Improving the delineation of hydrocarbon-impacted soils and water through induced polarization (IP) tomographies: a field study at an industrial waste land.

PubMed

Deceuster, John; Kaufmann, Olivier

2012-08-01

Without a good estimation of samples representativeness, the delineation of the contaminated plume extent and the evaluation of volumes of hydrocarbon-impacted soils may remain difficult. To contribute to this question, a time domain induced polarization (IP) field experiment was conducted on an industrial waste land. Boreholes were drilled to specify the local geological context. Cross-hole seismic tomographies were performed to extend borehole logs and to draw an interpreted geological cross-section. Soil samples taken during drillings were analysed in laboratory. A preliminary survey was conducted to locate the IP profile. The polarization signatures linked to the presence of clayey sediments were filtered out from the data set. Chargeability and resistivity depth soundings were computed and compared to mean concentrations of total organic products to overcome the data support issue between the geophysical models and the spot samples of soils. A logarithmic relation between chargeabilities and smoothed hydrocarbon concentrations in soils was found. Taking into account contaminant's concentration thresholds defined in local codes and regulations allows defining chargeability classes to delineate hotspots on this site. This showed that IP tomography can be an accurate screening methodology. A statistical methodology is proposed to assess the efficiency of the investigation strategy. Copyright © 2012 Elsevier B.V. All rights reserved.

Analysis of Induced Polarization effects in airborne TEM data - a case study from central East Greenland

NASA Astrophysics Data System (ADS)

Maack Rasmussen, Thorkild; Brethes, Anaïs; Pierpaolo Guarnieri, Pierpaolo; Bauer, Tobias

2017-04-01

Data from a high-resolution airborne SkyTEM time-domain electromagnetic survey conducted in central East Greenland were analysed. An analysis based on utilization of a Self Organizing Map procedure for response curve characterization and analyses based on data inversion and modelling are presented. The survey was flown in 2013 along the eastern margin of the Jameson Land basin with the purpose of base metal exploration and with sulphide mineralization as target. The survey area comprises crystalline basement to the East and layered Early Triassic to Jurassic sediments to the West. The layers are dipping a few degrees towards West. The Triassic sequence is 1 to 2 km thick and mostly of continental origin. The fluviatile Early Triassic arkoses and conglomerates, the Upper Triassic grey limestone and black shale beds and overlying gypsiferous sandstones and mudstones are known to host disseminated sulphides. E-W oriented lines were flown with an average terrain clearance of 30m and a separation of 300m. The data were initially processed and inverted by SkyTEM Aps. The conductivity models showed some conductive layers as well as induced polarization (IP) effects in the data. IP effects in TEM data reflect the relaxation of polarized charges in the ground which can be good indicators of the presence of metallic particles. Some of these locations were drilled during the following field season but unfortunately did not reveal the presence of mineralization. The aim of this study is therefore to understand the possible causes of these IP effects. Electrical charge accumulation in the ground can be related to the presence of sulphides, oxides or graphite or to the presence of clays or fibrous minerals. Permafrost may also cause IP effects and is then expected to be associated with a highly resistive subsurface. Several characteristics of the transient curves (IP indicators) of the SkyTEM survey were extracted and analysed by using the Kohonen Self-Organizing Map (SOM) technique. SOM is a type of neural network algorithm developed for analysis of non-linear relationships in multivariate data. The basic idea of SOM is to provide a method for easy visualizing of multi-dimensional data. The SOM may be viewed as a two-dimensional grid onto which multi-dimensional input data are projected or mapped from a multi-dimensional space. The space dimension is equal to the number of analysed variables containing the geo-referenced IP indicators that characterise the transient curves. Input data that are similar or close to each other, irrespectively of their geographic location, are mapped to the same or adjacent position in the SOM. Data that belongs to a particular cluster in the SOM space are afterwards mapped into a geographical space. Characteristics of the IP effects can therefore be mapped and spatially compared with the geology of the area. Once IP were identified and located, Cole-Cole parameters were recovered from the airborne TEM data in specific locations by inversion of the TEM data. An interpretation of the derived models is discussed in relation to possible causes of the observed IP effects.

Two different electrical properties can improve transoceanic cable-route mapping

USGS Publications Warehouse

Wynn, J.; McGinnis, T.

2001-01-01

Induced polarization (IP) measurements made in the marine environment were investigated to map and remotely characterize the top 6-10 meters of the seafloor. The continuous resistivity profiling with cone-penetrometer tests, providing important information to engineers planning transoceanic cable routes, was also described. The IP effect and resistivity were identified as the two electric properties to improve transoceanic cable-route mapping. The measurement of IP and resistivity was found to depend on electrical current.

Better band gaps with asymptotically corrected local exchange potentials

NASA Astrophysics Data System (ADS)

Singh, Prashant; Harbola, Manoj K.; Hemanadhan, M.; Mookerjee, Abhijit; Johnson, D. D.

2016-02-01

We formulate a spin-polarized van Leeuwen and Baerends (vLB) correction to the local density approximation (LDA) exchange potential [R. van Leeuwen and E. J. Baerends, Phys. Rev. A 49, 2421 (1994), 10.1103/PhysRevA.49.2421] that enforces the ionization potential (IP) theorem following T. Stein et al. [Phys. Rev. Lett. 105, 266802 (2010), 10.1103/PhysRevLett.105.266802]. For electronic-structure problems, the vLB correction replicates the behavior of exact-exchange potentials, with improved scaling and well-behaved asymptotics, but with the computational cost of semilocal functionals. The vLB + IP correction produces a large improvement in the eigenvalues over those from the LDA due to correct asymptotic behavior and atomic shell structures, as shown in rare-gas, alkaline-earth, zinc-based oxides, alkali halides, sulfides, and nitrides. In half-Heusler alloys, this asymptotically corrected LDA reproduces the spin-polarized properties correctly, including magnetism and half-metallicity. We also consider finite-sized systems [e.g., ringed boron nitride (B12N12 ) and graphene (C24)] to emphasize the wide applicability of the method.

Better band gaps with asymptotically corrected local exchange potentials

DOE PAGES

Singh, Prashant; Harbola, Manoj K.; Hemanadhan, M.; ...

2016-02-22

In this study, we formulate a spin-polarized van Leeuwen and Baerends (vLB) correction to the local density approximation (LDA) exchange potential [R. van Leeuwen and E. J. Baerends, Phys. Rev. A 49, 2421 (1994)] that enforces the ionization potential (IP) theorem following T. Stein et al. [Phys. Rev. Lett. 105, 266802 (2010)]. For electronic-structure problems, the vLB correction replicates the behavior of exact-exchange potentials, with improved scaling and well-behaved asymptotics, but with the computational cost of semilocal functionals. The vLB + IP correction produces a large improvement in the eigenvalues over those from the LDA due to correct asymptotic behaviormore » and atomic shell structures, as shown in rare-gas, alkaline-earth, zinc-based oxides, alkali halides, sulfides, and nitrides. In half-Heusler alloys, this asymptotically corrected LDA reproduces the spin-polarized properties correctly, including magnetism and half-metallicity. We also consider finite-sized systems [e.g., ringed boron nitride (B 12N 12) and graphene (C 24)] to emphasize the wide applicability of the method.« less

Induced Polarization Surveying for Acid Rock Screening in Highway Design

NASA Astrophysics Data System (ADS)

Butler, K. E.; Al, T.; Bishop, T.

2004-05-01

Highway and pipeline construction agencies have become increasingly vigilant in their efforts to avoid cutting through sulphide-bearing bedrock that has potential to produce acid rock drainage. Blasting and fragmentation of such rock increases the surface area available for sulphide oxidation and hence increases the risk of acid rock drainage unless the rock contains enough natural buffering capacity to neutralize the pH. In December, 2001, the New Brunswick Department of Transportation (NBOT) sponsored a field trial of geophysical surveying in order to assess its suitability as a screening tool for locating near-surface sulphides along proposed highway alignments. The goal was to develop a protocol that would allow existing programs of drilling and geochemical testing to be targeted more effectively, and provide design engineers with the information needed to reduce rock cuts where necessary and dispose of blasted material in a responsible fashion. Induced polarization (IP) was chosen as the primary geophysical method given its ability to detect low-grade disseminated mineralization. The survey was conducted in dipole-dipole mode using an exploration-style time domain IP system, dipoles 8 to 25 m in length, and six potential dipoles for each current dipole location (i.e. n = 1 - 6). Supplementary information was provided by resistivity and VLF-EM surveys sensitive to lateral changes in electrical conductivity, and by magnetic field surveying chosen for its sensitivity to the magnetic susceptibility of pyrrhotite. Geological and geochemical analyses of samples taken from several IP anomalies located along 4.3 line-km of proposed highway confirmed the effectiveness of the screening technique. IP pseudosections from a region of metamorphosed shales and volcaniclastic rocks identified discrete, well-defined mineralized zones. Stronger, overlapping, and more laterally extensive IP anomalies were observed over a section of graphitic and sulphide-bearing metasedimentary rocks. Attempts to use spectral IP characteristics to determine relative abundances of sulphides and graphite were not conclusive. The overall effectiveness of the screening technique however encouraged NBDOT to apply it to an additional 50 km of planned rock cuts along the corridor selected for the new Trans-Canada Highway.

Permeability Estimation Directly From Logging-While-Drilling Induced Polarization Data

NASA Astrophysics Data System (ADS)

Fiandaca, G.; Maurya, P. K.; Balbarini, N.; Hördt, A.; Christiansen, A. V.; Foged, N.; Bjerg, P. L.; Auken, E.

2018-04-01

In this study, we present the prediction of permeability from time domain spectral induced polarization (IP) data, measured in boreholes on undisturbed formations using the El-log logging-while-drilling technique. We collected El-log data and hydraulic properties on unconsolidated Quaternary and Miocene deposits in boreholes at three locations at a field site in Denmark, characterized by different electrical water conductivity and chemistry. The high vertical resolution of the El-log technique matches the lithological variability at the site, minimizing ambiguity in the interpretation originating from resolution issues. The permeability values were computed from IP data using a laboratory-derived empirical relationship presented in a recent study for saturated unconsolidated sediments, without any further calibration. A very good correlation, within 1 order of magnitude, was found between the IP-derived permeability estimates and those derived using grain size analyses and slug tests, with similar depth trends and permeability contrasts. Furthermore, the effect of water conductivity on the IP-derived permeability estimations was found negligible in comparison to the permeability uncertainties estimated from the inversion and the laboratory-derived empirical relationship.

Very long baseline IPS observations of the solar wind speed in the fast polar streams

NASA Technical Reports Server (NTRS)

Rao, A. Pramesh; Ananthakrishnan, S.; Balasubramanian, V.; Coles, William A.

1995-01-01

Observations of intensity scintillation (IPS) with two or more spaced antennas have been widely used to measure the solar wind velocity. Such methods are particularly valuable in regions which spacecraft have not yet penetrated, but they are also very useful in improving the spatial temporal sampling of the solar wind, even in regions where spacecraft data are available. The principle of the measurement is to measure the time delay tau(sub d) between the scintillations observed with an antenna baseline b. The velocity estimate is just V = b/tau(sub d). The error in estimation of the time delay delta tau(sub d) is independent of the baseline length, thus the error in the velocity estimate delta V given by delta(V)/V approximately equals to (delta tau(sub d))/tau(sub d) is inversely proportional to tau(sub d) and hence to b. However the use of a long baseline b has a less obvious advantage; it provides a means for separating fast and slow contributions when both are present in the scattering region. Here we will present recent observations made using the large cylinder antenna at Ooty in the Nilgiri Hills of South India, and one of the 45 m dishes of GMRT near Pune in West-Central India. The baseline of 900 km is, by a considerable margin, the longest ever used for IPS and provides excellent velocity resolution. These results compared with the ULYSSES observations and other IPS measurements made closer to the sun with higher frequency instruments such as EISCAT and the VLBA will provide a precise measure of the velocity profile of the fast north-polar stream.

ELRIS2D: A MATLAB Package for the 2D Inversion of DC Resistivity/IP Data

NASA Astrophysics Data System (ADS)

Akca, Irfan

2016-04-01

ELRIS2D is an open source code written in MATLAB for the two-dimensional inversion of direct current resistivity (DCR) and time domain induced polarization (IP) data. The user interface of the program is designed for functionality and ease of use. All available settings of the program can be reached from the main window. The subsurface is discre-tized using a hybrid mesh generated by the combination of structured and unstructured meshes, which reduces the computational cost of the whole inversion procedure. The inversion routine is based on the smoothness constrained least squares method. In order to verify the program, responses of two test models and field data sets were inverted. The models inverted from the synthetic data sets are consistent with the original test models in both DC resistivity and IP cases. A field data set acquired in an archaeological site is also used for the verification of outcomes of the program in comparison with the excavation results.

Restricted access Improved hydrogeophysical characterization and monitoring through parallel modeling and inversion of time-domain resistivity andinduced-polarization data

USGS Publications Warehouse

Johnson, Timothy C.; Versteeg, Roelof J.; Ward, Andy; Day-Lewis, Frederick D.; Revil, André

2010-01-01

Electrical geophysical methods have found wide use in the growing discipline of hydrogeophysics for characterizing the electrical properties of the subsurface and for monitoring subsurface processes in terms of the spatiotemporal changes in subsurface conductivity, chargeability, and source currents they govern. Presently, multichannel and multielectrode data collections systems can collect large data sets in relatively short periods of time. Practitioners, however, often are unable to fully utilize these large data sets and the information they contain because of standard desktop-computer processing limitations. These limitations can be addressed by utilizing the storage and processing capabilities of parallel computing environments. We have developed a parallel distributed-memory forward and inverse modeling algorithm for analyzing resistivity and time-domain induced polar-ization (IP) data. The primary components of the parallel computations include distributed computation of the pole solutions in forward mode, distributed storage and computation of the Jacobian matrix in inverse mode, and parallel execution of the inverse equation solver. We have tested the corresponding parallel code in three efforts: (1) resistivity characterization of the Hanford 300 Area Integrated Field Research Challenge site in Hanford, Washington, U.S.A., (2) resistivity characterization of a volcanic island in the southern Tyrrhenian Sea in Italy, and (3) resistivity and IP monitoring of biostimulation at a Superfund site in Brandywine, Maryland, U.S.A. Inverse analysis of each of these data sets would be limited or impossible in a standard serial computing environment, which underscores the need for parallel high-performance computing to fully utilize the potential of electrical geophysical methods in hydrogeophysical applications.

Induced polarization and its interaction with electromagnetic coupling in low-frequency geophysical exploration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gruszka, T.P.

1987-01-01

Starting from the dynamic equations of electromagnetics we derive mutual impedance formulas that include the effects of induced polarization (IP) and electromagnetic (EM) coupling. The mutual impedance formulas are given for four geometries: a fullspace, a cylinder in a fullspace, a halfspace, and a layer over a halfspace. IP effects are characterized by a Cole-Cole model, the properties of which are fully investigated. From the general mutual impedance formulas specific limiting forms are defined to characterize the IP and EM effects. Using these limiting forms a framework is developed to justify the addition or multiplication of the two effects. Themore » additive and multiplicative models are compared in the cylinder and layer geometries with the conclusion that the additive model proves to be more accurate over a wider range of frequencies than the multiplicative model. The nature of the IP and EM effects is illustrated in all four geometries showing the effects of relevant parameters. In all cases it is shown that the real part of the mutual impedance contains important IP information that is less influenced by EM effects. Finally the effects of boundaries are illustrated by the cylinder and layer geometries and a theory is developed to incorporate EM effects and IP effects from multiple regions which utilizes frequency dependent real dilution factors. The author also included a brief review of some EM removal schemes and dilution theory approximations.« less

Temperature dependence of the positronium yields in polar and nonpolar pure liquids; an experimental test of a phenomenological model

NASA Astrophysics Data System (ADS)

Lévay, B.

2004-08-01

A phenomenological model describing the temperature dependence of the positronium yields ( IPs, %) was tested in pure liquids of different polarity. The investigated solvents were: m-xylene (m-Xy) and iso-octane (i-C8) as aromatic and aliphatic nonpolar hydrocarbons, methanol (MeOH), water and dimethyl formamide as polar solvents with and without OH group. Arrhenius type linear relationship predicted by the model for the ln Q vs 1/ T function, where Q=(100/ IPs-1), was found to be valid in all cases. The slopes of the lines correspond to the activation energy differences (Δ E*= Erec- EPs) between the two main competing reaction pathways in the positron spur, i.e., solvent recombination (e - + M +) and positronium formation (e - + e +). The slopes were positive, i.e., Δ E*<0 and Erec< EPs. For polar liquids, correlation seems to exists between Δ E* and the electron mobility ( μ) or the activation energy of the viscosity ( Eη).

Crystal structure of human IPS-1/MAVS/VISA/Cardif caspase activation recruitment domain.

PubMed

Potter, Jane A; Randall, Richard E; Taylor, Garry L

2008-02-28

IPS-1/MAVS/VISA/Cardif is an adaptor protein that plays a crucial role in the induction of interferons in response to viral infection. In the initial stage of the intracellular antiviral response two RNA helicases, retinoic acid inducible gene-I (RIG-I) and melanoma differentiation-association gene 5 (MDA5), are independently able to bind viral RNA in the cytoplasm. The 62 kDa protein IPS-1/MAVS/VISA/Cardif contains an N-terminal caspase activation and recruitment (CARD) domain that associates with the CARD regions of RIG-I and MDA5, ultimately leading to the induction of type I interferons. As a first step towards understanding the molecular basis of this important adaptor protein we have undertaken structural studies of the IPS-1 MAVS/VISA/Cardif CARD region. The crystal structure of human IPS-1/MAVS/VISA/Cardif CARD has been determined to 2.1A resolution. The protein was expressed and crystallized as a maltose-binding protein (MBP) fusion protein. The MBP and IPS-1 components each form a distinct domain within the structure. IPS-1/MAVS/VISA/Cardif CARD adopts a characteristic six-helix bundle with a Greek-key topology and, in common with a number of other known CARD structures, contains two major polar surfaces on opposite sides of the molecule. One face has a surface-exposed, disordered tryptophan residue that may explain the poor solubility of untagged expression constructs. The IPS-1/MAVS/VISA/Cardif CARD domain adopts the classic CARD fold with an asymmetric surface charge distribution that is typical of CARD domains involved in homotypic protein-protein interactions. The location of the two polar areas on IPS-1/MAVS/VISA/Cardif CARD suggest possible types of associations that this domain makes with the two CARD domains of MDA5 or RIG-I. The N-terminal CARD domains of RIG-I and MDA5 share greatest sequence similarity with IPS-1/MAVS/VISA/Cardif CARD and this has allowed modelling of their structures. These models show a very different charge profile for the equivalent surfaces compared to IPS-1/MAVS/VISA/Cardif CARD.

New Geophysical Technique for Mineral Exploration and Mineral Discrimination Based on Electromagnetic Methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Michael S. Zhdanov

2005-03-09

The research during the first year of the project was focused on developing the foundations of a new geophysical technique for mineral exploration and mineral discrimination, based on electromagnetic (EM) methods. The proposed new technique is based on examining the spectral induced polarization effects in electromagnetic data using modern distributed acquisition systems and advanced methods of 3-D inversion. The analysis of IP phenomena is usually based on models with frequency dependent complex conductivity distribution. One of the most popular is the Cole-Cole relaxation model. In this progress report we have constructed and analyzed a different physical and mathematical model ofmore » the IP effect based on the effective-medium theory. We have developed a rigorous mathematical model of multi-phase conductive media, which can provide a quantitative tool for evaluation of the type of mineralization, using the conductivity relaxation model parameters. The parameters of the new conductivity relaxation model can be used for discrimination of the different types of rock formations, which is an important goal in mineral exploration. The solution of this problem requires development of an effective numerical method for EM forward modeling in 3-D inhomogeneous media. During the first year of the project we have developed a prototype 3-D IP modeling algorithm using the integral equation (IP) method. Our IE forward modeling code INTEM3DIP is based on the contraction IE method, which improves the convergence rate of the iterative solvers. This code can handle various types of sources and receivers to compute the effect of a complex resistivity model. We have tested the working version of the INTEM3DIP code for computer simulation of the IP data for several models including a southwest US porphyry model and a Kambalda-style nickel sulfide deposit. The numerical modeling study clearly demonstrates how the various complex resistivity models manifest differently in the observed EM data. These modeling studies lay a background for future development of the IP inversion method, directed at determining the electrical conductivity and the intrinsic chargeability distributions, as well as the other parameters of the relaxation model simultaneously. The new technology envisioned in this proposal, will be used for the discrimination of different rocks, and in this way will provide an ability to distinguish between uneconomic mineral deposits and the location of zones of economic mineralization and geothermal resources.« less

Modeling and inversion Matlab algorithms for resistivity, induced polarization and seismic data

NASA Astrophysics Data System (ADS)

Karaoulis, M.; Revil, A.; Minsley, B. J.; Werkema, D. D.

2011-12-01

M. Karaoulis (1), D.D. Werkema (3), A. Revil (1,2), A., B. Minsley (4), (1) Colorado School of Mines, Dept. of Geophysics, Golden, CO, USA. (2) ISTerre, CNRS, UMR 5559, Université de Savoie, Equipe Volcan, Le Bourget du Lac, France. (3) U.S. EPA, ORD, NERL, ESD, CMB, Las Vegas, Nevada, USA . (4) USGS, Federal Center, Lakewood, 10, 80225-0046, CO. Abstract We propose 2D and 3D forward modeling and inversion package for DC resistivity, time domain induced polarization (IP), frequency-domain IP, and seismic refraction data. For the resistivity and IP case, discretization is based on rectangular cells, where each cell has as unknown resistivity in the case of DC modelling, resistivity and chargeability in the time domain IP modelling, and complex resistivity in the spectral IP modelling. The governing partial-differential equations are solved with the finite element method, which can be applied to both real and complex variables that are solved for. For the seismic case, forward modeling is based on solving the eikonal equation using a second-order fast marching method. The wavepaths are materialized by Fresnel volumes rather than by conventional rays. This approach accounts for complicated velocity models and is advantageous because it considers frequency effects on the velocity resolution. The inversion can accommodate data at a single time step, or as a time-lapse dataset if the geophysical data are gathered for monitoring purposes. The aim of time-lapse inversion is to find the change in the velocities or resistivities of each model cell as a function of time. Different time-lapse algorithms can be applied such as independent inversion, difference inversion, 4D inversion, and 4D active time constraint inversion. The forward algorithms are benchmarked against analytical solutions and inversion results are compared with existing ones. The algorithms are packaged as Matlab codes with a simple Graphical User Interface. Although the code is parallelized for multi-core cpus, it is not as fast as machine code. In the case of large datasets, someone should consider transferring parts of the code to C or Fortran through mex files. This code is available through EPA's website on the following link http://www.epa.gov/esd/cmb/GeophysicsWebsite/index.html Although this work was reviewed by EPA and approved for publication, it may not necessarily reflect official Agency policy.

Theoretical and numerical evaluation of polarimeter using counter-circularly-polarized-probing-laser under the coupling between Faraday and Cotton-Mouton effect.

PubMed

Imazawa, Ryota; Kawano, Yasunori; Itami, Kiyoshi

2016-04-01

This study evaluated an effect of an coupling between the Faraday and Cotton-Mouton effect to a measurement signal of the Dodel-Kunz method which uses counter-circular-polarized probing-laser for measuring the Faraday effect. When the coupling is small (the Faraday effect is dominant and the characteristic eigenmodes are approximately circularly polarized), the measurement signal can be algebraically expressed and it is shown that the finite effect of the coupling is still significant. When the Faraday effect is not dominant, a numerical calculation is necessary. The numerical calculation under an ITER-like condition (Bt = 5.3 T, Ip = 15 MA, a = 2 m, ne = 10(20) m(-3) and λ = 119 μm) showed that difference between the pure Faraday rotation and the measurement signal of the Dodel-Kunz method was an order of one degree, which exceeds allowable error of ITER poloidal polarimeter. In conclusion, similar to other polarimeter techniques, the Dodel-Kunz method is not free from the coupling between the Faraday and Cotton-Mouton effect.

Msd1/SSX2IP-dependent microtubule anchorage ensures spindle orientation and primary cilia formation

PubMed Central

Hori, Akiko; Ikebe, Chiho; Tada, Masazumi; Toda, Takashi

2014-01-01

Anchoring microtubules to the centrosome is critical for cell geometry and polarity, yet the molecular mechanism remains unknown. Here we show that the conserved human Msd1/SSX2IP is required for microtubule anchoring. hMsd1/SSX2IP is delivered to the centrosome in a centriolar satellite-dependent manner and binds the microtubule-nucleator γ-tubulin complex. hMsd1/SSX2IP depletion leads to disorganised interphase microtubules and misoriented mitotic spindles with reduced length and intensity. Furthermore, hMsd1/SSX2IP is essential for ciliogenesis, and during zebrafish embryogenesis, knockdown of its orthologue results in ciliary defects and disturbs left-right asymmetry. We propose that the Msd1 family comprises conserved microtubule-anchoring proteins. PMID:24397932

Polarized light microscopy for 3-dimensional mapping of collagen fiber architecture in ocular tissues.

PubMed

Yang, Bin; Jan, Ning-Jiun; Brazile, Bryn; Voorhees, Andrew; Lathrop, Kira L; Sigal, Ian A

2018-04-06

Collagen fibers play a central role in normal eye mechanics and pathology. In ocular tissues, collagen fibers exhibit a complex 3-dimensional (3D) fiber orientation, with both in-plane (IP) and out-of-plane (OP) orientations. Imaging techniques traditionally applied to the study of ocular tissues only quantify IP fiber orientation, providing little information on OP fiber orientation. Accurate description of the complex 3D fiber microstructures of the eye requires quantifying full 3D fiber orientation. Herein, we present 3dPLM, a technique based on polarized light microscopy developed to quantify both IP and OP collagen fiber orientations of ocular tissues. The performance of 3dPLM was examined by simulation and experimental verification and validation. The experiments demonstrated an excellent agreement between extracted and true 3D fiber orientation. Both IP and OP fiber orientations can be extracted from the sclera and the cornea, providing previously unavailable quantitative 3D measures and insight into the tissue microarchitecture. Together, the results demonstrate that 3dPLM is a powerful imaging technique for the analysis of ocular tissues. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Theory of the high-frequency chiral optical response of a p(x) + ip(y) superconductor.

PubMed

Yakovenko, Victor M

2007-02-23

The optical Hall conductivity and the polar Kerr angle are calculated as functions of temperature for a two-dimensional chiral p(x) + ip(y) superconductor, where the time-reversal symmetry is spontaneously broken. The theoretical estimate for the polar Kerr angle agrees by the order of magnitude with the recent experimental measurement in Sr2RuO4 by Xia et al. [Phys. Rev. Lett. 97, 167002 (2006)10.1103/PhysRevLett.97.167002]. The theory predicts that the Kerr angle is proportional to the square of the superconducting energy gap and is inversely proportional to the cube of frequency, which can be verified experimentally.

Evidence for Intermediate Polars as the Origin of the Galactic Center Hard X-Ray Emission

NASA Technical Reports Server (NTRS)

Hailey, Charles J.; Mori, Kaya; Perez, Kerstin; Canipe, Alicia M.; Hong, Jaesub; Tomsick, John A.; Boggs, Steven E.; Christensen, Finn E.; Craig, William W.; Fornasini, Francesa;

Human Induced Pluripotent Stem Cell-Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation.

PubMed

Sharmin, Sazia; Taguchi, Atsuhiro; Kaku, Yusuke; Yoshimura, Yasuhiro; Ohmori, Tomoko; Sakuma, Tetsushi; Mukoyama, Masashi; Yamamoto, Takashi; Kurihara, Hidetake; Nishinakamura, Ryuichi

2016-06-01

Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator-like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in vitro These induced human podocytes exhibited apicobasal polarity, with nephrin proteins accumulated close to the basal domain, and possessed primary processes that were connected with slit diaphragm-like structures. Microarray analysis of sorted iPS cell-derived podocytes identified well conserved marker gene expression previously shown in mouse and human podocytes in vivo Furthermore, we developed a novel transplantation method using spacers that release the tension of host kidney capsules, thereby allowing the effective formation of glomeruli from human iPS cell-derived nephron progenitors. The human glomeruli were vascularized with the host mouse endothelial cells, and iPS cell-derived podocytes with numerous cell processes accumulated around the fenestrated endothelial cells. Therefore, the podocytes generated from iPS cells retain the podocyte-specific molecular and structural features, which will be useful for dissecting human glomerular development and diseases. Copyright © 2016 by the American Society of Nephrology.

Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation

PubMed Central

Sharmin, Sazia; Taguchi, Atsuhiro; Kaku, Yusuke; Yoshimura, Yasuhiro; Ohmori, Tomoko; Sakuma, Tetsushi; Mukoyama, Masashi; Yamamoto, Takashi; Kurihara, Hidetake

2016-01-01

Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in vitro. These induced human podocytes exhibited apicobasal polarity, with nephrin proteins accumulated close to the basal domain, and possessed primary processes that were connected with slit diaphragm–like structures. Microarray analysis of sorted iPS cell–derived podocytes identified well conserved marker gene expression previously shown in mouse and human podocytes in vivo. Furthermore, we developed a novel transplantation method using spacers that release the tension of host kidney capsules, thereby allowing the effective formation of glomeruli from human iPS cell–derived nephron progenitors. The human glomeruli were vascularized with the host mouse endothelial cells, and iPS cell–derived podocytes with numerous cell processes accumulated around the fenestrated endothelial cells. Therefore, the podocytes generated from iPS cells retain the podocyte-specific molecular and structural features, which will be useful for dissecting human glomerular development and diseases. PMID:26586691

Combined DC resistivity and induced polarization (DC-IP) for mapping the internal composition of a mine waste rock pile in Nova Scotia, Canada

NASA Astrophysics Data System (ADS)

Power, Christopher; Tsourlos, Panagiotis; Ramasamy, Murugan; Nivorlis, Aristeidis; Mkandawire, Martin

2018-03-01

Mine waste rock piles (WRPs) can contain sulfidic minerals whose interaction with oxygen and water can generate acid mine drainage (AMD). Thus, WRPs can be a long-term source of environmental pollution. Since the generation of AMD and its release into the environment is dependent on the net volume and bulk composition of waste rock, effective characterization of WRPs is necessary for successful remedial design and monitoring. In this study, a combined DC resistivity and induced polarization (DC-IP) approach was employed to characterize an AMD-generating WRP in the Sydney Coalfield, Nova Scotia, Canada. Two-dimensional (2D) DC-IP imaging with 6 survey lines was performed to capture the full WRP landform. 2D DC results indicated a highly heterogeneous and moderately conductive waste rock underlain by a resistive bedrock containing numerous fractures. 2D IP (chargeability) results identified several highly-chargeable regions within the waste, with normalized chargeability delineating regions specific to waste mineralogy only. Three-dimensional (3D) DC-IP imaging, using 17 parallel lines on the plateau of the pile, was then used to focus on the composition of the waste rock. The full 3D inverted DC-IP distributions were used to identify coincident and continuous zones (isosurfaces) of low resistivity (<30 Ω-m) and high normalized chargeability (>0.4 mS/m) that were inferred as generated AMD (leachate) and stored AMD (sulfides), respectively. Integrated geological, hydrogeological and geochemical data increased confidence in the geoelectrical interpretations. Knowledge on the location of potentially more reactive waste material is extremely valuable for improved long-term AMD monitoring at the WRP.

The application of induced polarization techniques to detect metal-bearing offshore anthropogenic waste and unexploded ordnance

USGS Publications Warehouse

Wynn, Jeff; Roberts, William

2009-01-01

Raw sewage and industrial waste have been dumped into sensitive estuaries, bays, and sounds for centuries. The full extents of the resulting sludge deposits are largely unknown, because they move in response to tidal and long‐shore currents, and because they are often buried by younger inert sediments. USGS field and laboratory measurements of toxic mine waste and organic effluent samples suggest that anthropogenic wastes typically contain finely‐divided metal and metal‐sulfide particles. The anoxic environment provided by anthropogenic wastes promotes the growth of anaerobic bacteria, creating a self‐reducing environment. We suggest that the finely‐divided metal and metal‐sulfide particles are the products of bacterial reduction and precipitation. The fine‐grained metallic precipitates are ideal targets for a surface‐effect electrochemical detection methodology called Induced Polarization (IP). A USGS‐patented (1998/2001) marine IP streamer technology has recently been commercialized and used to map “black smoker” sulfide deposits and their disseminated halos in the Bismarck Sea (2005), and titanium‐sand deposits offshore of South Africa (2007). The marine induced polarization system can do this mapping in three dimensions, more rapidly (it is towed at 3 knots), and with far higher resolution that land‐based measurements or vibracoring. Laboratory‐scale studies at the USGS suggest that anthropogenic wastes may display a specific multi‐frequency IP spectral signature that may be applicable to waste‐deposit mapping.

Upscaling of spectral induced polarization response using random tube networks

NASA Astrophysics Data System (ADS)

Maineult, Alexis; Revil, André; Camerlynck, Christian; Florsch, Nicolas; Titov, Konstantin

2017-05-01

In order to upscale the induced polarization (IP) response of porous media, from the pore scale to the sample scale, we implement a procedure to compute the macroscopic complex resistivity response of random tube networks. A network is made of a 2-D square-meshed grid of connected tubes, which obey to a given tube radius distribution. In a simplified approach, the electrical impedance of each tube follows a local Pelton resistivity model, with identical resistivity, chargeability and Cole-Cole exponent values for all the tubes-only the time constant varies, as it depends on the radius of each tube and on a diffusion coefficient also identical for all the tubes. By solving the conservation law for the electrical charge, the macroscopic IP response of the network is obtained. We fit successfully the macroscopic complex resistivity also by a Pelton resistivity model. Simulations on uncorrelated and correlated networks, for which the tube radius distribution is so that the decimal logarithm of the radius is normally distributed, evidence that the local and macroscopic model parameters are the same, except the Cole-Cole exponent: its macroscopic value diminishes with increasing heterogeneity (i.e. with increasing standard deviation of the radius distribution), compared to its local value. The methodology is also applied to six siliciclastic rock samples, for which the pore radius distributions from mercury porosimetry are available. These samples exhibit the same behaviour as synthetic media, that is, the macroscopic Cole-Cole exponent is always lower than the local one. As a conclusion, the pore network method seems to be a promising tool for studying the upscaling of the IP response of porous media.

Demonstration That Calibration of the Instrument Response to Polarizations Parallel and Perpendicular to the Object Space Projected Slit of an Imaging Spectrometer Enable Measurement of the Atmospheric Absorption Spectrum in Region of the Weak CO2 Band for the Case of Arbitrary Polarization: Implication for the Geocarb Mission

NASA Astrophysics Data System (ADS)

Kumer, J. B.; Rairden, R. L.; Polonsky, I. N.; O'Brien, D. M.

2014-12-01

The Tropospheric Infrared Mapping Spectrometer (TIMS) unit rebuilt to operate in a narrow spectral region, approximately 1603 to 1615 nm, of the weak CO2 band as described by Kumer et al. (2013, Proc. SPIE 8867, doi:10.1117/12.2022668) was used to conduct the demonstration. An integrating sphere (IS), linear polarizers and quarter wave plate were used to confirm that the instrument's spectral response to unpolarized light, to 45° linearly polarized light and to circular polarized light are identical. In all these cases the intensity components Ip = Is where Ip is the component parallel to the object space projected slit and Is is perpendicular to the slit. In the circular polarized case Ip = Is in the time averaged sense. The polarizer and IS were used to characterize the ratio Rθ of the instrument response to linearly polarized light at the angle θ relative to parallel from the slit, for increments of θ from 0 to 90°, to that of the unpolarized case. Spectra of diffusely reflected sunlight passed through the polarizer in increments of θ, and divided by the respective Rθ showed identical results, within the noise limit, for solar spectrum multiplied by the atmospheric transmission and convolved by the Instrument Line Shape (ILS). These measurements demonstrate that unknown polarization in the diffusely reflected sunlight on this small spectral range affect only the slow change across the narrow band in spectral response relative to that of unpolarized light and NOT the finely structured / high contrast spectral structure of the CO2 atmospheric absorption that is used to retrieve the atmospheric content of CO2. The latter is one of the geoCARB mission objectives (Kumer et al, 2013). The situation is similar for the other three narrow geoCARB bands; O2 A band 757.9 to 768.6 nm; strong CO2 band 2045.0 to 2085.0 nm; CH4 and CO region 2300.6 to 2345.6 nm. Polonsky et al have repeated the mission simulation study doi:10.5194/amt-7-959-2014 assuming no use of a geoCARB depolarizer or polarizer. Enabled by measurement of the geoCARB grating efficiencies the simulated intensities Ism include the slow polarization induced spectral change across the band. These Ism are input to the retrieval SW that was used in the original study. There is no significant change to the very positive previous results for the mission objective of gas column retrieval.

ERP44 inhibits human lung cancer cell migration mainly via IP3R2.

PubMed

Huang, Xue; Jin, Meng; Chen, Ying-Xiao; Wang, Jun; Zhai, Kui; Chang, Yan; Yuan, Qi; Yao, Kai-Tai; Ji, Guangju

2016-06-01

Cancer cell migration is involved in tumour metastasis. However, the relationship between calcium signalling and cancer migration is not well elucidated. In this study, we used the human lung adenocarcinoma A549 cell line to examine the role of endoplasmic reticulum protein 44 (ERP44), which has been reported to regulate calcium release inside of the endoplasmic reticulum (ER), in cell migration. We found that the inositol 1,4,5-trisphosphate receptors (IP3Rs/ITPRs) inhibitor 2-APB significantly inhibited A549 cell migration by inhibiting cell polarization and pseudopodium protrusion, which suggests that Ca2+ is necessary for A549 cell migration. Similarly, the overexpression of ERP44 reduced intracellular Ca2+ release via IP3Rs, altered cell morphology and significantly inhibited the migration of A549 cells. These phenomena were primarily dependent on IP3R2 because wound healing in A549 cells with IP3R2 rather than IP3R1 or IP3R3 siRNA was markedly inhibited. Moreover, the overexpression of ERP44 did not affect the migration of the human neuroblastoma cell line SH-SY5Y, which mainly expresses IP3R1. Based on the above observations, we conclude that ERP44 regulates A549 cell migration mainly via an IP3R2-dependent pathway.

ERP44 inhibits human lung cancer cell migration mainly via IP3R2

PubMed Central

Zhai, Kui; Chang, Yan; Yuan, Qi; Yao, Kai-Tai; Ji, Guangju

2016-01-01

Cancer cell migration is involved in tumour metastasis. However, the relationship between calcium signalling and cancer migration is not well elucidated. In this study, we used the human lung adenocarcinoma A549 cell line to examine the role of endoplasmic reticulum protein 44 (ERP44), which has been reported to regulate calcium release inside of the endoplasmic reticulum (ER), in cell migration. We found that the inositol 1,4,5-trisphosphate receptors (IP3Rs/ITPRs) inhibitor 2-APB significantly inhibited A549 cell migration by inhibiting cell polarization and pseudopodium protrusion, which suggests that Ca2+ is necessary for A549 cell migration. Similarly, the overexpression of ERP44 reduced intracellular Ca2+ release via IP3Rs, altered cell morphology and significantly inhibited the migration of A549 cells. These phenomena were primarily dependent on IP3R2 because wound healing in A549 cells with IP3R2 rather than IP3R1 or IP3R3 siRNA was markedly inhibited. Moreover, the overexpression of ERP44 did not affect the migration of the human neuroblastoma cell line SH-SY5Y, which mainly expresses IP3R1. Based on the above observations, we conclude that ERP44 regulates A549 cell migration mainly via an IP3R2-dependent pathway. PMID:27347718

Detection and quantification of hydrocarbons in sediments

USGS Publications Warehouse

Wynn, Jeff; Williamson, Mike; Frank, Jeff

2016-01-01

A new technology developed by the US Geological Survey now allows for fast, direct detection of hydrocarbon plumes both in rivers and drifting in the deep ocean. Recent experiments show that the method can also detect and quantify hydrocarbons buried in river sediments and estuaries. This approach uses a variant of induced polarization, a surface-sensitive physical property of certain polarizable materials immersed in an electrolyte that can accept and adsorb charge under an inducing voltage. Known polarizable materials include most sulfides, ilmenite (FeTiO3), metallic objects such as buried wrecks and pipelines, and now hydrocarbons. The hydrocarbon-in-water response to induced polarization is in fact nearly two orders of magnitude greater than the IP response of any of the hard minerals. The oil:water detection limit for hydrocarbons so far is down to 0.0002% in the laboratory.

myo-Inositol hexakisphosphate is a major component of an extracellular structure in the parasitic cestode Echinococcus granulosus.

PubMed Central

Irigoín, Florencia; Ferreira, Fernando; Fernández, Cecilia; Sim, Robert B; Díaz, Alvaro

2002-01-01

myo-Inositol hexakisphosphate (IP(6)) is an abundant intracellular component of animal cells. In this study we describe the presence of extracellular IP(6) in the hydatid cyst wall (HCW) of the larval stage of the cestode parasite Echinococcus granulosus. The HCW comprises an inner cellular layer and an outer, acellular (laminated) layer up to 2 mm in thickness that protects the parasite from host immune cells. A compound, subsequently identified as IP(6), was detected in and purified from an HCW extract on the basis of its capacity to inhibit complement activation. The identification of the isolated compound was carried out by a combination of NMR, MS and TLC. The majority of IP(6) in the HCW was found in the acellular layer, with only a small fraction of the compound being extracted from cells. In the laminated layer, IP(6) was present in association with calcium, and accounted for up to 15% of the total dry mass of the HCW. IP(6) was not detected in any other structures or stages of the parasite. Our results imply that IP(6) is secreted by the larval stage of the parasite in a polarized fashion towards the interface with the host. This is the first report of the secretion of IP(6), and the possible implications beyond the biology of E. granulosus are discussed. PMID:11853537

NICA project at JINR: status and prospects

NASA Astrophysics Data System (ADS)

Kekelidze, V. D.

2017-06-01

The project NICA (Nuclotron-based Ion Collider fAcility) is aimed to study hot and dense baryonic matter in heavy-ion collisions in the energy range up to 11.0 AGeV . The plan of NICA accelerator block development includes an upgrade of the existing superconducting (SC) synchrotron Nuclotron and construction of the new injection complex, SC Booster, and SC Collider with two interaction points (IP). The heavy-ion collision program will be performed with the fixed target experiment Baryonic Matter at Nuclotron (BM@N) at the beam extracted from the Nuclotron, and with Multi-Purpose Detector (MPD) at the first IP of NICA Collider. Investigation of nucleon spin structure and polarization phenomena is foreseen with the Spin Physics Detector (SPC) at the second IP of the Collider.

Characterization of riverbed sediments hydraulic conductivity using slug tests and electrical resistivity tomography and induced polarization tomogrpahy.

NASA Astrophysics Data System (ADS)

Nguyen, F.; Benoit, S.; Gommers, K.; Ghysels, G.; Hermans, T.; Huysmans, M.

2017-12-01

Hydraulic conductivity of river sediments ranges from values smaller than 10-9 m/s to values higher than 10-2 m/s, with a dominance in values between 10-7 m/s and 10-3 m/s. Both horizontal hydraulic conductivity and vertical hydraulic conductivity show spatial variation in a riverbed. The spatial variation in hydraulic conductivity is due to the influence of the sedimentary and geomorphological environment as well as the method of determination, including scale, size and imprecision of the applied method. The characterization of the spatial variability of hydraulic conductivity in riverbeds is important because of its effect on the interaction between river and groundwater. These river - groundwater interactions influence water resource management, water quality and functioning of the riparian ecosystem. It is necessary in the simulation of 3D flow between river and aquifer near the interface and thus, it also determines contaminant transport and biogeochemical modelling in this riparian or hyporheic zone. Different processes occur in this specific zone such as transport, degradation, transformation, precipitation and sorption of substances, all dependent on hydraulic conductivity. Several methods exist to determine the hydraulic conductivity in river beds, both direct and indirect methods, from field to laboratory experiments or numerical modelling, but the uncertainty on obtained K values is often large because of the large variability of K. In the recent years, research has been performed on the usefulness of geophysical methods on rivers, in particular Electrical Resistivity Tomography (ERT) and Induced Polarization (IP). The implementation of ERT and IP in rivers provides a continuous image of the resistivity and chargeability of the subsurface, respectively, and can be used in several applications as proxies for hydraulic conductivity. This work reports and investigate a correlation between hydraulic conductivity measured by slug tests at an experimental site, and electrical resistivity, chargeability and normalized chargeability for riverbeds sediments.

Antidiabetic activity of medium-polar extract from the leaves of Stevia rebaudiana Bert. (Bertoni) on alloxan-induced diabetic rats

PubMed Central

Misra, Himanshu; Soni, Manish; Silawat, Narendra; Mehta, Darshana; Mehta, B. K.; Jain, D. C.

2011-01-01

Objective: To investigate the medicative effects of medium-polar (benzene:acetone, 1:1, v/v) extract of leaves from Stevia rebaudiana (family Asteraceae) on alloxan-induced diabetic rats. Materials and Methods: Diabetes was induced in adult albino Wistar rats by intraperitoneal (i.p.) injection of alloxan (180 mg/kg). Medium-polar extract was administered orally at daily dose of 200 and 400 mg/kg body wt. basis for 10 days. The control group received normal saline (0.9%) for the same duration. Glibenclamide was used as positive control reference drug against Stevia extract. Results: Medium-polar leaf extract of S. rebaudiana (200 and 400 mg/kg) produced a delayed but significant (P < 0.01) decrease in the blood glucose level, without producing condition of hypoglycemia after treatment, together with lesser loss in the body weight as compared with standard positive control drug glibenclamide. Conclusions: Treatment of diabetes with sulfonylurea drugs (glibenclamide) causes hypoglycemia followed by greater reduction in body weight, which are the most worrisome effects of these drugs. Stevia extract was found to antagonize the necrotic action of alloxan and thus had a re-vitalizing effect on β-cells of pancreas. PMID:21687353

Flexoelectric effect in an in-plane switching (IPS) liquid crystal cell for low-power consumption display devices

NASA Astrophysics Data System (ADS)

Kim, Min Su; Bos, Philip J.; Kim, Dong-Woo; Yang, Deng-Ke; Lee, Joong Hee; Lee, Seung Hee

2016-10-01

Technology of displaying static images in portable displays, advertising panels and price tags pursues significant reduction in power consumption and in product cost. Driving at a low-frequency electric field in fringe-field switching (FFS) mode can be one of the efficient ways to save powers of the recent portable devices, but a serious drop of image-quality, so-called image-flickering, has been found in terms of the coupling of elastic deformation to not only quadratic dielectric effect but linear flexoelectric effect. Despite of the urgent requirement of solving the issue, understanding of such a phenomenon is yet vague. Here, we thoroughly analyze and firstly report the flexoelectric effect in in-plane switching (IPS) liquid crystal cell. The effect takes place on the area above electrodes due to splay and bend deformations of nematic liquid crystal along oblique electric fields, so that the obvious spatial shift of the optical transmittance is experimentally observed and is clearly demonstrated based on the relation between direction of flexoelectric polarization and electric field polarity. In addition, we report that the IPS mode has inherent characteristics to solve the image-flickering issue in the low-power consumption display in terms of the physical property of liquid crystal material and the electrode structure.

Flexoelectric effect in an in-plane switching (IPS) liquid crystal cell for low-power consumption display devices.

PubMed

Kim, Min Su; Bos, Philip J; Kim, Dong-Woo; Yang, Deng-Ke; Lee, Joong Hee; Lee, Seung Hee

2016-10-12

Technology of displaying static images in portable displays, advertising panels and price tags pursues significant reduction in power consumption and in product cost. Driving at a low-frequency electric field in fringe-field switching (FFS) mode can be one of the efficient ways to save powers of the recent portable devices, but a serious drop of image-quality, so-called image-flickering, has been found in terms of the coupling of elastic deformation to not only quadratic dielectric effect but linear flexoelectric effect. Despite of the urgent requirement of solving the issue, understanding of such a phenomenon is yet vague. Here, we thoroughly analyze and firstly report the flexoelectric effect in in-plane switching (IPS) liquid crystal cell. The effect takes place on the area above electrodes due to splay and bend deformations of nematic liquid crystal along oblique electric fields, so that the obvious spatial shift of the optical transmittance is experimentally observed and is clearly demonstrated based on the relation between direction of flexoelectric polarization and electric field polarity. In addition, we report that the IPS mode has inherent characteristics to solve the image-flickering issue in the low-power consumption display in terms of the physical property of liquid crystal material and the electrode structure.

Electrical imaging of subsurface nanoparticle propagation for in-situ groundwater remediation

NASA Astrophysics Data System (ADS)

Flores Orozco, Adrián; Gallistl, Jakob; Schmid, Doris; Micic Batka, Vesna; Bücker, Matthias; Hofmann, Thilo

2017-04-01

Application of nanoparticles has emerged as a promising in situ remediation technology for the remediation of contaminated groundwater, particularly for areas difficult to access by other remediation techniques. The performance of nanoparticle injections, as a foremost step within this technology, is usually assessed through the geochemical analysis of soil and groundwater samples. This approach is not well suited for a real-time monitoring, and often suffers from a poor spatio-temporal resolution and only provides information from areas close to the sampling points. To overcome these limitations we propose the application of non-invasive Induced Polarization (IP) imaging, a geophysical method that provides information on the electrical properties of the subsurface. The analysis of temporal changes in the electrical images allows tracking the propagation of the injected nanoparticle suspension and detection of the induced bio-geochemical changes in the subsurface. Here, we present IP monitoring results for data collected during the injection of Nano-Goethite particles (NGP) used for simulation of biodegradation of a BTEX plume (i.e., benzene, toluene, ethylbenzene, and xylene) at the Spolchemie II site, CZ. Frequency-domain IP measurements were collected parallel to the groundwater flow direction and centred on the NGP injection point. Pre-injection imaging results revealed high electrical conductivities (> 10 S/m) and negligible polarization effects in the BTEX-contaminated part of the saturated zone (below 5 m depth). The apparently contradictory observation - BTEX compounds are poor electrical conductors - can be explained by the release of carbonic acids (a metabolic by-product of the biodegradation of hydrocarbons), which leads to an increase of the electrical conductivity. Post-injection images revealed a significant decrease (> 50%) of the electrical conductivity, with even larger changes in the proximity of the injection points, most likely due to the relatively high resistivity of the NGP suspension. This is in line with geochemical data from both the injected NGP suspension and the groundwater samples. Furthermore, temporal changes in the IP images are consistent with variations in total iron concentration in groundwater (a proxy for the NGP concentration) as well as in situ groundwater parameters, such as pH and oxidation-reduction potential. Our results demonstrate the applicability of IP imaging for the real-time monitoring of nanoparticle injection, as well as of the accompanying geochemical changes. Part of this research is funded by the European Union's Seventh Framework Programme for research, technological development and demonstration under grant agreement no 309517.

Numerical modelling of electrochemical polarization around charged metallic particles

NASA Astrophysics Data System (ADS)

Bücker, Matthias; Undorf, Sabine; Flores Orozco, Adrián; Kemna, Andreas

2017-04-01

We extend an existing analytical model and carry out numerical simulations to study the polarization process around charged metallic particles immersed in an electrolyte solution. Electro-migration and diffusion processes in the electrolyte are described by the Poisson-Nernst-Planck system of partial differential equations. To model the surface charge density, we consider a time- and frequency-invariant electric potential at the particle surface, which leads to the build-up of a static electrical double layer (EDL). Upon excitation by an external electric field at low frequencies, we observe the superposition of two polarization processes. On the one hand, the induced dipole moment on the metallic particle leads to the accumulation of opposite charges in the electrolyte. This charge polarization corresponds to the long-known response of uncharged metallic particles. On the other hand, the unequal cation and anion concentrations in the EDL give rise to a salinity gradient between the two opposite sides of the metallic particle. The resulting concentration polarization enhances the magnitude of the overall polarization response. Furthermore, we use our numerical model to study the effect of relevant model parameters such as surface charge density and ionic strength of the electrolyte on the resulting spectra of the effective conductivity of the composite model system. Our results do not only give interesting new insight into the time-harmonic variation of electric potential and ion concentrations around charged metallic particle. They are also able to reduce incongruities between earlier model predictions and geophysical field and laboratory measurements. Our model thereby improves the general understanding of IP signatures of metallic particles and represents the next step towards a quantitative interpretation of IP imaging results. Part of this research is funded by the Austrian Federal Ministry of Science, Research and Economy under the Raw Materials Initiative.

The Expanding Marketplace for Applied Geophysics

NASA Astrophysics Data System (ADS)

Carlson, N.; Sirles, P.

2012-12-01

While the image of geophysics for the proverbial "layman" often seems limited to volcanoes and earthquakes, and to the geoscientist this image enlarges to include oil or minerals exploration and whole earth studies, there has been a steady increase in the application of geophysics into the realm of "daily life", such as real estate deals, highway infrastructure, and flood protection. This expansion of applications can be attributed to the improved economics from advances in equipment and interpretation. Traditional geophysical methods that at one time often only fit within the budgets of oil, gas, and minerals exploration programs can now be economically applied to much smaller scale needs like contaminant mapping, landfill delineation, and levee investigations. A real-world, economic example of this expanding marketplace is our company, which began very small and was aimed almost exclusively at the minerals exploration market. Most of our growth has been in the last 10 years, when we have expanded to five offices and a staff with almost 40 geoscientist degrees (21 in geophysics); much of this growth has been in the non-oil, non-minerals arenas. While much of our work still includes minerals exploration, other projects this year include wind-farm foundation studies, cavity detection above underground nuclear tests, landfill studies, acid mine drainage problems, and leaks in evaporation ponds. A methodology example of this expanding market is the induced polarization (IP) survey, once primarily used for minerals exploration, particularly large porphyry copper deposits, but now efficient enough to also use in environmental studies. The IP method has been particularly useful in delineating and characterizing old, poorly documented landfills, and recent research suggests it may also be useful in monitoring the accelerated biodegradation processes used in some cases to rehabilitate the sites. Compared to temperature monitoring systems, IP may be more useful in providing a better image of the subsurface to locate areas that are not being properly decomposed due to poor fluid flow or inefficient air circulation.Raw IP data in traditional pseudosection format, prior to modeling, showing the change in IP effects after four years of accelerated biodegradation of an old, buried, municipal solid waste landfill. Posted values are chargeability in milliseconds.

3-D Forward modeling of Induced Polarization Effects of Transient Electromagnetic Method

NASA Astrophysics Data System (ADS)

Wu, Y.; Ji, Y.; Guan, S.; Li, D.; Wang, A.

2017-12-01

In transient electromagnetic (TEM) detection, Induced polarization (IP) effects are so important that they cannot be ignored. The authors simulate the three-dimensional (3-D) induced polarization effects in time-domain directly by applying the finite-difference time-domain method (FDTD) based on Cole-Cole model. Due to the frequency dispersion characteristics of the electrical conductivity, the computations of convolution in the generalized Ohm's law of fractional order system makes the forward modeling particularly complicated. Firstly, we propose a method to approximate the fractional order function of Cole-Cole model using a lower order rational transfer function based on error minimum theory in the frequency domain. In this section, two auxiliary variables are introduced to transform nonlinear least square fitting problem of the fractional order system into a linear programming problem, thus avoiding having to solve a system of equations and nonlinear problems. Secondly, the time-domain expression of Cole-Cole model is obtained by using Inverse Laplace transform. Then, for the calculation of Ohm's law, we propose an e-index auxiliary equation of conductivity to transform the convolution to non-convolution integral; in this section, the trapezoid rule is applied to compute the integral. We then substitute the recursion equation into Maxwell's equations to derive the iterative equations of electromagnetic field using the FDTD method. Finally, we finish the stimulation of 3-D model and evaluate polarization parameters. The results are compared with those obtained from the digital filtering solution of the analytical equation in the homogeneous half space, as well as with the 3-D model results from the auxiliary ordinary differential equation method (ADE). Good agreements are obtained across the three methods. In terms of the 3-D model, the proposed method has higher efficiency and lower memory requirements as execution times and memory usage were reduced by 20% compared with ADE method.

Functional Polarity of Microvascular Brain Endothelial Cells Supported by Neurovascular Unit Computational Model of Large Neutral Amino Acid Homeostasis

PubMed Central

Taslimifar, Mehdi; Buoso, Stefano; Verrey, Francois; Kurtcuoglu, Vartan

2018-01-01

The homeostatic regulation of large neutral amino acid (LNAA) concentration in the brain interstitial fluid (ISF) is essential for proper brain function. LNAA passage into the brain is primarily mediated by the complex and dynamic interactions between various solute carrier (SLC) transporters expressed in the neurovascular unit (NVU), among which SLC7A5/LAT1 is considered to be the major contributor in microvascular brain endothelial cells (MBEC). The LAT1-mediated trans-endothelial transport of LNAAs, however, could not be characterized precisely by available in vitro and in vivo standard methods so far. To circumvent these limitations, we have incorporated published in vivo data of rat brain into a robust computational model of NVU-LNAA homeostasis, allowing us to evaluate hypotheses concerning LAT1-mediated trans-endothelial transport of LNAAs across the blood brain barrier (BBB). We show that accounting for functional polarity of MBECs with either asymmetric LAT1 distribution between membranes and/or intrinsic LAT1 asymmetry with low intraendothelial binding affinity is required to reproduce the experimentally measured brain ISF response to intraperitoneal (IP) L-tyrosine and L-phenylalanine injection. On the basis of these findings, we have also investigated the effect of IP administrated L-tyrosine and L-phenylalanine on the dynamics of LNAAs in MBECs, astrocytes and neurons. Finally, the computational model was shown to explain the trans-stimulation of LNAA uptake across the BBB observed upon ISF perfusion with a competitive LAT1 inhibitor. PMID:29593549

Optical Studies of 15 Hard X-Ray Selected Cataclysmic Binaries

NASA Astrophysics Data System (ADS)

Halpern, Jules P.; Thorstensen, John R.; Cho, Patricia; Collver, Gabriel; Motsoaledi, Mokhine; Breytenbach, Hannes; Buckley, David A. H.; Woudt, Patrick A.

2018-06-01

We conducted time-resolved optical spectroscopy and/or time-series photometry of 15 cataclysmic binaries that were discovered in hard X-ray surveys by the Swift Burst Alert Telescope and the International Gamma-Ray Astrophysics Laboratory, with the goal of measuring their orbital periods and searching for spin periods. Four of the objects in this study are new optical identifications: Swift J0535.2+2830, Swift J2006.4+3645, IGR J21095+4322, and Swift J2116.5+5336. Coherent pulsations are detected from three objects for the first time, Swift J0535.2+2830 (1523 s), 2PBC J1911.4+1412 (747 s), and 1SWXRT J230642.7+550817 (464 s), indicating that they are intermediate polars (IPs). We find two new eclipsing systems in time-series photometry: 2PBC J0658.0‑1746, a polar with a period of 2.38 hr, and Swift J2116.5+5336, a disk system that has an eclipse period of 6.56 hr. Exact or approximate spectroscopic orbital periods are found for six additional targets. Of note is the long 4.637-day orbit for Swift J0623.9‑0939, which is revealed by the radial velocities of the photospheric absorption lines of the secondary star. We also discover a 12.76 hr orbital period for RX J2015.6+3711, which confirms that the previously detected 2.00 hr X-ray period from this star is the spin period of an IP, as inferred by Coti Zelati et al. These results support the conclusion that hard X-ray selection favors magnetic CVs, with IPs outnumbering polars.

Polarization Studies for the eRHIC Electron Storage Ring

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gianfelice-Wendt, Eliana; Tepikian, S.

A hadron/lepton collider with polarized beams has been under consideration by the scientific community since some years, in the U.S. and Europe. Among the various proposals, those by JLAB and BNL with polarized electron and proton beams are currently under closer study in the U.S. Experimenters call for the simultaneous storage of electron bunches with both spin helicity. In the BNL based Ring-Ring design, electrons are stored at top energy in a ring to be accommodated in the existing RHIC tunnel. The transversely polarized electron beam is injected into the storage ring at variable energies, between 5 and 18 GeV.more » Polarization is brought into the longitudinal direction at the IP by a couple of spin rotators. In this paper results of first studies of the attainable beam polarization level and lifetime in the storage ring at 18 GeV are presented.« less

Studying the Polarization Switching in Polycrystalline BiFeO3 Films by 2D Piezoresponse Force Microscopy

NASA Astrophysics Data System (ADS)

Jin, Yaming; Lu, Xiaomei; Zhang, Junting; Kan, Yi; Bo, Huifeng; Huang, Fengzhen; Xu, Tingting; Du, Yingchao; Xiao, Shuyu; Zhu, Jinsong

2015-07-01

For rhombohedral multiferroelectrics, non-180° ferroelectric domain switching may induce ferroelastic and/or (anti-)ferromagnetic effect. So the determination and control of ferroelectric domain switching angles is crucial for nonvolatile information storage and exchange-coupled magnetoelectric devices. We try to study the intrinsic characters of polarization switching in BiFeO3 by introducing a special data processing method to determine the switching angle from 2D PFM (Piezoresponse Force Microscopy) images of randomly oriented samples. The response surface of BiFeO3 is first plotted using the piezoelectric tensor got from first principles calculations. Then from the normalized 2D PFM signals before and after switching, the switching angles of randomly oriented BiFeO3 grains can be determined through numerical calculations. In the polycrystalline BiFeO3 films, up to 34% of all switched area is that with original out-of-plane (OP) polarization parallel to the poling field. 71° polarization switching is more favorable, with the area percentages of 71°, 109° and 180° domain switching being about 42%, 29% and 29%, respectively. Our analysis further reveals that IP stress and charge migration have comparable effect on switching, and they are sensitive to the geometric arrangements. This work helps exploring a route to control polarization switching in BiFeO3, so as to realize desirable magnetoelectric coupling.

VoIP Accessibility: A Usability Study of Voice over Internet Protocol (VoIP) Systems and A Survey of VoIP Users with Vision Loss

ERIC Educational Resources Information Center

Packer, Jaclyn; Reuschel, William

2018-01-01

Introduction: Accessibility of Voice over Internet Protocol (VoIP) systems was tested with a hands-on usability study and an online survey of VoIP users who are visually impaired. The survey examined the importance of common VoIP features, and both methods assessed difficulty in using those features. Methods: The usability test included four paid…

Forward Tracking with the JLab/MEIC Detector Concept

NASA Astrophysics Data System (ADS)

Hyde, Charles; JLab/MEIC Design Team

2015-10-01

At a future electron ion collider (EIC), the quark-gluon structure of the NN force can be probed in e . g . deeply virtual exclusive scattering on a tensor polarized Deuteron and diffractive DIS on the deuteron with tagging of the NN final state. The MEIC design includes two Interaction Points (IPs), each of which can operate simultaneously at full luminosity. The detector and beam-line optics for IP1 are designed to be nearly hermetic for all particles outside the presumed 10-sigma admittance (longitudinal and transverse) of the figure-8 accelerator lattice. The integration of the IP1 detector with the lattice extends 40 m downstream of the IP in both the electron and ion directions. The central region of the detector is a new 4 m long 3 m diameter 3 Tesla solenoid. Analysis in the forward ion direction is enhanced by the 50 mrad crossing angle at the IP, and a two-stage spectrometer integrated into the first 36 m of the accelerator lattice. In this talk I will present the optics and resolution of the forward ion spectrometer, including resolution effects of an initial beam pipe design. Supported by U.S. Department of Energy.

Hydrothermal system of the Papandayan Volcano from temperature, self-potential (SP) and geochemical measurements

NASA Astrophysics Data System (ADS)

Byrdina, Svetlana; Revil, André; Gunawan, Hendra; Saing, Ugan B.; Grandis, Hendra

2017-07-01

Papandayan volcano in West Java, Indonesia, is characterized by intense hydrothermal activities manifested by numerous fumaroles at three craters or kawah, i.e. Mas, Manuk and Baru. The latter was created after November 2002 phreatic eruption. Since 2011, numerous volcano-tectonic B events are encountered and the volcano was set on alert status on several occasions. The purpose of the present study is to delineate the structure of the summital hydrothermal system from Self-Potential (SP), soil temperature and gas concentrations in the soil (CO2, SO2 and H2S) data. This combination of geophysical and geochemical methods allows identification of the weak permeable zones serving as preferential pathways for hydrothermal circulation and potential candidates to future landslides or flank collapses. This study is an on-going collaborative research project and we plan to conduct electrical resistivity tomography (ERT) and also Induced-Polarization (IP) surveys. Additional data would allow the 3D imaging of the studied area. The IP parameters will be used to characterise and to quantify the degree of alteration of the volcanic rocks as has been shown very recently in the laboratory studies. There are also rocks and soil samples that will undergo laboratory analyses at ISTerre for IP and complex resistivity parameters at the sample scale that will help to interpret the survey results.

1D Cole-Cole inversion of TEM transients influenced by induced polarization

NASA Astrophysics Data System (ADS)

Seidel, Marc; Tezkan, Bülent

2017-03-01

Effects of induced polarization (IP) can have an impact on time-domain electromagnetic measurements (TEM) and may lead to sign reversals in the recorded transients. To study these IP effects on TEM data, a new 1D inversion algorithm was developed for both, the central-loop and the separate-loop TEM configurations using the Cole-Cole relaxation model. 1D forward calculations for a homogeneous half-space were conducted with the aim of analyzing the impacts of the Cole-Cole parameters on TEM transients with respect to possible sign reversals. The forward modelings showed that the variation of different parameters have comparable effects on the TEM transients. This leads to an increasing number of equivalent models as a result of inversion calculations. Subsequently, 1D inversions of synthetic data were performed to study the potentials and limitations of the algorithm regarding the resolution of the Cole-Cole parameters. In order to achieve optimal inversion results, it was essential to error-weight the data points in the direct vicinity of sign reversals. The obtained findings were eventually adopted on the inversion of real field data which contained considerable IP signatures such as sign reversals. One field data set was recorded at the Nakyn kimberlite field in Western Yakutiya, Russia, in the central-loop configuration. Another field data set originates from a waste site in Cologne, Germany, and was measured utilizing the separate-loop configuration.

The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision.

PubMed

Perreault, Andrea A; Venters, Bryan J

2016-12-23

Chromatin immunoprecipitation (ChIP) is an indispensable tool in the fields of epigenetics and gene regulation that isolates specific protein-DNA interactions. ChIP coupled to high throughput sequencing (ChIP-seq) is commonly used to determine the genomic location of proteins that interact with chromatin. However, ChIP-seq is hampered by relatively low mapping resolution of several hundred base pairs and high background signal. The ChIP-exo method is a refined version of ChIP-seq that substantially improves upon both resolution and noise. The key distinction of the ChIP-exo methodology is the incorporation of lambda exonuclease digestion in the library preparation workflow to effectively footprint the left and right 5' DNA borders of the protein-DNA crosslink site. The ChIP-exo libraries are then subjected to high throughput sequencing. The resulting data can be leveraged to provide unique and ultra-high resolution insights into the functional organization of the genome. Here, we describe the ChIP-exo method that we have optimized and streamlined for mammalian systems and next-generation sequencing-by-synthesis platform.

Inorganic SnIP-Type Double Helices in Main-Group Chemistry.

PubMed

Baumgartner, Maximilian; Weihrich, Richard; Nilges, Tom

2017-05-05

Inspired by the synthesis of the first atomic-scale double-helix semiconductor SnIP, this study deals with the question of whether more atomistic, inorganic double-helix compounds are accessible. With the aid of quantum chemical calculations, we have identified 31 candidates by a homoatomic substitution in MXPn, varying the Group 14 M-element from Si to Pb, the Group 17 X-element from F to I and replacing the pnictide (Pn) phosphorus by arsenic. The double-helical structure of SnIP has been used as the starting model for all candidates and the electronic structure and vibrational spectra were determined within the framework of density functional theory (DFT). Varying the outer MX or the inner Pn helix led to the conclusion that iodide- and bromide-containing MXPn compounds show similar structures to SnIP. Here, the calculations indicate interesting effects for electronic band-gap tuning. For the highly polarized fluorides, a segregation of the helices to more complex MX substructures is predicted. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies

PubMed Central

Euskirchen, Ghia M.; Rozowsky, Joel S.; Wei, Chia-Lin; Lee, Wah Heng; Zhang, Zhengdong D.; Hartman, Stephen; Emanuelsson, Olof; Stolc, Viktor; Weissman, Sherman; Gerstein, Mark B.; Ruan, Yijun; Snyder, Michael

2007-01-01

Recent progress in mapping transcription factor (TF) binding regions can largely be credited to chromatin immunoprecipitation (ChIP) technologies. We compared strategies for mapping TF binding regions in mammalian cells using two different ChIP schemes: ChIP with DNA microarray analysis (ChIP-chip) and ChIP with DNA sequencing (ChIP-PET). We first investigated parameters central to obtaining robust ChIP-chip data sets by analyzing STAT1 targets in the ENCODE regions of the human genome, and then compared ChIP-chip to ChIP-PET. We devised methods for scoring and comparing results among various tiling arrays and examined parameters such as DNA microarray format, oligonucleotide length, hybridization conditions, and the use of competitor Cot-1 DNA. The best performance was achieved with high-density oligonucleotide arrays, oligonucleotides ≥50 bases (b), the presence of competitor Cot-1 DNA and hybridizations conducted in microfluidics stations. When target identification was evaluated as a function of array number, 80%–86% of targets were identified with three or more arrays. Comparison of ChIP-chip with ChIP-PET revealed strong agreement for the highest ranked targets with less overlap for the low ranked targets. With advantages and disadvantages unique to each approach, we found that ChIP-chip and ChIP-PET are frequently complementary in their relative abilities to detect STAT1 targets for the lower ranked targets; each method detected validated targets that were missed by the other method. The most comprehensive list of STAT1 binding regions is obtained by merging results from ChIP-chip and ChIP-sequencing. Overall, this study provides information for robust identification, scoring, and validation of TF targets using ChIP-based technologies. PMID:17568005

An open-water electrical geophysical tool for mapping sub-seafloor heavy placer minerals in 3D and migrating hydrocarbon plumes in 4D

USGS Publications Warehouse

Wynn, Jefferey C.; Urquhart, Scott; Williamson, Mike; Fleming, John B.

2011-01-01

A towed-streamer technology has been developed for mapping placer heavy minerals and dispersed hydrocarbon plumes in the open ocean. The approach uses induced polarization (IP), an electrical measurement that encompasses several different surface-reactive capacitive and electrochemical phenomena, and thus is ideally suited for mapping dispersed or disseminated targets. The application is operated at sea by towing active electrical geophysical streamers behind a ship; a wide area can be covered in three dimensions by folding tow-paths over each other in lawn-mower fashion. This technology has already been proven in laboratory and ocean settings to detect IP-reactive titanium- and rare-earth (REE) minerals such as ilmenite and monazite. By extension, minerals that weather and accumulate/concentrate by a similar mechanism, including gold, platinum, and diamonds, may be rapidly detected and mapped indirectly- even when dispersed and covered with thick, inert sediment. IP is also highly reactive to metal structures such as pipelines and cables. Currently, the only means for mapping an oil-spill plume is to park a large ship in the ocean and drop a sampling string over the side, requiring hours of time per sampling point. The samples must then be chemically analyzed, adding additional time and expense. We believe that an extension of the marine IP technology could also apply to rapidly mapping both seafloor- blanket and disseminated hydrocarbon plumes in the open ocean, as hydrocarbon droplets in conductive seawater are topologically equivalent to a metal-plates-and-dielectric capacitor. Because the effective capacitance would be frequency-dependent on droplet size, the approach we advocate holds the potential to not only map, but also to characterize the evolution and degradation of such a plume over time. In areas where offshore oil field development has been practiced for extended periods, making IP measurements from a towed streamer may be useful for locating buried - nd exposed pipelines, as well as pipeline leaks. We believe this technique will be a more cost-effective method than drop-sampling to map and monitor hydrocarbon plumes in open ocean settings. A marine induced polarization system was used successfully to map a 15 km × 45 km swath of the ocean floor off eastern South Africa with 3-meter sampling along 200-meter-separated profiles. The survey detected titanium-bearing sands up to 15 meters below the seafloor. From preliminary laboratory work it is apparent that we can extend this technology to monitor significant environmental problems including anthropogenic and industrial waste washed into sensitive estuaries and sounds during storm-water runoff episodes, and also to map and characterize dispersed oil plumes in the seawater column in three dimensions, as well as movement and dispersal of both over time.

ChIP-PIT: Enhancing the Analysis of ChIP-Seq Data Using Convex-Relaxed Pair-Wise Interaction Tensor Decomposition.

PubMed

Zhu, Lin; Guo, Wei-Li; Deng, Su-Ping; Huang, De-Shuang

2016-01-01

In recent years, thanks to the efforts of individual scientists and research consortiums, a huge amount of chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) experimental data have been accumulated. Instead of investigating them independently, several recent studies have convincingly demonstrated that a wealth of scientific insights can be gained by integrative analysis of these ChIP-seq data. However, when used for the purpose of integrative analysis, a serious drawback of current ChIP-seq technique is that it is still expensive and time-consuming to generate ChIP-seq datasets of high standard. Most researchers are therefore unable to obtain complete ChIP-seq data for several TFs in a wide variety of cell lines, which considerably limits the understanding of transcriptional regulation pattern. In this paper, we propose a novel method called ChIP-PIT to overcome the aforementioned limitation. In ChIP-PIT, ChIP-seq data corresponding to a diverse collection of cell types, TFs and genes are fused together using the three-mode pair-wise interaction tensor (PIT) model, and the prediction of unperformed ChIP-seq experimental results is formulated as a tensor completion problem. Computationally, we propose efficient first-order method based on extensions of coordinate descent method to learn the optimal solution of ChIP-PIT, which makes it particularly suitable for the analysis of massive scale ChIP-seq data. Experimental evaluation the ENCODE data illustrate the usefulness of the proposed model.

Correlation between oestrogen receptor protein expression in infiltrating ductal carcinoma of the breast by immunohistochemistry and cytosol measurements.

PubMed

Looi, L M; Yap, S F; Cheah, P L

1997-11-01

Fresh frozen neoplastic tissues from 70 infiltrating ductal breast carcinomas were analysed for cytosolic oestrogen receptor (ER) protein content using a solid phase enzyme immunoassay (EIA) method based on a "sandwich" principle (Abbott ER-EIA monoclonal). Formalin-fixed, paraffin-embedded sections from the same carcinomas were examined for nuclear immunoreactivity against a monoclonal antibody for ER protein (Dako) using the standard avidin-biotin complex immunoperoxidase (IP) method after microwave antigen retrieval. The degree of ER positivity by IP was also scored according to a visual estimation of the percentage of cells expressing immunopositivity and the intensity of staining. Twenty-eight (40%) of the carcinomas were ER-positive by EIA and 34 (48.6%) were positive by IP. Twenty-five (35.7%) were ER-positive and 33 (47.1%) were ER-negative by both methods. Nine (12.9%) were ER-negative by EIA but were positive by IP, this discrepancy being ascribed to sampling inadequacy for EIA. However, 3 (4.3%) tumours were ER-positive by EIA and negative by IP. This discrepancy may be variously due to inadequate antigen retrieval, faulty technique and the possibility that the two methods do not measure identical ER proteins. IP appears to have an advantage over EIA in that it has a higher pick-up rate, does not require fresh tissue and can be applied to archival material. However, to reduce false negative estimations, it may be necessary to run IP staining using more than one ER antibody. Standardisation of the IP method for ER is desirable before this method is to be widely adopted in Malaysian laboratories. Quantitation of ER positivity by IP scoring correlated poorly with actual cytosolic levels. Caution should be exercised in attaching patient management value to visual IP scoring.

Measuring Sister Chromatid Cohesion Protein Genome Occupancy in Drosophila melanogaster by ChIP-seq.

PubMed

Dorsett, Dale; Misulovin, Ziva

2017-01-01

This chapter presents methods to conduct and analyze genome-wide chromatin immunoprecipitation of the cohesin complex and the Nipped-B cohesin loading factor in Drosophila cells using high-throughput DNA sequencing (ChIP-seq). Procedures for isolation of chromatin, immunoprecipitation, and construction of sequencing libraries for the Ion Torrent Proton high throughput sequencer are detailed, and computational methods to calculate occupancy as input-normalized fold-enrichment are described. The results obtained by ChIP-seq are compared to those obtained by ChIP-chip (genomic ChIP using tiling microarrays), and the effects of sequencing depth on the accuracy are analyzed. ChIP-seq provides similar sensitivity and reproducibility as ChIP-chip, and identifies the same broad regions of occupancy. The locations of enrichment peaks, however, can differ between ChIP-chip and ChIP-seq, and low sequencing depth can splinter broad regions of occupancy into distinct peaks.

Efficient biotechnological approach for lentiviral transduction of induced pluripotent stem cells.

PubMed

Zare, Mehrak; Soleimani, Masoud; Mohammadian, Mozhdeh; Akbarzadeh, Abolfazl; Havasi, Parvaneh; Zarghami, Nosratollah

2016-01-01

Induced pluripotent stem (iPS) cells are generated from differentiated adult somatic cells by reprogramming them. Unlimited self-renewal, and the potential to differentiate into any cell type, make iPS cells very promising candidates for basic and clinical research. Furthermore, iPS cells can be genetically manipulated for use as therapeutic tools. DNA can be introduced into iPS cells, using lentiviral vectors, which represent a helpful choice for efficient transduction and stable integration of transgenes. In this study, we compare two methods of lentiviral transduction of iPS cells, namely, the suspension method and the hanging drop method. In contrast to the conventional suspension method, in the hanging drop method, embryoid body (EB) formation and transduction occur concurrently. The iPS cells were cultured to form EBs, and then transduced with lentiviruses, using the conventional suspension method and the hanging drop method, to express miR-128 and green fluorescent protein (GFP). The number of transduced cells were assessed by fluorescent microscopy and flow cytometry. MTT assay and real-time PCR were performed to determine the cell viability and transgene expression, respectively. Morphologically, GFP+ cells were more detectable in the hanging drop method, and this finding was quantified by flow cytometric analysis. According to the results of the MTT assay, cell viability was considerably higher in the hanging drop method, and real-time PCR represented a higher relative expression of miR-128 in the iPS cells introduced with lentiviruses in drops. Altogether, it seems that lentiviral transduction of challenging iPS cells using the hanging drop method offers a suitable and sufficient strategy in their gene transfer, with less toxicity than the conventional suspension method.

A new ionospheric storm scale based on TEC and foF2 statistics

NASA Astrophysics Data System (ADS)

Nishioka, Michi; Tsugawa, Takuya; Jin, Hidekatsu; Ishii, Mamoru

2017-01-01

In this paper, we propose the I-scale, a new ionospheric storm scale for general users in various regions in the world. With the I-scale, ionospheric storms can be classified at any season, local time, and location. Since the ionospheric condition largely depends on many factors such as solar irradiance, energy input from the magnetosphere, and lower atmospheric activity, it had been difficult to scale ionospheric storms, which are mainly caused by solar and geomagnetic activities. In this study, statistical analysis was carried out for total electron content (TEC) and F2 layer critical frequency (foF2) in Japan for 18 years from 1997 to 2014. Seasonal, local time, and latitudinal dependences of TEC and foF2 variabilities are excluded by normalizing each percentage variation using their statistical standard deviations. The I-scale is defined by setting thresholds to the normalized numbers to seven categories: I0, IP1, IP2, IP3, IN1, IN2, and IN3. I0 represents a quiet state, and IP1 (IN1), IP2 (IN2), and IP3 (IN3) represent moderate, strong, and severe positive (negative) storms, respectively. The proposed I-scale can be used for other locations, such as polar and equatorial regions. It is considered that the proposed I-scale can be a standardized scale to help the users to assess the impact of space weather on their systems.

Tailored liquid chromatography-mass spectrometry analysis improves the coverage of the intracellular metabolome of HepaRG cells.

PubMed

Cuykx, Matthias; Negreira, Noelia; Beirnaert, Charlie; Van den Eede, Nele; Rodrigues, Robim; Vanhaecke, Tamara; Laukens, Kris; Covaci, Adrian

2017-03-03

Metabolomics protocols are often combined with Liquid Chromatography-Mass Spectrometry (LC-MS) using mostly reversed phase chromatography coupled to accurate mass spectrometry, e.g. quadrupole time-of-flight (QTOF) mass spectrometers to measure as many metabolites as possible. In this study, we optimised the LC-MS separation of cell extracts after fractionation in polar and non-polar fractions. Both phases were analysed separately in a tailored approach in four different runs (two for the non-polar and two for the polar-fraction), each of them specifically adapted to improve the separation of the metabolites present in the extract. This approach improves the coverage of a broad range of the metabolome of the HepaRG cells and the separation of intra-class metabolites. The non-polar fraction was analysed using a C18-column with end-capping, mobile phase compositions were specifically adapted for each ionisation mode using different co-solvents and buffers. The polar extracts were analysed with a mixed mode Hydrophilic Interaction Liquid Chromatography (HILIC) system. Acidic metabolites from glycolysis and the Krebs cycle, together with phosphorylated compounds, were best detected with a method using ion pairing (IP) with tributylamine and separation on a phenyl-hexyl column. Accurate mass detection was performed with the QTOF in MS-mode only using an extended dynamic range to improve the quality of the dataset. Parameters with the greatest impact on the detection were the balance between mass accuracy and linear range, the fragmentor voltage, the capillary voltage, the nozzle voltage, and the nebuliser pressure. By using a tailored approach for the intracellular HepaRG metabolome, consisting of three different LC techniques, over 2200 metabolites can be measured with a high precision and acceptable linear range. The developed method is suited for qualitative untargeted LC-MS metabolomics studies. Copyright © 2017 Elsevier B.V. All rights reserved.

Dental Shade Guide Variability for Hues B, C, and D Using Cross-Polarized Photography.

PubMed

Sampaio, Camila S; Gurrea, Jon; Gurrea, Marta; Bruguera, August; Atria, Pablo J; Janal, Malvin; Bonfante, Estevam A; Coelho, Paulo G; Hirata, Ronaldo

2018-04-20

This study evaluated the color variability of hues B, C, and D between the VITA Classical shade guide (Vita Zahnfabrik) and four other VITA-coded ceramic shade guides using a digital camera (Canon EOS 60D) and computer software (Adobe Photoshop CC). A cross-polarizing filter was used to standardize external light sources influencing color match. A total of 275 pictures were taken, 5 per shade tab, for 11 shades (B1, B2, B3, B4, C1, C2, C3, C4, D2, D3, and D4), from the following shade guides: VITA Classical (control); IPS e.max Ceram (Ivoclar Vivadent); IPS d.SIGN (Ivoclar Vivadent); Initial ZI (GC); and Creation CC (Creation Willi Geller). Pictures were evaluated using Adobe Photoshop CC for standardization of hue, chroma, and value between shade tabs. The VITA-coded shade guides evaluated here showed an overall unmatched shade in all their tabs when compared to the control, suggesting that shade selection should be made with the corresponding manufacturer guide of the ceramic intended for the final restoration.

Density-functional study on the equilibria in the ThDP activation.

PubMed

Delgado, Eduardo J; Alderete, Joel B; Jaña, Gonzalo A

2011-11-01

The equilibria among the various ionization and tautomeric states involved in the activation of ThDP is addressed using high level density functional theory calculations, X3LYP/6-311++G(d,p)//X3LYP(PB)/6-31++G(d,p). This study provides the first theoretically derived thermodynamic data for the internal equilibria in the activation of ThDP. The role of the medium polarity on the geometry and thermodynamics of the diverse equilibria of ThDP is addressed. The media chosen are cyclohexane and water, as paradigms of apolar and polar media. The results suggest that all ionization and tautomeric states are accessible during the catalytic cycle, even in the absence of substrate, being APH(+) the form required to interconvert the AP and IP tautomers; and the generation of the ylide proceeds via the formation of the IP form. Additionally, the calculated ΔG° values allow to calculate all the equilibrium constants, including the pK(C2) for the thiazolium C2 atom whose ionization is believed to initiate the catalytic cycle.

IP Subsurface Imaging in the Presence of Buried Steel Infrastructure

NASA Astrophysics Data System (ADS)

Smart, N. H.; Everett, M. E.

2017-12-01

The purpose of this research is to explore the use of induced polarization to image closely-spaced steel columns at a controlled test site. Texas A&M University's Riverside Campus (RELLIS) was used as a control test site to examine the difference between actual and remotely-sensed observed depths. Known borehole depths and soil composition made this site ideal. The subsurface metal structures were assessed using a combination of ER (Electrical Resistivity) and IP (Induced Polarization), and later processed using data inversion. Surveying was set up in reference to known locations and depths of steel structures in order to maximize control data quality. In comparing of known and remotely-sensed foundation depths a series of questions is raised regarding how percent error between imaged and actual depths can be lowered. We are able to draw questions from the results of our survey, as we compare them with the known depth and width of the metal beams. As RELLIS offers a control for us to conduct research, ideal survey geometry and inversion parameters can be met to achieve optimal results and resolution

Study of gas-phase O-H bond dissociation enthalpies and ionization potentials of substituted phenols - Applicability of ab initio and DFT/B3LYP methods

NASA Astrophysics Data System (ADS)

Klein, Erik; Lukeš, Vladimír

2006-11-01

In this paper, the study of phenol and 37 compounds representing various ortho-, para-, and meta-substituted phenols is presented. Molecules and their radical structures were studied using ab initio methods with inclusion of correlation energy and DFT in order to calculate the O-H bond dissociation enthalpies (BDEs) and vertical ionization potentials (IPs). Calculated BDEs and IPs were compared with available experimental values to ascertain the suitability of used methods, especially for the description of the substituent induced changes in BDE and IP. MP2, MP3, and MP4 methods do not give reliable results, since they significantly underestimate substituent induced changes in BDE and do not reflect distinct effect of substituents related to para and meta position correctly. DFT/B3LYP method reflects the effect of substituents on BDE satisfactorily, though ΔBDEs are in narrower range than experimental values. BDE of phenol was calculated also using CCSD(T) method in various basis sets. Both, DFT and HF methods describe the effect of substituents on IP identically. However, DFT considerably underestimates individual values. HF method gives IPs in very good agreement with experimental data. Obtained results show that dependences of BDEs and IPs on Hammett constants of the substituents are linear. Linearity of DFT BDE vs. IP dependence is even better than the dependences on Hammett constants and obtained equations allow estimating of O-H BDEs of meta- and para-substituted phenols from calculated IPs.

