Pickering effect with amphiphilic properties similar to the surfactant. Taking advantage of these amphiphilic Pickering emulsifiers, miniemulsion polymerization of styrene was performed. Homogeneous polystyrene nanoparticles with size around 150 nm could thus be prepared.

  16. Orthogonal NGS for High Throughput Clinical Diagnostics.

    Science.gov (United States)

    Chennagiri, Niru; White, Eric J; Frieden, Alexander; Lopez, Edgardo; Lieber, Daniel S; Nikiforov, Anastasia; Ross, Tristen; Batorsky, Rebecca; Hansen, Sherry; Lip, Va; Luquette, Lovelace J; Mauceli, Evan; Margulies, David; Milos, Patrice M; Napolitano, Nichole; Nizzari, Marcia M; Yu, Timothy; Thompson, John F

    2016-04-19

    Next generation sequencing is a transformative technology for discovering and diagnosing genetic disorders. However, high-throughput sequencing remains error-prone, necessitating variant confirmation in order to meet the exacting demands of clinical diagnostic sequencing. To address this, we devised an orthogonal, dual platform approach employing complementary target capture and sequencing chemistries to improve speed and accuracy of variant calls at a genomic scale. We combined DNA selection by bait-based hybridization followed by Illumina NextSeq reversible terminator sequencing with DNA selection by amplification followed by Ion Proton semiconductor sequencing. This approach yields genomic scale orthogonal confirmation of ~95% of exome variants. Overall variant sensitivity improves as each method covers thousands of coding exons missed by the other. We conclude that orthogonal NGS offers improvements in variant calling sensitivity when two platforms are used, better specificity for variants identified on both platforms, and greatly reduces the time and expense of Sanger follow-up, thus enabling physicians to act on genomic results more quickly.

  17. Pickering Particles Prepared from Food Waste

    Science.gov (United States)

    Gould, Joanne; Garcia-Garcia, Guillermo; Wolf, Bettina

    2016-01-01

    In this paper, we demonstrate the functionality and functionalisation of waste particles as an emulsifier for oil-in-water (o/w) and water-in-oil (w/o) emulsions. Ground coffee waste was chosen as a candidate waste material due to its naturally high content of lignin, a chemical component imparting emulsifying ability. The waste coffee particles readily stabilised o/w emulsions and following hydrothermal treatment adapted from the bioenergy field they also stabilised w/o emulsions. The hydrothermal treatment relocated the lignin component of the cell walls within the coffee particles onto the particle surface thereby increasing the surface hydrophobicity of the particles as demonstrated by an emulsion assay. Emulsion droplet sizes were comparable to those found in processed foods in the case of hydrophilic waste coffee particles stabilizing o/w emulsions. These emulsions were stable against coalescence for at least 12 weeks, flocculated but stable against coalescence in shear and stable to pasteurisation conditions (10 min at 80 °C). Emulsion droplet size was also insensitive to pH of the aqueous phase during preparation (pH 3–pH 9). Stable against coalescence, the water droplets in w/o emulsions prepared with hydrothermally treated waste coffee particles were considerably larger and microscopic examination showed evidence of arrested coalescence indicative of particle jamming at the surface of the emulsion droplets. Refinement of the hydrothermal treatment and broadening out to other lignin-rich plant or plant based food waste material are promising routes to bring closer the development of commercially relevant lignin based food Pickering particles applicable to emulsion based processed foods ranging from fat continuous spreads and fillings to salad dressings. PMID:28773909

  18. Pickering Particles Prepared from Food Waste

    Directory of Open Access Journals (Sweden)

    Joanne Gould

    2016-09-01

    Full Text Available In this paper, we demonstrate the functionality and functionalisation of waste particles as an emulsifier for oil-in-water (o/w and water-in-oil (w/o emulsions. Ground coffee waste was chosen as a candidate waste material due to its naturally high content of lignin, a chemical component imparting emulsifying ability. The waste coffee particles readily stabilised o/w emulsions and following hydrothermal treatment adapted from the bioenergy field they also stabilised w/o emulsions. The hydrothermal treatment relocated the lignin component of the cell walls within the coffee particles onto the particle surface thereby increasing the surface hydrophobicity of the particles as demonstrated by an emulsion assay. Emulsion droplet sizes were comparable to those found in processed foods in the case of hydrophilic waste coffee particles stabilizing o/w emulsions. These emulsions were stable against coalescence for at least 12 weeks, flocculated but stable against coalescence in shear and stable to pasteurisation conditions (10 min at 80 °C. Emulsion droplet size was also insensitive to pH of the aqueous phase during preparation (pH 3–pH 9. Stable against coalescence, the water droplets in w/o emulsions prepared with hydrothermally treated waste coffee particles were considerably larger and microscopic examination showed evidence of arrested coalescence indicative of particle jamming at the surface of the emulsion droplets. Refinement of the hydrothermal treatment and broadening out to other lignin-rich plant or plant based food waste material are promising routes to bring closer the development of commercially relevant lignin based food Pickering particles applicable to emulsion based processed foods ranging from fat continuous spreads and fillings to salad dressings.

  19. Pickering Particles Prepared from Food Waste.

    Science.gov (United States)

    Gould, Joanne; Garcia-Garcia, Guillermo; Wolf, Bettina

    2016-09-21

    In this paper, we demonstrate the functionality and functionalisation of waste particles as an emulsifier for oil-in-water (o/w) and water-in-oil (w/o) emulsions. Ground coffee waste was chosen as a candidate waste material due to its naturally high content of lignin, a chemical component imparting emulsifying ability. The waste coffee particles readily stabilised o/w emulsions and following hydrothermal treatment adapted from the bioenergy field they also stabilised w/o emulsions. The hydrothermal treatment relocated the lignin component of the cell walls within the coffee particles onto the particle surface thereby increasing the surface hydrophobicity of the particles as demonstrated by an emulsion assay. Emulsion droplet sizes were comparable to those found in processed foods in the case of hydrophilic waste coffee particles stabilizing o/w emulsions. These emulsions were stable against coalescence for at least 12 weeks, flocculated but stable against coalescence in shear and stable to pasteurisation conditions (10 min at 80 °C). Emulsion droplet size was also insensitive to pH of the aqueous phase during preparation (pH 3-pH 9). Stable against coalescence, the water droplets in w/o emulsions prepared with hydrothermally treated waste coffee particles were considerably larger and microscopic examination showed evidence of arrested coalescence indicative of particle jamming at the surface of the emulsion droplets. Refinement of the hydrothermal treatment and broadening out to other lignin-rich plant or plant based food waste material are promising routes to bring closer the development of commercially relevant lignin based food Pickering particles applicable to emulsion based processed foods ranging from fat continuous spreads and fillings to salad dressings.

  20. CRCDA--Comprehensive resources for cancer NGS data analysis.

    Science.gov (United States)

    Thangam, Manonanthini; Gopal, Ramesh Kumar

    2015-01-01

    Next generation sequencing (NGS) innovations put a compelling landmark in life science and changed the direction of research in clinical oncology with its productivity to diagnose and treat cancer. The aim of our portal comprehensive resources for cancer NGS data analysis (CRCDA) is to provide a collection of different NGS tools and pipelines under diverse classes with cancer pathways and databases and furthermore, literature information from PubMed. The literature data was constrained to 18 most common cancer types such as breast cancer, colon cancer and other cancers that exhibit in worldwide population. NGS-cancer tools for the convenience have been categorized into cancer genomics, cancer transcriptomics, cancer epigenomics, quality control and visualization. Pipelines for variant detection, quality control and data analysis were listed to provide out-of-the box solution for NGS data analysis, which may help researchers to overcome challenges in selecting and configuring individual tools for analysing exome, whole genome and transcriptome data. An extensive search page was developed that can be queried by using (i) type of data [literature, gene data and sequence read archive (SRA) data] and (ii) type of cancer (selected based on global incidence and accessibility of data). For each category of analysis, variety of tools are available and the biggest challenge is in searching and using the right tool for the right application. The objective of the work is collecting tools in each category available at various places and arranging the tools and other data in a simple and user-friendly manner for biologists and oncologists to find information easier. To the best of our knowledge, we have collected and presented a comprehensive package of most of the resources available in cancer for NGS data analysis. Given these factors, we believe that this website will be an useful resource to the NGS research community working on cancer. Database URL: http://bioinfo.au-kbc.org.in/ngs/ngshome.html.

  1. Next generation sequencing (NGS)technologies and applications

    Energy Technology Data Exchange (ETDEWEB)

    Vuyisich, Momchilo [Los Alamos National Laboratory

    2012-09-11

    NGS technology overview: (1) NGS library preparation - Nucleic acids extraction, Sample quality control, RNA conversion to cDNA, Addition of sequencing adapters, Quality control of library; (2) Sequencing - Clonal amplification of library fragments, (except PacBio), Sequencing by synthesis, Data output (reads and quality); and (3) Data analysis - Read mapping, Genome assembly, Gene expression, Operon structure, sRNA discovery, and Epigenetic analyses.

  2. Pickering Emulsions for Food Applications: Background, Trends, and Challenges

    NARCIS (Netherlands)

    Berton-Carabin, C.C.; Schroën, C.G.P.H.

    2015-01-01

    Particle-stabilized emulsions, also referred to as Pickering emulsions, have garnered exponentially increasing interest in recent years. This has also led to the first food applications, although the number of related publications is still rather low. The involved stabilization mechanisms are fundam

  3. Particle Shape Anisotropy in Pickering Emulsions: Cubes and Peanuts

    NARCIS (Netherlands)

    de Folter, J.W.J.; Hutter, E.M.; Castillo, S.I.R.; Klop, K.E.; Philipse, A.P.; Kegel, W.K.

    2014-01-01

    We have investigated the effect of particle shape in Pickering emulsions by employing, for the first time, cubic and peanut-shaped particles. The interfacial packing and orientation of anisotropic microparticles are revealed at the single-particle level by direct microscopy observations. The uniform

  4. Pickering Emulsions for Food Applications: Background, Trends, and Challenges

    NARCIS (Netherlands)

    Berton-Carabin, C.C.; Schroën, C.G.P.H.

    2015-01-01

    Particle-stabilized emulsions, also referred to as Pickering emulsions, have garnered exponentially increasing interest in recent years. This has also led to the first food applications, although the number of related publications is still rather low. The involved stabilization mechanisms are

  5. tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species.

    Science.gov (United States)

    Russell, Joanne R; Hedley, Peter E; Cardle, Linda; Dancey, Siobhan; Morris, Jenny; Booth, Allan; Odee, David; Mwaura, Lucy; Omondi, William; Angaine, Peter; Machua, Joseph; Muchugi, Alice; Milne, Iain; Kindt, Roeland; Jamnadass, Ramni; Dawson, Ian K

    2014-01-01

    The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data.

  6. From pioneering to implementing automated blood pressure measurement in clinical practice: Thomas Pickering's legacy

    DEFF Research Database (Denmark)

    Stolarz-Skrzypek, Katarzyna; Thijs, Lutgarde; Wizner, Barbara

    2010-01-01

    Thomas G. Pickering spent most of his scientific career in carrying out research on clinical hypertension and blood pressure (BP) measurement. In our review of Pickering's seminal work, we first focused on white-coat hypertension and masked hypertension, two terms that he had introduced. Next, we...... highlighted the early publications of Pickering on diurnal BP variability and on the clinical application of self-measured BP. Pickering's work inspired many investigators worldwide and constituted a solid basis for further research. Pickering's original ideas led to algorithms for risk stratification...... involving white-coat hypertension and masked hypertension, diurnal BP variability, and self-measured BP. Recent studies validated Pickering's observations in terms of cardiovascular outcome and bridged the path from concept to application in clinical practice....

  7. Improved chemical shift based fragment selection for CS-Rosetta using Rosetta3 fragment picker

    Energy Technology Data Exchange (ETDEWEB)

    Vernon, Robert [Hospital for Sick Children, Program in Molecular Structure and Function (Canada); Shen, Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Baker, David [University of Washington, Department of Biochemistry (United States); Lange, Oliver F., E-mail: oliver.lange@tum.de [Technische Universitaet Muenchen, Department Chemie, Biomolecular NMR and Munich Center for Integrated Protein Science (Germany)

    2013-10-15

    A new fragment picker has been developed for CS-Rosetta that combines beneficial features of the original fragment picker, MFR, used with CS-Rosetta, and the fragment picker, NNMake, that was used for purely sequence based fragment selection in the context of ROSETTA de-novo structure prediction. Additionally, the new fragment picker has reduced sensitivity to outliers and other difficult to match data points rendering the protocol more robust and less likely to introduce bias towards wrong conformations in cases where data is bad, missing or inconclusive. The fragment picker protocol gives significant improvements on 6 of 23 CS-Rosetta targets. An independent benchmark on 39 protein targets, whose NMR data sets were published only after protocol optimization had been finished, also show significantly improved performance for the new fragment picker (van der Schot et al. in J Biomol NMR, 2013)

  8. Pickering emulsions stabilized by oppositely charged colloids: Stability and pattern formation

    Science.gov (United States)

    Christdoss Pushpam, Sam David; Basavaraj, Madivala G.; Mani, Ethayaraja

    2015-11-01

    A binary mixture of oppositely charged colloids can be used to stabilize water-in-oil or oil-in-water emulsions. A Monte Carlo simulation study to address the effect of charge ratio of colloids on the stability of Pickering emulsions is presented. The colloidal particles at the interface are modeled as aligned dipolar hard spheres, with attractive interaction between unlike-charged and repulsive interaction between like-charged particles. The optimum composition (fraction of positively charged particles) required for the stabilization corresponds to a minimum in the interaction energy per particle. In addition, for each charge ratio, there is a range of compositions where emulsions can be stabilized. The structural arrangement of particles or the pattern formation at the emulsion interface is strongly influenced by the charge ratio. We find well-mixed isotropic, square, and hexagonal arrangements of particles on the emulsion surface for different compositions at a given charge ratio. The distribution of coordination numbers is calculated to characterize structural features. The simulation study is useful for the rational design of Pickering emulsifications wherein oppositely charged colloids are used, and for the control of pattern formation that can be useful for the synthesis of colloidosomes and porous shells derived thereof.

  9. Pickering Emulsion-Based Marbles for Cellular Capsules

    Directory of Open Access Journals (Sweden)

    Guangzhao Zhang

    2016-07-01

    Full Text Available The biodegradable cellular capsule, being prepared from simple vaporization of liquid marbles, is an ideal vehicle for the potential application of drug encapsulation and release. This paper reports the fabrication of cellular capsules via facile vaporization of Pickering emulsion marbles in an ambient atmosphere. Stable Pickering emulsion (water in oil was prepared while utilizing dichloromethane (containing poly(l-lactic acid and partially hydrophobic silica particles as oil phase and stabilizing agents respectively. Then, the Pickering emulsion marbles were formed by dropping emulsion into a petri dish containing silica particles with a syringe followed by rolling. The cellular capsules were finally obtained after the complete vaporization of both oil and water phases. The technique of scanning electron microscope (SEM was employed to research the microstructure and surface morphology of the prepared capsules and the results showed the cellular structure as expected. An in vitro drug release test was implemented which showed a sustained release property of the prepared cellular capsules. In addition, the use of biodegradable poly(l-lactic acid and the biocompatible silica particles also made the fabricated cellular capsules of great potential in the application of sustained drug release.

  10. Barrier properties of heat treated starch Pickering emulsions.

    Science.gov (United States)

    Sjöö, Malin; Emek, Sinan Cem; Hall, Tina; Rayner, Marilyn; Wahlgren, Marie

    2015-07-15

    There is a recognized technological need for delivery systems encapsulating lipophilic substances in food and pharmaceutical products. Pickering emulsions can provide well-defined and highly stable systems, but may not provide good enough barrier properties. Starch granules, recently being used for Pickering stabilization, have the advantage of the ability to swell during gelatinization. Hence, this property could be used to tune and control barrier properties. Oil-in-water Pickering emulsions stabilized by starch were subject to heat treatment at different conditions. The influence of temperature, time, and storage on emulsion drop characteristics was evaluated. In order to further evaluate the barrier properties, lipolysis using the pH-stat method was applied and the effect of starch concentration, treatment temperature, and preliminary oral conditions were also investigated. A better encapsulating barrier was obtained by starch swelling at the oil drop interface. This was seen as reduced lipase activity. The internal oil drop size remained intact and the starch was kept at the interface during heat treatment. The extent of swelling could be controlled by the heating conditions and had impact on the ability to prevent lipase transport through the starch barrier layer. Addition of α-amylase simulating oral digestion only had minor impact on the barrier effect. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. NGS catalog: A database of next generation sequencing studies in humans.

    Science.gov (United States)

    Xia, Junfeng; Wang, Qingguo; Jia, Peilin; Wang, Bing; Pao, William; Zhao, Zhongming

    2012-06-01

    Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research since its advent only a few years ago, and they are expected to advance at an unprecedented pace in the following years. To provide the research community with a comprehensive NGS resource, we have developed the database Next Generation Sequencing Catalog (NGS Catalog, http://bioinfo.mc.vanderbilt.edu/NGS/index.html), a continually updated database that collects, curates and manages available human NGS data obtained from published literature. NGS Catalog deposits publication information of NGS studies and their mutation characteristics (SNVs, small insertions/deletions, copy number variations, and structural variants), as well as mutated genes and gene fusions detected by NGS. Other functions include user data upload, NGS general analysis pipelines, and NGS software. NGS Catalog is particularly useful for investigators who are new to NGS but would like to take advantage of these powerful technologies for their own research. Finally, based on the data deposited in NGS Catalog, we summarized features and findings from whole exome sequencing, whole genome sequencing, and transcriptome sequencing studies for human diseases or traits.

  12. Estimating IBD tracts from low coverage NGS data

    DEFF Research Database (Denmark)

    Garrett Vieira, Filipe Jorge; Albrechtsen, Anders; Nielsen, Rasmus

    2016-01-01

    that the new method provides a marked increase in accuracy even at low coverage. AVAILABILITY AND IMPLEMENTATION: The methods presented in this work were implemented in C/C ++ and are freely available for non-commercial use from https://github.com/fgvieira/ngsF-HMM CONTACT: fgvieira@snm.ku.dk SUPPLEMENTARY...

  13. Genetic counselors' (GC) knowledge, awareness, understanding of clinical next-generation sequencing (NGS) genomic testing.

    Science.gov (United States)

    Boland, P M; Ruth, K; Matro, J M; Rainey, K L; Fang, C Y; Wong, Y N; Daly, M B; Hall, M J

    2015-12-01

    Genomic tests are increasingly complex, less expensive, and more widely available with the advent of next-generation sequencing (NGS). We assessed knowledge and perceptions among genetic counselors pertaining to NGS genomic testing via an online survey. Associations between selected characteristics and perceptions were examined. Recent education on NGS testing was common, but practical experience limited. Perceived understanding of clinical NGS was modest, specifically concerning tumor testing. Greater perceived understanding of clinical NGS testing correlated with more time spent in cancer-related counseling, exposure to NGS testing, and NGS-focused education. Substantial disagreement about the role of counseling for tumor-based testing was seen. Finally, a majority of counselors agreed with the need for more education about clinical NGS testing, supporting this approach to optimizing implementation.

  14. NGS Catalog: A Database of Next Generation Sequencing Studies in Humans

    OpenAIRE

    Xia, Junfeng; Wang, Qingguo; Jia, Peilin; Wang, Bing; Pao, William; Zhao, Zhongming

    2012-01-01

    Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research since its advent only a few years ago, and they are expected to advance at an unprecedented pace in the following years. To provide the research community with a comprehensive NGS resource, we have developed the database Next Generation Sequencing Catalog (NGS Catalog, http://bioinfo.mc.vanderbilt.edu/NGS/index.html), a continually updated database that collects, curates and manages a...

  15. Edible foam based on Pickering effect of probiotic bacteria and milk proteins

    DEFF Research Database (Denmark)

    Yücel, Cigdem; Geng, Xiaolu; Cárdenas, Marité

    2017-01-01

    We report the preparation and characterization of aqueous Pickering foams using bio-particles constituted by lactic acid bacteria surface modified by oppositely charged milk proteins. Cell surface modification was shown by zeta potential measurements. Foams stabilized by bacterial Pickering bio-p...

  16. From pioneering to implementing automated blood pressure measurement in clinical practice: Thomas Pickering's legacy

    DEFF Research Database (Denmark)

    Stolarz-Skrzypek, Katarzyna; Thijs, Lutgarde; Wizner, Barbara;

    2010-01-01

    Thomas G. Pickering spent most of his scientific career in carrying out research on clinical hypertension and blood pressure (BP) measurement. In our review of Pickering's seminal work, we first focused on white-coat hypertension and masked hypertension, two terms that he had introduced. Next, we...

  17. Expanding worldwide urban solid waste recycling: The Brazilian social technology in waste pickers inclusion.

    Science.gov (United States)

    Rutkowski, Jacqueline E; Rutkowski, Emília W

    2015-12-01

    'If an integrated urban waste management system includes the informal recycling sector (IRS), there is a good chance that more solid waste is recycled' is common sense. However, informal integration brings additional social, environmental, and economic benefits, such as reduction of operational costs and environmental impacts of landfilling. Brazil is a global best practice example in terms of waste picker inclusion, and has received international recognition for its recycling levels. In addition to analysing the results of inclusive recycling approaches, this article evaluates a selection of the best Brazilian inclusive recycling practices and summaries and presents the resulting knowledge. The objective is to identify processes that enable the replication of the inclusion of the informal recycling sector model as part of municipal solid waste management. Qualitative and quantitative data have been collected in 25 Brazilian cities that have contracted waste pickers co-operatives for door-to-door selective collection of recyclables. Field data was collected in action research projects that worked with waste pickers co-operatives between 2006 and 2013. The Brazilian informal recycling sector integration model improves municipal solid waste recycling indicators: it shows an increase in the net tonness recycled, from 140 to 208 t month(-1), at a much lower cost per tonne than conventional selective collection systems. Inclusive systems show costs of US$35 per tonne of recyclables collected, well below the national average of US$195.26. This inclusive model improves the quality of collected material and the efficiency of municipal selective collection. It also diminishes the negative impacts of informal recycling, by reducing child labour, and by improving the conditions of work, occupational health and safety, and uncontrolled pollution. Although treating the Brazilian experience as a blueprint for transfer of experience in every case is unrealistic, the results

  18. An Overview of Pickering Emulsions: Solid-Particle Materials, Classification, Morphology, and Applications

    Directory of Open Access Journals (Sweden)

    Yunqi Yang

    2017-05-01

    Full Text Available Pickering emulsion, a kind of emulsion stabilized only by solid particles locating at oil–water interface, has been discovered a century ago, while being extensively studied in recent decades. Substituting solid particles for traditional surfactants, Pickering emulsions are more stable against coalescence and can obtain many useful properties. Besides, they are more biocompatible when solid particles employed are relatively safe in vivo. Pickering emulsions can be applied in a wide range of fields, such as biomedicine, food, fine chemical synthesis, cosmetics, and so on, by properly tuning types and properties of solid emulsifiers. In this article, we give an overview of Pickering emulsions, focusing on some kinds of solid particles commonly serving as emulsifiers, three main types of products from Pickering emulsions, morphology of solid particles and as-prepared materials, as well as applications in different fields.

  19. Development of Porous Polymers via Pickering HIPEs Template%Pickering HIPEs 模板构建多孔聚合物的研究进展

    Institute of Scientific and Technical Information of China (English)

    陈香; 潘建明; 闫永胜

    2016-01-01

    对近年来Pickering ( high internal phase emulsions , HIPEs )模板法制备多孔聚合物的工作进行了总结,阐述了Pickering HIPEs模板的形成机理和影响稳定性的因素,介绍了多孔材料( PolyHIPEs )的形貌控制和改性的有效手段,初步探讨了PolyHIPEs的应用现状和前景。 Pickering HIPEs模板法具有乳液稳定性好、形成过程环境友好、获得的多孔聚合物孔结构易控制等优点,有望应用于工业催化、能源转化、生物医学和化工分离等领域。%The porous polymers via Pickering HIPEs template were studied .The formation mechanism of Pickering HIPEs template and effects to the stability of template were discussed .The methods for controlling the porous structure and modification were demonstrated.Finally, the application status and prospect of porous polymers resulted from Pickering HIPEs template were also introduced .Pickering HIPEs possessed the advantages of stable emulsion , environment-friendly formation process , easy controlled the structure of as-prepared porous polymers.Thus, Pickering HIPEs had the potential to the fields of industrial catalysis , energy conversion , biomedicine and chemical separation .

  20. Next generation sequencing (NGS): a golden tool in forensic toolkit.

    Science.gov (United States)

    Aly, S M; Sabri, D M

    2015-01-01

    The DNA analysis is a cornerstone in contemporary forensic sciences. DNA sequencing technologies are powerful tools that enrich molecular sciences in the past based on Sanger sequencing and continue to glowing these sciences based on Next generation sequencing (NGS). Next generation sequencing has excellent potential to flourish and increase the molecular applications in forensic sciences by jumping over the pitfalls of the conventional method of sequencing. The main advantages of NGS compared to conventional method that it utilizes simultaneously a large number of genetic markers with high-resolution of genetic data. These advantages will help in solving several challenges such as mixture analysis and dealing with minute degraded samples. Based on these new technologies, many markers could be examined to get important biological data such as age, geographical origins, tissue type determination, external visible traits and monozygotic twins identification. It also could get data related to microbes, insects, plants and soil which are of great medico-legal importance. Despite the dozens of forensic research involving NGS, there are requirements before using this technology routinely in forensic cases. Thus, there is a great need to more studies that address robustness of these techniques. Therefore, this work highlights the applications of forensic sciences in the era of massively parallel sequencing.

  1. Reverse logistics network for municipal solid waste management: The inclusion of waste pickers as a Brazilian legal requirement.

    Science.gov (United States)

    Ferri, Giovane Lopes; Chaves, Gisele de Lorena Diniz; Ribeiro, Glaydston Mattos

    2015-06-01

    This study proposes a reverse logistics network involved in the management of municipal solid waste (MSW) to solve the challenge of economically managing these wastes considering the recent legal requirements of the Brazilian Waste Management Policy. The feasibility of the allocation of MSW material recovery facilities (MRF) as intermediate points between the generators of these wastes and the options for reuse and disposal was evaluated, as well as the participation of associations and cooperatives of waste pickers. This network was mathematically modelled and validated through a scenario analysis of the municipality of São Mateus, which makes the location model more complete and applicable in practice. The mathematical model allows the determination of the number of facilities required for the reverse logistics network, their location, capacities, and product flows between these facilities. The fixed costs of installation and operation of the proposed MRF were balanced with the reduction of transport costs, allowing the inclusion of waste pickers to the reverse logistics network. The main contribution of this study lies in the proposition of a reverse logistics network for MSW simultaneously involving legal, environmental, economic and social criteria, which is a very complex goal. This study can guide practices in other countries that have realities similar to those in Brazil of accelerated urbanisation without adequate planning for solid waste management, added to the strong presence of waste pickers that, through the characteristic of social vulnerability, must be included in the system. In addition to the theoretical contribution to the reverse logistics network problem, this study aids in decision-making for public managers who have limited technical and administrative capacities for the management of solid wastes. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Reverse logistics network for municipal solid waste management: The inclusion of waste pickers as a Brazilian legal requirement

    Energy Technology Data Exchange (ETDEWEB)

    Ferri, Giovane Lopes, E-mail: giovane.ferri@aluno.ufes.br [Department of Engineering and Technology, Federal University of Espírito Santo – UFES, Rodovia BR 101 Norte, Km 60, Bairro Litorâneo, São Mateus, ES, 29.932-540 (Brazil); Diniz Chaves, Gisele de Lorena, E-mail: gisele.chaves@ufes.br [Department of Engineering and Technology, Federal University of Espírito Santo – UFES, Rodovia BR 101 Norte, Km 60, Bairro Litorâneo, São Mateus, ES, 29.932-540 (Brazil); Ribeiro, Glaydston Mattos, E-mail: glaydston@pet.coppe.ufrj.br [Transportation Engineering Programme, Federal University of Rio de Janeiro – UFRJ, Centro de Tecnologia, Bloco H, Sala 106, Cidade Universitária, Rio de Janeiro, 21949-900 (Brazil)

    2015-06-15

    Highlights: • We propose a reverse logistics network for MSW involving waste pickers. • A generic facility location mathematical model was validated in a Brazilian city. • The results enable to predict the capacity for screening and storage centres (SSC). • We minimise the costs for transporting MSW with screening and storage centres. • The use of SSC can be a potential source of revenue and a better use of MSW. - Abstract: This study proposes a reverse logistics network involved in the management of municipal solid waste (MSW) to solve the challenge of economically managing these wastes considering the recent legal requirements of the Brazilian Waste Management Policy. The feasibility of the allocation of MSW material recovery facilities (MRF) as intermediate points between the generators of these wastes and the options for reuse and disposal was evaluated, as well as the participation of associations and cooperatives of waste pickers. This network was mathematically modelled and validated through a scenario analysis of the municipality of São Mateus, which makes the location model more complete and applicable in practice. The mathematical model allows the determination of the number of facilities required for the reverse logistics network, their location, capacities, and product flows between these facilities. The fixed costs of installation and operation of the proposed MRF were balanced with the reduction of transport costs, allowing the inclusion of waste pickers to the reverse logistics network. The main contribution of this study lies in the proposition of a reverse logistics network for MSW simultaneously involving legal, environmental, economic and social criteria, which is a very complex goal. This study can guide practices in other countries that have realities similar to those in Brazil of accelerated urbanisation without adequate planning for solid waste management, added to the strong presence of waste pickers that, through the

  3. Pickering emulsion templated interfacial atom transfer radical polymerization for microencapsulation.

    Science.gov (United States)

    Li, Jian; Hitchcock, Adam P; Stöver, Harald D H

    2010-12-01

    This Article describes a new microencapsulation method based on a Pickering emulsion templated interfacial atom transfer radical polymerization (PETI-ATRP). Cationic LUDOX CL nanoparticles were coated electrostatically with an anionic polymeric ATRP initiator, poly(sodium styrene sulfonate-co-2-(2-bromoisobutyryloxy)ethyl methacrylate) (PSB), prepared by radical copolymerization of sodium styrene sulfonate and 2-(2-bromoisobutyryloxy)ethyl methacrylate (BIEM). The resulting PSB-modified CL particles were surface active and could be used to stabilize oil-in-water Pickering emulsions. ATRP of water-soluble cross-linking monomers, confined to the oil-water interface by the surface-bound PSB, then led to nanoparticle/polymer composite shells. This method allowed encapsulation of core solvents (xylene, hexadecane, perfluoroheptane) with different solubility parameters. The microcapsule (MC) wall chemistry could accommodate different monomers, demonstrating the versatility of this method. Double-walled MCs were formed by sequentially carrying out PETI-ATRP and in situ polymerization of encapsulated monomers. The double-walled structure was verified by both transmission electron microscopy (TEM) and scanning transmission X-ray microscopy (STXM).

  4. Viscosity of the oil-in-water Pickering emulsion stabilized by surfactant-polymer and nanoparticle-surfactant-polymer system

    Science.gov (United States)

    Sharma, Tushar; Kumar, G. Suresh; Chon, Bo Hyun; Sangwai, Jitendra S.

    2014-11-01

    Information on the viscosity of Pickering emulsion is required for their successful application in upstream oil and gas industry to understand their stability at extreme environment. In this work, a novel formulation of oil-in-water (o/w) Pickering emulsion stabilized using nanoparticle-surfactant-polymer (polyacrylamide) system as formulated in our earlier work (Sharma et al., Journal of Industrial and Engineering Chemistry, 2014) is investigated for rheological stability at high pressure and high temperature (HPHT) conditions using a controlled-strain rheometer. The nanoparticle (SiO2 and clay) concentration is varied from 1.0 to 5.0 wt%. The results are compared with the rheological behavior of simple o/w emulsion stabilized by surfactant-polymer system. Both the emulsions exhibit non-Newtonian shear thinning behavior. A positive shift in this behavior is observed for surfactant-polymer stabilized emulsion at high pressure conditions. Yield stress is observed to increase with pressure for surfactant-polymer emulsion. In addition, increase in temperature has an adverse effect on the viscosity of emulsion stabilized by surfactant-polymer system. In case of nanoparticle-surfactant-polymer stabilized o/w emulsion system, the viscosity and yield stress are predominantly constant for varying pressure and temperature conditions. The viscosity data for both o/w emulsion systems are fitted by the Herschel-Bulkley model and found to be satisfactory. In general, the study indicates that the Pickering emulsion stabilized by nanoparticle-surfactant-polymer system shows improved and stable rheological properties as compared to conventional emulsion stabilized by surfactant-polymer system indicating their successful application for HPHT environment in upstream oil and gas industry.

  5. Tunable catalysts for solvent-free biphasic systems: pickering interfacial catalysts over amphiphilic silica nanoparticles.

    Science.gov (United States)

    Zhou, Wen-Juan; Fang, Lin; Fan, Zhaoyu; Albela, Belén; Bonneviot, Laurent; De Campo, Floryan; Pera-Titus, Marc; Clacens, Jean-Marc

    2014-04-02

    Stabilization of oil/oil Pickering emulsions using robust and recyclable catalytic amphiphilic silica nanoparticles bearing alkyl and propylsulfonic acid groups allows fast and efficient solvent-free acetalization of immiscible long-chain fatty aldehydes with ethylene glycol.

  6. Study of Pickering emulsions stabilized by mixed particles of silica and calcite

    Institute of Scientific and Technical Information of China (English)

    Sha Wang; Yongjun He; Yong Zou

    2010-01-01

    Picketing emulsions were prepared using mixed particles of silica and calcite as emulsifiers.The effects of the silica content in the mixed particles on the stability and the drop size of the Pickering emulsions were investigated.The results showed that the Pickering emulsions were of the oil-in-water type.With increasing silica content in the mixed particles,the stability and the drop size of the Pickering emulsions decreased.Larger silica particles had more influence on the stability of the emulsions,while smaller ones had more influence on the drop size of the emulsions.The effect of the silica particles on the emulsions was attributed to their adsorptive behavior at the oil-water interfaces of the Pickering emulsions.

  7. Fabrication of CMC-g-PAM superporous polymer monoliths via eco-friendly Pickering-MIPEs for superior adsorption of methyl violet and methylene blue

    Science.gov (United States)

    Wang, Feng; Zhu, Yongfeng; Wang, Wenbo; Zong, Li; Lu, Taotao; Wang, Aiqin

    2017-06-01

    A series of superporous carboxymethylcellulose-graft-poly(acrylamide) (CMC-g-PAM) polymer monoliths presenting interconnected pore structure and excellent adsorption properties were prepared by one-step free-radical grafting polymerization reaction of CMC and acrylamide (AM) in the oil-in-water (O/W) Pickering-medium internal phase emulsions (Pickering-MIPEs) composed of non-toxic edible oil as a dispersion phase and natural Pal nanorods as stabilizers. The effects of Pal dosage, AM dosage, and co-surfactant Tween-20 (T-20) on the pore structures of the monoliths were studied. It was revealed that the well-defined pores were formed when the dosages of Pal and T-20 are 9-14% and 3%, respectively. The porous monolith can rapidly adsorb 1585 mg/g of methyl violet (MV) and 1625 mg/g of methylene blue (MB). After the monolith was regenerated by adsorption-desorption process for 5 times, the adsorption capacities still reached 92.1% (for MV) and 93.5% (for MB) of the initial maximum adsorption capacities. The adsorption process was fitted with Langmuir adsorption isotherm model and pseudo-second-order adsorption kinetic model very well, which indicate that mono-layer chemical adsorption mainly contribute to the high-capacity adsorption for dyes. The superporous polymer monolith prepared from eco-friendly Pickering-MIPEs shows good adsorption capacity and fast adsorption rate, which is potential adsorbent for the decontimination of dye-containing wastewater.

  8. NGS-based Molecular diagnosis of 105 eyeGENE(®) probands with Retinitis Pigmentosa.

    Science.gov (United States)

    Ge, Zhongqi; Bowles, Kristen; Goetz, Kerry; Scholl, Hendrik P N; Wang, Feng; Wang, Xinjing; Xu, Shan; Wang, Keqing; Wang, Hui; Chen, Rui

    2015-12-15

    The National Ophthalmic Disease Genotyping and Phenotyping Network (eyeGENE(®)) was established in an effort to facilitate basic and clinical research of human inherited eye disease. In order to provide high quality genetic testing to eyeGENE(®)'s enrolled patients which potentially aids clinical diagnosis and disease treatment, we carried out a pilot study and performed Next-generation sequencing (NGS) based molecular diagnosis for 105 Retinitis Pigmentosa (RP) patients randomly selected from the network. A custom capture panel was designed, which incorporated 195 known retinal disease genes, including 61 known RP genes. As a result, disease-causing mutations were identified in 52 out of 105 probands (solving rate of 49.5%). A total of 82 mutations were identified, and 48 of them were novel. Interestingly, for three probands the molecular diagnosis was inconsistent with the initial clinical diagnosis, while for five probands the molecular information suggested a different inheritance model other than that assigned by the physician. In conclusion, our study demonstrated that NGS target sequencing is efficient and sufficiently precise for molecular diagnosis of a highly heterogeneous patient cohort from eyeGENE(®).

  9. An NGS Workflow Blueprint for DNA Sequencing Data and Its Application in Individualized Molecular Oncology

    OpenAIRE

    Jian Li; Aarif Mohamed Nazeer Batcha; Björn Grüning; Mansmann, Ulrich R.

    2016-01-01

    Next-generation sequencing (NGS) technologies that have advanced rapidly in the past few years possess the potential to classify diseases, decipher the molecular code of related cell processes, identify targets for decision-making on targeted therapy or prevention strategies, and predict clinical treatment response. Thus, NGS is on its way to revolutionize oncology. With the help of NGS, we can draw a finer map for the genetic basis of diseases and can improve our understanding of diagnostic ...

  10. An NGS Workflow Blueprint for DNA Sequencing Data and Its Application in Individualized Molecular Oncology.

    Science.gov (United States)

    Li, Jian; Batcha, Aarif Mohamed Nazeer; Grüning, Björn; Mansmann, Ulrich R

    2015-01-01

    Next-generation sequencing (NGS) technologies that have advanced rapidly in the past few years possess the potential to classify diseases, decipher the molecular code of related cell processes, identify targets for decision-making on targeted therapy or prevention strategies, and predict clinical treatment response. Thus, NGS is on its way to revolutionize oncology. With the help of NGS, we can draw a finer map for the genetic basis of diseases and can improve our understanding of diagnostic and prognostic applications and therapeutic methods. Despite these advantages and its potential, NGS is facing several critical challenges, including reduction of sequencing cost, enhancement of sequencing quality, improvement of technical simplicity and reliability, and development of semiautomated and integrated analysis workflow. In order to address these challenges, we conducted a literature research and summarized a four-stage NGS workflow for providing a systematic review on NGS-based analysis, explaining the strength and weakness of diverse NGS-based software tools, and elucidating its potential connection to individualized medicine. By presenting this four-stage NGS workflow, we try to provide a minimal structural layout required for NGS data storage and reproducibility.

  11. Non-monotonic dependence of Pickering emulsion gel rheology on particle volume fraction.

    Science.gov (United States)

    Kaganyuk, M; Mohraz, A

    2017-03-29

    The microstructure of Pickering emulsion gels features a tenuous network of faceted droplets, bridged together by shared monolayers of particles. In this investigation, we use standard oscillatory rheometry in conjunction with confocal microscopy to gain a more comprehensive understanding of the role particle bridged interfaces have on the rheology of Pickering emulsion gels. The zero-shear elastic modulus of Pickering emulsion gels shows a non-monotonic dependence on particle loading, with three separate regimes of power-law and linear gel strengthening, and subsequent gel weakening. The transition from power-law to linear scaling is found to coincide with a peak in the volume fraction of particles that participate in bridging, which we indirectly calculate using measureable quantities, and the transition to gel weakening is shown to result from a loss in network connectivity at high particle loadings. These observations are explained via a simple representation of how Pickering emulsion gels arise from an initial population of partially-covered droplets. Based on these considerations, we propose a combined variable related to the initial droplet coverage, to be used in reporting and rationalizing the rheology of Pickering emulsion gels. We demonstrate the applicability of this variable with Pickering emulsions prepared at variable fluid ratios and with different-sized colloidal particles. The results of our investigation have important implications for many technological applications that utilize solid stabilized multi-phase emulsions and require a priori knowledge or engineering of their flow characteristics.

  12. Processable high internal phase Pickering emulsions using depletion attraction.

    Science.gov (United States)

    Kim, KyuHan; Kim, Subeen; Ryu, Jiheun; Jeon, Jiyoon; Jang, Se Gyu; Kim, Hyunjun; Gweon, Dae-Gab; Im, Won Bin; Han, Yosep; Kim, Hyunjung; Choi, Siyoung Q

    2017-02-01

    High internal phase emulsions have been widely used as templates for various porous materials, but special strategies are required to form, in particular, particle-covered ones that have been more difficult to obtain. Here, we report a versatile strategy to produce a stable high internal phase Pickering emulsion by exploiting a depletion interaction between an emulsion droplet and a particle using water-soluble polymers as a depletant. This attractive interaction facilitating the adsorption of particles onto the droplet interface and simultaneously suppressing desorption once adsorbed. This technique can be universally applied to nearly any kind of particle to stabilize an interface with the help of various non- or weakly adsorbing polymers as a depletant, which can be solidified to provide porous materials for many applications.

  13. Tom Pickering as a clinical scientist: masked hypertension.

    Science.gov (United States)

    Eguchi, Kazuo

    2010-04-01

    Masked hypertension has been 'unmasked' by the use of the out-of-office measurement of blood pressure, as home BP monitoring or ambulatory blood pressure monitoring has become available. The term masked hypertension could be used more widely than the original version of masked hypertension; morning hypertension, stress-induced hypertension, and nocturnal hypertension are all classified as subtypes of masked hypertension. Masked hypertension can also be seen in patients with diabetes, that could change clinical practice in diabetes. Masked hypertension is associated with cardiovascular events, but most of the outcome studies are on antihypertensive medications. Therefore, masked hypertension includes insufficient treatment of hypertension. In Dr Pickering's latest review of masked hypertension, prehypertension or high normal blood pressure was stressed as an associating factor with masked hypertension. The biggest theme in the field of hypertension is how we can detect masked hypertension. I present two interesting cases of possible masked hypertension in this commentary.

  14. Pickering Emulsification to Mass Produce Nanoencapsulated Phase-change-material

    Science.gov (United States)

    Wang, Xuezhen; Zhang, Lecheng; Yu, Yi-Hsien; Mannan, S. Sam; Chen, Ying; Cheng, Zhengdong; Cheng's Group Team, Dr.

    2015-03-01

    Phase changing materials (PCM) have useful applications in thermal management. However, mass production of micro and nano encapsulated PCM has been a challenge. Here, we present a simple and scalable method via a two-step Pickering emulsification method. We have developed interface active nanoplates by asymmetric modification of nanoplates of layered crystal materials. Nanoencapsulated PCM is realized with exfoliated monolayer nanoplates surfactants using very little energy input for emulsification. Further chemical reactions are performed to convert the emulsions into core-shell structures. The resulted capsules are submicron in size with remarkable uniformity in size distribution. DSC characterization showed that the capsulation efficiency of NEPCM was 58.58% and were thermal stable which was characterized by the DSC data for the sample after 200 thermal cycling.

  15. Processable high internal phase Pickering emulsions using depletion attraction

    Science.gov (United States)

    Kim, Kyuhan; Kim, Subeen; Ryu, Jiheun; Jeon, Jiyoon; Jang, Se Gyu; Kim, Hyunjun; Gweon, Dae-Gab; Im, Won Bin; Han, Yosep; Kim, Hyunjung; Choi, Siyoung Q.

    2017-02-01

    High internal phase emulsions have been widely used as templates for various porous materials, but special strategies are required to form, in particular, particle-covered ones that have been more difficult to obtain. Here, we report a versatile strategy to produce a stable high internal phase Pickering emulsion by exploiting a depletion interaction between an emulsion droplet and a particle using water-soluble polymers as a depletant. This attractive interaction facilitating the adsorption of particles onto the droplet interface and simultaneously suppressing desorption once adsorbed. This technique can be universally applied to nearly any kind of particle to stabilize an interface with the help of various non- or weakly adsorbing polymers as a depletant, which can be solidified to provide porous materials for many applications.

  16. Coalescence of Pickering Emulsion Droplets Induced by an Electric Field

    Science.gov (United States)

    Chen, Guo; Tan, Peng; Chen, Shuyu; Huang, Jiping; Wen, Weijia; Xu, Lei

    2013-02-01

    Combining high-speed photography with electric current measurement, we investigate the electrocoalescence of Pickering emulsion droplets. Under a high enough electric field, the originally stable droplets coalesce via two distinct approaches: normal coalescence and abnormal coalescence. In the normal coalescence, a liquid bridge grows continuously and merges two droplets together, similar to the classical picture. In the abnormal coalescence, however, the bridge fails to grow indefinitely; instead, it breaks up spontaneously due to the geometric constraint from particle shells. Such connecting-then-breaking cycles repeat multiple times, until a stable connection is established. In depth analysis indicates that the defect size in particle shells determines the exact merging behaviors: when the defect size is larger than a critical size around the particle diameter, normal coalescence will show up, while abnormal coalescence will appear for coatings with smaller defects.

  17. Quantitative morphological characterization of bicontinuous Pickering emulsions via interfacial curvatures

    Science.gov (United States)

    Reeves, Matthew; Stratford, Kevin; Thijssen, Job H. J.

    Bicontinuous Pickering emulsions (bijels) are a physically interesting class of soft materials with many potential applications including catalysis, microfluidics and tissue engineering. They are created by arresting the spinodal decomposition of a partially-miscible liquid with a (jammed) layer of interfacial colloids. Porosity $L$ (average interfacial separation) of the bijel is controlled by varying the radius ($r$) and volume fraction ($\\phi$) of the colloids ($L \\propto r/\\phi$). However, to optimize the bijel structure with respect to other parameters, e.g. quench rate, characterizing by $L$ alone is insufficient. Hence, we have used confocal microscopy and X-ray CT to characterize a range of bijels in terms of local and area-averaged interfacial curvatures. In addition, the curvatures of bijels have been monitored as a function of time, which has revealed an intriguing evolution up to 60 minutes after bijel formation, contrary to previous understanding.

  18. Coalescence of Pickering emulsion droplets induced by electric-field

    Science.gov (United States)

    Chen, Guo; Tan, Peng; Chen, Shuyu; Huang, Jiping; Wen, Weijia; Xu, Lei

    2013-03-01

    Combining high-speed photography with electric current measurement, we investigate the coalescence of Pickering emulsion droplets. Under high enough electric field, the originally-stable droplets coalesce via two distinct approaches: normal coalescence and abnormal coalescence. In the normal coalescence, a liquid bridge grows continuously and merges two droplets together, similar to the classical picture. In the abnormal coalescence, however, the bridge fails to grow indefinitely; instead it breaks up spontaneously due to the geometric constraint from particle shells. Such connecting-then-breaking cycles repeat multiple times, until a stable connection is established. In depth analysis indicates that the defect size in particle shells determines the exact merging behaviors: when the defects are larger than a critical size, normal coalescence will show up; while abnormal coalescence will appear for smaller defects. This project is supported by the Hong Kong GRF Grant (Project No. CUHK404211).

  19. Processable high internal phase Pickering emulsions using depletion attraction

    Science.gov (United States)

    Kim, KyuHan; Kim, Subeen; Ryu, Jiheun; Jeon, Jiyoon; Jang, Se Gyu; Kim, Hyunjun; Gweon, Dae-Gab; Im, Won Bin; Han, Yosep; Kim, Hyunjung; Choi, Siyoung Q.

    2017-01-01

    High internal phase emulsions have been widely used as templates for various porous materials, but special strategies are required to form, in particular, particle-covered ones that have been more difficult to obtain. Here, we report a versatile strategy to produce a stable high internal phase Pickering emulsion by exploiting a depletion interaction between an emulsion droplet and a particle using water-soluble polymers as a depletant. This attractive interaction facilitating the adsorption of particles onto the droplet interface and simultaneously suppressing desorption once adsorbed. This technique can be universally applied to nearly any kind of particle to stabilize an interface with the help of various non- or weakly adsorbing polymers as a depletant, which can be solidified to provide porous materials for many applications. PMID:28145435

  20. Preparation of Pickering double emulsions using block copolymer worms.

    Science.gov (United States)

    Thompson, Kate L; Mable, Charlotte J; Lane, Jacob A; Derry, Mathew J; Fielding, Lee A; Armes, Steven P

    2015-04-14

    The rational formulation of Pickering double emulsions is described using a judicious combination of hydrophilic and hydrophobic block copolymer worms as highly anisotropic emulsifiers. More specifically, RAFT dispersion polymerization was utilized to prepare poly(lauryl methacrylate)-poly(benzyl methacrylate) worms at 20% w/w solids in n-dodecane and poly(glycerol monomethacrylate)-poly(2-hydroxypropyl methacrylate)-poly(benzyl methacrylate) worms at 13% w/w solids in water by polymerization-induced self-assembly (PISA). Water-in-oil-in-water (w/o/w) double emulsions can be readily prepared with mean droplet diameters ranging from 30 to 80 μm using a two-stage approach. First, a w/o precursor emulsion comprising 25 μm aqueous droplets is prepared using the hydrophobic worms, followed by encapsulation within oil droplets stabilized by the hydrophilic worms. The double emulsion droplet diameter and number of encapsulated water droplets can be readily varied by adjusting the stirring rate employed during the second stage. For each stage, the droplet volume fraction is relatively high at 0.50. The double emulsion nature of the final formulation was confirmed by optical and fluorescence microscopy studies. Such double emulsions are highly stable to coalescence, with little or no change in droplet diameter being detected over storage at 20 °C for 10 weeks as judged by laser diffraction. Preliminary experiments indicate that the complementary o/w/o emulsions can also be prepared using the same pair of worms by changing the order of homogenization, although somewhat lower droplet volume fractions were required in this case. Finally, we demonstrate that triple and even quadruple emulsions can be formulated using these new highly anisotropic Pickering emulsifiers.

  1. Tunable Pickering emulsions with polymer-grafted lignin nanoparticles (PGLNs).

    Science.gov (United States)

    Silmore, Kevin S; Gupta, Chetali; Washburn, Newell R

    2016-03-15

    Lignin is an abundant biopolymer that has native interfacial functions but aggregates strongly in aqueous media. Polyacrylamide was grafted onto kraft lignin nanoparticles using reversible addition-fragmentation chain transfer (RAFT) chemistry to form polymer-grafted lignin nanoparticles (PGLNs) that tune aggregation strength while retaining interfacial activities in forming Pickering emulsions. Polymer graft density on the particle surface, ionic strength, and initial water and cyclohexane volume fractions were varied and found to have profound effects on emulsion characteristics, including emulsion volume fraction, droplet size, and particle interfacial concentration that were attributed to changes in lignin aggregation and hydrophobic interactions. In particular, salt concentration was found to have a significant effect on aggregation, zeta potential, and interfacial tension, which was attributed to changes in solubility of both the kraft lignin and the polyacrylamide grafts. Dynamic light scattering, UV-vis spectroscopy, optical microscopy, and tensiometry were used to quantify emulsion properties and nanoparticle behavior. Under all conditions, the emulsions exhibited relatively fast creaming but were stable against coalescence and Ostwald ripening for a period of months. All emulsions were also oil-in-water (o/w) emulsions, as predicted by the Bancroft rule, and no catastrophic phase inversions were observed for any nanoparticle compositions. We conclude that lower grafting density of polyacrylamide on a lignin core resulted in high levels of interfacial activity, as characterized by higher concentration at the water-cyclohexane interface with a corresponding decrease in interfacial tension. These results indicate that the interfacial properties of polymer-grafted lignin nanoparticles are primarily due to the native hydrophobic interactions of the lignin core. These results suggest that the forces that drive aggregation are also correlated with interfacial

  2. NGS WFSs module for MAORY at E-ELT

    Science.gov (United States)

    Esposito, S.; Agapito, G.; Antichi, J.; Bonanno, A.; Carbonaro, L.; Giordano, C.; Spanò, P.

    We report on the natural guide star (NGS) wavefront sensors (WFS) module for MAORY, the multi-cojugate adaptive optics (MCAO) system for the ESO E-ELT. Three low-order, near-infrared (H-band), Shack-Hartmann sensors provide fast acquisition of the first 5 modes (tip, tilt, focus, astigmatism) on 3 natural guide stars over a 160 arcsec field of view. Three moderate-order (20x20), visible (600-800 nm), pyramid WFSs provide the slow Truth sensing to correct LGS wavefront estimates of low-order modes. These sensors are mounted onto three R-theta stages to patrol the field of view. The module is also equipped with a retractable, on-axis, high-order (80x80), visible, pyramid WFS for the single-conjugate AO (SCAO) mode of MAORY and MICADO. The visible WFSs share the same 80x80 pyramid WFS design. This choice enables also a MCAO NGS capability. Simulations show that Strehl ratios (SR) over 40% are reached with MCAO and three, 2x2 sub-apertures, NIR low-order WFSs working with H-mag=20 reference stars. In SCAO mode, 90% SR for a 8mag stars with a contrast down to 10-5, and 45% SR for a 16mag star, are achieved.

  3. Émulsions de Pickering : approche théorique et applications : analyse physico-chimique des phénomènes interfaciaux : obtention d'émulsions de Pickering nanométriques de manière spontanée et d'émulsions foisonnées de Pickering

    OpenAIRE

    Ridel, Laure

    2015-01-01

    Pickering emulsions are emulsions stabilized by solid particles in opposition to emulsifiers-stabilized emulsions. The stabilization of Pickering emulsions comes from a strong adsorption of solid particles at the oil-water interface that builds a rigid barrier against coalescence. The aim of this work was to understand, develop and optimize methods for the fabrication of different types of Pickering emulsions stabilized by silica nanoparticles. Three mains axes can be exposed: (i) Firstly, a ...

  4. RNA-CODE: a noncoding RNA classification tool for short reads in NGS data lacking reference genomes.

    Directory of Open Access Journals (Sweden)

    Cheng Yuan

    Full Text Available The number of transcriptomic sequencing projects of various non-model organisms is still accumulating rapidly. As non-coding RNAs (ncRNAs are highly abundant in living organism and play important roles in many biological processes, identifying fragmentary members of ncRNAs in small RNA-seq data is an important step in post-NGS analysis. However, the state-of-the-art ncRNA search tools are not optimized for next-generation sequencing (NGS data, especially for very short reads. In this work, we propose and implement a comprehensive ncRNA classification tool (RNA-CODE for very short reads. RNA-CODE is specifically designed for ncRNA identification in NGS data that lack quality reference genomes. Given a set of short reads, our tool classifies the reads into different types of ncRNA families. The classification results can be used to quantify the expression levels of different types of ncRNAs in RNA-seq data and ncRNA composition profiles in metagenomic data, respectively. The experimental results of applying RNA-CODE to RNA-seq of Arabidopsis and a metagenomic data set sampled from human guts demonstrate that RNA-CODE competes favorably in both sensitivity and specificity with other tools. The source codes of RNA-CODE can be downloaded at http://www.cse.msu.edu/~chengy/RNA_CODE.

  5. Research progress review of solid particles stabilized Pickering emulsion and polymerization%固体颗粒稳定的 Pickering 乳液及其聚合研究述评

    Institute of Scientific and Technical Information of China (English)

    刘瑞雪; 段瑞卿; 岳英英; 张晓静; 方少明

    2014-01-01

    Recent advances in Pickering emulsion stabilized by solid particles and Pickering emulsion poly-merization were reviewed.It pointed out that the main stability theories of Pickering emulsion were the in-terface theory and the contact angle theory.The influence factors of Pickering emulsion included solid par-ticle concentration,pH value and the type of electrolyte,etc.SiO2 ,Laponite and magnetite had been commonly used as solid stabilizers in Pickering emulsion polymerization.The shortages on Pickering emul-sion research were also pointed out,such as neglecting the influence of electrical properties of solid parti-cles and deficient research on lamellar colloidal particles as Pickering emulsion stabilizer.Preparing the new Pickering emulsion less affected by monomer with stable properties,so as to enrich Pickering emulsion and its joint technology will be the research focus in the future.%综观国内外学者近年对固体颗粒稳定的 Pickering 乳液及其聚合的研究,相关理论有界面理论和接触角理论,对其影响因素的分析主要有固体颗粒浓度、水相 pH 值和水相电解质。研究者已经将SiO2,Laponite 粘土,磁铁矿等一系列无机固体颗粒成功地应用于 Pickering 乳液中,并制备出一系列性能各异的材料,但研究工作仍存在一些不足,如忽略固体颗粒的电性质对 Pickering 乳液的影响,对 Pickering 乳液的片状胶体颗粒稳定剂的研究不系统等。制备受单体影响小、性能稳定的新型 Pick-ering 乳液聚合稳定剂,从而不断丰富 Pickering 乳液及其聚合技术将是未来研究的热点。

  6. IPv6与下一代服务(NGS)

    Institute of Scientific and Technical Information of China (English)

    雷振洲

    2005-01-01

    大家知道现在我们都在走PSTN电信网络NGN,下一代Internet就是NGI,移动网要走向3G/B3G.那么他们为什么要走向NGS,实际上特别是上个世纪90年代的移动通信告诉我们现在的网络不能适应将来的要求,为什么?互联网的大发展说明人对信息的需求、对数据的需求、对未来更有价值的服务应用的需求越来越高.移动的大发展说明移动性对个性化对无所不在的需求是越来越强烈了.

  7. Clinical validation of NGS technology for HLA: An early adopter's perspective.

    Science.gov (United States)

    Weimer, Eric T

    2016-10-01

    Clinical validation of NGS for HLA typing has been a topic of interest with many laboratories investigating the merits. NGS has proven effective at reducing ambiguities and costs while providing more detailed information on HLA genes not previously sequenced. The ability of NGS to multiplex many patients within a single run presents unique challenges and sequencing new regions of HLA genes requires application of our knowledge of genetics to accurately determine HLA typing. This review represents my laboratory's experience in validation of NGS for HLA typing. It describes the obstacles faced with validation of NGS and is broken down into pre-analytic, analytic, and post-analytic challenges. Each section includes solutions to address them.

  8. DeepPicker: A deep learning approach for fully automated particle picking in cryo-EM.

    Science.gov (United States)

    Wang, Feng; Gong, Huichao; Liu, Gaochao; Li, Meijing; Yan, Chuangye; Xia, Tian; Li, Xueming; Zeng, Jianyang

    2016-09-01

    Particle picking is a time-consuming step in single-particle analysis and often requires significant interventions from users, which has become a bottleneck for future automated electron cryo-microscopy (cryo-EM). Here we report a deep learning framework, called DeepPicker, to address this problem and fill the current gaps toward a fully automated cryo-EM pipeline. DeepPicker employs a novel cross-molecule training strategy to capture common features of particles from previously-analyzed micrographs, and thus does not require any human intervention during particle picking. Tests on the recently-published cryo-EM data of three complexes have demonstrated that our deep learning based scheme can successfully accomplish the human-level particle picking process and identify a sufficient number of particles that are comparable to those picked manually by human experts. These results indicate that DeepPicker can provide a practically useful tool to significantly reduce the time and manual effort spent in single-particle analysis and thus greatly facilitate high-resolution cryo-EM structure determination. DeepPicker is released as an open-source program, which can be downloaded from https://github.com/nejyeah/DeepPicker-python.

