Cerebral Apolipoprotein-D Is Hypoglycosylated Compared to Peripheral Tissues and Is Variably Expressed in Mouse and Human Brain Regions.

PubMed

Li, Hongyun; Ruberu, Kalani; Karl, Tim; Garner, Brett

2016-01-01

Recent studies have shown that cerebral apoD levels increase with age and in Alzheimer's disease (AD). In addition, loss of cerebral apoD in the mouse increases sensitivity to lipid peroxidation and accelerates AD pathology. Very little data are available, however, regarding the expression of apoD protein levels in different brain regions. This is important as both brain lipid peroxidation and neurodegeneration occur in a region-specific manner. Here we addressed this using western blotting of seven different regions (olfactory bulb, hippocampus, frontal cortex, striatum, cerebellum, thalamus and brain stem) of the mouse brain. Our data indicate that compared to most brain regions, the hippocampus is deficient in apoD. In comparison to other major organs and tissues (liver, spleen, kidney, adrenal gland, heart and skeletal muscle), brain apoD was approximately 10-fold higher (corrected for total protein levels). Our analysis also revealed that brain apoD was present at a lower apparent molecular weight than tissue and plasma apoD. Utilising peptide N-glycosidase-F and neuraminidase to remove N-glycans and sialic acids, respectively, we found that N-glycan composition (but not sialylation alone) were responsible for this reduction in molecular weight. We extended the studies to an analysis of human brain regions (hippocampus, frontal cortex, temporal cortex and cerebellum) where we found that the hippocampus had the lowest levels of apoD. We also confirmed that human brain apoD was present at a lower molecular weight than in plasma. In conclusion, we demonstrate apoD protein levels are variable across different brain regions, that apoD levels are much higher in the brain compared to other tissues and organs, and that cerebral apoD has a lower molecular weight than peripheral apoD; a phenomenon that is due to the N-glycan content of the protein.

Simulation, Design, and Test of Square, Apodized Photon Sieves for High Contrast, Exoplanet Imaging

DTIC Science & Technology

reason, square apodized photon sieves were simulated, designed, and tested for high-contrast performance and use in an exoplanet imaging telescope...for apodizing sieves, measuring PSFs, and characterizing high-contrast performance. Tests indicated that square apodized sieves could detect

Apolipoprotein D Internalization Is a Basigin-dependent Mechanism.

PubMed

Najyb, Ouafa; Brissette, Louise; Rassart, Eric

2015-06-26

Apolipoprotein D (apoD), a member of the lipocalin family, is a 29-kDa secreted glycoprotein that binds and transports small lipophilic molecules. Expressed in several tissues, apoD is up-regulated under different stress stimuli and in a variety of pathologies. Numerous studies have revealed that overexpression of apoD led to neuroprotection in various mouse models of acute stress and neurodegeneration. This multifunctional protein is internalized in several cells types, but the specific internalization mechanism remains unknown. In this study, we demonstrate that the internalization of apoD involves a specific cell surface receptor in 293T cells, identified as the transmembrane glycoprotein basigin (BSG, CD147); more particularly, its low glycosylated form. Our results show that internalized apoD colocalizes with BSG into vesicular compartments. Down-regulation of BSG disrupted the internalization of apoD in cells. In contrast, overexpression of basigin in SH-5YSY cells, which poorly express BSG, restored the uptake of apoD. Cyclophilin A, a known ligand of BSG, competitively reduced apoD internalization, confirming that BSG is a key player in the apoD internalization process. In summary, our results demonstrate that basigin is very likely the apoD receptor and provide additional clues on the mechanisms involved in apoD-mediated functions, including neuroprotection. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Can My Image Appear on APOD?: How APOD Really Works

NASA Astrophysics Data System (ADS)

Nemiroff, Robert J.; Bonnell, Jerry T.

2017-01-01

The Astronomy Picture of the Day (APOD) makes an effort to present and annotate the best astronomical images of our time. How "best" is defined in practice is debatable and will be discussed. However, if your image appears destined to appear in future astronomy textbooks, there is a good chance it will be highlighted on APOD. Perhaps the most ambitious goal of APOD is to bolster astronomy as a globally unifying medium, highlighting that all of humanity shares the night sky. Perhaps the least ambitious goal is to find enough time to prepare a reasonably interesting and error-free APOD for tomorrow. In practice, APOD has been cited by many teachers of astronomy as making educational images easily available to bolster their lectures and give a background understandable to their students. Feedback from teachers is therefore particularly encouraged.

Design and comparative performance analysis of different chirping profiles of tanh apodized fiber Bragg grating and comparison with the dispersion compensation fiber for long-haul transmission system

NASA Astrophysics Data System (ADS)

Dar, Aasif Bashir; Jha, Rakesh Kumar

2017-03-01

Various dispersion compensation units are presented and evaluated in this paper. These dispersion compensation units include dispersion compensation fiber (DCF), DCF merged with fiber Bragg grating (FBG) (joint technique), and linear, square root, and cube root chirped tanh apodized FBG. For the performance evaluation 10 Gb/s NRZ transmission system over 100-km-long single-mode fiber is used. The three chirped FBGs are optimized individually to yield pulse width reduction percentage (PWRP) of 86.66, 79.96, 62.42% for linear, square root, and cube root, respectively. The DCF and Joint technique both provide a remarkable PWRP of 94.45 and 96.96%, respectively. The performance of optimized linear chirped tanh apodized FBG and DCF is compared for long-haul transmission system on the basis of quality factor of received signal. For both the systems maximum transmission distance is calculated such that quality factor is ≥ 6 at the receiver and result shows that performance of FBG is comparable to that of DCF with advantages of very low cost, small size and reduced nonlinear effects.

Energy balance in apodized diffractive multifocal intaocular lenses

NASA Astrophysics Data System (ADS)

Alba-Bueno, Francisco; Vega, Fidel; Millán, María S.

2011-08-01

The energy distribution between the distance and near images formed in a model eye by three different apodized diffractive multifocal intraocular lenses (IOLs) is experimentally determined in an optical bench. The model eye has an artificial cornea with positive spherical aberration (SA) similar to human cornea. The level of SA upon the IOL, which is pupil size dependent, is controlled using a Hartmann-Shack wave sensor. The energy of the distance and near images as a function of the pupil size is experimentally obtained from image analysis. All three IOLs have the same base refractive power (20D) but different designs (aspheric, spherical) and add powers (+4.0 D, +3.0 D). The results show that in all the cases, the energy efficiency of the distance image decreases for large pupils, in contrast with the theoretical and simulated results that only consider the diffractive profile of the lens. As for the near image, since the diffractive zone responsible for the formation of this image has the same apodization factor in the spherical and aspheric lenses and the apertures involved are small (and so the level of SA), the results turn out to be similar for all the three IOL designs.

Air-Coupled Ultrasonic Measurements in Composites

NASA Astrophysics Data System (ADS)

Kommareddy, V.; Peters, J. J.; Dayal, V.; Hsu, D. K.

2004-02-01

Air-coupled ultrasound is a non-contact technique and has clear advantages over water-coupled testing. Research of air-coupled ultrasonics, especially using capacitance and micromachined transducers, has been extensively reported in the literature. This paper reports our experience of applying piezoceramic air-coupled transducers for nondestructive evaluation of composites. The beam profiles of air-coupled piezoceramic transducers, with and without apodization, were mapped out. The transmission of air-coupled ultrasonic energy through composite plates of different thickness was measured experimentally; model calculation of the transmission coefficient, taking into account the frequency bandwidth of the transducer, agreed with the measurement results. The occurrence of diffraction phenomenon ("Poisson bright spot") while imaging flaws in composite laminates was investigated. The resolution of scanned images obtained with air-coupled transducers was investigated for different frequency, focusing, and apodization conditions.

Schwann cell-derived Apolipoprotein D controls the dynamics of post-injury myelin recognition and degradation

PubMed Central

García-Mateo, Nadia; Ganfornina, Maria D.; Montero, Olimpio; Gijón, Miguel A.; Murphy, Robert C.; Sanchez, Diego

2014-01-01

Management of lipids, particularly signaling lipids that control neuroinflammation, is crucial for the regeneration capability of a damaged nervous system. Knowledge of pro- and anti-inflammatory signals after nervous system injury is extensive, most of them being proteins acting through well-known receptors and intracellular cascades. However, the role of lipid binding extracellular proteins able to modify the fate of lipids released after injury is not well understood. Apolipoprotein D (ApoD) is an extracellular lipid binding protein of the Lipocalin family induced upon nervous system injury. Our previous study shows that axon regeneration is delayed without ApoD, and suggests its participation in early events during Wallerian degeneration. Here we demonstrate that ApoD is expressed by myelinating and non-myelinating Schwann cells and is induced early upon nerve injury. We show that ApoD, known to bind arachidonic acid (AA), also interacts with lysophosphatidylcholine (LPC) in vitro. We use an in vivo model of nerve crush injury, a nerve explant injury model, and cultured macrophages exposed to purified myelin, to uncover that: (i) ApoD regulates denervated Schwann cell-macrophage signaling, dampening MCP1- and Tnf-dependent macrophage recruitment and activation upon injury; (ii) ApoD controls the over-expression of the phagocytosis activator Galectin-3 by infiltrated macrophages; (iii) ApoD controls the basal and injury-triggered levels of LPC and AA; (iv) ApoD modifies the dynamics of myelin-macrophage interaction, favoring the initiation of phagocytosis and promoting myelin degradation. Regulation of macrophage behavior by Schwann-derived ApoD is therefore a key mechanism conditioning nerve injury resolution. These results place ApoD as a lipid binding protein controlling the signals exchanged between glia, neurons and blood-borne cells during nerve recovery after injury, and open the possibility for a therapeutic use of ApoD as a regeneration-promoting agent. PMID:25426024

Apodizing functions for Fourier transform spectroscopy.

PubMed

Naylor, David A; Tahic, Margaret K

2007-11-01

Apodizing functions are used in Fourier transform spectroscopy (FTS) to reduce the magnitude of the sidelobes in the instrumental line shape (ILS), which are a direct result of the finite maximum optical path difference in the measured interferogram. Three apodizing functions, which are considered optimal in the sense of producing the smallest loss in spectral resolution for a given reduction in the magnitude of the largest sidelobe, find frequent use in FTS [J. Opt. Soc. Am.66, 259 (1976)]. We extend this series to include optimal apodizing functions corresponding to increases in the width of the ILS ranging from factors of 1.1 to 2.0 compared with its unapodized value, and we compare the results with other commonly used apodizing functions.

After APOD: From the Website to the Classroom and Beyond

NASA Astrophysics Data System (ADS)

Wilson, Teresa; APOD

2017-01-01

Astronomy Picture of the Day (APOD) images may start on the apod.nasa.gov website, but their reach goes much further than the individual sitting at their computer screen. They provoke questions that then prompts the reader to email the authors; teachers use the images in their classrooms; students use them in their projects. This presentation will take a look at some of the work done using APOD images and text, including public outreach via middle school presentations and email communications, and academic uses beyond astronomy such as lesson plans on atmospheric refraction and even plagiarism, copyright and fair use.

Spectral characterization of differential group delay in uniform fiber Bragg gratings.

PubMed

Bette, S; Caucheteur, C; Wuilpart, M; Mégret, P; Garcia-Olcina, R; Sales, S; Capmany, J

2005-12-12

In this paper, we completely study the wavelength dependency of differential group delay (DGD) in uniform fiber Bragg gratings (FBG) exhibiting birefringence. An analytical expression of DGD is established. We analyze the impact of grating parameters (physical length, index modulation and apodization profile) on the wavelength dependency of DGD. Experimental results complete the paper. A very good agreement between theory and experience is reported.

Current Status of the High Contrast Imager for Complex Aperture Telescopes (HiCAT) Testbed

NASA Astrophysics Data System (ADS)

Brooks, Keira; Brady, Gregory; Brito, Arturo; Comeau, Tom; Dillon, Thomas; Choquet, Elodie; Egron, Sylvain; Rob, Gontrum; John, Hagopian; Leboulleux, Lucie; Perrin, Marshall; Petrone, Peter; Pueyo, Laurent; Mazoyer, Johan; Moriarty, Christopher; N’Diaye, Mamadou; Eldorado Riggs, A. J.; Shiri, Ron; Sivaramakrishnan, Anand; St. Laurent, Kathryn; Valenzuela, Ana Maria; Zimmerman, Neil; Soummer, Remi; JHU Mechanical Engineering Senior Design Team

2018-01-01

The coming decades will bring the next space telescopes to take on the ambitious goal of exoplanet discovery via direct imaging, driving the development of innovative coronagraphic solutions. High contrast imager for Complex Aperture Telescopes (HiCAT) is an optical testbed meant to test such solutions for complex aperture telescopes, such as the Large UV/Optical/InfraRed surveyor (LUVOIR), or any other segmented space observatory. High contrast imaging becomes more demanding with the addition of segments, a secondary mirror obscuration, and support structure. LUVOIR, a candidate for the next-next generation major space telescope funded in part by NASA, will have all three. In the past year, HiCAT has made significant hardware and software updates in order to meet the needs of LUVOIR. In addition to completely overhauling the software that runs the testbed, we have received the first two custom-made apodizers for the Apodized Pupil Lyot Coronagraph (APLC) that we are testing for LUVOIR, and are continuing the development of the wavefront sensing and control. This poster will serve to give an update on these, and other, changes, as well as the most recent results.

3-D Vector Flow Estimation With Row-Column-Addressed Arrays.

PubMed

Holbek, Simon; Christiansen, Thomas Lehrmann; Stuart, Matthias Bo; Beers, Christopher; Thomsen, Erik Vilain; Jensen, Jorgen Arendt

2016-11-01

Simulation and experimental results from 3-D vector flow estimations for a 62 + 62 2-D row-column (RC) array with integrated apodization are presented. A method for implementing a 3-D transverse oscillation (TO) velocity estimator on a 3-MHz RC array is developed and validated. First, a parametric simulation study is conducted, where flow direction, ensemble length, number of pulse cycles, steering angles, transmit/receive apodization, and TO apodization profiles and spacing are varied, to find the optimal parameter configuration. The performance of the estimator is evaluated with respect to relative mean bias ~B and mean standard deviation ~σ . Second, the optimal parameter configuration is implemented on the prototype RC probe connected to the experimental ultrasound scanner SARUS. Results from measurements conducted in a flow-rig system containing a constant laminar flow and a straight-vessel phantom with a pulsating flow are presented. Both an M-mode and a steered transmit sequence are applied. The 3-D vector flow is estimated in the flow rig for four representative flow directions. In the setup with 90° beam-to-flow angle, the relative mean bias across the entire velocity profile is (-4.7, -0.9, 0.4)% with a relative standard deviation of (8.7, 5.1, 0.8)% for ( v x , v y , v z ). The estimated peak velocity is 48.5 ± 3 cm/s giving a -3% bias. The out-of-plane velocity component perpendicular to the cross section is used to estimate volumetric flow rates in the flow rig at a 90° beam-to-flow angle. The estimated mean flow rate in this setup is 91.2 ± 3.1 L/h corresponding to a bias of -11.1%. In a pulsating flow setup, flow rate measured during five cycles is 2.3 ± 0.1 mL/stroke giving a negative 9.7% bias. It is concluded that accurate 3-D vector flow estimation can be obtained using a 2-D RC-addressed array.

Scattering apodizer for laser beams

DOEpatents

Summers, Mark A.; Hagen, Wilhelm F.; Boyd, Robert D.

1985-01-01

A method is disclosed for apodizing a laser beam to smooth out the production of diffraction peaks due to optical discontinuities in the path of the laser beam, such method comprising introduction of a pattern of scattering elements for reducing the peak intensity in the region of such optical discontinuities, such pattern having smoothly tapering boundaries in which the distribution density of the scattering elements is tapered gradually to produce small gradients in the distribution density, such pattern of scattering elements being effective to reduce and smooth out the diffraction effects which would otherwise be produced. The apodizer pattern may be produced by selectively blasting a surface of a transparent member with fine abrasive particles to produce a multitude of minute pits. In one embodiment, a scattering apodizer pattern is employed to overcome diffraction patterns in a multiple element crystal array for harmonic conversion of a laser beam. The interstices and the supporting grid between the crystal elements are obscured by the gradually tapered apodizer pattern of scattering elements.

Imaging performance of annular apertures. IV - Apodization and point spread functions. V - Total and partial energy integral functions

NASA Technical Reports Server (NTRS)

Tschunko, H. F. A.

1983-01-01

Reference is made to a study by Tschunko (1979) in which it was discussed how apodization modifies the modulation transfer function for various central obstruction ratios. It is shown here how apodization, together with the central obstruction ratio, modifies the point spread function, which is the basic element for the comparison of imaging performance and for the derivation of energy integrals and other functions. At high apodization levels and lower central obstruction (less than 0.1), new extended radial zones are formed in the outer part of the central ring groups. These transmutation of the image functions are of more than theoretical interest, especially if the irradiance levels in the outer ring zones are to be compared to the background irradiance levels. Attention is then given to the energy distribution in point images generated by annular apertures apodized by various transmission functions. The total energy functions are derived; partial energy integrals are determined; and background irradiance functions are discussed.

Scattering apodizer for laser beams

DOEpatents

Summers, M.A.; Hagen, W.F.; Boyd, R.D.

1984-01-01

A method is disclosed for apodizing a laser beam to smooth out the production of diffraction peaks due to optical discontinuities in the path of the laser beam, such method comprising introduction of a pattern of scattering elements for reducing the peak intensity in the region of such optical discontinuities, such pattern having smoothly tapering boundaries in which the distribution density of the scattering elements is tapered gradually to produce small gradients in the distribution density, such pattern of scattering elements being effective to reduce and smooth out the diffraction effects which would otherwise be produced. The apodizer pattern may be produced by selectively blasting a surface of a transparent member with fine abrasive particles to produce a multitude of minute pits. In one embodiment, a scattering apodizer pattern is employed to overcome diffraction patterns in a multiple element crystal array for harmonic conversion of a laser beam. The interstices and the supporting grid between the crystal elements are obscured by the gradually tapered apodizer pattern of scattering elements.

The Phase-Induced Amplitude Apodization Coronagraph (PIAAC): A High Performance Coronagraph for Exoplanet Imaging

NASA Astrophysics Data System (ADS)

Guyon, O.; Pluzhnik, E.; Martinache, F.; Ridgway, S.; Galicher, R.

2004-12-01

Using 2 aspheric mirrors, it is possible to achromatically apodize a telescope beam without losing light (Phase-Induced Amplitude Apodization, PIAA). We propose a coronagraph concept using this technique: the telescope pupil is first apodized to yield a high contrast focal plane image, on which an occulting mask is placed. The exit pupil is then de-apodized to regain a large field of view. We show that the PIAAC combines all the qualities needed for efficient exoplanet imaging: full throughput, small inner working angle (1.2 l/d), high angular resolution (l/d), low sensitivity to tip-tilt, and large field of view (more than 200 l/d in diameter). We conclude that PIAAC is well adapted for exoplanet imaging with a 4m to 6m space telescope (TPF mission). This work was carried out under JPL contract numbers 1254445 and 1257767 for Development of Technologies for the Terrestrial Planet Finder Mission, with the support and hospitality of the National Astronomical Observatory of Japan.

Protecting cells by protecting their vulnerable lysosomes: Identification of a new mechanism for preserving lysosomal functional integrity upon oxidative stress.

PubMed

Pascua-Maestro, Raquel; Diez-Hermano, Sergio; Lillo, Concepción; Ganfornina, Maria D; Sanchez, Diego

2017-02-01

Environmental insults such as oxidative stress can damage cell membranes. Lysosomes are particularly sensitive to membrane permeabilization since their function depends on intraluminal acidic pH and requires stable membrane-dependent proton gradients. Among the catalog of oxidative stress-responsive genes is the Lipocalin Apolipoprotein D (ApoD), an extracellular lipid binding protein endowed with antioxidant capacity. Within the nervous system, cell types in the defense frontline, such as astrocytes, secrete ApoD to help neurons cope with the challenge. The protecting role of ApoD is known from cellular to organism level, and many of its downstream effects, including optimization of autophagy upon neurodegeneration, have been described. However, we still cannot assign a cellular mechanism to ApoD gene that explains how this protection is accomplished. Here we perform a comprehensive analysis of ApoD intracellular traffic and demonstrate its role in lysosomal pH homeostasis upon paraquat-induced oxidative stress. By combining single-lysosome in vivo pH measurements with immunodetection, we demonstrate that ApoD is endocytosed and targeted to a subset of vulnerable lysosomes in a stress-dependent manner. ApoD is functionally stable in this acidic environment, and its presence is sufficient and necessary for lysosomes to recover from oxidation-induced alkalinization, both in astrocytes and neurons. This function is accomplished by preventing lysosomal membrane permeabilization. Two lysosomal-dependent biological processes, myelin phagocytosis by astrocytes and optimization of neurodegeneration-triggered autophagy in a Drosophila in vivo model, require ApoD-related Lipocalins. Our results uncover a previously unknown biological function of ApoD, member of the finely regulated and evolutionary conserved gene family of extracellular Lipocalins. They set a lipoprotein-mediated regulation of lysosomal membrane integrity as a new mechanism at the hub of many cellular functions, critical for the outcome of a wide variety of neurodegenerative diseases. These results open therapeutic opportunities by providing a route of entry and a repair mechanism for lysosomes in pathological situations.

High-contrast imager for Complex Aperture Telescopes (HiCAT): APLC/shaped-pupil hybrid coronagraph designs

NASA Astrophysics Data System (ADS)

N'Diaye, Mamadou; Choquet, Elodie; Carlotti, Alexis; Pueyo, Laurent; Egron, Sylvain; Leboulleux, Lucie; Levecq, Olivier; Perrin, Marshall D.; Wallace, J. Kent; Long, Chris; Lajoie, Rachel; Lajoie, Charles-Philippe; Eldorado Riggs, A. J.; Zimmerman, Neil T.; Groff, Tyler Dean; Kasdin, N. Jeremy; Vanderbei, Robert J.; Mawet, Dimitri; Macintosh, Bruce; Shaklan, Stuart; Soummer, Remi

2015-01-01

HiCAT is a high-contrast imaging testbed designed to provide complete solutions in wavefront sensing, control and starlight suppression with complex aperture telescopes. Primary mirror segmentation, central obstruction and spiders in the pupil of an on-axis telescope introduces additional diffraction features in the point spread function, which make high-contrast imaging very challenging. The testbed alignment was completed in the summer of 2014, exceeding specifications with a total wavefront error of 12nm rms with a 18mm pupil. Two deformable mirrors are to be installed for wavefront control in the fall of 2014. In this communication, we report on the first testbed results using a classical Lyot coronagraph. We have developed novel coronagraph designs combining an Apodized Pupil Lyot Coronagraph (APLC) with shaped-pupil type optimizations. We present the results of these new APLC-type solutions with two-dimensional shaped-pupil apodizers for the HiCAT geometry. These solutions render the system quasi-insensitive to jitter and low-order aberrations, while improving the performance in terms of inner working angle, bandpass and contrast over a classical APLC.

High-contrast imager for complex aperture telescopes (HiCAT): 3. first lab results with wavefront control

NASA Astrophysics Data System (ADS)

N'Diaye, Mamadou; Mazoyer, Johan; Choquet, Élodie; Pueyo, Laurent; Perrin, Marshall D.; Egron, Sylvain; Leboulleux, Lucie; Levecq, Olivier; Carlotti, Alexis; Long, Chris A.; Lajoie, Rachel; Soummer, Rémi

2015-09-01

HiCAT is a high-contrast imaging testbed designed to provide complete solutions in wavefront sensing, control and starlight suppression with complex aperture telescopes. The pupil geometry of such observatories includes primary mirror segmentation, central obstruction, and spider vanes, which make the direct imaging of habitable worlds very challenging. The testbed alignment was completed in the summer of 2014, exceeding specifications with a total wavefront error of 12nm rms over a 18mm pupil. The installation of two deformable mirrors for wavefront control is to be completed in the winter of 2015. In this communication, we report on the first testbed results using a classical Lyot coronagraph. We also present the coronagraph design for HiCAT geometry, based on our recent development of Apodized Pupil Lyot Coronagraph (APLC) with shaped-pupil type optimizations. These new APLC-type solutions using two-dimensional shaped-pupil apodizer render the system quasi-insensitive to jitter and low-order aberrations, while improving the performance in terms of inner working angle, bandpass and contrast over a classical APLC.

Constrained Adaptive Beamforming for Improved Contrast in Breast Ultrasound

DTIC Science & Technology

2007-06-01

Contr., vol. 54, no. 5, pp. 1045-1054, May 2007. Ranganathan , K. and W.F. Walker, “Cystic Resolution: A Performance Metric for Ultrasound Imaging...Ultrasonics Symposium. D.A. Guenther, Ranganathan , K. and W.F. Walker, “Design of Apodization Profiles Using a Cystic Resolution Metric for Ultrasound...diagnosis. 22 References: [1] V. Jackson, " Management of solid breast nodules: what is the role of sonography?," Radiology, vol. 196, pp. 14-15, 1995

Improving the phase measurement by the apodization filter in the digital holography

NASA Astrophysics Data System (ADS)

Chang, Shifeng; Wang, Dayong; Wang, Yunxin; Zhao, Jie; Rong, Lu

2012-11-01

Due to the finite size of the hologram aperture in digital holography, high frequency intensity and phase fluctuations along the edges of the images, which reduce the precision of phase measurement. In this paper, the apodization filters are applied to improve the phase measurement in the digital holography. Firstly, the experimental setup of the lensless Fourier transform digital holography is built, where the sample is a standard phase grating with the grating constant of 300μm and the depth of 150nm. Then, apodization filters are applied to phase measurement of the sample with three kinds of the window functions: Tukey window, Hanning window and Blackman window, respectively. Finally, the results were compared to the detection data given by the commercial white-light interferometer. It is shown that aperture diffraction effects can be reduced by the digital apodization, and the phase measurement with the apodization is more accurate than in the unapodized case. Meanwhile, the Blackman window function produces better effect than the other two window functions in the measurement of the standard phase grating.

The Gemini Planet Imager Calibration Wavefront Sensor Instrument

NASA Technical Reports Server (NTRS)

Wallace, J. Kent; Burruss, Rick S.; Bartos, Randall D.; Trinh, Thang Q.; Pueyo, Laurent A.; Fregoso, Santos F.; Angione, John R.; Shelton, J. Chris

2010-01-01

The Gemini Planet Imager is an extreme adaptive optics system that will employ an apodized-pupil coronagraph to make direct detections of faint companions of nearby stars to a contrast level of the 10(exp -7) within a few lambda/D of the parent star. Such high contrasts from the ground require exquisite wavefront sensing and control both for the AO system as well as for the coronagraph. Un-sensed non-common path phase and amplitude errors after the wavefront sensor dichroic but before the coronagraph would lead to speckles which would ultimately limit the contrast. The calibration wavefront system for GPI will measure the complex wavefront at the system pupil before the apodizer and provide slow phase corrections to the AO system to mitigate errors that would cause a loss in contrast. The calibration wavefront sensor instrument for GPI has been built. We will describe the instrument and its performance.

An annular superposition integral for axisymmetric radiators.

PubMed

Kelly, James F; McGough, Robert J

2007-02-01

A fast integral expression for computing the nearfield pressure is derived for axisymmetric radiators. This method replaces the sum of contributions from concentric annuli with an exact double integral that converges much faster than methods that evaluate the Rayleigh-Sommerfeld integral or the generalized King integral. Expressions are derived for plane circular pistons using both continuous wave and pulsed excitations. Several commonly used apodization schemes for the surface velocity distribution are considered, including polynomial functions and a "smooth piston" function. The effect of different apodization functions on the spectral content of the wave field is explored. Quantitative error and time comparisons between the new method, the Rayleigh-Sommerfeld integral, and the generalized King integral are discussed. At all error levels considered, the annular superposition method achieves a speed-up of at least a factor of 4 relative to the point-source method and a factor of 3 relative to the generalized King integral without increasing the computational complexity.

Transmission and group-delay characterization of coupled resonator optical waveguides apodized through the longitudinal offset technique.

PubMed

Doménech, J D; Muñoz, P; Capmany, J

2011-01-15

In this Letter, the amplitude and group delay characteristics of coupled resonator optical waveguides apodized through the longitudinal offset technique are presented. The devices have been fabricated in silicon-on-insulator technology employing deep ultraviolet lithography. The structures analyzed consisted of three racetracks resonators uniform (nonapodized) and apodized with the aforementioned technique, showing a delay of 5 ± 3 ps and 4 ± 0.5 ps over 1.6 and 1.4 nm bandwidths, respectively.

PIZZA: a phase-induced zonal Zernike apodization designed for stellar coronagraphy

NASA Astrophysics Data System (ADS)

Martinache, Frantz

2004-08-01

I explore here the possibilities offered by the general formalism of coronagraphy for the very special case of phase contrast. This technique, invented by Zernike, is commonly used in microscopy, to see phase objects such as micro-organisms, and in strioscopy, to control the quality of optics polishing. It may find application in telescope pupil apodization with significant advantages over classical pupil apodization techniques, including high throughput and no off-axis resolution loss, which is essential for exoplanet imaging.

Protecting cells by protecting their vulnerable lysosomes: Identification of a new mechanism for preserving lysosomal functional integrity upon oxidative stress

PubMed Central

Pascua-Maestro, Raquel

2017-01-01

Environmental insults such as oxidative stress can damage cell membranes. Lysosomes are particularly sensitive to membrane permeabilization since their function depends on intraluminal acidic pH and requires stable membrane-dependent proton gradients. Among the catalog of oxidative stress-responsive genes is the Lipocalin Apolipoprotein D (ApoD), an extracellular lipid binding protein endowed with antioxidant capacity. Within the nervous system, cell types in the defense frontline, such as astrocytes, secrete ApoD to help neurons cope with the challenge. The protecting role of ApoD is known from cellular to organism level, and many of its downstream effects, including optimization of autophagy upon neurodegeneration, have been described. However, we still cannot assign a cellular mechanism to ApoD gene that explains how this protection is accomplished. Here we perform a comprehensive analysis of ApoD intracellular traffic and demonstrate its role in lysosomal pH homeostasis upon paraquat-induced oxidative stress. By combining single-lysosome in vivo pH measurements with immunodetection, we demonstrate that ApoD is endocytosed and targeted to a subset of vulnerable lysosomes in a stress-dependent manner. ApoD is functionally stable in this acidic environment, and its presence is sufficient and necessary for lysosomes to recover from oxidation-induced alkalinization, both in astrocytes and neurons. This function is accomplished by preventing lysosomal membrane permeabilization. Two lysosomal-dependent biological processes, myelin phagocytosis by astrocytes and optimization of neurodegeneration-triggered autophagy in a Drosophila in vivo model, require ApoD-related Lipocalins. Our results uncover a previously unknown biological function of ApoD, member of the finely regulated and evolutionary conserved gene family of extracellular Lipocalins. They set a lipoprotein-mediated regulation of lysosomal membrane integrity as a new mechanism at the hub of many cellular functions, critical for the outcome of a wide variety of neurodegenerative diseases. These results open therapeutic opportunities by providing a route of entry and a repair mechanism for lysosomes in pathological situations. PMID:28182653

Development of high damage threshold laser-machined apodizers and gain filters for laser applications

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

Rambo, Patrick; Schwarz, Jens; Kimmel, Mark

We have developed high damage threshold filters to modify the spatial profile of a high energy laser beam. The filters are formed by laser ablation of a transmissive window. The ablation sites constitute scattering centers which can be filtered in a subsequent spatial filter. Finally, by creating the filters in dielectric materials, we see an increased laser-induced damage threshold from previous filters created using ‘metal on glass’ lithography.

Development of high damage threshold laser-machined apodizers and gain filters for laser applications

DOE PAGES

Rambo, Patrick; Schwarz, Jens; Kimmel, Mark; ...

2016-09-27

We have developed high damage threshold filters to modify the spatial profile of a high energy laser beam. The filters are formed by laser ablation of a transmissive window. The ablation sites constitute scattering centers which can be filtered in a subsequent spatial filter. Finally, by creating the filters in dielectric materials, we see an increased laser-induced damage threshold from previous filters created using ‘metal on glass’ lithography.

APOD Mission Status and Observations by VLBI

NASA Astrophysics Data System (ADS)

Tang, Geshi; Sun, Jing; Li, Xie; Liu, Shushi; Chen, Guangming; Ren, Tianpeng; Wang, Guangli

2016-12-01

On September 20, 2015, 20 satellites were successfully launched from the TaiYuan Satellite Launch Center by a Chinese CZ-6 test rocket and are, since then, operated in a circular, near-polar orbit at an altitude of 520 km. Among these satellites, a set of four CubSats, named APOD (Atmospheric density detection and Precise Orbit Determination), are intended for atmospheric density in-situ detection and derivation via precise orbit. The APOD satellites, manufactured by DFH Co., carry a number of instruments including a density detector, a dual-frequency GNSS (GPS/BD) receiver, an SLR reflector, and a VLBI S/X beacon. The APOD mission aims at detecting the atmospheric density below 520 km. The ground segment is controlled by BACC (Beijing Aerospace Control Center) including payload operation as well as science data receiving, processing, archiving, and distribution. Currently, the in-orbit test of the nano-satellites and their payloads are completed, and preliminary results show that the precision of the orbit determination is about 10 cm derived from both an overlap comparison and an SLR observation validation. The in-situ detected density calibrated by orbit-derived density demonstrates that the accuracy of atmospheric mass density is approximately 4.191×10^{-14} kgm^{-3}, about 5.5% of the measurement value. Since three space-geodetic techniques (i.e., GNSS, SLR, and VLBI) are co-located on the APOD nano-satellites, the observations can be used for combination and validation in order to detect systematic differences. Furthermore, the observations of the APOD satellites by VLBI radio telescopes can be used in an ideal fashion to link the dynamical reference frames of the satellite with the terrestrial and, most importantly, with the celestial reference frame as defined by the positions of quasars. The possibility of observing the APOD satellites by IVS VLBI radio telescopes will be analyzed, considering continental-size VLBI observing networks and the small telescopes with sufficient speed.

New apodizing functions for Fourier spectrometry

NASA Technical Reports Server (NTRS)

Norton, R. H.; Beer, R.

1976-01-01

A new class of apodizing functions suitable for Fourier spectrometry (and similar applications) is introduced. From this class, three specific functions are discussed in detail, and the resulting instrumental line shapes are compared to numerous others proposed for the same purpose.

An annular superposition integral for axisymmetric radiators

PubMed Central

Kelly, James F.; McGough, Robert J.

2007-01-01

A fast integral expression for computing the nearfield pressure is derived for axisymmetric radiators. This method replaces the sum of contributions from concentric annuli with an exact double integral that converges much faster than methods that evaluate the Rayleigh-Sommerfeld integral or the generalized King integral. Expressions are derived for plane circular pistons using both continuous wave and pulsed excitations. Several commonly used apodization schemes for the surface velocity distribution are considered, including polynomial functions and a “smooth piston” function. The effect of different apodization functions on the spectral content of the wave field is explored. Quantitative error and time comparisons between the new method, the Rayleigh-Sommerfeld integral, and the generalized King integral are discussed. At all error levels considered, the annular superposition method achieves a speed-up of at least a factor of 4 relative to the point-source method and a factor of 3 relative to the generalized King integral without increasing the computational complexity. PMID:17348500

Identification of an AR Mutation-Negative Class of Androgen Insensitivity by Determining Endogenous AR Activity.