The TOTEM detector at LHC

NASA Astrophysics Data System (ADS)

Antchev, G.; Aspell, P.; Atanassov, I.; Avati, V.; Berardi, V.; Berretti, M.; Bozzo, M.; Brucken, E.; Buzzo, A.; Cafagna, F.; Calicchio, M.; Catanesi, M. G.; Ciocci, M. A.; Csanád, M.; Csörgő, T.; Deile, M.; Dénes, E.; Dimovasili, E.; Doubek, M.; Eggert, K.; Ferro, F.; Garcia, F.; Giani, S.; Greco, V.; Grzanka, L.; Heino, J.; Hilden, T.; Janda, M.; Kaˇspar, J.; Kopal, J.; Kundrat, V.; Kurvinen, K.; Lami, S.; Latino, G.; Lauhakangas, R.; Lippmaa, E.; Lokajicek, M.; Lo Vetere, M.; Lucas Rodriguez, F.; Macri`, M.; Magazzu`, G.; Minutoli, S.; Niewiadomski, H.; Notarnicola, G.; Novak, T.; Oliveri, E.; Oljemark, F.; Orava, R.; Oriunno, M.; Osterberg, K.; Palazzi, P.; Pedreschi, E.; Petajajarvi, J.; Quinto, M.; Radermacher, E.; Radicioni, E.; Ravotti, F.; Robutti, E.; Ropelewski, L.; Ruggiero, G.; Rummel, A.; Saarikko, H.; Sanguinetti, G.; Santroni, A.; Scribano, A.; Sette, G.; Snoeys, W.; Spearman, W.; Spinella, F.; Ster, A.; Taylor, C.; Trummal, A.; Turini, N.; Vacek, V.; Vitek, M.; Whitmore, J.; Wu, J.

2010-05-01

The TOTEM experiment, small in size compared to the others at the LHC, is dedicated to the measurement of the total proton-proton cross-sections with a luminosity-independent method and to the study of elastic and diffractive scattering at the LHC. To achieve optimum forward coverage for charged particles emitted by the pp collisions in the IP5 interaction point, two tracking telescopes, T1 and T2, will be installed on each side in the pseudo-rapidity region between 3.1 and 6.5, and Roman Pot stations will be placed at distances of 147 and 220 m from IP5. The telescope closest to the interaction point (T1, centred at z=9 m) consists of Cathode Strip Chambers (CSC), while the second one (T2, centred at 13.5 m), makes use of Gas Electron Multipliers (GEM). The proton detectors in the Roman Pots are silicon devices designed by TOTEM with the specific objective of reducing down to a few tens of microns the insensitive area at the edge. High efficiency as close as possible to the physical detector boundary is an essential feature. It maximizes the experimental acceptance for protons scattered elastically or interactively at polar angles down to a few micro-radians at IP5. To measure protons at the lowest possible emission angles, special beam optics have been conceived to optimize proton detection in terms of acceptance and resolution. The read-out of all TOTEM subsystems is based on the custom-developed digital VFAT chip with trigger capability.

A 3-D view of field-scale fault-zone cementation from geologically ground-truthed electrical resistivity

NASA Astrophysics Data System (ADS)

Barnes, H.; Spinelli, G. A.; Mozley, P.

2015-12-01

Fault-zones are an important control on fluid flow, affecting groundwater supply, hydrocarbon/contaminant migration, and waste/carbon storage. However, current models of fault seal are inadequate, primarily focusing on juxtaposition and entrainment effects, despite the recognition that fault-zone cementation is common and can dramatically reduce permeability. We map the 3D cementation patterns of the variably cemented Loma Blanca fault from the land surface to ~40 m depth, using electrical resistivity and induced polarization (IP). The carbonate-cemented fault zone is a region of anomalously low normalized chargeability, relative to the surrounding host material. Zones of low-normalized chargeability immediately under the exposed cement provide the first ground-truth that a cemented fault yields an observable IP anomaly. Low-normalized chargeability extends down from the surface exposure, surrounded by zones of high-normalized chargeability, at an orientation consistent with normal faults in the region; this likely indicates cementation of the fault zone at depth, which could be confirmed by drilling and coring. Our observations are consistent with: 1) the expectation that carbonate cement in a sandstone should lower normalized chargeability by reducing pore-surface area and bridging gaps in the pore space, and 2) laboratory experiments confirming that calcite precipitation within a column of glass beads decreases polarization magnitude. The ability to characterize spatial variations in the degree of fault-zone cementation with resistivity and IP has exciting implications for improving predictive models of the hydrogeologic impacts of cementation within faults.

Gigantic magnetic-field-induced polarization and magnetoelectric coupling in a ferrimagnetic oxide CaBaCo 4 O 7

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caignaert, V.; Maignan, A.; Singh, K.

2013-11-01

Below Tc, the single-crystal study of CaBaCo40,, a noncollinear ferrimagnet (Tc = 64 K) with a polar orthorhombic space group (Pbn21) between 4 and 293 K, shows a large change inthe electric polarization along its c axis reaching !!iP = 17 mC/m2 at 10 K. At 62.5 K, a magnetic-field-driven giant variation inpolarization P(9 T) - P(O T) = 8 mC/m2 is observed. Moreover, the present magnetoelectric measurements are fully consistent withthe m'm2' magnetic point group. This ferrimagnetic oxide, which belongs to the "114" structural family, opens an avenue for the search for new magnetoelectrics.

Using the MDCT thick slab MinIP method for the follow-up of pulmonary emphysema.

PubMed

Lan, Hai; Nishitani, Hiromu; Nishihara, Sadamitsu; Ueno, Junji; Takao, Shoichiro; Iwamoto, Seiji; Kawanaka, Takashi; Mahmut, Mawlan; Qingge, Si

2011-08-01

The purpose of this study was to evaluate the usefulness of thick slab minimum intensity projection (MinIP) as a follow-up method in patients with pulmonary emphysema. This method was used to determine the presence or absence of changes over time in the lung field based on multi-detector-row CT (MDCT) data. Among patients diagnosed with pulmonary emphysema who underwent 16-MDCT (slice thickness, 1 mm) twice at an interval of 6 months or more, 12 patients without changes in the lung field and 14 with clear changes in the lung field were selected as subjects. An image interpretation experiment was performed by five image interpreters. Pulmonary emphysema was followed up using two types of thick slab MinIP (thick slab MinIP 1 and 2) and multi-planar reformation (MPR), and the results of image interpretation were evaluated by receiver operating characteristic (ROC) analysis. In addition, the time required for image interpretation was compared among the three follow-up methods. The area under the ROC curve (Az) was 0.794 for thick slab MinIP 1, 0.778 for the thick slab MinIP 2, and 0.759 for MPR, showing no significant differences among the three methods. Individual differences in each item were significantly more marked for MPR than for thick slab MinIP. The time required for image interpretation was around 18 seconds for thick slab MinIP 1, 11 seconds for thick slab MinIP 2, and approximately 127 seconds for MPR, showing significant differences among the three methods. There were no significant differences in the results of image interpretation regarding the presence or absence of changes in the lung fields between thick slab MinIP and MPR. However, thick slab MinIP showed a shorter image interpretation time and smaller individual differences in the results among image interpreters than MPR, suggesting the usefulness of this method for determining the presence or absence of changes with time in the lung fields of patients with pulmonary emphysema.

ASTRO-2 Spacelab Instrument Pointing System mission performance

NASA Technical Reports Server (NTRS)

Wessling, Francis C., III; Singh, S. P.

1995-01-01

This paper reports the performance of the Instrument Pointing System (IPS) that flew on the National Aeronautics and Space Administration (NASA) ASTRO-2 Spacelab mission aboard the Space Shuttle Endeavour in March 1995. The IPS provides a stabilizing platform for the ASTRO-2 instrument payload complement that consists of three main experiments (telescopes). The telescopes observe stellar targets in the universe within the ultraviolet portion of the electromagnetic spectrum that must be observed from beyond the earth's atmospheric filtering effects. The three main experiments for observation are the Hopkins Ultraviolet Telescope (HUT), the Ultraviolet Imaging Telescope (UIT), and the Wisconsin Ultraviolet Photo-Polarimetry Experiment (WUPPE). The HUT uses spectroscopy to obtain the structure and chemical makeup of ultraviolet targets. UIT is responsible for wide field photographing to capture the hidden view of the ultraviolet universe. The WUPPE gathers data on the polarization of the ultraviolet electromagnetic energy coming from the astronomical targets. The capability of IPS enables the experiments to 'see' faint celestial objects. A brief explanation of the IPS is given followed by a review of engineering efforts to improve IPS performance over the ASTRO-1 mission. The main focus of improvements was on enhancing the star acquisition capability through improved guide star selection, lab simulations, computer upgrades, data display systems improvements, and software modifications. A star simulator was developed in the lab to enable IPS to be simulated on the ground pre-mission with flight hardware and software in the loop. The paper concludes with results from the ASTRO-2 mission. The number of targets acquired and the IPS pointing accuracy/stability is reported along with recommendations for the future use of the Instrument Pointing System.

Faster in-plane switching and reduced rotational viscosity characteristics in a graphene-nematic suspension

NASA Astrophysics Data System (ADS)

Basu, Rajratan; Kinnamon, Daniel; Skaggs, Nicole; Womack, James

2016-05-01

The in-plane switching (IPS) for a nematic liquid crystal (LC) was found to be considerably faster when the LC was doped with dilute concentrations of monolayer graphene flakes. Additional studies revealed that the presence of graphene reduced the rotational viscosity of the LC, permitting the nematic director to respond quicker in IPS mode on turning the electric field on. The studies were carried out with several graphene concentrations in the LC, and the experimental results coherently suggest that there exists an optimal concentration of graphene, allowing a reduction in the IPS response time and rotational viscosity in the LC. Above this optimal graphene concentration, the rotational viscosity was found to increase, and consequently, the LC no longer switched faster in IPS mode. The presence of graphene suspension was also found to decrease the LC's pretilt angle significantly due to the π-π electron stacking between the LC molecules and graphene flakes. To understand the π-π stacking interaction, the anchoring mechanism of the LC on a CVD grown monolayer graphene film on copper substrate was studied by reflected crossed polarized microscopy. Optical microphotographs revealed that the LC alignment direction depended on monolayer graphene's hexagonal crystal structure and its orientation.

Scrape-off-layer currents during MHD activity and disruptions in HBT-EP

NASA Astrophysics Data System (ADS)

Levesque, J. P.; Desanto, S.; Battey, A.; Bialek, J.; Brooks, J. W.; Mauel, M. E.; Navratil, G. A.

2017-10-01

We report scrape-off layer (SOL) current measurements during MHD mode activity and disruptions in the HBT-EP tokamak. Currents are measured via Rogowski coils mounted on tiles in the low-field-side SOL, toroidal jumpers between otherwise-isolated vessel sections, and segmented plasma current Rogowski coils. These currents strongly depend on the plasma's major radius, mode amplitude, and mode phase. Plasma current asymmetries and SOL currents during disruptions reach 4% of the plasma current. Asymmetric toroidal currents between vessel sections rotate at tens of kHz through most of the current quench, then symmetrize once Ip reaches 30% of its pre-disruptive value. Toroidal jumper currents oscillate between co- and counter-Ip, with co-Ip being dominant on average during disruptions. Increases in local plasma current correlate with counter-Ip current in the nearest toroidal jumper. Measurements are interpreted in the context of two models that produce contrary predictions for the toroidal vessel current polarity during disruptions. Plasma current asymmetries are consistent with both models, and scale with plasma displacement toward the wall. Progress of ongoing SOL current diagnostic upgrades is also presented. Supported by U.S. DOE Grant DE-FG02-86ER53222.

Plasma current ramp-up by lower hybrid wave using innovative antennas on TST-2

NASA Astrophysics Data System (ADS)

Takase, Yuichi; Ejiri, Akira; Moeller, Charles; Roidl, Benedikt; Shinya, Takahiro; Tsujii, Naoto; Yajima, Satoru; Yamazaki, Hibiki; Kitayama, Akichika; Matsumoto, Naoki; Sato, Akito; Sonehara, Masateru; Takahashi, Wataru; Tajiri, Yoshiyuki; Takei, Yuki; Togashi, Hiro; Toida, Kazuya; Yoshida, Yusuke

2016-10-01

Non-inductive plasma current (Ip) ramp-up by RF power in the lower hybrid frequency range is being studied on the TST-2 spherical tokamak (R = 0.36 m, a = 0.23 m, Bt = 0.3 T, Ip = 0.1 MA). Up to 400 kW of RF power is available at a frequency of 200 MHz. An innovative antenna called the capacitively-coupled combline (CCC) antenna was developed to excite a sharp, highly directional traveling wave with the electric field polarized in the toroidal direction. It is an array of resonant circuit elements made of capacitance and inductance, coupled to neighboring elements by mutual capacitance. Two CCC antennas are installed in TST-2, a 13-element outboard-launch antenna and a 6-element top-launch antenna. The latter was installed in March 2016 to improve accessibility to the core and to achieve single-pass damping. The suspected wave power loss in the scrape-off layer plasma should also be avoided. Ip ramp-up to 25 kA has been achieved so far. An upgrade of the Bt power supply is planned to take advantage of the observed improvement of Ip ramp-up with Bt. Higher Bt for longer pulses should improve the Ip ramp-up efficiency by improving wave accessibility and by reducing prompt orbit losses of energetic electrons.

cChIP-seq: a robust small-scale method for investigation of histone modifications.

PubMed

Valensisi, Cristina; Liao, Jo Ling; Andrus, Colin; Battle, Stephanie L; Hawkins, R David

2015-12-21

ChIP-seq is highly utilized for mapping histone modifications that are informative about gene regulation and genome annotations. For example, applying ChIP-seq to histone modifications such as H3K4me1 has facilitated generating epigenomic maps of putative enhancers. This powerful technology, however, is limited in its application by the large number of cells required. ChIP-seq involves extensive manipulation of sample material and multiple reactions with limited quality control at each step, therefore, scaling down the number of cells required has proven challenging. Recently, several methods have been proposed to overcome this limit but most of these methods require extensive optimization to tailor the protocol to the specific antibody used or number of cells being profiled. Here we describe a robust, yet facile method, which we named carrier ChIP-seq (cChIP-seq), for use on limited cell amounts. cChIP-seq employs a DNA-free histone carrier in order to maintain the working ChIP reaction scale, removing the need to tailor reactions to specific amounts of cells or histone modifications to be assayed. We have applied our method to three different histone modifications, H3K4me3, H3K4me1 and H3K27me3 in the K562 cell line, and H3K4me1 in H1 hESCs. We successfully obtained epigenomic maps for these histone modifications starting with as few as 10,000 cells. We compared cChIP-seq data to data generated as part of the ENCODE project. ENCODE data are the reference standard in the field and have been generated starting from tens of million of cells. Our results show that cChIP-seq successfully recapitulates bulk data. Furthermore, we showed that the differences observed between small-scale ChIP-seq data and ENCODE data are largely to be due to lab-to-lab variability rather than operating on a reduced scale. Data generated using cChIP-seq are equivalent to reference epigenomic maps from three orders of magnitude more cells. Our method offers a robust and straightforward approach to scale down ChIP-seq to as low as 10,000 cells. The underlying principle of our strategy makes it suitable for being applied to a vast range of chromatin modifications without requiring expensive optimization. Furthermore, our strategy of a DNA-free carrier can be adapted to most ChIP-seq protocols.

Direct Detection of the Ion Pair to Free Ions Transformation upon Complexation with an Ion Receptor in Non-Polar Solvents by using Conductometry.

PubMed

Iseda, Kazuya; Kokado, Kenta; Sada, Kazuki

2018-03-01

In this study, we performed conductometry in various organic solvents to directly detect the transformation from tetrabutylammonium chloride ( TBACl ) ion-pair salt to the free ions through complexation with meso -octamethylcalix[4]pyrrole ( CP ), which is a well-known receptor for chloride anions. In the presence of CP , the conductivity of TBACl increases in various non-polar solvents, indicating that complexation with CP enhances the ionic dissociation of TBACl in such non-polar solvents. In other words, CP recognizes chloride as an ion-paired salt as well as a free anion in non-polar solvents. Additionally, the TBA(CP - Cl ) complex exhibited a considerably lower ion-pairing constant ( K ip ) than TBACl in non-polar solvents, resulting in enhanced conductivity. Based on these findings, we can conclude that complexation of an anion with a hydrophobic anion receptor will be useful for creating functional and stimuli-responsive soft materials in organic solvents using coulombic forces.

Direct Detection of the Ion Pair to Free Ions Transformation upon Complexation with an Ion Receptor in Non‐Polar Solvents by using Conductometry

PubMed Central

Iseda, Kazuya

2018-01-01

Abstract In this study, we performed conductometry in various organic solvents to directly detect the transformation from tetrabutylammonium chloride (TBACl) ion‐pair salt to the free ions through complexation with meso‐octamethylcalix[4]pyrrole (CP), which is a well‐known receptor for chloride anions. In the presence of CP, the conductivity of TBACl increases in various non‐polar solvents, indicating that complexation with CP enhances the ionic dissociation of TBACl in such non‐polar solvents. In other words, CP recognizes chloride as an ion‐paired salt as well as a free anion in non‐polar solvents. Additionally, the TBA(CP–Cl) complex exhibited a considerably lower ion‐pairing constant (K ip) than TBACl in non‐polar solvents, resulting in enhanced conductivity. Based on these findings, we can conclude that complexation of an anion with a hydrophobic anion receptor will be useful for creating functional and stimuli‐responsive soft materials in organic solvents using coulombic forces. PMID:29610717

An open-water electrical geophysical tool for mapping sub-seafloor heavy placer minerals in 3D and migrating hydrocarbon plumes in 4D

USGS Publications Warehouse

Wynn, J.; Williamson, M.; Urquhart, S.; Fleming, J.

2011-01-01

A towed-streamer technology has been developed for mapping placer heavy minerals and dispersed hydrocarbon plumes in the open ocean. The approach uses induced polarization (IP), an electrical measurement that encompasses several different surface-reactive capacitive and electrochemical phenomena, and thus is ideally suited for mapping dispersed or disseminated targets. The application is operated at sea by towing active electrical geophysical streamers behind a ship; a wide area can be covered in three dimensions by folding tow-paths over each other in lawn-mower fashion. This technology has already been proven in laboratory and ocean settings to detect IP-reactive titanium-and rare-earth (REE) minerals such as ilmenite and monazite. By extension, minerals that weather and accumulate/concentrate by a similar mechanism, including gold, platinum, and diamonds, may be rapidly detected and mapped indirectly even when dispersed and covered with thick, inert sediment. IP is also highly reactive to metal structures such as pipelines and cables. ?? 2011 MTS.

Packet flow monitoring tool and method

DOEpatents

Thiede, David R [Richland, WA

2009-07-14

A system and method for converting packet streams into session summaries. Session summaries are a group of packets each having a common source and destination internet protocol (IP) address, and, if present in the packets, common ports. The system first captures packets from a transport layer of a network of computer systems, then decodes the packets captured to determine the destination IP address and the source IP address. The system then identifies packets having common destination IP addresses and source IP addresses, then writes the decoded packets to an allocated memory structure as session summaries in a queue.

Relativistic electron kinetic effects on laser diagnostics in burning plasmas

NASA Astrophysics Data System (ADS)

Mirnov, V. V.; Den Hartog, D. J.

2018-02-01

Toroidal interferometry/polarimetry (TIP), poloidal polarimetry (PoPola), and Thomson scattering systems (TS) are major optical diagnostics being designed and developed for ITER. Each of them relies upon a sophisticated quantitative understanding of the electron response to laser light propagating through a burning plasma. Review of the theoretical results for two different applications is presented: interferometry/polarimetry (I/P) and polarization of Thomson scattered light, unified by the importance of relativistic (quadratic in vTe/c) electron kinetic effects. For I/P applications, rigorous analytical results are obtained perturbatively by expansion in powers of the small parameter τ = Te/me c2, where Te is electron temperature and me is electron rest mass. Experimental validation of the analytical models has been made by analyzing data of more than 1200 pulses collected from high-Te JET discharges. Based on this validation the relativistic analytical expressions are included in the error analysis and design projects of the ITER TIP and PoPola systems. The polarization properties of incoherent Thomson scattered light are being examined as a method of Te measurement relevant to ITER operational regimes. The theory is based on Stokes vector transformation and Mueller matrices formalism. The general approach is subdivided into frequency-integrated and frequency-resolved cases. For each of them, the exact analytical relativistic solutions are presented in the form of Mueller matrix elements averaged over the relativistic Maxwellian distribution function. New results related to the detailed verification of the frequency-resolved solutions are reported. The precise analytic expressions provide output much more rapidly than relativistic kinetic numerical codes allowing for direct real-time feedback control of ITER device operation.

Using a multi-method approach based on soil radon deficit, resistivity, and induced polarization measurements to monitor non-aqueous phase liquid contamination in two study areas in Italy and India.

PubMed

Castelluccio, Mauro; Agrahari, Sudha; De Simone, Gabriele; Pompilj, Francesca; Lucchetti, Carlo; Sengupta, Debashish; Galli, Gianfranco; Friello, Pierluigi; Curatolo, Pierpaolo; Giorgi, Riccardo; Tuccimei, Paola

2018-05-01

Geochemical and geophysical surveys employing radon deficit, resistivity, and induced polarization (IP) measurements were undertaken on soil contaminated with non-aqueous phase liquids (NAPLs) in two different sites in India and in Italy. Radon deficit, validated through the comparison with average soil radon in reference unpolluted areas, shows the extension of contamination in the upper part of the unsaturated aquifers. In site 1 (Italy), the spill is not recent. A residual film of kerosene covers soil grains, inhibiting their chargeability and reducing electrical resistivity difference with background unpolluted areas. No correlation between the two parameters is observed. Soil volatile organic compounds (VOCs) concentration is not linked with radon deficit, supporting the old age of the spillage. NAPL pollution in sites 2a and 2b (India) is more recent and probably still active, as demonstrated by higher values of electrical resistivity. A good correlation with IP values suggests that NAPL is still distributed as droplets or as a continuous phase in the pores, strengthening the scenario of a fresh spill or leakage. Residual fraction of gasoline in the pore space of sites 2a and 2b is respectively 1.5 and 11.8 kg per cubic meter of terrain. This estimation is referred to the shallower portion of the unsaturated aquifer. Electrical resistivity is still very high indicating that the gasoline has not been strongly degraded yet. Temperature and soil water content influence differently radon deficit in the three areas, reducing soil radon concentration and partly masking the deficit in sites 2a and 2b.

Efficient genomic correction methods in human iPS cells using CRISPR-Cas9 system.

PubMed

Li, Hongmei Lisa; Gee, Peter; Ishida, Kentaro; Hotta, Akitsu

2016-05-15

Precise gene correction using the CRISPR-Cas9 system in human iPS cells holds great promise for various applications, such as the study of gene functions, disease modeling, and gene therapy. In this review article, we summarize methods for effective editing of genomic sequences of iPS cells based on our experiences correcting dystrophin gene mutations with the CRISPR-Cas9 system. Designing specific sgRNAs as well as having efficient transfection methods and proper detection assays to assess genomic cleavage activities are critical for successful genome editing in iPS cells. In addition, because iPS cells are fragile by nature when dissociated into single cells, a step-by-step confirmation during the cell recovery process is recommended to obtain an adequate number of genome-edited iPS cell clones. We hope that the techniques described here will be useful for researchers from diverse backgrounds who would like to perform genome editing in iPS cells. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Synchrotron Radiation X-Ray Microfluorescence Reveals Polarized Distribution of Atomic Elements during Differentiation of Pluripotent Stem Cells

PubMed Central

Paulsen, Bruna S.; Rehen, Stevens K.

2011-01-01

The mechanisms underlying pluripotency and differentiation in embryonic and reprogrammed stem cells are unclear. In this work, we characterized the pluripotent state towards neural differentiated state through analysis of trace elements distribution using the Synchrotron Radiation X-ray Fluorescence Spectroscopy. Naive and neural-stimulated embryoid bodies (EB) derived from embryonic and induced pluripotent stem (ES and iPS) cells were irradiated with a spatial resolution of 20 µm to make elemental maps and qualitative chemical analyses. Results show that these embryo-like aggregates exhibit self-organization at the atomic level. Metallic elements content rises and consistent elemental polarization pattern of P and S in both mouse and human pluripotent stem cells were observed, indicating that neural differentiation and elemental polarization are strongly correlated. PMID:22195032

Identification of polar, ionic, and highly water soluble organic pollutants in untreated industrial wastewaters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castillo, M.; Alonso, M.C.; Riu, J.

1999-04-15

This paper presents a generic protocol for the determination of polar, ionic, and highly water soluble organic pollutants on untreated industrial wastewaters involving the use of two different solid-phase extraction (SPE) methodologies followed by liquid chromatography-mass spectrometry (LC-MS). Untreated industrial wastewaters might contain natural and synthetic dissolved organic compounds with total organic carbon (TOC) values varying between 100 and 3000 mg/L. All polar, ionic and highly water soluble compounds comprising more than 95% of the organic content and with major contribution to the total toxicity of the sample cannot be analyzed by conventional gas chromatography-mass spectrometry (GC-MS), and LC-MS ismore » a good alternative. In this work two extraction procedures were used to obtain fractionated extracts of the nonionic polar compounds: a polymeric Isolute ENV + SPE cartridge for the preconcentration of anionic analytes and a sequential solid-phase extraction (SSPE) method percolating the samples first in octadecylsilica cartridge in series with the polymeric Lichrolut EN cartridge. Average recoveries ranging from 72% to 103% were obtained for a variety of 23 different analytes. Determination of nonionic pollutants was accomplished by reverse-phase liquid chromatography-atmospheric pressure chemical ionization-mass spectrometry (LC-APCI-MS), while anionic compounds were analyzed by ion pair chromatography-electrospray-mass spectrometry (IP-ESI-MS) and LC-ESI-MS. This protocol was applied to a pilot survey of textile and tannery wastewaters leading to the identification and quantification of 33 organic pollutants.« less

Monitoring the bio-stimulation of hydrocarbon-contaminated soils by measurements of soil electrical properties, and CO2 content and its 13C/12C isotopic signature

NASA Astrophysics Data System (ADS)

Noel, C.; Gourry, J.; Ignatiadis, I.; Colombano, S.; Dictor, M.; Guimbaud, C.; Chartier, M.; Dumestre, A.; Dehez, S.; Naudet, V.

2013-12-01

Hydrocarbon contaminated soils represent an environmental issue as it impacts on ecosystems and aquifers. Where significant subsurface heterogeneity exists, conventional intrusive investigations and groundwater sampling can be insufficient to obtain a robust monitoring of hydrocarbon contaminants, as the information they provide is restricted to vertical profiles at discrete locations, with no information between sampling points. In order to obtain wider information in space volume on subsurface modifications, complementary methods can be used like geophysics. Among geophysical methods, geoelectrical techniques such as electrical resistivity (ER) and induced polarization (IP) seem the more promising, especially to study the effects of biodegradation processes. Laboratory and field geoelectrical experiments to characterize soils contaminated by oil products have shown that mature hydrocarbon-contaminated soils are characterized by enhanced electrical conductivity although hydrocarbons are electrically resistive. This high bulk conductivity is due to bacterial impacts on geological media, resulting in changes in the chemical and physical properties and thus, to the geophysical properties of the ground. Moreover, microbial activity induced CO2 production and isotopic deviation of carbon. Indeed, produced CO2 will reflect the pollutant isotopic signature. Thus, the ratio δ13C(CO2) will come closer to δ13C(hydrocarbon). BIOPHY, project supported by the French National Research Agency (ANR), proposes to use electrical methods and gas analyses to develop an operational and non-destructive method for monitoring in situ biodegradation of hydrocarbons in order to optimize soil treatment. Demonstration field is located in the South of Paris (France), where liquid fuels (gasoline and diesel) leaked from some tanks in 1997. In order to stimulate biodegradation, a trench has been dug to supply oxygen to the water table and thus stimulate aerobic metabolic bioprocesses. ER and IP surveys are performed regularly to monitor the stimulated biodegradation and progress of remediation until soil cleanup. Microbial activity is characterized by CO2 production increase and δ13C isotopic deviation, in the produced CO2 measured by infrared laser spectroscopy, and by an evolution of electrical conductivity and IP responses in correlation with microbiological and chemical analyses.

Effects of Low-Level Laser Therapy on M1-Related Cytokine Expression in Monocytes via Histone Modification

PubMed Central

Chen, Chia-Hsin; Wang, Chau-Zen; Wang, Yan-Hsiung; Liao, Wei-Ting; Chen, Yi-Jen; Kuo, Hsuan-Fu; Hung, Chih-Hsing

2014-01-01

Low-level laser therapy (LLLT) has been used in the treatment of radiotherapy-induced oral mucositis and allergic rhinitis. However, the effects of LLLT on human monocyte polarization into M1 macrophages are unknown. To evaluate the effects of LLLT on M1-related cytokine and chemokine production and elucidate the mechanism, the human monocyte cell line THP-1 was treated with different doses of LLLT. The expression of M1-related cytokines and chemokines (CCL2, CXCL10, and TNF-α) was determined by ELISA and real-time PCR. LLLT-associated histone modifications were examined by chromatin immunoprecipitation (ChIP) assays. Mitochondrial involvement in the LLLT-induced M1-related cytokine expression was evaluated by quantitative real-time PCR. Flow cytometry was used to detect the cell surface markers for monocyte polarization. The results showed that LLLT (660 nm) significantly enhanced M1-related cytokine and chemokine expression in mRNA and protein levels. Mitochondrial copy number and mRNA levels of complex I-V protein were increased by LLLT (1 J/cm2). Activation of M1 polarization was concomitant with histone modification at TNF-α gene locus and IP-10 gene promoter area. This study indicates that LLLT (660 nm) enhanced M1-related cytokine and chemokine expression via mitochondrial biogenesis and histone modification, which may be a potent immune-enhancing agent for the treatment of allergic diseases. PMID:24692853

Antioxidant behavior of mearnsetin and myricetin flavonoid compounds — A DFT study

NASA Astrophysics Data System (ADS)

Sadasivam, K.; Kumaresan, R.

2011-06-01

The molecular characteristics of two naturally occurring flavonoid compounds mearnsetin and myricetin have been computed using density functional theory (DFT) approach with B3LYP/6-311G(d,p) level of theory. The computation and analysis of bond dissociation enthalpy magnitudes for all the OH sites for both the compounds clearly denotes the contribution of the B-ring for the antioxidant activity. The analysis has also indicated the higher values of BDE on the C5-OH radical species in both the compounds. The computed vibrational frequency analysis indicates the absence of imaginary frequency in the neutral as well as radical species of both the flavonoid compounds. The ionisation potential (IP) analysis was found to be within the range of the IP of synthetic food additives. In addition, various molecular descriptors such as electron affinity, hardness, softness, electronegativity, electrophilic index have also been calculated and the validity of Koopman's theorem is verified. The plot of frontier molecular orbital and spin density distribution analysis for neutral and the corresponding radical species for both the compounds have been computed and interpreted. The polar nature and their polarizing capacity are well established through the analysis of dipole moment and polarisability magnitudes.

Optimized HPLC method for analysis of polar and nonpolar heterocyclic amines in cooked meat products.

PubMed

Gibis, Monika

2009-01-01

A simple, precise, and specific column high-performance liquid chromatographic (HPLC) method with UV absorption diode array and fluorescence detection has been developed by optimizing a previously described method for the simultaneous quantification of 15 polar and nonpolar heterocyclic amines (HAs) in fried meat products. The HPLC determination could be improved due to the application of a silica-based reversed-phase column with octadecyl groups (TSK-gel Super ODS) and a particle size of 2 microm. The separation of HAs in the complex meat matrix was performed with a 21 min mobile phase gradient. The method was validated for instrumental precision, repeatability, and selectivity and compared with a previously published method. After liquid adsorption of the basic sample mixture on diatomaceous earth, HAs were extracted with ethyl acetate. For cleanup, solid-phase extraction (silica propylsulfonic acid and octadecyl cartridges) and different washing steps were applied. Both nonpolar and polar HAs were determined in one fraction. The calibration curves of all HAs were linear for the applied detection system (correlation coefficient = 0.990-0.995). The recoveries, with the exception of 3-amino-1-methyl-5H-pyrido [4,3-b]indole (Trp-P-2), were between 42 and 98% from meat samples spiked in a range of 1.5 to 3.3 ng/g for fluorescence-active and 4.3 to 8 ng/g for UV-active HAs. For quantification of HAs, the standard addition method was used for adjustment of different characteristics of HAs in the extraction. In fried meat samples (chicken breast and beef patties), 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MelQx), 2-amino-3,4,8-trimethylimidazo[4,5-f] quinoxaline(4,8-DiMelQx), 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), norharmane, and harmane were found in a concentration range of 0.02 to 14.3 ng/g.

Isotopic Randomness and Maxwell's Demon

NASA Astrophysics Data System (ADS)

Berezin, Alexander A.

2005-03-01

Isotopic disorder in crystals can lead to suppression of thermal conductivity, mobility variations and (weak) Anderson localization on isotopic fluctuations. The latter (AAB, J.ChemPhys.1984) is akin to polaron effect (self-localization due polarization). Possibility of isotopic patterning (IP) increases near melting point (thermally activated isotopic hopping swaps). Crystal near melting threshold become “informationally sensitive” as if its IP is operated by some external Maxwell’s Demon, MD (AAB, URAM J, 2002). At this state short range (e.g. electrostatic inverse square) forces evolve into long-range interactions (due to divergence of order parameter) and information sensitivity can be further amplified by (say) a single fast electron (e.g. beta-particle from decay of 14-C or other radioactive isotope) which may result in cascade of impact ionization events and (short time-scale) enhancement of screening by impact-generated non-equilibrium (non-thermal) electrons. In this state informationally driven (MD-controlled) IP (Eccles effect) can result in decrease of positional entropy signifying emergence of physical complexity out of pure information, similar to peculiar “jinni effect” on closed time loops in relativistic cosmology (R.J.Gott, 2001) or Wheeler’s “it from bit” metaphor. By selecting special IP, MD modifies ergodicity principle in favor of info rich states.

Faster in-plane switching and reduced rotational viscosity characteristics in a graphene-nematic suspension

DOE Office of Scientific and Technical Information (OSTI.GOV)

Basu, Rajratan, E-mail: basu@usna.edu; Kinnamon, Daniel; Skaggs, Nicole

2016-05-14

The in-plane switching (IPS) for a nematic liquid crystal (LC) was found to be considerably faster when the LC was doped with dilute concentrations of monolayer graphene flakes. Additional studies revealed that the presence of graphene reduced the rotational viscosity of the LC, permitting the nematic director to respond quicker in IPS mode on turning the electric field on. The studies were carried out with several graphene concentrations in the LC, and the experimental results coherently suggest that there exists an optimal concentration of graphene, allowing a reduction in the IPS response time and rotational viscosity in the LC. Abovemore » this optimal graphene concentration, the rotational viscosity was found to increase, and consequently, the LC no longer switched faster in IPS mode. The presence of graphene suspension was also found to decrease the LC's pretilt angle significantly due to the π-π electron stacking between the LC molecules and graphene flakes. To understand the π-π stacking interaction, the anchoring mechanism of the LC on a CVD grown monolayer graphene film on copper substrate was studied by reflected crossed polarized microscopy. Optical microphotographs revealed that the LC alignment direction depended on monolayer graphene's hexagonal crystal structure and its orientation.« less

Sub-corotating region of Saturn's magnetosphere: Cassini observations of the azimuthal field and implications for the ionospheric Pederesen Current (Invited)

NASA Astrophysics Data System (ADS)

Smith, E. J.; Dougherty, M. K.; Zhou, X.

2010-12-01

A consensus model of Saturn’s magnetosphere that has broad acceptance consists of four regions in which the plasma and field are corotating, sub-corotating or undergoing Vasyliunas or Dungey convection. In this model, the sub-corotating magnetosphere contains a large scale circuital current system comprised of radial, field-aligned and ionospheric currents. A quantitative rendering of this system developed by S. Cowley and E. Bunch relates the azimuthal field component, B phi, that causes the field to spiral to the ionospheric Pedersen current , Ip. Cassini measurements of B phi over the four year interval between 2005 and 2008 that are widely distributed in radial distance, latitude and local time have been used to compute Ip from a Bunce-Cowley formula. A striking north-south asymmetry of the global magnetosphere has been found. In the southern hemisphere, the magnitude and variation of Ip with invariant colatitude, θ, agree qualitatively with the model but Ip (θ) is shifted poleward by about 10°. In the northern hemisphere, however, the data fail to reproduce the profile of Ip (θ) predicted by the model but are dominated by two high latitude currents having the wrong polarities. Possible causes of this asymmetry are seasonal variations (summer in the southern hemisphere) and/or asymmetric plasma outflow from the inner magnetosphere such as the plumes extending southward from Enceladus. Another finding is a significant local time dependence of Ip(θ) rather than the axisymmetry assumed in the model. There is a close correspondence with the model in the noon sector. The currents in the midnight and dawn sectors are significantly larger than in the noon sector and the current in the dusk sector is dramatically weaker.

Magnetic novae

NASA Astrophysics Data System (ADS)

Zemko, Polina; Orio, Marina

2016-07-01

We present the results of optical and X-ray observations of two quiescent novae, V2491 Cyg and V4743 Sgr. Our observations suggest the intriguing possibility of localization of hydrogen burning in magnetic novae, in which accretion is streamed to the polar caps. V2491 Cyg was observed with Suzaku more than 2 years after the outburst and V4743 Sgr was observed with XMM Newton 2 and 3.5 years after maximum. In the framework of a monitoring program of novae previously observed as super soft X-ray sources we also obtained optical spectra of V4743 Sgr with the SALT telescope 11.5 years after the eruption and of V2491 Cyg with the 6m Big Azimutal Telescope 4 and 7 years post-outburst. In order to confirm the possible white dwarf spin period of V2491 Cyg measured in the Suzaku observations we obtained photometric data using the 90cm WIYN telescope at Kitt Peak and the 1.2 m telescope in Crimea. We found that V4743 Sgr is an intermediate polar (IP) and V2491 Cyg is a strong IP candidate. Both novae show modulation of their X-ray light curves and have X-ray spectra typical of IPs. The Suzaku and XMM Newton exposures revealed that the spectra of both novae have a very soft blackbody-like component with a temperature close to that of the hydrogen burning white dwarfs in their SSS phases, but with flux by at least two orders of magnitude lower, implying a possible shrinking of emitting regions in the thin atmosphere that is heated by nuclear burning underneath it. In quiescent IPs, independently of the burning, an ultrasoft X-ray flux component originates at times in the polar regions irradiated by the accretion column, but the soft component of V4743 Sgr disappeared in 2006, indicating that the origin may be different from accretion. We suggest it may have been due to an atmospheric temperature gradient on the white dwarf surface, or to continuing localized thermonuclear burning at the bottom of the envelope, before complete turn-off. The optical spectra of V2491 Cyg and V4743 Sgr showed the prominent He II 4686 A line and the Bowen blend, which indicate a hot region, with peak temperature in the ultraviolet range. This may be the same region that previously emitted supersoft X-rays, and later cooled shifting the peak of emission to the ultraviolet.

ChIP-seq.

PubMed

Kim, Tae Hoon; Dekker, Job

2018-05-01

Owing to its digital nature, ChIP-seq has become the standard method for genome-wide ChIP analysis. Using next-generation sequencing platforms (notably the Illumina Genome Analyzer), millions of short sequence reads can be obtained. The densities of recovered ChIP sequence reads along the genome are used to determine the binding sites of the protein. Although a relatively small amount of ChIP DNA is required for ChIP-seq, the current sequencing platforms still require amplification of the ChIP DNA by ligation-mediated PCR (LM-PCR). This protocol, which involves linker ligation followed by size selection, is the standard ChIP-seq protocol using an Illumina Genome Analyzer. The size-selected ChIP DNA is amplified by LM-PCR and size-selected for the second time. The purified ChIP DNA is then loaded into the Genome Analyzer. The ChIP DNA can also be processed in parallel for ChIP-chip results. © 2018 Cold Spring Harbor Laboratory Press.

Near surface IP investigations: Four case studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hearst, R.B.; Morris, W.A.; Clark, M.A.

1995-12-31

The use of the Induced Polarisation (IP) method of geophysical surveying for near surface site investigations is gaining acceptance within the geophysical community. In this study the IP method is evaluated as a tool for the delineation of ground water resources; contamination plume detection in a lateritic horizon; and acid mine drainage leak detection from decommissioned mine tailings. A time domain IP system was selected for this study primarily for the flexibility in the selection and setting of receiver time windows and diagnostic characteristics attributed to submitting the data to Cole-Cole analysis. Analysis of the acquired data in conjunction withmore » available borehole and geological information illustrates the effectiveness and usefulness of the survey method for solving near surface problems. In all of the locations tested, it was found that with a properly designed IP survey it was possible to resolve the target and/or related structures.« less

The value of DCIP geophysical surveys for contaminated site investigations

NASA Astrophysics Data System (ADS)

Balbarini, N.; Rønde, V.; Maurya, P. K.; Møller, I.; McKnight, U. S.; Christiansen, A. V.; Binning, P. J.; Bjerg, P. L.

2017-12-01

Geophysical methods are increasingly being used in contaminant hydrogeology to map lithology, hydraulic properties, and contaminant plumes with a high ionic strength. Advances in the Direct Current resistivity and Induced Polarization (DCIP) method allow the collection of high resolution three dimensional (3D) data sets. The DC resistivity can describe both soil properties and the water electrical conductivity, while the IP can describe the lithology and give information on hydrogeological properties. The aim of the study was to investigate a large contaminant plume discharging to a stream from an old factory site by combining traditional geological, hydrological, and contaminant concentration data with DCIP surveys. The plume consisted of xenobiotic organic compounds and inorganics. The study assesses benefits and limitations of DCIP geophysics for contaminated site investigations. A 3D geological model was developed from borehole logs and DCIP data as framework for the complex transport pathways near the meandering stream. IP data were useful in indicating the continuity and the changes in thickness of local clay layers between the borehole logs. The geological model was employed to develop a groundwater flow model describing groundwater flows to the stream. The hydraulic conductivity distribution was based on IP data, slug tests and grain size analysis. The distribution of contaminant concentrations revealed two chemically distinct plumes, separated by a clay layer, with different transport paths to the stream. The DC resistivity was useful in mapping ionic compounds, but also organic compounds whose spatial distribution coincided with the ionic compounds. A conceptual model describing the contaminant plume was developed, and it matched well with contaminant concentrations in stream water and below the streambed. Surface DCIP surveys supported the characterization of the spatial variability in geology, hydraulic conductivity and contaminant concentration. Though DCIP data interpretation required additional borehole data, the DCIP survey reduced the number of boreholes required and helped design field campaigns. The results suggest DCIP surveys are useful and inexpensive tools, which has potential as an integrated part of contaminated site investigations.

A Facile Method to Establish Human Induced Pluripotent Stem Cells From Adult Blood Cells Under Feeder-Free and Xeno-Free Culture Conditions: A Clinically Compliant Approach

PubMed Central

Chou, Bin-Kuan; Gu, Haihui; Gao, Yongxing; Dowey, Sarah N.; Wang, Ying; Shi, Jun; Li, Yanxin; Ye, Zhaohui; Cheng, Tao

2015-01-01

Reprogramming human adult blood mononuclear cells (MNCs) cells by transient plasmid expression is becoming increasingly popular as an attractive method for generating induced pluripotent stem (iPS) cells without the genomic alteration caused by genome-inserting vectors. However, its efficiency is relatively low with adult MNCs compared with cord blood MNCs and other fetal cells and is highly variable among different adult individuals. We report highly efficient iPS cell derivation under clinically compliant conditions via three major improvements. First, we revised a combination of three EBNA1/OriP episomal vectors expressing five transgenes, which increased reprogramming efficiency by ≥10–50-fold from our previous vectors. Second, human recombinant vitronectin proteins were used as cell culture substrates, alleviating the need for feeder cells or animal-sourced proteins. Finally, we eliminated the previously critical step of manually picking individual iPS cell clones by pooling newly emerged iPS cell colonies. Pooled cultures were then purified based on the presence of the TRA-1-60 pluripotency surface antigen, resulting in the ability to rapidly expand iPS cells for subsequent applications. These new improvements permit a consistent and reliable method to generate human iPS cells with minimal clonal variations from blood MNCs, including previously difficult samples such as those from patients with paroxysmal nocturnal hemoglobinuria. In addition, this method of efficiently generating iPS cells under feeder-free and xeno-free conditions allows for the establishment of clinically compliant iPS cell lines for future therapeutic applications. PMID:25742692

Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus.

PubMed

Hansen, Peter; Hecht, Jochen; Ibn-Salem, Jonas; Menkuec, Benjamin S; Roskosch, Sebastian; Truss, Matthias; Robinson, Peter N

2016-11-04

ChIP-nexus, an extension of the ChIP-exo protocol, can be used to map the borders of protein-bound DNA sequences at nucleotide resolution, requires less input DNA and enables selective PCR duplicate removal using random barcodes. However, the use of random barcodes requires additional preprocessing of the mapping data, which complicates the computational analysis. To date, only a very limited number of software packages are available for the analysis of ChIP-exo data, which have not yet been systematically tested and compared on ChIP-nexus data. Here, we present a comprehensive software package for ChIP-nexus data that exploits the random barcodes for selective removal of PCR duplicates and for quality control. Furthermore, we developed bespoke methods to estimate the width of the protected region resulting from protein-DNA binding and to infer binding positions from ChIP-nexus data. Finally, we applied our peak calling method as well as the two other methods MACE and MACS2 to the available ChIP-nexus data. The Q-nexus software is efficient and easy to use. Novel statistics about duplication rates in consideration of random barcodes are calculated. Our method for the estimation of the width of the protected region yields unbiased signatures that are highly reproducible for biological replicates and at the same time very specific for the respective factors analyzed. As judged by the irreproducible discovery rate (IDR), our peak calling algorithm shows a substantially better reproducibility. An implementation of Q-nexus is available at http://charite.github.io/Q/ .

Limitations and possibilities of low cell number ChIP-seq

PubMed Central

2012-01-01

Background Chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq) offers high resolution, genome-wide analysis of DNA-protein interactions. However, current standard methods require abundant starting material in the range of 1–20 million cells per immunoprecipitation, and remain a bottleneck to the acquisition of biologically relevant epigenetic data. Using a ChIP-seq protocol optimised for low cell numbers (down to 100,000 cells / IP), we examined the performance of the ChIP-seq technique on a series of decreasing cell numbers. Results We present an enhanced native ChIP-seq method tailored to low cell numbers that represents a 200-fold reduction in input requirements over existing protocols. The protocol was tested over a range of starting cell numbers covering three orders of magnitude, enabling determination of the lower limit of the technique. At low input cell numbers, increased levels of unmapped and duplicate reads reduce the number of unique reads generated, and can drive up sequencing costs and affect sensitivity if ChIP is attempted from too few cells. Conclusions The optimised method presented here considerably reduces the input requirements for performing native ChIP-seq. It extends the applicability of the technique to isolated primary cells and rare cell populations (e.g. biobank samples, stem cells), and in many cases will alleviate the need for cell culture and any associated alteration of epigenetic marks. However, this study highlights a challenge inherent to ChIP-seq from low cell numbers: as cell input numbers fall, levels of unmapped sequence reads and PCR-generated duplicate reads rise. We discuss a number of solutions to overcome the effects of reducing cell number that may aid further improvements to ChIP performance. PMID:23171294

System-level protection and hardware Trojan detection using weighted voting.

PubMed

Amin, Hany A M; Alkabani, Yousra; Selim, Gamal M I

2014-07-01

The problem of hardware Trojans is becoming more serious especially with the widespread of fabless design houses and design reuse. Hardware Trojans can be embedded on chip during manufacturing or in third party intellectual property cores (IPs) during the design process. Recent research is performed to detect Trojans embedded at manufacturing time by comparing the suspected chip with a golden chip that is fully trusted. However, Trojan detection in third party IP cores is more challenging than other logic modules especially that there is no golden chip. This paper proposes a new methodology to detect/prevent hardware Trojans in third party IP cores. The method works by gradually building trust in suspected IP cores by comparing the outputs of different untrusted implementations of the same IP core. Simulation results show that our method achieves higher probability of Trojan detection over a naive implementation of simple voting on the output of different IP cores. In addition, experimental results show that the proposed method requires less hardware overhead when compared with a simple voting technique achieving the same degree of security.

Chromatin Immunoprecipitation (ChIP) Protocol for Low-abundance Embryonic Samples.

PubMed

Rehimi, Rizwan; Bartusel, Michaela; Solinas, Francesca; Altmüller, Janine; Rada-Iglesias, Alvaro

2017-08-29

Chromatin immunoprecipitation (ChIP) is a widely-used technique for mapping the localization of post-translationally modified histones, histone variants, transcription factors, or chromatin-modifying enzymes at a given locus or on a genome-wide scale. The combination of ChIP assays with next-generation sequencing (i.e., ChIP-Seq) is a powerful approach to globally uncover gene regulatory networks and to improve the functional annotation of genomes, especially of non-coding regulatory sequences. ChIP protocols normally require large amounts of cellular material, thus precluding the applicability of this method to investigating rare cell types or small tissue biopsies. In order to make the ChIP assay compatible with the amount of biological material that can typically be obtained in vivo during early vertebrate embryogenesis, we describe here a simplified ChIP protocol in which the number of steps required to complete the assay were reduced to minimize sample loss. This ChIP protocol has been successfully used to investigate different histone modifications in various embryonic chicken and adult mouse tissues using low to medium cell numbers (5 x 10 4 - 5 x 10 5 cells). Importantly, this protocol is compatible with ChIP-seq technology using standard library preparation methods, thus providing global epigenomic maps in highly relevant embryonic tissues.

On recovering distributed IP information from inductive source time domain electromagnetic data

NASA Astrophysics Data System (ADS)

Kang, Seogi; Oldenburg, Douglas W.

2016-10-01

We develop a procedure to invert time domain induced polarization (IP) data for inductive sources. Our approach is based upon the inversion methodology in conventional electrical IP (EIP), which uses a sensitivity function that is independent of time. However, significant modifications are required for inductive source IP (ISIP) because electric fields in the ground do not achieve a steady state. The time-history for these fields needs to be evaluated and then used to define approximate IP currents. The resultant data, either a magnetic field or its derivative, are evaluated through the Biot-Savart law. This forms the desired linear relationship between data and pseudo-chargeability. Our inversion procedure has three steps: (1) Obtain a 3-D background conductivity model. We advocate, where possible, that this be obtained by inverting early-time data that do not suffer significantly from IP effects. (2) Decouple IP responses embedded in the observations by forward modelling the TEM data due to a background conductivity and subtracting these from the observations. (3) Use the linearized sensitivity function to invert data at each time channel and recover pseudo-chargeability. Post-interpretation of the recovered pseudo-chargeabilities at multiple times allows recovery of intrinsic Cole-Cole parameters such as time constant and chargeability. The procedure is applicable to all inductive source survey geometries but we focus upon airborne time domain EM (ATEM) data with a coincident-loop configuration because of the distinctive negative IP signal that is observed over a chargeable body. Several assumptions are adopted to generate our linearized modelling but we systematically test the capability and accuracy of the linearization for ISIP responses arising from different conductivity structures. On test examples we show: (1) our decoupling procedure enhances the ability to extract information about existence and location of chargeable targets directly from the data maps; (2) the horizontal location of a target body can be well recovered through inversion; (3) the overall geometry of a target body might be recovered but for ATEM data a depth weighting is required in the inversion; (4) we can recover estimates of intrinsic τ and η that may be useful for distinguishing between two chargeable targets.

[Modern research progress of traditional Chinese medicine based on integrative pharmacology].

PubMed

Wang, Ping; Tang, Shi-Huan; Su, Jin; Zhang, Jia-Qi; Cui, Ru-Yi; Xu, Hai-Yu; Yang, Hong-Jun

2018-04-01

Integrative pharmacology (IP) is a discipline that studies the interaction, integration and principle of action of multiple components with the body, emphasizing the integrations of multi-level and multi-link, such as "whole and part", " in vivo and in vitro ", " in vivo process and activity evaluation". After four years of development and practice, the theory and method of IP has received extensive attention and application.In order to better promote the development of IP, this paper systematically reviews the concepts, research contents, research methods and application fields about IP. Copyright© by the Chinese Pharmaceutical Association.

Covert Channels in SIP for VoIP Signalling

NASA Astrophysics Data System (ADS)

Mazurczyk, Wojciech; Szczypiorski, Krzysztof

In this paper, we evaluate available steganographic techniques for SIP (Session Initiation Protocol) that can be used for creating covert channels during signaling phase of VoIP (Voice over IP) call. Apart from characterizing existing steganographic methods we provide new insights by introducing new techniques. We also estimate amount of data that can be transferred in signalling messages for typical IP telephony call.

Ion-pair high-speed countercurrent chromatography in fractionation of a high-molecular weight variation of acyl-oligosaccharide linked betacyanins from purple bracts of Bougainvillea glabra.

PubMed

Wybraniec, Sławomir; Jerz, Gerold; Gebers, Nadine; Winterhalter, Peter

2010-02-15

The natural pigment composition of purple bracts of Bougainvillea glabra (Nyctaginaceae) consists of a highly complex mixture of betacyanins solely differing by the substitution with a variety of acyl-oligoglycoside units. This study was focused on a two-dimensional chromatography approach, a combination of preparative high-speed countercurrent chromatography (HSCCC) and analytical C18-HPLC with ESI-DAD-MS/MS detection which finally enabled a more detailed view into the pigment profile and elucidated the existence of an overwhelming amount of varying betacyanin structures occurring in Bougainvillea bracts. The detected molecular weights of the pigments reached so far unknown high values and ranged up to maximum values of 1653 and 1683 Da for the largest molecules due to oligosaccharide linkage and multiple acyl substitutions. The preparative IP-HSCCC separation yielded 15 complex fractions containing betacyanins of enhanced polarity as well as structures with highly increased lipophilicity. Betacyanin structures extended by large oligosaccharide chains with bigger number of glycoside units and also carrying a reduced number of hydroxycinnamic acid substitutions were characteristic for polar pigments occurring mainly in the early eluting CCC fractions. IP-HSCCC was proven to be extremely effective for fractionating this complex crude betalain pigment extract into more defined 'polarity-windows'. Structural analysis by analytical LC-ESI-MS/MS in the positive ionization mode detected a total sum of 146 different betacyanin pigments in the CCC fractions of reduced complexity. Copyright 2010 Elsevier B.V. All rights reserved.

Determination of solar proton fluxes and energies at high solar latitudes by UV radiation measurements

NASA Technical Reports Server (NTRS)

Witt, N.; Blum, P. W.; Ajello, J. M.

1981-01-01

The latitudinal variation of the solar proton flux and energy causes a density increase at high solar latitudes of the neutral gas penetrating the heliosphere. Measurements of the neutral density by UV resonance radiation observations from interplanetary spacecraft thus permit deductions on the dependence of the solar proton flux on heliographic latitude. Using both the results of Mariner 10 measurements and of other off-ecliptic solar wind observations, the values of the solar proton fluxes and energies at polar heliographic latitudes are determined for several cases of interest. The Mariner 10 analysis, together with IPS results, indicate a significant decrease of the solar proton flux at polar latitudes.

ChIP-re-ChIP: Co-occupancy Analysis by Sequential Chromatin Immunoprecipitation.

PubMed

Beischlag, Timothy V; Prefontaine, Gratien G; Hankinson, Oliver

2018-01-01

Chromatin immunoprecipitation (ChIP) exploits the specific interactions between DNA and DNA-associated proteins. It can be used to examine a wide range of experimental parameters. A number of proteins bound at the same genomic location can identify a multi-protein chromatin complex where several proteins work together to regulate gene transcription or chromatin configuration. In many instances, this can be achieved using sequential ChIP; or simply, ChIP-re-ChIP. Whether it is for the examination of specific transcriptional or epigenetic regulators, or for the identification of cistromes, the ability to perform a sequential ChIP adds a higher level of power and definition to these analyses. In this chapter, we describe a simple and reliable method for the sequential ChIP assay.

Calibration and application of the IP25 biomarker for Arctic sea ice reconstructions

NASA Astrophysics Data System (ADS)

Cabedo Sanz, P.; Navarro Rodriguez, A.; Belt, S. T.; Brown, T. A.; Knies, J.; Husum, K.; Giraudeau, J.; Andrews, J.

2012-04-01

The presence of the sea ice diatom biomarker IP25 in Arctic marine sediments has been used in previous studies as a proxy for past spring sea ice occurrence and as an indicator of wider palaeoenvironmental conditions for different regions of the Arctic over various timescales [e.g. 1, 3]. In addition, measurement of IP25 has also been applied as a sea ice origin tracer for studying the transfer of organic carbon through Arctic food-webs [2]. The current study focuses on three main areas: (1) In order to improve on the quantitative analytical aspects of IP25 based research, we present here the results of a large scale extraction, purification and identification procedure for IP25 from marine sediments. This has confirmed the structure of IP25 in sediments and enabled more robust quantitative measurements by gas chromatography - mass spectrometry (GC-MS) to be established. (2) Quantitative measurements of IP25 from a sediment core from Andfjord (continental shelf, Tromsø, Norway) have been determined for the period 6.3 to 14.3 ka BP. The results of this study add significant further information to that reported previously from other biomarker studies for this core (e.g. brassicasterol) [4]. (3) Analytical detection issues (GC-MS) regarding the occurrence of IP25 in other sub-Arctic regions (e.g. East Greenland - North Iceland area) will be presented and discussed with relation to other proxy data (e.g. IRD). Belt, S. T., Vare, L. L., Massé, G., Manners, H. R., Price, J. C., MacLachlan, S. E., Andrews, J. T. & Schmidt, S. (2010) 'Striking similarities in temporal changes to spring sea ice occurrence across the central Canadian Arctic Archipelago over the last 7000 years', Quaternary Science Reviews, 29 (25-26), pp. 3489-3504. Brown, T. A. & Belt, S. T. (2012) 'Identification of the sea ice diatom biomarker IP25 in Arctic benthic macrofauna: direct evidence for a sea ice diatom diet in Arctic heterotrophs', Polar Biology, 35, pp. 131-137. Müller, J., Massé, G., Stein, R. & Belt, S. T. (2009) 'Variability of sea-ice conditions in the Fram Strait over the past 30,000 years', Nature Geoscience, 2 (11), pp. 772-776. .Knies, J. (2005) 'Climate-induced changes in sedimentary regimes for organic matter supply on the continental shelf off northern Norway', Geochimica et Cosmochimica Acta, 69 (19), pp. 4631-4647.

A Method to Biomonitor the Cooked Meat Carcinogen 2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) in Dyed Hair by Ultra Performance Liquid Chromatography-Orbitrap High Resolution Multistage Mass Spectrometry

PubMed Central

Guo, Jingshu; Yonemori, Kim; Le Marchand, Loïc; Turesky, Robert J.

2015-01-01

2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) is a carcinogenic heterocyclic aromatic amine formed in cooked meat. The use of naturally colored hair containing PhIP can serve as a long-term biomarker of exposure to this carcinogen. However, the measurement of PhIP in dyed hair, a cosmetic treatment commonly used by the adult population, is challenging because the dye process introduces a complex mixture of chemicals into the hair matrix, which interfere with the measurement of PhIP. The high-resolution scanning features of the Orbitrap Fusion™ mass spectrometer were employed to biomonitor PhIP in dyed hair. Because of the complexity of chemicals in the hair dye, the consecutive reaction monitoring of PhIP at the MS3 scan stage was employed to selectively remove the isobaric interferences. The limit of quantification (LOQ) of PhIP was 84 parts-per-trillion (ppt) employing 50 mg hair. Calibration curves were generated in dyed hair matrices and showed good linearity (40 to 1000 pg PhIP/g hair) with a goodness-of-fit regression value r2 > 0.9978. The within-day (between-day) coefficients of variation were 7.7% (17%) and 5.4% (6.1%), respectively, with dyed hair samples spiked with PhIP at 200 and 600 ppt. The levels of PhIP accrued in dyed hair from volunteers on a semi-controlled feeding study who ingested known levels of PhIP were comparable to the levels of PhIP accrued in hair of subjects with natural hair color. The method was successfully employed to measure PhIP in non-dyed and dyed hair biospecimens of participants in a case-control study of colorectal adenoma on their regular diet. PMID:25969997

iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data.

PubMed

Yang, Chia-Chun; Andrews, Erik H; Chen, Min-Hsuan; Wang, Wan-Yu; Chen, Jeremy J W; Gerstein, Mark; Liu, Chun-Chi; Cheng, Chao

2016-08-12

Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) or microarray hybridization (ChIP-chip) has been widely used to determine the genomic occupation of transcription factors (TFs). We have previously developed a probabilistic method, called TIP (Target Identification from Profiles), to identify TF target genes using ChIP-seq/ChIP-chip data. To achieve high specificity, TIP applies a conservative method to estimate significance of target genes, with the trade-off being a relatively low sensitivity of target gene identification compared to other methods. Additionally, TIP's output does not render binding-peak locations or intensity, information highly useful for visualization and general experimental biological use, while the variability of ChIP-seq/ChIP-chip file formats has made input into TIP more difficult than desired. To improve upon these facets, here we present are fined TIP with key extensions. First, it implements a Gaussian mixture model for p-value estimation, increasing target gene identification sensitivity and more accurately capturing the shape of TF binding profile distributions. Second, it enables the incorporation of TF binding-peak data by identifying their locations in significant target gene promoter regions and quantifies their strengths. Finally, for full ease of implementation we have incorporated it into a web server ( http://syslab3.nchu.edu.tw/iTAR/ ) that enables flexibility of input file format, can be used across multiple species and genome assembly versions, and is freely available for public use. The web server additionally performs GO enrichment analysis for the identified target genes to reveal the potential function of the corresponding TF. The iTAR web server provides a user-friendly interface and supports target gene identification in seven species, ranging from yeast to human. To facilitate investigating the quality of ChIP-seq/ChIP-chip data, the web server generates the chart of the characteristic binding profiles and the density plot of normalized regulatory scores. The iTAR web server is a useful tool in identifying TF target genes from ChIP-seq/ChIP-chip data and discovering biological insights.

IRF5 regulates lung macrophages M2 polarization during severe acute pancreatitis in vitro

PubMed Central

Sun, Kang; He, Song-Bing; Qu, Jian-Guo; Dang, Sheng-Chun; Chen, Ji-Xiang; Gong, Ai-Hua; Xie, Rong; Zhang, Jian-Xin

2016-01-01

AIM To investigate the role of interferon regulatory factor 5 (IRF5) in reversing polarization of lung macrophages during severe acute pancreatitis (SAP) in vitro. METHODS A mouse SAP model was established by intraperitoneal (ip) injections of 20 μg/kg body weight caerulein. Pathological changes in the lung were observed by hematoxylin and eosin staining. Lung macrophages were isolated from bronchoalveolar lavage fluid. The quantity and purity of lung macrophages were detected by fluorescence-activated cell sorting and evaluated by real-time polymerase chain reaction (RT-PCR). They were treated with IL-4/IRF5 specific siRNA (IRF5 siRNA) to reverse their polarization and were evaluated by detecting markers expression of M1/M2 using RT-PCR. RESULTS SAP associated acute lung injury (ALI) was induced successfully by ip injections of caerulein, which was confirmed by histopathology. Lung macrophages expressed high levels of IRF5 as M1 phenotype during the early acute pancreatitis stages. Reduction of IRF5 expression by IRF5 siRNA reversed the action of macrophages from M1 to M2 phenotype in vitro. The expressions of M1 markers, including IRF5 (S + IRF5 siRNA vs S + PBS, 0.013 ± 0.01 vs 0.054 ± 0.047, P < 0.01), TNF-α (S + IRF5 siRNA vs S + PBS, 0.0003 ± 0.0002 vs 0.019 ± 0.018, P < 0.001), iNOS (S + IRF5 siRNA vs S + PBS, 0.0003 ± 0.0002 vs 0.026 ± 0.018, P < 0.001) and IL-12 (S + IRF5 siRNA vs S + PBS, 0.000005 ± 0.00004 vs 0.024 ± 0.016, P < 0.001), were decreased. In contrast, the expressions of M2 markers, including IL-10 (S + IRF5 siRNA vs S + PBS, 0.060 ± 0.055 vs 0.0230 ± 0.018, P < 0.01) and Arg-1 (S + IRF5 siRNA vs S + PBS, 0.910 ± 0.788 vs 0.0036 ± 0.0025, P < 0.001), were increased. IRF5 siRNA could reverse the lung macrophage polarization more effectively than IL-4. CONCLUSION Treatment with IRF5 siRNA can reverse the pancreatitis-induced activation of lung macrophages from M1 phenotype to M2 phenotype in SAP associated with ALI. PMID:27895424

Equation of motion coupled cluster methods for electron attachment and ionization potential in polyacenes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhaskaran-Nair, Kiran; Kowalski, Karol; Jarrell, Mark

2015-11-05

Polyacenes have attracted considerable attention due to their use in organic based optoelectronic materials. Polyacenes are polycyclic aromatic hydrocarbons composed of fused benzene rings. Key to understanding and design of new functional materials is an understanding of their excited state properties starting with their electron affinity (EA) and ionization potential (IP). We have developed a highly accurate and com- putationally e*fficient EA/IP equation of motion coupled cluster singles and doubles (EA/IP-EOMCCSD) method that is capable of treating large systems and large basis set. In this study we employ the EA/IP-EOMCCSD method to calculate the electron affinity and ionization potential ofmore » naphthalene, anthracene, tetracene, pentacene, hex- acene and heptacene. We have compared our results with other previous theoretical studies and experimental data. Our EA/IP results are in very good agreement with experiment and when compared with the other theoretical investigations our results represent the most accurate calculations as compared to experiment.« less

Examining Correlates of Problematic Internet Pornography Use Among University Students

PubMed Central

Harper, Cody; Hodgins, David C.

2016-01-01

Background and aims The phenomenon of Internet pornography (IP) addiction is gainingincreasing attention in the popular media and psychological research. What has not been tested empirically is how frequency and amount ofIP use, along with other individual characteristics, are related tosymptoms of IP addiction. Methods 105 female and 86 male university students (mean age 21) from Calgary,Canada, were administered measures of IP use, psychosocial functioning (anxiety and depression, life and relationship satisfaction), addictivepropensities, and addictive IP use. Results Men reported earlier age of exposure and more frequent current IP use than women. Individuals not in relationships reported more frequent use than those in relationships. Frequency of IP use wasnot generally correlated with psychosocial functioning but was significantly positively correlated with level of IP addiction. Higher level of IP addiction was associated with poorer psychosocial functioning and problematic alcohol, cannabis, gambling and, in particular, video game use. A curvilinear association was found between frequency of IP use and level of addiction such that daily or greater IP use was associated with a sharp rise in addictive IP scores. Discussion The failure to find a strong significant relationship between IP use and general psychosocial functioning suggests that the overall effect of IP use is not necessarily harmful in and of itself. Addictiveuse of IP, which is associated with poorer psychosocial functioning, emerges when people begin to use IP daily. PMID:27156383

Multiplexed ChIP-Seq Using Direct Nucleosome Barcoding: A Tool for High-Throughput Chromatin Analysis.

PubMed

Chabbert, Christophe D; Adjalley, Sophie H; Steinmetz, Lars M; Pelechano, Vicent

2018-01-01

Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) or microarray hybridization (ChIP-on-chip) are standard methods for the study of transcription factor binding sites and histone chemical modifications. However, these approaches only allow profiling of a single factor or protein modification at a time.In this chapter, we present Bar-ChIP, a higher throughput version of ChIP-Seq that relies on the direct ligation of molecular barcodes to chromatin fragments. Bar-ChIP enables the concurrent profiling of multiple DNA-protein interactions and is therefore amenable to experimental scale-up, without the need for any robotic instrumentation.

Spike-In Normalization of ChIP Data Using DNA-DIG-Antibody Complex.

PubMed

Eberle, Andrea B

2018-01-01

Chromatin immunoprecipitation (ChIP) is a widely used method to determine the occupancy of specific proteins within the genome, helping to unravel the function and activity of specific genomic regions. In ChIP experiments, normalization of the obtained data by a suitable internal reference is crucial. However, particularly when comparing differently treated samples, such a reference is difficult to identify. Here, a simple method to improve the accuracy and reliability of ChIP experiments by the help of an external reference is described. An artificial molecule, composed of a well-defined digoxigenin (DIG) labeled DNA fragment in complex with an anti-DIG antibody, is synthesized and added to each chromatin sample before immunoprecipitation. During the ChIP procedure, the DNA-DIG-antibody complex undergoes the same treatments as the chromatin and is therefore purified and quantified together with the chromatin of interest. This external reference compensates for variability during the ChIP routine and improves the similarity between replicates, thereby emphasizing the biological differences between samples.

Considerations on Experimental Design and Data Analysis of Chromatin Immunoprecipitation Experiments.

PubMed

Jordán-Pla, Antonio; Visa, Neus

2018-01-01

Arguably one of the most valuable techniques to study chromatin organization, ChIP is the method of choice to map the contacts established between proteins and genomic DNA. Ever since its inception, more than 30 years ago, ChIP has been constantly evolving, improving, and expanding its capabilities and reach. Despite its widespread use by many laboratories across a wide variety of disciplines, ChIP assays can be sometimes challenging to design, and are often sensitive to variations in practical implementation.In this chapter, we provide a general overview of the ChIP method and its most common variations, with a special focus on ChIP-seq. We try to address some of the most important aspects that need to be taken into account in order to design and perform experiments that generate the most reproducible, high-quality data. Some of the main topics covered include the use of properly characterized antibodies, alternatives to chromatin preparation, the need for proper controls, and some recommendations about ChIP-seq data analysis.

Quantification of histone modification ChIP-seq enrichment for data mining and machine learning applications

PubMed Central

2011-01-01

Background The advent of ChIP-seq technology has made the investigation of epigenetic regulatory networks a computationally tractable problem. Several groups have applied statistical computing methods to ChIP-seq datasets to gain insight into the epigenetic regulation of transcription. However, methods for estimating enrichment levels in ChIP-seq data for these computational studies are understudied and variable. Since the conclusions drawn from these data mining and machine learning applications strongly depend on the enrichment level inputs, a comparison of estimation methods with respect to the performance of statistical models should be made. Results Various methods were used to estimate the gene-wise ChIP-seq enrichment levels for 20 histone methylations and the histone variant H2A.Z. The Multivariate Adaptive Regression Splines (MARS) algorithm was applied for each estimation method using the estimation of enrichment levels as predictors and gene expression levels as responses. The methods used to estimate enrichment levels included tag counting and model-based methods that were applied to whole genes and specific gene regions. These methods were also applied to various sizes of estimation windows. The MARS model performance was assessed with the Generalized Cross-Validation Score (GCV). We determined that model-based methods of enrichment estimation that spatially weight enrichment based on average patterns provided an improvement over tag counting methods. Also, methods that included information across the entire gene body provided improvement over methods that focus on a specific sub-region of the gene (e.g., the 5' or 3' region). Conclusion The performance of data mining and machine learning methods when applied to histone modification ChIP-seq data can be improved by using data across the entire gene body, and incorporating the spatial distribution of enrichment. Refinement of enrichment estimation ultimately improved accuracy of model predictions. PMID:21834981

Method to Biomonitor the Cooked Meat Carcinogen 2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine in Dyed Hair by Ultra-Performance Liquid Chromatography-Orbitrap High Resolution Multistage Mass Spectrometry.

PubMed

Guo, Jingshu; Yonemori, Kim; Le Marchand, Loïc; Turesky, Robert J

2015-06-16

2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) is a carcinogenic heterocyclic aromatic amine formed in cooked meat. The use of naturally colored hair containing PhIP can serve as a long-term biomarker of exposure to this carcinogen. However, the measurement of PhIP in dyed hair, a cosmetic treatment commonly used by the adult population, is challenging because the dye process introduces into the hair matrix a complex mixture of chemicals that interferes with the measurement of PhIP. The high-resolution scanning features of the Orbitrap Fusion mass spectrometer were employed to biomonitor PhIP in dyed hair. Because of the complexity of chemicals in the hair dye, the consecutive reaction monitoring of PhIP at the MS(3) scan stage was employed to selectively remove the isobaric interferences. The limit of quantification (LOQ) of PhIP was 84 parts-per-trillion (ppt) employing 50 mg of hair. Calibration curves were generated in dyed hair matrixes and showed good linearity (40-1000 pg PhIP/g hair) with a goodness-of-fit regression value of r(2) > 0.9978. The within-day (between-day) coefficients of variation were 7.7% (17%) and 5.4% (6.1%), respectively, with dyed hair samples spiked with PhIP at 200 and 600 ppt. The levels of PhIP accrued in dyed hair from volunteers on a semicontrolled feeding study who ingested known levels of PhIP were comparable to the levels of PhIP accrued in hair of subjects with natural hair color. The method was successfully employed to measure PhIP in nondyed and dyed hair biospecimens of participants in a case-control study of colorectal adenoma on their regular diet.

A novel statistical method for quantitative comparison of multiple ChIP-seq datasets.

PubMed

Chen, Li; Wang, Chi; Qin, Zhaohui S; Wu, Hao

2015-06-15

ChIP-seq is a powerful technology to measure the protein binding or histone modification strength in the whole genome scale. Although there are a number of methods available for single ChIP-seq data analysis (e.g. 'peak detection'), rigorous statistical method for quantitative comparison of multiple ChIP-seq datasets with the considerations of data from control experiment, signal to noise ratios, biological variations and multiple-factor experimental designs is under-developed. In this work, we develop a statistical method to perform quantitative comparison of multiple ChIP-seq datasets and detect genomic regions showing differential protein binding or histone modification. We first detect peaks from all datasets and then union them to form a single set of candidate regions. The read counts from IP experiment at the candidate regions are assumed to follow Poisson distribution. The underlying Poisson rates are modeled as an experiment-specific function of artifacts and biological signals. We then obtain the estimated biological signals and compare them through the hypothesis testing procedure in a linear model framework. Simulations and real data analyses demonstrate that the proposed method provides more accurate and robust results compared with existing ones. An R software package ChIPComp is freely available at http://web1.sph.emory.edu/users/hwu30/software/ChIPComp.html. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Examining Correlates of Problematic Internet Pornography Use Among University Students.

PubMed

Harper, Cody; Hodgins, David C

2016-06-01

Background and aims The phenomenon of Internet pornography (IP) addiction is gainingincreasing attention in the popular media and psychological research.What has not been tested empirically is how frequency and amount ofIP use, along with other individual characteristics, are related tosymptoms of IP addiction. Methods 105 female and 86 male university students (mean age 21) from Calgary,Canada, were administered measures of IP use, psychosocial functioning(anxiety and depression, life and relationship satisfaction), addictivepropensities, and addictive IP use. Results Men reported earlier age of exposure and more frequent currentIP use than women. Individuals not in relationships reported morefrequent use than those in relationships. Frequency of IP use wasnot generally correlated with psychosocial functioning but was significantlypositively correlated with level of IP addiction. Higher level ofIP addiction was associated with poorer psychosocial functioning andproblematic alcohol, cannabis, gambling and, in particular, videogame use. A curvilinear association was found between frequency ofIP use and level of addiction such that daily or greater IP use wasassociated with a sharp rise in addictive IP scores. Discussion The failure to find a strong significant relationship between IPuse and general psychosocial functioning suggests that the overalleffect of IP use is not necessarily harmful in and of itself. Addictiveuse of IP, which is associated with poorer psychosocial functioning,emerges when people begin to use IP daily.

Circularly polarized harmonic generation by intense bicircular laser pulses: electron recollision dynamics and frequency dependent helicity

NASA Astrophysics Data System (ADS)

Bandrauk, André D.; Mauger, François; Yuan, Kai-Jun

2016-12-01

Numerical solutions of time-dependent Schrödinger equations for one and two electron cyclic molecules {{{H}}}nq+ exposed to intense bichromatic circularly polarized laser pulses of frequencies {ω }1 and {ω }2, such that {ω }1/{ω }2={n}1/{n}2 (integer) produce circularly polarized high order harmonics with a cut-off recollision maximum energy at and greater than the linear polarization law (in atomic units) {N}m{ω }1={I}p+3.17{U}p, where I p is the ionization potential and {U}p={(2{E}0)}2/4{ω }2 is the ponderomotive energy defined by the field E 0 (intensity I={{cE}}02/8π ) from each pulse and mean frequency ω =({ω }1+{ω }2)/2 . An electron recollision model in a rotating frame at rotating frequency {{Δ }}ω =({ω }1-{ω }2)/2 predicts this simple result as a result of recollision dynamics in a combination of bichromatic circularly polarized pulses. The harmonic helicities and their intensities are shown to depend on compatible symmetries of the net pulse electric fields with that of the molecules.

An improved ChIP-seq peak detection system for simultaneously identifying post-translational modified transcription factors by combinatorial fusion, using SUMOylation as an example.

PubMed

Cheng, Chia-Yang; Chu, Chia-Han; Hsu, Hung-Wei; Hsu, Fang-Rong; Tang, Chung Yi; Wang, Wen-Ching; Kung, Hsing-Jien; Chang, Pei-Ching

2014-01-01

Post-translational modification (PTM) of transcriptional factors and chromatin remodelling proteins is recognized as a major mechanism by which transcriptional regulation occurs. Chromatin immunoprecipitation (ChIP) in combination with high-throughput sequencing (ChIP-seq) is being applied as a gold standard when studying the genome-wide binding sites of transcription factor (TFs). This has greatly improved our understanding of protein-DNA interactions on a genomic-wide scale. However, current ChIP-seq peak calling tools are not sufficiently sensitive and are unable to simultaneously identify post-translational modified TFs based on ChIP-seq analysis; this is largely due to the wide-spread presence of multiple modified TFs. Using SUMO-1 modification as an example; we describe here an improved approach that allows the simultaneous identification of the particular genomic binding regions of all TFs with SUMO-1 modification. Traditional peak calling methods are inadequate when identifying multiple TF binding sites that involve long genomic regions and therefore we designed a ChIP-seq processing pipeline for the detection of peaks via a combinatorial fusion method. Then, we annotate the peaks with known transcription factor binding sites (TFBS) using the Transfac Matrix Database (v7.0), which predicts potential SUMOylated TFs. Next, the peak calling result was further analyzed based on the promoter proximity, TFBS annotation, a literature review, and was validated by ChIP-real-time quantitative PCR (qPCR) and ChIP-reChIP real-time qPCR. The results show clearly that SUMOylated TFs are able to be pinpointed using our pipeline. A methodology is presented that analyzes SUMO-1 ChIP-seq patterns and predicts related TFs. Our analysis uses three peak calling tools. The fusion of these different tools increases the precision of the peak calling results. TFBS annotation method is able to predict potential SUMOylated TFs. Here, we offer a new approach that enhances ChIP-seq data analysis and allows the identification of multiple SUMOylated TF binding sites simultaneously, which can then be utilized for other functional PTM binding site prediction in future.

78 FR 60301 - Agency Information Collection Activities: Proposed Collection; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-01

... Evaluation Program (HSEEP) After Action Report (AAR) Improvement Plan (IP). DATES: Comments must be submitted...) Improvement Plan (IP) provides a standardized method for reporting the results of preparedness exercises and identifying, correcting and sharing as appropriate strengths and areas for improvement. Thus, the HSEEP AAR/IP...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garg, L.C.; McArdle, S.; Crews, F.T.

The release of inositol phosphates (IP) from phosphoinositides (PI) by carbachol was studied in the tissue slices from cortex (C), outer medulla (OM) and inner medulla (IM) of rabbit kidneys. The method involved the incubation of the slices with (/sup 3/H)inositol for its incorporation into the PI and measurement of the release of IP in presence of lithium which prevents dephosphorylation of IP. The results of (/sup 3/H)IP formation are expressed as % of total (/sup 3/H)inositol incorporation in the tissue. No significant effect of carbachol was found on the release of IP in the C. The drug produced amore » 48% increase in IP release in the OM. In the IM, carbachol produced a concentration dependent increase in IP release with a maximum of 772% at 1 mM. The release of IP in the IM by 1 mM carbachol was completely blocked by 1 ..mu..M atropine. Our results indicate that IP release by carbachol is due to activation of muscarinic receptors in the IM of the rabbit kidney.« less

On the implementation of IP protection using biometrics based information hiding and firewall

NASA Astrophysics Data System (ADS)

Basu, Abhishek; Nandy, Kingshuk; Banerjee, Avishek; Giri, Supratick; Sarkar, Souvik; Sarkar, Subir Kumar

2016-02-01

System-on-chip-based design style creates a revolution in very large scale integration industry with design efficiency, operating speed and development time. To support this process, reuse and exchange of components are essential in electronic form called intellectual property (IP). This, however, increases the possibility of encroachment of IP of the design. So copyright protection of IP against piracy is the most important concern for IP vendors. The existing solutions for IP protection are still not secure enough with flexibility, cost, etc. This paper proposes an information-hiding-based solution for IP protection by embedding a biometric copyright information and firewall inside an IP in the form of a finite state machine with unique configuration. The scheme first introduces biometric signature-based copyright as ownership proof. Second, firewall interrupts the normal functionality of IP at the end of the user time period. The experimental outcomes of field-programmable-gate-array implementation illustrate the efficiency of the proposed method.

Geophysical Monitoring of Coupled Microbial and Geochemical Processes During Stimulated Subsurface Bioremediation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, Kenneth H.; Kemna, Andreas; Wilkins, Michael J.

2009-08-05

Understanding how microorganisms alter their physical and chemical environment during bioremediation is hindered by our inability to resolve subsurface microbial activity with high spatial resolution. Here we demonstrate the use of a minimally invasive geophysical technique to monitor stimulated microbial activity during acetate amendment in an aquifer near Rifle, Colorado. During electrical induced polarization (IP) measurements, spatiotemporal variations in the phase response between imposed electric current and the resultant electric field correlated with changes in groundwater geochemistry accompanying stimulated iron and sulfate reduction and sulfide mineral precipitation. The magnitude of the phase response varied with measurement frequency (0.125 and 1more » Hz) andwasdependent upon the dominant metabolic process. The spectral effect was corroborated using a biostimulated column experiment containing Rifle sediments and groundwater. Fluids and sediments recovered from regions exhibiting an anomalous phase response were enriched in Fe(II), dissolved sulfide, and cell-associated FeS nanoparticles. The accumulation of mineral precipitates and electroactive ions altered the ability of pore fluids to conduct electrical charge, accounting for the anomalous IP response and revealing the usefulness of multifrequency IP measurements for monitoring mineralogical and geochemical changes accompanying stimulated subsurface bioremediation.« less

[Microstructure and mechanical property of a new IPS-Empress 2 dental glass-ceramic].

PubMed

Luo, Xiao-ping; Watts, D C; Wilson, N H F; Silsons, N; Cheng, Ya-qin

2005-03-01

To investigate the microstructure and mechanical properties of a new IPS-Empress 2 dental glass-ceramic. AFM, SEM and XRD were used to analyze the microstructure and crystal phase of IPS-Empress 2 glass-ceramic. The flexural strength and fracture toughness were tested using 3-point bending method and indentation method respectively. IPS-Empress 2 glass-ceramic mainly consisted of lithium disilicate crystal, lithium phosphate and glass matrix, which formed a continuous interlocking structure. The crystal phases were not changed before and after hot-pressed treatment. AFM showed nucleating agent particles of different sizes distributed on the highly polished ceramic surface. The strength and fracture toughness were 300 MPa and 3.1 MPam(1/2). The high strength and fracture toughness of IPS-Empress 2 glass ceramic are attributed to the fine lithium disilicate crystalline, interlocking microstructure and crack deflection.

Analysis of ChIP-seq Data in R/Bioconductor.

PubMed

de Santiago, Ines; Carroll, Thomas

2018-01-01

The development of novel high-throughput sequencing methods for ChIP (chromatin immunoprecipitation) has provided a very powerful tool to study gene regulation in multiple conditions at unprecedented resolution and scale. Proactive quality-control and appropriate data analysis techniques are of critical importance to extract the most meaningful results from the data. Over the last years, an array of R/Bioconductor tools has been developed allowing researchers to process and analyze ChIP-seq data. This chapter provides an overview of the methods available to analyze ChIP-seq data based primarily on software packages from the open-source Bioconductor project. Protocols described in this chapter cover basic steps including data alignment, peak calling, quality control and data visualization, as well as more complex methods such as the identification of differentially bound regions and functional analyses to annotate regulatory regions. The steps in the data analysis process were demonstrated on publicly available data sets and will serve as a demonstration of the computational procedures routinely used for the analysis of ChIP-seq data in R/Bioconductor, from which readers can construct their own analysis pipelines.

Briefer assessment of social network drinking: A test of the Important People Instrument-5 (IP-5).

PubMed

Hallgren, Kevin A; Barnett, Nancy P

2016-12-01

The Important People instrument (IP; Longabaugh et al., 2010) is one of the most commonly used measures of social network drinking. Although its reliability and validity are well-supported, the length of the instrument may limit its use in many settings. The present study evaluated whether a briefer, 5-person version of the IP (IP-5) adequately reproduces scores from the full IP. College freshmen (N = 1,053) reported their own past-month drinking, alcohol-related consequences, and information about drinking in their close social networks at baseline and 1 year later. From this we derived network members' drinking frequency, percentage of drinkers, and percentage of heavy drinkers, assessed for up to 10 (full IP) or 5 (IP-5) network members. We first modeled the expected concordance between full-IP scores and scores from simulated shorter IP instruments by sampling smaller subsets of network members from full IP data. Then, using quasi-experimental methods, we administered the full IP and IP-5 and compared the 2 instruments' score distributions and concurrent and year-lagged associations with participants' alcohol consumption and consequences. Most of the full-IP variance was reproduced from simulated shorter versions of the IP (ICCs ≥ 0.80). The full IP and IP-5 yielded similar score distributions, concurrent associations with drinking (r = 0.22 to 0.52), and year-lagged associations with drinking. The IP-5 retains most of the information about social network drinking from the full IP. The shorter instrument may be useful in clinical and research settings that require frequent measure administration, yielding greater temporal resolution for monitoring social network drinking. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gopishankar, N; Agarwal, Priyanka; Bisht, Raj Kishor

Purpose: To evaluate forward and inverse planning methods for acoustic neuroma cases treated in Gamma Knife Perfexion. Methods: Five patients with acoustic neuroma tumour abutting brainstem were planned twice in LGP TPS (Version 10.1) using TMR10 algorithm. First plan was entirely based on forward planning (FP) in which each shot was chosen manually. Second plan was generated using inverse planning (IP) for which planning parameters like coverage, selectivity, gradient index (GI) and beam-on time threshold were set. Number of shots in IP was automatically selected by objective function using iterative process. In both planning methods MRI MPRAGE sequence images weremore » used for tumour localization and planning. A planning dose of 12Gy at 50% isodose level was chosen. Results and Discussion: Number of shots used in FP was greater than IP and beam-on time in FP was in average 1.4 times more than IP. One advantage of FP was that the brainstem volume subjected to 6Gy dose (25% isodose) was less in FP than IP. Our results showed use of more number of shots as in FP results in GI less than or equal to 2.55 which is close to its lower limit. Dose homogeneity index (DHI) analysis of FP and IP showed average values of 0.59 and 0.67 respectively. General trend in GK for planning in acoustic neuroma cases is to use small collimator shots to avoid dose to adjacent critical structures. More number of shots and prolonged treatment time causes inconvenience to the patients. Similarly overuse of automatic shot shaping as in IP results in increased scatter dose. A compromise is required in shot selection for these cases. Conclusion: IP method could be used in acoustic neuroma cases to decrease treatment time provided the source sector openings near brainstem are shielded or adjusted appropriately to reduce brainstem dose.« less

Chromatin analyses of Zymoseptoria tritici: Methods for chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq).