  9. Estimating the possible range of recycling rates achieved by dump waste pickers: The case of Bantar Gebang in Indonesia.

    Science.gov (United States)

    Sasaki, Shunsuke; Araki, Tetsuya

    2014-06-01

    This article presents informal recycling contributions made by scavengers in the surrounding area of Bantar Gebang final disposal site for municipal solid waste generated in Jakarta. Preliminary fieldwork was conducted through daily conversations with scavengers to identify recycling actors at the site, and then quantitative field surveys were conducted twice. The first survey (n = 504 households) covered 33% of all households in the area, and the second survey (n = 69 households) was conducted to quantify transactions of recyclables among scavengers. Mathematical equations were formulated with assumptions made to estimate the possible range of recycling rates achieved by dump waste pickers. Slightly over 60% of all respondents were involved in informal recycling and over 80% of heads of households were waste pickers, normally referred to as live-in waste pickers and live-out waste pickers at the site. The largest percentage of their spouses were family workers, followed by waste pickers and housewives. Over 95% of all households of respondents had at least one waste picker or one small boss who has a coequal status of a waste picker. Average weight of recyclables collected by waste pickers at the site was estimated to be approximately 100 kg day(-1) per household on the net weight basis. The recycling rate of solid wastes collected by all scavengers at the site was estimated to be in the range of 2.8-7.5% of all solid wastes transported to the site.

  10. Sculpting Pickering Emulsion Droplets by Arrest and Jamming

    Science.gov (United States)

    Burke, Christopher; Wei, Zengyi; Caggioni, Marco; Spicer, Patrick; Atherton, Tim

    Pickering emulsion droplets can be arrested into non-spherical shapes--useful for applications such as active delivery--through a general mechanism of deformation followed by absorption of additional colloidal particles onto the interface, relaxation of the droplet caused by surface tension and arrest at some point due to crowding of the particles. We perform simulations of the arrest process to clarify the relative importance of diffusive rearrangement of particles and collective forcing due to surface evolution. Experiment and theory are compared, giving insight into the stability of the resulting capsules and the robustness of the production process for higher-throughput production in, for example, microfluidic systems. We adapt theoretical tools from the jamming literature to better understand the arrested configurations and long timescale evolution of the system: using linear programming and a penalty function approach, we identify unjamming motions in kinetically arrested states. We propose a paradigm of ``metric jamming'' to describe the limiting behavior of this class of system: a structure is metric-jammed if it is stable with respect to collective motion of the particles as well as evolution of the hypersurface on which the packing is embedded. Supported by a Cottrell Award from the Research Corporation for Science Advancement.

  11. Particle shape anisotropy in pickering emulsions: cubes and peanuts.

    Science.gov (United States)

    de Folter, Julius W J; Hutter, Eline M; Castillo, Sonja I R; Klop, Kira E; Philipse, Albert P; Kegel, Willem K

    2014-02-04

    We have investigated the effect of particle shape in Pickering emulsions by employing, for the first time, cubic and peanut-shaped particles. The interfacial packing and orientation of anisotropic microparticles are revealed at the single-particle level by direct microscopy observations. The uniform anisotropic hematite microparticles adsorb irreversibly at the oil-water interface in monolayers and form solid-stabilized o/w emulsions via the process of limited coalescence. Emulsions were stable against further coalescence for at least 1 year. We found that cubes assembled at the interface in monolayers with a packing intermediate between hexagonal and cubic and average packing densities of up to 90%. Local domains displayed densities even higher than theoretically achievable for spheres. Cubes exclusively orient parallel with one of their flat sides at the oil-water interface, whereas peanuts preferentially attach parallel with their long side. Those peanut-shaped microparticles assemble in locally ordered, interfacial particle stacks that may interlock. Indications for long-range capillary interactions were not found, and we hypothesize that this is related to the observed stable orientations of cubes and peanuts that marginalize deformations of the interface.

  12. Pickering interfacial catalysis for biphasic systems: from emulsion design to green reactions.

    Science.gov (United States)

    Pera-Titus, Marc; Leclercq, Loïc; Clacens, Jean-Marc; De Campo, Floryan; Nardello-Rataj, Véronique

    2015-02-09

    Pickering emulsions are surfactant-free dispersions of two immiscible fluids that are kinetically stabilized by colloidal particles. For ecological reasons, these systems have undergone a resurgence of interest to mitigate the use of synthetic surfactants and solvents. Moreover, the use of colloidal particles as stabilizers provides emulsions with original properties compared to surfactant-stabilized emulsions, microemulsions, and micellar systems. Despite these specific advantages, the application of Pickering emulsions to catalysis has been rarely explored. This Minireview describes very recent examples of hybrid and composite amphiphilic materials for the design of interfacial catalysts in Pickering emulsions with special emphasis on their assets and challenges for industrially relevant biphasic reactions in fine chemistry, biofuel upgrading, and depollution.

  13. Controlling Pickering Emulsion Destabilisation: A Route to Fabricating New Materials by Phase Inversion

    Directory of Open Access Journals (Sweden)

    Catherine P. Whitby

    2016-07-01

    Full Text Available The aim of this paper is to review the key findings about how particle-stabilised (or Pickering emulsions respond to stress and break down. Over the last ten years, new insights have been gained into how particles attached to droplet (and bubble surfaces alter the destabilisation mechanisms in emulsions. The conditions under which chemical demulsifiers displace, or detach, particles from the interface were established. Mass transfer between drops and the continuous phase was shown to disrupt the layers of particles attached to drop surfaces. The criteria for causing coalescence by applying physical stress (shear or compression to Pickering emulsions were characterised. These findings are being used to design the structures of materials formed by breaking Pickering emulsions.

  14. Switchable Pickering emulsions stabilized by silica nanoparticles hydrophobized in situ with a conventional cationic surfactant.

    Science.gov (United States)

    Zhu, Yue; Jiang, Jianzhong; Liu, Kaihong; Cui, Zhenggang; Binks, Bernard P

    2015-03-24

    A stable oil-in-water Pickering emulsion stabilized by negatively charged silica nanoparticles hydrophobized in situ with a trace amount of a conventional cationic surfactant can be rendered unstable on addition of an equimolar amount of an anionic surfactant. The emulsion can be subsequently restabilized by adding a similar trace amount of cationic surfactant along with rehomogenization. This destabilization-stabilization behavior can be cycled many times, demonstrating that the Pickering emulsion is switchable. The trigger is the stronger electrostatic interaction between the oppositely charged ionic surfactants compared with that between the cationic surfactant and the (initially) negatively charged particle surfaces. The cationic surfactant prefers to form ion pairs with the added anionic surfactant and thus desorbs from particle surfaces rendering them surface-inactive. This access to switchable Pickering emulsions is easier than those employing switchable surfactants, polymers, or surface-active particles, avoiding both the complicated synthesis and the stringent switching conditions.

  15. A new drug nanocrystal self-stabilized Pickering emulsion for oral delivery of silybin.

    Science.gov (United States)

    Yi, Tao; Liu, Chuan; Zhang, Jiao; Wang, Fan; Wang, Jirui; Zhang, Jifen

    2017-01-01

    A new silybin nanocrystal self-stabilized Pickering emulsion (SN-SSPE) has been developed using a high pressure homogenization method to improve the oral bioavailability of silybin. Influences of homogenization pressure and drug content on the formation of SN-SSPE were studied. The morphology, structure and size of Pickering emulsion droplets were characterized using a scanning electron micrograph, confocal laser scanning microscopy and atomic force microscopy. The stability, in vitro release and in vivo oral bioavailability of SN-SSPE were investigated. Results indicated that the particle size of silybin nanocrystals (SN-NC) decreased when homogenization pressure increased until 100MPa. When the content of silybin reached 300mg or above, a stable Pickering emulsion of silybin could be formed by sufficient SN-NC covering surfaces of oil droplets completely and thus self-stabilizing the Pickering emulsion. The emulsion droplet of SN-SSPE with the size of 27.3±3.1μm showed a core-shell structure consisting of a core of oil and a shell of SN-NC. SN-SSPE has shown high stability over 40days. The in vitro release rate of SN-SSPE was faster than silybin coarse powder and similar to silybin nanocrystalline suspension (SN-NCS). The peak concentration of silybin of SN-SSPE following intragastric administration in rats was increased by 2.5-fold and 3.6-fold compared with SN-NCS and silybin coarse powder, respectively. The AUC of SN-SSPE was increased by 1.6-fold and 4.0-fold compared with SN-NCS and silybin coarse powder, respectively. All these results showed that the Pickering emulsion of silybin could be stabilized by nanocrystals of silybin itself and increased the oral bioavailability of silybin. The drug nanocrystalline self-stabilized Pickering emulsion was a promising oral drug delivery system for poorly soluble drugs.

  16. Cas-analyzer: an online tool for assessing genome editing results using NGS data.

    Science.gov (United States)

    Park, Jeongbin; Lim, Kayeong; Kim, Jin-Soo; Bae, Sangsu

    2017-01-15

    Genome editing with programmable nucleases has been widely adopted in research and medicine. Next generation sequencing (NGS) platforms are now widely used for measuring the frequencies of mutations induced by CRISPR-Cas9 and other programmable nucleases. Here, we present an online tool, Cas-Analyzer, a JavaScript-based implementation for NGS data analysis. Because Cas-Analyzer is completely used at a client-side web browser on-the-fly, there is no need to upload very large NGS datasets to a server, a time-consuming step in genome editing analysis. Currently, Cas-Analyzer supports various programmable nucleases, including single nucleases and paired nucleases.

  17. Colloidal particles as liquid dispersion stabilizer: Pickering emulsions and materials thereof

    Science.gov (United States)

    Schmitt, Véronique; Destribats, Mathieu; Backov, Rénal

    2014-10-01

    Solid stabilized emulsions, also referred to as Pickering emulsions, are very diverse owing to the large variety of available colloidal particles from naturally occurring to synthesized ones, from hard to very deformable ones and from spheres to more complex shaped particles. Here we illustrate this variety and, despite this huge diversity, we aim at highlighting the common features. We discuss next the remaining open questions that, in our point of view, should sustain special efforts in the future and we illustrate elaboration of original materials based on Pickering emulsions. xml:lang="fr"

  18. A Pure-Python Robust Frequency Band Automatic Phase Picker for Seismic Monitoring

    Science.gov (United States)

    Chen, C.; Holland, A. A.

    2013-12-01

    We modify the FPPICK algorithm of Lomax et al. (2012) and implement an automatic phase picking algorithm implemented in Python. The algorithm takes advantage of existing seismological Python libraries, Obspy. The algorithm is designed to work on a variety of instrumentation and automatically adapts to different sampling rates. The time series signals are band-pass filtered for each band, octave, considered within the picker algorithm. The energy of the signal is calculated over an averaging window and multiplied by the instantaneous energy of the signal. This energy time-series is the statistic we can then examine for each frequency band considered. The summary statistic, which allows the identification of a trigger, is simply the maximum value of any frequency bands energy statistic at each sample time. A trigger is identified by using a control chart type statistic to identify when our statistics summary is changing rapidly and exceeds a specified number of standard deviations from the mean of the summary energy statistic. This has the advantage that the picker parameters don't necessarily need to be modified when processing data from a wide variety of instrumentation with different response characteristics. The algorithm also contains a method to determine the first motion direction associated with a pick as well as an uncertainty for the pick. As with any automatic phase identification system false picks can and do occur. A few simple algorithms are implemented to avoid false-picks, the picker can be configured not to include these checks. These algorithms remove picks that occur very close in time, and picks for which a phase has a smaller RMS than the previous time interval. The algorithm uses many techniques within Numpy to improve computation times. The algorithm effectively picks both P- and S-phase from local and regional earthquakes with only small amounts of picker parameter modifications. The picker can pick both P and S phases on local and regional

  19. Aquivion Perfluorosulfonic Superacid as an Efficient Pickering Interfacial Catalyst for the Hydrolysis of Triglycerides.

    Science.gov (United States)

    Shi, Hui; Fan, Zhaoyu; Hong, Bing; Pera-Titus, Marc

    2017-09-11

    Rational design of the surface properties of heterogeneous catalysts can boost the interfacial activity in biphasic reactions through the generation of Pickering emulsions. This concept, termed Pickering interfacial catalysis (PIC), has shown promising credentials in acid-catalyzed transesterification, ester hydrolysis, acetalization, etherification, and alkylation reactions. PIC has now been applied to the efficient, solvent-free hydrolysis of the triglyceride glyceryl trilaurate to lauric acid, catalyzed by Aquivion perfluorosulfonic superacid at mild conditions (100 °C and ambient pressure). © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Using REDItools to Detect RNA Editing Events in NGS Datasets.

    Science.gov (United States)

    Picardi, Ernesto; D'Erchia, Anna Maria; Montalvo, Antonio; Pesole, Graziano

    2015-03-09

    RNA editing is a post-transcriptional/co-transcriptional molecular phenomenon whereby a genetic message is modified from the corresponding DNA template by means of substitutions, insertions, and/or deletions. It occurs in a variety of organisms and different cellular locations through evolutionally and biochemically unrelated proteins. RNA editing has a plethora of biological effects including the modulation of alternative splicing and fine-tuning of gene expression. RNA editing events by base substitutions can be detected on a genomic scale by NGS technologies through the REDItools package, an ad hoc suite of Python scripts to study RNA editing using RNA-Seq and DNA-Seq data or RNA-Seq data alone. REDItools implement effective filters to minimize biases due to sequencing errors, mapping errors, and SNPs. The package is freely available at Google Code repository (http://code.google.com/p/reditools/) and released under the MIT license. In the present unit we show three basic protocols corresponding to three main REDItools scripts.

  1. Porous and Magnetic Molecularly Imprinted Polymers via Pickering High Internal Phase Emulsions Polymerization for Selective Adsorption of λ-Cyhalothrin

    Science.gov (United States)

    Wu, Yunlong; Ma, Yue; Pan, Jianming; Gu, Runxing; Luo, Jialu

    2017-01-01

    A novel macroporous magnetic molecularly imprinted polymer (MMIPs) of was prepared by W/O Pickering (high internal phase emulsions) HIPEs polymerization, and then it was adopted as adsorbent for selective adsorption of λ-cyhalothrin (LC). In static conditions, adsorption capacity of LC increased rapidly in the first 60 min and reached to equilibrium in ~2.0 h. Excellent conformity of the second-order model confirmed the chemical nature of the interaction between the LC and imprinted sites. The fitting adsorption isotherm was a Langmuir type, and the maximum monolayer adsorption capacity at 298 K was 404.4 μmol g−1. Thermodynamic parameters suggested the specific adsorption at 298 K was an exothermic, spontaneous, and entropy decreased process. Competitive recognition studies of the MMIPs were performed with diethyl phthalate (DEP) and the structurally similar compound fenvalerate (FL), and the MMIPs, which displayed high selectivity for LC.

  2. The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability.

    Science.gov (United States)

    Li, Jing-Woei; Bolser, Dan; Manske, Magnus; Giorgi, Federico Manuel; Vyahhi, Nikolay; Usadel, Björn; Clavijo, Bernardo J; Chan, Ting-Fung; Wong, Nathalie; Zerbino, Daniel; Schneider, Maria Victoria

    2013-09-01

    Next-generation sequencing (NGS) is increasingly being adopted as the backbone of biomedical research. With the commercialization of various affordable desktop sequencers, NGS will be reached by increasing numbers of cellular and molecular biologists, necessitating community consensus on bioinformatics protocols to tackle the exponential increase in quantity of sequence data. The current resources for NGS informatics are extremely fragmented. Finding a centralized synthesis is difficult. A multitude of tools exist for NGS data analysis; however, none of these satisfies all possible uses and needs. This gap in functionality could be filled by integrating different methods in customized pipelines, an approach helped by the open-source nature of many NGS programmes. Drawing from community spirit and with the use of the Wikipedia framework, we have initiated a collaborative NGS resource: The NGS WikiBook. We have collected a sufficient amount of text to incentivize a broader community to contribute to it. Users can search, browse, edit and create new content, so as to facilitate self-learning and feedback to the community. The overall structure and style for this dynamic material is designed for the bench biologists and non-bioinformaticians. The flexibility of online material allows the readers to ignore details in a first read, yet have immediate access to the information they need. Each chapter comes with practical exercises so readers may familiarize themselves with each step. The NGS WikiBook aims to create a collective laboratory book and protocol that explains the key concepts and describes best practices in this fast-evolving field.

  3. Fabrication of CMC-g-PAM Superporous Polymer Monoliths via Eco-Friendly Pickering-MIPEs for Superior Adsorption of Methyl Violet and Methylene Blue

    Directory of Open Access Journals (Sweden)

    Feng Wang

    2017-06-01

    Full Text Available A series of superporous carboxymethylcellulose-graft-poly(acrylamide/palygorskite (CMC-g-PAM/Pal polymer monoliths presenting interconnected pore structure and excellent adsorption properties were prepared by one-step free-radical grafting polymerization reaction of CMC and acrylamide (AM in the oil-in-water (O/W Pickering-medium internal phase emulsions (Pickering-MIPEs composed of non-toxic edible oil as a dispersion phase and natural Pal nanorods as stabilizers. The effects of Pal dosage, AM dosage, and co-surfactant Tween-20 (T-20 on the pore structures of the monoliths were studied. It was revealed that the well-defined pores were formed when the dosages of Pal and T-20 are 9–14 and 3%, respectively. The porous monolith can rapidly adsorb 1,585 mg/g of methyl violet (MV and 1,625 mg/g of methylene blue (MB. After the monolith was regenerated by adsorption-desorption process for five times, the adsorption capacities still reached 92.1% (for MV and 93.5% (for MB of the initial maximum adsorption capacities. The adsorption process was fitted with Langmuir adsorption isotherm model and pseudo-second-order adsorption kinetic model very well, which indicate that mono-layer chemical adsorption mainly contribute to the high-capacity adsorption for dyes. The superporous polymer monolith prepared from eco-friendly Pickering-MIPEs shows good adsorption capacity and fast adsorption rate, which is potential adsorbent for the decontamination of dye-containing wastewater.

  4. Fabrication of CMC-g-PAM Superporous Polymer Monoliths via Eco-Friendly Pickering-MIPEs for Superior Adsorption of Methyl Violet and Methylene Blue

    Science.gov (United States)

    Wang, Feng; Zhu, Yongfeng; Wang, Wenbo; Zong, Li; Lu, Taotao; Wang, Aiqin

    2017-01-01

    A series of superporous carboxymethylcellulose-graft-poly(acrylamide)/palygorskite (CMC-g-PAM/Pal) polymer monoliths presenting interconnected pore structure and excellent adsorption properties were prepared by one-step free-radical grafting polymerization reaction of CMC and acrylamide (AM) in the oil-in-water (O/W) Pickering-medium internal phase emulsions (Pickering-MIPEs) composed of non-toxic edible oil as a dispersion phase and natural Pal nanorods as stabilizers. The effects of Pal dosage, AM dosage, and co-surfactant Tween-20 (T-20) on the pore structures of the monoliths were studied. It was revealed that the well-defined pores were formed when the dosages of Pal and T-20 are 9–14 and 3%, respectively. The porous monolith can rapidly adsorb 1,585 mg/g of methyl violet (MV) and 1,625 mg/g of methylene blue (MB). After the monolith was regenerated by adsorption-desorption process for five times, the adsorption capacities still reached 92.1% (for MV) and 93.5% (for MB) of the initial maximum adsorption capacities. The adsorption process was fitted with Langmuir adsorption isotherm model and pseudo-second-order adsorption kinetic model very well, which indicate that mono-layer chemical adsorption mainly contribute to the high-capacity adsorption for dyes. The superporous polymer monolith prepared from eco-friendly Pickering-MIPEs shows good adsorption capacity and fast adsorption rate, which is potential adsorbent for the decontamination of dye-containing wastewater. PMID:28642862

  5. Interventions for control of Salmonella: clearance of microbial growth from rubber picker fingers.

    Science.gov (United States)

    Arnold, J W; Yates, I E

    2009-06-01

    A study was conducted to determine if a surface material with antimicrobial properties combined with an effective disinfectant could achieve total clearance of bacterial contamination. Before beginning the project, new rubber picker fingers collected from 3 processing facilities were tested for endogenous microflora. Five species of bacteria common to soil and human handling were present: Bacillus amyloliquefaciens, Bacillus cereus/thuringiensis, Staphylococcus epidermidis, Staphylococcus hominis ssp. novobiosepticus, and Staphylococcus intermedius. In separate experiments, new (unused) rubber picker fingers from 3 manufacturers were exposed to broiler carcass rinses, and the kinetics of bacterial attachment to finger material was determined. Turbidity of the bacterial suspensions at varying dilutions containing picker finger sections was compared hourly with controls to evaluate inhibition. New rubber finger material from the 3 manufacturers significantly inhibited bacterial growth (P growth of pathogens and determined the activity of 5 disinfectant compounds. Two of the compounds were most effective against Pseudomonas aeruginosa, Listeria monocytogenes, Staphylococcus aureus, Salmonella Enteritidis, and Escherichia coli, and one of the compounds was selected for further study with Salmonella Enteritidis. Scanning electron microscopy confirmed the levels of Salmonella Enteritidis before and after treatment. The most effective compound was nontoxic and completely cleared Salmonella Enteritidis contamination from the rubber picker finger surface.

  6. Pickering Interfacial Catalysts for solvent-free biomass transformation: physicochemical behavior of non-aqueous emulsions.

    Science.gov (United States)

    Fan, Zhaoyu; Tay, Astrid; Pera-Titus, Marc; Zhou, Wen-Juan; Benhabbari, Samy; Feng, Xiaoshuang; Malcouronne, Guillaume; Bonneviot, Laurent; De Campo, Floryan; Wang, Limin; Clacens, Jean-Marc

    2014-08-01

    A key challenge in biomass conversion is how to achieve valuable molecules with optimal reactivity in the presence of immiscible reactants. This issue is usually tackled using either organic solvents or surfactants to promote emulsification, making industrial processes expensive and not environmentally friendly. As an alternative, Pickering emulsions using solid particles with tailored designed surface properties can promote phase contact within intrinsically biphasic systems. Here we show that amphiphilic silica nanoparticles bearing a proper combination of alkyl and strong acidic surface groups can generate stable Pickering emulsions of the glycerol/dodecanol system in the temperature range of 35-130°C. We also show that such particles can perform as Pickering Interfacial Catalysts for the acid-catalyzed etherification of glycerol with dodecanol at 150°C. Our findings shed light on some key parameters governing emulsion stability and catalytic activity of Pickering interfacial catalytic systems. This understanding is critical to pave the way toward technological solutions for biomass upgrading able to promote eco-efficient reactions between immiscible organic reagents with neither use of solvents nor surfactants.

  7. Synthesis of Covalently Cross-Linked Colloidosomes from Peroxidized Pickering Emulsions

    Directory of Open Access Journals (Sweden)

    Nadiya Popadyuk

    2016-10-01

    Full Text Available A new approach to the formation of cross-linked colloidosomes was developed on the basis of Pickering emulsions that were stabilized exclusively by peroxidized colloidal particles. Free radical polymerization and a soft template technique were used to convert droplets of a Pickering emulsion into colloidosomes. The peroxidized latex particles were synthesized in the emulsion polymerization process using amphiphilic polyperoxide copolymers poly(2-tert-butylperoxy-2-methyl-5-hexen-3-ine-co-maleic acid (PM-1-MAc or poly[N-(tert-butylperoxymethylacrylamide]-co-maleic acid (PM-2-MAc, which were applied as both initiators and surfactants (inisurfs. The polymerization in the presence of the inisurfs results in latexes with a controllable amount of peroxide and carboxyl groups at the particle surface. Peroxidized polystyrene latex particles with a covalently grafted layer of inisurf PM-1-MAc or PM-2-MAc were used as Pickering stabilizers to form Pickering emulsions. A mixture of styrene and/or butyl acrylate with divinylbenzene and hexadecane was applied as a template for the synthesis of colloidosomes. Peroxidized latex particles located at the interface are involved in the radical reactions of colloidosomes formation. As a result, covalently cross-linked colloidosomes were obtained. It was demonstrated that the structure of the synthesized (using peroxidized latex particles colloidosomes depends on the amount of functional groups and pH during the synthesis. Therefore, the size and morphology of colloidosomes can be controlled by latex particle surface properties.

  8. Pickering emulsions stabilized by whey protein nanoparticles prepared by thermal cross-linking

    NARCIS (Netherlands)

    Wu, Jiande; Shi, Mengxuan; Li, Wei; Zhao, Luhai; Wang, Ze; Yan, Xinzhong; Norde, Willem; Li, Yuan

    2015-01-01

    A Pickering (o/w) emulsion was formed and stabilized by whey protein isolate nanoparticles (WPI NPs). Those WPI NPs were prepared by thermal cross-linking of denatured WPI proteins within w/o emulsion droplets at 80. °C for 15. min. During heating of w/o emulsions containing 10% (w/v) WPI protein

  9. Poly(methyl methacrylate)-silica microcapsules synthesized by templating Pickering emulsion droplets

    NARCIS (Netherlands)

    Wijk, J. van; Salari, J.W.O.; Zaquen, N.; Meuldijk, J.; Klumperman, B.

    2013-01-01

    In this contribution, we present the silica microencapsulation of hydrophilic compounds by templating Pickering emulsion droplets without contamination of the dispersed phase by either the catalyst or the silica precursor. This is accomplished by the use of an amphiphilic catalyst, which situates ar

  10. Preparation of Pickering emulsions through interfacial adsorption by soft cyclodextrin nanogels

    Directory of Open Access Journals (Sweden)

    Shintaro Kawano

    2015-11-01

    Full Text Available Background: Emulsions stabilized by colloidal particles are known as Pickering emulsions. To date, soft microgel particles as well as inorganic and organic particles have been utilized as Pickering emulsifiers. Although cyclodextrin (CD works as an attractive emulsion stabilizer through the formation of a CD–oil complex at the oil–water interface, a high concentration of CD is normally required. Our research focuses on an effective Pickering emulsifier based on a soft colloidal CD polymer (CD nanogel with a unique surface-active property.Results: CD nanogels were prepared by crosslinking heptakis(2,6-di-O-methyl-β-cyclodextrin with phenyl diisocyanate and subsequent immersion of the resulting polymer in water. A dynamic light scattering study shows that primary CD nanogels with 30–50 nm diameter assemble into larger CD nanogels with 120 nm diameter by an increase in the concentration of CD nanogel from 0.01 to 0.1 wt %. The CD nanogel has a surface-active property at the air–water interface, which reduces the surface tension of water. The CD nanogel works as an effective Pickering emulsion stabilizer even at a low concentration (0.1 wt %, forming stable oil-in-water emulsions through interfacial adsorption by the CD nanogels.Conclusion: Soft CD nanogel particles adsorb at the oil–water interface with an effective coverage by forming a strong interconnected network and form a stable Pickering emulsion. The adsorption property of CD nanogels on the droplet surface has great potential to become new microcapsule building blocks with porous surfaces. These microcapsules may act as stimuli-responsive nanocarriers and nanocontainers.

  11. QuickNGS elevates Next-Generation Sequencing data analysis to a new level of automation.

    Science.gov (United States)

    Wagle, Prerana; Nikolić, Miloš; Frommolt, Peter

    2015-07-01

    Next-Generation Sequencing (NGS) has emerged as a widely used tool in molecular biology. While time and cost for the sequencing itself are decreasing, the analysis of the massive amounts of data remains challenging. Since multiple algorithmic approaches for the basic data analysis have been developed, there is now an increasing need to efficiently use these tools to obtain results in reasonable time. We have developed QuickNGS, a new workflow system for laboratories with the need to analyze data from multiple NGS projects at a time. QuickNGS takes advantage of parallel computing resources, a comprehensive back-end database, and a careful selection of previously published algorithmic approaches to build fully automated data analysis workflows. We demonstrate the efficiency of our new software by a comprehensive analysis of 10 RNA-Seq samples which we can finish in only a few minutes of hands-on time. The approach we have taken is suitable to process even much larger numbers of samples and multiple projects at a time. Our approach considerably reduces the barriers that still limit the usability of the powerful NGS technology and finally decreases the time to be spent before proceeding to further downstream analysis and interpretation of the data.

  12. Targeted NGS meets expert clinical characterization: Efficient diagnosis of spastic paraplegia type 11.

    Science.gov (United States)

    Castro-Fernández, Cristina; Arias, Manuel; Blanco-Arias, Patricia; Santomé-Collazo, Luis; Amigo, Jorge; Carracedo, Ángel; Sobrido, Maria-Jesús

    2015-06-01

    Next generation sequencing (NGS) is transforming the diagnostic approach for neurological disorders, since it allows simultaneous analysis of hundreds of genes, even based on just a broad, syndromic patient categorization. However, such an approach bears a high risk of incidental and uncertain genetic findings. We report a patient with spastic paraplegia whose comprehensive neurological and imaging examination raised a high clinical suspicion of SPG11. Thus, although our NGS pipeline for this group of disorders includes gene panel and exome sequencing, in this sample only the spatacsin gene region was captured and subsequently searched for mutations. Two probably pathogenic variants were quickly and clearly identified, confirming the diagnosis of SPG11. This case illustrates how combination of expert clinical characterization with highly oriented NGS protocols leads to a fast, cost-efficient diagnosis, minimizing the risk of findings with unclear significance.

  13. NGS-Trex: an automatic analysis workflow for RNA-Seq data.

    Science.gov (United States)

    Boria, Ilenia; Boatti, Lara; Saggese, Igor; Mignone, Flavio

    2015-01-01

    RNA-Seq technology allows the rapid analysis of whole transcriptomes taking advantage of next-generation sequencing platforms. Moreover with the constant decrease of the cost of NGS analysis RNA-Seq is becoming very popular and widespread. Unfortunately data analysis is quite demanding in terms of bioinformatic skills and infrastructures required, thus limiting the potential users of this method. Here we describe the complete analysis of sample data from raw sequences to data mining of results by using NGS-Trex platform, a low user interaction, fully automatic analysis workflow. Used through a web interface, NGS-Trex processes data and profiles the transcriptome of the samples identifying expressed genes, transcripts, and new and known splice variants. It also detects differentially expressed genes and transcripts across different experiments.

  14. Targeted NGS meets expert clinical characterization: Efficient diagnosis of spastic paraplegia type 11

    Directory of Open Access Journals (Sweden)

    Cristina Castro-Fernández

    2015-06-01

    Full Text Available Next generation sequencing (NGS is transforming the diagnostic approach for neurological disorders, since it allows simultaneous analysis of hundreds of genes, even based on just a broad, syndromic patient categorization. However, such an approach bears a high risk of incidental and uncertain genetic findings. We report a patient with spastic paraplegia whose comprehensive neurological and imaging examination raised a high clinical suspicion of SPG11. Thus, although our NGS pipeline for this group of disorders includes gene panel and exome sequencing, in this sample only the spatacsin gene region was captured and subsequently searched for mutations. Two probably pathogenic variants were quickly and clearly identified, confirming the diagnosis of SPG11. This case illustrates how combination of expert clinical characterization with highly oriented NGS protocols leads to a fast, cost-efficient diagnosis, minimizing the risk of findings with unclear significance.

  15. KNIME4NGS: a comprehensive toolbox for Next Generation Sequencing analysis.

    Science.gov (United States)

    Hastreiter, Maximilian; Jeske, Tim; Hoser, Jonathan; Kluge, Michael; Ahomaa, Kaarin; Friedl, Marie-Sophie; Kopetzky, Sebastian J; Quell, Jan-Dominik; Werner Mewes, H-; Küffner, Robert

    2017-01-09

    Analysis of Next Generation Sequencing (NGS) data requires the processing of large datasets by chaining various tools with complex input and output formats. In order to automate data analysis, we propose to standardize NGS tasks into modular workflows. This simplifies reliable handling and processing of NGS data, and corresponding solutions become substantially more reproducible and easier to maintain. Here, we present a documented, linux-based, toolbox of 42 processing modules that are combined to construct workflows facilitating a variety of tasks such as DNAseq and RNAseq analysis. We also describe important technical extensions. The high throughput executor (HTE) helps to increase the reliability and to reduce manual interventions when processing complex datasets. We also provide a dedicated binary manager that assists users in obtaining the modules' executables and keeping them up to date. As basis for this actively developed toolbox we use the workflow management software KNIME.

  16. Formation of Pickering emulsions stabilized via interaction between nanoparticles dispersed in aqueous phase and polymer end groups dissolved in oil phase.

    Science.gov (United States)

    Okada, Masahiro; Maeda, Hayata; Fujii, Syuji; Nakamura, Yoshinobu; Furuzono, Tsutomu

    2012-06-26

    The influence of end groups of a polymer dissolved in an oil phase on the formation of a Pickering-type hydroxyapatite (HAp) nanoparticle-stabilized emulsion and on the morphology of HAp nanoparticle-coated microspheres prepared by evaporating solvent from the emulsion was investigated. Polystyrene (PS) molecules with varying end groups and molecular weights were used as model polymers. Although HAp nanoparticles alone could not function as a particulate emulsifier for stabilizing dichloromethane (oil) droplets, oil droplets could be stabilized with the aid of carboxyl end groups of the polymers dissolved in the oil phase. Lower-molecular-weight PS molecules containing carboxyl end groups formed small droplets and deflated microspheres, due to the higher concentration of carboxyl groups on the droplet/microsphere surface and hence stronger adsorption of the nanoparticles at the water/oil interface. In addition, Pickering-type suspension polymerization of styrene droplets stabilized by PS molecules containing carboxyl end groups successfully led to the formation of spherical HAp-coated microspheres.

  17. The secret life of Pickering emulsions: particle exchange revealed using two colours of particle

    Science.gov (United States)

    French, David J.; Brown, Aidan T.; Schofield, Andrew B.; Fowler, Jeff; Taylor, Phil; Clegg, Paul S.

    2016-08-01

    Emulsion droplets stabilised by colloidal particles (Pickering emulsions) can be highly stable, so it is unsurprising that they are beginning to be exploited industrially. The individual colloidal particles have interfacial attachment energies that are vastly larger than the thermal energy, hence they are usually thought of as being irreversibly adsorbed. Here we show, for the first time, particles being exchanged between droplets in a Pickering emulsion. This occurs when the emulsion contains droplets that share particles, often called bridging. By starting with two emulsions showing bridging, each stabilised by a different colour of particle, the dynamics can be studied as they are gently mixed together on a roller bank. We find that particle exchange occurs by two routes: firstly, during a period of unbridging and rebridging whose duration can be tuned by varying the wettability of the particles, and secondly, during very rare events when particles are ejected from one droplet and re-adsorbed onto another.

  18. Seroepidemiology of infection with Toxoplasma gondii in waste pickers and waste workers in Durango, Mexico.

    Science.gov (United States)

    Alvarado-Esquivel, C; Liesenfeld, O; Márquez-Conde, J A; Cisneros-Camacho, A; Estrada-Martínez, S; Martínez-García, S A; González-Herrera, A; García-Corral, N

    2008-08-01

    Municipal waste is a potential source of infection for Toxoplasma gondii as it may contain contaminated meat with parasite tissue cysts and cat excrement with parasite oocysts. Therefore, we sought to determine the prevalence of T. gondii infection and associated characteristics in two populations exposed to municipal solid waste in Durango, Mexico. Ninety waste pickers and 83 waste workers of Durango City, Mexico were examined for T. gondii infection. They were tested for anti-T. gondii IgG and IgM antibodies using enzyme-linked immunoassays. In addition, socio-demographic and behavioural characteristics from each participant were obtained. Nineteen (21.1%) of the 90 waste pickers and seven (8.4%) of the 83 waste workers were positive for anti-T. gondii IgG antibodies. The difference in prevalence among the groups was statistically significant (P =0.03). Waste pickers aged 31-50 years showed a significantly higher prevalence (40.9%) than waste workers of the same age group (2.9%, P food found in the garbage [adjusted odds ratio (OR) = 4.4; 95% confidence interval (CI) 1.6-11.8] and with lack of education (adjusted OR = 3.2; 95% CI 1.1-8.8). From this study, we conclude: (i) waste pickers may represent a risk group for T. gondii infection; (ii) lack of education might be a contributing factor for T. gondii infection; (iii) the higher the exposure to garbage, the higher the seroprevalence of T. gondii infection; (iv) Eating food products from the garbage may represent an important route for T. gondii infection.

  19. Pickering emulsions stabilized by whey protein nanoparticles prepared by thermal cross-linking.

    Science.gov (United States)

    Wu, Jiande; Shi, Mengxuan; Li, Wei; Zhao, Luhai; Wang, Ze; Yan, Xinzhong; Norde, Willem; Li, Yuan

    2015-03-01

    A Pickering (o/w) emulsion was formed and stabilized by whey protein isolate nanoparticles (WPI NPs). Those WPI NPs were prepared by thermal cross-linking of denatured WPI proteins within w/o emulsion droplets at 80°C for 15 min. During heating of w/o emulsions containing 10% (w/v) WPI proteins in the water phase, the emulsions displayed turbid-transparent-turbid phase transitions, which is ascribed to the change in the size of the protein-containing water droplets caused by thermal cross-linking between denatured protein molecules. The transparent stage indicated the formation of WPI NPs. WPI NPs of different sizes were obtained by varying the mixing speed. WPI NPs of 200-500 nm were selected to prepare o/w Pickering emulsions because of their good stability against coalescence. By Confocal Laser Scanning Microscopy, it was observed that WPI NPs were closely packed and distributed at the surface of the emulsion droplets. By measuring water contact angles of WPI NPs films, it was found that under most conditions WPI NPs present good partial wetting properties, but that at the isoelectric point (pI) and high ionic strength the particles become more hydrophobic, resulting in less stable Pickering emulsion. Thus, at pH above and below the pI of WPI NPs and low to moderate ionic strengths (1-10 mM), and with a WPI NPs concentration of 2% (w/v), a stable Pickering emulsion can be obtained. The results may provide useful information for applications of WPI NPs in environmentally friendly and food grade applications, notably in food, pharmaceutical and cosmetic products.

  20. Effects of Water-Soluble Co-Solvent on Properties of W/O Pickering Emulsions

    Institute of Scientific and Technical Information of China (English)

    张旭斌; 谢世巍; 蔡旺锋; 王富民

    2016-01-01

    Effects of water-soluble co-solvents(WSCs)on the properties of water/oil Pickering emulsions were investigated. Pickering emulsions were prepared in the system of 1,2,4-trimethylbenzene(TMB)/ hydrophobic sil-ica/water with varied concentrations of WSCs(ethanol, acetic acid and glycerin). Mean droplet diameter distribu-tions of the obtained emulsions were studied to investigate the effects of WSCs types and concentrations. The re-sults demonstrated that mean droplet diameter distributions decreased at first and then increased with the increase of WSC concentration. Moreover, the effect of WSC concentration on the phase inversion locus was further investi-gated. At the same time, infrared radiation(IR)spectrometer was used to investigate the mechanism. The results showed that the WSC attaching on hydrophobic silica changed the wettability of the particles, which facilitated the formation and phase inversion of the emulsion. The hydrogen bonds between the co-solvent groups attaching on the solid particles made a great effect on the droplet size of the emulsion and strengthened the interaction among emul-sifiers. Overall, proper WSC was in favor of the stability of Pickering emulsion.

  1. Research progress of Pickering emulsions%Pickering乳液研究进展

    Institute of Scientific and Technical Information of China (English)

    刘悦; 陈朝霞; 段兰兰; 张玉红

    2014-01-01

    Pickering emulsifiers are the solid particles emulsifiers instead of the surfactant moleculars which are adsorbed at the oil-water interface and used as the robust barrier to prevent the aggregation of monomer droplets. In recent years,the Pickering emulsions have attracted increasing interest due to their widely application prospects in various fields, especially in the paper, emulsion polymerization, cosmetics, drug release and preparation of functional polymer. In this paper,the mechanism of Pickering emulsifier, emulsifiering stability factors, phase inversion and application aspects were summarized in details.%Pickering乳化剂是指用固体颗粒代替传统的化学乳化剂,固体颗粒在分散相液滴表面形成一层薄膜阻止了液滴之间的聚集,在造纸、乳液聚合、化妆品、药物缓释和制备功能高分子领域具有应用前景。本文从Pickering乳化剂的作用机理、乳化稳定因素、相转化以及应用几个方面进行总结。

  2. A Web-Hosted R Workflow to Simplify and Automate the Analysis of 16S NGS Data

    Science.gov (United States)

    Next-Generation Sequencing (NGS) produces large data sets that include tens-of-thousands of sequence reads per sample. For analysis of bacterial diversity, 16S NGS sequences are typically analyzed in a workflow that containing best-of-breed bioinformatics packages that may levera...

  3. Soy protein nanoparticle aggregates as pickering stabilizers for oil-in-water emulsions.

    Science.gov (United States)

    Liu, Fu; Tang, Chuan-He

    2013-09-18

    In recent years, there have been increasing interests in developing food-grade Pickering stabilizers, due to their potential applications in formulations of novel functional foods. The present work was to investigate the potential of soy proteins to be developed into a kind of Pickering-like stabilizer for oil-in-water emulsions. The nanoparticle aggregates of soy protein isolate (SPI) were formed by sequential treatments of heating at 95 °C for 15 min and then electrostatic screening with NaCl addition. The particle size and microstructure of these aggregates were characterized using dynamic light scattering and atomic force microscopy, indicating that the fabricated nanoparticle aggregates were ∼100 nm in size with more surface hydrophobic nature (relative to unheated SPI). The influence of particle concentration (c; 0.5-6.0%, w/w) and increasing oil fraction (ϕ; in the range 0.2-0.6) on the droplet size and coalescence and/or creaming stability of the emulsions stabilized by these nanoparticle aggregates was investigated. The results showed that, at ϕ = 0.2, increasing the c resulted in a progressive but slight decrease in droplet size, and improved the stability against coalescence and creaming; at a specific c, the creaming stability was progressively increased by increasing the ϕ, with better improvement observed at a higher c (e.g., 6.0% vs 2.0%). The improvement of creaming stability was largely associated with the formation of a gel-like network that could entrap the oil droplets within the network. The observations are generally consistent with those observed for the conventional Pickering emulsions, confirming that soy proteins could be applied as a kind of effective Pickering-like stabilizer. The finding may have important implications for the design and fabrication of protein-based emulsion formulations, and even for the development of soy protein products with some unique functions. To the authors' knowledge, this is the first work to report

  4. RepARK--de novo creation of repeat libraries from whole-genome NGS reads.

    Science.gov (United States)

    Koch, Philipp; Platzer, Matthias; Downie, Bryan R

    2014-05-01

    Generation of repeat libraries is a critical step for analysis of complex genomes. In the era of next-generation sequencing (NGS), such libraries are usually produced using a whole-genome shotgun (WGS) derived reference sequence whose completeness greatly influences the quality of derived repeat libraries. We describe here a de novo repeat assembly method--RepARK (Repetitive motif detection by Assembly of Repetitive K-mers)--which avoids potential biases by using abundant k-mers of NGS WGS reads without requiring a reference genome. For validation, repeat consensuses derived from simulated and real Drosophila melanogaster NGS WGS reads were compared to repeat libraries generated by four established methods. RepARK is orders of magnitude faster than the other methods and generates libraries that are: (i) composed almost entirely of repetitive motifs, (ii) more comprehensive and (iii) almost completely annotated by TEclass. Additionally, we show that the RepARK method is applicable to complex genomes like human and can even serve as a diagnostic tool to identify repetitive sequences contaminating NGS datasets.

  5. Detailed finite element analysis of Darlington NGS feeder pipes with locally thinned regions below pressure minimum thickness

    Energy Technology Data Exchange (ETDEWEB)

    Haq, I.; Stojakovic, M.; Li, M. [Ontario Power Generation Inc., Pickering, Ontario (Canada)

    2011-07-01

    Feeder Pipes in CANDU nuclear stations are experiencing wall thinning due to flow accelerated corrosion (FAC) resulting in locally thinned regions in addition to general thinning. In Darlington NGS these locally thinned regions can be below pressure based minimum thickness (t{sub min}), required as per ASME Code Section III NB-3600 Equation (1). A methodology is presented to qualify the locally thinned regions under NB-3200 (NB-3213 and NB-3221) for internal pressure loading only. Detailed finite element models are used for internal pressure analysis using ANSYS v11.0. All other loadings such as deadweight, thermal and seismic loadings are qualified under NB-3600 using a general purpose piping stress analysis software. The piping stress analysis is based on average thickness equal to t{sub min} along with maximum values of ASME Code stress indices (Table NB-3681(a)-1). The requirement for the use of this methodology is that the average thickness of each cross-section with the locally thinned region shall be at least t{sub min}. The finite element analysis models are thinned to 0.75 t{sub min} (in increments of 0.05 t{sub min}) all-around the circumference in the straight section region allowing for flexible inspection requirements. Two different thicknesses of 1.10 t{sub min} and 1.30 t{sub min} are assigned to the bends. Thickness vs the allowable axial extent curves were developed for different types of feeder pipes in service. Feeders differ in pipe size, straight section length, bend angle and orientation. The stress analysis results show that all Darlington NGS outlet feeder pipes are fit for service with locally thinned regions up to 75% of the pressure based minimum thickness. This paper demonstrates the effectiveness of finite element analysis in extending the useful life of degraded piping components. (author)

  6. MicNeSs: genotyping microsatellite loci from a collection of (NGS) reads.

    Science.gov (United States)

    Suez, Marie; Behdenna, Abdelkader; Brouillet, Sophie; Graça, Paula; Higuet, Dominique; Achaz, Guillaume

    2016-03-01

    Microsatellites are widely used in population genetics to uncover recent evolutionary events. They are typically genotyped using capillary sequencer, which capacity is usually limited to 9, at most 12 loci for each run, and which analysis is a tedious task that is performed by hand. With the rise of next-generation sequencing (NGS), a much larger number of loci and individuals are available from sequencing: for example, on a single run of a GS Junior, 28 loci from 96 individuals are sequenced with a 30X cover. We have developed an algorithm to automatically and efficiently genotype microsatellites from a collection of reads sorted by individual (e.g. specific PCR amplifications of a locus or a collection of reads that encompass a locus of interest). As the sequencing and the PCR amplification introduce artefactual insertions or deletions, the set of reads from a single microsatellite allele shows several length variants. The algorithm infers, without alignment, the true unknown allele(s) of each individual from the observed distributions of microsatellites length of all individuals. MicNeSs, a python implementation of the algorithm, can be used to genotype any microsatellite locus from any organism and has been tested on 454 pyrosequencing data of several loci from fruit flies (a model species) and red deers (a nonmodel species). Without any parallelization, it automatically genotypes 22 loci from 441 individuals in 11 hours on a standard computer. The comparison of MicNeSs inferences to the standard method shows an excellent agreement, with some differences illustrating the pros and cons of both methods.

  7. Next Generation Solvent (NGS): Development for Caustic-Side Solvent Extraction of Cesium

    Energy Technology Data Exchange (ETDEWEB)

    Moyer, Bruce A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Birdwell, Jr, Joseph F. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Bonnesen, Peter V. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Bruffey, Stephanie H. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Delmau, Laetitia Helene [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Duncan, Nathan C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Ensor, Dale [Tennessee Technological Univ., Cookeville, TN (United States); Hill, Talon G. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lee, Denise L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Rajbanshi, Arbin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Roach, Benjamin D. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Szczygiel, Patricia L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Sloop, Jr., Frederick V. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Stoner, Erica L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Williams, Neil J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2014-03-01

    This report summarizes the FY 2010 and 2011 accomplishments at Oak Ridge National Laboratory (ORNL) in developing the Next Generation Caustic-Side Solvent Extraction (NG-CSSX) process, referred to commonly as the Next Generation Solvent (NGS), under funding from the U.S. Department of Energy, Office of Environmental Management (DOE-EM), Office of Technology Innovation and Development. The primary product of this effort is a process solvent and preliminary flowsheet capable of meeting a target decontamination factor (DF) of 40,000 for worst-case Savannah River Site (SRS) waste with a concentration factor of 15 or higher in the 18-stage equipment configuration of the SRS Modular Caustic-Side Solvent Extraction Unit (MCU). In addition, the NG-CSSX process may be readily adapted for use in the SRS Salt Waste Processing Facility (SWPF) or in supplemental tank-waste treatment at Hanford upon appropriate solvent or flowsheet modifications. Efforts in FY 2010 focused on developing a solvent composition and process flowsheet for MCU implementation. In FY 2011 accomplishments at ORNL involved a wide array of chemical-development activities and testing up through single-stage hydraulic and mass-transfer tests in 5-cm centrifugal contactors. Under subcontract from ORNL, Argonne National Laboratory (ANL) designed a preliminary flowsheet using ORNL cesium distribution data, and Tennessee Technological University confirmed a chemical model for cesium distribution ratios (DCs) as a function of feed composition. Interlaboratory efforts were coordinated with complementary engineering tests carried out (and reported separately) by personnel at Savannah River National Laboratory (SRNL) and Savannah River Remediation (SRR) with helpful advice by Parsons Engineering and General Atomics on aspects of possible SWPF implementation.

  8. Introduction and application of South NGS - 200 type of GPS%南方NGS-2O0型GPS测量系统及其应用

    Institute of Scientific and Technical Information of China (English)

    郭胜利

    2002-01-01

    GPS(Global Positioning System)是全球卫星定位系统的缩写.南方NGS-200型GPS测量系统及其在永定河干堤加固工程中的应用表明,GPS测量相对传统的作业模式具有突破性的改变,这一新技术的应用使得广大测量工作者从繁重的外业劳动中解脱出来,并且工作效率有了根本性的提高.

  9. Application of modified starch to prepare pickering emulsions%变性淀粉在 Pickering乳液中应用

    Institute of Scientific and Technical Information of China (English)

    冯康; 黄强; 徐亚峰

    2013-01-01

    Pickering emulsions are one kind of new emulsions system. The solid particles replace the traditional surface active agent to stabilize the emulsions. The stability mechanism and classify of Pickering emulsions was summarized. The application of modified starch in Pickering emulsions was discussed. The new emulsions may be developed based on this paper.%  Pickering乳液是一种新型乳液稳定体系,以固体颗粒替代传统表面活性剂的稳定乳液,具有独特性质特性。该文综述Pickering乳液稳定机理和分类、变性淀粉制备Pickering乳液进展及其应用前景,并进行展望;以期为新型乳液研究与开发提供参考。

  10. Preparation of cellulose nanocrystals from asparagus (Asparagus officinalis L.) and their applications to palm oil/water Pickering emulsion.

    Science.gov (United States)

    Wang, Wenhang; Du, Guanhua; Li, Cong; Zhang, Hongjie; Long, Yunduo; Ni, Yonghao

    2016-10-20

    Nano cellulosic materials as promising emulsion stabilizers have attracted great interest in food industry. In this paper, five different sized cellulose nanocrystals (CNC) samples were prepared from stem of Asparagus officinalis L. using the same sulfuric acid hydrolysis conditions but different times (1.5, 2, 2.5, 3.0, and 3.5h). The sizes of these CNC ranged from 178.2 to 261.8nm, with their crystallinity of 72.4-77.2%. The CNC aqueous dispersions showed a typical shear thinning behavior. In a palm oil/water (30/70, v/v) model solution, stable Pickering emulsions were formed with the addition of CNC, and their sizes are in the range of 1-10μm based on the optical and confocal laser scanning microscopy (CLSM) observation. The CNC sample prepared at 3h hydrolysis time, showed a relative efficient emulsion capacity for palm oil droplets, among these CNCs. Other parameters including the CNC, salt, and casein concentrations on the emulsion stability were studied.

  11. Nanoscale trifunctional bovine hemoglobin for fabricating molecularly imprinted polydopamine via Pickering emulsions-hydrogels polymerization.

    Science.gov (United States)

    Sun, Yanhua; Zhong, Shian

    2017-07-29

    In this work, a novel strategy was developed for the selective recognition of protein based on oil-in-water Pickering emulsions-hydrogels polymerization and interfacial imprinting method. For the first time, nanoscale trifunctional bovine hemoglobin (BHb) played three roles simultaneously during the process, including emulsifier, template protein and sacrificial material for further exposing recognition sites. Prior to acting as stabilizers, bovine hemoglobin colloidal particles (BCPs) were firstly prepared by acidification and heat denaturation. Then the BCPs acted as "surfactant" to stabilize the Pickering emulsions composed of functional monomers in the water phase. After dopamine polymerized, the template proteins were removed, forming the BHb imprinted cavities on the surface of the polymeric materials. During this process, the interfacial BCPs also fell off, leaving more imprinted cavities exposed. FT-IR spectroscopy confirmed that BCPs were completely removed from the synthesized imprinted materials. The interconnected macropores structures of the materials encouraged nearly all of the rebinding sites located on its surface. Thus the prepared Hydro-MIPs exhibited rapid and selective recognition toward BHb. Owing to the hierarchical porous structure, the BHb imprinted polymers based on Pickering emulsions-hydrogels (Hydro-MIPs) possessed enhanced rebinding kinetics, and the maximum rebinding capacity is 449mgg(-1), 3.97 times higher than that of the non-imprinted polymers (Hydro-NIPs). Besides these, the regeneration ability test suggested that the Hydro-MIPs could be used repeatedly without distinct loss in adsorption capacity. Overall, the combination of high selectivity, good mass transfer efficiency, easy preparation and trifunctional BHb provide a new insight into bioseparation and proteomics research in biological area. Copyright © 2017. Published by Elsevier B.V.

  12. Nozzleless Fabrication of Oil-Core Biopolymeric Microcapsules by the Interfacial Gelation of Pickering Emulsion Templates.

    Science.gov (United States)

    Leong, Jun-Yee; Tey, Beng-Ti; Tan, Chin-Ping; Chan, Eng-Seng

    2015-08-05

    Ionotropic gelation has been an attractive method for the fabrication of biopolymeric oil-core microcapsules due to its safe and mild processing conditions. However, the mandatory use of a nozzle system to form the microcapsules restricts the process scalability and the production of small microcapsules (palm olein, cyclohexane, dichloromethane, and toluene). In addition, small microcapsules with a mean size smaller than 100 μm can be produced by selecting the appropriate conventional emulsification methods available to prepare the Pickering emulsion. The simplicity and versatility of this method allows biopolymeric microcapsules to be fabricated with ease by ionotropic gelation for numerous applications.

  13. Functional genomics of tomato: Opportunities and challenges in post-genome NGS era

    Indian Academy of Sciences (India)

    Rahul Kumar; Ashima Khurana

    2014-12-01

    The Tomato Genome Sequencing Project represented a landmark venture in the history of sequencing projects where both Sanger’s and next-generation sequencing (NGS) technologies were employed, and a highly accurate and one of the best assembled plant genomes along with a draft of the wild relative, Solanum pimpinellifolium, were released in 2012. However, the functional potential of the major portion of this newly generated resource is still undefined. The very first challenge before scientists working on tomato functional biology is to exploit this high-quality reference sequence for tapping of the wealth of genetic variants for improving agronomic traits in cultivated tomatoes. The sequence data generated recently by 150 Tomato Genome Consortium would further uncover the natural alleles present in different tomato genotypes. Therefore, we found it relevant to have a fresh outlook on tomato functional genomics in the context of application of NGS technologies in its post-genome sequencing phase. Herein, we provide an overview how NGS technologies vis-à-vis available reference sequence have assisted each other for their mutual improvement and how their combined use could further facilitate the development of other ‘omics’ tools, required to propel the Solanaceae research. Additionally, we highlight the challenges associated with the application of these cutting-edge technologies.

  14. HLA-genotyping of clinical specimens using Ion Torrent-based NGS.

    Science.gov (United States)

    Barone, Jonathan C; Saito, Katsuyuki; Beutner, Karl; Campo, Maria; Dong, Wei; Goswami, Chirayu P; Johnson, Erica S; Wang, Zi-Xuan; Hsu, Susan

    2015-12-01

    We have evaluated and validated the NXType™ workflow (One Lambda, Inc.) and the accompanying TypeStream™ software on the Ion Torrent Next Generation Sequencing (NGS) platform using a comprehensive testing panel. The panel consisted of 285 genomic DNA (gDNA) samples derived from four major ethnic populations and contained 59 PT samples and 226 clinical specimens. The total number of alleles from the six loci interrogated by NGS was 3420. This validation panel provided a wide range of HLA sequence variations including many rare alleles, new variants and homozygous alleles. The NXType™ system (reagents and software) was able to correctly genotype the vast majority of these specimens. The concordance rate between SBT-derived genotypes and those generated by TypeStream™ auto-analysis ranged from 99.5% to 99.8% for the HLA-A, B, C, DRB1 and DQB1 loci, and was 98.9% for HLA-DPB1. A strategy for data review was developed that would allow correction of most of the few remaining typing errors. The entire NGS workflow from gDNA amplification to genotype assignment could be completed within 3 working days. Through this validation study, the limitations and shortcomings of the platform, specific assay system, and software algorithm were also revealed for further evaluation and improvement.

  15. The variation game: Cracking complex genetic disorders with NGS and omics data.

    Science.gov (United States)

    Cui, Hongzhu; Dhroso, Andi; Johnson, Nathan; Korkin, Dmitry

    2015-06-01

    Tremendous advances in Next Generation Sequencing (NGS) and high-throughput omics methods have brought us one step closer towards mechanistic understanding of the complex disease at the molecular level. In this review, we discuss four basic regulatory mechanisms implicated in complex genetic diseases, such as cancer, neurological disorders, heart disease, diabetes, and many others. The mechanisms, including genetic variations, copy-number variations, posttranscriptional variations, and epigenetic variations, can be detected using a variety of NGS methods. We propose that malfunctions detected in these mechanisms are not necessarily independent, since these malfunctions are often found associated with the same disease and targeting the same gene, group of genes, or functional pathway. As an example, we discuss possible rewiring effects of the cancer-associated genetic, structural, and posttranscriptional variations on the protein-protein interaction (PPI) network centered around P53 protein. The review highlights multi-layered complexity of common genetic disorders and suggests that integration of NGS and omics data is a critical step in developing new computational methods capable of deciphering this complexity.

  16. Development of a high-resolution NGS-based HLA-typing and analysis pipeline.

    Science.gov (United States)

    Wittig, Michael; Anmarkrud, Jarl A; Kässens, Jan C; Koch, Simon; Forster, Michael; Ellinghaus, Eva; Hov, Johannes R; Sauer, Sascha; Schimmler, Manfred; Ziemann, Malte; Görg, Siegfried; Jacob, Frank; Karlsen, Tom H; Franke, Andre

    2015-06-23

    The human leukocyte antigen (HLA) complex contains the most polymorphic genes in the human genome. The classical HLA class I and II genes define the specificity of adaptive immune responses. Genetic variation at the HLA genes is associated with susceptibility to autoimmune and infectious diseases and plays a major role in transplantation medicine and immunology. Currently, the HLA genes are characterized using Sanger- or next-generation sequencing (NGS) of a limited amplicon repertoire or labeled oligonucleotides for allele-specific sequences. High-quality NGS-based methods are in proprietary use and not publicly available. Here, we introduce the first highly automated open-kit/open-source HLA-typing method for NGS. The method employs in-solution targeted capturing of the classical class I (HLA-A, HLA-B, HLA-C) and class II HLA genes (HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1, HLA-DPB1). The calling algorithm allows for highly confident allele-calling to three-field resolution (cDNA nucleotide variants). The method was validated on 357 commercially available DNA samples with known HLA alleles obtained by classical typing. Our results showed on average an accurate allele call rate of 0.99 in a fully automated manner, identifying also errors in the reference data. Finally, our method provides the flexibility to add further enrichment target regions.