PubMed

Hornig, N C; Ukat, M; Schweikert, H U; Hiort, O; Werner, R; Drop, S L S; Cools, M; Hughes, I A; Audi, L; Ahmed, S F; Demiri, J; Rodens, P; Worch, L; Wehner, G; Kulle, A E; Dunstheimer, D; Müller-Roßberg, E; Reinehr, T; Hadidi, A T; Eckstein, A K; van der Horst, C; Seif, C; Siebert, R; Ammerpohl, O; Holterhus, P-M

2016-11-01

Only approximately 85% of patients with a clinical diagnosis complete androgen insensitivity syndrome and less than 30% with partial androgen insensitivity syndrome can be explained by inactivating mutations in the androgen receptor (AR) gene. The objective of the study was to clarify this discrepancy by in vitro determination of AR transcriptional activity in individuals with disorders of sex development (DSD) and male controls. Quantification of DHT-dependent transcriptional induction of the AR target gene apolipoprotein D (APOD) in cultured genital fibroblasts (GFs) (APOD assay) and next-generation sequencing of the complete coding and noncoding AR locus. The study was conducted at a university hospital endocrine research laboratory. GFs from 169 individuals were studied encompassing control males (n = 68), molecular defined DSD other than androgen insensitivity syndrome (AIS; n = 18), AR mutation-positive AIS (n = 37), and previously undiagnosed DSD including patients with a clinical suspicion of AIS (n = 46). There were no interventions. DHT-dependent APOD expression in cultured GF and AR mutation status in 169 individuals was measured. The APOD assay clearly separated control individuals (healthy males and molecular defined DSD patients other than AIS) from genetically proven AIS (cutoff < 2.3-fold APOD-induction; 100% sensitivity, 93.3% specificity, P < .0001). Of 46 DSD individuals with no AR mutation, 17 (37%) fell below the cutoff, indicating disrupted androgen signaling. AR mutation-positive AIS can be reliably identified by the APOD assay. Its combination with next-generation sequencing of the AR locus uncovered an AR mutation-negative, new class of androgen resistance, which we propose to name AIS type II. Our data support the existence of cellular components outside the AR affecting androgen signaling during sexual differentiation with high clinical relevance.

Effect of central obscuration on the LDR point spread function

NASA Technical Reports Server (NTRS)

Vanzyl, Jakob J.

1988-01-01

It is well known that Gaussian apodization of an aperture reduces the sidelobe levels of its point spread function (PSF). In the limit where the standard deviation of the Gaussian function is much smaller than the diameter of the aperture, the sidelobes completely disappear. However, when Gaussian apodization is applied to the Large Deployable Reflector (LDR) array consisting of 84 hexagonal panels, it is found that the sidelobe level only decreases by about 2.5 dB. The reason for this is explained. The PSF is shown for an array consisting of 91 uniformly illuminated hexagonal apertures; this array is identical to the LDR array, except that the central hole in the LDR array is filled with seven additional panels. For comparison, the PSF of the uniformly illuminated LDR array is shown. Notice that it is already evident that the sidelobe structure of the LDR array is different from that of the full array of 91 panels. The PSF's of the same two arrays are shown, but with the illumination apodized with a Gaussian function to have 20 dB tapering at the edges of the arrays. While the sidelobes of the full array have decreased dramatically, those of the LDR array changed in structure, but stayed at almost the same level. This result is not completely surprising, since the Gaussian apodization tends to emphasize the contributions from the central portion of the array; exactly where the hole in the LDR array is located. The two most important conclusions are: the size of the central hole should be minimized, and a simple Gaussian apodization scheme to suppress the sidelobes in the PSF should not be used. A more suitable apodization scheme would be a Gaussian annular ring.

Apodization of beams in an optical interferometer

NASA Technical Reports Server (NTRS)

Ames, Lawrence L. (Inventor); Dutta, Kalyan (Inventor)

2006-01-01

An interferometry apparatus comprises one or more beam generators, a detector, and a plurality of optical paths along which one or more beams of light propagate. Disposed along at least one of the optical paths is an apodization mask to shape one of the beams.

Apodized RFI filtering of synthetic aperture radar images

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

Doerry, Armin Walter

2014-02-01

Fine resolution Synthetic Aperture Radar (SAR) systems necessarily require wide bandwidths that often overlap spectrum utilized by other wireless services. These other emitters pose a source of Radio Frequency Interference (RFI) to the SAR echo signals that degrades SAR image quality. Filtering, or excising, the offending spectral contaminants will mitigate the interference, but at a cost of often degrading the SAR image in other ways, notably by raising offensive sidelobe levels. This report proposes borrowing an idea from nonlinear sidelobe apodization techniques to suppress interference without the attendant increase in sidelobe levels. The simple post-processing technique is termed Apodized RFImore » Filtering (ARF).« less

History and development of the apodized diffractive intraocular lens.

PubMed

Davison, James A; Simpson, Michael J

2006-05-01

The ReSTOR intraocular lens presents a unique apodized diffractive design within a refractive foldable acrylic optic, which makes an unprecedented level of mulifocal optical performance available. We describe the history and principles of diffractive optics used in the development of this refractive-diffractive IOL.

ExSPO: A Discovery Class Apodized Square Aperture (ASA) Expo-Planet Imaging Space Telescope Concept

NASA Technical Reports Server (NTRS)

Gezari, D.; Harwit, M.; Lyon, R.; Melnick, G.; Papaliolos, G.; Ridgeway, S.; Woodruff, R.; Nisenson, P.; Oegerle, William (Technical Monitor)

2002-01-01

ExSPO is a Discovery Class (approx. 4 meter) apodized square aperture (ASA) space telescope mission designed for direct imaging of extrasolar Earth-like planets, as a precursor to TPF. The ASA telescope concept, instrument design, capabilities, mission plan and science goals are described.

Community Radiative Transfer Model Applications - A Study of the Retrieval of Trace Gases in the Atmosphere from Cross-track Infrared Sounder (CrIS) Data of a Full-spectral Resolution

NASA Astrophysics Data System (ADS)

Liu, Q.; Nalli, N. R.; Tan, C.; Zhang, K.; Iturbide, F.; Wilson, M.; Zhou, L.

2015-12-01

The Community Radiative Transfer Model (CRTM) [3] operationally supports satellite radiance assimilation for weather forecasting, sensor data verification, and the retrievals of satellite products. The CRTM has been applied to UV and visible sensors, infrared and microwave sensors. The paper will demonstrate the applications of the CRTM, in particular radiative transfer in the retrieva algorithm. The NOAA Unique CrIS/ATMS Processing System (NUCAPS) operationally generates vertical profiles of atmospheric temperature (AVTP) and moisture (AVMP) from Suomi NPP Cross-track Infrared Sounder (CrIS) and Advanced Technology Microwave Sounder (ATMS) measurements. Current operational CrIS data have reduced spectral resolution: 1.25 cm-1 for a middle wave band and 2.5 cm-1 for a short-wave wave band [1]. The reduced spectral data largely degraded the retrieval accuracy of trace gases. CrIS full spectral data are also available now which have single spectral resolution of 0.625 cm-1 for all of the three bands: long-wave band, middle wave band, and short-wave band. The CrIS full-spectral resolution data is critical to the retrieval of trace gases such as O3, CO [2], CO2, and CH4. In this paper, we use the Community Radiative Transfer Model (CRTM) to study the impact of the CrIS spectral resolution on the retrieval accuracy of trace gases. The newly released CRTM version 2.2.1 can simulates Hamming-apodized CrIS radiance of a full-spectral resolution. We developed a small utility that can convert the CRTM simulated radiance to un-apodized radiance. The latter has better spectral information which can be helpful to the retrievals of the trace gases. The retrievals will be validated using both NWP model data as well as the data collected during AEROSE expeditions [4]. We will also discuss the sensitivity on trace gases between apodized and un-apodized radiances. References[1] Gambacorta, A., et al.(2013), IEEE Lett., 11(9), doi:10.1109/LGRS.2014.230364, 1639-1643. [2] Han, Y., et al. (2013), JGR.,118, 12,734-12,748, doi:10.1002/2013JD020344. [3] Liu, Q., and S. Boukabara (2013), Remote Sen. Environ., 140 (2014) 744-754. [4] Nalli, N. R. et al(2011) . Bulletin of the American Meteorological Society, (92), 765-789.

VLBI observations to the APOD satellite

NASA Astrophysics Data System (ADS)

Sun, Jing; Tang, Geshi; Shu, Fengchun; Li, Xie; Liu, Shushi; Cao, Jianfeng; Hellerschmied, Andreas; Böhm, Johannes; McCallum, Lucia; McCallum, Jamie; Lovell, Jim; Haas, Rüdiger; Neidhardt, Alexander; Lu, Weitao; Han, Songtao; Ren, Tianpeng; Chen, Lue; Wang, Mei; Ping, Jinsong

2018-02-01

The APOD (Atmospheric density detection and Precise Orbit Determination) is the first LEO (Low Earth Orbit) satellite in orbit co-located with a dual-frequency GNSS (GPS/BD) receiver, an SLR reflector, and a VLBI X/S dual band beacon. From the overlap statistics between consecutive solution arcs and the independent validation by SLR measurements, the orbit position deviation was below 10 cm before the on-board GNSS receiver got partially operational. In this paper, the focus is on the VLBI observations to the LEO satellite from multiple geodetic VLBI radio telescopes, since this is the first implementation of a dedicated VLBI transmitter in low Earth orbit. The practical problems of tracking a fast moving spacecraft with current VLBI ground infrastructure were solved and strong interferometric fringes were obtained by cross-correlation of APOD carrier and DOR (Differential One-way Ranging) signals. The precision in X-band time delay derived from 0.1 s integration time of the correlator output is on the level of 0.1 ns. The APOD observations demonstrate encouraging prospects of co-location of multiple space geodetic techniques in space, as a first prototype.

A Millimetre-Wave Cuboid Solid Immersion Lens with Intensity-Enhanced Amplitude Mask Apodization

NASA Astrophysics Data System (ADS)

Yue, Liyang; Yan, Bing; Monks, James N.; Dhama, Rakesh; Wang, Zengbo; Minin, Oleg V.; Minin, Igor V.

2018-06-01

Photonic jet is a narrow, highly intensive, weak-diverging beam propagating into a background medium and can be produced by a cuboid solid immersion lens (SIL) in both transmission and reflection modes. Amplitude mask apodization is an optical method to further improve the spatial resolution of a SIL imaging system via reduction of waist size of photonic jet, but always leading to intensity loss due to central masking of the incoming plane wave. In this letter, we report a particularly sized millimetre-wave cuboid SIL with the intensity-enhanced amplitude mask apodization for the first time. It is able to simultaneously deliver extra intensity enhancement and waist narrowing to the produced photonic jet. Both numerical simulation and experimental verification of the intensity-enhanced apodization effect are demonstrated using a copper-masked Teflon cuboid SIL with 22-mm side length under radiation of a plane wave with 8-mm wavelength. Peak intensity enhancement and the lateral resolution of the optical system increase by about 36.0% and 36.4% in this approach, respectively.

Spacetime Symphony: APOD and Gravitational Waves

NASA Astrophysics Data System (ADS)

Cominsky, Lynn R.; Simonnet, Aurore; LIGO-Virgo Scientific Collaboration

2017-01-01

In 1915, Albert Einstein published his General Theory of Relativity. In this theory, gravity is not a force, but a property of space and time in the presence of massive objects. A century later, on September 14, 2015, the Laser Interferometer Gravitational-wave Observatory (LIGO) received the first confirmed gravitational wave signals. Now known as GW150914, the event represents the coalescence of two distant black holes that were previously in mutual orbit. The LIGO-Virgo Scientific Collaboration planned a detailed social media strategy to publicize the February 11, 2016 press conference that announced this discovery. Astronomy Picture of the Day (APOD) was a major factor in disseminating the now iconic imagery that was developed, and the LVC worked closely with APOD to ensure that the secrecy would be maintained throughout the press embargo period. Due to the success of our efforts, we repeated the process for the AAS press conference that announced GW151226, the second confirmed gravitational wave event. We have also repurposed the APOD imagery for an online course for community college instructors, as well as in a poster that will be available through CPEPphysics.org (Contemporary Physics Education Project).

Identification of an AR Mutation-Negative Class of Androgen Insensitivity by Determining Endogenous AR Activity

PubMed Central

Ukat, M.; Schweikert, H. U.; Hiort, O.; Werner, R.; Drop, S. L. S.; Cools, M.; Hughes, I. A.; Audi, L.; Ahmed, S. F.; Demiri, J.; Rodens, P.; Worch, L.; Wehner, G.; Kulle, A. E.; Dunstheimer, D.; Müller-Roßberg, E.; Reinehr, T.; Hadidi, A. T.; Eckstein, A. K.; van der Horst, C.; Seif, C.; Siebert, R.; Ammerpohl, O.; Holterhus, P.-M.

2016-01-01

Context: Only approximately 85% of patients with a clinical diagnosis complete androgen insensitivity syndrome and less than 30% with partial androgen insensitivity syndrome can be explained by inactivating mutations in the androgen receptor (AR) gene. Objective: The objective of the study was to clarify this discrepancy by in vitro determination of AR transcriptional activity in individuals with disorders of sex development (DSD) and male controls. Design: Quantification of DHT-dependent transcriptional induction of the AR target gene apolipoprotein D (APOD) in cultured genital fibroblasts (GFs) (APOD assay) and next-generation sequencing of the complete coding and noncoding AR locus. Setting: The study was conducted at a university hospital endocrine research laboratory. Patients: GFs from 169 individuals were studied encompassing control males (n = 68), molecular defined DSD other than androgen insensitivity syndrome (AIS; n = 18), AR mutation-positive AIS (n = 37), and previously undiagnosed DSD including patients with a clinical suspicion of AIS (n = 46). Intervention(s): There were no interventions. Main Outcome Measure(s): DHT-dependent APOD expression in cultured GF and AR mutation status in 169 individuals was measured. Results: The APOD assay clearly separated control individuals (healthy males and molecular defined DSD patients other than AIS) from genetically proven AIS (cutoff < 2.3-fold APOD-induction; 100% sensitivity, 93.3% specificity, P < .0001). Of 46 DSD individuals with no AR mutation, 17 (37%) fell below the cutoff, indicating disrupted androgen signaling. Conclusions: AR mutation-positive AIS can be reliably identified by the APOD assay. Its combination with next-generation sequencing of the AR locus uncovered an AR mutation-negative, new class of androgen resistance, which we propose to name AIS type II. Our data support the existence of cellular components outside the AR affecting androgen signaling during sexual differentiation with high clinical relevance. PMID:27583472

Application of CRAFT in two-dimensional NMR data processing.

PubMed

Krishnamurthy, Krish; Sefler, Andrea M; Russell, David J

2017-03-01

Two-dimensional (2D) data are typically truncated in both dimensions, but invariably and severely so in the indirect dimension. These truncated FIDs and/or interferograms are extensively zero filled, and Fourier transformation of such zero-filled data is always preceded by a rapidly decaying apodization function. Hence, the frequency line width in the spectrum (at least parallel to the evolution dimension) is almost always dominated by the apodization function. Such apodization-driven line broadening in the indirect (t 1 ) dimension leads to the lack of clear resolution of cross peaks in the 2D spectrum. Time-domain analysis (i.e. extraction of frequency, amplitudes, line width, and phase parameters directly from the FID, in this case via Bayesian modeling into a tabular format) of NMR data is another approach for spectral resonance characterization and quantification. The recently published complete reduction to amplitude frequency table (CRAFT) technique converts the raw FID data (i.e. time-domain data) into a table of frequencies, amplitudes, decay rate constants, and phases. CRAFT analyses of time-domain data require minimal or no apodization prior to extraction of the four parameters. We used the CRAFT processing approach for the decimation of the interferograms and compared the results from a variety of 2D spectra against conventional processing with and without linear prediction. The results show that use of the CRAFT technique to decimate the t 1 interferograms yields much narrower spectral line width of the resonances, circumventing the loss of resolution due to apodization. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Classification images for localization performance in ramp-spectrum noise.

PubMed

Abbey, Craig K; Samuelson, Frank W; Zeng, Rongping; Boone, John M; Eckstein, Miguel P; Myers, Kyle

2018-05-01

This study investigates forced localization of targets in simulated images with statistical properties similar to trans-axial sections of x-ray computed tomography (CT) volumes. A total of 24 imaging conditions are considered, comprising two target sizes, three levels of background variability, and four levels of frequency apodization. The goal of the study is to better understand how human observers perform forced-localization tasks in images with CT-like statistical properties. The transfer properties of CT systems are modeled by a shift-invariant transfer function in addition to apodization filters that modulate high spatial frequencies. The images contain noise that is the combination of a ramp-spectrum component, simulating the effect of acquisition noise in CT, and a power-law component, simulating the effect of normal anatomy in the background, which are modulated by the apodization filter as well. Observer performance is characterized using two psychophysical techniques: efficiency analysis and classification image analysis. Observer efficiency quantifies how much diagnostic information is being used by observers to perform a task, and classification images show how that information is being accessed in the form of a perceptual filter. Psychophysical studies from five subjects form the basis of the results. Observer efficiency ranges from 29% to 77% across the different conditions. The lowest efficiency is observed in conditions with uniform backgrounds, where significant effects of apodization are found. The classification images, estimated using smoothing windows, suggest that human observers use center-surround filters to perform the task, and these are subjected to a number of subsequent analyses. When implemented as a scanning linear filter, the classification images appear to capture most of the observer variability in efficiency (r 2 = 0.86). The frequency spectra of the classification images show that frequency weights generally appear bandpass in nature, with peak frequency and bandwidth that vary with statistical properties of the images. In these experiments, the classification images appear to capture important features of human-observer performance. Frequency apodization only appears to have a significant effect on performance in the absence of anatomical variability, where the observers appear to underweight low spatial frequencies that have relatively little noise. Frequency weights derived from the classification images generally have a bandpass structure, with adaptation to different conditions seen in the peak frequency and bandwidth. The classification image spectra show relatively modest changes in response to different levels of apodization, with some evidence that observers are attempting to rebalance the apodized spectrum presented to them. © 2018 American Association of Physicists in Medicine.

Photonic Hilbert transformers based on laterally apodized integrated waveguide Bragg gratings on a SOI wafer.

PubMed

Bazargani, Hamed Pishvai; Burla, Maurizio; Chrostowski, Lukas; Azaña, José

2016-11-01

We experimentally demonstrate high-performance integer and fractional-order photonic Hilbert transformers based on laterally apodized Bragg gratings in a silicon-on-insulator technology platform. The sub-millimeter-long gratings have been fabricated using single-etch electron beam lithography, and the resulting HT devices offer operation bandwidths approaching the THz range, with time-bandwidth products between 10 and 20.

The PIAA Coronagraph: Optical design and Diffraction Effects

NASA Astrophysics Data System (ADS)

Pluzhnik, E. A.; Guyon, O.; Ridgway, S.; Martinache, F.; Woodruff, R.; Blain, C.; Galicher, R.

2005-12-01

Properly apodized pupils are suitable for high dynamical range imaging of extrasolar terrestrial planets. Phase-induced amplitude apodization (PIAA) of the telescope pupil (Guyon 2003) combines the advantages of classical pupil apodization with full throughput, no loss of angular resolution and low chromaticity. Diffraction propagation effects can decrease both the achieved contrast and the spectral bandwidth of the coronagraph. We show here how the diffraction effects in the PIAA optics can be corrected by an appropriate optical design. The proposed hybrid coronagraph design preserves the 10-10 PSF contrast at ≈ 1.5 λ /d required for efficient exoplanet imaging over the whole visible spectrum. This work was carried out under JPL contract numbers 1254445 and 1257767 for Development of Technologies for the Terrestrial Planet Finder Mission, with the support and hospitality of the National Astronomical Observatory of Japan.

Effect of Nd:YAG laser capsulotomy on refraction in multifocal apodized diffractive pseudophakia.

PubMed

Vrijman, Violette; van der Linden, Jan Willem; Nieuwendaal, Carla P; van der Meulen, Ivanka J E; Mourits, Maarten P; Lapid-Gortzak, Ruth

2012-08-01

To evaluate the effect on refraction of neodymium:YAG (Nd:YAG) laser posterior capsulotomy for posterior capsule opacification (PCO), and to evaluate the correlation between automated and subjective refraction in multifocal apodized diffractive pseudophakia. A retrospective study of 75 pseudophakic eyes (50 patients) with multifocal apodized diffractive pseudophakia, treated for PCO with Nd:YAG laser posterior capsulotomy, was performed. Pre- and postintervention values of refractive and visual parameters were compared. The outcomes of autorefraction and subjective refraction were also compared. Uncorrected and corrected distance visual acuity improved significantly after Nd:YAG capsulotomy (P<.001). No significant changes were noted in defocus equivalent, astigmatic power vectors J(0) and J(45), and overall blurring strength in subjective refraction and autorefraction. Spherical equivalent changed significantly in autorefraction (P=.008), but not in subjective refraction. Autorefraction and subjective refraction were highly correlated in spherical equivalent, defocus equivalent, and blurring strength (r(2)>0.59). In approximately 7% of eyes, a change of more than 0.50 diopters in spherical equivalent in subjective refraction occurred. In most cases, Nd:YAG laser capsulotomy in patients with multifocal pseudophakia did not result in a change in refraction. However, 7% of eyes experienced a significant change in subjective refraction. Autorefraction correlated well with subjective refraction in apodized diffractive multifocal IOLs. Copyright 2012, SLACK Incorporated.

Variations in apolipoprotein D and sigma non-opioid intracellular receptor 1 genes with relation to risk, severity and outcome of ischemic stroke.

PubMed

Lövkvist, Håkan; Jönsson, Ann-Cathrin; Luthman, Holger; Jood, Katarina; Jern, Christina; Wieloch, Tadeusz; Lindgren, Arne

2014-09-28

In experimental studies, the apolipoprotein D (APOD) and the sigma receptor type 1 (SIGMAR1) have been related to processes of brain damage, repair and plasticity. We examined blood samples from 3081 ischemic stroke (IS) patients and 1595 control subjects regarding 10 single nucleotide polymorphisms (SNPs) in the APOD (chromosomal location 3q29) and SIGMAR1 (chromosomal location 9p13) genes to find possible associations with IS risk, IS severity (NIHSS-score) and recovery after IS (modified Rankin Scale, mRS, at 90 days). Simple/multiple logistic regression and Spearman's rho were utilized for the analyses. Among the SNPs analyzed, rs7659 within the APOD gene showed a possible association with stroke risk (OR = 1.12; 95% CI: 1.01-1.25; P = 0.029) and stroke severity (NIHSS ≥ 16) (OR = 0.70; 95% CI: 0.54-0.92; P = 0.009) when controlling for age, sex and vascular risk factors for stroke. No SNP showed an association with stroke recovery (mRS). We conclude that the SNP rs7659 within the APOD gene might be related to risk and severity of ischemic stroke in patients.

Optical apparatus using liquid crystals for shaping the spatial intensity of optical beams having designated wavelengths

DOEpatents

Jacobs, S.D.; Cerqua, K.A.

1987-07-14

The spatial intensity profile of an optical beam of designated wavelengths, such as a laser beam, is shaped (the beam is apodized) by means of cholesteric liquid crystals of opposite chirality disposed successively along the path of the beam. The crystals have curved surfaces, which may be defined by a lens which defines the thickness of the liquid crystal fluid gap in a liquid crystal cell, so as to vary the selective reflection of the designated wavelength across the aperture of the beam. In this way, a soft aperture is provided. By using tandem cell pairs having liquid crystals of opposite chirality, but of different pitch, and with lenses of different curvature, beams of different wavelengths which are projected colinearly along the path may be individually tailored in spatial intensity profile. 11 figs.

Optical apparatus using liquid crystals for shaping the spatial intensity of optical beams having designated wavelengths

DOEpatents

Jacobs, Stephen D.; Cerqua, Kathleen A.

1987-01-01

The spatial intensity profile of an optical beam of designated wavelengths, such as a laser beam, is shaped (the beam is apodized) by means of cholesteric liquid crystals of opposite chirality disposed successively along the path of the beam. The crystals have curved surfaces, which may be defined by a lens which defines the thickness of the liquid crystal fluid gap in a liquid crystal cell, so as to vary the selective reflection of the designated wavelength across the aperture of the beam. In this way, a soft aperture is provided. By using tandem cell pairs having liquid crystals of opposite chirality, but of different pitch, and with lenses of different curvature, beams of different wavelengths which are projected colinearly along the path may be individually tailored in spatial intensity profile.

Tip/tilt optimizations for polynomial apodized vortex coronagraphs on obscured telescope pupils

NASA Astrophysics Data System (ADS)

Fogarty, Kevin; Pueyo, Laurent; Mazoyer, Johan; N'Diaye, Mamadou

2017-09-01

Obstructions due to large secondary mirrors, primary mirror segmentation, and secondary mirror support struts all introduce diffraction artifacts that limit the performance offered by coronagraphs. However, just as vortex coronagraphs provides theoretically ideal cancellation of on-axis starlight for clear apertures, the Polynomial Apodized Vortex Coronagraph (PAVC) completely blocks on-axis light for apertures with central obscurations, and delivers off-axis throughput that improves as the topological charge of the vortex increases. We examine the sensitivity of PAVC designs to tip/tilt aberrations and stellar angular size, and discuss methods for mitigating these effects. By imposing additional constraints on the pupil plane apodization, we decrease the sensitivity of the PAVC to the small positional shifts of the on-axis source induced by either tip/tilt or stellar angular size; providing a route to overcoming an important hurdle facing the performance of vortex coronagraphs on telescopes with complicated pupils.

Defect of focus in two-line resolution with Hanning amplitude filters

NASA Astrophysics Data System (ADS)

Karunasagar, D.; Bhikshamaiah, G.; Keshavulu Goud, M.; Lacha Goud, S.

In the presence of defocusing the modified Sparrow limits of resolution for two-line objects have been investigated for a diffraction-limited coherent optical system apodized by generalized Hanning amplitude filters. These limits have been studied as a function of different parameters such as intensity ratio, the order of the filter for various amounts of apodization parameter. Results reveal that in some situations the defocusing is effective in enhancing the resolution of an optical system.

The Efffect of Image Apodization on Global Mode Parameters and Rotational Inversions

NASA Astrophysics Data System (ADS)

Larson, Tim; Schou, Jesper

2016-10-01

It has long been known that certain systematic errors in the global mode analysis of data from both MDI and HMI depend on how the input images were apodized. Recently it has come to light, while investigating a six-month period in f-mode frequencies, that mode coverage is highest when B0 is maximal. Recalling that the leakage matrix is calculated in the approximation that B0=0, it comes as a surprise that more modes are fitted when the leakage matrix is most incorrect. It is now believed that the six-month oscillation has primarily to do with what portion of the solar surface is visible. Other systematic errors that depend on the part of the disk used include high-latitude anomalies in the rotation rate and a prominent feature in the normalized residuals of odd a-coefficients. Although the most likely cause of all these errors is errors in the leakage matrix, extensive recalculation of the leaks has not made any difference. Thus we conjecture that another effect may be at play, such as errors in the noise model or one that has to do with the alignment of the apodization with the spherical harmonics. In this poster we explore how differently shaped apodizations affect the results of inversions for internal rotation, for both maximal and minimal absolute values of B0.

An apodized Kepler periodogram for separating planetary and stellar activity signals

PubMed Central

Gregory, Philip C.

2016-01-01

A new apodized Keplerian (AK) model is proposed for the analysis of precision radial velocity (RV) data to model both planetary and stellar activity (SA) induced RV signals. A symmetrical Gaussian apodization function with unknown width and centre can distinguish planetary signals from SA signals on the basis of the span of the apodization window. The general model for m AK signals includes a linear regression term between RV and the SA diagnostic log (R′hk), as well as an extra Gaussian noise term with unknown standard deviation. The model parameters are explored using a Bayesian fusion Markov chain Monte Carlo code. A differential version of the generalized Lomb–Scargle periodogram that employs a control diagnostic provides an additional way of distinguishing SA signals and helps guide the choice of new periods. Results are reported for a recent international RV blind challenge which included multiple state-of-the-art simulated data sets supported by a variety of SA diagnostics. In the current implementation, the AK method achieved a reduction in SA noise by a factor of approximately 6. Final parameter estimates for the planetary candidates are derived from fits that include AK signals to model the SA components and simple Keplerians to model the planetary candidates. Preliminary results are also reported for AK models augmented by a moving average component that allows for correlations in the residuals. PMID:27346979

Preliminary study of synthetic aperture tissue harmonic imaging on in-vivo data

NASA Astrophysics Data System (ADS)

Rasmussen, Joachim H.; Hemmsen, Martin C.; Madsen, Signe S.; Hansen, Peter M.; Nielsen, Michael B.; Jensen, Jørgen A.

2013-03-01

A method for synthetic aperture tissue harmonic imaging is investigated. It combines synthetic aperture sequen- tial beamforming (SASB) with tissue harmonic imaging (THI) to produce an increased and more uniform spatial resolution and improved side lobe reduction compared to conventional B-mode imaging. Synthetic aperture sequential beamforming tissue harmonic imaging (SASB-THI) was implemented on a commercially available BK 2202 Pro Focus UltraView ultrasound system and compared to dynamic receive focused tissue harmonic imag- ing (DRF-THI) in clinical scans. The scan sequence that was implemented on the UltraView system acquires both SASB-THI and DRF-THI simultaneously. Twenty-four simultaneously acquired video sequences of in-vivo abdominal SASB-THI and DRF-THI scans on 3 volunteers of 4 different sections of liver and kidney tissues were created. Videos of the in-vivo scans were presented in double blinded studies to two radiologists for image quality performance scoring. Limitations to the systems transmit stage prevented user defined transmit apodization to be applied. Field II simulations showed that side lobes in SASB could be improved by using Hanning transmit apodization. Results from the image quality study show, that in the current configuration on the UltraView system, where no transmit apodization was applied, SASB-THI and DRF-THI produced equally good images. It is expected that given the use of transmit apodization, SASB-THI could be further improved.

Post-Coronagraph Wavefront Sensor for Gemini Planet Imager

NASA Technical Reports Server (NTRS)

Wallace, J. Kent; Burruss, Rick; Pueyo, Laurent; Soummer, Remi; Shelton, Chris; Bartos, Randall; Fregoso, Felipe; Nemati, Bijan; Best, Paul; Angione, John

2009-01-01

The calibration wavefront system for the Gemini Planet Imager (GPI) will measure the complex wavefront at the apodized pupil and provide slow phase errors to the AO system to mitigate against image plane speckles that would cause a loss in contrast. This talk describes both the low-order and high-order sensors in the calibration wavefront sensor and how the information is combined to form the wavefront estimate before the coronagraph. We will show laboratory results from our calibration testbed that demonstrate the subsystem performance at levels commensurate with those required on the final instrument.

Steep and flat bandpass filter using linearly chirped and apodized fiber Bragg grating

NASA Astrophysics Data System (ADS)

Wu, Xunqi; Jacquet, Jo"l.; Duan, Guanghua

2010-02-01

The development of new optical systems requires the design of novel components that fulfill the market constraints. In particular, low loss, high optical rejection and low cost narrowband filters can play an important role for the introduction of the Wavelength Division Multiplexing (WDM) technology in the local network. So, a novel fiber filter is proposed in this article, with a special combined apodized Linearly Chirped Fiber Bragg Grating (LCFBG) which presents the preferable flat-top and steep-edge characteristics. In the design, we use a continuum cavity condition which is obtained when the effective round-trip phase of oscillated wavelength band is kept identical over the whole Bragg wavelength range. And the transmission spectra are calculated by the reconstruction of the matrixes with the continuum oscillation condition. Therefore, our works show that the ideal square shaped filter is obtained with a lower chirp value relatively together with symmetric reflectivity on both mirrors. The coupling coefficient of the FBG is adjusted to get the same reflectivity values and then to get a transmission filter close to unity. We have then introduced an apodization function of the filter to get a flatter transfer function. Various apodizations schemes have been tested. In this paper, we design and analyze a type of continuum fiber filter with the cavity formed between mirror and apodized LCFBG as reflectors. We calculate firstly the reflectivity, the transmissivity and the group time delay of LCFBG modeled by a simple and practical Transfer Matrix Method (TMM), and then the cavity is reconstructed by TMM, the length of the oscillated cavity is calculated by the continuum oscillation condition, so the output of transmission from the side of LCFBG is continuous in the corresponded reflected bandwidth of LCFBG. We obtain the results and discuss some characteristics of this type of continuum fiber filter.

A space telescope for infrared spectroscopy of earth-like planets

NASA Technical Reports Server (NTRS)

Angel, J. R. P.; Cheng, A. Y. S.; Woolf, N. J.

1986-01-01

It is shown here that a space telescope of 16 m diameter, apodized in a new way, could image and measure oxygen n in the thermal infrared spectral of earthlike planets up to 4 pc away. The problems of visible light imaging for this case are discussed, and it is argued that imaging the thermal emission, with greatly reduced requirements for gain and hence surface accuracy, is preferable. The requirements for such imaging are discussed, including the apodization solution.

Strange Horizons: Teaching Usual and Unusual Atmospheric Effects using APOD

NASA Astrophysics Data System (ADS)

Wilson, Teresa

2015-01-01

Unusual Sun and moonsets are not only photogenic -- they are educational. Images appearing on the Astronomy Picture of the Day (APOD) that demonstrate dramatic examples of the green flash, the Moon illusion, Fata Morgana, and the Etruscan vase effect are discussed in terms of how they demonstrate atmospheric refraction, chromatic aberration, and temperature inversions. A lesson plan is given for undergraduate classrooms as well as estimates of how each effect might alter the perceived time of a common sunset.

The pinwheel pupil discovery: exoplanet science & improved processing with segmented telescopes

NASA Astrophysics Data System (ADS)

Breckinridge, James Bernard

2018-01-01

In this paper, we show that by using a “pinwheel” architecture for the segmented primary mirror and curved supports for the secondary mirror, we can achieve a near uniform diffraction background in ground and space large telescope systems needed for high SNR exoplanet science. Also, the point spread function will be nearly rotationally symmetric, enabling improved digital image reconstruction. Large (>4-m) aperture space telescopes are needed to characterize terrestrial exoplanets by direct imaging coronagraphy. Launch vehicle volume constrains these apertures are segmented and deployed in space to form a large mirror aperture that is masked by the gaps between the hexagonal segments and the shadows of the secondary support system. These gaps and shadows over the pupil result in an image plane point spread function that has bright spikes, which may mask or obscure exoplanets.These telescope artifact mask faint exoplanets, making it necessary for the spacecraft to make a roll about the boresight and integrate again to make sure no planets are missed. This increases integration time, and requires expensive space-craft resources to do bore-sight roll.Currently the LUVOIR and HabEx studies have several significant efforts to develop special purpose A/O technology and to place complex absorbing apodizers over their Hex pupils to shape the unwanted diffracted light. These strong apodizers absorb light, decreasing system transmittance and reducing SNR. Implementing curved pupil obscurations will eliminate the need for the highly absorbing apodizers and thus result in higher SNR.Quantitative analysis of diffraction patterns that use the pinwheel architecture are compared to straight hex-segment edges with a straight-line secondary shadow mask to show a gain of over a factor of 100 by reducing the background. For the first-time astronomers are able to control and minimize image plane diffraction background “noise”. This technology will enable 10-m segmented apertures to perform nearly the same as a 10-meter monolith filled aperture. The pinwheel pupil will enable a significant gain in exoplanet SNR.