PubMed

Soyer, Jessica L; Möller, Mareike; Schotanus, Klaas; Connolly, Lanelle R; Galazka, Jonathan M; Freitag, Michael; Stukenbrock, Eva H

2015-06-01

The presence or absence of specific transcription factors, chromatin remodeling machineries, chromatin modification enzymes, post-translational histone modifications and histone variants all play crucial roles in the regulation of pathogenicity genes. Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) provides an important tool to study genome-wide protein-DNA interactions to help understand gene regulation in the context of native chromatin. ChIP-seq is a convenient in vivo technique to identify, map and characterize occupancy of specific DNA fragments with proteins against which specific antibodies exist or which can be epitope-tagged in vivo. We optimized existing ChIP protocols for use in the wheat pathogen Zymoseptoria tritici and closely related sister species. Here, we provide a detailed method, underscoring which aspects of the technique are organism-specific. Library preparation for Illumina sequencing is described, as this is currently the most widely used ChIP-seq method. One approach for the analysis and visualization of representative sequence is described; improved tools for these analyses are constantly being developed. Using ChIP-seq with antibodies against H3K4me2, which is considered a mark for euchromatin or H3K9me3 and H3K27me3, which are considered marks for heterochromatin, the overall distribution of euchromatin and heterochromatin in the genome of Z. tritici can be determined. Our ChIP-seq protocol was also successfully applied to Z. tritici strains with high levels of melanization or aberrant colony morphology, and to different species of the genus (Z. ardabiliae and Z. pseudotritici), suggesting that our technique is robust. The methods described here provide a powerful framework to study new aspects of chromatin biology and gene regulation in this prominent wheat pathogen. Copyright © 2015 Elsevier Inc. All rights reserved.

Kinetic Description of the Impedance Probe

NASA Astrophysics Data System (ADS)

Oberrath, Jens; Lapke, Martin; Mussenbrock, Thomas; Brinkmann, Ralf

2011-10-01

Active plasma resonance spectroscopy is a well known diagnostic method. Many concepts of this method are theoretically investigated and realized as a diagnostic tool, one of which is the impedance probe (IP). The application of such a probe in plasmas with pressures of a few Pa raises the question whether kinetic effects have to be taken into account or not. To address this question a kinetic model is necessary. A general kinetic model for an electrostatic concept of active plasma spectroscopy was presented by R.P. Brinkmann and can be used to describe the multipole resonance probe (MRP). In principle the IP is interpretable as a special case of the MRP in lower order. Thus, we are able to describe the IP by the kinetic model of the MRP. Based on this model we derive a solution to investigate the influence of kinetic effects to the resonance behavior of the IP. Active plasma resonance spectroscopy is a well known diagnostic method. Many concepts of this method are theoretically investigated and realized as a diagnostic tool, one of which is the impedance probe (IP). The application of such a probe in plasmas with pressures of a few Pa raises the question whether kinetic effects have to be taken into account or not. To address this question a kinetic model is necessary. A general kinetic model for an electrostatic concept of active plasma spectroscopy was presented by R.P. Brinkmann and can be used to describe the multipole resonance probe (MRP). In principle the IP is interpretable as a special case of the MRP in lower order. Thus, we are able to describe the IP by the kinetic model of the MRP. Based on this model we derive a solution to investigate the influence of kinetic effects to the resonance behavior of the IP. The authors acknowledge the support by the Deutsche Forschungsgemeinschaft (DFG) via the Ruhr University Research School and the Federal Ministry of Education and Research in frame of the PluTO project.

Chromatin immunoprecipitation (ChIP) method for non-model fruit flies (Diptera: Tephritidae) and evidence of histone modifications.

PubMed

Nagalingam, Kumaran; Lorenc, Michał T; Manoli, Sahana; Cameron, Stephen L; Clarke, Anthony R; Dudley, Kevin J

2018-01-01

Interactions between DNA and proteins located in the cell nucleus play an important role in controlling physiological processes by specifying, augmenting and regulating context-specific transcription events. Chromatin immunoprecipitation (ChIP) is a widely used methodology to study DNA-protein interactions and has been successfully used in various cell types for over three decades. More recently, by combining ChIP with genomic screening technologies and Next Generation Sequencing (e.g. ChIP-seq), it has become possible to profile DNA-protein interactions (including covalent histone modifications) across entire genomes. However, the applicability of ChIP-chip and ChIP-seq has rarely been extended to non-model species because of a number of technical challenges. Here we report a method that can be used to identify genome wide covalent histone modifications in a group of non-model fruit fly species (Diptera: Tephritidae). The method was developed by testing and refining protocols that have been used in model organisms, including Drosophila melanogaster. We demonstrate that this method is suitable for a group of economically important pest fruit fly species, viz., Bactrocera dorsalis, Ceratitis capitata, Zeugodacus cucurbitae and Bactrocera tryoni. We also report an example ChIP-seq dataset for B. tryoni, providing evidence for histone modifications in the genome of a tephritid fruit fly for the first time. Since tephritids are major agricultural pests globally, this methodology will be a valuable resource to study taxa-specific evolutionary questions and to assist with pest management. It also provides a basis for researchers working with other non-model species to undertake genome wide DNA-protein interaction studies.

Polarity governed selective amplification of through plane proton shuttling in proton exchange membrane fuel cells.

PubMed

Gautam, Manu; Chattanahalli Devendrachari, Mruthyunjayachari; Thimmappa, Ravikumar; Raja Kottaichamy, Alagar; Pottachola Shafi, Shahid; Gaikwad, Pramod; Makri Nimbegondi Kotresh, Harish; Ottakam Thotiyl, Musthafa

2017-03-15

Graphene oxide (GO) anisotropically conducts protons with directional dominance of in plane ionic transport (σ IP) over the through plane (σ TP). In a typical H 2 -O 2 fuel cell, since the proton conduction occurs through the plane during its generation at the fuel electrode, it is indeed inevitable to selectively accelerate GO's σ TP for advancement towards a potential fuel cell membrane. We successfully achieved ∼7 times selective amplification of GO's σ TP by tuning the polarity of the dopant molecule in its nanoporous matrix. The coexistence of strongly non-polar and polar domains in the dopant demonstrated a synergistic effect towards σ TP with the former decreasing the number of water molecules coordinated to protons by ∼3 times, diminishing the effects of electroosmotic drag exerted on ionic movements, and the latter selectively accelerating σ TP across the catalytic layers by bridging the individual GO planes via extensive host guest H-bonding interactions. When they are decoupled, the dopant with mainly non-polar or polar features only marginally enhances the σ TP, revealing that polarity factors contribute to fuel cell relevant transport properties of GO membranes only when they coexist. Fuel cell polarization and kinetic analyses revealed that these multitask dopants increased the fuel cell performance metrics of the power and current densities by ∼3 times compared to the pure GO membranes, suggesting that the functional group factors of the dopants are of utmost importance in GO-based proton exchange membrane fuel cells.

ChIP-seq and RNA-seq methods to study circadian control of transcription in mammals

PubMed Central

Takahashi, Joseph S.; Kumar, Vivek; Nakashe, Prachi; Koike, Nobuya; Huang, Hung-Chung; Green, Carla B.; Kim, Tae-Kyung

2015-01-01

Genome-wide analyses have revolutionized our ability to study the transcriptional regulation of circadian rhythms. The advent of next-generation sequencing methods has facilitated the use of two such technologies, ChIP-seq and RNA-seq. In this chapter, we describe detailed methods and protocols for these two techniques, with emphasis on their usage in circadian rhythm experiments in the mouse liver, a major target organ of the circadian clock system. Critical factors for these methods are highlighted and issues arising with time series samples for ChIP-seq and RNA-seq are discussed. Finally detailed protocols for library preparation suitable for Illumina sequencing platforms are presented. PMID:25662462

High throughput mutagenesis for identification of residues regulating human prostacyclin (hIP) receptor expression and function.

PubMed

Bill, Anke; Rosethorne, Elizabeth M; Kent, Toby C; Fawcett, Lindsay; Burchell, Lynn; van Diepen, Michiel T; Marelli, Anthony; Batalov, Sergey; Miraglia, Loren; Orth, Anthony P; Renaud, Nicole A; Charlton, Steven J; Gosling, Martin; Gaither, L Alex; Groot-Kormelink, Paul J

2014-01-01

The human prostacyclin receptor (hIP receptor) is a seven-transmembrane G protein-coupled receptor (GPCR) that plays a critical role in vascular smooth muscle relaxation and platelet aggregation. hIP receptor dysfunction has been implicated in numerous cardiovascular abnormalities, including myocardial infarction, hypertension, thrombosis and atherosclerosis. Genomic sequencing has discovered several genetic variations in the PTGIR gene coding for hIP receptor, however, its structure-function relationship has not been sufficiently explored. Here we set out to investigate the applicability of high throughput random mutagenesis to study the structure-function relationship of hIP receptor. While chemical mutagenesis was not suitable to generate a mutagenesis library with sufficient coverage, our data demonstrate error-prone PCR (epPCR) mediated mutagenesis as a valuable method for the unbiased screening of residues regulating hIP receptor function and expression. Here we describe the generation and functional characterization of an epPCR derived mutagenesis library compromising >4000 mutants of the hIP receptor. We introduce next generation sequencing as a useful tool to validate the quality of mutagenesis libraries by providing information about the coverage, mutation rate and mutational bias. We identified 18 mutants of the hIP receptor that were expressed at the cell surface, but demonstrated impaired receptor function. A total of 38 non-synonymous mutations were identified within the coding region of the hIP receptor, mapping to 36 distinct residues, including several mutations previously reported to affect the signaling of the hIP receptor. Thus, our data demonstrates epPCR mediated random mutagenesis as a valuable and practical method to study the structure-function relationship of GPCRs.

High Throughput Mutagenesis for Identification of Residues Regulating Human Prostacyclin (hIP) Receptor Expression and Function

PubMed Central

Kent, Toby C.; Fawcett, Lindsay; Burchell, Lynn; van Diepen, Michiel T.; Marelli, Anthony; Batalov, Sergey; Miraglia, Loren; Orth, Anthony P.; Renaud, Nicole A.; Charlton, Steven J.; Gosling, Martin; Gaither, L. Alex; Groot-Kormelink, Paul J.

2014-01-01

The human prostacyclin receptor (hIP receptor) is a seven-transmembrane G protein-coupled receptor (GPCR) that plays a critical role in vascular smooth muscle relaxation and platelet aggregation. hIP receptor dysfunction has been implicated in numerous cardiovascular abnormalities, including myocardial infarction, hypertension, thrombosis and atherosclerosis. Genomic sequencing has discovered several genetic variations in the PTGIR gene coding for hIP receptor, however, its structure-function relationship has not been sufficiently explored. Here we set out to investigate the applicability of high throughput random mutagenesis to study the structure-function relationship of hIP receptor. While chemical mutagenesis was not suitable to generate a mutagenesis library with sufficient coverage, our data demonstrate error-prone PCR (epPCR) mediated mutagenesis as a valuable method for the unbiased screening of residues regulating hIP receptor function and expression. Here we describe the generation and functional characterization of an epPCR derived mutagenesis library compromising >4000 mutants of the hIP receptor. We introduce next generation sequencing as a useful tool to validate the quality of mutagenesis libraries by providing information about the coverage, mutation rate and mutational bias. We identified 18 mutants of the hIP receptor that were expressed at the cell surface, but demonstrated impaired receptor function. A total of 38 non-synonymous mutations were identified within the coding region of the hIP receptor, mapping to 36 distinct residues, including several mutations previously reported to affect the signaling of the hIP receptor. Thus, our data demonstrates epPCR mediated random mutagenesis as a valuable and practical method to study the structure-function relationship of GPCRs. PMID:24886841

Measuring the impostor phenomenon: a comparison of Clance's IP Scale and Harvey's I-P Scale.

PubMed

Holmes, S W; Kertay, L; Adamson, L B; Holland, C L; Clance, P R

1993-02-01

Many of the discrepancies reported to date in empirical investigations of the impostor phenomenon (IP) may be due in part to (a) the use of different methods for identifying individuals suffering from this syndrome (impostors), (b) the common use of a median split procedure to classify subjects and (c) the fact that subjects in many studies were drawn from impostor-prone samples. In this study, we compared the scores of independently identified impostors and nonimpostors on two instruments designed to measure the IP: Harvey's I-P Scale and Clance's IP Scale. The results suggest that Clance's scale may be the more sensitive and reliable instrument. Cutoff score suggestions for both instruments are offered.

Generation of transgene-free induced pluripotent stem cells with non-viral methods.

PubMed

Wang, Tao; Zhao, Hua-shan; Zhang, Qiu-ling; Xu, Chang-lin; Liu, Chang-bai

2013-03-01

Induced pluripotent stem (iPS) cells were originally generated from mouse fibroblasts by enforced expression of Yamanaka factors (Oct3/4, Sox2, Klf4, and c-Myc). The technique was quickly reproduced with human fibroblasts or mesenchymal stem cells. Although having been showed therapeutic potential in animal models of sickle cell anemia and Parkinson's disease, iPS cells generated by viral methods do not suit all the clinical applications. Various non-viral methods have appeared in recent years for application of iPS cells in cell transplantation therapy. These methods mainly include DNA vector-based approaches, transfection of mRNA, and transduction of reprogramming proteins. This review summarized these non-viral methods and compare the advantages, disadvantages, efficiency, and safety of these methods.

Hubble Space Telescope Ultraviolet Light Curves Reveal Interesting Properties of CC Sculptoris and RZ Leonis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Szkody, Paula; Mukadam, Anjum S.; Toloza, Odette

2017-03-01

Time-tag ultraviolet data obtained on the Hubble Space Telescope in 2013 reveal interesting variability related to the white dwarf spin in the two cataclysmic variables RZ Leo and CC Scl. RZ Leo shows a period at 220 s and its harmonic at 110 s, thus identifying it as a likely Intermediate Polar (IP). The spin signal is not visible in a short single night of ground-based data in 2016, but the shorter exposures in that data set indicate a possible partial eclipse. The much larger UV amplitude of the spin signal in the known IP CC Scl allows the spinmore » of 389 s, previously only seen at outburst, to be visible at quiescence. Spectra created from the peaks and troughs of the spin times indicate a hotter temperature of several thousand degrees during the peak phases, with multiple components contributing to the UV light.« less

ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq data.

PubMed

Wu, Song; Wang, Jianmin; Zhao, Wei; Pounds, Stanley; Cheng, Cheng

2010-06-03

ChIP-Seq is a powerful tool for identifying the interaction between genomic regulators and their bound DNAs, especially for locating transcription factor binding sites. However, high cost and high rate of false discovery of transcription factor binding sites identified from ChIP-Seq data significantly limit its application. Here we report a new algorithm, ChIP-PaM, for identifying transcription factor target regions in ChIP-Seq datasets. This algorithm makes full use of a protein-DNA binding pattern by capitalizing on three lines of evidence: 1) the tag count modelling at the peak position, 2) pattern matching of a specific tag count distribution, and 3) motif searching along the genome. A novel data-based two-step eFDR procedure is proposed to integrate the three lines of evidence to determine significantly enriched regions. Our algorithm requires no technical controls and efficiently discriminates falsely enriched regions from regions enriched by true transcription factor (TF) binding on the basis of ChIP-Seq data only. An analysis of real genomic data is presented to demonstrate our method. In a comparison with other existing methods, we found that our algorithm provides more accurate binding site discovery while maintaining comparable statistical power.

Morphological Analysis of Live Undifferentiated Cells Derived from Induced Pluripotent Stem Cells.

PubMed

Osawa, Yukihiko; Miyamoto, Tomoyuki; Ohno, Setsuyo; Ohno, Eiji

2018-01-01

Induced pluripotent stem (iPS) cells possess pluripotency and self-renewal ability. Therefore, iPS cells are expected to be useful in regenerative medicine. However, iPS cells form malignant immature teratomas after transplantation into animals, even after differentiation induction. It has been suggested that undifferentiated cells expressing Nanog that remain after differentiation induction are responsible for teratoma formation. Various methods of removing these undifferentiated cells have therefore been investigated, but few methods involve morphological approaches, which may induce less cell damage. In addition, for cells derived from iPS cells to be applied in regenerative medicine, they must be alive. However, detailed morphological analysis of live undifferentiated cells has not been performed. For the above reasons, we assessed the morphological features of live undifferentiated cells remaining after differentiation induction as a basic investigation into the clinical application of iPS cells. As a result, live undifferentiated cells remaining after differentiation induction exhibited a round or oval cytoplasm about 12 μm in diameter and a nucleus. They exhibited nucleo-cytoplasmic (N/C) ratio of about 60% and eccentric nuclei, and they possessed partially granule-like structures in the cytoplasm and prominent nucleoli. Although they were similar to iPS cells, they were smaller than live iPS cells. Furthermore, very small cells were present among undifferentiated cells after differentiation induction. These results suggest that the removal of undifferentiated cells may be possible using the morphological features of live iPS cells and undifferentiated cells after differentiation induction. In addition, this study supports safe regenerative medicine using iPS cells.

DNA adducts of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine and 4-aminobiphenyl are infrequently detected in human mammary tissue by liquid chromatography/tandem mass spectrometry

PubMed Central

Gu, Dan; Turesky, Robert J.; Tao, Yeqing; Langouët, Sophie A.; Nauwelaërs, Gwendoline C.; Yuan, Jian-Min; Yee, Douglas; Yu, Mimi C.

2012-01-01

Some epidemiological investigations have revealed that frequent consumption of well-done cooked meats and tobacco smoking are risk factors for breast cancer in women. 2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) is a heterocyclic aromatic amine that is formed in well-done cooked meat, and 4-aminobiphenyl (4-ABP) is an aromatic amine that arises in tobacco smoke and occurs as a contaminant in the atmosphere. Both compounds are rodent mammary carcinogens, and putative DNA adducts of PhIP and 4-ABP have been frequently detected, by immunohistochemistry (IHC) or 32P-post-labeling methods, in mammary tissue of USA women. Because of these findings, PhIP and 4-ABP have been implicated as causal agents of human breast cancer. However, the biomarker data are controversial: both IHC and 32P-post-labeling are non-selective screening methods and fail to provide confirmatory spectral data. Consequently, the identities of the lesions are equivocal. We employed a specific and sensitive liquid chromatography/mass spectrometry (MS) method, to screen tumor-adjacent normal mammary tissue for DNA adducts of PhIP and 4-ABP. Only 1 of 70 biopsy samples obtained from Minneapolis, Minnesota breast cancer patients contained a PhIP-DNA adduct. The level was three adducts per 109 nucleotides, a level that is 100-fold lower than the mean level of PhIP adducts reported by IHC or 32P-post-labeling methods. The occurrence of 4-ABP-DNA adducts was nil in those same breast tissues. Our findings, derived from a specific mass spectrometry method, signify that PhIP and 4-ABP are not major DNA-damaging agents in mammary tissue of USA women and raise questions about the roles of these chemicals in breast cancer. PMID:22072616

Response functions of Fuji imaging plates to monoenergetic protons in the energy range 0.6-3.2 MeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bonnet, T.; Denis-Petit, D.; Gobet, F.

2013-01-15

We have measured the responses of Fuji MS, SR, and TR imaging plates (IPs) to protons with energies ranging from 0.6 to 3.2 MeV. Monoenergetic protons were produced with the 3.5 MV AIFIRA (Applications Interdisciplinaires de Faisceaux d'Ions en Region Aquitaine) accelerator at the Centre d'Etudes Nucleaires de Bordeaux Gradignan (CENBG). The IPs were irradiated with protons backscattered off a tantalum target. We present the photo-stimulated luminescence response of the IPs together with the fading measurements for these IPs. A method is applied to allow correction of fading effects for variable proton irradiation duration. Using the IP fading corrections, amore » model of the IP response function to protons was developed. The model enables extrapolation of the IP response to protons up to proton energies of 10 MeV. Our work is finally compared to previous works conducted on Fuji TR IP response to protons.« less

Intrinsic polarization switching in BaTi O3 crystal under uniaxial electromechanical loading

NASA Astrophysics Data System (ADS)

Li, Yingwei; Wang, Jie; Li, Faxin

2016-11-01

Both 180∘ and 90∘ intrinsic polarization switching (IPS) in BaTi O3 crystal were investigated by Landau-Ginzburg-Devonshire (LGD) theory under combined electric field and stress loading. Results show that for 180∘PS , the coercive electric field (EIC 180∘) increases under tension but decreases under compression with increasing stresses. The 90∘PS was classified into two types. For type I 90∘PS , EIC I (90∘) increases under tension but decreases under compression with increasing stresses, similar to 180∘PS ; while for type II 90∘PS , an opposite variation trend is observed. (The definition of the type I and the type II 90∘PS is given in the text.) Additionally, the calculation demonstrates that under tensile stresses or under compressive stresses between -140 and 0 MPa, the electric field needed to drive both types of 90∘PS is smaller than that needed for driving 180∘PS , implying that 180∘PS is favorable to accomplish by two-step 90∘PS . As EI C refers to 180∘PS in the past investigations, these demonstrate that the EI C calculated by others may be overestimated. Moreover, the coercive stresses needed to drive 90∘ ferroelastic IPS was also calculated as a function of preloading bias electric fields.

Life History and Biology of Ips latidens (LeConte) (Coleoptera: Scolytidae)\\t

Treesearch

D.R. Miller; J.H. Borden

1985-01-01

The life history and biology of Ips latidens (LeConte) were investigated using bark-sandwich and whole-log rearing methods. In contrast with other Ips spp., some females initiated galleries under conditions of female-biased sex ratios, and sometimes 2 or more males were present in a gallery. In general, however, I....

Normalization, bias correction, and peak calling for ChIP-seq

PubMed Central

Diaz, Aaron; Park, Kiyoub; Lim, Daniel A.; Song, Jun S.

2012-01-01

Next-generation sequencing is rapidly transforming our ability to profile the transcriptional, genetic, and epigenetic states of a cell. In particular, sequencing DNA from the immunoprecipitation of protein-DNA complexes (ChIP-seq) and methylated DNA (MeDIP-seq) can reveal the locations of protein binding sites and epigenetic modifications. These approaches contain numerous biases which may significantly influence the interpretation of the resulting data. Rigorous computational methods for detecting and removing such biases are still lacking. Also, multi-sample normalization still remains an important open problem. This theoretical paper systematically characterizes the biases and properties of ChIP-seq data by comparing 62 separate publicly available datasets, using rigorous statistical models and signal processing techniques. Statistical methods for separating ChIP-seq signal from background noise, as well as correcting enrichment test statistics for sequence-dependent and sonication biases, are presented. Our method effectively separates reads into signal and background components prior to normalization, improving the signal-to-noise ratio. Moreover, most peak callers currently use a generic null model which suffers from low specificity at the sensitivity level requisite for detecting subtle, but true, ChIP enrichment. The proposed method of determining a cell type-specific null model, which accounts for cell type-specific biases, is shown to be capable of achieving a lower false discovery rate at a given significance threshold than current methods. PMID:22499706

Ionization potential and electron affinity for six common explosive compounds by DFT, MP2, and CBS-QB3

DOE PAGES

Cooper, Jason K.; Grant, Christian D.; Zhang, Jin Z.

2012-07-20

The vertical and adiabatic ionization potential (IP V and IP A) and vertical electron affinity (EA V) for six explosives (RDX, HMX, TNT, PETN, HMTD, and TATP) have been studied by ab initio computational methods. The IPV was calculated using MP2 and CBS-QB3 while the IP A was calculated with B3LYP, CAM-B3LYP, ω B97XD, B2PLYP, and MP2. RDX and TNT IP A’s were also reported using CBS -QB3. Excluding results by CBS-QB3, B3LYP and B2PLYPD provided superior and more consistent results for calculating the IP. The EA V were calculated using the same methods however B3LYP performed the worst inmore » this case with MP2 and B2PLYPD predicting values closest to those made by CBS-QB3, which was used a reference due to lacking experimental data. Basis set effects were evaluated using 6- 31+G(d,p), 6-311+G(d,p), and 6-311+(3df,2p) for both IP and EA. 6-31+G(d,p) gave satisfactory results for calculating both IP however 6-311+G(3df,2p) had improved results in calculating the EA. The four nitro containing compounds had exothermic reduction potentials while the peroxides were unfavorable. Additionally, it was seen that RDX, HMX, TATP and HMTD were unstable in their reduced forms. Results are aimed to assist detection and screening methods.« less

Fostering interprofessional learning in a rehabilitation setting: development of an interprofessional clinical learning unit.

PubMed

Vanderzalm, Jeanne; Hall, Mark D; McFarlane, Lu-Anne; Rutherford, Laurie; Patterson, Steven K

2013-01-01

The development and implementation of interprofessional (IP) clinical learning units as a method to enhance IP clinical education and improve patient care in a rehabilitation setting are described. Using a community-based participatory research approach, academia and healthcare delivery agencies formed a partnership to create an IP clinical learning unit in a rehabilitation setting. Preimplementation data from surveys and focus group data identified areas for improvement to enhance IP understanding and collaboration. A working group developed and implemented initiatives to enhance IP practice. Preimplementation, eight themes emerged from which the working group identified goals and implemented strategies to strengthen IP learning. Goals included Creation of an IP Learning Environment, Increased Awareness of IP Practice, Role Clarification, Enhanced IP Communication, and Reflection and Evaluation. Postimplementation data revealed six themes: Communication, Informal IP Learning, Role Awareness, Positive Learning Environment, Logistics, and Challenges. The development of the IP clinical learning unit was successful and rewarding, but not without its challenges. Formal IP education was necessary to enhance collaborative practice, even in a multidisciplinary environment. Commitment and support from all participants, particularly managers and administrators from the healthcare agency, were critical to success. The focus of this unit was on a stroke rehabilitation unit; however, the development and implementation principles identified may be applicable to any team-based clinical setting. © 2013 Association of Rehabilitation Nurses.

Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq.

PubMed

Guertin, Michael J; Cullen, Amy E; Markowetz, Florian; Holding, Andrew N

2018-04-17

A key challenge in quantitative ChIP combined with high-throughput sequencing (ChIP-seq) is the normalization of data in the presence of genome-wide changes in occupancy. Analysis-based normalization methods were developed for transcriptomic data and these are dependent on the underlying assumption that total transcription does not change between conditions. For genome-wide changes in transcription factor (TF) binding, these assumptions do not hold true. The challenges in normalization are confounded by experimental variability during sample preparation, processing and recovery. We present a novel normalization strategy utilizing an internal standard of unchanged peaks for reference. Our method can be readily applied to monitor genome-wide changes by ChIP-seq that are otherwise lost or misrepresented through analytical normalization. We compare our approach to normalization by total read depth and two alternative methods that utilize external experimental controls to study TF binding. We successfully resolve the key challenges in quantitative ChIP-seq analysis and demonstrate its application by monitoring the loss of Estrogen Receptor-alpha (ER) binding upon fulvestrant treatment, ER binding in response to estrodiol, ER mediated change in H4K12 acetylation and profiling ER binding in patient-derived xenographs. This is supported by an adaptable pipeline to normalize and quantify differential TF binding genome-wide and generate metrics for differential binding at individual sites.

BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates.

PubMed

Goren, Emily; Liu, Peng; Wang, Chao; Wang, Chong

2018-04-19

ChIP-seq experiments that are aimed at detecting DNA-protein interactions require biological replication to draw inferential conclusions, however there is no current consensus on how to analyze ChIP-seq data with biological replicates. Very few methodologies exist for the joint analysis of replicated ChIP-seq data, with approaches ranging from combining the results of analyzing replicates individually to joint modeling of all replicates. Combining the results of individual replicates analyzed separately can lead to reduced peak classification performance compared to joint modeling. Currently available methods for joint analysis may fail to control the false discovery rate at the nominal level. We propose BinQuasi, a peak caller for replicated ChIP-seq data, that jointly models biological replicates using a generalized linear model framework and employs a one-sided quasi-likelihood ratio test to detect peaks. When applied to simulated data and real datasets, BinQuasi performs favorably compared to existing methods, including better control of false discovery rate than existing joint modeling approaches. BinQuasi offers a flexible approach to joint modeling of replicated ChIP-seq data which is preferable to combining the results of replicates analyzed individually. Source code is freely available for download at https://cran.r-project.org/package=BinQuasi, implemented in R. pliu@iastate.edu or egoren@iastate.edu. Supplementary material is available at Bioinformatics online.

Epidermal wound repair is regulated by the planar cell polarity signaling pathway.

PubMed

Caddy, Jacinta; Wilanowski, Tomasz; Darido, Charbel; Dworkin, Sebastian; Ting, Stephen B; Zhao, Quan; Rank, Gerhard; Auden, Alana; Srivastava, Seema; Papenfuss, Tony A; Murdoch, Jennifer N; Humbert, Patrick O; Parekh, Vishwas; Boulos, Nidal; Weber, Thomas; Zuo, Jian; Cunningham, John M; Jane, Stephen M

2010-07-20

The mammalian PCP pathway regulates diverse developmental processes requiring coordinated cellular movement, including neural tube closure and cochlear stereociliary orientation. Here, we show that epidermal wound repair is regulated by PCP signaling. Mice carrying mutant alleles of PCP genes Vangl2, Celsr1, PTK7, and Scrb1, and the transcription factor Grhl3, interact genetically, exhibiting failed wound healing, neural tube defects, and disordered cochlear polarity. Using phylogenetic analysis, ChIP, and gene expression in Grhl3(-)(/-) mice, we identified RhoGEF19, a homolog of a RhoA activator involved in PCP signaling in Xenopus, as a direct target of GRHL3. Knockdown of Grhl3 or RhoGEF19 in keratinocytes induced defects in actin polymerization, cellular polarity, and wound healing, and re-expression of RhoGEF19 rescued these defects in Grhl3-kd cells. These results define a role for Grhl3 in PCP signaling and broadly implicate this pathway in epidermal repair. (c) 2010 Elsevier Inc. All rights reserved.

Epidermal wound repair is regulated by the planar cell polarity signaling pathway

PubMed Central

Caddy, Jacinta; Wilanowski, Tomasz; Darido, Charbel; Dworkin, Sebastian; Ting, Stephen B.; Zhao, Quan; Rank, Gerhard; Auden, Alana; Srivastava, Seema; Papenfuss, Tony A.; Murdoch, Jennifer N.; Humbert, Patrick O.; Boulos, Nidal; Weber, Thomas; Zuo, Jian; Cunningham, John M.; Jane, Stephen M.

2010-01-01

SUMMARY The mammalian PCP pathway regulates diverse developmental processes requiring coordinated cellular movement, including neural tube closure and cochlear stereociliary orientation. Here, we show that epidermal wound repair is regulated by PCP signaling. Mice carrying mutant alleles of PCP genes Vangl2, Celsr1, PTK7, and Scrb1, and the transcription factor Grhl3, interact genetically, exhibiting failed wound healing, neural tube defects and disordered cochlear polarity. Using phylogenetic analysis, ChIP, and gene expression in Grhl3−/− mice, we identified RhoGEF19, a homologue of a RhoA activator involved in PCP signaling in Xenopus, as a direct target of GRHL3. Knockdown of Grhl3 or RhoGEF19 in keratinocytes induced defects in actin polymerisation, cellular polarity and wound healing, and re-expression of RhoGEF19 rescued these defects in Grhl3-kd cells. These results define a role for Grhl3 in PCP signaling, and broadly implicate this pathway in epidermal repair. PMID:20643356

Call progress time measurement in IP telephony

NASA Astrophysics Data System (ADS)

Khasnabish, Bhumip

1999-11-01

Usually a voice call is established through multiple stages in IP telephony. In the first stage, a phone number is dialed to reach a near-end or call-originating IP-telephony gateway. The next stages involve user identification through delivering an m-digit user-id to the authentication and/or billing server, and then user authentication by using an n- digit PIN. After that, the caller is allowed (last stage dial tone is provided) to dial a destination phone number provided that authentication is successful. In this paper, we present a very flexible method for measuring call progress time in IP telephony. The proposed technique can be used to measure the system response time at every stage. It is flexible, so that it can be easily modified to include new `tone' or a set of tones, or `voice begin' can be used in every stage to detect the system's response. The proposed method has been implemented using scripts written in Hammer visual basic language for testing with a few commercially available IP telephony gateways.

Combining multiple ChIP-seq peak detection systems using combinatorial fusion.

PubMed

Schweikert, Christina; Brown, Stuart; Tang, Zuojian; Smith, Phillip R; Hsu, D Frank

2012-01-01

Due to the recent rapid development in ChIP-seq technologies, which uses high-throughput next-generation DNA sequencing to identify the targets of Chromatin Immunoprecipitation, there is an increasing amount of sequencing data being generated that provides us with greater opportunity to analyze genome-wide protein-DNA interactions. In particular, we are interested in evaluating and enhancing computational and statistical techniques for locating protein binding sites. Many peak detection systems have been developed; in this study, we utilize the following six: CisGenome, MACS, PeakSeq, QuEST, SISSRs, and TRLocator. We define two methods to merge and rescore the regions of two peak detection systems and analyze the performance based on average precision and coverage of transcription start sites. The results indicate that ChIP-seq peak detection can be improved by fusion using score or rank combination. Our method of combination and fusion analysis would provide a means for generic assessment of available technologies and systems and assist researchers in choosing an appropriate system (or fusion method) for analyzing ChIP-seq data. This analysis offers an alternate approach for increasing true positive rates, while decreasing false positive rates and hence improving the ChIP-seq peak identification process.

Biomonitoring the Cooked Meat Carcinogen 2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) in Hair: Impact of Exposure, Pigmentation and Cytochrome P450 1A2 Phenotype

PubMed Central

Turesky, Robert J.; Liu, Lin; Gu, Dan; Yonemori, Kim M.; White, Kami K.; Wilkens, Lynne R.; Marchand, Loic Le

2013-01-01

Background Hair is a promising tissue to assess exposure to 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), a carcinogen formed in cooked meats. However, an understanding of how dietary exposure to PhIP, cytochrome P450 1A2 activity - a key enzyme involved in PhIP metabolism, and hair pigmentation affect the level of PhIP accrued in hair is required in order to determine the reliability of the PhIP hair level as a biomarker of exposure to this carcinogen. Methods We examined the impact of PhIP exposure, cytochrome P450 1A2 activity, and hair pigmentation on the levels of PhIP accumulated in the hair of volunteers on a 4-week semi-controlled diet of cooked meat containing known quantities of PhIP. Results The amount of PhIP in hair increased, on average, 15-fold in light- and dark-haired individuals during consumption of cooked meat. PhIP levels in hair were correlated to PhIP intake (ρ = 0.53; p < 0.001), and the relationship was strengthened when PhIP levels were normalized for the melanin content of hair (ρ = 0.71; p < 0.001). However, PhIP accrual in hair was not correlated to cytochrome P450 1A2 activity, as assessed by the caffeine test, or to the levels of unmetabolized PhIP in urine, or to the metabolic ratio of the major urinary metabolite N2-(ß-1-glucosiduronyl-2-(hydroxyamino)-1-methyl-6-phenylimidazo[4,5-b]pyridine to unmetabolized PhIP. Conclusions The employment of the PhIP hair biomarker should take hair pigmentation into account for accurate exposure assessment. Impact PhIP hair levels can serve as a biomarker in epidemiological studies investigating the association of HAAs, cooked meat and cancer risk. PMID:23329727

Astronomy in Denver: Probing Interstellar Circular Polarization with Polvis, a Full Stokes Single Shot Polarimeter

NASA Astrophysics Data System (ADS)

Wolfe, Tristan; Stencel, Robert E.

2018-06-01

Measurements of optical circular polarization (Stokes V) introduced by dust grains in the ISM are important for two main reasons. First of all, the polarization itself contains information about the metallic versus dielectric composition of the dust grains themselves (H. C. van de Hulst 1957, textbook). Additionally, circular polarization can help constrain the interstellar component of the polarization of any source that may have intrinsic polarization, which needs to be calibrated for astrophysical study. Though interstellar circular polarization has been observed (P. G. Martin 1972, MNRAS 159), most broadband measurements of ISM polarization include linear polarization only (Stokes Q and U), due to the relatively low circular polarization signal and the added instrumentation complexity of including V-measurement capability. Prior circular polarization measurements have also received very little follow-up in the past several decades, even as polarimeters have become more accurate due to advances in technology. The University of Denver is pursuing these studies with POLVIS, a prototype polarimeter that utilizes a stress-engineered optic ("SEO", A. K. Spilman and T. G. Brown 2007, Applied Optics IP 46) to produce polarization-dependent PSFs (A. M. Beckley and T. G. Brown 2010, Proc SPIE 7570). These PSFs are analyzed to provide simultaneous Stokes I, Q, U, and V measurements, in a single beam and single image, along the line-of-sight to point source-like objects. Polvis is the first polarimeter to apply these optics and measurement techniques for astronomical observations. We present the first results of this instrument in B, V, and R wavebands, providing a fresh look at full Stokes interstellar polarization. Importantly, this set of efforts will constrain the ISM contribution to the polarization with respect to intrinsic stellar components. The authors are grateful to the estate of William Herschel Womble for the support of astronomy at the University of Denver, and for funding provided by the Mt. Cuba Astronomical Foundation.

[Predominant polarity in type-I bipolar patients: Study in an isolated population with a high prevalence of mood disorders].

PubMed

Obando, Antonio Carlos Toro; García, Ángela María Agudelo; Rodríguez, María Aurora Gallo; Palacio, Tomás Felipe Restrepo; Ontoso, Miguel Soto; Tamayo, Alejandra; Jaramillo, Carlos Alberto López

2012-12-01

Recent studies have shown that the predominant description of polarity has effects upon early detection and the timely beginning of treatment in patients with bipolar affective disorder (BAD). Cross sectional cut and descriptive study in 101 BAD patients coming from a genetically isolated population from the Colombian Region of Antioquia. The study covered a population of 101 patients with type-I BAD diagnosis, out of which 57,4% met the criteria for maniac polarity (MP), 10,1% exhibited depressive polarity (DP) and 25,7% were classified with Indefinite Polarity (IP). In comparison, MP patients have a lower education level and less starting age, including a greater number of single people. The MP group showed the greatest prevalence of suicide and greater use of cannabinoids and cocaine. Within the DP group there was a strong tendency to cigarette and alcohol consumption. With respect to pharmaceutical drugs consumed by the study patients during their lives, antipsychotics were the most widely used group, followed by lithium and anti-convulsivants. There is high percentage of MP patients who have used antidepressants during their lives. The polarity of the first episode of the disease seems to be a valid predictive parameter concerning the polarity of subsequent episodes; therefore, it works indirectly as a valid predictor of the disease's course. Copyright © 2012 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

Differentiation of Odontoblast-Like Cells From Mouse Induced Pluripotent Stem Cells by Pax9 and Bmp4 Transfection.

PubMed

Seki, Daisuke; Takeshita, Nobuo; Oyanagi, Toshihito; Sasaki, Shutaro; Takano, Ikuko; Hasegawa, Masakazu; Takano-Yamamoto, Teruko

2015-09-01

The field of tooth regeneration has progressed in recent years, and human tooth regeneration could become viable in the future. Because induced pluripotent stem (iPS) cells can differentiate into odontogenic cells given appropriate conditions, iPS cells are a potential cell source for tooth regeneration. However, a definitive method to induce iPS cell-derived odontogenic cells has not been established. We describe a novel method of odontoblast differentiation from iPS cells using gene transfection. We generated mouse iPS cell-derived neural crest-like cells (iNCLCs), which exhibited neural crest markers. Next, we differentiated iNCLCs into odontoblast-like cells by transfection of Pax9 and Bmp4 expression plasmids. Exogenous Pax9 upregulated expression of Msx1 and dentin matrix protein 1 (Dmp1) in iNCLCs but not bone morphogenetic protein 4 (Bmp4) or dentin sialophosphoprotein (Dspp). Exogenous Bmp4 upregulated expression of Msx1, Dmp1, and Dspp in iNCLCs, but not Pax9. Moreover, cotransfection of Pax9 and Bmp4 plasmids in iNCLCs revealed a higher expression of Pax9 than when Pax9 plasmid was used alone. In contrast, exogenous Pax9 downregulated Bmp4 overexpression. Cotransfection of Pax9 and Bmp4 synergistically upregulated Dmp1 expression; however, Pax9 overexpression downregulated exogenous Bmp4-induced Dspp expression. Together, these findings suggest that an interaction between exogenous Pax9- and Bmp4-induced signaling modulated Dmp1 and Dspp expression. In conclusion, transfection of Pax9 and Bmp4 expression plasmids in iNCLCs induced gene expression associated with odontoblast differentiation, suggesting that iNCLCs differentiated into odontoblast-like cells. The iPS cell-derived odontoblast-like cells could be a useful cell source for tooth regeneration. It has been reported that induced pluripotent stem (iPS) cells differentiate into odontogenic cells by administration of recombinant growth factors and coculture with odontogenic cells. Therefore, they can be potential cell sources for tooth regeneration. However, these previous methods still have problems, such as usage of other cell types, heterogeneity of differentiated cells, and tumorigenicity. In the present study, a novel method to differentiate iPS cells into odontoblast-like cells without tumorigenicity using gene transfection was established. It is an important advance in the establishment of efficient methods to generate homogeneous functional odontogenic cells derived from iPS cells. ©AlphaMed Press.

Nonlinear Magnetic Dynamics and The Switching Phase Diagrams in Spintronic Devices

NASA Astrophysics Data System (ADS)

Yan, Shu

Spin-transfer torque induced magnetic switching, by which the spin-polarized current transfers its magnetic moment to the ferromagnetic layer and changes its magnetization, holds great promise towards faster and smaller magnetic bits in data-storage applications due to the lower power consumption and better scalability. We propose an analytic approach which can be used to calculate the switching phase diagram of a nanomagnetic system in the presence of both magnetic field and spin-transfer torque in an exact fashion. This method is applied to the study of switching conditions for the uniaxial, single domain magnetic layers in different spin-transfer devices. In a spin valve with spin polarization collinear with the easy axis, we get a modified Stoner-Wohlfarth astroid which represents many of the features that have been found in experiment. It also shows a self-crossing boundary and demonstrates a region with three stable equilibria. We demonstrate that the region of stable equilibria with energy near the maximum can be reached only through a narrow bottleneck in the field space, which sets a stringent requirement for magnetic field alignment in the experiments. Switching diagrams are then calculated for the setups with magnetic field not perfectly aligned with the easy axis. In a ferromagnet-heavy-metal bilayer device with strong spin Hall effect, the in plane current becomes spin-polarized and transfers its magnetic moment to the ferromagnetic layer by diffusion. The three-dimensional asymmetric phase diagram is calculated. In the case that the external field is confined in the vertical plane defined by the direction of the current and the easy axis, the spin-transfer torque shifts the conventional in-plane (IP) equilibria within the same plane, and also creates two out-of-plane (OOP) equilibria, one of which can be stable. The threshold switching currents for IP switching and OOP switching are discussed. We also address the magnetic switching processes. Damping switching and precessional switching are two different switching types that are typically considered in recent studies. In the damping mode the switching is slow and heavily depends on the initial deviation, while in the precessional mode the accurate manipulation of the field or current pulse is required. We propose a switching scenario for a fast and reliable switching by taking advantage of the out-of-plane stable equilibrium in the SHE induced magnetic switching. The magnetization is first driven by a pulse of field and current towards the OOP equilibrium without precession. Since it is in the lower half of the unit sphere, no backwards pulse is required for a complete switching. This indicates a potentially feasible method of reliable ultra-fast magnetic control.

Achieving quality of service in IP networks

NASA Astrophysics Data System (ADS)

Hays, Tim

2001-07-01

The Internet Protocol (IP) has served global networks well, providing a standardized method to transmit data among many disparate systems. But IP is designed for simplicity, and only enables a `best effort' service that can be subject to delays and loss of data. For data networks, this is an acceptable trade-off. In the emerging world of convergence, driven by new applications such as video streaming and IP telephony, minimizing latency and packet loss as well as jitter can be critical. Simply increasing the size of the IP network `pipe' to meet those demands is not always sufficient. In this environment, vendors and standards bodies are endeavoring to create technologies and techniques to enable IP to improve the quality of service it can provide, while retaining the characteristics that has enabled it to become the dominant networking protocol.

The Long Wavelength Array (LWA): A Large HF/VHF Array for Solar Physics, Ionospheric Science, and Solar Radar

DTIC Science & Technology

2010-09-01

adds an extra dimension to both IPS and other observations. The polarization of the CME synchrotron emission observed by [3] will be of great...base funding. 8. REFERENCES 1. Kassim et al., The 74 MHz System on the Very Large Array, The Astrophysical Journal Supplement Series, Vol. 172...The Long Wavelength Array (LWA): A Large HF/VHF Array for Solar Physics, Ionospheric Science, and Solar Radar Namir E. Kassim Naval Research

3D Inversion of Induced Polarization Data From Borehole Measurements to Map Subsurface Contaminations of Tetrachloroethylene and Trichloroethylene.

NASA Astrophysics Data System (ADS)

Briggs, V. A.; Sogade, J.; Minsley, B.; Lambert, M.; Coles, D.; Repert, P.; Morgan, F.; Rossabi, J.; Riha, B.

2003-12-01

The purpose of this study is to image contaminant plumes of tetrachloroethylene (PCE) and Trichloroethylene (TCE) in a subsurface environment. PCE and TCE have been used in the metals fabrication industry since the start of the second word war and subsequently millions of tons of these chemicals have been released in to the environment. Once in the water supply these contaminants are difficult to remove and can be toxic at the part per billion level. Remediation at the source of many of these contaminated sites, in the form of vapour extraction, can effectively remove alot of the chemicals but without techniques to delineate the size and shape of the contaminated zone, or to monitor the effectiveness of the remediation effort, it is difficult to quantify the remediation success. Using complex resistivity methods it is possible to determine the spatial extent and concentration of these chemicals due to their effect on the pore space chemistry. Even at parts per billion the contaminantas can significantly alter the IP signature enabling detection. Data were collected from a site in South Carolina where these chemcals are known to have been released in large quantities from the 1950's through to the 1980's. Induced Polarization data were measured in a multi-borehole environment to ensure good data coverage. Data is inverted using a 3D finite difference bi-conjugate gradient method and correlated to ground truth boreholes within the region of interest.

The synergistic effect of micro/nano-structured and Cu2+-doped hydroxyapatite particles to promote osteoblast viability and antibacterial activity.

PubMed

Shi, Feng; Liu, Yumei; Zhi, Wei; Xiao, Dongqin; Li, Hongyu; Duan, Ke; Qu, Shuxin; Weng, Jie

2017-06-06

Microstructure and chemical constitution are important factors affecting the biological activity of biomaterials. This study aimed to fabricate hydroxyapatite (HAp) particles with both micro/nanohybrid structure and Cu 2+ doping to promote osteogenic differentiation and antibacterial property. In the presence of inositol hexakisphosphate (IP6), micro/nano-structured and Cu 2+ -doped HAp (HAp-IP6-Cu) microspheres were successfully fabricated via hydrothermal method. Morphological observation showed that HAp-IP6-Cu microspheres with a diameter of 3.1-4.1 μm were chrysanthemum-like and composed of nano-flakes approximately 50 nm in thickness. Compared with the HAp micro-rods or IP6 modified HAp (HAp-IP6) microspheres, HAp-IP6-Cu microspheres had a larger specific surface area, better hydrophilicity and stronger ability to adsorb bovine serum albumin. To evaluate the synergistic effects of micro/nanohybrid structure and Cu 2+ on cell behavior, rat calvarial osteoblasts (RCOs) were cultured on HAp-IP6-Cu, HAp-IP6 and HAp layers as well as their extracts, respectively. Results demonstrated that HAp-IP6-Cu layer promoted the adhesion, proliferation and osteogenic differentiation of RCOs. The cells grew on HAp-IP6-Cu and HAp-IP6 layers exhibited greater spreading than those on HAp layer. In addition, quantitative test by the agar disk diffusion technique found that HAp-IP6-Cu microspheres were effectively against S taphylococcus aureus and E scherichia coli. These results demonstrated that HAp-IP6-Cu microspheres may be a potential candidate as a bioactive and anti-infective biomaterial for bone regeneration.

14 CFR Appendix A to Part 420 - Method for Defining a Flight Corridor

Code of Federal Regulations, 2010 CFR

2010-01-01

... impact range factor [IP(Hap)] and a dispersion factor [DISP(Hap)] as shown below: (A) An applicant shall... maximum apogee altitude (Hap) multiplied by the impact range factor as shown below: ER19OC00.048 where: IP(Hap) = 0.4 for an apogee less than 100 km; and IP(Hap) = 0.7 for an apogee 100 km or greater. (B) An...

14 CFR Appendix A to Part 420 - Method for Defining a Flight Corridor

Code of Federal Regulations, 2011 CFR

2011-01-01

... impact range factor [IP(Hap)] and a dispersion factor [DISP(Hap)] as shown below: (A) An applicant shall... maximum apogee altitude (Hap) multiplied by the impact range factor as shown below: ER19OC00.048 where: IP(Hap) = 0.4 for an apogee less than 100 km; and IP(Hap) = 0.7 for an apogee 100 km or greater. (B) An...

Paradoxical ventilator associated pneumonia incidences among selective digestive decontamination studies versus other studies of mechanically ventilated patients: benchmarking the evidence base

PubMed Central

2011-01-01

Introduction Selective digestive decontamination (SDD) appears to have a more compelling evidence base than non-antimicrobial methods for the prevention of ventilator associated pneumonia (VAP). However, the striking variability in ventilator associated pneumonia-incidence proportion (VAP-IP) among the SDD studies remains unexplained and a postulated contextual effect remains untested for. Methods Nine reviews were used to source 45 observational (benchmark) groups and 137 component (control and intervention) groups of studies of SDD and studies of three non-antimicrobial methods of VAP prevention. The logit VAP-IP data were summarized by meta-analysis using random effects methods and the associated heterogeneity (tau2) was measured. As group level predictors of logit VAP-IP, the mode of VAP diagnosis, proportion of trauma admissions, the proportion receiving prolonged ventilation and the intervention method under study were examined in meta-regression models containing the benchmark groups together with either the control (models 1 to 3) or intervention (models 4 to 6) groups of the prevention studies. Results The VAP-IP benchmark derived here is 22.1% (95% confidence interval; 95% CI; 19.2 to 25.5; tau2 0.34) whereas the mean VAP-IP of control groups from studies of SDD and of non-antimicrobial methods, is 35.7 (29.7 to 41.8; tau2 0.63) versus 20.4 (17.2 to 24.0; tau2 0.41), respectively (P < 0.001). The disparity between the benchmark groups and the control groups of the SDD studies, which was most apparent for the highest quality studies, could not be explained in the meta-regression models after adjusting for various group level factors. The mean VAP-IP (95% CI) of intervention groups is 16.0 (12.6 to 20.3; tau2 0.59) and 17.1 (14.2 to 20.3; tau2 0.35) for SDD studies versus studies of non-antimicrobial methods, respectively. Conclusions The VAP-IP among the intervention groups within the SDD evidence base is less variable and more similar to the benchmark than among the control groups. These paradoxical observations cannot readily be explained. The interpretation of the SDD evidence base cannot proceed without further consideration of this contextual effect. PMID:21214897

Cooking methods and the formation of PhIP (2-Amino, 1-methyl, 6-phenylimidazo[4,5-b] pyridine) in the crust of the habitually consumed meat in Argentina.

PubMed

Reartes, Gabriela Angelina; Di Paola Naranjo, Romina Daniela; Eynard, Aldo Renato; Muñoz, Sonia Edith

2016-06-01

Content of carcinogenic molecules like, 2-Amino, 1-methyl, 6-phenylimidazo[4,5-b] pyridine in meals is one of the main mutagenic substances formed during meat cooking, and it can be used as a dietary exposure marker. Our objective was to estimate the amount of PhIP consumed from habitual Argentinean diet, rich in red meats, comparing different cooking procedures and meat type. Samples (n = 240) of lean and fatty beef, chicken, pork, and fish were cooked using different methods: griddle, grill, sauté pan, and oven. Samples were: Overcooked, or cooked with a microbiologically suitable or "healthy technique" (HT). The PhIP was determined by HPLC-MS. Meats cooked using HT formed little crust amounts and PhIP was below the detection levels. In overcooked meats, large amounts of crust were formed in lean meats, fatty beef, fatty chicken and baked pork. PhIP was measured in lean meats sauted or cooked on a griddle, a method reaching temperatures until 250 °C.It was estimated that Argentine people eats about 12,268.0 ng/day of PhIP being these values above those tolerated limits for total dietary heterocyclic amines in some developed countries. Hence, cooking small meat portions, at medium temperature, avoiding prolonged cooking and preferring baked lean meats could be recommended as a healthier habit. Copyright © 2016. Published by Elsevier Ltd.

High concentrations of the carcinogen 2-amino-1-methyl-6-phenylimidazo- [4,5-b]pyridine (PhIP) occur in chicken but are dependent on the cooking method.

PubMed

Sinha, R; Rothman, N; Brown, E D; Salmon, C P; Knize, M G; Swanson, C A; Rossi, S C; Mark, S D; Levander, O A; Felton, J S

1995-10-15

Heterocyclic aromatic amines (HAAs) are mutagenic and carcinogenic compounds found in meats cooked at high temperatures. Although chicken is consumed in large quantities in the United States, there is little information on its HAA content. The objective of this study was to measure the five predominant HAAs (IQ, MeIQ, MeIQx, DiMeIQx, and PhIP) in chicken cooked by various methods to different degrees of doneness. Chicken breasts were panfried, oven-broiled, or grilled/barbecued. Whole chickens were roasted or stewed. Skinless, boneless chicken breasts were cooked to three degrees of doneness: just until done, well done, or very well done. High levels of PhIP (ranging from 12 to 480 ng/g cooked meat) were found in chicken breasts when panfried, oven-broiled, and grilled/barbecued but not in while roasted or stewed chicken. PhIP concentration increased in skinless, boneless chicken breast with longer cooking time, higher internal temperature, and greater degree of surface browning. PhIP concentration was also high in chicken breasts cooked with skin and bones. MeIQx and DiMeIQx levels increased with the degree of doneness, whereas IQ and MeIQ were not detectable in any of these chicken samples. Certain cooking methods produce PhIP, a known colon and breast carcinogen in rodents and possibly a human carcinogen, at substantially higher levels in chicken than has been reported previously in red meat.

Effect of xanthotoxin (8-methoxypsoralen) on the anticonvulsant activity of classical antiepileptic drugs against maximal electroshock-induced seizures in mice.

PubMed

Zagaja, Miroslaw; Pyrka, Daniel; Skalicka-Wozniak, Krystyna; Glowniak, Kazimierz; Florek-Luszczki, Magdalena; Glensk, Michał; Luszczki, Jarogniew J

2015-09-01

The effects of xanthotoxin (8-methoxypsoralen) on the anticonvulsant activity of four classical antiepileptic drugs (carbamazepine, phenobarbital, phenytoin and valproate) were studied in the mouse maximal electroshock seizure model. Tonic hind limb extension (seizure activity) was evoked in adult male albino Swiss mice by a current (25 mA, 500 V, 50 Hz, 0.2 s stimulus duration) delivered via auricular electrodes. Total brain concentrations of antiepileptic drugs were measured by fluorescence polarization immunoassay to ascertain any pharmacokinetic contribution to the observed anticonvulsant effects. Results indicate that xanthotoxin (50 and 100 mg/kg, i.p.) significantly potentiated the anticonvulsant activity of carbamazepine against maximal electroshock-induced seizures (P<0.05 and P<0.001, respectively). Similarly, xanthotoxin (100 mg/kg, i.p.) markedly enhanced the anticonvulsant action of valproate in the maximal electroshock seizure test (P<0.001). In contrast, xanthotoxin (100 mg/kg, i.p.) did not affect the protective action of phenobarbital and phenytoin against maximal electroshock-induced seizures in mice. Moreover, xanthotoxin (100 mg/kg, i.p.) significantly increased total brain concentrations of carbamazepine (P<0.001) and valproate (P<0.05), but not those of phenytoin and phenobarbital, indicating pharmacokinetic nature of interactions between drugs. In conclusion, the combinations of xanthotoxin with carbamazepine and valproate, despite their beneficial effects in terms of seizure suppression in mice, were probably due to a pharmacokinetic increase in total brain concentrations of these antiepileptic drugs in experimental animals. Copyright © 2015. Published by Elsevier B.V.

A comparative study of ChIP-seq sequencing library preparation methods.

PubMed

Sundaram, Arvind Y M; Hughes, Timothy; Biondi, Shea; Bolduc, Nathalie; Bowman, Sarah K; Camilli, Andrew; Chew, Yap C; Couture, Catherine; Farmer, Andrew; Jerome, John P; Lazinski, David W; McUsic, Andrew; Peng, Xu; Shazand, Kamran; Xu, Feng; Lyle, Robert; Gilfillan, Gregor D

2016-10-21

ChIP-seq is the primary technique used to investigate genome-wide protein-DNA interactions. As part of this procedure, immunoprecipitated DNA must undergo "library preparation" to enable subsequent high-throughput sequencing. To facilitate the analysis of biopsy samples and rare cell populations, there has been a recent proliferation of methods allowing sequencing library preparation from low-input DNA amounts. However, little information exists on the relative merits, performance, comparability and biases inherent to these procedures. Notably, recently developed single-cell ChIP procedures employing microfluidics must also employ library preparation reagents to allow downstream sequencing. In this study, seven methods designed for low-input DNA/ChIP-seq sample preparation (Accel-NGS® 2S, Bowman-method, HTML-PCR, SeqPlex™, DNA SMART™, TELP and ThruPLEX®) were performed on five replicates of 1 ng and 0.1 ng input H3K4me3 ChIP material, and compared to a "gold standard" reference PCR-free dataset. The performance of each method was examined for the prevalence of unmappable reads, amplification-derived duplicate reads, reproducibility, and for the sensitivity and specificity of peak calling. We identified consistent high performance in a subset of the tested reagents, which should aid researchers in choosing the most appropriate reagents for their studies. Furthermore, we expect this work to drive future advances by identifying and encouraging use of the most promising methods and reagents. The results may also aid judgements on how comparable are existing datasets that have been prepared with different sample library preparation reagents.

Multi-frequency electrical and electromagnetic measurements for imaging water flows: application to catchment and landslide hydrology.

NASA Astrophysics Data System (ADS)

Lajaunie, Myriam; Sailhac, Pascal; Malet, Jean-Philippe; Larnier, Hugo; Gance, Julien; Gautier, Stéphanie; Pierret, Marie-Claire

2017-04-01

Imaging water flows in mountainous watersheds is a difficult task, not only because of the topography and the dimensions of the existing structures, but also because the soils and rocks consist of unsaturated porous and heterogeneous fractured media, leading to multi-scale water-flow properties. In addition, these properties can change in time, in relation to temperature, rainfall and biological forcings. Electrical properties are relevant proxies of the subsurface hydrological properties. In order to image water flows, we consider measurements of the complex electrical conductivity (conduction and polarization/chargeability effects) which translate into a frequency dependance of the conductivity at the sample scale. We further discuss the combined use of electromagnetic (CS-AMT) and electric (DC and IP) measurements at the slope scale. The solving of processing, calibration and modelling issues allows the estimation of hydrological properties (i.e. permeability, soil humidity) giving master constraints for slope-scale hydrological modelling. We illustrate the application of these methods for the identification of the hydrological role of weathered structures of granitic catchments (e.g. Strengbach, Vosges mountains, ca. 80 km from Strasbourg, North East France) where new AMT processing has been developed in the AMT dead band to improve DC electrical imaging. We also illustrate the use of these methods to document the seasonal regime of the groundwater of the Lodève landslide (unstable slope located at Pégairolles, foot of the Cévennes mountain, ca. 80 km from Montpellier, South of France) where a new detailed time-lapse DC and IP setup (surface and borehole) is being tested. The works are supported by the research projects HYDROCRISZTO and HYDROSLIDE, and the large infrastructure project CRITEX.

Development of monitoring method of spatial neutron distribution in neutrons-gamma rays mixed field using imaging plate for NCT--depression of the field.

PubMed

Tanaka, Kenichi; Endo, Satoru; Hoshi, Masaharu; Takada, Jun

2011-12-01

The degree of depression in the neutron field caused by neutron absorption in the materials of an imaging plate (IP) was investigated using MCNP-4C. Consequently, the IP doped with Gd, which reproduced the distribution of (157)Gd(n,γ)(158)Gd reaction rate in the previous study, depresses the relative distribution by about 50%. The depression for the IP in which Gd is replaced with similar amount of B atoms was estimated to be about 10%. The signal intensity for this IP is estimated to be at a similar level with that for Gd-doped IP. Copyright © 2011 Elsevier Ltd. All rights reserved.

Improved Discovery of Molecular Interactions in Genome-Scale Data with Adaptive Model-Based Normalization

PubMed Central

Brown, Patrick O.

2013-01-01

Background High throughput molecular-interaction studies using immunoprecipitations (IP) or affinity purifications are powerful and widely used in biology research. One of many important applications of this method is to identify the set of RNAs that interact with a particular RNA-binding protein (RBP). Here, the unique statistical challenge presented is to delineate a specific set of RNAs that are enriched in one sample relative to another, typically a specific IP compared to a non-specific control to model background. The choice of normalization procedure critically impacts the number of RNAs that will be identified as interacting with an RBP at a given significance threshold – yet existing normalization methods make assumptions that are often fundamentally inaccurate when applied to IP enrichment data. Methods In this paper, we present a new normalization methodology that is specifically designed for identifying enriched RNA or DNA sequences in an IP. The normalization (called adaptive or AD normalization) uses a basic model of the IP experiment and is not a variant of mean, quantile, or other methodology previously proposed. The approach is evaluated statistically and tested with simulated and empirical data. Results and Conclusions The adaptive (AD) normalization method results in a greatly increased range in the number of enriched RNAs identified, fewer false positives, and overall better concordance with independent biological evidence, for the RBPs we analyzed, compared to median normalization. The approach is also applicable to the study of pairwise RNA, DNA and protein interactions such as the analysis of transcription factors via chromatin immunoprecipitation (ChIP) or any other experiments where samples from two conditions, one of which contains an enriched subset of the other, are studied. PMID:23349766

Transplantation of neurons derived from human iPS cells cultured on collagen matrix into guinea-pig cochleae.

PubMed

Ishikawa, Masaaki; Ohnishi, Hiroe; Skerleva, Desislava; Sakamoto, Tatsunori; Yamamoto, Norio; Hotta, Akitsu; Ito, Juichi; Nakagawa, Takayuki

2017-06-01

The present study examined the efficacy of a neural induction method for human induced pluripotent stem (iPS) cells to eliminate undifferentiated cells and to determine the feasibility of transplanting neurally induced cells into guinea-pig cochleae for replacement of spiral ganglion neurons (SGNs). A stepwise method for differentiation of human iPS cells into neurons was used. First, a neural induction method was established on Matrigel-coated plates; characteristics of cell populations at each differentiation step were assessed. Second, neural stem cells were differentiated into neurons on a three-dimensional (3D) collagen matrix, using the same protocol of culture on Matrigel-coated plates; neuron subtypes in differentiated cells on a 3D collagen matrix were examined. Then, human iPS cell-derived neurons cultured on a 3D collagen matrix were transplanted into intact guinea-pig cochleae, followed by histological analysis. In vitro analyses revealed successful induction of neural stem cells from human iPS cells, with no retention of undifferentiated cells expressing OCT3/4. After the neural differentiation of neural stem cells, approximately 70% of cells expressed a neuronal marker, 90% of which were positive for vesicular glutamate transporter 1 (VGLUT1). The expression pattern of neuron subtypes in differentiated cells on a 3D collagen matrix was identical to that of the differentiated cells on Matrigel-coated plates. In addition, the survival of transplant-derived neurons was achieved when inflammatory responses were appropriately controlled. Our preparation method for human iPS cell-derived neurons efficiently eliminated undifferentiated cells and contributed to the settlement of transplant-derived neurons expressing VGLUT1 in guinea-pig cochleae. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Additional Interventions to Enhance the Effectiveness of Individual Placement and Support: A Rapid Evidence Assessment

PubMed Central

Boycott, Naomi; Schneider, Justine; McMurran, Mary

2012-01-01

Topic. Additional interventions used to enhance the effectiveness of individual placement and support (IPS). Aim. To establish whether additional interventions improve the vocational outcomes of IPS alone for people with severe mental illness. Method. A rapid evidence assessment of the literature was conducted for studies where behavioural or psychological interventions have been used to supplement standard IPS. Published and unpublished empirical studies of IPS with additional interventions were considered for inclusion. Conclusions. Six published studies were found which compared IPS alone to IPS plus a supplementary intervention. Of these, three used skills training and three used cognitive remediation. The contribution of each discrete intervention is difficult to establish. Some evidence suggests that work-related social skills and cognitive training are effective adjuncts, but this is an area where large RCTs are required to yield conclusive evidence. PMID:22685665

Development of a cyclic voltammetry method for the detection of Clostridium novyi in black disease.

PubMed

Liu, L L; Jiang, D N; Xiang, G M; Liu, C; Yu, J C; Pu, X Y

2014-03-17

Black disease is an acute disease of sheep and cattle. The pathogen is the obligate anaerobe, Clostridium novyi. Due to difficulties of anaerobic culturing in the country or disaster sites, a simple, rapid, and sensitive method is required. In this study, an electrochemical method, the cyclic voltammetry method, basing on loop-mediated isothermal amplification (LAMP), electrochemical ion bonding (positive dye, methylene blue), was introduced. DNA extracted from C. novyi specimens was amplified through the LAMP reaction. Then the products combined were with methylene blue, which lead to a reduction in the oxidation peak current (ipA) and the reduction peak current (ipC) of the cyclic voltammetry. The changes of ipA/ipC were real-time measured by special designed electrode, so the DNA was quantitatively detected. The results displayed that this electrochemical detection of C. novyi could be completed in 1-2 h with the lowest bacterial concentration of 10(2) colony forming units/mL, and high accuracy (96.5%), sensitivity (96%), and specificity (97%) compared to polymerase chain reation. The cyclic voltammetry method was a simple and fast method, with high sensitivity and high specificity, and has great potential to be a usable molecular tool for fast diagnosis of Black disease.

Effects of the Voice over Internet Protocol on Perturbation Analysis of Normal and Pathological Phonation

PubMed Central

Zhu, Yanmei; Witt, Rachel E.; MacCallum, Julia K.; Jiang, Jack J.

2010-01-01

Objective In this study, a Voice over Internet Protocol (VoIP) communication based on G.729 protocol was simulated to determine the effects of this system on acoustic perturbation parameters of normal and pathological voice signals. Patients and Methods: Fifty recordings of normal voice and 48 recordings of pathological voice affected by laryngeal paralysis were transmitted through a VoIP communication system. The acoustic analysis programs of CSpeech and MDVP were used to determine the percent jitter and percent shimmer from the voice samples before and after VoIP transmission. The effects of three frequently used audio compression protocols (MP3, WMA, and FLAC) on the perturbation measures were also studied. Results It was found that VoIP transmission disrupts the waveform and increases the percent jitter and percent shimmer of voice samples. However, after VoIP transmission, significant discrimination between normal and pathological voices affected by laryngeal paralysis was still possible. It was found that the lossless compression method FLAC does not exert any influence on the perturbation measures. The lossy compression methods MP3 and WMA increase percent jitter and percent shimmer values. Conclusion This study validates the feasibility of these transmission and compression protocols in developing remote voice signal data collection and assessment systems. PMID:20588051

Interferon-gamma inducible protein-10 as a potential biomarker in localized scleroderma

PubMed Central

2013-01-01

Introduction The purpose of this study was to evaluate the presence and levels of interferon-gamma inducible protein-10 (IP-10) in the plasma and skin of pediatric localized scleroderma (LS) patients compared to those of healthy pediatric controls and to determine if IP-10 levels correlate to clinical disease activity measures. Methods The presence of IP-10 in the plasma was analyzed using a Luminex panel in 69 pediatric patients with LS and compared to 71 healthy pediatric controls. Of these patients, five had available skin biopsy specimens with concurrent clinical and serological data during the active disease phase, which were used to analyze the presence and location of IP-10 in the skin by immunohistochemistry (IHC). Results IP-10 levels were significantly elevated in the plasma of LS patients compared to that of healthy controls and correlated to clinical disease activity measures in LS. Immunohistochemistry staining of IP-10 was present in the dermal infiltrate of LS patients and was similar to that found in psoriasis skin specimens, the positive disease control. Conclusions Elevation of IP-10 levels in the plasma compared to those of healthy controls and the presence of IP-10 staining in the affected skin of LS patients indicates that IP-10 is a potential biomarker in LS. Furthermore, significant elevation of IP-10 in LS patients with active versus inactive disease and correlations between IP-10 levels and standardized disease outcome measures of activity in LS strongly suggest that IP-10 may be a biomarker for disease activity in LS. PMID:24499523

Elimination of remaining undifferentiated induced pluripotent stem cells in the process of human cardiac cell sheet fabrication using a methionine-free culture condition.

PubMed

Matsuura, Katsuhisa; Kodama, Fumiko; Sugiyama, Kasumi; Shimizu, Tatsuya; Hagiwara, Nobuhisa; Okano, Teruo

2015-03-01

Cardiac tissue engineering is a promising method for regenerative medicine. Although we have developed human cardiac cell sheets by integration of cell sheet-based tissue engineering and scalable bioreactor culture, the risk of contamination by induced pluripotent stem (iPS) cells in cardiac cell sheets remains unresolved. In the present study, we established a novel culture method to fabricate human cardiac cell sheets with a decreased risk of iPS cell contamination while maintaining viabilities of iPS cell-derived cells, including cardiomyocytes and fibroblasts, using a methionine-free culture condition. When cultured in the methionine-free condition, human iPS cells did not survive without feeder cells and could not proliferate or form colonies on feeder cells or in coculture with cells for cardiac cell sheet fabrication. When iPS cell-derived cells after the cardiac differentiation were transiently cultured in the methionine-free condition, gene expression of OCT3/4 and NANOG was downregulated significantly compared with that in the standard culture condition. Furthermore, in fabricated cardiac cell sheets, spontaneous and synchronous beating was observed in the whole area while maintaining or upregulating the expression of various cardiac and extracellular matrix genes. These findings suggest that human iPS cells are methionine dependent and a methionine-free culture condition for cardiac cell sheet fabrication might reduce the risk of iPS cell contamination.

Measurements of neutron distribution in neutrons-gamma-rays mixed field using imaging plate for neutron capture therapy.

PubMed

Tanaka, Kenichi; Endo, Satoru; Hoshi, Masaharu

2010-01-01

The imaging plate (IP) technique is tried to be used as a handy method to measure the spatial neutron distribution via the (157)Gd(n,gamma)(158)Gd reaction for neutron capture therapy (NCT). For this purpose, IP is set in a water phantom and irradiated in a mixed field of neutrons and gamma-rays. The Hiroshima University Radiobiological Research Accelerator is utilized for this experiment. The neutrons are moderated with 20-cm-thick D(2)O to obtain suitable neutron field for NCT. The signal for IP doped with Gd as a neutron-response enhancer is subtracted with its contribution by gamma-rays, which was estimated using IP without Gd. The gamma-ray response of Gd-doped IP to non-Gd IP is set at 1.34, the value measured for (60)Co gamma-rays, in estimating the gamma-ray contribution to Gd-doped IP signal. Then measured distribution of the (157)Gd(n,gamma)(158)Gd reaction rate agrees within 10% with the calculated value based on the method that has already been validated for its reproducibility of Au activation. However, the evaluated distribution of the (157)Gd(n,gamma)(158)Gd reaction rate is so sensitive to gamma-ray energy, e.g. the discrepancy of the (157)Gd(n,gamma)(158)Gd reaction rate between measurement and calculation becomes 30% for the photon energy change from 33keV to 1.253MeV.

Limited hair cell induction from human induced pluripotent stem cells using a simple stepwise method.

PubMed

Ohnishi, Hiroe; Skerleva, Desislava; Kitajiri, Shin-ichiro; Sakamoto, Tatsunori; Yamamoto, Norio; Ito, Juichi; Nakagawa, Takayuki

2015-07-10

Disease-specific induced pluripotent stem cells (iPS) cells are expected to contribute to exploring useful tools for studying the pathophysiology of inner ear diseases and to drug discovery for treating inner ear diseases. For this purpose, stable induction methods for the differentiation of human iPS cells into inner ear hair cells are required. In the present study, we examined the efficacy of a simple induction method for inducing the differentiation of human iPS cells into hair cells. The induction of inner ear hair cell-like cells was performed using a stepwise method mimicking inner ear development. Human iPS cells were sequentially transformed into the preplacodal ectoderm, otic placode, and hair cell-like cells. As a first step, preplacodal ectoderm induction, human iPS cells were seeded on a Matrigel-coated plate and cultured in a serum free N2/B27 medium for 8 days according to a previous study that demonstrated spontaneous differentiation of human ES cells into the preplacodal ectoderm. As the second step, the cells after preplacodal ectoderm induction were treated with basic fibroblast growth factor (bFGF) for induction of differentiation into otic-placode-like cells for 15 days. As the final step, cultured cells were incubated in a serum free medium containing Matrigel for 48 days. After preplacodal ectoderm induction, over 90% of cultured cells expressed the genes that express in preplacodal ectoderm. By culture with bFGF, otic placode marker-positive cells were obtained, although their number was limited. Further 48-day culture in serum free media resulted in the induction of hair cell-like cells, which expressed a hair cell marker and had stereocilia bundle-like constructions on their apical surface. Our results indicate that hair cell-like cells are induced from human iPS cells using a simple stepwise method with only bFGF, without the use of xenogeneic cells. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Characterization of New Hard X-ray Cataclysmic Variables

NASA Technical Reports Server (NTRS)

Bernardini, F.; deMartino, D.; Falanga, M.; Mukai, K.; Matt, G.; Bonnet-Bidaud, J.-M.; Masetti, N.; Mouchet, M.

2012-01-01

Aims. We aim at characterizing a sample of nine new hard X-ray selected Cataclysmic Variable (CVs), to unambiguously identify them as magnetic systems of the Intermediate Polar (IP) type. Methods. We performed detailed timing and spectral analysis by using X-ray, and simultaneous UV and optical data collected by XMM-Newton, complemented with hard X-ray data provided by INTEGRAL and Swift. The pulse arrival time were used to estimate the orbital periods. The broad band X-ray spectra were fitted using composite models consisting of different absorbing columns and emission components. Results. Strong X-ray pulses at the White Dwarf (WD) spin period are detected and found to decrease with energy. Most sources are spin-dominated systems in the X-rays, though four are beat dominated at optical wavelengths. We estimated the orbital period in all system (except for IGR J16500-3307), providing the first estimate for IGRJ08390-4833, IGRJ18308-1232, and IGR J18173-2509. All X-ray spectra are multi-temperature. V2069 Cyg and RX J0636+3535 poses a soft X-ray optically thick component at kT approx. 80 eV. An intense K (sub alpha) Fe line at 6.4 keV is detected in all sources. An absorption edge at 0.76 keV from OVII is detected in IGR J08390-4833. The WD masses and lower limits to the accretion rates are also estimated. Conclusions. We found all sources to be IPs. IGR J08390-4833, V2069 Cyg, and IGR J16500-3307 are pure disc accretors, while IGR J18308-1232, IGR J1509-6649, IGR J17195-4100, and RX J0636+3535 display a disc-overflow accretion mode. All sources show a temperature gradient in the post-shock regions and a highly absorbed emission from material located in the pre-shock flow which is also responsible for the X-ray pulsations. Reflection at the WD surface is likely the origin of the fluorescent iron line. There is an increasing evidence for the presence of a warm absorber in IPs, a feature that needs future exploration. The addition of two systems to the subgroup of soft X-ray IPs confirms a relatively large ( 30%) incidence.

Apiaceous Vegetable Consumption Decreases PhIP-Induced DNA Adducts and Increases Methylated PhIP Metabolites in the Urine Metabolome in Rats123

PubMed Central

Kim, Jae Kyeom; Gallaher, Daniel D; Chen, Chi; Yao, Dan; Trudo, Sabrina P

2015-01-01

Background: Heterocyclic aromatic amines, such as 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), are carcinogenic compounds produced during heating of protein-containing foods. Apiaceous vegetables inhibit PhIP-activating enzymes, whereas cruciferous vegetables induce both PhIP-activating and -detoxifying enzymes. Objective: We investigated the effects of these vegetables, either alone or combined, on PhIP metabolism and colonic DNA adduct formation in rats. Methods: Male Wistar rats were fed cruciferous vegetables (21%, wt:wt), apiaceous vegetables (21%, wt:wt), or a combination of both vegetables (10.5% wt:wt of each). Negative and positive control groups were fed an AIN-93G diet. After 6 d, all groups received an intraperitoneal injection of PhIP (10 mg · kg body weight−1) except for the negative control group, which received only vehicle. Urine was collected for 24 h after the injection for LC–tandem mass spectrometry metabolomic analyses. On day 7, rats were killed and tissues processed. Results: Compared with the positive control, cruciferous vegetables increased the activity of hepatic PhIP-activating enzymes [39.5% and 45.1% for cytochrome P450 (CYP) 1A1 (P = 0.0006) and CYP1A2 (P < 0.0001), respectively] and of uridine 5′-diphospho-glucuronosyltransferase 1A (PhIP-detoxifying) by 24.5% (P = 0.0267). Apiaceous vegetables did not inhibit PhIP-activating enzymes, yet reduced colonic PhIP-DNA adducts by 20.4% (P = 0.0496). Metabolomic analyses indicated that apiaceous vegetables increased the relative abundance of urinary methylated PhIP metabolites. The sum of these methylated metabolites inversely correlated with colonic PhIP-DNA adducts (r = −0.43, P = 0.01). We detected a novel methylated urinary PhIP metabolite and demonstrated that methylated metabolites are produced in the human liver S9 fraction. Conclusions: Apiaceous vegetables did not inhibit the activity of PhIP-activating enzymes in rats, suggesting that the reduction in PhIP-DNA adducts may involve other pathways. Further investigation of the importance of PhIP methylation in carcinogen metabolism is warranted, given the inverse correlation of methylated PhIP metabolites with a biomarker of carcinogenesis and the detection of a novel methylated PhIP metabolite. PMID:25733458

Micro-chromatin Immunoprecipation (μChIP) Protocol for Real-time PCR Analysis of a Limited Amount of Cells.

PubMed

Gillotin, Sébastien; Guillemot, François

2016-06-20

Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) is an important strategy to study gene regulation. When availability of cells is limited, however, it can be useful to focus on specific genes to investigate in depth the role of transcription factors or histone marks. Unfortunately, performing ChIP experiments to study transcription factors' binding to DNA can be difficult when biological material is restricted. This protocol describes a robust method to perform μChIP for over-expressed or endogenous transcription factors using ~100,000 cells per ChIP experiment (Masserdotti et al ., 2015). We also describe optimization steps, which we think are critical for this protocol to work and which can be used to further reduce the number of cells.

Research on TCP/IP network communication based on Node.js

NASA Astrophysics Data System (ADS)

Huang, Jing; Cai, Lixiong

2018-04-01

In the face of big data, long connection and high synchronization, TCP/IP network communication will cause performance bottlenecks due to its blocking multi-threading service model. This paper presents a method of TCP/IP network communication protocol based on Node.js. On the basis of analyzing the characteristics of Node.js architecture and asynchronous non-blocking I/O model, the principle of its efficiency is discussed, and then compare and analyze the network communication model of TCP/IP protocol to expound the reasons why TCP/IP protocol stack is widely used in network communication. Finally, according to the large data and high concurrency in the large-scale grape growing environment monitoring process, a TCP server design based on Node.js is completed. The results show that the example runs stably and efficiently.

Evaluation of Dental Shade Guide Variability Using Cross-Polarized Photography.

PubMed

Gurrea, Jon; Gurrea, Marta; Bruguera, August; Sampaio, Camila S; Janal, Malvin; Bonfante, Estevam; Coelho, Paulo G; Hirata, Ronaldo

2016-01-01

This study evaluated color variability in the A hue between the VITA Classical (VITA Zahnfabrik) shade guide and four other VITA-coded ceramic shade guides using a Canon EOS 60D camera and software (Photoshop CC, Adobe). A total of 125 photographs were taken, 5 per shade tab for each of 5 shades (A1 to A4) from the following shade guides: VITA Classical (control), IPS e.max Ceram (Ivoclar Vivadent), IPS d.SIGN (Ivoclar Vivadent), Initial ZI (GC), and Creation CC (Creation Willi Geller). Photos were processed with Adobe Photoshop CC to allow standardized evaluation of hue, chroma, and value between shade tabs. None of the VITA-coded shade tabs fully matched the VITA Classical shade tab for hue, chroma, or value. The VITA-coded shade guides evaluated herein showed an overall unmatched shade in all tabs when compared with the control, suggesting that shade selection should be made using the guide produced by the manufacturer of the ceramic intended for the final restoration.

The role of the human papillomavirus in the pathogenesis of Schneiderian inverted papillomas: an analytic overview of the evidence.

PubMed

Lawson, William; Schlecht, Nicolas F; Brandwein-Gensler, Margaret

2008-06-01

Evidence of an etiological role for human papillomavirus (HPV) in Schneiderian inverted papillomas IP arose in the late 1980's; yet almost three decades later, the association between HPV and IP has yet to be universally accepted. This is probably due to the disparate HPV detection rates in IP reported in the literature. We analyzed the weight of published data in order to address the following questions: why do the HPV detection rates in IP vary so greatly? What is the relationship between low-risk (LR) and high-risk (HR) HPV types and HPV detection rates in IP? Is there a relationship between the presence and type of HPV in IP and recurrence and malignant progression? A search using the Pubmed search engine was performed to identify studies published in English from 01/87 through 12/06 using the MeSH terms ''HPV'' and ''Inverted", "Exophytic", "Oncocytic Schneiderian" or "Fungiform papilloma''. Data was abstracted from publications including histology, HPV target, HPV type, method of detection, etc. HPV results were stratified by histology and other variables. Tests for heterogeneity (between-study variability) were conducted, and weighted prevalence (WP) estimates and 95% confidence intervals (CI) were calculated using a random-effects inverse-variance model stratified on study. The association between HPV IP recurrence was estimated by random-effects inverse-variance weighted odds ratio (OR). Weighted estimates revealed similar detection rates across detection methods, 26.8% (95%CI 16.4-37.2%) by ISH, 25.2% (95%CI 14.7-35.6%) by consensus PCR, and 23.6% (95%CI 12.2-35.0%) by type-specific PCR. A preponderance of HPV 6/11 is found in IP as compared to HPV 16/18; the overall unadjusted ratio of LR to high-risk HR HPV types is 2.8:1 The HPV detection rates significantly increase (Wald t-test P < 0.02) in IPs with high-grade dysplasia (WP 55.8%, 95%CI 30.5-81.0%) and carcinoma (WP 55.1%, 95%CI 37.0-73.2%) as compared to IPs with no dysplasia or mild dysplasia (WP 22.3%, 95%CI 15.9-28.6%). Furthermore, the preponderance of LR HPV in benign IP (ratio LR/HR = 4.8:1) shifts in dysplastic and malignant IP. The LR/HR ratio is 1.1:1 for IPs with high-grade dysplasias, this ratio is inverted to favor HR HPV (1:2.4) for malignant IP. Recurrences developed in 44 of 236 patients; HPV was detected in 27 of 44 IPs (WP 57.9%, 95%CI 31.6-84.2%) that developed recurrences and in 24 of 192 IPs (WP 9.7%, 95%CI 4.4-15.0%) that did not develop recurrence. The presence of HPV was significantly associated with the likelihood of developing recurrence (weighted OR of 10.2, 95%CI 3.2-32.8). We hypothesize that LR HPV may induce IP formation, and then are lost as infected cells are shed, as a "hit and run" phenomenon. HPV detection rates increase in dysplastic IP and SCC-ex-IP with increasing ratio of HR to LR HPV types, compared to nondysplastic IP. We believe that one explanation for the variation in HPV detection rates between different studies may be the actual histologic composition of the cohort. That is, if one series contains a higher frequency of dysplastic and malignant IP, it may have a higher detection rate than another series which contains only nondysplastic IP. We hypothesize that the higher rates of HPV detection in dysplastic and malignant IP may be related to HPV integration. The implication of this is that HPV sub-type testing may identify patients at risk for recurrence, or progression to dysplasia and malignancy, and thus may impact surveillance protocols.

Direct Covalent Grafting of Phytate to Titanium Surfaces through Ti-O-P Bonding Shows Bone Stimulating Surface Properties and Decreased Bacterial Adhesion.