  17. Parallel WGA and WTA for Comparative Genome and Transcriptome NGS Analysis Using Tiny Cell Numbers.

    Science.gov (United States)

    Korfhage, Christian; Fricke, Evelyn; Meier, Andreas

    2015-07-01

    Genomic DNA determines how and when the transcriptome is changed by a trigger or environmental change and how cellular metabolism is influenced. Comparative genome and transcriptome analysis of the same cell sample links a defined genome with all changes in the bases, structure, or numbers of the transcriptome. However, comparative genome and transcriptome analysis using next-generation sequencing (NGS) or real-time PCR is often limited by the small amount of sample available. In mammals, the amount of DNA and RNA in a single cell is ∼10 picograms, but deep analysis of the genome and transcriptome currently requires several hundred nanograms of nucleic acids for library preparation for NGS sequencing. Consequently, accurate whole-genome amplification (WGA) and whole-transcriptome amplification (WTA) is required for such quantitative analysis. This unit describes how the genome and the transcriptome of a tiny number of cells can be amplified in a highly parallel and comparable process. Protocols for quality control of amplified DNA and application of amplified DNA for NGS are included.

  18. Functional genomics of tomato: opportunities and challenges in post-genome NGS era.

    Science.gov (United States)

    Kumar, Rahul; Khurana, Ashima

    2014-12-01

    The Tomato Genome Sequencing Project represented a landmark venture in the history of sequencing projects where both Sanger's and next-generation sequencing (NGS) technologies were employed, and a highly accurate and one of the best assembled plant genomes along with a draft of the wild relative, Solanum pimpinellifolium, were released in 2012. However, the functional potential of the major portion of this newly generated resource is still undefined. The very first challenge before scientists working on tomato functional biology is to exploit this high-quality reference sequence for tapping of the wealth of genetic variants for improving agronomic traits in cultivated tomatoes. The sequence data generated recently by 150 Tomato Genome Consortium would further uncover the natural alleles present in different tomato genotypes. Therefore, we found it relevant to have a fresh outlook on tomato functional genomics in the context of application of NGS technologies in its post-genome sequencing phase. Herein, we provide an overview how NGS technologies vis-a-vis available reference sequence have assisted each other for their mutual improvement and how their combined use could further facilitate the development of other 'omics' tools, required to propel the Solanaceae research. Additionally, we highlight the challenges associated with the application of these cutting-edge technologies.

  19. BAL31-NGS approach for identification of telomeres de novo in large genomes.

    Science.gov (United States)

    Peška, Vratislav; Sitová, Zdeňka; Fajkus, Petr; Fajkus, Jiří

    2017-02-01

    This article describes a novel method to identify as yet undiscovered telomere sequences, which combines next generation sequencing (NGS) with BAL31 digestion of high molecular weight DNA. The method was applied to two groups of plants: i) dicots, genus Cestrum, and ii) monocots, Allium species (e.g. A. ursinum and A. cepa). Both groups consist of species with large genomes (tens of Gb) and a low number of chromosomes (2n=14-16), full of repeat elements. Both genera lack typical telomeric repeats and multiple studies have attempted to characterize alternative telomeric sequences. However, despite interesting hypotheses and suggestions of alternative candidate telomeres (retrotransposons, rDNA, satellite repeats) these studies have not resolved the question. In a novel approach based on the two most general features of eukaryotic telomeres, their repetitive character and sensitivity to BAL31 nuclease digestion, we have taken advantage of the capacity and current affordability of NGS in combination with the robustness of classical BAL31 nuclease digestion of chromosomal termini. While representative samples of most repeat elements were ensured by low-coverage (less than 5%) genomic shot-gun NGS, candidate telomeres were identified as under-represented sequences in BAL31-treated samples.

  20. Palm olein-in-water Pickering emulsion stabilized by Fe3O4-cellulose nanocrystal nanocomposites and their responses to pH.

    Science.gov (United States)

    Low, Liang Ee; Tey, Beng Ti; Ong, Boon Hoong; Chan, Eng Seng; Tang, Siah Ying

    2017-01-02

    We studied the formation of palm olein-in-water (O/W) Pickering emulsion stabilized by Fe3O4-cellulose nanocrystals (MCNC) nanocomposites obtained by ultrasound assisted in-situ co-precipitation method. The synthesized MCNC nanocomposites successfully stabilized Pickering emulsion with dual responses. The magnetic tests revealed a direct-relation between attractability of MCNC-stabilized Pickering emulsions and the emulsion droplet diameter. The Pickering emulsions were stable under pH ranging from 3 to 6. The stability substantially reduced around pH 8-10, and regained slowly when approaching pH 13. From microscopic and mastersizer analysis, monodisperse emulsion droplets were noticed at pH 3-6, and 13, while polydisperse emulsion were obtained at pH 8-12. The Pickering emulsions prepared at pH 6 are stable up to 14 days, while Pickering emulsions at pH 8 experienced coalescence. In this study, the dual stimuli-responsive Pickering emulsion stabilized by MCNC may hold potentials for biomedical and drug delivery as new generation of smart nanotherapeutic carrier.

  1. Sticky Genomes: Using NGS Evidence to Test Hybrid Speciation Hypotheses.

    Directory of Open Access Journals (Sweden)

    Mary Morgan-Richards

    Full Text Available Hypotheses of hybrid origin are common. Here we use next generation sequencing to test a hybrid hypothesis for a non-model insect with a large genome. We compared a putative hybrid triploid stick insect species (Acanthoxyla geisovii with its putative paternal diploid taxon (Clitarchus hookeri, a relationship that provides clear predictions for the relative genetic diversity within each genome. The parental taxon is expected to have comparatively low allelic diversity that is nested within the diversity of the hybrid daughter genome. The scale of genome sequencing required was conveniently achieved by extracting mRNA and sequencing cDNA to examine expressed allelic diversity. This allowed us to test hybrid-progenitor relationships among non-model organisms with large genomes and different ploidy levels. Examination of thousands of independent loci avoids potential problems produced by the silencing of parts of one or other of the parental genomes, a phenomenon sometimes associated with the process of stabilisation of a hybrid genome. Transcript assembles were assessed for evidence of paralogs and/or alternative splice variants before proceeding. Comparison of transcript assemblies was not an appropriate measure of genetic variability, but by mapping reads back to clusters derived from each species we determined levels of allelic diversity. We found greater cDNA sequence diversity among alleles in the putative hybrid species (Acanthoxyla geisovii than the non-hybrid. The allelic diversity within the putative paternal species (Clitachus hookeri nested within the hybrid-daughter genome, supports the current view of a hybrid-progenitor relationship for these stick insect species. Next generation sequencing technology provides opportunities for testing evolutionary hypotheses with non-model organisms, including, as here, genomes that are large due to polyploidy.

  2. Interfacial behaviour of sodium stearoyllactylate (SSL) as an oil-in-water pickering emulsion stabiliser.

    Science.gov (United States)

    Kurukji, D; Pichot, R; Spyropoulos, F; Norton, I T

    2013-11-01

    The ability of a food ingredient, sodium stearoyllactylate (SSL), to stabilise oil-in-water (O/W) emulsions against coalescence was investigated, and closely linked to its capacity to act as a Pickering stabiliser. Results showed that emulsion stability could be achieved with a relatively low SSL concentration (≥0.1 wt%), and cryogenic-scanning electron microscopy (cryo-SEM) visualisation of emulsion structure revealed the presence of colloidal SSL aggregates adsorbed at the oil-water interface. Surface properties of SSL could be modified by altering the size of these aggregates in water; a faster decrease in surface tension was observed when SSL dispersions were subjected to high pressure homogenisation (HPH). The rate of SSL adsorption at the sunflower oil-water interface also increased after HPH, and a higher interfacial tension (IFT) was observed with increasing SSL concentration. Differential scanning calorimetry (DSC) enabled a comparison of the thermal behaviour of SSL in aqueous dispersions with SSL-stabilised O/W emulsions. SSL melting enthalpy depended on emulsion interfacial area and the corresponding DSC data was used to determine the amount of SSL adsorbed at the oil-water interface. An idealised theoretical interfacial coverage calculation based on Pickering emulsion theory was in general agreement with the mass of SSL adsorbed as predicted by DSC.

  3. Pickering Emulsion Gels Prepared by Hydrogen-Bonded Zein/Tannic Acid Complex Colloidal Particles.

    Science.gov (United States)

    Zou, Yuan; Guo, Jian; Yin, Shou-Wei; Wang, Jin-Mei; Yang, Xiao-Quan

    2015-08-26

    Food-grade colloidal particles and complexes, which are formed via modulation of the noncovalent interactions between macromolecules and natural small molecules, can be developed as novel functional ingredients in a safe and sustainable way. For this study was prepared a novel zein/tannic acid (TA) complex colloidal particle (ZTP) based on the hydrogen-bonding interaction between zein and TA in aqueous ethanol solution by using a simple antisolvent approach. Pickering emulsion gels with high oil volume fraction (φ(oil) > 50%) were successfully fabricated via one-step homogenization. Circular dichroism (CD) and small-angle X-ray scattering (SAXS) measurements, which were used to characterize the structure of zein/TA complexes in ethanol solution, clearly showed that TA binding generated a conformational change of zein without altering their supramolecular structure at pH 5.0 and intermediate TA concentrations. Consequently, the resultant ZTP had tuned near neutral wettability (θ(ow) ∼ 86°) and enhanced interfacial reactivity, but without significantly decreased surface charge. These allowed the ZTP to stabilize the oil droplets and further triggered cross-linking to form a continuous network among and around the oil droplets and protein particles, leading to the formation of stable Pickering emulsion gels. Layer-by-layer (LbL) interfacial architecture on the oil-water surface of the droplets was observed, which implied a possibility to fabricate hierarchical interface microstructure via modulation of the noncovalent interaction between hydrophobic protein and natural polyphenol.

  4. Inorganic/organic hybrid microcapsules: melamine formaldehyde-coated Laponite-based Pickering emulsions.

    Science.gov (United States)

    Williams, Mark; Olland, Birte; Armes, Steven P; Verstraete, Pierre; Smets, Johan

    2015-12-15

    A facile synthesis route to novel inorganic/organic hybrid microcapsules is reported. Laponite nanoparticles are surface-modified via electrostatic adsorption of Magnafloc, an amine-based polyelectrolyte allowing the formation of stable oil-in-water Pickering emulsions. Hybrid microcapsules can be subsequently prepared by coating these Pickering emulsion precursors with dense melamine formaldehyde (MF) shells. Employing a water-soluble polymeric stabiliser, poly(acrylamide-co-sodium acrylate) leads to stable hybrid microcapsules that survive an alcohol challenge and the ultrahigh vacuum conditions required for SEM studies. Unfortunately, the presence of this copolymer also leads to secondary nucleation of excess MF latex particles in the aqueous continuous phase. However, since the Magnafloc is utilised at submonolayer coverage when coating the Laponite particles, the nascent cationic MF nanoparticles can deposit onto anionic surface sites on the Laponite, which removes the requirement for the poly(acrylamide-co-sodium acrylate) component. Following this electrostatic adsorption, the secondary amine groups on the Magnafloc chains can react with the MF, leading to highly robust cross-linked MF shells. The absence of the copolymer leads to minimal secondary nucleation of MF latex particles, ensuring more efficient deposition at the surface of the emulsion droplets. However, the MF shells appear to become more brittle, as SEM studies reveal cracking on addition of ethanol.

  5. Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities.

    Science.gov (United States)

    Tan, BoonFei; Ng, Charmaine; Nshimyimana, Jean Pierre; Loh, Lay Leng; Gin, Karina Y-H; Thompson, Janelle R

    2015-01-01

    Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools.

  6. Quiescent water-in-oil Pickering emulsions as a route toward healthier fruit juice infused chocolate confectionary

    NARCIS (Netherlands)

    Skelhon, T.S.; Grossiord, N.; Morgan, A.R.; Bon, S.A.F.

    2012-01-01

    We demonstrate a route toward the preparation of healthier fruit juice infused chocolate candy. Up to 50 wt% of the fat content in chocolate, that is cocoa butter and milk fats, is replaced with fruit juice in the form of emulsion droplets using a quiescent Pickering emulsion fabrication strategy.

  7. Quiescent water-in-oil Pickering emulsions as a route toward healthier fruit juice infused chocolate confectionary

    NARCIS (Netherlands)

    Skelhon, T.S.; Grossiord, N.; Morgan, A.R.; Bon, S.A.F.

    2012-01-01

    We demonstrate a route toward the preparation of healthier fruit juice infused chocolate candy. Up to 50 wt% of the fat content in chocolate, that is cocoa butter and milk fats, is replaced with fruit juice in the form of emulsion droplets using a quiescent Pickering emulsion fabrication strategy. F

  8. Quiescent water-in-oil Pickering emulsions as a route toward healthier fruit juice infused chocolate confectionary

    NARCIS (Netherlands)

    Skelhon, T.S.; Grossiord, N.; Morgan, A.R.; Bon, S.A.F.

    2012-01-01

    We demonstrate a route toward the preparation of healthier fruit juice infused chocolate candy. Up to 50 wt% of the fat content in chocolate, that is cocoa butter and milk fats, is replaced with fruit juice in the form of emulsion droplets using a quiescent Pickering emulsion fabrication strategy. F

  9. Next-generation sequencing (NGS) in the microbiological world: How to make the most of your money.

    Science.gov (United States)

    Vincent, Antony T; Derome, Nicolas; Boyle, Brian; Culley, Alexander I; Charette, Steve J

    2017-07-01

    The Sanger sequencing method produces relatively long DNA sequences of unmatched quality and has been considered for long time as the gold standard for sequencing DNA. Many improvements of the Sanger method that culminated with fluorescent dyes coupled with automated capillary electrophoresis enabled the sequencing of the first genomes. Nevertheless, using this technology to sequence whole genomes was costly, laborious and time consuming even for genomes that are relatively small in size. A major technological advance was the introduction of next-generation sequencing (NGS) pioneered by 454 Life Sciences in the early part of the 21th century. NGS allowed scientists to sequence thousands to millions of DNA molecules in a single machine run. Since then, new NGS technologies have emerged and existing NGS platforms have been improved, enabling the production of genome sequences at an unprecedented rate as well as broadening the spectrum of NGS applications. The current affordability of generating genomic information, especially with microbial samples, has resulted in a false sense of simplicity that belies the fact that many researchers still consider these technologies a black box. In this review, our objective is to identify and discuss four steps that we consider crucial to the success of any NGS-related project. These steps are: (1) the definition of the research objectives beyond sequencing and appropriate experimental planning, (2) library preparation, (3) sequencing and (4) data analysis. The goal of this review is to give an overview of the process, from sample to analysis, and discuss how to optimize your resources to achieve the most from your NGS-based research. Regardless of the evolution and improvement of the sequencing technologies, these four steps will remain relevant. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Critical review of NGS analyses for de novo genotyping multigene families.

    Science.gov (United States)

    Lighten, Jackie; van Oosterhout, Cock; Bentzen, Paul

    2014-08-01

    The genotyping of highly polymorphic multigene families across many individuals used to be a particularly challenging task because of methodological limitations associated with traditional approaches. Next-generation sequencing (NGS) can overcome most of these limitations, and it is increasingly being applied in population genetic studies of multigene families. Here, we critically review NGS bioinformatic approaches that have been used to genotype the major histocompatibility complex (MHC) immune genes, and we discuss how the significant advances made in this field are applicable to population genetic studies of gene families. Increasingly, approaches are introduced that apply thresholds of sequencing depth and sequence similarity to separate alleles from methodological artefacts. We explain why these approaches are particularly sensitive to methodological biases by violating fundamental genotyping assumptions. An alternative strategy that utilizes ultra-deep sequencing (hundreds to thousands of sequences per amplicon) to reconstruct genotypes and applies statistical methods on the sequencing depth to separate alleles from artefacts appears to be more robust. Importantly, the 'degree of change' (DOC) method avoids using arbitrary cut-off thresholds by looking for statistical boundaries between the sequencing depth for alleles and artefacts, and hence, it is entirely repeatable across studies. Although the advances made in generating NGS data are still far ahead of our ability to perform reliable processing, analysis and interpretation, the community is developing statistically rigorous protocols that will allow us to address novel questions in evolution, ecology and genetics of multigene families. Future developments in third-generation single molecule sequencing may potentially help overcome problems that still persist in de novo multigene amplicon genotyping when using current second-generation sequencing approaches.

  11. Sample Results From The Extraction, Scrub, And Strip Test For The Blended NGS Solvent

    Energy Technology Data Exchange (ETDEWEB)

    Washington, A. L. II; Peters, T. B.

    2014-03-03

    This report summarizes the results of the extraction, scrub, and strip testing for the September 2013 sampling of the Next Generation Solvent (NGS) Blended solvent from the Modular Caustic Side-Solvent Extraction Unit (MCU) Solvent Hold Tank. MCU is in the process of transitioning from the BOBCalixC6 solvent to the NGS Blend solvent. As part of that transition, MCU has intentionally created a blended solvent to be processed using the Salt Batch program. This sample represents the first sample received from that blended solvent. There were two ESS tests performed where NGS blended solvent performance was assessed using either the Tank 21 material utilized in the Salt Batch 7 analyses or a simulant waste material used in the V-5/V-10 contactor testing. This report tabulates the temperature corrected cesium distribution, or DCs values, step recovery percentage, and actual temperatures recorded during the experiment. This report also identifies the sample receipt date, preparation method, and analysis performed in the accumulation of the listed values. The calculated extraction DCs values using the Tank 21H material and simulant are 59.4 and 53.8, respectively. The DCs values for two scrub and three strip processes for the Tank 21 material are 4.58, 2.91, 0.00184, 0.0252, and 0.00575, respectively. The D-values for two scrub and three strip processes for the simulant are 3.47, 2.18, 0.00468, 0.00057, and 0.00572, respectively. These values are similar to previous measurements of Salt Batch 7 feed with lab-prepared blended solvent. These numbers are considered compatible to allow simulant testing to be completed in place of actual waste due to the limited availability of feed material.

  12. New genes and pathomechanisms in mitochondrial disorders unraveled by NGS technologies.

    Science.gov (United States)

    Legati, Andrea; Reyes, Aurelio; Nasca, Alessia; Invernizzi, Federica; Lamantea, Eleonora; Tiranti, Valeria; Garavaglia, Barbara; Lamperti, Costanza; Ardissone, Anna; Moroni, Isabella; Robinson, Alan; Ghezzi, Daniele; Zeviani, Massimo

    2016-08-01

    Next Generation Sequencing (NGS) technologies are revolutionizing the diagnostic screening for rare disease entities, including primary mitochondrial disorders, particularly those caused by nuclear gene defects. NGS approaches are able to identify the causative gene defects in small families and even single individuals, unsuitable for investigation by traditional linkage analysis. These technologies are contributing to fill the gap between mitochondrial disease cases defined on the basis of clinical, neuroimaging and biochemical readouts, which still outnumber by approximately 50% the cases for which a molecular-genetic diagnosis is attained. We have been using a combined, two-step strategy, based on targeted genes panel as a first NGS screening, followed by whole exome sequencing (WES) in still unsolved cases, to analyze a large cohort of subjects, that failed to show mutations in mtDNA and in ad hoc sets of specific nuclear genes, sequenced by the Sanger's method. Not only this approach has allowed us to reach molecular diagnosis in a significant fraction (20%) of these difficult cases, but it has also revealed unexpected and conceptually new findings. These include the possibility of marked variable penetrance of recessive mutations, the identification of large-scale DNA rearrangements, which explain spuriously heterozygous cases, and the association of mutations in known genes with unusual, previously unreported clinical phenotypes. Importantly, WES on selected cases has unraveled the presence of pathogenic mutations in genes encoding non-mitochondrial proteins (e.g. the transcription factor E4F1), an observation that further expands the intricate genetics of mitochondrial disease and suggests a new area of investigation in mitochondrial medicine. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.

  13. Fast extraction from SPS LSS4 for the LHC and NGS projects

    CERN Document Server

    Goddard, B

    1998-01-01

    The proton and lead ion beams for the anti-clockwise ring of the LHC will be extracted from the SPS in LSS4 and transferred to LHC point 8 via the transfer line TT40-TI8. A conventional single turn 'fast' extraction will be used. The same extraction channel may be used to transfer protons to a neutrino target for the proposed long baseline Neutrino to Gran Sasso (NGS) project. The planned layout for the extraction channel in LSS4 now has the extraction septum in SPS half period 418, and is outlined for both fast-pulsed and DC septum designs.

  14. Precise GPS ephemerides from DMA and NGS tested by time transfer

    Science.gov (United States)

    Lewandowski, Wlodzimierz W.; Petit, Gerard; Thomas, Claudine

    1992-01-01

    It was shown that the use of the Defense Mapping Agency's (DMA) precise ephemerides brings a significant improvement to the accuracy of GPS time transfer. At present a new set of precise ephemerides produced by the National Geodetic Survey (NGS) has been made available to the timing community. This study demonstrates that both types of precise ephemerides improve long-distance GPS time transfer and remove the effects of Selective Availability (SA) degradation of broadcast ephemerides. The issue of overcoming SA is also discussed in terms of the routine availability of precise ephemerides.

  15. Bespoke contrast-matched diblock copolymer nanoparticles enable the rational design of highly transparent Pickering double emulsions

    Science.gov (United States)

    Rymaruk, Matthew J.; Thompson, Kate L.; Derry, Matthew J.; Warren, Nicholas J.; Ratcliffe, Liam P. D.; Williams, Clive N.; Brown, Steven L.; Armes, Steven P.

    2016-07-01

    We report the preparation of highly transparent oil-in-water Pickering emulsions using contrast-matched organic nanoparticles. This is achieved via addition of judicious amounts of either sucrose or glycerol to an aqueous dispersion of poly(glycerol monomethacrylate)56-poly(2,2,2-trifluoroethyl methacrylate)500 [PGMA-PTFEMA] diblock copolymer nanoparticles prior to high shear homogenization with an equal volume of n-dodecane. The resulting Pickering emulsions comprise polydisperse n-dodecane droplets of 20-100 μm diameter and exhibit up to 96% transmittance across the visible spectrum. In contrast, control experiments using non-contrast-matched poly(glycerol monomethacrylate)56-poly(benzyl methacrylate)300 [PGMA56-PBzMA300] diblock copolymer nanoparticles as a Pickering emulsifier only produced conventional highly turbid emulsions. Thus contrast-matching of the two immiscible phases is a necessary but not sufficient condition for the preparation of highly transparent Pickering emulsions: it is essential to use isorefractive nanoparticles in order to minimize light scattering. Furthermore, highly transparent oil-in-water-in-oil Pickering double emulsions can be obtained by homogenizing the contrast-matched oil-in-water Pickering emulsion prepared using the PGMA56-PTFEMA500 nanoparticles with a contrast-matched dispersion of hydrophobic poly(lauryl methacrylate)39-poly(2,2,2-trifluoroethyl methacrylate)800 [PLMA39-PTFEMA800] diblock copolymer nanoparticles in n-dodecane. Finally, we show that an isorefractive oil-in-water Pickering emulsion enables fluorescence spectroscopy to be used to monitor the transport of water-insoluble small molecules (pyrene and benzophenone) between n-dodecane droplets. Such transport is significantly less efficient than that observed for the equivalent isorefractive surfactant-stabilized emulsion. Conventional turbid emulsions do not enable such a comparison to be made because the intense light scattering leads to substantial spectral

  16. Facile fabrication of Pickering emulsion polymerized polystyrene/laponite composite nanoparticles and their electrorheology.

    Science.gov (United States)

    Kim, Young Jae; Liu, Ying Dan; Choi, Hyoung Jin; Park, Soo-Jin

    2013-03-15

    Polystyrene (PS)/laponite composite nanoparticles were fabricated using a surfactant-free Pickering emulsion polymerization method, in which emulsions of styrene dispersed in water were stabilized by hydrophilic laponite modified with cetyltrimethylammonium bromide. The PS/laponite nanoparticles, of which their surface was covered compactly by laponite clay platelets, were observed by scanning electron microscopy. Fourier-transform infrared spectroscopy, X-ray diffraction, and thermogravimetric analysis confirmed their chemical composition, crystallographic structure, and thermal properties and weight loss percentage of the laponite located on the surface of the PS particle, respectively. When an external electrical field was applied, the chain-like structure of the laponite coated nano-sized PS particle exhibiting electrorheological characteristics was observed by optical microscopy. The electrorheological performance of the bulk properties was also examined using a rotational rheometer equipped with a high voltage generator.

  17. Effects of pH on the ability of flavonoids to act as Pickering emulsion stabilizers.

    Science.gov (United States)

    Luo, Zijun; Murray, Brent S; Ross, Anne-Lise; Povey, Malcolm J W; Morgan, Michael R A; Day, Andrea J

    2012-04-01

    The flavonoids tiliroside, rutin and naringin have been investigated as stabilizers of Pickering oil-in-water (O/W) emulsions. The mean droplet size of tetradecane emulsions was considerably smaller at higher pH, especially for rutin. The solubility of flavonoids in the aqueous phase was 4-6 times higher at pH 8 compared to pH 2 for tiliroside and rutin, although all absolute solubilities remained low (tiliroside and rutin at the O-W interface at pH 8 compared to pH 2. However, improved emulsion stabilization at higher pH is better explained by the significant increase in ζ-potential of the flavonoid particles to more negative values at pH 8, which will improve particle dispersion and increase the charge on the droplets stabilized by them. A buckwheat tea extract, rich in rutin, was also shown to be an effective stabilizer of sunflower O/W emulsions.

  18. Grafting amphiphilic brushes onto halloysite nanotubes via a living RAFT polymerization and their Pickering emulsification behavior.

    Science.gov (United States)

    Hou, Yifan; Jiang, Junqing; Li, Kai; Zhang, Yanwu; Liu, Jindun

    2014-02-20

    Amphiphilic brushes of poly(4-vinylpyridine)-block-polystyrene (P4VP-b-PS) and polystyrene-block-poly(4-vinylpyridine) (PS-b-P4VP) are grafted onto halloysite nanotubes (HNTs) via a surface reversible addition-fragmentation chain transfer (RAFT) living polymerization through anchoring R group in RAFT agent S-1-dodecyl-S'-(R,R'-dimethyl-R″-acetic acid) trithiocarbonates (DDMAT). The characterization of TGA, TEM, and GPC show that amphiphilic brushes are successfully grafted onto HNTs in a living manner. To verify the amphiphilicity of HNTs grafted with block copolymers, their Pickering emulsification behavior in water/soybean oil diphase mixture is studied. The results show that modified HNTs can emulsify water/soybean oil diphase mixture and the emulsification performance is dependent on microstructure of amphiphilic brushes such as hydrophilic/hydrophobic segment size and sequence.

  19. Open Cherry Picker simulation results. [manned platform for satellite servicing from Shuttle

    Science.gov (United States)

    Nathan, C. A.

    1982-01-01

    The Open Cherry Picker (OCP) is a manned platform, mounted at the end of the Remote Manipulator System (RMS), which is used to enhance extravehicular activities. The objective of the simulation program described was to reduce the existing complexity of those OCP design features that are mandatory for initial Space Shuttle applications. The OCP development test article consists of a torque box, a rotating foot restraint, a rotating stanchion that houses handholds, and a tool storage section with an interface with payload modules. If the size or complexity of the payload increases, payload handling devices may be added at a later data. The simulations have shown that the crew can control the RMS from the Aft Flight Deck of the Shuttle, using voice commands from the EVA crewman. No need for a stabilizer was evident, and RMS dynamics due to crew-induced workloads were found to be minor.

  20. THE INFLUENCE OF TRUST IN THE CONSTITUTION OF A BRAZILIAN COOPERATIVE OF SELECTIVE WASTE PICKERS

    Directory of Open Access Journals (Sweden)

    Dayanne Marciane Gonçalves

    2016-03-01

    Full Text Available Since the Brazilian public policy started to encourage solidarity economy in 2003, the number of projects and enterprises in this sector has steadily increased. Embeddedness has contributed to the understanding of organizational phenomena of solidarity economy and cooperatives. The aim of this study was to understand the influence of trust, from the perspective of Mark Granovetter’s social networks, on the constitution of a cooperative of urban recyclable waste pickers in southern Brazil between 1996 until early 2012, considered the foundation period. We used the qualitative method with a historical approach to social relationships and content analysis. Possible influences of trust were analysed based on the economic, social and political history of the cooperative. Among the main results, we highlight the existence of social relations before the constitution, defined by trust due to family identity and reputation built over time.

  1. A high-throughput optomechanical retrieval method for sequence-verified clonal DNA from the NGS platform.

    Science.gov (United States)

    Lee, Howon; Kim, Hyoki; Kim, Sungsik; Ryu, Taehoon; Kim, Hwangbeom; Bang, Duhee; Kwon, Sunghoon

    2015-02-02

    Writing DNA plays a significant role in the fields of synthetic biology, functional genomics and bioengineering. DNA clones on next-generation sequencing (NGS) platforms have the potential to be a rich and cost-effective source of sequence-verified DNAs as a precursor for DNA writing. However, it is still very challenging to retrieve target clonal DNA from high-density NGS platforms. Here we propose an enabling technology called 'Sniper Cloning' that enables the precise mapping of target clone features on NGS platforms and non-contact rapid retrieval of targets for the full utilization of DNA clones. By merging the three cutting-edge technologies of NGS, DNA microarray and our pulse laser retrieval system, Sniper Cloning is a week-long process that produces 5,188 error-free synthetic DNAs in a single run of NGS with a single microarray DNA pool. We believe that this technology has potential as a universal tool for DNA writing in biological sciences.

  2. Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses.

    Science.gov (United States)

    Golosova, Olga; Henderson, Ross; Vaskin, Yuriy; Gabrielian, Andrei; Grekhov, German; Nagarajan, Vijayaraj; Oler, Andrew J; Quiñones, Mariam; Hurt, Darrell; Fursov, Mikhail; Huyen, Yentram

    2014-01-01

    The advent of Next Generation Sequencing (NGS) technologies has opened new possibilities for researchers. However, the more biology becomes a data-intensive field, the more biologists have to learn how to process and analyze NGS data with complex computational tools. Even with the availability of common pipeline specifications, it is often a time-consuming and cumbersome task for a bench scientist to install and configure the pipeline tools. We believe that a unified, desktop and biologist-friendly front end to NGS data analysis tools will substantially improve productivity in this field. Here we present NGS pipelines "Variant Calling with SAMtools", "Tuxedo Pipeline for RNA-seq Data Analysis" and "Cistrome Pipeline for ChIP-seq Data Analysis" integrated into the Unipro UGENE desktop toolkit. We describe the available UGENE infrastructure that helps researchers run these pipelines on different datasets, store and investigate the results and re-run the pipelines with the same parameters. These pipeline tools are included in the UGENE NGS package. Individual blocks of these pipelines are also available for expert users to create their own advanced workflows.

  3. lociNGS: a lightweight alternative for assessing suitability of next-generation loci for evolutionary analysis.

    Directory of Open Access Journals (Sweden)

    Sarah M Hird

    Full Text Available Genomic enrichment methods and next-generation sequencing produce uneven coverage for the portions of the genome (the loci they target; this information is essential for ascertaining the suitability of each locus for further analysis. lociNGS is a user-friendly accessory program that takes multi-FASTA formatted loci, next-generation sequence alignments and demographic data as input and collates, displays and outputs information about the data. Summary information includes the parameters coverage per locus, coverage per individual and number of polymorphic sites, among others. The program can output the raw sequences used to call loci from next-generation sequencing data. lociNGS also reformats subsets of loci in three commonly used formats for multi-locus phylogeographic and population genetics analyses - NEXUS, IMa2 and Migrate. lociNGS is available at https://github.com/SHird/lociNGS and is dependent on installation of MongoDB (freely available at http://www.mongodb.org/downloads. lociNGS is written in Python and is supported on MacOSX and Unix; it is distributed under a GNU General Public License.

  4. Analysis and Visualization of ChIP-Seq and RNA-Seq Sequence Alignments Using ngs.plot.

    Science.gov (United States)

    Loh, Yong-Hwee Eddie; Shen, Li

    2016-01-01

    The continual maturation and increasing applications of next-generation sequencing technology in scientific research have yielded ever-increasing amounts of data that need to be effectively and efficiently analyzed and innovatively mined for new biological insights. We have developed ngs.plot-a quick and easy-to-use bioinformatics tool that performs visualizations of the spatial relationships between sequencing alignment enrichment and specific genomic features or regions. More importantly, ngs.plot is customizable beyond the use of standard genomic feature databases to allow the analysis and visualization of user-specified regions of interest generated by the user's own hypotheses. In this protocol, we demonstrate and explain the use of ngs.plot using command line executions, as well as a web-based workflow on the Galaxy framework. We replicate the underlying commands used in the analysis of a true biological dataset that we had reported and published earlier and demonstrate how ngs.plot can easily generate publication-ready figures. With ngs.plot, users would be able to efficiently and innovatively mine their own datasets without having to be involved in the technical aspects of sequence coverage calculations and genomic databases.

  5. Facile fabrication of biocompatible PLGA drug-carrying microspheres by O/W pickering emulsions.

    Science.gov (United States)

    Wei, Zengjiang; Wang, Chaoyang; Liu, Hao; Zou, Shengwen; Tong, Zhen

    2012-03-01

    This study is focused on the preparation of Ibuprofen (IBU) loaded micrometer-sized poly(lactic-co-glycolic acid) (PLGA) microspheres and process variables on the size, drug loading and release during preparation of formulation. Silicon dioxide (SiO(2)) nanoparticle-coated PLGA microspheres were fabricated via a combined system of "Pickering-type" emulsion route and solvent volatilization method in the absence of any molecular surfactants. Stable oil-in-water emulsions were prepared using SiO(2) nanoparticles as a particulate emulsifier and a dichloromethane (CH(2)Cl(2)) solution of PLGA as an oil phase. The SiO(2) nanoparticle-coated PLGA microspheres were fabricated by the evaporation of CH(2)Cl(2) in situ, and then bare-PLGA microspheres were prepared by removal of the SiO(2) nanoparticles using HF aqueous solution. The two types of microspheres were characterized in terms of size, component and morphology using scanning electronic microscope (SEM), Fourier-transform infrared, optical microscope, and so on. Moreover, IBU was encapsulated into the hybrid beads by dispersing them in the CH(2)Cl(2) solution of PLGA in the fabrication process. The sustained release could be obtained due to the barrier of the polymeric matrix (PLGA). More over, the release curves were nicely fitted by the Weibull equation and the release followed Fickian diffusion. The combined system of Pickering emulsion and solvent volatilization opens up a new route to fabricate a variety of microspheres. The resulting microspheres may find applications as delivery vehicles for biomolecules, drugs, cosmetics and living cells. Copyright © 2011 Elsevier B.V. All rights reserved.

  6. NGS-Based Assay for the Identification of Individuals Carrying Recessive Genetic Mutations in Reproductive Medicine.

    Science.gov (United States)

    Abulí, Anna; Boada, Montserrat; Rodríguez-Santiago, Benjamín; Coroleu, Buenaventura; Veiga, Anna; Armengol, Lluís; Barri, Pedro N; Pérez-Jurado, Luis A; Estivill, Xavier

    2016-06-01

    Next-generation sequencing (NGS) has the capacity of carrier screening in gamete donation (GD) programs. We have developed and validated an NGS carrier-screening test (qCarrier test) that includes 200 genes associated with 368 disorders (277 autosomal recessive and 37 X-linked). Carrier screening is performed on oocyte donation candidates and the male partner of oocyte recipient. Carriers of X-linked conditions are excluded from the GD program, whereas donors are chosen who do not carry mutations for the same gene/disease as the recipients. The validation phase showed a high sensitivity (>99% sensitivity) detecting all single-nucleotide variants, 13 indels, and 25 copy-number variants included in the validation set. A total of 1,301 individuals were analysed with the qCarrier test, including 483 candidate oocyte donors and 635 receptor couples, 105 females receiving sperm donation, and 39 couples seeking pregnancy. We identified 56% of individuals who are carriers for at least one genetic condition and 1.7% of female donors who were excluded from the program due to a carrier state of X-linked conditions. Globally, 3% of a priori assigned donations had a high reproductive risk that could be minimized after testing. Genetic counselling at different stages is essential for helping to facilitate a successful and healthy pregnancy.

  7. Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions.

    Science.gov (United States)

    Bianchi, Valerio; Ceol, Arnaud; Ogier, Alessandro G E; de Pretis, Stefano; Galeota, Eugenia; Kishore, Kamal; Bora, Pranami; Croci, Ottavio; Campaner, Stefano; Amati, Bruno; Morelli, Marco J; Pelizzola, Mattia

    2016-01-01

    Next-generation sequencing (NGS) technologies have deeply changed our understanding of cellular processes by delivering an astonishing amount of data at affordable prices; nowadays, many biology laboratories have already accumulated a large number of sequenced samples. However, managing and analyzing these data poses new challenges, which may easily be underestimated by research groups devoid of IT and quantitative skills. In this perspective, we identify five issues that should be carefully addressed by research groups approaching NGS technologies. In particular, the five key issues to be considered concern: (1) adopting a laboratory management system (LIMS) and safeguard the resulting raw data structure in downstream analyses; (2) monitoring the flow of the data and standardizing input and output directories and file names, even when multiple analysis protocols are used on the same data; (3) ensuring complete traceability of the analysis performed; (4) enabling non-experienced users to run analyses through a graphical user interface (GUI) acting as a front-end for the pipelines; (5) relying on standard metadata to annotate the datasets, and when possible using controlled vocabularies, ideally derived from biomedical ontologies. Finally, we discuss the currently available tools in the light of these issues, and we introduce HTS-flow, a new workflow management system conceived to address the concerns we raised. HTS-flow is able to retrieve information from a LIMS database, manages data analyses through a simple GUI, outputs data in standard locations and allows the complete traceability of datasets, accompanying metadata and analysis scripts.

  8. Integrated systems for NGS data management and analysis: open issues and available solutions

    Directory of Open Access Journals (Sweden)

    Valerio eBianchi

    2016-05-01

    Full Text Available Next-generation sequencing (NGS technologies have deeply changed our understanding of cellular processes by delivering an astonishing amount of data at affordable prices; nowadays, many biology laboratories have already accumulated a large number of sequenced samples. However, managing and analyzing these data poses new challenges, which may easily be underestimated by research groups devoid of IT and quantitative skills. In this perspective, we identify five issues that should be carefully addressed by research groups approaching NGS technologies. In particular, the five key issues to be considered concern: 1 adopting a laboratory management system (LIMS and safeguard the resulting raw data structure in downstream analyses; 2 monitoring the flow of the data and standardizing input and output directories and file names, even when multiple analysis protocols are used on the same data; 3 ensuring complete traceability of the analysis performed; 4 enabling non-experienced users to run analyses through a graphical user interface (GUI acting as a front-end for the pipelines; 5 relying on standard metadata to annotate the datasets, and when possible using controlled vocabularies, ideally derived from biomedical ontologies. Finally, we discuss the currently available tools in the light of these issues, and we introduce HTS-flow, a new workflow management system (WMS conceived to address the concerns we raised. HTS-flow is able to retrieve information from a LIMS database, manages data analyses through a simple GUI, outputs data in standard locations and allows the complete traceability of datasets, accompanying metadata and analysis scripts.

  9. CDH1 mutations in gastric cancer patients from northern Brazil identified by Next- Generation Sequencing (NGS).

    Science.gov (United States)

    El-Husny, Antonette; Raiol-Moraes, Milene; Amador, Marcos; Ribeiro-Dos-Santos, André M; Montagnini, André; Barbosa, Silvanira; Silva, Artur; Assumpção, Paulo; Ishak, Geraldo; Santos, Sidney; Pinto, Pablo; Cruz, Aline; Ribeiro-Dos-Santos, Ândrea

    2016-05-13

    Gastric cancer is considered to be the fifth highest incident tumor worldwide and the third leading cause of cancer deaths. Developing regions report a higher number of sporadic cases, but there are only a few local studies related to hereditary cases of gastric cancer in Brazil to confirm this fact. CDH1 germline mutations have been described both in familial and sporadic cases, but there is only one recent molecular description of individuals from Brazil. In this study we performed Next Generation Sequencing (NGS) to assess CDH1 germline mutations in individuals who match the clinical criteria for Hereditary Diffuse Gastric Cancer (HDGC), or who exhibit very early diagnosis of gastric cancer. Among five probands we detected CDH1 germline mutations in two cases (40%). The mutation c.1023T > G was found in a HDGC family and the mutation c.1849G > A, which is nearly exclusive to African populations, was found in an early-onset case of gastric adenocarcinoma. The mutations described highlight the existence of gastric cancer cases caused by CDH1 germline mutations in northern Brazil, although such information is frequently ignored due to the existence of a large number of environmental factors locally. Our report represent the first CDH1 mutations in HDGC described from Brazil by an NGS platform.

  10. Assessment of the latest NGS enrichment capture methods in clinical context.

    Science.gov (United States)

    García-García, Gema; Baux, David; Faugère, Valérie; Moclyn, Mélody; Koenig, Michel; Claustres, Mireille; Roux, Anne-Françoise

    2016-02-11

    Enrichment capture methods for NGS are widely used, however, they evolve rapidly and it is necessary to periodically measure their strengths and weaknesses before transfer to diagnostic services. We assessed two recently released custom DNA solution-capture enrichment methods for NGS, namely Illumina NRCCE and Agilent SureSelect(QXT), against a reference method NimbleGen SeqCap EZ Choice on a similar gene panel, sharing 678 kb and 110 genes. Two Illumina MiSeq runs of 12 samples each have been performed, for each of the three methods, using the same 24 patients (affected with sensorineural disorders). Technical outcomes have been computed and compared, including depth and evenness of coverage, enrichment in targeted regions, performance in GC-rich regions and ability to generate consistent variant datasets. While we show that the three methods resulted in suitable datasets for standard DNA variant discovery, we describe significant differences between the results for the above parameters. NimbleGen offered the best depth of coverage and evenness, while NRCCE showed the highest on target levels but high duplicate rates. SureSelect(QXT) showed an overall quality close to that of NimbleGen. The new methods exhibit reduced preparation time but behave differently. These findings will guide laboratories in their choice of library enrichment approach.

  11. Panel-based NGS Reveals Novel Pathogenic Mutations in Autosomal Recessive Retinitis Pigmentosa.

    Science.gov (United States)

    Perez-Carro, Raquel; Corton, Marta; Sánchez-Navarro, Iker; Zurita, Olga; Sanchez-Bolivar, Noelia; Sánchez-Alcudia, Rocío; Lelieveld, Stefan H; Aller, Elena; Lopez-Martinez, Miguel Angel; López-Molina, Ma Isabel; Fernandez-San Jose, Patricia; Blanco-Kelly, Fiona; Riveiro-Alvarez, Rosa; Gilissen, Christian; Millan, Jose M; Avila-Fernandez, Almudena; Ayuso, Carmen

    2016-01-25

    Retinitis pigmentosa (RP) is a group of inherited progressive retinal dystrophies (RD) characterized by photoreceptor degeneration. RP is highly heterogeneous both clinically and genetically, which complicates the identification of causative genes and mutations. Targeted next-generation sequencing (NGS) has been demonstrated to be an effective strategy for the detection of mutations in RP. In our study, an in-house gene panel comprising 75 known RP genes was used to analyze a cohort of 47 unrelated Spanish families pre-classified as autosomal recessive or isolated RP. Disease-causing mutations were found in 27 out of 47 cases achieving a mutation detection rate of 57.4%. In total, 33 pathogenic mutations were identified, 20 of which were novel mutations (60.6%). Furthermore, not only single nucleotide variations but also copy-number variations, including three large deletions in the USH2A and EYS genes, were identified. Finally seven out of 27 families, displaying mutations in the ABCA4, RP1, RP2 and USH2A genes, could be genetically or clinically reclassified. These results demonstrate the potential of our panel-based NGS strategy in RP diagnosis.

  12. Next generation sequencing (NGS database for tandem repeats with multiple pattern 2°-shaft multicore string matching

    Directory of Open Access Journals (Sweden)

    Chinta Someswara Rao

    2016-03-01

    Full Text Available Next generation sequencing (NGS technologies have been rapidly applied in biomedical and biological research in recent years. To provide the comprehensive NGS resource for the research, in this paper , we have considered 10 loci/codi/repeats TAGA, TCAT, GAAT, AGAT, AGAA, GATA, TATC, CTTT, TCTG and TCTA. Then we developed the NGS Tandem Repeat Database (TandemRepeatDB for all the chromosomes of Homo sapiens, Callithrix jacchus, Chlorocebus sabaeus, Gorilla gorilla, Macaca fascicularis, Macaca mulatta, Nomascus leucogenys, Pan troglodytes, Papio anubis and Pongo abelii genome data sets for all those locis. We find the successive occurence frequency for all the above 10 SSR (simple sequence repeats in the above genome data sets on a chromosome-by-chromosome basis with multiple pattern 2° shaft multicore string matching.

  13. Next generation sequencing (NGS) database for tandem repeats with multiple pattern 2°-shaft multicore string matching

    Science.gov (United States)

    Someswara Rao, Chinta; Raju, S. Viswanadha

    2016-01-01

    Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research in recent years. To provide the comprehensive NGS resource for the research, in this paper , we have considered 10 loci/codi/repeats TAGA, TCAT, GAAT, AGAT, AGAA, GATA, TATC, CTTT, TCTG and TCTA. Then we developed the NGS Tandem Repeat Database (TandemRepeatDB) for all the chromosomes of Homo sapiens, Callithrix jacchus, Chlorocebus sabaeus, Gorilla gorilla, Macaca fascicularis, Macaca mulatta, Nomascus leucogenys, Pan troglodytes, Papio anubis and Pongo abelii genome data sets for all those locis. We find the successive occurence frequency for all the above 10 SSR (simple sequence repeats) in the above genome data sets on a chromosome-by-chromosome basis with multiple pattern 2° shaft multicore string matching. PMID:26981434

  14. A case study for cloud based high throughput analysis of NGS data using the globus genomics system.

    Science.gov (United States)

    Bhuvaneshwar, Krithika; Sulakhe, Dinanath; Gauba, Robinder; Rodriguez, Alex; Madduri, Ravi; Dave, Utpal; Lacinski, Lukasz; Foster, Ian; Gusev, Yuriy; Madhavan, Subha

    2015-01-01

    Next generation sequencing (NGS) technologies produce massive amounts of data requiring a powerful computational infrastructure, high quality bioinformatics software, and skilled personnel to operate the tools. We present a case study of a practical solution to this data management and analysis challenge that simplifies terabyte scale data handling and provides advanced tools for NGS data analysis. These capabilities are implemented using the "Globus Genomics" system, which is an enhanced Galaxy workflow system made available as a service that offers users the capability to process and transfer data easily, reliably and quickly to address end-to-endNGS analysis requirements. The Globus Genomics system is built on Amazon 's cloud computing infrastructure. The system takes advantage of elastic scaling of compute resources to run multiple workflows in parallel and it also helps meet the scale-out analysis needs of modern translational genomics research.

  15. Next generation sequencing (NGS) database for tandem repeats with multiple pattern 2°-shaft multicore string matching.

    Science.gov (United States)

    Someswara Rao, Chinta; Raju, S Viswanadha

    2016-03-01

    Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research in recent years. To provide the comprehensive NGS resource for the research, in this paper , we have considered 10 loci/codi/repeats TAGA, TCAT, GAAT, AGAT, AGAA, GATA, TATC, CTTT, TCTG and TCTA. Then we developed the NGS Tandem Repeat Database (TandemRepeatDB) for all the chromosomes of Homo sapiens, Callithrix jacchus, Chlorocebus sabaeus, Gorilla gorilla, Macaca fascicularis, Macaca mulatta, Nomascus leucogenys, Pan troglodytes, Papio anubis and Pongo abelii genome data sets for all those locis. We find the successive occurence frequency for all the above 10 SSR (simple sequence repeats) in the above genome data sets on a chromosome-by-chromosome basis with multiple pattern 2° shaft multicore string matching.

  16. A case study for cloud based high throughput analysis of NGS data using the globus genomics system

    Directory of Open Access Journals (Sweden)

    Krithika Bhuvaneshwar

    2015-01-01

    Full Text Available Next generation sequencing (NGS technologies produce massive amounts of data requiring a powerful computational infrastructure, high quality bioinformatics software, and skilled personnel to operate the tools. We present a case study of a practical solution to this data management and analysis challenge that simplifies terabyte scale data handling and provides advanced tools for NGS data analysis. These capabilities are implemented using the “Globus Genomics” system, which is an enhanced Galaxy workflow system made available as a service that offers users the capability to process and transfer data easily, reliably and quickly to address end-to-endNGS analysis requirements. The Globus Genomics system is built on Amazon's cloud computing infrastructure. The system takes advantage of elastic scaling of compute resources to run multiple workflows in parallel and it also helps meet the scale-out analysis needs of modern translational genomics research.

  17. Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities

    Science.gov (United States)

    Tan, BoonFei; Ng, Charmaine; Nshimyimana, Jean Pierre; Loh, Lay Leng; Gin, Karina Y.-H.; Thompson, Janelle R.

    2015-01-01

    Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools. PMID:26441948

  18. Next-generation sequencing (NGS for assessment of microbial water quality: current progress, challenges, and future opportunities

    Directory of Open Access Journals (Sweden)

    BoonFei eTan

    2015-09-01

    Full Text Available Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools.

  19. Heterogeneous nanoparticles at water-oil interfaces: Structure, Order, Diffusion, and Implications for the stability of Pickering emulsions

    Science.gov (United States)

    Striolo, Alberto; Luu, Xuan-Cuong; Molecular Science and Engineering Team

    2013-03-01

    Pickering emulsions find applications, e.g., in food processing, personal care products, and drug delivery. The emulsions stability is naturally related to the structural and dynamical properties of the nanoparticles adsorbed at oil-water interfaces. Such properties are investigated here by means of dissipative particle dynamics simulations, informed by atomistic molecular dynamics simulations results (Langmuir2011, 27, (9), 5264-5274). Several nanoparticles are considered, including Janus and homogeneous, and of several different shapes (spherical, elliptical, discoid, etc.) Structural and transport properties are quantified as a function of surface density and system composition. Results for radial distribution functions, hexagonal order parameters, and self-diffusion coefficients are reported. We sometimes find unexpected behavior. For example, self-diffusion coefficient maxima are observed in mixed systems. Implications of such observations on macroscopic observables (i.e., the stability of Pickering emulsions) are discussed. Acknowledgments: NSF

  20. Exact Solutions of Nonlinear Dynamics Equation in a New Double-Chain Model of DNA

    Institute of Scientific and Technical Information of China (English)

    QIAN Xian-Min; LOU Sen-Yue

    2003-01-01

    The exact solutions of the general nonlinear dynamic system in a new double-chain model of DNA are studiedkink shape excitations can be found in both the Conte's truncation expansion and the Pickering's truncation expansion.Three types of new localized excitations, the asymmetric kink-kink excitations, the soliton-kink excitation, and thekink-soliton excitations, are found by using the Pickering's nonstandard truncation expansion.

  1. Pickering emulsions stabilized by a metal-organic framework (MOF) and graphene oxide (GO) for producing MOF/GO composites.

    Science.gov (United States)

    Zhang, Fanyu; Liu, Lifei; Tan, Xiuniang; Sang, Xinxin; Zhang, Jianling; Liu, Chengcheng; Zhang, Bingxing; Han, Buxing; Yang, Guanying

    2017-10-02

    Herein we demonstrate the formation of a novel kind of Pickering emulsion that is stabilized by a Zr-based metal-organic framework (Zr-MOF) and graphene oxide (GO). It was found that the Zr-BDC-NO2 and GO solids assembling at the oil/water interface can effectively stabilize the oil droplets that are dispersed in the water phase. Such a Pickering emulsion offers a facile route for fabricating Zr-MOF/GO composite materials. After removing water and oil by freeze drying from Pickering emulsions, the Zr-MOF/GO composites were obtained and their morphologies, structures and interaction properties were characterized by scanning electron microscopy, transmission electron microscopy, X-ray diffraction and Fourier transform infrared spectrometry, respectively. The influences of the concentration of GO and Zr-MOF on the emulsion microstructures and the properties of the MOF/GO composites were studied. Based on experimental results, the mechanisms for the emulsion formation by Zr-MOF and GO and the as-synthesized superstructures of the Zr-MOF/GO composite were proposed. It is expected that this facile and tunable route can be applied to the synthesis of different kinds of MOF-based or GO-based composite materials.

  2. Polystyrene/nano-SiO2 composite microspheres fabricated by Pickering emulsion polymerization: Preparation, mechanisms and thermal properties

    Directory of Open Access Journals (Sweden)

    W. H. Zhang

    2012-07-01

    Full Text Available We report the preparation, mechanisms and thermal properties of core-shell structured polymer/inorganic nanoparticle composite microspheres prepared by Pickering emulsion polymerization. Stable Pickering emulsion was firstly fabricated by using surface-modified nano-SiO2 particles as stabilizer. And then, two kinds of polystyrene/nano-SiO2 (PS/SiO2 composite microspheres with different sizes and morphologies were synthesized using hydrophobic azobisisobutyronitrile (AIBN and hydrophilic ammonium persulfate (APS as initiator, respectively. The possible mechanisms of Pickering emulsion polymerization initiated by different initiators were proposed according to the results of transmission electron microscope (TEM and scanning electron microscope (SEM. The chemical structure and molecular weight of the composite microspheres were characterized by Fourier transform infrared spectroscopy (FTIR, X-ray diffractometer (XRD and gel permeation chromatography coupled with a multi-angle laser light scattering photometer (GPC-MALLS. Thermogravimetric analysis (TGA and differential scanning calorimeter (DSC were used to comparatively analyze the thermal properties of nanocomposites and corresponding pure polymer. The results indicated that the decomposition temperature and glass transition temperature (Tg of nanocomposites were elevated to a certain degree due to the existence of nano-SiO2.

  3. IgH-V(D)J NGS-MRD measurement pre- and early post-allotransplant defines very low- and very high-risk ALL patients.

    Science.gov (United States)

    Pulsipher, Michael A; Carlson, Chris; Langholz, Bryan; Wall, Donna A; Schultz, Kirk R; Bunin, Nancy; Kirsch, Ilan; Gastier-Foster, Julie M; Borowitz, Michael; Desmarais, Cindy; Williamson, David; Kalos, Michael; Grupp, Stephan A

    2015-05-28

    Positive detection of minimal residual disease (MRD) by multichannel flow cytometry (MFC) prior to hematopoietic cell transplantation (HCT) of patients with acute lymphoblastic leukemia (ALL) identifies patients at high risk for relapse, but many pre-HCT MFC-MRD negative patients also relapse, and the predictive power MFC-MRD early post-HCT is poor. To test whether the increased sensitivity of next-generation sequencing (NGS)-MRD better identifies pre- and post-HCT relapse risk, we performed immunoglobulin heavy chain (IgH) variable, diversity, and joining (V[D]J) DNA sequences J NGS-MRD on 56 patients with B-cell ALL enrolled in Children's Oncology Group trial ASCT0431. NGS-MRD predicted relapse and survival more accurately than MFC-MRD (P NGS-MRD detection was better at predicting relapse than MFC-MRD (P NGS-MRD positive relapse rate, 67%; P = .004). Any post-HCT NGS positivity resulted in an increase in relapse risk by multivariate analysis (hazard ratio, 7.7; P = .05). Absence of detectable IgH-V(D)J NGS-MRD pre-HCT defines good-risk patients potentially eligible for less intense treatment approaches. Post-HCT NGS-MRD is highly predictive of relapse and survival, suggesting a role for this technique in defining patients early who would be eligible for post-HCT interventions. The trial was registered at www.clinicaltrials.gov as #NCT00382109.

  4. [Molecular-genetic analysis of DNA pol and TK of HSV-1 population using NGS technology].

    Science.gov (United States)

    Gus'kova, A A; Skoblov, M Iu; Lavrov, A V; Zubtsov, D A; Andronova, V L; Gol'dshteĭn, D V; Galegov, G A; Skoblov, Iu S

    2013-01-01

    It was determined the ratio of viral DNA and DNA from Vero cells using the polymerase chain reaction in real time in Vero cell lysate, infected with L2 strain of the herpes simplex virus type 1. Copy number of the virus reached a maximum after 24 hours of incubation of infection. Total DNA was isolated and sequenced using NGS technology by Ion Torrent device. Nucleotide sequences of the thymidine kinase gene (UL23) and DNA polymerase (UL30) were determined for a population of HSV-1 strain L2. Comparison of the primary structure of these genes with the corresponding nucleotide sequences of known strains of HSV-1 KOS and 17 was conducted. Differences in the structure of genes UL23 and UL30 between strain L2 and reference strains KOS and 17 are not important, because changes are found in non-conservative regions.

  5. ascatNgs: Identifying Somatically Acquired Copy-Number Alterations from Whole-Genome Sequencing Data.

    Science.gov (United States)

    Raine, Keiran M; Van Loo, Peter; Wedge, David C; Jones, David; Menzies, Andrew; Butler, Adam P; Teague, Jon W; Tarpey, Patrick; Nik-Zainal, Serena; Campbell, Peter J

    2016-12-08

    We have developed ascatNgs to aid researchers in carrying out Allele-Specific Copy number Analysis of Tumours (ASCAT). ASCAT is capable of detecting DNA copy number changes affecting a tumor genome when comparing to a matched normal sample. Additionally, the algorithm estimates the amount of tumor DNA in the sample, known as Aberrant Cell Fraction (ACF). ASCAT itself is an R-package which requires the generation of many file types. Here, we present a suite of tools to help handle this for the user. Our code is available on our GitHub site (https://github.com/cancerit). This unit describes both 'one-shot' execution and approaches more suitable for large-scale compute farms. © 2016 by John Wiley & Sons, Inc.

  6. Pickering乳液的制备及稳定性研究%Preparation of Pickering Emulsion and Its Stability

    Institute of Scientific and Technical Information of China (English)

    田梅娟

    2016-01-01

    Pickering emulsion is a kind of new one with solid particles replacing organic surfactants.Using Stöbe method,with anhydrous ethanol as a co-solvent and ammonia as a catalyst,solid silica nanoparticles were prepared by decomposing ethyl orthosilicate.Using solid silica nanoparticles as a stable agent,Pickering emul-sion of chloroform/water was prepared.The effects of the amount of solid silica nanoparticles,oil/water volume ratio,alkali concentration on Pickering emulsion stability were investigated.The results showed that,when the amount of solid silica nanoparticles was 0.035 g,oil/water volume ratio was 1∶350,alkali concentration was 0.01 mol·L-1 ,the emulsion stability was the best.%Pickering 乳液是一种由固体粒子取代有机表面活性剂稳定乳液体系的新式乳液。采用 Stöbe法,以无水乙醇作共溶剂,用氨作催化剂,分解正硅酸乙酯(TEOS)制备纳米固体 SiO2粒子,然后用纳米固体 SiO2粒子作稳定剂,制备三氯甲烷/水的Pickering乳液。考察了纳米固体 SiO2粒子加入量、油水体积比、氢氧化钠溶液浓度对 Pickering 乳液稳定性的影响。结果表明:当纳米固体 SiO2粒子加入量为0.035 g、油水体积比为1∶350、氢氧化钠溶液浓度为0.01 mol·L-1时,制备的乳液稳定性最好。

  7. Epigenetic DNA Methylation Profiling with MSRE: A Quantitative NGS Approach Using a Parkinson's Disease Test Case

    Directory of Open Access Journals (Sweden)

    Adam G. Marsh

    2016-11-01

    Full Text Available Epigenetics is a rapidly developing field focused on deciphering chemical fingerprints that accumulate on human genomes over time. As the nascent idea of precision medicine expands to encompass epigenetic signatures of diagnostic and prognostic relevance, there is a need for methodologies that provide high-throughput DNA methylation profiling measurements. Here we report a novel quantification methodology for computationally reconstructing site-specific CpG methylation status from next generation sequencing (NGS data using methyl-sensitive restriction endonucleases (MSRE. An integrated pipeline efficiently incorporates raw NGS metrics into a statistical discrimination platform to identify functional linkages between shifts in epigenetic DNA methylation and disease phenotypes in samples being analyzed. In this pilot proof-of-concept study we quantify and compare DNA methylation in blood serum of individuals with Parkinson's Disease relative to matched healthy blood profiles. Even with a small study of only six samples, a high degree of statistical discrimination was achieved based on CpG methylation profiles between groups, with 1,008 statistically different CpG sites (p textless 0.0025, after false discovery rate correction. A methylation load calculation was used to assess higher order impacts of methylation shifts on genes and pathways and most notably identified FGF3, FGF8, HTT, KMTA5, MIR8073, and YWHAG as differentially methylated genes with high relevance to Parkinson's Disease and neurodegeneration (based on PubMed literature citations. Of these, KMTA5 is a histone methyl-transferase gene and HTT is Huntington Disease Protein or Huntingtin, for which there are well established neurodegenerative impacts. The future need for precision diagnostics now requires more tools for exploring epigenetic processes that may be linked to cellular dysfunction and subsequent disease progression.