Apodized Pupil Lyot Coronagraphs for Arbitrary Apertures. II. Theoretical Properties and Application to Extremely Large Telescopes

NASA Astrophysics Data System (ADS)

Soummer, Rémi; Pueyo, Laurent; Ferrari, André; Aime, Claude; Sivaramakrishnan, Anand; Yaitskova, Natalia

2009-04-01

We study the application of Lyot coronagraphy to future Extremely Large Telescopes (ELTs), showing that Apodized Pupil Lyot Coronagraphs enable high-contrast imaging for exoplanet detection and characterization with ELTs. We discuss the properties of the optimal pupil apodizers for this application (generalized prolate spheroidal functions). The case of a circular aperture telescope with a central obstruction is considered in detail, and we discuss the effects of primary mirror segmentation and secondary mirror support structures as a function of the occulting mask size. In most cases where inner working distance is critical, e.g., for exoplanet detection, these additional features do not alter the solutions derived with just the central obstruction, although certain applications such as quasar-host galaxy coronagraphic observations could benefit from designs that explicitly accomodate ELT spider geometries. We illustrate coronagraphic designs for several ELT geometries including ESO/OWL, the Thirty Mirror Telescope, the Giant Magellan Telescope, and describe numerical methods for generating these designs.

Apodized grating coupler using fully-etched nanostructures

NASA Astrophysics Data System (ADS)

Wu, Hua; Li, Chong; Li, Zhi-Yong; Guo, Xia

2016-08-01

A two-dimensional apodized grating coupler for interfacing between single-mode fiber and photonic circuit is demonstrated in order to bridge the mode gap between the grating coupler and optical fiber. The grating grooves of the grating couplers are realized by columns of fully etched nanostructures, which are utilized to digitally tailor the effective refractive index of each groove in order to obtain the Gaussian-like output diffractive mode and then enhance the coupling efficiency. Compared with that of the uniform grating coupler, the coupling efficiency of the apodized grating coupler is increased by 4.3% and 5.7%, respectively, for the nanoholes and nanorectangles as refractive index tunes layer. Project supported by the National Natural Science Foundation of China (Grant Nos. 61222501, 61335004, and 61505003), the Specialized Research Fund for the Doctoral Program of Higher Education of China (Grant No. 20111103110019), the Postdoctoral Science Foundation of Beijing Funded Project, China (Grant No. Q6002012201502), and the Science and Technology Research Project of Jiangxi Provincial Education Department, China (Grant No. GJJ150998).

Coherent diffraction imaging of non-isolated object with apodized illumination.

PubMed

Khakurel, Krishna P; Kimura, Takashi; Joti, Yasumasa; Matsuyama, Satoshi; Yamauchi, Kazuto; Nishino, Yoshinori

2015-11-02

Coherent diffraction imaging (CDI) is an established lensless imaging method widely used at the x-ray regime applicable to the imaging of non-periodic materials. Conventional CDI can practically image isolated objects only, which hinders the broader application of the method. We present the imaging of non-isolated objects by employing recently proposed "non-scanning" apodized-illumination CDI at an optical wavelength. We realized isolated apodized illumination with a specially designed optical configuration and succeeded in imaging phase objects as well as amplitude objects. The non-scanning nature of the method is important particularly in imaging live cells and tissues, where fast imaging is required for non-isolated objects, and is an advantage over ptychography. We believe that our result of phase contrast imaging at an optical wavelength can be extended to the quantitative phase imaging of cells and tissues. The method also provides the feasibility of the lensless single-shot imaging of extended objects with x-ray free-electron lasers.

pureS2HAT: S 2HAT-based Pure E/B Harmonic Transforms

NASA Astrophysics Data System (ADS)

Grain, J.; Stompor, R.; Tristram, M.

2011-10-01

The pS2HAT routines allow efficient, parallel calculation of the so-called 'pure' polarized multipoles. The computed multipole coefficients are equal to the standard pseudo-multipoles calculated for the apodized sky maps of the Stokes parameters Q and U subsequently corrected by so-called counterterms. If the applied apodizations fullfill certain boundary conditions, these multipoles correspond to the pure multipoles. Pure multipoles of one type, i.e., either E or B, are ensured not to contain contributions from the other one, at least to within numerical artifacts. They can be therefore further used in the estimation of the sky power spectra via the pseudo power spectrum technique, which has to however correctly account for the applied apodization on the one hand, and the presence of the counterterms, on the other. In addition, the package contains the routines permitting calculation of the spin-weighted apodizations, given an input scalar, i.e., spin-0 window. The former are needed to compute the counterterms. It also provides routines for maps and window manipulations. The routines are written in C and based on the S2HAT library, which is used to perform all required spherical harmonic transforms as well as all inter-processor communication. They are therefore parallelized using MPI and follow the distributed-memory computational model. The data distribution patterns, pixelization choices, conventions etc are all as those assumed/allowed by the S2HAT library.

Fine tuning of optical signals in nanoporous anodic alumina photonic crystals by apodized sinusoidal pulse anodisation.

PubMed

Santos, Abel; Law, Cheryl Suwen; Chin Lei, Dominique Wong; Pereira, Taj; Losic, Dusan

2016-11-03

In this study, we present an advanced nanofabrication approach to produce gradient-index photonic crystal structures based on nanoporous anodic alumina. An apodization strategy is for the first time applied to a sinusoidal pulse anodisation process in order to engineer the photonic stop band of nanoporous anodic alumina (NAA) in depth. Four apodization functions are explored, including linear positive, linear negative, logarithmic positive and logarithmic negative, with the aim of finely tuning the characteristic photonic stop band of these photonic crystal structures. We systematically analyse the effect of the amplitude difference (from 0.105 to 0.840 mA cm -2 ), the pore widening time (from 0 to 6 min), the anodisation period (from 650 to 950 s) and the anodisation time (from 15 to 30 h) on the quality and the position of the characteristic photonic stop band and the interferometric colour of these photonic crystal structures using the aforementioned apodization functions. Our results reveal that a logarithmic negative apodisation function is the most optimal approach to obtain unprecedented well-resolved and narrow photonic stop bands across the UV-visible-NIR spectrum of NAA-based gradient-index photonic crystals. Our study establishes a fully comprehensive rationale towards the development of unique NAA-based photonic crystal structures with finely engineered optical properties for advanced photonic devices such as ultra-sensitive optical sensors, selective optical filters and all-optical platforms for quantum computing.

A Demonstration of Optimal Apodization Determination for Proper Lateral Modulation

NASA Astrophysics Data System (ADS)

Sumi, Chikayoshi; Komiya, Yuichi; Uga, Shinya

2009-07-01

We have realized effective ultrasound (US) beamformings by the steering of plural beams and apodizations for B-mode imaging with a high lateral resolution and accurate measurement of tissue or blood displacement vector and/or strain tensor using the multidimensional cross-spectrum phase gradient method (MCSPGM), or multidimensional autocorrelation or Doppler methods (MAM and MDM) using multidimensional analytic signals. For instance, the coherent superposition of the steered beams performed in the lateral cosine modulation method (LCM) has a higher potential for realizing a more accurate measurement of a displacement vector than the synthesis of the displacement vector using the accurately measured axial displacements obtained by the multidimensional synthetic aperture method (MDSAM), multidirectional transmission method (MTM) or the use of plural US transducers. Originally, the apodization function to be used for realizing a designed point spread function (PSF) was obtained by the Fraunhofer approximation (FA). However, to obtain the best approximated, designed PSF in the least-squares sense, we proposed a linear optimization (LO) method. Furthermore, on the basis of the knowledge about the losts of US energy during the propagation, we have recently developed a nonlinear optimization (NLO) method, in which the feet of the main lobes in apodization function are properly truncated. Thus, NLO also allows the decrease in the number of channels or the confinement of the effective aperture. In this study, to gain insight into the ideal shape of the PSF, the accuracies of the two-dimensional (2D) displacement vector measurements were compared for typical PSFs with distinct lateral envelope shapes, particularly, in terms of full width at half maximum (FWHM) and the length of the feet, i.e., the Gaussian function, Hanning window and parabolic function. It was confirmed that a PSF having a wide FWHM and short feet was ideal. Such a PSF yielded an echo with a high signal-to-noise ratio (SNR), a large bandwidth and a large maximum spectrum of the center frequency. Moreover, for the three PSFs used, by calculating the PSFs using a typical transducer model and the apodization functions obtained by the respective LO and NLO methods and FA, we compare the approximation accuracies of the realized PSFs. NLO was effective for realizing such an ideal PSF. In addition, NLO allowed the significant decrease in the number of channels or the confinement of the effective aperture. Thus, in the comparisons of the three distinct PSFs, we obtain an appropriate apodization function. This study will assist the realization of the best lateral modulation.

What types of astronomy images are most popular?

NASA Astrophysics Data System (ADS)

Allen, Alice; Bonnell, Jerry T.; Connelly, Paul; Haring, Ralf; Lowe, Stuart R.; Nemiroff, Robert J.

2015-01-01

Stunning imagery helps make astronomy one of the most popular sciences -- but what types of astronomy images are most popular? To help answer this question, public response to images posted to various public venues of the Astronomy Picture of the Day (APOD) are investigated. APOD portals queried included the main NASA website and the social media mirrors on Facebook, Google Plus, and Twitter. Popularity measures include polls, downloads, page views, likes, shares, and retweets; these measures are used to assess how image popularity varies in relation to various image attributes including topic and topicality.

An optimized Fresnel array for a test space mission in UV

NASA Astrophysics Data System (ADS)

Roux, W.; Koechlin, L.

2016-07-01

The Fresnel Diffractive Imager is based on a new optical concept for space telescopes, developed at Institut de Recherche en Astrophysique et Planétologie (IRAP) in Toulouse, France. We propose it for space missions dedicated to science cases in the Ultra-Violet with aperture ranges from 6 to 30 meters. Instead of a classical mirror to focus light, this concept uses very light-weight diffractive optics : the Fresnel array. Our project has already proved its performances in terms of resolution and high dynamic range in the laboratory, in the visible and near IR. It has been tested successfully on real astrophysical sources from the ground. At present, the project has reached the stage where a probatory mission is needed to validate its operation in space. In collaboration with institutes in Spain and Russia, we will propose a mission to the Russian space agency Roscosmos, to board a small prototype Fresnel imager on the International Space Station (ISS) for a UV astronomy program. We have improved the Fresnel array design to get a better Point Spread Function (PSF), 2 different ways. Numerical simulations have first allowed us to confirm these optical improvements, before manufacturing the diffractive optics and using them for new lab tests. In our previous setups, the opaque Fresnel zones in the primary Fresnel array (playing the role of the telescope objective) were maintained with an orthogonal bars mesh, following the pseudo-period of the Fresnel zones. We show that the PSF improves when these bars are regularly spaced. Furthermore, the optical system is apodized to get a better peaked PSF, and increase its high contrast performances. In our case, to apodize a binary mask the solution is to modulate the Fresnel zones in relative thickness ratio (opaque versus void), thus driving the local light transmission ratio. In earlier implementations, our Fresnel arrays were apodized with a circularly symmetric law, but an orthogonal apodization law is more efficient. That is why we are developing this particular type of apodized square aperture Fresnel arrays.

Non-imaging ray-tracing for sputtering simulation with apodization

NASA Astrophysics Data System (ADS)

Ou, Chung-Jen

2018-04-01

Although apodization patterns have been adopted for the analysis of sputtering sources, the analytical solutions for the film thickness equations are yet limited to only simple conditions. Empirical formulations for thin film sputtering lacking the flexibility in dealing with multi-substrate conditions, a suitable cost-effective procedure is required to estimate the film thickness distribution. This study reports a cross-discipline simulation program, which is based on discrete particle Monte-Carlo methods and has been successfully applied to a non-imaging design to solve problems associated with sputtering uniformity. Robustness of the present method is first proved by comparing it with a typical analytical solution. Further, this report also investigates the overall all effects cause by the sizes of the deposited substrate, such that the determination of the distance between the target surface and the apodization index can be complete. This verifies the capability of the proposed method for solving the sputtering film thickness problems. The benefit is that an optical thin film engineer can, using the same optical software, design a specific optical component and consider the possible coating qualities with thickness tolerance, during the design stage.

Non-imaging ray-tracing for sputtering simulation with apodization

NASA Astrophysics Data System (ADS)

Ou, Chung-Jen

2018-06-01

Although apodization patterns have been adopted for the analysis of sputtering sources, the analytical solutions for the film thickness equations are yet limited to only simple conditions. Empirical formulations for thin film sputtering lacking the flexibility in dealing with multi-substrate conditions, a suitable cost-effective procedure is required to estimate the film thickness distribution. This study reports a cross-discipline simulation program, which is based on discrete particle Monte-Carlo methods and has been successfully applied to a non-imaging design to solve problems associated with sputtering uniformity. Robustness of the present method is first proved by comparing it with a typical analytical solution. Further, this report also investigates the overall all effects cause by the sizes of the deposited substrate, such that the determination of the distance between the target surface and the apodization index can be complete. This verifies the capability of the proposed method for solving the sputtering film thickness problems. The benefit is that an optical thin film engineer can, using the same optical software, design a specific optical component and consider the possible coating qualities with thickness tolerance, during the design stage.

Equivalence of time and aperture domain additive noise in ultrasound coherence.

PubMed

Bottenus, Nick B; Trahey, Gregg E

2015-01-01

Ultrasonic echoes backscattered from diffuse media, recorded by an array transducer and appropriately focused, demonstrate coherence predicted by the van Cittert-Zernike theorem. Additive noise signals from off-axis scattering, reverberation, phase aberration, and electronic (thermal) noise can all superimpose incoherent or partially coherent signals onto the recorded echoes, altering the measured coherence. An expression is derived to describe the effect of uncorrelated random channel noise in terms of the noise-to-signal ratio. Equivalent descriptions are made in the aperture dimension to describe uncorrelated magnitude and phase apodizations of the array. Binary apodization is specifically described as an example of magnitude apodization and adjustments are presented to minimize the artifacts caused by finite signal length. The effects of additive noise are explored in short-lag spatial coherence imaging, an image formation technique that integrates the calculated coherence curve of acquired signals up to a small fraction of the array length for each lateral and axial location. A derivation of the expected contrast as a function of noise-to-signal ratio is provided and validation is performed in simulation.

Apodization in high-contrast long-slit spectroscopy. Closer, deeper, fainter, cooler

NASA Astrophysics Data System (ADS)

Vigan, A.; N'Diaye, M.; Dohlen, K.

2013-07-01

The spectroscopy of faint planetary-mass companions to nearby stars is one of the main challenges that new-generation high-contrast spectro-imagers are going to face. However, the high contrast ratio between main-sequence stars and young planets makes it difficult to extract a companion spectrum that is not biased by the signal from the star. In a previous work we demonstrated that coupling long-slit spectroscopy (LSS) and classical Lyot coronagraphy (CLC) to form a long-slit coronagraph (LSC) allows low-mass companions to be properly characterized when combined with an innovative a posteriori data analysis methods based on the spectral deconvolution (SD). However, the presence of a slit in the coronagraphic focal plane induces a complex distribution of energy in the Lyot pupil plane that cannot be easily masked with a binary Lyot stop, creating strong diffraction residuals at close angular separation. To alleviate this concern, we propose to use a pupil apodization to suppress diffraction, creating an apodized long-slit coronagraph (ALSC). We show that this concept allows looking at a closer separation from the star, at deeper contrast, which enables the characterization of fainter substellar companions. After describing how the apodization was optimized, we demonstrate its advantages with respect to the CLC in the context of SPHERE/IRDIS LSS mode at low resolution with a 0.12'' slit and 0.18'' coronagraphic mask. We performed different sets of simulations with and without aberrations, and with and without a slit to demonstrate that the apodization is a more appropriate concept for LSS, at the expense of a significantly reduced throughput (37%) compared to the LSC. Then we performed detailed end-to-end simulations of the LSC and the ALSC that include realistic levels of aberrations to obtain several datasets representing 1 h of integration time on stars of spectral type A0 to M0 located at 10 pc. We inserted the spectra of planetary companions at different effective temperatures (Teff) and surface gravities (log g) into the data at angular separations of 0.3'' to 1.5'' and with contrast ratios from 6 to 18 mag. Using the SD method to subtract the speckles, we show that the ALSC brings a gain in sensitivity of up to ~3 mag at 0.3'' over the LSC and that both concepts are essentially equivalent for separations larger than 0.5''. The gain at small separation is the result of suppressing of the bright Airy rings that are difficult to estimate at very small angular separations because of the point spread function chromaticity. The improved sensitivity is confirmed by extracting the simulated companions spectra from the data and comparing them to libraries of models to determine their Teff and log g. Using a restoration factor that quantitatively compares the input and output spectra, we show that the ALSC data systematically leads to better quality spectra below 0.5''. In terms of Teff, we demonstrate that at small angular separations the limit with the ALSC is always lower by at least 100 K, inducing an increase in sensitivity of a factor up to 1.8 in objects' masses at young ages. Finally, for the determination of log g, we show that the ALSC provides a less biased estimation than the LSC.

APODIZED PUPIL LYOT CORONAGRAPHS FOR ARBITRARY APERTURES. IV. REDUCED INNER WORKING ANGLE AND INCREASED ROBUSTNESS TO LOW-ORDER ABERRATIONS

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

N'Diaye, Mamadou; Pueyo, Laurent; Soummer, Rémi, E-mail: mamadou@stsci.edu

The Apodized Pupil Lyot Coronagraph (APLC) is a diffraction suppression system installed in the recently deployed instruments Palomar/P1640, Gemini/GPI, and VLT/SPHERE to allow direct imaging and spectroscopy of circumstellar environments. Using a prolate apodization, the current implementations offer raw contrasts down to 10{sup –7} at 0.2 arcsec from a star over a wide bandpass (20%), in the presence of central obstruction and struts, enabling the study of young or massive gaseous planets. Observations of older or lighter companions at smaller separations would require improvements in terms of the inner working angle (IWA) and contrast, but the methods originally used for thesemore » designs were not able to fully explore the parameter space. We propose a novel approach to improve the APLC performance. Our method relies on the linear properties of the coronagraphic electric field with the apodization at any wavelength to develop numerical solutions producing coronagraphic star images with high-contrast region in broadband light. We explore the parameter space by considering different aperture geometries, contrast levels, dark-zone sizes, bandpasses, and focal plane mask sizes. We present an application of these solutions to the case of Gemini/GPI with a design delivering a 10{sup –8} raw contrast at 0.19 arcsec and offering a significantly reduced sensitivity to low-order aberrations compared to the current implementation. Optimal solutions have also been found to reach 10{sup –10} contrast in broadband light regardless of the aperture shape, with effective IWA in the 2-3.5 λ/D range, therefore making the APLC a suitable option for the future exoplanet direct imagers on the ground or in space.« less

A novel scoring system for gastric cancer risk assessment based on the expression of three CLIP4 DNA methylation-associated genes

PubMed Central

Hu, Chenggong; Zhou, Yongfang; Liu, Chang; Kang, Yan

2018-01-01

Gastric cancer (GC) is the fifth most common cancer and the third leading cause of cancer-associated mortality worldwide. In the current study, comprehensive bioinformatic analyses were performed to develop a novel scoring system for GC risk assessment based on CAP-Gly domain containing linker protein family member 4 (CLIP4) DNA methylation status. Two GC datasets with methylation sequencing information and mRNA expression profiling were downloaded from the The Cancer Genome Atlas and Gene Expression Omnibus databases. Differentially expressed genes (DEGs) between the CLIP4 hypermethylation and CLIP4 hypomethylation groups were screened using the limma package in R 3.3.1, and survival analysis of these DEGs was performed using the survival package. A risk scoring system was established via regression factor-weighted gene expression based on linear combination to screen the most important genes associated with CLIP4 methylation and prognosis. Genes associated with high/low-risk value were selected using the limma package. Functional enrichment analysis of the top 500 DEGs that positively and negatively associated with risk values was performed using DAVID 6.8 online and the gene set enrichment analysis (GSEA) software. In total, 35 genes were identified to be that significantly associated with prognosis and CLIP4 DNA methylation, and three prognostic signature genes, claudin-11 (CLDN11), apolipoprotein D (APOD), and chordin like 1 (CHRDL1), were used to establish a risk assessment system. The prognostic scoring system exhibited efficiency in classifying patients with different prognoses, where the low-risk groups had significantly longer overall survival times than those in the high-risk groups. CLDN11, APOD and CHRDL1 exhibited reduced expression in the hypermethylation and low-risk groups compare with the hypomethylation and high-risk groups, respectively. Multivariate Cox analysis indicated that risk value could be used as an independent prognostic factor. In functional analysis, six functional gene ontology terms and five GSEA pathways were associated with CLDN11, APOD and CHRDL1. The results established the credibility of the scoring system in this study. Additionally, these three genes, which were significantly associated with CLIP4 DNA methylation and GC risk assessment, were identified as potential prognostic biomarkers. PMID:29901187

[Halos and multifocal intraocular lenses: origin and interpretation].

PubMed

Alba-Bueno, F; Vega, F; Millán, M S

2014-10-01

To present the theoretical and experimental characterization of the halo in multifocal intraocular lenses (MIOL). The origin of the halo in a MIOL is the overlaying of 2 or more images. Using geometrical optics, it can be demonstrated that the diameter of each halo depends on the addition of the lens (ΔP), the base power (P(d)), and the diameter of the IOL that contributes to the «non-focused» focus. In the image plane that corresponds to the distance focus, the halo diameter (δH(d)) is given by: δH(d)=d(pn) ΔP/P(d), where d(pn) is the diameter of the IOL that contributes to the near focus. Analogously, in the near image plane the halo diameter (δH(n)) is: δH(n)=d(pd) ΔP/P(d), where d(pd) is the diameter of the IOL that contributes to the distance focus. Patients perceive halos when they see bright objects over a relatively dark background. In vitro, the halo can be characterized by analyzing the intensity profile of the image of a pinhole that is focused by each of the foci of a MIOL. A comparison has been made between the halos induced by different MIOL of the same base power (20D) in an optical bench. As predicted by theory, the larger the addition of the MIOL, the larger the halo diameter. For large pupils and with MIOL with similar aspheric designs and addition (SN6AD3 vs ZMA00), the apodized MIOL has a smaller halo diameter than a non-apodized one in distance vision, while in near vision the size is very similar, but the relative intensity is higher in the apodized MIOL. When comparing lenses with the same diffractive design, but with different spherical-aspheric base design (SN60D3 vs SN6AD3), the halo in distance vision of the spherical MIOL is larger, while in near vision the spherical IOL induces a smaller halo, but with higher intensity due to the spherical aberration of the distance focus in the near image. In the case of a trifocal-diffractive IOL (AT LISA 839MP) the most noticeable characteristic is the double-halo formation due to the 2 non-focused powers. Copyright © 2013 Sociedad Española de Oftalmología. Published by Elsevier Espana. All rights reserved.

Binarization of apodizers by adapted one-dimensional error diffusion method

NASA Astrophysics Data System (ADS)

Kowalczyk, Marek; Cichocki, Tomasz; Martinez-Corral, Manuel; Andres, Pedro

1994-10-01

Two novel algorithms for the binarization of continuous rotationally symmetric real positive pupil filters are presented. Both algorithms are based on 1-D error diffusion concept. The original gray-tone apodizer is substituted by a set of transparent and opaque concentric annular zones. Depending on the algorithm the resulting binary mask consists of either equal width or equal area zones. The diffractive behavior of binary filters is evaluated. It is shown that the pupils with equal width zones give Fraunhofer diffraction pattern more similar to that of the original continuous-tone pupil than those with equal area zones, assuming in both cases the same resolution limit of printing device.

A coronagraph based on two spatial light modulators for active amplitude apodizing and phase corrections

NASA Astrophysics Data System (ADS)

Dou, Jiangpei; Ren, Deqing; Zhang, Xi; Zhu, Yongtian; Zhao, Gang; Wu, Zhen; Chen, Rui; Liu, Chengchao; Yang, Feng; Yang, Chao

2014-08-01

Almost all high-contrast imaging coronagraphs proposed until now are based on passive coronagraph optical components. Recently, Ren and Zhu proposed for the first time a coronagraph that integrates a liquid crystal array (LCA) for the active pupil apodizing and a deformable mirror (DM) for the phase corrections. Here, for demonstration purpose, we present the initial test result of a coronagraphic system that is based on two liquid crystal spatial light modulators (SLM). In the system, one SLM is served as active pupil apodizing and amplitude correction to suppress the diffraction light; another SLM is used to correct the speckle noise that is caused by the wave-front distortions. In this way, both amplitude and phase error can be actively and efficiently compensated. In the test, we use the stochastic parallel gradient descent (SPGD) algorithm to control two SLMs, which is based on the point spread function (PSF) sensing and evaluation and optimized for a maximum contrast in the discovery area. Finally, it has demonstrated a contrast of 10-6 at an inner working angular distance of ~6.2 λ/D, which is a promising technique to be used for the direct imaging of young exoplanets on ground-based telescopes.

The Phase-Induced Amplitude Apodization Coronagraph (PIAAC): Performance for Imaging of Earth-like Exoplanets.

NASA Astrophysics Data System (ADS)

Martinache, F.; Guyon, O.; Pluzhnik, E.; Ridgway, S.; Galicher, R.

2004-12-01

PIAA is one of the powerful applications of pupil remapping. A set of two aspheric mirrors changes the distribution of light and provides an apodized pupil, suitable for coronagraphy, without light loss on an absorbing mask. Deployed on to a space telescope with coronagraphic quality optics, it may allow planet detection from a 1.2 λ /d inner working distance and a full working field. We describe the performance of a PIAA version of NASA's Terrestrial Planet Finder (TPF) in terms of Signal to Noise Ratio and compare it to Classical Pupil Apodization (CPA) performance. We also discuss the necessity of using different occulting masks and give an estimate of the total exposure time for the planet detection phase of the TPF mission. This study is based on realistic Monte Carlo simulations of terrestrial planets orbiting around F, G, K stars within 30 pc around the solar system and includes planet phase and angular separation probabilities. This work was carried out under JPL contract numbers 1254445 and 1257767 for Development of Technologies for the Terrestrial Planet Finder Mission, with the support and hospitality of the National Astronomical Observatory of Japan.

Coherent x-ray zoom condenser lens for diffractive and scanning microscopy.

PubMed

Kimura, Takashi; Matsuyama, Satoshi; Yamauchi, Kazuto; Nishino, Yoshinori

2013-04-22

We propose a coherent x-ray zoom condenser lens composed of two-stage deformable Kirkpatrick-Baez mirrors. The lens delivers coherent x-rays with a controllable beam size, from one micrometer to a few tens of nanometers, at a fixed focal position. The lens is suitable for diffractive and scanning microscopy. We also propose non-scanning coherent diffraction microscopy for extended objects by using an apodized focused beam produced by the lens with a spatial filter. The proposed apodized-illumination method will be useful in highly efficient imaging with ultimate storage ring sources, and will also open the way to single-shot coherent diffraction microscopy of extended objects with x-ray free-electron lasers.

Spatially variant apodization for squinted synthetic aperture radar images.

PubMed

Castillo-Rubio, Carlos F; Llorente-Romano, Sergio; Burgos-García, Mateo

2007-08-01

Spatially variant apodization (SVA) is a nonlinear sidelobe reduction technique that improves sidelobe level and preserves resolution at the same time. This method implements a bidimensional finite impulse response filter with adaptive taps depending on image information. Some papers that have been previously published analyze SVA at the Nyquist rate or at higher rates focused on strip synthetic aperture radar (SAR). This paper shows that traditional SVA techniques are useless when the sensor operates with a squint angle. The reasons for this behaviour are analyzed, and a new implementation that largely improves the results is presented. The algorithm is applied to simulated SAR images in order to demonstrate the good quality achieved along with efficient computation.

Quadratic grating apodized photon sieves for simultaneous multiplane microscopy

NASA Astrophysics Data System (ADS)

Cheng, Yiguang; Zhu, Jiangping; He, Yu; Tang, Yan; Hu, Song; Zhao, Lixin

2017-10-01

We present a new type of imaging device, named quadratic grating apodized photon sieve (QGPS), used as the objective for simultaneous multiplane imaging in X-rays. The proposed QGPS is structured based on the combination of two concepts: photon sieves and quadratic gratings. Its design principles are also expounded in detail. Analysis of imaging properties of QGPS in terms of point-spread function shows that QGPS can image multiple layers within an object field onto a single image plane. Simulated and experimental results in visible light both demonstrate the feasibility of QGPS for simultaneous multiplane imaging, which is extremely promising to detect dynamic specimens by X-ray microscopy in the physical and life sciences.

Differential alterations in gene expression profiles contribute to time-dependent effects of nandrolone to prevent denervation atrophy

PubMed Central

2010-01-01

Background Anabolic steroids, such as nandrolone, slow muscle atrophy, but the mechanisms responsible for this effect are largely unknown. Their effects on muscle size and gene expression depend upon time, and the cause of muscle atrophy. Administration of nandrolone for 7 days beginning either concomitantly with sciatic nerve transection (7 days) or 29 days later (35 days) attenuated denervation atrophy at 35 but not 7 days. We reasoned that this model could be used to identify genes that are regulated by nandrolone and slow denervation atrophy, as well as genes that might explain the time-dependence of nandrolone effects on such atrophy. Affymetrix microarrays were used to profile gene expression changes due to nandrolone at 7 and 35 days and to identify major gene expression changes in denervated muscle between 7 and 35 days. Results Nandrolone selectively altered expression of 124 genes at 7 days and 122 genes at 35 days, with only 20 genes being regulated at both time points. Marked differences in biological function of genes regulated by nandrolone at 7 and 35 days were observed. At 35, but not 7 days, nandrolone reduced mRNA and protein levels for FOXO1, the mTOR inhibitor REDD2, and the calcineurin inhibitor RCAN2 and increased those for ApoD. At 35 days, correlations between mRNA levels and the size of denervated muscle were negative for RCAN2, and positive for ApoD. Nandrolone also regulated genes for Wnt signaling molecules. Comparison of gene expression at 7 and 35 days after denervation revealed marked alterations in the expression of 9 transcriptional coregulators, including Ankrd1 and 2, and many transcription factors and kinases. Conclusions Genes regulated in denervated muscle after 7 days administration of nandrolone are almost entirely different at 7 versus 35 days. Alterations in levels of FOXO1, and of genes involved in signaling through calcineurin, mTOR and Wnt may be linked to the favorable action of nandrolone on denervated muscle. Marked changes in the expression of genes regulating transcription and intracellular signaling may contribute to the time-dependent effects of nandrolone on gene expression. PMID:20969782

Differential alterations in gene expression profiles contribute to time-dependent effects of nandrolone to prevent denervation atrophy.

PubMed

Qin, Weiping; Pan, Jiangping; Bauman, William A; Cardozo, Christopher P

2010-10-22

Anabolic steroids, such as nandrolone, slow muscle atrophy, but the mechanisms responsible for this effect are largely unknown. Their effects on muscle size and gene expression depend upon time, and the cause of muscle atrophy. Administration of nandrolone for 7 days beginning either concomitantly with sciatic nerve transection (7 days) or 29 days later (35 days) attenuated denervation atrophy at 35 but not 7 days. We reasoned that this model could be used to identify genes that are regulated by nandrolone and slow denervation atrophy, as well as genes that might explain the time-dependence of nandrolone effects on such atrophy. Affymetrix microarrays were used to profile gene expression changes due to nandrolone at 7 and 35 days and to identify major gene expression changes in denervated muscle between 7 and 35 days. Nandrolone selectively altered expression of 124 genes at 7 days and 122 genes at 35 days, with only 20 genes being regulated at both time points. Marked differences in biological function of genes regulated by nandrolone at 7 and 35 days were observed. At 35, but not 7 days, nandrolone reduced mRNA and protein levels for FOXO1, the mTOR inhibitor REDD2, and the calcineurin inhibitor RCAN2 and increased those for ApoD. At 35 days, correlations between mRNA levels and the size of denervated muscle were negative for RCAN2, and positive for ApoD. Nandrolone also regulated genes for Wnt signaling molecules. Comparison of gene expression at 7 and 35 days after denervation revealed marked alterations in the expression of 9 transcriptional coregulators, including Ankrd1 and 2, and many transcription factors and kinases. Genes regulated in denervated muscle after 7 days administration of nandrolone are almost entirely different at 7 versus 35 days. Alterations in levels of FOXO1, and of genes involved in signaling through calcineurin, mTOR and Wnt may be linked to the favorable action of nandrolone on denervated muscle. Marked changes in the expression of genes regulating transcription and intracellular signaling may contribute to the time-dependent effects of nandrolone on gene expression.

Performance Evaluation of Adaptive Imaging Based on Multiphase Apodization with Cross-correlation: A Pilot Study in Abdominal Ultrasound.

PubMed

Shin, Junseob; Chen, Yu; Malhi, Harshawn; Chen, Frank; Yen, Jesse

2018-05-01

Degradation of image contrast caused by phase aberration, off-axis clutter, and reverberation clutter remains one of the most important problems in abdominal ultrasound imaging. Multiphase apodization with cross-correlation (MPAX) is a novel beamforming technique that enhances ultrasound image contrast by adaptively suppressing unwanted acoustic clutter. MPAX employs multiple pairs of complementary sinusoidal phase apodizations to intentionally introduce grating lobes that can be used to derive a weighting matrix, which mostly preserves the on-axis signals from tissue but reduces acoustic clutter contributions when multiplied with the beamformed radio-frequency (RF) signals. In this paper, in vivo performance of the MPAX technique was evaluated in abdominal ultrasound using data sets obtained from 10 human subjects referred for abdominal ultrasound at the USC Keck School of Medicine. Improvement in image contrast was quantified, first, by the contrast-to-noise ratio (CNR) and, second, by the rating of two experienced radiologists. The MPAX technique was evaluated for longitudinal and transverse views of the abdominal aorta, the inferior vena cava, the gallbladder, and the portal vein. Our in vivo results and analyses demonstrate the feasibility of the MPAX technique in enhancing image contrast in abdominal ultrasound and show potential for creating high contrast ultrasound images with improved target detectability and diagnostic confidence.

Coil combination for receive array spectroscopy: Are data-driven methods superior to methods using computed field maps?