PubMed

Córdoba, Alba; Hierro-Oliva, Margarita; Pacha-Olivenza, Miguel Ángel; Fernández-Calderón, María Coronada; Perelló, Joan; Isern, Bernat; González-Martín, María Luisa; Monjo, Marta; Ramis, Joana M

2016-05-11

Myo-inositol hexaphosphate, also called phytic acid or phytate (IP6), is a natural molecule abundant in vegetable seeds and legumes. Among other functions, IP6 inhibits bone resorption. It is adsorbed on the surface of hydroxyapatite, inhibiting its dissolution and decreasing the progressive loss of bone mass. We present here a method to directly functionalize Ti surfaces covalently with IP6, without using a cross-linker molecule, through the reaction of the phosphate groups of IP6 with the TiO2 layer of Ti substrates. The grafting reaction consisted of an immersion in an IP6 solution to allow the physisorption of the molecules onto the substrate, followed by a heating step to obtain its chemisorption, in an adaptation of the T-Bag method. The reaction was highly dependent on the IP6 solution pH, only achieving a covalent Ti-O-P bond at pH 0. We evaluated two acidic pretreatments of the Ti surface, to increase its hydroxylic content, HNO3 30% and HF 0.2%. The structure of the coated surfaces was characterized by X-ray photoelectron spectroscopy, time-of-flight secondary ion mass spectrometry, and ellipsometry. The stability of the IP6 coating after three months of storage and after sterilization with γ-irradiation was also determined. Then, we evaluated the biological effect of Ti-IP6 surfaces in vitro on MC3T3-E1 osteoblastic cells, showing an osteogenic effect. Finally, the effect of the surfaces on the adhesion and biofilm viability of oral microorganisms S. mutans and S. sanguinis was also studied, and we found that Ti-IP6 surfaces decreased the adhesion of S. sanguinis. A surface that actively improves osseointegration while decreasing the bacterial adhesion could be suitable for use in bone implants.

A Simple Method to Quantitate IP-10 in Dried Blood and Plasma Spots

PubMed Central

Aabye, Martine G.; Eugen-Olsen, Jesper; Werlinrud, Anne Marie; Holm, Line Lindebo; Tuuminen, Tamara; Ravn, Pernille; Ruhwald, Morten

2012-01-01

Background Antigen specific release of IP-10 is an established marker for infection with M.tuberculosis. Compared to IFN-γ, IP-10 is released in 100-fold higher concentrations enabling the development of novel assays for detection. Dried blood spots are a convenient sample for high throughput newborn screening. Aim To develop a robust and sensitive ELISA-based assay for IP-10 detection in plasma, dried blood spots (DBS) and dried plasma spots (DPS); to validate the ELISA in clinically relevant samples; and to assess the performance of the assay for detection of Cytomegalovirus (CMV) and M.tuberculosis specific immune responses. Method We raised mice and rat monoclonal antibodies against human IP-10 and developed an ELISA. The assay was validated and applied to the detection of CMV and M.tuberculosis specific responses in 18 patients with immune reactivity towards M.tuberculosis and 32 healthy controls of which 22 had immune reactivity towards CMV and none towards M.tuberculosis. We compared the performance of this new assay to IFN-γ. Results The ELISA was reliable for IP-10 detection in both plasma and filter paper samples. The linear range of the ELISA was 2.5–600 pg/ml. IFN-γ was not readily detectable in DPS samples. IP-10 was stabile in filter paper samples for at least 4 weeks at 37°C. The correlation between IP-10 detected in plasma, DPS and DBS samples was excellent (r2>0.97). Conclusions This newly developed assay is reliable for IP-10 quantification in plasma, DBS and DPS samples from antigen stimulated and non-stimulated whole blood. The filter paper assays enable easy sample acquisition and transport at ambient temperature e.g. via the postal system. The system can potentially simplify diagnostic assays for M.tuberculosis and CMV infection. PMID:22761744

Qualitative and quantitative evaluation of solvent systems for countercurrent separation.

PubMed

Friesen, J Brent; Ahmed, Sana; Pauli, Guido F

2015-01-16

Rational solvent system selection for countercurrent chromatography and centrifugal partition chromatography technology (collectively known as countercurrent separation) studies continues to be a scientific challenge as the fundamental questions of comparing polarity range and selectivity within a solvent system family and between putative orthogonal solvent systems remain unanswered. The current emphasis on metabolomic investigations and analysis of complex mixtures necessitates the use of successive orthogonal countercurrent separation (CS) steps as part of complex fractionation protocols. Addressing the broad range of metabolite polarities demands development of new CS solvent systems with appropriate composition, polarity (π), selectivity (σ), and suitability. In this study, a mixture of twenty commercially available natural products, called the GUESSmix, was utilized to evaluate both solvent system polarity and selectively characteristics. Comparisons of GUESSmix analyte partition coefficient (K) values give rise to a measure of solvent system polarity range called the GUESSmix polarity index (GUPI). Solvatochromic dye and electrical permittivity measurements were also evaluated in quantitatively assessing solvent system polarity. The relative selectivity of solvent systems were evaluated with the GUESSmix by calculating the pairwise resolution (αip), the number of analytes found in the sweet spot (Nsw), and the pairwise resolution of those sweet spot analytes (αsw). The combination of these parameters allowed for both intra- and inter-family comparison of solvent system selectivity. Finally, 2-dimensional reciprocal shifted symmetry plots (ReSS(2)) were created to visually compare both the polarities and selectivities of solvent system pairs. This study helps to pave the way to the development of new solvent systems that are amenable to successive orthogonal CS protocols employed in metabolomic studies. Copyright © 2014 Elsevier B.V. All rights reserved.

Preparation of Low-Input and Ligation-Free ChIP-seq Libraries Using Template-Switching Technology.

PubMed

Bolduc, Nathalie; Lehman, Alisa P; Farmer, Andrew

2016-10-10

Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) has become the gold standard for mapping of transcription factors and histone modifications throughout the genome. However, for ChIP experiments involving few cells or targeting low-abundance transcription factors, the small amount of DNA recovered makes ligation of adapters very challenging. In this unit, we describe a ChIP-seq workflow that can be applied to small cell numbers, including a robust single-tube and ligation-free method for preparation of sequencing libraries from sub-nanogram amounts of ChIP DNA. An example ChIP protocol is first presented, resulting in selective enrichment of DNA-binding proteins and cross-linked DNA fragments immobilized on beads via an antibody bridge. This is followed by a protocol for fast and easy cross-linking reversal and DNA recovery. Finally, we describe a fast, ligation-free library preparation protocol, featuring DNA SMART technology, resulting in samples ready for Illumina sequencing. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

Enhancing interacting residue prediction with integrated contact matrix prediction in protein-protein interaction.

PubMed

Du, Tianchuan; Liao, Li; Wu, Cathy H

2016-12-01

Identifying the residues in a protein that are involved in protein-protein interaction and identifying the contact matrix for a pair of interacting proteins are two computational tasks at different levels of an in-depth analysis of protein-protein interaction. Various methods for solving these two problems have been reported in the literature. However, the interacting residue prediction and contact matrix prediction were handled by and large independently in those existing methods, though intuitively good prediction of interacting residues will help with predicting the contact matrix. In this work, we developed a novel protein interacting residue prediction system, contact matrix-interaction profile hidden Markov model (CM-ipHMM), with the integration of contact matrix prediction and the ipHMM interaction residue prediction. We propose to leverage what is learned from the contact matrix prediction and utilize the predicted contact matrix as "feedback" to enhance the interaction residue prediction. The CM-ipHMM model showed significant improvement over the previous method that uses the ipHMM for predicting interaction residues only. It indicates that the downstream contact matrix prediction could help the interaction site prediction.

Higher-order equation-of-motion coupled-cluster methods for ionization processes.

PubMed

Kamiya, Muneaki; Hirata, So

2006-08-21

Compact algebraic equations defining the equation-of-motion coupled-cluster (EOM-CC) methods for ionization potentials (IP-EOM-CC) have been derived and computer implemented by virtue of a symbolic algebra system largely automating these processes. Models with connected cluster excitation operators truncated after double, triple, or quadruple level and with linear ionization operators truncated after two-hole-one-particle (2h1p), three-hole-two-particle (3h2p), or four-hole-three-particle (4h3p) level (abbreviated as IP-EOM-CCSD, CCSDT, and CCSDTQ, respectively) have been realized into parallel algorithms taking advantage of spin, spatial, and permutation symmetries with optimal size dependence of the computational costs. They are based on spin-orbital formalisms and can describe both alpha and beta ionizations from open-shell (doublet, triplet, etc.) reference states into ionized states with various spin magnetic quantum numbers. The application of these methods to Koopmans and satellite ionizations of N2 and CO (with the ambiguity due to finite basis sets eliminated by extrapolation) has shown that IP-EOM-CCSD frequently accounts for orbital relaxation inadequately and displays errors exceeding a couple of eV. However, these errors can be systematically reduced to tenths or even hundredths of an eV by IP-EOM-CCSDT or CCSDTQ. Comparison of spectroscopic parameters of the FH+ and NH+ radicals between IP-EOM-CC and experiments has also underscored the importance of higher-order IP-EOM-CC treatments. For instance, the harmonic frequencies of the A 2Sigma- state of NH+ are predicted to be 1285, 1723, and 1705 cm(-1) by IP-EOM-CCSD, CCSDT, and CCSDTQ, respectively, as compared to the observed value of 1707 cm(-1). The small adiabatic energy separation (observed 0.04 eV) between the X 2Pi and a 4Sigma- states of NH+ also requires IP-EOM-CCSDTQ for a quantitative prediction (0.06 eV) when the a 4Sigma- state has the low-spin magnetic quantum number (s(z) = 1/2). When the state with s(z) = 3/2 is sought, the energy separations converge much more rapidly with the IP-EOM-CCSD value (0.03 eV) already being close to the observed (0.04 eV).

Stem/progenitor cells from inflamed human dental pulp retain tissue regeneration potential

PubMed Central

Alongi, Dominick J; Yamaza, Takayoshi; Song, Yingjie; Fouad, Ashraf F; Romberg, Elaine E; Shi, Songtao; Tuan, Rocky S; Huang, George T-J

2011-01-01

Background Potent stem/progenitor cells have been isolated from normal human dental pulps termed dental pulp stem cells (DPSCs). However, it is unknown whether these cells exist in inflamed pulps (IPs). Aims To determine whether DPSCs can be identified and isolated from IPs; and if they can be successfully cultured, whether they retain tissue regeneration potential in vivo. Materials & methods DPSCs from freshly collected normal pulps (NPs) and IPs were characterized in vitro and their tissue regeneration potential tested using an in vivo study model. Results The immunohistochemical analysis showed that IPs expressed higher levels of mesenchymal stem cell markers STRO-1, CD90, CD105 and CD146 compared with NPs (p < 0.05). Flow cytometry analysis showed that DPSCs from both NPs and IPs expressed moderate to high levels of CD146, stage-specific embryonic antigen-4, CD73 and CD166. Total population doubling of DPSCs-IPs (44.6 ± 2.9) was lower than that of DPSCs-NPs (58.9 ± 2.5) (p < 0.05), and DPSCs-IPs appeared to have a decreased osteo/dentinogenic potential compared with DPSCs-NPs based on the mineral deposition in cultures. Nonetheless, DPSCs-IPs formed pulp/dentin complexes similar to DPSCs-NPs when transplanted into immunocompromised mice. Conclusion DPSCs-IPs can be isolated and their mesenchymal stem cell marker profiles are similar to those from NPs. Although some stem cell properties of DPSCs-IPs were altered, cells from some samples remained potent in tissue regeneration in vivo. PMID:20465527

Geophysical Signitures From Hydrocarbon Contaminated Aquifers

NASA Astrophysics Data System (ADS)

Abbas, M.; Jardani, A.

2015-12-01

The task of delineating the contamination plumes as well as studying their impact on the soil and groundwater biogeochemical properties is needed to support the remediation efforts and plans. Geophysical methods including electrical resistivity tomography (ERT), induced polarization (IP), ground penetrating radar (GPR), and self-potential (SP) have been previously used to characterize contaminant plumes and investigate their impact on soil and groundwater properties (Atekwana et al., 2002, 2004; Benson et al., 1997; Campbell et al., 1996; Cassidy et al., 2001; Revil et al., 2003; Werkema et al., 2000). Our objective was to: estimate the hydrocarbon contamination extent in a contaminated site in northern France, and to adverse the effects of the oil spill on the groundwater properties. We aim to find a good combination of non-intrusive and low cost methods which we can use to follow the bio-remediation process, which is planned to proceed next year. We used four geophysical methods including electrical resistivity tomography, IP, GPR, and SP. The geophysical data was compared to geochemical ones obtained from 30 boreholes installed in the site during the geophysical surveys. Our results have shown: low electrical resistivity values; high chargeability values; negative SP anomalies; and attenuated GPR reflections coincident with groundwater contamination. Laboratory and field geochemical measurements have demonstrated increased groundwater electrical conductivity and increased microbial activity associated with hydrocarbon contamination of groundwater. Our study results support the conductive model suggested by studies such as Sauck (2000) and Atekwana et al., (2004), who suggest that biological alterations of hydrocarbon contamination can substantially modify the chemical and physical properties of the subsurface, producing a dramatic shift in the geo-electrical signature from resistive to conductive. The next stage of the research will include time lapse borehole and 3D geophysical measurements coupled to biological and chemical surface phase experiments in order to monitor the bioremediation processes.

Genome-wide profiling of DNA-binding proteins using barcode-based multiplex Solexa sequencing.

PubMed

Raghav, Sunil Kumar; Deplancke, Bart

2012-01-01

Chromatin immunoprecipitation (ChIP) is a commonly used technique to detect the in vivo binding of proteins to DNA. ChIP is now routinely paired to microarray analysis (ChIP-chip) or next-generation sequencing (ChIP-Seq) to profile the DNA occupancy of proteins of interest on a genome-wide level. Because ChIP-chip introduces several biases, most notably due to the use of a fixed number of probes, ChIP-Seq has quickly become the method of choice as, depending on the sequencing depth, it is more sensitive, quantitative, and provides a greater binding site location resolution. With the ever increasing number of reads that can be generated per sequencing run, it has now become possible to analyze several samples simultaneously while maintaining sufficient sequence coverage, thus significantly reducing the cost per ChIP-Seq experiment. In this chapter, we provide a step-by-step guide on how to perform multiplexed ChIP-Seq analyses. As a proof-of-concept, we focus on the genome-wide profiling of RNA Polymerase II as measuring its DNA occupancy at different stages of any biological process can provide insights into the gene regulatory mechanisms involved. However, the protocol can also be used to perform multiplexed ChIP-Seq analyses of other DNA-binding proteins such as chromatin modifiers and transcription factors.

Phenotypic Detection of Metallo-β-Lactamase in Imipenem-Resistant Pseudomonas aeruginosa

PubMed Central

Khosravi, Yalda; Loke, Mun Fai; Chua, Eng Guan; Tay, Sun Tee; Vadivelu, Jamuna

2012-01-01

Carbapenems are the primary choice of treatment for severe Pseudomonas aeruginosa infection. However, the emergence of carbapenem resistance due to the production of metallo-β-lactamases (MBLs) is of global concern. In this study, 90 imipenem- (IPM- or IP-) resistant P. aeruginosa (IRPA) isolates, including 32 previously tested positive and genotyped for MBL genes by PCR, were subjected to double-disk synergy test (DDST), combined disk test (CDT), and imipenem/imipenem-inhibitor (IP/IPI) E-test to evaluate their MBLs detection capability. All three methods were shown to have a sensitivity of 100%. However, DDST was the most specific of the three (96.6%), followed by IP/IPI E-test interpreted based on the single criteria of IP/IPI ≥8 as positive (62.1%), and CDT was the least specific (43.1%). Based on the data from this evaluation, we propose that only IRPA with IP MIC >16 μg/mL and IP/IPI ≥8 by IP/IPI E-test should be taken as positive for MBL activity. With the new dual interpretation criteria, the MBL IP/IPI E-test was shown to achieve 100% sensitivity as well as specificity for the IRPA in this study. Therefore, the IP/IPI E-test is a viable alternative phenotypic assay to detect MBL production in IRPA in our population in circumstances where PCR detection is not a feasible option. PMID:22792048

Equation-of-motion coupled-cluster method for ionised states with spin-orbit coupling using open-shell reference wavefunction

NASA Astrophysics Data System (ADS)

Wang, Zhifan; Wang, Fan

2018-04-01

The equation-of-motion coupled-cluster method for ionised states at the singles and doubles level (EOM-IP-CCSD) with spin-orbit coupling (SOC) included in post-Hartree-Fock (HF) steps is extended to spatially non-degenerate open-shell systems such as high spin states of s1, p3, σ1 or π2 configuration in this work. Pseudopotentials are employed to treat relativistic effects and spin-unrestricted scalar relativistic HF determinant is adopted as reference in calculations. Symmetry is not exploited in the implementation since both time-reversal and spatial symmetry is broken due to SOC. IPs with the EOM-IP-CCSD approach are those from the 3Σ1- states for high spin state of π2 configuration, while the ground state is the 3Σ0- state. When removing an electron from the high spin state of p3 configuration, only the 3P2 state can be reached. The open-shell EOM-IP-CCSD approach with SOC was employed in calculating IPs of some open-shell atoms with s1 configuration, diatomic molecules with π2 configuration and SOC splitting of the ionised π1 state, as well as IPs of VA atoms with p3 configuration. Our results demonstrate that this approach can be applied to ionised states of spatially non-degenerate open-shell states containing heavy elements with reasonable accuracy.

Comparison of Protein Immunoprecipitation-Multiple Reaction Monitoring with ELISA for Assay of Biomarker Candidates in Plasma

PubMed Central

2013-01-01

Quantitative analysis of protein biomarkers in plasma is typically done by ELISA, but this method is limited by the availability of high-quality antibodies. An alternative approach is protein immunoprecipitation combined with multiple reaction monitoring mass spectrometry (IP-MRM). We compared IP-MRM to ELISA for the analysis of six colon cancer biomarker candidates (metalloproteinase inhibitor 1 (TIMP1), cartilage oligomeric matrix protein (COMP), thrombospondin-2 (THBS2), endoglin (ENG), mesothelin (MSLN) and matrix metalloproteinase-9 (MMP9)) in plasma from colon cancer patients and noncancer controls. Proteins were analyzed by multiplex immunoprecipitation from plasma with the ELISA capture antibodies, further purified by SDS-PAGE, digested and analyzed by stable isotope dilution MRM. IP-MRM provided linear responses (r = 0.978–0.995) between 10 and 640 ng/mL for the target proteins spiked into a “mock plasma” matrix consisting of 60 mg/mL bovine serum albumin. Measurement variation (coefficient of variation at the limit of detection) for IP-MRM assays ranged from 2.3 to 19%, which was similar to variation for ELISAs of the same samples. IP-MRM and ELISA measurements for all target proteins except ENG were highly correlated (r = 0.67–0.97). IP-MRM with high-quality capture antibodies thus provides an effective alternative method to ELISA for protein quantitation in biological fluids. PMID:24224610

Pattern-based IP block detection, verification, and variability analysis

NASA Astrophysics Data System (ADS)

Ahmad Ibrahim, Muhamad Asraf Bin; Muhsain, Mohamad Fahmi Bin; Kamal Baharin, Ezni Aznida Binti; Sweis, Jason; Lai, Ya-Chieh; Hurat, Philippe

2018-03-01

The goal of a foundry partner is to deliver high quality silicon product to its customers on time. There is an assumed trust that the silicon will yield, function and perform as expected when the design fits all the sign-off criteria. The use of Intellectual Property (IP) blocks is very common today and provides the customer with pre-qualified and optimized functions for their design thus shortening the design cycle. There are many methods by which an IP Block can be generated and placed within layout. Even with the most careful methods and following of guidelines comes the responsibility of sign-off checking. A foundry needs to detect where these IP Blocks have been placed and look for any violations. This includes DRC clean modifications to the IP Block which may or may not be intentional. Using a pattern-based approach to detect all IP Blocks used provides the foundry advanced capabilities to analyze them further for any kind of changes which could void the OPC and process window optimizations. Having any changes in an IP Block could cause functionality changes or even failures. This also opens the foundry to legal and cost issues while at the same time forcing re-spins of the design. In this publication, we discuss the methodology we have employed to avoid process issues and tape-out errors while at the same time reduce our manual work and improve the turnaround time. We are also able to use our pattern analysis to improve our OPC optimizations when modifications are encountered which have not been seen before.

IGR J14257-6117, a magnetic accreting white dwarf with a very strong strong X-ray orbital modulation

NASA Astrophysics Data System (ADS)

Bernardini, F.; de Martino, D.; Mukai, K.; Falanga, M.

2018-04-01

IGR J14257-6117 is an unclassified source in the hard X-ray catalogues. Optical follow-ups suggest it could be a Cataclysmic Variable of the magnetic type. We present the first high S/N X-ray observation performed by XMM-Newton at 0.3-10 keV, complemented with 10-80 keV coverage by Swift/BAT, aimed at revealing the source nature. We detected for the first time a fast periodic variability at 509.5 s and a longer periodic variability at 4.05 h, ascribed to the white dwarf (WD) spin and binary orbital periods, respectively. These unambiguously identify IGR J14257-6117 as a magnetic CV of the Intermediate Polar (IP) type. The energy resolved light curves at both periods reveal amplitudes decreasing with increasing energy, with the orbital modulation reaching ˜100% in the softest band. The energy spectrum shows optically thin thermal emission with an excess at the iron complex, absorbed by two dense media (NH ˜ 1022 - 23 cm-2), partially covering the X-ray source. These are likely localised in the magnetically confined accretion flow above the WD surface and at the disc rim, producing the energy dependent spin and orbital variabilities, respectively. IGR J14257-6117, joins the group of strongest orbitally modulated IPs now counting four systems. Drawing similarities with low-mass X-ray binaries displaying orbital dips, these IPs should be seen at large orbital inclinations allowing azimuthally extended absorbing material fixed in the binary frame to intercept the line of sight. For IGR J14257-6117, we estimate (50o ≲ i ≲ 70o). Whether also the mass accretion rate plays a role in the large orbital modulations in IPs cannot be established with the present data.

Solar--geophysical data. Prompt reports. [Number 405, May 1978. Data for A/pril 1978--March 1978

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coffey, H.E.

1978-05-01

This prompt report provides data for April 1978 on alert period, daily solar indices, solar flares, solar radio waves, solar x-ray radiation, coronal holes, inferred IP magnetic field polarities, mean solar magnetic field, solar wind measurements, geomagnetic substorms, and magnetograms of geomagnetic storm. It also provides data for March 1978 on daily solar activity center, sudden ionospheric disturbances, solar x-ray radiation, solar radio waves, cosmic rays, geomagnetic indices and radio propagation indices. A new data page lists the North American magnetometer network.

The Effect of Internal Possession Laws on Underage Drinking Among High School Students: A 12-State Analysis

PubMed Central

Disney, Lynn D.; Yi, Hsiao-ye

2013-01-01

Objectives. We assessed the effect of internal possession (IP) laws, which allow law enforcement to charge underage drinkers with alcohol possession if they have ingested alcohol, on underage drinking behaviors. Methods. We examined Youth Risk Behavior Survey (YRBS) data from 12 states with IP laws and with YRBS data before and after each law’s implementation. We used logistic regression models with fixed effects for state to assess the effects of IP laws on drinking and binge drinking among high school students. Results. Implementation of IP laws is associated with reductions in the odds of past-month drinking. This reduction was bigger among male than among female adolescents (27% vs 15%) and only significant among younger students aged 14 and 15 years (15% and 11%, respectively). Male adolescents also reported a significant reduction (24%) in the odds of past-month binge drinking under IP laws. Conclusions. These findings suggest that IP laws are effective in reducing underage drinking, particularly among younger adolescents. PMID:23597385

Advancing interprofessional education through the use of high fidelity human patient simulators

PubMed Central

Smithburger, Pamela L.; Kane-Gill, Sandra L.; Kloet, Megan A.; Lohr, Brian; Seybert, Amy L.

Background Modern medical care increasingly requires coordinated teamwork and communication between healthcare professionals of different disciplines. Unfortunately, healthcare professional students are rarely afforded the opportunity to learn effective methods of interprofessional (IP) communication and teamwork strategies during their education. The question of how to best incorporate IP interactions in the curricula of the schools of health professions remains unanswered. Objective We aim to solve the lack of IP education in the pharmacy curricula through the use of high fidelity simulation (HFS) to allow teams of medical, pharmacy, nursing, physician assistant, and social work students to work together in a controlled environment to solve cases of complex medical and social issues. Methods Once weekly for a 4-week time period, students worked together to complete complex simulation scenarios in small IP teams consisting of pharmacy, medical, nursing, social work, and physician assistant students. Student perception of the use of HFS was evaluated by a survey given at the conclusion of the HFS sessions. Team communication was evaluated through the use of Communication and Teamwork Skills (CATS) Assessment by 2 independent evaluators external to the project. Results The CATS scores improved from the HFS sessions 1 to 2 (p = 0.01), 2 to 3 (p = 0.035), and overall from 1 to 4 (p = 0.001). The inter-rater reliability between evaluators was high (0.85, 95% CI 0.71, 0.99). Students perceived the HFS improved: their ability to communicate with other professionals (median =4); confidence in patient care in an IP team (median=4). It also stimulated student interest in IP work (median=4.5), and was an efficient use of student time (median=4.5) Conclusions The use of HFS improved student teamwork and communication and was an accepted teaching modality. This method of exposing students of the health sciences to IP care should be incorporated throughout the curricula. PMID:24155851

IPS analysis on relationship among velocity, density and temperature of the solar wind

NASA Astrophysics Data System (ADS)

Hayashi, K.; Tokumaru, M.; Fujiki, K.

2015-12-01

The IPS(Interplanetary Scintillation)-MHD(magnetohydrodynamics) tomography is a method we have developed to determine three-dimensional MHD solution of the solar wind that best matches the line-of-sight IPS solar-wind speed data (Hayashi et al., 2003). The tomographic approach is an iteration method in which IPS observations are simulated in MHD steady-state solution, then differences between the simulated observation and the actual IPS observation is reduced by modifying solar-wind boundary map at 50 solar radii. This forward model needs to assume solar wind density and temperature as function of speed. We use empirical functions, N(V) and T(V), derived from Helios in-situ measurement data within 0.5 AU in 1970s. For recent years, especially after 2006, these functions yield higher densities and lower temperatures than in-situ measurements indicate. To characterize the differences between the simulated and actual solar wind plasma, we tune parameters in the functions so that agreements with in-situ data (near the Earth and at Ulysses) will be optimized. This optimization approach can help better simulations of the solar corona and heliosphere, and will help our understandings on roles of magnetic field in solar wind heating and acceleration.

Resolution Properties Of A Computed Radiographic System

NASA Astrophysics Data System (ADS)

Fujita, Hiroshi; Morishita, Junji; Ueda, Katsuhiko; Tsai, Du Y.; Ohtsuka, Akiyoshi; Fujikawa, Tsuyoshi

1989-05-01

The analysis of spatial-resolution properties in terms of the modulation transfer function (MTF) has been presented in a computed radiographic (CR) system (FCR-101) with the photostimulable-phosphor plate (imaging plate, IP). The newly devised method of determining the presampling MTF which includes the x-ray detector (IP) unsharpness and the unsharpness of the sampling aperture is described in which an image of a slightly-angulated lead slit relative to a horizontal or vertical direction is employed. The IP MTFs as an analog MTF in the system, the presampling MTFs for different types of IPs, different sampling distances, different versions of IPs, simultaneous multisection tomography and magnification radiography, and the laser-printer MTFs as display MTF are measured and shown. The effective sampling aperture MTFs calculated indicate that the noticeable degradation of resolution occurs at the stage of image data sampling. The usefulness of the magnification technique for mammography and bone radiography is demonstrated. It is shown that both of the digital MTF and the overall MTF are difficult to use for general purpose due to the aliasing artifacts. The effect of glare on the contrast is also characterized by lead-disk method. The glare fraction is found to be approximately 6.5%.

High-resolution IP25-based reconstruction of sea-ice variability in the western North Pacific and Bering Sea during the past 18,000 years

NASA Astrophysics Data System (ADS)

Méheust, Marie; Stein, Ruediger; Fahl, Kirsten; Max, Lars; Riethdorf, Jan-Rainer

2016-04-01

Due to its strong influence on heat and moisture exchange between the ocean and the atmosphere, sea ice is an essential component of the global climate system. In the context of its alarming decrease in terms of concentration, thickness and duration, understanding the processes controlling sea-ice variability and reconstructing paleo-sea-ice extent in polar regions have become of great interest for the scientific community. In this study, for the first time, IP25, a recently developed biomarker sea-ice proxy, was used for a high-resolution reconstruction of the sea-ice extent and its variability in the western North Pacific and western Bering Sea during the past 18,000 years. To identify mechanisms controlling the sea-ice variability, IP25 data were associated with published sea-surface temperature as well as diatom and biogenic opal data. The results indicate that a seasonal sea-ice cover existed during cold periods (Heinrich Stadial 1 and Younger Dryas), whereas during warmer intervals (Bølling-Allerød and Holocene) reduced sea ice or ice-free conditions prevailed in the study area. The variability in sea-ice extent seems to be linked to climate anomalies and sea-level changes controlling the oceanographic circulation between the subarctic Pacific and the Bering Sea, especially the Alaskan Stream injection though the Aleutian passes.

Multi-method Quantification of Sea-ice Production in Weddell Sea Polynyas (Antarctica)

NASA Astrophysics Data System (ADS)

Heinemann, G.; Zentek, R.; Stulic, L.; Paul, S.; Preusser, A.; Timmermann, R.

2017-12-01

Coastal polynyas occur frequently during winter in the Weddell Sea, which leads to strong sea ice production and to the formation of a highly saline water mass which is considered to be a major source of bottom water and one of the main drivers of the circulation beneath the Filchner-Ronne Ice Shelf. Thus the quantification of sea ice production in Weddell Sea polynyas is of vital interest for understanding water mass modification in this region. We use a multi-method approach to quantify sea ice production. Method 1) is based on the energy balance simulated by the regional climate model COSMO-CLM (CCLM) with 15 / 5 km resolution for the period 2002-2015 (nested in ERA-Interim data). Daily sea ice concentrations were taken from microwave satellite measurements. Method 2) is based on remote sensing using MODIS thermal infrared data at a resolution of 1-2km and a surface energy balance model taking atmospheric data from different reanalyses (ERA-Interim, JRA55, NCEP2) as well as data of CCLM. Method 3) relies on simulations using the Finite Element Sea ice-Ocean Model (FESOM). FESOM is run on a global grid with a resolution of about 5 km along the coast of the Weddell Sea using atmospheric forcing from reanalyses (ERA-Interim (80km) and CFSR (38km)) as well as from CCLM. In addition, an experiment with assimilation of MODIS thin ice retrievals was conducted. Estimates of polynya area (POLA) and sea ice production (IP) from the different methods are presented. The MODIS-based method with ERA-Interim shows the largest POLA as well as the largest IP for the Ronne polynya (RO, POLA / IP = 2800 km² / 29 km³/a) and for the polynya off Brunt Ice Shelf (BR, 3400 km² / 30 km³/a). Sensitivity to the choice of atmosphere data is high. In particular, too low temperatures in JRA55 cause very large ice production events and a strong overestimation of IP rates. Estimates based on CCLM simulations agree generally well with MODIS/ERA-Interim. FESOM yields a generally larger ice production and shows also a pronounced sensitivity to the atmospheric forcing, but the effect on POLA and IP depends on the region. For BR the FESOM simulations show much larger POLA and IP than other methods.

Remote Monitoring of the Polarized Target's Control for E1039

NASA Astrophysics Data System (ADS)

Fox, David; SeaQuest Collaboration

2017-09-01

The 1039 experiment at FNAL will further our understanding of spin structure by measuring the contribution that sea quarks orbital angular momentum provide to overall nucleon spin. It is accepted that the valence-quarks of nucleons only provide 30% of the total nucleon spin. To study the nucleon's sea quark contribution, E1039 will use the Drell-Yan process by colliding 120 GeV un-polarized beam protons with polarized ammonia targets of hydrogen and deuterium. The asymmetric spin distributions of resulting dimuons will be measured. These asymmetries are sensitive, among other effects, to the orbital angular momentum contribution of the sea quarks. The polarized target requires a multi-stage vacuum pump located near the target. Since access to its present controls will not be possible during running, remote control and monitoring upgrades were required. A secondary control panel was purchased and tested. Information from the programmable logic controller (PLC) must be fed into our data stream to enable remote monitoring and to signal possible alarm conditions. This solution and the program created using explicit TCP/IP messaging to extract data tags from the PLC and log it within our databases will be presented. Supported by U.S. D.O.E. Medium Energy Nuclear Physics under Grant DE-FG02-03ER41243.

Cytokinin, auxin and physiological polarity in the aquatic carnivorous plants Aldrovanda vesiculosa and Utricularia australis

PubMed Central

Šimura, Jan; Spíchal, Lukáš; Adamec, Lubomír; Pěnčík, Aleš; Rolčík, Jakub; Novák, Ondřej; Strnad, Miroslav

2016-01-01

Background and Aims The typical rootless linear shoots of aquatic carnivorous plants exhibit clear, steep polarity associated with very rapid apical shoot growth. The aim of this study was to determine how auxin and cytokinin contents are related to polarity and shoot growth in such plants. Methods The main auxin and cytokinin metabolites in separated shoot segments and turions of two carnivorous plants, Aldrovanda vesiculosa and Utricularia australis, were analysed using ultra-high-performance liquid chromatography coupled with triple quad mass spectrometry. Key Results In both species, only isoprenoid cytokinins were identified. Zeatin cytokinins predominated in the apical parts, with their concentrations decreasing basipetally, and the trans isomer predominated in A. vesiculosa whereas the cis form was more abundant in U australis. Isopentenyladenine-type cytokinins, in contrast, increased basipetally. Conjugated cytokinin metabolites, the O-glucosides, were present at high concentrations in A. vesiculosa but only in minute amounts in U. australis. N9-glucoside forms were detected only in U. australis, with isopentenyladenine-9-glucoside (iP9G) being most abundant. In addition to free indole-3-acetic acid (IAA), indole-3-acetamide (IAM), IAA-aspartate (IAAsp), IAA-glutamate (IAGlu) and IAA-glycine (IAGly) conjugates were identified. Conclusions Both species show common trends in auxin and cytokinin levels, the apical localization of the cytokinin biosynthesis and basipetal change in the ratio of active cytokinins to auxin, in favour of auxin. However, our detailed study of cytokinin metabolic profiles also revealed that both species developed different regulatory mechanisms of active cytokinin content; on the level of their degradation, in U. australis, or in the biosynthesis itself, in the case of A. vesiculosa. Results indicate that the rapid turnover of these signalling molecules along the shoots is essential for maintaining the dynamic balance between the rapid polar growth and development of the apical parts and senescence of the older, basal parts of the shoots. PMID:27098087

ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis

PubMed Central

2011-01-01

Background Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription factor bindings and histone modifications. Previous reports only compared a small number of profiles, and little has been done to compare histone modification profiles generated by the two technologies or to assess the impact of input DNA libraries in ChIP-seq analysis. Here, we performed a systematic analysis of a modENCODE dataset consisting of 31 pairs of ChIP-chip/ChIP-seq profiles of the coactivator CBP, RNA polymerase II (RNA PolII), and six histone modifications across four developmental stages of Drosophila melanogaster. Results Both technologies produce highly reproducible profiles within each platform, ChIP-seq generally produces profiles with a better signal-to-noise ratio, and allows detection of more peaks and narrower peaks. The set of peaks identified by the two technologies can be significantly different, but the extent to which they differ varies depending on the factor and the analysis algorithm. Importantly, we found that there is a significant variation among multiple sequencing profiles of input DNA libraries and that this variation most likely arises from both differences in experimental condition and sequencing depth. We further show that using an inappropriate input DNA profile can impact the average signal profiles around genomic features and peak calling results, highlighting the importance of having high quality input DNA data for normalization in ChIP-seq analysis. Conclusions Our findings highlight the biases present in each of the platforms, show the variability that can arise from both technology and analysis methods, and emphasize the importance of obtaining high quality and deeply sequenced input DNA libraries for ChIP-seq analysis. PMID:21356108

Benchmark study of ionization potentials and electron affinities of armchair single-walled carbon nanotubes using density functional theory

NASA Astrophysics Data System (ADS)

Zhou, Bin; Hu, Zhubin; Jiang, Yanrong; He, Xiao; Sun, Zhenrong; Sun, Haitao

2018-05-01

The intrinsic parameters of carbon nanotubes (CNTs) such as ionization potential (IP) and electron affinity (EA) are closely related to their unique properties and associated applications. In this work, we demonstrated the success of optimal tuning method based on range-separated (RS) density functionals for both accurate and efficient prediction of vertical IPs and electron affinities (EAs) of a series of armchair single-walled carbon nanotubes C20n H20 (n  =  2–6) compared to the high-level IP/EA equation-of-motion coupled-cluster method with single and double substitutions (IP/EA-EOM-CCSD). Notably, the resulting frontier orbital energies (–ε HOMO and –ε LUMO) from the tuning method exhibit an excellent approximation to the corresponding IPs and EAs, that significantly outperform other conventional density functionals. In addition, it is suggested that the RS density functionals that possess both a fixed amount of exact exchange in the short-range and a correct long-range asymptotic behavior are suitable for calculating electronic structures of finite-sized CNTs. Next the performance of density functionals for description of various molecular properties such as chemical potential, hardness and electrophilicity are assessed as a function of tube length. Thanks to the efficiency and accuracy of this tuning method, the related behaviors of much longer armchair single-walled CNTs until C200H20 were studied. Lastly, the present work is proved to provide an efficient theoretical tool for future materials design and reliable characterization of other interesting properties of CNT-based systems.

Strand-Specific Analysis of DNA Synthesis and Proteins Association with DNA Replication Forks in Budding Yeast.

PubMed

Yu, Chuanhe; Gan, Haiyun; Zhang, Zhiguo

2018-01-01

DNA replication initiates at DNA replication origins after unwinding of double-strand DNA(dsDNA) by replicative helicase to generate single-stranded DNA (ssDNA) templates for the continuous synthesis of leading-strand and the discontinuous synthesis of lagging-strand. Therefore, methods capable of detecting strand-specific information will likely yield insight into the association of proteins at leading and lagging strand of DNA replication forks and the regulation of leading and lagging strand synthesis during DNA replication. The enrichment and Sequencing of Protein-Associated Nascent DNA (eSPAN), which measure the relative amounts of proteins at nascent leading and lagging strands of DNA replication forks, is a step-wise procedure involving the chromatin immunoprecipitation (ChIP) of a protein of interest followed by the enrichment of protein-associated nascent DNA through BrdU immunoprecipitation. The isolated ssDNA is then subjected to strand-specific sequencing. This method can detect whether a protein is enriched at leading or lagging strand of DNA replication forks. In addition to eSPAN, two other strand-specific methods, (ChIP-ssSeq), which detects potential protein-ssDNA binding and BrdU-IP-ssSeq, which can measure synthesis of both leading and lagging strand, were developed along the way. These methods can provide strand-specific and complementary information about the association of the target protein with DNA replication forks as well as synthesis of leading and lagging strands genome wide. Below, we describe the detailed eSPAN, ChIP-ssSeq, and BrdU-IP-ssSeq protocols.

A Spiking Strategy for ChIP-chip Data Normalization in S. cerevisiae.

PubMed

Jeronimo, Célia; Robert, François

2017-01-01

Chromatin immunoprecipitation coupled to DNA microarrays (ChIP-chip) is widely used in the chromatin field, notably to map the position of histone variants or histone modifications along the genome. Often, the position and the occupancy of these epigenetic marks are to be compared between different experiments. It is now increasingly recognized that such cross-sample comparison is better done using externally added exogenous controls for normalization but no such method has been described for ChIP-chip. Here we describe a spiking normalization strategy that makes use of phiX174 phage DNA as a spiked control for normalization of ChIP-chip signals across different experiments.

Broad-band characteristics of seven new hard X-ray selected cataclysmic variables

NASA Astrophysics Data System (ADS)

Bernardini, F.; de Martino, D.; Mukai, K.; Russell, D. M.; Falanga, M.; Masetti, N.; Ferrigno, C.; Israel, G.

2017-10-01

We present timing and spectral analysis of a sample of seven hard X-ray selected cataclysmic variable candidates based on simultaneous X-ray and optical observations collected with XMM-Newton, complemented with Swift/BAT and INTEGRAL /IBIS hard X-ray data and ground-based optical photometry. For six sources, X-ray pulsations are detected for the first time in the range of ˜296-6098 s, identifying them as members of the magnetic class. Swift J0927.7-6945, Swift J0958.0-4208, Swift J1701.3-4304, Swift J2113.5+5422 and possibly PBC J0801.2-4625 are intermediate polars (IPs), while Swift J0706.8+0325 is a short (1.7 h) orbital period polar, the 11th hard X-ray-selected identified so far. X-ray orbital modulation is also observed in Swift J0927.7-6945 (5.2 h) and Swift J2113.5+5422 (4.1 h). Swift J1701.3-4304 is discovered as the longest orbital period (12.8 h) deep eclipsing IP. The spectra of the magnetic systems reveal optically thin multitemperature emission between 0.2 and 60 keV. Energy-dependent spin pulses and the orbital modulation in Swift J0927.7-6945 and Swift J2113.5+5422 are due to intervening local high-density absorbing material (NH ˜ 1022 - 23 cm-2). In Swift J0958.0-4208 and Swift J1701.3-4304, a soft X-ray blackbody (kT ˜ 50 and ˜80 eV) is detected, adding them to the growing group of `soft' IPs. White dwarf masses are determined in the range of ˜ 0.58-1.18 M⊙, indicating massive accreting primaries in five of them. Most sources accrete at rates lower than the expected secular value for their orbital period. Formerly proposed as a long-period (9.4 h) nova-like CV, Swift J0746.3-1608 shows peculiar spectrum and light curves suggesting either an atypical low-luminosity CV or a low-mass X-ray binary.

Method for observing phase objects without halos and directional shadows

NASA Astrophysics Data System (ADS)

Suzuki, Yoshimasa; Kajitani, Kazuo; Ohde, Hisashi

2015-03-01

A new microscopy method for observing phase objects without halos and directional shadows is proposed. The key optical element is an annular aperture at the front focal plane of a condenser with a larger diameter than those used in standard phase contrast microscopy. The light flux passing through the annular aperture is changed by the specimen's surface profile and then passes through an objective and contributes to image formation. This paper presents essential conditions for realizing the method. In this paper, images of colonies formed by induced pluripotent stem (iPS) cells using this method are compared with the conventional phase contrast method and the bright-field method when the NA of the illumination is small to identify differences among these techniques. The outlines of the iPS cells are clearly visible with this method, whereas they are not clearly visible due to halos when using the phase contrast method or due to weak contrast when using the bright-field method. Other images using this method are also presented to demonstrate a capacity of this method: a mouse ovum and superimposition of several different images of mouse iPS cells.

Determining ERβ Binding Affinity to Singly Mutant ERE Using Dual Polarization Interferometry

NASA Astrophysics Data System (ADS)

Song, Hong Yan; Su, Xiaodi

In a classic mode of estrogen action, estrogen receptors (ERs) bind to estrogen responsive element (ERE) to activate gene transcription. A perfect ERE contains a 13-base pair sequence of a palindromic repeat separated by a three-base spacer, 5‧-GGTCAnnnTGACC-3‧. In addition to the consensus or wild-type ERE (wtERE), naturally occurring EREs often have one or two base pairs’ alternation. Based on the newly constructed Thermodynamic Modeling of ChIP-seq (TherMos) model, binding energy between ERβ and a series of 34-bp mutant EREs (mutERE) was simulated to predict the binding affinity between ERs and EREs with single base pair deviation at different sites of the 13-bp inverted sequence. Experimentally, dual polarization interferometry (DPI) method was developed to measure ERβ-mutEREs binding affinity. On a biotin-NeutrAvidin (NA)-biotin treated DPI chip, wtERE is immobilized. In a direct binding assay, ERβ-wtERE binding affinity is determined. In a competition assay, ERβ was preincubated with mutant EREs before being added for competitive binding to the immobilized wtERE. This competition strategy provided a successful platform to evaluate the binding affinity variation among large number of ERE with different base mutations. The experimental result correlates well with the mathematically predicted binding energy with a Spearman correlation coefficient of 0.97.

IP-10 measured by Dry Plasma Spots as biomarker for therapy responses in Mycobacterium Tuberculosis infection.

PubMed

Tonby, Kristian; Ruhwald, Morten; Kvale, Dag; Dyrhol-Riise, Anne Ma

2015-03-18

Tuberculosis (TB) has huge impact on human morbidity and mortality and biomarkers to support rapid TB diagnosis and ensure treatment initiation and cure are needed, especially in regions with high prevalence of multi-drug resistant TB. Soluble interferon gamma inducible protein 10 (IP-10) analyzed from dry plasma spots (DPS) has potential as an immunodiagnostic marker in TB infection. We analyzed IP-10 levels in plasma directly and extracted from DPS in parallel by ELISA from 34 clinically well characterized patients with TB disease before and throughout 24 weeks of effective anti-TB chemotherapy. We detected a significant decline of IP-10 levels in both plasma and DPS already after two weeks of therapy with good correlation between the tests. This was observed both in pulmonary and extrapulmonary TB. In conclusion, plasma IP-10 may serve as an early biomarker for anti-TB chemotherapy responses and the IP-10 DPS method has potential to be developed into a point-of care test for use in resource-limited settings. Further studies must be performed to validate the use of IP-10 DPS in TB high endemic countries.

Biosphere Reserve for All: Potentials for Involving Underrepresented Age Groups in the Development of a Biosphere Reserve through Intergenerational Practice.

PubMed

Mitrofanenko, Tamara; Snajdr, Julia; Muhar, Andreas; Penker, Marianne; Schauppenlehner-Kloyber, Elisabeth

2018-05-22

Stakeholder participation is of high importance in UNESCO biosphere reserves as model regions for sustainable development; however, certain groups remain underrepresented. The paper proposes Intergenerational Practice (IP) as a means of involving youth and elderly women and explores its options and barriers, using the example of the Salzburger Lungau and Kärntner Nockberge Biosphere Reserve in Austria. Case study analysis is used involving mixed methods. The results reveal obstacles and motivations to participating in biosphere reserve implementation and intergenerational activities for the youth and the elderly women and imply that much potential for IP exists in the biosphere reserve region. The authors propose suitable solutions from the intergenerational field to overcome identified participation obstacles and suggest benefits of incorporating IP as a management tool into biosphere reserve activities. Suggestions for future research include evaluating applications of IP in the context of protected areas, testing of methods used in other contexts, and contribution to theory development.

Broad-Enrich: functional interpretation of large sets of broad genomic regions.

PubMed

Cavalcante, Raymond G; Lee, Chee; Welch, Ryan P; Patil, Snehal; Weymouth, Terry; Scott, Laura J; Sartor, Maureen A

2014-09-01

Functional enrichment testing facilitates the interpretation of Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) data in terms of pathways and other biological contexts. Previous methods developed and used to test for key gene sets affected in ChIP-seq experiments treat peaks as points, and are based on the number of peaks associated with a gene or a binary score for each gene. These approaches work well for transcription factors, but histone modifications often occur over broad domains, and across multiple genes. To incorporate the unique properties of broad domains into functional enrichment testing, we developed Broad-Enrich, a method that uses the proportion of each gene's locus covered by a peak. We show that our method has a well-calibrated false-positive rate, performing well with ChIP-seq data having broad domains compared with alternative approaches. We illustrate Broad-Enrich with 55 ENCODE ChIP-seq datasets using different methods to define gene loci. Broad-Enrich can also be applied to other datasets consisting of broad genomic domains such as copy number variations. http://broad-enrich.med.umich.edu for Web version and R package. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

An Alternative Approach to ChIP-Seq Normalization Enables Detection of Genome-Wide Changes in Histone H3 Lysine 27 Trimethylation upon EZH2 Inhibition

PubMed Central

Yuan, Chih-Chi; Craske, Madeleine Lisa; Labhart, Paul; Guler, Gulfem D.; Arnott, David; Maile, Tobias M.; Busby, Jennifer; Henry, Chisato; Kelly, Theresa K.; Tindell, Charles A.; Jhunjhunwala, Suchit; Zhao, Feng; Hatton, Charlie; Bryant, Barbara M.

2016-01-01

Chromatin immunoprecipitation and DNA sequencing (ChIP-seq) has been instrumental in inferring the roles of histone post-translational modifications in the regulation of transcription, chromatin compaction and other cellular processes that require modulation of chromatin structure. However, analysis of ChIP-seq data is challenging when the manipulation of a chromatin-modifying enzyme significantly affects global levels of histone post-translational modifications. For example, small molecule inhibition of the methyltransferase EZH2 reduces global levels of histone H3 lysine 27 trimethylation (H3K27me3). However, standard ChIP-seq normalization and analysis methods fail to detect a decrease upon EZH2 inhibitor treatment. We overcome this challenge by employing an alternative normalization approach that is based on the addition of Drosophila melanogaster chromatin and a D. melanogaster-specific antibody into standard ChIP reactions. Specifically, the use of an antibody that exclusively recognizes the D. melanogaster histone variant H2Av enables precipitation of D. melanogaster chromatin as a minor fraction of the total ChIP DNA. The D. melanogaster ChIP-seq tags are used to normalize the human ChIP-seq data from DMSO and EZH2 inhibitor-treated samples. Employing this strategy, a substantial reduction in H3K27me3 signal is now observed in ChIP-seq data from EZH2 inhibitor treated samples. PMID:27875550

An Alternative Approach to ChIP-Seq Normalization Enables Detection of Genome-Wide Changes in Histone H3 Lysine 27 Trimethylation upon EZH2 Inhibition.

PubMed

Egan, Brian; Yuan, Chih-Chi; Craske, Madeleine Lisa; Labhart, Paul; Guler, Gulfem D; Arnott, David; Maile, Tobias M; Busby, Jennifer; Henry, Chisato; Kelly, Theresa K; Tindell, Charles A; Jhunjhunwala, Suchit; Zhao, Feng; Hatton, Charlie; Bryant, Barbara M; Classon, Marie; Trojer, Patrick

2016-01-01

Chromatin immunoprecipitation and DNA sequencing (ChIP-seq) has been instrumental in inferring the roles of histone post-translational modifications in the regulation of transcription, chromatin compaction and other cellular processes that require modulation of chromatin structure. However, analysis of ChIP-seq data is challenging when the manipulation of a chromatin-modifying enzyme significantly affects global levels of histone post-translational modifications. For example, small molecule inhibition of the methyltransferase EZH2 reduces global levels of histone H3 lysine 27 trimethylation (H3K27me3). However, standard ChIP-seq normalization and analysis methods fail to detect a decrease upon EZH2 inhibitor treatment. We overcome this challenge by employing an alternative normalization approach that is based on the addition of Drosophila melanogaster chromatin and a D. melanogaster-specific antibody into standard ChIP reactions. Specifically, the use of an antibody that exclusively recognizes the D. melanogaster histone variant H2Av enables precipitation of D. melanogaster chromatin as a minor fraction of the total ChIP DNA. The D. melanogaster ChIP-seq tags are used to normalize the human ChIP-seq data from DMSO and EZH2 inhibitor-treated samples. Employing this strategy, a substantial reduction in H3K27me3 signal is now observed in ChIP-seq data from EZH2 inhibitor treated samples.

An improved grey wolf optimizer algorithm for the inversion of geoelectrical data

NASA Astrophysics Data System (ADS)

Li, Si-Yu; Wang, Shu-Ming; Wang, Peng-Fei; Su, Xiao-Lu; Zhang, Xin-Song; Dong, Zhi-Hui

2018-05-01

The grey wolf optimizer (GWO) is a novel bionics algorithm inspired by the social rank and prey-seeking behaviors of grey wolves. The GWO algorithm is easy to implement because of its basic concept, simple formula, and small number of parameters. This paper develops a GWO algorithm with a nonlinear convergence factor and an adaptive location updating strategy and applies this improved grey wolf optimizer (improved grey wolf optimizer, IGWO) algorithm to geophysical inversion problems using magnetotelluric (MT), DC resistivity and induced polarization (IP) methods. Numerical tests in MATLAB 2010b for the forward modeling data and the observed data show that the IGWO algorithm can find the global minimum and rarely sinks to the local minima. For further study, inverted results using the IGWO are contrasted with particle swarm optimization (PSO) and the simulated annealing (SA) algorithm. The outcomes of the comparison reveal that the IGWO and PSO similarly perform better in counterpoising exploration and exploitation with a given number of iterations than the SA.

Validity of a self-administered food frequency questionnaire in the estimation of heterocyclic aromatic amines.

PubMed

Iwasaki, Motoki; Mukai, Tomomi; Takachi, Ribeka; Ishihara, Junko; Totsuka, Yukari; Tsugane, Shoichiro

2014-08-01

Clarification of the putative etiologic role of heterocyclic aromatic amines (HAAs) in the development of cancer requires a validated assessment tool for dietary HAAs. This study primarily aimed to evaluate the validity of a food frequency questionnaire (FFQ) in estimating HAA intake, using 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) level in human hair as the reference method. We first updated analytical methods of PhIP using liquid chromatography-electrospray ionization/tandem mass spectrometry (LC-ESI/MS/MS) and measured 44 fur samples from nine rats from a feeding study as part-verification of the quantitative performance of LC-ESI/MS/MS. We next measured PhIP level in human hair samples from a validation study of the FFQ (n = 65). HAA intake from the FFQ was estimated using information on intake from six fish items and seven meat items and data on HAA content in each food item. Correlation coefficients between PhIP level in human hair and HAA intake from the FFQ were calculated. The animal feeding study of PhIP found a significant dose-response relationship between dosage and PhIP in rat fur. Mean level was 53.8 pg/g hair among subjects with values over the limit of detection (LOD) (n = 57). We found significant positive correlation coefficients between PhIP in human hair and HAA intake from the FFQ, with Spearman rank correlation coefficients of 0.35 for all subjects, 0.21 for subjects with over LOD values, and 0.34 for subjects with over limit of quantification. Findings from the validation study suggest that the FFQ is reasonably valid for the assessment of HAA intake.

Teaching Network Security with IP Darkspace Data

ERIC Educational Resources Information Center

Zseby, Tanja; Iglesias Vázquez, Félix; King, Alistair; Claffy, K. C.

2016-01-01

This paper presents a network security laboratory project for teaching network traffic anomaly detection methods to electrical engineering students. The project design follows a research-oriented teaching principle, enabling students to make their own discoveries in real network traffic, using data captured from a large IP darkspace monitor…

Real-time capture and reconstruction system with multiple GPUs for a 3D live scene by a generation from 4K IP images to 8K holograms.

PubMed

Ichihashi, Yasuyuki; Oi, Ryutaro; Senoh, Takanori; Yamamoto, Kenji; Kurita, Taiichiro

2012-09-10

We developed a real-time capture and reconstruction system for three-dimensional (3D) live scenes. In previous research, we used integral photography (IP) to capture 3D images and then generated holograms from the IP images to implement a real-time reconstruction system. In this paper, we use a 4K (3,840 × 2,160) camera to capture IP images and 8K (7,680 × 4,320) liquid crystal display (LCD) panels for the reconstruction of holograms. We investigate two methods for enlarging the 4K images that were captured by integral photography to 8K images. One of the methods increases the number of pixels of each elemental image. The other increases the number of elemental images. In addition, we developed a personal computer (PC) cluster system with graphics processing units (GPUs) for the enlargement of IP images and the generation of holograms from the IP images using fast Fourier transform (FFT). We used the Compute Unified Device Architecture (CUDA) as the development environment for the GPUs. The Fast Fourier transform is performed using the CUFFT (CUDA FFT) library. As a result, we developed an integrated system for performing all processing from the capture to the reconstruction of 3D images by using these components and successfully used this system to reconstruct a 3D live scene at 12 frames per second.

Phosphoinositide and Inositol Phosphate Analysis in Lymphocyte Activation

PubMed Central

Sauer, Karsten; Huang, Yina Hsing; Lin, Hongying; Sandberg, Mark; Mayr, Georg W.

2015-01-01

Lymphocyte antigen receptor engagement profoundly changes the cellular content of phosphoinositide lipids and soluble inositol phosphates. Among these, the phosphoinositides phosphatidylinositol 4,5-bisphosphate (PIP2) and phosphatidylinositol 3,4,5-trisphosphate (PIP3) play key signaling roles by acting as pleckstrin homology (PH) domain ligands that recruit signaling proteins to the plasma membrane. Moreover, PIP2 acts as a precursor for the second messenger molecules diacylglycerol and soluble inositol 1,4,5-trisphosphate (IP3), essential mediators of PKC, Ras/Erk, and Ca2+ signaling in lymphocytes. IP3 phosphorylation by IP3 3-kinases generates inositol 1,3,4,5-tetrakisphosphate (IP4), an essential soluble regulator of PH domain binding to PIP3 in developing T cells. Besides PIP2, PIP3, IP3, and IP4, lymphocytes produce multiple other phosphoinositides and soluble inositol phosphates that could have important physiological functions. To aid their analysis, detailed protocols that allow one to simultaneously measure the levels of multiple different phosphoinositide or inositol phosphate isomers in lymphocytes are provided here. They are based on thin layer, conventional and high-performance liquid chromatographic separation methods followed by radiolabeling or non-radioactive metal-dye detection. Finally, less broadly applicable nonchromatographic methods for detection of specific phosphoinositide or inositol phosphate isomers are discussed. Support protocols describe how to obtain pure unstimulated CD4+CD8+ thymocyte populations for analyses of inositol phosphate turnover during positive and negative selection, key steps in T cell development. PMID:19918943

IRF5 regulates lung macrophages M2 polarization during severe acute pancreatitis in vitro.

PubMed

Sun, Kang; He, Song-Bing; Qu, Jian-Guo; Dang, Sheng-Chun; Chen, Ji-Xiang; Gong, Ai-Hua; Xie, Rong; Zhang, Jian-Xin

2016-11-14

To investigate the role of interferon regulatory factor 5 (IRF5) in reversing polarization of lung macrophages during severe acute pancreatitis (SAP) in vitro . A mouse SAP model was established by intraperitoneal (ip) injections of 20 μg/kg body weight caerulein. Pathological changes in the lung were observed by hematoxylin and eosin staining. Lung macrophages were isolated from bronchoalveolar lavage fluid. The quantity and purity of lung macrophages were detected by fluorescence-activated cell sorting and evaluated by real-time polymerase chain reaction (RT-PCR). They were treated with IL-4/IRF5 specific siRNA (IRF5 siRNA) to reverse their polarization and were evaluated by detecting markers expression of M1/M2 using RT-PCR. SAP associated acute lung injury (ALI) was induced successfully by ip injections of caerulein, which was confirmed by histopathology. Lung macrophages expressed high levels of IRF5 as M1 phenotype during the early acute pancreatitis stages. Reduction of IRF5 expression by IRF5 siRNA reversed the action of macrophages from M1 to M2 phenotype in vitro . The expressions of M1 markers, including IRF5 (S + IRF5 siRNA vs S + PBS, 0.013 ± 0.01 vs 0.054 ± 0.047, P < 0.01), TNF-α (S + IRF5 siRNA vs S + PBS, 0.0003 ± 0.0002 vs 0.019 ± 0.018, P < 0.001), iNOS (S + IRF5 siRNA vs S + PBS, 0.0003 ± 0.0002 vs 0.026 ± 0.018, P < 0.001) and IL-12 (S + IRF5 siRNA vs S + PBS, 0.000005 ± 0.00004 vs 0.024 ± 0.016, P < 0.001), were decreased. In contrast, the expressions of M2 markers, including IL-10 (S + IRF5 siRNA vs S + PBS, 0.060 ± 0.055 vs 0.0230 ± 0.018, P < 0.01) and Arg-1 (S + IRF5 siRNA vs S + PBS, 0.910 ± 0.788 vs 0.0036 ± 0.0025, P < 0.001), were increased. IRF5 siRNA could reverse the lung macrophage polarization more effectively than IL-4. Treatment with IRF5 siRNA can reverse the pancreatitis-induced activation of lung macrophages from M1 phenotype to M2 phenotype in SAP associated with ALI.

Creation of a competency-based professional development program for infection preventionists guided by the APIC Competency Model: steps in the process.

PubMed

Bernard, Heather; Hackbarth, Diana; Olmsted, Russell N; Murphy, Denise

2018-06-07

Infection Preventionists have varying levels of educational preparation. Many have no prior experience in IP. The diversity makes design of professional development programs challenging. Recent surveys suggest that only about half of practicing IPs are board certified. There is an urgent need to employ competent IP's to drive improvement in patient outcomes. This is a project that utilized the APIC Competency Model to create a professional development program characterizing three career stages. Methods included a review of literature on professional development; a survey of IP competence; an assessment of job descriptions and performance evaluations; and a crosswalk of IP competencies. The professional development program includes competency - based IP job descriptions and performance evaluations for each career stage; a professional portfolio; and a toolkit for supervisors. Participants agreed that application of the model resulted in tools which are more closely aligned with current roles for IPs; and increased satisfaction and motivation with the new program. Competent and knowledgeable IP's are crucial to optimizing efficacy of IPC programs. A professional development program has the potential to guide staff orientation, improve satisfaction and retention, improve patient outcomes and promote a positive trajectory in advancing practice. Copyright © 2018 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Practical Integration-Free Episomal Methods for Generating Human Induced Pluripotent Stem Cells.

PubMed

Kime, Cody; Rand, Tim A; Ivey, Kathryn N; Srivastava, Deepak; Yamanaka, Shinya; Tomoda, Kiichiro

2015-10-06

The advent of induced pluripotent stem (iPS) cell technology has revolutionized biomedicine and basic research by yielding cells with embryonic stem (ES) cell-like properties. The use of iPS-derived cells for cell-based therapies and modeling of human disease holds great potential. While the initial description of iPS cells involved overexpression of four transcription factors via viral vectors that integrated within genomic DNA, advances in recent years by our group and others have led to safer and higher quality iPS cells with greater efficiency. Here, we describe commonly practiced methods for non-integrating induced pluripotent stem cell generation using nucleofection of episomal reprogramming plasmids. These methods are adapted from recent studies that demonstrate increased hiPS cell reprogramming efficacy with the application of three powerful episomal hiPS cell reprogramming factor vectors and the inclusion of an accessory vector expressing EBNA1. Copyright © 2015 John Wiley & Sons, Inc.

Using Importance-Performance Analysis To Evaluate Teaching Effectiveness.

ERIC Educational Resources Information Center

Attarian, Aram

This paper introduces Importance-Performance (IP) analysis as a method to evaluate teaching effectiveness in a university outdoor program. Originally developed for use in the field of marketing, IP analysis is simple and easy to administer, and provides the instructor with a visual representation of what teaching attributes are important, how…

Migration features of Ips typographus in the Tatra Mountains: using a genetic method

Treesearch

Ferenc Lakatos

2003-01-01

The genetic structure of Ips typographus populations in the Tatra Mountains was studied based on the observed differences of gene flow and migration rate. It was a highlighted question as to what extent different natural barriers influence the migration potential of the species.

Induction of pluripotency by defined factors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Okita, Keisuke, E-mail: okita@cira.kyoto-u.ac.jp; Yamanaka, Shinya; Department of Stem Cell Biology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507

2010-10-01

Somatic cells can be reprogrammed into pluripotent stem cells by introducing a combination of several transcription factors. The induced pluripotent stem (iPS) cells from a patient's somatic cells could be useful source of cells for drug discovery and cell transplantation therapies. However, most human iPS cells are made by viral vectors, such as retrovirus and lentivirus, which integrate the reprogramming factors into host genomes and may increase the risk of tumor formation. Studies of the mechanisms underlying the reprogramming and establishment of non-integration methods contribute evidence to resolve the safety concerns associated with iPS cells. On the other hand, patient-specificmore » iPS cells have already been established and used for recapitulating disease pathology.« less

Synthesis and characterization of non-hydrolysable diphosphoinositol polyphosphate second messengers.

PubMed

Wu, Mingxuan; Dul, Barbara E; Trevisan, Alexandra J; Fiedler, Dorothea

2013-01-01

The diphosphoinositol polyphosphates (PP-IPs) are a central group of eukaryotic second messengers. They regulate numerous processes, including cellular energy homeostasis and adaptation to environmental stresses. To date, most of the molecular details in PP-IP signalling have remained elusive, due to a lack of appropriate methods and reagents. Here we describe the expedient synthesis of methylene-bisphosphonate PP-IP analogues. Their characterization revealed that the analogues exhibit significant stability and mimic their natural counterparts very well. This was further confirmed in two independent biochemical assays, in which our analogues potently inhibited phosphorylation of the protein kinase Akt and hydrolytic activity of the Ddp1 phosphohydrolase. The non-hydrolysable PP-IPs thus emerge as important tools and hold great promise for a variety of applications.

Analytical method development and validation of simultaneous estimation of rabeprazole, pantoprazole, and itopride by reverse-phase high-performance liquid chromatography.

PubMed

Perumal, Senthamil Selvan; Ekambaram, Sanmuga Priya; Raja, Samundeswari

2014-12-01

A simple, selective, rapid, and precise reverse-phase high-performance liquid chromatography (RP-HPLC) method for the simultaneous estimation of rabeprazole (RP), pantoprazole (PP), and itopride (IP) has been developed. The compounds were well separated on a Phenomenex C 18 (Luna) column (250 mm × 4.6 mm, dp = 5 μm) with C 18 guard column (4 mm × 3 mm × 5 μm) with a mobile phase consisting of buffer containing 10 mM potassium dihydrogen orthophosphate (adjusted to pH 6.8): acetonitrile (70:30 v/v) at a flow rate of 1.0 mL/min and ultraviolet detection at 288 nm. The retention time of RP, PP, and IP were 5.35, 7.92, and 11.16 minutes, respectively. Validation of the proposed method was carried out according to International Conference on Harmonisation (ICH) guidelines. Linearity range was obtained for RP, PP, and IP over the concentration range of 2.5-25, 1-30, and 3-35 μg/mL and the r 2 values were 0.994, 0.978, and 0.991, respectively. The calculated limit of detection (LOD) values were 1, 0.3, and 1 μg/mL and limit of quantitation (LOQ) values were 2.5, 1, and 3 μg/mL for RP, PP, and IP correspondingly. Thus, the current study showed that the developed reverse-phase liquid chromatography method is sensitive and selective for the estimation of RP, PP, and IP in combined dosage form. Copyright © 2014. Published by Elsevier B.V.

Vectors to Increase Production Efficiency of Inducible Pluripotent Stem Cell (iPSC) | NCI Technology Transfer Center | TTC

Cancer.gov

This invention describes the discovery that specific p53 isoform increase the number of inducible pluripotent stem cells (iPS). It is known that the activity of p53 regulates the self-renewal and pluripotency of normal and cancer stem cells, and also affects re-programming efficiency of iPS cells. This p53 isoform-based technology provides a more natural process of increasing iPS cell production than previous methods of decreasing p53. NCI seeks licensees for this technology.

Novel Methods for Imaging PET Biomarkers and Gene Therapy of Cancer

DTIC Science & Technology

2009-05-01

sphingosine 1-phosphate; GFP, g reen fluorescent protein. ???? ??, 2009•VOLUME 284• NUMBER?? angiogenesis, and platelet aggregation (1, 2). At least eight...FLAG·LPA2 - - ·-...... ---- ---.,_.-. IB: GFP·TRIP6 -- _ ...... IP: FLAG•LPA2 - - --~~-~IB:FLAG·LPA2 lysates • ... IB: GFP·TRIP6 ... N < < < < C) < u < s...Ill Ill Ill IP: FLAGoLPA2 Ill <!I " <!I <!I <!I GST puldown - IB: stv .. t IP: FLAG.f..PA2 c:oomusleblue - lysates ------ 18: MYC..Siva•1

Human induced pluripotent stem cells labeled with fluorescent magnetic nanoparticles for targeted imaging and hyperthermia therapy for gastric cancer.

PubMed

Li, Chao; Ruan, Jing; Yang, Meng; Pan, Fei; Gao, Guo; Qu, Su; Shen, You-Lan; Dang, Yong-Jun; Wang, Kan; Jin, Wei-Lin; Cui, Da-Xiang

2015-09-01

Human induced pluripotent stem (iPS) cells exhibit great potential for generating functional human cells for medical therapies. In this paper, we report for use of human iPS cells labeled with fluorescent magnetic nanoparticles (FMNPs) for targeted imaging and synergistic therapy of gastric cancer cells in vivo. Human iPS cells were prepared and cultured for 72 h. The culture medium was collected, and then was co-incubated with MGC803 cells. Cell viability was analyzed by the MTT method. FMNP-labeled human iPS cells were prepared and injected into gastric cancer-bearing nude mice. The mouse model was observed using a small-animal imaging system. The nude mice were irradiated under an external alternating magnetic field and evaluated using an infrared thermal mapping instrument. Tumor sizes were measured weekly. iPS cells and the collected culture medium inhibited the growth of MGC803 cells. FMNP-labeled human iPS cells targeted and imaged gastric cancer cells in vivo, as well as inhibited cancer growth in vivo through the external magnetic field. FMNP-labeled human iPS cells exhibit considerable potential in applications such as targeted dual-mode imaging and synergistic therapy for early gastric cancer.

Impact of electronic healthcare-associated infection surveillance software on infection prevention resources: a systematic review of the literature.

PubMed

Russo, P L; Shaban, R Z; Macbeth, D; Carter, A; Mitchell, B G

2018-05-01

Surveillance of healthcare-associated infections is fundamental for infection prevention. The methods and practices for surveillance have evolved as technology becomes more advanced. The availability of electronic surveillance software (ESS) has increased, and yet adoption of ESS is slow. It is argued that ESS delivers savings through automation, particularly in terms of human resourcing and infection prevention (IP) staff time. To describe the findings of a systematic review on the impact of ESS on IP resources. A systematic search was conducted of electronic databases Medline and the Cumulative Index to Nursing and Allied Health Literature published between January 1 st , 2006 and December 31 st , 2016 with analysis using the Newcastle-Ottawa Scale. In all, 2832 articles were reviewed, of which 16 studies met the inclusion criteria. IP resources were identified as time undertaken on surveillance. A reduction in IP staff time to undertake surveillance was demonstrated in 13 studies. The reduction proportion ranged from 12.5% to 98.4% (mean: 73.9%). The remaining three did not allow for any estimation of the effect in terms of IP staff time. None of the studies demonstrated an increase in IP staff time. The results of this review demonstrate that adopting ESS yields considerable dividends in IP staff time relating to data collection and case ascertainment while maintaining high levels of sensitivity and specificity. This has the potential to enable reinvestment into other components of IP to maximize efficient use of scarce IP resources. Copyright © 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Improved phase shift approach to the energy correction of the infinite order sudden approximation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, B.; Eno, L.; Rabitz, H.

1980-07-15

A new method is presented for obtaining energy corrections to the infinite order sudden (IOS) approximation by incorporating the effect of the internal molecular Hamiltonian into the IOS wave function. This is done by utilizing the JWKB approximation to transform the Schroedinger equation into a differential equation for the phase. It is found that the internal Hamiltonian generates an effective potential from which a new improved phase shift is obtained. This phase shift is then used in place of the IOS phase shift to generate new transition probabilities. As an illustration the resulting improved phase shift (IPS) method is appliedmore » to the Secrest--Johnson model for the collinear collision of an atom and diatom. In the vicinity of the sudden limit, the IPS method gives results for transition probabilities, P/sub n/..-->..n+..delta..n, in significantly better agreement with the 'exact' close coupling calculations than the IOS method, particularly for large ..delta..n. However, when the IOS results are not even qualitatively correct, the IPS method is unable to satisfactorily provide improvements.« less

MAPPING INDUCED POLARIZATION WITH NATURAL ELECTROMAGNETIC FIELDS FOR EXPLORATION AND RESOURCES CHARACTERIZATION BY THE MINING INDUSTRY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edward Nichols

2002-05-03

In this quarter we continued the processing of the Safford IP survey data. The processing identified a time shift problem between the sites that was caused by a GPS firmware error. A software procedure was developed to identify and correct the shift, and this was applied to the data. Preliminary estimates were made of the remote referenced MT parameters, and initial data quality assessment showed the data quality was good for most of the line. The multi-site robust processing code of Egbert was linked to the new data and processing initiated.

The predominant WT1 isoform (+KTS) encodes a DNA binding protein targeting the planar cell polarity gene Scribble in renal podocytes

PubMed Central

Wells, Julie; Rivera, Miguel N.; Kim, Woo Jae; Starbuck, Kristen; Haber, Daniel A.

2010-01-01

WT1 encodes a tumor suppressor, first identified by its inactivation in Wilms Tumor. While one WT1 splicing variant encodes a well-characterized zinc finger transcription factor, little is known about the function of the most prevalent WT1 isoform, whose DNA binding domain is disrupted by a three amino acid (KTS) insertion. Using cells which conditionally express WT1(+KTS), we undertook a genome-wide chromatin immunoprecipitation and cloning (ChIP-cloning) analysis to identify candidate WT1(+KTS) regulated promoters. We identified the planar cell polarity (PCP) gene Scribble (SCRB) as the first WT1(+KTS) target gene in podocytes of the kidney. WT1 and SCRB expression patterns overlap precisely in developing renal glomeruli of mice, and WT1(+KTS) binds to a 33 nucleotide region within the Scribble promoter in both mouse and human cell lines and kidneys. Together, our results support a role for the predominant WT1(+KTS) isoform in transcriptional regulation and suggest a link between the WT1-dependent tumor suppressor pathway and a key component of the planar cell polarity pathway. PMID:20571064

A Network Steganography Lab on Detecting TCP/IP Covert Channels

ERIC Educational Resources Information Center

Zseby, Tanja; Vázquez, Félix Iglesias; Bernhardt, Valentin; Frkat, Davor; Annessi, Robert

2016-01-01

This paper presents a network security laboratory to teach data analysis for detecting TCP/IP covert channels. The laboratory is mainly designed for students of electrical engineering, but is open to students of other technical disciplines with similar background. Covert channels provide a method for leaking data from protected systems, which is a…

65nm RadSafe™ Technology for RC64 and Advanced SOCs

NASA Astrophysics Data System (ADS)

Liran, Tuvia; Ginosar, Ran; Lange, Fredy; Mandler, Alberto; Aviely, Peleg; Meirov, Henri; Goldberg, Michael; Meister, Zeev; Oliel, Mickey

2015-09-01

The trend of scaling of microelectronic provides certain advantages for space components, as well as some challenges. It enables implementing highly integrated and high performance ASICs, reducing power, area and weight. Scaling also improves the immunity to TID and SEL in most cases, but increases soft error rate significantly. Ramon Chips adopted the 65nm technology for implementing RC64 [1,2], a 64 core DSP for space applications, and for making other future products. The 65nm process node is widely used, very mature, and supported by wide range of IP providers. Thus the need for full custom design of cores and IPs is minimized, and radiation hardening is achievable by mitigating the radiation effects on the available IPs, and developing proprietary IPs only for complementing the available IPs. The RadSafe_65TM technology includes hardened standard cells and I/O libraries, methods for mitigation of radiation effects in COTS IP cores (SRAM, PLL, SERDES, DDR2/3 interface) and adding unique cores for monitoring radiation effects and junction temperature. We had developed RADIC6, a technology development vehicle, for verification of all hard cores and verification of the methodologies and design flow required for RC64. RADIC6 includes the test structures for characterizing the IP cores for immunity to all radiation effects. This paper describes the main elements and IP cores of RadSafe_65TM, as well as the contents of RADIC6 test chip.

Proteomics to study DNA-bound and chromatin-associated gene regulatory complexes

PubMed Central

Wierer, Michael; Mann, Matthias

2016-01-01

High-resolution mass spectrometry (MS)-based proteomics is a powerful method for the identification of soluble protein complexes and large-scale affinity purification screens can decode entire protein interaction networks. In contrast, protein complexes residing on chromatin have been much more challenging, because they are difficult to purify and often of very low abundance. However, this is changing due to recent methodological and technological advances in proteomics. Proteins interacting with chromatin marks can directly be identified by pulldowns with synthesized histone tails containing posttranslational modifications (PTMs). Similarly, pulldowns with DNA baits harbouring single nucleotide polymorphisms or DNA modifications reveal the impact of those DNA alterations on the recruitment of transcription factors. Accurate quantitation – either isotope-based or label free – unambiguously pinpoints proteins that are significantly enriched over control pulldowns. In addition, protocols that combine classical chromatin immunoprecipitation (ChIP) methods with mass spectrometry (ChIP-MS) target gene regulatory complexes in their in-vivo context. Similar to classical ChIP, cells are crosslinked with formaldehyde and chromatin sheared by sonication or nuclease digested. ChIP-MS baits can be proteins in tagged or endogenous form, histone PTMs, or lncRNAs. Locus-specific ChIP-MS methods would allow direct purification of a single genomic locus and the proteins associated with it. There, loci can be targeted either by artificial DNA-binding sites and corresponding binding proteins or via proteins with sequence specificity such as TAL or nuclease deficient Cas9 in combination with a specific guide RNA. We predict that advances in MS technology will soon make such approaches generally applicable tools in epigenetics. PMID:27402878

A Learning-Based Approach for IP Geolocation

NASA Astrophysics Data System (ADS)

Eriksson, Brian; Barford, Paul; Sommers, Joel; Nowak, Robert

The ability to pinpoint the geographic location of IP hosts is compelling for applications such as on-line advertising and network attack diagnosis. While prior methods can accurately identify the location of hosts in some regions of the Internet, they produce erroneous results when the delay or topology measurement on which they are based is limited. The hypothesis of our work is that the accuracy of IP geolocation can be improved through the creation of a flexible analytic framework that accommodates different types of geolocation information. In this paper, we describe a new framework for IP geolocation that reduces to a machine-learning classification problem. Our methodology considers a set of lightweight measurements from a set of known monitors to a target, and then classifies the location of that target based on the most probable geographic region given probability densities learned from a training set. For this study, we employ a Naive Bayes framework that has low computational complexity and enables additional environmental information to be easily added to enhance the classification process. To demonstrate the feasibility and accuracy of our approach, we test IP geolocation on over 16,000 routers given ping measurements from 78 monitors with known geographic placement. Our results show that the simple application of our method improves geolocation accuracy for over 96% of the nodes identified in our data set, with on average accuracy 70 miles closer to the true geographic location versus prior constraint-based geolocation. These results highlight the promise of our method and indicate how future expansion of the classifier can lead to further improvements in geolocation accuracy.

Effective Leadership and Management of an ACS Injury Prevention Program: Current Opinions and Perspectives From Where the Rubber Meets the Road.

PubMed

Wolfe, Elizabeth S; Bryant, Elizabeth A

The American College of Surgeons (ACS) mandates that each verified trauma center must have an injury prevention coordinator (IPC); however, Chapter 18 in the Resources for Optimal Care of the Injured Patient (2014) provides minimal information on how to effectively lead or manage an injury prevention (IP) program. This opinion article addresses 3 fundamental components of an effective IP program: (1) construction of an innovative vision of IP programming using current technology; (2) intentional investment and involvement; and (3) stakeholder leadership, engagement, and sustainability. This article also provides leadership and management methods from other professions both within and outside of the health care field that can be translated into sustainable IP program planning, implementation, and longevity.

Synthesis and characterization of non-hydrolysable diphosphoinositol polyphosphate second messengers

PubMed Central

Wu, Mingxuan; Dul, Barbara E.; Trevisan, Alexandra J.; Fiedler, Dorothea

2012-01-01

The diphosphoinositol polyphosphates (PP-IPs) are a central group of eukaryotic second messengers. They regulate numerous processes, including cellular energy homeostasis and adaptation to environmental stresses. To date, most of the molecular details in PP-IP signalling have remained elusive, due to a lack of appropriate methods and reagents. Here we describe the expedient synthesis of methylene-bisphosphonate PP-IP analogues. Their characterization revealed that the analogues exhibit significant stability and mimic their natural counterparts very well. This was further confirmed in two independent biochemical assays, in which our analogues potently inhibited phosphorylation of the protein kinase Akt and hydrolytic activity of the Ddp1 phosphohydrolase. The non-hydrolysable PP-IPs thus emerge as important tools and hold great promise for a variety of applications. PMID:23378892

Historical data learning based dynamic LSP routing for overlay IP/MPLS over WDM networks

NASA Astrophysics Data System (ADS)

Yu, Xiaojun; Xiao, Gaoxi; Cheng, Tee Hiang

2013-08-01

Overlay IP/MPLS over WDM network is a promising network architecture starting to gain wide deployments recently. A desirable feature of such a network is to achieve efficient routing with limited information exchanges between the IP/MPLS and the WDM layers. This paper studies dynamic label switched path (LSP) routing in the overlay IP/MPLS over WDM networks. To enhance network performance while maintaining its simplicity, we propose to learn from the historical data of lightpath setup costs maintained by the IP-layer integrated service provider (ISP) when making routing decisions. Using a novel historical data learning scheme for logical link cost estimation, we develop a new dynamic LSP routing method named Existing Link First (ELF) algorithm. Simulation results show that the proposed algorithm significantly outperforms the existing ones under different traffic loads, with either limited or unlimited numbers of optical ports. Effects of the number of candidate routes, add/drop ratio and the amount of historical data are also evaluated.

Telebation: next-generation telemedicine in remote airway management using current wireless technologies.

PubMed

Mosier, Jarrod; Joseph, Bellal; Sakles, John C

2013-02-01

Since the first remote intubation with telemedicine guidance, wireless technology has advanced to enable more portable methods of telemedicine involvement in remote airway management. Three voice over Internet protocol (VoIP) services were evaluated for quality of image transmitted, data lag, and audio quality with remotely observed and assisted intubations in an academic emergency department. The VoIP clients evaluated were Apple (Cupertino, CA) FaceTime(®), Skype™ (a division of Microsoft, Luxembourg City, Luxembourg), and Tango(®) (TangoMe, Palo Alto, CA). Each client was tested over a Wi-Fi network as well as cellular third generation (3G) (Skype and Tango). All three VoIP clients provided acceptable image and audio quality. There is a significant data lag in image transmission and quality when VoIP clients are used over cellular broadband (3G) compared with Wi-Fi. Portable remote telemedicine guidance is possible with newer technology devices such as a smartphone or tablet, as well as VoIP clients used over Wi-Fi or cellular broadband.

Motif-based analysis of large nucleotide data sets using MEME-ChIP

PubMed Central

Ma, Wenxiu; Noble, William S; Bailey, Timothy L

2014-01-01

MEME-ChIP is a web-based tool for analyzing motifs in large DNA or RNA data sets. It can analyze peak regions identified by ChIP-seq, cross-linking sites identified by cLIP-seq and related assays, as well as sets of genomic regions selected using other criteria. MEME-ChIP performs de novo motif discovery, motif enrichment analysis, motif location analysis and motif clustering, providing a comprehensive picture of the DNA or RNA motifs that are enriched in the input sequences. MEME-ChIP performs two complementary types of de novo motif discovery: weight matrix–based discovery for high accuracy; and word-based discovery for high sensitivity. Motif enrichment analysis using DNA or RNA motifs from human, mouse, worm, fly and other model organisms provides even greater sensitivity. MEME-ChIP’s interactive HTML output groups and aligns significant motifs to ease interpretation. this protocol takes less than 3 h, and it provides motif discovery approaches that are distinct and complementary to other online methods. PMID:24853928

In-situ calibration: migrating control system IP module calibration from the bench to the storage ring

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weber, Jonah M.; Chin, Michael

2002-04-30

The Control System for the Advanced Light Source (ALS) at Lawrence Berkeley National Lab (LBNL) uses in-house designed IndustryPack(registered trademark) (IP) modules contained in compact PCI (cPCI) crates with 16-bit analog I/O to control instrumentation. To make the IP modules interchangeable, each module is calibrated for gain and offset compensation. We initially developed a method of verifying and calibrating the IP modules in a lab bench test environment using a PC with LabVIEW. The subsequent discovery that the ADCs have significant drift characteristics over periods of days of installed operation prompted development of an ''in-situ'' calibration process--one in which themore » IP modules can be calibrated without removing them from the cPCI crates in the storage ring. This paper discusses the original LabVIEW PC calibration and the migration to the proposed in-situ EPICS control system calibration.« less

Application of modern autoradiography to nuclear forensic analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parsons-Davis, Tashi; Knight, Kim; Fitzgerald, Marc

Modern autoradiography techniques based on phosphorimaging technology using image plates (IPs) and digital scanning can identify heterogeneities in activity distributions and reveal material properties, serving to inform subsequent analyses. Here, we have adopted these advantages for applications in nuclear forensics, the technical analysis of radioactive or nuclear materials found outside of legal control to provide data related to provenance, production history, and trafficking route for the materials. IP autoradiography is a relatively simple, non-destructive method for sample characterization that records an image reflecting the relative intensity of alpha and beta emissions from a two-dimensional surface. Such data are complementary tomore » information gathered from radiochemical characterization via bulk counting techniques, and can guide the application of other spatially resolved techniques such as scanning electron microscopy (SEM) and secondary ion mass spectrometry (SIMS). IP autoradiography can image large 2-dimenstional areas (up to 20 × 40 cm), with relatively low detection limits for actinides and other radioactive nuclides, and sensitivity to a wide dynamic range (10 5) of activity density in a single image. Distributions of radioactivity in nuclear materials can be generated with a spatial resolution of approximately 50 μm using IP autoradiography and digital scanning. While the finest grain silver halide films still provide the best possible resolution (down to ~10 μm), IP autoradiography has distinct practical advantages such as shorter exposure times, no chemical post-processing, reusability, rapid plate scanning, and automated image digitization. Sample preparation requirements are minimal, and the analytical method does not consume or alter the sample. These advantages make IP autoradiography ideal for routine screening of nuclear materials, and for the identification of areas of interest for subsequent micro-characterization methods. Here in this article we present a summary of our setup, as modified for nuclear forensic sample analysis and related research, and provide examples of data from select samples from the nuclear fuel cycle and historical nuclear test debris.« less

Application of modern autoradiography to nuclear forensic analysis

DOE PAGES

Parsons-Davis, Tashi; Knight, Kim; Fitzgerald, Marc; ...