  8. Determining performance characteristics of an NGS-based HLA typing method for clinical applications.

    Science.gov (United States)

    Duke, J L; Lind, C; Mackiewicz, K; Ferriola, D; Papazoglou, A; Gasiewski, A; Heron, S; Huynh, A; McLaughlin, L; Rogers, M; Slavich, L; Walker, R; Monos, D S

    2016-03-01

    This study presents performance specifications of an in-house developed human leukocyte antigen (HLA) typing assay using next-generation sequencing (NGS) on the Illumina MiSeq platform. A total of 253 samples, previously characterized for HLA-A, -B, -C, -DRB1 and -DQB1 were included in this study, which were typed at high-resolution using a combination of Sanger sequencing, sequence-specific primer (SSP) and sequence-specific oligonucleotide probe (SSOP) technologies and recorded at the two-field level. Samples were selected with alleles that cover a high percentage of HLA specificities in each of five different race/ethnic groups: European, African-American, Asian Pacific Islander, Hispanic and Native American. Sequencing data were analyzed by two software programs, Omixon's target and GenDx's NGSengine. A number of metrics including allele balance, sensitivity, specificity, precision, accuracy and remaining ambiguity were assessed. Data analyzed by the two software systems are shown independently. The majority of alleles were identical in the exonic sequences (third field) with both programs for HLA-A, -B, -C and -DQB1 in 97.7% of allele determinations. Among the remaining discrepant genotype calls at least one of the analysis programs agreed with the reference typing. Upon additional manual analysis 100% of the 2530 alleles were concordant with the reference HLA genotypes; the remaining ambiguities did not exceed 0.8%. The results demonstrate the feasibility and significant benefit of HLA typing by NGS as this technology is highly accurate, eliminates virtually all ambiguities, provides complete sequencing information for the length of the HLA gene and forms the basis for utilizing a single methodology for HLA typing in the immunogenetics labs.

  9. RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application.

    Science.gov (United States)

    D'Antonio, Mattia; D'Onorio De Meo, Paolo; Pallocca, Matteo; Picardi, Ernesto; D'Erchia, Anna Maria; Calogero, Raffaele A; Castrignanò, Tiziana; Pesole, Graziano

    2015-01-01

    The study of RNA has been dramatically improved by the introduction of Next Generation Sequencing platforms allowing massive and cheap sequencing of selected RNA fractions, also providing information on strand orientation (RNA-Seq). The complexity of transcriptomes and of their regulative pathways make RNA-Seq one of most complex field of NGS applications, addressing several aspects of the expression process (e.g. identification and quantification of expressed genes and transcripts, alternative splicing and polyadenylation, fusion genes and trans-splicing, post-transcriptional events, etc.). In order to provide researchers with an effective and friendly resource for analyzing RNA-Seq data, we present here RAP (RNA-Seq Analysis Pipeline), a cloud computing web application implementing a complete but modular analysis workflow. This pipeline integrates both state-of-the-art bioinformatics tools for RNA-Seq analysis and in-house developed scripts to offer to the user a comprehensive strategy for data analysis. RAP is able to perform quality checks (adopting FastQC and NGS QC Toolkit), identify and quantify expressed genes and transcripts (with Tophat, Cufflinks and HTSeq), detect alternative splicing events (using SpliceTrap) and chimeric transcripts (with ChimeraScan). This pipeline is also able to identify splicing junctions and constitutive or alternative polyadenylation sites (implementing custom analysis modules) and call for statistically significant differences in genes and transcripts expression, splicing pattern and polyadenylation site usage (using Cuffdiff2 and DESeq). Through a user friendly web interface, the RAP workflow can be suitably customized by the user and it is automatically executed on our cloud computing environment. This strategy allows to access to bioinformatics tools and computational resources without specific bioinformatics and IT skills. RAP provides a set of tabular and graphical results that can be helpful to browse, filter and export

  10. DEVELOPMENT OF ANALYTICAL METHODS FOR DETERMINING SUPPRESSOR CONCENTRATION IN THE MCU NEXT GENERATION SOLVENT (NGS)

    Energy Technology Data Exchange (ETDEWEB)

    Taylor-Pashow, K.; Fondeur, F.; White, T.; Diprete, D.; Milliken, C.

    2013-07-31

    Savannah River National Laboratory (SRNL) was tasked with identifying and developing at least one, but preferably two methods for quantifying the suppressor in the Next Generation Solvent (NGS) system. The suppressor is a guanidine derivative, N,N',N"-tris(3,7-dimethyloctyl)guanidine (TiDG). A list of 10 possible methods was generated, and screening experiments were performed for 8 of the 10 methods. After completion of the screening experiments, the non-aqueous acid-base titration was determined to be the most promising, and was selected for further development as the primary method. {sup 1}H NMR also showed promising results from the screening experiments, and this method was selected for further development as the secondary method. Other methods, including {sup 36}Cl radiocounting and ion chromatography, also showed promise; however, due to the similarity to the primary method (titration) and the inability to differentiate between TiDG and TOA (tri-n-ocytlamine) in the blended solvent, {sup 1}H NMR was selected over these methods. Analysis of radioactive samples obtained from real waste ESS (extraction, scrub, strip) testing using the titration method showed good results. Based on these results, the titration method was selected as the method of choice for TiDG measurement. {sup 1}H NMR has been selected as the secondary (back-up) method, and additional work is planned to further develop this method and to verify the method using radioactive samples. Procedures for analyzing radioactive samples of both pure NGS and blended solvent were developed and issued for the both methods.

  11. MutAid: Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics.

    Science.gov (United States)

    Pandey, Ram Vinay; Pabinger, Stephan; Kriegner, Albert; Weinhäusel, Andreas

    2016-01-01

    Traditional Sanger sequencing as well as Next-Generation Sequencing have been used for the identification of disease causing mutations in human molecular research. The majority of currently available tools are developed for research and explorative purposes and often do not provide a complete, efficient, one-stop solution. As the focus of currently developed tools is mainly on NGS data analysis, no integrative solution for the analysis of Sanger data is provided and consequently a one-stop solution to analyze reads from both sequencing platforms is not available. We have therefore developed a new pipeline called MutAid to analyze and interpret raw sequencing data produced by Sanger or several NGS sequencing platforms. It performs format conversion, base calling, quality trimming, filtering, read mapping, variant calling, variant annotation and analysis of Sanger and NGS data under a single platform. It is capable of analyzing reads from multiple patients in a single run to create a list of potential disease causing base substitutions as well as insertions and deletions. MutAid has been developed for expert and non-expert users and supports four sequencing platforms including Sanger, Illumina, 454 and Ion Torrent. Furthermore, for NGS data analysis, five read mappers including BWA, TMAP, Bowtie, Bowtie2 and GSNAP and four variant callers including GATK-HaplotypeCaller, SAMTOOLS, Freebayes and VarScan2 pipelines are supported. MutAid is freely available at https://sourceforge.net/projects/mutaid.

  12. NGS-QC Generator: A Quality Control System for ChIP-Seq and Related Deep Sequencing-Generated Datasets.

    Science.gov (United States)

    Mendoza-Parra, Marco Antonio; Saleem, Mohamed-Ashick M; Blum, Matthias; Cholley, Pierre-Etienne; Gronemeyer, Hinrich

    2016-01-01

    The combination of massive parallel sequencing with a variety of modern DNA/RNA enrichment technologies provides means for interrogating functional protein-genome interactions (ChIP-seq), genome-wide transcriptional activity (RNA-seq; GRO-seq), chromatin accessibility (DNase-seq, FAIRE-seq, MNase-seq), and more recently the three-dimensional organization of chromatin (Hi-C, ChIA-PET). In systems biology-based approaches several of these readouts are generally cumulated with the aim of describing living systems through a reconstitution of the genome-regulatory functions. However, an issue that is often underestimated is that conclusions drawn from such multidimensional analyses of NGS-derived datasets critically depend on the quality of the compared datasets. To address this problem, we have developed the NGS-QC Generator, a quality control system that infers quality descriptors for any kind of ChIP-sequencing and related datasets. In this chapter we provide a detailed protocol for (1) assessing quality descriptors with the NGS-QC Generator; (2) to interpret the generated reports; and (3) to explore the database of QC indicators (www.ngs-qc.org) for >21,000 publicly available datasets.

  13. ngs (notochord granular surface) gene encodes a novel type of intermediate filament family protein essential for notochord maintenance in zebrafish.

    Science.gov (United States)

    Tong, Xiangjun; Xia, Zhidan; Zu, Yao; Telfer, Helena; Hu, Jing; Yu, Jingyi; Liu, Huan; Zhang, Quan; Sodmergen; Lin, Shuo; Zhang, Bo

    2013-01-25

    The notochord is an important organ involved in embryonic patterning and locomotion. In zebrafish, the mature notochord consists of a single stack of fully differentiated, large vacuolated cells called chordocytes, surrounded by a single layer of less differentiated notochordal epithelial cells called chordoblasts. Through genetic analysis of zebrafish lines carrying pseudo-typed retroviral insertions, a mutant exhibiting a defective notochord with a granular appearance was isolated, and the corresponding gene was identified as ngs (notochord granular surface), which was specifically expressed in the notochord. In the mutants, the notochord started to degenerate from 32 hours post-fertilization, and the chordocytes were then gradually replaced by smaller cells derived from chordoblasts. The granular notochord phenotype was alleviated by anesthetizing the mutant embryos with tricaine to prevent muscle contraction and locomotion. Phylogenetic analysis showed that ngs encodes a new type of intermediate filament (IF) family protein, which we named chordostatin based on its function. Under the transmission electron microcopy, bundles of 10-nm-thick IF-like filaments were enriched in the chordocytes of wild-type zebrafish embryos, whereas the chordocytes in ngs mutants lacked IF-like structures. Furthermore, chordostatin-enhanced GFP (EGFP) fusion protein assembled into a filamentous network specifically in chordocytes. Taken together, our work demonstrates that ngs encodes a novel type of IF protein and functions to maintain notochord integrity for larval development and locomotion. Our work sheds light on the mechanisms of notochord structural maintenance, as well as the evolution and biological function of IF family proteins.

  14. Genotype-phenotype correlation in a cohort of Portuguese patients comprising the entire spectrum of VWD types: impact of NGS.

    Science.gov (United States)

    Fidalgo, Teresa; Salvado, Ramon; Corrales, Irene; Pinto, Silva Catarina; Borràs, Nina; Oliveira, Ana; Martinho, Patricia; Ferreira, Gisela; Almeida, Helena; Oliveira, Cristina; Marques, Dalila; Gonçalves, Elsa; Diniz, MJoão; Antunes, Margarida; Tavares, Alice; Caetano, Gonçalo; Kjöllerström, Paula; Maia, Raquel; Sevivas, Teresa S; Vidal, Francisco; Ribeiro, Leticia

    2016-07-01

    The diagnosis of von Willebrand disease (VWD), the most common inherited bleeding disorder, is characterised by a variable bleeding tendency and heterogeneous laboratory phenotype. The sequencing of the entire VWF coding region has not yet become a routine practice in diagnostic laboratories owing to its high costs. Nevertheless, next-generation sequencing (NGS) has emerged as an alternative to overcome this limitation. We aimed to determine the correlation of genotype and phenotype in 92 Portuguese individuals from 60 unrelated families with VWD; therefore, we directly sequenced VWF. We compared the classical Sanger sequencing approach and NGS to assess the value-added effect on the analysis of the mutation distribution in different types of VWD. Sixty-two different VWF mutations were identified, 27 of which had not been previously described. NGS detected 26 additional mutations, contributing to a broad overview of the mutant alleles present in each VWD type. Twenty-nine probands (48.3 %) had two or more mutations; in addition, mutations with pleiotropic effects were detected, and NGS allowed an appropriate classification for seven of them. Furthermore, the differential diagnosis between VWD 2B and platelet type VWD (n = 1), Bernard-Soulier syndrome and VWD 2B (n = 1), and mild haemophilia A and VWD 2N (n = 2) was possible. NGS provided an efficient laboratory workflow for analysing VWF. These findings in our cohort of Portuguese patients support the proposal that improving VWD diagnosis strategies will enhance clinical and laboratory approaches, allowing to establish the most appropriate treatment for each patient.

  15. Production of Concentrated Pickering Emulsions with Narrow Size Distributions Using Stirred Cell Membrane Emulsification.

    Science.gov (United States)

    Manga, Mohamed S; York, David W

    2017-09-12

    Stirred cell membrane emulsification (SCME) has been employed to prepare concentrated Pickering oil in water emulsions solely stabilized by fumed silica nanoparticles. The optimal conditions under which highly stable and low-polydispersity concentrated emulsions using the SCME approach are highlighted. Optimization of the oil flux rates and the paddle stirrer speeds are critical to achieving control over the droplet size and size distribution. Investigating the influence of oil volume fraction highlights the criticality of the initial particle loading in the continuous phase on the final droplet size and polydispersity. At a particle loading of 4 wt %, both the droplet size and polydispersity increase with increasing of the oil volume fraction above 50%. As more interfacial area is produced, the number of particles available in the continuous phase diminishes, and coincidently a reduction in the kinetics of particle adsorption to the interface resulting in larger polydisperse droplets occurs. Increasing the particle loading to 10 wt % leads to significant improvements in both size and polydispersity with oil volume fractions as high as 70% produced with coefficient of variation values as low as ∼30% compared to ∼75% using conventional homogenization techniques.

  16. Interfacial Polymerization of Dopamine in a Pickering Emulsion: Synthesis of Cross-Linkable Colloidosomes and Enzyme Immobilization at Oil/Water Interfaces.

    Science.gov (United States)

    Qu, Yanning; Huang, Renliang; Qi, Wei; Su, Rongxin; He, Zhimin

    2015-07-15

    Colloidosomes are promising carriers for immobilizing enzyme for catalytic purposes in aqueous/organic media. However, they often suffer from one or more problems regarding catalytic performance, stability, and recyclability. Here, we report a novel approach for the synthesis of cross-linkable colloidosomes by the selective polymerization of dopamine at oil/water interfaces in a Pickering emulsion. An efficient enzyme immobilization method was further developed by covalently bonding enzymes to the polydopamine (PDA) layer along with the formation of such colloidosomes with lipase as a model enzyme. In this enzyme system, the PDA layer served as a cross-linking layer and enzyme support for simultaneously enhancing the colloidosomes' stability and improving surface availability of the enzymes for catalytic reaction. It was found that the specific activity of lipases immobilized on the colloidosome shells was 8 and 1.4 times higher than that of free lipase and encapsulated lipase positioned in the aqueous cores of colloidosomes, respectively. Moreover, the immobilized lipases demonstrated excellent operational stability and recyclability, retaining 86.6% of enzyme activity after 15 cycles. It is therefore reasonable to expect that this novel approach for enzyme immobilization has great potential to serve as an important technique for the construction of biocatalytic systems.

  17. A comparative study on the capacity of a range of food-grade particles to form stable O/W and W/O Pickering emulsions.

    Science.gov (United States)

    Duffus, Laudina J; Norton, Jennifer E; Smith, Paul; Norton, Ian T; Spyropoulos, Fotios

    2016-07-01

    Whilst literature describing edible Pickering emulsions is becoming increasingly available, current understanding of these systems still suffers from a lack of consistency in terms of the (processing and formulation) conditions within which these structures have been studied. The current study aims to provide a comparative analysis of the behaviour of different edible Pickering candidates and their ability to stabilise emulsion droplets, under well-controlled and uniform experimental conditions, in order to clearly identify the particle properties necessary for successful Pickering functionality. More specifically, an extensive investigation into the suitability of various food-grade material to act as Pickering particles and provide stable oil-in-water (O/W) and water-in-oil (W/O) emulsions was carried out. Polysaccharide and flavonoid particles were characterised in terms of their size, ζ-potential, interfacial activity and wettability, under equivalent conditions. Particles were subsequently used to stabilise 20% w/w O/W and W/O emulsions, in the absence of added surfactant or other known emulsifying agents, through different processing routes. All formed Pickering emulsions were shown to resist significant droplet size variation and remain stable at particle concentrations between 2 and 3% w/w. The main particle prerequisites for successful Pickering stabilisation were: particle size (200nm - 1μm); an affinity for the emulsion continuous phase and a sufficient particle charge to extend stability. Depending upon the employed emulsification process, the resulting emulsion formation and stability behaviour can be reasonably predicted a priori from the evaluation of specific particle characteristics.

  18. e-DNA meta-barcoding: from NGS raw data to taxonomic profiling.

    Science.gov (United States)

    Bruno, Fosso; Marinella, Marzano; Santamaria, Monica

    2015-01-01

    In recent years, thanks to the essential support provided by the Next-Generation Sequencing (NGS) technologies, Metagenomics is enabling the direct access to the taxonomic and functional composition of mixed microbial communities living in any environmental niche, without the prerequisite to isolate or culture the single organisms. This approach has already been successfully applied for the analysis of many habitats, such as water or soil natural environments, also characterized by extreme physical and chemical conditions, food supply chains, and animal organisms, including humans. A shotgun sequencing approach can lead to investigate both organisms and genes diversity. Anyway, if the purpose is limited to explore the taxonomic complexity, an amplicon-based approach, based on PCR-targeted sequencing of selected genetic species markers, commonly named "meta-barcodes", is desirable. Among the genomic regions most widely used for the discrimination of bacterial organisms, in some cases up to the species level, some hypervariable domains of the gene coding for the 16S rRNA occupy a prominent place. The amplification of a certain meta-barcode from a microbial community through the use of PCR primers able to work in the entire considered taxonomic group is the first task after the extraction of the total DNA. Generally, this step is followed by the high-throughput sequencing of the resulting amplicons libraries by means of a selected NGS platform. Finally, the interpretation of the huge amount of produced data requires appropriate bioinformatics tools and know-how in addition to efficient computational resources. Here a computational methodology suitable for the taxonomic characterization of 454 meta-barcode sequences is described in detail. In particular, a dataset covering the V1-V3 region belonging to the bacterial 16S rRNA coding gene and produced in the Human Microbiome Project (HMP) from a palatine tonsils sample is analyzed. The proposed exercise includes the

  19. NGS-200型GPS测量系统在建立三维控制网中的应用%Application of NGS-200 GPS in Establishment of Three-Dimensional Control Network

    Institute of Scientific and Technical Information of China (English)

    赵俊兰; 冯建秋

    2001-01-01

    介绍了NGS-200GPS测量系统的组成及原理,阐述了利用该系统在北京八大处公园建立测区首级平面控制网的具体做法,对布网方案、数据处理、平差计算和测量结果可靠性进行了分析.实践表明NGS-200GPS在八大处公园山地地形复杂,树木覆盖较密的情况下 ,其性能仍然比较稳定,所取得的测量结果达到了国家有关规范要求.该系统替代常规测量技术是经济、合理可靠的.

  20. NGS-based identification of druggable alterations and signaling pathways – hepatocellular carcinoma case report

    Directory of Open Access Journals (Sweden)

    Kotelnikova E. A.

    2015-12-01

    Full Text Available Aim. To identify potential cancer driving or clinically relevant molecular events for a patient with hepatocellular carcinoma. Methods. In order to achieve this goal, we performed RNA-seq and exome sequencing for the tumor tissue and its matched control. We annotated the alterations found using several publicly available databases and bioinformatics tools. Results. We identified several differentially expressed genes linked to the classical sorafenib treatment as well as additional pathways potentially druggable by therapies studied in clinical trials (Erlotinib, Lapatinib and Temsirolimus. Several germline mutations, found in XRCC1, TP53 and DPYD, according to the data from other clinical trials, could be related to the increased sensitivity to platinum therapies and reduced sensitivity to 5-Fluorouracil. We also identified several potentially driving mutations that could not be currently linked to therapies, like deletion in CIRBP, SNVs in BTG1, ERBB3, TCF7L2 et al. Conclusions. The presented study shows the potential usefulness of the integrated approach to the NGS data analysis, including the analysis of germline mutations and transcriptome in addition to the cancer panel or the exome sequencing data.

  1. Photometric calibration of NGS/POSS and ESO/SRC plates using the NOAO PDS measuring engine. II - Surface photometry

    Science.gov (United States)

    Cutri, Roc M.; Low, Frank J.; Guhathakurta, Puragra

    1993-01-01

    In this paper we present a method to calibrate surface photometry of faint sources measured from direct photographic plates, such as those of the NGS/POSS and ESO/SRC Sky Survey. This calibration procedure does not require scanning sensitometer spots on the plates, but instead uses measurements of the brightness profiles of many faint stars of known brightness to fit a linearized approximation to the characteristic curve. The approximation is valid for only low- to medium-density emulsions, so this technique is appropriate only for relatively faint emission. Comparison between measurements of representative extended sources on the NGS/POSS and CCD images indicates that surface photometry can be obtained from the Sky Survey plates accurate to 0.1-0.3 mag in the range mu(B) between 23 and 27 and mu(R) between 22 and 26 mag/sq arcsec.

  2. Tratamento de dados de NGS para pesquisa de novas mutações associadas à miocardiopatia hipertrófica

    OpenAIRE

    2012-01-01

    Tese de mestrado em Bioestatística, apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2012 A Sequenciação de Nova Geração (NGS - Next Generation Sequencing) está a revolucionar a investigação na área da biomédica, contribuindo significativamente para o avanço da medicina personalizada. A NGS, apoiando-se nos conhecimentos da Estatística Bayesiana e da Bioinformática para a análise e tratamento dos dados que esta técnica origina, torna-se num excelente exemplo dos novo...

  3. Improvement of PCR-free NGS Library Preparation to Obtain Uniform Read Coverage of Genome with Extremely High AT Content

    OpenAIRE

    Williams, A.; Storton, D.; Buckles, J.; Llinas, M.; Wang, Wei

    2012-01-01

    PCR amplification is commonly used in generating libraries for Next-Generation Sequencing (NGS) to efficiently enrich and amplify sequenceable DNA fragments. However, it introduces bias in the representation of the original complex template DNA. Such artifact has devastating effects in sequencing genomes with highly unbalanced base composition: regions of extremely high or low GC content, which are a substantial fraction of such genomes, are often covered with zero or near-zero read depth. PC...

  4. An NGS-Independent Strategy for Proteome-Wide Identification of Single Amino Acid Polymorphisms by Mass Spectrometry.

    Science.gov (United States)

    Xiong, Yun; Guo, Yufeng; Xiao, Weidi; Cao, Qichen; Li, Shanshan; Qi, Xianni; Zhang, Zhidan; Wang, Qinhong; Shui, Wenqing

    2016-03-01

    Detection of proteins containing single amino acid polymorphisms (SAPs) encoded by nonsynonymous SNPs (nsSNPs) can aid researchers in studying the functional significance of protein variants. Most proteogenomic approaches for large-scale SAPs mapping require construction of a sample-specific database containing protein variants predicted from the next-generation sequencing (NGS) data. Searching shotgun proteomic data sets against these NGS-derived databases allowed for identification of SAP peptides, thus validating the proteome-level sequence variation. Contrary to the conventional approaches, our study presents a novel strategy for proteome-wide SAP detection without relying on sample-specific NGS data. By searching a deep-coverage proteomic data set from an industrial thermotolerant yeast strain using our strategy, we identified 337 putative SAPs compared to the reference genome. Among the SAP peptides identified with stringent criteria, 85.2% of SAP sites were validated using whole-genome sequencing data obtained for this organism, which indicates high accuracy of SAP identification with our strategy. More interestingly, for certain SAP peptides that cannot be predicted by genomic sequencing, we used synthetic peptide standards to verify expression of peptide variants in the proteome. Our study has provided a unique tool for proteogenomics to enable proteome-wide direct SAP identification and capture nongenetic protein variants not linked to nsSNPs.

  5. Intra-individual polymorphism in chloroplasts from NGS data: where does it come from and how to handle it?

    Science.gov (United States)

    Scarcelli, N; Mariac, C; Couvreur, T L P; Faye, A; Richard, D; Sabot, F; Berthouly-Salazar, C; Vigouroux, Y

    2016-03-01

    Next-generation sequencing allows access to a large quantity of genomic data. In plants, several studies used whole chloroplast genome sequences for inferring phylogeography or phylogeny. Even though the chloroplast is a haploid organelle, NGS plastome data identified a nonnegligible number of intra-individual polymorphic SNPs. Such observations could have several causes such as sequencing errors, the presence of heteroplasmy or transfer of chloroplast sequences in the nuclear and mitochondrial genomes. The occurrence of allelic diversity has practical important impacts on the identification of diversity, the analysis of the chloroplast data and beyond that, significant evolutionary questions. In this study, we show that the observed intra-individual polymorphism of chloroplast sequence data is probably the result of plastid DNA transferred into the mitochondrial and/or the nuclear genomes. We further assess nine different bioinformatics pipelines' error rates for SNP and genotypes calling using SNPs identified in Sanger sequencing. Specific pipelines are adequate to deal with this issue, optimizing both specificity and sensitivity. Our results will allow a proper use of whole chloroplast NGS sequence and will allow a better handling of NGS chloroplast sequence diversity.

  6. COV2HTML: a visualization and analysis tool of bacterial next generation sequencing (NGS) data for postgenomics life scientists.

    Science.gov (United States)

    Monot, Marc; Orgeur, Mickael; Camiade, Emilie; Brehier, Clément; Dupuy, Bruno

    2014-03-01

    COV2HTML is an interactive web interface, which is addressed to biologists, and allows performing both coverage visualization and analysis of NGS alignments performed on prokaryotic organisms (bacteria and phages). It combines two processes: a tool that converts the huge NGS mapping or coverage files into light specific coverage files containing information on genetic elements; and a visualization interface allowing a real-time analysis of data with optional integration of statistical results. To demonstrate the scope of COV2HTML, the program was tested with data from two published studies. The first data were from RNA-seq analysis of Campylobacter jejuni, based on comparison of two conditions with two replicates. We were able to recover 26 out of 27 genes highlighted in the publication using COV2HTML. The second data comprised of stranded TSS and RNA-seq data sets on the Archaea Sulfolobus solfataricus. COV2HTML was able to highlight most of the TSSs from the article and allows biologists to visualize both TSS and RNA-seq on the same screen. The strength of the COV2HTML interface is making possible NGS data analysis without software installation, login, or a long training period. A web version is accessible at https://mmonot.eu/COV2HTML/ . This website is free and open to users without any login requirement.

  7. A new method to prevent carry-over contaminations in two-step PCR NGS library preparations.

    Science.gov (United States)

    Seitz, Volkhard; Schaper, Sigrid; Dröge, Anja; Lenze, Dido; Hummel, Michael; Hennig, Steffen

    2015-11-16

    Two-step PCR procedures are an efficient and well established way to generate amplicon libraries for NGS sequencing. However, there is a high risk of cross-contamination by carry-over of amplicons from first to second amplification rounds, potentially leading to severe misinterpretation of results. Here we describe a new method able to prevent and/or to identify carry-over contaminations by introducing the K-box, a series of three synergistically acting short sequence elements. Our K-boxes are composed of (i) K1 sequences for suppression of contaminations, (ii) K2 sequences for detection of possible residual contaminations and (iii) S sequences acting as separators to avoid amplification bias. In order to demonstrate the effectiveness of our method we analyzed two-step PCR NGS libraries derived from a multiplex PCR system for detection of T-cell receptor beta gene rearrangements. We used this system since it is of high clinical relevance and may be affected by very low amounts of contaminations. Spike-in contaminations are effectively blocked by the K-box even at high rates as demonstrated by ultra-deep sequencing of the amplicons. Thus, we recommend implementation of the K-box in two-step PCR-based NGS systems for research and diagnostic applications demanding high sensitivity and accuracy.

  8. Pickering emulsion stabilized by lipase-containing periodic mesoporous organosilica particles: a robust biocatalyst system for biodiesel production.

    Science.gov (United States)

    Jiang, Yanjun; Liu, Xinlong; Chen, Yafei; Zhou, Liya; He, Ying; Ma, Li; Gao, Jing

    2014-02-01

    A novel catalytic system of Pickering emulsion stabilized by lipase-containing periodic mesoporous organosilica was constructed (named LP@PE) and used as biocatalyst for biodiesel production. The reaction parameters were optimized and the optimum conditions were as follows: the water fraction 0.65%, molar ratio of ethanol to oleic acid 2:1, immobilized lipase particles 150mg, phosphate buffer pH 7.0 and temperature 30°C. Under these conditions, the maximum biodiesel yield obtained via esterification of oleic acid with ethanol could reach 95.8%. The biodiesel yield could maintain 88.6% after LP@PE was used 15times. The LP@PE was also used in the synthesis of biodiesel from Jatropha curcas oil. The highest yield could reach 87.1% and the yield was 73.0% after 10 cycles. All these results demonstrated that Pickering emulsion system stabilized by immobilized enzyme may possess much potential in many enzymatic industrial applications.

  9. Kafirin Nanoparticle-Stabilized Pickering Emulsions as Oral Delivery Vehicles: Physicochemical Stability and in Vitro Digestion Profile.

    Science.gov (United States)

    Xiao, Jie; Li, Chao; Huang, Qingrong

    2015-12-01

    Kafirin nanoparticle-stabilized Pickering emulsions (KPEs) were used to encapsulate curcumin. The stability of KPEs under processing conditions and their protective effects against photo-oxidation of curcumin and lipid oxidation of oil in emulsions, as well as the digestion profiles in gastrointestinal tract, were investigated. KPEs were found to be more stable under acidic than basic environment, and elevated temperature induced their structural instability. The protective effect of KPEs on the chemical stability of curcumin was manifested when subjected to UV radiation as compared to other comparable formulations, such as bulk oil or Tween 80 stabilized emulsions (TEs). Meanwhile, the lipid oxidation rate was retarded in KPEs as compared to those of TEs. Due to hydrolysis of pepsin, KPEs could not survive through the gastric digestion process. After the intestinal digestion process, the extent of lipolysis of KPEs and the curcumin bioaccessibility fell between those of TEs and bulk oil. These results will fill the gap between the physicochemical properties of protein particle-based Pickering emulsions and their realistic applications in the oral delivery of functional food ingredients.

  10. Networks of recyclable material waste-picker's cooperatives: an alternative for the solid waste management in the city of Rio de Janeiro.

    Science.gov (United States)

    Tirado-Soto, Magda Martina; Zamberlan, Fabio Luiz

    2013-04-01

    The objective of this study is to discuss the role of networks formed of waste-picker cooperatives in ameliorating problems of final disposal of solid waste in the city of Rio de Janeiro, since the city's main landfill will soon have to close because of exhausted capacity. However, it is estimated that in the city of Rio de Janeiro there are around five thousand waste-pickers working in poor conditions, with lack of physical infrastructure and training, but contributing significantly by diverting solid waste from landfills. According to the Sustainable Development Indicators (IBGE, 2010a,b) in Brazil, recycling rates hover between 45% and 55%. In the municipality of Rio de Janeiro, only 1% of the waste produced is collected selectively by the government (COMLURB, 2010), demonstrating that recycling is mainly performed by waste-pickers. Furthermore, since the recycling market is an oligopsony that requires economies of scale to negotiate directly with industries, the idea of working in networks of cooperatives meets the demands for joint marketing of recyclable materials. Thus, this work presents a method for creating and structuring a network of recycling cooperatives, with prior training for working in networks, so that the expected synergies and joint efforts can lead to concrete results. We intend to demonstrate that it is first essential to strengthen the waste-pickers' cooperatives in terms of infrastructure, governance and training so that solid waste management can be environmentally, socially and economically sustainable in the city of Rio de Janeiro.

  11. Preparation of stable Pickering emulsions with short, medium and long chain fats and starch nanocrystals and their in vitro digestion properties

    Science.gov (United States)

    Pickering emulsions are receiving more attention as delivery systems in food and pharmaceuticals because they can be formulated with nontoxic food ingredients to form stable emulsions. In this study, 40-100 nm starch nanocrystals (SNCs) prepared from acid hydrolysis of waxy maize starches were used ...

  12. AG-NGS: a powerful and user-friendly computing application for the semi-automated preparation of next-generation sequencing libraries using open liquid handling platforms.

    Science.gov (United States)

    Callejas, Sergio; Álvarez, Rebeca; Benguria, Alberto; Dopazo, Ana

    2014-01-01

    Next-generation sequencing (NGS) is becoming one of the most widely used technologies in the field of genomics. Library preparation is one of the most critical, hands-on, and time-consuming steps in the NGS workflow. Each library must be prepared in an independent well, increasing the number of hours required for a sequencing run and the risk of human-introduced error. Automation of library preparation is the best option to avoid these problems. With this in mind, we have developed automatic genomics NGS (AG-NGS), a computing application that allows an open liquid handling platform to be transformed into a library preparation station without losing the potential of an open platform. Implementation of AG-NGS does not require programming experience, and the application has also been designed to minimize implementation costs. Automated library preparation with AG-NGS generated high-quality libraries from different samples, demonstrating its efficiency, and all quality control parameters fell within the range of optimal values.

  13. Optimizing information in Next-Generation-Sequencing (NGS) reads for improving de novo genome assembly.

    Science.gov (United States)

    Liu, Tsunglin; Tsai, Cheng-Hung; Lee, Wen-Bin; Chiang, Jung-Hsien

    2013-01-01

    Next-Generation-Sequencing is advantageous because of its much higher data throughput and much lower cost compared with the traditional Sanger method. However, NGS reads are shorter than Sanger reads, making de novo genome assembly very challenging. Because genome assembly is essential for all downstream biological studies, great efforts have been made to enhance the completeness of genome assembly, which requires the presence of long reads or long distance information. To improve de novo genome assembly, we develop a computational program, ARF-PE, to increase the length of Illumina reads. ARF-PE takes as input Illumina paired-end (PE) reads and recovers the original DNA fragments from which two ends the paired reads are obtained. On the PE data of four bacteria, ARF-PE recovered >87% of the DNA fragments and achieved >98% of perfect DNA fragment recovery. Using Velvet, SOAPdenovo, Newbler, and CABOG, we evaluated the benefits of recovered DNA fragments to genome assembly. For all four bacteria, the recovered DNA fragments increased the assembly contiguity. For example, the N50 lengths of the P. brasiliensis contigs assembled by SOAPdenovo and Newbler increased from 80,524 bp to 166,573 bp and from 80,655 bp to 193,388 bp, respectively. ARF-PE also increased assembly accuracy in many cases. On the PE data of two fungi and a human chromosome, ARF-PE doubled and tripled the N50 length. However, the assembly accuracies dropped, but still remained >91%. In general, ARF-PE can increase both assembly contiguity and accuracy for bacterial genomes. For complex eukaryotic genomes, ARF-PE is promising because it raises assembly contiguity. But future error correction is needed for ARF-PE to also increase the assembly accuracy. ARF-PE is freely available at http://140.116.235.124/~tliu/arf-pe/.

  14. Pickering乳液的制备和应用研究进展%Advance in the Investigations of the Preparation and Application of Pickering Emulsion

    Institute of Scientific and Technical Information of China (English)

    周君; 乔秀颖; 孙康

    2012-01-01

    Pickering emulsion is a new kind of emulsion stabilized by solid particles instead of traditional organic surfactants. Compared with the traditional emulsion, Pickering emulsion has the advantages of strong interfacial stability, reduced bubbles, regeneration, low toxicity and low cost, and possesses wide applicable prospects in the fields of cosmetic, food, medicine, petroleum, and the waste water disposal, so the investigations of Pickering emulsions attract great attentions of more and more researchers. In this paper, the features and advantages of Pickering emulsions over the surfactant stabilized emulsions were introduced. Furthermore,the advances in the preparation and application of Pickering emulsions were introduced.%Pickering乳液是一种由固体粒子代替传统有机表面活性剂稳定乳液体系的新型乳液。与传统乳液相比,Pickering乳液具有强界面稳定性、减少泡沫出现、可再生、低毒、低成本等优势,在化妆品、食品、制药、石油和废水处理等行业具有广阔的应用前景,受到越来越多研究者们的关注。本文综述了近年来Pickering乳液的研究进展,先介绍Pickering乳液相对于表面活性剂乳液的特色与优势,然后介绍Pickering乳液的制备研究进展,最后介绍Pickering乳液的应用研究进展。

  15. Comparison of targeted next-generation sequencing (NGS) and real-time PCR in the detection of EGFR, KRAS, and BRAF mutations on formalin-fixed, paraffin-embedded tumor material of non-small cell lung carcinoma-superiority of NGS.

    Science.gov (United States)

    Tuononen, Katja; Mäki-Nevala, Satu; Sarhadi, Virinder Kaur; Wirtanen, Aino; Rönty, Mikko; Salmenkivi, Kaisa; Andrews, Jenny M; Telaranta-Keerie, Aino I; Hannula, Sari; Lagström, Sonja; Ellonen, Pekka; Knuuttila, Aija; Knuutila, Sakari

    2013-05-01

    The development of tyrosine kinase inhibitor treatments has made it important to test cancer patients for clinically significant gene mutations that influence the benefit of treatment. Targeted next-generation sequencing (NGS) provides a promising method for diagnostic purposes by enabling the simultaneous detection of multiple mutations in various genes in a single test. The aim of our study was to screen EGFR, KRAS, and BRAF mutations by targeted NGS and commonly used real-time polymerase chain reaction (PCR) methods to evaluate the feasibility of targeted NGS for the detection of the mutations. Furthermore, we aimed to identify potential novel mutations by targeted NGS. We analyzed formalin-fixed, paraffin-embedded (FFPE) tumor tissue specimens from 81 non-small cell lung carcinoma patients. We observed a significant concordance (from 96.3 to 100%) of the EGFR, KRAS, and BRAF mutation detection results between targeted NGS and real-time PCR. Moreover, targeted NGS revealed seven nonsynonymous single-nucleotide variations and one insertion-deletion variation in EGFR not detectable by the real-time PCR methods. The potential clinical significance of these variants requires elucidation in future studies. Our results support the use of targeted NGS in the screening of EGFR, KRAS, and BRAF mutations in FFPE tissue material.

  16. 基于氧化淀粉的新型 Pickering 苯丙乳液表面施胶剂的合成%Preparation of the styrene acrylic emulsion surface sizing agent through oxidized starch-based Pickering emulsion method

    Institute of Scientific and Technical Information of China (English)

    张恒; 宋雪; 李素香; 孙嘉浩

    2016-01-01

    以苯乙烯、丙烯酸丁酯为单体,过硫酸铵为引发剂,氧化淀粉作固体粒子乳化剂,采用无皂乳液聚合的方法来制备 Pickering 苯丙聚合物乳液,考察了不同含量的氧化淀粉对乳液固含量、转化率、卡伯值以及稳定性的影响,并对制备的 Pickering 苯丙聚合物乳液进行了粒径、红外光谱表征,当氧化淀粉的含量为2%时,制备的Pickering 苯丙聚合物乳液转化率为96%,粒径为264.4 nm,卡伯值为71.4 g/m2,抗水性和稳定性较好.%Pickering emulsion was prepared using styrene and butyl acrylate as monomers,am-monium persulfate as initiator,oxidized starch as solid emulsifier,which adopts the method of soap-free emulsion polymerization.This study discusses the influence on latex solid content and conversion rate by different dosage of oxidized starch.At the same time,infrared spectra and particle size of the Pickering emulsion were obtained.When oxidation starch content was 2%, conversion rate was 96%,the particle size was 264.4 nm,and cobb value was 71.4 g/m2 ,the stability of Pickering emulsion is optimal.

  17. HCV genotyping from NGS short reads and its application in genotype detection from HCV mixed infected plasma.

    Science.gov (United States)

    Qiu, Ping; Stevens, Richard; Wei, Bo; Lahser, Fred; Howe, Anita Y M; Klappenbach, Joel A; Marton, Matthew J

    2015-01-01

    Genotyping of hepatitis C virus (HCV) plays an important role in the treatment of HCV. As new genotype-specific treatment options become available, it has become increasingly important to have accurate HCV genotype and subtype information to ensure that the most appropriate treatment regimen is selected. Most current genotyping methods are unable to detect mixed genotypes from two or more HCV infections. Next generation sequencing (NGS) allows for rapid and low cost mass sequencing of viral genomes and provides an opportunity to probe the viral population from a single host. In this paper, the possibility of using short NGS reads for direct HCV genotyping without genome assembly was evaluated. We surveyed the publicly-available genetic content of three HCV drug target regions (NS3, NS5A, NS5B) in terms of whether these genes contained genotype-specific regions that could predict genotype. Six genotypes and 38 subtypes were included in this study. An automated phylogenetic analysis based HCV genotyping method was implemented and used to assess different HCV target gene regions. Candidate regions of 250-bp each were found for all three genes that have enough genetic information to predict HCV genotypes/subtypes. Validation using public datasets shows 100% genotyping accuracy. To test whether these 250-bp regions were sufficient to identify mixed genotypes, we developed a random primer-based method to sequence HCV plasma samples containing mixtures of two HCV genotypes in different ratios. We were able to determine the genotypes without ambiguity and to quantify the ratio of the abundances of the mixed genotypes in the samples. These data provide a proof-of-concept that this random primed, NGS-based short-read genotyping approach does not need prior information about the viral population and is capable of detecting mixed viral infection.

  18. HCV genotyping from NGS short reads and its application in genotype detection from HCV mixed infected plasma.

    Directory of Open Access Journals (Sweden)

    Ping Qiu

    Full Text Available Genotyping of hepatitis C virus (HCV plays an important role in the treatment of HCV. As new genotype-specific treatment options become available, it has become increasingly important to have accurate HCV genotype and subtype information to ensure that the most appropriate treatment regimen is selected. Most current genotyping methods are unable to detect mixed genotypes from two or more HCV infections. Next generation sequencing (NGS allows for rapid and low cost mass sequencing of viral genomes and provides an opportunity to probe the viral population from a single host. In this paper, the possibility of using short NGS reads for direct HCV genotyping without genome assembly was evaluated. We surveyed the publicly-available genetic content of three HCV drug target regions (NS3, NS5A, NS5B in terms of whether these genes contained genotype-specific regions that could predict genotype. Six genotypes and 38 subtypes were included in this study. An automated phylogenetic analysis based HCV genotyping method was implemented and used to assess different HCV target gene regions. Candidate regions of 250-bp each were found for all three genes that have enough genetic information to predict HCV genotypes/subtypes. Validation using public datasets shows 100% genotyping accuracy. To test whether these 250-bp regions were sufficient to identify mixed genotypes, we developed a random primer-based method to sequence HCV plasma samples containing mixtures of two HCV genotypes in different ratios. We were able to determine the genotypes without ambiguity and to quantify the ratio of the abundances of the mixed genotypes in the samples. These data provide a proof-of-concept that this random primed, NGS-based short-read genotyping approach does not need prior information about the viral population and is capable of detecting mixed viral infection.

  19. A techno-economic assessment of primary heat transport system decontamination in support of decommissioning Pickering Nuclear Generating Stations

    Energy Technology Data Exchange (ETDEWEB)

    Husain, A.; Krasznai, J. [Kinectrics, Inc., Analytical and Waste Services Dept., Toronto, Ontario, (Canada); Vijay, R. [Ontario Power Generation, Nuclear Decommissioning Organization, Toronto, Ontario, (Canada)

    2013-07-01

    The operating reactor units at Pickering are expected to be permanently shut down by approximately 2020 (this nominal date is for planning purposes only) and then decommissioned. OPG has adopted the 'Deferred Dismantling' strategy for decommissioning its nuclear plants. In contrast with prompt dismantling, radioactive decay leads to reduced dose expenditure during deferred dismantling. As part of the decommissioning strategy, chemical decontamination of the primary heat transport (PHT) system may be undertaken prior to Safe Storage. Decommissioning costs depend significantly on the chosen deferral period. The overall objective of the present work was to contribute to the optimization of the existing decommissioning plan by assessing the benefits of decontamination. Accordingly, an overall cost-benefit analysis for PHT system decontamination was performed. Details are presented in this paper. (author)

  20. One-pot fabrication of rattle-like capsules with multicores by pickering-based polymerization with nanoparticle nucleation.

    Science.gov (United States)

    Zou, Shengwen; Hu, Yang; Wang, Chaoyang

    2014-08-01

    Rattle-like polymer capsules with multicores in one shell are facilely fabricated by oil-in-water Pickering emulsion polymerization for the first time. The oil phase contains hydrophobic silica nanoparticles dispersed in polymerizable monomer, styrene, and unpolymerizable solvent, hexadecane. The multicore rattle-like capsules are facilely produced after the polymerization of monomers in the oil droplets. The key point of this one-pot method lies in the nucleation of hydrophobic silica and the phase separation between the resulting polystyrene and hexadecane. The influences of the contents of silica, hexadecane, cross-linker, and stabilizer on the structure and morphology of rattle-like capsules are systematically investigated. Moreover, functionalization of the rattle-like capsules can be developed easily by varying hydrophobic nucleation nanoparticles in the oil phase. This work opens up a new route to fabricate multilevel capsules or spheres. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Hollow microsphere with mesoporous shell by Pickering emulsion polymerization as a potential colloidal collector for organic contaminants in water.

    Science.gov (United States)

    Guan, Yinyan; Meng, Xiaohui; Qiu, Dong

    2014-04-08

    Submicrometer hollow microspheres with mesoporous shells were prepared by a simple one-pot strategy. Colloidal silica particles were used as a particle stabilizer to emulsify the oil phase, which was composed of a polymerizable silicon monomer (TPM) and an inert organic solvent (PEA). The low interfacial tension between colloidal silica particles and TPM helped to form a Pickering emulsion with small droplet sizes. After the polymerization of TPM, the more hydrophobic PEA formed a liquid core, leading to a hollow structure after its removal by evaporation. BET results indicated that the shell of a hollow particle was mesoporous with a specific surface area over 400 m(2)·g(-1). With PEA as the core and silica as the shell, each resultant hollow particle had a hydrophobic cavity and an amphiphilic surface, thus serving as a good colloidal collector for hydrophobic contaminants in water.

  2. Introduction of the Python script STRinNGS for analysis of STR regions in FASTQ or BAM files and expansion of the Danish STR sequence database to 11 STRs

    DEFF Research Database (Denmark)

    Friis, Susanne L; Buchard, Anders; Rockenbauer, Eszter

    2016-01-01

    This work introduces the in-house developed Python application STRinNGS for analysis of STR sequence elements in BAM or FASTQ files. STRinNGS identifies sequence reads with STR loci by their flanking sequences, it analyses the STR sequence and the flanking regions, and generates a report with the......This work introduces the in-house developed Python application STRinNGS for analysis of STR sequence elements in BAM or FASTQ files. STRinNGS identifies sequence reads with STR loci by their flanking sequences, it analyses the STR sequence and the flanking regions, and generates a report...

  3. Using GC-FID to Quantify the Removal of 4-sec-Butylphenol from NGS Solvent by NaOH

    Energy Technology Data Exchange (ETDEWEB)

    Sloop, Jr., Frederick V. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Moyer, Bruce A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2014-12-01

    A caustic wash of the solvent used in the Next-Generation Caustic-Side Solvent Extraction (NG-CSSX) process was found to remove the modifier breakdown product 4-sec-butylphenol (SBP) with varying efficiency depending on the aqueous NaOH concentration. Recent efforts at ORNL have aimed at characterizing the flowsheet chemistry and reducing the technical uncertainties of the NG-CSSX process. One technical uncertainty has been the efficacy of caustic washing of the solvent for the removal of lipophilic anions, in particular, the efficient removal of SBP, an important degradation product of the solvent modifier, Cs-7SB. In order to make this determination, it was necessary to develop a sensitive and reliable analytical technique for the detection and quantitation of SBP. This report recounts the development of a GC-FID-based (Gas Chromatography Flame Ionization Detection) technique for analyzing SBP and the utilization of the technique to subsequently confirm the ability of the caustic wash to efficiently remove SBP from the Next Generation Solvent (NGS) used in NG-CSSX. In particular, the developed technique was used to monitor the amount of SBP removed from a simple solvent and the full NGS by contact with sodium hydroxide wash solutions over a range of concentrations. The results show that caustic washing removes SBP with effectively the same efficiency as it did in the original Caustic-Side Solvent Extraction (CSSX) process.

  4. Preparation of polystyrene/SiO2 microsphere via Pickering emulsion polymerization: Synergistic effect of SiO2 concentrations and initiator sorts

    Science.gov (United States)

    Zhou, Haiou; Shi, Tiejun; Zhou, Xun

    2013-02-01

    In this paper, polystyrene (PS)/SiO2 microspheres were successfully prepared via Pickering emulsion polymerization stabilized solely by ethacryloxypropyltrimethoxysilane (MPTMS) modified SiO2 nanoparticles. The formation mechanisms of PS/SiO2 microspheres with different morphology were investigated under various Pickering emulsion polymerization conditions. The results showed that SiO2 concentrations and initiator sorts would synergistically impact on the morphology of products corresponding to distinct formation mechanisms. When SiO2 concentrations was low and water-solute initiator potassium persulfate (KPS) was used, aqueous nucleation was dominant, which was deduced to the formation of dispersive microspheres sparsely anchored by SiO2 particles. When SiO2 concentrations was increased and oil-solute initiator azobisisobutyronitrile (AIBN) was applied, nucleation in oil phase prevailed which lead to the formation of microspheres densely packed by SiO2 particles.

  5. 4MSB-300型背负式采棉机的改进%Improvement of 4MSB-300 backpack cotton picker

    Institute of Scientific and Technical Information of China (English)

    李红斌; 郑炫; 何艳红

    2015-01-01

    针对目前背负式采棉机存在的连接方式不合理,造成田间转弯困难,卸棉箱的开门机构需要人工进行开启、锁紧,浪费劳力等问题,对其结构进行改进,并进行了试验,达到改进效果.%The present type of backpack cotton picker has many defects and existing problems such as unreasonable link mode and so on, these defects result in difficulties in turning around in field and waste of labour force when opening and locking the opening mechanism of cotton unloading trunk. Aim at these problems,researchers have improved the structure of these mechinery and carried on related experiments and tests, the results indicted that, through the improvement, each index and function of the backpack cotton picker have both met the requirments.

  6. NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data

    Science.gov (United States)

    Katta, Mohan A. V. S. K.; Khan, Aamir W.; Doddamani, Dadakhalandar; Thudi, Mahendar; Varshney, Rajeev K.

    2015-01-01

    Rapid popularity and adaptation of next generation sequencing (NGS) approaches have generated huge volumes of data. High throughput platforms like Illumina HiSeq produce terabytes of raw data that requires quick processing. Quality control of the data is an important component prior to the downstream analyses. To address these issues, we have developed a quality control pipeline, NGS-QCbox that scales up to process hundreds or thousands of samples. Raspberry is an in-house tool, developed in C language utilizing HTSlib (v1.2.1) (http://htslib.org), for computing read/base level statistics. It can be used as stand-alone application and can process both compressed and uncompressed FASTQ format files. NGS-QCbox integrates Raspberry with other open-source tools for alignment (Bowtie2), SNP calling (SAMtools) and other utilities (bedtools) towards analyzing raw NGS data at higher efficiency and in high-throughput manner. The pipeline implements batch processing of jobs using Bpipe (https://github.com/ssadedin/bpipe) in parallel and internally, a fine grained task parallelization utilizing OpenMP. It reports read and base statistics along with genome coverage and variants in a user friendly format. The pipeline developed presents a simple menu driven interface and can be used in either quick or complete mode. In addition, the pipeline in quick mode outperforms in speed against other similar existing QC pipeline/tools. The NGS-QCbox pipeline, Raspberry tool and associated scripts are made available at the URL https://github.com/CEG-ICRISAT/NGS-QCbox and https://github.com/CEG-ICRISAT/Raspberry for rapid quality control analysis of large-scale next generation sequencing (Illumina) data. PMID:26460497

  7. NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data.

    Science.gov (United States)

    Katta, Mohan A V S K; Khan, Aamir W; Doddamani, Dadakhalandar; Thudi, Mahendar; Varshney, Rajeev K

    2015-01-01

    Rapid popularity and adaptation of next generation sequencing (NGS) approaches have generated huge volumes of data. High throughput platforms like Illumina HiSeq produce terabytes of raw data that requires quick processing. Quality control of the data is an important component prior to the downstream analyses. To address these issues, we have developed a quality control pipeline, NGS-QCbox that scales up to process hundreds or thousands of samples. Raspberry is an in-house tool, developed in C language utilizing HTSlib (v1.2.1) (http://htslib.org), for computing read/base level statistics. It can be used as stand-alone application and can process both compressed and uncompressed FASTQ format files. NGS-QCbox integrates Raspberry with other open-source tools for alignment (Bowtie2), SNP calling (SAMtools) and other utilities (bedtools) towards analyzing raw NGS data at higher efficiency and in high-throughput manner. The pipeline implements batch processing of jobs using Bpipe (https://github.com/ssadedin/bpipe) in parallel and internally, a fine grained task parallelization utilizing OpenMP. It reports read and base statistics along with genome coverage and variants in a user friendly format. The pipeline developed presents a simple menu driven interface and can be used in either quick or complete mode. In addition, the pipeline in quick mode outperforms in speed against other similar existing QC pipeline/tools. The NGS-QCbox pipeline, Raspberry tool and associated scripts are made available at the URL https://github.com/CEG-ICRISAT/NGS-QCbox and https://github.com/CEG-ICRISAT/Raspberry for rapid quality control analysis of large-scale next generation sequencing (Illumina) data.

  8. NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina Data.

    Directory of Open Access Journals (Sweden)

    Mohan A V S K Katta

    Full Text Available Rapid popularity and adaptation of next generation sequencing (NGS approaches have generated huge volumes of data. High throughput platforms like Illumina HiSeq produce terabytes of raw data that requires quick processing. Quality control of the data is an important component prior to the downstream analyses. To address these issues, we have developed a quality control pipeline, NGS-QCbox that scales up to process hundreds or thousands of samples. Raspberry is an in-house tool, developed in C language utilizing HTSlib (v1.2.1 (http://htslib.org, for computing read/base level statistics. It can be used as stand-alone application and can process both compressed and uncompressed FASTQ format files. NGS-QCbox integrates Raspberry with other open-source tools for alignment (Bowtie2, SNP calling (SAMtools and other utilities (bedtools towards analyzing raw NGS data at higher efficiency and in high-throughput manner. The pipeline implements batch processing of jobs using Bpipe (https://github.com/ssadedin/bpipe in parallel and internally, a fine grained task parallelization utilizing OpenMP. It reports read and base statistics along with genome coverage and variants in a user friendly format. The pipeline developed presents a simple menu driven interface and can be used in either quick or complete mode. In addition, the pipeline in quick mode outperforms in speed against other similar existing QC pipeline/tools. The NGS-QCbox pipeline, Raspberry tool and associated scripts are made available at the URL https://github.com/CEG-ICRISAT/NGS-QCbox and https://github.com/CEG-ICRISAT/Raspberry for rapid quality control analysis of large-scale next generation sequencing (Illumina data.

  9. Grid平台上的NGS编译技术%The Compiler Technology of NGS on the Grid

    Institute of Scientific and Technical Information of China (English)

    丛杨; 王雷; 朱凯佳; 刘又诚

    2003-01-01

    随着网络技术的发展,在异构平台上使用共同的计算和信息资源将很快成为可能.Grid(网格)就是这样一种提供资源共享的新兴平台,而在其之上的下一代软件程序(NGS)则对编译器提出了新的挑战[1].未来Grid平台上的编译系统将是能够进行动态编译和优化,根据实时系统以及网络的性能不断进行自我调整的软件模型,同时它还能为具有自适应性的应用程序提供编译支持.

  10. NGS metabarcoding proves successful for quantitative assessment of symbiont abundance: the case of feather mites on birds.

    Science.gov (United States)

    Diaz-Real, J; Serrano, D; Piriz, A; Jovani, R

    2015-10-01

    Understanding the ecological function of species and the structure of communities is crucial in the study of ecological interactions among species. For this purpose, not only the occurrence of particular species but also their abundance in ecological communities is required. However, abundance quantification of species through morphological characters is often difficult or time/money consuming when dealing with elusive or small taxa. Here we tested the use of next-generation sequencing (NGS) for abundance estimation of two species of feather mites (Proctophyllodes stylifer and Pteronyssoides parinus) under five proportions (16:1, 16:4, 16:16, 16:64, and 16:256 mites) against a mock community composed by Proctophyllodes clavatus and Proctophyllodes sylviae. In all mixtures, we retrieved sequence reads from all species. We found a strong linear relationship between 454 reads and the real proportion of individuals in the mixture for both focal species. The slope for Pr. stylifer was close to one (0.904), and the intercept close to zero (-0.007), thus showing an almost perfect correspondence between real and estimated proportions. The slope for Pt. parinus was 0.351 and the intercept 0.307, showing that while the estimated proportion increased linearly relative to real proportions of individuals in the samples, proportions were overestimated at low real proportions and underestimated at larger ones. Additionally, pyrosequencing replicates from each DNA extraction were highly repeatable (R = 0.920 and 0.972, respectively), showing that the quantification method is highly consistent given a DNA extract. Our study suggests that NGS is a promising tool for abundance estimation of feather mites' communities in birds.

  11. ICO amplicon NGS data analysis: a Web tool for variant detection in common high-risk hereditary cancer genes analyzed by amplicon GS Junior next-generation sequencing.

    Science.gov (United States)

    Lopez-Doriga, Adriana; Feliubadaló, Lídia; Menéndez, Mireia; Lopez-Doriga, Sergio; Morón-Duran, Francisco D; del Valle, Jesús; Tornero, Eva; Montes, Eva; Cuesta, Raquel; Campos, Olga; Gómez, Carolina; Pineda, Marta; González, Sara; Moreno, Victor; Capellá, Gabriel; Lázaro, Conxi

    2014-03-01

    Next-generation sequencing (NGS) has revolutionized genomic research and is set to have a major impact on genetic diagnostics thanks to the advent of benchtop sequencers and flexible kits for targeted libraries. Among the main hurdles in NGS are the difficulty of performing bioinformatic analysis of the huge volume of data generated and the high number of false positive calls that could be obtained, depending on the NGS technology and the analysis pipeline. Here, we present the development of a free and user-friendly Web data analysis tool that detects and filters sequence variants, provides coverage information, and allows the user to customize some basic parameters. The tool has been developed to provide accurate genetic analysis of targeted sequencing of common high-risk hereditary cancer genes using amplicon libraries run in a GS Junior System. The Web resource is linked to our own mutation database, to assist in the clinical classification of identified variants. We believe that this tool will greatly facilitate the use of the NGS approach in routine laboratories.