PubMed

Rodgers, Christopher T; Robson, Matthew D

2016-02-01

Combining spectra from receive arrays, particularly X-nuclear spectra with low signal-to-noise ratios (SNRs), is challenging. We test whether data-driven combination methods are better than using computed coil sensitivities. Several combination algorithms are recast into the notation of Roemer's classic formula, showing that they differ primarily in their estimation of coil receive sensitivities. This viewpoint reveals two extensions of the whitened singular-value decomposition (WSVD) algorithm, using temporal or temporal + spatial apodization to improve the coil sensitivities, and thus the combined spectral SNR. Radiofrequency fields from an array were simulated and used to make synthetic spectra. These were combined with 10 algorithms. The combined spectra were then assessed in terms of their SNR. Validation used phantoms and cardiac (31) P spectra from five subjects at 3T. Combined spectral SNRs from simulations, phantoms, and humans showed the same trends. In phantoms, the combined SNR using computed coil sensitivities was lower than with WSVD combination whenever the WSVD SNR was >14 (or >11 with temporal apodization, or >9 with temporal + spatial apodization). These new apodized WSVD methods gave higher SNRs than other data-driven methods. In the human torso, at frequencies ≥49 MHz, data-driven combination is preferable to using computed coil sensitivities. Magn Reson, 2015. © 2015 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Magn Reson Med 75:473-487, 2016. © 2015 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. © 2015 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.

In-flight performance analysis of MEMS GPS receiver and its application to precise orbit determination of APOD-A satellite

NASA Astrophysics Data System (ADS)

Gu, Defeng; Liu, Ye; Yi, Bin; Cao, Jianfeng; Li, Xie

2017-12-01

An experimental satellite mission termed atmospheric density detection and precise orbit determination (APOD) was developed by China and launched on 20 September 2015. The micro-electro-mechanical system (MEMS) GPS receiver provides the basis for precise orbit determination (POD) within the range of a few decimetres. The in-flight performance of the MEMS GPS receiver was assessed. The average number of tracked GPS satellites is 10.7. However, only 5.1 GPS satellites are available for dual-frequency navigation because of the loss of many L2 observations at low elevations. The variations in the multipath error for C1 and P2 were estimated, and the maximum multipath error could reach up to 0.8 m. The average code noises are 0.28 m (C1) and 0.69 m (P2). Using the MEMS GPS receiver, the orbit of the APOD nanosatellite (APOD-A) was precisely determined. Two types of orbit solutions are proposed: a dual-frequency solution and a single-frequency solution. The antenna phase center variations (PCVs) and code residual variations (CRVs) were estimated, and the maximum value of the PCVs is 4.0 cm. After correcting the antenna PCVs and CRVs, the final orbit precision for the dual-frequency and single-frequency solutions were 7.71 cm and 12.91 cm, respectively, validated using the satellite laser ranging (SLR) data, which were significantly improved by 3.35 cm and 25.25 cm. The average RMS of the 6-h overlap differences in the dual-frequency solution between two consecutive days in three dimensions (3D) is 4.59 cm. The MEMS GPS receiver is the Chinese indigenous onboard receiver, which was successfully used in the POD of a nanosatellite. This study has important reference value for improving the MEMS GPS receiver and its application in other low Earth orbit (LEO) nanosatellites.

Impact of Primary Spherical Aberration, Spatial Frequency and Stiles Crawford Apodization on Wavefront determined Refractive Error: A Computational Study

PubMed Central

Xu, Renfeng; Bradley, Arthur; Thibos, Larry N.

2013-01-01

Purpose We tested the hypothesis that pupil apodization is the basis for central pupil bias of spherical refractions in eyes with spherical aberration. Methods We employed Fourier computational optics in which we vary spherical aberration levels, pupil size, and pupil apodization (Stiles Crawford Effect) within the pupil function, from which point spread functions and optical transfer functions were computed. Through-focus analysis determined the refractive correction that optimized retinal image quality. Results For a large pupil (7 mm), as spherical aberration levels increase, refractions that optimize the visual Strehl ratio mirror refractions that maximize high spatial frequency modulation in the image and both focus a near paraxial region of the pupil. These refractions are not affected by Stiles Crawford Effect apodization. Refractions that optimize low spatial frequency modulation come close to minimizing wavefront RMS, and vary with level of spherical aberration and Stiles Crawford Effect. In the presence of significant levels of spherical aberration (e.g. C40 = 0.4 µm, 7mm pupil), low spatial frequency refractions can induce −0.7D myopic shift compared to high SF refraction, and refractions that maximize image contrast of a 3 cycle per degree square-wave grating can cause −0.75D myopic drift relative to refractions that maximize image sharpness. Discussion Because of small depth of focus associated with high spatial frequency stimuli, the large change in dioptric power across the pupil caused by spherical aberration limits the effective aperture contributing to the image of high spatial frequencies. Thus, when imaging high spatial frequencies, spherical aberration effectively induces an annular aperture defining that portion of the pupil contributing to a well-focused image. As spherical focus is manipulated during the refraction procedure, the dimensions of the annular aperture change. Image quality is maximized when the inner radius of the induced annulus falls to zero, thus defining a circular near paraxial region of the pupil that determines refraction outcome. PMID:23683093

Mitigation of cross-beam energy transfer: Implication of two-state focal zooming on OMEGA

NASA Astrophysics Data System (ADS)

Froula, D. H.; Kessler, T. J.; Igumenshchev, I. V.; Betti, R.; Goncharov, V. N.; Huang, H.; Hu, S. X.; Hill, E.; Kelly, J. H.; Meyerhofer, D. D.; Shvydky, A.; Zuegel, J. D.

2013-08-01

Cross-beam energy transfer (CBET) during OMEGA low-adiabat cryogenic experiments reduces the hydrodynamic efficiency by ˜35%, which lowers the calculated one-dimensional (1-D) yield by a factor of 7. CBET can be mitigated by reducing the diameter of the laser beams relative to the target diameter. Reducing the diameter of the laser beams by 30%, after a sufficient conduction zone has been generated (two-state zooming), is predicted to maintain low-mode uniformity while recovering 90% of the kinetic energy lost to CBET. A radially varying phase plate is proposed to implement two-state zooming on OMEGA. A beam propagating through the central half-diameter of the phase plate will produce a large spot, while a beam propagating through the outer annular region of the phase plate will produce a narrower spot. To generate the required two-state near-field laser-beam profile, a picket driver with smoothing by spectral dispersion (SSD) would pass through an apodizer, forming a beam of half the standard diameter. A second main-pulse driver would co-propagate without SSD through its own apodizer, forming a full-diameter annular beam. Hydrodynamic simulations, using the designed laser spots produced by the proposed zooming scheme on OMEGA, show that implementing zooming will increase the implosion velocity by 25% resulting in a 4.5× increase in the 1-D neutron yield. Demonstrating zooming on OMEGA would validate a viable direct-drive CBET mitigation scheme and help establish a pathway to hydrodynamically equivalent direct-drive-ignition implosions by increasing the ablation pressure (1.6×), which will allow for more stable implosions at ignition-relevant velocities.

LLE review

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

Bradley, D.K.

1989-01-01

This volume of the LLE Review, covering the period October--December 1989, contains an article discussing saturation effects and power-balance considerations in the design of high-power lasers and an article describing numerical modeling of the effects of power imbalances on target behavior. The advanced technology section reports on the development of a liquid crystal laser-beam apodizer and an experiment to study the high-intensity ionization of noble gases. Finally, the activities of the National Laser Users Facility and the GDL and OMEGA laser facilities are summarized. The highlights of this issue are: The problem of achieving power balance in high-efficiency, multibeam lasersmore » has been studied in terms of gain-saturation effects and the nonlinear nature of harmonic frequency conversion. It is shown that power imbalance can be minimized by balancing the gains and losses in equivalent amplification stages in each beamline. The effects of target implosion behavior of various power-imbalance sources in the OMEGA laser system have been studied using the two-dimensional hydrodynamics code ORCHID. The simulations show good agreement with an experiment in which a deliberate power imbalance was applied to the target drive. Laser-beam apodizers with large clear apertures have been fabricated using cholesteric liquid crystals. A soft-edge profile has been achieved by filling a cell with two separate liquid crystals with different selective-reflection bands, and allowing them to partially mix at the interface. A study of the ionization of noble gases in the tunneling regime using high- intensity, 1-ps pulses from the tabletop terawatt laser (T{sup 3}) has been carried out. The measured ion production is well predicted by a Coulomb barrier suppression ionization theory.« less

Theoretical performance of serrated external occulters for solar coronagraphy. Application to ASPIICS

NASA Astrophysics Data System (ADS)

Rougeot, R.; Aime, C.

2018-04-01

Context. This study is made in the context of the future solar coronagraph ASPIICS of the ESA formation-flying mission Proba-3. Aims: In the context of solar coronagraphy, we provide a comparative study of the theoretical performance of serrated (or toothed) external occulters by varying the number and size of the teeth, which we compare to the sharp-edged and apodized disks. The tooth height is small (a few centimeters), to avoid hindering the observation of the solar corona near the limb. We first analyze the diffraction pattern produced by such occulters. In a second step, we compute the umbra profile by integration over the Sun. Methods: We explored a few methods to compute the diffraction pattern. Two of them were implemented. The first is based on 2D fast Fourier transformation (FFT) routines and a multiplication by the Fresnel filter of the form exp(-iπλzu2). Simple rules were derived and discussed to set the sampling conditions. The Maggi-Rubinowicz representation is then proposed as an alternative method, and is proven to be very efficient for this study. Results: Serrated occulters tend to create a two-level intensity pattern, the inner being the darker, which perfectly matches a previously reported geometrical prediction. The diffraction in this central region is lower by two to four orders of magnitude when compared to the sharp-edged disk. The achieved umbra level at the center ranges from 10-4 to below 10-7, depending on the geometry of the teeth. Conclusions: Our study shows that serrated occulters can achieve a high rejection and can almost reach the performance of the apodized disk when very many teeth are used. We prove that shaped occulters must be preferred to simple disks in solar and stellar coronagraphy.

ANALYTIC MODELING OF STARSHADES

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

Cash, Webster

2011-09-01

External occulters, otherwise known as starshades, have been proposed as a solution to one of the highest priority yet technically vexing problems facing astrophysics-the direct imaging and characterization of terrestrial planets around other stars. New apodization functions, developed over the past few years, now enable starshades of just a few tens of meters diameter to occult central stars so efficiently that the orbiting exoplanets can be revealed and other high-contrast imaging challenges addressed. In this paper, an analytic approach to the analysis of these apodization functions is presented. It is used to develop a tolerance analysis suitable for use inmore » designing practical starshades. The results provide a mathematical basis for understanding starshades and a quantitative approach to setting tolerances.« less

One-dimensional error-diffusion technique adapted for binarization of rotationally symmetric pupil filters

NASA Astrophysics Data System (ADS)

Kowalczyk, Marek; Martínez-Corral, Manuel; Cichocki, Tomasz; Andrés, Pedro

1995-02-01

Two novel algorithms for the binarization of continuous rotationally symmetric real and positive pupil filters are presented. Both algorithms are based on the one-dimensional error diffusion concept. In our numerical experiment an original gray-tone apodizer is substituted by a set of transparent and opaque concentric annular zones. Depending on the algorithm the resulting binary mask consists of either equal width or equal area zones. The diffractive behavior of binary filters is evaluated. It is shown that the filter with equal width zones gives Fraunhofer diffraction pattern more similar to that of the original gray-tone apodizer than that with equal area zones, assuming in both cases the same resolution limit of device used to print both filters.

Super-resolving random-Gaussian apodized photon sieve.

PubMed

Sabatyan, Arash; Roshaninejad, Parisa

2012-09-10

A novel apodized photon sieve is presented in which random dense Gaussian distribution is implemented to modulate the pinhole density in each zone. The random distribution in dense Gaussian distribution causes intrazone discontinuities. Also, the dense Gaussian distribution generates a substantial number of pinholes in order to form a large degree of overlap between the holes in a few innermost zones of the photon sieve; thereby, clear zones are formed. The role of the discontinuities on the focusing properties of the photon sieve is examined as well. Analysis shows that secondary maxima have evidently been suppressed, transmission has increased enormously, and the central maxima width is approximately unchanged in comparison to the dense Gaussian distribution. Theoretical results have been completely verified by experiment.

Terahertz bandwidth all-optical Hilbert transformers based on long-period gratings.

PubMed

Ashrafi, Reza; Azaña, José

2012-07-01

A novel, all-optical design for implementing terahertz (THz) bandwidth real-time Hilbert transformers is proposed and numerically demonstrated. An all-optical Hilbert transformer can be implemented using a uniform-period long-period grating (LPG) with a properly designed amplitude-only grating apodization profile, incorporating a single π-phase shift in the middle of the grating length. The designed LPG-based Hilbert transformers can be practically implemented using either fiber-optic or integrated-waveguide technologies. As a generalization, photonic fractional Hilbert transformers are also designed based on the same optical platform. In this general case, the resulting LPGs have multiple π-phase shifts along the grating length. Our numerical simulations confirm that all-optical Hilbert transformers capable of processing arbitrary optical signals with bandwidths well in the THz range can be implemented using feasible fiber/waveguide LPG designs.

Improved First Pass Spiral Myocardial Perfusion Imaging with Variable Density Trajectories

PubMed Central

Salerno, Michael; Sica, Christopher; Kramer, Christopher M.; Meyer, Craig H.

2013-01-01

Purpose To develop and evaluate variable-density (VD) spiral first-pass perfusion pulse sequences for improved efficiency and off-resonance performance and to demonstrate the utility of an apodizing density compensation function (DCF) to improve SNR and reduce dark-rim artifact caused by cardiac motion and Gibbs Ringing. Methods Three variable density spiral trajectories were designed, simulated, and evaluated in 18 normal subjects, and in 8 patients with cardiac pathology on a 1.5T scanner. Results By utilizing a density compensation function (DCF) which intentionally apodizes the k-space data, the side-lobe amplitude of the theoretical PSF is reduced by 68%, with only a 13% increase in the FWHM of the main-lobe as compared to the same data corrected with a conventional VD DCF, and has an 8% higher resolution than a uniform density spiral with the same number of interleaves and readout duration. Furthermore, this strategy results in a greater than 60% increase in measured SNR as compared to the same VD spiral data corrected with a conventional DCF (p<0.01). Perfusion defects could be clearly visualized with minimal off-resonance and dark-rim artifacts. Conclusion VD spiral pulse sequences using an apodized DCF produce high-quality first-pass perfusion images with minimal dark-rim and off-resonance artifacts, high SNR and CNR and good delineation of resting perfusion abnormalities. PMID:23280884

Teaching Astronomy with Podcasts of the APOD

NASA Astrophysics Data System (ADS)

Wagner, Robert M.

2017-01-01

The APOD website provides many excellent astronomy photos that are used to enhance introductory astronomy classes. For nearly six years, podcasts have been used to enhance learning in introductory astronomy classes at Harrisburg Area Community College. Daily 3-5 minute podcasts have been created and made available through iTunes to students in these classes at no charge. Students are asked to subscribe to the podcast collections and are quizzed on the images discussed throughout the semester. Because the images often focus on current findings in astronomy, the students are given instruction on findings that will not appear in their textbooks for several years. The students also receive a taste of some topics that may not be covered or that are just touched upon because of time limits in the classes. The podcasts have been used successfully with both traditional and fully online classes. The use of the podcasts enhances mobile learning as students can download and listen to the podcasts on their smartphones or tablets at their convenience. The student response to the podcasts has been excellent with some students noting that they continue to follow the website and podcasts even after they have completed the class. With mobile learning expanding, this is an excellent way to reach students and encourage them to further research the various topics in astronomy that are covered in the APOD images.

Acoustical tweezers using single spherically focused piston, X-cut, and Gaussian beams.

PubMed

Mitri, Farid G

2015-10-01

Partial-wave series expansions (PWSEs) satisfying the Helmholtz equation in spherical coordinates are derived for circular spherically focused piston (i.e., apodized by a uniform velocity amplitude normal to its surface), X-cut (i.e., apodized by a velocity amplitude parallel to the axis of wave propagation), and Gaussian (i.e., apodized by a Gaussian distribution of the velocity amplitude) beams. The Rayleigh-Sommerfeld diffraction integral and the addition theorems for the Legendre and spherical wave functions are used to obtain the PWSEs assuming weakly focused beams (with focusing angle α ⩽ 20°) in the Fresnel-Kirchhoff (parabolic) approximation. In contrast with previous analytical models, the derived expressions allow computing the scattering and acoustic radiation force from a sphere of radius a without restriction to either the Rayleigh (a ≪ λ, where λ is the wavelength of the incident radiation) or the ray acoustics (a ≫λ) regimes. The analytical formulations are valid for wavelengths largely exceeding the radius of the focused acoustic radiator, when the viscosity of the surrounding fluid can be neglected, and when the sphere is translated along the axis of wave propagation. Computational results illustrate the analysis with particular emphasis on the sphere's elastic properties and the axial distance to the center of the concave surface, with close connection of the emergence of negative trapping forces. Potential applications are in single-beam acoustical tweezers, acoustic levitation, and particle manipulation.

Apodization of two-dimensional pupils with aberrations

NASA Astrophysics Data System (ADS)

Reddy, Andra Naresh Kumar; Hashemi, Mahdieh; Khonina, Svetlana Nikolaevna

2018-06-01

The technique proposed to enhance the resolution of the point spread function (PSF) of an optical system underneath defocussing and spherical aberrations. The method of approach is based on the amplitude and phase masking in a ring aperture for modifying the light intensity distribution in the Gaussian focal plane (YD = 0) and in the defocussed planes (YD= π and YD= 2π ). The width of the annulus modifies the distribution of the light intensity in the side lobes of the resultant PSF. In the presence of an asymmetry in the phase of the annulus, the Hanning amplitude apodizer [cos(π β ρ )] employed in the pupil function can modify the spatial distribution of light in the maximum defocussed plane ({Y}D = 2π ), results in PSF with improved resolution.

The PIAA Coronagraph Prototype: First Laboratory Results.

NASA Astrophysics Data System (ADS)

Pluzhnik, Eugene; Guyon, O.; Colley, S.; Gallet, B.; Ridgway, S.; Woodruff, R.; Tanaka, S.; Warren, M.

2006-12-01

The phase-induced amplitude apodization (PIAA) coronagraph combines the main advantages of classical pupil apodization with high throughput ( 100%), high angular resolution ( 2λ/D) and low chromaticity. These advantages can allow direct imaging of nearby extrasolar planets with a 4-meter telescope. The PIAA coronagraph laboratory prototype has been successfully manufactured and starts to operate at the Subary Telescope facility. We present here our first laboratory results with this prototype where we have achieved 2x10-6 contrast within 2 λ/D. We also discuss the main constrains limiting the contrast and describe our future efforts. This work was carried out under JPL contract numbers 1254445 and 1257767 for Development of Technologies for the Terrestrial Planet Finder Mission, with the support and hospitality of the National Astronomical Observatory of Japan.

Unidirectional waveguide grating antennas with uniform emission for optical phased arrays.

PubMed

Raval, Manan; Poulton, Christopher V; Watts, Michael R

2017-07-01

We demonstrate millimeter-scale optical waveguide grating antennas with unidirectional emission for integrated optical phased arrays. Unidirectional emission eliminates the fundamental problem of blind spots in the element factor of a phased array caused by reflections of antenna radiation within the substrate. Over 90% directionality is demonstrated using a design consisting of two silicon nitride layers. Furthermore, the perturbation strength along the antenna is apodized to achieve uniform emission for the first time, to the best of our knowledge, on a millimeter scale. This allows for a high effective aperture and receiving efficiency. The emission profile of the measured 3 mm long antenna has a standard deviation of 8.65% of the mean. These antennas are state of the art and will allow for integrated optical phased arrays with blind-spot-free high transmission output power and high receiving efficiency for LIDAR and free-space communication systems.

Fraunhofer Diffraction and Polarization.

ERIC Educational Resources Information Center

Fortin, E.

1979-01-01

Describes an experiment for the intermediate undergraduate optics laboratory designed to illustrate simultaneously some aspects of the phenomena of diffraction; interference, coherence, apodization, the Fresnel-Arago law; as well as of the interrelations between these concepts. (HM)

Improved first-pass spiral myocardial perfusion imaging with variable density trajectories.

PubMed

Salerno, Michael; Sica, Christopher; Kramer, Christopher M; Meyer, Craig H

2013-11-01

To develop and evaluate variable-density spiral first-pass perfusion pulse sequences for improved efficiency and off-resonance performance and to demonstrate the utility of an apodizing density compensation function (DCF) to improve signal-to-noise ratio (SNR) and reduce dark-rim artifact caused by cardiac motion and Gibbs Ringing. Three variable density spiral trajectories were designed, simulated, and evaluated in 18 normal subjects, and in eight patients with cardiac pathology on a 1.5T scanner. By using a DCF, which intentionally apodizes the k-space data, the sidelobe amplitude of the theoretical point spread function (PSF) is reduced by 68%, with only a 13% increase in the full-width at half-maximum of the main-lobe when compared with the same data corrected with a conventional variable-density DCF, and has an 8% higher resolution than a uniform density spiral with the same number of interleaves and readout duration. Furthermore, this strategy results in a greater than 60% increase in measured SNR when compared with the same variable-density spiral data corrected with a conventional DCF (P < 0.01). Perfusion defects could be clearly visualized with minimal off-resonance and dark-rim artifacts. Variable-density spiral pulse sequences using an apodized DCF produce high-quality first-pass perfusion images with minimal dark-rim and off-resonance artifacts, high SNR and contrast-to-noise ratio, and good delineation of resting perfusion abnormalities. Copyright © 2012 Wiley Periodicals, Inc.

Removal of central obscuration and spiders for coronagraphy

NASA Astrophysics Data System (ADS)

Abe, L.; Nishikawa, J.; Murakami, N.; Tamura, M.

2006-06-01

We present a method to remove the central obscuration and spiders, or any kind of geometry inside a telescope pupil. The technique relies on the combination of a first focal plane diffracting mask, and a complex amplitude pupil mask. In this combination, the central obscuration and eventual spider arms patterns in the re-imaged pupil (after the diffracting mask) are filled with coherent light. Adding an appropriate complex amplitude pupil mask allows virtually any kind of pupil shaping (in both amplitude and/or phase). We show that the obtained output pupil can feed a high efficiency coronagraph (any kind) with a very reasonable overall throughput and good performance even when considering pointing errors. In this paper, we specifically assess the performance of this technique when using apodized entrance pupils. This technique is relevant for ground based telescopes foreseeing the advent of higher order (so called ExAO) adaptive optics systems providing very high Strehl ratios. Some feasibility points are also discussed. adaptive optics systems providing very high Strehl ratios. Some feasibility points are also discussed.

Complex Pupil Masks for Aberrated Imaging of Closely Spaced Objects

NASA Astrophysics Data System (ADS)

Reddy, A. N. K.; Sagar, D. K.; Khonina, S. N.

2017-12-01

Current approach demonstrates the suppression of optical side-lobes and the contraction of the main lobe in the composite image of two object points of the optical system under the influence of defocusing effect when an asymmetric phase edges are imposed over the apodized circular aperture. The resolution of two point sources having different intensity ratio is discussed in terms of the modified Sparrow criterion, functions of the degree of coherence of the illumination, the intensity difference and the degree of asymmetric phase masking. Here we have introduced and explored the effects of focus aberration (defect-of-focus) on the two-point resolution of the optical systems. Results on the aberrated composite image of closely spaced objects with amplitude mask and asymmetric phase masks forms a significant contribution in astronomical and microscopic observations.

Silicon graphene Bragg gratings.

PubMed

Capmany, José; Domenech, David; Muñoz, Pascual

2014-03-10

We propose the use of interleaved graphene sections on top of a silicon waveguide to implement tunable Bragg gratings. The filter central wavelength and bandwidth can be controlled changing the chemical potential of the graphene sections. Apodization techniques are also presented.

Apodization of spurs in radar receivers using multi-channel processing

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

Doerry, Armin W.; Bickel, Douglas L.

The various technologies presented herein relate to identification and mitigation of spurious energies or signals (aka "spurs") in radar imaging. Spurious energy in received radar data can be a consequence of non-ideal component and circuit behavior. Such behavior can result from I/Q imbalance, nonlinear component behavior, additive interference (e.g. cross-talk, etc.), etc. The manifestation of the spurious energy in a radar image (e.g., a range-Doppler map) can be influenced by appropriate pulse-to-pulse phase modulation. Comparing multiple images which have been processed using the same data but of different signal paths and modulations enables identification of undesired spurs, with subsequent croppingmore » or apodization of the undesired spurs from a radar image. Spurs can be identified by comparison with a threshold energy. Removal of an undesired spur enables enhanced identification of true targets in a radar image.« less

Increasing Accuracy of Tissue Shear Modulus Reconstruction Using Ultrasonic Strain Tensor Measurement

NASA Astrophysics Data System (ADS)

Sumi, C.

Previously, we developed three displacement vector measurement methods, i.e., the multidimensional cross-spectrum phase gradient method (MCSPGM), the multidimensional autocorrelation method (MAM), and the multidimensional Doppler method (MDM). To increase the accuracies and stabilities of lateral and elevational displacement measurements, we also developed spatially variant, displacement component-dependent regularization. In particular, the regularization of only the lateral/elevational displacements is advantageous for the lateral unmodulated case. The demonstrated measurements of the displacement vector distributions in experiments using an inhomogeneous shear modulus agar phantom confirm that displacement-component-dependent regularization enables more stable shear modulus reconstruction. In this report, we also review our developed lateral modulation methods that use Parabolic functions, Hanning windows, and Gaussian functions in the apodization function and the optimized apodization function that realizes the designed point spread function (PSF). The modulations significantly increase the accuracy of the strain tensor measurement and shear modulus reconstruction (demonstrated using an agar phantom).

Absorber for terahertz radiation management

DOEpatents

Biallas, George Herman; Apeldoorn, Cornelis; Williams, Gwyn P.; Benson, Stephen V.; Shinn, Michelle D.; Heckman, John D.

2015-12-08

A method and apparatus for minimizing the degradation of power in a free electron laser (FEL) generating terahertz (THz) radiation. The method includes inserting an absorber ring in the FEL beam path for absorbing any irregular THz radiation and thus minimizes the degradation of downstream optics and the resulting degradation of the FEL output power. The absorber ring includes an upstream side, a downstream side, and a plurality of wedges spaced radially around the absorber ring. The wedges form a scallop-like feature on the innermost edges of the absorber ring that acts as an apodizer, stopping diffractive focusing of the THz radiation that is not intercepted by the absorber. Spacing between the scallop-like features and the shape of the features approximates the Bartlett apodization function. The absorber ring provides a smooth intensity distribution, rather than one that is peaked on-center, thereby eliminating minor distortion downstream of the absorber.

Optimization of coronagraph design for segmented aperture telescopes

NASA Astrophysics Data System (ADS)

Jewell, Jeffrey; Ruane, Garreth; Shaklan, Stuart; Mawet, Dimitri; Redding, Dave

2017-09-01

The goal of directly imaging Earth-like planets in the habitable zone of other stars has motivated the design of coronagraphs for use with large segmented aperture space telescopes. In order to achieve an optimal trade-off between planet light throughput and diffracted starlight suppression, we consider coronagraphs comprised of a stage of phase control implemented with deformable mirrors (or other optical elements), pupil plane apodization masks (gray scale or complex valued), and focal plane masks (either amplitude only or complex-valued, including phase only such as the vector vortex coronagraph). The optimization of these optical elements, with the goal of achieving 10 or more orders of magnitude in the suppression of on-axis (starlight) diffracted light, represents a challenging non-convex optimization problem with a nonlinear dependence on control degrees of freedom. We develop a new algorithmic approach to the design optimization problem, which we call the "Auxiliary Field Optimization" (AFO) algorithm. The central idea of the algorithm is to embed the original optimization problem, for either phase or amplitude (apodization) in various planes of the coronagraph, into a problem containing additional degrees of freedom, specifically fictitious "auxiliary" electric fields which serve as targets to inform the variation of our phase or amplitude parameters leading to good feasible designs. We present the algorithm, discuss details of its numerical implementation, and prove convergence to local minima of the objective function (here taken to be the intensity of the on-axis source in a "dark hole" region in the science focal plane). Finally, we present results showing application of the algorithm to both unobscured off-axis and obscured on-axis segmented telescope aperture designs. The application of the AFO algorithm to the coronagraph design problem has produced solutions which are capable of directly imaging planets in the habitable zone, provided end-to-end telescope system stability requirements can be met. Ongoing work includes advances of the AFO algorithm reported here to design in additional robustness to a resolved star, and other phase or amplitude aberrations to be encountered in a real segmented aperture space telescope.

Comparison of the visual and intraocular optical performance of a refractive multifocal IOL with rotational asymmetry and an apodized diffractive multifocal IOL.

PubMed

Alió, Jorge L; Plaza-Puche, Ana B; Javaloy, Jaime; Ayala, María José

2012-02-01

To compare the visual outcomes and intraocular optical quality observed postoperatively in patients implanted with a rotationally asymmetric multifocal intraocular lens (IOL) and an apodized diffractive multifocal IOL. Seventy-four consecutive eyes of 40 cataract patients (age range: 36 to 79 years) were divided into two groups: zonal refractive group, 39 eyes implanted with a rotationally asymmetric multifocal IOL (Lentis Mplus LS-312 IOL, Oculentis GmbH); and diffractive group, 35 eyes implanted with an apodized diffractive multifocal IOL (ReSTOR SN6AD3, Alcon Laboratories Inc). Distance and near visual acuity outcomes, contrast sensitivity, intraocular optical quality, and defocus curves were evaluated during 3-month follow-up. Calculation of the intraocular aberrations was performed by subtracting corneal aberrations from total ocular aberrations. Uncorrected near visual acuity and distance-corrected near visual acuity were better in the diffractive group than in the zonal refractive group (P=.01), whereas intermediate visual acuity (defocus +1.00 and +1.50 diopters) was better in the zonal refractive group. Photopic contrast sensitivity was significantly better in the zonal refractive group (P=.04). Wavefront aberrations (total, higher order, tilt, primary coma) were significantly higher in the zonal refractive group than in the diffractive group (P=.02). Both multifocal IOLs are able to successfully restore visual function after cataract surgery. The zonal refractive multifocal IOL provides better results in contrast sensitivity and intermediate vision, whereas the diffractive multifocal IOL provides better near vision at a closer distance. Copyright 2012, SLACK Incorporated.

Secreted glycoprotein BmApoD1 plays a critical role in anti-oxidation and anti-apoptosis in Bombyx mori.

PubMed

Zhou, Yanyan; Wang, Li; Li, Rongqiao; Liu, Minmin; Li, Xiaotong; Su, Hang; Xu, Yusong; Wang, Huabing

2018-01-01

Recent studies highlighted that apolipoprotein D (ApoD) and its homologs exert neuroprotective and antioxidant functions in mammals and Drosophila. Unlike mammals and Drosophila, lepidopteran insects possess three distinct ApoD homologs. However, few information on their functions in lepidopteran insects are available. In this study, we investigated the protective potential of a novel ApoD homolog, BmApoD1, in Bombyx mori. Quantitative PCR analyses demonstrated that BmApoD1 is extensively expressed at low levels during the larval stage but abundantly expressed in the testis during the pupal and adult stages. Tryptophan fluorescence titration demonstrated that recombinant BmApoD1 protein can bind retinoic acid and ergosterol. In addition, we provided evidence that N-linked glycans of BmApoD1 are essential to BmApoD1 secretion, and three residues, namely, Asp69, Asp104, and Asp196, are the glycosylation sites of BmApoD1. Furthermore, we showed that BmApoD1 is significantly up-regulated in the larvae after oxidant or starvation treatment. The recombinant BmApoD1 protein can protect cells from oxidative stress induced by H 2 O 2 and reduce actinomycin D-induced cell apoptosis. These observations, together with the transcriptional up-regulation of BmApoD1 in several tissues upon oxidative insult, identify BmApoD1 as a potent antioxidant. Our results demonstrate that BmApoD1 is critical for metabolic adaptation of B. mori to environmental challenges. Copyright © 2017 Elsevier Inc. All rights reserved.

Instrument Line Shape Modeling and Correction for Off-Axis Detectors in Fourier Transform Spectrometry

NASA Technical Reports Server (NTRS)

Bowman, K.; Worden, H.; Beer, R.

1999-01-01

Spectra measured by off-axis detectors in a high-resolution Fourier transform spectrometer (FTS) are characterized by frequency scaling, asymmetry and broadening of their line shape, and self-apodization in the corresponding interferogram.

Fully optimized shaped pupils: preparation for a test at the Subaru Telescope

NASA Astrophysics Data System (ADS)

Carlotti, Alexis; Kasdin, N. Jeremy; Martinache, Frantz; Vanderbei, Robert J.; Young, Elizabeth J.; Che, George; Groff, Tyler D.; Guyon, Olivier

2012-09-01

The SCExAO instrument at the Subaru telescope, mainly based on a PIAA coronagraph can benefit from the addition of a robust and simple shaped pupil coronagraph. New shaped pupils, fully optimized in 2 dimensions, make it possible to design optimal apodizers for arbitrarily complex apertures, for instance on-axis telescopes such as the Subaru telescope. We have designed several masks with inner working angles as small as 2.5 λ / D, and for high-contrast regions with different shapes. Using Princeton University nanofabrication facilities, we have manufactured two masks by photolithography. These masks have been tested in the laboratory, both in Princeton and in the facilities of the National Astronomical Observatory of Japan (NAOJ) in Hilo. The goal of this work is to prepare tests on the sky of a shaped pupil coronagraph in 2012.

Nanostructure Secondary-Mirror Apodizing Mask for Transmitter Signal Suppression in a Duplex Telescope

NASA Technical Reports Server (NTRS)

Hagopian, John; Livas, Jeffrey; Shiri, Shahram; Getty, Stephanie; Tveekrem, June; Butler, James

2012-01-01

A document discusses a nanostructure apodizing mask, made of multi-walled carbon nanotubes, that is applied to the centers (or in and around the holes) of the secondary mirrors of telescopes that are used to interferometrically measure the strain of space-time in response to gravitational waves. The shape of this ultra-black mask can be adjusted to provide a smooth transition to the clear aperture of the secondary mirror to minimize diffracted light. Carbon nanotubes grown on silicon are a viable telescope mirror substrate, and can absorb significantly more light than other black treatments. The hemispherical reflectance of multi-walled carbon nanotubes grown at GSFC is approximately 3 to 10 times better than a standard aerospace paint used for stray light control. At the LISA (Laser Interferometer Space Antenna) wavelength of 1 micron, the advantage over paint is a factor of 10. Primarily, in the center of the secondary mirror (in the region of central obscuration, where no received light is lost) a black mask is applied to absorb transmitted light that could be reflected back into the receiver. In the LISA telescope, this is in the center couple of millimeters. The shape of this absorber is critical to suppress diffraction at the edge. By using the correct shape, the stray light can be reduced by approximately 10 to the 9 orders of magnitude versus no center mask. The effect of the nanotubes has been simulated in a stray-light model. The effect of the apodizing mask has been simulated in a near-field diffraction model. Specifications are geometry-dependent, but the baseline design for the LISA telescope has been modeled as well. The coatings are somewhat fragile, but work is continuing to enhance adhesion.