2018-05-20

Modern autoradiography techniques based on phosphorimaging technology using image plates (IPs) and digital scanning can identify heterogeneities in activity distributions and reveal material properties, serving to inform subsequent analyses. Here, we have adopted these advantages for applications in nuclear forensics, the technical analysis of radioactive or nuclear materials found outside of legal control to provide data related to provenance, production history, and trafficking route for the materials. IP autoradiography is a relatively simple, non-destructive method for sample characterization that records an image reflecting the relative intensity of alpha and beta emissions from a two-dimensional surface. Such data are complementary tomore » information gathered from radiochemical characterization via bulk counting techniques, and can guide the application of other spatially resolved techniques such as scanning electron microscopy (SEM) and secondary ion mass spectrometry (SIMS). IP autoradiography can image large 2-dimenstional areas (up to 20 × 40 cm), with relatively low detection limits for actinides and other radioactive nuclides, and sensitivity to a wide dynamic range (10 5) of activity density in a single image. Distributions of radioactivity in nuclear materials can be generated with a spatial resolution of approximately 50 μm using IP autoradiography and digital scanning. While the finest grain silver halide films still provide the best possible resolution (down to ~10 μm), IP autoradiography has distinct practical advantages such as shorter exposure times, no chemical post-processing, reusability, rapid plate scanning, and automated image digitization. Sample preparation requirements are minimal, and the analytical method does not consume or alter the sample. These advantages make IP autoradiography ideal for routine screening of nuclear materials, and for the identification of areas of interest for subsequent micro-characterization methods. Here in this article we present a summary of our setup, as modified for nuclear forensic sample analysis and related research, and provide examples of data from select samples from the nuclear fuel cycle and historical nuclear test debris.« less

Application of modern autoradiography to nuclear forensic analysis.

PubMed

Parsons-Davis, Tashi; Knight, Kim; Fitzgerald, Marc; Stone, Gary; Caldeira, Lee; Ramon, Christina; Kristo, Michael

2018-05-01

Modern autoradiography techniques based on phosphorimaging technology using image plates (IPs) and digital scanning can identify heterogeneities in activity distributions and reveal material properties, serving to inform subsequent analyses. Here, we have adopted these advantages for applications in nuclear forensics, the technical analysis of radioactive or nuclear materials found outside of legal control to provide data related to provenance, production history, and trafficking route for the materials. IP autoradiography is a relatively simple, non-destructive method for sample characterization that records an image reflecting the relative intensity of alpha and beta emissions from a two-dimensional surface. Such data are complementary to information gathered from radiochemical characterization via bulk counting techniques, and can guide the application of other spatially resolved techniques such as scanning electron microscopy (SEM) and secondary ion mass spectrometry (SIMS). IP autoradiography can image large 2-dimenstional areas (up to 20×40cm), with relatively low detection limits for actinides and other radioactive nuclides, and sensitivity to a wide dynamic range (10 5 ) of activity density in a single image. Distributions of radioactivity in nuclear materials can be generated with a spatial resolution of approximately 50μm using IP autoradiography and digital scanning. While the finest grain silver halide films still provide the best possible resolution (down to ∼10μm), IP autoradiography has distinct practical advantages such as shorter exposure times, no chemical post-processing, reusability, rapid plate scanning, and automated image digitization. Sample preparation requirements are minimal, and the analytical method does not consume or alter the sample. These advantages make IP autoradiography ideal for routine screening of nuclear materials, and for the identification of areas of interest for subsequent micro-characterization methods. In this paper we present a summary of our setup, as modified for nuclear forensic sample analysis and related research, and provide examples of data from select samples from the nuclear fuel cycle and historical nuclear test debris. Copyright © 2018 Elsevier B.V. All rights reserved.

Fluorescence Fluctuations and Equivalence Classes of Ca 2+ Imaging Experiments

PubMed Central

Piegari, Estefanía; Lopez, Lucía; Perez Ipiña, Emiliano; Ponce Dawson, Silvina

2014-01-01

release into the cytosol through inositol 1,4,5-trisphosphate receptors (IP3Rs) plays a relevant role in numerous physiological processes. IP3R-mediated signals involve -induced -release (CICR) whereby release through one open IP3R induces the opening of other channels. IP3Rs are apparently organized in clusters. The signals can remain localized (i.e., puffs) if CICR is limited to one cluster or become waves that propagate between clusters. puffs are the building blocks of waves. Thus, there is great interest in determining puff properties, especially in view of the current controversy on the spatial distribution of activatable IP3Rs. puffs have been observed in intact cells with optical techniques proving that they are intrinsically stochastic. Obtaining a correct picture of their dynamics then entails being able to detect the whole range of puff sizes. puffs are observed using visible single-wavelength dyes, slow exogenous buffers (e.g., EGTA) to disrupt inter-cluster CICR and UV-photolyzable caged IP3. Single-wavelength dyes increase their fluorescence upon calcium binding producing images that are strongly dependent on their kinetic, transport and photophysical properties. Determining the artifacts that the imaging setting introduces is particularly relevant when trying to analyze the smallest signals. In this paper we introduce a method to estimate the expected signal-to-noise ratio of imaging experiments that use single-wavelength dyes. The method is based on the Number and Brightness technique. It involves the performance of a series of experiments and their subsequent analysis in terms of a fluorescence fluctuation model with which the model parameters are quantified. Using the model, the expected signal-to-noise ratio is then computed. Equivalence classes between different experimental conditions that produce images with similar signal-to-noise ratios can then be established. The method may also be used to estimate the smallest signals that can reliably be observed with each setting. PMID:24776736

An exploratory study on the peroxyl-radical-scavenging activity of 2,6-dimethyl-5-hepten-2-ol and its heterocyclic analogues

NASA Astrophysics Data System (ADS)

Stobiecka, Agnieszka; Sikora, Magdalena; Bonikowski, Radosław; Kula, Józef

2016-03-01

The structural properties and radical scavenging activity of 2,6-dimethyl-5-hepten-2-ol (1) and its new heterocyclic analogues, i.e. 2-methyl-4-(5-methylfuran-2-yl)-butan-2-ol (2) and 2-methyl-4-(5-methylthiophen-2-yl)-butan-2-ol (3) and have been studied by using the experimental and theoretical methods for the first time. Activity of title compounds against the peroxyl radical was determined by using standard fluorimetric test, i.e. the Oxygen Radical Absorbance Capacity assay (ORACFL). Furthermore, the electron-donating ability of odorants has been evaluated by using colorimetric ABTS assay. According to the experimental results obtained from the ORACFL test 2,6-dimethyl-5-hepten-2-ol was characterized by the highest activity in comparison with the novel counterparts. Nevertheless, all investigated compounds exhibited pronounced anti-peroxyl radical activity comparable to that exerted by the one of the most prominent antioxidant among the monoterpene alcohols, i.e. by linalool. On the other hand, the title compounds exerted relatively low capacity to quench the radical cation of ABTS. Theoretical calculations based on the Density Functional Theory (DFT) method with the hybrid functional B3LYP were carried out in order to investigate selected structural and electronic properties including the geometrical parameters as well as the energy of frontier molecular orbitals of parent molecules and the resulting radicals. Furthermore, the possible mechanism of peroxyl-radical-scavenging has been determined by using the thermodynamic descriptors such as the bond dissociation enthalpies (BDEs) and ionization potentials (IPs). These theoretical data pointed out the relevance of HAT mechanism in the peroxyl-radical-scavenging exhibited by 2,6-dimethyl-5-hepten-2-ol and its new heterocyclic analogues in polar and non-polar medium.

Impact of the codec and various QoS methods on the final quality of the transferred voice in an IP network

NASA Astrophysics Data System (ADS)

Slavata, Oldřich; Holub, Jan

2015-02-01

This paper deals with an analysis of the relation between the codec that is used, the QoS method, and the final voice transmission quality. The Cisco 2811 router is used for adjusting QoS. VoIP client Linphone is used for adjusting the codec. The criterion for transmission quality is the MOS parameter investigated with the ITU-T P.862 PESQ and P.863 POLQA algorithms.

[Progress and application prospect of pig induced pluripotent stem cells].

PubMed

Yan, Yi-Bo; Zhang, Yan-Li; Qi, Wei-Wei; Wan, Yong-Jie; Fan, Yi-Xuan; Wang, Feng

2011-04-01

Pig has always been the focus of establishing a big ungulate animal ES cell lines because of its convenient source, genetic similarity with humans, and their importance in animal husbandry, but little development is achieved. Induced pluripotent stem cells technology creates a new method of reprogramming somatic cells to pluripotent state. As the pig iPS cells is established and perfected, pig ES cells will be established in the coming years. The pig iPS cells will give a hint on other livestock ES cells. On the other hand, pig iPS cells can be used to improve the efficiency of transgenic cloning pigs to conduct effective breeding and conservation of breeds. It is particularly important that the pig iPS cells can provide new model for human medical research, a new donor cells for human tissue and organ engineering, and have extensive and far-reaching impact on the biomedical field. Here, we briefly review the major progress of iPS cells, and emphasize current state of pig iPS cells and its application prospect in biomedicine and animal husbandry in order to provide a useful reference for researchers working in this area.

Evaluation of the route dependency of the pharmacokinetics and neuro-pharmacokinetics of tramadol and its main metabolites in rats.

PubMed

Sheikholeslami, Behjat; Gholami, Mahdi; Lavasani, Hoda; Rouini, Mohammadreza

2016-09-20

Tramadol hydrochloride is a centrally acting analgesic used for the treatment of moderate-to-severe pain. It has three main metabolites: O-desmethyltramadol (M1), N-desmethyltramadol (M2), and N,O-didesmethyltramadol (M5). Because of the frequent use of tramadol by patients and drug abusers, the ability to determine the parent drug and its metabolites in plasma and cerebrospinal fluid is of great importance. In the present study, a pharmacokinetic approach was applied using two groups of five male Wistar rats administered a 20mg/kg dose of tramadol via intravenous (i.v.) or intraperitoneal (i.p.) routes. Plasma and CSF samples were collected at 5-360min following tramadol administration. Our results demonstrate that the plasma values of Cmax (C0 in i.v. group) and area under the curve (AUC)0-t for tramadol were 23,314.40±6944.85 vs. 3187.39±760.25ng/mL (Cmax) and 871.15±165.98 vs. 414.04±149.25μg·min/mL in the i.v. and i.p. groups, respectively (p<0.05). However, there were no significant differences between i.v. and i.p. plasma values for tramadol metabolites (p>0.05). Tramadol rapidly penetrated the blood-brain barrier (BBB) and blood-cerebrospinal fluid barrier (BCSFB) (5.00±0.00 vs. 10.00±5.77min in i.v. and i.p. groups, respectively). Tramadol and its metabolites (M1 and M2) were present to a lesser extent in the cerebrospinal fluid (CSF) than in the plasma. M5 hardly penetrated the CSF, owing to its high polarity. There was no significant difference between the AUC0-t of tramadol in plasma (414.04±149.25μg·min/mL) and CSF (221.81±83.02μg·min/mL) in the i.p. group. In addition, the amounts of metabolites (M1 and M2) in the CSF showed no significant differences following both routes of administration. There were also no significant differences among the Kp,uu,CSF(0-360) (0.51±0.12 vs. 0.63±0.04) and Kp,uu,CSF(0-∞) (0.61±0.10 vs. 0.62±0.02) for i.v. and i.p. pathways, respectively (p>0.05). Drug targeting efficiency (DTE) values of tramadol after i.p. injection were more than unity for all scheduled time points. Considering the main analgesic effect of M1, it is hypothesized that both routes of administration may produce the same amount of analgesia. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecularly imprinted polymer coupled with dispersive liquid-liquid microextraction and injector port silylation: a novel approach for the determination of 3-phenoxybenzoic acid in complex biological samples using gas chromatography-tandem mass spectrometry.

PubMed

Mudiam, Mohana Krishna Reddy; Chauhan, Abhishek; Jain, Rajeev; Dhuriya, Yogesh Kumar; Saxena, Prem Narain; Khanna, Vinay Kumar

2014-01-15

A novel analytical approach based on molecularly imprinted solid phase extraction (MISPE) coupled with dispersive liquid-liquid microextraction (DLLME), and injector port silylation (IPS) has been developed for the selective preconcentration, derivatization and analysis of 3-phenoxybenzoic acid (3-PBA) using gas chromatography-tandem mass spectrometry (GC-MS/MS) in complex biological samples such as rat blood and liver. Factors affecting the synthesis of MIP were evaluated and the best monomer and cross-linker were selected based on binding affinity studies. Various parameters of MISPE, DLLME and IPS were optimized for the selective preconcentration and derivatization of 3-PBA. The developed method offers a good linearity over the calibration range of 0.02-2.5ngmg(-1) and 7.5-2000ngmL(-1) for liver and blood respectively. Under optimized conditions, the recovery of 3-PBA in liver and blood samples were found to be in the range of 83-91%. The detection limit was found to be 0.0045ngmg(-1) and 1.82ngmL(-1) in liver and blood respectively. SRM transition of 271→227 and 271→197 has been selected as quantifier and qualifier transition for 3-PBA derivative. Intra and inter-day precision for five replicates in a day and for five, successive days was found to be less than 8%. The method developed was successfully applied to real samples, i.e. rat blood and tissue for quantitative evaluation of 3-PBA. The analytical approach developed is rapid, economic, simple, eco-friendly and possess immense utility for the analysis of analytes with polar functional groups in complex biological samples by GC-MS/MS. Copyright © 2013 Elsevier B.V. All rights reserved.

Preparation of pancreatic β-cells from human iPS cells with small molecules

PubMed Central

2012-01-01

Human induced pluripotent stem (iPS) cells obtained from patients are expected to be a useful source for cell transplantation therapy, because many patients (including those with type 1 diabetes and severe type 2 diabetes) are on waiting lists for transplantation for a long time due to the shortage of donors. At present, many concerns related to clinical application of human iPS cells have been raised, but rapid development of methods for the establishment, culture, and standardization of iPS cells will lead autologous cell therapy to be realistic sooner or later. However, establishment of a method for preparing some of desired cell types is still challenging. Regarding pancreatic β-cells, there have been many reports about differentiation of these cells from human embryonic stem (ES)/iPS cells, but a protocol for clinical application has still not been established. Since there is clear proof that cell transplantation therapy is effective for diabetes based on the results of clinical islet transplantation, pancreatic β-cells prepared from human iPS cells are considered likely to be effective for reducing the burden on patients. In this article, the current status of procedures for preparing pancreatic β-cells from human ES/iPS cells, including effective use of small molecules, is summarized, and some of the problems that still need to be overcome are discussed. PMID:22722666

Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection

PubMed Central

Sun, Hong; Guns, Tias; Fierro, Ana Carolina; Thorrez, Lieven; Nijssen, Siegfried; Marchal, Kathleen

2012-01-01

Computationally retrieving biologically relevant cis-regulatory modules (CRMs) is not straightforward. Because of the large number of candidates and the imperfection of the screening methods, many spurious CRMs are detected that are as high scoring as the biologically true ones. Using ChIP-information allows not only to reduce the regions in which the binding sites of the assayed transcription factor (TF) should be located, but also allows restricting the valid CRMs to those that contain the assayed TF (here referred to as applying CRM detection in a query-based mode). In this study, we show that exploiting ChIP-information in a query-based way makes in silico CRM detection a much more feasible endeavor. To be able to handle the large datasets, the query-based setting and other specificities proper to CRM detection on ChIP-Seq based data, we developed a novel powerful CRM detection method ‘CPModule’. By applying it on a well-studied ChIP-Seq data set involved in self-renewal of mouse embryonic stem cells, we demonstrate how our tool can recover combinatorial regulation of five known TFs that are key in the self-renewal of mouse embryonic stem cells. Additionally, we make a number of new predictions on combinatorial regulation of these five key TFs with other TFs documented in TRANSFAC. PMID:22422841

Determination of the optimum number of cardiac cycles to differentiate intra-pulmonary shunt and patent foramen ovale by saline contrast two- and three-dimensional echocardiography.

PubMed

Bhatia, Nirmanmoh; Abushora, Mohannad Y; Donneyong, Macarius M; Stoddard, Marcus F

2014-03-01

Patent foramen ovale (PFO) and intra-pulmonary shunt (IPS) are potential causes of stroke. The most optimum cardiac cycle cutoff for bubbles to appear in the left heart on saline contrast transthoracic echocardiography (TTE) as criteria to differentiate the 2 entities is unknown. Ninety-five adult patients had saline contrast transesophageal echocardiography (TEE), two-dimensional (2D) and 3DTTE. Sensitivity and specificity of each cardiac cycle as cutoff to differentiate a PFO and IPS were obtained. Transesophageal echocardiography showed IPS in 28 and PFO in 15 patients. If bubbles appeared in the left heart within the first 4 cardiac cycles (the 4th cardiac cycle rule) as compared to alternate cutoffs, a PFO was most accurately diagnosed by both 2D and 3DTTE. Bubbles appearing at or after the 5th cardiac cycle most accurately determined an IPS. 3D versus 2DTTE had a trend for a higher sensitivity (61% vs. 36%, P = 0.06), but similar specificity (94% vs. 91%) for IPS. Accuracy of 3DTTE was 84% and 2DTTE was 75% (P = 0.08) for IPS. For PFO, 2DTTE sensitivity (87%) and specificity (98%) did not differ (P = NS) from that of 3DTTE sensitivity (73%) and specificity (100%). This study demonstrates for the first time that the 4th cardiac cycle rule differentiates PFO and IPS most optimally by 2D and 3DTTE. 3DTTE appears to have higher sensitivity for diagnosing IPS. These data suggest that 3DTTE is preferable when IPS is to be diagnosed. Both methods are similar for diagnosing PFO. © 2013, Wiley Periodicals, Inc.

Evaluating an undergraduate interprofessional simulation-based educational module: communication, teamwork, and confidence performing cardiac resuscitation skills

PubMed Central

Luctkar-Flude, Marian; Baker, Cynthia; Pulling, Cheryl; Mcgraw, Robert; Dagnone, Damon; Medves, Jennifer; Turner-Kelly, Carly

2010-01-01

Purpose Interprofessional (IP) collaboration during cardiac resuscitation is essential and contributes to patient wellbeing. The purpose of this study is to evaluate an innovative simulation-based IP educational module for undergraduate nursing and medical students on cardiac resuscitation skills. Methods Nursing and medical trainees participated in a new cardiac resuscitation curriculum involving a 2-hour IP foundational cardiac resuscitation skills lab, followed by three 2-hour IP simulation sessions. Control group participants attended the existing two 2-hour IP simulation sessions. Study respondents (N = 71) completed a survey regarding their confidence performing cardiac resuscitation skills and their perceptions of IP collaboration. Results Despite a consistent positive trend, only one out of 17 quantitative survey items were significantly improved for learners in the new curriculum. They were more likely to report feeling confident managing the airway during cardiac resuscitation (P = 0.001). Overall, quantitative results suggest that senior nursing and medical students were comfortable with IP communication and teamwork and confident with cardiac resuscitation skills. There were no significant differences between nursing students’ and medical students’ results. Through qualitative feedback, participants reported feeling comfortable learning with students from other professions and found value in the IP simulation sessions. Conclusion Results from this study will inform ongoing restructuring of the IP cardiac resuscitation skills simulation module as defined by the action research process. Specific improvements that are suggested by these findings include strengthening the team leader component of the resuscitation skills lab and identifying learners who may benefit from additional practice in the role of team leader and with other skills where they lack confidence. PMID:23745064

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Ying, E-mail: ying.chen@hc.msu.edu; Wang, Kai; Chandramouli, Gadisetti V.R.

Highlights: •Epithelial-like phenotype of trophoblast lineage cells derived from human iPS cells. •Trophoblast lineage cells derived from human iPS cells exhibit trophoblast function. •Trophoblasts from iPS cells provides a proof-of-concept in regenerative medicine. -- Abstract: Background: During implantation, the blastocyst trophectoderm attaches to the endometrial epithelium and continues to differentiate into all trophoblast subtypes, which are the major components of a placenta. Aberrant trophoblast proliferation and differentiation are associated with placental diseases. However, due to ethical and practical issues, there is almost no available cell or tissue source to study the molecular mechanism of human trophoblast differentiation, which further becomesmore » a barrier to the study of the pathogenesis of trophoblast-associated diseases of pregnancy. In this study, our goal was to generate a proof-of-concept model for deriving trophoblast lineage cells from induced pluripotency stem (iPS) cells from human fibroblasts. In future studies the generation of trophoblast lineage cells from iPS cells established from patient’s placenta will be extremely useful for studying the pathogenesis of individual trophoblast-associated diseases and for drug testing. Methods and results: Combining iPS cell technology with BMP4 induction, we derived trophoblast lineage cells from human iPS cells. The gene expression profile of these trophoblast lineage cells was distinct from fibroblasts and iPS cells. These cells expressed markers of human trophoblasts. Furthermore, when these cells were differentiated they exhibited invasive capacity and placental hormone secretive capacity, suggesting extravillous trophoblasts and syncytiotrophoblasts. Conclusion: Trophoblast lineage cells can be successfully derived from human iPS cells, which provide a proof-of-concept tool to recapitulate pathogenesis of patient placental trophoblasts in vitro.« less

Study on improved Ip-iq APF control algorithm and its application in micro grid

NASA Astrophysics Data System (ADS)

Xie, Xifeng; Shi, Hua; Deng, Haiyingv

2018-01-01

In order to enhance the tracking velocity and accuracy of harmonic detection by ip-iq algorithm, a novel ip-iq control algorithm based on the Instantaneous reactive power theory is presented, the improved algorithm adds the lead correction link to adjust the zero point of the detection system, the Fuzzy Self-Tuning Adaptive PI control is introduced to dynamically adjust the DC-link Voltage, which meets the requirement of the harmonic compensation of the micro grid. Simulation and experimental results verify the proposed method is feasible and effective in micro grid.

oPOSSUM-3: Advanced Analysis of Regulatory Motif Over-Representation Across Genes or ChIP-Seq Datasets

PubMed Central

Kwon, Andrew T.; Arenillas, David J.; Hunt, Rebecca Worsley; Wasserman, Wyeth W.

2012-01-01

oPOSSUM-3 is a web-accessible software system for identification of over-represented transcription factor binding sites (TFBS) and TFBS families in either DNA sequences of co-expressed genes or sequences generated from high-throughput methods, such as ChIP-Seq. Validation of the system with known sets of co-regulated genes and published ChIP-Seq data demonstrates the capacity for oPOSSUM-3 to identify mediating transcription factors (TF) for co-regulated genes or co-recovered sequences. oPOSSUM-3 is available at http://opossum.cisreg.ca. PMID:22973536

oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.

PubMed

Kwon, Andrew T; Arenillas, David J; Worsley Hunt, Rebecca; Wasserman, Wyeth W

2012-09-01

oPOSSUM-3 is a web-accessible software system for identification of over-represented transcription factor binding sites (TFBS) and TFBS families in either DNA sequences of co-expressed genes or sequences generated from high-throughput methods, such as ChIP-Seq. Validation of the system with known sets of co-regulated genes and published ChIP-Seq data demonstrates the capacity for oPOSSUM-3 to identify mediating transcription factors (TF) for co-regulated genes or co-recovered sequences. oPOSSUM-3 is available at http://opossum.cisreg.ca.

Multi-board kernel communication using socket programming for embedded applications

NASA Astrophysics Data System (ADS)

Mishra, Ashish; Girdhar, Neha; Krishnia, Nikita

2016-03-01

It is often seen in large application projects, there is a need to communicate between two different processors or two different kernels. The aim of this paper is to communicate between two different kernels and use efficient method to do so. The TCP/IP protocol is implemented to communicate between two boards via the Ethernet port and use lwIP (lightweight IP) stack, which is a smaller independent implementation of the TCP/IP stack suitable for use in embedded systems. While retaining TCP/IP functionality, lwIP stack reduces the use of memory and even size of the code. In this process of communication we made Raspberry pi as an active client and Field programmable gate array(FPGA) board as a passive server and they are allowed to communicate via Ethernet. Three applications based on TCP/IP client-server network communication have been implemented. The Echo server application is used to communicate between two different kernels of two different boards. Socket programming is used as it is independent of platform and programming language used. TCP transmit and receive throughput test applications are used to measure maximum throughput of the transmission of data. These applications are based on communication to an open source tool called iperf. It is used to measure the throughput transmission rate by sending or receiving some constant piece of data to the client or server according to the test application.

Chromatin immunoprecipitation in microfluidic droplets: towards fast and cheap analyses.

PubMed

Teste, Bruno; Champ, Jerome; Londono-Vallejo, Arturo; Descroix, Stéphanie; Malaquin, Laurent; Viovy, Jean-Louis; Draskovic, Irena; Mottet, Guillaume

2017-01-31

Genetic organization is governed by the interaction of DNA with histone proteins, and differential modifications of these proteins is a fundamental mechanism of gene regulation. Histone modifications are primarily studied through chromatin immunoprecipitation (ChIP) assays, however conventional ChIP procedures are time consuming, laborious and require a large number of cells. Here we report for the first time the development of ChIP in droplets based on a microfluidic platform combining nanoliter droplets, magnetic beads (MB) and magnetic tweezers (MT). The droplet approach enabled compartmentalization and improved mixing, while reducing the consumption of samples and reagents in an integrated workflow. Anti-histone antibodies grafted to MB were used as a solid support to capture and transfer the target chromatin from droplets to droplets in order to perform chromatin immunoprecipitation, washing, elution and purification of DNA. We designed a new ChIP protocol to investigate four different types of modified histones with known roles in gene activation or repression. We evaluated the performances of this new ChIP in droplet assay in comparison with conventional methods. The proposed technology dramatically reduces analytical time from a few days to 7 hours, simplifies the ChIP protocol and decreases the number of cells required by 100 fold while maintaining a high degree of sensitivity and specificity. Therefore this droplet-based ChIP assay represents a new, highly advantageous and convenient approach to epigenetic analyses.

Effectiveness of Individual Placement and Support Supported Employment for Young Adults

PubMed Central

Bond, Gary R.; Drake, Robert E.; Campbell, Kikuko

2015-01-01

Objective The Individual Placement and Support (IPS) model of supported employment was first developed in community mental health centers for adults with severe mental illness. While IPS is an established evidence-based practice in this broad population, evidence on its effectiveness focused specifically on young adults has been limited. The current study aimed to address this gap. Methods To investigate the effects of IPS on young adults, the authors conducted a secondary analysis on a pooled sample of 109 unemployed young adults (under age 30) from four randomized controlled trials employing a common research protocol that included a standardized measurement battery and rigorous fidelity monitoring. Researchers assessed these participants over 18 months on nine competitive employment outcome measures. Results On all measures the IPS group had significantly better employment outcomes. Overall, 40 (82%) of IPS participants obtained employment during follow-up compared to 25 (42%) of control participants, Χ2 =17.9, p < .001. IPS participants averaged 25.0 weeks of employment, compared to 7.0 weeks for control participants, t = 4.50, p < .001. Conclusions The current analysis supports a small number of previous studies in showing that IPS is highly effective in helping young adults to attain competitive employment. When young adults acquire competitive jobs and initiate a path toward normal adult roles, they may avoid the cycle of disability and psychiatric patient roles that are demeaning and demoralizing. PMID:25138195

ROVER: A DNS-Based Method to Detect and Prevent IP Hijacks

ERIC Educational Resources Information Center

Gersch, Joseph E.

2013-01-01

The Border Gateway Protocol (BGP) is critical to the global internet infrastructure. Unfortunately BGP routing was designed with limited regard for security. As a result, IP route hijacking has been observed for more than 16 years. Well known incidents include a 2008 hijack of YouTube, loss of connectivity for Australia in February 2012, and an…

Gated Word Recognition by Postlingually Deafened Adults with Cochlear Implants: Influence of Semantic Context

ERIC Educational Resources Information Center

Patro, Chhayakanta; Mendel, Lisa Lucks

2018-01-01

Purpose: The main goal of this study was to investigate the minimum amount of sensory information required to recognize spoken words (isolation points [IPs]) in listeners with cochlear implants (CIs) and investigate facilitative effects of semantic contexts on the IPs. Method: Listeners with CIs as well as those with normal hearing (NH)…

Quantifying intermolecular interactions of ionic liquids using cohesive energy densities.

PubMed

Lovelock, Kevin R J

2017-12-01

For ionic liquids (ILs), both the large number of possible cation + anion combinations and their ionic nature provide a unique challenge for understanding intermolecular interactions. Cohesive energy density, ced , is used to quantify the strength of intermolecular interactions for molecular liquids, and is determined using the enthalpy of vaporization. A critical analysis of the experimental challenges and data to obtain ced for ILs is provided. For ILs there are two methods to judge the strength of intermolecular interactions, due to the presence of multiple constituents in the vapour phase of ILs. Firstly, ced IP , where the ionic vapour constituent is neutral ion pairs, the major constituent of the IL vapour. Secondly, ced C+A , where the ionic vapour constituents are isolated ions. A ced IP dataset is presented for 64 ILs. For the first time an experimental ced C+A , a measure of the strength of the total intermolecular interaction for an IL, is presented. ced C+A is significantly larger for ILs than ced for most molecular liquids, reflecting the need to break all of the relatively strong electrostatic interactions present in ILs. However, the van der Waals interactions contribute significantly to IL volatility due to the very strong electrostatic interaction in the neutral ion pair ionic vapour. An excellent linear correlation is found between ced IP and the inverse of the molecular volume. A good linear correlation is found between IL ced IP and IL Gordon parameter (which are dependent primarily on surface tension). ced values obtained through indirect methods gave similar magnitude values to ced IP . These findings show that ced IP is very important for understanding IL intermolecular interactions, in spite of ced IP not being a measure of the total intermolecular interactions of an IL. In the outlook section, remaining challenges for understanding IL intermolecular interactions are outlined.

Quantifying intermolecular interactions of ionic liquids using cohesive energy densities

PubMed Central

2017-01-01

For ionic liquids (ILs), both the large number of possible cation + anion combinations and their ionic nature provide a unique challenge for understanding intermolecular interactions. Cohesive energy density, ced, is used to quantify the strength of intermolecular interactions for molecular liquids, and is determined using the enthalpy of vaporization. A critical analysis of the experimental challenges and data to obtain ced for ILs is provided. For ILs there are two methods to judge the strength of intermolecular interactions, due to the presence of multiple constituents in the vapour phase of ILs. Firstly, cedIP, where the ionic vapour constituent is neutral ion pairs, the major constituent of the IL vapour. Secondly, cedC+A, where the ionic vapour constituents are isolated ions. A cedIP dataset is presented for 64 ILs. For the first time an experimental cedC+A, a measure of the strength of the total intermolecular interaction for an IL, is presented. cedC+A is significantly larger for ILs than ced for most molecular liquids, reflecting the need to break all of the relatively strong electrostatic interactions present in ILs. However, the van der Waals interactions contribute significantly to IL volatility due to the very strong electrostatic interaction in the neutral ion pair ionic vapour. An excellent linear correlation is found between cedIP and the inverse of the molecular volume. A good linear correlation is found between IL cedIP and IL Gordon parameter (which are dependent primarily on surface tension). ced values obtained through indirect methods gave similar magnitude values to cedIP. These findings show that cedIP is very important for understanding IL intermolecular interactions, in spite of cedIP not being a measure of the total intermolecular interactions of an IL. In the outlook section, remaining challenges for understanding IL intermolecular interactions are outlined. PMID:29308254

Application of the new comprehensive X-ray spectral model to the two brightest intermediate polars EX Hydrae and V1223 Sagittarii

NASA Astrophysics Data System (ADS)

Hayashi, Takayuki; Ishida, Manabu

2014-07-01

We applied the new comprehensive X-ray spectral model for the post-shock accretion column (PSAC) of the intermediate polars (IPs) constructed by Hayashi and Ishida to the Suzaku data of the two brightest IPs EX Hydrae and V1223 Sagittarii. The white dwarf (WD) mass and the specific accretion rate of EX Hya are estimated to be M_WD= 0.63_{-0.14}^{+0.17} M⊙ and a=0.049_{-0.035}^{+0.66} g cm-2 s-1. Our WD mass of EX Hya is greater than that of previous X-ray estimations (˜0.4-0.5 M⊙), where higher specific accretion rate than ours is assumed, and marginally consistent with 0.790 ± 0.026 M⊙ measured by Beuermann and Reinsch using a binary motion. On the other hand, with the aid of the PSAC height of V1223 Sgr hV1223 < 0.07RWD, we estimated M_WD= 0.87_{-0.06}^{+0.10} M_{⊙} and a > 2.0 g cm-2 s-1 for V1223 Sgr. We evaluated the fractional accreting area of EX Hya and V1223 Sgr at 0.0033_{-0.0030}^{+0.0067} and <0.007, respectively. Calculation of the hydrodynamical equations with these best-fitting parameters show that the PSAC height of EX Hya is 0.33 RWD = 2.8 × 108 cm. The maximum temperature of the EX Hya and V1223 Sgr are calculated at 18.0 keV and 43.1 keV, respectively. In EX Hya, the temperature distribution is flatter and the density at the top of the PSAC is smaller than those of the previous PSAC models because of its low specific accretion rate.

On the Nature of the Hard X-ray Sources SWIFT J1907.3-2050, IGR J12123-5802 and IGR J19552+0044

NASA Technical Reports Server (NTRS)

Bernardini, F.; De Martino, D.; Mukai, K.; Falanga, M.; Andruchow, I.; Bonnet-Bidaud, J.-M.; Masetti, N.; Gonzalez Buitrago, D. H.; Mouchet, M.; Tovmassian, G.

2013-01-01

The INTEGRAL and Swift hard X-ray surveys have identified a large number of new sources, among which many are proposed as Cataclysmic Variables (CVs). Here we present the first detailed study of three X-ray selected CVs, Swift J1907.3-2050, IGRJ12123-5802, and IGRJ19552+0044 based on XMM-Newton, Suzaku, Swift observations and ground based optical and archival near-infrared/infrared data. Swift J1907.3-2050 is highly variable from hours to months-years at all wavelengths. No coherent X-ray pulses are detected but rather transient features. The X-ray spectrum reveals a multi-temperature optically thin plasma absorbed by complex neutral material and a soft black body component arising from a small area. These characteristics are remarkably similar to those observed in magnetic CVs. A supra-solar abundance of nitrogen could arise from nuclear processed material from the donor star. Swift J1907.3-2050 could be a peculiar magnetic CV with the second longest (20.82 hours) binary period. IGRJ12123-5802 is variable in the X-rays on a timescale of greater than or approximately 7.6 hours. No coherent pulsations are detected, but its spectral characteristics suggest that it could be a magnetic CV of the Intermediate Polar (IP) type. IGRJ19552+0044 shows two X-ray periods, approximately 1.38 hours and approximately 1.69 hours and a X-ray spectrum characterized by a multi-temperature plasma with little absorption. We derive a low accretion rate, consistent with a CV below the orbital period gap. Its peculiar near-infrared/infrared spectrum suggests a contribution from cyclotron emission. It could either be a pre-polar or an IP with the lowest degree of asynchronism.

On the Nature of the Hard X-Ray Sources SWIFT J1907.3-2050, IGR J12123-5802 and IGR J19552+0044

NASA Technical Reports Server (NTRS)

Bernardini, F.; deMartino, D; Mukai, K.; Falanga, M.; Andruchow, I.; Bonnet-Bidaud, J.-M.; Masetti, N.; GonzalezBuitrago, D. H.; Mouchet, M.; Tovmassian, G.

2014-01-01

The INTEGRAL and Swift hard X-ray surveys have identified a large number of new sources, among which many are proposed as Cataclysmic Variables (CVs). Here we present the first detailed study of three X-ray selected CVs, Swift J1907.3-2050, IGRJ12123-5802, and IGRJ19552+0044 based on XMM-Newton, Suzaku, Swift observations and ground based optical and archival nIR/IR data. Swift J1907.3-2050 is highly variable from hours to monthsyears at all wavelengths. No coherent X-ray pulses are detected but rather transient features. The X-ray spectrum reveals a multi-temperature optically thin plasma absorbed by complex neutral material and a soft black body component arising from a small area. These characteristics are remarkably similar to those observed in magnetic CVs. A supra-solar abundance of nitrogen could arise from nuclear processed material from the donor star. Swift J1907.3-2050 could be a peculiar magnetic CV with the second longest (20.82 h) binary period. IGRJ12123-5802 is variable in the X-rays on a timescale of approximately or greater than 7.6 h. No coherent pulsations are detected, but its spectral characteristics suggest that it could be a magnetic CV of the Intermediate Polar (IP) type. IGRJ19552+0044 shows two X-ray periods, approximately 1.38 h and approximately 1.69 h and a X-ray spectrum characterized by a multi-temperature plasma with little absorption.We derive a low accretion rate, consistent with a CV below the orbital period gap. Its peculiar nIR/IR spectrum suggests a contribution from cyclotron emission. It could either be a pre-polar or an IP with the lowest degree of asynchronism.

Research on polarization imaging information parsing method

NASA Astrophysics Data System (ADS)

Yuan, Hongwu; Zhou, Pucheng; Wang, Xiaolong

2016-11-01

Polarization information parsing plays an important role in polarization imaging detection. This paper focus on the polarization information parsing method: Firstly, the general process of polarization information parsing is given, mainly including polarization image preprocessing, multiple polarization parameters calculation, polarization image fusion and polarization image tracking, etc.; And then the research achievements of the polarization information parsing method are presented, in terms of polarization image preprocessing, the polarization image registration method based on the maximum mutual information is designed. The experiment shows that this method can improve the precision of registration and be satisfied the need of polarization information parsing; In terms of multiple polarization parameters calculation, based on the omnidirectional polarization inversion model is built, a variety of polarization parameter images are obtained and the precision of inversion is to be improve obviously; In terms of polarization image fusion , using fuzzy integral and sparse representation, the multiple polarization parameters adaptive optimal fusion method is given, and the targets detection in complex scene is completed by using the clustering image segmentation algorithm based on fractal characters; In polarization image tracking, the average displacement polarization image characteristics of auxiliary particle filtering fusion tracking algorithm is put forward to achieve the smooth tracking of moving targets. Finally, the polarization information parsing method is applied to the polarization imaging detection of typical targets such as the camouflage target, the fog and latent fingerprints.

Serum Immune Responses Predict Rapid Disease Progression among Children with Crohn’s Disease: Immune Responses Predict Disease Progression

PubMed Central

Dubinsky, Marla C.; Lin, Ying-Chao; Dutridge, Debra; Picornell, Yoana; Landers, Carol J.; Farrior, Sharmayne; Wrobel, Iwona; Quiros, Antonio; Vasiliauskas, Eric A.; Grill, Bruce; Israel, David; Bahar, Ron; Christie, Dennis; Wahbeh, Ghassan; Silber, Gary; Dallazadeh, Saied; Shah, Praful; Thomas, Danny; Kelts, Drew; Hershberg, Robert M.; Elson, Charles O.; Targan, Stephan R.; Taylor, Kent D.; Rotter, Jerome I.; Yang, Huiying

2007-01-01

BACKGROUND AND AIM Crohn’s disease (CD) is a heterogeneous disorder characterized by diverse clinical phenotypes. Childhood-onset CD has been described as a more aggressive phenotype. Genetic and immune factors may influence disease phenotype and clinical course. We examined the association of immune responses to microbial antigens with disease behavior and prospectively determined the influence of immune reactivity on disease progression in pediatric CD patients. METHODS Sera were collected from 196 pediatric CD cases and tested for immune responses: anti-I2, anti-outer membrane protein C (anti-OmpC), anti-CBir1 flagellin (anti-CBir1), and anti-Saccharomyces-cerevisiae (ASCA) using ELISA. Associations between immune responses and clinical phenotype were evaluated. RESULTS Fifty-eight patients (28%) developed internal penetrating and/or stricturing (IP/S) disease after a median follow-up of 18 months. Both anti-OmpC (p < 0.0006) and anti-I2 (p < 0.003) were associated with IP/S disease. The frequency of IP/S disease increased with increasing number of immune responses (p trend = 0.002). The odds of developing IP/S disease were highest in patients positive for all four immune responses (OR (95% CI): 11 (1.5–80.4); p = 0.03). Pediatric CD patients positive for ≥1 immune response progressed to IP/S disease sooner after diagnosis as compared to those negative for all immune responses (p < 0.03). CONCLUSIONS The presence and magnitude of immune responses to microbial antigens are significantly associated with more aggressive disease phenotypes among children with CD. This is the first study to prospectively demonstrate that the time to develop a disease complication in children is significantly faster in the presence of immune reactivity, thereby predicting disease progression to more aggressive disease phenotypes among pediatric CD patients. PMID:16454844

Anomalous diffusion of Ibuprofen in cyclodextrin nanosponge hydrogels: an HRMAS NMR study.

PubMed

Ferro, Monica; Castiglione, Franca; Punta, Carlo; Melone, Lucio; Panzeri, Walter; Rossi, Barbara; Trotta, Francesco; Mele, Andrea

2014-01-01

Ibuprofen sodium salt (IP) was encapsulated in cyclodextrin nanosponges (CDNS) obtained by cross-linking of β-cyclodextrin with ethylenediaminetetraacetic acid dianhydride (EDTAn) in two different preparations: CDNSEDTA 1:4 and 1:8, where the 1:n notation indicates the CD to EDTAn molar ratio. The entrapment of IP was achieved by swelling the two polymers with a 0.27 M solution of IP in D2O, leading to colourless, homogeneous hydrogels loaded with IP. The molecular environment and the transport properties of IP in the hydrogels were studied by high resolution magic angle spinning (HRMAS) NMR spectroscopy. The mean square displacement (MSD) of IP in the gels was obtained by a pulsed field gradient spin echo (PGSE) NMR pulse sequence at different observation times t d. The MSD is proportional to the observation time elevated to a scaling factor α. The α values define the normal Gaussian random motion (α = 1), or the anomalous diffusion (α < 1, subdiffusion, α > 1 superdiffusion). The experimental data here reported point out that IP undergoes subdiffusive regime in CDNSEDTA 1:4, while a slightly superdiffusive behaviour is observed in CDNSEDTA 1:8. The transition between the two dynamic regimes is triggered by the polymer structure. CDNSEDTA 1:4 is characterized by a nanoporous structure able to induce confinement effects on IP, thus causing subdiffusive random motion. CDNSEDTA 1:8 is characterized not only by nanopores, but also by dangling EDTA groups ending with ionized COO(-) groups. The negative potential provided by such groups to the polymer backbone is responsible for the acceleration effects on the IP anion thus leading to the superdiffusive behaviour observed. These results point out that HRMAS NMR spectroscopy is a powerful direct method for the assessment of the transport properties of a drug encapsulated in polymeric scaffolds. The diffusion properties of IP in CDNS can be modulated by suitable polymer synthesis; this finding opens the possibility to design suitable systems for drug delivery with predictable and desired drug release properties.

Observations of Heliospheric Faraday Rotation (FR) and Interplanetary Scintillation (IPS) with the LOw Frequency ARray (LOFAR): Steps Towards Improving Space-Weather Forecasting Capabilities

NASA Astrophysics Data System (ADS)

Bisi, M. M.; Fallows, R. A.; Sobey, C.; Eftekhari, T.; Jensen, E. A.; Jackson, B. V.; Yu, H. S.; Hick, P. P.; Odstrcil, D.; Tokumaru, M.

2015-12-01

The phenomenon of space weather - analogous to terrestrial weather which describes the changing pressure, temperature, wind, and humidity conditions on Earth - is essentially a description of the changes in velocity, density, magnetic field, high-energy particles, and radiation in the near-Earth space environment including the effects of such changes on the Earth's magnetosphere, radiation belts, ionosphere, and thermosphere. Space weather can be considered to have two main strands: (i) scientific research, and (ii) applications. The former is self-explanatory, but the latter covers operational aspects which includes its forecasting. Understanding and forecasting space weather in the near-Earth environment is vitally important to protecting our modern-day reliance (militarily and commercially) on satellites, global-communication and navigation networks, high-altitude air travel (radiation concerns particularly on polar routes), long-distance power/oil/gas lines and piping, and for any future human exploration of space to list but a few. Two ground-based radio-observing remote-sensing techniques that can aid our understanding and forecasting of heliospheric space weather are those of interplanetary scintillation (IPS) and heliospheric Faraday rotation (FR). The LOw Frequency ARray (LOFAR) is a next-generation 'software' radio telescope centered in The Netherlands with international stations spread across central and northwest Europe. For several years, scientific observations of IPS on LOFAR have been undertaken on a campaign basis and the experiment is now well developed. More recently, LOFAR has been used to attempt scientific heliospheric FR observations aimed at remotely sensing the magnetic field of the plasma traversing the inner heliosphere. We present our latest progress using these two radio heliospheric-imaging remote-sensing techniques including the use of three-dimensional (3-D) modeling and reconstruction techniques using other, additional data as input (such as IPS data from the Solar Terrestrial Environment Laboratory - STELab) to support and better-interpret the LOFAR results.

Monocyte-derived dendritic cells exposed to Der p 1 allergen enhance the recruitment of Th2 cells: major involvement of the chemokines TARC/CCL17 and MDC/CCL22.

PubMed

Hammad, Hamida; Smits, Hermelijn H; Ratajczak, Céline; Nithiananthan, Asokananthan; Wierenga, Eddy A; Stewart, Geoffrey A; Jacquet, Alain; Tonnel, Andre-Bernard; Pestel, Joël

2003-01-01

Dendritic cells (DC) are potent antigen - presenting cells that can orientate the immune response towards a Th1 or a Th2 type. DC produce chemokines that are involved in the recruitment of either Th1 cells, such as IP10 (CXCL10), Th2 cells such as TARC (CCL17) and MDC (CCL22), or non-polarized T cells such as RANTES (CCL5) and MIP-lalpha (CCL3). We investigated whether monocyte-derived DC (MD-DC) generated from healthy donors or from patients sensitive to Dermatophagoides pteronyssinus (Dpt) and exposed to the cysteine-protease Der p 1(allergen of Dpt), could upregulate the expression of chemokines involved in type 1 or type 2 T cell recruitment. MD-DC were pulsed with either Der p 1 or with LPS as the control and the chemokines produced were evaluated using ELISA and chemotaxis assays. Der p 1-pulsed DC from allergic patients showed increased TARC (CCL17) and MDC (CCL22) production without modifying IP-10 (CXCL10) release. Der p 1-pulsed DC from healthy donors showed only increased IP-10 (CXCL10) secretion. RANTES (CCL5) and MIP-lalpha (CCL3) production were similarly increased when DC were from healthy or allergic donors. The selective Th2 clone recruitment activity of supernatants from Der p 1-pulsed DC of allergic patients was inhibited by anti-TARC (CCL17) and anti-MDC (CCL22) neutralizing Abs. By using anti-IP10 (CXCL10) blocking Abs, supernatants of Der p 1-pulsed DC from healthy donors were shown to be involved in the recruitment of Th1 cells. These results suggest that in allergic patients exposed to house dust mites, DC may favour the exacerbation of the Th2 response via the increase in type 2 chemokine production. Copyright John Libbey Eurotext 2003.

An In Vitro Expansion System for Generation of Human iPS Cell-Derived Hepatic Progenitor-Like Cells Exhibiting a Bipotent Differentiation Potential

PubMed Central

Yanagida, Ayaka; Ito, Keiichi; Chikada, Hiromi; Nakauchi, Hiromitsu; Kamiya, Akihide

2013-01-01

Hepatoblasts, hepatic stem/progenitor cells in liver development, have a high proliferative potential and the ability to differentiate into both hepatocytes and cholangiocytes. In regenerative medicine and drug screening for the treatment of severe liver diseases, human induced pluripotent stem (iPS) cell-derived mature functional hepatocytes are considered to be a potentially good cell source. However, induction of proliferation of these cells is difficult ex vivo. To circumvent this problem, we generated hepatic progenitor-like cells from human iPS cells using serial cytokine treatments in vitro. Highly proliferative hepatic progenitor-like cells were purified by fluorescence-activated cell sorting using antibodies against CD13 and CD133 that are known cell surface markers of hepatic stem/progenitor cells in fetal and adult mouse livers. When the purified CD13highCD133+ cells were cultured at a low density with feeder cells in the presence of suitable growth factors and signaling inhibitors (ALK inhibitor A-83-01 and ROCK inhibitor Y-27632), individual cells gave rise to relatively large colonies. These colonies consisted of two types of cells expressing hepatocytic marker genes (hepatocyte nuclear factor 4α and α-fetoprotein) and a cholangiocytic marker gene (cytokeratin 7), and continued to proliferate over long periods of time. In a spheroid formation assay, these cells were found to express genes required for mature liver function, such as cytochrome P450 enzymes, and secrete albumin. When these cells were cultured in a suitable extracellular matrix gel, they eventually formed a cholangiocytic cyst-like structure with epithelial polarity, suggesting that human iPS cell-derived hepatic progenitor-like cells have a bipotent differentiation ability. Collectively these data indicate that this novel procedure using an in vitro expansion system is useful for not only liver regeneration but also for the determination of molecular mechanisms that regulate liver development. PMID:23935837

An in vitro expansion system for generation of human iPS cell-derived hepatic progenitor-like cells exhibiting a bipotent differentiation potential.

PubMed

Yanagida, Ayaka; Ito, Keiichi; Chikada, Hiromi; Nakauchi, Hiromitsu; Kamiya, Akihide

2013-01-01

Hepatoblasts, hepatic stem/progenitor cells in liver development, have a high proliferative potential and the ability to differentiate into both hepatocytes and cholangiocytes. In regenerative medicine and drug screening for the treatment of severe liver diseases, human induced pluripotent stem (iPS) cell-derived mature functional hepatocytes are considered to be a potentially good cell source. However, induction of proliferation of these cells is difficult ex vivo. To circumvent this problem, we generated hepatic progenitor-like cells from human iPS cells using serial cytokine treatments in vitro. Highly proliferative hepatic progenitor-like cells were purified by fluorescence-activated cell sorting using antibodies against CD13 and CD133 that are known cell surface markers of hepatic stem/progenitor cells in fetal and adult mouse livers. When the purified CD13(high)CD133(+) cells were cultured at a low density with feeder cells in the presence of suitable growth factors and signaling inhibitors (ALK inhibitor A-83-01 and ROCK inhibitor Y-27632), individual cells gave rise to relatively large colonies. These colonies consisted of two types of cells expressing hepatocytic marker genes (hepatocyte nuclear factor 4α and α-fetoprotein) and a cholangiocytic marker gene (cytokeratin 7), and continued to proliferate over long periods of time. In a spheroid formation assay, these cells were found to express genes required for mature liver function, such as cytochrome P450 enzymes, and secrete albumin. When these cells were cultured in a suitable extracellular matrix gel, they eventually formed a cholangiocytic cyst-like structure with epithelial polarity, suggesting that human iPS cell-derived hepatic progenitor-like cells have a bipotent differentiation ability. Collectively these data indicate that this novel procedure using an in vitro expansion system is useful for not only liver regeneration but also for the determination of molecular mechanisms that regulate liver development.

IGR J14257-6117, a magnetic accreting white dwarf with a very strong strong X-ray orbital modulation

NASA Astrophysics Data System (ADS)

Bernardini, F.; de Martino, D.; Mukai, K.; Falanga, M.

2018-07-01

IGR J14257-6117 is an unclassified source in the hard X-ray catalogues. Optical follow-ups suggest it could be a Cataclysmic Variable (CV) of the magnetic type. We present the first high signal-to-noise (S/N) X-ray observation performed by XMM-Newton at 0.3-10 keV, complemented with 10-80 keV coverage by Swift/BAT, aimed at revealing the source nature. We detected for the first time a fast periodic variability at 509.5 s and a longer periodic variability at 4.05 h, ascribed to the white dwarf (WD) spin and binary orbital periods, respectively. These unambiguously identify IGR J14257-6117 as a magnetic CV of the intermediate polar (IP) type. The energy-resolved light curves at both periods reveal amplitudes decreasing with increasing energy, with the orbital modulation reaching ˜ 100 per cent in the softest band. The energy spectrum shows optically thin thermal emission with an excess at the iron complex, absorbed by two dense media (NH ˜ 1022 - 23 cm-2), partially covering the X-ray source. These are likely localized in the magnetically confined accretion flow above the WD surface and at the disc rim, producing the energy-dependent spin and orbital variabilities, respectively. IGR J14257-6117 joins the group of strongest orbitally modulated IPs now counting four systems. Drawing similarities with low-mass X-ray binaries displaying orbital dips, these IPs should be seen at large orbital inclinations allowing azimuthally extended absorbing material fixed in the binary frame to intercept the line of sight. For IGR J14257-6117, we estimate 50o ≲ i ≲ 70o. Whether also the mass accretion rate plays a role in the large orbital modulations in IPs cannot be established with the present data.

Predictive IP controller for robust position control of linear servo system.

PubMed

Lu, Shaowu; Zhou, Fengxing; Ma, Yajie; Tang, Xiaoqi

2016-07-01

Position control is a typical application of linear servo system. In this paper, to reduce the system overshoot, an integral plus proportional (IP) controller is used in the position control implementation. To further improve the control performance, a gain-tuning IP controller based on a generalized predictive control (GPC) law is proposed. Firstly, to represent the dynamics of the position loop, a second-order linear model is used and its model parameters are estimated on-line by using a recursive least squares method. Secondly, based on the GPC law, an optimal control sequence is obtained by using receding horizon, then directly supplies the IP controller with the corresponding control parameters in the real operations. Finally, simulation and experimental results are presented to show the efficiency of proposed scheme. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries.

PubMed

Nair, Nishanth Ulhas; Sahu, Avinash Das; Bucher, Philipp; Moret, Bernard M E

2012-01-01

The advent of high-throughput technologies such as ChIP-seq has made possible the study of histone modifications. A problem of particular interest is the identification of regions of the genome where different cell types from the same organism exhibit different patterns of histone enrichment. This problem turns out to be surprisingly difficult, even in simple pairwise comparisons, because of the significant level of noise in ChIP-seq data. In this paper we propose a two-stage statistical method, called ChIPnorm, to normalize ChIP-seq data, and to find differential regions in the genome, given two libraries of histone modifications of different cell types. We show that the ChIPnorm method removes most of the noise and bias in the data and outperforms other normalization methods. We correlate the histone marks with gene expression data and confirm that histone modifications H3K27me3 and H3K4me3 act as respectively a repressor and an activator of genes. Compared to what was previously reported in the literature, we find that a substantially higher fraction of bivalent marks in ES cells for H3K27me3 and H3K4me3 move into a K27-only state. We find that most of the promoter regions in protein-coding genes have differential histone-modification sites. The software for this work can be downloaded from http://lcbb.epfl.ch/software.html.

Efficient generation of rat induced pluripotent stem cells using a non-viral inducible vector.

PubMed

Merkl, Claudia; Saalfrank, Anja; Riesen, Nathalie; Kühn, Ralf; Pertek, Anna; Eser, Stefan; Hardt, Markus Sebastian; Kind, Alexander; Saur, Dieter; Wurst, Wolfgang; Iglesias, Antonio; Schnieke, Angelika

2013-01-01

Current methods of generating rat induced pluripotent stem cells are based on viral transduction of pluripotency inducing genes (Oct4, Sox2, c-myc and Klf4) into somatic cells. These activate endogenous pluripotency genes and reprogram the identity of the cell to an undifferentiated state. Epigenetic silencing of exogenous genes has to occur to allow normal iPS cell differentiation. To gain more control over the expression of exogenous reprogramming factors, we used a novel doxycycline-inducible plasmid vector encoding Oct4, Sox2, c-Myc and Klf4. To ensure efficient and controlled generation of iPS cells by plasmid transfection we equipped the reprogramming vector with a bacteriophage φC31 attB site and used a φC31 integrase expression vector to enhance vector integration. A series of doxycycline-independent rat iPS cell lines were established. These were characterized by immunocytochemical detection of Oct4, SSEA1 and SSEA4, alkaline phosphatase staining, methylation analysis of the endogenous Oct4 promoter and RT-PCR analysis of endogenous rat pluripotency genes. We also determined the number of vector integrations and the extent to which reprogramming factor gene expression was controlled. Protocols were developed to generate embryoid bodies and rat iPS cells demonstrated as pluripotent by generating derivatives of all three embryonic germ layers in vitro, and teratoma formation in vivo. All data suggest that our rat iPS cells, generated by plasmid based reprogramming, are similar to rat ES cells. Methods of DNA transfection, protein transduction and feeder-free monolayer culture of rat iPS cells were established to enable future applications.

A MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets.

PubMed

Zuo, Chandler; Chen, Kailei; Keleş, Sündüz

2017-06-01

Current analytic approaches for querying large collections of chromatin immunoprecipitation followed by sequencing (ChIP-seq) data from multiple cell types rely on individual analysis of each data set (i.e., peak calling) independently. This approach discards the fact that functional elements are frequently shared among related cell types and leads to overestimation of the extent of divergence between different ChIP-seq samples. Methods geared toward multisample investigations have limited applicability in settings that aim to integrate 100s to 1000s of ChIP-seq data sets for query loci (e.g., thousands of genomic loci with a specific binding site). Recently, Zuo et al. developed a hierarchical framework for state-space matrix inference and clustering, named MBASIC, to enable joint analysis of user-specified loci across multiple ChIP-seq data sets. Although this versatile framework estimates both the underlying state-space (e.g., bound vs. unbound) and also groups loci with similar patterns together, its Expectation-Maximization-based estimation structure hinders its applicability with large number of loci and samples. We address this limitation by developing MAP-based asymptotic derivations from Bayes (MAD-Bayes) framework for MBASIC. This results in a K-means-like optimization algorithm that converges rapidly and hence enables exploring multiple initialization schemes and flexibility in tuning. Comparison with MBASIC indicates that this speed comes at a relatively insignificant loss in estimation accuracy. Although MAD-Bayes MBASIC is specifically designed for the analysis of user-specified loci, it is able to capture overall patterns of histone marks from multiple ChIP-seq data sets similar to those identified by genome-wide segmentation methods such as ChromHMM and Spectacle.

Validating a conceptual model for an inter-professional approach to shared decision making: a mixed methods study

PubMed Central

Légaré, France; Stacey, Dawn; Gagnon, Susie; Dunn, Sandy; Pluye, Pierre; Frosch, Dominick; Kryworuchko, Jennifer; Elwyn, Glyn; Gagnon, Marie-Pierre; Graham, Ian D

2011-01-01

Rationale, aims and objectives Following increased interest in having inter-professional (IP) health care teams engage patients in decision making, we developed a conceptual model for an IP approach to shared decision making (SDM) in primary care. We assessed the validity of the model with stakeholders in Canada. Methods In 15 individual interviews and 7 group interviews with 79 stakeholders, we asked them to: (1) propose changes to the IP-SDM model; (2) identify barriers and facilitators to the model's implementation in clinical practice; and (3) assess the model using a theory appraisal questionnaire. We performed a thematic analysis of the transcripts and a descriptive analysis of the questionnaires. Results Stakeholders suggested placing the patient at its centre; extending the concept of family to include significant others; clarifying outcomes; highlighting the concept of time; merging the micro, meso and macro levels in one figure; and recognizing the influence of the environment and emotions. The most common barriers identified were time constraints, insufficient resources and an imbalance of power among health professionals. The most common facilitators were education and training in inter-professionalism and SDM, motivation to achieve an IP approach to SDM, and mutual knowledge and understanding of disciplinary roles. Most stakeholders considered that the concepts and relationships between the concepts were clear and rated the model as logical, testable, having clear schematic representation, and being relevant to inter-professional collaboration, SDM and primary care. Conclusions Stakeholders validated the new IP-SDM model for primary care settings and proposed few modifications. Future research should assess if the model helps implement SDM in IP clinical practice. PMID:20695950

A comparative DFT study on the antioxidant activity of apigenin and scutellarein flavonoid compounds

NASA Astrophysics Data System (ADS)

Sadasivam, K.; Kumaresan, R.

2011-03-01

The potent antioxidant activity of flavonoids relevant to their ability to scavenge reactive oxygen species is the most important function of flavonoids. Density functional theory calculations were explored to investigate the antioxidant activity of flavonoid compounds such as apigenin and scutellarein. The biological characteristics are dependent on electronic parameters, describing the charge distribution on the rings of the flavonoid molecules. The computation of structural and various molecular descriptors such as polarizability, dipole moment, energy gap, homolytic O-H bond dissociation enthalpies (BDEs), ionization potential (IP), electron affinity, hardness, softness, electronegativity, electrophilic index and density plot of molecular orbital for neutral as well as radical species were carried out and studied. The B3LYP/6-311G(d,p) basis set was adopted for all the computations. This computation reveals that scutellarein exhibits higher degree of antioxidant activity than apigenin. Their dipole moment and polarizability analysis show that both the compounds are polar in nature and have the capacity to polarize other atoms.

Investigation of the antioxidant and radical scavenging activities of some phenolic Schiff bases with different free radicals.

PubMed

Marković, Zoran; Đorović, Jelena; Petrović, Zorica D; Petrović, Vladimir P; Simijonović, Dušica

2015-11-01

The antioxidant properties of some phenolic Schiff bases in the presence of different reactive particles such as (•)OH, (•)OOH, (CH2=CH-O-O(•)), and (-•)O2 were investigated. The thermodynamic values, ΔH BDE, ΔH IP, and ΔH PA, were used for this purpose. Three possible mechanisms for transfer of hydrogen atom, concerted proton-electron transfer (CPET), single electron transfer followed by proton transfer (SET-PT), and sequential proton loss electron transfer (SPLET) were considered. These mechanisms were tested in solvents of different polarity. On the basis of the obtained results it was shown that SET-PT antioxidant mechanism can be the dominant mechanism when Schiff bases react with radical cation, while SPLET and CPET are competitive mechanisms for radical scavenging of hydroxy radical in all solvents under investigation. Examined Schiff bases react with the peroxy radicals via SPLET mechanism in polar and nonpolar solvents. The superoxide radical anion reacts with these Schiff bases very slowly.

Evaluation of the filter paper IP-10 tests in school children after exposure to tuberculosis: a prospective cohort study with a 4-year follow-up

PubMed Central

Tuuminen, Tamara; Salo, Eeva; Kotilainen, Hannele; Ruhwald, Morten

2012-01-01

Objectives The prevalence of active tuberculosis (TB) is low in Finland, but outbreaks do occur. Following exposure national guidelines recommend either tuberculosis skin test or interferon-γ-release assay-testing of asymptomatic children. The aim of this study was to compare QuantiFERON-TB Gold In-Tube test (QFT) and interferon-γ-inducible protein (IP-10) release assay for detection of Mycobacterium tuberculosis infection following exposure to TB in a primary school. Design A prospective cohort study. Setting School children in Helsinki, Finland. Participants Two siblings of the index case and 58 classmates exposed to M tuberculosis. Intervention All the children were screened using the QFT, which was used to guide preventive treatment. All those exposed were followed up through the national TB registry. Outcome measures IP-10 was measured in plasma supernatants from the QFT test supernatants and in plasma dried and stored for 1 year on filter paper. IP-10 test results were calculated using preset algorithms for positive and indeterminate tests. The negative predictive values of the tests were assessed. Results At an initial screening 2 months after the debut of symptoms in the index case, QFT was positive in two children; 56 tests were negative; one was indeterminate and one was borderline. IP-10 showed a perfect concordance between the dried plasma spot and plasma method; two children were IP-10 positive and two were IP-10 indeterminate. There were two (3%) discordant results between the QFT and IP-10 tests. Four children converted to positive QFT at a 1–3 month follow-up. None of the QFT negative/borderline children developed TB in the 4-year period since exposure. Conclusions We demonstrated that IP-10 and QFT perform comparably as screening tools for infection with M tuberculosis in a contact investigation. IP-10 determined in dried plasma spots was at par with IP-10 determined in plasma, which further supports the usefulness of this alternative approach. PMID:23212994

a New Ubiquitous-Based Indoor Positioning System with Minimum Extra Hardware Using Smart Phones

NASA Astrophysics Data System (ADS)

Hassany Pazoky, S.; Chehreghan, A.; Sadeghi Niaraki, A.; Abbaspour, R. Ali

2014-10-01

Knowing the position has been an ambition in many areas such as science, military, business, etc. GPS was the realization of this wish in 1970s. Technological advances such as ubiquitous computing, as a conquering perspective, requires any service to work for any user, any place, anytime, and via any network. As GPS cannot provide services in indoor environments, many scientists began to develop indoor positioning systems (IPS). Smart phones penetrating our everyday lives were a great platform to host IPS applications. Sensors in smart phones were another big motive to develop IPS applications. Many researchers have been working on the topic developing various applications. However, the applications introduced lack simplicity. In other words, they need to install a step counter or smart phone on the ankle, which makes it awkward and inapplicable in many situations. In the current study, a new IPS methodology is introduced using only the usual embedded sensors in the smart phones. The robustness of this methodology cannot compete with those of the aforementioned approaches. The price paid for simplicity was decreasing robustness and complicating the methods and formulations. However, methods or tricks to harness the errors to an acceptable range are introduced as the future works.

Highly Expandable Human iPS Cell-Derived Neural Progenitor Cells (NPC) and Neurons for Central Nervous System Disease Modeling and High-Throughput Screening.

PubMed

Cheng, Chialin; Fass, Daniel M; Folz-Donahue, Kat; MacDonald, Marcy E; Haggarty, Stephen J

2017-01-11

Reprogramming of human somatic cells into induced pluripotent stem (iPS) cells has greatly expanded the set of research tools available to investigate the molecular and cellular mechanisms underlying central nervous system (CNS) disorders. Realizing the promise of iPS cell technology for the identification of novel therapeutic targets and for high-throughput drug screening requires implementation of methods for the large-scale production of defined CNS cell types. Here we describe a protocol for generating stable, highly expandable, iPS cell-derived CNS neural progenitor cells (NPC) using multi-dimensional fluorescence activated cell sorting (FACS) to purify NPC defined by cell surface markers. In addition, we describe a rapid, efficient, and reproducible method for generating excitatory cortical-like neurons from these NPC through inducible expression of the pro-neural transcription factor Neurogenin 2 (iNgn2-NPC). Finally, we describe methodology for the use of iNgn2-NPC for probing human neuroplasticity and mechanisms underlying CNS disorders using high-content, single-cell-level automated microscopy assays. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

A study on efficient detection of network-based IP spoofing DDoS and malware-infected Systems.

PubMed

Seo, Jung Woo; Lee, Sang Jin

2016-01-01

Large-scale network environments require effective detection and response methods against DDoS attacks. Depending on the advancement of IT infrastructure such as the server or network equipment, DDoS attack traffic arising from a few malware-infected systems capable of crippling the organization's internal network has become a significant threat. This study calculates the frequency of network-based packet attributes and analyzes the anomalies of the attributes in order to detect IP-spoofed DDoS attacks. Also, a method is proposed for the effective detection of malware infection systems triggering IP-spoofed DDoS attacks on an edge network. Detection accuracy and performance of the collected real-time traffic on a core network is analyzed thru the use of the proposed algorithm, and a prototype was developed to evaluate the performance of the algorithm. As a result, DDoS attacks on the internal network were detected in real-time and whether or not IP addresses were spoofed was confirmed. Detecting hosts infected by malware in real-time allowed the execution of intrusion responses before stoppage of the internal network caused by large-scale attack traffic.

ChIPWig: a random access-enabling lossless and lossy compression method for ChIP-seq data.

PubMed

Ravanmehr, Vida; Kim, Minji; Wang, Zhiying; Milenkovic, Olgica

2018-03-15

Chromatin immunoprecipitation sequencing (ChIP-seq) experiments are inexpensive and time-efficient, and result in massive datasets that introduce significant storage and maintenance challenges. To address the resulting Big Data problems, we propose a lossless and lossy compression framework specifically designed for ChIP-seq Wig data, termed ChIPWig. ChIPWig enables random access, summary statistics lookups and it is based on the asymptotic theory of optimal point density design for nonuniform quantizers. We tested the ChIPWig compressor on 10 ChIP-seq datasets generated by the ENCODE consortium. On average, lossless ChIPWig reduced the file sizes to merely 6% of the original, and offered 6-fold compression rate improvement compared to bigWig. The lossy feature further reduced file sizes 2-fold compared to the lossless mode, with little or no effects on peak calling and motif discovery using specialized NarrowPeaks methods. The compression and decompression speed rates are of the order of 0.2 sec/MB using general purpose computers. The source code and binaries are freely available for download at https://github.com/vidarmehr/ChIPWig-v2, implemented in C ++. milenkov@illinois.edu. Supplementary data are available at Bioinformatics online.

49 CFR 173.427 - Transport requirements for low specific activity (LSA) Class 7 (radioactive) materials and...

Code of Federal Regulations, 2010 CFR

2010-10-01

... package (IP-1, IP-2 or IP-3; § 173.411), subject to the limitations of Table 6; (2) In a DOT Specification... use shipment 1. LSA-I: Solid IP-1 IP-1 Liquid IP-1 IP-2 2. LSA-II: Solid IP-2 IP-2 Liquid and gas IP-2 IP-3 3. LSA-III IP-2 IP-3 4. SCO-I IP-1 IP-1 5. SCO-II IP-2 IP-2 [69 FR 3676, Jan. 26, 2004; 69 FR...

49 CFR 173.427 - Transport requirements for low specific activity (LSA) Class 7 (radioactive) materials and...

Code of Federal Regulations, 2011 CFR

2011-10-01

... package (IP-1, IP-2 or IP-3; § 173.411), subject to the limitations of Table 6; (2) In a DOT Specification... use shipment 1. LSA-I: Solid IP-1 IP-1 Liquid IP-1 IP-2 2. LSA-II: Solid IP-2 IP-2 Liquid and gas IP-2 IP-3 3. LSA-III IP-2 IP-3 4. SCO-I IP-1 IP-1 5. SCO-II IP-2 IP-2 [69 FR 3676, Jan. 26, 2004; 69 FR...

Scalable Electrophysiological Investigation of iPS Cell-Derived Cardiomyocytes Obtained by a Lentiviral Purification Strategy.

PubMed

Friedrichs, Stephanie; Malan, Daniela; Voss, Yvonne; Sasse, Philipp

2015-01-08

Disease-specific induced pluripotent stem (iPS) cells can be generated from patients and differentiated into functional cardiomyocytes for characterization of the disease and for drug screening. In order to obtain pure cardiomyocytes for automated electrophysiological investigation, we here report a novel non-clonal purification strategy by using lentiviral gene transfer of a puromycin resistance gene under the control of a cardiac-specific promoter. We have applied this method to our previous reported wild-type and long QT syndrome 3 (LQTS 3)-specific mouse iPS cells and obtained a pure cardiomyocyte population. These cells were investigated by action potential analysis with manual and automatic planar patch clamp technologies, as well as by recording extracellular field potentials using a microelectrode array system. Action potentials and field potentials showed the characteristic prolongation at low heart rates in LQTS 3-specific, but not in wild-type iPS cell-derived cardiomyocytes. Hence, LQTS 3-specific cardiomyocytes can be purified from iPS cells with a lentiviral strategy, maintain the hallmarks of the LQTS 3 disease and can be used for automated electrophysiological characterization and drug screening.

iASeq: integrative analysis of allele-specificity of protein-DNA interactions in multiple ChIP-seq datasets

PubMed Central

2012-01-01

Background ChIP-seq provides new opportunities to study allele-specific protein-DNA binding (ASB). However, detecting allelic imbalance from a single ChIP-seq dataset often has low statistical power since only sequence reads mapped to heterozygote SNPs are informative for discriminating two alleles. Results We develop a new method iASeq to address this issue by jointly analyzing multiple ChIP-seq datasets. iASeq uses a Bayesian hierarchical mixture model to learn correlation patterns of allele-specificity among multiple proteins. Using the discovered correlation patterns, the model allows one to borrow information across datasets to improve detection of allelic imbalance. Application of iASeq to 77 ChIP-seq samples from 40 ENCODE datasets and 1 genomic DNA sample in GM12878 cells reveals that allele-specificity of multiple proteins are highly correlated, and demonstrates the ability of iASeq to improve allelic inference compared to analyzing each individual dataset separately. Conclusions iASeq illustrates the value of integrating multiple datasets in the allele-specificity inference and offers a new tool to better analyze ASB. PMID:23194258

Who Benefits From Supported Employment: A Meta-analytic Study

PubMed Central

Campbell, Kikuko; Drake, Robert E.

2011-01-01

Aims: This meta-analysis sought to identify which subgroups of clients with severe mental illness (SMI) benefited from evidence-based supported employment. Methods: We used meta-analysis to pool the samples from 4 randomized controlled trials comparing the Individual Placement and Support (IPS) model of supported employment to well-regarded vocational approaches using stepwise models and brokered services. Meta-analysis was used to determine the magnitude of effects for IPS/control group differences within specific client subgroups (defined by 2 work history, 7 sociodemographic, and 8 clinical variables) on 3 competitive employment outcomes (obtaining a job, total weeks worked, and job tenure). Results: The findings strongly favored IPS, with large effect sizes across all outcomes: 0.96 for job acquisition, 0.79 for total weeks worked, and 0.74 for job tenure. Overall, 90 (77%) of the 117 effect sizes calculated for the 39 subgroups exceeded 0.70, and all 117 favored IPS. Conclusions: IPS produces better competitive employment outcomes for persons with SMI than alternative vocational programs regardless of background demographic, clinical, and employment characteristics. PMID:19661196

Elastic Multilayer Bandages for Chronic Venous Insufficiency: Features of Our Technique

PubMed Central

2012-01-01

Objectives: To evaluate the interface pressure (IP) and stiffness of our elastic multilayer bandages (eMLB). Methods: Three medical staff wrapped the legs of 10 healthy volunteers with one to six rolls of elastic bandages. The IP was measured at the medial aspect of the lower leg at the level of transposition of the medial gastrocnemius muscle into the Achilles tendon (level of B1) with the patient supine and then standing, for each number of bandages worn. The static stiffness index (SSI) was calculated as a difference between these IPs. Results: The IPs in the standing position increased linearly for up to five bandages (21.8 ± 7.2, 32.5 ± 6.1, 41.8 ± 8.5, 52.0 ± 10.4, 60.3 ± 11.8, and 66.7 ± 13.4 mmHg, with one to six bandages). SSI also increased linearly for up to five bandages (6.8 ± 5.1, 10.2 ± 4.8, 13.4 ± 7.2, 17.4 ± 8.8, 19.7 ± 9.1, and 20.4 ± 9.4 mmHg, with one to six bandages). No significant technical variation in the IP was observed among the three operators. Conclusions: Our eMLB provided stable, predictable and sufficient IPs and SSIs in healthy volunteers. PMID:23555535

Potential of laryngeal muscle regeneration using induced pluripotent stem cell-derived skeletal muscle cells.

PubMed

Dirja, Bayu Tirta; Yoshie, Susumu; Ikeda, Masakazu; Imaizumi, Mitsuyoshi; Nakamura, Ryosuke; Otsuki, Koshi; Nomoto, Yukio; Wada, Ikuo; Hazama, Akihiro; Omori, Koichi

2016-01-01

Conclusion Induced pluripotent stem (iPS) cells may be a new potential cell source for laryngeal muscle regeneration in the treatment of vocal fold atrophy after recurrent laryngeal nerve paralysis. Objectives Unilateral vocal fold paralysis can lead to degeneration, atrophy, and loss of force of the thyroarytenoid muscle. At present, there are some treatments such as thyroplasty, arytenoid adduction, and vocal fold injection. However, such treatments cannot restore reduced mass of the thyroarytenoid muscle. iPS cells have been recognized as supplying a potential resource for cell transplantation. The aim of this study was to assess the effectiveness of the use of iPS cells for the regeneration of laryngeal muscle through the evaluation of both in vitro and in vivo experiments. Methods Skeletal muscle cells were generated from tdTomato-labeled iPS cells using embryoid body formation. Differentiation into skeletal muscle cells was analyzed by gene expression and immunocytochemistry. The tdTomato-labeled iPS cell-derived skeletal muscle cells were transplanted into the left atrophied thyroarytenoid muscle. To evaluate the engraftment of these cells after transplantation, immunohistochemistry was performed. Results The tdTomato-labeled iPS cells were successfully differentiated into skeletal muscle cells through an in vitro experiment. These cells survived in the atrophied thyroarytenoid muscle after transplantation.

Long-term Culture of Human iPS Cell-derived Telencephalic Neuron Aggregates on Collagen Gel.

PubMed

Oyama, Hiroshi; Takahashi, Koji; Tanaka, Yoshikazu; Takemoto, Hiroshi; Haga, Hisashi

2018-01-01

It takes several months to form the 3-dimensional morphology of the human embryonic brain. Therefore, establishing a long-term culture method for neuronal tissues derived from human induced pluripotent stem (iPS) cells is very important for studying human brain development. However, it is difficult to keep primary neurons alive for more than 3 weeks in culture. Moreover, long-term adherent culture to maintain the morphology of telencephalic neuron aggregates induced from human iPS cells is also difficult. Although collagen gel has been widely used to support long-term culture of cells, it is not clear whether human iPS cell-derived neuron aggregates can be cultured for long periods on this substrate. In the present study, we differentiated human iPS cells to telencephalic neuron aggregates and examined long-term culture of these aggregates on collagen gel. The results indicated that these aggregates could be cultured for over 3 months by adhering tightly onto collagen gel. Furthermore, telencephalic neuronal precursors within these aggregates matured over time and formed layered structures. Thus, long-term culture of telencephalic neuron aggregates derived from human iPS cells on collagen gel would be useful for studying human cerebral cortex development.Key words: Induced pluripotent stem cell, forebrain neuron, collagen gel, long-term culture.

Safety incentive and penalty provisions in Indian construction projects and their impact on safety performance.

PubMed

Hasan, Abid; Jha, Kumar Neeraj

2013-01-01

Safety incentive and penalty (I/P) provisions in construction contracts are one of the most common forms of I/P. Contradictory opinions on the effectiveness of these provisions have been expressed in the literature. Statistics on safety provisions were collected from 32 construction projects, which include both types of contracts - those with safety I/P provisions and those without them. Although inclusion of safety I/P provisions in contracts helps in improving the overall safety performance in construction projects, further scope for improvement still exists. Literature review and structured personal interviews, coupled with a survey based on preliminary questionnaire, revealed that successful formulation and implementation of such provisions are dependent on 25 attributes which need the attention of both clients and contractors. A questionnaire-based survey was conducted to evaluate these attributes. The six factors extracted by carrying out factor analysis are: incentive distribution method, proper labour training, special attention to risky situations, role of safety committee and sub-contractors, specialised works and safety equipments, and right form of I/P. If taken care of, these attributes have the potential to improve the safety performance in construction projects. The results would be useful to clients and contractors in implementing the safety I/P provisions and thereby improving safety performance.

Linear photonic frequency discriminator on As₂S₃-ring-on-Ti:LiNbO₃ hybrid platform.

PubMed

Kim, Jaehyun; Sung, Won Ju; Eknoyan, Ohannes; Madsen, Christi K

2013-10-21

We report a photonic frequency discriminator built on the vertically integrated As₂S₃-ring-on-Ti:LiNbO₃ hybrid platform. The discriminator consists of a Mach Zehnder interferometer (MZI) formed by the optical path length difference (OPD) between polarization modes of Ti-diffused waveguide on LiNbO₃ substrate and a vertically integrated As₂S₃ race-track ring resonator on top of the substrate. The figures of merit of the device, enhancement of the signal-to-3rd order intermodulation distortion (IMD3) power ratio and corresponding 3rd order intercept point (IP3) over a traditional MZI, are demonstrated through device characterization.

Molecular mechanism of Danshensu on platelet antiaggregation

NASA Astrophysics Data System (ADS)

Yu, Chen; Geng, Feng; Fan, Hua-Ying; Luan, Hai-Yun; Liu, Yue; Ji, Kai; Fu, Feng-Hua

2018-04-01

In this study, we detected the effect of Danshensu on PARs-PLCβsignaling pathway to elucidate molecular mechanism of Danshensu on platelet anti-aggregation. Our results demonstrate that Danshensu is able to decrease the levels of IP3, Ca2+ and AA secretion, which indicate that Danshensu may involve in PARs-PLCβ signaling pathways. Molecular docking study shows that Danshesu has similar polar interactions with PAR1 receptors as BMS200261 at the same position. The findings from our study enable a better understanding of Danshensu biological properties, which could ultimately lead to the development of multi-target antiplatelet natural medicine for the treatment and/or prevention of some thrombotic diseases.

Tier-1 assays for assessing the toxicity of insecticidal proteins produced by genetically engineered plants to non-target arthropods.

PubMed

Li, Yun-He; Romeis, Jörg; Wu, Kong-Ming; Peng, Yu-Fa

2014-04-01

In assessing an insect-resistant genetically engineered (IRGE) crop before its commercialization, researchers normally use so-called "Tier-1 assays" as the initial step to determine the effects of the crop on non-target organisms. In these tests, the insecticidal proteins (IPs) produced by the IRGEs are added to the diets of test organisms in the laboratory. Test organisms in such assays can be directly exposed to much higher concentrations of the test IPs than they would encounter in the field. The results of Tier-1 assays are thus more conservative than those generated in studies in which the organisms are exposed to the IPs by feeding on IRGE plant tissue or in the case of predators or parasites, by feeding on invertebrate prey or hosts that have fed on IRGE plant tissue. In this report, we consider three important factors that must be considered in Tier-1 assays: (i) methods for delivery of the IP to the test organisms; (ii) the need for and selection of compounds used as positive controls; and (iii) methods for monitoring the concentration, stability and bioactivity of the IP during the assay. We also analyze the existing data from Tier-1 assays regarding the toxicity of Bt Cry proteins to non-target arthropod species. The data indicate that the widely used Bt proteins have no direct toxicity to non-target organisms. © 2013 Institute of Zoology, Chinese Academy of Sciences.

A five-primary photostimulator suitable for studying intrinsically photosensitive retinal ganglion cell functions in humans

PubMed Central

Cao, Dingcai; Nicandro, Nathaniel; Barrionuevo, Pablo A.

2015-01-01

Intrinsically photosensitive retinal ganglion cells (ipRGCs) can respond to light directly through self-contained photopigment, melanopsin. IpRGCs also receive synaptic inputs from rods and cones. Thus, studying ipRGC functions requires a novel photostimulating method that can account for all of the photoreceptor inputs. Here, we introduced an inexpensive LED-based five-primary photostimulator that can control the excitations of rods, S-, M-, L-cones, and melanopsin-containing ipRGCs in humans at constant background photoreceptor excitation levels, a critical requirement for studying the adaptation behavior of ipRGCs with rod, cone, or melanopsin input. We described the theory and technical aspects (including optics, electronics, software, and calibration) of the five-primary photostimulator. Then we presented two preliminary studies using the photostimulator we have implemented to measure melanopsin-mediated pupil responses and temporal contrast sensitivity function (TCSF). The results showed that the S-cone input to pupil responses was antagonistic to the L-, M- or melanopsin inputs, consistent with an S-OFF and (L + M)-ON response property of primate ipRGCs (Dacey et al., 2005). In addition, the melanopsin-mediated TCSF had a distinctive pattern compared with L + M or S-cone mediated TCSF. Other than controlling individual photoreceptor excitation independently, the five-primary photostimulator has the flexibility in presenting stimuli modulating any combination of photoreceptor excitations, which allows researchers to study the mechanisms by which ipRGCs combine various photoreceptor inputs. PMID:25624466

Voice over Internet protocol for the orthodontic practice: a sensible switch from plain old telephone service.

PubMed

Mupparapu, Muralidhar

2008-03-01

Voice over Internet protocol (VoIP) is a revolutionary new technology that is causing a stir in the telecommunications industry and threatening the existence of traditional telephone service providers. Based on a simple method of converting analog audio signals into digital data before being transmitted over the Internet, VoIP has gained immense popularity among consumers. The technology is now regarded as an alternative to traditional telephone service for the orthodontic office. When the economics are considered, it is cost-effective, especially for a busy orthodontic practice where the call volumes both in and out are always high. VoIP has the potential to reduce costs, break the barriers between local vs long-distance calling, and make life easier for the office staff. However, deploying VoIP requires a cautious and thought-out process. Users should fully understand the risks and benefits before switching from the public switched telephone network. VoIP customers and service providers are vulnerable to many of the same impersonation-based attacks by those who attempt toll fraud, and identity and information theft. In this article, VoIP is introduced to orthodontic practitioners, who might be unfamiliar with this technology. Internet protocol based private branch exchange systems that are currently marketed as open-source technologies are also reviewed. Additionally, VoIP is compared with the traditional public switched telephone network technology and evaluated for its potential applications in an orthodontic office for both increased efficiency and cost savings.

Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation.

PubMed

Nakato, Ryuichiro; Shirahige, Katsuhiko

2017-03-01

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis can detect protein/DNA-binding and histone-modification sites across an entire genome. Recent advances in sequencing technologies and analyses enable us to compare hundreds of samples simultaneously; such large-scale analysis has potential to reveal the high-dimensional interrelationship level for regulatory elements and annotate novel functional genomic regions de novo. Because many experimental considerations are relevant to the choice of a method in a ChIP-seq analysis, the overall design and quality management of the experiment are of critical importance. This review offers guiding principles of computation and sample preparation for ChIP-seq analyses, highlighting the validity and limitations of the state-of-the-art procedures at each step. We also discuss the latest challenges of single-cell analysis that will encourage a new era in this field. © The Author 2016. Published by Oxford University Press.

Assessing the role of Hartree-Fock exchange, correlation energy and long range corrections in evaluating ionization potential, and electron affinity in density functional theory.

PubMed

Vikramaditya, Talapunur; Lin, Shiang-Tai

2017-06-05

Accurate determination of ionization potentials (IPs), electron affinities (EAs), fundamental gaps (FGs), and HOMO, LUMO energy levels of organic molecules play an important role in modeling and predicting the efficiencies of organic photovoltaics, OLEDs etc. In this work, we investigate the effects of Hartree Fock (HF) Exchange, correlation energy, and long range corrections in predicting IP and EA in Hybrid Functionals. We observe increase in percentage of HF exchange results in increase of IPs and decrease in EAs. Contrary to the general expectations inclusion of both HF exchange and correlation energy (from the second order perturbation theory MP2) leads to poor prediction. Range separated Hybrid Functionals are found to be more reliable among various DFT Functionals investigated. DFT Functionals predict accurate IPs whereas post HF methods predict accurate EAs. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

In vivo anticancer activity of vanillin semicarbazone

PubMed Central

Ali, Shaikh M Mohsin; Azad, M Abul Kalam; Jesmin, Mele; Ahsan, Shamim; Rahman, M Mijanur; Khanam, Jahan Ara; Islam, M Nazrul; Shahriar, Sha M Shahan

2012-01-01

Objective To evaluate the anticancer activity of vanillin semicarbazone (VSC) against Ehrlich ascites carcinoma (EAC) cells in Swiss albino mice. Methods The compound VSC at three doses (5, 7.5 and 10 mg/kg i.p.) was administered into the intraperitoneal cavity of the EAC inoculated mice to observe its efficiency by studying the cell growth inhibition, reduction of tumour weight, enhancement of survival time as well as the changes in depleted hematological parameters. All such parameters were also studied with a known standard drug bleomycin at the dose of 0.3 mg/kg (i.p.). Results Among the doses studied, 10 mg/kg (i.p.) was found to be quite comparable in potency to that of bleomycin at the dose of 0.3 mg/kg (i.p.). The host toxic effects of VSC was found to be negligible. Conclusions It can be concluded that VSC can therefore be considered as potent anticancer agent. PMID:23569946

IP-FCM measures physiologic protein-protein interactions modulated by signal transduction and small-molecule drug inhibition.