  12. A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).

    Science.gov (United States)

    Wu, Tsung-Jung; Shamsaddini, Amirhossein; Pan, Yang; Smith, Krista; Crichton, Daniel J; Simonyan, Vahan; Mazumder, Raja

    2014-01-01

    Years of sequence feature curation by UniProtKB/Swiss-Prot, PIR-PSD, NCBI-CDD, RefSeq and other database biocurators has led to a rich repository of information on functional sites of genes and proteins. This information along with variation-related annotation can be used to scan human short sequence reads from next-generation sequencing (NGS) pipelines for presence of non-synonymous single-nucleotide variations (nsSNVs) that affect functional sites. This and similar workflows are becoming more important because thousands of NGS data sets are being made available through projects such as The Cancer Genome Atlas (TCGA), and researchers want to evaluate their biomarkers in genomic data. BioMuta, an integrated sequence feature database, provides a framework for automated and manual curation and integration of cancer-related sequence features so that they can be used in NGS analysis pipelines. Sequence feature information in BioMuta is collected from the Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, UniProtKB and through biocuration of information available from publications. Additionally, nsSNVs identified through automated analysis of NGS data from TCGA are also included in the database. Because of the petabytes of data and information present in NGS primary repositories, a platform HIVE (High-performance Integrated Virtual Environment) for storing, analyzing, computing and curating NGS data and associated metadata has been developed. Using HIVE, 31 979 nsSNVs were identified in TCGA-derived NGS data from breast cancer patients. All variations identified through this process are stored in a Curated Short Read archive, and the nsSNVs from the tumor samples are included in BioMuta. Currently, BioMuta has 26 cancer types with 13 896 small-scale and 308 986 large-scale study-derived variations. Integration of variation data allows identifications of novel or common nsSNVs that can be prioritized in validation studies. Database URL: BioMuta: http

  13. Points to consider in the clinical use of NGS panels for mitochondrial disease: an analysis of gene inclusion and consent forms.

    Science.gov (United States)

    Platt, Julia; Cox, Rachel; Enns, Gregory M

    2014-08-01

    Mitochondrial next generation sequencing (NGS) panels offer single-step analysis of the numerous nuclear genes involved in the structure, function, and maintenance of mitochondria. However, the complexities of mitochondrial biology and genetics raise points for consideration in clinical use of these tests. To understand the current status of mitochondrial genetic testing, we assessed the gene offerings and consent forms of mitochondrial NGS panels available from seven US-based clinical laboratories. The NGS panels varied markedly in number of genes (101-1204 genes), and the proportion of genes causing "classic" mitochondrial diseases and their phenocopies ranged widely between labs (18 %-94 % of panel contents). All panels included genes not associated with classic mitochondrial diseases (6 %-28 % of panel contents), including genes causing adult-onset neurodegenerative disorders, cancer predisposition, and other genetic syndromes or inborn errors of metabolism. Five of the panels included genes that are not listed in OMIM to be associated with a disease phenotype (5 %-49 % of panel contents). None of the consent documents reviewed had options for patient preference regarding receipt of incidental findings. These findings raise points of discussion applicable to mitochondrial diagnostics, but also to the larger arenas of exome and genome sequencing, including the need to consider the boundaries between clinical and research testing, the necessity of appropriate informed consent, and the responsibilities of clinical laboratories and clinicians. Based on these findings, we recommend careful evaluation by laboratories of the genes offered on NGS panels, clear communication of the predicted phenotypes, and revised consent forms to allow patients to make choices about receiving incidental findings. We hope that our analysis and recommendations will help to maximize the considerable clinical utility of NGS panels for the diagnosis of mitochondrial disease.

  14. Switchable Pickering Emulsions Stabilized by Awakened TiO2 Nanoparticle Emulsifiers Using UV/Dark Actuation.

    Science.gov (United States)

    Zhang, Qing; Bai, Rui-Xue; Guo, Ting; Meng, Tao

    2015-08-26

    In this work, switchable Pickering emulsions that utilize UV/dark manipulation employ a type of smart TiO2 nanoparticle as emulsifiers. The emulsifiers can be awakened when needed via UV-induced degradation of grafted silanes on TiO2 nanoparticles. By tuning the surface wettability of TiO2 nanoparticles in situ via UV/dark actuation, emulsions stabilized by the nanoparticles can be reversibly switched between the water-in-oil (W/O) type and oil-in-water (O/W) type for several cycles. Due to the convertible wettability, the smart nanoparticle emulsifiers can be settled in either the oil phase or the water phase as desired during phase separation, making it convenient for recycling. The present work provides a facile and noninvasive method to freely manipulate the formation, breakage, and switching of the emulsion; this method has promising potential as a powerful technique for use in energy-efficient and environmentally friendly industries.

  15. Comparison of Dijkstra's algorithm and dynamic programming method in finding shortest path for order picker in a warehouse

    Science.gov (United States)

    Nordin, Noraimi Azlin Mohd; Omar, Mohd; Sharif, S. Sarifah Radiah

    2017-04-01

    Companies are looking forward to improve their productivity within their warehouse operations and distribution centres. In a typical warehouse operation, order picking contributes more than half percentage of the operating costs. Order picking is a benchmark in measuring the performance and productivity improvement of any warehouse management. Solving order picking problem is crucial in reducing response time and waiting time of a customer in receiving his demands. To reduce the response time, proper routing for picking orders is vital. Moreover, in production line, it is vital to always make sure the supplies arrive on time. Hence, a sample routing network will be applied on EP Manufacturing Berhad (EPMB) as a case study. The Dijkstra's algorithm and Dynamic Programming method are applied to find the shortest distance for an order picker in order picking. The results show that the Dynamic programming method is a simple yet competent approach in finding the shortest distance to pick an order that is applicable in a warehouse within a short time period.

  16. Life Cycle Cost Dynamic Software Design of Cotton Picker%采棉机全生命周期成本动态软件设计

    Institute of Scientific and Technical Information of China (English)

    雷福祥; 陈晓川; 王伟; 许晓东

    2014-01-01

    The fundamental way out for agriculture lies in mechanization. This is the practical needs of high efficiency which is sought after by people. Therefore, The wide application of cotton pickers frees man from the labour of cotton production. But because foreign machine maintenance costs and its price are high,the piched cotton cost is high too,while the core technology of domestic cotton picker is not up to standard, its recovery cost and the equipment failure rate are high. This paper uses Matlab software to establish the simulation software for the cost estimation of the cotton picker. A new method is provided for the cotton cost estimation. It can be used to Predict the price of the machine pick up cotton.%农业的根本出路在于机械化,也是人们追求效率、提高效益的现实需要。因此兵团棉花迫切需要摆脱生产量对劳力数量的依存关系,全面推广采棉机械化势在必行。由于国外机型维护成本高、价格高,而国产采棉机的核心技术没有过关、采收成本过高、设备故障率太高导致机采棉成本居高不下。所以利用Matlab软件建立了机采棉成本动态仿真软件,为机采棉成本估算提供了一种方法。预测了机采棉成本的价格走势。

  17. Catador de material reciclável: uma profissão para além da sobrevivência? Recycled garbage pickers: a profession beyond survival?

    Directory of Open Access Journals (Sweden)

    Luiza Ferreira Rezende de Medeiros

    2006-08-01

    Full Text Available O artigo apresenta resultados de uma pesquisa que objetivou investigar as relações de trabalho entre catadores de materiais recicláveis e organizações de reciclagem dos materiais coletados. Os catadores atuam no município de Goiânia. A reciclagem de lixo urbano figura como atividade emergente após movimentos ambientalistas e de preservação ambiental. Embora gere vantagens ambientais indiscutíveis, sobressaem os aspectos econômicos. A catação de materiais recicláveis constitui, para muitos trabalhadores, única forma de garantir sobrevivência e possibilidade de inclusão num mercado de trabalho excludente. Essa pesquisa investigou como os catadores percebem suas relações de trabalho, as condições em que desempenham suas funções e as práticas do trabalho em cooperativas de reciclagem. Utilizou-se entrevistas com 10 catadores, que foram tratadas pela análise de conteúdo. Os dados revelaram relações de trabalho precárias e informais entre catadores e organizações de reciclagem. Os trabalhadores são expostos à periculosidade, vítimas de preconceitos e estigmas e excluídos de alguns ambientes sociais.The article presents results of a research that investigated the work relations between recycled garbage pickers working in Goiânia and organizations that recycle such materials. The recycling of urban garbage figure as an emergent activity after environmentalist movements and environment preservation. Although it generates unquestionable environmental advantages, the economic benefits excel. Collecting garbage, to many workers, is the only way of guaranteing survival and inclusion in the excluding market. This research investigated the way garbage pickers understand their work relations, under what conditions perform their functions, and the work practices in garbage picking cooperatives. Ten garbage pickers were interviewed and data analyzed by content analysis. Data showed precarious and informal work relations

  18. Photometric calibration of NGS/POSS and ESO/SRC plates using the NOAO PDS measuring engine. I - Stellar photometry

    Science.gov (United States)

    Cutri, Roc M.; Low, Frank J.; Marvel, Kevin B.

    1992-01-01

    The PDS/Monet measuring engine at the National Optical Astronomy Observatory was used to obtain photometry of nearly 10,000 stars on the NGS/POSS and 2000 stars on the ESO/SRC Survey glass plates. These measurements have been used to show that global transformation functions exist that allow calibration of stellar photometry from any blue or red plate to equivalent Johnson B and Cousins R photoelectric magnitudes. The four transformation functions appropriate for the POSS O and E and ESO/SRC J and R plates were characterized, and it was found that, within the measurement uncertainties, they vary from plate to plate only by photometric zero-point offsets. A method is described to correct for the zero-point shifts and to obtain calibrated B and R photometry of stellar sources to an average accuracy of 0.3-0.4 mag within the range R between values of 8 and 19.5 for red plates in both surveys, B between values of 9 and 20.5 on POSS blue plates, and B between values of 10 and 20.5 on ESO/SRC blue plates. This calibration procedure makes it possible to obtain rapid photometry of very large numbers of stellar sources.

  19. Fast admixture analysis and population tree estimation for SNP and NGS data

    DEFF Research Database (Denmark)

    Cheng, Jade Yu; Mailund, Thomas; Nielsen, Rasmus

    2017-01-01

    analyses of real data we show that the new method finds solutions with higher likelihoods than the state-of-the-art method in the same computational time. The optimization algorithm is also applicable to models based on genotype likelihoods, that can account for the uncertainty in genotype...

  20. IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST.

    Science.gov (United States)

    Aouinti, Safa; Giudicelli, Véronique; Duroux, Patrice; Malouche, Dhafer; Kossida, Sofia; Lefranc, Marie-Paule

    2016-01-01

    There is a huge need for standardized analysis and statistical procedures in order to compare the complex immune repertoires of antigen receptors immunoglobulins (IG) and T cell receptors (TR) obtained by next generation sequencing (NGS). NGS technologies generate millions of nucleotide sequences and have led to the development of new tools. The IMGT/HighV-QUEST, available since 2010, is the first global web portal for the analysis of IG and TR high throughput sequences. IMGT/HighV-QUEST provides standardized outputs for the characterization of the "IMGT clonotype (AA)" (AA for amino acids) and their comparison in up to one million sequences. Standardized statistical procedures for "IMGT clonotype (AA)" diversity or expression comparisons have recently been described, however, no tool was yet available. IMGT/StatClonotype, a new IMGT(®) tool, evaluates and visualizes statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per V (variable), D (diversity), and J (joining) gene of a given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. IMGT/StatClonotype tool is incorporated in the R package "IMGTStatClonotype," with a user-friendly interface. IMGT/StatClonotype is downloadable at IMGT(®) for users to evaluate pairwise comparison of IG and TR NGS statistical output from IMGT/HighV-QUEST and to visualize, on their web browser, the statistical significance of IMGT clonotype (AA) diversity or expression, per gene, the comparative analysis of CDR-IMGT and the V-D-J associations, in immunoprofiles from normal or pathological immune responses.

  1. IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST

    Science.gov (United States)

    Aouinti, Safa; Giudicelli, Véronique; Duroux, Patrice; Malouche, Dhafer; Kossida, Sofia; Lefranc, Marie-Paule

    2016-01-01

    There is a huge need for standardized analysis and statistical procedures in order to compare the complex immune repertoires of antigen receptors immunoglobulins (IG) and T cell receptors (TR) obtained by next generation sequencing (NGS). NGS technologies generate millions of nucleotide sequences and have led to the development of new tools. The IMGT/HighV-QUEST, available since 2010, is the first global web portal for the analysis of IG and TR high throughput sequences. IMGT/HighV-QUEST provides standardized outputs for the characterization of the “IMGT clonotype (AA)” (AA for amino acids) and their comparison in up to one million sequences. Standardized statistical procedures for “IMGT clonotype (AA)” diversity or expression comparisons have recently been described, however, no tool was yet available. IMGT/StatClonotype, a new IMGT® tool, evaluates and visualizes statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per V (variable), D (diversity), and J (joining) gene of a given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. IMGT/StatClonotype tool is incorporated in the R package “IMGTStatClonotype,” with a user-friendly interface. IMGT/StatClonotype is downloadable at IMGT®1 for users to evaluate pairwise comparison of IG and TR NGS statistical output from IMGT/HighV-QUEST and to visualize, on their web browser, the statistical significance of IMGT clonotype (AA) diversity or expression, per gene, the comparative analysis of CDR-IMGT and the V–D–J associations, in immunoprofiles from normal or pathological immune responses. PMID:27667992

  2. FGFR2 mutation in a patient without typical features of Pfeiffer syndrome--The emerging role of combined NGS and phenotype based strategies.

    Science.gov (United States)

    Flöttmann, Ricarda; Knaus, Alexej; Zemojtel, Tomasz; Robinson, Peter N; Mundlos, Stefan; Horn, Denise; Spielmann, Malte

    2015-08-01

    Pfeiffer syndrome (MIM: #101600) is a rare autosomal dominant disorder classically characterized by limb and craniofacial anomalies. It is caused by heterozygous mutations in the fibroblast growth factor receptors types 1 and 2 (FGFR1 and FGFR2). We applied a next generation sequencing (NGS) panel approach comprising all 2877 genes currently known to be causative for one or more Mendelian diseases combined with the phenotype based computational tool PhenIX (Phenotypic Interpretation of eXomes). We report on a patient presenting with multiple anomalies of hands and feet including brachydactyly and symphalangism. No clinical diagnosis could be established based on the clinical findings and testing of several genes associated with brachydactyly and symphalangism failed to identify mutations. Via next generation sequencing (NGS) panel approach we then identified a novel de novo missense FGFR2 mutation affecting an amino acid reported to be mutated in Pfeiffer syndrome. Since our patient shows typical radiological findings of Pfeiffer syndrome in hands and feet but at the same time lacks several characteristic features such as clinical signs of craniosynostosis and prominent eyes we suggest introducing the term "FGFR2 associated phenotypes" for similar cases. Our results highlight the emerging role of combined NGS and phenotype based bioinformatics strategies to establish clinical diagnoses.

  3. Neurofibromatosis type 1 molecular diagnosis: what can NGS do for you when you have a large gene with loss of function mutations?

    Science.gov (United States)

    Pasmant, Eric; Parfait, Béatrice; Luscan, Armelle; Goussard, Philippe; Briand-Suleau, Audrey; Laurendeau, Ingrid; Fouveaut, Corinne; Leroy, Chrystel; Montadert, Annelore; Wolkenstein, Pierre; Vidaud, Michel; Vidaud, Dominique

    2015-05-01

    Molecular diagnosis of neurofibromatosis type 1 (NF1) is challenging owing to the large size of the tumour suppressor gene NF1, and the lack of mutation hotspots. A somatic alteration of the wild-type NF1 allele is observed in NF1-associated tumours. Genetic heterogeneity in NF1 was confirmed in patients with SPRED1 mutations. Here, we present a targeted next-generation sequencing (NGS) of NF1 and SPRED1 using a multiplex PCR approach (230 amplicons of ∼150 bp) on a PGM sequencer. The chip capacity allowed mixing 48 bar-coded samples in a 4-day workflow. We validated the NGS approach by retrospectively testing 30 NF1-mutated samples, and then prospectively analysed 279 patients in routine diagnosis. On average, 98.5% of all targeted bases were covered by at least 20X and 96% by at least 100X. An NF1 or SPRED1 alteration was found in 246/279 (88%) and 10/279 (4%) patients, respectively. Genotyping throughput was increased over 10 times, as compared with Sanger, with ∼90[euro ] for consumables per sample. Interestingly, our targeted NGS approach also provided quantitative information based on sequencing depth allowing identification of multiexons deletion or duplication. We then addressed the NF1 somatic mutation detection sensitivity in mosaic NF1 patients and tumours.

  4. Neurofibromatosis type 1 molecular diagnosis: what can NGS do for you when you have a large gene with loss of function mutations?

    Science.gov (United States)

    Pasmant, Eric; Parfait, Béatrice; Luscan, Armelle; Goussard, Philippe; Briand-Suleau, Audrey; Laurendeau, Ingrid; Fouveaut, Corinne; Leroy, Chrystel; Montadert, Annelore; Wolkenstein, Pierre; Vidaud, Michel; Vidaud, Dominique

    2015-01-01

    Molecular diagnosis of neurofibromatosis type 1 (NF1) is challenging owing to the large size of the tumour suppressor gene NF1, and the lack of mutation hotspots. A somatic alteration of the wild-type NF1 allele is observed in NF1-associated tumours. Genetic heterogeneity in NF1 was confirmed in patients with SPRED1 mutations. Here, we present a targeted next-generation sequencing (NGS) of NF1 and SPRED1 using a multiplex PCR approach (230 amplicons of ∼150 bp) on a PGM sequencer. The chip capacity allowed mixing 48 bar-coded samples in a 4-day workflow. We validated the NGS approach by retrospectively testing 30 NF1-mutated samples, and then prospectively analysed 279 patients in routine diagnosis. On average, 98.5% of all targeted bases were covered by at least 20X and 96% by at least 100X. An NF1 or SPRED1 alteration was found in 246/279 (88%) and 10/279 (4%) patients, respectively. Genotyping throughput was increased over 10 times, as compared with Sanger, with ∼90€ for consumables per sample. Interestingly, our targeted NGS approach also provided quantitative information based on sequencing depth allowing identification of multiexons deletion or duplication. We then addressed the NF1 somatic mutation detection sensitivity in mosaic NF1 patients and tumours. PMID:25074460

  5. Two-step sequential cross-linking of sugar beet pectin for transforming zein nanoparticle-based Pickering emulsions to emulgels.

    Science.gov (United States)

    Soltani, Sahar; Madadlou, Ashkan

    2016-01-20

    Nanosized (<100 nm) zein spheres were employed for fabrication of a series of fish O/W Pickering emulsions. Although surface tension measurement informed the high potency of zein particles for interfacial adsorption, the prepared emulsions destabilized shortly. Electrostatic deposition of sugar beet pectin onto zein particles interfacial layer at pH 4.0 increased significantly the emulsion stability which was attributed to enhanced steric and electrostatic repulsions based on ζ-potential measurements. Pectin enrichment also increased the viscosity of the continuous phase of emulsion. Injection of the oxidative enzyme laccase into the pectin-enriched emulsion to cross-link the feruloyl-bearing pectin molecules and the subsequent addition of CaCl2 to set ion-mediated cross-linkages between carboxyl groups of pectin chains transformed Pickering emulsions to emulgels. The higher the pectin content, the shorter was the gelation time of emulsions. The obtained emulgels were self-standing and became harder along with increasing pectin content.

  6. Error correction and diversity analysis of population mixtures determined by NGS.

    Science.gov (United States)

    Wood, Graham R; Burroughs, Nigel J; Evans, David J; Ryabov, Eugene V

    2014-01-01

    The impetus for this work was the need to analyse nucleotide diversity in a viral mix taken from honeybees. The paper has two findings. First, a method for correction of next generation sequencing error in the distribution of nucleotides at a site is developed. Second, a package of methods for assessment of nucleotide diversity is assembled. The error correction method is statistically based and works at the level of the nucleotide distribution rather than the level of individual nucleotides. The method relies on an error model and a sample of known viral genotypes that is used for model calibration. A compendium of existing and new diversity analysis tools is also presented, allowing hypotheses about diversity and mean diversity to be tested and associated confidence intervals to be calculated. The methods are illustrated using honeybee viral samples. Software in both Excel and Matlab and a guide are available at http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software/, the Warwick University Systems Biology Centre software download site.

  7. Pickering乳液模板法制备多孔分子印迹聚合物的进展%Development of Porous Imprinted Polymers Synthesized via Pickering Emulsion Template

    Institute of Scientific and Technical Information of China (English)

    潘建明; 殷毅杰

    2016-01-01

    This work reviews the studies about porous imprinted polymers via Pickering emulsion template .The hollow imprinted polymers , porous imprinted polymers and imprinted polymer foams can be prepared by Pickering single emulsion ,Pickering double emulsion and Pickering high internal phase emulsion ,respectively , and their interface behaviors and structure-activity relationship were described .Meanwhile, the merits, disadvantages and application fields of three emulsion template were commented .Finally ,the expectation of this research containing the selection of micro/nano particles ,formation ways of stable emulsion was illustrated .%对近年来Pickering乳液模板法制备多孔分子印迹聚合物的工作进行了总结,阐述了Pickering单乳液、Pickering双乳液以及Pickering高内相乳液法分别制备中空、多孔微球以及泡沫的结构分子印迹聚合物的过程、界面行为调控和对应构效关系;指出了3类方法的优势、适用范围与存在的不足之处,并对微纳米稳定粒子选择、乳液形成方式、应用领域拓展等方面的研究设想进行了展望。

  8. 用于水性涂料的Pickering乳液包覆抗蚀活性助剂的研究进展%Progress of the Corrosion of Active Additives Pickering Emulsion Coating

    Institute of Scientific and Technical Information of China (English)

    梁晟源; 许凯; 彭军; 桂雪峰; 邢玉秀; 高树曦; 任圆圆

    2016-01-01

    简述了五种包覆技术和Pickering乳液,综述了Pickering乳液包覆技术制备的复合微球,重点论述了采用Pickering乳液包覆抗蚀性活性助剂的原理以及在水性涂料中的应用,目前研究情况及应用优势,最后展望了Pickering乳液包覆技术的深入研究会对推动水性涂料行业的迅猛发展起到关键性作用。%Five kinds of coating technology, Pickering emulsion and reviews of Pickering emulsion coating technology were introduced. The preparation of nanocomposite by Pickering emulsion was emphasized the principle of corrosion resistance of coated active additives as well as the application of waterborne coatings, the current research situation and the advantage of application. Pickering emulsion coating technology discussed in-depth research will play a key role to promote the rapid development of coating industry.

  9. Identification and Characterization of Microsatellite Loci in Maqui (Aristotelia chilensis [Molina] Stunz) Using Next-Generation Sequencing (NGS)

    Science.gov (United States)

    Bastías, Adriana; Correa, Francisco; Rojas, Pamela; Almada, Rubén; Muñoz, Carlos; Sagredo, Boris

    2016-01-01

    Maqui (Aristotelia chilensis [Molina] Stunz) is a small dioecious tree native to South America with edible fruit characterized by very high antioxidant capacity and anthocyanin content. To preserve maqui as a genetic resource it is essential to study its genetic diversity. However, the complete genome is unknown and only a few gene sequences are available in databases. Simple sequence repeats (SSR) markers, which are neutral, co-dominant, reproducible and highly variable, are desirable to support genetic studies in maqui populations. By means of identification and characterization of microsatellite loci from a maqui genotype, using 454 sequencing technology, we develop a set of SSR for this species. Obtaining a total of 165,043 shotgun genome sequences, with an average read length of 387 bases, we covered 64 Mb of the maqui genome. Reads were assembled into 4,832 contigs, while 98,546 reads remained as singletons, generating a total of 103,378 consensus genomic sequences. A total of 24,494 SSR maqui markers were identified. Of them, 15,950 SSR maqui markers were classified as perfects. The most common SSR motifs were dinucleotide (31%), followed by tetranucleotide (26%) and trinucleotide motifs (24%). The motif AG/CT (28.4%) was the most abundant, while the motif AC (89 bp) was the largest. Eleven polymorphic SSRs were selected and used to analyze a population of 40 maqui genotypes. Polymorphism information content (PIC) ranged from 0.117 to 0.82, with an average of 0.58. Non-significant groups were observed in the maqui population, showing a panmictic genetic structure. In addition, we also predicted 11150 putative genes and 3 microRNAs (miRNAs) in maqui sequences. This results, including partial sequences of genes, some miRNAs and SSR markers from high throughput next generation sequencing (NGS) of maqui genomic DNA, constitute the first platform to undertake genetic and molecular studies of this important species. PMID:27459734

  10. Identification and Characterization of Microsatellite Loci in Maqui (Aristotelia chilensis [Molina] Stunz Using Next-Generation Sequencing (NGS.

    Directory of Open Access Journals (Sweden)

    Adriana Bastías

    Full Text Available Maqui (Aristotelia chilensis [Molina] Stunz is a small dioecious tree native to South America with edible fruit characterized by very high antioxidant capacity and anthocyanin content. To preserve maqui as a genetic resource it is essential to study its genetic diversity. However, the complete genome is unknown and only a few gene sequences are available in databases. Simple sequence repeats (SSR markers, which are neutral, co-dominant, reproducible and highly variable, are desirable to support genetic studies in maqui populations. By means of identification and characterization of microsatellite loci from a maqui genotype, using 454 sequencing technology, we develop a set of SSR for this species. Obtaining a total of 165,043 shotgun genome sequences, with an average read length of 387 bases, we covered 64 Mb of the maqui genome. Reads were assembled into 4,832 contigs, while 98,546 reads remained as singletons, generating a total of 103,378 consensus genomic sequences. A total of 24,494 SSR maqui markers were identified. Of them, 15,950 SSR maqui markers were classified as perfects. The most common SSR motifs were dinucleotide (31%, followed by tetranucleotide (26% and trinucleotide motifs (24%. The motif AG/CT (28.4% was the most abundant, while the motif AC (89 bp was the largest. Eleven polymorphic SSRs were selected and used to analyze a population of 40 maqui genotypes. Polymorphism information content (PIC ranged from 0.117 to 0.82, with an average of 0.58. Non-significant groups were observed in the maqui population, showing a panmictic genetic structure. In addition, we also predicted 11150 putative genes and 3 microRNAs (miRNAs in maqui sequences. This results, including partial sequences of genes, some miRNAs and SSR markers from high throughput next generation sequencing (NGS of maqui genomic DNA, constitute the first platform to undertake genetic and molecular studies of this important species.

  11. Pickering emulsions: Wetting and colloidal stability of hairy particles - A self-consistent field theory

    NARCIS (Netherlands)

    Salari, J.W.O.; Leermakers, F.A.M.; Klumperman, B.

    2011-01-01

    The assembly of sterically stabilized colloids at liquid–liquid interfaces is studied with the self-consistent field (SCF) theory using the discretization scheme that was developed by Scheutjens, Fleer, and co-workers. The model is based on a poly(methyl methacrylate) (pMMA) particle with poly(isobu

  12. Preference of multi-walled carbon nanotube (MWCNT) to single-walled carbon nanotube (SWCNT) and activated carbon for preparing silica nanohybrid pickering emulsion for chemical enhanced oil recovery (C-EOR)

    Science.gov (United States)

    AfzaliTabar, M.; Alaei, M.; Ranjineh Khojasteh, R.; Motiee, F.; Rashidi, A. M.

    2017-01-01

    The aim of this research was to determine the best nano hybrid that can be used as a Pickering emulsion Chemical Enhanced Oil Recovery (C-EOR). Therefore, we have prepared different carbon structures nano hybrids with SiO2 nano particles with different weight percent using sol-gel method. The as-prepared nano materials were characterized with X-Ray Diffraction (XRD), Field Emission Scanning Electron Microscopy (FE-SEM) and Thermal Gravimetric Analysis (TGA). Pickering emulsions of these nanohybrids were prepared at pH=7 in ambient temperature and with distilled water. Stability of the mentioned Pickering emulsions was controlled for one month. Emulsion phase morphology was investigated using optical microscopic imaging. Evaluation results demonstrated that the best sample is the 70% MWCNT/SiO2 nanohybrid. Stability of the selected nanohybrid (70% MWCNT/SiO2 nanohybrid) was investigated by alteration of salinity, pH and temperature. Results showed that the mentioned Pickering emulsion has very good stability at 0.1%, 1% salinity, moderate and high temperature (25 °C and 90 °C) and neutral and alkaline pH (7, 10) that is suitable for the oil reservoirs conditions. The effect of the related nano fluid on the wettability of carbonate rock was investigated by measuring the contact angle and interfacial tension. Results show that the nanofluid could significantly change the wettability of the carbonate rock from oil wet to water wet and can decrease the interfacial tension. Therefore, the 70% MWCNT/SiO2 nanohybrid Pickering emulsion can be used for Chemical Enhanced Oil Recovery (C-EOR).

  13. Clustering and gelation of hard spheres induced by the Pickering effect

    Science.gov (United States)

    Fortini, Andrea

    2012-04-01

    A mixture of hard-sphere particles and model emulsion droplets is studied with a Brownian dynamics simulation. We find that the addition of nonwetting emulsion droplets to a suspension of pure hard spheres can lead to both gas-liquid and fluid-solid phase separations. Furthermore, we find a stable fluid of hard-sphere clusters. The stability is due to the saturation of the attraction that occurs when the surface of the droplets is completely covered with colloidal particles. At larger emulsion droplet densities a percolation transition is observed. The resulting networks of colloidal particles show dynamical and mechanical properties typical of a colloidal gel. The results of the model are in good qualitative agreement with recent experimental findings [E. Koos and N. Willenbacher, ScienceSCIEAS0036-807510.1126/science.1199243 331, 897 (2011)] in a mixture of colloidal particles and two immiscible fluids.

  14. Exploring the genes of yerba mate (Ilex paraguariensis A. St.-Hil. by NGS and de novo transcriptome assembly.

    Directory of Open Access Journals (Sweden)

    Humberto J Debat

    Full Text Available Yerba mate (Ilex paraguariensis A. St.-Hil. is an important subtropical tree crop cultivated on 326,000 ha in Argentina, Brazil and Paraguay, with a total yield production of more than 1,000,000 t. Yerba mate presents a strong limitation regarding sequence information. The NCBI GenBank lacks an EST database of yerba mate and depicts only 80 DNA sequences, mostly uncharacterized. In this scenario, in order to elucidate the yerba mate gene landscape by means of NGS, we explored and discovered a vast collection of I. paraguariensis transcripts. Total RNA from I. paraguariensis was sequenced by Illumina HiSeq-2000 obtaining 72,031,388 pair-end 100 bp sequences. High quality reads were de novo assembled into 44,907 transcripts encompassing 40 million bases with an estimated coverage of 180X. Multiple sequence analysis allowed us to predict that yerba mate contains ∼ 32,355 genes and 12,551 gene variants or isoforms. We identified and categorized members of more than 100 metabolic pathways. Overall, we have identified ∼ 1,000 putative transcription factors, genes involved in heat and oxidative stress, pathogen response, as well as disease resistance and hormone response. We have also identified, based in sequence homology searches, novel transcripts related to osmotic, drought, salinity and cold stress, senescence and early flowering. We have also pinpointed several members of the gene silencing pathway, and characterized the silencing effector Argonaute1. We predicted a diverse supply of putative microRNA precursors involved in developmental processes. We present here the first draft of the transcribed genomes of the yerba mate chloroplast and mitochondrion. The putative sequence and predicted structure of the caffeine synthase of yerba mate is presented. Moreover, we provide a collection of over 10,800 SSR accessible to the scientific community interested in yerba mate genetic improvement. This contribution broadly expands the limited knowledge

  15. NGS-based BRCA1/2 mutation testing of high-grade serous ovarian cancer tissue: results and conclusions of the first international round robin trial.

    Science.gov (United States)

    Endris, Volker; Stenzinger, Albrecht; Pfarr, Nicole; Penzel, Roland; Möbs, Markus; Lenze, Dido; Darb-Esfahani, Silvia; Hummel, Michael; Sabine-Merkelbach-Bruse; Jung, Andreas; Lehmann, Ulrich; Kreipe, Hans; Kirchner, Thomas; Büttner, Reinhard; Jochum, Wolfram; Höfler, Gerald; Dietel, Manfred; Weichert, Wilko; Schirmacher, Peter

    2016-06-01

    With the approval of olaparib as monotherapy treatment in platinum-sensitive, relapsed high-grade serous ovarian cancer by the European Medical Agency (EMA), comprehensive genotyping of BRCA1 and BRCA2 in tumor tissue has become a mandatory pre-therapeutic test. This requires significant advances in routine tumor test methodologies due to the large size of both genes and the lack of mutational hot spots. Classical focused screening approaches, like Sanger sequencing, do not allow for a sensitive, rapid, and economic analysis of tumor tissue. Next-generation sequencing (NGS) approaches employing targeted panels for BRCA1/2 to interrogate formalin-fixed and paraffin-embedded tumor samples from either surgical resection or biopsy specimens can overcome these limitations. Although focused NGS methods have been implemented by few centers in routine molecular diagnostics for the analysis of some druggable oncogenic mutations, the reliable diagnostic testing of the entire coding regions of BRCA1 and BRCA2 was a new challenge requiring extensive technological improvement and quality management. Here, we describe the implementation and results of the first round robin trial for BRCA1/2 mutation testing in tumor tissue that was conducted in central Europe on May 2015, shortly after the approval and prior to the official release of olaparib. The high success rate of 81 % (21/26 test centers) demonstrates that BRCA1/2 multicenter mutation testing is well feasible in FFPE tumor tissue, extending to other tumor entities beyond ovarian cancer. The high number of test centers passing the trial demonstrates the success of the concerted efforts by German, Swiss, and Austrian pathology centers to ensure quality-controlled NGS-based testing and proves the potential of this technology in routine molecular pathology. On the basis of our results, we provide recommendations for predictive testing of tumor tissue for BRCA1/2 to clinical decision making in ovarian cancer patients.

  16. 基于Pickering乳液介质萃取苯胺的研究%Study on the Aniline Extraction Process Based on Pickering Emulsion Medium

    Institute of Scientific and Technical Information of China (English)

    刘登卫; 贺拥军; 郭晓滨; 张超; 李紫萱; 高绮

    2012-01-01

    The static and dynamic extraction of aniline from aqueous solution was carried out with the Pickering emulsions as extraction media. The effects of the volume amount of emulsions, the amount of MgO particles and the extraction stages on the static extraction efficiency were investigated. The influences of the influent rate, the inlet concentration of aniline, and the amount of emulsion on the efficiency of the dynamic extraction were also investigated. The results show that the static extraction efficiency of single-stage is 70%, while that of three-stages exceeds 98%. With the increase of the volume amount of the Pickering emulsions and the extraction stages, the static extraction efficiency increases. With increasing the amount of MgO particles, the static extraction efficiency raises at first and then decreases. The dynamic extraction behavior of aniline from aqueous solution is similar to that of adsorption procedure in fixed bed. With the increase of the volume amount of Pickering emulsions, and the decrease of inlet rate and initial aniline concentration, the dynamic extraction efficiency increases. The extraction procedure based on Pickering emulsions provides a potential way for many industrial processes, such as sewage treatment and the extraction of the active ingredients of traditional Chinese medicines.%以Pickering乳液为介质,研究了苯胺的静态和动态萃取过程.考察了乳液用量、氧化镁粒子用量和萃取级数对静态萃取效率的影响作用,以及苯胺进水浓度、乳液用量和进水流速对动态萃取过程的影响作用.结果表明,在静态条件下,乳液单级萃取苯胺的效率为70%,三级萃取效率超过98%.随着Pickering乳液的用量和萃取级数的增加,静态萃取效率提高:随着MgO粒子用量的增大,静态萃取效率呈现先提高后减小的变化趋势.苯胺的动态萃取行为与固定床吸附过程类似,随着乳液用量增加、进水流速减小和进水浓度的减

  17. Impact of NGS in the medical sciences: Genetic syndromes with an increased risk of developing cancer as an example of the use of new technologies.

    Science.gov (United States)

    Lapunzina, Pablo; López, Rocío Ortiz; Rodríguez-Laguna, Lara; García-Miguel, Purificación; Martínez, Augusto Rojas; Martínez-Glez, Víctor

    2014-03-01

    The increased speed and decreasing cost of sequencing, along with an understanding of the clinical relevance of emerging information for patient management, has led to an explosion of potential applications in healthcare. Currently, SNP arrays and Next-Generation Sequencing (NGS) technologies are relatively new techniques used to scan genomes for gains and losses, losses of heterozygosity (LOH), SNPs, and indel variants as well as to perform complete sequencing of a panel of candidate genes, the entire exome (whole exome sequencing) or even the whole genome. As a result, these new high-throughput technologies have facilitated progress in the understanding and diagnosis of genetic syndromes and cancers, two disorders traditionally considered to be separate diseases but that can share causal genetic alterations in a group of developmental disorders associated with congenital malformations and cancer risk. The purpose of this work is to review these syndromes as an example of a group of disorders that has been included in a panel of genes for NGS analysis. We also highlight the relationship between development and cancer and underline the connections between these syndromes.

  18. Impact of NGS in the medical sciences: genetic syndromes with an increased risk of developing cancer as an example of the use of new technologies

    Directory of Open Access Journals (Sweden)

    Pablo Lapunzina

    2014-01-01

    Full Text Available The increased speed and decreasing cost of sequencing, along with an understanding of the clinical relevance of emerging information for patient management, has led to an explosion of potential applications in healthcare. Currently, SNP arrays and Next-Generation Sequencing (NGS technologies are relatively new techniques used to scan genomes for gains and losses, losses of heterozygosity (LOH, SNPs, and indel variants as well as to perform complete sequencing of a panel of candidate genes, the entire exome (whole exome sequencing or even the whole genome. As a result, these new high-throughput technologies have facilitated progress in the understanding and diagnosis of genetic syndromes and cancers, two disorders traditionally considered to be separate diseases but that can share causal genetic alterations in a group of developmental disorders associated with congenital malformations and cancer risk. The purpose of this work is to review these syndromes as an example of a group of disorders that has been included in a panel of genes for NGS analysis. We also highlight the relationship between development and cancer and underline the connections between these syndromes.

  19. Next-generation sequencing (NGS) as a fast molecular diagnosis tool for left ventricular noncompaction in an infant with compound mutations in the MYBPC3 gene.

    Science.gov (United States)

    Schaefer, Elise; Helms, Pauline; Marcellin, Luc; Desprez, Philippe; Billaud, Philippe; Chanavat, Valérie; Rousson, Robert; Millat, Gilles

    2014-03-01

    Left ventricular noncompaction (LVNC) is a clinically heterogeneous disorder characterized by a trabecular meshwork and deep intertrabecular myocardial recesses that communicate with the left ventricular cavity. LVNC is classified as a rare genetic cardiomyopathy. Molecular diagnosis is a challenge for the medical community as the condition shares morphologic features of hypertrophic and dilated cardiomyopathies. Several genetic causes of LVNC have been reported, with variable modes of inheritance, including autosomal dominant and X-linked inheritance, but relatively few responsible genes have been identified. In this report, we describe a case of a severe form of LVNC leading to death at 6 months of life. NGS sequencing using a custom design for hypertrophic cardiomyopathy panel allowed us to identify compound heterozygosity in the MYBPC3 gene (p.Lys505del, p.Pro955fs) in 3 days, confirming NGS sequencing as a fast molecular diagnosis tool. Other studies have reported neonatal presentation of cardiomyopathies associated with compound heterozygous or homozygous MYBPC3 mutations. In this family and in families in which parental truncating MYBPC3 mutations are identified, preimplantation or prenatal genetic screening should be considered as these genotypes leads to neonatal mortality and morbidity.

  20. Impact of NGS in the medical sciences: Genetic syndromes with an increased risk of developing cancer as an example of the use of new technologies

    Science.gov (United States)

    Lapunzina, Pablo; López, Rocío Ortiz; Rodríguez-Laguna, Lara; García-Miguel, Purificación; Martínez, Augusto Rojas; Martínez-Glez, Víctor

    2014-01-01

    The increased speed and decreasing cost of sequencing, along with an understanding of the clinical relevance of emerging information for patient management, has led to an explosion of potential applications in healthcare. Currently, SNP arrays and Next-Generation Sequencing (NGS) technologies are relatively new techniques used to scan genomes for gains and losses, losses of heterozygosity (LOH), SNPs, and indel variants as well as to perform complete sequencing of a panel of candidate genes, the entire exome (whole exome sequencing) or even the whole genome. As a result, these new high-throughput technologies have facilitated progress in the understanding and diagnosis of genetic syndromes and cancers, two disorders traditionally considered to be separate diseases but that can share causal genetic alterations in a group of developmental disorders associated with congenital malformations and cancer risk. The purpose of this work is to review these syndromes as an example of a group of disorders that has been included in a panel of genes for NGS analysis. We also highlight the relationship between development and cancer and underline the connections between these syndromes. PMID:24764758

  1. Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies

    Directory of Open Access Journals (Sweden)

    Alexandre G. de Brevern

    2015-01-01

    Full Text Available Sequencing the human genome began in 1994, and 10 years of work were necessary in order to provide a nearly complete sequence. Nowadays, NGS technologies allow sequencing of a whole human genome in a few days. This deluge of data challenges scientists in many ways, as they are faced with data management issues and analysis and visualization drawbacks due to the limitations of current bioinformatics tools. In this paper, we describe how the NGS Big Data revolution changes the way of managing and analysing data. We present how biologists are confronted with abundance of methods, tools, and data formats. To overcome these problems, focus on Big Data Information Technology innovations from web and business intelligence. We underline the interest of NoSQL databases, which are much more efficient than relational databases. Since Big Data leads to the loss of interactivity with data during analysis due to high processing time, we describe solutions from the Business Intelligence that allow one to regain interactivity whatever the volume of data is. We illustrate this point with a focus on the Amadea platform. Finally, we discuss visualization challenges posed by Big Data and present the latest innovations with JavaScript graphic libraries.

  2. Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies.

    Science.gov (United States)

    de Brevern, Alexandre G; Meyniel, Jean-Philippe; Fairhead, Cécile; Neuvéglise, Cécile; Malpertuy, Alain

    2015-01-01

    Sequencing the human genome began in 1994, and 10 years of work were necessary in order to provide a nearly complete sequence. Nowadays, NGS technologies allow sequencing of a whole human genome in a few days. This deluge of data challenges scientists in many ways, as they are faced with data management issues and analysis and visualization drawbacks due to the limitations of current bioinformatics tools. In this paper, we describe how the NGS Big Data revolution changes the way of managing and analysing data. We present how biologists are confronted with abundance of methods, tools, and data formats. To overcome these problems, focus on Big Data Information Technology innovations from web and business intelligence. We underline the interest of NoSQL databases, which are much more efficient than relational databases. Since Big Data leads to the loss of interactivity with data during analysis due to high processing time, we describe solutions from the Business Intelligence that allow one to regain interactivity whatever the volume of data is. We illustrate this point with a focus on the Amadea platform. Finally, we discuss visualization challenges posed by Big Data and present the latest innovations with JavaScript graphic libraries.

  3. [Identification of key markers of normal and pathogenic microbiota determining health of periodontium by NGS-sequencing 16S-rDNA libraries of periodontal swabs].

    Science.gov (United States)

    Zorina, O A; Petrukhina, N B; Basova, A A; Shibaeva, A V; Trubnikova, E V; Shevelev, A B

    2014-01-01

    By using NGS-sequencing libraries of DNA from periodontal swabs with primers specific to V6 region of 16S rDNA prevalence of bacterial genera and species in periodontal microbiota of patients with aggressive periodontitis and healthy donors was analyzed. Six genera of putative periodontal protectors and eight periodontal pathogens were identified with respect to aggressive (but not chronic) periodontitis. Statistically relevant over-colonization by general Porphyromonas, Treponema, Synergistes, Tannerella, Filifactor, Ruminococcus, Parvimonas and Mycoplasma was found to be associated with the condition. From these, only three genera Porphyromonas, Treponema and Tannerella are traditionally considered as periodontal pathogens. Statistically confidential over-colonization by genus Veillonella was found in healthy patients. This genus should be considered as a relevant marker of a healthy periodontium. Genera Streptococcus, Bergeyella, Granulicatella, Kingella and Corynebacterium may be considered as putative periodontal protectors. Comparison of data of NGS-sequencing and real-time PCR demonstrated a good agreement if different PCR efficiency using independent primer pairs is taken into account.

  4. Progress in Surface Modification of Nano-micron Particles and Its Application to Pickering Emulsions%纳微米颗粒的表面改性及其在Pickering乳液中的应用进展

    Institute of Scientific and Technical Information of China (English)

    张明; 王爱娟; 李均明; 宋娜

    2016-01-01

    以固体粒子替代表面活性剂稳定的Pickering乳液,不仅可以赋予乳液许多特殊的性能(电磁和温度感应性能等),还可消除由添加表面活性剂所带来的副作用(过敏性和毒性等),这使得Pickering乳液可以应用到对表面活性物质具有很大限制的生物材料领域。系统综述了常见Pickering乳液用固体粒子,以及为了获得不同类型的乳液而对固体粒子进行表面改性的主要方法,着重归纳了表面改性前亲水性羟基磷灰石(HAp)和改性后疏水性HAp作为颗粒乳化剂稳定的Pickering乳液的类型及其进一步合成的产物。%Pickering emulsion is stabilized by solid particles instead of surfactant,which can not only adj ust the special properties of emulsion (electromagnetic and temperature sensitive performance),but also avoid the side effects of surfactant (irritability and toxicity).Accordingly,Pickering emulsions can be applied to the field of biological mate-rials which have great limitations on surfactant.This paper summarized the solid particles widely used in common Pickering emulsion,and some methods used for surface modification of solid particles in order to obtain different types of emulsion.The emulsion types and further synthetic products of Pickering emulsion stabilized by using hydroxyapa-tite (HAp)as particle emulsifier before and after surface modification are concluded.

  5. Bespoke contrast-matched diblock copolymer nanoparticles enable the rational design of highly transparent Pickering double emulsions† †Electronic supplementary information (ESI) available: GPC chromatograms, additional transmission electron micrographs, digital photographs, visible absorption spectra and laser diffraction data, further optical and fluorescence micrographs. See DOI: 10.1039/c6nr03856e Click here for additional data file.

    Science.gov (United States)

    Thompson, Kate L.; Derry, Matthew J.; Warren, Nicholas J.; Ratcliffe, Liam P. D.; Williams, Clive N.; Brown, Steven L.

    2016-01-01

    We report the preparation of highly transparent oil-in-water Pickering emulsions using contrast-matched organic nanoparticles. This is achieved via addition of judicious amounts of either sucrose or glycerol to an aqueous dispersion of poly(glycerol monomethacrylate)56–poly(2,2,2-trifluoroethyl methacrylate)500 [PGMA–PTFEMA] diblock copolymer nanoparticles prior to high shear homogenization with an equal volume of n-dodecane. The resulting Pickering emulsions comprise polydisperse n-dodecane droplets of 20–100 μm diameter and exhibit up to 96% transmittance across the visible spectrum. In contrast, control experiments using non-contrast-matched poly(glycerol monomethacrylate)56–poly(benzyl methacrylate)300 [PGMA56–PBzMA300] diblock copolymer nanoparticles as a Pickering emulsifier only produced conventional highly turbid emulsions. Thus contrast-matching of the two immiscible phases is a necessary but not sufficient condition for the preparation of highly transparent Pickering emulsions: it is essential to use isorefractive nanoparticles in order to minimize light scattering. Furthermore, highly transparent oil-in-water-in-oil Pickering double emulsions can be obtained by homogenizing the contrast-matched oil-in-water Pickering emulsion prepared using the PGMA56–PTFEMA500 nanoparticles with a contrast-matched dispersion of hydrophobic poly(lauryl methacrylate)39–poly(2,2,2-trifluoroethyl methacrylate)800 [PLMA39–PTFEMA800] diblock copolymer nanoparticles in n-dodecane. Finally, we show that an isorefractive oil-in-water Pickering emulsion enables fluorescence spectroscopy to be used to monitor the transport of water-insoluble small molecules (pyrene and benzophenone) between n-dodecane droplets. Such transport is significantly less efficient than that observed for the equivalent isorefractive surfactant-stabilized emulsion. Conventional turbid emulsions do not enable such a comparison to be made because the intense light scattering leads to

  6. Increased genetic diversity and prevalence of co-infection with Trypanosoma spp. in koalas (Phascolarctos cinereus) and their ticks identified using next-generation sequencing (NGS).

    Science.gov (United States)

    Barbosa, Amanda D; Gofton, Alexander W; Paparini, Andrea; Codello, Annachiara; Greay, Telleasha; Gillett, Amber; Warren, Kristin; Irwin, Peter; Ryan, Una

    2017-01-01

    Infections with Trypanosoma spp. have been associated with poor health and decreased survival of koalas (Phascolarctos cinereus), particularly in the presence of concurrent pathogens such as Chlamydia and koala retrovirus. The present study describes the application of a next-generation sequencing (NGS)-based assay to characterise the prevalence and genetic diversity of trypanosome communities in koalas and two native species of ticks (Ixodes holocyclus and I. tasmani) removed from koala hosts. Among 168 koalas tested, 32.2% (95% CI: 25.2-39.8%) were positive for at least one Trypanosoma sp. Previously described Trypanosoma spp. from koalas were identified, including T. irwini (32.1%, 95% CI: 25.2-39.8%), T. gilletti (25%, 95% CI: 18.7-32.3%), T. copemani (27.4%, 95% CI: 20.8-34.8%) and T. vegrandis (10.1%, 95% CI: 6.0-15.7%). Trypanosoma noyesi was detected for the first time in koalas, although at a low prevalence (0.6% 95% CI: 0-3.3%), and a novel species (Trypanosoma sp. AB-2017) was identified at a prevalence of 4.8% (95% CI: 2.1-9.2%). Mixed infections with up to five species were present in 27.4% (95% CI: 21-35%) of the koalas, which was significantly higher than the prevalence of single infections 4.8% (95% CI: 2-9%). Overall, a considerably higher proportion (79.7%) of the Trypanosoma sequences isolated from koala blood samples were identified as T. irwini, suggesting this is the dominant species. Co-infections involving T. gilletti, T. irwini, T. copemani, T. vegrandis and Trypanosoma sp. AB-2017 were also detected in ticks, with T. gilletti and T. copemani being the dominant species within the invertebrate hosts. Direct Sanger sequencing of Trypanosoma 18S rRNA gene amplicons was also performed and results revealed that this method was only able to identify the genotypes with greater amount of reads (according to NGS) within koala samples, which highlights the advantages of NGS in detecting mixed infections. The present study provides new insights on the

  7. Synthesis and Analytical Centrifugation of Magnetic Model Colloids

    OpenAIRE

    Luigjes, B.

    2012-01-01

    This thesis is a study of the preparation and thermodynamic properties of magnetic colloids. First, two types of magnetic model colloids are investigated: composite colloids and single-domain nanoparticles. Thermodynamics of magnetic colloids is studied using analytical centrifugation, including a specially adapted centrifuge for measuring heavy and strongly light absorbing colloids. Magnetic composite colloids can be prepared from thermodynamically stable Pickering emulsions of 3-methacrylox...

  8. Molecularly imprinted polymer microspheres prepared by Pickering emulsion polymerization for selective solid-phase extraction of eight bisphenols from human urine samples

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Jiajia [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Li, Yun; Wang, Jincheng [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China); Sun, Xiaoli; Cao, Rong [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Sun, Hao [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China); Department of Chemistry, Liaoning University, Shenyang 110000 (China); Huang, Chaonan [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Chen, Jiping, E-mail: chenjp@dicp.ac.cn [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China)

    2015-05-04

    Highlights: • BPA imprinted polymer microspheres were prepared by Pickering emulsion polymerization. • Regular spherical shape and narrow diameter distribution. • Good specific adsorption capacity for BPA. • Good class-selectivity and clean-up efficiency for bisphenols in human urine under SPE mode. • Good recoveries and sensitivity for bisphenols using the MIPMS-SPE coupled with HPLC-DAD method. - Abstract: The bisphenol A (BPA) imprinted polymer microspheres were prepared by simple Pickering emulsion polymerization. Compared to traditional bulk polymerization, both high yields of polymer and good control of particle sizes were achieved. The characterization results of scanning electron microscopy and nitrogen adsorption–desorption measurements showed that the obtained molecularly imprinted polymer microsphere (MIPMS) particles possessed regular spherical shape, narrow diameter distribution (30–60 μm), a specific surface area (S{sub BET}) of 281.26 m{sup 2} g{sup −1} and a total pore volume (V{sub t}) of 0.459 cm{sup 3} g{sup −1}. Good specific adsorption capacity for BPA was obtained in the sorption experiment and good class selectivity for BPA and its seven structural analogs (bisphenol F, bisphenol B, bisphenol E, bisphenol AF, bisphenol S, bisphenol AP and bisphenol Z) was demonstrated by the chromatographic evaluation experiment. The MIPMS as solid-phase extraction (SPE) packing material was then evaluated for extraction and clean-up of these bisphenols (BPs) from human urine samples. An accurate and sensitive analytical method based on the MIPMS-SPE coupled with HPLC-DAD has been successfully established for simultaneous determination of eight BPs from human urine samples with detection limits of 1.2–2.2 ng mL{sup −1}. The recoveries of BPs for urine samples at two spiking levels (100 and 500 ng mL{sup −1} for each BP) were in the range of 81.3–106.7% with RSD values below 8.3%.

  9. DUSTiNGS. III. Distribution of Intermediate-age and Old Stellar Populations in Disks and Outer Extremities of Dwarf Galaxies

    Science.gov (United States)

    McQuinn, Kristen B.; Boyer, Martha; DUSTiNGS Team

    2017-06-01

    As part of the DUST in Nearby Galaxies with Spitzer (DUSTiNGS) survey, we have traced the spatial distributions of intermediate-age and old stars in nine dwarf galaxies in the distant parts of the Local Group. We find intermediate age stars are well mixed with the older populations and extend to large radii, indicating that chemical enrichment from these dust-producing stars may occur in the outer regions of galaxies with some frequency. Theories of structure formation in dwarf galaxies must account for the lack of radial gradients in intermediate-age populations and the presence of these stars in the outer extremities of dwarfs. We also identify the tip of the red giant branch (TRGB) in Spitzer IRAC 3.6 μm photometry. Unlike the constant TRGB in the I band, at 3.6 μm, the TRGB magnitude varies by ˜0.7 mag and is not a metallicity independent distance indicator.

  10. A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies

    Science.gov (United States)

    Massart, Sebastien; Candresse, Thierry; Gil, José; Lacomme, Christophe; Predajna, Lukas; Ravnikar, Maja; Reynard, Jean-Sébastien; Rumbou, Artemis; Saldarelli, Pasquale; Škorić, Dijana; Vainio, Eeva J.; Valkonen, Jari P. T.; Vanderschuren, Hervé; Varveri, Christina; Wetzel, Thierry

    2017-01-01

    Recent advances in high-throughput sequencing technologies and bioinformatics have generated huge new opportunities for discovering and diagnosing plant viruses and viroids. Plant virology has undoubtedly benefited from these new methodologies, but at the same time, faces now substantial bottlenecks, namely the biological characterization of the newly discovered viruses and the analysis of their impact at the biosecurity, commercial, regulatory, and scientific levels. This paper proposes a scaled and progressive scientific framework for efficient biological characterization and risk assessment when a previously known or a new plant virus is detected by next generation sequencing (NGS) technologies. Four case studies are also presented to illustrate the need for such a framework, and to discuss the scenarios. PMID:28174561

  11. Diagnosis for choroideremia in a large Chinese pedigree by next-generation sequencing (NGS) and non-invasive prenatal testing (NIPT)

    Science.gov (United States)

    Zhu, Li; Cheng, Jingliang; Zhou, Boxu; Wei, Chunli; Yang, Weichan; Jiang, Dong; Ijaz, Iqra; Tan, Xiaojun; Chen, Rui; Fu, Junjiang

    2017-01-01

    To develop an effective strategy to isolate and use cell-free fetal DNA (cffDNA) for the combined use of next-generation sequencing (NGS) for diagnosing choroideremia and non-invasive prenatal testing (NIPT) for Y chromosome determination, a large Chinese family with an X-linked recessive disease, choroideremia, was recruited. Cell-free DNA was extracted from maternal plasma, and SRY polymerase chain reaction amplification was performed using NIPT. Sanger sequencing was subsequently used for fetal amniotic fluid DNA verification. A nonsense mutation (c.C799T:p.R267X) of the CHM gene on the X chromosome of the proband (IV:7) and another 5 males with choroideremia were detected, while 3 female carriers with no symptoms were also identified. The fetus (VI:7) was identified as female from the cffDNA, and the same heterozygous nonsense mutation present in her mother was also confirmed. At one and a half years of age, the female baby did not present with any associated symptoms of choroideremia. Therefore, cffDNA was successfully used for the combined use of NGS for diagnosing choroideremia in a large Chinese pedigree, and NIPT for Y chromosome determination. This approach should result in a markedly increased use of prenatal diagnosis and improvement, and more sophisticated clinical management of diseases in China and other developing countries. The establishment of a highly accurate method for prenatal gene diagnosis will allow for more reliable gene diagnosis, improved genetic counseling, and personalized clinical management of our patients. PMID:28098911

  12. Molecularly imprinted polymer microspheres prepared by Pickering emulsion polymerization for selective solid-phase extraction of eight bisphenols from human urine samples.

    Science.gov (United States)

    Yang, Jiajia; Li, Yun; Wang, Jincheng; Sun, Xiaoli; Cao, Rong; Sun, Hao; Huang, Chaonan; Chen, Jiping

    2015-05-01

    The bisphenol A (BPA) imprinted polymer microspheres were prepared by simple Pickering emulsion polymerization. Compared to traditional bulk polymerization, both high yields of polymer and good control of particle sizes were achieved. The characterization results of scanning electron microscopy and nitrogen adsorption-desorption measurements showed that the obtained molecularly imprinted polymer microsphere (MIPMS) particles possessed regular spherical shape, narrow diameter distribution (30-60 μm), a specific surface area (S(BET)) of 281.26 m(2) g(-1) and a total pore volume (V(t)) of 0.459 cm(3) g(-1). Good specific adsorption capacity for BPA was obtained in the sorption experiment and good class selectivity for BPA and its seven structural analogs (bisphenol F, bisphenol B, bisphenol E, bisphenol AF, bisphenol S, bisphenol AP and bisphenol Z) was demonstrated by the chromatographic evaluation experiment. The MIPMS as solid-phase extraction (SPE) packing material was then evaluated for extraction and clean-up of these bisphenols (BPs) from human urine samples. An accurate and sensitive analytical method based on the MIPMS-SPE coupled with HPLC-DAD has been successfully established for simultaneous determination of eight BPs from human urine samples with detection limits of 1.2-2.2 ng mL(-1). The recoveries of BPs for urine samples at two spiking levels (100 and 500 ng mL(-1) for each BP) were in the range of 81.3-106.7% with RSD values below 8.3%.