Distribution of CO2 in Saturn's Atmosphere from Cassini/cirs Infrared Observations

NASA Astrophysics Data System (ADS)

Abbas, M. M.; LeClair, A.; Woodard, E.; Young, M.; Stanbro, M.; Flasar, F. M.; Kunde, V. G.; Achterberg, R. K.; Bjoraker, G.; Brasunas, J.; Jennings, D. E.; the Cassini/CIRS Team

2013-10-01

This paper focuses on the CO2 distribution in Saturn's atmosphere based on analysis of infrared spectral observations of Saturn made by the Composite Infrared Spectrometer aboard the Cassini spacecraft. The Cassini spacecraft was launched in 1997 October, inserted in Saturn's orbit in 2004 July, and has been successfully making infrared observations of Saturn, its rings, Titan, and other icy satellites during well-planned orbital tours. The infrared observations, made with a dual Fourier transform spectrometer in both nadir- and limb-viewing modes, cover spectral regions of 10-1400 cm-1, with the option of variable apodized spectral resolutions from 0.53 to 15 cm-1. An analysis of the observed spectra with well-developed radiative transfer models and spectral inversion techniques has the potential to provide knowledge of Saturn's thermal structure and composition with global distributions of a series of gases. In this paper, we present an analysis of a large observational data set for retrieval of Saturn's CO2 distribution utilizing spectral features of CO2 in the Q-branch of the ν2 band, and discuss its possible relationship to the influx of interstellar dust grains. With limited spectral regions available for analysis, due to low densities of CO2 and interference from other gases, the retrieved CO2 profile is obtained as a function of a model photochemical profile, with the retrieved values at atmospheric pressures in the region of ~1-10 mbar levels. The retrieved CO2 profile is found to be in good agreement with the model profile based on Infrared Space Observatory measurements with mixing ratios of ~4.9 × 10-10 at atmospheric pressures of ~1 mbar.

Microwave photonic filter using multiwavelength Brillouin-erbium fiber laser with double-Brillouin-frequency shift

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

Loh, K. K.; Yeo, K. S.; Shee, Y. G.

2015-04-24

A microwave photonic filter based on double-Brillouin-frequency spaced multiwavelength Brillouin-erbium fiber laser (BEFL) is experimentally demonstrated. The filter selectivity can be easily adjusted by tuning and apodizing the optical taps generated from the multiwavelength BEFL. Reconfiguration of different frequency responses are demonstrated.

The Operational Impacts of Joint Seabasing

DTIC Science & Technology

2007-05-08

carry the equivalent of 200 C-17 Globemaster IIIs or 220 C-5A Galaxies . 59 The benefits of increasing the nations capacity to transport more cargo...already possesses a forced entry capability in the Marine Corps, Army Rangers , and Army Airborne forces which can seize APODs and SPODs for follow-on

Plasma-derived Extracellular Vesicles Contain Predictive Biomarkers and Potential Therapeutic Targets for Myocardial Ischemic (MI) Injury*

PubMed Central

Cheow, Esther Sok Hwee; Cheng, Woo Chin; Lee, Chuen Neng; de Kleijn, Dominique; Sorokin, Vitaly; Sze, Siu Kwan

2016-01-01

Myocardial infarction (MI) triggers a potent inflammatory response via the release of circulatory mediators, including extracellular vesicles (EVs) by damaged cardiac cells, necessary for myocardial healing. Timely repression of inflammatory response are critical to prevent and minimize cardiac tissue injuries, nonetheless, progression in this aspect remains challenging. The ability of EVs to trigger a functional response upon delivery of carried bioactive cargos, have made them clinically attractive diagnostic biomarkers and vectors for therapeutic interventions. Using label-free quantitative proteomics approach, we compared the protein cargo of plasma EVs between patients with MI and from patients with stable angina (NMI). We report, for the first time, the proteomics profiling on 252 EV proteins that were modulated with >1.2-fold after MI. We identified six up-regulated biomarkers with potential for clinical applications; these reflected post-infarct pathways of complement activation (Complement C1q subcomponent subunit A (C1QA), 3.23-fold change, p = 0.012; Complement C5 (C5), 1.27-fold change, p = 0.087), lipoprotein metabolism (Apoliporotein D (APOD), 1.86-fold change, p = 0.033; Apolipoprotein C-III (APOCC3), 2.63-fold change, p = 0.029) and platelet activation (Platelet glycoprotein Ib alpha chain (GP1BA), 9.18-fold change, p < 0.0001; Platelet basic protein (PPBP), 4.72-fold change, p = 0.027). The data have been deposited to the ProteomeXchange with identifier PXD002950. This novel biomarker panel was validated in 43 patients using antibody-based assays (C1QA (p = 0.005); C5 (p = 0.0047), APOD (p = 0.0267); APOC3 (p = 0.0064); GP1BA (p = 0.0031); PPBP (p = 0.0465)). We further present that EV-derived fibrinogen components were paradoxically down-regulated in MI, suggesting that a compensatory mechanism may suppress post-infarct coagulation pathways, indicating potential for therapeutic targeting of this mechanism in MI. Taken together, these data demonstrated that plasma EVs contain novel diagnostic biomarkers and therapeutic targets that can be further developed for clinical use to benefit patients with coronary artery diseases (CADs). PMID:27234505

Topics in Chemical Instrumentation: Fourier Transform-Infrared Spectroscopy: Part I. Instrumentation.

ERIC Educational Resources Information Center

Perkins, W. D.

1986-01-01

Discusses: (1) the design of the Fourier Transform-Infrared Spectroscopy (FT-IR) spectrometer; (2) the computation of the spectrum from the interferogram; and (3) the use of apodization. (Part II will discuss advantages of FT-IR over dispersive techniques and show applications of FT-IR to difficult spectroscopic measurements.) (JN)

Zonal Winds Between 25 and 120 Km Retrieved from Solar Occultation Spectra. Ph.D. Thesis Final Report

NASA Technical Reports Server (NTRS)

Vancleef, Garrett Warren; Shaw, John H.

1989-01-01

Atmospheric winds at heights between 25 and 120 km have been retrieved with precisions of 5/ms from the Doppler shifts of atmospheric absorption lines measured from a satellite-borne instrument. Lines of the upsilon 3 CO2 and upsilon 2 H2O rotation-vibration bands caused by gases in the instrument allowed the instrumental frequency scale to be absolutely calibrated so that accurate relative speeds could be obtained. By comparing the positions of both sets of instrumental lines the calibration of the frequency scale was determined to be stable to a precision of less than 2 x 10(-5) cm during the course of each occultation. It was found that the instrumental resolution of 0.015 cm after apodization, the signal to noise ratio of about 100 and stable calibration allowed relative speeds to be determined to a precision of 5 ms or better by using small numbers of absorption lines between 1600 and 3200 cm. Absolute absorption line positions were simultaneously recovered to precisions of 5 x 10(-5) cm or better. The wind speed profiles determined from four sunset occultations and one sunrise occultation show remarkable similarities in the magnitudes and directions of the zonal wind velocities as functions of height. These wind profiles appear to be manifestations of atmospheric tides.

Comparison of Simulated Contrast Performance of Different Phase Induced Amplitude Apodization (PIAA) Coronagraph Configurations

NASA Technical Reports Server (NTRS)

Sidick, Erkin; Kern, Brian; Kuhnert, Andreas; Shaklan, Stuart

2013-01-01

We compare the broadband contrast performances of several Phase Induced Amplitude Apodization (PIAA) coronagraph configurations through modeling and simulations. The basic optical design of the PIAA coronagraph is the same as NASA's High Contrast Imaging Testbed (HCIT) setup at the Jet Propulsion Laboratory (JPL). Using a deformable mirror and a broadband wavefront sensing and control algorithm, we create a "dark hole" in the broadband point-spread function (PSF) with an inner working angle (IWA) of 2(f lambda/D)(sub sky). We evaluate two systems in parallel. One is a perfect system having a design PIAA output amplitude and not having any wavefront error at its exit-pupil. The other is a realistic system having a design PIAA output amplitude and the measured residual wavefront error. We also investigate the effect of Lyot stops of various sizes when a postapodizer is and is not present. Our simulations show that the best 7.5%-broadband contrast value achievable with the current PIAA coronagraph is approximately 1.5x10(exp -8).

Evaluation of the effect of filter apodization for volume PET imaging using the 3-D RP algorithm

NASA Astrophysics Data System (ADS)

Baghaei, H.; Wong, Wai-Hoi; Li, Hongdi; Uribe, J.; Wang, Yu; Aykac, M.; Liu, Yaqiang; Xing, Tao

2003-02-01

We investigated the influence of filter apodization and cutoff frequency on the image quality of volume positron emission tomography (PET) imaging using the three-dimensional reprojection (3-D RP) algorithm. An important parameter in 3-D RP and other filtered backprojection algorithms is the choice of the filter window function. In this study, the Hann, Hamming, and Butterworth low-pass window functions were investigated. For each window, a range of cutoff frequencies was considered. Projection data were acquired by scanning a uniform cylindrical phantom, a cylindrical phantom containing four small lesion phantoms having diameters of 3, 4, 5, and 6 mm and the 3-D Hoffman brain phantom. All measurements were performed using the high-resolution PET camera developed at the M.D. Anderson Cancer Center (MDAPET), University of Texas, Houston, TX. This prototype camera, which is a multiring scanner with no septa, has an intrinsic transaxial resolution of 2.8 mm. The evaluation was performed by computing the noise level in the reconstructed images of the uniform phantom and the contrast recovery of the 6-mm hot lesion in a warm background and also by visually inspecting images, especially those of the Hoffman brain phantom. For this work, we mainly studied the central slices which are less affected by the incompleteness of the 3-D data. Overall, the Butterworth window offered a better contrast-noise performance over the Hann and Hamming windows. For our high statistics data, for the Hann and Hamming apodization functions a cutoff frequency of 0.6-0.8 of the Nyquist frequency resulted in a reasonable compromise between the contrast recovery and noise level and for the Butterworth window a cutoff frequency of 0.4-0.6 of the Nyquist frequency was a reasonable choice. For the low statistics data, use of lower cutoff frequencies was more appropriate.

Real time en face Fourier-domain optical coherence tomography with direct hardware frequency demodulation

PubMed Central

Biedermann, Benjamin R.; Wieser, Wolfgang; Eigenwillig, Christoph M.; Palte, Gesa; Adler, Desmond C.; Srinivasan, Vivek J.; Fujimoto, James G.; Huber, Robert

2009-01-01

We demonstrate en face swept source optical coherence tomography (ss-OCT) without requiring a Fourier transformation step. The electronic optical coherence tomography (OCT) interference signal from a k-space linear Fourier domain mode-locked laser is mixed with an adjustable local oscillator, yielding the analytic reflectance signal from one image depth for each frequency sweep of the laser. Furthermore, a method for arbitrarily shaping the spectral intensity profile of the laser is presented, without requiring the step of numerical apodization. In combination, these two techniques enable sampling of the in-phase and quadrature signal with a slow analog-to-digital converter and allow for real-time display of en face projections even for highest axial scan rates. Image data generated with this technique is compared to en face images extracted from a three-dimensional OCT data set. This technique can allow for real-time visualization of arbitrarily oriented en face planes for the purpose of alignment, registration, or operator-guided survey scans while simultaneously maintaining the full capability of high-speed volumetric ss-OCT functionality. PMID:18978919

Assessment of Infrared Sounder Radiometric Noise from Analysis of Spectral Residuals

NASA Astrophysics Data System (ADS)

Dufour, E.; Klonecki, A.; Standfuss, C.; Tournier, B.; Serio, C.; Masiello, G.; Tjemkes, S.; Stuhlmann, R.

2016-08-01

For the preparation and performance monitoring of the future generation of hyperspectral InfraRed sounders dedicated to the precise vertical profiling of the atmospheric state, such as the Meteosat Third Generation hyperspectral InfraRed Sounder, a reliable assessment of the instrument radiometric error covariance matrix is needed.Ideally, an inflight estimation of the radiometrric noise is recommended as certain sources of noise can be driven by the spectral signature of the observed Earth/ atmosphere radiance. Also, unknown correlated noise sources, generally related to incomplete knowledge of the instrument state, can be present, so a caracterisation of the noise spectral correlation is also neeed.A methodology, relying on the analysis of post-retreival spectral residuals, is designed and implemented to derive in-flight the covariance matrix on the basis of Earth scenes measurements. This methodology is successfully demonstrated using IASI observations as MTG-IRS proxy data and made it possible to highlight anticipated correlation structures explained by apodization and micro-vibration effects (ghost). This analysis is corroborated by a parallel estimation based on an IASI black body measurement dataset and the results of an independent micro-vibration model.

Finite element area and line integral transforms for generalization of aperture function and geometry in Kirchhoff scalar diffraction theory

NASA Astrophysics Data System (ADS)

Kraus, Hal G.

1993-02-01

Two finite element-based methods for calculating Fresnel region and near-field region intensities resulting from diffraction of light by two-dimensional apertures are presented. The first is derived using the Kirchhoff area diffraction integral and the second is derived using a displaced vector potential to achieve a line integral transformation. The specific form of each of these formulations is presented for incident spherical waves and for Gaussian laser beams. The geometry of the two-dimensional diffracting aperture(s) is based on biquadratic isoparametric elements, which are used to define apertures of complex geometry. These elements are also used to build complex amplitude and phase functions across the aperture(s), which may be of continuous or discontinuous form. The finite element transform integrals are accurately and efficiently integrated numerically using Gaussian quadrature. The power of these methods is illustrated in several examples which include secondary obstructions, secondary spider supports, multiple mirror arrays, synthetic aperture arrays, apertures covered by screens, apodization, phase plates, and off-axis apertures. Typically, the finite element line integral transform results in significant gains in computational efficiency over the finite element Kirchhoff transform method, but is also subject to some loss in generality.

Apodizer aperture for lasers

DOEpatents

Jorna, Siebe; Siebert, Larry D.; Brueckner, Keith A.

1976-11-09

An aperture attenuator for use with high power lasers which includes glass windows shaped and assembled to form an annulus chamber which is filled with a dye solution. The annulus chamber is shaped such that the section in alignment with the axis of the incident beam follows a curve which is represented by the equation y = (r - r.sub.o).sup.n.

Design of Off-Axis PIAACMC Mirrors

NASA Technical Reports Server (NTRS)

Pluzhnik, Eugene; Guyon, Olivier; Belikov, Ruslan; Kern, Brian; Bendek, Eduardo

2015-01-01

The Phase-Induced Amplitude Apodization Complex Mask Coronagraph (PIAACMC) provides an efficient way to control diffraction propagation effects caused by the central obstruction/segmented mirrors of the telescope. PIAACMC can be optimized in a way that takes into account both chromatic diffraction effects caused by the telescope obstructed aperture and tip/tilt sensitivity of the coronagraph. As a result, unlike classic PIAA, the PIAACMC mirror shapes are often slightly asymmetric even for an on-axis configuration and require more care in calculating off-axis shapes when an off-axis configuration is preferred. A method to design off-axis PIAA mirror shapes given an on-axis mirror design is presented. The algorithm is based on geometrical ray tracing and is able to calculate off-axis PIAA mirror shapes for an arbitrary geometry of the input and output beams. The method is demonstrated using the third generation PIAACMC design for WFIRST-AFTA (Wide Field Infrared Survey Telescope-Astrophysics Focused Telescope Assets) telescope. Geometrical optics design issues related to the off-axis diffraction propagation effects are also discussed.

Optimization of homonuclear 2D NMR for fast quantitative analysis: application to tropine-nortropine mixtures.

PubMed

Giraudeau, Patrick; Guignard, Nadia; Hillion, Emilie; Baguet, Evelyne; Akoka, Serge

2007-03-12

Quantitative analysis by (1)H NMR is often hampered by heavily overlapping signals that may occur for complex mixtures, especially those containing similar compounds. Bidimensional homonuclear NMR spectroscopy can overcome this difficulty. A thorough review of acquisition and post-processing parameters was carried out to obtain accurate and precise, quantitative 2D J-resolved and DQF-COSY spectra in a much reduced time, thus limiting the spectrometer instabilities in the course of time. The number of t(1) increments was reduced as much as possible, and standard deviation was improved by optimization of spectral width, number of transients, phase cycling and apodization function. Localized polynomial baseline corrections were applied to the relevant chemical shift areas. Our method was applied to tropine-nortropine mixtures. Quantitative J-resolved spectra were obtained in less than 3 min and quantitative DQF-COSY spectra in 12 min, with an accuracy of 3% for J-spectroscopy and 2% for DQF-COSY, and a standard deviation smaller than 1%.

Nitrogen-broadened lines of ethane at 150 K

NASA Technical Reports Server (NTRS)

Chudamani, S.; Varanasi, P.; Giver, L. P.; Valero, F. P. J.

1985-01-01

Spectral transmittance has been measured in the nu9 fundamental band of C2H6 at 150 K using a Fourier transform spectrometer with apodized spectral resolution of 0.06/cm. Comparison of observed spectral transmittance with a line-by-line computation using the spectral catalog of Atakan et al. (1983) has yielded N2-broadened half-widths at 150 K.

Abriendo Puertas: Opening Doors to Opportunity--A National Evaluation of Second-Generation Trainers

ERIC Educational Resources Information Center

Bridges, Margaret; Cohen, Shana R.; Fuller, Bruce

2012-01-01

Abriendo Puertas/Opening Doors (AP/OD) is a comprehensive, 10-session parenting skills and advocacy program developed by and for low-income Latino parents with children ages 0 to 5. Drawing from the real-life experiences of Latino parents and local data about their schools and communities, sessions are filled with interactive activities that aim…

Gemini Planet Imager coronagraph testbed results

NASA Astrophysics Data System (ADS)

Sivaramakrishnan, Anand; Soummer, Rémi; Oppenheimer, Ben R.; Carr, G. Lawrence; Mey, Jacob L.; Brenner, Doug; Mandeville, Charles W.; Zimmerman, Neil; Macintosh, Bruce A.; Graham, James R.; Saddlemyer, Les; Bauman, Brian; Carlotti, Alexis; Pueyo, Laurent; Tuthill, Peter G.; Dorrer, Christophe; Roberts, Robin; Greenbaum, Alexandra

2010-07-01

The Gemini Planet Imager (GPI) is an extreme AO coronagraphic integral field unit YJHK spectrograph destined for first light on the 8m Gemini South telescope in 2011. GPI fields a 1500 channel AO system feeding an apodized pupil Lyot coronagraph, and a nIR non-common-path slow wavefront sensor. It targets detection and characterizion of relatively young (<2GYr), self luminous planets up to 10 million times as faint as their primary star. We present the coronagraph subsystem's in-lab performance, and describe the studies required to specify and fabricate the coronagraph. Coronagraphic pupil apodization is implemented with metallic half-tone screens on glass, and the focal plane occulters are deep reactive ion etched holes in optically polished silicon mirrors. Our JH testbed achieves H-band contrast below a million at separations above 5 resolution elements, without using an AO system. We present an overview of the coronagraphic masks and our testbed coronagraphic data. We also demonstrate the performance of an astrometric and photometric grid that enables coronagraphic astrometry relative to the primary star in every exposure, a proven technique that has yielded on-sky precision of the order of a milliarsecond.

Image enhancement by spatial frequency post-processing of images obtained with pupil filters

NASA Astrophysics Data System (ADS)

Estévez, Irene; Escalera, Juan C.; Stefano, Quimey Pears; Iemmi, Claudio; Ledesma, Silvia; Yzuel, María J.; Campos, Juan

2016-12-01

The use of apodizing or superresolving filters improves the performance of an optical system in different frequency bands. This improvement can be seen as an increase in the OTF value compared to the OTF for the clear aperture. In this paper we propose a method to enhance the contrast of an image in both its low and its high frequencies. The method is based on the generation of a synthetic Optical Transfer Function, by multiplexing the OTFs given by the use of different non-uniform transmission filters on the pupil. We propose to capture three images, one obtained with a clear pupil, one obtained with an apodizing filter that enhances the low frequencies and another one taken with a superresolving filter that improves the high frequencies. In the Fourier domain the three spectra are combined by using smoothed passband filters, and then the inverse transform is performed. We show that we can create an enhanced image better than the image obtained with the clear aperture. To evaluate the performance of the method, bar tests (sinusoidal tests) with different frequency content are used. The results show that a contrast improvement in the high and low frequencies is obtained.

An Assessment of Hickam Air Force Base's Capability to Support Strategic Airlift Throughput when Operating under an Avian Flu Pandemic

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

Brigantic, Robert T.; Campbell, James R.; Doctor, Pamela G.

Hickam Air Force Base (AFB), Hawaii provides an ideal waypoint for U.S. strategic airlift aircraft to refuel and receive other services on their way to Northeast and Southeast Asia from the continental United States. Hickam AFB also serves as a critical aerial port of debarkation (APOD) for deploying U.S. forces and equipment to more distant lands as needed. Making use of the United States Transportation Command’s Aerial Port of Debarkation Plus model, this paper examines the ability of Hickam AFB to serve in its important role as an APOD when operating under the effects of a major avian flu pandemic.more » In this regard, the major influence on Hickam AFB will be a serious degradation to the number of available personnel to service aircraft and operate Hickam AFB’s aerial port. It is noted that the results presented herein are based on simplistic attrition rate assumptions. Nonetheless, it is envisioned that this work is applicable to more realistic input attrition rates as avian flu epidemiological models are refined, as well as attrition associated with other types of contagious pandemic disease or willful biological warfare attack.« less

Single photons to multiple octaves: Engineering nonlinear optics in micro- and nano-structured media

DTIC Science & Technology

2017-05-18

generation and amplification of ultrafast IR pulses. Both efforts took advantage of microstructured nonlinear media, e.g. quasi -phasematched (QPM...enhance the wave-mixing efficiency, especially for low-power devices. Because errors in fabrication of waveguides and quasi - phasematching gratings are... experimental demonstration of optical parametric chirped pulse amplifiers (OPCPA) in apodized aperiodic QPMgratings for high repetition rate, high

Optical microwave filter based on spectral slicing by use of arrayed waveguide gratings.

PubMed

Pastor, Daniel; Ortega, Beatriz; Capmany, José; Sales, Salvador; Martinez, Alfonso; Muñoz, Pascual

2003-10-01

We have experimentally demonstrated a new optical signal processor based on the use of arrayed waveguide gratings. The structure exploits the concept of spectral slicing combined with the use of an optical dispersive medium. The approach presents increased flexibility from previous slicing-based structures in terms of tunability, reconfiguration, and apodization of the samples or coefficients of the transversal optical filter.

Applications That Participate in Their Own Defense (APOD)

DTIC Science & Technology

2003-05-01

bandwidth requirements from multiple applications and uses ssh to directly login the RSVP routers to reconfigure the priority queues. This approach...detect flooding. 3 Emerald makes use of some signature matching techniques on BSM logs, but the unique strength of Emerald technology is in event...mechanisms that provide awareness, and IDSs form an important class of these4. We investigated several COTS and research IDSs including Emerald

Microcomb-Based True-Time-Delay Network for Microwave Beamforming With Arbitrary Beam Pattern Control

NASA Astrophysics Data System (ADS)

Xue, Xiaoxiao; Xuan, Yi; Bao, Chengying; Li, Shangyuan; Zheng, Xiaoping; Zhou, Bingkun; Qi, Minghao; Weiner, Andrew M.

2018-06-01

Microwave phased array antennas (PAAs) are very attractive to defense applications and high-speed wireless communications for their abilities of fast beam scanning and complex beam pattern control. However, traditional PAAs based on phase shifters suffer from the beam-squint problem and have limited bandwidths. True-time-delay (TTD) beamforming based on low-loss photonic delay lines can solve this problem. But it is still quite challenging to build large-scale photonic TTD beamformers due to their high hardware complexity. In this paper, we demonstrate a photonic TTD beamforming network based on a miniature microresonator frequency comb (microcomb) source and dispersive time delay. A method incorporating optical phase modulation and programmable spectral shaping is proposed for positive and negative apodization weighting to achieve arbitrary microwave beam pattern control. The experimentally demonstrated TTD beamforming network can support a PAA with 21 elements. The microwave frequency range is $\\mathbf{8\\sim20\\ {GHz}}$, and the beam scanning range is $\\mathbf{\\pm 60.2^\\circ}$. Detailed measurements of the microwave amplitudes and phases are performed. The beamforming performances of Gaussian, rectangular beams and beam notch steering are evaluated through simulations by assuming a uniform radiating antenna array. The scheme can potentially support larger PAAs with hundreds of elements by increasing the number of comb lines with broadband microcomb generation.

High Contrast Tests with a PIAA Coronagraph in Air

NASA Astrophysics Data System (ADS)

Totems, J.; Guyon, O.

2007-06-01

The Phase-Induced Amplitude Apodization Coronagraph, which allows high contrast imaging with a small inner working angle, is extremely attractive for future space and ground-based high contrast missions. An experiment is currently under development in our lab at the Subaru Telescope in Hilo, Hawaii, to qualify its capabilities. We will describe the optical configuration adopted and our efforts to stabilize the wavefront in order to improve its performance.

Demonstration of Broadband Contrast at 1.2 Lambda/D for the EXCEDE Phase-Induced Amplitude Apodization Coronagraph

NASA Technical Reports Server (NTRS)

Sirbu, Dan; Thomas, Sandrine J.; Belikov, Ruslan; Lozi, Julien; Bendek, Eduardo; Pluzhnik, Eugene; Lynch, Dana H.; Hix, Troy; Zell, Peter; Schneider, Glenn;

Spiders in Lyot Coronagraphs

NASA Astrophysics Data System (ADS)

Sivaramakrishnan, Anand; Lloyd, James P.

2005-11-01

In principle, suppression of on-axis stellar light by a coronagraph is easier on an unobscured aperture telescope than on one with an obscured aperture. Recent designs such as the apodized pupil Lyot coronagraph, the ``band-limited'' Lyot coronagraph, and several variants of phase-mask coronagraphs work best on unobscured circular aperture telescopes. These designs were developed to enable the discovery and characterization of nearby Jovian or even terrestrial exoplanets. All of today's major space-based and adaptive optics-equipped ground-based telescopes are obscured-aperture systems with a secondary mirror held in place by secondary support ``spider'' vanes. The presence of a secondary obscuration can be dealt with by ingenious coronagraph designs, but the spider vanes themselves cause diffracted light, which can hamper the search for Jovian exoplanets around nearby stars. We look at the problem of suppressing spider vane diffraction in Lyot coronagraphs, including apodized pupil and band-limited designs. We show how spider vane diffraction can be reduced drastically and in fact contained in the final coronagraphic image, within one resolution element of the geometric image of the focal plane mask's occulting spot. This makes adaptive optics coronagraphic searches for exojupiters possible with the next generation of adaptive optics systems being developed for 8-10 m class telescopes such as Gemini and the Very Large Telescopes.

Imagine the Universe!

NASA Technical Reports Server (NTRS)

White, N.

2003-01-01

Welcome to the 2004 edition of the education CD from the Laboratory for High Energy Astrophysics at NASA Goddard Space Flight Center. We hope that you will find it to be an exciting and fun learning experience. We have tried very hard to make this CD as user-friendly as possible and along the way we have discovered some things that every user may need to know. Please read the README file found on the CD if you have any questions or problems using the disk. Then, after that, if you still have problems, email us at itu@athena.gsfc.nasa.gov. We will be happy to help you 'get going'! Below are links to all of the sites included on the CD. You will also find the addresses for the on-line version of each of these sites. If you have a good Internet connection available, we recommend that you view the sites on-line. There you will find the latest updated information, interactive activities, and active links to other sites. Included on the disk are: Imagine The Universe! This site is dedicated to a discussion about our Universe... what we know about it, how it is evolving, and the kinds of objects and phenomena it contains. Emphasizing the X-ray and gamma-ray parts of the electromagnetic spectrum, it also discusses how scientists know what they know, what mysteries remain, and how the answers to remaining mysteries may one day be found. Lots of movies, quizzes, and a special section for educators. Geared for ages 14 and up. This site can be viewed on-line at http://imagine.gsfc.nasa.gov/. StarChild: A learning center for young astronomers The 1998 Webby Award Winner for Best Education Website, StarChild is aimed at ages 4-14. It contains easy-to-understand information about our Solar System, the Universe, and space exploration. There are also activities, songs, movies, and puzzles! This site can be viewed on-line at http://starchild.gsfc.nasa.gov/. Astronomy Picture of the Day APOD offers a new astronomical image and caption each calendar day. We have captured the year 2003 entries of this award-winning site and included them on the disk. The images and information provide a wonderful resource for all ages. This site can be viewed on-line at http://apod.gsfc.nasa.gov/apod/astropix.html.

Molecular, anatomical, and biochemical events associated with neurodegeneration in mice with Niemann-Pick type C disease.

PubMed

Li, Hao; Repa, Joyce J; Valasek, Mark A; Beltroy, Eduardo P; Turley, Stephen D; German, Dwight C; Dietschy, John M

2005-04-01

In Niemann-Pick type C (NPC) disease, cholesterol associated with either apoE or apoB100 is taken up by cells in all tissues, including the central nervous system, through clathrin-coated pits and becomes trapped in late endosomes and lysosomes. This study defines the functional, biochemical, and molecular events that ensue as nerve cell death occurs. In mice homozygous for a mutation in NPC1, neuromuscular dysfunction begins at 5 weeks and death occurs at 13 weeks of age. Cholesterol accumulates in every tissue in the body. Purkinje cell loss in the cerebellum begins at 3 to 4 weeks of age and is nearly complete by 11 weeks. This neurodegeneration in the cerebellum is associated with increases in the levels of mRNA for caspase 1, caspase 3, NPC2, LipA, apoE, apoD, glial fibrillary acidic protein, and tumor necrosis factor-alpha, but not for most target genes of the LXR nuclear receptors. The level for apoER2 is significantly reduced. These studies show there is a compensatory increase in NPC2 and LipA in an attempt to overcome the physiological defect caused by the mutation. Nevertheless, neurodegeneration proceeds utilizing apoptosis with activation of glial cells, increased apoE and apoD synthesis, and increased cholesterol turnover across the CNS.

Application of CRAFT (complete reduction to amplitude frequency table) in nonuniformly sampled (NUS) 2D NMR data processing.

PubMed

Krishnamurthy, Krish; Hari, Natarajan

2017-09-15

The recently published CRAFT (complete reduction to amplitude frequency table) technique converts the raw FID data (i.e., time domain data) into a table of frequencies, amplitudes, decay rate constants, and phases. It offers an alternate approach to decimate time-domain data, with minimal preprocessing step. It has been shown that application of CRAFT technique to process the t 1 dimension of the 2D data significantly improved the detectable resolution by its ability to analyze without the use of ubiquitous apodization of extensively zero-filled data. It was noted earlier that CRAFT did not resolve sinusoids that were not already resolvable in time-domain (i.e., t 1 max dependent resolution). We present a combined NUS-IST-CRAFT approach wherein the NUS acquisition technique (sparse sampling technique) increases the intrinsic resolution in time-domain (by increasing t 1 max), IST fills the gap in the sparse sampling, and CRAFT processing extracts the information without loss due to any severe apodization. NUS and CRAFT are thus complementary techniques to improve intrinsic and usable resolution. We show that significant improvement can be achieved with this combination over conventional NUS-IST processing. With reasonable sensitivity, the models can be extended to significantly higher t 1 max to generate an indirect-DEPT spectrum that rivals the direct observe counterpart. Copyright © 2017 John Wiley & Sons, Ltd.

Observing APOD with the AuScope VLBI Array

PubMed Central

Sun, Jing; Cao, Jianfeng

2018-01-01

The possibility to observe satellites with the geodetic Very Long Baseline Interferometry (VLBI) technique is vividly discussed in the geodetic community, particularly with regard to future co-location satellite missions. The Chinese APOD-A nano satellite can be considered as a first prototype—suitable for practical observation tests—combining the techniques Satellite Laser Ranging (SLR), Global Navigation Satellite Systems (GNSS) and VLBI on a single platform in a Low Earth Orbit (LEO). Unfortunately, it has hardly been observed by VLBI, so major studies towards actual frame ties could not be performed. The main reason for the lack of observations was that VLBI observations of satellites are non-standard, and suitable observing strategies were not in place for this mission. This work now presents the first serious attempt to observe the satellite with a VLBI network over multiple passes. We introduce a series of experiments with the AuScope geodetic VLBI array which were carried out in November 2016, and describe all steps integrated in the established process chain: the experiment design and observation planning, the antenna tracking and control scheme, correlation and derivation of baseline-delays, and the data analysis yielding delay residuals on the level of 10 ns. The developed procedure chain can now serve as reference for future experiments, hopefully enabling the global VLBI network to be prepared for the next co-location satellite mission. PMID:29772732

Observing APOD with the AuScope VLBI Array.

PubMed

Hellerschmied, Andreas; McCallum, Lucia; McCallum, Jamie; Sun, Jing; Böhm, Johannes; Cao, Jianfeng

2018-05-16

The possibility to observe satellites with the geodetic Very Long Baseline Interferometry (VLBI) technique is vividly discussed in the geodetic community, particularly with regard to future co-location satellite missions. The Chinese APOD-A nano satellite can be considered as a first prototype-suitable for practical observation tests-combining the techniques Satellite Laser Ranging (SLR), Global Navigation Satellite Systems (GNSS) and VLBI on a single platform in a Low Earth Orbit (LEO). Unfortunately, it has hardly been observed by VLBI, so major studies towards actual frame ties could not be performed. The main reason for the lack of observations was that VLBI observations of satellites are non-standard, and suitable observing strategies were not in place for this mission. This work now presents the first serious attempt to observe the satellite with a VLBI network over multiple passes. We introduce a series of experiments with the AuScope geodetic VLBI array which were carried out in November 2016, and describe all steps integrated in the established process chain: the experiment design and observation planning, the antenna tracking and control scheme, correlation and derivation of baseline-delays, and the data analysis yielding delay residuals on the level of 10 ns. The developed procedure chain can now serve as reference for future experiments, hopefully enabling the global VLBI network to be prepared for the next co-location satellite mission.