PubMed

Smith, Stephen E P; Bida, Anya T; Davis, Tessa R; Sicotte, Hugues; Patterson, Steven E; Gil, Diana; Schrum, Adam G

2012-01-01

Protein-protein interactions (PPI) mediate the formation of intermolecular networks that control biological signaling. For this reason, PPIs are of outstanding interest in pharmacology, as they display high specificity and may represent a vast pool of potentially druggable targets. However, the study of physiologic PPIs can be limited by conventional assays that often have large sample requirements and relatively low sensitivity. Here, we build on a novel method, immunoprecipitation detected by flow cytometry (IP-FCM), to assess PPI modulation during either signal transduction or pharmacologic inhibition by two different classes of small-molecule compounds. First, we showed that IP-FCM can detect statistically significant differences in samples possessing a defined PPI change as low as 10%. This sensitivity allowed IP-FCM to detect a PPI that increases transiently during T cell signaling, the antigen-inducible interaction between ZAP70 and the T cell antigen receptor (TCR)/CD3 complex. In contrast, IP-FCM detected no ZAP70 recruitment when T cells were stimulated with antigen in the presence of the src-family kinase inhibitor, PP2. Further, we tested whether IP-FCM possessed sufficient sensitivity to detect the effect of a second, rare class of compounds called SMIPPI (small-molecule inhibitor of PPI). We found that the first-generation non-optimized SMIPPI, Ro-26-4550, inhibited the IL-2:CD25 interaction detected by IP-FCM. This inhibition was detectable using either a recombinant CD25-Fc chimera or physiologic full-length CD25 captured from T cell lysates. Thus, we demonstrate that IP-FCM is a sensitive tool for measuring physiologic PPIs that are modulated by signal transduction and pharmacologic inhibition.

Bias in diet determination: incorporating traditional methods in Bayesian mixing models.

PubMed

Franco-Trecu, Valentina; Drago, Massimiliano; Riet-Sapriza, Federico G; Parnell, Andrew; Frau, Rosina; Inchausti, Pablo

2013-01-01

There are not "universal methods" to determine diet composition of predators. Most traditional methods are biased because of their reliance on differential digestibility and the recovery of hard items. By relying on assimilated food, stable isotope and Bayesian mixing models (SIMMs) resolve many biases of traditional methods. SIMMs can incorporate prior information (i.e. proportional diet composition) that may improve the precision in the estimated dietary composition. However few studies have assessed the performance of traditional methods and SIMMs with and without informative priors to study the predators' diets. Here we compare the diet compositions of the South American fur seal and sea lions obtained by scats analysis and by SIMMs-UP (uninformative priors) and assess whether informative priors (SIMMs-IP) from the scat analysis improved the estimated diet composition compared to SIMMs-UP. According to the SIMM-UP, while pelagic species dominated the fur seal's diet the sea lion's did not have a clear dominance of any prey. In contrast, SIMM-IP's diets compositions were dominated by the same preys as in scat analyses. When prior information influenced SIMMs' estimates, incorporating informative priors improved the precision in the estimated diet composition at the risk of inducing biases in the estimates. If preys isotopic data allow discriminating preys' contributions to diets, informative priors should lead to more precise but unbiased estimated diet composition. Just as estimates of diet composition obtained from traditional methods are critically interpreted because of their biases, care must be exercised when interpreting diet composition obtained by SIMMs-IP. The best approach to obtain a near-complete view of predators' diet composition should involve the simultaneous consideration of different sources of partial evidence (traditional methods, SIMM-UP and SIMM-IP) in the light of natural history of the predator species so as to reliably ascertain and weight the information yielded by each method.

Novel LC-ESI/MS/MSn Method for the Characterization and Quantification of 2′-Deoxyguanosine Adducts of the Dietary Carcinogen 2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine by 2-D Linear Quadrupole Ion Trap Mass Spectrometry

PubMed Central

Goodenough, Angela K.; Schut, Herman A. J.; Turesky, Robert J.

2008-01-01

An accurate and sensitive liquid chromatography-electrospray ionization/multi-stage mass spectrometry (LC-ESI/MS/MSn) technique has been developed for the characterization and quantification of 2′-deoxyguanosine (dG) adducts of the dietary mutagen, 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP). PhIP is an animal and potential human carcinogen that occurs in grilled meats. Following enzymatic digestion and adduct enrichment by solid-phase extraction (SPE), PhIP—DNA adducts were analyzed by MS/MS and MSn scan modes on a 2-D linear quadrupole ion trap mass spectrometer (QIT/MS). The major DNA adduct, N-(deoxyguanosin-8-yl)-2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (dG-C8-PhIP), was detected in calf thymus (CT) DNA modified in vitro with a bioactivated form of PhIP and in the colon and liver of rats given PhIP as part of the diet. The lower limit of detection (LOD) was 1 adduct per 108 DNA bases, and the limit of quantification (LOQ) was 3 adducts per 108 DNA bases in both MS/MS and MS3 scan modes, using 27 μg of DNA for analysis. Measurements were based on isotope dilution with the internal standard, N-(deoxyguanosin-8-yl)-2-amino-1-(trideutero)methyl-6-phenylimidazo[4,5-b]pyridine (dG-C8-[2H3C]-PhIP). The selected reaction monitoring (SRM) scan mode in MS/MS was employed to monitor the loss of deoxyribose (dR) from the protonated molecules of the adducts ([M + H - 116]+). The consecutive reaction monitoring (CRM) scan modes in MS3 and MS4 were used to measure and further characterize product ions of the aglycone ion (BH2+) (Guanyl-PhIP). The MS3 scan mode was effective in eliminating isobaric interferences observed in the MS/MS scan mode and resulted in an improved signal-to-noise (S/N) ratio. Moreover, the product ion spectra obtained by the MSn scan modes provided rich structural information about the adduct and were used to corroborate the identity of dG-C8-PhIP. In addition, an isomeric dG-PhIP adduct was detected in vivo. This LCESI/MS/MSn method is the first reported application on the use of the MS3 scan mode for the analysis of DNA adducts in vivo. PMID:17305409

Transient IP Structures Associated with Short-Period Variations in the Solar Energetic Particle and Galactic Cosmic Ray Flux

NASA Astrophysics Data System (ADS)

Mulligan, T.; Blake, J.; Spence, H. E.; Jordan, A. P.; Quenby, J. J.; Shaul, D.

2006-12-01

Short-period variations in the integral SEP ( > 10 MeV) and GCR fluence ( > 100 MeV), often observed in neutron monitor data have also been seen by the High Sensitivity Telescope (HIST) aboard the Polar Spacecraft. Although HIST was designed to measure radiation-belt electrons, it makes clean measurements of the integral SEP and GCR fluence when Polar is outside the radiation belts. These measurements show variability on a variety of timescales including 0.1~mHz - 1~mHz. We examine these variations from Polar and compare them with IMF and plasma solar wind conditions at L1 using ACE data. We find coherent short-term variability occurs when Earth is in close proximity to the HCS and when Earth is either inside an ICME or when an ICME has just transited the Earth. Also, when a flux rope ICME signature is present, the rope axis is nearly parallel to the radial direction and the HCS. The launch of STEREO will enable detailed 3-D analyses of such solar wind disturbances along spatial scales on the same order of typical SEP and GCR proton gyroradii, which are needed to elucidate the mechanism behind this short-period variability.

Orchestrating BMD Control in Extended BPEL

DTIC Science & Technology

2008-05-21

Orchestration of secure WebMail , Technical Report ISE-TR-06-08, George Mason University, Fairfax, VA, August 2006. [9] E. Christensen, F. Curbera...methods to access and dissemination control, securing circuit switched (SS7) and IP based telecommunication (VoIP) systems, multimedia, security ...decorating the Business Process Execution Language (BPEL) with Quality of Service (QoS), Measures of Performance (MoP), Measures of Effectiveness (MoE

Ion Pair Formation between Tertiary Aliphatic Amines and Perchlorate in the Biphasic Water/Dichloromethane System.

PubMed

Badocco, Denis; Di Marco, Valerio; Venzo, Alfonso; Frasconi, Marco; Frezzato, Diego; Pastore, Paolo

2017-10-12

The ability of aliphatic amines (AAs), namely, tripropylamine (TPrA), trisobutylamine (TisoBuA), and tributylamine (TBuA), to form ion pairs with perchlorate anion (ClO 4 - ) in biphasic aqueous/dichloromethane (CH 2 Cl 2 ) mixtures containing ClO 4 - 0.1 M has been demonstrated by GC with flame ionization (FID) and mass detectors (MS) and by NMR measurements. The extraction efficiency of the AAs to the organic phase was modeled by equations that were used to fit the experimental GC data, allowing us to determine values for K P (partition constant of the free AA), K IP (formation constant of the ion pair), and K P IP (partition constant of the ion pair) for TPrA, TisoBuA, and TBuA at 25 °C. Ion pairs were shown to form in CH 2 Cl 2 also when ClO 4 - is replaced by other inorganic anions, like NO 3 - , ClO 3 - , Cl - , H 2 PO 4 - , and IO 3 - . No ion pairs formed when CH 2 Cl 2 was replaced by n-hexane, suggesting that aliphatic amine ion pairs can form in polar organic solvents but not in nonpolar ones.

Refinement of intraperitoneal injection of sodium pentobarbital for euthanasia in laboratory rats (Rattus norvegicus).

PubMed

Zatroch, Katie K; Knight, Cameron G; Reimer, Julie N; Pang, Daniel S J

2017-02-21

The Canadian Council on Animal Care and American Veterinary Medical Association classify intraperitoneal (IP) pentobarbital as an acceptable euthanasia method in rats. However, national guidelines do not exist for a recommended dose or volume and IP euthanasia has been described as unreliable, with misinjections leading to variable success in ensuring a timely death. The aims of this study were to assess and improve efficacy and consistency of IP euthanasia. In a randomized, blinded study, 51 adult female Sprague-Dawley rats (170-495 g) received one of four treatments: low-dose low-volume (LL) IP pentobarbital (n = 13, 200 mg/kg pentobarbital), low-dose high-volume (LH) IP pentobarbital (n = 14, 200 mg/kg diluted 1:3 with phosphate buffered saline), high-dose high-volume (HH, n = 14, 800 mg/kg pentobarbital), or saline. Times to loss of righting reflex (LORR) and cessation of heartbeat (CHB) were recorded. To identify misinjections, necropsy examinations were performed on all rats. Video recordings of LL and HH groups were analyzed for pain-associated behaviors. Between-group comparisons were performed with 1-way ANOVA and Games-Howell post hoc tests. Variability in CHB was assessed by calculating the coefficient of variation (CV). The fastest euthanasia method (CHB) was HH (283.7 ± 38.0 s), compared with LL (485.8 ± 140.7 s, p = 0.002) and LH (347.7 ± 72.0 s, p = 0.039). Values for CV were: HH, 13.4%; LH, 20.7%; LL, 29.0%. LORR time was longest in LL (139.5 ± 29.6 s), compared with HH (111.6 ± 19.7 s, p = 0.046) and LH (104.2 ± 19.3 s, p = 0.01). Misinjections occurred in 17.0% (7/41) of euthanasia attempts. Pain-associated behavior incidence ranged from 36% (4/11, LL) to 46% (5/11, HH). These data illustrate refinement of the IP pentobarbital euthanasia technique. Both dose and volume contribute to speed of death, with a dose of 800 mg/kg (HH) being the most effective method. An increase in volume alone does not significantly reduce variability. The proportion of misinjections was similar to that of previous studies.

The Worldwide Interplanetary Scintillation (IPS) Stations (WIPSS) Network October 2016 Observing Campaign: Initial WIPSS Data Analyses

NASA Astrophysics Data System (ADS)

Bisi, M. M.; Fallows, R. A.; Jackson, B. V.; Tokumaru, M.; Gonzalez-Esparza, A.; Morgan, J.; Chashei, I. V.; Mejia-Ambriz, J.; Tyul'bashev, S. A.; Manoharan, P. K.; De la Luz, V.; Aguilar-Rodriguez, E.; Yu, H. S.; Barnes, D.; Chang, O.; Odstrcil, D.; Fujiki, K.; Shishov, V.

2017-12-01

Interplanetary Scintillation (IPS) allows for the determination of velocity and a proxy for plasma density to be made throughout the corona and inner heliosphere. Where sufficient observations are undertaken, the results can be used as input to the University of California, San Diego (UCSD) three-dimensional (3-D) time-dependent tomography suite to allow for the full 3-D reconstruction of both velocity and density throughout the inner heliosphere. By combining IPS results from multiple observing locations around the planet, we can increase both the temporal and spatial coverage across the whole of the inner heliosphere and hence improve forecast capability. During October 2016, a unique opportunity arose whereby the European-based LOw Frequency ARray (LOFAR) radio telescope was used to make nearly four weeks of continuous observations of IPS as a heliospheric space-weather trial campaign. This was expanded into a global effort to include observations of IPS from the Murchison Widefield Array (MWA) in Western Australia and many more observations from various IPS-dedicated WIPSS Network systems. LOFAR is a next-generation low-frequency radio interferometer capable of observing in the radio frequency range 10-250 MHz, nominally with up to 80 MHz bandwidth at a time. MWA in Western Australia is capable of observing in the 80-300 MHz frequency range nominally using up to 32 MHz of bandwidth. IPS data from LOFAR, ISEE, the MEXican Array Radio Telescope (MEXART), and, where possible, other WIPSS Network systems (such as LPI-BSA and Ooty), will be used in this study and we will present some initial findings for these data sets. We also make a first attempt at the 3-D reconstruction of multiple pertinent WIPSS results in the UCSD tomography. We will also try to highlight some of the potential future tools that make LOFAR a very unique system to be able to test and validate a whole plethora of IPS analysis methods with the same set of IPS data.

Use and Effectiveness of Intraperitoneal Chemotherapy for Treatment of Ovarian Cancer

PubMed Central

Wright, Alexi A.; Cronin, Angel; Milne, Dana E.; Bookman, Michael A.; Burger, Robert A.; Cohn, David E.; Cristea, Mihaela C.; Griggs, Jennifer J.; Keating, Nancy L.; Levenback, Charles F.; Mantia-Smaldone, Gina; Matulonis, Ursula A.; Meyer, Larissa A.; Niland, Joyce C.; Weeks, Jane C.; O'Malley, David M.

2015-01-01

Purpose A 2006 randomized trial demonstrated a 16-month survival benefit with intraperitoneal and intravenous (IP/IV) chemotherapy administered to patients who had ovarian cancer, compared with IV chemotherapy alone, but more treatment-related toxicities. The objective of this study was to examine the use and effectiveness of IP/IV chemotherapy in clinical practice. Patients and Methods Prospective cohort study of 823 women with stage III, optimally cytoreduced ovarian cancer diagnosed at six National Comprehensive Cancer Network institutions. We examined IP/IV chemotherapy use in all patients diagnosed between 2003 and 2012 (N = 823), and overall survival and treatment-related toxicities with Cox regression and logistic regression, respectively, in a propensity score–matched sample (n = 402) of patients diagnosed from 2006 to 2012, excluding trial participants, to minimize selection bias. Results Use of IP/IV chemotherapy increased from 0% to 33% between 2003 and 2006, increased to 50% from 2007 to 2008, and plateaued thereafter. Between 2006 and 2012, adoption of IP/IV chemotherapy varied by institution from 4% to 67% (P < .001) and 43% of patients received modified IP/IV regimens at treatment initiation. In the propensity score–matched sample, IP/IV chemotherapy was associated with significantly improved overall survival (3-year overall survival, 81% v 71%; hazard ratio, 0.68; 95% CI, 0.47 to 0.99), compared with IV chemotherapy, but also more frequent alterations in chemotherapy delivery route (adjusted rates discontinuation or change, 20.4% v 10.0%; adjusted odds ratio, 2.83; 95% CI, 1.47 to 5.47). Conclusion Although the use of IP/IV chemotherapy increased significantly at National Comprehensive Cancer Network centers between 2003 and 2012, fewer than 50% of eligible patients received it. Increasing IP/IV chemotherapy use in clinical practice may be an important and underused strategy to improve ovarian cancer outcomes. PMID:26240233

Extemporaneously preparative biodegradable injectable polymer systems exhibiting temperature-responsive irreversible gelation.

PubMed

Yoshida, Yasuyuki; Takata, Kazuyuki; Takai, Hiroki; Kawahara, Keisuke; Kuzuya, Akinori; Ohya, Yuichi

2017-10-01

On clinical application of biodegradable injectable polymer (IP) systems, quick extemporaneous preparation of IP formulations and longer duration time gel state after injection into the body are the important targets to be developed. Previously, we had reported temperature-responsive covalent gelation systems via bio-orthogonal thiol-ene reaction by 'mixing strategy' of amphiphilic biodegradable tri-block copolymer (tri-PCG) attaching acryloyl groups on both termini (tri-PCG-Acryl) with reactive polythiol. In other previous works, we found 'freeze-dry with PEG/dispersion' method as quick extemporaneous preparation method of biodegradable IP formulations. In this study, we applied this quick preparative method to the temperature-triggered covalent gelation system. The instant formulation (D-sample) could be prepared by 'freeze-dry with PEG/dispersion' just mixing of tri-PCG-Acryl micelle dispersion and tri-PCG/DPMP micelle dispersion with PEG, that can be prepared in 30 s from the dried samples. The obtained D-sample showed irreversible gelation and long duration time of gel state, which was basically the same as the formulations prepared by the usual heating dissolution method (S-sample). Interestingly, the D-sample could maintain its sol state for a longer time (24 h) after preparing the formulation at r.t. compared with the S-sample, which became a gel in 3 h after preparing. The IP system showed good biocompatibility and long duration time of the gel state after subcutaneous implantation. These characteristics of D-samples, quick extemporaneous preparation and high stability in the sol state before injection, would be very convenient in a clinical setting.

Performance of local optimization in single-plane fluoroscopic analysis for total knee arthroplasty.

PubMed

Prins, A H; Kaptein, B L; Stoel, B C; Lahaye, D J P; Valstar, E R

2015-11-05

Fluoroscopy-derived joint kinematics plays an important role in the evaluation of knee prostheses. Fluoroscopic analysis requires estimation of the 3D prosthesis pose from its 2D silhouette in the fluoroscopic image, by optimizing a dissimilarity measure. Currently, extensive user-interaction is needed, which makes analysis labor-intensive and operator-dependent. The aim of this study was to review five optimization methods for 3D pose estimation and to assess their performance in finding the correct solution. Two derivative-free optimizers (DHSAnn and IIPM) and three gradient-based optimizers (LevMar, DoNLP2 and IpOpt) were evaluated. For the latter three optimizers two different implementations were evaluated: one with a numerically approximated gradient and one with an analytically derived gradient for computational efficiency. On phantom data, all methods were able to find the 3D pose within 1mm and 1° in more than 85% of cases. IpOpt had the highest success-rate: 97%. On clinical data, the success rates were higher than 85% for the in-plane positions, but not for the rotations. IpOpt was the most expensive method and the application of an analytically derived gradients accelerated the gradient-based methods by a factor 3-4 without any differences in success rate. In conclusion, 85% of the frames can be analyzed automatically in clinical data and only 15% of the frames require manual supervision. The optimal success-rate on phantom data (97% with IpOpt) on phantom data indicates that even less supervision may become feasible. Copyright © 2015 Elsevier Ltd. All rights reserved.

Molecular simulation of small Knudsen number flows

NASA Astrophysics Data System (ADS)

Fei, Fei; Fan, Jing

2012-11-01

The direct simulation Monte Carlo (DSMC) method is a powerful particle-based method for modeling gas flows. It works well for relatively large Knudsen (Kn) numbers, typically larger than 0.01, but quickly becomes computationally intensive as Kn decreases due to its time step and cell size limitations. An alternative approach was proposed to relax or remove these limitations, based on replacing pairwise collisions with a stochastic model corresponding to the Fokker-Planck equation [J. Comput. Phys., 229, 1077 (2010); J. Fluid Mech., 680, 574 (2011)]. Similar to the DSMC method, the downside of that approach suffers from computationally statistical noise. To solve the problem, a diffusion-based information preservation (D-IP) method has been developed. The main idea is to track the motion of a simulated molecule from the diffusive standpoint, and obtain the flow velocity and temperature through sampling and averaging the IP quantities. To validate the idea and the corresponding model, several benchmark problems with Kn ˜ 10-3-10-4 have been investigated. It is shown that the IP calculations are not only accurate, but also efficient because they make possible using a time step and cell size over an order of magnitude larger than the mean collision time and mean free path, respectively.

Saturation analysis of ChIP-seq data for reproducible identification of binding peaks

PubMed Central

Hansen, Peter; Hecht, Jochen; Ibrahim, Daniel M.; Krannich, Alexander; Truss, Matthias; Robinson, Peter N.

2015-01-01

Chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) is a powerful technology to identify the genome-wide locations of transcription factors and other DNA binding proteins. Computational ChIP-seq peak calling infers the location of protein–DNA interactions based on various measures of enrichment of sequence reads. In this work, we introduce an algorithm, Q, that uses an assessment of the quadratic enrichment of reads to center candidate peaks followed by statistical analysis of saturation of candidate peaks by 5′ ends of reads. We show that our method not only is substantially faster than several competing methods but also demonstrates statistically significant advantages with respect to reproducibility of results and in its ability to identify peaks with reproducible binding site motifs. We show that Q has superior performance in the delineation of double RNAPII and H3K4me3 peaks surrounding transcription start sites related to a better ability to resolve individual peaks. The method is implemented in C+l+ and is freely available under an open source license. PMID:26163319

Machine Learning Approach to Automated Quality Identification of Human Induced Pluripotent Stem Cell Colony Images.

PubMed

Joutsijoki, Henry; Haponen, Markus; Rasku, Jyrki; Aalto-Setälä, Katriina; Juhola, Martti

2016-01-01

The focus of this research is on automated identification of the quality of human induced pluripotent stem cell (iPSC) colony images. iPS cell technology is a contemporary method by which the patient's cells are reprogrammed back to stem cells and are differentiated to any cell type wanted. iPS cell technology will be used in future to patient specific drug screening, disease modeling, and tissue repairing, for instance. However, there are technical challenges before iPS cell technology can be used in practice and one of them is quality control of growing iPSC colonies which is currently done manually but is unfeasible solution in large-scale cultures. The monitoring problem returns to image analysis and classification problem. In this paper, we tackle this problem using machine learning methods such as multiclass Support Vector Machines and several baseline methods together with Scaled Invariant Feature Transformation based features. We perform over 80 test arrangements and do a thorough parameter value search. The best accuracy (62.4%) for classification was obtained by using a k-NN classifier showing improved accuracy compared to earlier studies.

Anomalous diffusion of Ibuprofen in cyclodextrin nanosponge hydrogels: an HRMAS NMR study

PubMed Central

Ferro, Monica; Punta, Carlo; Melone, Lucio; Panzeri, Walter; Rossi, Barbara; Trotta, Francesco

2014-01-01

Summary Ibuprofen sodium salt (IP) was encapsulated in cyclodextrin nanosponges (CDNS) obtained by cross-linking of β-cyclodextrin with ethylenediaminetetraacetic acid dianhydride (EDTAn) in two different preparations: CDNSEDTA 1:4 and 1:8, where the 1:n notation indicates the CD to EDTAn molar ratio. The entrapment of IP was achieved by swelling the two polymers with a 0.27 M solution of IP in D2O, leading to colourless, homogeneous hydrogels loaded with IP. The molecular environment and the transport properties of IP in the hydrogels were studied by high resolution magic angle spinning (HRMAS) NMR spectroscopy. The mean square displacement (MSD) of IP in the gels was obtained by a pulsed field gradient spin echo (PGSE) NMR pulse sequence at different observation times t d. The MSD is proportional to the observation time elevated to a scaling factor α. The α values define the normal Gaussian random motion (α = 1), or the anomalous diffusion (α < 1, subdiffusion, α > 1 superdiffusion). The experimental data here reported point out that IP undergoes subdiffusive regime in CDNSEDTA 1:4, while a slightly superdiffusive behaviour is observed in CDNSEDTA 1:8. The transition between the two dynamic regimes is triggered by the polymer structure. CDNSEDTA 1:4 is characterized by a nanoporous structure able to induce confinement effects on IP, thus causing subdiffusive random motion. CDNSEDTA 1:8 is characterized not only by nanopores, but also by dangling EDTA groups ending with ionized COO− groups. The negative potential provided by such groups to the polymer backbone is responsible for the acceleration effects on the IP anion thus leading to the superdiffusive behaviour observed. These results point out that HRMAS NMR spectroscopy is a powerful direct method for the assessment of the transport properties of a drug encapsulated in polymeric scaffolds. The diffusion properties of IP in CDNS can be modulated by suitable polymer synthesis; this finding opens the possibility to design suitable systems for drug delivery with predictable and desired drug release properties. PMID:25550735

What is the role of retroperitoneal exploration in optimally debulked stage IIIC epithelial ovarian cancer? An NRG Oncology/Gynecologic Oncology Group ancillary data study.

PubMed

Rungruang, Bunja J; Miller, Austin; Krivak, Thomas C; Horowitz, Neil S; Rodriguez, Noah; Hamilton, Chad A; Backes, Floor J; Carson, Linda F; Friedlander, Michael; Mutch, David G; Goodheart, Michael J; Tewari, Krishnansu S; Wenham, Robert M; Bookman, Michael A; Maxwell, G Larry; Richard, Scott D

2017-05-15

The purpose of this study was to determine the effect of retroperitoneal (RP) exploration on progression-free survival (PFS) and overall survival (OS) in epithelial ovarian cancer (EOC) patients with stage IIIC disease who underwent optimal debulking surgery. Data were collected from records of the Gynecologic Oncology Group 182 (GOG-182) study of stage IIIC EOC patients cytoreduced to no gross residual disease (R0) or minimal gross residual (<1 cm) disease (MGRD) at primary surgery. Patients with stage IIIC disease by intraperitoneal (IP) tumor were included and divided into 3 groups: 1) > 2 cm IP tumor without lymph node involvement (IP/RP-), 2) > 2 cm IP tumor with lymph node involvement (IP/RP+), and 3) > 2 cm IP tumor with no RP exploration (IP/RP?). The effects of disease distribution and RP exploration on PFS and OS were assessed using Kaplan-Meier and proportional hazards methods. There were 1871 stage IIIC patients in GOG-182 who underwent optimal primary debulking surgery. Of these, 689 (36.8%) underwent RP exploration with removal of lymph nodes from at least 1 para-aortic site, and 1182 (63.2%) did not. There were 269 patients in the IP/RP- group, 420 patients in the IP/RP + group, and 1182 patients in the IP/RP? group. Improved PFS (18.5 vs 16.0 months; P < .0001) and OS (53.3 vs 42.8 months; P < .0001) were associated with RP exploration versus no exploration. Patients with MGRD had improved PFS (16.8 vs 15.1 months, P = 0.0108) and OS (44.9 vs 40.5 months, P = 0.0076) versus no exploration. RP exploration at the time of primary surgery in patients with optimally debulked stage IIIC EOC is associated with a survival benefit. Cancer 2017;123:985-93. © 2016 American Cancer Society. © 2016 American Cancer Society.

Calibration of BAS-TR image plate response to high energy (3-300 MeV) carbon ions

NASA Astrophysics Data System (ADS)

Doria, D.; Kar, S.; Ahmed, H.; Alejo, A.; Fernandez, J.; Cerchez, M.; Gray, R. J.; Hanton, F.; MacLellan, D. A.; McKenna, P.; Najmudin, Z.; Neely, D.; Romagnani, L.; Ruiz, J. A.; Sarri, G.; Scullion, C.; Streeter, M.; Swantusch, M.; Willi, O.; Zepf, M.; Borghesi, M.

2015-12-01

The paper presents the calibration of Fuji BAS-TR image plate (IP) response to high energy carbon ions of different charge states by employing an intense laser-driven ion source, which allowed access to carbon energies up to 270 MeV. The calibration method consists of employing a Thomson parabola spectrometer to separate and spectrally resolve different ion species, and a slotted CR-39 solid state detector overlayed onto an image plate for an absolute calibration of the IP signal. An empirical response function was obtained which can be reasonably extrapolated to higher ion energies. The experimental data also show that the IP response is independent of ion charge states.

Calibration of BAS-TR image plate response to high energy (3-300 MeV) carbon ions.

PubMed

Doria, D; Kar, S; Ahmed, H; Alejo, A; Fernandez, J; Cerchez, M; Gray, R J; Hanton, F; MacLellan, D A; McKenna, P; Najmudin, Z; Neely, D; Romagnani, L; Ruiz, J A; Sarri, G; Scullion, C; Streeter, M; Swantusch, M; Willi, O; Zepf, M; Borghesi, M

2015-12-01

The paper presents the calibration of Fuji BAS-TR image plate (IP) response to high energy carbon ions of different charge states by employing an intense laser-driven ion source, which allowed access to carbon energies up to 270 MeV. The calibration method consists of employing a Thomson parabola spectrometer to separate and spectrally resolve different ion species, and a slotted CR-39 solid state detector overlayed onto an image plate for an absolute calibration of the IP signal. An empirical response function was obtained which can be reasonably extrapolated to higher ion energies. The experimental data also show that the IP response is independent of ion charge states.

Energy star compliant voice over internet protocol (VoIP) telecommunications network including energy star compliant VoIP devices

DOEpatents

Kouchri, Farrokh Mohammadzadeh

2012-11-06

A Voice over Internet Protocol (VoIP) communications system, a method of managing a communications network in such a system and a program product therefore. The system/network includes an ENERGY STAR (E-star) aware softswitch and E-star compliant communications devices at system endpoints. The E-star aware softswitch allows E-star compliant communications devices to enter and remain in power saving mode. The E-star aware softswitch spools messages and forwards only selected messages (e.g., calls) to the devices in power saving mode. When the E-star compliant communications devices exit power saving mode, the E-star aware softswitch forwards spooled messages.

A diffusive information preservation method for small Knudsen number flows

NASA Astrophysics Data System (ADS)

Fei, Fei; Fan, Jing

2013-06-01

The direct simulation Monte Carlo (DSMC) method is a powerful particle-based method for modeling gas flows. It works well for relatively large Knudsen (Kn) numbers, typically larger than 0.01, but quickly becomes computationally intensive as Kn decreases due to its time step and cell size limitations. An alternative approach was proposed to relax or remove these limitations, based on replacing pairwise collisions with a stochastic model corresponding to the Fokker-Planck equation [J. Comput. Phys., 229, 1077 (2010); J. Fluid Mech., 680, 574 (2011)]. Similar to the DSMC method, the downside of that approach suffers from computationally statistical noise. To solve the problem, a diffusion-based information preservation (D-IP) method has been developed. The main idea is to track the motion of a simulated molecule from the diffusive standpoint, and obtain the flow velocity and temperature through sampling and averaging the IP quantities. To validate the idea and the corresponding model, several benchmark problems with Kn ˜ 10-3-10-4 have been investigated. It is shown that the IP calculations are not only accurate, but also efficient because they make possible using a time step and cell size over an order of magnitude larger than the mean collision time and mean free path, respectively.

Spectral inversion of frequency-domain IP data obtained in Haenam, South Korea

NASA Astrophysics Data System (ADS)

Kim, B.; Nam, M. J.; Son, J. S.

2017-12-01

Spectral induced polarization (SIP) method using a range of source frequencies have been performed for not only exploring minerals resources, but also engineering or environmental application. SIP interpretation first makes inversion of individual frequency data to obtain complex resistivity structures, which will further analyzed employing Cole-Cole model to explain the frequency-dependent characteristics. However, due to the difficulty in fitting Cole-Cole model, there is a movement to interpret complex resistivity structure inverted only from a single frequency data: that is so-called "complex resistivity survey". Further, simultaneous inversion of multi-frequency SIP data, rather than making a single frequency SIP data, has been studied to improve ambiguity and artefacts of independent single frequency inversion in obtaining a complex resistivity structure, even though the dispersion characteristics of complex resistivity with respect to source frequency. Employing the simultaneous inversion method, this study makes inversion of field SIP data obtained over epithermal mineralized area, Haenam, in the southernmost tip of South Korea. The area has a polarizable structure because of extensive hydrothermal alteration, gold-silver deposits. After the inversion, we compare between inversion results considering multi-frequency data and single frequency data set to evaluate the performance of simultaneous inversion of multi-frequency SIP data.

Impact of Environmental Exposures on the Mutagenicity/Carcinogenicity of Heterocyclic Amines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Felton, J S; Knize, M G; Bennett, L M

2003-12-19

Carcinogenic heterocyclic amines are produced from overcooked foods and are highly mutagenic in most short-term test systems. One of the most abundant of these amines, 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), induces breast, colon and prostate tumors in rats. Human dietary epidemiology studies suggest a strong correlation between either meat consumption or well-done muscle meat consumption and cancers of the colon, breast, stomach, lung and esophagus. For over 20 years our laboratory has helped define the human exposure to these dietary carcinogens. In this report we describe how various environmental exposures may modulate the risk from exposure to heterocyclic amines, especially PhIP. To assessmore » the impact of foods on PhIP metabolism in humans, we developed an LC/MS/MS method to analyze the four major PhIP urinary metabolites following the consumption of a single portion of grilled chicken. Adding broccoli to the volunteers' diet altered the kinetics of PhIP metabolism. At the cellular level we have found that PhIP itself stimulates a significant estrogenic response in MCF-7 cells, but even more interestingly, co-incubation of the cells with herbal teas appear to enhance the response. Numerous environmental chemicals found in food or the atmosphere can impact the exposure, metabolism, and cell proliferation response of heterocyclic amines.« less

Are Current Insulin Pumps Accessible to Blind and Visually Impaired People?

PubMed Central

Burton, Darren M.; Uslan, Mark M.; Blubaugh, Morgan V.; Clements, Charles W.

2009-01-01

Background In 2004, Uslan and colleagues determined that insulin pumps (IPs) on the market were largely inaccessible to blind and visually impaired persons. The objective of this study is to determine if accessibility status changed in the ensuing 4 years. Methods Five IPs on the market in 2008 were acquired and analyzed for key accessibility traits such as speech and other audio output, tactual nature of control buttons, and the quality of visual displays. It was also determined whether or not a blind or visually impaired person could independently complete tasks such as programming the IP for insulin delivery, replacing batteries, and reading manuals and other documentation. Results It was found that IPs have not improved in accessibility since 2004. None have speech output, and with the exception of the Animas IR 2020, no significantly improved visual display characteristics were found. Documentation is still not completely accessible. Conclusion Insulin pumps are relatively complex devices, with serious health consequences resulting from improper use. For IPs to be used safely and independently by blind and visually impaired patients, they must include voice output to communicate all the information presented on their display screens. Enhancing display contrast and the size of the displayed information would also improve accessibility for visually impaired users. The IPs must also come with accessible user documentation in alternate formats. PMID:20144301

State of the Art of Interpersonal Physiology in Psychotherapy: A Systematic Review.

PubMed

Kleinbub, Johann R

2017-01-01

Introduction: The fast expanding field of Interpersonal Physiology (IP) focuses on the study of co-ordination or synchronization dynamics between the physiological activities of two, or more, individuals. IP has been associated with various relational features (e.g., empathy, attachment security, rapport, closeness…) that overlap with desirable characteristics of clinical relationships, suggesting that the relevant studies might provide objective, economical, and theory-free techniques to investigate the clinical process. The goal of the present work is to systematically retrieve and review the literature on IP in the field of psychotherapy and psychological intervention, in order to consolidate the knowledge of this research domain, highlight its critical issues, and delineate possible developments. Method: Following the guidelines by Okoli and Schabram (2010), a systematic literature search was performed in Scopus, Web of Science, PsycINFO, and PubMed databases by means of multiple keyword combinations; the results were integrated with references to the retrieved articles' bibliography as well as to other published reviews on IP. Results: All the retrieved documents reported clinical interactions that are characterized, at least partially, by IP phenomena. They appear to use fragmented and sometimes ambiguous terminology and show a lack of both specific theory-informed hypotheses and sound analytical procedures. Conclusion: Although the psychological nature of IP and its role in the clinical relationship are still mostly unknown, the potential value of a physiology-based measure of implicit exchanges in psychotherapy drives an acceleration in this research field. On the basis of the highlighted critical issues, possible future directions for clinical IP researchers are discussed.

Provider-identified barriers and facilitators to implementing a supported employment program in spinal cord injury.

PubMed

Cotner, Bridget A; Ottomanelli, Lisa; O'Connor, Danielle R; Trainor, John K

2018-06-01

In a 5-year study, individual placement and support (IPS) significantly increased employment rate of United States Veterans with spinal cord injury (SCI), a historically underemployed population. In a follow-up study, data on barriers and facilitators to IPS implementation were identified. Over 24 months of implementation, 82 key medical and vocational staff underwent semi-structured interviews (n = 130). Interviews were digitally recorded and qualitatively analyzed (ATLAS.ti v0.7) using a constant comparative method to generate themes. Some barriers to implementation occurred throughout the study, such as Veterans' lack of motivation and providers' difficulty integrating vocational and medical rehabilitation. Other barriers emerged at specific stages, for example, early barriers included a large geographic service area and a large patient caseload, and late barriers included need for staff education. Facilitators were mostly constant throughout implementation and included leadership support and successful integration of vocational staff into the medical care team. Implementation strategies need to be adjusted as implementation progresses and matures. The strategies that succeeded in this setting, which were situated in a real-world context of providing IPS as a part of SCI medical care, may inform implementation of IPS for other populations with physical disabilities. Implications for Rehabilitation Key facilitators to IPS in SCI implementation are integrating vocational staff with expertise in IPS and SCI on clinical rehabilitation teams and providing leadership support. Ongoing barriers to IPS in SCI include patient specific and program administration factors such as caseload size and staffing patterns. Varying implementation strategies are needed to address barriers as they arise and facilitate successful implementation.

c-MYC independent nuclear reprogramming favors cardiogenic potential of induced pluripotent stem cells

PubMed Central

Martinez-Fernandez, Almudena; Nelson, Timothy J.; Ikeda, Yasuhiro; Terzic, Andre

2010-01-01

Induced pluripotent stem cell (iPS) technology has launched a new platform in regenerative medicine aimed at deriving unlimited replacement tissue from autologous sources through somatic cell reprogramming using stemness factor sets. In this way, authentic cardiomyocytes have been obtained from iPS and recently demonstrated in proof-of-principle studies to repair infarcted heart. Optimizing the cardiogenic potential of iPS progeny would ensure a maximized yield of bioengineered cardiac tissue. Here, we reprogrammed fibroblasts in the presence or absence of c-MYC to determine if the acquired cardiogenicity is sensitive to the method of nuclear reprogramming. Using lentiviral constructs that expressed stemness factors SOX2, OCT4, and KLF4 with or without c-MYC, iPS clones generated through fibroblast reprogramming demonstrated indistinguishable characteristics for 5 days of differentiation with similar cell morphology, growth rates, and chimeric embryo integration. However, 4-factor c-MYC dependent nuclear reprogramming produced iPS progeny that consistently prolonged the expression of pluripotent Oct-4 and Fgf4 genes and repressed cardiac differentiation. In contrast, 3-factor c-MYC-less iPS clones efficiently up-regulated pre-cardiac (CXCR4, Flk-1, and Mesp1/2) and cardiac (Nkx2.5, Mef2c, and Myocardin) gene expression patterns. In fact, 3-factor iPS progeny demonstrated early and robust cardiogenesis during in vitro differentiation with consistent beating activity, sarcomere maturation, and rhythmical intracellular calcium dynamics. Thus, nuclear reprogramming independent of c-MYC enhances production of pluripotent stem cells with innate cardiogenic potential. PMID:20221419

Multi-views storage model and access methods of conversation history in converged IP messaging system

NASA Astrophysics Data System (ADS)

Lu, Meilian; Yang, Dong; Zhou, Xing

2013-03-01

Based on the analysis of the requirements of conversation history storage in CPM (Converged IP Messaging) system, a Multi-views storage model and access methods of conversation history are proposed. The storage model separates logical views from physical storage and divides the storage into system managed region and user managed region. It simultaneously supports conversation view, system pre-defined view and user-defined view of storage. The rationality and feasibility of multi-view presentation, the physical storage model and access methods are validated through the implemented prototype. It proves that, this proposal has good scalability, which will help to optimize the physical data storage structure and improve storage performance.

Composition of the bacterial community in the gut of the pine engraver, Ips pini (Say) (Coloptera) colonizing red pine

Treesearch

Italo Jr. Delalibera; Archana Vasanthakumar; Benjamin J. Burwitz; Patrick D. Schloss; Kier D. Klepzig; Jo Handelsman; Kenneth F. Raffa

2007-01-01

The gut bacterial community of a bark beetle, the pine engraver Ips pini (Say), was characterized using culture-dependent and culture-independent methods. Bacteria from individual guts of larvae, pupae and adults were cultured and DNA was extracted from samples of pooled larval guts. Analysis of 16S rRNA gene sequences amplified directly from the gut...

Calculation of photoelectron spectra of molybdenum and tungsten complexes using Green's functions methods.

PubMed

Bayse, Craig A; Ortwine, Kristine N

2007-08-16

Green's functions calculations are presented for several complexes of molybdenum and tungsten, two metals that are similar structurally but display subtle, but significant, differences in electronic structure. Outer valence Green's functions IPs for M(CO)6, M(Me)6, MH6, [MCl4O](-), and [MO4](-) (M = Mo, W) are generally within +/-0.2 eV of available experimental photoelectron spectra. The calculations show that electrons in M-L bonding orbitals are ejected at lower energies for Mo while the detachment energy for electrons in d orbitals varies with metal and complex. For the metal carbonyls, the quasiparticle picture assumed in OVGF breaks down for the inner valence pi CO molecular orbitals due to the coupling of two-hole-one-particle charge transfer states to the one-hole states. Incorporation of the 2h1p states through a Tamm-Dancoff approximation calculation accurately represents the band due to detachment from these molecular orbitals. Though the ordering of IPs for Green's functions methods and DFT Koopmans' theorem IPs is similar for the highest IPs for most compounds considered, the breakdown of the quasiparticle picture for the metal carbonyls suggests that scaling of the latter values may result in a fortuitous or incorrect assignment of experimental VDEs.

Sampling and data handling methods for inhalable particulate sampling. Final report nov 78-dec 80

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, W.B.; Cushing, K.M.; Johnson, J.W.

1982-05-01

The report reviews the objectives of a research program on sampling and measuring particles in the inhalable particulate (IP) size range in emissions from stationary sources, and describes methods and equipment required. A computer technique was developed to analyze data on particle-size distributions of samples taken with cascade impactors from industrial process streams. Research in sampling systems for IP matter included concepts for maintaining isokinetic sampling conditions, necessary for representative sampling of the larger particles, while flowrates in the particle-sizing device were constant. Laboratory studies were conducted to develop suitable IP sampling systems with overall cut diameters of 15 micrometersmore » and conforming to a specified collection efficiency curve. Collection efficiencies were similarly measured for a horizontal elutriator. Design parameters were calculated for horizontal elutriators to be used with impactors, the EPA SASS train, and the EPA FAS train. Two cyclone systems were designed and evaluated. Tests on an Andersen Size Selective Inlet, a 15-micrometer precollector for high-volume samplers, showed its performance to be with the proposed limits for IP samplers. A stack sampling system was designed in which the aerosol is diluted in flow patterns and with mixing times simulating those in stack plumes.« less

Bayesian reconstruction of transmission within outbreaks using genomic variants.

PubMed

De Maio, Nicola; Worby, Colin J; Wilson, Daniel J; Stoesser, Nicole

2018-04-01

Pathogen genome sequencing can reveal details of transmission histories and is a powerful tool in the fight against infectious disease. In particular, within-host pathogen genomic variants identified through heterozygous nucleotide base calls are a potential source of information to identify linked cases and infer direction and time of transmission. However, using such data effectively to model disease transmission presents a number of challenges, including differentiating genuine variants from those observed due to sequencing error, as well as the specification of a realistic model for within-host pathogen population dynamics. Here we propose a new Bayesian approach to transmission inference, BadTrIP (BAyesian epiDemiological TRansmission Inference from Polymorphisms), that explicitly models evolution of pathogen populations in an outbreak, transmission (including transmission bottlenecks), and sequencing error. BadTrIP enables the inference of host-to-host transmission from pathogen sequencing data and epidemiological data. By assuming that genomic variants are unlinked, our method does not require the computationally intensive and unreliable reconstruction of individual haplotypes. Using simulations we show that BadTrIP is robust in most scenarios and can accurately infer transmission events by efficiently combining information from genetic and epidemiological sources; thanks to its realistic model of pathogen evolution and the inclusion of epidemiological data, BadTrIP is also more accurate than existing approaches. BadTrIP is distributed as an open source package (https://bitbucket.org/nicofmay/badtrip) for the phylogenetic software BEAST2. We apply our method to reconstruct transmission history at the early stages of the 2014 Ebola outbreak, showcasing the power of within-host genomic variants to reconstruct transmission events.

GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis.

PubMed

Stricker, Georg; Engelhardt, Alexander; Schulz, Daniel; Schmid, Matthias; Tresch, Achim; Gagneur, Julien

2017-08-01

Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) is a widely used approach to study protein-DNA interactions. Often, the quantities of interest are the differential occupancies relative to controls, between genetic backgrounds, treatments, or combinations thereof. Current methods for differential occupancy of ChIP-Seq data rely however on binning or sliding window techniques, for which the choice of the window and bin sizes are subjective. Here, we present GenoGAM (Genome-wide Generalized Additive Model), which brings the well-established and flexible generalized additive models framework to genomic applications using a data parallelism strategy. We model ChIP-Seq read count frequencies as products of smooth functions along chromosomes. Smoothing parameters are objectively estimated from the data by cross-validation, eliminating ad hoc binning and windowing needed by current approaches. GenoGAM provides base-level and region-level significance testing for full factorial designs. Application to a ChIP-Seq dataset in yeast showed increased sensitivity over existing differential occupancy methods while controlling for type I error rate. By analyzing a set of DNA methylation data and illustrating an extension to a peak caller, we further demonstrate the potential of GenoGAM as a generic statistical modeling tool for genome-wide assays. Software is available from Bioconductor: https://www.bioconductor.org/packages/release/bioc/html/GenoGAM.html . gagneur@in.tum.de. Supplementary information is available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Consensus in controversy: The modified Delphi method applied to Gynecologic Oncology practice.

PubMed

Cohn, David E; Havrilesky, Laura J; Osann, Kathryn; Lipscomb, Joseph; Hsieh, Susie; Walker, Joan L; Wright, Alexi A; Alvarez, Ronald D; Karlan, Beth Y; Bristow, Robert E; DiSilvestro, Paul A; Wakabayashi, Mark T; Morgan, Robert; Mukamel, Dana B; Wenzel, Lari

2015-09-01

To determine the degree of consensus regarding the probabilities of outcomes associated with IP/IV and IV chemotherapy. A survey was administered to an expert panel using the Delphi method. Ten ovarian cancer experts were asked to estimate outcomes for patients receiving IP/IV or IV chemotherapy. The clinical estimates were: 1) probability of completing six cycles of chemotherapy, 2) probability of surviving five years, 3) median survival, and 4) probability of ER/hospital visits during treatment. Estimates for two patients, one with a low comorbidity index (patient 1) and the other with a moderate index (patient 2), were included. The survey was administered in three rounds, and panelists could revise their subsequent responses based on review of the anonymous opinions of their peers. The ranges were smaller for IV compared with IP/IV therapy. Ranges decreased with each round. Consensus converged around outcomes related to IP/IV chemotherapy for: 1) completion of 6 cycles of therapy (type 1 patient, 62%, type 2 patient, 43%); 2) percentage of patients surviving 5 years (type 1 patient, 66%, type 2 patient, 47%); and 3) median survival (type 1 patient, 83 months, type 2 patient, 58 months). The group required three rounds to achieve consensus on the probabilities of ER/hospital visits (type 1 patient, 24%, type 2 patient, 35%). Initial estimates of survival and adverse events associated with IP/IV chemotherapy differ among experts. The Delphi process works to build consensus and may be a pragmatic tool to inform patients of their expected outcomes. Copyright © 2015 Elsevier Inc. All rights reserved.

Global Mapping of Transcription Factor Binding Sites by Sequencing Chromatin Surrogates: a Perspective on Experimental Design, Data Analysis, and Open Problems.

PubMed

Wei, Yingying; Wu, George; Ji, Hongkai

2013-05-01

Mapping genome-wide binding sites of all transcription factors (TFs) in all biological contexts is a critical step toward understanding gene regulation. The state-of-the-art technologies for mapping transcription factor binding sites (TFBSs) couple chromatin immunoprecipitation (ChIP) with high-throughput sequencing (ChIP-seq) or tiling array hybridization (ChIP-chip). These technologies have limitations: they are low-throughput with respect to surveying many TFs. Recent advances in genome-wide chromatin profiling, including development of technologies such as DNase-seq, FAIRE-seq and ChIP-seq for histone modifications, make it possible to predict in vivo TFBSs by analyzing chromatin features at computationally determined DNA motif sites. This promising new approach may allow researchers to monitor the genome-wide binding sites of many TFs simultaneously. In this article, we discuss various experimental design and data analysis issues that arise when applying this approach. Through a systematic analysis of the data from the Encyclopedia Of DNA Elements (ENCODE) project, we compare the predictive power of individual and combinations of chromatin marks using supervised and unsupervised learning methods, and evaluate the value of integrating information from public ChIP and gene expression data. We also highlight the challenges and opportunities for developing novel analytical methods, such as resolving the one-motif-multiple-TF ambiguity and distinguishing functional and non-functional TF binding targets from the predicted binding sites. The online version of this article (doi:10.1007/s12561-012-9066-5) contains supplementary material, which is available to authorized users.

Picking ChIP-seq peak detectors for analyzing chromatin modification experiments

PubMed Central

Micsinai, Mariann; Parisi, Fabio; Strino, Francesco; Asp, Patrik; Dynlacht, Brian D.; Kluger, Yuval

2012-01-01

Numerous algorithms have been developed to analyze ChIP-Seq data. However, the complexity of analyzing diverse patterns of ChIP-Seq signals, especially for epigenetic marks, still calls for the development of new algorithms and objective comparisons of existing methods. We developed Qeseq, an algorithm to detect regions of increased ChIP read density relative to background. Qeseq employs critical novel elements, such as iterative recalibration and neighbor joining of reads to identify enriched regions of any length. To objectively assess its performance relative to other 14 ChIP-Seq peak finders, we designed a novel protocol based on Validation Discriminant Analysis (VDA) to optimally select validation sites and generated two validation datasets, which are the most comprehensive to date for algorithmic benchmarking of key epigenetic marks. In addition, we systematically explored a total of 315 diverse parameter configurations from these algorithms and found that typically optimal parameters in one dataset do not generalize to other datasets. Nevertheless, default parameters show the most stable performance, suggesting that they should be used. This study also provides a reproducible and generalizable methodology for unbiased comparative analysis of high-throughput sequencing tools that can facilitate future algorithmic development. PMID:22307239

Chromatin immunoprecipitation of mouse embryos.

PubMed

Voss, Anne K; Dixon, Mathew P; McLennan, Tamara; Kueh, Andrew J; Thomas, Tim

2012-01-01

During prenatal development, a large number of different cell types are formed, the vast majority of which contain identical genetic material. The basis of the great variety in cell phenotype and function is the differential expression of the approximately 25,000 genes in the mammalian genome. Transcriptional activity is regulated at many levels by proteins, including members of the basal transcriptional apparatus, DNA-binding transcription factors, and chromatin-binding proteins. Importantly, chromatin structure dictates the availability of a specific genomic locus for transcriptional activation as well as the efficiency, with which transcription can occur. Chromatin immunoprecipitation (ChIP) is a method to assess if chromatin modifications or proteins are present at a specific locus. ChIP involves the cross linking of DNA and associated proteins and immunoprecipitation using specific antibodies to DNA-associated proteins followed by examination of the co-precipitated DNA sequences or proteins. In the last few years, ChIP has become an essential technique for scientists studying transcriptional regulation and chromatin structure. Using ChIP on mouse embryos, we can document the presence or absence of specific proteins and chromatin modifications at genomic loci in vivo during mammalian development. Here, we describe a ChIP technique adapted for mouse embryos.

Picking ChIP-seq peak detectors for analyzing chromatin modification experiments.

PubMed

Micsinai, Mariann; Parisi, Fabio; Strino, Francesco; Asp, Patrik; Dynlacht, Brian D; Kluger, Yuval

2012-05-01

Numerous algorithms have been developed to analyze ChIP-Seq data. However, the complexity of analyzing diverse patterns of ChIP-Seq signals, especially for epigenetic marks, still calls for the development of new algorithms and objective comparisons of existing methods. We developed Qeseq, an algorithm to detect regions of increased ChIP read density relative to background. Qeseq employs critical novel elements, such as iterative recalibration and neighbor joining of reads to identify enriched regions of any length. To objectively assess its performance relative to other 14 ChIP-Seq peak finders, we designed a novel protocol based on Validation Discriminant Analysis (VDA) to optimally select validation sites and generated two validation datasets, which are the most comprehensive to date for algorithmic benchmarking of key epigenetic marks. In addition, we systematically explored a total of 315 diverse parameter configurations from these algorithms and found that typically optimal parameters in one dataset do not generalize to other datasets. Nevertheless, default parameters show the most stable performance, suggesting that they should be used. This study also provides a reproducible and generalizable methodology for unbiased comparative analysis of high-throughput sequencing tools that can facilitate future algorithmic development.

Chromatin Immunoprecipitation in Early Mouse Embryos.

PubMed

García-González, Estela G; Roque-Ramirez, Bladimir; Palma-Flores, Carlos; Hernández-Hernández, J Manuel

2018-01-01

Epigenetic regulation is achieved at many levels by different factors such as tissue-specific transcription factors, members of the basal transcriptional apparatus, chromatin-binding proteins, and noncoding RNAs. Importantly, chromatin structure dictates the availability of a specific genomic locus for transcriptional activation as well as the efficiency with which transcription can occur. Chromatin immunoprecipitation (ChIP) is a method that allows elucidating gene regulation at the molecular level by assessing if chromatin modifications or proteins are present at a specific locus. Initially, the majority of ChIP experiments were performed on cultured cell lines and more recently this technique has been adapted to a variety of tissues in different model organisms. Using ChIP on mouse embryos, it is possible to document the presence or absence of specific proteins and chromatin modifications at genomic loci in vivo during mammalian development and to get biological meaning from observations made on tissue culture analyses. We describe here a ChIP protocol on freshly isolated mouse embryonic somites for in vivo analysis of muscle specific transcription factor binding on chromatin. This protocol has been easily adapted to other mouse embryonic tissues and has also been successfully scaled up to perform ChIP-Seq.

Scalable Electrophysiological Investigation of iPS Cell-Derived Cardiomyocytes Obtained by a Lentiviral Purification Strategy

PubMed Central

Friedrichs, Stephanie; Malan, Daniela; Voss, Yvonne; Sasse, Philipp

2015-01-01

Disease-specific induced pluripotent stem (iPS) cells can be generated from patients and differentiated into functional cardiomyocytes for characterization of the disease and for drug screening. In order to obtain pure cardiomyocytes for automated electrophysiological investigation, we here report a novel non-clonal purification strategy by using lentiviral gene transfer of a puromycin resistance gene under the control of a cardiac-specific promoter. We have applied this method to our previous reported wild-type and long QT syndrome 3 (LQTS 3)-specific mouse iPS cells and obtained a pure cardiomyocyte population. These cells were investigated by action potential analysis with manual and automatic planar patch clamp technologies, as well as by recording extracellular field potentials using a microelectrode array system. Action potentials and field potentials showed the characteristic prolongation at low heart rates in LQTS 3-specific, but not in wild-type iPS cell-derived cardiomyocytes. Hence, LQTS 3-specific cardiomyocytes can be purified from iPS cells with a lentiviral strategy, maintain the hallmarks of the LQTS 3 disease and can be used for automated electrophysiological characterization and drug screening. PMID:26237021

Cross State-dependent Learning Interaction Between Scopolamine and Morphine in Mice: The Role of Dorsal Hippocampus

PubMed Central

Maleki, Morteza; Hassanpour-Ezatti, Majid; Navaeian, Majid

2017-01-01

Introduction: The current study aimed at investigating the existence of the cross state-dependent learning between morphine and scopolamine (SCO) in mice by passive avoidance method, pointing to the role of CA1 area. Methods: The effects of pre-training SCO (0.75, 1.5, and 3 μg, Intra-CA1), or morphine (1, 3, and 6 mg/kg, intraperitoneal (i.p.) was evaluated on the retrieval of passive avoidance learning using step-down task in mice (n=10). Then, the effect of pretest administration of morphine (1.5, 3, and 6 mg/kg, i.p.) was examined on passive avoidance retrieval impairment induced by pre-training SCO (3 μg/mice, Intra-CA1). Next, the effect of pretest Intra-CA1 injection of scopolamine (0.75, 1.5, and 3 μg/mice) was evaluated on morphine (6 mg/kg, i.p.) pre-training deficits in this task in mice. Results: The pre-training Intra-CA1 injection of scopolamine (1.5 and 3 μg/mouse), or morphine (3 and 6 mg/kg, i.p.) impaired the avoidance memory retrieval when it was tested 24 hours later. Pretest injection of both drugs improved its pre-training impairing effects on mice memory. Moreover, the amnesia induced by the pre-training injections of scopolamine (3 μg/mice) was restored significantly (P<0.01) by pretest injections of morphine (3 and 6 mg/kg, i.p.). Similarly, pretest injection of scopolamine (3 μg/mice) restored amnesia induced by the pre-training injections of morphine (6 mg/kg, i.p.), significantly (P<0.01). Conclusion: The current study findings indicated a cross state-dependent learning between SCO and morphine at CA1 level. Therefore, it seems that muscarinic and opioid receptors may act reciprocally on modulation of passive avoidance memory retrieval, at the level of dorsal hippocampus, in mice. PMID:28781727

High‐resolution mass spectrometric analysis of myo‐inositol hexakisphosphate using electrospray ionisation Orbitrap

PubMed Central

McIntyre, Catherine A.; Arthur, Christopher J.

2017-01-01

Rationale The phosphorus storage compound in grains, phytic acid, or myo‐inositol hexakisphosphate (IP6), is important for nutrition and human health, and is reportedly the most abundant organic phosphorus compound in soils. Methods for its determination have traditionally relied on complexation with iron and precipitation, acid digestion and measurement of phosphate concentration, or 31P NMR spectroscopy. Direct determination of phytic acid (and its homologues) using mass spectrometry has, as yet, found limited application to environmental or other complex matrices. The behaviour of phytic acid in electrospray ionisation high‐resolution mass spectrometry (ESI‐HRMS) and its fragmentation, both in‐source and via collision‐induced dissociation, have not been studied so far. Methods The negative ion mass spectrometry and tandem mass spectrometry (MS/MS) of IP6, and the lower inositol pentakisphosphate (IP5), using an ESI‐Orbitrap mass spectrometer is described. The purity of the compounds was investigated using anion‐exchange chromatography. Results IP6 is highly anionic, forming multiply charged ions and sodium adduct ions, which readily undergo dissociation in the ESI source. MS/MS analysis of the phytic acid [M−2H]2− ion and fragment ions and comparison with the full MS of the IP5 reference standard, and the MS/MS spectrum of the pentakisphosphate [M−2H]2− ion, confirm the fragmentation pattern of inositol phosphates in ESI. Further evidence for dissociation in the ion source is shown by the effect of increasing the source voltage on the mass spectrum of phytic acid. Conclusions The ESI‐HRMS of inositol phosphates is unusual and highly characteristic. The study of the full mass spectrum of IP6 in ESI‐HRMS mode indicates the detection of the compound in environmental matrices using this technique is preferable to the use of multiple reaction monitoring (MRM). PMID:28696018

Accelerated generation of human induced pluripotent stem cells with retroviral transduction and chemical inhibitors under physiological hypoxia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shimada, Hidenori; Hashimoto, Yoshiya; Nakada, Akira

2012-01-13

Highlights: Black-Right-Pointing-Pointer Very rapid generation of human iPS cells under optimized conditions. Black-Right-Pointing-Pointer Five chemical inhibitors under hypoxia boosted reprogramming. Black-Right-Pointing-Pointer We performed genome-wide DNA methylation analysis. -- Abstract: Induced pluripotent stem (iPS) cells are generated from somatic cells by the forced expression of a defined set of pluripotency-associated transcription factors. Human iPS cells can be propagated indefinitely, while maintaining the capacity to differentiate into all cell types in the body except for extra-embryonic tissues. This technology not only represents a new way to use individual-specific stem cells for regenerative medicine but also constitutes a novel method to obtain largemore » amounts of disease-specific cells for biomedical research. Despite their great potential, the long reprogramming process (up to 1 month) remains one of the most significant challenges facing standard virus-mediated methodology. In this study, we report the accelerated generation of human iPS cells from adipose-derived stem (ADS) cells, using a new combination of chemical inhibitors under a setting of physiological hypoxia in conjunction with retroviral transduction of Oct4, Sox2, Klf4, and L-Myc. Under optimized conditions, we observed human embryonic stem (ES)-like cells as early as 6 days after the initial retroviral transduction. This was followed by the emergence of fully reprogrammed cells bearing Tra-1-81-positive and DsRed transgene-silencing properties on day 10. The resulting cell lines resembled human ES cells in many respects including proliferation rate, morphology, pluripotency-associated markers, global gene expression patterns, genome-wide DNA methylation states, and the ability to differentiate into all three of the germ layers, both in vitro and in vivo. Our method, when combined with chemical inhibitors under conditions of physiological hypoxia, offers a powerful tool for rapidly generating bona fide human iPS cells and facilitates the application of iPS cell technology to biomedical research.« less

Polar and non-polar heterocyclic amines in cooked fish and meat products and their corresponding pan residues.

PubMed

Skog, K; Augustsson, K; Steineck, G; Stenberg, M; Jägerstad, M

1997-06-01

Fourteen cooked dishes with their corresponding pan residues were analysed for polar and non-polar heterocyclic amines using HPLC. The choice of foods, including beef, pork, poultry, game, fish, egg and sausages, was based on an investigation of an elderly population in Stockholm participating in an analytical epidemiological case-control study on cancer risks after intake of heterocyclic amines. The food items were prepared using normal household cooking practices, and to reflect the wide range of surface browning of the cooked dishes that would be encountered in this population, four cooking temperatures were used in the range 150-225 degrees C. For all food samples, the total amount of heterocyclic amines formed at 150 degrees C was less than 1 ng/g cooked product, and at 175 degrees C less than 2 ng/g. The highest concentrations of heterocyclic amines were detected in fillet of pork, reindeer meat and chicken breast fried at 200 and 225 degrees C and their corresponding pan residues. The total sum of 2-amino-3,8-dimethylimidazo-[4,5-f]quinoxaline, 2-amino-3,4,8-trimethylimidazo[4,5-f]quinoxaline and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine was about 1 microgram per 100 g portion (including pan residues) for reindeer meat and chicken breast, and between 1.9 and 6.3 micrograms per 100-g portion for fillet of pork. PhIP was the most abundant heterocyclic amine, identified in 73 of 84 samples, and the highest concentration of PhIP, 32.0 ng/g, was found in the pan residue from fillet of pork cooked at 225 degrees C. The non-polar heterocyclic amines 3-amino-1,4-dimethyl-5H-pyrido[4,3-b]indole and 3-amino-1-methyl-5H-pyrido[4,3-b]indole were detected in the range of 0.5-7.4 ng/g in most foods cooked at 225 degrees C, and also in meat sauce prepared at 200 and 175 degrees C. The other heterocyclic amines tested for: 2-amino-3-methylimidazo-[4,5-f]quinoline, 2-amino-3,4-dimethylimidazo[4,5-f]quinoline, 2-amino-6-methyl-pyrido-[1,2-a:3',2'-d]-imidazole and 2-aminodipyrido-[1,2-a:3',2'-d]imidazole, were present only at very low or non-detectable levels. The low recoveries of the amino-alpha-carbolines 2-amino-9H-pyrido[2,3-b]indole and 2-amino-3-methyl-9H-pyrido[2,3-b]indole made it impossible to quantify them. However, the co-mutagenic substances 1-methyl-9H-pyrido-[3,4-b]indole and 9H-pyrido[3,4-b]indole were detected at levels of about 1-30 ng/g in most of the dishes cooked at 200 and 225 degrees C.

Excision of a viral reprogramming cassette by delivery of synthetic Cre mRNA

PubMed Central

Loh, Yuin-Han; Yang, Jimmy Chen; De Los Angeles, Alejandro; Guo, Chunguang; Cherry, Anne; Rossi, Derrick J.; Park, In-Hyun; Daley, George Q.

2012-01-01

The generation of patient-specific induced pluripotent stem (iPS) cells provides an invaluable resource for cell therapy, in vitro modeling of human disease, and drug screening. To date, most human iPS cells have been generated with integrating retro- and lenti-viruses and are limited in their potential utility because residual transgene expression may alter their differentiation potential or induce malignant transformation. Alternatively, transgene-free methods using adenovirus and protein transduction are limited by low efficiency. This report describes a protocol for the generation of transgene-free human induced pluripotent stem cells using retroviral transfection of a single vector, which includes the coding sequences of human OCT4, SOX2, KLF4, and cMYC linked with picornaviral 2A plasmids. Moreover, after reprogramming has been achieved, this cassette can be removed using mRNA transfection of Cre recombinase. The method described herein to excise reprogramming factors with ease and efficiency facilitates the experimental generation and use of transgene-free human iPS cells. PMID:22605648

Effects of rhamnolipid and initial compost particle size on the two-stage composting of green waste.

PubMed

Zhang, Lu; Sun, Xiangyang

2014-07-01

Composting is a potential alternative to green waste incineration or deposition in landfills. The effects of the biosurfactant rhamnolipid (RL) (at 0.0%, 0.15%, and 0.30%) and initial compost particle size (IPS) (10, 15, and 25 mm) on a new, two-stage method for composting green waste was investigated. A combination of RL addition and IPS adjustment improved the quality of the finished compost in terms of its physical characteristics, pH, C/N ratio, nutrient content, cellulose and hemicellulose contents, water-soluble carbon (WSC) content, xylanase and CMCase activities, numbers of culturable microorganisms (bacteria, actinomycetes, and fungi), and toxicity to germinating seeds. The production of a stable and mature compost required only 24 days with the optimized two-stage composting method described here rather than the 90-270 days required with traditional composting. The best quality compost was obtained with 0.15% RL and an IPS of 15 mm. Copyright © 2014 Elsevier Ltd. All rights reserved.

Intake of meat mutagens and risk of prostate cancer in a cohort of U.S. health professionals

PubMed Central

Rohrmann, Sabine; Nimptsch, Katharina; Sinha, Rashmi; Willett, Walter C; Giovannucci, Edward L.; Platz, Elizabeth A; Wu, Kana

2015-01-01

Background Evidence relating heterocyclic aromatic amines (HCA), associated with high-temperature cooking methods, to prostate cancer risk is inconsistent Methods In a large US cohort study, intakes of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx) and 2-amino-3,4,8-trimethylimidazo[4,5-f]quinoxaline (DiMeIQx) and a meat-derived mutagenicity index (MDM) were assessed using a cooking method questionnaire administered in 1996. Until 2010, 2,770 prostate cancer cases were observed among 26,030 participants. Results Intake of PhIP from red meat was statistically significantly associated with total prostate cancer risk (top vs. bottom quintile HR=1.18, 95% CI 1.03–1.35), but not other HCAs (MeIQx, 1.12, 0.98–1.27, PhIP from white meat, 1.08, 0.95–1.22, DiMeIQx, 1.09, 0.97–1.21) or MDM (1.13, 1.00–1.28). For high grade (Gleason sum 7 with pattern 4+3 and Gleason sum 8–10, n=483 cases) and advanced cancers (n=281), we only observed positive associations for PhIP from red meat (top vs. bottom quintile: high grade: HR=1.44, 95% CI 1.04–1.98, p-trend=0.03; advanced: HR=1.50, 95% 0.99–2.26; p-trend=0.12), but associations for advanced cancers did not reach statistical significance. Observed associations remained similar after adjustment for total, unprocessed or processed red meat intake. Conclusion Observed positive associations between PhIP intake from red meat and prostate cancer, particularly high-grade and possibly also advanced prostate cancer need to be confirmed in other studies. Impact Results do not provide strong evidence that HCAs increase risk of prostate cancers. PMID:26224797

Generating Porcine Chimeras Using Inner Cell Mass Cells and Parthenogenetic Preimplantation Embryos

PubMed Central

Nakano, Kazuaki; Watanabe, Masahito; Matsunari, Hitomi; Matsuda, Taisuke; Honda, Kasumi; Maehara, Miki; Kanai, Takahiro; Hayashida, Gota; Kobayashi, Mirina; Kuramoto, Momoko; Arai, Yoshikazu; Umeyama, Kazuhiro; Fujishiro, Shuh-hei; Mizukami, Yoshihisa; Nagaya, Masaki; Hanazono, Yutaka; Nagashima, Hiroshi

2013-01-01

Background The development and validation of stem cell therapies using induced pluripotent stem (iPS) cells can be optimized through translational research using pigs as large animal models, because pigs have the closest characteristics to humans among non-primate animals. As the recent investigations have been heading for establishment of the human iPS cells with naïve type characteristics, it is an indispensable challenge to develop naïve type porcine iPS cells. The pluripotency of the porcine iPS cells can be evaluated using their abilities to form chimeras. Here, we describe a simple aggregation method using parthenogenetic host embryos that offers a reliable and effective means of determining the chimera formation ability of pluripotent porcine cells. Methodology/Significant Principal Findings In this study, we show that a high yield of chimeric blastocysts can be achieved by aggregating the inner cell mass (ICM) from porcine blastocysts with parthenogenetic porcine embryos. ICMs cultured with morulae or 4–8 cell-stage parthenogenetic embryos derived from in vitro-matured (IVM) oocytes can aggregate to form chimeric blastocysts that can develop into chimeric fetuses after transfer. The rate of production of chimeric blastocysts after aggregation with host morulae (20/24, 83.3%) was similar to that after the injection of ICMs into morulae (24/29, 82.8%). We also found that 4–8 cell-stage embryos could be used; chimeric blastocysts were produced with a similar efficiency (17/26, 65.4%). After transfer into recipients, these blastocysts yielded chimeric fetuses at frequencies of 36.0% and 13.6%, respectively. Conclusion/Significance Our findings indicate that the aggregation method using parthenogenetic morulae or 4–8 cell-stage embryos offers a highly reproducible approach for producing chimeric fetuses from porcine pluripotent cells. This method provides a practical and highly accurate system for evaluating pluripotency of undifferentiated cells, such as iPS cells, based on their ability to form chimeras. PMID:23626746

Angle-resolved photoelectron spectroscopy of formaldehyde and methanol

NASA Astrophysics Data System (ADS)

Keller, P. R.; Taylor, J. W.; Grimm, F. A.; Carlson, Thomas A.

1984-10-01

Angle-resolved photoelectron spectroscopy was employed to obtain the angular distribution parameter, β, for the valence orbitals (IP < 21.1 eV) of formaldehyde and methanol over the 10-30 eV photon energy range using dispersed polarized synchrotron radiation as the excitation source. It was found that the energy dependence of β in the photoelectron energy range between 2 and 10 eV can be related to the molecular-orbital type from which ionization occurs. This generalized energy behavior is discussed with regard to earlier energy-dependence studies on molecules of different orbital character. Evidence is presented for the presence of resonance photoionization phenomena in formaldehyde in agreement with theoretical cross-section calculations.

Permeable polyaniline articles for gas separation

DOEpatents

Wang, Hsing-Lin [Los Alamos, NM; Mattes, Benjamin R [Santa Fe, NM

2009-07-21

Immersion precipitation of solutions having 15%-30% (w/w) and various molecular weights of the emeraldine base form of polyaniline in polar aprotic solvents are shown to form integrally skinned asymmetric membranes and fibers having skin layers <1 .mu.m thick which exhibit improved rates of gas transport while preserving good selectivity. These membranes can be further transformed by an acid doping process after fabrication to achieve excellent permeation rates and high selectivities for particular gas separations. Prior to the use of concentrated EB solutions, the formation of integrally skinned asymmetric membranes was not possible, since films and fibers made from <5% w/w polyaniline solutions were found to disintegrate during the IP process.

Permeable polyaniline articles for gas separation

DOEpatents

Wang, Hsing-Lin; Mattes, Benjamin R.

2004-09-28

Immersion precipitation of solutions having 15%-30% (w/w) and various molecular weights of the emeraldine base form of polyaniline in polar aprotic solvents are shown to form integrally skinned asymmetric membranes and fibers having skin layers <1 .mu.m thick which exhibit improved rates of gas transport while preserving good selectivity. These membranes can be further transformed by an acid doping process after fabrication to achieve excellent permeation rates and high selectivities for particular gas separations. Prior to the use of concentrated EB solutions, the formation of integrally skinned asymmetric membranes was not possible, since films and fibers made from <5% w/w polyaniline solutions were found to disintegrate during the IP process.

Coupled Cluster Studies of Ionization Potentials and Electron Affinities of Single-Walled Carbon Nanotubes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peng, Bo; Govind, Niranjan; Aprà, Edoardo

In this paper we apply equation-of-motion coupled cluster (EOMCC) methods in studies of vertical ionization potentials (IP) and electron affinities (EA) for sin- gled walled carbon nanotubes. EOMCC formulations for ionization potentials and electron affinities employing excitation manifolds spanned by single and double ex- citations (IP/EA-EOMCCSD) are used to study IPs and EAs of nanotubes as a function of nanotube length. Several armchair nanotubes corresponding to C20nH20 models with n = 2 - 6 have been used in benchmark calculations. In agreement with previous studies, we demonstrate that the electronegativity of C20nH20 systems remains, to a large extent, independent ofmore » nanotube length. We also compare IP/EA- EOMCCSD results with those obtained with the coupled cluster models with single and double excitations corrected by perturbative triples, CCSD(T), and density func- tional theory (DFT) using global and range-separated hybrid exchange-correlation functionals.« less

Clinical performance of IPS-Empress 2 ceramic crowns inserted by general dental practitioners.

PubMed

Mansour, Yasar F; Al-Omiri, Mahmoud K; Khader, Yousef Saleh; Al-Wahadni, Ahed

2008-05-01

The aim of this study was to evaluate the clinical performance of IPS-Empress 2(R) all-ceramic crowns placed by general dental practitioners. Eighty-two IPS-Empress 2 crowns placed in 64 patients (27 females and 37 males) were evaluated. These crowns had been in place for 15.2 to 57.2 months (mean 25.3 months, SD=9.3). Survival analysis was conducted using the Kaplan-Meier method. Of the 82 crowns 93.9% were rated satisfactory. In terms of the integrity of the restorations, fracture was observed in three crowns and two showed a crack upon transillumination. Five crowns were rated unsatisfactory for color match; one for marginal adaptation; and none for discoloration, secondary caries, or sensitivity. IPS-Empress 2(R) is a suitable material to fabricate all-ceramic crowns; when these all-ceramic crowns were inserted by general dental practitioners, they functioned satisfactorily with low failure rates during an observation period ranging between 15.2 to 57.2 months.

Assigning Polarity to Causal Information in Financial Articles on Business Performance of Companies

NASA Astrophysics Data System (ADS)

Sakai, Hiroyuki; Masuyama, Shigeru

We propose a method of assigning polarity to causal information extracted from Japanese financial articles concerning business performance of companies. Our method assigns polarity (positive or negative) to causal information in accordance with business performance, e.g. “zidousya no uriage ga koutyou: (Sales of cars are good)” (The polarity positive is assigned in this example). We may use causal expressions assigned polarity by our method, e.g., to analyze content of articles concerning business performance circumstantially. First, our method classifies articles concerning business performance into positive articles and negative articles. Using them, our method assigns polarity (positive or negative) to causal information extracted from the set of articles concerning business performance. Although our method needs training dataset for classifying articles concerning business performance into positive and negative ones, our method does not need a training dataset for assigning polarity to causal information. Hence, even if causal information not appearing in the training dataset for classifying articles concerning business performance into positive and negative ones exist, our method is able to assign it polarity by using statistical information of this classified sets of articles. We evaluated our method and confirmed that it attained 74.4% precision and 50.4% recall of assigning polarity positive, and 76.8% precision and 61.5% recall of assigning polarity negative, respectively.

Evaluation of VIIRS, GOCI, and MODIS Collection 6 AOD Retrievals Against Ground Sunphotometer Observations Over East Asia

NASA Technical Reports Server (NTRS)

Xiao, Q.; Zhang, H.; Choi, M.; Li, S.; Kondragunta, S.; Kim, J.; Holben, B.; Levy, R. C.; Liu, Y.

2016-01-01

Persistent high aerosol loadings together with extremely high population densities have raised serious air quality and public health concerns in many urban centers in East Asia. However, ground-based air quality monitoring is relatively limited in this area. Recently, satellite-retrieved Aerosol Optical Depth (AOD) at high resolution has become a powerful tool to characterize aerosol patterns in space and time. Using ground AOD observations from the Aerosol Robotic Network (AERONET) and the Distributed Regional Aerosol Gridded Observation Networks (DRAGON)-Asia Campaign, as well as from handheld sunphotometers, we evaluated emerging aerosol products from the Visible Infrared Imaging Radiometer Suite (VIIRS) aboard the Suomi National Polar-orbiting Partnership (S-NPP), the Geostationary Ocean Color Imager (GOCI) aboard the Communication, Ocean, and Meteorology Satellite (COMS), and Terra and Aqua Moderate Resolution Imaging Spectroradiometer (MODIS) (Collection 6) in East Asia in 2012 and 2013. In the case study in Beijing, when compared with AOD observations from handheld sunphotometers, 51% of VIIRS Environmental Data Record (EDR) AOD, 37% of GOCI AOD, 33% of VIIRS Intermediate Product (IP) AOD, 26% of Terra MODIS C6 3km AOD, and 16% of Aqua MODIS C6 3km AOD fell within the reference expected error (EE) envelope (+/-0.05/+/- 0.15 AOD). Comparing against AERONET AOD over the JapanSouth Korea region, 64% of EDR, 37% of IP, 61% of GOCI, 39% of Terra MODIS, and 56% of Aqua MODIS C6 3km AOD fell within the EE. In general, satellite aerosol products performed better in tracking the day-to-day variability than tracking the spatial variability at high resolutions. The VIIRS EDR and GOCI products provided the most accurate AOD retrievals, while VIIRS IP and MODIS C6 3km products had positive biases.

Evaluation of VIIRS, GOCI, and MODIS Collection 6 AOD retrievals against ground sunphotometer observations over East Asia

NASA Astrophysics Data System (ADS)

Xiao, Q.; Zhang, H.; Choi, M.; Li, S.; Kondragunta, S.; Kim, J.; Holben, B.; Levy, R. C.; Liu, Y.

2016-02-01

Persistent high aerosol loadings together with extremely high population densities have raised serious air quality and public health concerns in many urban centers in East Asia. However, ground-based air quality monitoring is relatively limited in this area. Recently, satellite-retrieved Aerosol Optical Depth (AOD) at high resolution has become a powerful tool to characterize aerosol patterns in space and time. Using ground AOD observations from the Aerosol Robotic Network (AERONET) and the Distributed Regional Aerosol Gridded Observation Networks (DRAGON)-Asia Campaign, as well as from handheld sunphotometers, we evaluated emerging aerosol products from the Visible Infrared Imaging Radiometer Suite (VIIRS) aboard the Suomi National Polar-orbiting Partnership (S-NPP), the Geostationary Ocean Color Imager (GOCI) aboard the Communication, Ocean, and Meteorology Satellite (COMS), and Terra and Aqua Moderate Resolution Imaging Spectroradiometer (MODIS) (Collection 6) in East Asia in 2012 and 2013. In the case study in Beijing, when compared with AOD observations from handheld sunphotometers, 51 % of VIIRS Environmental Data Record (EDR) AOD, 37 % of GOCI AOD, 33 % of VIIRS Intermediate Product (IP) AOD, 26 % of Terra MODIS C6 3 km AOD, and 16 % of Aqua MODIS C6 3 km AOD fell within the reference expected error (EE) envelope (±0.05 ± 0.15 AOD). Comparing against AERONET AOD over the Japan-South Korea region, 64 % of EDR, 37 % of IP, 61 % of GOCI, 39 % of Terra MODIS, and 56 % of Aqua MODIS C6 3 km AOD fell within the EE. In general, satellite aerosol products performed better in tracking the day-to-day variability than tracking the spatial variability at high resolutions. The VIIRS EDR and GOCI products provided the most accurate AOD retrievals, while VIIRS IP and MODIS C6 3 km products had positive biases.

IP over fiber technologies: ATM/POS/SDL

NASA Astrophysics Data System (ADS)

Jin, Depeng; Zeng, Lieguang

2001-10-01

The explosive growth of Internet traffic has created the need to transport IP over high-speed links such as fiber. Three main IP over fiber technologies have been developed: ATM, POS and SDL. As ATM has been widely researched and developed, this paper mainly discusses the POS and SDL. POS is a traditional mapping method of packets, and this paper presents the realization state machine of POS and analyzes the Probability of Packet Loss. SDL is a new framing protocol for variable/fixed length of packet, which extends the HEC-liking framing mechanism used in ATM. This paper analyzes this new protocol and gives the performance results such as MTTF and PFP. Finally, the comparison of POS and SDL is provided.

Characterization for imperfect polarizers under imperfect conditions.

PubMed

Nee, S M; Yoo, C; Cole, T; Burge, D

1998-01-01

The principles for measuring the extinction ratio and transmittance of a polarizer are formulated by use of the principal Mueller matrix, which includes both polarization and depolarization. The extinction ratio is about half of the depolarization, and the contrast is the inverse of the extinction ratio. Errors in the extinction ratio caused by partially polarized incident light and the misalignment of polarizers can be corrected by the devised zone average method and the null method. Used with a laser source, the null method can measure contrasts for very good polarizers. Correct algorithms are established to deduce the depolarization for three comparable polarizers calibrated mutually. These methods are tested with wire-grid polarizers used in the 3-5-microm wavelength region with a laser source and also a lamp source. The contrasts obtained from both methods agree.

MeRHIC - staging approach to eRHIC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ptitsyn,V.; Beebe-Wang, J.; Ben-Zvi, I.

Design of a medium energy electron-ion collider (MeRHIC) is under development at the Collider-Accelerator Department at BNL. The design envisions construction of a 4 GeV electron accelerator in a local area inside and near the RHIC tunnel. Electrons will be produced by a polarized electron source and accelerated in energy recovery linacs. Collisions of the electron beam with 100 GeV/u heavy ions or with 250 GeV polarized protons will be arranged in the existing IP2 interaction region of RHIC. The luminosity of electron-proton collisions at the 10{sup 32} cm{sup -2}s{sup -1} level will be achieved with 50 mA CW electronmore » current and presently available proton beam parameters. Efficient proton beam cooling at collision energy may bring the luminosity to 10{sup 33} cm{sup -2}s{sup -1}. An important feature of MeRHIC is that it serves as a first stage of eRHIC, a future electron-ion collider at BNL with both higher luminosity and energy reach. The majority of MeRHIC accelerator components will be used in eRHIC.« less

Subtype-selective regulation of IP(3) receptors by thimerosal via cysteine residues within the IP(3)-binding core and suppressor domain.

PubMed

Khan, Samir A; Rossi, Ana M; Riley, Andrew M; Potter, Barry V L; Taylor, Colin W

2013-04-15

IP(3)R (IP(3) [inositol 1,4,5-trisphosphate] receptors) and ryanodine receptors are the most widely expressed intracellular Ca(2+) channels and both are regulated by thiol reagents. In DT40 cells stably expressing single subtypes of mammalian IP(3)R, low concentrations of thimerosal (also known as thiomersal), which oxidizes thiols to form a thiomercurylethyl complex, increased the sensitivity of IP(3)-evoked Ca(2+) release via IP(3)R1 and IP(3)R2, but inhibited IP(3)R3. Activation of IP(3)R is initiated by IP(3) binding to the IBC (IP(3)-binding core; residues 224-604) and proceeds via re-arrangement of an interface between the IBC and SD (suppressor domain; residues 1-223). Thimerosal (100 μM) stimulated IP(3) binding to the isolated NT (N-terminal; residues 1-604) of IP(3)R1 and IP(3)R2, but not to that of IP(3)R3. Binding of a competitive antagonist (heparin) or partial agonist (dimeric-IP(3)) to NT1 was unaffected by thiomersal, suggesting that the effect of thimerosal is specifically related to IP(3)R activation. IP(3) binding to NT1 in which all cysteine residues were replaced by alanine was insensitive to thimerosal, so too were NT1 in which cysteine residues were replaced in either the SD or IBC. This demonstrates that thimerosal interacts directly with cysteine in both the SD and IBC. Chimaeric proteins in which the SD of the IP(3)R was replaced by the structurally related A domain of a ryanodine receptor were functional, but thimerosal inhibited both IP(3) binding to the chimaeric NT and IP(3)-evoked Ca(2+) release from the chimaeric IP(3)R. This is the first systematic analysis of the effects of a thiol reagent on each IP(3)R subtype. We conclude that thimerosal selectively sensitizes IP(3)R1 and IP(3)R2 to IP(3) by modifying cysteine residues within both the SD and IBC and thereby stabilizing an active conformation of the receptor.