  13. 紫外光引发Pickering乳液聚合制备中空复合微球的研究%Synthesis of Hollow Microspheres by Pickering Emulsion Polymerization Initiated by Ultraviolet Light

    Institute of Scientific and Technical Information of China (English)

    张卫红; 范晓东; 田威; 范伟伟; 程广文

    2011-01-01

    Hollow composite microspheres can be prepared rapidly by Pickering emulsion polymerization initiated by ultraviolet light.Firstly,nano-SiO2 were endowed with amphipathy and photosensitivity by grafting with 2-hydroxy-4'-(2-hydroxyethoxy)-2-methyl-propiophenone(IHT-PI 659).Secondly,stable Pickering emulsion was fabricated by using this functional nano-SiO2 particles as stabilizer.Finally,the SiO2/polymethylmethacrylate composite microspheres with hollow structure were successfully synthesized by Pickering emulsion polymerization initiated by ultraviolet light at room temperature.The products were characterized by Fourier transformation infrared spectrum(FTIR),thermogravimetric analysis(TGA),transmission electron microscopy(TEM) and scanning electron microscope(SEM).A possible mechanism for the formation of the hollow composites by photo-initiation Pickering emulsion polymerization was also proposed.%用光引发剂2-羟基-4'-(2-羟乙氧基)-2-甲基苯丙酮(IHT-PI 659)对纳米SiO2表面进行接枝使之兼具两亲性及光引发特性;以该功能性纳米SiO2为稳定剂构筑O/W(水包油)型Pickering乳液;用紫外光引发处于内油相的甲基丙烯酸甲酯单体聚合,制备出具有中空结构的SiO2/PMMA复合微球,采用傅里叶变换红外光谱(FTIR)、热失重分析仪(TGA)、透射电镜(TEM)及扫描电子显微镜(SEM)对复合微球进行了表征,并提出了紫外光引发Pickering乳液聚合制备中空复合微球的机理.

  14. Pickering Emulsion Stabilized by Graphene Oxide and Its Polymerization%氧化石墨烯稳定的Pickering乳液及其聚合反应

    Institute of Scientific and Technical Information of China (English)

    黄颖; 金小荀; 王新龙

    2014-01-01

    通过改进的Hummers法制备氧化石墨烯(GO),以GO做稳定剂,甲基丙烯酸甲酯(MMA)为油相,制备了Pickering 乳液,并研究了GO浓度、水相pH值对其稳定性的影响;通过加入引发剂成功进行了Pickering乳液聚合制备PMMA/GO复合微球,利用透射电镜对该复合微球的微观结构进行了表征.研究表明,GO稳定的Pickering乳液相比于SDBS稳定的普通乳液,液滴粒径更小且分散性更好;GO浓度对Pickering乳液的稳定性影响不大,但随其浓度的增加,Pickering乳液液滴尺寸变小,液滴更为分散;酸性连续相更有利于GO在油水界面的吸附而形成稳定的Pickering乳液,随着pH值增大,液滴尺寸逐渐变大,但碱性条件下乳液无法稳定存在;乳液聚合产物形貌为PMMA颗粒由GO片均匀包覆形成的复合微球,尺寸分布约200nm左右.

  15. Facile fabrication of poly(L-lactic acid) microsphere-incorporated calcium alginate/hydroxyapatite porous scaffolds based on Pickering emulsion templates.

    Science.gov (United States)

    Hu, Yang; Ma, Shanshan; Yang, Zhuohong; Zhou, Wuyi; Du, Zhengshan; Huang, Jian; Yi, Huan; Wang, Chaoyang

    2016-04-01

    In this study, we develop a facile one-pot approach to the fabrication of poly(L-lactic acid) (PLLA) microsphere-incorporated calcium alginate (ALG-Ca)/hydroxyapatite (HAp) porous scaffolds based on HAp nanoparticle-stabilized oil-in-water Pickering emulsion templates, which contain alginate in the aqueous phase and PLLA in the oil phase. The emulsion aqueous phase is solidified by in situ gelation of alginate with Ca(2+) released from HAp by decreasing pH with slow hydrolysis of D-gluconic acid δ-lactone (GDL) to produce emulsion droplet-incorporated gels, followed by freeze-drying to form porous scaffolds containing microspheres. The pore structure of porous scaffolds can be adjusted by varying the HAp or GDL concentration. The compressive tests show that the increase of HAp or GDL concentration is beneficial to improve the compressive property of porous scaffolds, while the excessive HAp can lead to the decrease in compressive property. Moreover, the swelling behavior studies display that the swelling ratios of porous scaffolds reduce with increasing HAp or GDL concentration. Furthermore, hydrophobic drug ibuprofen (IBU) and hydrophilic drug bovine serum albumin (BSA) are loaded into the microspheres and scaffold matrix, respectively. In vitro drug release results indicate that BSA has a rapid release while IBU has a sustained release in the dual drug-loaded scaffolds. In vitro cell culture experiments verify that mouse bone mesenchymal stem cells can proliferate on the porous scaffolds well, indicating the good biocompatibility of porous scaffolds. All these results demonstrate that the PLLA microsphere-incorporated ALG-Ca/HAp porous scaffolds have a promising potential for tissue engineering and drug delivery applications.

  16. 多颜色空间取色器的设计与实现%Research and Implementation of Color Picker Based on Multi Color Space

    Institute of Scientific and Technical Information of China (English)

    徐尤华; 熊传玉

    2014-01-01

    目前常用软件使用颜色时多以RGB颜色空间为主,也有少数软件使用了HSB、Lab、CMYK等颜色空间。在肤色检测研究领域,RGB颜色空间已经满足不了研究需要,通常会采用HSI、HSV、YCbCr、YIQ、YUV等颜色空间,用于提高肤色检测的准确率和检测效率。针对常见软件的不足,给出了一款基于多颜色空间的取色器,实时抓取光标位置的颜色,并转换为HSI、HSV、YCbCr、YIQ、YUV颜色空间的表示形式,能让用户直观的看到同一颜色在不同颜色空间的各个分量值,加深用户对各种颜色的理解。%Currently, common software usually use RGB color space, while a few software use HSB, Lab, and CMYK as well. In skin color detection research field, as RGB can’t meet the researches’ requirements, HSI, HSV, YCbCr, YIQ and YUV color space is usually used, to improve the skin detection accuracy and efficiency. Aiming at the insufficient of common software, the paper create a color picker based on multiply color space, getting the color on the position of cursor, converting to HIS, HSV, YCbCr, YIQ,YUV color space representation. It can help users observe assignment component of different color space to one color intui-tively, and enhance user’s understanding on various colors.

  17. Modeling Cancer Metastasis using Global, Quantitative and Integrative Network Biology

    DEFF Research Database (Denmark)

    Schoof, Erwin; Erler, Janine

    phosphorylation dynamics in a given biological sample. In Chapter III, we move into Integrative Network Biology, where, by combining two fundamental technologies (MS & NGS), we can obtain more in-depth insights into the links between cellular phenotype and genotype. Article 4 describes the proof...... cancer networks using Network Biology. Technologies key to this, such as Mass Spectrometry (MS), Next-Generation Sequencing (NGS) and High-Content Screening (HCS) are briefly described. In Chapter II, we cover how signaling networks and mutational data can be modeled in order to gain a better...

  18. DUSTiNGS III: Distribution of Intermediate-Age and Old Stellar Populations in Disks and Outer Extremities of Dwarf Galaxies

    CERN Document Server

    McQuinn, Kristen B W; Mitchell, Mallory B; Skillman, Evan D; Gehrz, R D; Groenewegen, Martin A T; McDonald, Iain; Sloan, G C; van Loon, Jacco Th; Whitelock, Patricia A; Zijlstra, Albert A

    2016-01-01

    We have traced the spatial distributions of intermediate-age and old stars in nine dwarf galaxies in the distant parts of the Local Group, using multi-epoch 3.6 and 4.5 micron data from the DUST in Nearby Galaxies with Spitzer (DUSTiNGS) survey. Using complementary optical imaging from the Hubble Space Telescope, we identify the tip of the red giant branch (TRGB) in the 3.6 micron photometry, separating thermally-pulsating asymptotic giant branch (TP-AGB) stars from the larger red giant branch (RGB) populations. Unlike the constant TRGB in the I-band, at 3.6 micron the TRGB magnitude varies by ~0.7 mag, making it unreliable as a distance indicator. The intermediate-age and old stars are well mixed in two-thirds of the sample with no evidence of a gradient in the ratio of the intermediate-age to old stellar populations outside the central ~1-2'. Variable AGB stars are detected in the outer extremities of the galaxies, indicating that chemical enrichment from these dust-producing stars may occur in the outer re...

  19. Detection and characterization of two co-infection variant strains of avian orthoreovirus (ARV) in young layer chickens using next-generation sequencing (NGS).

    Science.gov (United States)

    Tang, Yi; Lin, Lin; Sebastian, Aswathy; Lu, Huaguang

    2016-04-19

    Using next-generation sequencing (NGS) for full genomic characterization studies of the newly emerging avian orthoreovirus (ARV) field strains isolated in Pennsylvania poultry, we identified two co-infection ARV variant strains from one ARV isolate obtained from ARV-affected young layer chickens. The de novo assembly of the ARV reads generated 19 contigs of two different ARV variant strains according to 10 genome segments of each ARV strain. The two variants had the same M2 segment. The complete genomes of each of the two variant strains were 23,493 bp in length, and 10 dsRNA segments ranged from 1192 bp (S4) to 3958 bp (L1), encoding 12 viral proteins. Sequence comparison of nucleotide (nt) and amino acid (aa) sequences of all 10 genome segments revealed 58.1-100% and 51.4-100% aa identity between the two variant strains, and 54.3-89.4% and 49.5-98.1% aa identity between the two variants and classic vaccine strains. Phylogenetic analysis revealed a moderate to significant nt sequence divergence between the two variant and ARV reference strains. These findings have demonstrated the first naturally occurring co-infection of two ARV variants in commercial young layer chickens, providing scientific evidence that multiple ARV strains can be simultaneously present in one host species of chickens.

  20. Rapid identification of fruit length loci in cucumber (Cucumis sativus L.) using next-generation sequencing (NGS)-based QTL analysis.

    Science.gov (United States)

    Wei, Qing-Zhen; Fu, Wen-Yuan; Wang, Yun-Zhu; Qin, Xiao-Dong; Wang, Jing; Li, Ji; Lou, Qun-Feng; Chen, Jin-Feng

    2016-06-07

    The cucumber (Cucumis sativus L.) exhibits extensive variations in fruit size and shape. Fruit length is an important agronomic and domesticated trait controlled by quantitative trait loci (QTLs). Nonetheless, the underlying molecular and genetic mechanisms that determine cucumber fruit length remain unclear. QTL-seq is an efficient strategy for QTL identification that takes advantage of bulked-segregant analysis (BSA) and next-generation sequencing (NGS). In the present study, we conducted QTL mapping and QTL-seq of cucumber fruit length. QTL mapping identified 8 QTLs for immature and mature fruit length. A major-effect QTL fl3.2, which explained a maximum of 38.87% of the phenotypic variation, was detected. A genome-wide comparison of SNP profiles between two DNA bulks identified 6 QTLs for ovary length. QTLs ovl3.1 and ovl3.2 both had major effects on ovary length with a △ (SNP-index) of 0.80 (P < 0.01) and 0.74 (P < 0.01), respectively. Quantitative RT-PCR of fruit size-related homologous genes localized in the consensus QTL FL3.2 was conducted. Four candidate genes exhibited increased expression levels in long fruit genotypes. Our results demonstrated the power of the QTL-seq method in rapid QTL detection and provided reliable QTL regions for fine mapping of fruit length-related loci and for identifying candidate genes.

  1. An Infrared Census of DUST in Nearby Galaxies with Spitzer (DUSTiNGS), II. Discovery of Metal-poor Dusty AGB Stars

    CERN Document Server

    Boyer, Martha L; Barmby, P; Bonanos, A Z; Gehrz, R D; Gordon, K D; Groenewegen, M A T; Lagadec, E; Lennon, D; Marengo, M; McDonald, I; Meixner, M; Skillman, E; Sloan, G C; Sonneborn, G; van Loon, J Th; Zijlstra, A

    2014-01-01

    The DUSTiNGS survey (DUST in Nearby Galaxies with Spitzer) is a 3.6 and 4.5 micron imaging survey of 50 nearby dwarf galaxies designed to identify dust-producing Asymptotic Giant Branch (AGB) stars and massive stars. Using two epochs, spaced approximately six months apart, we identify a total of 526 dusty variable AGB stars (sometimes called "extreme" or x-AGB stars; [3.6]-[4.5]>0.1 mag). Of these, 111 are in galaxies with [Fe/H] < -1.5 and 12 are in galaxies with [Fe/H] < -2.0, making them the most metal-poor dust-producing AGB stars known. We compare these identifications to those in the literature and find that most are newly discovered large-amplitude variables, with the exception of approximately 30 stars in NGC 185 and NGC 147, one star in IC 1613, and one star in Phoenix. The chemical abundances of the x-AGB variables are unknown, but the low metallicities suggest that they are more likely to be carbon-rich than oxygen-rich and comparisons with existing optical and near-IR photometry confirms tha...

  2. Pre-Analytical Considerations for Successful Next-Generation Sequencing (NGS: Challenges and Opportunities for Formalin-Fixed and Paraffin-Embedded Tumor Tissue (FFPE Samples

    Directory of Open Access Journals (Sweden)

    Gladys Arreaza

    2016-09-01

    Full Text Available In cancer drug discovery, it is important to investigate the genetic determinants of response or resistance to cancer therapy as well as factors that contribute to adverse events in the course of clinical trials. Despite the emergence of new technologies and the ability to measure more diverse analytes (e.g., circulating tumor cell (CTC, circulating tumor DNA (ctDNA, etc., tumor tissue is still the most common and reliable source for biomarker investigation. Because of its worldwide use and ability to preserve samples for many decades at ambient temperature, formalin-fixed, paraffin-embedded tumor tissue (FFPE is likely to be the preferred choice for tissue preservation in clinical practice for the foreseeable future. Multiple analyses are routinely performed on the same FFPE samples (such as Immunohistochemistry (IHC, in situ hybridization, RNAseq, DNAseq, TILseq, Methyl-Seq, etc.. Thus, specimen prioritization and optimization of the isolation of analytes is critical to ensure successful completion of each assay. FFPE is notorious for producing suboptimal DNA quality and low DNA yield. However, commercial vendors tend to request higher DNA sample mass than what is actually required for downstream assays, which restricts the breadth of biomarker work that can be performed. We evaluated multiple genomics service laboratories to assess the current state of NGS pre-analytical processing of FFPE. Significant differences in pre-analytical capabilities were observed. Key aspects are highlighted and recommendations are made to improve the current practice in translational research.

  3. Adaptive optics sky coverage modeling for extremely large telescopes.

    Science.gov (United States)

    Clare, Richard M; Ellerbroek, Brent L; Herriot, Glen; Véran, Jean-Pierre

    2006-12-10

    A Monte Carlo sky coverage model for laser guide star adaptive optics systems was proposed by Clare and Ellerbroek [J. Opt. Soc. Am. A 23, 418 (2006)]. We refine the model to include (i) natural guide star (NGS) statistics using published star count models, (ii) noise on the NGS measurements, (iii) the effect of telescope wind shake, (iv) a model for how the Strehl and hence NGS wavefront sensor measurement noise varies across the field, (v) the focus error due to imperfectly tracking the range to the sodium layer, (vi) the mechanical bandwidths of the tip-tilt (TT) stage and deformable mirror actuators, and (vii) temporal filtering of the NGS measurements to balance errors due to noise and servo lag. From this model, we are able to generate a TT error budget for the Thirty Meter Telescope facility narrow-field infrared adaptive optics system (NFIRAOS) and perform several design trade studies. With the current NFIRAOS design, the median TT error at the galactic pole with median seeing is calculated to be 65 nm or 1.8 mas rms.

  4. NGS tools for traceability in candies as high processed food products: Ion Torrent PGM versus conventional PCR-cloning.

    Science.gov (United States)

    Muñoz-Colmenero, Marta; Martínez, Jose Luis; Roca, Agustín; Garcia-Vazquez, Eva

    2017-01-01

    The Next Generation Sequencing methodologies are considered the next step within DNA-based methods and their applicability in different fields is being evaluated. Here, we tested the usefulness of the Ion Torrent Personal Genome Machine (PGM) in food traceability analyzing candies as a model of high processed foods, and compared the results with those obtained by PCR-cloning-sequencing (PCR-CS). The majority of samples exhibited consistency between methodologies, yielding more information and species per product from the PGM platform than PCR-CS. Significantly higher AT-content in sequences of the same species was also obtained from PGM. This together with some taxonomical discrepancies between methodologies suggest that the PGM platform is still pre-mature for its use in food traceability of complex highly processed products. It could be a good option for analysis of less complex food, saving time and cost per sample.

  5. Introduction of the Python script STRinNGS for analysis of STR regions in FASTQ or BAM files and expansion of the Danish STR sequence database to 11 STRs.

    Science.gov (United States)

    Friis, Susanne L; Buchard, Anders; Rockenbauer, Eszter; Børsting, Claus; Morling, Niels

    2016-03-01

    This work introduces the in-house developed Python application STRinNGS for analysis of STR sequence elements in BAM or FASTQ files. STRinNGS identifies sequence reads with STR loci by their flanking sequences, it analyses the STR sequence and the flanking regions, and generates a report with the assigned SNP-STR alleles. The main output file from STRinNGS contains all sequences with read counts above 1% of the total number of reads per locus. STR sequences are automatically named according to the nomenclature used previously and according to the repeat unit definitions in STRBase (http://www.cstl.nist.gov/strbase/). The sequences are named with (1) the locus name, (2) the length of the repeat region divided by the length of the repeat unit, (3) the sequence(s) of the repeat unit(s) followed by the number of repeats and (4) variations in the flanking regions. Lower case letters in the main output file are used to flag sequences with previously unknown variations in the STRs. SNPs in the flanking regions are named by their "rs" numbers and the nucleotides in the SNP position. Data from 207 Danes sequenced with the Ion Torrent™ HID STR 10-plex that amplified nine STRs (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D16S539, TH01, TPOX, vWA), and Amelogenin was analysed with STRinNGS. Sequencing uncovered five common SNPs near four STRs and revealed 20 new alleles in the 207 Danes. Three short homopolymers in the D8S1179 flanking regions caused frequent sequencing errors. In 29 of 3726 allele calls (0.8%), sequences with homopolymer errors were falsely assigned as true alleles. An in-house developed script in R compensated for these errors by compiling sequence reads that had identical STR sequences and identical nucleotides in the five common SNPs. In the output file from the R script, all SNP-STR haplotype calls were correct. The 207 samples and six additional samples were sequenced for D3S1358, D12S391, and D21S11 using the 454 GS Junior platform in this and a

  6. AN INFRARED CENSUS OF DUST IN NEARBY GALAXIES WITH SPITZER (DUSTiNGS). II. DISCOVERY OF METAL-POOR DUSTY AGB STARS

    Energy Technology Data Exchange (ETDEWEB)

    Boyer, Martha L.; Sonneborn, George [Observational Cosmology Lab, Code 665, NASA Goddard Space Flight Center, Greenbelt, MD 20771 (United States); McQuinn, Kristen B. W.; Gehrz, Robert D.; Skillman, Evan [Minnesota Institute for Astrophysics, School of Physics and Astronomy, 116 Church Street SE, University of Minnesota, Minneapolis, MN 55455 (United States); Barmby, Pauline [Department of Physics and Astronomy, University of Western Ontario, London, ON N6A 3K7 (Canada); Bonanos, Alceste Z. [IAASARS, National Observatory of Athens, GR-15236 Penteli (Greece); Gordon, Karl D.; Meixner, Margaret [STScI, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Groenewegen, M. A. T. [Royal Observatory of Belgium, Ringlaan 3, B-1180 Brussels (Belgium); Lagadec, Eric [Laboratoire Lagrange, UMR7293, Univ. Nice Sophia-Antipolis, CNRS, Observatoire de la Côte d' Azur, F-06300 Nice (France); Lennon, Daniel [ESA-European Space Astronomy Centre, Apdo. de Correo 78, E-28691 Villanueva de la Cañada, Madrid (Spain); Marengo, Massimo [Department of Physics and Astronomy, Iowa State University, Ames, IA 50011 (United States); McDonald, Iain; Zijlstra, Albert [Jodrell Bank Centre for Astrophysics, Alan Turing Building, University of Manchester, Manchester M13 9PL (United Kingdom); Sloan, G. C. [Astronomy Department, Cornell University, Ithaca, NY 14853-6801 (United States); Van Loon, Jacco Th., E-mail: martha.boyer@nasa.gov [Astrophysics Group, Lennard-Jones Laboratories, Keele University, Staffordshire ST5 5BG (United Kingdom)

    2015-02-10

    The DUSTiNGS survey (DUST in Nearby Galaxies with Spitzer) is a 3.6 and 4.5 μm imaging survey of 50 nearby dwarf galaxies designed to identify dust-producing asymptotic giant branch (AGB) stars and massive stars. Using two epochs, spaced approximately six months apart, we identify a total of 526 dusty variable AGB stars (sometimes called ''extreme'' or x-AGB stars; [3.6]-[4.5] > 0.1 mag). Of these, 111 are in galaxies with [Fe/H] < –1.5 and 12 are in galaxies with [Fe/H] < –2.0, making them the most metal-poor dust-producing AGB stars known. We compare these identifications to those in the literature and find that most are newly discovered large-amplitude variables, with the exception of ≈30 stars in NGC 185 and NGC 147, 1 star in IC 1613, and 1 star in Phoenix. The chemical abundances of the x-AGB variables are unknown, but the low metallicities suggest that they are more likely to be carbon-rich than oxygen-rich and comparisons with existing optical and near-IR photometry confirm that 70 of the x-AGB variables are confirmed or likely carbon stars. We see an increase in the pulsation amplitude with increased dust production, supporting previous studies suggesting that dust production and pulsation are linked. We find no strong evidence linking dust production with metallicity, indicating that dust can form in very metal-poor environments.

  7. A NGS approach to the encrusting Mediterranean sponge Crella elegans (Porifera, Demospongiae, Poecilosclerida): transcriptome sequencing, characterization and overview of the gene expression along three life cycle stages.

    Science.gov (United States)

    Pérez-Porro, A R; Navarro-Gómez, D; Uriz, M J; Giribet, G

    2013-05-01

    Sponges can be dominant organisms in many marine and freshwater habitats where they play essential ecological roles. They also represent a key group to address important questions in early metazoan evolution. Recent approaches for improving knowledge on sponge biological and ecological functions as well as on animal evolution have focused on the genetic toolkits involved in ecological responses to environmental changes (biotic and abiotic), development and reproduction. These approaches are possible thanks to newly available, massive sequencing technologies-such as the Illumina platform, which facilitate genome and transcriptome sequencing in a cost-effective manner. Here we present the first NGS (next-generation sequencing) approach to understanding the life cycle of an encrusting marine sponge. For this we sequenced libraries of three different life cycle stages of the Mediterranean sponge Crella elegans and generated de novo transcriptome assemblies. Three assemblies were based on sponge tissue of a particular life cycle stage, including non-reproductive tissue, tissue with sperm cysts and tissue with larvae. The fourth assembly pooled the data from all three stages. By aggregating data from all the different life cycle stages we obtained a higher total number of contigs, contigs with blast hit and annotated contigs than from one stage-based assemblies. In that multi-stage assembly we obtained a larger number of the developmental regulatory genes known for metazoans than in any other assembly. We also advance the differential expression of selected genes in the three life cycle stages to explore the potential of RNA-seq for improving knowledge on functional processes along the sponge life cycle.

  8. NGS-based transcriptome profiling reveals biomarkers for companion diagnostics of the TGF-β receptor blocker galunisertib in HCC.

    Science.gov (United States)

    Cao, Yuan; Agarwal, Rahul; Dituri, Francesco; Lupo, Luigi; Trerotoli, Paolo; Mancarella, Serena; Winter, Peter; Giannelli, Gianluigi

    2017-02-23

    Transforming growth factor-beta (TGF-β) signaling has gained extensive interest in hepatocellular carcinoma (HCC). The small molecule kinase inhibitor galunisertib, targeting the TGF-β receptor I (TGF-βRI), blocks HCC progression in preclinical models and shows promising effects in ongoing clinical trials. As the drug is not similarly effective in all patients, this study was aimed at identifying new companion diagnostics biomarkers for patient stratification. Next-generation sequencing-based massive analysis of cDNA ends was used to investigate the transcriptome of an invasive HCC cell line responses to TGF-β1 and galunisertib. These identified mRNA were validated in 78 frozen HCC samples and in 26 ex-vivo HCC tissues treated in culture with galunisertib. Respective protein levels in patients blood were measured by enzyme-linked immunosorbent assay. SKIL, PMEPA1 ANGPTL4, SNAI1, Il11 and c4orf26 were strongly upregulated by TGF-β1 and downregulated by galunisertib in different HCC cell lines. In the 78 HCC samples, only SKIL and PMEPA1 (P<0.001) were correlated with endogenous TGF-β1. In ex-vivo samples, SKIL and PMEPA1 were strongly downregulated (P<0.001), and correlated (P<0.001) with endogenous TGF-β1. SKIL and PMEPA1 mRNA expression in tumor tissues was significantly increased compared with controls and not correlated with protein levels in the blood of paired HCC patients. SKIL and PMEPA1 mRNA levels were positively correlated with TGF-β1 mRNA concentrations in HCC tissues and strongly downregulated by galunisertib. The target genes identified here may serve as biomarkers for the stratification of HCC patients undergoing treatment with galunisertib.

  9. Suppression substractive hybridisation and NGS reveal differential transcriptome expression profiles in Wayfaring Tree (Viburnum lantana L. treated with ozone

    Directory of Open Access Journals (Sweden)

    Elena eGottardini

    2016-06-01

    specific transcription factors (MYB and WRKY. This study demonstrates that a complex sequence of events takes place in the cells at intracellular and membrane level following O3 exposure and elucidates the effects of this oxidative stress on the transcriptional machinery of the non-model plant species V. lantana, with the final aim to provide the molecular supportive knowledge for the use of this plant as O3-bioindicator.

  10. Synergistic Emulsification of Pickering ASA Emulsion by Dodecane and Nano-montmorillonite Modified with Silane Coupling Agent%硅烷偶联剂改性纳米蒙脱石协同正十二烷乳化ASA

    Institute of Scientific and Technical Information of China (English)

    林兆云; 李友明; 于得海

    2012-01-01

    ASA(烯基琥珀酸酐)是在造纸过程中赋予纸和纸板抗渗透性的一种浆内施胶剂。本文研究了硅烷偶联剂改性纳米蒙脱石协同正十二烷乳化ASA,及其乳液稳定性和施胶性能,对改性纳米蒙脱石(MMT)利用X射线衍射(XRD)、傅里叶红外FT—IR、表面接触角等方法进行分析表征。结果表明,KH570成功改性纳米蒙脱石颗粒,并与蒙脱石表面羟基反应而改变颗粒亲水性;当油水比中为0.4时,改性蒙脱石用量为2%时,由KH570改性蒙脱石固体颗粒与正十二烷协同乳化稳定的Pickering乳液型ASA乳液稳定性最好;硫酸铝用量为0.6%时,随ASA用量的增加,纸页施胶效果明显提高。%Alkenyl succinic anhydride (ASA) is an internal sizing agent used to hydrophobize paper and paper- board in papermaking process. The stability and sizing performance of ASA Pickering emulsions (o/w) stabilized by nano-montmorillonite (nano-MMT) modified with silane coupling agent KH570 are reported. The modified nano-MMT particles were characterized by XRD, FTIR and interfacial contact angles. And the morphology of ASA emulsions was observed by optical microscopy. The results show that KH570 successfully modified nano-MMT and improved hydrophobicity due to the reaction between KH570 and hydroxyl group of MMT particle. With 0.4 oil vol- ume fraction, stable ASA Pickering emulsions (o/w) was prepared by the synergistic effect of KH570 modified nano-MMT (2wt%) and dodecane. The obtained ASA Pickering emulsion exhibited increased sizing performance with 0.6wt% aluminum sulfate and increasing dosage of ASA.

  11. The organic/inorganic hybrid microspheres with supracolloidal structure prepared by Pickering emulsion droplet template%Pickering乳滴模板法制备超粒子结构有机/无机杂化微球

    Institute of Scientific and Technical Information of China (English)

    王朝阳; 刘浩; 刘红霞; 高权星; 陈云华; 李煜; 童真

    2011-01-01

    Pickering乳滴模板法制备有机/无机杂化的核壳微球越来越引起人们的关注,主要因为该方法制备出的微球具有以无机粒子为壳层的超粒子结构(supracolloidal structure),能够赋予微球独特的功能.胶体粒子在乳滴表面自组装形成有序的球面胶体壳,得到稳定Pickering乳液,固定乳滴表面的胶体粒子来制备核壳结构的微球或者以胶体粒子为壳层的微胶囊(colloidosome).本文综述了我们课题组以Pickering乳滴模板法制备超粒子结构有机/无机杂化微胶囊包括实心微球方面的工作.我们选择具有不同性能、种类的胶体粒子以及具有不同性质和功能的核材料,采用Pickering乳滴模板法,对吸附在乳滴表面的胶体粒子用不同的固定方法制备具有不同结构和性能的微球和微胶囊,利用基于多重Pickering乳液的聚合技术制备双纳米复合的超粒子结构多核聚合物微球.%The organic/inorganic hybrid core-shell microspheres fabricated by Pickering emulsion droplet template are attracting more attentions. The microspheres obtained by this method have a supracolloidal structure, which endows the microspheres with some special functions. In a Pickering emulsion, colloid particles adsorb on the surface of the emulsion droplets and self-assemble into an ordered spherical solid shell. Then, the colloid particles are fixed to prepare the core-shell microparticles or microcapsules. The microcapsules with the shell of colloid particles are also called the colloidosomes. In this paper, we summarize the research about using the Pickering emulsion droplet template to fabricate the organic/inorganic hybrid core-shell colloidosomes, including the supracolloidal-structured microsphere. The different organic core matrices, inorganic colloid particles and the fixing methods of colloid particles on the surface of the emulsion droplets have been chosen to obtain the colloidosomes or the supracolloidal

  12. Mechanism and Formation of Pickering-Type Multiple Emulsions Made by One Step Method%Pickering多重乳状液的一步法合成及形成机理研究

    Institute of Scientific and Technical Information of China (English)

    王一平; 姚志良; 李彦超; 刘陈伟

    2011-01-01

    It was found that Pickering-type persistent multiple emulsions would be generated by one step method through mixing aqueous Laponite particle dispersion diluted with water before emulsification and oil solution containg Span80.The effect of Span80 concentration,Laponite concentration and water ratio on the stability of emulsions was studied.The formation and mechanism of Pickering-type persistent multiple emulsions by one step method were discussed.The experimental results showed that the dilution of Laponite particle suspension was the key factor of generating Pickering-type persistent multiple emulsions.The water ratio determined the inner water drop volume.With the increase of Span80 concentration,mean diameter of multiple emulsions decreased while stability increased greatly.Concentration of Laponite particles could impact the style of emulsions,but had little influence on the stability and diameter of emulsions.The lower diffusion rate of Laponite particles in water disperse system is the main reason of forming Pickering-type persistent multiple emulsions by one step method.%使用锂皂石层状纳米颗粒与表面活性剂(Span80)复配制备乳状液的过程中,在乳化之前对锂皂石颗粒水分散体系进行稀释,则可以通过一步法制备出性能稳定的W/O/W型Pickering多重乳状液.研究了Span80浓度、锂皂石浓度以及稀释用水的量对生成乳状液的类型及稳定性的影响规律,对一步法合成Pickering多重乳状液的成因及机理进行了探讨和分析.实验结果表明,对锂皂石颗粒水分散体系的稀释是一步法合成稳定Pickering多重乳状液的关键因素,稀释用水的量决定了多重乳状液中的内水相体积.随着Span80浓度的增加,多重乳状液的粒径减小,稳定性迅速增加.锂皂石颗粒的浓度能够影响乳状液的类型,但对乳状液的稳定性以及乳状液的粒径影响不大.锂皂石颗粒在水分散体系中缓慢的扩散速率是一步法

  13. The Preparation of Metal ion Crosslinking Pickering Emulsion and Its Application in Resistance to Formaldehyde Coating%金属离子交联Pickering乳液的制备及其在抗甲醛涂料中应用

    Institute of Scientific and Technical Information of China (English)

    张少飞; 何九军; 杨建东; 崔文辉; 贾如琰

    2015-01-01

    ZnCl2作为金属离子交联剂,纳米Ti02作为表面活性剂,甲基丙烯酸甲酯(MMA)、丙烯酸丁酯(BA)和丙烯酸(AA)作为单体,制备了金属离子交联Pickering乳液,将其与多孔颜填料制备了抗甲醛涂料.研究结果表明,金属离子交联Pickering乳液基抗甲醛涂料(Pickering-C)具有良好的吸甲醛性能,由于该涂料不含挥发性有机溶剂,且安全环保,可以应用于建筑物室内墙壁涂饰与涂装.

  14. Synergistic Stabilization of High Internal Phase Pickering Emulsions by a Mixture of Nanoparticle and Polymer%粒子与聚合物协同稳定高内相Pickering乳液

    Institute of Scientific and Technical Information of China (English)

    邹声文; 王朝阳; 魏增江; 刘浩; 童真

    2012-01-01

    选用二氧化硅纳米粒子(H30)和聚(乳酸-羟基乙酸)共聚物(PLGA)为复合稳定剂,成功制备出内相体积分数高达90%的高内相Pickering乳液.对照实验表明:单独用H30粒子作稳定剂,内相体积分数上限为75%;单独用PLGA作稳定剂,发生严重相分离,不能形成乳液.无机纳米粒子与聚合物之间的协同作用在制备高内相乳液的过程中起到了关键作用.因此,使用无机粒子和聚合物作为混合稳定剂制备高内相乳液是一种新型而有效的方法.%In this paper,we have prepared high internal phase Pickering emulsions(Pickering HIPEs) with internal phase volume fraction 90% which are stabilized by a mixture of silica nanoparticles(H30) and poly(L-lactide-co-glycolide)(PLGA).HIPEs with an internal phase volume not more than 75% could be prepared solely by H30 nanoparticles.Using PLGA as stabilizer,phase separation takes place and stable emulsions are not formed.Synergistic interaction between H30 particles and PLGA molecules plays an im-portant part in preparation of HIPEs.Using inorganic particles and polymer as co-stabilizer will be a new and effective method to prepare HIPEs.

  15. Pickering-type ASA emulsions stabilized by Fe3O4 nanoparticles%纳米Fe3O4稳定的Pickering型ASA乳液

    Institute of Scientific and Technical Information of China (English)

    林兆云; 于得海; 李友明

    2014-01-01

    利用纳米Fe3O4作为稳定剂和乳化剂来制备Pickering型ASA(alkenyl succinic anhydride)施胶乳液,并研究了固体颗粒浓度、油水比、水分散相pH对乳液类型、稳定性、形态及施胶性能的影响。结果表明,纳米Fe3O4能够乳化制备均一稳定的Pickering型ASA乳液。乳液在室温下静置稳定,析出油相体积分数随固体颗粒用量的增加而增大,随油水比的增大而减小。油水比为2:1,水分散相浓度为0.1%(质量分数)时制备的ASA乳液稳定性最佳。固体颗粒部分吸附在油/水界面处,部分分散在分散相中,随分散相中固体颗粒浓度的增加,乳液稳定性变差。乳液静置分层之前,ASA发生部分水解。在放置1 h后用于纸页浆内施胶,随ASA乳液用量的增加,纸页表面接触角逐渐增大,且纸页表面粗糙度下降。在ASA的添加量为1.0%(质量分数)时,纸页表面接触角达到93.5°,纸页表面粗糙度为15.924μm。%Fe3O4 nanoparticles were used as stabilizer and emulsifier to prepare Pickering-type ASA (alkenyl succinic anhydride) emulsions, and the effects of particles concentration, volume ratio of oil/water and pH value on the type, stability, morphology and sizing performance of the emulsions were investigated. Fe3O4 nanoparticles were able to emulsify ASA to prepare homogeneous emulsions. When emulsions were placed without stirring at room temperature, the separated oil phase fraction increased with increasing particles concentration and decreased with increasing volume ratio of oil/water. Emulsions could keep homogeneous phase for 6 h as volume ratio of oil/water was 2 and particles concentration was 0.1%(mass). For stable emulsions, part of particles was absorbed at liquid-liquid interface and part of particles entered the dispersed phase, the stability of emulsions reduced with increasing particles concentration. Before the emulsions creamed, hydrolysis resistance was investigated

  16. Capillary interactions in Pickering emulsions

    Science.gov (United States)

    Guzowski, J.; Tasinkevych, M.; Dietrich, S.

    2011-09-01

    The effective capillary interaction potentials for small colloidal particles trapped at the surface of liquid droplets are calculated analytically. Pair potentials between capillary monopoles and dipoles, corresponding to particles floating on a droplet with a fixed center of mass and subjected to external forces and torques, respectively, exhibit a repulsion at large angular separations and an attraction at smaller separations, with the latter resembling the typical behavior for flat interfaces. This change of character is not observed for quadrupoles, corresponding to free particles on a mechanically isolated droplet. The analytical results are compared with the numerical minimization of the surface free energy of the droplet in the presence of spherical or ellipsoidal particles.

  17. Extracting data from the muck: deriving biological insight from complex microbial communities and non-model organisms with next generation sequencing.

    Science.gov (United States)

    Solomon, Kevin V; Haitjema, Charles H; Thompson, Dawn A; O'Malley, Michelle A

    2014-08-01

    It is becoming increasingly clear that microbes within microbial communities, for which cultured isolates have not yet been obtained, have an immense, untapped reservoir of enzymes that could help address grand challenges in human health, energy, and sustainability. Despite the obstacles associated with culturing these microbes, recent advances in next-generation sequencing (NGS) have made it possible to explore complex microbial communities in their native context for the first time. Key to extracting meaning from rapidly growing NGS datasets are bioinformatics tools that assemble the sequence data, annotate homologous sequences and interrogate it to reveal regulatory patterns. Complementing this are advances in proteomics that can link NGS data to biological function. This combination of next generation sequencing, proteomics and bioinformatic analysis forms a powerful tool to study non-model microbes, which will transform what we know about these dynamic systems.

  18. NGS detection for Chinese primary lung cancer patients gene mutation on EGFR, KRAS, BRAF and PIK3CA%NGS技术检测中国原发性肺癌患者的EGFR、KRAS、BRAF和PIK3CA基因突变

    Institute of Scientific and Technical Information of China (English)

    支修益; 胡牧; 王鑫

    2015-01-01

    Objective To evaluate the feasibility of application of next generation sequencing (NGS) technology in clinical molecular diagnosis of lung cancer. Method The NGS platform-Ion Torrent was utilized in this study to examine the mutational status of EGFR, KRAS, BRAF and PIK3CA in 30 cases of lung cancer. The NGS results were compared with qPCR results. Result The technical parameters of NGS method were stable and the NGS results were entirely consistent with qPCR results (100%). Conclusion After further technical validation of more clinical samples, NGS technology is expected to be applied broadly in clinical setting. It is believed to elevate the molecular diagnosis and individualized treatment of lung cancer to a new level.%目的:评估下一代测序(NGS)技术在原发性肺癌临床分子诊断中应用的可行性。方法本研究应用Ion Torrent NGS平台,一次性检测30例肺癌病理样本EGFR、KRAS、BRAF和PIK3CA基因的突变情况,并与实时荧光定量核酸扩增检测(qPCR)技术检测结果进行对比。结果 NGS检测方法技术参数稳定,且与qPCR技术检测结果完全一致(100%)。结论经过更多临床样本的方法验证后, NGS技术有望得到临床推广,并将原发性肺癌分子诊断和个体化诊疗提高到一个新的水平。

  19. SiO2纳米颗粒与聚氧乙烯对Pickering乳液的协同稳定作用%Stability Mechanisms of Pickering Emulsion Co-stabilized by Silica Nanoparticles and PEO

    Institute of Scientific and Technical Information of China (English)

    谭伟强; 臧渡洋; 李云飞; 张永建; 陆晨君; 栗志广

    2014-01-01

    The Pickering emulsions with 65% water and 35% xylene system stabilized by silica nanoparticles or by both the particles and polyethylene oxide(PEO) additives were prepared. The emulsification was per-formed using a rotor-stator homogenizer under varied rotation speeds from 5000 r/min to 24000 r/min. The emulsion droplets were observed using an optical microscope, consequently, the droplet diameters vs. rotation speed and aging time were obtained. For most cases, W/O type emulsion was obtained. It is found that the mean diameter of water droplets decreases with increasing shear rate or shear duration. With the presence of PEO, the diameters of the droplets are significantly reduced and the phase inversion from W/O to W/O/W is prevented, which occurs in the system without PEO when prolong the shear duration. In addition, the coales-cence of droplets is completely inhibited. To elucidate the ultrastability of the Pickering emulsion resulted from co-stabilization by silica nanoparticles and PEO, we study the rheological properties of the particle layers at the gas-liquid interface using the Langmuir trough equipped with a Wilhelmy plate. The silica nanoparticles were spreaded on the surface of either water or PEO water solution, consequently and the effect of PEO additives on particle layer properties was investigated. The results confirm that PEO additives can favor the trapping of par-ticles at the water/xylene interface, due to the formation of larger size aggregates with the presence of PEO. Therefore, the particle layer has a higher compression modulus. The stronger mechanical property of the parti-cle layer protects the water/xylene interface from rupture when exerted turbulent shearing, hence preventing the occurrence of phase inversion from W/O emulsion to the W/O/W one. Owing to the satisfaction of the Gibbs stability criterion, the coalescence of droplets is almost completely inhibited. The results demonstrate that the rheological properties of the liquid

  20. 水飞蓟宾纳米晶自稳定Pickering乳液的制备及评价%Preparation and evaluation of silybin nanocrystallines self-stabilizing Pickering emulsion

    Institute of Scientific and Technical Information of China (English)

    张继芬; 刘川; 张焦; 易涛

    2016-01-01

    为提高水飞蓟宾的口服生物利用度,以水飞蓟宾纳米晶为固体微粒,采用高压匀质法制备水飞蓟宾纳米晶自稳定Pickering乳液(silybin nanocrystalline self-stabilizing Pickering emulsion,SN-SSPE).考察匀质压力、药物加入量对SN-SSPE形成的影响,以激光共聚焦显微镜、扫描电镜和原子力显微镜等研究表征SN-SSPE的乳滴粒径与形态结构.从乳液的稳定性、体外药物释放和体内药物吸收等方面对SN-SSPE进行评价.结果发现,匀质压力越大,纳米晶粒径越小,压力大于100 MPa时粒径变化较小;水飞蓟宾加入量达到300 mg及其以上时,纳米晶能够完全覆盖油滴表面,形成稳定的SN-SSPE.优化的SN-SSPE乳滴粒径为27.3±3.1 μm,具有明显的核壳状结构.SN-SSPE的稳定性比SN纳米晶混悬液高,至少可稳定40天以上.SN-SSPE的体外释放速率与纳米晶混悬液相似,比原料药显著加快.大鼠灌胃后,SN-SSPE的血药峰浓度相对于纳米晶混悬液和原料药分别提高了2.5倍和2.3倍,AUC分别提高了1.4倍和3.8倍.研究结果表明,难溶性药物纳米晶可以稳定Pickering 乳液;药物纳米晶自稳定Pickering乳液对于提高难溶性药物的口服生物利用度有着广阔的应用前景.

  1. Pickering乳液聚合制备共价键连接的磁性复合微球%Preparation of Covalently-Bonded Magnetic Microspheres by Pickering Emulsion Polymerization

    Institute of Scientific and Technical Information of China (English)

    杜筱; 尹德忠; 刘浩; 马荔; 贾佳

    2012-01-01

    Fe3O4/PMMA Magnetic microspheres with PMMA core and Fe3O4 nanoparticles shell were prepared by Pickering emulsion polymerization. Fe3 O4 Nanoparticles were modified sequentially by TEOS and KH570, which endowed Fe3O4 particles with reactive C=C groups on surface and suitable surface hydrophilicity for Pickering stabilization. The magnetic microspheres were characterized by grain size analyzer,optical microscopy, SEM,FTIR,TGA, and vibration sample magnetometer (VSM). The results indicated that Fe3 O4 in the shell was connected with polymer core by covalent bond which was formed by copolymerization of MMA and reactive C=C group on Fe3O4 stabilizer. The microspheres were spherical in shape,with a diameter of 15-20 /urn, a magnetic content was 4. 9% and a specific saturated magnetization intensity of 2. 38 emu · g-1 .which could be separated easily in a outer magnetic field.%以先后用TEOS和KH570改性的表面含双键的Fe3O4纳米粒子为唯一乳化剂,以甲基丙烯酸甲酯(MMA)为单体,制备了稳定的Pickering乳液,并通过Pickering乳液聚合制备了以PMMA为核、Fe3O4为壳的Fe3O4/PMMA磁性复合微球.用粒度分析仪、光学显微镜、扫描电镜、傅立叶红外光谱仪、热失重分析仪、振动样品磁强计对所制备的改性Fe3O4纳米粒子和磁性复合微球的结构、形态和性能进行了表征.结果表明:通过Fe3O4表面双键与单体的共聚,使微球表面的Fe3O4通过化学键与PMMA连接,所制备磁性复合微球粒径为15~20μm、磁含量为4.9%、比饱和磁化强度为2.38 emu · g-1,可在外磁场下方便地分离.

  2. 科学史与后人文主义--析皮克林的后人文主义科学史观%History of Science and Posthumanism--An Analysis of Pickering's Posthumanism on the Historical Development of Science

    Institute of Scientific and Technical Information of China (English)

    王延锋

    2005-01-01

    分析了当代美国科学知识社会学家安德鲁·皮克林(Andrew Pickering)的科学史观.指出他欲建立独立于科学家的解释方式的"历史解释",以超越传统的逻辑实证(经验)主义的科学史观;摆脱爱丁堡学派的"利益模式"在实践上的困境,以"后人文主义"(posthumanism)的观点来看待当代科学技术的发展;以文化的多样性、异质性来理解实验室中的科学文化.这些新观念对沟通科学文化与人文文化,对科学史与科学哲学、科学社会学等多学科的沟通与融合带来新的理解.

  3. 光交联Pickering乳液中的粒子稳定剂制备胶体体微胶囊%Preparation of Colloidosome Microcapsules Based on Particle Stabilized Photo-Crosslinkable Pickering Emulsions

    Institute of Scientific and Technical Information of China (English)

    王朝阳; 宁印; 陈云华; 童真

    2012-01-01

    In this work,we studied the preparation and emulsification behavior of nanoparticles with photo-sensitive polymer brushes and presented a method for the preparation of novel colloidosome microcapsules based on single Pickering emulsion template,which is stabilized by surface-modified silica nanoparticles with photodimerizable coumarin group.Firstly,silica nanoparticles were self-made by using a st ber method with a diameter of about 180 nm,following aminated by 3-aminopropyltriethoxysilane(APS) and further modified by 2-bromo-2-methylpropionyl bromide,endowing these nanoparticles with ATRP-initiator reactive group.After that,silica nanoparticles with photo-sensitive polymer brushes(SiO2PMMA-PCMA) were obtained through graft reaction of methyl methacrylate(MMA) and 7-(2-methacryloyloxyethoxy)-4-methylcoumarin(CMA) monomers(with a molar fraction of 4∶1) onto silica nanoparticles by surface-initiated atom transfer radical polymerization(SI-ATRP) method.Here,CMA was synthesized via a two-step method and was detected by UV-visible spectrophotometer.Secondly,the as-prepared hydrophobic SiO2-PMMA-PCMA nanoparticles were dispersed in 2 mL of toluene with a ultrasonic for 5 min(with an interval of 30 s per min),then 0.5 mL of deionized water was rapidly added,afterwards,water-in-oil type Pickering emulsions were prepared by hand-shake for 3 min.Finally,colloidosome microcapsules were produced through cross-linking reaction of the coumarin group of CMA initiated by UV irradiation,in this step,the SiO2-PMMA-PCMA nanoparticles were locked.The average size and size distribution of as-synthesized Pickering emulsion droplets and colloidosomes were observed with an optical microscope.The results show that both CMA and SiO2-PMMA-PCMA nanoparticles can be initiated to cross-link through the dimerization of the coumarin groups of CMA from different SiO2-PMMA-PCMA nanoparticles via UV irradiation,the dimerization rate of CMA reached about 80% in 6 min

  4. 纳米SiO2稳定Pickering乳液的研究进展%Progress in research of Pickering emulsion stabilized by nano-SiO2

    Institute of Scientific and Technical Information of China (English)

    高党鸽; 段羲颖; 吕斌; 马建中

    2015-01-01

    介绍了纳米SiO2稳定Picketing乳液的类型、特点和稳定机理.详细介绍了Pickering乳液的制备方法(传统法、微通道乳化法、借助表面活性剂法和表面活性剂与纳米SiO2协同乳化法),以及纳米SiO2稳定Picker-ing乳液的影响因素,包括纳米SiO2的润湿性、纳米SiO2浓度、油相种类和油水比、电解质浓度及水相pH值、SiO2粒子的初始分散位置等;并对其在药物缓释、萃取分离、功能材料以及纺织工业中的应用和发展进行了展望.

  5. Hétérogenéité quantitative et qualitative de la matière organique dans les argiles du Kimmeridgien du val de Pickering (Yorkshire, UK. Cadre sédimentologique et stratigraphique Quantitative and Qualitative Heterogeneity of the Organic Matter Within the Kimmeridge Clay of the Vale of Pickering (Yorkshire, Uk. Sedimentological and Stratigraphical Framework

    Directory of Open Access Journals (Sweden)

    Penn I. E.

    2006-11-01

    Full Text Available Les argiles du Kimméridgien contribuent à l'alimentation de nombreux gisements en mer du Nord. L'étude de quatre puits localisés sur une coupe Est-Ouest dans le Val de Pickering (Bassin de Cleveland permet d'illustrer dans cette formation l'hétérogénéité de distribution verticale et latérale de la matière organique en terme de quantité et de qualité. La coupe étudiée (35 km de long, 200 m de haut représente environ 6,5 millions d'années d'histoire géologique. Les analyses minéralogiques montrent que la formation est caractérisée par une grande homogénéité des apports sédimentaires, ce qui suppose des conditions de sédimentation stables dans le temps et dans l'espace. Le matériel sédimentaire, déposé dans un environnement calme, est composé de minéraux argileux (kaolinite, illite, et interstratifiés irréguliers illite/smectite avec des niveaux carbonatés résultant d'une production biogénique. Ces niveaux carbonatés intercalés au sein des argiles peuvent être corrélés entre les puits. Pour la plupart dolomitisés, ils résultent d'une transformation plus importante àl'ouest (Marton qu'à l'est (Reighton de couches presque exclusivement formées de coccolithes. L'extension horizontale de ces niveaux indique qu'ils correspondent à des événements géodynamiques régionaux. L'étude des ammonites permet de reconnaitre, dans le Yorkshire, la succession de 10 zones du Kimméridgien (sensu anglico et d'identifier 8 sous-zones depuis la zone à Cymodoce (- 144 m. a. jusqu'à celle à Pectinatus (- 137,5 m. a. . Les zonations reconnues permettent de corréler ces quatre puits avec les autres régions d'Angleterre. L'existence de repères stratigraphiques et de repères diagraphiques caractéristiques au sein des zones d'ammonites permet d'établir des zones de corrélation entre une partie bassin (puits de Marton 87, Ebberston 87, Flixton 87 et une zone haute appartenant à la plate-forme Est de l

  6. Preparation of water-based silicone rubber based on nano SiO2/OTAC collaborative Pickering emulsion%纳米SiO2/OTAC协同稳定Pickering乳液聚合制备水基硅橡胶

    Institute of Scientific and Technical Information of China (English)

    翟俊菱; 沈敏敏; 孙淳宁; 王俊凤; 哈成勇

    2015-01-01

    以十八烷基三甲基氯化铵(OTAC)协同纳米SiO2制备Pickering乳液,碱性条件下引发D4开环聚合制备线性聚硅氧烷(PDMS),然后加入交联剂 KH560制备阳离子型水基硅橡胶乳液。考察了纳米 SiO2与 OTAC 用量对Pickering乳液性能的影响,通过zeta电位、TEM及SEM研究了OTAC在SiO2表面的吸附状态,用FT-IR、29Si NMR对水基硅橡胶的结构进行了表征,研究了 KH560用量对橡胶膜对水接触角和邵氏硬度的影响。结果表明:w(SiO2)=2.0%时,乳液流动性和稳定性最优;w(OTAC)=1.75%时,OTAC在纳米SiO2表面的单层吸附达到饱和,单体转化率为89%,粒径为617 nm,zeta电位接近零点,PDMS的数均分子量为16036,PDI为1.485;w(KH560)=5.0%时,KH560与PDMS充分水解缩合,硅橡胶膜憎水性和硬度显著提高。%Pickering emulsion was obtained by using octadecyl trimethyl ammonium chloride (OTAC) in combination with nano SiO2, and linear polysiloxane (PDMS) was synthesized with D4 through ring-open polymerization under alkaline condition, and then cross-linking agent KH560 was added to prepare cationic water-based silicone rubber emulsion. The effects of SiO2 and OTAC contents on Pickering emulsion were investigated. The absorption behavior of OTAC on the surface of SiO2 was revealed by zeta potential, TEM and SEM. The structure of water-based silicone rubber was characterized with FT-IR, 29Si NMR spectra. The effects of KH560 on the contact angle and Shore A hardness of the rubber film were also investigated. The emulsion possessed optimal liquidity and stability when w(SiO2)=2.0%. When w(OTAC)=1.75%, the absorption of OTAC reached saturation on the surface of SiO2, monomer conversion was about 89%, particle size was about 617 nm, zeta potential was close to zero, Mn and PDI for PDMS were 16036 and 1.485 respectively. When w(KH560)=5.0%, PDMS hydrolyzed and condensed fully with KH560, and the obtained rubber film possessed optimal

  7. Hydrophobic Modification of Nano-silica and Its Stabilizing Effect on Pickering Emulsions%纳米二氧化硅的疏水改性及其对Pickering乳液的稳定作用

    Institute of Scientific and Technical Information of China (English)

    王丽; 周宏伟; 蒋文远; 黄畴; 易英

    2016-01-01

    为了探究固体粒子对乳液的稳定作用,采用L-赖氨酸作为催化剂合成纳米SiO2粒子,并用六甲基二硅胺烷(HMDS)对纳米SiO2粒子进行表面疏水改性,将经过HMDS改性后的纳米SiO2粒子作为稳定剂制备出Pickering乳液.通过粒径分析仪、场发射透射电子显微镜、FTIR、TG-DSC、接触角测量仪、光学显微镜、电导率仪分别对纳米SiO2的制备、表面改性和Pickering乳液的性能进行了表征.结果表明,成功合成出粒径小且形貌均一的硅球,具有疏水性的三甲基硅基成功接枝到纳米SiO2的表面;不同纳米SiO2浓度制备的Picketing乳液,发现随着SiO2浓度的增大,乳液的稳定性逐渐增强,乳液液滴直径呈现减小的趋势;不同油水比制备的Pickering乳液,发现随着油相体积的增大,乳液的稳定性呈现增大的趋势.

  8. Preparation of liquid paraffin Pickering emulsions by bacterial cellulose nanocrystals%细菌纤维素纳米晶稳定液体石蜡Pickering乳液的制备

    Institute of Scientific and Technical Information of China (English)

    颜慧琼; 陈秀琼; 刘海芳; 冯玉红; 王向辉; 林强

    2016-01-01

    Bacterial cellulose (BC )was prepared by biological method,and bacterial cellulose nanocrystals (BCN)were prepared by hydrolysis of the BC with concentrate sulfuric acid. Then O/W Pickering emulsions were prepared by liquid paraffin as the oil phase and BCN as the solid emulsifier under the assistance of ultrasonic wave. BC and BCN were characterized by SEM,TEM,FT -IR,XRD,contact angle meter,laser particle size and Zeta potential analyzer. The effects of BCN mass concentration,pH value of the aqueous phase and ionic strength on the stability of the Pickering emulsions were also investigated. Experimental results showed that oxidation of BC occurs during the process of acid hydrolysis and the hydrolysis mainly occurs in the amorphous region,making the crystallization index of BCN be as high as 97%. BCN suspension with the size of 462.5 nm,the Zeta potential value of-40.8 mV and the three phase contact angle of 95.7°,exhibits good emulsifying performance. The particle size of the emulsions prepared under the assistance of ultrasonic wave is 8.6-17.3 μm. Adjustment of pH value of aqueous phase could change the surface charge density of BCN,thereby changing the stability of the emulsions. With the increase of pH value,the volume fraction of the emulsions increases and the stability of the emulsions also improves. With the increase of NaCl concentration, thestabilityoftheemulsionsreducesandthevolumefractionoftheemulsionsdecreases.Inaddition,fromthe SEM observation,the BCN reveal two kinds of morphologies as fiber line and aggregated particles in the stabilizing process of Pickering emulsions.%采用生物法合成了高纯度的细菌纤维素(BC),通过浓硫酸水解制得细菌纤维素纳米晶(BCN)。以液体石蜡为油相,BCN为固体乳化剂,在超声作用下制得O/W型Pickering乳液。通过SEM,TEM,FT-IR,XRD,接触角测量仪及激光粒度和Zeta电位分析仪对BC及BCN进行了表征。考察了BCN质量浓度、水相pH

  9. Modeling the mechanical behaviour of CANDU fuel cladding

    Energy Technology Data Exchange (ETDEWEB)

    Holt, R.A. [Queen' s Univ., Dept. of Mechanical Engineering, Kingston, Ontario (Canada)

    2003-07-01

    Models for the mechanical behaviour of fuel cladding were developed in the period 1973-1983 by staff at AECL CRNL. The models for the mechanical properties of fuel cladding during normal operation were a by-product of programs during the period 1970-1975 to understand the origin of fuel-cladding defects caused by power ramps at Douglas Point and Pickering A. Models for accident conditions were, initially, based heavily on mechanical properties data generated by McGill University and Westinghouse Canada under contract to AECL in the late 1960's and early 1970's and attempts to interpret the data in terms of the underlying deformation mechanisms. The model for normal operating conditions was embodied in the ELESTRES/ELESIM series of codes, and the models for accident conditions were embodied in NIRVANA. (author)

  10. Identification of a novel, CF-causing compound genotype (p.S1159P and p.Y569H) using an NGS-based assay: Novel CF-causing compound p.S1159P and p.Y569H genotype.

    Science.gov (United States)

    Simakova, Tamara; Kondratyeva, Elena; Avakian, Lusine; Bragin, Anton; Zaytseva, Maria; Pavlov, Alexander

    2016-01-10

    A novel combination of two rare pathogenic cystic fibrosis-causing mutations, p.S1159P and p.Y569H, was detected in a patient of 17 years age who suffered from pancreatic insufficiency of unknown etiology. Both mutations were previously described in compound heterozygous patients with moderate lung disease, who carried p.F508del on the other allele. However, this newly described combination of alleles is unusually associated with general gastrointestinal manifestations. Both mutations managed to be identified by virtue of using the Ion PGM next-generation sequencing (NGS) platform, thereby making our work a “proof of concept” for clinical application of a new NGS technology in conjunction with the developed software for variant annotation.