Low-loss adiabatically-tapered high-contrast gratings for slow-wave modulators on SOI

NASA Astrophysics Data System (ADS)

Sciancalepore, Corrado; Hassan, Karim; Ferrotti, Thomas; Harduin, Julie; Duprez, Hélène; Menezo, Sylvie; Ben Bakir, Badhise

2015-02-01

In this communication, we report about the design, fabrication, and testing of Silicon-based photonic integrated circuits (Si-PICs) including low-loss flat-band slow-light high-contrast-gratings (HCGs) waveguides at 1.31 μm. The light slowdown is achieved in 300-nm-thick silicon-on-insulator (SOI) rib waveguides by patterning adiabatically-tapered highcontrast gratings, capable of providing slow-light propagation with extremely low optical losses, back-scattering, and Fabry-Pérot noise. In detail, the one-dimensional (1-D) grating architecture is capable to provide band-edge group indices ng ~ 25, characterized by overall propagation losses equivalent to those of the index-like propagation regime (~ 1-2 dB/cm). Such photonic band-edge slow-light regime at low propagation losses is made possible by the adiabatic apodization of such 1-D HCGs, thus resulting in a win-win approach where light slow-down regime is reached without additional optical losses penalty. As well as that, a tailored apodization optimized via genetic algorithms allows the flattening of slow-light regime over the wavelength window of interest, therefore suiting well needs for group index stability for modulation purposes and non-linear effects generation. In conclusion, such architectures provide key features suitable for power-efficient high-speed modulators in silicon as well as an extremely low-loss building block for non-linear optics (NLO) which is now available in the Si photonics toolbox.

Apodized coupled resonator waveguides.

PubMed

Capmany, J; Muñoz, P; Domenech, J D; Muriel, M A

2007-08-06

In this paper we propose analyse the apodisation or windowing of the coupling coefficients in the unit cells of coupled resonator waveguide devices (CROWs) as a means to reduce the level of secondary sidelobes in the bandpass characteristic of their transfer functions. This technique is regularly employed in the design of digital filters and has been applied as well in the design of other photonic devices such as corrugated waveguide filters and fiber Bragg gratings. The apodisation of both Type-I and Type-II structures is discussed for several windowing functions.

Method for conducting nonlinear electrochemical impedance spectroscopy

DOEpatents

Adler, Stuart B.; Wilson, Jamie R.; Huff, Shawn L.; Schwartz, Daniel T.

2015-06-02

A method for conducting nonlinear electrochemical impedance spectroscopy. The method includes quantifying the nonlinear response of an electrochemical system by measuring higher-order current or voltage harmonics generated by moderate-amplitude sinusoidal current or voltage perturbations. The method involves acquisition of the response signal followed by time apodization and fast Fourier transformation of the data into the frequency domain, where the magnitude and phase of each harmonic signal can be readily quantified. The method can be implemented on a computer as a software program.

Computationally Efficient Adaptive Beamformer for Ultrasound Imaging Based on QR Decomposition.

PubMed

Park, Jongin; Wi, Seok-Min; Lee, Jin S

2016-02-01

Adaptive beamforming methods for ultrasound imaging have been studied to improve image resolution and contrast. The most common approach is the minimum variance (MV) beamformer which minimizes the power of the beamformed output while maintaining the response from the direction of interest constant. The method achieves higher resolution and better contrast than the delay-and-sum (DAS) beamformer, but it suffers from high computational cost. This cost is mainly due to the computation of the spatial covariance matrix and its inverse, which requires O(L(3)) computations, where L denotes the subarray size. In this study, we propose a computationally efficient MV beamformer based on QR decomposition. The idea behind our approach is to transform the spatial covariance matrix to be a scalar matrix σI and we subsequently obtain the apodization weights and the beamformed output without computing the matrix inverse. To do that, QR decomposition algorithm is used and also can be executed at low cost, and therefore, the computational complexity is reduced to O(L(2)). In addition, our approach is mathematically equivalent to the conventional MV beamformer, thereby showing the equivalent performances. The simulation and experimental results support the validity of our approach.

Optimal fitting of Gaussian-apodized or under-resolved emission lines in Fourier transform spectra providing new insights on the velocity structure of NGC 6720

NASA Astrophysics Data System (ADS)

Martin, Thomas B.; Prunet, Simon; Drissen, Laurent

2016-12-01

An analysis of the kinematics of NGC 6720 is performed on the commissioning data obtained with SITELLE, the Canada-France-Hawaii Telescope's new imaging Fourier transform spectrometer. In order to measure carefully the small broadening effect of a shell expansion on an unresolved emission line, we have determined a computationally robust implementation of the convolution of a Gaussian with a sinc instrumental line shape which avoids arithmetic overflows. This model can be used to measure line broadening of typically a few km s-1 even at low spectral resolution (R < 5000). We have also designed the corresponding set of Gaussian apodizing functions that are now used by ORBS, the SITELLE's reduction pipeline. We have implemented this model in ORCS, a fitting engine for SITELLE's data, and used it to derive the [S II] density map of the central part of the nebula. The study of the broadening of the [N II] lines shows that the main ring and the central lobe are two different shells with different expansion velocities. We have also derived deep and spatially resolved velocity maps of the halo in [N II] and Hα and found that the brightest bubbles are originating from two bipolar structures with a velocity difference of more than 35 km s-1 lying at the poles of a possibly unique halo shell expanding at a velocity of more than 15 km s-1.

On the Use of Fourier Transform Infrared (FT-IR) Spectroscopy and Synthetic Calibration Spectra to Quantify Gas Concentrations in a Fischer-Tropsch Catalyst System

NASA Technical Reports Server (NTRS)

Ferguson, Frank T.; Johnson, Natasha M.; Nuth, Joseph A., III

2015-01-01

One possible origin of prebiotic organic material is that these compounds were formed via Fischer-Tropsch-type (FTT) reactions of carbon monoxide and hydrogen on silicate and oxide grains in the warm, inner-solar nebula. To investigate this possibility, an experimental system has been built in which the catalytic efficiency of different grain-analog materials can be tested. During such runs, the gas phase above these grain analogs is sampled using Fourier transform infrared (FT-IR) spectroscopy. To provide quantitative estimates of the concentration of these gases, a technique in which high-resolution spectra of the gases are calculated using the high-resolution transmission molecular absorption (HITRAN) database is used. Next, these spectra are processed via a method that mimics the processes giving rise to the instrumental line shape of the FT-IR spectrometer, including apodization, self-apodization, and broadening due to the finite resolution. The result is a very close match between the measured and computed spectra. This technique was tested using four major gases found in the FTT reactions: carbon monoxide, methane, carbon dioxide, and water. For the ranges typical of the FTT reactions, the carbon monoxide results were found to be accurate to within 5% and the remaining gases accurate to within 10%. These spectra can then be used to generate synthetic calibration data, allowing the rapid computation of the gas concentrations in the FTT experiments.

Multicapillary Gas Chromatography-Temperature Modulated Metal Oxide Semiconductor Sensors Array Detector for Monitoring of Volatile Organic Compounds in Closed Atmosphere Using Gaussian Apodization Factor Analysis.

PubMed

Alinoori, Amir Hossein; Masoum, Saeed

2018-05-22

A unique metal oxide semiconductor sensor (MOS) array detector with eight sensors was designed and fabricated in a PTFE chamber as an interface for coupling with multicapillary gas chromatography. This design consists of eight transfer lines with equal length between the multicapillary columns (MCC) and sensors. The deactivated capillary columns were passed through each transfer line and homemade flow splitter to distribute the same gas flow on each sensor. Using the eight ports flow splitter design helps us to equal the length of carrier gas path and flow for each sensor, minimizing the dead volume of the sensor's chamber and increasing chromatographic resolution. In addition to coupling of MCC to MOS array detector and other considerations in hardware design, modulation of MOS temperature was used to increase sensitivity and selectivity, and data analysis was enhanced with adapted Gaussian apodization factor analysis (GAFA) as a multivariate curve resolution algorithm. Continues air sampling and injecting system (CASI) design provides a fast and easily applied method for continues injection of air sample with no additional sample preparation. The analysis cycle time required for each run is less than 300 s. The high sample load and sharp injection with the fast separation by MCC decrease the peak widths and improve detection limits. This homemade customized instrument is an alternative to other time-consuming and expensive technologies for continuous monitoring of outgassing in air samples.

On the Use of Fourier Transform Infrared (FT-IR) Spectroscopy and Synthetic Calibration Spectra to Quantify Gas Concentrations in a Fischer-Tropsch Catalyst System.

PubMed

Ferguson, Frank T; Johnson, Natasha M; Nuth, Joseph A

2015-10-01

One possible origin of prebiotic organic material is that these compounds were formed via Fischer-Tropsch-type (FTT) reactions of carbon monoxide and hydrogen on silicate and oxide grains in the warm, inner-solar nebula. To investigate this possibility, an experimental system has been built in which the catalytic efficiency of different grain-analog materials can be tested. During such runs, the gas phase above these grain analogs is sampled using Fourier transform infrared (FT-IR) spectroscopy. To provide quantitative estimates of the concentration of these gases, a technique in which high-resolution spectra of the gases are calculated using the High-Resolution Transmission Molecular Absorption (HITRAN) database is used. Next, these spectra are processed via a method that mimics the processes giving rise to the instrumental line shape of the FT-IR spectrometer, including apodization, self-apodization, and broadening due to the finite resolution. The result is a very close match between the measured and computed spectra. This technique was tested using four major gases found in the FTT reactions: carbon monoxide, methane, carbon dioxide, and water. For the ranges typical of the FTT reactions, the carbon monoxide results were found to be accurate to within 5% and the remaining gases accurate to within 10%. These spectra can then be used to generate synthetic calibration data, allowing the rapid computation of the gas concentrations in the FTT experiments.

Infrared absorption cross sections of alternative CFCs

NASA Technical Reports Server (NTRS)

Clerbaux, Cathy; Colin, Reginald; Simon, Paul C.

1994-01-01

Absorption cross sections have obtained in the infrared atmospheric window, between 600 and 1500 cm(exp -1), for 10 alternative hydrohalocarbons: HCFC-22, HCFC-123, HCFC-124, HCFC-141b, HCFC-142b, HCFC-225ca, HCFC-225cb, HFC-125, HFC-134a, and HFC-152a. The measurements were made at three temperatures (287K, 270K and 253K) with a Fourier transform spectrometer operating at 0.03 cm(exp -1) apodized resolution. Integrated cross sections are also derived for use in radiative models to calculate the global warming potentials.

Evolutionary multidimensional access architecture featuring cost-reduced components

NASA Astrophysics Data System (ADS)

Farjady, Farsheed; Parker, Michael C.; Walker, Stuart D.

1998-12-01

We describe a three-stage wavelength-routed optical access network, utilizing coarse passband-flattened arrayed- waveguide grating routers. An N-dimensional addressing strategy enables 6912 customers to be bi-directionally addressed with multi-Gb/s data using only 24 wavelengths spaced by 1.6 nm. Coarse wavelength separation allows use of increased tolerance WDM components at the exchange and customer premises. The architecture is designed to map onto standard access network topologies, allowing elegant upgradability from legacy PON infrastructures at low cost. Passband-flattening of the routers is achieved through phase apodization.

Teaching Fair Use with Astronomy Imagery

NASA Astrophysics Data System (ADS)

Wilson, Teresa

2016-01-01

Plagiarism among students is most common because of a misunderstanding of copyright and fair use. Images and text are frequently used without proper credit to the original author, and works are frequently acknowledged improperly. For example, space imagery is often used in posters, presentations, on the web, on Facebook, and even in the classrooms, but often are not properly cited. A lesson plan on fair use is presented, outlining what constitutes fair use and how to properly acknowledge the work done by artists and authors everywhere, with examples drawn from the Astronomy Picture of the Day (APOD).

Effects of Molecular Adsorption on the Electronic Structure of Single-Layer Graphene

DTIC Science & Technology

2011-08-03

HgxCd1xTe ( MCT -A) detector at a resolution of 4 cm1. 1000 scans were averaged in about 8 min, and 2-fold zero-filling and triangle apodization were...range was∼10007500 cm1, limited on the low end by the Si transmission and on the high end by the detector response. Note that the spectrometer low-pass...reflections) and without any arbitrary vertical displacement. The dashed line shows the position of δR/R = 0. The increased noise at the high-energy end is

Introduction of Total Variation Regularization into Filtered Backprojection Algorithm

NASA Astrophysics Data System (ADS)

Raczyński, L.; Wiślicki, W.; Klimaszewski, K.; Krzemień, W.; Kowalski, P.; Shopa, R. Y.; Białas, P.; Curceanu, C.; Czerwiński, E.; Dulski, K.; Gajos, A.; Głowacz, B.; Gorgol, M.; Hiesmayr, B.; Jasińska, B.; Kisielewska-Kamińska, D.; Korcyl, G.; Kozik, T.; Krawczyk, N.; Kubicz, E.; Mohammed, M.; Pawlik-Niedźwiecka, M.; Niedźwiecki, S.; Pałka, M.; Rudy, Z.; Sharma, N. G.; Sharma, S.; Silarski, M.; Skurzok, M.; Wieczorek, A.; Zgardzińska, B.; Zieliński, M.; Moskal, P.

In this paper we extend the state-of-the-art filtered backprojection (FBP) method with application of the concept of Total Variation regularization. We compare the performance of the new algorithm with the most common form of regularizing in the FBP image reconstruction via apodizing functions. The methods are validated in terms of cross-correlation coefficient between reconstructed and real image of radioactive tracer distribution using standard Derenzo-type phantom. We demonstrate that the proposed approach results in higher cross-correlation values with respect to the standard FBP method.

Fabrication of 1-D Photonic Crystal Cavity on a Nanofiber Using Femtosecond Laser-induced Ablation.

PubMed

Nayak, Kali Prasanna; Keloth, Jameesh; Hakuta, Kohzo

2017-02-25

We present a protocol for fabricating 1-D Photonic Crystal (PhC) cavities on subwavelength-diameter tapered optical fibers, optical nanofibers, using femtosecond laser-induced ablation. We show that thousands of periodic nano-craters are fabricated on an optical nanofiber by irradiating with just a single femtosecond laser pulse. For a typical sample, periodic nano-craters with a period of 350 nm and with diameter gradually varying from 50 - 250 nm over a length of 1 mm are fabricated on a nanofiber with diameter around 450 - 550 nm. A key aspect of such a nanofabrication is that the nanofiber itself acts as a cylindrical lens and focuses the femtosecond laser beam on its shadow surface. Moreover, the single-shot fabrication makes it immune to mechanical instabilities and other fabrication imperfections. Such periodic nano-craters on nanofiber, act as a 1-D PhC and enable strong and broadband reflection while maintaining the high transmission out of the stopband. We also present a method to control the profile of the nano-crater array to fabricate apodized and defect-induced PhC cavities on the nanofiber. The strong confinement of the field, both transverse and longitudinal, in the nanofiber-based PhC cavities and the efficient integration to the fiber networks, may open new possibilities for nanophotonic applications and quantum information science.

Imagine the Universe!

NASA Technical Reports Server (NTRS)

2001-01-01

Welcome to Imagine the Universe! Contained on this CD-ROM you will find three astronomy and space science learning centers, individually captured from the World Wide Web in December of 2000. Each site contains its own learning adventure full of facts, fun, beautiful images, movies, and excitement. (1) Imagine The Universe: this site is dedicated to a discussion about our Universe... what we know about it, how it is evolving, and the kinds of objects and phenomena it contains. Emphasizing the X-ray and gamma-ray parts of the electromagnetic spectrum, it also discusses how scientists know what they know, what mysteries remain, and how the answers to remaining mysteries may one day be found. Lots of movies, quizzes, and a special section for educators. Geared for ages 14 and up. This site can be viewed on-line at http://imagine.gsfc.nasa.gov/. (2) StarChild- a learning center for young astronomers: the 1998 Webby Award Winner for Best Education Website, StarChild is aimed at ages 4-14. It contains easy-to-understand information about our Solar System, the Universe, and space exploration. There are also activities, songs, movies, and puzzles. This site can be viewed on-line at http://starchild.gsfc.nasa.gov/. (3) Astronomy Picture of the Day: APOD offers a new astronomical image and caption each calendar day. We have captured the year 2000 entries of this award-winning site and included them on the disk. The images and information provide a wonderful resource for all ages. This site can be viewed on-line at http://antwrp.gsfc.nasa.gov/apod/astropix.html.

IBIS: An Interferometer-Based Imaging System for Detecting Extrasolar Planets with a Next Generation Space Telescope

NASA Technical Reports Server (NTRS)

Diner, David J.

1989-01-01

The direct detection of extrasolar planetary systems is a challenging observational objective. The observing system must be able to detect faint planetary signals against the background of diffracted and scattered starlight, zodiacal light, and in the IR, mirror thermal radiation. As part of a JPL study, we concluded that the best long-term approach is a 10-20 m filled-aperture telescope operating in the thermal IR (10-15 microns). At these wavelengths, the star/planet flux ratio is on the order of 10(exp 6)-10(exp 8). Our study supports the work of Angel et al., who proposed a cooled 16-m IR telescope and a special apodization mask to suppress the stellar light within a limited angular region around the star. Our scheme differs in that it is capable of stellar suppression over a much broader field-of- view, enabling more efficient planet searches. To do this, certain key optical signal-processing components are needed, including a coronagraph to apodize the stellar diffraction pattern, an infrared interferometer to provide further starlight suppression, a complementary visible-wavelength interferometer to sense figure errors in the telescope optics, and a deformable mirror to adaptively compensate for these errors. Because of the central role of interferometry we have designated this concept the Interferometer-Based Imaging System (IBIS). IBIS incorporates techniques originally suggested by Ken Knight for extrasolar planet detection at visible wavelengths. The type of telescope discussed at this workshop is well suited to implementation of the IBIS concept.

Exploiting three kinds of interface propensities to identify protein binding sites.

PubMed

Liu, Bin; Wang, Xiaolong; Lin, Lei; Dong, Qiwen; Wang, Xuan

2009-08-01

Predicting the binding sites between two interacting proteins provides important clues to the function of a protein. In this study, we present a building block of proteins called order profiles to use the evolutionary information of the protein sequence frequency profiles and apply this building block to produce a class of propensities called order profile interface propensities. For comparisons, we revisit the usage of residue interface propensities and binary profile interface propensities for protein binding site prediction. Each kind of propensities combined with sequence profiles and accessible surface areas are inputted into SVM. When tested on four types of complexes (hetero-permanent complexes, hetero-transient complexes, homo-permanent complexes and homo-transient complexes), experimental results show that the order profile interface propensities are better than residue interface propensities and binary profile interface propensities. Therefore, order profile is a suitable profile-level building block of the protein sequences and can be widely used in many tasks of computational biology, such as the sequence alignment, the prediction of domain boundary, the designation of knowledge-based potentials and the protein remote homology detection.

[Research on spatially modulated Fourier transform imaging spectrometer data processing method].

PubMed

Huang, Min; Xiangli, Bin; Lü, Qun-Bo; Zhou, Jin-Song; Jing, Juan-Juan; Cui, Yan

2010-03-01

Fourier transform imaging spectrometer is a new technic, and has been developed very rapidly in nearly ten years. The data catched by Fourier transform imaging spectrometer is indirect data, can not be used by user, and need to be processed by various approaches, including data pretreatment, apodization, phase correction, FFT, and spectral radicalization calibration. No paper so far has been found roundly to introduce this method. In the present paper, the author will give an effective method to process the interfering data to spectral data, and with this method we can obtain good result.

Multiplexing of adjacent vortex modes with the forked grating coupler

NASA Astrophysics Data System (ADS)

Nadovich, Christopher T.; Kosciolek, Derek J.; Crouse, David T.; Jemison, William D.

2017-08-01

For vortex fiber multiplexing to reach practical commercial viability, simple silicon photonic interfaces with vortex fiber will be required. These interfaces must support multiplexing. Toward this goal, an efficient singlefed multimode Forked Grating Coupler (FGC) for coupling two different optical vortex OAM charges to or from the TE0 and TE1 rectangular waveguide modes has been developed. A simple, apodized device implemented with e-beam lithography and a conventional dual-etch processing on SOI wafer exhibits low crosstalk and reasonable mode match. Advanced designs using this concept are expected to further improve performance.

Initial Results from Fitting Resolved Modes using HMI Intensity Observations

NASA Astrophysics Data System (ADS)

Korzennik, Sylvain G.

2017-08-01

The HMI project recently started processing the continuum intensity images following global helioseismology procedures similar to those used to process the velocity images. The spatial decomposition of these images has produced time series of spherical harmonic coefficients for degrees up to l=300, using a different apodization than the one used for velocity observations. The first 360 days of observations were processed and made available. I present initial results from fitting these time series using my state of the art fitting methodology and compare the derived mode characteristics to those estimated using co-eval velocity observations.

Notable Images of the 2017 Total Solar Eclipse

NASA Astrophysics Data System (ADS)

Wilson, Teresa; Dahiwale, Aishwarya; Nemiroff, Robert; Bonnell, Jerry

2018-01-01

The "Great American Eclipse" – the total solar eclipse visible across the USA on 21 August 2017 – resulted in some notable eclipse images and videos high in educational and scientific value. Some of the images that were selected to appear on the Astronomy Picture of the Day (APOD) website are shown in high resolution accompanied by educational descriptions. The questions of whether this eclipse was the most viewed and the most photographed event of any type in human history will be discussed. People are invited to come by and share their own eclipse images and stories.

Performance Sensitivity Studies on the PIAA Implementation of the High-Contrast Imaging Testbed

NASA Technical Reports Server (NTRS)

Sidick, Erkin; Lou, John; Shaklan, Stuart; Levine, Marie

2010-01-01

This slide presentation reviews the sensitivity studies on the Phase-Induced Amplitude Apodization (PIAA), or pupil mapping using the High-Contrast Imaging Testbed (HCIT). PIAA is a promising technique in high-dynamic range stellar coronagraph. This presentation reports on the investigation of the effects of the phase and rigid-body errors of various optics on the narrowband contrast performance of the PIAA/HCIT hybrid system. The results have shown that the 2-step wavefront control method utilizing 2-DMs is quite effective in compensating the effects of realistic phase and rigid-body errors of various optics

Performance Sensitivity Studies on the PIAA Implementation of the High-Contrast Imaging Testbed

NASA Technical Reports Server (NTRS)

Sidick, Erkin; Lou, John Z.; Shaklan, Stuart; Levine, Marie

2009-01-01

We have investigated the dependence of the High Contrast Imaging Testbed (HCIT) Phase Induced Amplitude Apodization (PIAA) coronagraph system performance on the rigid-body perturbations of various optics. The structural design of the optical system as well as the parameters of various optical elements used in the analysis are drawn from those of the PIAA/HCIT system that have been and will be implemented, and the simulation takes into account the surface errors of various optics. In this paper, we report our findings when the input light is a narrowband beam.

Expression profiling suggests a regulatory role of gallbladder in lipid homeostasis

PubMed Central

Yuan, Zuo-Biao; Han, Tian-Quan; Jiang, Zhao-Yan; Fei, Jian; Zhang, Yi; Qin, Jian; Tian, Zhi-Jie; Shang, Jun; Jiang, Zhi-Hong; Cai, Xing-Xing; Jiang, Yu; Zhang, Sheng-Dao; Jin, Gang

2005-01-01

AIM: To examine expression profile of gallbladder using microarray and to investigate the role of gallbladder in lipid homeostasis. METHODS: 33P-labelled cDNA derived from total RNA of gallbladder tissue was hybridized to a cDNA array representing 17000 cDNA clusters. Genes with intensities ≥2 and variation <0.33 between two samples were considered as positive signals with subtraction of background chosen from an area where no cDNA was spotted. The average gray level of two gallbladders was adopted to analyze its bioinformatics. Identified target genes were confirmed by touch-down polymerase chain reaction and sequencing. RESULTS: A total of 11 047 genes expressed in normal gallbladder, which was more than that predicted by another author, and the first 10 genes highly expressed (high gray level in hybridization image), e.g., ARPC5 (2225.88±90.46), LOC55972 (2220.32±446.51) and SLC20A2 (1865.21±98.02), were related to the function of smooth muscle contraction and material transport. Meanwhile, 149 lipid-related genes were expressed in the gallbladder, 89 of which were first identified (with gray level in hybridization image), e.g., FASN (11.42±2.62), APOD (92.61±8.90) and CYP21A2 (246.11±42.36), and they were involved in each step of lipid metabolism pathway. In addition, 19 of those 149 genes were gallstone candidate susceptibility genes (with gray level in hybridization image), e.g., HMGCR (10.98±0.31), NPC1 (34.88±12.12) and NR1H4 (16.8±0.65), which were previously thought to be expressed in the liver and/or intestine tissue only. CONCLUSION: Gallbladder expresses 11 047 genes and takes part in lipid homeostasis. PMID:15810076

IASI-NG: a new generation of infrared sounders for meteorology and atmospheric composition

NASA Astrophysics Data System (ADS)

Deschamps, A.; Bermudo, F.; Rousseau, S.; Bernard, F.; Pequignot, E.

2016-12-01

IASI-NG is the main payload of the future Metop-SG satellite of the Eumetsat EPS-SG program. This infrared atmospheric sounder generates radiance spectra at high resolution between 645cm-1 and 2760cm-1 and takes benefits from the IASI heritage. As for the first generation, the development of IASI-NG is under CNES responsibility. The first goal of the IASI-NG mission is to support Numerical Weather Prediction (NWP) by improving the estimation of humidity and temperature profiles, especially in the troposphere. To reach this goal, the spectral resolution will be two times better than for IASI first generation, and the radiometric noise will be divided by a factor of two. These performances will enable to support pollution monitoring, climate and atmospheric composition studies as well. CH4 and CO2 columns (but also O3, SO2, CO, NH3, HNO3 concentrations) are some of the products which will be derived from the IASI-NG measurements, in addition to NWP products (such as temperature and water vapor profiles, surface temperature and cloud information). This presentation describes in a first part the main characteristics of the instrument, which allow it to reach this level of performances. The interferometer, developed by Airbus Defense and Space, is based on the Mertz concept and allows to assess the self apodization by a field effect compensation (IASI-NG will be the first mission to implement Mertz Interferometer). In a second part, we present the main performances of the IASI-NG system, in terms of radiometric noise, spectral resolution and geolocation. We describe also the main algorithms which will be used in the ground segment to calibrate the data and correct the instrumental effects. Lastly, we give some information about the status of the project which is currently is the C/D phase and the major milestones in the IASI-NG agenda.

Comparison of high resolution x-ray detectors with conventional FPDs using experimental MTFs and apodized aperture pixel design for reduced aliasing

NASA Astrophysics Data System (ADS)

Shankar, A.; Russ, M.; Vijayan, S.; Bednarek, D. R.; Rudin, S.

2017-03-01

Apodized Aperture Pixel (AAP) design, proposed by Ismailova et.al, is an alternative to the conventional pixel design. The advantages of AAP processing with a sinc filter in comparison with using other filters include non-degradation of MTF values and elimination of signal and noise aliasing, resulting in an increased performance at higher frequencies, approaching the Nyquist frequency. If high resolution small field-of-view (FOV) detectors with small pixels used during critical stages of Endovascular Image Guided Interventions (EIGIs) could also be extended to cover a full field-of-view typical of flat panel detectors (FPDs) and made to have larger effective pixels, then methods must be used to preserve the MTF over the frequency range up to the Nyquist frequency of the FPD while minimizing aliasing. In this work, we convolve the experimentally measured MTFs of an Microangiographic Fluoroscope (MAF) detector, (the MAF-CCD with 35μm pixels) and a High Resolution Fluoroscope (HRF) detector (HRF-CMOS50 with 49.5μm pixels) with the AAP filter and show the superiority of the results compared to MTFs resulting from moving average pixel binning and to the MTF of a standard FPD. The effect of using AAP is also shown in the spatial domain, when used to image an infinitely small point object. For detectors in neurovascular interventions, where high resolution is the priority during critical parts of the intervention, but full FOV with larger pixels are needed during less critical parts, AAP design provides an alternative to simple pixel binning while effectively eliminating signal and noise aliasing yet allowing the small FOV high resolution imaging to be maintained during critical parts of the EIGI.

Apodized Pupil Lyot Coronagraphs designs for future segmented space telescopes

NASA Astrophysics Data System (ADS)

St. Laurent, Kathryn; Fogarty, Kevin; Zimmerman, Neil; N’Diaye, Mamadou; Stark, Chris; Sivaramakrishnan, Anand; Pueyo, Laurent; Vanderbei, Robert; Soummer, Remi

2018-01-01

A coronagraphic starlight suppression system situated on a future flagship space observatory offers a promising avenue to image Earth-like exoplanets and search for biomarkers in their atmospheric spectra. One NASA mission concept that could serve as the platform to realize this scientific breakthrough is the Large UV/Optical/IR Surveyor (LUVOIR). Such a mission would also address a broad range of topics in astrophysics with a multi-wavelength suite of instruments.In support of the community’s assessment of the scientific capability of a LUVOIR mission, the Exoplanet Exploration Program (ExEP) has launched a multi-team technical study: Segmented Coronagraph Design and Analysis (SCDA). The goal of this study is to develop viable coronagraph instrument concepts for a LUVOIR-type mission. Results of the SCDA effort will directly inform the mission concept evaluation being carried out by the LUVOIR Science and Technology Definition Team. The apodized pupil Lyot coronagraph (APLC) is one of several coronagraph design families that the SCDA study is assessing. The APLC is a Lyot-style coronagraph that suppresses starlight through a series of amplitude operations on the on-axis field. Given a suite of seven plausible segmented telescope apertures, we have developed an object-oriented software toolkit to automate the exploration of thousands of APLC design parameter combinations. In the course of exploring this parameter space we have established relationships between APLC throughput and telescope aperture geometry, Lyot stop, inner working angle, bandwidth, and contrast level. In parallel with the parameter space exploration, we have investigated several strategies to improve the robustness of APLC designs to fabrication and alignment errors and integrated a Design Reference Mission framework to evaluate designs with scientific yield metrics.

High intensity ultrasound transducer used in gene transfection

NASA Astrophysics Data System (ADS)

Morrison, Kyle P.; Keilman, George W.; Noble, Misty L.; Brayman, Andrew A.; Miao, Carol H.

2012-11-01

This paper describes a novel therapeutic high intensity non-focused ultrasound (HIU) transducer designed with uniform pressure distribution to aid in accelerated gene transfer in large animal liver tissues in vivo. The underlying HIU transducer was used to initiate homogeneous cavitation throughout the tissue while delivering up to 2.7 MPa at 1.1 MHz across its radiating surface. The HIU transducer was built into a 6 cm diameter x 1.3 cm tall housing ergonomically designed to avoid collateral damage to the surrounding anatomy during dynamic motion. The ultrasound (US) radiation was applied in a 'paintbrush-like' manner to the surface of the liver. The layers and geometry of the transducer were carefully selected to maximize the active diameter (5.74 cm), maximize the electrical to acoustic conversion efficiency (85%) to achieve 2.7 MPa of peak negative pressure, maximize the frequency operating band at the fundamental resonance to within a power transfer delta of 1 dB, and reduce the pressure delta to within 2 dB across the radiating surface. For maximum peak voltage into the transducer, a high performance piezoceramic was chosen and a DC bias circuit was built integral to the system. An apodized two element annular pattern was made from a single piezoceramic element, resulting in significant pressure uniformity enhancement. In addition to using apodization for pressure uniformity, a proprietary multi-layered structure was used to improve efficiency while sustaining an operating band from 900 kHz to 1.3 MHz. The resultant operating band allowed for dithering techniques using frequency modulation. The underlying HIU transducer for use in large animals enhances gene expression up to 6300-fold.

Uranium and cadmium provoke different oxidative stress responses in Lemna minor L.

PubMed

Horemans, N; Van Hees, M; Van Hoeck, A; Saenen, E; De Meutter, T; Nauts, R; Blust, R; Vandenhove, H

2015-01-01

Common duckweed (Lemna minor L.) is ideally suited to test the impact of metals on freshwater vascular plants. Literature on cadmium (Cd) and uranium (U) oxidative responses in L. minor are sparse or, for U, non-existent. It was hypothesised that both metals impose concentration-dependent oxidative stress and growth retardation on L. minor. Using a standardised 7-day growth inhibition test, the adverse impact of these metals on L. minor growth was confirmed, with EC50 values for Cd and U of 24.1 ± 2.8 and 29.5 ± 1.9 μm, respectively, and EC10 values of 1.5 ± 0.2 and 6.5 ± 0.9 μm, respectively. The metal-induced oxidative stress response was compared through assessing the activity of different antioxidative enzymes [catalase, glutathione reductase, superoxide dismutase (SOD), ascorbate peroxidase (APOD), guaiacol peroxidase (GPOD) and syringaldizyne peroxidase (SPOD)]. Significant changes in almost all antioxidative enzymes indicated their importance in counteracting the U- and Cd-imposed oxidative burden. However, some striking differences were also observed. For activity of APODs and SODs, a biphasic but opposite response at low Cd compared to U concentrations was found. In addition, Cd (0.5-20 μm) strongly enhanced plant GPOD activity, whereas U inhibited it. Finally, in contrast to Cd, U up to 10 μm increased the level of chlorophyll a and b and carotenoids. In conclusion, although U and Cd induce similar growth arrest in L. minor, the U-induced oxidative stress responses, studied here for the first time, differ greatly from those of Cd. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

Comparative visual performance with monofocal and multifocal intraocular lenses

PubMed Central

Gundersen, Kjell Gunnar; Potvin, Richard

2013-01-01

Background To compare near, intermediate, and distance vision, and quality of vision using appropriate subjective questionnaires, when monofocal or apodized diffractive multifocal intraocular lenses (IOLs) are binocularly implanted. Methods Patients with different binocular IOLs implanted were recruited after surgery and had their visual acuity tested, and quality of vision evaluated, at a single diagnostic visit between 3 and 8 months after second-eye surgery. Lenses tested included an aspheric monofocal and two apodized diffractive multifocal IOLs with slightly different design parameters. A total of 94 patients were evaluated. Results Subjects with the ReSTOR® +2.5 D IOL had better near and intermediate vision than those subjects with a monofocal IOL. Intermediate vision was similar to, and near vision slightly lower than, that of subjects with a ReSTOR® +3.0 D IOL implanted. The preferred reading distance was slightly farther out for the +2.5 D relative to the +3.0 D lens, and farthest for the monofocal. Visual acuity at the preferred reading distance was equal with the two multifocal IOLs and significantly worse with the monofocal IOL. Quality of vision measures were highest with the monofocal IOL and similar between the two multifocal IOLs. Conclusion The data indicate that the ReSTOR +2.5 D IOL provided good intermediate and functional near vision for patients who did not want to accept a higher potential for visual disturbances associated with the ReSTOR +3.0 D IOL, but wanted more near vision than a monofocal IOL generally provides. Quality of vision was not significantly different between the multifocal IOLs, but patient self-selection for each lens type may have been a factor. PMID:24143064

Design of refractive laser beam shapers to generate complex irradiance profiles

NASA Astrophysics Data System (ADS)

Li, Meijie; Meuret, Youri; Duerr, Fabian; Vervaeke, Michael; Thienpont, Hugo

2014-05-01

A Gaussian laser beam is reshaped to have specific irradiance distributions in many applications in order to ensure optimal system performance. Refractive optics are commonly used for laser beam shaping. A refractive laser beam shaper is typically formed by either two plano-aspheric lenses or by one thick lens with two aspherical surfaces. Ray mapping is a general optical design technique to design refractive beam shapers based on geometric optics. This design technique in principle allows to generate any rotational-symmetric irradiance profile, yet in literature ray mapping is mainly developed to transform a Gaussian irradiance profile to a uniform profile. For more complex profiles especially with low intensity in the inner region, like a Dark Hollow Gaussian (DHG) irradiance profile, ray mapping technique is not directly applicable in practice. In order to these complex profiles, the numerical effort of calculating the aspherical surface points and fitting a surface with sufficient accuracy increases considerably. In this work we evaluate different sampling approaches and surface fitting methods. This allows us to propose and demonstrate a comprehensive numerical approach to efficiently design refractive laser beam shapers to generate rotational-symmetric collimated beams with a complex irradiance profile. Ray tracing analysis for several complex irradiance profiles demonstrates excellent performance of the designed lenses and the versatility of our design procedure.