What Is the Role of Informal Healthcare Providers in Developing Countries? A Systematic Review

PubMed Central

Sudhinaraset, May; Ingram, Matthew; Lofthouse, Heather Kinlaw; Montagu, Dominic

2013-01-01

Informal health care providers (IPs) comprise a significant component of health systems in developing nations. Yet little is known about the most basic characteristics of performance, cost, quality, utilization, and size of this sector. To address this gap we conducted a comprehensive literature review on the informal health care sector in developing countries. We searched for studies published since 2000 through electronic databases PubMed, Google Scholar, and relevant grey literature from The New York Academy of Medicine, The World Bank, The Center for Global Development, USAID, SHOPS (formerly PSP-One), The World Health Organization, DFID, Human Resources for Health Global Resource Center. In total, 334 articles were retrieved, and 122 met inclusion criteria and chosen for data abstraction. Results indicate that IPs make up a significant portion of the healthcare sector globally, with almost half of studies (48%) from Sub-Saharan Africa. Utilization estimates from 24 studies in the literature of IP for healthcare services ranged from 9% to 90% of all healthcare interactions, depending on the country, the disease in question, and methods of measurement. IPs operate in a variety of health areas, although baseline information on quality is notably incomplete and poor quality of care is generally assumed. There was a wide variation in how quality of care is measured. The review found that IPs reported inadequate drug provision, poor adherence to clinical national guidelines, and that there were gaps in knowledge and provider practice; however, studies also found that the formal sector also reported poor provider practices. Reasons for using IPs included convenience, affordability, and social and cultural effects. Recommendations from the literature amount to a call for more engagement with the IP sector. IPs are a large component of nearly all developing country health systems. Research and policies of engagement are needed. PMID:23405101

Interferon-γ–Inducible Protein 10 (IP-10) as a Screening Tool to Optimize Human Immunodeficiency Virus RNA Monitoring in Resource-Limited Settings

PubMed Central

Pastor, Lucía; Casellas, Aina; Carrillo, Jorge; Maculuve, Sonia; Jairoce, Chenjerai; Paredes, Roger; Blanco, Julià; Naniche, Denise

2017-01-01

Abstract Background Achieving effective antiretroviral treatment (ART) monitoring is a key determinant to ensure viral suppression and reach the UNAIDS 90-90-90 targets. The gold standard for detecting virological failure is plasma human immunodeficiency virus (HIV) RNA (viral load [VL]) testing; however, its availability is very limited in low-income countries due to cost and operational constraints. Methods HIV-1–infected adults on first-line ART attending routine visits at the Manhiça District Hospital, Mozambique, were previously evaluated for virologic failure. Plasma levels of interferon-γ–inducible protein 10 (IP-10) were quantified by enzyme-linked immunosorbent assay. Logistic regression was used to build an IP-10–based model able to identify individuals with VL >150 copies/mL. From the 316 individuals analyzed, 253 (80%) were used for model training and 63 (20%) for validation. Receiver operating characteristic curves were employed to evaluate model prediction. Results From the individuals included in the training set, 34% had detectable VL. Mean age was 41 years, 70% were females, and median time on ART was 3.4 years. IP-10 levels were significantly higher in subjects with detectable VL (108.2 pg/mL) as compared to those with undetectable VL (38.0 pg/mL) (P < .0001, U test). IP-10 univariate model demonstrated high classification performance (area under the curve = 0.85 [95% confidence interval {CI}, .80–.90]). Using a cutoff value of IP-10 ≥44.2 pg/mL, the model identified detectable VL with 91.9% sensitivity (95% CI, 83.9%–96.7%) and 59.9% specificity (95% CI, 52.0%–67.4%), values confirmed in the validation set. Conclusions IP-10 is an accurate biomarker to screen individuals on ART for detectable viremia. Further studies should evaluate the benefits of IP-10 as a triage approach to monitor ART in resource-limited settings. PMID:29020145

Interferon-γ-inducible protein-10 in chronic hepatitis C: Correlations with insulin resistance, histological features & sustained virological response.

PubMed

Crisan, Dana; Grigorescu, Mircea Dan; Radu, Corina; Suciu, Alina; Grigorescu, Mircea

2017-04-01

One of the multiple factors contributing to virological response in chronic hepatitis C (CHC) is interferon-gamma-inducible protein-10 (IP-10). Its level reflects the status of interferon-stimulated genes, which in turn is associated with virological response to antiviral therapy. The aim of this study was to evaluate the role of serum IP-10 levels on sustained virological response (SVR) and the association of this parameter with insulin resistance (IR) and liver histology. Two hundred and three consecutive biopsy proven CHC patients were included in the study. Serum levels of IP-10 were determined using ELISA method. IR was evaluated by homeostasis model assessment-IR (HOMA-IR). Histological features were assessed invasively by liver biopsy and noninvasively using FibroTest, ActiTest and SteatoTest. Predictive factors for SVR and their interrelations were assessed. A cut-off value for IP-10 of 392 pg/ml was obtained to discriminate between responders and non-responders. SVR was obtained in 107 patients (52.70%). Area under the receiver operating characteristic curve for SVR was 0.875 with a sensitivity of 91.6 per cent, specificity 74.7 per cent, positive predictive value 80.3 per cent and negative predictive value 88.7 per cent. Higher values of IP-10 were associated with increasing stages of fibrosis (P<0.01) and higher grades of inflammation (P=0.02, P=0.07) assessed morphologically and noninvasively through FibroTest and ActiTest. Significant steatosis and IR were also associated with increased levels of IP-10 (P=0.01 and P=0.02). In multivariate analysis, IP-10 levels and fibrosis stages were independently associated with SVR. Our findings showed that the assessment of serum IP-10 level could be a predictive factor for SVR and it was associated with fibrosis, necroinflammatory activity, significant steatosis and IR in patients with chronic HCV infection.

MicroRNA‐199b Modulates Vascular Cell Fate During iPS Cell Differentiation by Targeting the Notch Ligand Jagged1 and Enhancing VEGF Signaling

PubMed Central

Chen, Ting; Kelaini, Sophia; Cochrane, Amy; Guha, Shaunta T.; Hu, Yanhua; Stitt, Alan W.; Xu, Qingbo

2015-01-01

Abstract Aims: Recent ability to derive endothelial cells (ECs) from induced pluripotent stem (iPS) cells holds a great therapeutic potential for personalized medicine and stem cell therapy. We aimed that better understanding of the complex molecular signals that are evoked during iPS cell differentiation toward ECs may allow specific targeting of their activities to enhance cell differentiation and promote tissue regeneration. Methods and Results: In this study, we have generated mouse iPS cells from fibroblasts using established protocol. When iPS cells were cultivated on type IV mouse collagen‐coated dishes in differentiation medium, cell differentiation toward vascular lineages were observed. To study the molecular mechanisms of iPS cell differentiation, we found that miR‐199b is involved in EC differentiation. A step‐wise increase in expression of miR‐199 was detected during EC differentiation. Notably, miR‐199b targeted the Notch ligand JAG1, resulting in vascular endothelial growth factor (VEGF) transcriptional activation and secretion through the transcription factor STAT3. Upon shRNA‐mediated knockdown of the Notch ligand JAG1, the regulatory effect of miR‐199b was ablated and there was robust induction of STAT3 and VEGF during EC differentiation. Knockdown of JAG1 also inhibited miR‐199b‐mediated inhibition of iPS cell differentiation toward smooth muscle markers. Using the in vitro tube formation assay and implanted Matrigel plugs, in vivo, miR‐199b also regulated VEGF expression and angiogenesis. Conclusions: This study indicates a novel role for miR‐199b as a regulator of the phenotypic switch during vascular cell differentiation derived from iPS cells by regulating critical signaling angiogenic responses. Stem Cells 2015;33:1405–1418 PMID:25535084

A geometric analysis of hallux valgus: correlation with clinical assessment of severity

PubMed Central

Piqué-Vidal, Carlos; Vila, Joan

2009-01-01

Background Application of plane geometry to the study of bunion deformity may represent an interesting and novel approach in the research field of hallux valgus. For the purpose of contributing to development of a different perspective in the assessment of hallux valgus, this study was conducted with three objectives: a) to determine the position on the intersection point of the perpendicular bisectors of the longitudinal axes of the first metatarsal and proximal phalanx (IP), b) to correlate the location of this point with hallux valgus deformity according to angular measurements and according to visual assessment of the severity carried out by three independent observers, and c) to assess whether this IP correlated with the radius of the first metatarsophalangeal arc circumference. Methods Measurements evaluated were intermetatarsal angle (IMA), hallux valgus angle (HVA), and proximal phalangeal articular angle (PPAA). The Autocad® program computed the location of the IP inside or outside of the foot. Three independent observers rated the severity of hallux valgus in photographs using a 100-mm visual analogue scale (VAS). Results Measurements of all angles except PPAA showed significantly lower values when the IP was located out of the foot more distantly and vice versa, significantly higher values for severe deformities in which the IP was found inside the foot (p < 0.001). The IP correlated significantly with VAS scores and with the length of the radius of the circle that included the first metatarsophalangeal arc circumference (p < 0.001) Conclusion The IP is a useful indicator of hallux valgus deformity because correlated significantly with IMA and HVA measurements, VAS scores obtained by visual inspection of the degree of deformity, and location of the center of the first metatarsophalangeal arc circumference. PMID:19442286

Microdistribution of fluorescently-labeled monoclonal antibody in a peritoneal dissemination model of ovarian cancer

NASA Astrophysics Data System (ADS)

Kosaka, Nobuyuki; Ogawa, Mikako; Paik, David S.; Paik, Chang H.; Choyke, Peter L.; Kobayashi, Hisataka

2010-02-01

The microdistribution of therapeutic monoclonal antibodies within a tumor is important for determining clinical response. Nonuniform microdistribution predicts therapy failure. Herein, we developed a semiquantitative method for measuring microdistribution of an antibody within a tumor using in situ fluorescence microscopy and sought to modulate the microdistribution by altering the route and timing of antibody dosing. The microdistribution of a fluorescently-labeled antibody, trastuzumab (50-μg and 150-μg intraperitoneal injection (i.p.), and 100-μg intravenous injection (i.v.)) was evaluated in a peritoneal dissemination mouse model of ovarian cancer. In addition, we evaluated the microdistribution of concurrently-injected (30-μg i.p. and 100-μg i.v.) or serial (two doses of 30-μg i.p.) trastuzumab using in situ multicolor fluorescence microscopy. After the administration of 50-μg i.p. and 100-μg i.v. trastuzumab fluorescence imaging showed no significant difference in the central to peripheral signal ratio (C/P ratio) and demonstrated a peripheral-dominant accumulation, whereas administration of 150-μg i.p. trastuzumab showed relatively uniform, central dominant accumulation. With concurrent-i.p.-i.v. injections trastuzumab showed slightly higher C/P ratio than concurrently-injected i.p. trastuzumab. Moreover, in the serial injection study, the second injection of trastuzumab distributed more centrally than the first injection, while no difference was observed in the control group. Our results suggest that injection routes do not affect the microdistribution pattern of antibody in small peritoneal disseminations. However, increasing the dose results in a more uniform antibody distribution within peritoneal nodules. Furthermore, the serial i.p. injection of antibody can modify the microdistribution within tumor nodules. This work has implications for the optimal delivery of antibody based cancer therapies.

Improvement of the course “Management of intellectual property” based on the mixed state contract in the field of scientific R&D

NASA Astrophysics Data System (ADS)

Yakovlev, D.; Ageev, A.; Yushkov, E.; Bogatyreova, M.

2017-01-01

Intellectual property (IP) is one of the forms of storing knowledge - intangible assets of knowledge economy. The translation of IP knowledge to the young generation is one of the challenges of nuclear knowledge management. At the NRNU MEPhI (National Research Nuclear University MEPhI), the subject is studied within the framework of the academic course “Management of intellectual property. The aim of the course is to train qualified specialists, ready to use modern methods of strategic management of IP in commercial firms. The article is devoted to the strengthening and transfer of IP rights for scientific output application in industry and commerce. The state remains the main source that finances all the significant developments in the field of science and technology. Therefore, the primary task is to effectively utilize the R&D output created at the expense of the Federal budget, both within the state order and the estimated budget financing. Currently, there exist contradictions in the area of strengthening and transfer of rights for R&D in the field of science. The newly borne concept dealing with the strengthening of IP rights for the scientific R&D output, centers on the theory of a mixed state contract and is conveniently integrated with the academic course mentioned. Knowledge itself takes the form of IP, as soon as it becomes formalized. The academic course when supplemented with various approaches to strengthening and transfer of IP rights for the scientific R&D output certainly gives a better understanding of the commercialization process of the intellectual capital and structures relevance to intellectual property. The research material is integrated with the educational process, and the academic course “Management of intellectual property” is designed both for economic and engineering specialties.

A Filtration-based Method of Preparing High-quality Nuclei from Cross-linked Skeletal Muscle for Chromatin Immunoprecipitation.

PubMed

Nohara, Kazunari; Chen, Zheng; Yoo, Seung-Hee

2017-07-06

Chromatin immunoprecipitation (ChIP) is a powerful method to determine protein binding to chromatin DNA. Fiber-rich skeletal muscle, however, has been a challenge for ChIP due to technical difficulty in isolation of high-quality nuclei with minimal contamination of myofibrils. Previous protocols have attempted to purify nuclei before cross-linking, which incurs the risk of altered DNA-protein interaction during the prolonged nuclei preparation process. In the current protocol, we first cross-linked the skeletal muscle tissue collected from mice, and the tissues were minced and sonicated. Since we found that ultracentrifugation was not able to separate nuclei from myofibrils using cross-linked muscle tissue, we devised a sequential filtration procedure to obtain high-quality nuclei devoid of significant myofibril contamination. We subsequently prepared chromatin by using an ultrasonicator, and ChIP assays with anti-BMAL1 antibody revealed robust circadian binding pattern of BMAL1 to target gene promoters. This filtration protocol constitutes an easily applicable method to isolate high-quality nuclei from cross-linked skeletal muscle tissue, allowing consistent sample processing for circadian and other time-sensitive studies. In combination with next-generation sequencing (NGS), our method can be deployed for various mechanistic and genomic studies focusing on skeletal muscle function.

Effects of bacterial contamination of media on the diagnosis of Tritrichomonas foetus by culture and real-time PCR.

PubMed

Clothier, Kristin A; Villanueva, Michelle; Torain, Andrea; Hult, Cynthia; Wallace, Rachel

2015-03-15

The venereal pathogen Tritrichomonas foetus causes early embryonic death and abortion in cattle. With no approved treatment, control involves detection of infected animals and their removal from the herd. Culture is the traditional diagnostic method; standard media are formulated to support protozoal growth while suppressing competing organisms which may prevent microscopic recognition of T. foetus. Real-time PCR increases diagnostic sensitivity and specificity over culture but requires intact T. foetus DNA for detection. The purposes of this study were 1) to evaluate the effects of resident preputial bacteria that are not suppressed by antimicrobials in a commercial culture medium (InPouch™) on T. foetus detection by culture and PCR, and 2) to determine the performance of a laboratory-prepared culture medium on T. foetus detection by culture and PCR in samples with and without this bacterial contamination. A known concentration of one of three different strains of T. foetus inoculated into InPouch™ (IP) or modified Diamonds-Plastridge media (DPM) were co-incubated with a smegma culture media (CONTAM) for 24h and examined microscopically for the presence of identifiable T. foetus. PCR was performed on IP samples to determine if CONTAM also affected T. foetus DNA detection. A PCR protocol was then validated in DPM that performed similarly to the established IP PCR method. IP and DPM with CONTAM were spiked with serial dilutions that mimic field infections of one of four T. foetus strains and evaluated by real-time PCR; cycles to threshold (Ct) values and "positive" classification were compared between media. T. foetus motility and morphology as well as media pH were severely altered in IP samples with CONTAM compared to those without as well as to DPM medium with and without CONTAM (P<0.0001). PCR testing demonstrated significantly greater Ct values were for T. foetus DNA (P<0.001) in IP contaminated with smegma bacteria compared to those without. When using T foetus concentrations that mimic field infections, IP samples with CONTAM had significantly higher Ct values (P<0.001) than DPM with CONTAM. Using the laboratory cut-off for "positive" on mean Ct values from these samples, significantly (P<0.01) more bulls would be identified using DPM than with IP if CONTAM was present. Results of this study indicate that bacteria which are not inhibited in media interfere with T. foetus identification by culture and PCR and adversely affect diagnostic sensitivity for this fastidious pathogen. Copyright © 2015 Elsevier B.V. All rights reserved.

Traffic-engineering-aware shortest-path routing and its application in IP-over-WDM networks [Invited

NASA Astrophysics Data System (ADS)

Lee, Youngseok; Mukherjee, Biswanath

2004-03-01

Single shortest-path routing is known to perform poorly for Internet traffic engineering (TE) where the typical optimization objective is to minimize the maximum link load. Splitting traffic uniformly over equal-cost multiple shortest paths in open shortest path first and intermediate system-intermediate system protocols does not always minimize the maximum link load when multiple paths are not carefully selected for the global traffic demand matrix. However, a TE-aware shortest path among all the equal-cost multiple shortest paths between each ingress-egress pair can be selected such that the maximum link load is significantly reduced. IP routers can use the globally optimal TE-aware shortest path without any change to existing routing protocols and without any serious configuration overhead. While calculating TE-aware shortest paths, the destination-based forwarding constraint at a node should be satisfied, because an IP router will forward a packet to the next hop toward the destination by looking up the destination prefix. We present a mathematical problem formulation for finding a set of TE-aware shortest paths for the given network as an integer linear program, and we propose a simple heuristic for solving large instances of the problem. Then we explore the usage of our proposed algorithm for the integrated TE method in IP-over-WDM networks. The proposed algorithm is evaluated through simulations in IP networks as well as in IP-over-WDM networks.

Acquisition and reinstatement of ethanol-induced conditioned place preference in rats: Effects of the cholinesterase inhibitors donepezil and rivastigmine.

PubMed

Gawel, Kinga; Labuz, Krzysztof; Gibula-Bruzda, Ewa; Jenda, Malgorzata; Marszalek-Grabska, Marta; Silberring, Jerzy; Kotlinska, Jolanta H

2016-07-01

The present study examined the influence of the cholinesterase inhibitors donepezil (a selective inhibitor of acetylcholinesterase) and rivastigmine (also an inhibitor of butyrylcholinesterase) on the acquisition and reinstatement of ethanol-induced conditioned place preference (CPP) in rats. Before the CPP procedure, animals received a single injection of ethanol (0.5 g/kg, 10% w/v, intraperitoneally [i.p.]) for 15 days. The ethanol-induced CPP (biased method) was developed by four injections of ethanol (0.5 g/kg, 10% w/v, i.p.) every second day. Control rats received saline instead of ethanol. Donepezil (0.5, 1 or 3 mg/kg, i.p.) or rivastigmine (0.03, 0.5 or 1 mg/kg, i.p.) were administered before ethanol during conditioning or before the reinstatement of ethanol-induced CPP. The cholinesterase inhibitors were equally effective in increasing (dose dependently) the acquisition of ethanol-induced CPP. Furthermore, priming injections of both inhibitors reinstated (cross-reinstatement) the ethanol-induced CPP with similar efficacy. These effects of both cholinesterase inhibitors were reversed by mecamylamine (3 mg/kg, i.p.), a nicotinic acetylcholine receptor antagonist, but not by scopolamine (0.5 mg/kg, i.p.), a muscarinic acetylcholine receptor antagonist. Thus, our results show that the cholinergic system is involved in the reinforcing properties of ethanol, and nicotinic acetylcholine receptors play an important role in the relapse to ethanol-seeking behaviour. © The Author(s) 2016.

Systems Modeling of Ca2+ Homeostasis and Mobilization in Platelets Mediated by IP3 and Store-Operated Ca2+ Entry

PubMed Central

Dolan, Andrew T.; Diamond, Scott L.

2014-01-01

Resting platelets maintain a stable level of low cytoplasmic calcium ([Ca2+]cyt) and high dense tubular system calcium ([Ca2+]dts). During thrombosis, activators cause a transient rise in inositol trisphosphate (IP3) to trigger calcium mobilization from stores and elevation of [Ca2+]cyt. Another major source of [Ca2+]cyt elevation is store-operated calcium entry (SOCE) through plasmalemmal calcium channels that open in response to store depletion as [Ca2+]dts drops. A 34-species systems model employed kinetics describing IP3-receptor, DTS-plasmalemma puncta formation, SOCE via assembly of STIM1 and Orai1, and the plasmalemma and sarco/endoplasmic reticulum Ca2+-ATPases. Four constraints were imposed: calcium homeostasis before activation; stable in zero extracellular calcium; IP3-activatable; and functional SOCE. Using a Monte Carlo method to sample three unknown parameters and nine initial concentrations in a 12-dimensional space near measured or expected values, we found that model configurations that were responsive to stimuli and demonstrated significant SOCE required high inner membrane electric potential (>−70 mV) and low resting IP3 concentrations. The absence of puncta in resting cells was required to prevent spontaneous store depletion in calcium-free media. Ten-fold increases in IP3 caused saturated calcium mobilization. This systems model represents a critical step in being able to predict platelets’ phenotypes during hemostasis or thrombosis. PMID:24806937

Using lifestyle factors to identify individuals at higher risk of inflammatory polyarthritis (results from the European Prospective Investigation of Cancer-Norfolk and the Norfolk Arthritis Register—the EPIC-2-NOAR Study)

PubMed Central

Lahiri, Manjari; Luben, Robert N; Morgan, Catharine; Bunn, Diane K; Marshall, Tarnya; Lunt, Mark; Verstappen, Suzanne M M; Symmons, Deborah P M; Khaw, Kay-Tee; Wareham, Nick; Bruce, Ian N

2014-01-01

Objectives To investigate the association of lifestyle factors with risk of inflammatory polyarthritis (IP) and rheumatoid arthritis (RA). Methods The European Prospective Investigation of Cancer, Norfolk, UK (EPIC-Norfolk) gathered lifestyle data from participants aged 40–79 years from 1993 to 1997. Individuals who subsequently developed IP were identified by linkage with the Norfolk Arthritis Register. A Cox proportional hazard model was developed, and a score assigned to each risk factor to calculate the odds of developing IP. Results 25 455 EPIC participants were followed for a median (IQR) of 14.2 (12.9, 15.3) years; 184 developed incident IP (138 cumulatively fulfilled criteria for RA; 107 were seropositive). Pack-years of smoking were associated with increased risk of IP and RA in men (HR 1.21 (95% CI 1.08 to 1.37) per 10-pack-years) and seropositive IP (HR 1.24 (95% CI 1.10 to 1.41)) for all. Diabetes mellitus was associated with increased risk of IP (HR 2.54 (95% CI 1.26 to 5.09)), while alcohol (HR 0.86 (95% CI 0.74 to 0.99) per unit/day) and higher social class (HR 0.36 (95% CI 0.15 to 0.89) for professionals vs manual workers) were associated with reduced risk. Body mass index was associated with seronegative IP (HR 2.75 (95% CI 1.39 to 5.46) for obese vs normal-weight participants). In women, parity (HR 2.81 (95% CI 1.37 to 5.76) for ≥2 vs no children) was associated with increased risk, and breast feeding (HR 0.66 (95% CI 0.46 to 0.94) for every 52 weeks of breast feeding) was inversely associated with risk. Risk factors from the model were used to generate a ‘risk score’. A total of 1159 (8.4%) women had scores reflecting a >3-fold increased risk of IP over those with a score of 0. Conclusions Several easily ascertained clinical and lifestyle factors can be used to stratify populations for risk of IP. PMID:23505230

DOC-2/DAB2 Interacting Protein Status in High-Risk Prostate Cancer Correlates With Outcome for Patients Treated With Radiation Therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jacobs, Corbin; Tumati, Vasu; Kapur, Payal

2014-07-15

Purpose: This pilot study investigates the role of DOC-2/DAB2 Interacting Protein (DAB2IP) and enhancer of zeste homolog 2 (EZH2) as prognostic biomarkers in high-risk prostate cancer patients receiving definitive radiation therapy. Methods and Materials: Immunohistochemistry was performed and scored by an expert genitourinary pathologist. Clinical endpoints evaluated were freedom from biochemical failure (FFBF), castration resistance–free survival (CRFS), and distant metastasis–free survival (DMFS). Log-rank test and Cox regression were used to determine significance of biomarker levels with clinical outcome. Results: Fifty-four patients with high-risk prostate cancer (stage ≥T3a, or Gleason score ≥8, or prostate-specific antigen level ≥20 ng/mL) treated with radiation therapy frommore » 2005 to 2012 at our institution were evaluated. Nearly all patients expressed EZH2 (98%), whereas 28% of patients revealed DAB2IP reduction and 72% retained DAB2IP. Median follow-up was 34.0 months for DAB2IP-reduced patients, 29.9 months for DAB2IP-retained patients, and 32.6 months in the EZH2 study. Reduction in DAB2IP portended worse outcome compared with DAB2IP-retained patients, including FFBF (4-year: 37% vs 89%, P=.04), CRFS (4-year: 50% vs 90%, P=.02), and DMFS (4-year: 36% vs 97%, P=.05). Stratified EZH2 expression trended toward significance for worse FFBF and CRFS (P=.07). Patients with reduced DAB2IP or highest-intensity EZH2 expression exhibited worse FFBF (4-year: 32% vs 95%, P=.02), CRFS (4-year: 28% vs 100%, P<.01), and DMFS (4-year: 39% vs 100%, P=.04) compared with the control group. Conclusion: Loss of DAB2IP is a potent biomarker that portends worse outcome despite definitive radiation therapy for patients with high-risk prostate cancer. Enhancer of zeste homolog 2 is expressed in most high-risk tumors and is a less potent discriminator of outcome in this study. The DAB2IP status in combination with degree of EZH2 expression may be useful for determining patients with worse outcome within the high-risk prostate cancer population.« less

PolyaPeak: Detecting Transcription Factor Binding Sites from ChIP-seq Using Peak Shape Information

PubMed Central

Wu, Hao; Ji, Hongkai

2014-01-01

ChIP-seq is a powerful technology for detecting genomic regions where a protein of interest interacts with DNA. ChIP-seq data for mapping transcription factor binding sites (TFBSs) have a characteristic pattern: around each binding site, sequence reads aligned to the forward and reverse strands of the reference genome form two separate peaks shifted away from each other, and the true binding site is located in between these two peaks. While it has been shown previously that the accuracy and resolution of binding site detection can be improved by modeling the pattern, efficient methods are unavailable to fully utilize that information in TFBS detection procedure. We present PolyaPeak, a new method to improve TFBS detection by incorporating the peak shape information. PolyaPeak describes peak shapes using a flexible Pólya model. The shapes are automatically learnt from the data using Minorization-Maximization (MM) algorithm, then integrated with the read count information via a hierarchical model to distinguish true binding sites from background noises. Extensive real data analyses show that PolyaPeak is capable of robustly improving TFBS detection compared with existing methods. An R package is freely available. PMID:24608116

Focal Activation of Cells by Plasmon Resonance Assisted Optical Injection of Signaling Molecules

PubMed Central

2015-01-01

Experimental methods for single cell intracellular delivery are essential for probing cell signaling dynamics within complex cellular networks, such as those making up the tumor microenvironment. Here, we show a quantitative and general method of interrogation of signaling pathways. We applied highly focused near-infrared laser light to optically inject gold-coated liposomes encapsulating bioactive molecules into single cells for focal activation of cell signaling. For this demonstration, we encapsulated either inositol trisphosphate (IP3), an endogenous cell signaling second messenger, or adenophostin A (AdA), a potent analogue of IP, within 100 nm gold-coated liposomes, and injected these gold-coated liposomes and their contents into the cytosol of single ovarian carcinoma cells to initiate calcium (Ca2+) release from intracellular stores. Upon optical injection of IP3 or AdA at doses above the activation threshold, we observed increases in cytosolic Ca2+ concentration within the injected cell initiating the propagation of a Ca2+ wave throughout nearby cells. As confirmed by octanol-induced inhibition, the intercellular Ca2+ wave traveled via gap junctions. Optical injection of gold-coated liposomes represents a quantitative method of focal activation of signaling cascades of broad interest in biomedical research. PMID:24877558

MOCCS: Clarifying DNA-binding motif ambiguity using ChIP-Seq data.

PubMed

Ozaki, Haruka; Iwasaki, Wataru

2016-08-01

As a key mechanism of gene regulation, transcription factors (TFs) bind to DNA by recognizing specific short sequence patterns that are called DNA-binding motifs. A single TF can accept ambiguity within its DNA-binding motifs, which comprise both canonical (typical) and non-canonical motifs. Clarification of such DNA-binding motif ambiguity is crucial for revealing gene regulatory networks and evaluating mutations in cis-regulatory elements. Although chromatin immunoprecipitation sequencing (ChIP-seq) now provides abundant data on the genomic sequences to which a given TF binds, existing motif discovery methods are unable to directly answer whether a given TF can bind to a specific DNA-binding motif. Here, we report a method for clarifying the DNA-binding motif ambiguity, MOCCS. Given ChIP-Seq data of any TF, MOCCS comprehensively analyzes and describes every k-mer to which that TF binds. Analysis of simulated datasets revealed that MOCCS is applicable to various ChIP-Seq datasets, requiring only a few minutes per dataset. Application to the ENCODE ChIP-Seq datasets proved that MOCCS directly evaluates whether a given TF binds to each DNA-binding motif, even if known position weight matrix models do not provide sufficient information on DNA-binding motif ambiguity. Furthermore, users are not required to provide numerous parameters or background genomic sequence models that are typically unavailable. MOCCS is implemented in Perl and R and is freely available via https://github.com/yuifu/moccs. By complementing existing motif-discovery software, MOCCS will contribute to the basic understanding of how the genome controls diverse cellular processes via DNA-protein interactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Direct Delta-MBPT(2) method for ionization potentials, electron affinities, and excitation energies using fractional occupation numbers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beste, Ariana; Vazquez-Mayagoitia, Alvaro; Ortiz, J. Vincent

2013-01-01

A direct method (D-Delta-MBPT(2)) to calculate second-order ionization potentials (IPs), electron affinities (EAs), and excitation energies is developed. The Delta-MBPT(2) method is defined as the correlated extension of the Delta-HF method. Energy differences are obtained by integrating the energy derivative with respect to occupation numbers over the appropriate parameter range. This is made possible by writing the second-order energy as a function of the occupation numbers. Relaxation effects are fully included at the SCF level. This is in contrast to linear response theory, which makes the D-Delta-MBPT(2) applicable not only to single excited but also higher excited states. We showmore » the relationship of the D-Delta-MBPT(2) method for IPs and EAs to a second-order approximation of the effective Fock-space coupled-cluster Hamiltonian and a second-order electron propagator method. We also discuss the connection between the D-Delta-MBPT(2) method for excitation energies and the CIS-MP2 method. Finally, as a proof of principle, we apply our method to calculate ionization potentials and excitation energies of some small molecules. For IPs, the Delta-MBPT(2) results compare well to the second-order solution of the Dyson equation. For excitation energies, the deviation from EOM-CCSD increases when correlation becomes more important. When using the numerical integration technique, we encounter difficulties that prevented us from reaching the Delta-MBPT(2) values. Most importantly, relaxation beyond the Hartree Fock level is significant and needs to be included in future research.« less

Speech Perception Benefits of Internet Versus Conventional Telephony for Hearing-Impaired Individuals

PubMed Central

Dubach, Patrick; Pfiffner, Flurin; Kompis, Martin; Caversaccio, Marco

2012-01-01

Background Telephone communication is a challenge for many hearing-impaired individuals. One important technical reason for this difficulty is the restricted frequency range (0.3–3.4 kHz) of conventional landline telephones. Internet telephony (voice over Internet protocol [VoIP]) is transmitted with a larger frequency range (0.1–8 kHz) and therefore includes more frequencies relevant to speech perception. According to a recently published, laboratory-based study, the theoretical advantage of ideal VoIP conditions over conventional telephone quality has translated into improved speech perception by hearing-impaired individuals. However, the speech perception benefits of nonideal VoIP network conditions, which may occur in daily life, have not been explored. VoIP use cannot be recommended to hearing-impaired individuals before its potential under more realistic conditions has been examined. Objective To compare realistic VoIP network conditions, under which digital data packets may be lost, with ideal conventional telephone quality with respect to their impact on speech perception by hearing-impaired individuals. Methods We assessed speech perception using standardized test material presented under simulated VoIP conditions with increasing digital data packet loss (from 0% to 20%) and compared with simulated ideal conventional telephone quality. We monaurally tested 10 adult users of cochlear implants, 10 adult users of hearing aids, and 10 normal-hearing adults in the free sound field, both in quiet and with background noise. Results Across all participant groups, mean speech perception scores using VoIP with 0%, 5%, and 10% packet loss were 15.2% (range 0%–53%), 10.6% (4%–46%), and 8.8% (7%–33%) higher, respectively, than with ideal conventional telephone quality. Speech perception did not differ between VoIP with 20% packet loss and conventional telephone quality. The maximum benefits were observed under ideal VoIP conditions without packet loss and were 36% (P = .001) for cochlear implant users, 18% (P = .002) for hearing aid users, and 53% (P = .001) for normal-hearing adults. With a packet loss of 10%, the maximum benefits were 30% (P = .002) for cochlear implant users, 6% (P = .38) for hearing aid users, and 33% (P = .002) for normal-hearing adults. Conclusions VoIP offers a speech perception benefit over conventional telephone quality, even when mild or moderate packet loss scenarios are created in the laboratory. VoIP, therefore, has the potential to significantly improve telecommunication abilities for the large community of hearing-impaired individuals. PMID:22805169

Importance of brain-gut axis in the gastroprotection induced by gastric and remote preconditioning.

PubMed

Brzozowski, T; Konturek, P C; Pajdo, R; Kwiecień, S; Sliwowski, Z; Drozdowicz, D; Ptak-Belowska, A; Pawlik, M; Konturek, S J; Pawlik, W W; Hahn, G G

2004-03-01

Limitation of the damage to the organs such as heart, liver, intestine, stomach and brain by an earlier brief complete occlusion of their arteries is defined as ischemic preconditioning (IP). No study so for has been undertaken to check whether brain-gut axis is involved in the gastroprotection exhibited by gastric IP or in that induced by repeated brief episodes of ischemia of remote organs such as heart and liver. This study was designed to determine the possible involvement of vagal and sensory afferent nerves, in the mechanism of gastric and remote organ IP on the gastric mucosa in rats exposed to prolonged ischemia-reperfusion with or without functional ablation of sensory nerves by capsaicin or in those with removed vagal innervation by vagotomy. This gastric IP was induced by short ischemia episodes (occlusion of celiac artery 1-5 times for 5 min) applied 30 min before subsequent ischemia followed by 3 h of reperfusion (I/R) and compared with remote IP induced by occlusion of left descending coronary artery or hepatic artery plus portal vein. The area of gastric lesions was determined by planimetry, gastric blood flow (GBF) was measured by H(2)-gas clearance method and mucosal biopsy samples were taken for the assessment of calcitonin gene-related peptide (CGRP) by RIA. Exposure of gastric mucosa to standard 3 h of I/R produced numerous gastric lesions and significant fall in the GBF and mucosal CGRP content. Two 5 min short ischemic episodes by occlusion of coronary or hepatic arteries, significantly reduced gastric damage induced by I/R with the extent similar to that exhibited by two short (5 min) episodes of gastric ischemia. These protective effects of gastric and remote IPs were accompanied by a restoration of the fall in the CGRP content caused by I/R alone. Protection and hyperemia induced by gastric IP were significantly attenuated in capsaicin-denervated or vagotomized animals and completely removed in those exposed to the combination of vagotomy and capsaicin-denervation. The IP-induced protection and hyperemia were restored by the administration of exogenous CGRP to gastric IP in capsaicin-treated animals. Gastroprotective and hyperemic actions of remote IP were markedly diminished in capsaicin-denervated rats and in those subjected to vagotomy. We conclude that brief ischemia in remote organs such as heart and liver protects gastric mucosa against gastric injury induced by I/R as effectively as gastric IP via mechanism involving both vagal and sensory nerves releasing vasodilatatory mediators such as CGRP.

Subtype-selective regulation of IP3 receptors by thimerosal via cysteine residues within the IP3-binding core and suppressor domain

PubMed Central

Khan, Samir A.; Rossi, Ana M.; Riley, Andrew M.; Potter, Barry V. L.; Taylor, Colin W.

2013-01-01

IP3R (IP3 [inositol 1,4,5-trisphosphate] receptors) and ryanodine receptors are the most widely expressed intracellular Ca2+ channels and both are regulated by thiol reagents. In DT40 cells stably expressing single subtypes of mammalian IP3R, low concentrations of thimerosal (also known as thiomersal), which oxidizes thiols to form a thiomercurylethyl complex, increased the sensitivity of IP3-evoked Ca2+ release via IP3R1 and IP3R2, but inhibited IP3R3. Activation of IP3R is initiated by IP3 binding to the IBC (IP3-binding core; residues 224–604) and proceeds via re-arrangement of an interface between the IBC and SD (suppressor domain; residues 1–223). Thimerosal (100 μM) stimulated IP3 binding to the isolated NT (N-terminal; residues 1–604) of IP3R1 and IP3R2, but not to that of IP3R3. Binding of a competitive antagonist (heparin) or partial agonist (dimeric-IP3) to NT1 was unaffected by thiomersal, suggesting that the effect of thimerosal is specifically related to IP3R activation. IP3 binding to NT1 in which all cysteine residues were replaced by alanine was insensitive to thimerosal, so too were NT1 in which cysteine residues were replaced in either the SD or IBC. This demonstrates that thimerosal interacts directly with cysteine in both the SD and IBC. Chimaeric proteins in which the SD of the IP3R was replaced by the structurally related A domain of a ryanodine receptor were functional, but thimerosal inhibited both IP3 binding to the chimaeric NT and IP3-evoked Ca2+ release from the chimaeric IP3R. This is the first systematic analysis of the effects of a thiol reagent on each IP3R subtype. We conclude that thimerosal selectively sensitizes IP3R1 and IP3R2 to IP3 by modifying cysteine residues within both the SD and IBC and thereby stabilizing an active conformation of the receptor. PMID:23282150

Influence of dental resin material composition on cross-polarization-optical coherence tomography imaging

PubMed Central

Lammeier, Carmen; Li, YuPing; Lunos, Scott; Fok, Alex; Rudney, Joel

2012-01-01

Abstract. The purpose of this study was to investigate cross-polarization-optical coherence tomography (CP-OCT) signal attenuation through different resin material compositions. Four distinct composite systems were used: Filtek supreme ultra (FSU) (3M ESPE), IPS empress direct (EMD) (Ivoclar Vivadent), estelite sigma quick (SQK) (Tokuyama Dental), and Z100 (3M ESPE). Cross-sectional images of different composite-demineralized phantoms (n=108) were collected using a 1310-nm intraoral cross-polarization swept source OCT (CP-OCT) imaging system. %T quantified the CP-OCT signal attenuation. Scanning electron microscopy, transmission electron microscopy, and energy-dispersive x-ray spectrometer chemical analysis was utilized to determine how different matrix/filler compositions affected attenuation of the near infrared (NIR) signal. CP-OCT imaging of dental resin composites showed enormous variation in signal attenuation. For each of our composite systems, there was not a consistent attenuation difference in the NIR signal for A to D shades. The four composites had similar measured backscattering values but attenuated the overall signal to different degrees. When comparing the A2 shades between the four different composite systems, the order of highest to lowest of %T was EMD>Z100, FSU>SQK (ANOVA, Tukey, p<0.0001). As a result, we demonstrate the importance of understanding how the constituents of composite materials affect CP-OCT signal attenuation. PMID:23224001

Influence of dental resin material composition on cross-polarization-optical coherence tomography imaging

NASA Astrophysics Data System (ADS)

Lammeier, Carmen; Li, YuPing; Lunos, Scott; Fok, Alex; Rudney, Joel; Jones, Robert S.

2012-10-01

The purpose of this study was to investigate cross-polarization-optical coherence tomography (CP-OCT) signal attenuation through different resin material compositions. Four distinct composite systems were used: Filtek supreme ultra (FSU) (3M ESPE), IPS empress direct (EMD) (Ivoclar Vivadent), estelite sigma quick (SQK) (Tokuyama Dental), and Z100 (3M ESPE). Cross-sectional images of different composite-demineralized phantoms (n=108) were collected using a 1310-nm intraoral cross-polarization swept source OCT (CP-OCT) imaging system. %T quantified the CP-OCT signal attenuation. Scanning electron microscopy, transmission electron microscopy, and energy-dispersive x-ray spectrometer chemical analysis was utilized to determine how different matrix/filler compositions affected attenuation of the near infrared (NIR) signal. CP-OCT imaging of dental resin composites showed enormous variation in signal attenuation. For each of our composite systems, there was not a consistent attenuation difference in the NIR signal for A to D shades. The four composites had similar measured backscattering values but attenuated the overall signal to different degrees. When comparing the A2 shades between the four different composite systems, the order of highest to lowest of %T was EMD>Z100, FSU>SQK (ANOVA, Tukey, p<0.0001). As a result, we demonstrate the importance of understanding how the constituents of composite materials affect CP-OCT signal attenuation.

A Laboratory Practical Illustrating the Use of the ChIP-qPCR Method in a Robust Model: Estrogen Receptor Alpha Immunoprecipitation Using MCF-7 Culture Cells

ERIC Educational Resources Information Center

Lacazette, Eric

2017-01-01

Chromatin immunoprecipitation followed by qPCR analysis (ChIP-qPCR) is a widely used technique to study gene expression. A large number of students in molecular biology and more generally in life sciences will be confronted with the use of this technique, which is quite difficult to set up and can lead to misinterpretation if not carefully…

Adrenal hormones and liver cAMP in exercising rats--different modes of anesthesia.

PubMed

Winder, W W; Fuller, E O; Conlee, R K

1983-11-01

We have compared five different modes of anesthesia (iv and ip pentobarbital sodium, ether, CO2, and cervical dislocation) with respect to their effects on liver glycogen, liver adenosine 3',5'-cyclic monophosphate (cAMP), blood glucose and lactate, plasma corticosterone, norepinephrine, and epinephrine in resting rats and in rats run on a treadmill at 26 m/min for 30 min. Ether, CO2, and cervical dislocation were found to be unsuitable due to the marked elevation in plasma catecholamines seen in both resting and exercising rats. Injection of pentobarbital sodium ip required an average of 8 min before onset of surgical anesthesia as opposed to less than 5 s for iv pentobarbital. Exercising rats anesthetized with ip pentobarbital showed markedly lower plasma catecholamines compared with rats given iv pentobarbital. Hepatic cAMP increased in response to exercise in all groups except the ip pentobarbital group. This is most likely due to the long delay between the end of the exercise and freezing of the liver in the ip pentobarbital-anesthetized animals. We conclude that iv injection of pentobarbital is the most suitable method of anesthesia for obtaining accurate measurements of plasma stress hormones, substrates, and metabolites and of hepatic cAMP and glycogen in resting and exercising rats.

Methods for assessing the energy-saving efficiency of industrial symbiosis in industrial parks.

PubMed

Li, Wenfeng; Cui, Zhaojie; Han, Feng

2015-01-01

The available energy resources are being depleted worldwide. Industrial symbiosis (IS) provides a promising approach for increasing the efficiency of energy utilization, with numerous studies reporting the superiority of this technology. However, studies quantifying the energy-saving efficiency of IS remain insufficient. This paper proposes an index system for the quantitative evaluation of the energy-saving efficiency of IS. Both energy-saving and financial indexes were selected, the former include the IS energy-saving index, the contribution rate of energy saved through IS, fractional energy savings, and cut rate of energy consumption per total output value; and the latter include the IS investment payback period, IS input-output ratio, net present value (NPV), and internal rate of return (IRR) of IS. The proposed methods were applied to a case study on the XF Industrial Park (XF IP), in the city of Liaocheng in Shandong Province of China. Three energy-saving channels using IS were found in the XF IP: (a) utilizing the energy of high-temperature materials among industrial processes, (b) recovering waste heat and steam between different processes, and (c) saving energy by sharing infrastructures. The results showed that the energy efficiency index of IS was 0.326, accounting for 34.6% of the comprehensive energy-saving index in 2011, and the fractional energy-savings were 12.42%. The index of energy consumption per total industrial output value varied from 90.9 tce/MRMB to 51.6 tce/MRMB. Thus, the cut rate of energy consumption per total industrial output value was 43.42%. The average values of the IS input-output ratio was 406.2 RMB/tce, 57.2% lower than the price of standard coal. Static investment payback period in the XF IP was 8.5 months, indicating that the XF IP began to earn profit 8.5 months after the construction of all IS modes. The NVP and IRR of each IS mode in the XF IP were greater than zero, with average values equal to 1,789.96 MRMB and 140.96%, respectively. The computation result for each indicator revealed that IS could lead to the use of energy with high efficiency and lighten the financial burden of enterprises in the XF IP. And the proposed index system may help IPs and EIPs to make strategic decisions when designing IS modes.

Cell-Penetrating Peptide as a Means of Directing the Differentiation of Induced-Pluripotent Stem Cells.

PubMed

Kaitsuka, Taku; Tomizawa, Kazuhito

2015-11-06

Protein transduction using cell-penetrating peptides (CPPs) is useful for the delivery of large protein molecules, including some transcription factors. This method is safer than gene transfection methods with a viral vector because there is no risk of genomic integration of the exogenous DNA. Recently, this method was reported as a means for the induction of induced pluripotent stem (iPS) cells, directing the differentiation into specific cell types and supporting gene editing/correction. Furthermore, we developed a direct differentiation method to obtain a pancreatic lineage from mouse and human pluripotent stem cells via the protein transduction of three transcription factors, Pdx1, NeuroD, and MafA. Here, we discuss the possibility of using CPPs as a means of directing the differentiation of iPS cells and other stem cell technologies.

Inositol Hexakisphosphate Kinase-3 Regulates the Morphology and Synapse Formation of Cerebellar Purkinje Cells via Spectrin/Adducin

PubMed Central

Fu, Chenglai; Xu, Jing; Li, Ruo-Jing; Crawford, Joshua A.; Khan, A. Basit; Ma, Ting Martin; Cha, Jiyoung Y.; Snowman, Adele M.; Pletnikov, Mikhail V.

2015-01-01

The inositol hexakisphosphate kinases (IP6Ks) are the principal enzymes that generate inositol pyrophosphates. There are three IP6Ks (IP6K1, 2, and 3). Functions of IP6K1 and IP6K2 have been substantially delineated, but little is known of IP6K3's role in normal physiology, especially in the brain. To elucidate functions of IP6K3, we generated mice with targeted deletion of IP6K3. We demonstrate that IP6K3 is highly concentrated in the brain in cerebellar Purkinje cells. IP6K3 physiologically binds to the cytoskeletal proteins adducin and spectrin, whose mutual interactions are perturbed in IP6K3-null mutants. Consequently, IP6K3 knock-out cerebella manifest abnormalities in Purkinje cell structure and synapse number, and the mutant mice display deficits in motor learning and coordination. Thus, IP6K3 is a major determinant of cytoskeletal disposition and function of cerebellar Purkinje cells. SIGNIFICANCE STATEMENT We identified and cloned a family of three inositol hexakisphosphate kinases (IP6Ks) that generate the inositol pyrophosphates, most notably 5-diphosphoinositol pentakisphosphate (IP7). Of these, IP6K3 has been least characterized. In the present study we generated IP6K3 knock-out mice and show that IP6K3 is highly expressed in cerebellar Purkinje cells. IP6K3-deleted mice display defects of motor learning and coordination. IP6K3-null mice manifest aberrations of Purkinje cells with a diminished number of synapses. IP6K3 interacts with the cytoskeletal proteins spectrin and adducin whose altered disposition in IP6K3 knock-out mice may mediate phenotypic features of the mutant mice. These findings afford molecular/cytoskeletal mechanisms by which the inositol polyphosphate system impacts brain function. PMID:26245967

Role of Ipsdienol, Ipsenol, and cis-Verbenol in chemical ecology of Ips avulsus, Ips calligraphus, and Ips grandicollis (Coleoptera: Curculionidae: Scolytinae)

Treesearch

Jeremy D. Allison; Jessica I. McKenney; Daniel R. Miller; Matthew L. Gimmel

2012-01-01

ABSTRACT Stressed or damaged pine (Pinus sp.) trees in the southeastern United States are often colonized simultaneously by three southern Ips species (Coleoptera: Curculionidae: Scolytinae): small southern pine engraver, Ips avulsus (Eichhoff); sixspined ips, Ips calligraphus (Germar); and...

Comparison of gating dynamics of different IP3R channels with immune algorithm searching for channel parameter distributions

NASA Astrophysics Data System (ADS)

Cai, Xiuhong; Li, Xiang; Qi, Hong; Wei, Fang; Chen, Jianyong; Shuai, Jianwei

2016-10-01

The gating properties of the inositol 1, 4, 5-trisphosphate (IP3) receptor (IP3R) are determined by the binding and unbinding capability of Ca2+ ions and IP3 messengers. With the patch clamp experiments, the stationary properties have been discussed for Xenopus oocyte type-1 IP3R (Oo-IP3R1), type-3 IP3R (Oo-IP3R3) and Spodoptera frugiperda IP3R (Sf-IP3R). In this paper, in order to provide insights about the relation between the observed gating characteristics and the gating parameters in different IP3Rs, we apply the immune algorithm to fit the parameters of a modified DeYoung-Keizer model. By comparing the fitting parameter distributions of three IP3Rs, we suggest that the three types of IP3Rs have the similar open sensitivity in responding to IP3. The Oo-IP3R3 channel is easy to open in responding to low Ca2+ concentration, while Sf-IP3R channel is easily inhibited in responding to high Ca2+ concentration. We also show that the IP3 binding rate is not a sensitive parameter for stationary gating dynamics for three IP3Rs, but the inhibitory Ca2+ binding/unbinding rates are sensitive parameters for gating dynamics for both Oo-IP3R1 and Oo-IP3R3 channels. Such differences may be important in generating the spatially and temporally complex Ca2+ oscillations in cells. Our study also demonstrates that the immune algorithm can be applied for model parameter searching in biological systems.

Method and apparatus for measuring birefringent particles

DOEpatents

Bishop, James K.; Guay, Christopher K.

2006-04-18

A method and apparatus for measuring birefringent particles is provided comprising a source lamp, a grating, a first polarizer having a first transmission axis, a sample cell and a second polarizer having a second polarization axis. The second polarizer has a second polarization axis that is set to be perpendicular to the first polarization axis, and thereby blocks linearly polarized light with the orientation of the beam of light passing through the first polarizer. The beam of light passing through the second polarizer is measured using a detector.

Combining genomic and proteomic approaches for epigenetics research

PubMed Central

Han, Yumiao; Garcia, Benjamin A

2014-01-01

Epigenetics is the study of changes in gene expression or cellular phenotype that do not change the DNA sequence. In this review, current methods, both genomic and proteomic, associated with epigenetics research are discussed. Among them, chromatin immunoprecipitation (ChIP) followed by sequencing and other ChIP-based techniques are powerful techniques for genome-wide profiling of DNA-binding proteins, histone post-translational modifications or nucleosome positions. However, mass spectrometry-based proteomics is increasingly being used in functional biological studies and has proved to be an indispensable tool to characterize histone modifications, as well as DNA–protein and protein–protein interactions. With the development of genomic and proteomic approaches, combination of ChIP and mass spectrometry has the potential to expand our knowledge of epigenetics research to a higher level. PMID:23895656

Polarization-polarization correlation measurement --- Experimental test of the PPCO methods

NASA Astrophysics Data System (ADS)

Droste, Ch.; Starosta, K.; Wierzchucka, A.; Morek, T.; Rohoziński, S. G.; Srebrny, J.; Wesolowski, E.; Bergstrem, M.; Herskind, B.

1998-04-01

A significant fraction of modern multidetector arrays used for "in-beam" gamma-ray spectroscopy consist of a detectors which are sensitive to linear polarization of gamma quanta. This yields the opportunity to carry out correlation measurements between the gamma rays registered in polarimeters to get information concerning spins and parities of excited nuclear states. The aim of the present work was to study the ability of the polarization- polarization correlation method (the PPCO method). The correlation between the linear polarization of one gamma quantum and the polarization of the second quantum emitted in a cascade from an oriented nucleus (due to a heavy ion reaction) was studied in detail. The appropriate formulae and methods of analysis are presented. The experimental test of the method was performed using the EUROGAM II array. The CLOVER detectors are the parts of the array used as polarimeters. The ^164Yb nucleus was produced via the ^138Ba(^30Si, 4n) reaction. It was found that the PPCO method together with the standard DCO analysis and the polarization- direction correlation method (PDCO) can be helpful for spin, parity and multipolarity assignments. The results suggest that the PPCO method can be applied to modern spectrometers in which a large number of detectors (e.g. CLOVER) are sensitive to polarization of gamma rays.

Measuring fluorescence polarization with a dichrometer.

PubMed

Sutherland, John C

2017-09-01

A method for obtaining fluorescence polarization data from an instrument designed to measure circular and linear dichroism is compared with a previously reported approach. The new method places a polarizer between the sample and a detector mounted perpendicular to the direction of the incident beam and results in determination of the fluorescence polarization ratio, whereas the previous method does not use a polarizer and yields the fluorescence anisotropy. A similar analysis with the detector located axially with the excitation beam demonstrates that there is no frequency modulated signal due to fluorescence polarization in the absence of a polarizer. Copyright © 2017. Published by Elsevier Inc.

Evaluation and Compensation of Detector Solenoid Effects in the JLEIC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wei, Guohui; Morozov, Vasiliy; Zhang, Yuhong

2016-05-01

The JLEIC detector solenoid has a strong 3 T field in the IR area, and its tails extend over a range of several meters. One of the main effects of the solenoid field is coupling of the horizontal and vertical betatron motions which must be corrected in order to preserve the dynamical stability and beam spot size match at the IP. Additional effects include influence on the orbit and dispersion caused by the angle between the solenoid axis and the beam orbit. Meanwhile it affects ion polarization breaking the figure-8 spin symmetry. Crab dynamics further complicates the picture. All ofmore » these effects have to be compensated or accounted for. The proposed correction system is equivalent to the Rotating Frame Method. However, it does not involve physical rotation of elements. It provides local compensation of the solenoid effects independently for each side of the IR. It includes skew quadrupoles, dipole correctors and anti-solenoids to cancel perturbations to the orbit and linear optics. The skew quadrupoles and FFQ together generate an effect equivalent to adjustable rotation angle to do the decoupling task. Details of all of the correction systems are presented.« less

3D imaging of geological structures by R-VSP utilizing vibrations caused by shaft excavations at the Mizunami Underground Research Laboratory in Japan

NASA Astrophysics Data System (ADS)

Matsuoka, T.; Hodotsuka, Y.; Ishigaki, K.; Lee, C.

2009-12-01

Japan Atomic Energy Agency is now conducting the Mizunami Underground Research Laboratory (MIU) project. The MIU consists of two shafts (main shaft: 6.5m, ventilation shaft: 4.5m diameter) and horizontal research galleries, in sedimentary and granitic rocks at Mizunami City, Central Japan. The MIU project is a broad scientific study of the deep geological environment providing the basis for research and development for geological disposal of high level radioactive waste. One of the main goals is to establish techniques for investigation, analysis and assessment of the deep geological environment in fractured crystalline rock. As a part of the MIU project, we carried out the Reverse-Vertical Seismic Profile (R-VSP) using vibrations from the blasting for the shaft excavations and drilling of boreholes in the horizontal research galleries and examined the applicability of this method to imaging of geological structures around underground facilities, such as the unconformity between the sedimentary rocks and the basal granite, and faults and fracture zones in the granite. R-VSP method is a seismic method utilizing the receiver arrays on surface and seismic sources underground (e.g. in boreholes). This method is advantageous in that planning of 3-dimensional surveys is easy compared with reflection seismic surveying and conventional VSP because seismic source arrays that are major constraint for conducting surveys on surface are unnecessary. The receiver arrays consist of six radial lines on surface with a central focus on the main shaft. Seven blast rounds for the main shaft excavation from GL-52.8m to GL-250m and the borehole drilling in the GL-200m horizontal research gallery were observed. Three types of data processing, conventional VSP data processing (VSP-CDP transform and VSP migration), Reflection data processing utilizing Seismic interferometry method (“Seismic interferometry”) and Reflection mapping utilizing Image Point transform method (“IP transform”), were performed to obtain reflection images from heterogeneous geological structure. As the results, the reflective events that seemed to correspond with sedimentary layers, the unconformity between sedimentary rocks and granite, and fracture zones in granite could be detected by reflection profiles using “conventional VSP data processing” and “Seismic interferometry”. However, it is difficult to identify the faults around the MIU because they are generally at a high-angle. “IP transform” is one type of Radon transform which change common shot gather to IP domain. Image Points are defined through geometries of sources and reflectors. Reflection signals in time domain can be accumulated and enhanced in IP domain by “IP transform” on the condition of the right angle to a fault. So, by a search of the direction that reflection signals are enhanced using “IP transform”, the locations of faults can be inferred. By this method, the distribution of faults that correspond with faults in the current geological model constructed from investigation data in the MIU project could be detected.

Optimized methods of chromatin immunoprecipitation for profiling histone modifications in industrial microalgae Nannochloropsis spp.

PubMed

Wei, Li; Xu, Jian

2018-06-01

Epigenetic factors such as histone modifications play integral roles in plant development and stress response, yet their implications in algae remain poorly understood. In the industrial oleaginous microalgae Nannochloropsis spp., the lack of an efficient methodology for chromatin immunoprecipitation (ChIP), which determines the specific genomic location of various histone modifications, has hindered probing the epigenetic basis of their photosynthetic carbon conversion and storage as oil. Here, a detailed ChIP protocol was developed for Nannochloropsis oceanica, which represents a reliable approach for the analysis of histone modifications, chromatin state, and transcription factor-binding sites at the epigenetic level. Using ChIP-qPCR, genes related to photosynthetic carbon fixation in this microalga were systematically assessed. Furthermore, a ChIP-Seq protocol was established and optimized, which generated a genome-wide profile of histone modification events, using histone mark H3K9Ac as an example. These results are the first step for appreciation of the chromatin landscape in industrial oleaginous microalgae and for epigenetics-based microalgal feedstock development. © 2018 Phycological Society of America.

Abnormalities in human pluripotent cells due to reprogramming mechanisms

PubMed Central

Ma, Hong; Morey, Robert; O’Neil, Ryan C.; He, Yupeng; Daughtry, Brittany; Schultz, Matthew D.; Hariharan, Manoj; Nery, Joseph R.; Castanon, Rosa; Sabatini, Karen; Thiagarajan, Rathi D.; Tachibana, Masahito; Kang, Eunju; Tippner-Hedges, Rebecca; Ahmed, Riffat; Gutierrez, Nuria Marti; Van Dyken, Crystal; Polat, Alim; Sugawara, Atsushi; Sparman, Michelle; Gokhale, Sumita; Amato, Paula; Wolf, Don P.; Ecker, Joseph R.; Laurent, Louise C.; Mitalipov, Shoukhrat

2016-01-01

Human pluripotent stem cells hold potential for regenerative medicine, but available cell types have significant limitations. Although embryonic stem cells (ES cells) from in vitro fertilized embryos (IVF ES cells) represent the ‘gold standard’, they are allogeneic to patients. Autologous induced pluripotent stem cells (iPS cells) are prone to epigenetic and transcriptional aberrations. To determine whether such abnormalities are intrinsic to somatic cell reprogramming or secondary to the reprogramming method, genetically matched sets of human IVF ES cells, iPS cells and nuclear transfer ES cells (NT ES cells) derived by somatic cell nuclear transfer (SCNT) were subjected to genome-wide analyses. Both NT ES cells and iPS cells derived from the same somatic cells contained comparable numbers of de novo copy number variations. In contrast, DNA methylation and transcriptome profiles of NT ES cells corresponded closely to those of IVF ES cells, whereas iPS cells differed and retained residual DNA methylation patterns typical of parental somatic cells. Thus, human somatic cells can be faithfully reprogrammed to pluripotency by SCNT and are therefore ideal for cell replacement therapies. PMID:25008523

Immunoaffinity purification of dietary heterocyclic amine carcinogens

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vanderlaan, M.; Hwang, M.; Djanegara, T.

1993-03-01

Cooking meats produces a family of heterocyclic aromatic amines that are carcinogens in rodents and genotoxic in many short-term assays. Concern that these compounds may be human carcinogens has prompted us to develop immunochemical methods for quantifying these compounds in the human diet and for identifying the parent compounds and metabolites in urine and feces. Previously reported monoclonal antibodies to 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx) and 6-phenyl-2-amino-1-methylimidazo[4,5-f]pyridine (PhIP) were used to purify by immunoaffinity these known mutagens and cross-reacting structural analogs from well-done cooked beef and urine samples. Materials recovered from the immunoaffinity columns were subsequently separated by HPLC to purify the knownmore » mutagens from cross-reacting chemicals that co-purify by immunoaffinity. Immunoaffinity chromatography was found to be a rapid means of quantifying individual known mutagens, with a minimum of precolumn sample clean-up required. In addition, this procedure has yielded several new mutagens present in cooked meats that are apparently structural analogs of PhIP. Immunoaffinity techniques were also used to purify metabolites from the urine of rats and humans exposed to MeIQx or PhIP. For MeIQx-exposed rats, the combination antibodies immunoconcentrated 75% of the total urinary radioactivity. Analysis of PhIP metabolites recovered from antibody columns is facilitated by the intrinsic fluorescence of PhIP and its metabolites, providing sufficient sensitivity to monitor individuals for the levels of PhIP excreted following consumption of typical western diets. 6 refs., 3 figs.« less

Prospective study of Centurion® versus Infiniti® phacoemulsification systems: surgical and visual outcomes

PubMed Central

Oh, Lawrence J.; Nguyen, Chu Luan; Wong, Eugene; Wang, Samuel S.Y.; Francis, Ian C.

2017-01-01

AIM To evaluate surgical outcomes (SOs) and visual outcomes (VOs) in cataract surgery comparing the Centurion® phacoemulsification system (CPS) with the Infiniti® phacoemulsification system (IPS). METHODS Prospective, consecutive study in a single-site private practice. Totally 412 patients undergoing cataract surgery with either the CPS using the 30-degree balanced® tip (n=207) or the IPS using the 30-degree Kelman® tip (n=205). Intraoperative and postoperative outcomes were documented prospectively up to one month follow-up. Nuclear sclerosis (NS) grade, cumulated dissipated energy (CDE), preoperative corrected distance visual acuity (CDVA), and CDVA at one month were recorded. RESULTS CDE was 13.50% less in the whole CPS compared with the whole IPS subcohort. In eyes with NS grade III or greater, CDE was 28.87% less with CPS (n=70) compared with IPS (n=44) (P=0.010). Surgical complications were not statistically different between the two subcohorts (P=0.083), but in the one case of vitreous loss using the CPS, CDVA of 6/4 was achieved at one month. The mean CDVAs (VOs) at one month for NS grade III and above cataracts were -0.17 logMAR (6/4.5) in the CPS and -0.15 logMAR (6/4.5) in the IPS subcohort respectively (P=0.033). CONCLUSION CDE is 28.87% less, and VOs are significantly improved, in denser cataracts in the CPS compared with the IPS. The authors recommend the CPS for cases with denser nuclei. PMID:29181313

The impact of the duration of an untreated episode on improvement of depression and somatic symptoms

PubMed Central

Hung, Ching-I; Yu, Nan-Wen; Liu, Chia-Yih; Wu, Kuan-Yi; Yang, Ching-Hui

2015-01-01

Purpose The aim of this study was to investigate the impact of the duration of an untreated episode (DUE) on the improvement of depression and somatic symptoms among patients with major depressive disorder (MDD), after the patients had received 4 weeks of pharmacotherapy. Methods In this open-label study, there were 155 participants with MDD who were treated daily with 75 mg of venlafaxine for 4 weeks. DUE was defined as the interval between the onset of the index major depressive episode and the start of pharmacotherapy. The Depression and Somatic Symptoms Scale (DSSS), composed of the depression subscale (DS) and the somatic subscale (SS), was used. The SS included the pain subscale (PS) and the nonpain somatic subscale (NPSS). Multiple linear regressions were used to test the impacts of DUE on the improvement percentages (IPs) of depression and somatic symptoms. Results Eighty-five subjects completed the 4-week treatment. The IPs of the DS, SS, and NPSS were significantly negatively correlated with DUE. A shorter DUE was related to higher IPs. DUE was an independent factor, predicting the IPs of the DS, SS, and NPSS. DUE <1 month was the most powerful time-point to predict the IPs of the DS, SS, and NPSS. However, DUE was unable to predict the IP of the PS at all time-points. Conclusion A shorter DUE might be one of the factors related to greater improvement of depression and somatic symptoms. DUE should be considered as an important factor when investigating the prognosis of depression and somatic symptoms. PMID:26346571

ChIP and ChIP-Related Techniques: Expanding the Fields of Application and Improving ChIP Performance.

PubMed

Visa, Neus; Jordán-Pla, Antonio

2018-01-01

Protein-DNA interactions in vivo can be detected and quantified by chromatin immunoprecipitation (ChIP). ChIP has been instrumental for the advancement of epigenetics and has set the groundwork for the development of a number of ChIP-related techniques that have provided valuable information about the organization and function of genomes. Here, we provide an introduction to ChIP and discuss the applications of ChIP in different research areas. We also review some of the strategies that have been devised to improve ChIP performance.

The prevalence of human papillomavirus infection in Iranian patients with sinonasal inverted papilloma.

PubMed

Jalilvand, Somayeh; Saidi, Masoumeh; Shoja, Zabihollah; Ghavami, Nastaran; Hamkar, Rasool

2016-03-01

Inverted papilloma (IP) is an uncommon disease which arises in the mucosal membrane of the nasal cavity and paranasal sinus. It has been proposed that human papillomavirus (HPV) is the causal agent in the pathogenesis of IP and plays a key role in the progression from benign IP to malignancy. As there are no prior studies that focus on an Iranian population, this study intended to characterize the prevalence of HPV types in benign and malignant forms of IP. In this retrospective study, we included a total of 40 IP patients [37 benign IP and 3 IP/squamous cell carcinoma (SCC)] who were referred to Amiralam Hospital in Tehran from 2004-2006. HPV was detected in 18.9% and 100% of IP and IP/SCC cases, respectively. In all HPV positive cases of IP and IP/SCC cases, HPV6/11 and HPV16/18 were detected, respectively. Therefore, HPV types were different between the IP and IP/SCC patients, and this difference was statistically significant (p = 0.002). This study suggests that HPV6 and 11 may be involved in the development of IP, but HPV16 and 18 likely play an important role in the progression from benign to malignant form of IP. Copyright © 2015. Published by Elsevier Taiwan LLC.

Parametric Optimization of Wire Electrical Discharge Machining of Powder Metallurgical Cold Worked Tool Steel using Taguchi Method

NASA Astrophysics Data System (ADS)

Sudhakara, Dara; Prasanthi, Guvvala

2017-04-01

Wire Cut EDM is an unconventional machining process used to build components of complex shape. The current work mainly deals with optimization of surface roughness while machining P/M CW TOOL STEEL by Wire cut EDM using Taguchi method. The process parameters of the Wire Cut EDM is ON, OFF, IP, SV, WT, and WP. L27 OA is used for to design of the experiments for conducting experimentation. In order to find out the effecting parameters on the surface roughness, ANOVA analysis is engaged. The optimum levels for getting minimum surface roughness is ON = 108 µs, OFF = 63 µs, IP = 11 A, SV = 68 V and WT = 8 g.

KChIP2 genotype dependence of transient outward current (Ito) properties in cardiomyocytes isolated from male and female mice

PubMed Central

Waldschmidt, Lara; Junkereit, Vera; Bähring, Robert

2017-01-01

The transient outward current (Ito) in cardiomyocytes is largely mediated by Kv4 channels associated with Kv Channel Interacting Protein 2 (KChIP2). A knockout model has documented the critical role of KChIP2 in Ito expression. The present study was conducted to characterize in both sexes the dependence of Ito properties, including current magnitude, inactivation kinetics, recovery from inactivation and voltage dependence of inactivation, on the number of functional KChIP2 alleles. For this purpose we performed whole-cell patch-clamp experiments on isolated left ventricular cardiomyocytes from male and female mice which had different KChIP2 genotypes; i.e., wild-type (KChIP2+/+), heterozygous knockout (KChIP2+/-) or complete knockout of KChIP2 (KChIP2-/-). We found in both sexes a KChIP2 gene dosage effect (i.e., a proportionality between number of alleles and phenotype) on Ito magnitude, however, concerning other Ito properties, KChIP2+/- resembled KChIP2+/+. Only in the total absence of KChIP2 (KChIP2-/-) we observed a slowing of Ito kinetics, a slowing of recovery from inactivation and a negative shift of a portion of the voltage dependence of inactivation. In a minor fraction of KChIP2-/- myocytes Ito was completely lost. The distinct KChIP2 genotype dependences of Ito magnitude and inactivation kinetics, respectively, seen in cardiomyocytes were reproduced with two-electrode voltage-clamp experiments on Xenopus oocytes expressing Kv4.2 and different amounts of KChIP2. Our results corroborate the critical role of KChIP2 in controlling Ito properties. They demonstrate that the Kv4.2/KChIP2 interaction in cardiomyocytes is highly dynamic, with a clear KChIP2 gene dosage effect on Kv4 channel surface expression but not on inactivation gating. PMID:28141821

KChIP2 genotype dependence of transient outward current (Ito) properties in cardiomyocytes isolated from male and female mice.

PubMed

Waldschmidt, Lara; Junkereit, Vera; Bähring, Robert

2017-01-01

The transient outward current (Ito) in cardiomyocytes is largely mediated by Kv4 channels associated with Kv Channel Interacting Protein 2 (KChIP2). A knockout model has documented the critical role of KChIP2 in Ito expression. The present study was conducted to characterize in both sexes the dependence of Ito properties, including current magnitude, inactivation kinetics, recovery from inactivation and voltage dependence of inactivation, on the number of functional KChIP2 alleles. For this purpose we performed whole-cell patch-clamp experiments on isolated left ventricular cardiomyocytes from male and female mice which had different KChIP2 genotypes; i.e., wild-type (KChIP2+/+), heterozygous knockout (KChIP2+/-) or complete knockout of KChIP2 (KChIP2-/-). We found in both sexes a KChIP2 gene dosage effect (i.e., a proportionality between number of alleles and phenotype) on Ito magnitude, however, concerning other Ito properties, KChIP2+/- resembled KChIP2+/+. Only in the total absence of KChIP2 (KChIP2-/-) we observed a slowing of Ito kinetics, a slowing of recovery from inactivation and a negative shift of a portion of the voltage dependence of inactivation. In a minor fraction of KChIP2-/- myocytes Ito was completely lost. The distinct KChIP2 genotype dependences of Ito magnitude and inactivation kinetics, respectively, seen in cardiomyocytes were reproduced with two-electrode voltage-clamp experiments on Xenopus oocytes expressing Kv4.2 and different amounts of KChIP2. Our results corroborate the critical role of KChIP2 in controlling Ito properties. They demonstrate that the Kv4.2/KChIP2 interaction in cardiomyocytes is highly dynamic, with a clear KChIP2 gene dosage effect on Kv4 channel surface expression but not on inactivation gating.

Anticonvulsant activity of Cotyledon orbiculata L. (Crassulaceae) leaf extract in mice.

PubMed

Amabeoku, G J; Green, I; Kabatende, J

2007-05-30

The anticonvulsant activity of Cotyledon orbiculata L. (Crassulaceae) was investigated by studying the effects of both aqueous and methanol extracts of the plant species on seizures induced by pentylenetetrazole, bicuculline, picrotoxin and N-methyl-dl-aspartic in mice. Aqueous extract of Cotyledon orbiculata (50-400mg/kg, i.p.) and methanol extract (100-400mg/kg, i.p.) significantly prolonged the onset of tonic seizures induced by pentylenetetrazole (95mg/kg, i.p.). Methanol extract (400mg/kg, i.p.) also significantly reduced the incidence of the seizures. One hundred to two hundred milligrams/kilogram (i.p.) of aqueous extract of Cotyledon orbiculata significantly delayed the onset of the tonic seizures induced by bicuculline (40mg/kg, i.p.), picrotoxin (12mg/kg, i.p.) and N-methyl-dl-aspartic acid (NMDLA, 400mg/kg, i.p.). Similarly, methanol extract (100-400mg/kg, i.p.) significantly delayed the onset of the tonic seizures induced by bicuculline (40mg/kg, i.p.) and picrotoxin (12mg/kg, i.p.) while 100mg/kg (i.p.) significantly delayed the onset of N-methyl-dl-aspartic acid (NMDLA, 400mg/kg, i.p.)-induced seizures. Methanol extract (200mg/kg, i.p.) significantly reduced the incidence of the seizures induced by bicuculline (40mg/kg, i.p.). Phenobarbitone (12mg/kg, i.p.) and diazepam (0.5mg/kg, i.p.) effectively antagonized only seizures induced by PTZ (95mg/kg, i.p.), bicuculline (40mg/kg, i.p.) and picrotoxin (12mg/kg, i.p.). Phenytoin (30mg/kg, i.p.) did not affect any of the seizures to any significant extent. The data obtained suggest that both aqueous and methanol extracts of Cotyledon orbiculata have anticonvulsant property and may probably be affecting both gabaergic and glutaminergic mechanisms to exert its effect. The phytochemical analysis carried out revealed the presence of cardiac glycosides, saponins, tannins, reducing sugar and triterpene steroids in the plant extract.

Phorbol 12,13-dibutyrate and 1-oleyl-2-acetyldiacylglycerol stimulate inositol trisphosphate dephosphorylation in human platelets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Molina y Vedia, L.M.; Lapetina, E.G.

1986-08-15

Inositol trisphosphate (IP3) is formed in response to specific agonists that cause activation of phospholipase C and degradation of phosphatidylinositol bisphosphate. IP3 is a second messenger that releases Ca/sup 2 +/ from the dense tubular system to the cytosol in stimulated platelets. Our present information indicates that (/sup 3/H)IP3 is dephosphorylated to (/sup 3/H)inositol bisphosphate (IP2) and (/sup 3/H)inositol monophosphate (IP) by human platelets treated with 0.05-0.10% Triton X-100. This dephosphorylation of (/sup 3/H)IP3 to (/sup 3/H)IP2 and (/sup 3/H)IP is also observed when platelets are permeabilized by electrical stimulation or by 20 micrograms/ml saponin. These detergents or electropermeabilization allowmore » IP3 to access cytosolic IP3 phosphatase. Pretreatment of intact platelets with phorbol dibutyrate and 1-oleyl-2-acetyldiacylglycerol for 30 s, at concentrations that maximally activate protein kinase C, stimulates the conversion of IP3 to IP2 and IP. This suggests a role for protein kinase C in the regulation of IP3 degradation.« less

Ultraperformance liquid chromatography-tandem mass spectrometry method for biomonitoring cooked meat carcinogens and their metabolites in human urine.

PubMed

Gu, Dan; Raymundo, Melissa M; Kadlubar, Fred F; Turesky, Robert J

2011-02-01

The cooked meat carcinogens 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx), and their principal metabolites produced by cytochrome P450 and/or uridine diphosphate glucuronosyl transferases were simultaneously measured at the parts per trillion level in urine of omnivores, by ultraperformance liquid chromatography (UPLC) with a Michrom Advance CaptiveSpray source and a triple stage quadrupole mass spectrometer. Quantitation was performed in the selected reaction monitoring mode. The UPLC method is much more rapid and sensitive than our earlier capillary HPLC method: the duty cycle of the UPLC method is 19 min compared to 57 min for capillary HPLC. The performance of the UPLC assay was evaluated with urine samples from three subjects over 4 different days. The intraday and interday precisions of the estimates of PhIP, MeIQx, and their metabolites, reported as the coefficients of variation, were ≤10%. The limit of quantification (LOQ) values for PhIP and MeIQx were about 5 pg/mL, whereas the LOQ values of their metabolites ranged from 10 to 40 pg/mL. Furthermore, the identities of the analytes were corroborated by acquisition of full scan product ion spectra, employing between 0.5 and 5 pg of analyte for assay.

Quantitative determination of biological activity of botulinum toxins utilizing compound muscle action potentials (CMAP), and comparison of neuromuscular transmission blockage and muscle flaccidity among toxins.

PubMed

Torii, Yasushi; Goto, Yoshitaka; Takahashi, Motohide; Ishida, Setsuji; Harakawa, Tetsuhiro; Sakamoto, Takashi; Kaji, Ryuji; Kozaki, Shunji; Ginnaga, Akihiro

2010-01-01

The biological activity of various types of botulinum toxin has been evaluated using the mouse intraperitoneal LD(50) test (ip LD(50)). This method requires a large number of mice to precisely determine toxin activity, and so has posed a problem with regard to animal welfare. We have used a direct measure of neuromuscular transmission, the compound muscle action potential (CMAP), to evaluate the effect of different types of botulinum neurotoxin (NTX), and we compared the effects of these toxins to evaluate muscle relaxation by employing the digit abduction scoring (DAS) assay. This method can be used to measure a broad range of toxin activities the day after administration. Types A, C, C/D, and E NTX reduced the CMAP amplitude one day after administration at below 1 ip LD(50), an effect that cannot be detected using the mouse ip LD(50) assay. The method is useful not only for measuring toxin activity, but also for evaluating the characteristics of different types of NTX. The rat CMAP test is straightforward, highly reproducible, and can directly determine the efficacy of toxin preparations through their inhibition of neuromuscular transmission. Thus, this method may be suitable for pharmacology studies and the quality control of toxin preparations. Copyright 2009 Elsevier Ltd. All rights reserved.

Interfacial modulus mapping of layered dental ceramics using nanoindentation

PubMed Central

Bushby, Andrew J; P'ng, Ken MY; Wilson, Rory M

2016-01-01

PURPOSE The aim of this study was to test the modulus of elasticity (E) across the interfaces of yttria stabilized zirconia (YTZP) / veneer multilayers using nanoindentation. MATERIALS AND METHODS YTZP core material (KaVo-Everest, Germany) specimens were either coated with a liner (IPS e.max ZirLiner, Ivoclar-Vivadent) (Type-1) or left as-sintered (Type-2) and subsequently veneered with a pressable glass-ceramic (IPS e.max ZirPress, Ivoclar-Vivadent). A 5 µm (nominal tip diameter) spherical indenter was used with a UMIS CSIRO 2000 (ASI, Canberra, Australia) nanoindenter system to test E across the exposed and polished interfaces of both specimen types. The multiple point load – partial unload method was used for E determination. All materials used were characterized using Scanning Electron Microscopy (SEM) and X – ray powder diffraction (XRD). E mappings of the areas tested were produced from the nanoindentation data. RESULTS A significantly (P<.05) lower E value between Type-1 and Type-2 specimens at a distance of 40 µm in the veneer material was associated with the liner. XRD and SEM characterization of the zirconia sample showed a fine grained bulk tetragonal phase. IPS e-max ZirPress and IPS e-max ZirLiner materials were characterized as amorphous. CONCLUSION The liner between the YTZP core and the heat pressed veneer may act as a weak link in this dental multilayer due to its significantly (P<.05) lower E. The present study has shown nanoindentation using spherical indentation and the multiple point load - partial unload method to be reliable predictors of E and useful evaluation tools for layered dental ceramic interfaces. PMID:28018566

Harnessing Data to Assess Equity of Care by Race, Ethnicity and Language

PubMed Central

Gracia, Amber; Cheirif, Jorge; Veliz, Juana; Reyna, Melissa; Vecchio, Mara; Aryal, Subhash

2015-01-01

Objective: Determine any disparities in care based on race, ethnicity and language (REaL) by utilizing inpatient (IP) core measures at Texas Health Resources, a large, faith-based, non-profit health care delivery system located in a large, ethnically diverse metropolitan area in Texas. These measures, which were established by the U.S. Centers for Medicare and Medicaid Services (CMS) and The Joint Commission (TJC), help to ensure better accountability for patient outcomes throughout the U.S. health care system. Methods: Sample analysis to understand the architecture of race, ethnicity and language (REaL) variables within the Texas Health clinical database, followed by development of the logic, method and framework for isolating populations and evaluating disparities by race (non-Hispanic White, non-Hispanic Black, Native American/Native Hawaiian/Pacific Islander, Asian and Other); ethnicity (Hispanic and non-Hispanic); and preferred language (English and Spanish). The study is based on use of existing clinical data for four inpatient (IP) core measures: Acute Myocardial Infarction (AMI), Congestive Heart Failure (CHF), Pneumonia (PN) and Surgical Care (SCIP), representing 100% of the sample population. These comprise a high number of cases presenting in our acute care facilities. Findings are based on a sample of clinical data (N = 19,873 cases) for the four inpatient (IP) core measures derived from 13 of Texas Health’s wholly-owned facilities, formulating a set of baseline data. Results: Based on applied method, Texas Health facilities consistently scored high with no discernable race, ethnicity and language (REaL) disparities as evidenced by a low percentage difference to the reference point (non-Hispanic White) on IP core measures, including: AMI (0.3%–1.2%), CHF (0.7%–3.0%), PN (0.5%–3.7%), and SCIP (0–0.7%). PMID:26703665

IP3-mediated gating mechanism of the IP3 receptor revealed by mutagenesis and X-ray crystallography.

PubMed

Hamada, Kozo; Miyatake, Hideyuki; Terauchi, Akiko; Mikoshiba, Katsuhiko

2017-05-02

The inositol 1,4,5-trisphosphate (IP 3 ) receptor (IP 3 R) is an IP 3 -gated ion channel that releases calcium ions (Ca 2+ ) from the endoplasmic reticulum. The IP 3 -binding sites in the large cytosolic domain are distant from the Ca 2+ conducting pore, and the allosteric mechanism of how IP 3 opens the Ca 2+ channel remains elusive. Here, we identify a long-range gating mechanism uncovered by channel mutagenesis and X-ray crystallography of the large cytosolic domain of mouse type 1 IP 3 R in the absence and presence of IP 3 Analyses of two distinct space group crystals uncovered an IP 3 -dependent global translocation of the curvature α-helical domain interfacing with the cytosolic and channel domains. Mutagenesis of the IP 3 R channel revealed an essential role of a leaflet structure in the α-helical domain. These results suggest that the curvature α-helical domain relays IP 3 -controlled global conformational dynamics to the channel through the leaflet, conferring long-range allosteric coupling from IP 3 binding to the Ca 2+ channel.

Inositol 1,4,5-trisphosphate receptor regulates replication, differentiation, infectivity and virulence of the parasitic protist Trypanosoma cruzi.

PubMed

Hashimoto, Muneaki; Enomoto, Masahiro; Morales, Jorge; Kurebayashi, Nagomi; Sakurai, Takashi; Hashimoto, Tetsuo; Nara, Takeshi; Mikoshiba, Katsuhiko

2013-03-01

In animals, inositol 1,4,5-trisphosphate receptors (IP3 Rs) are ion channels that play a pivotal role in many biological processes by mediating Ca(2+) release from the endoplasmic reticulum. Here, we report the identification and characterization of a novel IP3 R in the parasitic protist, Trypanosoma cruzi, the pathogen responsible for Chagas disease. DT40 cells lacking endogenous IP3 R genes expressing T. cruzi IP3 R (TcIP3 R) exhibited IP3 -mediated Ca(2+) release from the ER, and demonstrated receptor binding to IP3 . TcIP3 R was expressed throughout the parasite life cycle but the expression level was much lower in bloodstream trypomastigotes than in intracellular amastigotes or epimastigotes. Disruption of two of the three TcIP3 R gene loci led to the death of the parasite, suggesting that IP3 R is essential for T. cruzi. Parasites expressing reduced or increased levels of TcIP3 R displayed defects in growth, transformation and infectivity, indicating that TcIP3 R is an important regulator of the parasite's life cycle. Furthermore, mice infected with T. cruzi expressing reduced levels of TcIP3 R exhibited a reduction of disease symptoms, indicating that TcIP3 R is an important virulence factor. Combined with the fact that the primary structure of TcIP3 R has low similarity to that of mammalian IP3 Rs, TcIP3 R is a promising drug target for Chagas disease. © 2013 Blackwell Publishing Ltd.

Global positioning method based on polarized light compass system

NASA Astrophysics Data System (ADS)

Liu, Jun; Yang, Jiangtao; Wang, Yubo; Tang, Jun; Shen, Chong

2018-05-01

This paper presents a global positioning method based on a polarized light compass system. A main limitation of polarization positioning is the environment such as weak and locally destroyed polarization environments, and the solution to the positioning problem is given in this paper which is polarization image de-noising and segmentation. Therefore, the pulse coupled neural network is employed for enhancing positioning performance. The prominent advantages of the present positioning technique are as follows: (i) compared to the existing position method based on polarized light, better sun tracking accuracy can be achieved and (ii) the robustness and accuracy of positioning under weak and locally destroyed polarization environments, such as cloudy or building shielding, are improved significantly. Finally, some field experiments are given to demonstrate the effectiveness and applicability of the proposed global positioning technique. The experiments have shown that our proposed method outperforms the conventional polarization positioning method, the real time longitude and latitude with accuracy up to 0.0461° and 0.0911°, respectively.

A method to measure neutron polarization using P-even asymmetry of {gamma}-quantum emission in the neutron-nuclear interaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gledenov, Yu. M.; Nesvizhevsky, V. V.; Sedyshev, P. V.

2012-07-15

A new method to measure polarization of cold/thermal neutrons using P-even asymmetry in nuclear reactions induced by polarized neutrons is proposed. A scheme profiting from a large correlation of the neutron spin and the circular {gamma}-quantum polarization in the reaction (n, {gamma}) of polarized neutrons with nuclei is analyzed. This method could be used, for instance, to measure the neutron-beam polarization in experiments with frequently varying configuration. We show that high accuracy and reliability of measurements could be expected.

Postoperative Outcomes of Extremely Low Birth-Weight Infants With Necrotizing Enterocolitis or Isolated Intestinal Perforation

PubMed Central

Blakely, Martin L.; Lally, Kevin P.; McDonald, Scott; Brown, Rebeccah L.; Barnhart, Douglas C.; Ricketts, Richard R.; Thompson, W Raleigh; Scherer, L R.; Klein, Michael D.; Letton, Robert W.; Chwals, Walter J.; Touloukian, Robert J.; Kurkchubasche, Arlett G.; Skinner, Michael A.; Moss, R Lawrence; Hilfiker, Mary L.