  11. Modelling dopaminergic and other processes involved in learning from reward prediction error: Contributions from an individual differences perspective

    Directory of Open Access Journals (Sweden)

    Alan David Pickering

    2014-09-01

    Full Text Available Phasic firing changes of midbrain dopamine neurons have been widely characterised as reflecting a reward prediction error (RPE. Major personality traits (e.g. extraversion have been linked to inter-individual variations in dopaminergic neurotransmission. Consistent with these two claims, recent research (Smillie, Cooper, & Pickering, 2011; Cooper, Duke, Pickering, & Smillie, 2014 found that extraverts exhibited larger RPEs than introverts, as reflected in feedback related negativity (FRN effects in EEG recordings. Using an established, biologically-localised RPE computational model, we successfully simulated dopaminergic cell firing changes which are thought to modulate the FRN. We introduced simulated individual differences into the model: parameters were systematically varied, with stable values for each simulated individual. We explored whether a model parameter might be responsible for the observed covariance between extraversion and the FRN changes in real data, and argued that a parameter is a plausible source of such covariance if parameter variance, across simulated individuals, correlated almost perfectly with the size of the simulated dopaminergic FRN modulation, and created as much variance as possible in this simulated output. Several model parameters met these criteria, while others did not. In particular, variations in the strength of connections carrying excitatory reward drive inputs to midbrain dopaminergic cells were considered plausible candidates, along with variations in a parameter which scales the effects of dopamine cell firing bursts on synaptic modification in ventral striatum. We suggest possible neurotransmitter mechanisms underpinning these model parameters. Finally, the limitations and possible extensions of our approach are discussed.

  12. 2014 NOAA NGS Topobathy Lidar: Connecticut

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ820G system. The data...

  13. The NGS Pyramid wavefront sensor for ERIS

    Science.gov (United States)

    Riccardi, A.; Antichi, J.; Quirós-Pacheco, F.; Esposito, S.; Carbonaro, L.; Agapito, G.; Biliotti, V.; Briguglio, R.; Di Rico, G.; Dolci, M.; Ferruzzi, D.; Pinna, E.; Puglisi, A.; Xompero, M.; Marchetti, E.; Fedrigo, E.; Le Louarn, M.; Conzelmann, R.; Delabre, B.; Amico, P.; Hubin, N.

    2014-07-01

    ERIS is the new Single Conjugate Adaptive Optics (AO) instrument for VLT in construction at ESO with the collaboration of Max-Planck Institut fuer Extraterrestrische Physik, ETH-Institute for Astronomy and INAF - Osservatorio Astrofisico di Arcetri. The ERIS AO system relies on a 40×40 sub-aperture Pyramid Wavefront Sensor (PWFS) for two operating modes: a pure Natural Guide Star high-order sensing for high Strehl and contrast correction and a low-order visible sensing in support of the Laser Guide Star AO mode. In this paper we present in detail the preliminary design of the ERIS PWFS that is developed under the responsibility of INAF-Osservatorio Astrofisico di Arcetri in collaboration with ESO.

  14. Genetic Testing Requires NGS and Sanger Methodologies.

    Science.gov (United States)

    Jennings, Lawrence J; Kirschmann, Dawn

    2016-09-01

    Investigators from the EuroEPINOMICS rare epilepsy syndromes Dravet working group performed whole-exome sequencing on 31 trios that had been reported negative for SCN1A mutations by Sanger sequencing.

  15. Sambamba : Fast processing of NGS alignment formats

    NARCIS (Netherlands)

    Tarasov, Artem; Vilella, Albert J.; Cuppen, Edwin; Nijman, Isaac J.; Prins, Pjotr

    2015-01-01

    Summary: Sambamba is a high-performance robust tool and library for working with SAM, BAM and CRAM sequence alignment files; the most common file formats for aligned next generation sequencing data. Sambamba is a faster alternative to samtools that exploits multi-core processing and dramatically red

  16. Converting NAD83 GPS Heights Into NAVD88 Elevations With LVGEOID, a Hybrid Geoid Height Model for the Long Valley Volcanic Region, California

    Science.gov (United States)

    Battaglia, Maurizio; Dzurisin, Daniel; Langbein, John; Svarc, Jerry; Hill, David P.

    2008-01-01

    A GPS survey of leveling benchmarks done in Long Valley Caldera in 1999 showed that the application of the National Geodetic Survey (NGS) geoid model GEOID99 to tie GPS heights to historical leveling measurements would significantly underestimate the caldera ground deformation (known from other geodetic measurements). The NGS geoid model was able to correctly reproduce the shape of the deformation, but required a local adjustment to give a realistic estimate of the magnitude of the uplift. In summer 2006, the U.S. Geological Survey conducted a new leveling survey along two major routes crossing the Long Valley region from north to south (Hwy 395) and from east to west (Hwy 203 - Benton Crossing). At the same time, 25 leveling bench marks were occupied with dual frequency GPS receivers to provide a measurement of the ellipsoid heights. Using the heights from these two surveys, we were able to compute a precise geoid height model (LVGEOID) for the Long Valley volcanic region. Our results show that although the LVGEOID and the latest NGS GEOID03 model practically coincide in areas outside the caldera, there is a difference of up to 0.2 m between the two models within the caldera. Accounting for this difference is critical when using the geoid height model to estimate the ground deformation due to magmatic or tectonic activity in the caldera.

  17. Modeling Interfacial Adsorption of Polymer-Grafted Nanoparticles

    Science.gov (United States)

    Yong, Xin

    2014-11-01

    Numerous natural and industrial processes demand advances in our fundamental understanding of colloidal adsorption at liquid interfaces. Using dissipative particle dynamics (DPD), we model the interfacial adsorption of core-shell nanoparticles at the water-oil interface. The solid core of the nanoparticle encompasses beads arranged in an fcc lattice structure and its surface is uniformly grafted with polymer chains. The nanoparticles bind to the interface from either phase to minimize total surface energy. With a single nanoparticle, we demonstrate detailed kinetics of different stages in the adsorption process. Prominent effect of grafted polymer chains is characterized by varying molecular weight and polydispersity of the chains. We also preload nanoparticles straddling the interface to reveal the influence of nanoparticle surface density on further adsorption. Importantly, these studies show how surface-grafted polymer chains can alter the interfacial behavior of colloidal particles and provide guidelines for designing on-demand Pickering emulsion.

  18. NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL

    NARCIS (Netherlands)

    A. May; S. Abeln; M.J. Buijs; J. Heringa; W. Crielaard; B.W. Brandt

    2015-01-01

    Massively parallel sequencing of microbial genetic markers (MGMs) is used to uncover the species composition in a multitude of ecological niches. These sequencing runs often contain a sample with known composition that can be used to evaluate the sequencing quality or to detect novel sequence varian

  19. National Geodetic Control Stations, Geographic NAD83, NGS (2004) [geodetic_ctrl_point_la_NGS_2004

    Data.gov (United States)

    Louisiana Geographic Information Center — This data contains a set of geodetic control stations maintained by the National Geodetic Survey. Each geodetic control station in this dataset has either a precise...

  20. 基于ZigBee无线传输的果园机车防撞防倾翻预警系统%Anti-collision and anti-tipping pre-alarm system of orchard picker based on ZigBee wireless transmission

    Institute of Scientific and Technical Information of China (English)

    杨柳; 穆浩淼; 邓钧文; 宋雨瑶; 刘武

    2014-01-01

    Exploitation of orchard fruit picking locomotive has broad prospects and brings huge economic interests. Meanwhile, China has more complex terrains for orchard distribution, such as plain, hill and terraced hillside, which bring a big security risk for safe and stable driving of orchard locomotive. In order to monitor and prevent tipping, obstacle distance system is particularly important for orchard locomotives in its walking and picking process in the orchard. At present, most pre-alarm system researches are about anti-collision for heavy-duty vehicles or locomotives. There is no system on small vehicles in the orchard, which is working on complex terrain and whose quality is unevenly distributed in the process of moving. This article studies this anti-collision and anti-tipping pre-alarm system of orchard locomotive for further research and improvement. While orchard picker is operating in the orchard, collision and tipping happens easily due to the obstacles and rugged land, which brings danger to the orchard locomotive. In order to give accurate early warning about collision and tipping and ensure to operate orchard picker stably and reliably, this article presents the pre-warning system of anti-rollover collision based on ZigBee wireless transmission. The designed ZigBee wireless network is based on CC2530. The end device collects data from ultrasonic sensor module and spoke type pressure sensors. The design uses a pressure sensor to measure positive pressure between the body and the ground to give rollover warning by comparing with rollover threshold, and uses lateral load transfer ratio (LTR) as an indicator to determine the stability of locomotive tipping. Through the network, the sensor data is sent to the coordinator and then transferred to the computer via RS232 serial port. Alarm is working after the comparison between obtained data and the threshold value. Wireless data transmission test shows that the pre-alarm device realizes the alarm when LTR is 0

  1. 非球形的剑麻纤维素纳米晶须稳定Pickering乳液的制备及稳定因素探讨%Fabrication and Factors of Stabilization of Pickering Emulsion Based on Cellulose Nanowhiskers Extracted from Sisal Fiber

    Institute of Scientific and Technical Information of China (English)

    胡盼盼; 覃倩伊; 刘红霞; 韦春; 吕建

    2015-01-01

    首先利用硫酸酸解剑麻微晶来制备剑麻纤维素纳米晶须(SCNW),继而通过非球形的SCNW来稳定环氧氯丙烷(EPC)/水型Pickering乳液.研究了SCNW的用量、水油体积比及超声时间等因素对SCNW稳定的EPC/水型Pickering乳液的稳定性、结构和形貌的影响.结果表明,当SCNW的量和水油体积比大于1时,SCNW才能稳定EPC/水型Pickering乳液.并且随着SCNW用量的增多、水油体积比的增大,EPC/水型乳液体系中乳滴的粒径越小,而超声乳化时间对乳滴粒径大小则没有多大影响.

  2. Near-surface traveltime tomographic inversion using multiple first break picks

    KAUST Repository

    Saragiotis, Christos

    2013-01-01

    The input data for refraction traveltime tomography are the traveltimes of the first breaks, which are picked using automatic pickers. Although automatic pickers perform satisfactorily overall, no one automatic picker can be characterized as the best one; one picker might fail for traces for which other pickers are accurate and vice versa for other traces. We introduce an iterative method for traveltime tomography, which takes as input traveltimes from a number of pickers. During the inversion scheme inconsistent traveltimes are replaced with more meaningful ones to obtain a smooth near-surface velocity model. The scheme is easily parallelizable and a byproduct of the inversion scheme is a set of consistent traveltimes which is close to the actual traveltimes of the first breaks.

  3. Pickering乳液聚合制备草莓型PSt/SiO_2有机-无机复合微球%Preparation of Raspberry-Like PSt/Si02 Organic-Inorganic Nanocomposite Microspheres Through Pickering Emulsion Polymerization

    Institute of Scientific and Technical Information of China (English)

    张玉红; 董正凤; 王治国; 何培新

    2012-01-01

    Polystyrene /SiO2 composite microspheres were successfully prepared by Pickering emulsion polymerization using a cationic azo initiator (2, 2'-azobis (isobutyramidine) dihydrochloride (AIBA)) in combination with a commercially available glycerol-functionalized ultrafine aqueous silica sol in the absence of any auxiliary comonomer. Transmission electron microscope (TEM) indicates polystyrene/silica particles with raspberry-like morphology. The particle sizes and final silica content range from 190 nm to 300 nm and 28 % to 44 %, respectively. The influences of initial silica content, AIBA content, reaction temperature on the average diameters and silica contents of the composite microspheres were studied. The result indicates that with the initial silica content increase, the diameter of the composite microspheres tends to decrease and the silica contents adsorbed on the latexes surface increase. The silica content increases with the increase of the AIBA amount. With the reaction temperature increase, the average diameter increases, but the variance of silica content is less.%在纳米硅溶胶分散介质中,以苯乙烯(St)为单体,偶氮二异丁脒盐酸盐(AIBA)为引发剂,不添加任何辅助单体,通过Pickering乳液聚合,成功制备了PSt/SiO2有机-无机复合微球,透射电镜研究显示,复合微球具有草莓型形态。所得复合微球粒径在190 nm-300 nm之间,二氧化硅吸附量介于28%-44%之间。研究了初始硅溶胶用量、AIBA用量和反应温度等因素对复合微球粒子粒径和二氧化硅吸附量的影响。结果发现,初始硅溶胶用量增大,复合微球粒径减小、二氧化硅吸附量增大;引发剂用量增加,二氧化硅吸附量增大;反应温度升高,复合微球粒径增大,但对二氧化硅吸附量影响较小。

  4. Detection of deletion mutations of FBN1 in two patients with Marfan syndrome using next generation sequencing (NGS) and multiplex ligation-dependent probe amplification (MLPA) technique%NGS和MLPA技术检测2例马凡综合征患者FBN1基因缺失突变

    Institute of Scientific and Technical Information of China (English)

    卢鑫鑫; 黄肖利; 王韧; 陈喜军; 饶慧英; 吴文冰; 丘丽萍; 黄毅; 伍严安

    2015-01-01

    目的 对2例马凡综合征(Marfan's syndrome,MFS)患者的原纤维蛋白-1基因(FBN1)进行突变检测.方法 提取患者的外周血全基因组DNA,用第二代测序技术(NGS)和多重连接探针扩增技术(MLPA)对FBN1进行突变筛查,对这2种方法提示有拷贝数异常的外显子进行PCR和DNA Sanger测序以证实突变.结果 NGS和MLPA技术检测均显示1例患者有18号外显子缺失突变,另1例患者其56号外显子有缺失突变.经PCR和Sanger测序证实前者18号外显子及其两侧翼区有大片段缺失c.2114-2357_2167+747de13158bp,后者第56号外显子及其内含子有9 bp的缺失突变c.6864_c.6871+1delCTGTGTAGG.结论 NGS和MLPA技术有助于筛查基因组缺失突变,但仍需借助Sanger测序等方法验证.

  5. Models

    DEFF Research Database (Denmark)

    Juel-Christiansen, Carsten

    2005-01-01

    Artiklen fremhæver den visuelle rotation - billeder, tegninger, modeller, værker - som det privilligerede medium i kommunikationen af ideer imellem skabende arkitekter......Artiklen fremhæver den visuelle rotation - billeder, tegninger, modeller, værker - som det privilligerede medium i kommunikationen af ideer imellem skabende arkitekter...

  6. DOMINO: development of informative molecular markers for phylogenetic and genome-wide population genetic studies in non-model organisms.

    Science.gov (United States)

    Frías-López, Cristina; Sánchez-Herrero, José F; Guirao-Rico, Sara; Mora, Elisa; Arnedo, Miquel A; Sánchez-Gracia, Alejandro; Rozas, Julio

    2016-12-15

    The development of molecular markers is one of the most important challenges in phylogenetic and genome wide population genetics studies, especially in studies with non-model organisms. A highly promising approach for obtaining suitable markers is the utilization of genomic partitioning strategies for the simultaneous discovery and genotyping of a large number of markers. Unfortunately, not all markers obtained from these strategies provide enough information for solving multiple evolutionary questions at a reasonable taxonomic resolution. We have developed Development Of Molecular markers In Non-model Organisms (DOMINO), a bioinformatics tool for informative marker development from both next generation sequencing (NGS) data and pre-computed sequence alignments. The application implements popular NGS tools with new utilities in a highly versatile pipeline specifically designed to discover or select personalized markers at different levels of taxonomic resolution. These markers can be directly used to study the taxa surveyed for their design, utilized for further downstream PCR amplification in a broader set taxonomic scope, or exploited as suitable templates to bait design for target DNA enrichment techniques. We conducted an exhaustive evaluation of the performance of DOMINO via computer simulations and illustrate its utility to find informative markers in an empirical dataset. DOMINO is freely available from www.ub.edu/softevol/domino CONTACT: elsanchez@ub.edu or jrozas@ub.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  7. 2014 NOAA NGS Topobathy Lidar: Post Sandy, Rhode Island

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ820G system. The data...

  8. Airborne Gravity: NGS' Gravity Data for EN08 (2013)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for New York, Vermont, New Hampshire, Massachusettes, Maine, and Canada collected in 2013 over 1 survey. This data set is part of the Gravity...

  9. Airborne Gravity: NGS' Gravity Data for EN01 (2011)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for New York, Canada, and Lake Ontario collected in 2011 over 1 survey. This data set is part of the Gravity for the Re-definition of the...

  10. Airborne Gravity: NGS' Gravity Data for CS01 (2014)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alabama and Florida collected in 2008 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical...

  11. Airborne Gravity: NGS' Gravity Data for ES02 (2013)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Florida and the Gulf of Mexico collected in 2013 over 1 survey. This data set is part of the Gravity for the Re-definition of the American...

  12. Airborne Gravity: NGS' Gravity Data for AN05 (2011)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2011 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  13. Airborne Gravity: NGS' Gravity Data for CN02 (2013 & 2014)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Nebraska collected in 2013 & 2014 over 3 surveys. This data set is part of the Gravity for the Re-definition of the American Vertical...

  14. 2014 NOAA NGS Lidar: Intracoastal Waterway, Florida Keys (FL)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ820G system. The data...

  15. Airborne Gravity: NGS' Gravity Data for CS04 (2009)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Texas collected in 2009 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  16. Airborne Gravity: NGS' Gravity Data for CS03 (2009)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Texas and Louisiana collected in 2009 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American Vertical...

  17. 2013 NOAA NGS Topobathy Lidar: Great Egg (NJ)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ820G system. The data...

  18. NGS Gravity Station Data for the U.S.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The gravity station data (1,633,499 records) were gathered by various governmental organizations (and academia) using a variety of methods. This data base was...

  19. Airborne Gravity: NGS' Gravity Data for EN09 (2016)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Massachusetts, Connecticut, Rhode Island, New Hampshire, New York, and the Atlantic Ocean collected in 2012 over 1 survey. This data set is...

  20. Airborne Gravity: NGS' Gravity Data for AS02 (2010)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2010 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  1. Airborne Gravity: NGS' Gravity Data for TS01 (2014)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Puerto Rico and the Virgin Islands collected in 2009 over 1 survey. This data set is part of the Gravity for the Re-definition of the...

  2. Airborne Gravity: NGS' Gravity Data for AN02 (2010)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2010 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  3. Airborne Gravity: NGS' Gravity Data for EN04 (2013)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Michigan and Lake Huron collected in 2012 over 1 survey. This data set is part of the Gravity for the Re-definition of the American...

  4. Airborne Gravity: NGS' Gravity Data for AN03 (2010)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2010 and 2012 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American Vertical Datum...

  5. Airborne Gravity: NGS' Gravity Data for EN06 (2016)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Maine, Canada, and the Atlantic Ocean collected in 2012 over 2 surveys. This data set is part of the Gravity for the Re-definition of the...

  6. Airborne Gravity: NGS' Gravity Data for EN05 (2012)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Minnesota, Wisconsin, and Michigan collected in 2012 over 1 survey. This data set is part of the Gravity for the Re-definition of the...

  7. Airborne Gravity: NGS' Gravity Data for EN10 (2013)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for New York, Pennsylvania, New Jersey, Connecticut and the Atlantic Ocean collected in 2013 over 1 survey. This data set is part of the...

  8. Airborne Gravity: NGS' Gravity Data for AN06 (2011)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2011 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  9. Airborne Gravity: NGS' Gravity Data for AN04 (2010)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2010 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  10. Airborne Gravity: NGS' Gravity Data for PN01 (2014)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for California and Oregon collected in 2011 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical...

  11. Airborne Gravity: NGS' Gravity Data for CS05 (2014)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Texas collected in 2014 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  12. Airborne Gravity: NGS' Gravity Data for ES01 (2013)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Florida, the Bahamas, and the Atlantic Ocean collected in 2013 over 1 survey. This data set is part of the Gravity for the Re-definition of...

  13. Airborne Gravity: NGS' Gravity Data for AS01 (2008)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2008 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  14. Airborne Gravity: NGS' Gravity Data for CS08 (2015)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for CS08 collected in 2006 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  15. Deep characterization of blood cell miRNomes by NGS.

    Science.gov (United States)

    Schwarz, Eva C; Backes, Christina; Knörck, Arne; Ludwig, Nicole; Leidinger, Petra; Hoxha, Cora; Schwär, Gertrud; Grossmann, Thomas; Müller, Sabine C; Hart, Martin; Haas, Jan; Galata, Valentina; Müller, Isabelle; Fehlmann, Tobias; Eichler, Hermann; Franke, Andre; Meder, Benjamin; Meese, Eckart; Hoth, Markus; Keller, Andreas

    2016-08-01

    A systematic understanding of different factors influencing cell type specific microRNA profiles is essential for state-of-the art biomarker research. We carried out a comprehensive analysis of the biological variability and changes in cell type pattern over time for different cell types and different isolation approaches in technical replicates. All combinations of the parameters mentioned above have been measured, resulting in 108 miRNA profiles that were evaluated by next-generation-sequencing. The largest miRNA variability was due to inter-individual differences (34 %), followed by the cell types (23.4 %) and the isolation technique (17.2 %). The change over time in cell miRNA composition was moderate (web resource.

  16. Simplifier: a web tool to eliminate redundant NGS contigs.

    Science.gov (United States)

    Ramos, Rommel Thiago Jucá; Carneiro, Adriana Ribeiro; Azevedo, Vasco; Schneider, Maria Paula; Barh, Debmalya; Silva, Artur

    2012-01-01

    Modern genomic sequencing technologies produce a large amount of data with reduced cost per base; however, this data consists of short reads. This reduction in the size of the reads, compared to those obtained with previous methodologies, presents new challenges, including a need for efficient algorithms for the assembly of genomes from short reads and for resolving repetitions. Additionally after abinitio assembly, curation of the hundreds or thousands of contigs generated by assemblers demands considerable time and computational resources. We developed Simplifier, a stand-alone software that selectively eliminates redundant sequences from the collection of contigs generated by ab initio assembly of genomes. Application of Simplifier to data generated by assembly of the genome of Corynebacterium pseudotuberculosis strain 258 reduced the number of contigs generated by ab initio methods from 8,004 to 5,272, a reduction of 34.14%; in addition, N50 increased from 1 kb to 1.5 kb. Processing the contigs of Escherichia coli DH10B with Simplifier reduced the mate-paired library 17.47% and the fragment library 23.91%. Simplifier removed redundant sequences from datasets produced by assemblers, thereby reducing the effort required for finalization of genome assembly in tests with data from Prokaryotic organisms. Simplifier is available at http://www.genoma.ufpa.br/rramos/softwares/simplifier.xhtmlIt requires Sun jdk 6 or higher.

  17. NGS Gravity Network Data for the U.S.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The gravity network data (7,298 records) were gathered by various governmental organizations (and academia) using a variety of methods.

  18. Airborne Gravity: NGS' Gravity Data for CN03 (2014)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Nebraska collected in 2014 over one survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum...

  19. 2014 NOAA NGS Topobathy Lidar: Post Sandy, Rhode Island

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ820G system. The data...

  20. 2015 NOAA NGS Topobathy Lidar: Buzzards Bay (MA)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ880G system. The data...

  1. 2013 NOAA NGS Topobathy Lidar: Little Egg (NJ)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ820G system. The data...

  2. Airborne Gravity: NGS' Gravity Data for ES03 (2013)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Maryland, Pennsylvania, New Jersey, West Virginia, Virginia, Delaware, and the Atlantic Ocean collected in 2013 over 1 survey. This data...

  3. Detection of chromosome aneuploidy and copy number variation in abortion fetus or chorionic villi using NGS technology%NGS技术检测自然流产胚胎或绒毛染色体非整倍体及拷贝数变异的研究

    Institute of Scientific and Technical Information of China (English)

    赵佳; 毕川; 高雅; 季刚; 汪凌云; 张红云; 李云; 王军; 王威

    2015-01-01

    目的 探索新一代测序技术(NGS)在检测自然流产胚胎或绒毛组织染色体非整倍体和拷贝数变异(CNV)应用中的价值.方法 选择20例自然流产患者的绒毛进行染色体核型分析,同时应用NGS技术进行染色体非整倍体和拷贝数变异的检测,并以染色体核型分析结果为“金标准”进行NGS方法的评估.后于201 3年共收集1 074例自然流产胚胎或绒毛组织,应用NGS技术完成染色体非整倍体和CNV的检测,并对检测结果进行分析.结果 20例自然流产样本的NGS结果与核型分析结果对比,检测灵敏度和特异性均为100%.临床检测的1 074例流产组织样本中,42例样本DNA不符合质控标准,实际完成检测1032例.1 032例组织样本中阳性445例(43.12%),其中非整倍体369例(82.92%),以16、X、22、21、15、1 8号染色体高发;CNV共76例(17.08%),阳性样本集中发生在8-12w.阴性587例(56.88%).根据孕妇年龄将样本分为三组比较,差异有统计学意义(P<0.01).结论 NGS技术用于检测流产组织的非整倍体和拷贝数变异具有较高的灵敏度和特异性,是适用于临床的有效检测方法.

  4. Modelling

    CERN Document Server

    Spädtke, P

    2013-01-01

    Modeling of technical machines became a standard technique since computer became powerful enough to handle the amount of data relevant to the specific system. Simulation of an existing physical device requires the knowledge of all relevant quantities. Electric fields given by the surrounding boundary as well as magnetic fields caused by coils or permanent magnets have to be known. Internal sources for both fields are sometimes taken into account, such as space charge forces or the internal magnetic field of a moving bunch of charged particles. Used solver routines are briefly described and some bench-marking is shown to estimate necessary computing times for different problems. Different types of charged particle sources will be shown together with a suitable model to describe the physical model. Electron guns are covered as well as different ion sources (volume ion sources, laser ion sources, Penning ion sources, electron resonance ion sources, and H$^-$-sources) together with some remarks on beam transport.

  5. Aqueous Dispersions of MgAl Double Hydroxide Particles of Different Forms and Stabilized Pickering Emulsions%不同形态双金属氢氧化物颗粒水分散体系及其稳定的Pickering乳液

    Institute of Scientific and Technical Information of China (English)

    刘国鹏; 王君; 李伟; 刘尚营; 孙德军

    2013-01-01

    3.山东省材料化学安全检测技术重点实验室,济南250103采用共沉淀法制备了3种形态的MgAl双金属氢氧化物颗粒的水分散体系,并以其为乳化剂制备了Pickering乳液.比较了3种颗粒的分散体系及其稳定的Pickering乳液的性质.X射线衍射(XRD)和透射电子显微镜(TEM)表征结果表明,低结晶度的颗粒以形状不规则、结构疏松、表面粗糙的絮状体形式分散于水中,且颗粒尺寸随高速搅拌分散时间的延长而减小;而良好结晶的颗粒以形状规则、结构致密、表面平滑的六角片存在于水中.Zeta电位测试表明,3种颗粒在水中均带正电荷,NaCl可降低颗粒的Zeta电位而使其发生絮凝,但良好结晶颗粒的分散体系在更高NaCl浓度时才出现明显沉淀.分别采用3种双金属氢氧化物颗/NaCl水分散体系制备了水包油(O/w)型Pickering乳液,并比较了乳液的稳定性.结果表明,NaCl的引入在一定程度上可提高3类乳液的稳定性;良好结晶颗粒稳定乳液的能力强于低结晶度的颗粒;对于低结晶度颗粒,大颗粒稳定乳液的能力比小颗粒更强.%Three aqueous dispersions of MgAl double hydroxide particles with different forms were prepared by a copreeipitation method. And then Pickering emulsions were prepared from them. The properties of the aqueous particle dispersions and the emulsions were studied. X-ray diffraction (XRD) and transmission electron mieroseope(TEM) characterizations indicate that the low crystallized particles dispersed in water in the manner of irregular shaped and loose structured particles with rough surfaces, while the well crystallized particles were the compact structured hexagonal platelets with smooth surfaces. Zeta potential measurements show that NaCl reduced the zeta potential of the three particles, resulting in particle floceulation in water. But the well crystallized particle dispersion flocculated in a higher salt concentration. The three

  6. 凹凸棒颗粒稳定的Pickering乳状液的制备条件及形成机理研究%Study on the Preparation Conditions of Olive Oil in Water Pickering Emulsions Stabilized by Attapulgite Particles and Formation Mechanism

    Institute of Scientific and Technical Information of China (English)

    陈浩; 张晓优; 徐樟浩; 赵杰

    2013-01-01

    In this work, attapulgite was selected as emulsifier and the effects of pH value, particle concentration, volume fraction of oil phase and salts of different valences on stability of olive oil-in-water Pickering emulsion were systematically investigated. The results show that the pH value in the range of 4~9 favours the formation of stable emulsions. The increase in concentration of particles can enhance coalescence stability of emulsion. With the increasing volume fraction of oil phase, diameter of the emulsion droplets increases firstly and then decreases. Introduction of the inorganic salt into system doesn’t impact the volumes of the emulsion phase and water phase, but the size distribution of the emulsion droplets are significantly affected. Herein, the increase of NaCl concentration is conducive to the increase in average diameter of emulsion droplets. While CaCl2 concentration increases, average diameter of emulsion droplets increases first and then decreases. Microscope image shows attapulgite particles are mainly attached in the oil-water interface through network structure of aggregates, which plays a role in stabilizing emulsion droplets.%  选取凹凸棒作为乳化剂,系统研究pH值、颗粒质量分数、油相体积分数以及不同价态盐对橄榄油/水型Pickering乳状液稳定性的影响。结果表明,体系pH值在4~9范围内可制备出稳定的乳状液;颗粒质量分数提高可增强乳液的分层和聚结稳定性;乳液液滴直径随油相体积分数的增加先增大后减小;无机盐的引入不会对乳液相及水相体积产生影响,但对乳液液滴的尺寸分布影响显著,其中NaCl浓度的增加有利于乳状液液滴数均直径的增加,而CaCl2浓度增加时,乳状液液滴数均直径呈现先增大后减小的变化趋势。显微镜图片显示,凹凸棒颗粒主要以聚集体网状结构的方式附着在油-水界面处,从而起到稳定乳液液滴的效果。

  7. model

    African Journals Online (AJOL)

    trie neural construction oí inoiviouo! unci communal identities in ... occurs, Including models based on Information processing,1 ... Applying the DSM descriptive approach to dissociation in the ... a personal, narrative path lhal connects personal lo ethnic ..... managed the problem in the context of the community, using a.

  8. A comparison of clinical vs subclinical skin pickers in Israel

    DEFF Research Database (Denmark)

    Keuthen, Nancy J.; Curley, Erin E.; Tung, Esther S.;

    2016-01-01

    BACKGROUND: Skin-picking disorder (SPD) was recognized as its own entity for the first time in DSM-5. The existing SPD literature is limited and, to date, no study has examined the differences between clinical and sub- clinical SPD. Identifying differences between these 2 groups may improve...

  9. A low-cost real color picker based on Arduino.

    Science.gov (United States)

    Agudo, Juan Enrique; Pardo, Pedro J; Sánchez, Héctor; Pérez, Ángel Luis; Suero, María Isabel

    2014-07-07

    Color measurements have traditionally been linked to expensive and difficult to handle equipment. The set of mathematical transformations that are needed to transfer a color that we observe in any object that doesn't emit its own light (which is usually called a color-object) so that it can be displayed on a computer screen or printed on paper is not at all trivial. This usually requires a thorough knowledge of color spaces, colorimetric transformations and color management systems. The TCS3414CS color sensor (I2C Sensor Color Grove), a system for capturing, processing and color management that allows the colors of any non-self-luminous object using a low-cost hardware based on Arduino, is presented in this paper. Specific software has been developed in Matlab and a study of the linearity of chromatic channels and accuracy of color measurements for this device has been undertaken. All used scripts (Arduino and Matlab) are attached as supplementary material. The results show acceptable accuracy values that, although obviously do not reach the levels obtained with the other scientific instruments, for the price difference they present a good low cost option.

  10. Food-grade Pickering emulsions stabilised with solid lipid particles.

    Science.gov (United States)

    Pawlik, Aleksandra; Kurukji, Daniel; Norton, Ian; Spyropoulos, Fotis

    2016-06-15

    Aqueous dispersions of tripalmitin particles (with a minimum size of 130 nm) were produced, via a hot sonication method, with and without the addition of food-grade emulsifiers. Depending on their relative size and chemistry, the emulsifiers altered the properties of the fat particles (e.g. crystal form, dispersion state and surface properties) by two proposed mechanisms. Firstly, emulsifiers modify the rate and/or extent of polymorphic transitions, resulting in the formation of fat crystals with a range of polarities. Secondly, the adsorption of emulsifiers at the particle interface modifies crystal surface properties. Such emulsifier-modified fat particles were then used to stabilise emulsions. As the behaviour of these particles was predisposed by the kind of emulsifier employed for their manufacture, the resulting particles showed different preferences to which of the emulsion phases (oil or water) became the continuous one. The polarity of the fat particles decreased as follows: Whey Protein Isolate > Soy Lecithin > Soy Lecithin + Tween 20 > Tween 20 > Polyglycerol Polyricinoleate > no emulsifier. Consequently, particles stabilised with WPI formed oil-in-water emulsions (O/W); particles stabilised solely with lecithin produced a highly unstable W/O emulsion; and particles stabilised with a mixture of lecithin and Tween 20 gave a stable W/O emulsion with drop size up to 30 μm. Coalescence stable, oil-continuous emulsions (W/O) with drop sizes between 5 and 15 μm were produced when the tripalmitin particles were stabilised with solely with Tween 20, solely with polyglycerol polyricinoleate, or with no emulsifier at all. It is proposed that the stability of the latter three emulsions was additionally enhanced by sintering of fat particles at the oil-water interface, providing a mechanical barrier against coalescence.

  11. Thermodynamically Stable Pickering Emulsions Stabilized by Janus Dumbbells

    Science.gov (United States)

    Tu, Fuquan; Park, Bum Jun; Lee, Daeyeon

    2013-03-01

    Janus particles have two sides with different, often opposite, surface properties. Janus dumbbell is one type of Janus particles that consists of two partially fused spherical lobes. It is possible to independently control the geometry and surface wettability of Janus dumbbells. Janus dumbbells can also be produced in a large quantity, making them useful for practical applications such as emulsion stabilization. In this work, we calculate the free energy of emulsion formation using amphiphilic Janus dumbbells as solid surfactants. In contrast to kinetically stable emulsions stabilized by homogeneous particles, emulsion stabilized by Janus dumbbells can be thermodynamically stable. There also exists an optimal radius of droplets that can be stabilized by infinite or limited number of amphiphilic dumbbells in the continuous phase. We demonstrate that the optimal radius of dumbbell-stabilized droplets can be predicted based on the volume of the dispersed phase and the volume fraction of dumbbells in the continuous phase. We believe our calculation will provide guidelines for using Janus dumbbells as colloid surfactants to generate stable emulsions.

  12. Multiwalled Carbon Nanotubes at the Interface of Pickering Emulsions.

    Science.gov (United States)

    Briggs, Nicholas M; Weston, Javen S; Li, Brian; Venkataramani, Deepika; Aichele, Clint P; Harwell, Jeffrey H; Crossley, Steven P

    2015-12-01

    Carbon nanotubes exhibit very unique properties in biphasic systems. Their interparticle attraction leads to reduced droplet coalescence rates and corresponding improvements in emulsion stability. Here we use covalent and noncovalent techniques to modify the hydrophilicity of multiwalled carbon nanotubes (MWCNTs) and study their resulting behavior at an oil-water interface. By using both paraffin wax/water and dodecane/water systems, the thickness of the layer of MWNTs at the interface and resulting emulsion stability are shown to vary significantly with the approach used to modify the MWNTs. Increased hydrophilicity of the MWNTs shifts the emulsions from water-in-oil to oil-in-water. The stability of the emulsion is found to correlate with the thickness of nanotubes populating the oil-water interface and relative strength of the carbon nanotube network. The addition of a surfactant decreases the thickness of nanotubes at the interface and enhances the overall interfacial area stabilized at the expense of increased droplet coalescence rates. To the best of our knowledge, this is the first time the interfacial thickness of modified carbon nanotubes has been quantified and correlated to emulsion stability.

  13. Destabilising Pickering emulsions by drop flocculation and adhesion.

    Science.gov (United States)

    Whitby, Catherine P; Khairul Anwar, Hunainah; Hughes, James

    2016-03-01

    We have investigated how emulsions of water drops coated by organoclay particles destabilise in organic solvents. The drops destabilise and the emulsions undergo a fluid-solid transition if the particles are poorly wetted by the solvent. We show that the drops adhere together and form three-dimensional networks as the fraction of the poor-quality solvent in the mixture increases. Microscopic observations revealed that the drops coalesce into buckled, non-spherical shapes in mixtures rich in poor-quality solvent. A key finding is that destabilisation is favoured under conditions where the energy of adhesion between the particle layers coating drops is comparable to the energy required to detach the particles from the drops. Rupture of the interfacial layer produces particle flocs and uncoated, unstable water drops that settle out of the emulsion.

  14. An automatic P‐Phase arrival‐time picker

    Science.gov (United States)

    Kalkan, Erol

    2016-01-01

    Presented is a new approach for picking P‐phase arrival time in single‐component acceleration or broadband velocity records without requiring detection interval or threshold settings. The algorithm PPHASEPICKER transforms the signal into a response domain of a single‐degree‐of‐freedom (SDOF) oscillator with viscous damping and then tracks the rate of change of dissipated damping energy to pick P‐wave phases. The SDOF oscillator has a short natural period and a correspondingly high resonant frequency, which is higher than most frequencies in a seismic wave. It also has a high damping ratio (60% of critical). At this damping level, the frequency response approaches the Butterworth maximally flat magnitude filter, and phase angles are preserved. The relative input energy imparted to the oscillator by the input signal is converted to elastic strain energy and then dissipated by the damping element as damping energy. The damping energy yields a smooth envelope over time; it is zero in the beginning of the signal, zero or near zero before theP‐phase arrival, and builds up rapidly with the P wave. Because the damping energy function changes considerably at the onset of the P wave, it is used as a metric to track and pick the P‐phase arrival time. The PPHASEPICKER detects P‐phase onset using the histogram method. Its performance is compared with picking techniques using short‐term‐average to long‐term‐average ratio, and a picking method that finds the first P‐phase arrival time using the Akaike information criterion. A large set of records with various intensities and signal‐to‐noise ratios is used for testing the PPHASEPICKER, and it is demonstrated thatPPHASEPICKER is able to more accurately pick the onset of genuine signals against the background noise and to correctly distinguish between whether the first arrival is a P wave (emergent or impulsive) or whether the signal is from a faulty sensor.

  15. Pickering emulsions stabilized by paraffin wax and Laponite clay particles.

    Science.gov (United States)

    Li, Caifu; Liu, Qian; Mei, Zhen; Wang, Jun; Xu, Jian; Sun, Dejun

    2009-08-01

    Emulsions containing wax in dispersed droplets stabilized by disc-like Laponite clay particles are prepared. Properties of the emulsions prepared at different temperatures are examined using stability, microscopy and droplet-size analysis. At low temperature, the wax crystals in the oil droplets can protrude through the interface, leading to droplet coalescence. But at higher temperatures, the droplet size decreases with wax concentration. Considering the viscosity of the oil phase and the interfacial tension, we conclude that the wax is liquid-like during the high temperature emulsification process, but during cooling wax crystals appear around the oil/water interface and stabilize the droplets. The oil/water ratio has minimal effect on the emulsions between ratios of 3:7 and 7:3. The Laponite is believed to stabilize the emulsions by increasing the viscosity of the continuous phase and also by adsorbing at the oil/water interface, thus providing a physical barrier to coalescence.

  16. A phase-field point-particle model for particle-laden interfaces

    Science.gov (United States)

    Gu, Chuan; Botto, Lorenzo

    2014-11-01

    The irreversible attachment of solid particles to fluid interfaces is exploited in a variety of applications, such as froth flotation and Pickering emulsions. Critical in these applications is to predict particle transport in and near the interface, and the two-way coupling between the particles and the interface. While it is now possible to carry out particle-resolved simulations of these systems, simulating relatively large systems with many particles remains challenging. We present validation studies and preliminary results for a hybrid Eulerian-Lagrangian simulation method, in which the dynamics of the interface is fully-resolved by a phase-field approach, while the particles are treated in the ``point-particle'' approximation. With this method, which represents a compromise between the competing needs of resolving particle and interface scale phenomena, we are able to simulate the adsorption of a large number of particles in the interface of drops, and particle-interface interactions during the spinodal coarsening of a multiphase system. While this method models the adsorption phenomenon efficiently and with reasonable accuracy, it still requires understanding subtle issues related to the modelling of hydrodynamic and capillary forces for particles in contact with interface.

  17. H-TArget model: Early technology assessment for ext generation sequencing in oncology

    NARCIS (Netherlands)

    Retel, Valesca P.; Joore, Manuela A.; Ramaekers, Bram; Heuvel, van den Michel M.; Heijden, van der Michiel Simon; Harten, van W.H.

    2015-01-01

    Background: Next Generation Sequencing (NGS) promises to find mutations (targets) in individual cancer patients, to subsequently prescribe targeted therapy. Currently, NGS is in development, the effects on choice of therapy and prognosis are still unclear, and the costs for targeted therapies are hi

  18. Model-independent analyses of non-Gaussianity in Planck CMB maps using Minkowski functionals

    Science.gov (United States)

    Buchert, Thomas; France, Martin J.; Steiner, Frank

    2017-05-01

    Despite the wealth of Planck results, there are difficulties in disentangling the primordial non-Gaussianity of the Cosmic Microwave Background (CMB) from the secondary and the foreground non-Gaussianity (NG). For each of these forms of NG the lack of complete data introduces model-dependences. Aiming at detecting the NGs of the CMB temperature anisotropy δ T , while paying particular attention to a model-independent quantification of NGs, our analysis is based upon statistical and morphological univariate descriptors, respectively: the probability density function P(δ T) , related to v0, the first Minkowski Functional (MF), and the two other MFs, v1 and v2. From their analytical Gaussian predictions we build the discrepancy functions {{ Δ }k} (k  =  P, 0, 1, 2) which are applied to an ensemble of 105 CMB realization maps of the Λ CDM model and to the Planck CMB maps. In our analysis we use general Hermite expansions of the {{ Δ }k} up to the 12th order, where the coefficients are explicitly given in terms of cumulants. Assuming hierarchical ordering of the cumulants, we obtain the perturbative expansions generalizing the second order expansions of Matsubara to arbitrary order in the standard deviation {σ0} for P(δ T) and v0, where the perturbative expansion coefficients are explicitly given in terms of complete Bell polynomials. The comparison of the Hermite expansions and the perturbative expansions is performed for the Λ CDM map sample and the Planck data. We confirm the weak level of non-Gaussianity (1-2)σ of the foreground corrected masked Planck 2015 maps.

  19. Modeling and interoperability of heterogeneous genomic big data for integrative processing and querying.

    Science.gov (United States)

    Masseroli, Marco; Kaitoua, Abdulrahman; Pinoli, Pietro; Ceri, Stefano

    2016-12-01

    While a huge amount of (epi)genomic data of multiple types is becoming available by using Next Generation Sequencing (NGS) technologies, the most important emerging problem is the so-called tertiary analysis, concerned with sense making, e.g., discovering how different (epi)genomic regions and their products interact and cooperate with each other. We propose a paradigm shift in tertiary analysis, based on the use of the Genomic Data Model (GDM), a simple data model which links genomic feature data to their associated experimental, biological and clinical metadata. GDM encompasses all the data formats which have been produced for feature extraction from (epi)genomic datasets. We specifically describe the mapping to GDM of SAM (Sequence Alignment/Map), VCF (Variant Call Format), NARROWPEAK (for called peaks produced by NGS ChIP-seq or DNase-seq methods), and BED (Browser Extensible Data) formats, but GDM supports as well all the formats describing experimental datasets (e.g., including copy number variations, DNA somatic mutations, or gene expressions) and annotations (e.g., regarding transcription start sites, genes, enhancers or CpG islands). We downloaded and integrated samples of all the above-mentioned data types and formats from multiple sources. The GDM is able to homogeneously describe semantically heterogeneous data and makes the ground for providing data interoperability, e.g., achieved through the GenoMetric Query Language (GMQL), a high-level, declarative query language for genomic big data. The combined use of the data model and the query language allows comprehensive processing of multiple heterogeneous data, and supports the development of domain-specific data-driven computations and bio-molecular knowledge discovery. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Large animal models of rare genetic disorders: sheep as phenotypically relevant models of human genetic disease.

    Science.gov (United States)

    Pinnapureddy, Ashish R; Stayner, Cherie; McEwan, John; Baddeley, Olivia; Forman, John; Eccles, Michael R

    2015-09-02

    Animals that accurately model human disease are invaluable in medical research, allowing a critical understanding of disease mechanisms, and the opportunity to evaluate the effect of therapeutic compounds in pre-clinical studies. Many types of animal models are used world-wide, with the most common being small laboratory animals, such as mice. However, rodents often do not faithfully replicate human disease, despite their predominant use in research. This discordancy is due in part to physiological differences, such as body size and longevity. In contrast, large animal models, including sheep, provide an alternative to mice for biomedical research due to their greater physiological parallels with humans. Completion of the full genome sequences of many species, and the advent of Next Generation Sequencing (NGS) technologies, means it is now feasible to screen large populations of domesticated animals for genetic variants that resemble human genetic diseases, and generate models that more accurately model rare human pathologies. In this review, we discuss the notion of using sheep as large animal models, and their advantages in modelling human genetic disease. We exemplify several existing naturally occurring ovine variants in genes that are orthologous to human disease genes, such as the Cln6 sheep model for Batten disease. These, and other sheep models, have contributed significantly to our understanding of the relevant human disease process, in addition to providing opportunities to trial new therapies in animals with similar body and organ size to humans. Therefore sheep are a significant species with respect to the modelling of rare genetic human disease, which we summarize in this review.

  1. Animal Models of Ionizing Radiation Damage

    Science.gov (United States)

    1992-01-01

    Haggbloom, and R.A. Gazzara, Effects of Hippocampal X-irradiation-Produced Granule-Cell Agenesis on Instrumental Runway Performance in Rats, Physiol...Bowden, and J.P. Wyatt, A Pathway To Pulmonary Fibrosis: An Ultrastructural Study Of Mouse and Rat Following Radiation to the Whole Body and Hemithorax...532-536, 1956. 27. Brooks, P.M., E.O. Richey, and J.E. Pickering, Prompt Pulmonary Ventilation and Oxygen Consumption Changes in Rhesus Monkeys

  2. TESTING OF HOME-MADE NANFANG NGS-200 STATIC GPS RECEIVER%国产南方NGS-200静态GPS接收机的测试

    Institute of Scientific and Technical Information of China (English)

    朱开文; 陈现春

    2000-01-01

    本文通过在原有GPS网上使用南方GPS接收机布设GPS网进行观测,同时以武汉测绘科技大学GPS处理软件与南方GPS处理软件分别进行计算与平差,在资料分析比较的基础上,对南方GPS软硬件的优缺点提出了自己的见解和看法.

  3. Epistasis analysis for quantitative traits by functional regression model.

    Science.gov (United States)

    Zhang, Futao; Boerwinkle, Eric; Xiong, Momiao

    2014-06-01

    The critical barrier in interaction analysis for rare variants is that most traditional statistical methods for testing interactions were originally designed for testing the interaction between common variants and are difficult to apply to rare variants because of their prohibitive computational time and poor ability. The great challenges for successful detection of interactions with next-generation sequencing (NGS) data are (1) lack of methods for interaction analysis with rare variants, (2) severe multiple testing, and (3) time-consuming computations. To meet these challenges, we shift the paradigm of interaction analysis between two loci to interaction analysis between two sets of loci or genomic regions and collectively test interactions between all possible pairs of SNPs within two genomic regions. In other words, we take a genome region as a basic unit of interaction analysis and use high-dimensional data reduction and functional data analysis techniques to develop a novel functional regression model to collectively test interactions between all possible pairs of single nucleotide polymorphisms (SNPs) within two genome regions. By intensive simulations, we demonstrate that the functional regression models for interaction analysis of the quantitative trait have the correct type 1 error rates and a much better ability to detect interactions than the current pairwise interaction analysis. The proposed method was applied to exome sequence data from the NHLBI's Exome Sequencing Project (ESP) and CHARGE-S study. We discovered 27 pairs of genes showing significant interactions after applying the Bonferroni correction (P-values < 4.58 × 10(-10)) in the ESP, and 11 were replicated in the CHARGE-S study.

  4. Bayesian state space models for dynamic genetic network construction across multiple tissues.

    Science.gov (United States)

    Liang, Yulan; Kelemen, Arpad

    2016-08-01

    Construction of gene-gene interaction networks and potential pathways is a challenging and important problem in genomic research for complex diseases while estimating the dynamic changes of the temporal correlations and non-stationarity are the keys in this process. In this paper, we develop dynamic state space models with hierarchical Bayesian settings to tackle this challenge for inferring the dynamic profiles and genetic networks associated with disease treatments. We treat both the stochastic transition matrix and the observation matrix time-variant and include temporal correlation structures in the covariance matrix estimations in the multivariate Bayesian state space models. The unevenly spaced short time courses with unseen time points are treated as hidden state variables. Hierarchical Bayesian approaches with various prior and hyper-prior models with Monte Carlo Markov Chain and Gibbs sampling algorithms are used to estimate the model parameters and the hidden state variables. We apply the proposed Hierarchical Bayesian state space models to multiple tissues (liver, skeletal muscle, and kidney) Affymetrix time course data sets following corticosteroid (CS) drug administration. Both simulation and real data analysis results show that the genomic changes over time and gene-gene interaction in response to CS treatment can be well captured by the proposed models. The proposed dynamic Hierarchical Bayesian state space modeling approaches could be expanded and applied to other large scale genomic data, such as next generation sequence (NGS) combined with real time and time varying electronic health record (EHR) for more comprehensive and robust systematic and network based analysis in order to transform big biomedical data into predictions and diagnostics for precision medicine and personalized healthcare with better decision making and patient outcomes.

  5. Airborne Gravity: NGS' Airborne Gravity Data for AN01 (2009-2010)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2009-2010 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American Vertical Datum...

  6. 2016 NOAA NGS Ortho-rectified Color Mosaic of Baton Rouge, Louisiana

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  7. Bioinformatics for NGS-based metagenomics and the application to biogas research.

    Science.gov (United States)

    Jünemann, Sebastian; Kleinbölting, Nils; Jaenicke, Sebastian; Henke, Christian; Hassa, Julia; Nelkner, Johanna; Stolze, Yvonne; Albaum, Stefan P; Schlüter, Andreas; Goesmann, Alexander; Sczyrba, Alexander; Stoye, Jens

    2017-08-18

    Metagenomics has proven to be one of the most important research fields for microbial ecology during the last decade. Starting from 16S rRNA marker gene analysis for the characterization of community compositions to whole metagenome shotgun sequencing which additionally allows for functional analysis, metagenomics has been applied in a wide spectrum of research areas. The cost reduction paired with the increase in the amount of data due to the advent of next-generation sequencing led to a rapidly growing demand for bioinformatic software in metagenomics. By now, a large number of tools that can be used to analyze metagenomic datasets has been developed. The Bielefeld-Gießen center for microbial bioinformatics as part of the German Network for Bioinformatics Infrastructure bundles and imparts expert knowledge in the analysis of metagenomic datasets, especially in research on microbial communities involved in anaerobic digestion residing in biogas reactors. In this review, we give an overview of the field of metagenomics, introduce into important bioinformatic tools and possible workflows, accompanied by application examples of biogas surveys successfully conducted at the Center for Biotechnology of Bielefeld University. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

  8. 2016 NOAA NGS Ortho-rectified Color Mosaic of Corpus Christi and Port Ingleside, Texas

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  9. An Infrared Census of DUST in Nearby Galaxies with Spitzer (DUSTiNGS), I. Overview

    CERN Document Server

    Boyer, Martha L; Barmby, Pauline; Bonanos, Alceste Z; Gehrz, Robert D; Gordon, Karl D; Groenewegen, M A T; Lagadec, Eric; Lennon, Daniel; Marengo, Massimo; Meixner, Margaret; Skillman, Evan; Sloan, G C; Sonneborn, George; van Loon, Jacco Th; Zijlstra, Albert

    2014-01-01

    Nearby resolved dwarf galaxies provide excellent opportunities for studying the dust-producing late stages of stellar evolution over a wide range of metallicity (-2.7 75% complete at the tip of the Red Giant Branch for all targeted galaxies, with the exception of the crowded inner regions of IC 10, NGC 185, and NGC 147. This photometric depth ensures that the majority of the dust-producing stars, including the thermally-pulsing AGB stars, are detected in each galaxy. The images map each galaxy to at least twice the half-light radius to ensure that the entire evolved star population is included and to facilitate the statistical subtraction of background and foreground contamination, which is severe at these wavelengths. In this overview, we describe the survey, the data products, and preliminary results. We show evidence for the presence of dust-producing AGB stars in 8 of the targeted galaxies, with metallicities as low as [Fe/H] = -1.9, suggesting that dust production occurs even at low metallicity.

  10. National Geodetic Survey (NGS) Geodetic Control Stations, (Horizontal and/or Vertical Control), March 2009

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — This data contains a set of geodetic control stations maintained by the National Geodetic Survey. Each geodetic control station in this dataset has either a precise...

  11. 2016 NOAA NGS Ortho-rectified Near-Infrared Mosaic of St. Paul Island, Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  12. Airborne Gravity: NGS' Gravity Data for EN03 (2011-2013)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Michigan, Wisconsin, Illinois, Indiana, and Lake Michigan collected in 2011 to 2013 over 3 surveys. This data set is part of the Gravity...

  13. Airborne Gravity: NGS' Gravity Data for EN02 (2011-2012)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for New York, Pennsylvania, Ohio, Michigan, Canada and Lake Erie collected in 2011 and 2012 over 3 surveys. This data set is part of the...

  14. The Power of Inbreeding: NGS-Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication.

    Science.gov (United States)

    Wang, Hongru; Xu, Xun; Vieira, Filipe Garrett; Xiao, Yunhua; Li, Zhikang; Wang, Jun; Nielsen, Rasmus; Chu, Chengcai

    2016-07-01

    Low-coverage whole-genome sequencing is an effective strategy for genome-wide association studies in humans, due to the availability of large reference panels for genotype imputation. However, it is unclear whether this strategy can be utilized in other species without reference panels. Using simulations, we show that this approach is even more relevant in inbred species such as rice (Oryza sativa L.), which are effectively haploid, allowing easy haplotype construction and imputation-based genotype calling, even without the availability of large reference panels. We sequenced 203 rice varieties with well-characterized phenotypes from the United States Department of Agriculture Rice Mini-Core Collection at an average depth of 1.5× and used the data for mapping three traits. For the first two traits, amylose content and seed length, our approach leads to direct identification of the previously identified causal SNPs in the major-effect loci. For the third trait, pericarp color, an important trait underwent selection during domestication, we identified a new major-effect locus. Although known loci can explain color variation in the varieties of two main subspecies of Asian domesticated rice, japonica and indica, the new locus identified is unique to another domesticated rice subgroup, aus, and together with existing loci, can fully explain the major variation in pericarp color in aus. Our discovery of a unique genetic basis of white pericarp in aus provides an example of convergent evolution during rice domestication and suggests that aus may have a domestication history independent of japonica and indica.

  15. Airborne Gravity: NGS' Gravity Data for ES04 (2013-2014)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for North Carolina, South Carolina, Virginia, and the Atlantic Ocean collected in 2013 and 2014 over two surveys. This data set is part of the...

  16. 2016 NOAA NGS Ortho-rectified Color Mosaic of Skagway, Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  17. 2016 NOAA NGS Ortho-rectified Color Mosaic of Snug Harbor, Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  18. 2016 NOAA NGS Ortho-rectified Near-Infrared Mosaic of Kenai and Nikiski, Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  19. NOS/NGS activities to support development of radio interferometric surveying techniques

    Science.gov (United States)

    Carter, W. E.; Dracup, J. F.; Hothem, L. D.; Robertson, D. S.; Strange, W. E.

    1980-01-01

    National Geodetic Survey activities towards the development of operational geodetic survey systems based on radio interferometry are reviewed. Information about the field procedures, data reduction and analysis, and the results obtained to date is presented.

  20. 2016 NOAA NGS Ortho-rectified Color Mosaic of Cordova, Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  1. Darlington NGS A: SGECS condensation induced waterhammer analysis and SGECS hot commissioning test

    Energy Technology Data Exchange (ETDEWEB)

    So, C.W. [Atomic Energy of Canada Limited, Darlington Nuclear Generating Station, Bowmanville, ON (Canada); Chang, P.L.; Meranda, D.G. [Ontario Hydro, Darlington Nuclear Generating Station, Bowmanville, ON (Canada)

    1997-07-01

    In the event of an accident such as the main steam line break, the reheater drain pump and the feedwater pump could fail. As a result, feedwater to the steam generators (SG-1 and SG-3) will stop, and the inventory in the SGs flash. This would cause depressurization of the SGs and formation of steam void in the piping of the Steam Generator Emergency Cooling System (SGECS). The subsequent low SG pressure will initiate the SGECS injection into the SGs. Upon the injection of the cold SGECS fluid to the steam filled SGECS piping, condensation would take place, and condensation induced waterhammer in the SGECS may occur. As an interim measure to protect the SGECS piping, the Second Stage Reheater Drain (RHD) flow to the SGs was suspended. This resulted in a 3% loss of power, a significant economic penalty to the heat cycle of the turbine. To remove the economic penalty, the original design of the SGECS was revised. To ensure the adequacy of the revised design, condensation induced waterhammer analysis were performed. The predicted pressure transients have passed the allowable level of stress limits. The analysis was presented to the AECB. Although the AECB has accepted the analytical results, the AECB requested a 'hot' commissioning test at site to demonstrate that the revised design does meet the operation requirement. The test was successfully performed. Subsequently, the AECB has allowed OH to re-instate the Second Stage Reheater Drain flow to the SGs. (author)

  2. 2016 NOAA NGS Ortho-rectified Color Mosaic of St. Paul Island, Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  3. 2016 NOAA NGS Ortho-rectified Near-Infrared Mosaic of Juneau and Auke Bay, Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  4. Detection of a Novel DSPP Mutation by NGS in a Population Isolate in Madagascar

    Science.gov (United States)

    Bloch-Zupan, Agnès; Huckert, Mathilde; Stoetzel, Corinne; Meyer, Julia; Geoffroy, Véronique; Razafindrakoto, Rabisoa W.; Ralison, Saholy N.; Randrianaivo, Jean-Claude; Ralison, Georgette; Andriamasinoro, Rija O.; Ramanampamaharana, Rija H.; Randrianazary, Solofomanantsoa E.; Ralimanana, Louise H.; Richard, Béatrice; Gorry, Philippe; Manière, Marie-Cécile; Rasoamananjara, Jeanne A.; Rakoto Alson, Simone; Dollfus, Hélène

    2016-01-01

    A large family from a small village in Madagascar, Antanetilava, is known to present with colored teeth. Through previous collaboration and 4 successive visits in 1994, 2004, 2005, and 2012, we provided dental care to the inhabitants and diagnosed dentinogenesis imperfecta. Recently, using whole exome sequencing we confirmed the clinical diagnosis by identifying a novel single nucleotide deletion in exon 5 of DSPP. This paper underlines the necessity of long run research, the importance of international and interpersonal collaborations as well as the major contribution of next generation sequencing tools in the genetic diagnosis of rare oro-dental anomalies. This study is registered in ClinicalTrials (https://clinicaltrials.gov) under the number NCT02397824. PMID:26973538

  5. Building A NGS Genomic Resource: Towards Molecular Breeding In L. Perenne

    DEFF Research Database (Denmark)

    Ruttink, Tom; Roldán-Ruiz, Isabel; Asp, Torben

    To advance the application of molecular breeding in Lolium perenne, we have generated a sequence resource to facilitate gene discovery and SNP marker development. Illumina GAII transcriptome sequencing was performed on meristem-enriched samples of 14 Lolium genotypes. De novo assemblies for indiv......To advance the application of molecular breeding in Lolium perenne, we have generated a sequence resource to facilitate gene discovery and SNP marker development. Illumina GAII transcriptome sequencing was performed on meristem-enriched samples of 14 Lolium genotypes. De novo assemblies...... of SNP markers in selected candidate genes. In parallel, a germplasm collection of 602 Lolium genotypes was established and is being phenotyped for plant architecture, reproductive characteristics, flowering time, and forage quality traits. We will test through association genetics whether phenotypic...