Scientific Discovery through Citizen Science via Popular Amateur Astrophotography

NASA Astrophysics Data System (ADS)

Nemiroff, Robert J.; Bonnell, Jerry T.; Allen, Alice

2015-01-01

Can popular astrophotography stimulate real astronomical discovery? Perhaps surprisingly, in some cases, the answer is yes. Several examples are given using the Astronomy Picture of the Day (APOD) site as an example venue. One reason is angular -- popular wide and deep images sometimes complement professional images which typically span a more narrow field. Another reason is temporal -- an amateur is at the right place and time to take a unique and illuminating image. Additionally, popular venues can be informational -- alerting professionals to cutting-edge amateur astrophotography about which they might not have known previously. Methods of further encouraging this unusual brand of citizen science are considered.

Tunable radio-frequency photonic filter based on an actively mode-locked fiber laser.

PubMed

Ortigosa-Blanch, A; Mora, J; Capmany, J; Ortega, B; Pastor, D

2006-03-15

We propose the use of an actively mode-locked fiber laser as a multitap optical source for a microwave photonic filter. The fiber laser provides multiple optical taps with an optical frequency separation equal to the external driving radio-frequency signal of the laser that governs its repetition rate. All the optical taps show equal polarization and an overall Gaussian apodization, which reduces the sidelobes. We demonstrate continuous tunability of the filter by changing the external driving radio-frequency signal of the laser, which shows good fine tunability in the operating range of the laser from 5 to 10 GHz.

The characteristics of grating structure in magnetic field measurements based on polarization properties of fiber gratings

NASA Astrophysics Data System (ADS)

Su, Yang; Peng, Hui; Feng, Kui; Li, Yu-quan

2009-11-01

In this paper the characteristics of grating structure in magnetic field measurements based on differential group delay of fiber gratings are analyzed. Theoretical simulations are realized using the coupled-mode theory and transfer matrix method. The effects of grating parameters of uniform Bragg grating on measurement range and sensitivity are analyzed. The impacts of chirped, phase-shifted and apodized gratings on DGD peak values are also monitored. FBG transmitted spectrums and DGD spectrums are recorded by means of an optical vector analyzer (OVA). Both the simulations and experiments demonstrate that the phase-shifted gratings can obviously improve the sensitivity.

Reconfigurable ultra-wideband waveform generation with simple photonic devices

NASA Astrophysics Data System (ADS)

Dastmalchi, Mansour; Abtahi, Mohammad; Lemus, David; Rusch, Leslie A.; LaRochelle, Sophie

2012-08-01

We propose and experimentally demonstrate a low cost, low power consumption technique for ultra-wideband pulse shaping. Our approach is based on thermal apodization of two identical linearly chirped fiber Bragg gratings (LCFBG) placed in both arms of a balanced photodetector. Resistive heating elements with low electrical power consumption are used to tune the LCFBG spectral responses. Using a standard gain switched distributed feedback laser as a pulsed optical source and a simple energy detector receiver, we measured a bit error rate of 1.5×10-4 at a data rate of 1 Gb/s after RF transmission over a 1-m link.

Diamond Turned High Precision PIAA Optics and Four Mirror PIAA System for High Contrast Imaging of Exo-planets

NASA Technical Reports Server (NTRS)

Balasubramanian, Kunjithapatham; Cady, Eric; Pueyo, Laurent; Ana, Xin; Shaklan, Stuart; Guyon, Olivier; Belikov, Ruslan

2011-01-01

Off-axis, high-sag PIAA optics for high contrast imaging present challenges in manufacturing and testing. With smaller form factors and consequently smaller surface deformations (< 80 microns), diamond turned fabrication of these mirrors becomes feasible. Though such a design reduces the system throughput, it still provides 2(lambda)D inner working angle. We report on the design, fabrication, measurements, and initial assessment of the novel PIAA optics in a coronagraph testbed. We also describe, for the first time, a four mirror PIAA coronagraph that relaxes apodizer requirements and significantly improves throughput while preserving the low-cost benefits.

Delay-tunable gap-soliton-based slow-light system

NASA Astrophysics Data System (ADS)

Mok, Joe T.; de Sterke, C. Martijn; Eggleton, Benjamin J.

2006-12-01

We numerically and analytically evaluate the delay of solitons propagating slowly, and without broadening, in an apodized Bragg grating. Simulations indicate that a 100 mm Bragg grating with Δn = 10-3 can delay sub-nanosecond pulses by nearly 20 pulse widths without any change in the output pulse width. Delay tunability is achieved by simultaneously adjusting the launch power and detuning. A simple analytic model is developed to describe the monotonic dependence of delay on Δn and compared with simulations. As the intensity may be greatly enhanced due to a reduced velocity, a procedure for improving the delay while avoiding material damage is outlined.

Science simulations for the New Worlds Observer

NASA Astrophysics Data System (ADS)

Schindhelm, Eric; Cash, Webster; Seager, Sara

2005-08-01

The New Worlds Observer, currently studied under a NASA Institute for Advanced Concepts grant, will be a pinhole camera in space designed to directly detect and study extrasolar terrestrial planets. An apodized occultor or pinhole creates an image of the planetary system in the focal plane far away, where a second telescope craft orbits to detect the light. In this study we simulate the expected signal of NWO to find the optimal configuration and specifications of the two craft. The efficiency of direct detection through photometric imaging depends strongly on occulter and telescope size, while preliminary studies on absorption biomarker detection and photometric variability measurements are summarized.

Dictionary-based image reconstruction for superresolution in integrated circuit imaging.

PubMed

Cilingiroglu, T Berkin; Uyar, Aydan; Tuysuzoglu, Ahmet; Karl, W Clem; Konrad, Janusz; Goldberg, Bennett B; Ünlü, M Selim

2015-06-01

Resolution improvement through signal processing techniques for integrated circuit imaging is becoming more crucial as the rapid decrease in integrated circuit dimensions continues. Although there is a significant effort to push the limits of optical resolution for backside fault analysis through the use of solid immersion lenses, higher order laser beams, and beam apodization, signal processing techniques are required for additional improvement. In this work, we propose a sparse image reconstruction framework which couples overcomplete dictionary-based representation with a physics-based forward model to improve resolution and localization accuracy in high numerical aperture confocal microscopy systems for backside optical integrated circuit analysis. The effectiveness of the framework is demonstrated on experimental data.

Space telescope low scattered light camera - A model

NASA Technical Reports Server (NTRS)

Breckinridge, J. B.; Kuper, T. G.; Shack, R. V.

1982-01-01

A design approach for a camera to be used with the space telescope is given. Camera optics relay the system pupil onto an annular Gaussian ring apodizing mask to control scattered light. One and two dimensional models of ripple on the primary mirror were calculated. Scattered light calculations using ripple amplitudes between wavelength/20 wavelength/200 with spatial correlations of the ripple across the primary mirror between 0.2 and 2.0 centimeters indicate that the detection of an object a billion times fainter than a bright source in the field is possible. Detection of a Jovian type planet in orbit about alpha Centauri with a camera on the space telescope may be possible.

Technology development towards WFIRST-AFTA coronagraph

NASA Astrophysics Data System (ADS)

Poberezhskiy, Ilya; Zhao, Feng; An, Xin; Balasubramanian, Kunjithapatham; Belikov, Ruslan; Cady, Eric; Demers, Richard; Diaz, Rosemary; Gong, Qian; Gordon, Brian; Goullioud, Renaud; Greer, Frank; Guyon, Olivier; Hoenk, Michael; Kasdin, N. Jeremy; Kern, Brian; Krist, John; Kuhnert, Andreas; McElwain, Michael; Mennesson, Bertrand; Moody, Dwight; Muller, Richard; Nemati, Bijan; Patterson, Keith; Riggs, A. J.; Ryan, Daniel; Seo, Byoung-Joon; Shaklan, Stuart; Sidick, Erkin; Shi, Fang; Siegler, Nicholas; Soummer, Rémi; Tang, Hong; Trauger, John; Wallace, J. Kent; Wang, Xu; White, Victor; Wilson, Daniel; Yee, Karl; Zhou, Hanying; Zimmerman, Neil

2014-08-01

NASA's WFIRST-AFTA mission concept includes the first high-contrast stellar coronagraph in space. This coronagraph will be capable of directly imaging and spectrally characterizing giant exoplanets similar to Neptune and Jupiter, and possibly even super-Earths, around nearby stars. In this paper we present the plan for maturing coronagraph technology to TRL5 in 2014-2016, and the results achieved in the first 6 months of the technology development work. The specific areas that are discussed include coronagraph testbed demonstrations in static and simulated dynamic environment, design and fabrication of occulting masks and apodizers used for starlight suppression, low-order wavefront sensing and control subsystem, deformable mirrors, ultra-low-noise spectrograph detector, and data post-processing.

Global-Mode Analysis of Full-Disk Data from the Michelson Doppler Imager and the Helioseismic and Magnetic Imager

NASA Astrophysics Data System (ADS)

Larson, Timothy P.; Schou, Jesper

2018-02-01

Building upon our previous work, in which we analyzed smoothed and subsampled velocity data from the Michelson Doppler Imager (MDI), we extend our analysis to unsmoothed, full-resolution MDI data. We also present results from the Helioseismic and Magnetic Imager (HMI), in both full resolution and processed to be a proxy for the low-resolution MDI data. We find that the systematic errors that we saw previously, namely peaks in both the high-latitude rotation rate and the normalized residuals of odd a-coefficients, are almost entirely absent in the two full-resolution analyses. Furthermore, we find that both systematic errors seem to depend almost entirely on how the input images are apodized, rather than on resolution or smoothing. Using the full-resolution HMI data, we confirm our previous findings regarding the effect of using asymmetric profiles on mode parameters, and also find that they occasionally result in more stable fits. We also confirm our previous findings regarding discrepancies between 360-day and 72-day analyses. We further investigate a six-month period previously seen in f-mode frequency shifts using the low-resolution datasets, this time accounting for solar-cycle dependence using magnetic-field data. Both HMI and MDI saw prominent six-month signals in the frequency shifts, but we were surprised to discover that the strongest signal at that frequency occurred in the mode coverage for the low-resolution proxy. Finally, a comparison of mode parameters from HMI and MDI shows that the frequencies and a-coefficients agree closely, encouraging the concatenation of the two datasets.

Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling*

PubMed Central

Larance, Mark; Kirkwood, Kathryn J.; Tinti, Michele; Brenes Murillo, Alejandro; Ferguson, Michael A. J.; Lamond, Angus I.

2016-01-01

We present a methodology using in vivo crosslinking combined with HPLC-MS for the global analysis of endogenous protein complexes by protein correlation profiling. Formaldehyde crosslinked protein complexes were extracted with high yield using denaturing buffers that maintained complex solubility during chromatographic separation. We show this efficiently detects both integral membrane and membrane-associated protein complexes,in addition to soluble complexes, allowing identification and analysis of complexes not accessible in native extracts. We compare the protein complexes detected by HPLC-MS protein correlation profiling in both native and formaldehyde crosslinked U2OS cell extracts. These proteome-wide data sets of both in vivo crosslinked and native protein complexes from U2OS cells are freely available via a searchable online database (www.peptracker.com/epd). Raw data are also available via ProteomeXchange (identifier PXD003754). PMID:27114452

Rethinking the longitudinal stream temperature paradigm: region-wide comparison of thermal infrared imagery reveals unexpected complexity of river temperatures

USGS Publications Warehouse

Fullerton, Aimee H.; Torgersen, Christian E.; Lawler, Joshua J.; Faux, Russell N.; Steel, E. Ashley; Beechie, Timothy J.; Ebersole, Joseph L.; Leibowitz, Scott J.

2015-01-01

Prevailing theory suggests that stream temperature warms asymptotically in a downstream direction, beginning at the temperature of the source in the headwaters and leveling off downstream as it converges to match meteorological conditions. However, there have been few empirical examples of longitudinal patterns of temperature in large rivers due to a paucity of data. We constructed longitudinal thermal profiles (temperature versus distance) for 53 rivers in the Pacific Northwest (USA) using an extensive dataset of remotely sensed summertime river temperatures and classified each profile into one of five patterns of downstream warming: asymptotic (increasing then flattening), linear (increasing steadily), uniform (not changing), parabolic (increasing then decreasing), or complex (not fitting other classes). We evaluated (1) how frequently profiles warmed asymptotically downstream as expected, and (2) whether relationships between river temperature and common hydroclimatic variables differed by profile class. We found considerable diversity in profile shape, with 47% of rivers warming asymptotically, and 53% having alternative profile shapes. Water temperature did not warm substantially over the course of the river for coastal parabolic and uniform profiles, and for some linear and complex profiles. Profile classes showed no clear geographical trends. The degree of correlation between river temperature and hydroclimatic variables differed among profile classes, but there was overlap among classes. Water temperature in rivers with asymptotic or parabolic profiles was positively correlated with August air temperature, tributary temperature and velocity, and negatively correlated with elevation, August precipitation, gradient, and distance upstream. Conversely, associations were less apparent in rivers with linear, uniform, or complex profiles. Factors contributing to the unique shape of parabolic profiles differed for coastal and inland rivers, where downstream cooling was influenced locally by climate or cool water inputs, respectively. Potential drivers of shape for complex profiles were specific to each river. These thermal patterns indicate diverse thermal habitats that may promote resilience of aquatic biota to climate change. Without this spatial context, climate change models may incorrectly estimate loss of thermally suitable habitat.

Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles

PubMed Central

Schneidman-Duhovny, Dina; Hammel, Michal

2018-01-01

Small-angle X-ray scattering (SAXS) is an increasingly common and useful technique for structural characterization of molecules in solution. A SAXS experiment determines the scattering intensity of a molecule as a function of spatial frequency, termed SAXS profile. SAXS profiles can be utilized in a variety of molecular modeling applications, such as comparing solution and crystal structures, structural characterization of flexible proteins, assembly of multi-protein complexes, and modeling of missing regions in the high-resolution structure. Here, we describe protocols for modeling atomic structures based on SAXS profiles. The first protocol is for comparing solution and crystal structures including modeling of missing regions and determination of the oligomeric state. The second protocol performs multi-state modeling by finding a set of conformations and their weights that fit the SAXS profile starting from a single-input structure. The third protocol is for protein-protein docking based on the SAXS profile of the complex. We describe the underlying software, followed by demonstrating their application on interleukin 33 (IL33) with its primary receptor ST2 and DNA ligase IV-XRCC4 complex. PMID:29605933

Bilateral implantation of +3.0 D multifocal toric intraocular lenses: results of a US Food and Drug Administration clinical trial.

PubMed

Lehmann, Robert; Modi, Satish; Fisher, Bret; Michna, Magda; Snyder, Michael

2017-01-01

The purpose of this study was to evaluate the clinical outcomes of apodized diffractive +3.0 D multifocal toric intraocular lens (IOL) implantations in subjects with preoperative corneal astigmatism. This was a prospective cohort study conducted at 21 US sites. The study population consisted of 574 subjects, aged ≥21 years, with preoperative astigmatism 0.75-2.82 D, and potential postoperative visual acuity (VA) ≥0.2 logMAR, undergoing bilateral cataract removal by phacoemulsification. The intervention was bilateral implantation of aspheric apodized diffractive +3.0 D multifocal toric or spherical multifocal nontoric IOLs. The main outcome measures were monocular uncorrected near and distance VA and safety at 12 months. A total of 373/386 and 182/188 subjects implanted with multifocal toric and nontoric IOLs, respectively, completed 12-month follow-up after the second implantation. Toric IOLs were nonin-ferior in monocular uncorrected distance (4 m) and near (40 cm) VA but had >1 line better binocular uncorrected intermediate VA (50, 60, and 70 cm) than nontoric IOLs. Toric IOLs reduced cylinder to within 0.50 D and 1.0 D of target in 278 (74.5%) and 351 (94.1%) subjects, respectively. Mean ± standard deviation (SD) differences between intended and achieved axis orientation in the first and second implanted eyes were 5.0°±6.1° and 4.7°±4.0°, respectively. Mean ± SD 12-month IOL rotations in the first and second implanted eyes were 2.7°±5.8° and 2.2°±2.7°, respectively. No subject receiving toric IOLs required secondary surgical intervention due to optical lens properties. Multifocal toric IOLs were noninferior to multifocal nontoric IOLs in uncorrected distance and near VAs in subjects with preexisting corneal astigmatism and effectively corrected astigmatism of 0.75-2.82 D.

Early Science Results from the Williams College Eclipse Expedition

NASA Astrophysics Data System (ADS)

Pasachoff, Jay M.; Person, Michael J.; Dantowitz, Ron; Lockwood, Christian A.; Nagle-McNaughton, Tim; Meadors, Erin N.; Perez, Cielo C.; Marti, Connor J.; Yu, Ross; Rosseau, Brendan; Daly, Declan M.; Ide, Charles A.; Davis, Allen B.; Lu, Muzhou; Sliski, David; Seiradakis, John; Voulgaris, Aris; Rusin, Vojtech; Peñaloza-Murillo, Marcos A.; Roman, Michael; Seaton, Daniel B.; Steele, Amy; Lee, Duane M.; Freeman, Marcus J.

2018-01-01

We describe our first cut of data reduction on a wide variety of observations of the solar corona and of the effect of the penumbra and umbra on the terrestrial atmosphere, carried out from our eclipse site on the campus of Willamette University in Salem, Oregon. Our team of faculty, undergraduate students, graduate students, and other colleagues observed the eclipse, taking images and spectra with a variety of sensors and telescopes. Equipment included frame-transfer cameras observing at 3 Hz in 0.3 nm filters at the coronal green and red lines to measure the power spectrum of oscillations in coronal loops or elsewhere in the lower corona; 3 spectrographs; a variety of telescopes and telephotos for white-light imaging; a double Lyot system tuned at Fe XIV 530.3 nm (FWHM 0.4 nm) and Fe X 637.4 nm (FWHM 0.5 nm); and a weather station to record changes in the terrestrial atmosphere. We are comparing our observations with predictions based on the previous mapping of the photospheric magnetic field, and preparing wide-field complete coronal imaging incorporating NOAA/NASA GOES-16 SUVI and NRL/NASA/LASCO for the corona outside our own images (which extend, given the completely clear skies we had, at least 4 solar radii), and NASA SDO/AIA and NOAA/NASA GOES-16 SUVI for the solar disk. One of our early composites appeared as Astronomy Picture of the Day for September 27: https://apod.nasa.gov/apod/ap170927.htmlOur expedition was supported in large part by grants from the Committee for Research and Exploration of the National Geographic Society and from the Solar Terrestrial Program of the Atmospheric and Geospace Sciences Division of the National Science Foundation, with additional student support from the STP/AGS of NSF, the NASA Massachusetts Space Grant Consortium, the Sigma Xi honorary scientific society, the Clare Booth Luce Foundation studentship and the Freeman Foote Expeditionary Fund at Williams College, other Williams College funds, and U. Pennsylvania funds.

Pre-control relationship of onchocercal skin disease with onchocercal infection in Guinea Savanna, Northern Nigeria

PubMed Central

Murdoch, Michele E.; Murdoch, Ian E.; Evans, Jennifer; Yahaya, Haliru; Njepuome, Ngozi; Cousens, Simon; Abiose, Adenike

2017-01-01

Background Onchocerca volvulus infection can result in blindness, itching and skin lesions. Previous research concentrated on blindness. Methods A clinical classification system of the cutaneous changes in onchocerciasis was used for the first time in this study within the context of an early ivermectin drug trial in the savanna region of Kaduna State, northern Nigeria. Skin examinations were performed in 6,790 individuals aged 5+ years in endemic communities and 1,343 individuals in nonendemic communities. Results / Discussion There was increased risk for all forms of onchocercal skin disease in endemic communities with the most common finding being the presence of nodules (1,438 individuals, 21.2%), followed by atrophy (367, 6.1% of those < 50 years), acute papular onchodermatitis, APOD (233, 3.4%), depigmentation (216, 3.2%) and chronic papular onchodermatitis, CPOD (155, 2.3%). A further 645 individuals (9.5%) complained of pruritus but had completely normal skin. APOD was more common in males whereas atrophy, hanging groin and nodules were more common in females. After controlling for age and sex, microfilarial positivity was a risk factor for CPOD, depigmentation, hanging groin and nodules (OR 1.54, p = 0.046; OR 2.29, p = 0.002; OR 2.18, p = 0.002 and OR 3.80, p <0.001 respectively). Comparable results were found using presence of nodules as the marker for infection. Microfilarial load showed similar, though weaker, results. A total of 2621(38.6%) endemic residents had itching with normal skin, or had one or more types of onchocercal skin disease including nodules, which may be considered as a composite index of the overall prevalence of onchocercal skin disease. Conclusion Significant levels of onchocercal skin disease were documented in this savanna area, which subsequently resulted in a reassessment of the true burden of skin disease in onchocerciasis. This paper represents the first detailed report of the association of onchocercal skin disease with markers for onchocercal infection. PMID:28355223

Optimal 2D-SIM reconstruction by two filtering steps with Richardson-Lucy deconvolution.

PubMed

Perez, Victor; Chang, Bo-Jui; Stelzer, Ernst Hans Karl

2016-11-16

Structured illumination microscopy relies on reconstruction algorithms to yield super-resolution images. Artifacts can arise in the reconstruction and affect the image quality. Current reconstruction methods involve a parametrized apodization function and a Wiener filter. Empirically tuning the parameters in these functions can minimize artifacts, but such an approach is subjective and produces volatile results. We present a robust and objective method that yields optimal results by two straightforward filtering steps with Richardson-Lucy-based deconvolutions. We provide a resource to identify artifacts in 2D-SIM images by analyzing two main reasons for artifacts, out-of-focus background and a fluctuating reconstruction spectrum. We show how the filtering steps improve images of test specimens, microtubules, yeast and mammalian cells.

Optimal 2D-SIM reconstruction by two filtering steps with Richardson-Lucy deconvolution

NASA Astrophysics Data System (ADS)

Perez, Victor; Chang, Bo-Jui; Stelzer, Ernst Hans Karl

2016-11-01

Structured illumination microscopy relies on reconstruction algorithms to yield super-resolution images. Artifacts can arise in the reconstruction and affect the image quality. Current reconstruction methods involve a parametrized apodization function and a Wiener filter. Empirically tuning the parameters in these functions can minimize artifacts, but such an approach is subjective and produces volatile results. We present a robust and objective method that yields optimal results by two straightforward filtering steps with Richardson-Lucy-based deconvolutions. We provide a resource to identify artifacts in 2D-SIM images by analyzing two main reasons for artifacts, out-of-focus background and a fluctuating reconstruction spectrum. We show how the filtering steps improve images of test specimens, microtubules, yeast and mammalian cells.

Laboratory demonstration of a broadband six-level phase mask coronagraph.

PubMed

Patru, Fabien; Baudoz, Pierre; Galicher, Raphaël; Cao, Qing; Wang, Kai; Xing, Lujing; Boussaha, Faouzi; Firminy, Josiane; Bonafous, Marion

2018-04-16

The six-level phase mask (SLPM) can be used in a focal plane as an efficient coronagraph [Opt. Express 22, 1884 (2014)]. It has several advantages: high-contrast imaging in broadband with small inner working angle; easy fabrication at low cost by photolithography and reactive ion etching processes; easy implementation with no need of pupil apodization. We present in this paper the first laboratory results demonstrating the high performance of a SLPM with an unobscured pupil. The on-axis attenuation reaches 2 × 10 -5 at λ = 800 nm and is better than 10 -4 over a 10% spectral bandwidth and better than 10 -3 over a 20% bandwidth. Finally, the detection of a planet can be achieved down to 1 λ/D.

Smoothing of the spectrum of fibre Bragg gratings in the Lloyd-interferometer recording scheme

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

Abdullina, S R; Vlasov, Aleksandr A; Babin, Sergei A

2010-05-26

The possibility of apodization of fibre Bragg gratings (FBGs) recorded in the region of interference of the two parts of a Gaussian beam in a Lloyd interferometer is considered. The reflection spectra of FBGs are numerically simulated for different parameters of the recording beam and its displacement with respect to the dividing axis in the interferometer. Aconsiderable suppression of sidelobe resonances in the FBG spectrum during the displacement of the beam centre with respect to the dividing axis by half the beam radius is predicted and experimentally demonstrated. It is shown that this is caused by the equating of themore » mean value of the refractive index in the FBG region. (fibres)« less

Noise normalization and windowing functions for VALIDAR in wind parameter estimation

NASA Astrophysics Data System (ADS)

Beyon, Jeffrey Y.; Koch, Grady J.; Li, Zhiwen

2006-05-01

The wind parameter estimates from a state-of-the-art 2-μm coherent lidar system located at NASA Langley, Virginia, named VALIDAR (validation lidar), were compared after normalizing the noise by its estimated power spectra via the periodogram and the linear predictive coding (LPC) scheme. The power spectra and the Doppler shift estimates were the main parameter estimates for comparison. Different types of windowing functions were implemented in VALIDAR data processing algorithm and their impact on the wind parameter estimates was observed. Time and frequency independent windowing functions such as Rectangular, Hanning, and Kaiser-Bessel and time and frequency dependent apodized windowing function were compared. The briefing of current nonlinear algorithm development for Doppler shift correction subsequently follows.

The Gemini Planet Imager: integration and status

NASA Astrophysics Data System (ADS)

Macintosh, Bruce A.; Anthony, Andre; Atwood, Jennifer; Barriga, Nicolas; Bauman, Brian; Caputa, Kris; Chilcote, Jeffery; Dillon, Daren; Doyon, René; Dunn, Jennifer; Gavel, Donald T.; Galvez, Ramon; Goodsell, Stephen J.; Graham, James R.; Hartung, Markus; Isaacs, Joshua; Kerley, Dan; Konopacky, Quinn; Labrie, Kathleen; Larkin, James E.; Maire, Jerome; Marois, Christian; Millar-Blanchaer, Max; Nunez, Arturo; Oppenheimer, Ben R.; Palmer, David W.; Pazder, John; Perrin, Marshall; Poyneer, Lisa A.; Quirez, Carlos; Rantakyro, Frederik; Reshtov, Vlad; Saddlemyer, Leslie; Sadakuni, Naru; Savransky, Dmitry; Sivaramakrishnan, Anand; Smith, Malcolm; Soummer, Remi; Thomas, Sandrine; Wallace, J. Kent; Weiss, Jason; Wiktorowicz, Sloane

2012-09-01

The Gemini Planet Imager is a next-generation instrument for the direct detection and characterization of young warm exoplanets, designed to be an order of magnitude more sensitive than existing facilities. It combines a 1700-actuator adaptive optics system, an apodized-pupil Lyot coronagraph, a precision interferometric infrared wavefront sensor, and a integral field spectrograph. All hardware and software subsystems are now complete and undergoing integration and test at UC Santa Cruz. We will present test results on each subsystem and the results of end-to-end testing. In laboratory testing, GPI has achieved a raw contrast (without post-processing) of 10-6 5σ at 0.4", and with multiwavelength speckle suppression, 2x10-7 at the same separation.

Weighted SAW reflector gratings for orthogonal frequency coded SAW tags and sensors

NASA Technical Reports Server (NTRS)

Puccio, Derek (Inventor); Malocha, Donald (Inventor)

2011-01-01

Weighted surface acoustic wave reflector gratings for coding identification tags and sensors to enable unique sensor operation and identification for a multi-sensor environment. In an embodiment, the weighted reflectors are variable while in another embodiment the reflector gratings are apodized. The weighting technique allows the designer to decrease reflectively and allows for more chips to be implemented in a device and, consequently, more coding diversity. As a result, more tags and sensors can be implemented using a given bandwidth when compared with uniform reflectors. Use of weighted reflector gratings with OFC makes various phase shifting schemes possible, such as in-phase and quadrature implementations of coded waveforms resulting in reduced device size and increased coding.

Evolution of Cuticular Hydrocarbons in the Hymenoptera: a Meta-Analysis.

PubMed

Kather, Ricarda; Martin, Stephen J

2015-10-01

Chemical communication is the oldest form of communication, spreading across all forms of life. In insects, cuticular hydrocarbons (CHC) function as chemical cues for the recognition of mates, species, and nest-mates in social insects. Although much is known about the function of individual hydrocarbons and their biosynthesis, a phylogenetic overview is lacking. Here, we review the CHC profiles of 241 species of Hymenoptera, one of the largest and most important insect orders, which includes the Symphyta (sawflies), the polyphyletic Parasitica (parasitoid wasps), and the Aculeata (wasps, bees, and ants). We investigated whether these taxonomic groups differed in the presence and absence of CHC classes and whether the sociality of a species (solitarily vs. social) had an effect on CHC profile complexity. We found that the main CHC classes (i.e., n-alkanes, alkenes, and methylalkanes) were all present early in the evolutionary history of the Hymenoptera, as evidenced by their presence in ancient Symphyta and primitive Parasitica wasps. Throughout all groups within the Hymenoptera, the more complex a CHC the fewer species that produce it, which may reflect the Occam's razor principle that insects' only biosynthesize the most simple compound that fulfil its needs. Surprisingly, there was no difference in the complexity of CHC profiles between social and solitary species, with some of the most complex CHC profiles belonging to the Parasitica. This profile complexity has been maintained in the ants, but some specialization in biosynthetic pathways has led to a simplification of profiles in the aculeate wasps and bees. The absence of CHC classes in some taxa or species may be due to gene silencing or down-regulation rather than gene loss, as demonstrated by sister species having highly divergent CHC profiles, and cannot be predicted by their phylogenetic history. The presence of highly complex CHC profiles prior to the vast radiation of the social Hymenoptera indicates a 'spring-loaded' system where the diversity of CHC needed for the complex communication systems of social insects were already present for natural selection to act upon, rather than having evolved independently. This diversity may have aided the multiple independent evolution of sociality within the Aculeata.

Modeling Bivariate Longitudinal Hormone Profiles by Hierarchical State Space Models

PubMed Central

Liu, Ziyue; Cappola, Anne R.; Crofford, Leslie J.; Guo, Wensheng

2013-01-01

The hypothalamic-pituitary-adrenal (HPA) axis is crucial in coping with stress and maintaining homeostasis. Hormones produced by the HPA axis exhibit both complex univariate longitudinal profiles and complex relationships among different hormones. Consequently, modeling these multivariate longitudinal hormone profiles is a challenging task. In this paper, we propose a bivariate hierarchical state space model, in which each hormone profile is modeled by a hierarchical state space model, with both population-average and subject-specific components. The bivariate model is constructed by concatenating the univariate models based on the hypothesized relationship. Because of the flexible framework of state space form, the resultant models not only can handle complex individual profiles, but also can incorporate complex relationships between two hormones, including both concurrent and feedback relationship. Estimation and inference are based on marginal likelihood and posterior means and variances. Computationally efficient Kalman filtering and smoothing algorithms are used for implementation. Application of the proposed method to a study of chronic fatigue syndrome and fibromyalgia reveals that the relationships between adrenocorticotropic hormone and cortisol in the patient group are weaker than in healthy controls. PMID:24729646

Modeling Bivariate Longitudinal Hormone Profiles by Hierarchical State Space Models.

PubMed

Liu, Ziyue; Cappola, Anne R; Crofford, Leslie J; Guo, Wensheng

2014-01-01

The hypothalamic-pituitary-adrenal (HPA) axis is crucial in coping with stress and maintaining homeostasis. Hormones produced by the HPA axis exhibit both complex univariate longitudinal profiles and complex relationships among different hormones. Consequently, modeling these multivariate longitudinal hormone profiles is a challenging task. In this paper, we propose a bivariate hierarchical state space model, in which each hormone profile is modeled by a hierarchical state space model, with both population-average and subject-specific components. The bivariate model is constructed by concatenating the univariate models based on the hypothesized relationship. Because of the flexible framework of state space form, the resultant models not only can handle complex individual profiles, but also can incorporate complex relationships between two hormones, including both concurrent and feedback relationship. Estimation and inference are based on marginal likelihood and posterior means and variances. Computationally efficient Kalman filtering and smoothing algorithms are used for implementation. Application of the proposed method to a study of chronic fatigue syndrome and fibromyalgia reveals that the relationships between adrenocorticotropic hormone and cortisol in the patient group are weaker than in healthy controls.

Results of an inter and intra laboratory exercise on the assessment of complex autosomal DNA profiles.

PubMed

Benschop, Corina C G; Connolly, Edward; Ansell, Ricky; Kokshoorn, Bas

2017-01-01

The interpretation of complex DNA profiles may differ between laboratories and reporting officers, which can lead to discrepancies in the final reports. In this study, we assessed the intra and inter laboratory variation in DNA mixture interpretation for three European ISO17025-accredited laboratories. To this aim, 26 reporting officers analyzed five sets of DNA profiles. Three main aspects were considered: 1) whether the mixed DNA profiles met the criteria for comparison to a reference profile, 2) the actual result of the comparison between references and DNA profiling data and 3) whether the weight of the DNA evidence could be assessed. Similarity in answers depended mostly on the complexity of the tasks. This study showed less variation within laboratories than between laboratories which could be the result of differences between internal laboratory guidelines and methods and tools available. Results show the profile types for which the three laboratories report differently, which informs indirectly on the complexity threshold the laboratories employ. Largest differences between laboratories were caused by the methods available to assess the weight of the DNA evidence. This exercise aids in training forensic scientists, refining laboratory guidelines and explaining differences between laboratories in court. Undertaking more collaborative exercises in future may stimulate dialog and consensus regarding interpretation. For training purposes, DNA profiles of the mixed stains and questioned references are made available. Copyright © 2016 The Chartered Society of Forensic Sciences. Published by Elsevier Ireland Ltd. All rights reserved.