2005-01-01

Objective: Purposes of this study were: 1) to compare mortality and postoperative morbidities (intra-abdominal abscess, wound dehiscence, and intestinal stricture) in extremely low birth weight (ELBW) infants who underwent initial laparotomy or drainage for necrotizing enterocolitis (NEC) or isolated intestinal perforation (IP); 2) to determine the ability to distinguish NEC from IP preoperatively and the importance of this distinction on outcome measures; and 3) to evaluate the association between extent of intestinal disease determined at operation and outcome measures. Background: ELBW infants who undergo operation for NEC or IP have a postoperative, in-hospital mortality rate of approximately 50%. Whether to perform laparotomy or drainage initially is controversial. Also unknown is the importance of distinguishing NEC from IP and the current ability to make this distinction based on objective data available prior to operation. Methods: A prospective, multicenter cohort study of 156 ELBW infants at 16 neonatal intensive care units (NICU) within the NICHD Neonatal Research Network. Results: Among the 156 enrolled infants, 80 underwent initial peritoneal drainage and 76 initial laparotomy. Mortality rate was 49% (76 of 156). Ninety-six patients had a preoperative diagnosis of NEC and 60 had presumed IP. There was a high level of agreement between the presumed preoperative diagnosis and intraoperative diagnosis in patients undergoing initial laparotomy (kappa = 0.85). The relative risk for death with a preoperative diagnosis of NEC (versus IP) was 1.4 (95% confidence interval, 0.99–2.1, P = 0.052). The overall incidence of postoperative intestinal stricture was 10.3%, wound dehiscence 4.4%, and intra-abdominal abscess 5.8%, and did not significantly differ between groups undergoing initial laparotomy versus initial drainage. Conclusions: Survival to hospital discharge after operation for NEC or IP in ELBW neonates remains poor (51%). Patients with a preoperative diagnosis of NEC have a relative risk for death of 1.4 compared with those with a preoperative diagnosis of IP. A distinction can be made preoperatively between NEC and IP based on abdominal radiographic findings and the patient's age at operation. Future randomized trials that compare laparotomy versus drainage would likely benefit from stratification of treatment assignment based on preoperative diagnosis. PMID:15912048

Equivalent intraperitoneal doses of ibuprofen supplemented in drinking water or in diet: a behavioral and biochemical assay using antinociceptive and thromboxane inhibitory dose–response curves in mice

PubMed Central

El Gayar, Nesreen H.; Georgy, Sonia S.

2016-01-01

Background. Ibuprofen is used chronically in different animal models of inflammation by administration in drinking water or in diet due to its short half-life. Though this practice has been used for years, ibuprofen doses were never assayed against parenteral dose–response curves. This study aims at identifying the equivalent intraperitoneal (i.p.) doses of ibuprofen, when it is administered in drinking water or in diet. Methods. Bioassays were performed using formalin test and incisional pain model for antinociceptive efficacy and serum TXB2 for eicosanoid inhibitory activity. The dose–response curve of i.p. administered ibuprofen was constructed for each test using 50, 75, 100 and 200 mg/kg body weight (b.w.). The dose–response curves were constructed of phase 2a of the formalin test (the most sensitive phase to COX inhibitory agents), the area under the ‘change in mechanical threshold’-time curve in the incisional pain model and serum TXB2 levels. The assayed ibuprofen concentrations administered in drinking water were 0.2, 0.35, 0.6 mg/ml and those administered in diet were 82, 263, 375 mg/kg diet. Results. The 3 concentrations applied in drinking water lay between 73.6 and 85.5 mg/kg b.w., i.p., in case of the formalin test; between 58.9 and 77.8 mg/kg b.w., i.p., in case of the incisional pain model; and between 71.8 and 125.8 mg/kg b.w., i.p., in case of serum TXB2 levels. The 3 concentrations administered in diet lay between 67.6 and 83.8 mg/kg b.w., i.p., in case of the formalin test; between 52.7 and 68.6 mg/kg b.w., i.p., in case of the incisional pain model; and between 63.6 and 92.5 mg/kg b.w., i.p., in case of serum TXB2 levels. Discussion. The increment in pharmacological effects of different doses of continuously administered ibuprofen in drinking water or diet do not parallel those of i.p. administered ibuprofen. It is therefore difficult to assume the equivalent parenteral daily doses based on mathematical calculations. PMID:27547547

Elastic Properties of Lithium Disilicate Versus Feldspathic Inlays: Effect on the Bonding by 3D Finite Element Analysis.

PubMed

Trindade, Flávia Zardo; Valandro, Luiz Felipe; de Jager, Niek; Bottino, Marco Antônio; Kleverlaan, Cornelis Johannes

2016-10-03

To determine the elastic properties of five ceramic systems with different compositions (lithium disilicate vs. feldspathic ceramics) and processing methods and compare the stress distribution in premolars in the interface with inlays made with these systems loaded with the maximum normal bite force (665 N) using 3D finite element analysis (FEA). The elastic properties of five ceramic restoration materials (IPS e.max Press, IPS e.max CAD, Vita PM9, Vita Mark II, Vita VM7) were obtained using the ultrasonic pulse-echo method. Three-dimensional FEA simplified models of maxillary premolars restored with these ceramic materials were created. The models were loaded with a load at the two nodes on the occlusal surface in the middle of the tooth, 2 mm from the outside of the tooth, simulating a loading ball with a radius of 6 mm. The means values of density (g/cm³), Young's modulus (GPa), and Poison's ratio was 2.6 ± 0.3, 82.3 ± 18.3, and 0.22 ± 0.01 for IPS e.max Press; 2.3 ± 0.1, 83.5 ± 15.0, and 0.21 ± 0.01 for IPS e.max CAD; 2.5 ± 0.1, 44.4 ± 11.5, and 0.26 ± 0.08 for PM9; 2.4 ± 0.1, 70.6 ± 4.9, and 0.22 ± 0.01 for Vitamark II; 2.4 ± 0.1, 63.3 ± 3.9, and 0.23 ± 0.01 for VM7, respectively. The 3D FEA showed the tensile stress at the interface between the tooth and the inlay was dependent on the elastic properties of the materials, since the Vita PM9 and IPS e.max CAD ceramics presented the lowest and the highest stress concentration in the interface, respectively. The elastic properties of ceramic materials were influenced by composition and processing methods, and these differences influenced the stress concentration at the bonding interface between tooth and restoration. The lower the elastic modulus of inlays, the lower is the stress concentration at the bonding interfaces. © 2016 by the American College of Prosthodontists.

Measuring fluorescence polarization with a dichrometer

DOE PAGES

Sutherland, John C.

2017-04-06

In this article, a method for obtaining fluorescence polarization data from an instrument designed to measure circular and linear dichroism is compared with a previously reported approach. The new method places a polarizer between the sample and a detector mounted perpendicular to the direction of the incident beam and results in determination of the fluorescence polarization ratio, whereas the previous method does not use a polarizer and yields the fluorescence anisotropy. A similar analysis with the detector located axially with the excitation beam demonstrates that there is no frequency modulated signal due to fluorescence polarization in the absence of amore » polarizer.« less

Clinical Diagnostic Utility of IP-10 and LAM Antigen Levels for the Diagnosis of Tuberculous Pleural Effusions in a High Burden Setting

PubMed Central

Dheda, Keertan; Van-Zyl Smit, Richard N.; Sechi, Leonardo A.; Badri, Motasim; Meldau, Richard; Symons, Gregory; Khalfey, Hoosein; Carr, Igshaan; Maredza, Alice; Dawson, Rodney; Wainright, Helen; Whitelaw, Andrew; Bateman, Eric D.; Zumla, Alimuddin

2009-01-01

Background Current tools for the diagnosis of tuberculosis pleural effusions are sub-optimal. Data about the value of new diagnostic technologies are limited, particularly, in high burden settings. Preliminary case control studies have identified IFN-γ-inducible-10kDa protein (IP-10) as a promising diagnostic marker; however, its diagnostic utility in a day-to-day clinical setting is unclear. Detection of LAM antigen has not previously been evaluated in pleural fluid. Methods We investigated the comparative diagnostic utility of established (adenosine deaminase [ADA]), more recent (standardized nucleic-acid-amplification-test [NAAT]) and newer technologies (a standardized LAM mycobacterial antigen-detection assay and IP-10 levels) for the evaluation of pleural effusions in 78 consecutively recruited South African tuberculosis suspects. All consenting participants underwent pleural biopsy unless contra-indicated or refused. The reference standard comprised culture positivity for M. tuberculosis or histology suggestive of tuberculosis. Principal Findings Of 74 evaluable subjects 48, 7 and 19 had definite, probable and non-TB, respectively. IP-10 levels were significantly higher in TB vs non-TB participants (p<0.0001). The respective outcomes [sensitivity, specificity, PPV, NPV %] for the different diagnostic modalities were: ADA at the 30 IU/L cut-point [96; 69; 90; 85], NAAT [6; 93; 67; 28], IP-10 at the 28,170 pg/ml ROC-derived cut-point [80; 82; 91; 64], and IP-10 at the 4035 pg/ml cut-point [100; 53; 83; 100]. Thus IP-10, using the ROC-derived cut-point, missed ∼20% of TB cases and mis-diagnosed ∼20% of non-TB cases. By contrast, when a lower cut-point was used a negative test excluded TB. The NAAT had a poor sensitivity but high specificity. LAM antigen-detection was not diagnostically useful. Conclusion Although IP-10, like ADA, has sub-optimal specificity, it may be a clinically useful rule-out test for tuberculous pleural effusions. Larger multi-centric studies are now required to confirm our findings. PMID:19277111

Lessons Learned in the Design and Use of IP1 / IP2 Flexible Packaging - 13621

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanchez, Mike; Reeves, Wendall; Smart, Bill

2013-07-01

For many years in the USA, Low Level Radioactive Waste (LLW), contaminated soils and construction debris, have been transported, interim stored, and disposed of, using IP1 / IP2 metal containers. The performance of these containers has been more than adequate, with few safety occurrences. The containers are used under the regulatory oversight of the US Department of Transportation (DOT), 49 Code of Federal Regulations (CFR). In the late 90's the introduction of flexible packaging for the transport, storage, and disposal of low level contaminated soils and construction debris was introduced. The development of flexible packaging came out of a needmore » for a more cost effective package, for the large volumes of waste generated by the decommissioning of many of the US Department of Energy (DOE) legacy sites across the US. Flexible packaging had to be designed to handle a wide array of waste streams, including soil, gravel, construction debris, and fine particulate dust migration. The design also had to meet all of the IP1 requirements under 49CFR 173.410, and be robust enough to pass the IP2 testing 49 CFR 173.465 required for many LLW shipments. Tens of thousands of flexible packages have been safely deployed and used across the US nuclear industry as well as for hazardous non-radioactive applications, with no recorded release of radioactive materials. To ensure that flexible packages are designed properly, the manufacturer must use lessons learned over the years, and the tests performed to provide evidence that these packages are suitable for transporting low level radioactive wastes. The design and testing of flexible packaging for LLW, VLLW and other hazardous waste streams must be as strict and stringent as the design and testing of metal containers. The design should take into consideration the materials being loaded into the package, and should incorporate the right materials, and manufacturing methods, to provide a quality, safe product. Flexible packaging can be shown to meet the criteria for safe and fit for purpose packaging, by meeting the US DOT regulations, and the IAEA Standards for IP-1 and IP-2 including leak tightness. (authors)« less

COMPARISON OF LAPAROSCOPIC SKILLS PERFORMANCE USING SINGLE-SITE ACCESS (SSA) DEVICES VS. AN INDEPENDENT-PORT SSA APPROACH

PubMed Central

Schill, Matthew R.; Varela, J. Esteban; Frisella, Margaret M.; Brunt, L. Michael

2015-01-01

Background We compared performance of validated laparoscopic tasks on four commercially available single site access (SSA) access devices (AD) versus an independent port (IP) SSA set-up. Methods A prospective, randomized comparison of laparoscopic skills performance on four AD (GelPOINT™, SILS™ Port, SSL Access System™, TriPort™) and one IP SSA set-up was conducted. Eighteen medical students (2nd–4th year), four surgical residents, and five attending surgeons were trained to proficiency in multi-port laparoscopy using four laparoscopic drills (peg transfer, bean drop, pattern cutting, extracorporeal suturing) in a laparoscopic trainer box. Drills were then performed in random order on each IP-SSA and AD-SSA set-up using straight laparoscopic instruments. Repetitions were timed and errors recorded. Data are mean ± SD, and statistical analysis was by two-way ANOVA with Tukey HSD post-hoc tests. Results Attending surgeons had significantly faster total task times than residents or students (p< 0.001), but the difference between residents and students was NS. Pair-wise comparisons revealed significantly faster total task times for the IP-SSA set-up compared to all four AD-SSA’s within the student group only (p<0.05). Total task times for residents and attending surgeons showed a similar profile, but the differences were NS. When data for the three groups was combined, the total task time was less for the IP-SSA set-up than for each of the four AD-SSA set-ups (p < 0.001). Similarly,, the IP-SSA set-up was significantly faster than 3 of 4 AD-SSA set-ups for peg transfer, 3 of 4 for pattern cutting, and 2 of 4 for suturing. No significant differences in error rates between IP-SSA and AD-SSA set-ups were detected. Conclusions When compared to an IP-SSA laparoscopic set-up, single site access devices are associated with longer task performance times in a trainer box model, independent of level of training. Task performance was similar across different SSA devices. PMID:21993938

TRAF3IP2 mediates atherosclerotic plaque development and vulnerability in ApoE−/− mice

PubMed Central

Prasad, Sakamuri Siva Sankara Vara; Higashi, Yusuke; Sukhanov, Sergiy; Siddesha, Jalahalli M; Delafontaine, Patrice; Siebenlist, Ulrich; Chandrasekar, Bysani

2016-01-01

Background and aims Atherosclerosis is a major cause of heart attack and stroke. Inflammation plays a critical role in the development of atherosclerosis. Since the cytoplasmic adaptor molecule TRAF3IP2 (TRAF3-Interacting Protein 2) plays a causal role in various autoimmune and inflammatory diseases, we hypothesized that TRAF3IP2 mediates atherosclerotic plaque development. Methods TRAF3IP2/ApoE double knockout (DKO) mice were generated by crossing TRAF3IP2−/− and ApoE−/− mice. ApoE−/− mice served as controls. Both DKO and control mice were fed a high-fat diet for 12 weeks. Plasma lipids were measured by ELISA, atherosclerosis by en face analysis of aorta and plaque cross-section measurements at the aortic valve region, plaque necrotic core area, collagen and smooth muscle cell content by histomorphometry, and aortic gene expression by RT-qPCR. Results The plasma lipoprotein profile was not altered by TRAF3IP2 gene deletion in ApoE−/− mice. While total aortic plaque area was decreased in DKO female, but not male mice, the plaque necrotic area was significantly decreased in DKO mice of both genders. Plaque collagen and smooth muscle cell contents were increased significantly in both female and male DKO mice compared to respective controls. Aortic expression of proinflammatory cytokine (Tumor necrosis factor α, TNFα), chemokine (Chemokine (C-X-C motif) Ligand 1, CXCL1) and adhesion molecule (Vascular cell adhesion molecule 1, VCAM1; and Intercellular adhesion molecule 1, ICAM1) gene expression were decreased in both male and female DKO mice. In addition, the male DKO mice showed a markedly reduced expression of extracellular matrix (ECM)-related genes, including TIMP1 (Tissue inhibitor of metalloproteinase 1), RECK (Reversion-Inducing- Cysteine-Rich Protein with Kazal Motifs) and ADAM17 (A Disintegrin And Metalloproteinase 17). Conclusions TRAF3IP2 plays a causal role in atherosclerotic plaque development and vulnerability, possibly by inducing the expression of multiple proinflammatory mediators. TRAF3IP2 could be a potential therapeutic target in atherosclerotic vascular diseases. PMID:27237075

Pharmacokinetics of Intraperitoneal Cefalothin and Cefazolin in Patients Being Treated for Peritoneal Dialysis-Associated Peritonitis.

PubMed

Roberts, Darren M; Ranganathan, Dwarakanathan; Wallis, Steven C; Varghese, Julie M; Kark, Adrian; Lipman, Jeffrey; Roberts, Jason A

2016-01-01

♦ The standard treatment of peritoneal dialysis (PD)-associated peritonitis (PD-peritonitis) is intraperitoneal (IP) administration of antibiotics. Only limited data on the pharmacokinetics and appropriateness of contemporary dose recommendations of IP cefalothin and cefazolin exist. The aim of this study was to describe the pharmacokinetics of IP cefalothin and cefazolin in patients treated for PD-peritonitis. ♦ As per international guidelines, IP cefalothin or cefazolin 15 mg/kg once daily was dosed with gentamicin in a 6-hour dwell to patients with PD-peritonitis during routine care. Serial plasma and PD effluent samples were collected over the first 24 hours of therapy. Antibiotic concentrations were quantified using a validated chromatographic method with pharmacokinetic analysis performed using a non-compartmental approach. ♦ Nineteen patients were included (cefalothin n = 8, cefazolin n = 11). The median bioavailability for both antibiotics exceeded 92%, but other pharmacokinetic parameters varied markedly between antibiotics. Both antibiotics achieved high PD effluent concentrations throughout the antibiotic dwell. Cefazolin had a smaller volume of distribution compared with cefalothin (14 vs 40 L, p = 0.003). The median trough total plasma antibiotic concentration for cefazolin and cefalothin during the dwell differed (plasma 56 vs 13 mg/L, p < 0.0001) despite a similar concentration in PD effluent (37 vs 38 mg/L, p = 0.58). Lower antibiotic concentrations were noted during PD dwells not containing antibiotic, particularly cefalothin, which was frequently undetectable in plasma and PD effluent. The median duration that the unbound antibiotic concentration was above the minimum inhibitory concentration (MIC) was approximately 13% (plasma) and 25% (IP) for cefalothin, and 100% (plasma and IP) for cefazolin, of the dosing interval. ♦ When IP cefalothin or cefazolin is allowed to dwell for 6 hours, sufficient PD effluent concentrations are present for common pathogens during this time. However, with once-daily IP dosing, in contrast to cefazolin, there is a risk of subtherapeutic plasma and PD effluent cefalothin concentrations, so more frequent dosing may be required. Copyright © 2016 International Society for Peritoneal Dialysis.

Consumer motivation towards purchasing fruit from integrated production in Belgium.

PubMed

Vannoppen, J; Verbeke, W; Van Huylenbroeck, G

2001-01-01

Consumer concerns about food safety have been steadily growing during the last decade. Along with the recognition of the increasing power from the consumer side of food chains, this has forced agricultural producers to innovate and adapt their production methods. One of those developments is integrated production of pip fruit (IFP). This research analyses and presents motivational structures of consumers towards purchasing IP fruit in Belgium. The research methodology builds on means-end-chain (MEC) theory, with data collected through personal laddering interviews with consumers. A hierarchical value map, indicating motivational structures for farm shop purchase of IP-labelled apples, is presented. IP-apple buyers pursue typical values, with health being paramount. The findings reveal interactions between market channel characteristics and product attributes, including characteristics that refer to production methods. Also, the study shows how outlet choice influences the perception and the motivation structure of the respondents for the specific product, fresh fruit in this case. From the findings, two sets of implications are set forth. First, marketing implications pertaining to advertising through the application of the "Means-End Conceptualization of the Components of Advertising Strategy" or MECCAS model. Second, implications to producers with respect to adapting their production methods to the needs and wants of the present end consumers.

Chromatin immunoprecipitation assays: application of ChIP-on-chip for defining dynamic transcriptional mechanisms in bone cells.

PubMed

van der Deen, Margaretha; Hassan, Mohammad Q; Pratap, Jitesh; Teplyuk, Nadiya M; Young, Daniel W; Javed, Amjad; Zaidi, Sayyed K; Lian, Jane B; Montecino, Martin; Stein, Janet L; Stein, Gary S; van Wijnen, Andre J

2008-01-01

Normal cell growth and differentiation of bone cells requires the sequential expression of cell type specific genes to permit lineage specification and development of cellular phenotypes. Transcriptional activation and repression of distinct sets of genes support the anabolic functions of osteoblasts and the catabolic properties of osteoclasts. Furthermore, metastasis of tumors to the bone environment is controlled by transcriptional mechanisms. Insights into the transcriptional regulation of genes in bone cells may provide a conceptual basis for improved therapeutic approaches to treat bone fractures, genetic osteopathologies, and/or cancer metastases to bone. Chromatin immunoprecipitation (ChIP) is a powerful technique to establish in vivo binding of transcription factors to the promoters of genes that are either activated or repressed in bone cells. Combining ChIP with genomic microarray analysis, colloquially referred to as "ChIP-on-chip," has become a valuable method for analysis of endogenous protein/DNA interactions. This technique permits assessment of chromosomal binding sites for transcription factors or the location of histone modifications at a genomic scale. This chapter discusses protocols for performing chromatin immunoprecipitation experiments, with a focus on ChIP-on-chip analysis. The information presented is based on the authors' experience with defining interactions of Runt-related (RUNX) transcription factors with bone-related genes within the context of the native nucleosomal organization of intact osteoblastic cells.

Isolation of centromeric-tandem repetitive DNA sequences by chromatin affinity purification using a HaloTag7-fused centromere-specific histone H3 in tobacco.

PubMed

Nagaki, Kiyotaka; Shibata, Fukashi; Kanatani, Asaka; Kashihara, Kazunari; Murata, Minoru

2012-04-01

The centromere is a multi-functional complex comprising centromeric DNA and a number of proteins. To isolate unidentified centromeric DNA sequences, centromere-specific histone H3 variants (CENH3) and chromatin immunoprecipitation (ChIP) have been utilized in some plant species. However, anti-CENH3 antibody for ChIP must be raised in each species because of its species specificity. Production of the antibodies is time-consuming and costly, and it is not easy to produce ChIP-grade antibodies. In this study, we applied a HaloTag7-based chromatin affinity purification system to isolate centromeric DNA sequences in tobacco. This system required no specific antibody, and made it possible to apply a highly stringent wash to remove contaminated DNA. As a result, we succeeded in isolating five tandem repetitive DNA sequences in addition to the centromeric retrotransposons that were previously identified by ChIP. Three of the tandem repeats were centromere-specific sequences located on different chromosomes. These results confirm the validity of the HaloTag7-based chromatin affinity purification system as an alternative method to ChIP for isolating unknown centromeric DNA sequences. The discovery of more than two chromosome-specific centromeric DNA sequences indicates the mosaic structure of tobacco centromeres. © Springer-Verlag 2011

Effect of cytokinins on in vitro multiplication of Sophora tonkinensis

PubMed Central

Jana, Sonali; Sivanesan, Iyyakkannu; Jeong, Byoung Ryong

2013-01-01

Objective To determine the effects of different cytokinins at various concentrations on in vitro shoot multiplication of an important medicinal plant. Methods Nodal explants (1.5-2.0 cm) of Sophora tonkinensis were used. Multiple shoots were induced from nodal explants cultured on the Murashige and Skoog (MS) medium supplemented with 0.0, 0.5, 1.0, 2.0, 4.0, 8.0, or 16.0 µmol 2-isopentyladenine (2iP), N6 benzyladenine, kinetin or thiadiazuron. Results Among the four investigated cytokinins, 2iP showed the best response for shoot multiplication. Maximum shoot induction (75%) was achieved on the MS medium supplemented with 2.0 µmol 2iP, with a mean number of 5.0 shoots per explant. In comparison to other cytokinins tried, 2iP showed the highest shoot elongation with a mean shoot length of 4.8 cm. Root initiation was observed within 15 d within the transfer of shoots onto the MS basal medium, and the rooting percentage was 100% with a mean number of 5.4 roots per shoot and root length of 6.2 cm over a period of 4 weeks. The healthy plants, hardened and transferred to a greenhouse for proper acclimatization, exhibited 100% survival. Conclusions It can be summarized that 2iP is the optimal plant growth regulator for Sophora multiplication. PMID:23836310

Three-dimensional exploration of the solar wind using observations of interplanetary scintillation

PubMed Central

TOKUMARU, Munetoshi

2013-01-01

The solar wind, a supersonic plasma flow continuously emanating from the Sun, governs the space environment in a vast region extending to the boundary of the heliosphere (∼100 AU). Precise understanding of the solar wind is of importance not only because it will satisfy scientific interest in an enigmatic astrophysical phenomenon, but because it has broad impacts on relevant fields. Interplanetary scintillation (IPS) of compact radio sources at meter to centimeter wavelengths serves as a useful ground-based method for investigating the solar wind. IPS measurements of the solar wind at a frequency of 327 MHz have been carried out regularly since the 1980s using the multi-station system of the Solar-Terrestrial Environment Laboratory (STEL) of Nagoya University. This paper reviews new aspects of the solar wind revealed from our IPS observations. PMID:23391604

Spatio Temporal EEG Source Imaging with the Hierarchical Bayesian Elastic Net and Elitist Lasso Models

PubMed Central

Paz-Linares, Deirel; Vega-Hernández, Mayrim; Rojas-López, Pedro A.; Valdés-Hernández, Pedro A.; Martínez-Montes, Eduardo; Valdés-Sosa, Pedro A.

2017-01-01

The estimation of EEG generating sources constitutes an Inverse Problem (IP) in Neuroscience. This is an ill-posed problem due to the non-uniqueness of the solution and regularization or prior information is needed to undertake Electrophysiology Source Imaging. Structured Sparsity priors can be attained through combinations of (L1 norm-based) and (L2 norm-based) constraints such as the Elastic Net (ENET) and Elitist Lasso (ELASSO) models. The former model is used to find solutions with a small number of smooth nonzero patches, while the latter imposes different degrees of sparsity simultaneously along different dimensions of the spatio-temporal matrix solutions. Both models have been addressed within the penalized regression approach, where the regularization parameters are selected heuristically, leading usually to non-optimal and computationally expensive solutions. The existing Bayesian formulation of ENET allows hyperparameter learning, but using the computationally intensive Monte Carlo/Expectation Maximization methods, which makes impractical its application to the EEG IP. While the ELASSO have not been considered before into the Bayesian context. In this work, we attempt to solve the EEG IP using a Bayesian framework for ENET and ELASSO models. We propose a Structured Sparse Bayesian Learning algorithm based on combining the Empirical Bayes and the iterative coordinate descent procedures to estimate both the parameters and hyperparameters. Using realistic simulations and avoiding the inverse crime we illustrate that our methods are able to recover complicated source setups more accurately and with a more robust estimation of the hyperparameters and behavior under different sparsity scenarios than classical LORETA, ENET and LASSO Fusion solutions. We also solve the EEG IP using data from a visual attention experiment, finding more interpretable neurophysiological patterns with our methods. The Matlab codes used in this work, including Simulations, Methods, Quality Measures and Visualization Routines are freely available in a public website. PMID:29200994

Spatio Temporal EEG Source Imaging with the Hierarchical Bayesian Elastic Net and Elitist Lasso Models.

PubMed

Paz-Linares, Deirel; Vega-Hernández, Mayrim; Rojas-López, Pedro A; Valdés-Hernández, Pedro A; Martínez-Montes, Eduardo; Valdés-Sosa, Pedro A

2017-01-01

The estimation of EEG generating sources constitutes an Inverse Problem (IP) in Neuroscience. This is an ill-posed problem due to the non-uniqueness of the solution and regularization or prior information is needed to undertake Electrophysiology Source Imaging. Structured Sparsity priors can be attained through combinations of (L1 norm-based) and (L2 norm-based) constraints such as the Elastic Net (ENET) and Elitist Lasso (ELASSO) models. The former model is used to find solutions with a small number of smooth nonzero patches, while the latter imposes different degrees of sparsity simultaneously along different dimensions of the spatio-temporal matrix solutions. Both models have been addressed within the penalized regression approach, where the regularization parameters are selected heuristically, leading usually to non-optimal and computationally expensive solutions. The existing Bayesian formulation of ENET allows hyperparameter learning, but using the computationally intensive Monte Carlo/Expectation Maximization methods, which makes impractical its application to the EEG IP. While the ELASSO have not been considered before into the Bayesian context. In this work, we attempt to solve the EEG IP using a Bayesian framework for ENET and ELASSO models. We propose a Structured Sparse Bayesian Learning algorithm based on combining the Empirical Bayes and the iterative coordinate descent procedures to estimate both the parameters and hyperparameters. Using realistic simulations and avoiding the inverse crime we illustrate that our methods are able to recover complicated source setups more accurately and with a more robust estimation of the hyperparameters and behavior under different sparsity scenarios than classical LORETA, ENET and LASSO Fusion solutions. We also solve the EEG IP using data from a visual attention experiment, finding more interpretable neurophysiological patterns with our methods. The Matlab codes used in this work, including Simulations, Methods, Quality Measures and Visualization Routines are freely available in a public website.

IP3-mediated gating mechanism of the IP3 receptor revealed by mutagenesis and X-ray crystallography

PubMed Central

Hamada, Kozo; Miyatake, Hideyuki; Terauchi, Akiko; Mikoshiba, Katsuhiko

2017-01-01

The inositol 1,4,5-trisphosphate (IP3) receptor (IP3R) is an IP3-gated ion channel that releases calcium ions (Ca2+) from the endoplasmic reticulum. The IP3-binding sites in the large cytosolic domain are distant from the Ca2+ conducting pore, and the allosteric mechanism of how IP3 opens the Ca2+ channel remains elusive. Here, we identify a long-range gating mechanism uncovered by channel mutagenesis and X-ray crystallography of the large cytosolic domain of mouse type 1 IP3R in the absence and presence of IP3. Analyses of two distinct space group crystals uncovered an IP3-dependent global translocation of the curvature α-helical domain interfacing with the cytosolic and channel domains. Mutagenesis of the IP3R channel revealed an essential role of a leaflet structure in the α-helical domain. These results suggest that the curvature α-helical domain relays IP3-controlled global conformational dynamics to the channel through the leaflet, conferring long-range allosteric coupling from IP3 binding to the Ca2+ channel. PMID:28416699

N-terminal pro-brain-type natriuretic peptide (NT-pro-BNP) and mortality risk in early inflammatory polyarthritis: results from the Norfolk Arthritis Registry (NOAR)

PubMed Central

Mirjafari, Hoda; Welsh, Paul; Verstappen, Suzanne M M; Wilson, Paddy; Marshall, Tarnya; Edlin, Helena; Bunn, Diane; Chipping, Jacqueline; Lunt, Mark; Symmons, Deborah P M; Sattar, Naveed; Bruce, Ian N

2014-01-01

Background We measured N-terminal pro-brain natriuretic peptide (NT-pro-BNP), a marker of cardiac dysfunction, in an inception cohort with early inflammatory polyarthritis (IP) and assessed its association with disease phenotype, cardiovascular disease (CVD), all-cause and CVD related mortality. Methods Subjects with early IP were recruited to the Norfolk Arthritis Register from January 2000 to December 2008 and followed up to death or until March 2010 including any data from the national death register. The associations of baseline NT-pro-BNP with IP related factors and CVD were assessed by linear regression. Cox proportional hazards models examined the independent association of baseline NT-pro-BNP with all-cause and CVD mortality. Results We studied 960 early IP subjects; 163 (17%) had prior CVD. 373 (39%) patients had a baseline NT-pro-BNP levels ≥100 pg/ml. NT-pro-BNP was associated with age, female gender, HAQ score, CRP, current smoking, history of hypertension, prior CVD and the presence of carotid plaque. 92 (10%) IP subjects died including 31 (3%) from CVD. In an age and gender adjusted analysis, having a raised NT-pro-BNP level (≥100 pg/ml) was associated with both all-cause and CVD mortality (adjusted HR (95% CI) 2.36 (1.42 to 3.94) and 3.40 (1.28 to 9.03), respectively). These findings were robust to adjustment for conventional CVD risk factors and prevalent CVD. Conclusions In early IP patients, elevated NT-pro-BNP is related to HAQ and CRP and predicts all-cause and CVD mortality independently of conventional CVD risk factors. Further study is required to identify whether NT-pro-BNP may be clinically useful in targeting intensive interventions to IP patients at greatest risk of CVD. PMID:23511225

Generation of Healthy Mice from Gene-Corrected Disease-Specific Induced Pluripotent Stem Cells

PubMed Central

Rittelmeyer, Ina; Sharma, Amar Deep; Sgodda, Malte; Zaehres, Holm; Bleidißel, Martina; Greber, Boris; Gentile, Luca; Han, Dong Wook; Rudolph, Cornelia; Steinemann, Doris; Schambach, Axel; Ott, Michael; Schöler, Hans R.; Cantz, Tobias

2011-01-01

Using the murine model of tyrosinemia type 1 (fumarylacetoacetate hydrolase [FAH] deficiency; FAH −/− mice) as a paradigm for orphan disorders, such as hereditary metabolic liver diseases, we evaluated fibroblast-derived FAH −/−-induced pluripotent stem cells (iPS cells) as targets for gene correction in combination with the tetraploid embryo complementation method. First, after characterizing the FAH −/− iPS cell lines, we aggregated FAH −/−-iPS cells with tetraploid embryos and obtained entirely FAH −/−-iPS cell–derived mice that were viable and exhibited the phenotype of the founding FAH −/− mice. Then, we transduced FAH cDNA into the FAH −/−-iPS cells using a third-generation lentiviral vector to generate gene-corrected iPS cells. We could not detect any chromosomal alterations in these cells by high-resolution array CGH analysis, and after their aggregation with tetraploid embryos, we obtained fully iPS cell–derived healthy mice with an astonishing high efficiency for full-term development of up to 63.3%. The gene correction was validated functionally by the long-term survival and expansion of FAH-positive cells of these mice after withdrawal of the rescuing drug NTBC (2-(2-nitro-4-fluoromethylbenzoyl)-1,3-cyclohexanedione). Furthermore, our results demonstrate that both a liver-specific promoter (transthyretin, TTR)-driven FAH transgene and a strong viral promoter (from spleen focus-forming virus, SFFV)-driven FAH transgene rescued the FAH-deficiency phenotypes in the mice derived from the respective gene-corrected iPS cells. In conclusion, our data demonstrate that a lentiviral gene repair strategy does not abrogate the full pluripotent potential of fibroblast-derived iPS cells, and genetic manipulation of iPS cells in combination with tetraploid embryo aggregation provides a practical and rapid approach to evaluate the efficacy of gene correction of human diseases in mouse models. PMID:21765802

North Atlantic Oscillation and moisture transport towards the Iberian Peninsula during winter

NASA Astrophysics Data System (ADS)

Ordóñez, Paulina; Liberato, Margarida L. R.; Gouveia, Célia; Trigo, Ricardo M.

2013-04-01

The North Atlantic Oscillation (NAO) is the major source of interannual variability in winter precipitation over the Iberian Peninsula (IP). Recent works have identified the most important sources of moisture that supply the IP during different seasons of the year, including the nearby western Mediterranean and the tropical-subtropical North Atlantic corridor that extends from the Gulf of Mexico to the IP, and the IP itself (Gimeno et al., 2010). However, although rainfall is directly related to the moisture supply, the relationship between the water vapor transported towards IP and the NAO phase remains unclear. In this work the moisture transport towards IP was analyzed using a Lagrangian diagnosis method, which relies on the Lagrangian particle dispersion model FLEXPART. This methodology computes budgets of evaporation minus precipitation (E-P) by evaluating changes in the specific humidity along back-trajectories. Here we have computed (for each day) the evolution of moisture of the particles bound for Iberia up to 10 days prior to their arrival. The analysis was constrained to the winter (DJF) season, responsible for the largest fraction of precipitation, for the 20 years of ECMWF Reanalyses ERA40 dataset from 1980 to 2000. The contribution of the NAO phase on the water budgets is examined using composites of the obtained (E - P) fields for the 5 most extreme positive and negative NAO years of the study period. Results confirm that the IP is dominated by positive (negative) E-P anomalies during positive (negative) NAO phase. Additionally an anomalous water vapor sink (source) region located approximately over the Gulf Stream is found during positive (negative) NAO phase. Gimeno L., Nieto R., Trigo R.M. , Vicente-Serrano S.M, Lopes-Moreno J.I., (2010) "Where does the Iberian Peninsula moisture come from? An answer based on a Lagrangian approach". J. Hydrometeorology, 11, 421-436 DOI: 10.1175/2009JHM1182.1.

Effect of Withania somnifera on forced swimming test induced immobility in mice and its interaction with various drugs.

PubMed

Shah, P C; Trivedi, N A; Bhatt, J D; Hemavathi, K G

2006-01-01

The objective of the present study was to evaluate the antidepressant action of Withania somnifera (WS) as well as its interaction with the conventional antidepressant drugs and to delineate the possible mechanism of its antidepressant action using forced swimming model in mice. Effect of different doses of WS, fluoxetine and imipramine were studied on forced swimming test induced mean immobility time (MIT). Moreover effect of WS 100 mg/kg, i.p. was observed at different time intervals. Effect produced by combination of sub therapeutic doses of WS with imipramine (2.5 mg/kg, i.p.) as well as fluoxetine (2.5 mg/kg, i.p.) were also observed. Effect of WS (100 mg/kg, i.p.) as well as combination of WS (37.5 mg/kg, i.p.) with either imipramine (2.5 mg/kg, i.p.) or fluoxetine (2.5 mg/kg, i.p.) were observed in mice pretreated with reserpine (2 mg/kg, i.p.) and clonidine (0.15 mg/kg, i.p.). Effects of prazosin (3 mg/kg, i.p.) or haloperidol (0.1 mg/kg, i.p.) pre-treatment were also observed on WS induced decrease in MIT. WS produced dose dependent decrease in MIT. Maximum effect in MIT was observed after 30 min of treatment with WS 100 mg/kg, i.p. Combination of WS (37.5 mg/kg, i.p.) with imipramine (2.5 mg/kg, i.p.) or fluoxetine (2.5 mg/kg, i.p.) also produced significant decrease in the MIT. Clonidine and reserpine induced increase in MIT, was significantly reversed by treatment with WS (100 mg/kg, i.p.) as well as combination of WS (37.5 mg/kg, i.p.) with either imipramine (2.5 mg/kg, i.p.) or fluoxetine (2.5 mg/kg, i.p.). Pre-treatment with prazosin but not haloperidol, significantly antagonized the WS (100 mg/kg, i.p.) induced decrease in MIT. It is concluded that, WS produced significant decrease in MIT in mice which could be mediated partly through a adrenoceptor as well as alteration in the level of central biogenic amines.

Potassium Channel Interacting Protein 2 (KChIP2) is not a transcriptional regulator of cardiac electrical remodeling

PubMed Central

Winther, Sine V.; Tuomainen, Tomi; Borup, Rehannah; Tavi, Pasi; Antoons, Gudrun; Thomsen, Morten B.

2016-01-01

The heart-failure relevant Potassium Channel Interacting Protein 2 (KChIP2) augments CaV1.2 and KV4.3. KChIP3 represses CaV1.2 transcription in cardiomyocytes via interaction with regulatory DNA elements. Hence, we tested nuclear presence of KChIP2 and if KChIP2 translocates into the nucleus in a Ca2+ dependent manner. Cardiac biopsies from human heart-failure patients and healthy donor controls showed that nuclear KChIP2 abundance was significantly increased in heart failure; however, this was secondary to a large variation of total KChIP2 content. Administration of ouabain did not increase KChIP2 content in nuclear protein fractions in anesthetized mice. KChIP2 was expressed in cell lines, and Ca2+ ionophores were applied in a concentration- and time-dependent manner. The cell lines had KChIP2-immunoreactive protein in the nucleus in the absence of treatments to modulate intracellular Ca2+ concentration. Neither increasing nor decreasing intracellular Ca2+ concentrations caused translocation of KChIP2. Microarray analysis did not identify relief of transcriptional repression in murine KChIP2−/− heart samples. We conclude that although there is a baseline presence of KChIP2 in the nucleus both in vivo and in vitro, KChIP2 does not directly regulate transcriptional activity. Moreover, the nuclear transport of KChIP2 is not dependent on Ca2+. Thus, KChIP2 does not function as a conventional transcription factor in the heart. PMID:27349185

One Approach for Transitioning the iNET Standards into the IRIG 106 Telemetry Standards

DTIC Science & Technology

2015-05-26

Protocol Suite. Figure 1 illustrates the Open Systems Interconnection ( OSI ) Model, the corresponding TCP/IP Model, and the major components of the TCP...IP Protocol Suite. Figure 2 represents the iNET-specific protocols layered onto the TCP/IP Model. Figure 1. OSI and TCP/IP Model with TCP/IP...Protocol Suite TCP/IP Protocol Suite Major Components IPv4 IPv6 TCP/IP Model OSI Model Application Presentation

Attraction of Southern Pine Engravers and Associated Bark Beetles (Coleoptera: Scolytidae) to Ipsenol, Ipsdienol, and Lanierone in Southeastern United States

Treesearch

D. R. Miller; C. Asaro; C. W. Berisford

2005-01-01

We determined the response of the small southern pine engraver, Ips avulses (Eichhoff); eastern fivespined ips, Ips grandicollis (Eichhoff); sixspined ips, Ips calligraphus (Germar); and pine engraver, Ips pini (Say) to the pheromones (±)-ipsenol, (±)-ipsdienol, and lanierone in the...

78 FR 49693 - Speech-to-Speech and Internet Protocol (IP) Speech-to-Speech Telecommunications Relay Services...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-15

...] Speech-to-Speech and Internet Protocol (IP) Speech-to-Speech Telecommunications Relay Services...: This is a summary of the Commission's Speech-to-Speech and Internet Protocol (IP) Speech-to-Speech...), Internet Protocol Relay (IP Relay), and IP captioned telephone service (IP CTS) as compensable forms of TRS...

Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data

PubMed Central

Carroll, Thomas S.; Liang, Ziwei; Salama, Rafik; Stark, Rory; de Santiago, Ines

2014-01-01

With the advent of ChIP-seq multiplexing technologies and the subsequent increase in ChIP-seq throughput, the development of working standards for the quality assessment of ChIP-seq studies has received significant attention. The ENCODE consortium's large scale analysis of transcription factor binding and epigenetic marks as well as concordant work on ChIP-seq by other laboratories has established a new generation of ChIP-seq quality control measures. The use of these metrics alongside common processing steps has however not been evaluated. In this study, we investigate the effects of blacklisting and removal of duplicated reads on established metrics of ChIP-seq quality and show that the interpretation of these metrics is highly dependent on the ChIP-seq preprocessing steps applied. Further to this we perform the first investigation of the use of these metrics for ChIP-exo data and make recommendations for the adaptation of the NSC statistic to allow for the assessment of ChIP-exo efficiency. PMID:24782889

Inositol trisphosphate metabolism in carrot (Daucus carota L. ) cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Memon, A.R.; Rincon, M.; Boss, W.F.

1989-10-01

The metabolism of exogenously added D-myo-(1-{sup 3}H)inositol 1,4,5-trisphosphate (IP{sub 3}) has been examined in microsomal membrane and soluble fractions of carrot cells grown in suspension culture. When ({sup 3}H)IP{sub 3} was added to a microsomal membrane fraction, ({sup 3}H)IP{sub 2} was the primary metabolite consisting of approximately 83% of the total recovered ({sup 3}H) by electrophoresis. ({sup 3}H)IP was only 6% of the ({sup 3}H) recovered, and 10% of the ({sup 3}H)IP{sub 3} was not further metabolized. In contrast, when ({sup 3}H)IP{sub 3} was added to the soluble fraction, approximately equal amounts of ({sup 3}H)IP{sub 2} and ({sup 3}H)IP weremore » recovered. Ca{sup 2+} (100 micromolar) tended to enhance IP{sub 3} dephosphorylation but inhibited the IP{sub 2} dephosphorylation in the soluble fraction by about 20%. MoO{sub 4}{sup 2{minus}} (1 millimolar) inhibited the dephosphorylation of IP{sub 3} by the microsomal fraction and the dephosphorylation of IP{sub 2} by the soluble fraction. MoO{sub 4}{sup 2{minus}}, however, did not inhibit the dephosphorylation of IP{sub 3} by the soluble fraction. Li{sup +} (10 and 50 millimolar) had no effect on IP{sub 3} metabolism in either the soluble or membrane fraction; however, Li{sup +} (50 millimolar) inhibited IP{sub 2} dephosphorylation in the soluble fraction about 25%.« less

Stimulation of Inositol 1,4,5-Trisphosphate (IP3) Receptor Subtypes by Adenophostin A and Its Analogues

PubMed Central

Saleem, Huma; Tovey, Stephen C.; Riley, Andrew M.; Potter, Barry V. L.; Taylor, Colin W.

2013-01-01

Inositol 1,4,5-trisphosphate receptors (IP3R) are intracellular Ca2+ channels. Most animal cells express mixtures of the three IP3R subtypes encoded by vertebrate genomes. Adenophostin A (AdA) is the most potent naturally occurring agonist of IP3R and it shares with IP3 the essential features of all IP3R agonists, namely structures equivalent to the 4,5-bisphosphate and 6-hydroxyl of IP3. The two essential phosphate groups contribute to closure of the clam-like IP3-binding core (IBC), and thereby IP3R activation, by binding to each of its sides (the α- and β-domains). Regulation of the three subtypes of IP3R by AdA and its analogues has not been examined in cells expressing defined homogenous populations of IP3R. We measured Ca2+ release evoked by synthetic adenophostin A (AdA) and its analogues in permeabilized DT40 cells devoid of native IP3R and stably expressing single subtypes of mammalian IP3R. The determinants of high-affinity binding of AdA and its analogues were indistinguishable for each IP3R subtype. The results are consistent with a cation-π interaction between the adenine of AdA and a conserved arginine within the IBC α-domain contributing to closure of the IBC. The two complementary contacts between AdA and the α-domain (cation-π interaction and 3″-phosphate) allow activation of IP3R by an analogue of AdA (3″-dephospho-AdA) that lacks a phosphate group equivalent to the essential 5-phosphate of IP3. These data provide the first structure-activity analyses of key AdA analogues using homogenous populations of all mammalian IP3R subtypes. They demonstrate that differences in the Ca2+ signals evoked by AdA analogues are unlikely to be due to selective regulation of IP3R subtypes. PMID:23469136

Biomonitoring the cooked meat carcinogen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine in hair: impact of exposure, hair pigmentation, and cytochrome P450 1A2 phenotype.

PubMed

Turesky, Robert J; Liu, Lin; Gu, Dan; Yonemori, Kim M; White, Kami K; Wilkens, Lynne R; Le Marchand, Loïc

2013-03-01

Hair is a promising tissue to assess exposure to 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), a carcinogen formed in cooked meats. However, an understanding of how dietary exposure to PhIP, cytochrome P450 1A2 activity-a key enzyme involved in PhIP metabolism, and hair pigmentation affect the level of PhIP accrued in hair is required to determine the reliability of the PhIP hair level as a biomarker of exposure to this carcinogen. We examined the impact of PhIP exposure, cytochrome P450 1A2 activity, and hair pigmentation on the levels of PhIP accumulated in the hair of volunteers on a 4-week semicontrolled diet of cooked meat containing known quantities of PhIP. The amount of PhIP in hair increased, on average, 15-fold in light- and dark-haired individuals during consumption of cooked meat. PhIP levels in hair were correlated to PhIP intake (ρ = 0.53; P < 0.001), and the relationship was strengthened when PhIP levels were normalized for the melanin content of hair (ρ = 0.71; P < 0.001). However, PhIP accrual in hair was not correlated to cytochrome P450 1A2 activity, as assessed by the caffeine test, or to the levels of unmetabolized PhIP in urine or to the metabolic ratio of the major urinary metabolite N(2)-(β-1-glucosiduronyl-2-(hydroxyamino)-1-methyl-6-phenylimidazo[4,5-b]pyridine to unmetabolized PhIP. The use of the PhIP hair biomarker should take hair pigmentation into account for accurate exposure assessment of PhIP. PhIP hair levels can serve as a biomarker in epidemiologic studies investigating the association of heterocyclic aromatic amine (HAA), cooked meat, and cancer risk.

Repliscan: a tool for classifying replication timing regions.

PubMed

Zynda, Gregory J; Song, Jawon; Concia, Lorenzo; Wear, Emily E; Hanley-Bowdoin, Linda; Thompson, William F; Vaughn, Matthew W

2017-08-07

Replication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density, and possible results make traditional ChIP-Seq analysis methods inappropriate for use with replication timing. To accurately detect and classify regions of replication across the genome, we present Repliscan. Repliscan robustly normalizes, automatically removes outlying and uninformative data points, and classifies Repli-seq signals into discrete combinations of replication signatures. The quality control steps and self-fitting methods make Repliscan generally applicable and more robust than previous methods that classify regions based on thresholds. Repliscan is simple and effective to use on organisms with different genome sizes. Even with analysis window sizes as small as 1 kilobase, reliable profiles can be generated with as little as 2.4x coverage.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sutherland, John C.

In this article, a method for obtaining fluorescence polarization data from an instrument designed to measure circular and linear dichroism is compared with a previously reported approach. The new method places a polarizer between the sample and a detector mounted perpendicular to the direction of the incident beam and results in determination of the fluorescence polarization ratio, whereas the previous method does not use a polarizer and yields the fluorescence anisotropy. A similar analysis with the detector located axially with the excitation beam demonstrates that there is no frequency modulated signal due to fluorescence polarization in the absence of amore » polarizer.« less

Study on polarization image methods in turbid medium

NASA Astrophysics Data System (ADS)

Fu, Qiang; Mo, Chunhe; Liu, Boyu; Duan, Jin; Zhang, Su; Zhu, Yong

2014-11-01

Polarization imaging detection technology in addition to the traditional imaging information, also can get polarization multi-dimensional information, thus improve the probability of target detection and recognition.Image fusion in turbid medium target polarization image research, is helpful to obtain high quality images. Based on visible light wavelength of light wavelength of laser polarization imaging, through the rotation Angle of polaroid get corresponding linear polarized light intensity, respectively to obtain the concentration range from 5% to 10% of turbid medium target stocks of polarization parameters, introduces the processing of image fusion technology, main research on access to the polarization of the image by using different polarization image fusion methods for image processing, discusses several kinds of turbid medium has superior performance of polarization image fusion method, and gives the treatment effect and analysis of data tables. Then use pixel level, feature level and decision level fusion algorithm on three levels of information fusion, DOLP polarization image fusion, the results show that: with the increase of the polarization Angle, polarization image will be more and more fuzzy, quality worse and worse. Than a single fused image contrast of the image be improved obviously, the finally analysis on reasons of the increase the image contrast and polarized light.

Curcumin modifies Apc(min) apoptosis resistance and inhibits 2-amino 1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) induced tumour formation in Apc(min) mice.

PubMed

Collett, G P; Robson, C N; Mathers, J C; Campbell, F C

2001-05-01

Curcumin, the active ingredient of the rhizome of Curcuma longa, promotes apoptosis and may have chemopreventive properties. This study investigates the effects of curcumin on apoptosis and tumorigenesis in male Apc(min) mice treated with the human dietary carcinogen, 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP). Intestinal epithelial apoptotic index in response to PhIP treatment was approximately twice as great in the wild-type C57BL/6 APC(+/+) strain than in Apc(min) mice (3.7% Apc(+/+) versus 1.9% Apc(min); P < 0.001). PhIP promoted tumour formation in Apc(min) proximal small intestine (4.6 tumours per mouse, PhIP treated versus 2.1 tumours per mouse, control untreated; P < 0.05). Curcumin enhanced PhIP-induced apoptosis (4.0% curcumin + PhIP versus 2.1% PhIP alone; P < 0.01) and inhibited PhIP-induced tumorigenesis in the proximal small intestine of Apc(min) mice (2.2 tumours per mouse, curcumin + PhIP versus 4.6 tumours per mouse PhIP alone; P < 0.05). This study shows that the Apc(min) genotype is associated with resistance to PhIP-induced apoptosis in intestinal epithelium. Curcumin attenuates Apc(min) resistance to PhIP-induced apoptosis and inhibits PhIP-induced tumorigenesis in proximal Apc(min) mouse small intestine.

Resonant Polarization Spectroscopy for Hot X-ray Plasmas

DOE PAGES

Chen, Guo -Xin

2016-04-28

X-ray line polarization spectroscopy is a method of choice for probing hot plasma conditions. The precise roles of resonant structures in this method have not been realized and fully understood. With a sophisticated relativistic close coupling Dirac R-matrix calculation of polarized radiation of the quadrupole magnetic M2 line at 2.717 Å in Ba 46+, we revealed the nature of resonant structures in x-ray line polarization spectroscopy. We found that signatures with a heavy resonance forest imprinting on polarization may be used for a sensitive new spectroscopic method. The resonant polarization spectrum was used to determine or constrain the directional beammore » electron distribution of the laboratory Ba plasma. Lastly, our results provide a start of resonant polarization spectroscopy as a method for diagnostics of laboratory, fusion and astrophysical plasma source conditions.« less

Determination of priority among air pollution factors in preventing COPD in residents of Shanghai City proper

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xuguang, Tao; Chuan-jie, Hong; Shun-zhang, Yu

The purpose of our study is to determine the priority among ambient sulphur dioxide (SO{sub 2}), inhalable particulates (IP), and indoor use of coal for cooking or heating to prevent COPD in residents of Shanghai city proper. We describe spatial and temporal distribution of the concentration of ambient SO{sub 2}, IP, and the proportion of families who use coal (1980-1985) by the trend surface simulating method and other statistics. Stratified by two sets of extreme levels of ambient SO{sub 2}, IP, and the proportion of coal-using families, we selected eight groups with different combinations of exposure levels. We analyzed themore » relationship between air pollution factors and their health effects at levels of mortality (1978-1987, 232,459 person years), prevalence (1987, 12,037 persons), lung function and local immunologic function (1987, 514 women) with logistic and stepwise regression, and ridit analysis. After controlling for possible confounders, e.g., tobacco smoking and occupational exposure, we found that indoor use of coal is a more important risk factor than ambient SO{sub 2} and IP. We then used canonical correlation analysis to evaluate the overall exposure-effect relationship between one set of air pollution and confounding factors and the other set of health effect indices. High correlation is found between the two. The indoor use of coal is more important for the overall health effects than the ambient SO{sub 2} and IP, to change from coal to gas could reduce the environmental exposure canonical variable more readily, with an effect equivalent to a reduction of 0.1839 mg/m{sup 3} for ambient SO{sub 2}, or 0.2806 mg/m{sup 3} for ambient IP in concentration.« less

Probing ionization potential, electron affinity and self-energy effect on the spectral shape and exciton binding energy of quantum liquid water with self-consistent many-body perturbation theory and the Bethe-Salpeter equation.

PubMed

Ziaei, Vafa; Bredow, Thomas

2018-05-31

An accurate theoretical prediction of ionization potential (IP) and electron affinity (EA) is key in understanding complex photochemical processes in aqueous environments. There have been numerous efforts in literature to accurately predict IP and EA of liquid water, however with often conflicting results depending on the level of theory and the underlying water structures. In a recent study based on hybrid-non-self-consistent many-body perturbation theory (MBPT) Gaiduk et al (2018 Nat. Commun. 9 247) predicted an IP of 10.2 eV and EA of 0.2 eV, resulting in an electronic band gap (i.e. electronic gap (IP-EA) as measured by photoelectron spectroscopy) of about 10 eV, redefining the widely cited experimental gap of 8.7 eV in literature. In the present work, we show that GW self-consistency and an implicit vertex correction in MBPT considerably affect recently reported EA values by Gaiduk et al (2018 Nat. Commun. 9 247) by about 1 eV. Furthermore, the choice of pseudo-potential is critical for an accurate determination of the absolute band positions. Consequently, the self-consistent GW approach with an implicit vertex correction based on projector augmented wave (PAW) method on top of quantum water structures predicts an IP of 10.2, an EA of 1.1, a fundamental gap of 9.1 eV and an exciton binding (Eb) energy of 0.9 eV for the first absorption band of liquid water via the Bethe-Salpeter equation (BSE). Only within such a self-consistent approach a simultanously accurate prediction of IP, EA, Eg, Eb is possible.

Post-fatigue fracture resistance of metal core crowns: press-on metal ceramic versus a conventional veneering system

PubMed Central

Agustín-Panadero, Rubén; Campos-Estellés, Carlos; Labaig-Rueda, Carlos

2015-01-01

Background The aim of this in vitro study was to compare the mechanical failure behavior and to analyze fracture characteristics of metal ceramic crowns with two veneering systems – press-on metal (PoM) ceramic versus a conventional veneering system – subjected to static compressive loading. Material and Methods Forty-six crowns were constructed and divided into two groups according to porcelain veneer manufacture. Group A: 23 metal copings with porcelain IPS-InLine veneering (conventional metal ceramic). Group B: 23 metal copings with IPS-InLine PoM veneering porcelain. After 120,000 fatigue cycles, the crowns were axially loaded to the moment of fracture with a universal testing machine. The fractured specimens were examined under optical stereomicroscopy and scanning electron microscope. Results Fracture resistance values showed statistically significant differences (Student’s t-test) regarding the type of ceramic veneering technique (p=0.001): Group A (conventional metal ceramics) obtained a mean fracture resistance of 1933.17 N, and Group B 1325.74N (Press-on metal ceramics). The most common type of fracture was adhesive failure (with metal exposure) (p=0.000). Veneer porcelain fractured on the occlusal surface following a radial pattern. Conclusions Metal ceramic crowns made of IPS InLine or IPS InLine PoM ceramics with different laboratory techniques all achieved above-average values for clinical survival in the oral environment according to ISO 6872. Crowns made with IPS InLine by conventional technique resisted fracture an average of 45% more than IPS InLine PoM fabricated with the press-on technique. Key words:Mechanical failure, conventional feldspathic, pressable ceramic, chewing simulator, thermocycling, compressive testing, fracture types, scanning electron microscope. PMID:26155346

Probing ionization potential, electron affinity and self-energy effect on the spectral shape and exciton binding energy of quantum liquid water with self-consistent many-body perturbation theory and the Bethe–Salpeter equation

NASA Astrophysics Data System (ADS)

Ziaei, Vafa; Bredow, Thomas

2018-05-01

An accurate theoretical prediction of ionization potential (IP) and electron affinity (EA) is key in understanding complex photochemical processes in aqueous environments. There have been numerous efforts in literature to accurately predict IP and EA of liquid water, however with often conflicting results depending on the level of theory and the underlying water structures. In a recent study based on hybrid-non-self-consistent many-body perturbation theory (MBPT) Gaiduk et al (2018 Nat. Commun. 9 247) predicted an IP of 10.2 eV and EA of 0.2 eV, resulting in an electronic band gap (i.e. electronic gap (IP-EA) as measured by photoelectron spectroscopy) of about 10 eV, redefining the widely cited experimental gap of 8.7 eV in literature. In the present work, we show that GW self-consistency and an implicit vertex correction in MBPT considerably affect recently reported EA values by Gaiduk et al (2018 Nat. Commun. 9 247) by about 1 eV. Furthermore, the choice of pseudo-potential is critical for an accurate determination of the absolute band positions. Consequently, the self-consistent GW approach with an implicit vertex correction based on projector augmented wave (PAW) method on top of quantum water structures predicts an IP of 10.2, an EA of 1.1, a fundamental gap of 9.1 eV and an exciton binding (Eb) energy of 0.9 eV for the first absorption band of liquid water via the Bethe–Salpeter equation (BSE). Only within such a self-consistent approach a simultanously accurate prediction of IP, EA, Eg, Eb is possible.

[Chromatic study of all-ceramic crown--IPS Empress: difference of color by manufacturing technique and cements].

PubMed

Hata, Utako; Sadamitsu, Kenichiro; Yamamura, Osamu; Kawauchi, Daisuke; Fujii, Teruhisa

2004-12-01

In recent years,aesthetic appearance and function are called for and all-ceramic crowns are spreading. By choosing an all-ceramic crown the problem of metal ceramics is avoided. There are difficulties of color tone reproducibility of cervical margin and darkness of gingival margin. We examined IPS Empress also in various all-ceramic crowns. IPS Empress has high permeability a ceramic ingot of various color tones and excellent color tone reproducibility of natural teeth. Generally a layering technique is used for an anterior tooth and the staining technique is used for a molar. However the details are unknown We examined how differences of manufacturing method and cement affect the color tone of all ceramics clinically. Two kinds of Empress crown were fabricated for a 27 year-old woman's upper left-side central incisors:the staining technique of IPS Empress and the layering technique of IPS Empress II. Various try-in pastes(transparent opaque white white and yellow) of VariolinkII of the IPS Empress System were used for cementing. Color was measured using a spectrophotometer CMS 35FS. The L*a*b* color system was used for showing a color. The right-side central incisors on the opposite side of the same name teeth were used for comparison. We analyzed the color difference (DeltaE* ab)with a natural tooth. Consequently when it had no cement of staining technique and was tranceparent small values were obtained. It is considered that the color tone can be adjusted by color cement. It is effective to use the staining technique for an anterior tooth crown depending on the case. The crown manufactured using the layering technique is not easily influenced by cement. The crown manufactured by the staining technique tends to be influenced by cement.

Validating a conceptual model for an inter-professional approach to shared decision making: a mixed methods study.

PubMed

Légaré, France; Stacey, Dawn; Gagnon, Susie; Dunn, Sandy; Pluye, Pierre; Frosch, Dominick; Kryworuchko, Jennifer; Elwyn, Glyn; Gagnon, Marie-Pierre; Graham, Ian D

2011-08-01

Following increased interest in having inter-professional (IP) health care teams engage patients in decision making, we developed a conceptual model for an IP approach to shared decision making (SDM) in primary care. We assessed the validity of the model with stakeholders in Canada. In 15 individual interviews and 7 group interviews with 79 stakeholders, we asked them to: (1) propose changes to the IP-SDM model; (2) identify barriers and facilitators to the model's implementation in clinical practice; and (3) assess the model using a theory appraisal questionnaire. We performed a thematic analysis of the transcripts and a descriptive analysis of the questionnaires. Stakeholders suggested placing the patient at its centre; extending the concept of family to include significant others; clarifying outcomes; highlighting the concept of time; merging the micro, meso and macro levels in one figure; and recognizing the influence of the environment and emotions. The most common barriers identified were time constraints, insufficient resources and an imbalance of power among health professionals. The most common facilitators were education and training in inter-professionalism and SDM, motivation to achieve an IP approach to SDM, and mutual knowledge and understanding of disciplinary roles. Most stakeholders considered that the concepts and relationships between the concepts were clear and rated the model as logical, testable, having clear schematic representation, and being relevant to inter-professional collaboration, SDM and primary care. Stakeholders validated the new IP-SDM model for primary care settings and proposed few modifications. Future research should assess if the model helps implement SDM in IP clinical practice. © 2010 Blackwell Publishing Ltd.

The molecular products and biogeochemical significance of lipid photooxidation in West Antarctic surface waters

NASA Astrophysics Data System (ADS)

Collins, James R.; Fredricks, Helen F.; Bowman, Jeff S.; Ward, Collin P.; Moreno, Carly; Longnecker, Krista; Marchetti, Adrian; Hansel, Colleen M.; Ducklow, Hugh W.; Van Mooy, Benjamin A. S.

2018-07-01

The seasonal depletion of stratospheric ozone over the Southern Hemisphere allows abnormally high doses of ultraviolet radiation (UVR) to reach surface waters of the West Antarctic Peninsula (WAP) in the austral spring, creating a natural laboratory for the study of lipid photooxidation in the shallow mixed layer of the marginal ice zone. The photooxidation of lipids under such conditions has been identified as a significant source of stress to microorganisms and short-chain fatty acids altered by photochemical processes have been found in both marine aerosols and sinking marine particle material. However, the biogeochemical impact of lipid photooxidation has not been quantitatively compared at ecosystem scale to the many other biological and abiotic processes that can transform particulate organic matter in the surface ocean. We combined results from field experiments with diverse environmental data, including high-resolution, accurate-mass HPLC-ESI-MS analysis of lipid extracts and in situ measurements of ultraviolet irradiance, to address several unresolved questions about lipid photooxidation in the marine environment. In our experiments, we used liposomes-nonliving, cell-like aggregations of lipids-to examine the photolability of various moieties of the intact polar diacylglycerol (IP-DAG) phosphatidylcholine (PC), a structural component of membranes in a broad range of microorganisms. We observed significant rates of photooxidation only when the molecule contained the polyunsaturated fatty acid (PUFA) docosahexaenoic acid (DHA). As the DHA-containing lipid was oxidized, we observed the steady ingrowth of a diversity of oxylipins and oxidized IP-DAG; our results suggest both the intact IP-DAG the degradation products were amenable to heterotrophic assimilation. To complement our experiments, we used an enhanced version of a new lipidomics discovery software package to identify the lipids in water column samples and in several diatom isolates. The galactolipid digalactosyldiacylglycerol (DGDG), the sulfolipid sulfoquinovosyldiacylglycerol (SQDG) and the phospholipids PC and phosphatidylglycerol (PG) accounted for the majority of IP-DAG in the water column particulate (≥0.2 μm) size fraction; between 3.4 and 5.3% of the IP-DAG contained fatty acids that were both highly polyunsaturated (i.e., each containing ≥5 double bonds). Using a broadband apparent quantum yield (AQY) that accounted for direct and Type I (i.e., radical-mediated) photooxidation of PUFA-containing IP-DAG, we estimated that 0.7 ± 0.2 μmol IP-DAG m-2 d-1 (0.5 ± 0.1 mg C m-2 d-1) were oxidized by photochemical processes in the mixed layer. This rate represented 4.4% (range, 3-21%) of the mean bacterial production rate measured in the same waters immediately following the retreat of the sea ice. Because our liposome experiments were not designed to account for oxidation by Type II photosensitized processes that often dominate in marine phytodetritus, our rate estimates may represent a sizeable underestimate of the true rate of lipid photooxidation in the water column. While production of such diverse oxidized lipids and oxylipins has been previously observed in terrestrial plants and mammals in response to biological stressors such as disease, we show here that a similar suite of molecules can be produced via an abiotic process in the environment and that the effect can be commensurate in magnitude with other ecosystem-scale biogeochemical processes.

Compressive Spectral Embedding: Sidestepping the SVD

DTIC Science & Technology

2015-09-28

of Rn, the distance between the p, q-th rows of f̃(S) can be written as ‖f̃L(S) (ip − iq)‖ = ‖f(S) (ip − iq)− Z (ip − iq)‖ ≤ ‖ ET (ip − iq)‖+ δ √ 2...2) Similarly, we have that ‖f̃L(S) (ip − iq)‖ ≥ ‖ ET (ip − iq)‖ − δ √ 2. Thus pairwise distances be- tween the rows of f̃L(S) approximate those between...iq) ∥∥∥ = ∥∥∥ΩT f̃L(S) (ip − iq) ∥∥∥ ≤ √ 1 + ǫ ∥∥∥f̃L(S) (ip − iq) ∥∥∥ Using (2), we can show that ‖ẼT (ip − iq)‖ ≤ √ 1 + ǫ ( ‖ ET (ip − iq)‖+ δ √ 2

Optics measurement and correction during beam acceleration in the Relativistic Heavy Ion Collider

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, C.; Marusic, A.; Minty, M.

2014-09-09

To minimize operational complexities, setup of collisions in high energy circular colliders typically involves acceleration with near constant β-functions followed by application of strong focusing quadrupoles at the interaction points (IPs) for the final beta-squeeze. At the Relativistic Heavy Ion Collider (RHIC) beam acceleration and optics squeeze are performed simultaneously. In the past, beam optics correction at RHIC has taken place at injection and at final energy with some interpolation of corrections into the acceleration cycle. Recent measurements of the beam optics during acceleration and squeeze have evidenced significant beta-beats which if corrected could minimize undesirable emittance dilutions and maximizemore » the spin polarization of polarized proton beams by avoidance of higher-order multipole fields sampled by particles within the bunch. In this report the methodology now operational at RHIC for beam optics corrections during acceleration with simultaneous beta-squeeze will be presented together with measurements which conclusively demonstrate the superior beam control. As a valuable by-product, the corrections have minimized the beta-beat at the profile monitors so reducing the dominant error in and providing more precise measurements of the evolution of the beam emittances during acceleration.« less

Space exploration by dendritic cells requires maintenance of myosin II activity by IP3 receptor 1.

PubMed

Solanes, Paola; Heuzé, Mélina L; Maurin, Mathieu; Bretou, Marine; Lautenschlaeger, Franziska; Maiuri, Paolo; Terriac, Emmanuel; Thoulouze, Maria-Isabel; Launay, Pierre; Piel, Matthieu; Vargas, Pablo; Lennon-Duménil, Ana-Maria

2015-03-12

Dendritic cells (DCs) patrol the interstitial space of peripheral tissues. The mechanisms that regulate their migration in such constrained environment remain unknown. We here investigated the role of calcium in immature DCs migrating in confinement. We found that they displayed calcium oscillations that were independent of extracellular calcium and more frequently observed in DCs undergoing strong speed fluctuations. In these cells, calcium spikes were associated with fast motility phases. IP₃ receptors (IP₃Rs) channels, which allow calcium release from the endoplasmic reticulum, were identified as required for immature DCs to migrate at fast speed. The IP₃R1 isoform was further shown to specifically regulate the locomotion persistence of immature DCs, that is, their capacity to maintain directional migration. This function of IP₃R1 results from its ability to control the phosphorylation levels of myosin II regulatory light chain (MLC) and the back/front polarization of the motor protein. We propose that by upholding myosin II activity, constitutive calcium release from the ER through IP₃R1 maintains DC polarity during migration in confinement, facilitating the exploration of their environment. © 2015 Institut Curie/Inserm. Published under the terms of the CC BY NC ND 4.0 license.

New Epigenetic Therapeutic Intervention for Metastatic Breast Cancer

DTIC Science & Technology

2017-04-01

papers as listed in 3.4B. Article Distinct Roles of Brd2 and Brd4 in Potentiating the Transcriptional Program for Th17 Cell Differentiation Graphical...this paper and include the following:d KEY RESOURCES TABLE d CONTACT FOR REAGENT AND RESOURCE SHARING d EXPERIMENTAL MODEL AND SUBJECT DETAILS d METHOD...Brd4, Smc1, Smc3, Nipbl, H3K27ac, H3K4me1 ChIP-seq data This paper GEO: GSE90788 and GSE63778 Other ChIP-seq data Ciofani et al., 2012 GEO: GSE40918

GraphPrints: Towards a Graph Analytic Method for Network Anomaly Detection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harshaw, Chris R; Bridges, Robert A; Iannacone, Michael D

This paper introduces a novel graph-analytic approach for detecting anomalies in network flow data called \\textit{GraphPrints}. Building on foundational network-mining techniques, our method represents time slices of traffic as a graph, then counts graphlets\\textemdash small induced subgraphs that describe local topology. By performing outlier detection on the sequence of graphlet counts, anomalous intervals of traffic are identified, and furthermore, individual IPs experiencing abnormal behavior are singled-out. Initial testing of GraphPrints is performed on real network data with an implanted anomaly. Evaluation shows false positive rates bounded by 2.84\\% at the time-interval level, and 0.05\\% at the IP-level with 100\\% truemore » positive rates at both.« less

Intake of Meat Mutagens and Risk of Prostate Cancer in a Cohort of U.S. Health Professionals.

PubMed

Rohrmann, Sabine; Nimptsch, Katharina; Sinha, Rashmi; Willett, Walter C; Giovannucci, Edward L; Platz, Elizabeth A; Wu, Kana

2015-10-01

Evidence relating heterocyclic aromatic amines (HCA), associated with high-temperature cooking methods, to prostate cancer risk is inconsistent. In a large U.S. cohort study, intakes of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx), and 2-amino-3,4,8-trimethylimidazo[4,5-f]quinoxaline (DiMeIQx) and a meat-derived mutagenicity (MDM) index were assessed using a cooking method questionnaire administered in 1996. Until 2010, 2,770 prostate cancer cases were observed among 26,030 participants. Intake of PhIP from red meat was statistically significantly associated with total prostate cancer risk (top vs. bottom quintile HR, 1.18; 95% confidence intervals; CI, 1.03-1.35), but not other HCAs (MeIQx, 1.12; 0.98-1.27, PhIP from white meat, 1.08; 0.95-1.22, DiMeIQx, 1.09; 0.97-1.21) or MDM (1.13; 1.00-1.28). For high-grade (Gleason sum 7 with pattern 4+3 and Gleason sum 8-10, n = 483 cases) and advanced cancers (n = 281), we only observed positive associations for PhIP from red meat (top vs. bottom quintile: high grade: HR, 1.44; 95% CI, 1.04-1.98, Ptrend = 0.03; advanced: HR, 1.50; 95% CI, 0.99-2.26; Ptrend = 0.12), but associations for advanced cancers did not reach statistical significance. Observed associations remained similar after adjustment for total, unprocessed, or processed red meat intake. Observed positive associations between PhIP intake from red meat and prostate cancer, particularly high-grade and possibly also advanced prostate cancer, need to be confirmed in other studies. Results do not provide strong evidence that HCAs increase risk of prostate cancers. ©2015 American Association for Cancer Research.

Model calibration for ice sheets and glaciers dynamics: a general theory of inverse problems in glaciology

NASA Astrophysics Data System (ADS)

Giudici, Mauro; Baratelli, Fulvia; Vassena, Chiara; Cattaneo, Laura

2014-05-01

Numerical modelling of the dynamic evolution of ice sheets and glaciers requires the solution of discrete equations which are based on physical principles (e.g. conservation of mass, linear momentum and energy) and phenomenological constitutive laws (e.g. Glen's and Fourier's laws). These equations must be accompanied by information on the forcing term and by initial and boundary conditions (IBC) on ice velocity, stress and temperature; on the other hand the constitutive laws involves many physical parameters, which possibly depend on the ice thermodynamical state. The proper forecast of the dynamics of ice sheets and glaciers (forward problem, FP) requires a precise knowledge of several quantities which appear in the IBCs, in the forcing terms and in the phenomenological laws and which cannot be easily measured at the study scale in the field. Therefore these quantities can be obtained through model calibration, i.e. by the solution of an inverse problem (IP). Roughly speaking, the IP aims at finding the optimal values of the model parameters that yield the best agreement of the model output with the field observations and data. The practical application of IPs is usually formulated as a generalised least squares approach, which can be cast in the framework of Bayesian inference. IPs are well developed in several areas of science and geophysics and several applications were proposed also in glaciology. The objective of this paper is to provide a further step towards a thorough and rigorous theoretical framework in cryospheric studies. Although the IP is often claimed to be ill-posed, this is rigorously true for continuous domain models, whereas for numerical models, which require the solution of algebraic equations, the properties of the IP must be analysed with more care. First of all, it is necessary to clarify the role of experimental and monitoring data to determine the calibration targets and the values of the parameters that can be considered to be fixed, whereas only the model output should depend on the subset of the parameters that can be identified with the calibration procedure and the solution to the IP. It is actually difficult to guarantee the existence and uniqueness of a solution to the IP for complex non-linear models. Also identifiability, a property related to the solution to the FP, and resolution should be carefully considered. Moreover, instability of the IP should not be confused with ill-conditioning and with the properties of the method applied to compute a solution. Finally, sensitivity analysis is of paramount importance to assess the reliability of the estimated parameters and of the model output, but it is often based on the one-at-a-time approach, through the application of the adjoint-state method, to compute local sensitivity, i.e. the uncertainty on the model output due to small variations of the input parameters, whereas first-order approaches that consider the whole possible variability of the model parameters should be considered. This theoretical framework and the relevant properties are illustrated by means of a simple numerical example of isothermal ice flow, based on the shallow ice approximation.

Inlet patch: heterotopic gastric mucosa--another contributor to supraesophageal symptoms?

PubMed

Macha, Suhasini; Reddy, Sushma; Rabah, Raja; Thomas, Ronald; Tolia, Vasundhara

2005-09-01

To determine prospectively the incidence of an inlet patch (IP) in children requiring esophagogastroduodenoscopy (EGD) and assess the prevalence of presenting symptoms between children with and without an IP. All patients undergoing EGD in a 2-year period were assessed for the presence of an IP with biopsy confirmation. IP, distal esophagus, and stomach biopsy specimens were blindly reviewed by a pathologist for the presence and degree of inflammation and intestinal metaplasia. Symptoms from children with and without an IP were compared. From 407 EGDs done by a single endoscopist, 24 patients had confirmed IP (incidence of 5.9%). The presence and degree of inflammation were always relatively greater in the columnar mucosa of the IP than in the antral/body gastric mucosa in the same patient (P = .0027) Inflammation was similar in the squamous epithelium around the IP and in the distal esophagus (P=.46). Two patients had intestinal metaplasia of the IP. The patients with IPs had a higher prevalence of respiratory symptoms than the control group (P = .03). Children with IPs may have a higher frequency of respiratory symptoms. Periodic surveillance should be performed in children with intestinal metaplasia of an IP.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hashimoto, Muneaki, E-mail: muneaki@juntendo.ac.jp; Nara, Takeshi, E-mail: tnara@juntendo.ac.jp; Enomoto, Masahiro, E-mail: menomoto@uhnres.utoronto.ca

Inositol 1,4,5-trisphosphate receptor (IP{sub 3}R) is a key regulator of intracellular Ca{sup 2+} concentration that release Ca{sup 2+} from Ca{sup 2+} stores in response to various external stimuli. IP{sub 3}R also works as a signal hub which form a platform for interacting with various proteins involved in diverse cell signaling. Previously, we have identified an IP{sub 3}R homolog in the parasitic protist, Trypanosoma cruzi (TcIP{sub 3}R). Parasites expressing reduced or increased levels of TcIP{sub 3}R displayed defects in growth, transformation, and infectivity. In the present study, we established parasitic strains expressing a dominant negative form of TcIP{sub 3}R, named DN-TcIP{submore » 3}R, to further investigate the physiological role(s) of TcIP{sub 3}R. We found that the growth of epimastigotes expressing DN-TcIP{sub 3}R was significantly slower than that of parasites with TcIP{sub 3}R expression levels that were approximately 65% of wild-type levels. The expression of DN-TcIP{sub 3}R in epimastigotes induced metacyclogenesis even in the normal growth medium. Furthermore, these epimastigotes showed the presence of dense mitochondria under a transmission electron microscope. Our findings confirm that TcIP{sub 3}R is crucial for epimastigote growth, as previously reported. They also suggest that a strong inhibition of the IP{sub 3}R-mediated signaling induces metacyclogenesis and that mitochondrial integrity is closely associated with this signaling. - Highlights: • We established T. cruzi strains expressing a dominant negative form of the TcIP{sub 3}R. • DN-TcIP{sub 3}R expression inhibits epimastigote growth and induces metacyclogenesis. • Microscopic analysis indicated TcIP{sub 3}R role in maintaining mitochondrial integrity. • Growth, but not microbial density, was altered by mammalian IP{sub 3}R inhibitor (2-APB).« less

Protein kinase C (PKC) phosphorylates human platelet inositol trisphosphate 5/sup +/-/-phosphomonoesterase (IP/sub 3/ 5'-p'tase) increasing phosphatase activity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Connolly, T.M.; Majerus, P.W.

1986-05-01

Phosphoinositide breakdown in response to thrombin stimulation of human platelets generates messenger molecules that activate PKC (diglyceride) and mobilize Ca/sup + +/ (inositol tris-phosphates). The water soluble products of phospholipase C-mediated metabolism of phosphatidylinositol 4,5-diphosphate are inositol 1,4,5 P/sub 3/ (IP/sub 3/) and inositol 1:2-cyclic 4,5 P/sub 3/ (cIP/sub 3/). A specific phosphatase, IP/sub 3/ 5'-p'tase, cleaves the 5 phosphate from IP/sub 3/ or cIP/sub 3/ to form IP/sub 2/ or cIP/sub 2/ and P/sub i/, none of which mobilizes Ca/sup + +/. Thus, the IP/sub 3/ 5'-p'tase may regulate cellular responses to IP/sub 3/ or cIP/sub 3/. The authorsmore » find that IP/sub 3/ 5'-p'tase isolated from human platelets is phosphorylated by rat brain PKC, resulting in a 4-fold increase in IP/sub 3/ 5'-p'tase activity. The authors phosphorylated IP/sub 3/ 5'-p'tase using ..gamma.. /sup 32/P-ATP and found that the labeled enzyme comigrated on SDS-PAGE with the previously described 40K protein phosphorylated in response to thrombin stimulation of platelets. The similarity of the PKC-phosphorylated IP/sub 3/ 5'-p'tase observed in vitro and the thrombin-stimulated phosphorylated 40K protein known to be phosphorylated by PKC in vivo, suggests that these proteins may be the same. These results suggest that platelet Ca/sup + +/ mobilization maybe regulated by PKC phosphorylation of the IP/sub 3/ 5'-p'tase and can explain the observation that phorbol ester treatment of intact human platelets results in decreased production of IP/sub 3/ and decreased Ca/sup + +/ mobilization upon subsequent thrombin addition.« less

Different KChIPs compete for heteromultimeric assembly with pore-forming Kv4 subunits.

PubMed

Zhou, Jingheng; Tang, Yiquan; Zheng, Qin; Li, Meng; Yuan, Tianyi; Chen, Liangyi; Huang, Zhuo; Wang, KeWei

2015-06-02

Auxiliary Kv channel-interacting proteins 1-4 (KChIPs1-4) coassemble with pore-forming Kv4 α-subunits to form channel complexes underlying somatodendritic subthreshold A-type current that regulates neuronal excitability. It has been hypothesized that different KChIPs can competitively bind to Kv4 α-subunit to form variable channel complexes that can exhibit distinct biophysical properties for modulation of neural function. In this study, we use single-molecule subunit counting by total internal reflection fluorescence microscopy in combinations with electrophysiology and biochemistry to investigate whether different isoforms of auxiliary KChIPs, KChIP4a, and KChIP4bl, can compete for binding of Kv4.3 to coassemble heteromultimeric channel complexes for modulation of channel function. To count the number of photobleaching steps solely from cell membrane, we take advantage of a membrane tethered k-ras-CAAX peptide that anchors cytosolic KChIP4 proteins to the surface for reduction of background noise. Single-molecule subunit counting reveals that the number of KChIP4 isoforms in Kv4.3-KChIP4 complexes can vary depending on the KChIP4 expression level. Increasing the amount of KChIP4bl gradually reduces bleaching steps of KChIP4a isoform proteins, and vice versa. Further analysis of channel gating kinetics from different Kv4-KChIP4 subunit compositions confirms that both KChIP4a and KChIP4bl can modulate the channel complex function upon coassembly. Taken together, our findings show that auxiliary KChIPs can heteroassemble with Kv4 in a competitive manner to form heteromultimeric Kv4-KChIP4 channel complexes that are biophysically distinct and regulated under physiological or pathological conditions. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Enabling IP Header Compression in COTS Routers via Frame Relay on a Simplex Link

NASA Technical Reports Server (NTRS)

Nguyen, Sam P.; Pang, Jackson; Clare, Loren P.; Cheng, Michael K.

2010-01-01

NASA is moving toward a networkcentric communications architecture and, in particular, is building toward use of Internet Protocol (IP) in space. The use of IP is motivated by its ubiquitous application in many communications networks and in available commercial off-the-shelf (COTS) technology. The Constellation Program intends to fit two or more voice (over IP) channels on both the forward link to, and the return link from, the Orion Crew Exploration Vehicle (CEV) during all mission phases. Efficient bandwidth utilization of the links is key for voice applications. In Voice over IP (VoIP), the IP packets are limited to small sizes to keep voice latency at a minimum. The common voice codec used in VoIP is G.729. This new algorithm produces voice audio at 8 kbps and in packets of 10-milliseconds duration. Constellation has designed the VoIP communications stack to use the combination of IP/UDP/RTP protocols where IP carries a 20-byte header, UDP (User Datagram Protocol) carries an 8-byte header, and RTP (Real Time Transport Protocol) carries a 12-byte header. The protocol headers total 40 bytes and are equal in length to a 40-byte G.729 payload, doubling the VoIP latency. Since much of the IP/UDP/RTP header information does not change from IP packet to IP packet, IP/UDP/RTP header compression can avoid transmission of much redundant data as well as reduce VoIP latency. The benefits of IP header compression are more pronounced at low data rate links such as the forward and return links during CEV launch. IP/UDP/RTP header compression codecs are well supported by many COTS routers. A common interface to the COTS routers is through frame relay. However, enabling IP header compression over frame relay, according to industry standard (Frame Relay IP Header Compression Agreement FRF.20), requires a duplex link and negotiations between the compressor router and the decompressor router. In Constellation, each forward to and return link from the CEV in space is treated independently as a simplex link. Without negotiation, the COTS routers are prevented from entering into the IP header compression mode, and no IP header compression would be performed. An algorithm is proposed to enable IP header compression in COTS routers on a simplex link with no negotiation or with a one-way messaging. In doing so, COTS routers can enter IP header compression mode without the need to handshake through a bidirectional link as required by FRF.20. This technique would spoof the routers locally and thereby allow the routers to enter into IP header compression mode without having the negotiations between routers actually occur. The spoofing function is conducted by a frame relay adapter (also COTS) with the capability to generate control messages according to the FRF.20 descriptions. Therefore, negotiation is actually performed between the FRF.20 adapter and the connecting COTS router locally and never occurs over the space link. Through understanding of the handshaking protocol described by FRF.20, the necessary FRF.20 negotiations messages can be generated to control the connecting router, not only to turn on IP header compression but also to adjust the compression parameters. The FRF.20 negotiation (or control) message is composed in the FRF.20 adapter by interpreting the incoming router request message. Many of the fields are simply transcribed from request to response while the control field indicating response and type are modified.

Negative regulation of DAB2IP by Akt and SCFFbw7 pathways.

PubMed

Dai, Xiangping; North, Brian J; Inuzuka, Hiroyuki

2014-05-30

Deletion of ovarian carcinoma 2/disabled homolog 2 (DOC-2/DAB2) interacting protein (DAB2IP), is a tumor suppressor that serves as a scaffold protein involved in coordinately regulating cell proliferation, survival and apoptotic pathways. DAB2IP is epigenetically down-regulated in a variety of tumors through the action of the histone methyltransferase EZH2. Although DAB2IP is transcriptionally down-regulated in a variety of tumors, it remains unclear if other mechanisms contribute to functional inactivation of DAB2IP. Here we demonstrate that DAB2IP can be functionally down-regulated by two independent mechanisms. First, we identified that Akt1 can phosphorylate DAB2IP on S847, which regulates the interaction between DAB2IP and its effector molecules H-Ras and TRAF2. Second, we demonstrated that DAB2IP can be degraded in part through ubiquitin-proteasome pathway by SCF(Fbw7). DAB2IP harbors two Fbw7 phosho-degron motifs, which can be regulated by the kinase, CK1δ. Our data hence indicate that in addition to epigenetic down-regulation, two additional pathways can functional inactivate DAB2IP. Given that DAB2IP has previously been identified to possess direct causal role in tumorigenesis and metastasis, our data indicate that a variety of pathways may pass through DAB2IP to govern cancer development, and therefore highlight DAB2IP agonists as potential therapeutic approaches for future anti-cancer drug development.