  6. Discriminating metastasised from non-metastasised seminoma based on transcriptional changes in primary tumours using NGS.

    Science.gov (United States)

    Ruf, C G; Schmelz, H-U; Port, M; Wagner, W; Matthies, C; Müller-Myhsok, B; Meineke, V; Abend, M

    2014-05-27

    We aimed to better discriminate (occult) metastasised from non-metastasised seminoma based on transcriptional changes of small RNAs in the primary tumour. Total RNAs including small RNAs were isolated from five testicular tumours of each, lymphogenic, occult and non-metastasised patients. Next-generation sequencing (SOLID, Life Technologies) was used to examine transcriptional changes. Small RNAs showing ⩾50 reads and a significant ⩾2-fold difference using non-metastasised tumours as the reference group were examined in univariate logistic regression analysis and combinations of two small RNAs were further examined using support vector machines. On average, 1.3 × 10(7), 1.4 × 10(7) and 1.7 × 10(7) small RNA reads were detectable in non-metastasised, occult and lymphogenic metastasised seminoma, respectively, of which 30-32% remained after trimming. Between 59 and 68% represented annotated reads and between 8.6 and 11% were annotated small RNA tags. Of them, 137 small RNAs showed>50 reads and a two-fold difference to the reference. In univariate analysis, 32-38 small RNAs significantly discriminated lymphogenic/occult from non-metastasised seminoma, and among these different comparisons, it were the same small RNAs in 51-88%. Many combinations of two of these small RNAs allowed a complete discrimination of metastasised from non-metastasised seminoma irrespective of the metastasis subtype. Metastasised and non-metastasised seminoma can be completely discriminated with a combination of two small RNAs.

  7. 2015 NOAA NGS Ortho-rectified Mean High Water Color Mosaic of Augusta to Newcastle, Maine

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  8. 2008 NOAA/NGS Integrated Ocean and Coastal Mapping (IOCM) LIDAR: Kenai Peninsula Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using an OPTECH ALTM system. The data...

  9. 2016 NOAA NGS Ortho-rectified Near-Infrared Mosaic of Grays Harbor and Westport, Washington

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  10. 2016 NOAA NGS Ortho-rectified Near-Infrared Mosaic of Skagway, Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  11. 2016 NOAA NGS Ortho-rectified Near-Infrared Mosaic of Ketchikan Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  12. 2015 NOAA NGS Ortho-rectified Near-Infrared Mosaic of Ashtabula, Ohio

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  13. 2016 NOAA NGS Ortho-rectified Near-Infrared Mosaic of Baton Rouge, Louisiana

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  14. 2016 NOAA NGS Ortho-rectified Near-Infrared Mosaic of South Slough NERR, Oregon

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  15. 2016 NOAA NGS Ortho-rectified Color Mosaic of Homer and Seldovia, Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  16. 2016 NOAA NGS Ortho-rectified Color Mosaic of Ketchikan Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  17. 2016 NOAA NGS Ortho-rectified Near-Infrared Mosaic of Dillingham, Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  18. 2016 NOAA NGS Ortho-rectified Color Mosaic of Valdez, Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  19. Building A NGS Genomic Resource: Towards Molecular Breeding In L. Perenne

    DEFF Research Database (Denmark)

    Ruttink, Tom; Roldán-Ruiz, Isabel; Asp, Torben;

    predicted genes from seven completely sequenced genomes together with the Lolium contigs, orthologous groups are established and most probable candidate orthologues in Lolium are assigned. We are currently validating the de novo transcriptome assembly by Sanger sequencing and will develop and validate a set......To advance the application of molecular breeding in Lolium perenne, we have generated a sequence resource to facilitate gene discovery and SNP marker development. Illumina GAII transcriptome sequencing was performed on meristem-enriched samples of 14 Lolium genotypes. De novo assemblies...... for individual genotypes was carried out with 12-30M paired-end reads per genotype using the CLCBio Genomics Workbench, yielding around 70,000 contigs per genotype. 54% of these contigs have a significant BLAST hit with a predicted Brachypodium gene. Vice versa, for around 60% of the 26,552 predicted...

  20. High Accuracy Reference Network (HARN), Points generated from coordinates supplied by NGS, Published in 1993, MARIS.

    Data.gov (United States)

    NSGIC GIS Inventory (aka Ramona) — This High Accuracy Reference Network (HARN) dataset, was produced all or in part from Field Survey/GPS information as of 1993. It is described as 'Points generated...

  1. Geodetic Networks, geodetic control points within the National Spatial Reference System, Published in unknown, NGS.

    Data.gov (United States)

    NSGIC GIS Inventory (aka Ramona) — This Geodetic Networks dataset, was produced all or in part from Field Survey/GPS information as of unknown. It is described as 'geodetic control points within the...

  2. Detection of a Novel DSPP Mutation by NGS in a Population Isolate in Madagascar.

    Science.gov (United States)

    Bloch-Zupan, Agnès; Huckert, Mathilde; Stoetzel, Corinne; Meyer, Julia; Geoffroy, Véronique; Razafindrakoto, Rabisoa W; Ralison, Saholy N; Randrianaivo, Jean-Claude; Ralison, Georgette; Andriamasinoro, Rija O; Ramanampamaharana, Rija H; Randrianazary, Solofomanantsoa E; Richard, Béatrice; Gorry, Philippe; Manière, Marie-Cécile; Rakoto Alson, Simone; Dollfus, Hélène

    2016-01-01

    A large family from a small village in Madagascar, Antanetilava, is known to present with colored teeth. Through previous collaboration and 4 successive visits in 1994, 2004, 2005, and 2012, we provided dental care to the inhabitants and diagnosed dentinogenesis imperfecta. Recently, using whole exome sequencing we confirmed the clinical diagnosis by identifying a novel single nucleotide deletion in exon 5 of DSPP. This paper underlines the necessity of long run research, the importance of international and interpersonal collaborations as well as the major contribution of next generation sequencing tools in the genetic diagnosis of rare oro-dental anomalies. This study is registered in ClinicalTrials (https://clinicaltrials.gov) under the number NCT02397824.

  3. CoNVaDING: Single Exon Variation Detection in Targeted NGS Data.

    Science.gov (United States)

    Johansson, Lennart F; van Dijk, Freerk; de Boer, Eddy N; van Dijk-Bos, Krista K; Jongbloed, Jan D H; van der Hout, Annemieke H; Westers, Helga; Sinke, Richard J; Swertz, Morris A; Sijmons, Rolf H; Sikkema-Raddatz, Birgit

    2016-05-01

    We have developed a tool for detecting single exon copy-number variations (CNVs) in targeted next-generation sequencing data: CoNVaDING (Copy Number Variation Detection In Next-generation sequencing Gene panels). CoNVaDING includes a stringent quality control (QC) metric, that excludes or flags low-quality exons. Since this QC shows exactly which exons can be reliably analyzed and which exons are in need of an alternative analysis method, CoNVaDING is not only useful for CNV detection in a research setting, but also in clinical diagnostics. During the validation phase, CoNVaDING detected all known CNVs in high-quality targets in 320 samples analyzed, giving 100% sensitivity and 99.998% specificity for 308,574 exons. CoNVaDING outperforms existing tools by exhibiting a higher sensitivity and specificity and by precisely identifying low-quality samples and regions.

  4. Airborne Gravity: NGS' Gravity Data for AS03 (2010-2012)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2010 and 2012 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American Vertical Datum...

  5. Airborne Gravity: NGS' Gravity Data for CS02 (2008-2009)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Louisana and Mississippi collected in 2008-2009 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American...

  6. Airborne Gravity: NGS' Gravity Data for EN07 (2012-2013)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Maine and Canada collected in 2012 and 2013 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American...

  7. 2008 NOAA/NGS Integrated Ocean and Coastal Mapping (IOCM) LIDAR: Kenai Peninsula Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using an OPTECH ALTM system. The data...

  8. Prioritizing and selecting likely novel miRNAs from NGS data.

    Science.gov (United States)

    Backes, Christina; Meder, Benjamin; Hart, Martin; Ludwig, Nicole; Leidinger, Petra; Vogel, Britta; Galata, Valentina; Roth, Patrick; Menegatti, Jennifer; Grässer, Friedrich; Ruprecht, Klemens; Kahraman, Mustafa; Grossmann, Thomas; Haas, Jan; Meese, Eckart; Keller, Andreas

    2016-04-07

    Small non-coding RNAs play a key role in many physiological and pathological processes. Since 2004, miRNA sequences have been catalogued in miRBase, which is currently in its 21st version. We investigated sequence and structural features of miRNAs annotated in the miRBase and compared them between different versions of this reference database. We have identified that the two most recent releases (v20 and v21) are influenced by next-generation sequencing based miRNA predictions and show significant deviation from miRNAs discovered prior to the high-throughput profiling period. From the analysis of miRBase, we derived a set of key characteristics to predict new miRNAs and applied the implemented algorithm to evaluate novel blood-borne miRNA candidates. We carried out 705 individual whole miRNA sequencings of blood cells and collected a total of 9.7 billion reads. Using miRDeep2 we initially predicted 1452 potentially novel miRNAs. After excluding false positives, 518 candidates remained. These novel candidates were ranked according to their distance to the features in the early miRBase versions allowing for an easier selection of a subset of putative miRNAs for validation. Selected candidates were successfully validated by qRT-PCR and northern blotting. In addition, we implemented a web-server for ranking potential miRNA candidates, which is available at:www.ccb.uni-saarland.de/novomirank.

  9. An integrated strategy combining DNA walking and NGS to detect GMOs.

    Science.gov (United States)

    Fraiture, Marie-Alice; Herman, Philippe; Papazova, Nina; De Loose, Marc; Deforce, Dieter; Ruttink, Tom; Roosens, Nancy H

    2017-10-01

    Recently, we developed a DNA walking system for the detection and characterization of a broad spectrum of GMOs in routine analysis of food/feed matrices. Here, we present a new version with improved throughput and sensitivity by coupling the DNA walking system to Pacific Bioscience® Next-generation sequencing technology. The performance of the new strategy was thoroughly assessed through several assays. First, we tested its detection and identification capability on grains with high or low GMO content. Second, the potential impacts of food processing were investigated using rice noodle samples. Finally, GMO mixtures and a real-life sample were analyzed to illustrate the applicability of the proposed strategy in routine GMO analysis. In all tested samples, the presence of multiple GMOs was unambiguously proven by the characterization of transgene flanking regions and the combinations of elements that are typical for transgene constructs. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  10. 2016 NOAA NGS Ortho-rectified Color Mosaic of Big Carlos Pass, Florida

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  11. 2014 NOAA NGS Topobathy Lidar: Key West National Wildlife Refuge (FL)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ880G system. The data...

  12. Report on the NGS3 Working Group on Safeguards by Design For Aqueous Reprocessing Plants

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Shirley J.; Ehinger, Michael; Schanfein, Mark

    2011-02-01

    The objective of the Working Group on SBD for Aqueous Reprocessing Facilities was to provide recommendations, for facility operators and designers, which would aid in the coordination and integration of nuclear material accountancy and the safeguards requirements of all concerned parties - operators, state/regional authorities, and the IAEA. The recommendations, which are to be provided to the IAEA, are intended to assist in optimizing facility design and operating parameters to ensure the safeguardability of the facility while minimizing impact on the operations. The one day Working Group session addressed a wide range of design and operating topics.

  13. 2016 NOAA NGS Ortho-rectified Color Mosaic of Seward, Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  14. Colorectal cancer molecular profiling: from IHC to NGS in search of optimal algorithm.

    Science.gov (United States)

    Furtado, Larissa V; Samowitz, Wade S

    2017-05-27

    Advances in defining the mutational landscape of colorectal cancer (CRC) over the past decades have revolutionized the molecular understanding and clinical testing algorithms for this disease. Mutation testing is standard of care for the work-up of CRCs. This review focuses on the current indications and strategies for molecular testing in CRC and discusses the potential changes in CRC testing approach associated with the emerging clinical application of genomic-based technologies.

  15. 2015 NOAA NGS Ortho-rectified Color Mosaic of Jacksonville Beach to Mosquito Lagoon, Florida

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  16. 2016 NOAA NGS Ortho-rectified Near-Infrared Mosaic of Whittier, Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  17. Detection of a novel DSPP mutation by NGS in a population isolate in Madagascar

    Directory of Open Access Journals (Sweden)

    Agnes eBloch-Zupan

    2016-03-01

    Full Text Available A large family from a small village in Madagascar, Antanetilava, is known to present with coloured teeth. Through previous collaboration and 4 successive visits in 1994, 2004, 2005 and 2012, we provided dental care to the inhabitants and diagnosed dentinogenesis imperfecta. Recently, using whole exome sequencing we confirmed the clinical diagnosis by identifying a novel single nucleotide deletion in exon 5 of DSPP. This paper underlines the necessity of long run research, the importance of international and interpersonal collaborations as well as the major contribution of next generation sequencing tools in the genetic diagnosis of rare oro-dental anomalies. This study is registered in ClinicalTrials (https://clinicaltrials.gov under the number NCT02397824.

  18. Genetics of Adiposity in Large Animal Models for Human Obesity-Studies on Pigs and Dogs.

    Science.gov (United States)

    Stachowiak, M; Szczerbal, I; Switonski, M

    2016-01-01

    The role of domestic mammals in the development of human biomedical sciences has been widely documented. Among these model species the pig and dog are of special importance. Both are useful for studies on the etiology of human obesity. Genome sequences of both species are known and advanced genetic tools [eg, microarray SNP for genome wide association studies (GWAS), next generation sequencing (NGS), etc.] are commonly used in such studies. In the domestic pig the accumulation of adipose tissue is an important trait, which influences meat quality and fattening efficiency. Numerous quantitative trait loci (QTLs) for pig fatness traits were identified, while gene polymorphisms associated with these traits were also described. The situation is different in dog population. Generally, excessive accumulation of adipose tissue is considered, similar to humans, as a complex disease. However, research on the genetic background of canine obesity is still in its infancy. Between-breed differences in terms of adipose tissue accumulation are well known in both animal species. In this review we show recent advances of studies on adipose tissue accumulation in pigs and dogs, and their potential importance for studies on human obesity. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. Investigation of Four Different Laponite Clays as Stabilizers in Pickering Emulsion Polymerization.

    Science.gov (United States)

    Brunier, Barthélémy; Sheibat-Othman, Nida; Chniguir, Mehdi; Chevalier, Yves; Bourgeat-Lami, Elodie

    2016-06-21

    Clay-armored polymer particles were prepared by emulsion polymerization in the presence of Laponite platelets that adsorb at the surface of latex particles and act as stabilizers during the course of the polymerization. While Laponite RDS clay platelets are most often used, the choice of the type of clay still remains an open issue that is addressed in the present article. Four different grades of Laponite were investigated as stabilizers in the emulsion polymerization of styrene. First, the adsorption isotherms of the clays, on preformed polystyrene particles, were determined by ICP-AES analysis of the residual clay in the aqueous phase. Adsorption of clay depended on the type of clay at low concentrations corresponding to adsorption as a monolayer. Adsorption of clay particles as multilayers was observed for all the grades above a certain concentration under the considered ionic strength (mainly due to the initiator ionic species). The stabilization efficiency of these clays was investigated during the polymerization reaction (free of any other stabilizer). The clays did not have the same effect on stabilization, which was related to differences in their compositions and in their adsorption isotherms. The different grades led to different polymer particles sizes and therefore to different polymerization reaction rates. Laponite RDS and S482 gave similar results, ensuring the best stabilization efficiency and the fastest reaction rate; the number of particles increased as the clay concentration increased. Stabilization with Laponite XLS gave the same particles size and number as the latter two clays at low clay concentrations, but it reached an upper limit in the number of nucleated polymer particles at higher concentrations indicating a decrease of stabilization efficiency at high concentrations. Laponite JS did not ensure a sufficient stability of the polymer particles, as the polymerization results were comparable to a stabilizer-free polymerization system.

  20. The order-picking routing problem for low-level order picker in a warehouse

    OpenAIRE

    Antonio Carlos Bonassa; Claudio Barbieri da Cunha

    2011-01-01

    O presente trabalho trata do problema da determinação de rota de separação manual de peças em armazéns que minimize a distância total percorrida pelo separador. O problema abordado é prático e comum a várias empresas, com impacto nos custos operacionais e relevância para a assertividade em relação aos itens coletados. Ainda assim, o tema é pouco explorado nos estudos de roteirização disponíveis em língua portuguesa e muitas empresas optam por confiar nas rotas criadas empiricamente pelos sepa...

  1. Influence of nanoscale particle roughness on the stability of Pickering emulsions.

    Science.gov (United States)

    San-Miguel, Adriana; Behrens, Sven H

    2012-08-21

    The wetting behavior of solid surfaces can be altered dramatically by introducing surface roughness on the nanometer scale. Some of nature's most fascinating wetting phenomena are associated with surface roughness; they have inspired both fundamental research and the adoption of surface roughness as a design parameter for man-made functional coatings. So far the attention has focused primarily on macroscopic surfaces, but one should expect the wetting properties of colloidal particles to be strongly affected by roughness, too. Particle wettability, in turn, is a key parameter for the adsorption of particles at liquid interfaces and for the industrially important use of particles as emulsion stabilizers; yet, the consequence of particle roughness for emulsion stability remains poorly understood. In order to investigate the matter systematically, we have developed a surface treatment, applicable to micrometer-sized particles and macroscopic surfaces alike, that produces surface coatings with finely tunable nanoscale roughness and identical surface chemistry. Coatings with different degrees of roughness were characterized with regard to their morphology, charging, and wetting properties, and the results were correlated with the stability of emulsions prepared with coated particles of different roughness. We find that the maximum capillary pressure, a metric of the emulsions' resistance to droplet coalescence, varies significantly and in a nonmonotonic fashion with particle roughness. Surface topography and contact angle hysteresis suggest that particle roughness benefits the stability of our emulsions as long as wetting occurs homogeneously (Wenzel regime), whereas the transition toward heterogeneous wetting (Cassie-Baxter regime) is associated with a loss of stability.

  2. The second Sir George Pickering memorial lecture. What regulates whole body autoregulation? Clinical observations.

    Science.gov (United States)

    Schalekamp, M A; Man in't Veld, A J; Wenting, G J

    1985-04-01

    The autoregulation theory of essential hypertension states that the characteristic haemodynamic derangement of this disease, i.e. increased vascular resistance, is a homeostatic response to abnormal sodium retention by the kidneys. The postulated relationship between arterial pressure and urinary sodium excretion is disturbed in such a way that a higher than normal pressure is required for sodium excretion to keep up with intake. This will initially expand plasma volume and raise cardiac output. However, hyperperfusion of the tissues will ultimately induce vasoconstriction, presumably by greater than normal wash-out of vasodilator metabolic products. Thus, cardiac output will be restored. Some elements of this theory are not supported by current evidence, but the key element, i.e. the assumption that increased vascular resistance is somehow dependent on abnormal renal sodium handling, is consistent with the following clinical observations: Arterial pressure and urinary sodium excretion are directly correlated over a wide range of pressures in patients with autonomic failure, both acutely during titling and chronically with changes in posture during a 24-h period. The failure to demonstrate pressure-natriuresis in normal subjects may therefore be related to the amplifying effect of the sympathetic nervous system on this mechanism, so that small changes in pressure are capable of inducing large changes in sodium excretion. The pressure-natriuresis curve in patients with autonomic failure is shifted to higher pressures by administration of aldosterone, which is consistent with an important role of renal sodium retention in mineralocorticoid hypertension. Measurements of total extracellular fluid volume, plasma volume/interstitial fluid volume ratio, transcapillary escape rate of serum albumin, cardiac output and arterial pressure at timed intervals during the development of hypertension, in patients exposed to mineralocorticoid excess, or during the reversal of hypertension in nephrectomized patients treated with ultrafiltration haemodialysis, revealed an association of increased total peripheral resistance with a reduced plasma volume/interstitial fluid volume ratio and an increased transcapillary escape rate of serum albumin. This association has also been observed in cross-sectional studies of patients with essential hypertension and suggests that part of the increase in resistance is located at a post-capillary level. It may be related to compression of collapsible venules and veins due to abnormally increased interstitial fluid pressure, not only in sodium-dependent secondary forms of hypertension but also in essential hypertension.(ABSTRACT TRUNCATED AT 400 WORDS)

  3. Size-dependent properties of silica nanoparticles for Pickering stabilization of emulsions and foams

    Science.gov (United States)

    Kim, Ijung; Worthen, Andrew J.; Johnston, Keith P.; DiCarlo, David A.; Huh, Chun

    2016-04-01

    Nanoparticles are a promising alternative to surfactants to stabilize emulsions or foams in enhanced oil recovery (EOR) processes due to their effectiveness in very harsh environments found in many of the oilfields around the world. While the size-dependent properties of nanoparticles have been extensively studied in the area of optics or cellular uptake, little is known on the effects of nanoparticle size on emulsion/foam generation, especially for EOR applications. In this study, silica nanoparticles with four different sizes (5, 12, 25, and 80 nm nominal diameter) but with the same surface treatment were employed to test their emulsion or foam generation behavior in high-salinity conditions. The decane-in-brine emulsion generated by sonication or flowing through sandpack showed smaller droplet size and higher apparent viscosity as the nanoparticle size decreased. Similarly, the CO2-in-brine foam generation in sandstone or sandpacks was also significantly affected by the nanoparticle size, exhibiting higher apparent foam viscosity as the nanoparticle size decreased. In case of foam generation in sandstone cores with 5 nm nanoparticles, a noticeable hysteresis occurred when the flow velocity was initially increased and then decreased, implying a strong foam generation initially; and then the trapping of the generated foam in the rock pores, as the flow velocity decreased. On the other hand, weak foams stabilized with larger nanoparticles indicated a rapid coalescence of bubbles which prevented foam generation. Overall, stable emulsions/foams were achievable by the smaller particles as a result of greater diffusivity and/or higher number concentration, thus allowing more nanoparticles with higher surface area to volume ratio to be adsorbed at the fluid/fluid interfaces of the emulsion/foam dispersion.

  4. Pickering石蜡乳状液的研制%Preparation of Paraffin Pickering Emulsions

    Institute of Scientific and Technical Information of China (English)

    田鹏飞; 刘温霞

    2008-01-01

    研究了带正电荷的氢氧化镁铝微粒对液体石蜡/水体系的乳化与稳定作用.结果发现,氢氧化镁铝胶体可将液体石蜡/水体系乳化成O/W型石蜡乳状液.随液体石蜡体积分数和氢氧化镁铝加入量的增加,乳状液稳定性提高,黏度也随之增加.但乳状液液滴分别表现为增大和减小趋势.初始油水体积比例为3:1时,加入w(氢氧化镁铝)=0.25%,便可得到稳定性良好的石蜡乳液.

  5. Particle-size effects in the formation of bicontinuous Pickering emulsions

    Science.gov (United States)

    Reeves, M.; Brown, A. T.; Schofield, A. B.; Cates, M. E.; Thijssen, J. H. J.

    2015-09-01

    We demonstrate that the formation of bicontinuous emulsions stabilized by interfacial particles (bijels) is more robust when nanoparticles rather than microparticles are used. Emulsification via spinodal demixing in the presence of nearly neutrally wetting particles is induced by rapid heating. Using confocal microscopy, we show that nanospheres allow successful bijel formation at heating rates two orders of magnitude slower than is possible with microspheres. In order to explain our results, we introduce the concept of mechanical leeway, i.e., nanoparticles benefit from a smaller driving force towards disruptive curvature. Finally, we suggest that leeway mechanisms may benefit any formulation in which challenges arise due to tight restrictions on a pivotal parameter, but where the restrictions can be relaxed by rationally changing the value of a more accessible parameter.

  6. Controlled microfluidic emulsification of oil in a clay nanofluid: Role of salt for Pickering stabilization

    Science.gov (United States)

    Gholamipour-Shirazi, A.; Carvalho, M. S.; Fossum, J. O.

    2016-07-01

    Research on emulsions is driven by their widespread use in different industries, such as food, cosmetic, pharmaceutical and oil recovery. Emulsions are stabilized by suitable surfactants, polymers, solid particles or a combination of them. Microfluidic emulsification is the process of droplet formation out of two or more liquids under strictly controlled conditions, without pre-emulsification step. Microfluidic technology offers a powerful tool for investigating the properties of emulsions themselves. In this work stable oil in water emulsions were formed with hydrophilic Laponite RD® nanoparticles adsorbed at the interface of the oil phase and aqueous clay nanofluid in a T junction microfluidic chip. Emulsion stability up to at least 40 days could be observed.

  7. Food-grade Pickering stabilisation of foams by in situ hydrophobisation of calcium carbonate particles

    NARCIS (Netherlands)

    Binks, Bernard P.; Muijlwijk, K.; Koman, Henriëtte; Poortinga, A.T.

    2017-01-01

    The aim of this study was to investigate the possibility of stabilising foam bubbles in water by adsorption of calcium carbonate (CaCO3) particles. Because CaCO3 is hydrophilic and not surface-active, particles were hydrophobised in situ with several emulsifiers. The used emulsifiers were food-grade

  8. Intensified photocatalytic degradation of nitrobenzene by Pickering emulsion of ZnO nanoparticles

    Institute of Scientific and Technical Information of China (English)

    Wei Wu; Shuang Gao; Weixia Tu; Jianfeng Chen; Pengyuan Zhang

    2010-01-01

    In this paper,zinc oxide nanoparticles were first prepared and surface-modified.A Picketing emulsion was then prepared,consisting of nitrobenzene(oil phase),water(water phase)and the modified zinc oxide nanoparticles located on the water-oil interface.The effects of different emulsions on the removal rate of nitrobenzene by photocatalytic degradation were studied.The results proved that use of a Pick-eting emulsion stabilized by surface-modified ZnO nanoparticles provides an effective and novel way to intensify the photocatalytic degradation of the organic contaminant.

  9. ""Thames Valley cotton pickers"": Race and youth in London blues culture

    OpenAIRE

    2005-01-01

    This study addresses the reception of African American blues music and the ensuing production of English blues in London from 1955 to 1966. It concentrates on London adolescents' unexpected fascination with a musical style that they virtually had no contact with prior to 1955, while analyzing how this immersion in African American culture shaped their cultural identity. Analysis of the influence of African American blues music in London during this period highlights the BBC's weakened influen...

  10. Flash pulmonary edema in patients with renal artery stenosis--the Pickering Syndrome

    DEFF Research Database (Denmark)

    Pelta, Anna; Andersen, Ulrik B; Just, Sven

    2010-01-01

    We report the prevalence of flash pulmonary edema in patients consecutively referred for balloon angioplasty of uni- or bilateral renal artery stenosis (PTRA), and describe the characteristics of this special fraction of the patients. We further report two unusual cases.......We report the prevalence of flash pulmonary edema in patients consecutively referred for balloon angioplasty of uni- or bilateral renal artery stenosis (PTRA), and describe the characteristics of this special fraction of the patients. We further report two unusual cases....

  11. Extending Pickering Fuel Channel Life to 247,000 EFPH (2020)

    Energy Technology Data Exchange (ETDEWEB)

    Malek, I. [Ontario Power Generation, Toronto, Ontario (Canada)

    2013-07-01

    This presentation is about extending the life of PNGS Pressure tubes from 210,000 EFPH (Effective Full Power Hours) to 247,000 EFPH. The l license renewal is in 2013 (R & D defined in 2009). The unknowns are the extent of degradation in some key areas. There are regulatory requirements for fuel channel extended life. It is necessary to integrate inspection capability and do-ability in outages. This would result in safe operation and demonstrated margin to extend life with operation to 2020.

  12. Compilation and Analysis of 20 and 30 GHz Rain Fade Events at the ACTS NASA Ground Station: Statistics and Model Assessment

    Science.gov (United States)

    Manning, Robert M.

    1996-01-01

    The purpose of the propagation studies within the ACTS Project Office is to acquire 20 and 30 GHz rain fade statistics using the ACTS beacon links received at the NGS (NASA Ground Station) in Cleveland. Other than the raw, statistically unprocessed rain fade events that occur in real time, relevant rain fade statistics derived from such events are the cumulative rain fade statistics as well as fade duration statistics (beyond given fade thresholds) over monthly and yearly time intervals. Concurrent with the data logging exercise, monthly maximum rainfall levels recorded at the US Weather Service at Hopkins Airport are appended to the database to facilitate comparison of observed fade statistics with those predicted by the ACTS Rain Attenuation Model. Also, the raw fade data will be in a format, complete with documentation, for use by other investigators who require realistic fade event evolution in time for simulation purposes or further analysis for comparisons with other rain fade prediction models, etc. The raw time series data from the 20 and 30 GHz beacon signals is purged of non relevant data intervals where no rain fading has occurred. All other data intervals which contain rain fade events are archived with the accompanying time stamps. The definition of just what constitutes a rain fade event will be discussed later. The archived data serves two purposes. First, all rain fade event data is recombined into a contiguous data series every month and every year; this will represent an uninterrupted record of the actual (i.e., not statistically processed) temporal evolution of rain fade at 20 and 30 GHz at the location of the NGS. The second purpose of the data in such a format is to enable a statistical analysis of prevailing propagation parameters such as cumulative distributions of attenuation on a monthly and yearly basis as well as fade duration probabilities below given fade thresholds, also on a monthly and yearly basis. In addition, various subsidiary

  13. Surface Gravity Data Contribution to the Puerto Rico and U.S. Virgin Islands Geoid Model

    Science.gov (United States)

    Li, X.; Gerhards, C.; Holmes, S. A.; Saleh, J.; Shaw, B.

    2015-12-01

    The Gravity for the Redefinition of the American Vertical Datum (GRAV-D) project provides updated local gravity field information for the XGEOID15 models. In particular, its airborne gravity data in the area of Puerto Rico and U.S. Virgin Islands (PRVI) made substantial improvements (~60%) on the precision of the geoid models at the local GNSS/Leveling bench marks in the target area. Fortunately, PRVI is free of the huge systematic error in the North American Vertical Datum of 1988 (NAVD88). Thus, the airborne contribution was evaluated more realistically. In addition, the airborne data picked up more detailed gravity field information in the medium wavelength band (spherical harmonic degree 200 to 600) that are largely beyond the resolution of the current satellite missions, especially along the nearby ocean trench areas. Under this circumstance (significant airborne contributions in the medium band), local surface gravity data need to be examined more carefully than before during merging with the satellite and airborne information for local geoid improvement, especially considering the well-known systematic problems in the NGS historical gravity holdings (Saleh et al 2013 JoG). Initial tests showed that it is very important to maintain high consistency between the surface data sets and the airborne enhanced reference model. In addition, a new aggregation method (Gerhards 2014, Inverse Problems) will also be tested to optimally combine the local surface data with the reference model. The data cleaning and combining procedures in the target area will be summarized here as reference for future applications.

  14. ALS Along the Axons – Expression of Coding and Noncoding RNA Differs in Axons of ALS models

    Science.gov (United States)

    Rotem, Nimrod; Magen, Iddo; Ionescu, Ariel; Gershoni-Emek, Noga; Altman, Topaz; Costa, Christopher J.; Gradus, Tal; Pasmanik-Chor, Metsada; Willis, Dianna E.; Ben-Dov, Iddo Z.; Hornstein, Eran; Perlson, Eran

    2017-01-01

    Amyotrophic lateral sclerosis (ALS) is a multifactorial lethal motor neuron disease with no known treatment. Although the basic mechanism of its degenerative pathogenesis remains poorly understood, a subcellular spatial alteration in RNA metabolism is thought to play a key role. The nature of these RNAs remains elusive, and a comprehensive characterization of the axonal RNAs involved in maintaining neuronal health has yet to be described. Here, using cultured spinal cord (SC) neurons grown using a compartmented platform followed by next-generation sequencing (NGS) technology, we find that RNA expression differs between the somatic and axonal compartments of the neuron, for both mRNA and microRNA (miRNA). Further, the introduction of SOD1G93A and TDP43A315T, established ALS-related mutations, changed the subcellular expression and localization of RNAs within the neurons, showing a spatial specificity to either the soma or the axon. Altogether, we provide here the first combined inclusive profile of mRNA and miRNA expression in two ALS models at the subcellular level. These data provide an important resource for studies on the roles of local protein synthesis and axon degeneration in ALS and can serve as a possible target pool for ALS treatment. PMID:28300211

  15. Modeling and characterization of multiple coupled lines

    Science.gov (United States)

    Tripathi, Alok

    1999-10-01

    order to demonstrate the procedure, a typical microstrip structure with three lines is synthesized from the time-domain reflection (TDR) data. In order to compliment known field theoretic techniques for characterization of multiconductor structures a network analog method is employed to solve the magnetic vector potential equation to characterize multilayer Metal-Insulator-Semiconductor (NGS) transmission line structures. This approach leads to the frequency dependent distributed inductance and the resistance matrices of a multilayer MIS transmission line structure. It is shown that the frequency dependent transmission line parameters can be modeled by an efficient quasi- static formulation for all propagating modes including the slow-wave and skin-effect modes. To demonstrate the proposed approach for single and multilevel structures, the frequency dependent distributed inductance and resistance matrices corresponding to the propagating modes classified as the slow-wave and skin-effect modes are calculated and validated by comparison with full-wave solutions.

  16. Genome-wide ENU mutagenesis in combination with high density SNP analysis and exome sequencing provides rapid identification of novel mouse models of developmental disease.

    Directory of Open Access Journals (Sweden)

    Georgina Caruana

    Full Text Available BACKGROUND: Mice harbouring gene mutations that cause phenotypic abnormalities during organogenesis are invaluable tools for linking gene function to normal development and human disorders. To generate mouse models harbouring novel alleles that are involved in organogenesis we conducted a phenotype-driven, genome-wide mutagenesis screen in mice using the mutagen N-ethyl-N-nitrosourea (ENU. METHODOLOGY/PRINCIPAL FINDINGS: ENU was injected into male C57BL/6 mice and the mutations transmitted through the germ-line. ENU-induced mutations were bred to homozygosity and G3 embryos screened at embryonic day (E 13.5 and E18.5 for abnormalities in limb and craniofacial structures, skin, blood, vasculature, lungs, gut, kidneys, ureters and gonads. From 52 pedigrees screened 15 were detected with anomalies in one or more of the structures/organs screened. Using single nucleotide polymorphism (SNP-based linkage analysis in conjunction with candidate gene or next-generation sequencing (NGS we identified novel recessive alleles for Fras1, Ift140 and Lig1. CONCLUSIONS/SIGNIFICANCE: In this study we have generated mouse models in which the anomalies closely mimic those seen in human disorders. The association between novel mutant alleles and phenotypes will lead to a better understanding of gene function in normal development and establish how their dysfunction causes human anomalies and disease.

  17. Using genotyping data to assign markers to their chromosome type and to infer the sex of individuals: a Bayesian model-based classifier.

    Science.gov (United States)

    Gautier, Mathieu

    2014-11-01

    The recent democratization of next-generation-sequencing-based approaches towards nonmodel species has made it cost-effective to produce large genotyping data sets for a wider range of species. However, when no detailed genome assembly is available, poor knowledge about the organization of the markers within the genome might hamper the optimal use of this abundant information. At the most basic level of genomic organization, the type of chromosome (autosomes, sex chromosomes, mitochondria or chloroplast in plants) may remain unknown for most markers which might be limiting or even misleading in some applications, particularly in population genetics. Conversely, the characterization of sex-linked markers allows molecular sexing of the individuals. In this study, we propose a Bayesian model-based classifier named detsex, to assign markers to their chromosome type and/or to perform sexing of individuals based on genotyping data. The performance of detsex is further evaluated by a comprehensive simulation study and by the analysis of real data sets from various origins (microsatellite and SNP data derived from genotyping assay designs and NGS experiments). Irrespective of the origin of the markers or the size of the data set, detsex was proved efficient (i) to identify the sex-linked markers, (ii) to perform molecular sexing of the individuals and (iii) to perform basic quality check of the genotyping data sets. The underlying structure of the model also allows to consider each of these potential applications either separately or jointly.

  18. A novel procedure on next generation sequencing data analysis using text mining algorithm.

    Science.gov (United States)

    Zhao, Weizhong; Chen, James J; Perkins, Roger; Wang, Yuping; Liu, Zhichao; Hong, Huixiao; Tong, Weida; Zou, Wen

    2016-05-13

    Next-generation sequencing (NGS) technologies have provided researchers with vast possibilities in various biological and biomedical research areas. Efficient data mining strategies are in high demand for large scale comparative and evolutional studies to be performed on the large amounts of data derived from NGS projects. Topic modeling is an active research field in machine learning and has been mainly used as an analytical tool to structure large textual corpora for data mining. We report a novel procedure to analyse NGS data using topic modeling. It consists of four major procedures: NGS data retrieval, preprocessing, topic modeling, and data mining using Latent Dirichlet Allocation (LDA) topic outputs. The NGS data set of the Salmonella enterica strains were used as a case study to show the workflow of this procedure. The perplexity measurement of the topic numbers and the convergence efficiencies of Gibbs sampling were calculated and discussed for achieving the best result from the proposed procedure. The output topics by LDA algorithms could be treated as features of Salmonella strains to accurately describe the genetic diversity of fliC gene in various serotypes. The results of a two-way hierarchical clustering and data matrix analysis on LDA-derived matrices successfully classified Salmonella serotypes based on the NGS data. The implementation of topic modeling in NGS data analysis procedure provides a new way to elucidate genetic information from NGS data, and identify the gene-phenotype relationships and biomarkers, especially in the era of biological and medical big data. The implementation of topic modeling in NGS data analysis provides a new way to elucidate genetic information from NGS data, and identify the gene-phenotype relationships and biomarkers, especially in the era of biological and medical big data.

  19. Topobathymetric model of Mobile Bay, Alabama

    Science.gov (United States)

    Danielson, Jeffrey J.; Brock, John C.; Howard, Daniel M.; Gesch, Dean B.; Bonisteel-Cormier, Jamie M.; Travers, Laurinda J.

    2013-01-01

    were made to these input data. The NGDC hydrographic, multibeam, and trackline surveys were transformed from mean low water (MLW) or mean lower low water (MLLW) to NAVD 88 using VDatum (http://vdatum.noaa.gov). VDatum is a tool developed by the National Geodetic Survey (NGS) that performs transformations among tidal, ellipsoid-based, geoid-based, and orthometric datums using calibrated hydrodynamic models. The vertical accuracy of the input topographic data varied depending on the input source. Because the input elevation data were derived primarily from lidar, the vertical accuracy ranges from 6 to 20 centimeters in root mean square error (RMSE). he horizontal datum of the Mobile Bay topobathymetric model is the North American Datum of 1983 (NAD 83), geographic coordinates. All the topographic and bathymetric datasets were originally referenced to NAD 83, and no transformations were made to the input data. The bathymetric surveys were downloaded referenced to NAD 83 geographic, and therefore no horizontal transformations were required. The topbathymetric model of Mobile Bay and detailed metadata can be obtained from the USGS Web sites: http://nationalmap.gov/.

  20. Leadership Models.

    Science.gov (United States)

    Freeman, Thomas J.

    This paper discusses six different models of organizational structure and leadership, including the scalar chain or pyramid model, the continuum model, the grid model, the linking pin model, the contingency model, and the circle or democratic model. Each model is examined in a separate section that describes the model and its development, lists…

  1. Computer-aided design and rapid prototyping technique for individualized artificial semi-knee joint prosthesis: Establishment of three-dimensional model of femoral condyle%个体化人工半膝关节假体计算机辅助设计和快速成型的基础:股骨髁三维建模

    Institute of Scientific and Technical Information of China (English)

    滕勇; 王臻; 李迪尘; 宦怡; 胡蕴玉; 张峰

    2006-01-01

    BACKGROUND:At present, there are several limb-preserving methods,such as xenogenic bone joint replacement, artificial metal prothesis replacement and inactivation and replantation of tumor bone segment, etc.Each method has its advantages and disadvantages. In addition, mismatch of xenogenic and autogeneic joints and articular cartilage necrosis in the late stage, which affects joint function, are two important problems for large frozen bone-joint allograft at ultra-low temperature in repair of bone defect following bone tumor resections in extremities.OBJECTIVE:To evaluate a method to obtain outline information on the cartilage surface through spiral CT scanning data, so as to lay foundation for study on individualized artifical semi-knee joint based on rapid prototyping (RP) technique.DESIGN: Open experiment.SETTING: First Department of Trauma, Urumqi General Hospital of Lanzhou Military Area Command of Chinese PLA.MATERIALS: This experiment was carried out at Institute of Orthopaedics, Xijing Hospital, Fourth Military Medical University of Chinese PLA, and Institute of Advanced Manufacturing, Xi'an Jiaotong University from September 2001 to May 2003. CT scanning subject was a 25-year-old healthy male volunteer.METHODS:Distal femur was performed 1 mm in thickness scanning with Picker 6 000 spiral CT. Three-dimensional volume reconstruction was conducted at the Voxel Q Image workstation on Picker 6000 CT, then, two-dimensional tomography image of reconstruction data were downloaded with spacing of 0.1 mm. Data format converter software was self-developed. The downloaded image was treated through smoothing, de-noise and so on.Vector data of two-dimensional borderline outline of tomography image was calculated and input into Surfacer 9.0 software (American Imageware company) for vectorial three-dimensional reconstruction. According to recognition of articular cartilage outline and request of prothesis design, the threedimensional images of interested articular

  2. Model Transformations? Transformation Models!

    NARCIS (Netherlands)

    Bézivin, J.; Büttner, F.; Gogolla, M.; Jouault, F.; Kurtev, I.; Lindow, A.

    2006-01-01

    Much of the current work on model transformations seems essentially operational and executable in nature. Executable descriptions are necessary from the point of view of implementation. But from a conceptual point of view, transformations can also be viewed as descriptive models by stating only the

  3. Modelling business models

    NARCIS (Netherlands)

    Simonse, W.L.

    2014-01-01

    Business model design does not always produce a “design” or “model” as the expected result. However, when designers are involved, a visual model or artifact is produced. To assist strategic managers in thinking about how they can act, the designers’ challenge is to combine both strategy and design n

  4. Naval Reseaarch Laboratory Gulf of Mexico Geoid Model Texas Reference Center Pilot Project

    Science.gov (United States)

    Prouty, D. B.; Lyle, S. D.; Roman, D. R.; Mulcare, D. M.; Jeffress, G.; Sadovski, A.; Aiken, C. L.; Smith, R.; Childers, V. A.; Brozena, J. M.

    2007-05-01

    The purpose of this project is to improve elevations in Texas and nearby regions for flooding, mapping and hurricane preparedness. The U.S. Navy Department's Naval Research Laboratory and Texas A&M University- Corpus Christi are planning an aircraft-based gravity data collection effort along the Gulf of Mexico and the southern boundary of the United States. This project will utilize the Naval Airborne Gravity modeling system to improve elevations along the coast and throughout the United States in support of shallow-water navigation, aviation, and ground monitoring systems used by federal, state and local public safety agencies. The current project plan will address the issue of inconsistencies in the gravity field from onshore to offshore, facilitate the identification of systematic problems and otherwise help resolve issues related to existing, legacy gravity data. The widespread and increasing use of GPS for height determinations fundamentally depends on the use of a geoid height model to convert GPS-derived heights into heights above mean sea level. Current geoid models are inadequate. Accurate, homogeneous gravity measurements are essential for the computation of geoid models. To address the inadequate gravity data set for the US, the Naval Research Laboratory (NRL) and National Geodetic Survey (NGS) have developed a new approach based on airborne methods. The new approach yields spatially well distributed high-quality, consistent, and contemporary gravity data. The method to be employed has undergone extensive testing and is now ready for additional investigation. The airborne gravitational data will be used in conjunction with existing ground and marine gravity data sets and data from the Texas Coastal Ocean Observation Network (TCOON), a network of 32 tide gauges, to be used to help identify problems of tying the geoid to mean sea-level. These improved gravity data will lead to the creation of new and improved US geoid models. Accurate geoid models will

  5. Nested high resolution models for the coastal areas of the North Indian Ocean

    Science.gov (United States)

    Wobus, Fred; Shapiro, Georgy

    2017-04-01

    . The results reveal an optimal tidal nesting strategy which forces tidal SSH from the parent model at 1-hourly intervals whilst non-tidal parameters are forced at 24-hourly intervals. The analysis includes comparisons with tidal gauges in the Gulf of Oman and inside the Arabian Gulf. The accuracy of tides inside the Gulf is inhibited by the narrow Straits of Hormuz, and tidal nesting doesn't achieve the same level of agreement with observation as traditional nesting. We also found that a further increase in the SSH forcing frequency to 30 minutes does not further improve the results. The forcing at intervals of 1h/24h for tidal/non-tidal parameters shows that a 2-step tidal nesting chain is viable and thus tides can be represented in more than just the last model of a nesting chain. References: Shapiro, G., Luneva, M., Pickering, J., and Storkey, D.: The effect of various vertical discretization schemes and horizontal diffusion parameterization on the performance of a 3-D ocean model: the Black Sea case study, Ocean Sci., 9, 377-390, doi:10.5194/os-9-377-2013, 2013.

  6. Modelling SDL, Modelling Languages

    Directory of Open Access Journals (Sweden)

    Michael Piefel

    2007-02-01

    Full Text Available Today's software systems are too complex to implement them and model them using only one language. As a result, modern software engineering uses different languages for different levels of abstraction and different system aspects. Thus to handle an increasing number of related or integrated languages is the most challenging task in the development of tools. We use object oriented metamodelling to describe languages. Object orientation allows us to derive abstract reusable concept definitions (concept classes from existing languages. This language definition technique concentrates on semantic abstractions rather than syntactical peculiarities. We present a set of common concept classes that describe structure, behaviour, and data aspects of high-level modelling languages. Our models contain syntax modelling using the OMG MOF as well as static semantic constraints written in OMG OCL. We derive metamodels for subsets of SDL and UML from these common concepts, and we show for parts of these languages that they can be modelled and related to each other through the same abstract concepts.

  7. Actant Models

    DEFF Research Database (Denmark)

    Poulsen, Helle

    1996-01-01

    This paper presents a functional modelling method called Actant Modelling rooted in linguistics and semiotics. Actant modelling can be integrated with Multilevel Flow Modelling (MFM) in order to give an interpretation of actants.......This paper presents a functional modelling method called Actant Modelling rooted in linguistics and semiotics. Actant modelling can be integrated with Multilevel Flow Modelling (MFM) in order to give an interpretation of actants....

  8. Modelling the models

    CERN Multimedia

    Anaïs Schaeffer

    2012-01-01

    By analysing the production of mesons in the forward region of LHC proton-proton collisions, the LHCf collaboration has provided key information needed to calibrate extremely high-energy cosmic ray models.   Average transverse momentum (pT) as a function of rapidity loss ∆y. Black dots represent LHCf data and the red diamonds represent SPS experiment UA7 results. The predictions of hadronic interaction models are shown by open boxes (sibyll 2.1), open circles (qgsjet II-03) and open triangles (epos 1.99). Among these models, epos 1.99 shows the best overall agreement with the LHCf data. LHCf is dedicated to the measurement of neutral particles emitted at extremely small angles in the very forward region of LHC collisions. Two imaging calorimeters – Arm1 and Arm2 – take data 140 m either side of the ATLAS interaction point. “The physics goal of this type of analysis is to provide data for calibrating the hadron interaction models – the well-known &...

  9. Modelling Practice

    DEFF Research Database (Denmark)

    2011-01-01

    This chapter deals with the practicalities of building, testing, deploying and maintaining models. It gives specific advice for each phase of the modelling cycle. To do this, a modelling framework is introduced which covers: problem and model definition; model conceptualization; model data...... requirements; model construction; model solution; model verification; model validation and finally model deployment and maintenance. Within the adopted methodology, each step is discussedthrough the consideration of key issues and questions relevant to the modelling activity. Practical advice, based on many...... years of experience is providing in directing the reader in their activities.Traps and pitfalls are discussed and strategies also given to improve model development towards “fit-for-purpose” models. The emphasis in this chapter is the adoption and exercise of a modelling methodology that has proven very...

  10. THE AFFECTION OF TIME AND DISTANCE TO NGS-2000GPS SURVEYING PRECISION%时间距离因子对南方NGS-200GPS测量精度的影响

    Institute of Scientific and Technical Information of China (English)

    费鲜芸; 亓学翔; 刘文杰; 高祥伟

    2003-01-01

    GPS是一项在逐渐兴起的技术.与传统的测量技术相比,它具有无可比拟的优越性.本文通过对观测分析,得出测量时间的长短及测量时段的分布对测量结果都具有明显的影响.

  11. Prediction in processing is a by-product of language learning.

    Science.gov (United States)

    Chang, Franklin; Kidd, Evan; Rowland, Caroline F

    2013-08-01

    Both children and adults predict the content of upcoming language, suggesting that prediction is useful for learning as well as processing. We present an alternative model which can explain prediction behaviour as a by-product of language learning. We suggest that a consideration of language acquisition places important constraints on Pickering & Garrod's (P&G's) theory.

  12. Interactive Alignment: A Teaching-Friendly View of Second Language Pronunciation Learning

    Science.gov (United States)

    Trofimovich, Pavel

    2016-01-01

    Interactive alignment is a phenomenon whereby interlocutors adopt and re-use each other's language patterns in the course of authentic interaction. According to the interactive alignment model, originally proposed by Pickering & Garrod (2004), this linguistic coordination is one way in which interlocutors achieve understanding in dialogue,…

  13. Next-generation sequencing as a powerful motor for advances in the biological and environmental sciences.

    Science.gov (United States)

    Faure, Denis; Joly, Dominique

    2015-04-01

    Next-generation sequencing (NGS) provides unprecedented insight into (meta)genomes, (meta)transcriptomes (cDNA) and (meta)barcodes of individuals, populations and communities of Archaea, Bacteria and Eukarya, as well as viruses. This special issue combines reviews and original papers reporting technical and scientific advances in genomics and transcriptomics of non-model species, as well as quantification and functional analyses of biodiversity using NGS technologies of the second and third generations. In addition, certain papers also exemplify the transition from Sanger to NGS barcodes in molecular taxonomy.

  14. Validation of the Narcissistic Grandiosity Scale and creation of reduced item variants.

    Science.gov (United States)

    Crowe, Michael; Carter, Nathan T; Campbell, W Keith; Miller, Joshua D

    2016-12-01

    The Narcissistic Grandiosity Scale (NGS) is a short adjective-based measure of narcissistic grandiosity (Rosenthal, Hooley, & Steshenko, 2007). The NGS has already shown promise as a measure of grandiose narcissism, but it has never been the subject of a formal validation study. In the current study (N = 870 across 3 samples), the factor structure of NGS was examined and item response theory analyses were used to generate abbreviated versions of the scale. The NGS scales' relations to measures of grandiose and vulnerable narcissism, the five-factor model (FFM), the interpersonal circumplex, self-esteem, and the Personality Inventory of the Diagnostic and Statistical Manual for Mental Disorders-Fifth Edition (DSM-5, PID-5) were assessed. The correlation profile of the NGS was also correlated with expert ratings of prototypical cases of narcissistic personality disorder using both the FFM and PID-5 trait profiles. Overall, the NGS was found to be a unidimensional measure of narcissistic grandiosity with good convergent, discriminant, and criterion validity. The abbreviated versions of the NGS manifested strong reliability and associations entirely consistent with the full version. (PsycINFO Database Record

  15. Improving mapping and SNP-calling performance in multiplexed targeted next-generation sequencing

    Directory of Open Access Journals (Sweden)

    ElSharawy Abdou

    2012-08-01

    Full Text Available Abstract Background Compared to classical genotyping, targeted next-generation sequencing (tNGS can be custom-designed to interrogate entire genomic regions of interest, in order to detect novel as well as known variants. To bring down the per-sample cost, one approach is to pool barcoded NGS libraries before sample enrichment. Still, we lack a complete understanding of how this multiplexed tNGS approach and the varying performance of the ever-evolving analytical tools can affect the quality of variant discovery. Therefore, we evaluated the impact of different software tools and analytical approaches on the discovery of single nucleotide polymorphisms (SNPs in multiplexed tNGS data. To generate our own test model, we combined a sequence capture method with NGS in three experimental stages of increasing complexity (E. coli genes, multiplexed E. coli, and multiplexed HapMap BRCA1/2 regions. Results We successfully enriched barcoded NGS libraries instead of genomic DNA, achieving reproducible coverage profiles (Pearson correlation coefficients of up to 0.99 across multiplexed samples, with Conclusions We recommend applying our general ‘two-step’ mapping approach for more efficient SNP discovery in tNGS. Our study has also shown the benefit of computing inter-sample SNP-concordances and inspecting read alignments in order to attain more confident results.

  16. Promoting Models

    Science.gov (United States)

    Li, Qin; Zhao, Yongxin; Wu, Xiaofeng; Liu, Si

    There can be multitudinous models specifying aspects of the same system. Each model has a bias towards one aspect. These models often override in specific aspects though they have different expressions. A specification written in one model can be refined by introducing additional information from other models. The paper proposes a concept of promoting models which is a methodology to obtain refinements with support from cooperating models. It refines a primary model by integrating the information from a secondary model. The promotion principle is not merely an academic point, but also a reliable and robust engineering technique which can be used to develop software and hardware systems. It can also check the consistency between two specifications from different models. A case of modeling a simple online shopping system with the cooperation of the guarded design model and CSP model illustrates the practicability of the promotion principle.

  17. Cadastral Modeling

    DEFF Research Database (Denmark)

    Stubkjær, Erik

    2005-01-01

    Modeling is a term that refers to a variety of efforts, including data and process modeling. The domain to be modeled may be a department, an organization, or even an industrial sector. E-business presupposes the modeling of an industrial sector, a substantial task. Cadastral modeling compares to...

  18. De Novo Transcriptome Assembly (NGS) of Curcuma longa L. Rhizome Reveals Novel Transcripts Related to Anticancer and Antimalarial Terpenoids

    Science.gov (United States)

    Jayakumar, Vasanthan; Damodaran, Anand C.; Rao, Sudha Narayana; Katta, Mohan A. V. S. K.; Gopinathan, Sreeja; Sarma, Santosh Prasad; Senthilkumar, Vanitha; Niranjan, Vidya; Gopinath, Ashok; Mugasimangalam, Raja C.

    2013-01-01

    Herbal remedies are increasingly being recognised in recent years as alternative medicine for a number of diseases including cancer. Curcuma longa L., commonly known as turmeric is used as a culinary spice in India and in many Asian countries has been attributed to lower incidences of gastrointestinal cancers. Curcumin, a secondary metabolite isolated from the rhizomes of this plant has been shown to have significant anticancer properties, in addition to antimalarial and antioxidant effects. We sequenced the transcriptome of the rhizome of the 3 varieties of Curcuma longa L. using Illumina reversible dye terminator sequencing followed by de novo transcriptome assembly. Multiple databases were used to obtain a comprehensive annotation and the transcripts were functionally classified using GO, KOG and PlantCyc. Special emphasis was given for annotating the secondary metabolite pathways and terpenoid biosynthesis pathways. We report for the first time, the presence of transcripts related to biosynthetic pathways of several anti-cancer compounds like taxol, curcumin, and vinblastine in addition to anti-malarial compounds like artemisinin and acridone alkaloids, emphasizing turmeric's importance as a highly potent phytochemical. Our data not only provides molecular signatures for several terpenoids but also a comprehensive molecular resource for facilitating deeper insights into the transcriptome of C. longa. PMID:23468859

  19. De Novo transcriptome assembly (NGS) of Curcuma longa L. rhizome reveals novel transcripts related to anticancer and antimalarial terpenoids.

    Science.gov (United States)

    Annadurai, Ramasamy S; Neethiraj, Ramprasad; Jayakumar, Vasanthan; Damodaran, Anand C; Rao, Sudha Narayana; Katta, Mohan A V S K; Gopinathan, Sreeja; Sarma, Santosh Prasad; Senthilkumar, Vanitha; Niranjan, Vidya; Gopinath, Ashok; Mugasimangalam, Raja C

    2013-01-01

    Herbal remedies are increasingly being recognised in recent years as alternative medicine for a number of diseases including cancer. Curcuma longa L., commonly known as turmeric is used as a culinary spice in India and in many Asian countries has been attributed to lower incidences of gastrointestinal cancers. Curcumin, a secondary metabolite isolated from the rhizomes of this plant has been shown to have significant anticancer properties, in addition to antimalarial and antioxidant effects. We sequenced the transcriptome of the rhizome of the 3 varieties of Curcuma longa L. using Illumina reversible dye terminator sequencing followed by de novo transcriptome assembly. Multiple databases were used to obtain a comprehensive annotation and the transcripts were functionally classified using GO, KOG and PlantCyc. Special emphasis was given for annotating the secondary metabolite pathways and terpenoid biosynthesis pathways. We report for the first time, the presence of transcripts related to biosynthetic pathways of several anti-cancer compounds like taxol, curcumin, and vinblastine in addition to anti-malarial compounds like artemisinin and acridone alkaloids, emphasizing turmeric's importance as a highly potent phytochemical. Our data not only provides molecular signatures for several terpenoids but also a comprehensive molecular resource for facilitating deeper insights into the transcriptome of C. longa.

  20. De Novo transcriptome assembly (NGS of Curcuma longa L. rhizome reveals novel transcripts related to anticancer and antimalarial terpenoids.

    Directory of Open Access Journals (Sweden)

    Ramasamy S Annadurai

    Full Text Available Herbal remedies are increasingly being recognised in recent years as alternative medicine for a number of diseases including cancer. Curcuma longa L., commonly known as turmeric is used as a culinary spice in India and in many Asian countries has been attributed to lower incidences of gastrointestinal cancers. Curcumin, a secondary metabolite isolated from the rhizomes of this plant has been shown to have significant anticancer properties, in addition to antimalarial and antioxidant effects. We sequenced the transcriptome of the rhizome of the 3 varieties of Curcuma longa L. using Illumina reversible dye terminator sequencing followed by de novo transcriptome assembly. Multiple databases were used to obtain a comprehensive annotation and the transcripts were functionally classified using GO, KOG and PlantCyc. Special emphasis was given for annotating the secondary metabolite pathways and terpenoid biosynthesis pathways. We report for the first time, the presence of transcripts related to biosynthetic pathways of several anti-cancer compounds like taxol, curcumin, and vinblastine in addition to anti-malarial compounds like artemisinin and acridone alkaloids, emphasizing turmeric's importance as a highly potent phytochemical. Our data not only provides molecular signatures for several terpenoids but also a comprehensive molecular resource for facilitating deeper insights into the transcriptome of C. longa.