Genomic profiling of bovine corpus luteum maturation

PubMed Central

Wigoda, Noa; Ben-Dor, Shifra; Orr, Irit; Meidan, Rina

2018-01-01

To unveil novel global changes associated with corpus luteum (CL) maturation, we analyzed transcriptome data for the bovine CL on days 4 and 11, representing the developing vs. mature gland. Our analyses revealed 681 differentially expressed genes (363 and 318 on day 4 and 11, respectively), with ≥2 fold change and FDR of <5%. Different gene ontology (GO) categories were represented prominently in transcriptome data at these stages (e.g. days 4: cell cycle, chromosome, DNA metabolic process and replication and on day 11: immune response; lipid metabolic process and complement activation). Based on bioinformatic analyses, select genes expression in day 4 and 11 CL was validated with quantitative real-time PCR. Cell specific expression was also determined in enriched luteal endothelial and steroidogenic cells. Genes related to the angiogenic process such as NOS3, which maintains dilated vessels and MMP9, matrix degrading enzyme, were higher on day 4. Importantly, our data suggests day 11 CL acquire mechanisms to prevent blood vessel sprouting and promote their maturation by expressing NOTCH4 and JAG1, greatly enriched in luteal endothelial cells. Another endothelial specific gene, CD300LG, was identified here in the CL for the first time. CD300LG is an adhesion molecule enabling lymphocyte migration, its higher levels at mid cycle are expected to support the transmigration of immune cells into the CL at this stage. Together with steroidogenic genes, most of the genes regulating de-novo cholesterol biosynthetic pathway (e.g HMGCS, HMGCR) and cholesterol uptake from plasma (LDLR, APOD and APOE) were upregulated in the mature CL. These findings provide new insight of the processes involved in CL maturation including blood vessel growth and stabilization, leucocyte transmigration as well as progesterone synthesis as the CL matures. PMID:29590145

Modelling exoplanet detection with the LUVOIR Coronagraph: aberration sensitivity and error tolerances

NASA Astrophysics Data System (ADS)

Juanola-Parramon, Roser; Zimmerman, Neil; Bolcar, Matthew R.; Rizzo, Maxime; Roberge, Aki

2018-01-01

The Coronagraph is a key instrument on the Large UV-Optical-Infrared (LUVOIR) Surveyor mission concept. The Apodized Pupil Lyot Coronagraph (APLC) is one of the baselined mask technologies to enable 1E10 contrast observations in the habitable zones of nearby stars. Both the LUVOIR architectures A and B present a segmented aperture as input pupil, introducing a set of random tip/tilt and piston errors, among others, that greatly affect the performance of the coronagraph instrument by increasing the wavefront errors hence reducing the instrument sensitivity. In this poster we present the latest results of the simulation of these effects for different working angle regions and discuss the achieved contrast for exoplanet detection and characterization, including simulated observations under these circumstances, setting boundaries for the tolerance of such errors.

Visualization of retinal vascular structure and perfusion with a nonconfocal adaptive optics scanning light ophthalmoscope

PubMed Central

Sulai, Yusufu N.; Scoles, Drew; Harvey, Zachary; Dubra, Alfredo

2015-01-01

Imaging of the retinal vascular structure and perfusion was explored by confocal illumination and nonconfocal detection in an adaptive optics scanning light ophthalmoscope (AOSLO), as an extension of the work by Chui et al. [Biomed. Opt. Express 3, 2537 (2012)]. Five different detection schemes were evaluated at multiple retinal locations: circular mask, annular mask, circular mask with filament, knife-edge, and split-detector. Given the superior image contrast in the reflectance and perfusion maps, the split-detection method was further tested using pupil apodization, polarized detection, and four different wavelengths. None of these variations provided noticeable contrast improvement. The noninvasive visualization of capillary flow and structure provided by AOSLO split-detection shows great promise for studying ocular and systemic conditions that affect the retinal vasculature. PMID:24690655

On the dynamics of Airy beams in nonlinear media with nonlinear losses.

PubMed

Ruiz-Jiménez, Carlos; Nóbrega, K Z; Porras, Miguel A

2015-04-06

We investigate on the nonlinear dynamics of Airy beams in a regime where nonlinear losses due to multi-photon absorption are significant. We identify the nonlinear Airy beam (NAB) that preserves the amplitude of the inward Hänkel component as an attractor of the dynamics. This attractor governs also the dynamics of finite-power (apodized) Airy beams, irrespective of the location of the entrance plane in the medium with respect to the Airy waist plane. A soft (linear) input long before the waist, however, strongly speeds up NAB formation and its persistence as a quasi-stationary beam in comparison to an abrupt input at the Airy waist plane, and promotes the formation of a new type of highly dissipative, fully nonlinear Airy beam not described so far.

Mathematical Formulation used by MATLAB Code to Convert FTIR Interferograms to Calibrated Spectra

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

Armstrong, Derek Elswick

This report discusses the mathematical procedures used to convert raw interferograms from Fourier transform infrared (FTIR) sensors to calibrated spectra. The work discussed in this report was completed as part of the Helios project at Los Alamos National Laboratory. MATLAB code was developed to convert the raw interferograms to calibrated spectra. The report summarizes the developed MATLAB scripts and functions, along with a description of the mathematical methods used by the code. The first step in working with raw interferograms is to convert them to uncalibrated spectra by applying an apodization function to the raw data and then by performingmore » a Fourier transform. The developed MATLAB code also addresses phase error correction by applying the Mertz method. This report provides documentation for the MATLAB scripts.« less

Fabrication of Extremely Short Length Fiber Bragg Gratings for Sensor Applications

NASA Technical Reports Server (NTRS)

Wu, Meng-Chou; Rogowski, Robert S.; Tedjojuwono, Ken K.

2002-01-01

A new technique and a physical model for writing extremely short length Bragg gratings in optical fibers have been developed. The model describes the effects of diffraction on the spatial spectra and therefore, the wavelength spectra of the Bragg gratings. Using an interferometric technique and a variable aperture, short gratings of various lengths and center wavelengths were written in optical fibers. By selecting the related parameters, the Bragg gratings with typical length of several hundred microns and bandwidth of several nanometers can be obtained. These short gratings can be apodized with selected diffraction patterns and hence their broadband spectra have a well-defined bell shape. They are suitable for use as miniaturized distributed strain sensors, which have broad applications to aerospace research and industry as well.

Sidelobe apodization in optical pulse compression reflectometry for fiber optic distributed acoustic sensing.

PubMed

Mompó, Juan José; Martín-López, Sonia; González-Herráez, Miguel; Loayssa, Alayn

2018-04-01

We demonstrate a technique to reduce the sidelobes in optical pulse compression reflectometry for distributed acoustic sensing. The technique is based on using a Gaussian probe pulse with linear frequency modulation. This is shown to improve the sidelobe suppression by 13 dB compared to the use of square pulses without any significant penalty in terms of spatial resolution. In addition, a 2.25 dB enhancement in signal-to-noise ratio is calculated compared to the use of receiver-side windowing. The method is tested by measuring 700 Hz vibrations with a 140  nε amplitude at the end of a 50 km fiber sensing link with 34 cm spatial resolution, giving a record 147,058 spatially resolved points.

Highly uniform parallel microfabrication using a large numerical aperture system

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

Zhang, Zi-Yu; Su, Ya-Hui, E-mail: ustcsyh@ahu.edu.cn, E-mail: dongwu@ustc.edu.cn; Zhang, Chen-Chu

In this letter, we report an improved algorithm to produce accurate phase patterns for generating highly uniform diffraction-limited multifocal arrays in a large numerical aperture objective system. It is shown that based on the original diffraction integral, the uniformity of the diffraction-limited focal arrays can be improved from ∼75% to >97%, owing to the critical consideration of the aperture function and apodization effect associated with a large numerical aperture objective. The experimental results, e.g., 3 × 3 arrays of square and triangle, seven microlens arrays with high uniformity, further verify the advantage of the improved algorithm. This algorithm enables the laser parallelmore » processing technology to realize uniform microstructures and functional devices in the microfabrication system with a large numerical aperture objective.« less

Extreme coronagraphy with an adaptive hologram. Simulations of exo-planet imaging

NASA Astrophysics Data System (ADS)

Ricci, D.; Le Coroller, H.; Labeyrie, A.

2009-08-01

Aims: We present a solution to improve the performance of coronagraphs for the detection of exo-planets. Methods: We simulate numerically several kinds of coronagraphic systems, with the aim of evaluating the gain obtained with an adaptive hologram. Results: The detection limit in flux ratio between a star and a planet (F_s/F_p) observed with an apodized Lyot coronagraph characterized by wavefront bumpiness imperfections of λ/20 (resp. λ/100) turns out to be increased by a factor of 103.4 (resp. 105.1) when equipped with a hologram. Conclusions: This technique could provide direct imaging of an exo-Earth at a distance of 11 parsec with a 6.5 m space telescope such as the JWST with the optical quality of the HST.

Electrolyte-stimulated biphasic dissolution profile and stability enhancement for tablets containing drug-polyelectrolyte complexes.

PubMed

Kindermann, Christoph; Matthée, Karin; Sievert, Frank; Breitkreutz, Jörg

2012-10-01

Recently introduced drug-polyelectrolyte complexes prepared by hot-melt extrusion should be processed to solid dosage forms with tailor-made release properties. Their potential of stability enhancement should be investigated. Milled hot-melt extruded naproxen-EUDRAGIT® E PO polyelectrolyte complexes were subsequently processed to double-layer tablets with varying complex loadings on a rotary-die press. Physicochemical interactions were studied under ICH guideline conditions and using the Gordon-Taylor equation. Sorption and desorption were determined to investigate the influence of moisture and temperature on the complex and related to stability tests under accelerated conditions. Naproxen release from the drug-polyelectrolyte complex is triggered by electrolyte concentration. Depending on the complex loading, phosphate buffer pH 6.8 stimulated a biphasic dissolution profile of the produced double-layer tablets: immediate release from the first layer with 65% loading and prolonged release from the second layer within 24 h (98.5% loading). XRPD patterns proved pseudopolymorphism for tablets containing the pure drug under common storage conditions whereas the drug-complex was stable in the amorphous state. Drug-polyelectrolyte complexes enable tailor-made dissolution profiles of solid dosage forms by electrolyte stimulation and increase stability under common storage conditions.

Digital sorting of complex tissues for cell type-specific gene expression profiles.

PubMed

Zhong, Yi; Wan, Ying-Wooi; Pang, Kaifang; Chow, Lionel M L; Liu, Zhandong

2013-03-07

Cellular heterogeneity is present in almost all gene expression profiles. However, transcriptome analysis of tissue specimens often ignores the cellular heterogeneity present in these samples. Standard deconvolution algorithms require prior knowledge of the cell type frequencies within a tissue or their in vitro expression profiles. Furthermore, these algorithms tend to report biased estimations. Here, we describe a Digital Sorting Algorithm (DSA) for extracting cell-type specific gene expression profiles from mixed tissue samples that is unbiased and does not require prior knowledge of cell type frequencies. The results suggest that DSA is a specific and sensitivity algorithm in gene expression profile deconvolution and will be useful in studying individual cell types of complex tissues.

Profiling Bioactivity of the ToxCast Chemical Library Using BioMAP Primary Human Cell Systems

EPA Science Inventory

The complexity of human biology has made prediction of health effects as a consequence of exposure to environmental chemicals especially challenging. Complex cell systems, such as the Biologically Multiplexed Activity Profiling (BioMAP) primary, human, cell-based disease models, ...

Exploring the oxidation and iron binding profile of a cyclodextrin encapsulated quercetin complex unveiled a controlled complex dissociation through a chemical stimulus.

PubMed

Diamantis, Dimitrios A; Ramesova, Sarka; Chatzigiannis, Christos M; Degano, Ilaria; Gerogianni, Paraskevi S; Karadima, Constantina; Perikleous, Sonia; Rekkas, Dimitrios; Gerothanassis, Ioannis P; Galaris, Dimitrios; Mavromoustakos, Thomas; Valsami, Georgia; Sokolova, Romana; Tzakos, Andreas G

2018-06-07

Flavonoids possess a rich polypharmacological profile and their biological role is linked to their oxidation state protecting DNA from oxidative stress damage. However, their bioavailability is hampered due to their poor aqueous solubility. This can be surpassed through encapsulation to supramolecular carriers as cyclodextrin (CD). A quercetin- 2HP-β-CD complex has been formerly reported by us. However, once the flavonoid is in its 2HP-β-CD encapsulated state its oxidation potential, its decomplexation mechanism, its potential to protect DNA damage from oxidative stress remained elusive. To unveil this, an array of biophysical techniques was used. The quercetin-2HP-β-CD complex was evaluated through solubility and dissolution experiments, electrochemical and spectroelectrochemical studies (Cyclic Voltammetry) UV-Vis spectroscopy, HPLC-ESI-MS/MS and HPLC-DAD, fluorescence spectroscopy, NMR Spectroscopy, theoretical calculations (density functional theory (DFT)) and biological evaluation of the protection offered against H 2 O 2 -induced DNA damage. Encapsulation of quercetin inside the supramolecule's cavity enhanced its solubility and oxidation profile is retained in its encapsulated state. Although the protective ability of the quercetin-2HP-β-CD complex against H 2 O 2 was diminished, iron serves as a chemical stimulus to dissociate the complex and release quercetin. We found that in a quercetin-2HP-β-CD inclusion complex quercetin retains its oxidation profile similarly to its native state, while iron can operate as a chemical stimulus to release quercetin from its host cavity. The oxidation profile of a natural product once it is encapsulated in a supramolecular cyclodextrin carrier as also it was discovered that decomplexation can be triggered by a chemical stimulus. Copyright © 2018. Published by Elsevier B.V.

A new method for the identification of non-Gaussian line profiles in elliptical galaxies

NASA Technical Reports Server (NTRS)

Van Der Marel, Roeland P.; Franx, Marijn

1993-01-01

A new parameterization for the line profiles of elliptical galaxies, the Gauss-Hermite series, is proposed. This approach expands the line profile as a sum of orthogonal functions which minimizes the correlations between the errors in the parameters of the fit. This method also make use of the fact that Gaussians provide good low-order fits to observed line profiles. The method yields measurements of the line strength, mean radial velocity, and the velocity dispersion as well as two extra parameters, h3 and h4, that measure asymmetric and symmetric deviations of the line profiles from a Gaussian, respectively. The new method was used to derive profiles for three elliptical galaxies which all have asymmetric line profiles on the major axis with symmetric deviations from a Gaussian. Results confirm that elliptical galaxies have complex structures due to their complex formation history.

Improving protein complex classification accuracy using amino acid composition profile.

PubMed

Huang, Chien-Hung; Chou, Szu-Yu; Ng, Ka-Lok

2013-09-01

Protein complex prediction approaches are based on the assumptions that complexes have dense protein-protein interactions and high functional similarity between their subunits. We investigated those assumptions by studying the subunits' interaction topology, sequence similarity and molecular function for human and yeast protein complexes. Inclusion of amino acids' physicochemical properties can provide better understanding of protein complex properties. Principal component analysis is carried out to determine the major features. Adopting amino acid composition profile information with the SVM classifier serves as an effective post-processing step for complexes classification. Improvement is based on primary sequence information only, which is easy to obtain. Copyright © 2013 Elsevier Ltd. All rights reserved.

A low-complexity add-on score for protein remote homology search with COMER.

PubMed

Margelevicius, Mindaugas

2018-06-15

Protein sequence alignment forms the basis for comparative modeling, the most reliable approach to protein structure prediction, among many other applications. Alignment between sequence families, or profile-profile alignment, represents one of the most, if not the most, sensitive means for homology detection but still necessitates improvement. We aim at improving the quality of profile-profile alignments and the sensitivity induced by them by refining profile-profile substitution scores. We have developed a new score that represents an additional component of profile-profile substitution scores. A comprehensive evaluation shows that the new add-on score statistically significantly improves both the sensitivity and the alignment quality of the COMER method. We discuss why the score leads to the improvement and its almost optimal computational complexity that makes it easily implementable in any profile-profile alignment method. An implementation of the add-on score in the open-source COMER software and data are available at https://sourceforge.net/projects/comer. The COMER software is also available on Github at https://github.com/minmarg/comer and as a Docker image (minmar/comer). Supplementary data are available at Bioinformatics online.

Molecular Mechanisms Underlying the Epileptogenesis and Seizure Progression in Tuberous Sclerosis Complex 1 Deficient Mouse Models

DTIC Science & Technology

2016-10-01

growth and metabolism known as mammalian target of rapamycin complex 1 (mTORC1). The pathological hallmark of TSC brains are cortical tubers...molecule players that respond to or do not respond to mTORC1 inhibitors. We will examine the effects of rapamycin on the molecular changes associated...ribosome profiling and conventional ribosome profiling. Ligation-Free Ribosome Profiling in CamK2a-Cre Tsc1fl/fl Mice following Rapamycin Treatment One

Field lens multiplexing in holographic 3D displays by using Bragg diffraction based volume gratings

NASA Astrophysics Data System (ADS)

Fütterer, G.

2016-11-01

Applications, which can profit from holographic 3D displays, are the visualization of 3D data, computer-integrated manufacturing, 3D teleconferencing and mobile infotainment. However, one problem of holographic 3D displays, which are e.g. based on space bandwidth limited reconstruction of wave segments, is to realize a small form factor. Another problem is to provide a reasonable large volume for the user placement, which means to provide an acceptable freedom of movement. Both problems should be solved without decreasing the image quality of virtual and real object points, which are generated within the 3D display volume. A diffractive optical design using thick hologram gratings, which can be referred to as Bragg diffraction based volume gratings, can provide a small form factor and high definition natural viewing experience of 3D objects. A large collimated wave can be provided by an anamorphic backlight unit. The complex valued spatial light modulator add local curvatures to the wave field he is illuminated with. The modulated wave field is focused onto to the user plane by using a volume grating based field lens. Active type liquid crystal gratings provide 1D fine tracking of approximately +/- 8° deg. Diffractive multiplex has to be implemented for each color and for a set of focus functions providing coarse tracking. Boundary conditions of the diffractive multiplexing are explained. This is done in regards to the display layout and by using the coupled wave theory (CWT). Aspects of diffractive cross talk and its suppression will be discussed including longitudinal apodized volume gratings.

PCoM-DB Update: A Protein Co-Migration Database for Photosynthetic Organisms.

PubMed

Takabayashi, Atsushi; Takabayashi, Saeka; Takahashi, Kaori; Watanabe, Mai; Uchida, Hiroko; Murakami, Akio; Fujita, Tomomichi; Ikeuchi, Masahiko; Tanaka, Ayumi

2017-01-01

The identification of protein complexes is important for the understanding of protein structure and function and the regulation of cellular processes. We used blue-native PAGE and tandem mass spectrometry to identify protein complexes systematically, and built a web database, the protein co-migration database (PCoM-DB, http://pcomdb.lowtem.hokudai.ac.jp/proteins/top), to provide prediction tools for protein complexes. PCoM-DB provides migration profiles for any given protein of interest, and allows users to compare them with migration profiles of other proteins, showing the oligomeric states of proteins and thus identifying potential interaction partners. The initial version of PCoM-DB (launched in January 2013) included protein complex data for Synechocystis whole cells and Arabidopsis thaliana thylakoid membranes. Here we report PCoM-DB version 2.0, which includes new data sets and analytical tools. Additional data are included from whole cells of the pelagic marine picocyanobacterium Prochlorococcus marinus, the thermophilic cyanobacterium Thermosynechococcus elongatus, the unicellular green alga Chlamydomonas reinhardtii and the bryophyte Physcomitrella patens. The Arabidopsis protein data now include data for intact mitochondria, intact chloroplasts, chloroplast stroma and chloroplast envelopes. The new tools comprise a multiple-protein search form and a heat map viewer for protein migration profiles. Users can compare migration profiles of a protein of interest among different organelles or compare migration profiles among different proteins within the same sample. For Arabidopsis proteins, users can compare migration profiles of a protein of interest with putative homologous proteins from non-Arabidopsis organisms. The updated PCoM-DB will help researchers find novel protein complexes and estimate their evolutionary changes in the green lineage. © The Author 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Measurement of refractive index profile of non-symmetric, complex silica preforms with high refractive index differences

NASA Astrophysics Data System (ADS)

Probostova, Jana; Slanicka, Jiri; Mrazek, Jan; Podrazky, Ondrej; Benda, Adam; Peterka, Pavel

2016-04-01

Refractive index profile measurement is a key instrument for characterization of optical properties of preforms, which are used for drawing of high-quality optical fibers. Common industrial optical preform analyzers have been designed for measurement of simple symmetric structures such as step-index or graded-index preforms with refractive index close to the silica (n=1.457 at 633 nm). However, these conditions are usually far from more complex structures used in fiber lasers or in fiber sensor area. Preforms for the drawing of advanced optical fibers, such as Bragg, microstructure or photonic crystal fibers, are usually constituted from stacks with non-symmetric internal structure or composed of alternating layers with high refractive index contrasts. In this paper we present comparison of refractive index profile measurements of simple as well as complex structures with high refractive index differences simulating the Bragg structures. Commercial Photon Kinetics 2600 preform analyzer was used for the refractive index profile measurements. A set of concentrically arranged silica tubes was welded to form a complex preforms. Free space between the tubes was filled by immersion with varying refractive indices to simulate the Bragg structure. Up to three tubes were used for the analysis and the refractive indices of immersion were changed from 1.4 to 1.5. When refractive index of immersion was independently measured the structure of preform was defined. Profiles of these "known" structures were compared to measured data processed by originally proposed algorithm. The work provides an extension of issues of refractive index profile measurements in non-symmetric complex silica structures by a commercial preform analyzer and proposes more convenient methods of numeric data processing.

Resonance Raman study of a two-chromophore system. The 2:1 complex of hexamethylbenzene with tetracyanoethylene

NASA Astrophysics Data System (ADS)

Mark Britt, B.; McHale, Jeanne L.

1997-05-01

Raman excitation profiles are presented for the 2:1 electron donor-acceptor (EDA) complex of hexamethylbenzene (HMB) and tetracyanoethylene (TCNE) in cyclohexane. Though the absorption and Raman spectra of the 1:1 and 2:1 complexes are similar, distinct differences are found in the Raman excitation profiles (REPs) of vibrational modes common to both systems. REPs of the 2:1 complex show intensity cancellation that is taken as evidence for interference of two charge-transfer excited states. The implications of the observed spectra concerning excited state electron delocalization are considered.

Planet detection and spectroscopy in visible light with a single aperture telescope and a nulling coronagraph

NASA Technical Reports Server (NTRS)

Shao, Michael; Serabyn, Eugene; Levine, Bruce Martin; Beichman, Charles; Liu, Duncan; Martin, Stefan; Orton, Glen; Mennesson, Bertrand; Morgan, Rhonda; Velusamy, Thangasamy;

A new crustacean from the Herefordshire (Silurian) Lagerstätte, UK, and its significance in malacostracan evolution

PubMed Central

Briggs, Derek E. G.; Siveter, Derek J.; Sutton, Mark D.; Legg, David

2017-01-01

Cascolus ravitis gen. et sp. nov. is a three-dimensionally preserved fossil crustacean with soft parts from the Herefordshire (Silurian) Lagerstätte, UK. It is characterized by a head with a head shield and five limb pairs, and a thorax (pereon) with nine appendage-bearing segments followed by an apodous abdomen (pleon). All the appendages except the first are biramous and have a gnathobase. The post-mandibular appendages are similar one to another, and bear petal-shaped epipods that probably functioned as a part of the respiratory–circulatory system. Cladistic analysis resolves the new taxon as a stem-group leptostracan (Malacostraca). This well-preserved arthropod provides novel insights into the evolution of appendage morphology, tagmosis and the possible respiratory–circulatory physiology of a basal malacostracan. PMID:28330926

Application of image processing technology to problems in manuscript encapsulation. [Codex Hammer

NASA Technical Reports Server (NTRS)

Glackin, D. L.; Korsmo, E. P.

1983-01-01

The long term effects of encapsulation individual sheets of the Codex Hammer were investigated. The manuscript was simulated with similar sheets of paper which were photographed under repeatable raking light conditions to enhance their surface texture, encapsulated in plexiglas, cycled in an environmental test chamber, and rephotographed at selected intervals. The film images were digitized, contrast enhanced, geometrically registered, and apodized. An FFT analysis of a control sheet and two experimental sheets indicates no micro-burnishing, but reveals that the ""mesoscale'' deformations with sizes 8mm are degrading monotonically, which is of no concern. Difference image analysis indicates that the sheets were increasingly stressed with time and that the plexiglas did not provide a sufficient environmental barrier under the simulation conditions. The relationship of these results to the Codex itself is to be determined.

Matrix form for the instrument line shape of Fourier-transform spectrometers yielding a fast integration algorithm to theoretical spectra.

PubMed

Desbiens, Raphaël; Tremblay, Pierre; Genest, Jérôme; Bouchard, Jean-Pierre

2006-01-20

The instrument line shape (ILS) of a Fourier-transform spectrometer is expressed in a matrix form. For all line shape effects that scale with wavenumber, the ILS matrix is shown to be transposed in the spectral and interferogram domains. The novel representation of the ILS matrix in the interferogram domain yields an insightful physical interpretation of the underlying process producing self-apodization. Working in the interferogram domain circumvents the problem of taking into account the effects of finite optical path difference and permits a proper discretization of the equations. A fast algorithm in O(N log2 N), based on the fractional Fourier transform, is introduced that permits the application of a constant resolving power line shape to theoretical spectra or forward models. The ILS integration formalism is validated with experimental data.

On the asymptotic evolution of finite energy Airy wave functions.

PubMed

Chamorro-Posada, P; Sánchez-Curto, J; Aceves, A B; McDonald, G S

2015-06-15

In general, there is an inverse relation between the degree of localization of a wave function of a certain class and its transform representation dictated by the scaling property of the Fourier transform. We report that in the case of finite energy Airy wave packets a simultaneous increase in their localization in the direct and transform domains can be obtained as the apodization parameter is varied. One consequence of this is that the far-field diffraction rate of a finite energy Airy beam decreases as the beam localization at the launch plane increases. We analyze the asymptotic properties of finite energy Airy wave functions using the stationary phase method. We obtain one dominant contribution to the long-term evolution that admits a Gaussian-like approximation, which displays the expected reduction of its broadening rate as the input localization is increased.

Web-Based Analysis for Student-Generated Complex Genetic Profiles

ERIC Educational Resources Information Center

Kass, David H.; LaRoe, Robert

2007-01-01

A simple, rapid method for generating complex genetic profiles using Alu-based markers was recently developed for students primarily at the undergraduate level to learn more about forensics and paternity analysis. On the basis of the Cold Spring Harbor Allele Server, which provides an excellent tool for analyzing a single Alu variant, we present a…

Profile of Neonatal Sepsis due to Burkholderia capacia Complex.

PubMed

Chandrasekaran, Aparna; Subburaju, Nivedhana; Mustafa, Muzamil; Putlibai, Sulochana

2016-12-15

We report the result of retrospective record review of the clinical profile of 59 neonates who presented to a tertiary-care extramural neonatal unit with Burkholderia cepacia complex infection. Among the 3265 admissions over 45 months, incidence of Burkholderia sepsis was 18 per 1000 admissions. Case fatality rate was 17%. Most (95%) isolates were sensitive to cotrimoxazole.

Comparative evaluation of humic substances in oral drug delivery.

PubMed

Mirza, Mohd Aamir; Ahmad, Niyaz; Agarwal, Suraj Prakash; Mahmood, Danish; Khalid Anwer, M; Iqbal, Z

2011-05-01

Major and biologically most explored components of natural organic matter (NOM) are humic acid (HA) and fulvic acid (FA). We have explored rock shilajit as a source of NOM. On the other hand carbamazepine (CBZ) is a well known anticonvulsant drug and has a limited accessibility to brain. Bioavailability and pharmacokinetic profiles of CBZ have been improved by complexation and different techniques also. Present study has assessed the comparative abilities of FA and HA as complexing agent for CBZ in order to enhance pharmacokinetic profile of CBZ and accessibility to the brain. These two complexing agents have been compared on various indices such as their abilities to cause complexation and enhance solubility, permeability and dissolution. The present study also compared pharmacodynamic and biochemical profiles after oral administration of complexes. With the help of various pharmaceutical techniques such as freeze drying, physical mixture, kneading and solvent evaporation, two molar ratios (1:1 and 1:2) were selected for complexation and evaluated for conformational analysis (molecular modeling). Complex formed was further characterized by differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FT-IR), mass spectroscopy and X-ray diffraction (XRD). Preclinical study on rodents with CBZ-HA and CBZ-FA has yielded appreciable results in terms of their anticonvulsant and antioxidants activities. However, CBZ-HA (1:2) demonstrated better result than any other complex.

Chabazite and dolomite formation in a dolocrete profile: An example of a complex alkaline paragenesis in Lanzarote, Canary Islands

NASA Astrophysics Data System (ADS)

Alonso-Zarza, Ana M.; Bustamante, Leticia; Huerta, Pedro; Rodríguez-Berriguete, Álvaro; Huertas, María José

2016-05-01

This paper studies the weathering and soil formation processes operating on detrital sediments containing alkaline volcanic rock fragments of the Mirador del Río dolocrete profile. The profile consists of a lower horizon of removilised weathered basalts, an intermediate red sandy mudstones horizon with irregular carbonate layers and a topmost horizon of amalgamated carbonate layers with root traces. Formation occurred in arid to semiarid climates, giving place to a complex mineralogical association, including Mg-carbonates and chabazite, rarely described in cal/dolocretes profiles. Initial vadose weathering processes occurred in the basalts and in directly overlying detrital sediments, producing (Stage 1) red-smectites and dolomicrite. Dominant phreatic (Stage 2) conditions allowed precipitation of coarse-zoned dolomite and chabazite filling porosities. In Stages 3 and 4, mostly pedogenic, biogenic processes played an important role in dolomite and calcite accumulation in the profile. Overall evolution of the profile and its mineralogical association involved initial processes dominated by alteration of host rock, to provide silica and Mg-rich alkaline waters, suitable for chabazite and dolomite formation, without a previous carbonate phase. Dolomite formed both abiogenically and biogenically, but without a previous carbonate precursor and in the absence of evaporites. Dominance of calcite towards the profile top is the result of Mg/Ca decrease in the interstitial meteoric waters due to decreased supply of Mg from weathering, and increased supply of Ca in aeolian dust. Meteoric origin of the water is confirmed by C and O isotope values, which also indicate lack of deep sourced CO2. The dolocrete studied and its complex mineral association reveal the complex interactions that occur at surface during weathering and pedogenesis of basalt-sourced rocks.

Metabolic pathway profiling of mitochondrial respiratory chain mutants in C. elegans

PubMed Central

MJ, Falk; Z, Zhang; Rosenjack; Nissim; E, Daikhin; Nissim; MM, Sedensky; M, Yudkoff; PG, Morgan

2008-01-01

C. elegans affords a model of primary mitochondrial dysfunction that provides insight into cellular adaptations which accompany mutations in nuclear gene that encode mitochondrial proteins. To this end, we characterized genome-wide expression profiles of C. elegans strains with mutations in nuclear-encoded subunits of respiratory chain complexes. Our goal was to detect concordant changes among clusters of genes that comprise defined metabolic pathways. Results indicate that respiratory chain mutants significantly upregulate a variety of basic cellular metabolic pathways involved in carbohydrate, amino acid, and fatty acid metabolism, as well as cellular defense pathways such as the metabolism of P450 and glutathione. To further confirm and extend expression analysis findings, quantitation of whole worm free amino acid levels was performed in C. elegans mitochondrial mutants for subunits of complexes I, II, and III. Significant differences were seen for 13 of 16 amino acid levels in complex I mutants compared with controls, as well as overarching similarities among profiles of complex I, II, and III mutants compared with controls. The specific pattern of amino acid alterations observed provides novel evidence to suggest that an increase in glutamate-linked transamination reactions caused by the failure of NAD+ dependent oxidation of ketoacids occurs in primary mitochondrial respiratory chain mutants. Recognition of consistent alterations among patterns of nuclear gene expression for multiple biochemical pathways and in quantitative amino acid profiles in a translational genetic model of mitochondrial dysfunction allows insight into the complex pathogenesis underlying primary mitochondrial disease. Such knowledge may enable the development of a metabolomic profiling diagnostic tool applicable to human mitochondrial disease. PMID:18178500

Health-related fitness profiles in adolescents with complex congenital heart disease.

PubMed

Klausen, Susanne Hwiid; Wetterslev, Jørn; Søndergaard, Lars; Andersen, Lars L; Mikkelsen, Ulla Ramer; Dideriksen, Kasper; Zoffmann, Vibeke; Moons, Philip

2015-04-01

This study investigates whether subgroups of different health-related fitness (HrF) profiles exist among girls and boys with complex congenital heart disease (ConHD) and how these are associated with lifestyle behaviors. We measured the cardiorespiratory fitness, muscle strength, and body composition of 158 adolescents aged 13-16 years with previous surgery for a complex ConHD. Data on lifestyle behaviors were collected concomitantly between October 2010 and April 2013. A cluster analysis was conducted to identify profiles with similar HrF. For comparisons between clusters, multivariate analyses of covariance were used to test the differences in lifestyle behaviors. Three distinct profiles were formed: (1) Robust (43, 27%; 20 girls and 23 boys); (2) Moderately Robust (85, 54%; 37 girls and 48 boys); and (3) Less robust (30, 19%; 9 girls and 21 boys). The participants in the Robust clusters reported leading a physically active lifestyle and participants in the Less robust cluster reported leading a sedentary lifestyle. Diagnoses were evenly distributed between clusters. The cluster analysis attributed some of the variability in cardiorespiratory fitness among adolescents with complex ConHD to lifestyle behaviors and physical activity. Profiling of HrF offers a valuable new option in the management of person-centered health promotion. Copyright © 2015 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

In-vitro dissolution rate and molecular docking studies of cabergoline drug with β-cyclodextrin

NASA Astrophysics Data System (ADS)

Shanmuga priya, Arumugam; Balakrishnan, Suganya bharathi; Veerakanellore, Giri Babu; Stalin, Thambusamy

2018-05-01

The physicochemical properties and dissolution profile of cabergoline drug (CAB) with β-cyclodextrin (β-CD) inclusion complex were investigated by the UV spectroscopy. The inclusion complex has used to calculate the stability constant and gives the stoichiometry molar ratio is 1:1 between CAB and β-CD. The phase solubility diagram and the aqueous solubility of CAB (60%) was found to be enhanced by β-CD. In addition, the phase solubility profile of CAB with β-CD was classified as AL-type. Binary systems of CAB with β-CD were prepared by Physical mixture, Kneading and solvent evaporation methods. The solid-state properties of the inclusion complex were characterized by Fourier transformation-infrared spectroscopy, Differential scanning calorimetry, Powder X-ray diffractometric patterns and Scanning electron microscopic techniques. Theoretically, β-CD and CAB inclusion complex obtained by molecular docking studies, it is in good correlation with the results obtained through experimental methods using the Schrödinger software program. In-vitro dissolution profiles of the inclusion complexes were carried out and obvious increase in dissolution rate was observed when compared with pure CAB drug and the complexes.

Autism Phenotypes in Tuberous Sclerosis Complex: Diagnostic and Treatment Considerations.

PubMed

Gipson, Tanjala T; Poretti, Andrea; Thomas, Emily A; Jenkins, Kosunique T; Desai, Sonal; Johnston, Michael V

2015-12-01

Tuberous sclerosis complex is a multisystem, chronic genetic condition characterized by systemic growth of benign tumors and often accompanied by epilepsy, autism spectrum disorders, and intellectual disability. Nonetheless, the neurodevelopmental phenotype of these patients is not often detailed. The authors describe 3 individuals with tuberous sclerosis complex who share common characteristics that can help to identify a distinct profile of autism spectrum disorder. These findings include typical cognitive development, expressive and pragmatic language deficits, and anxiety. The authors also describe features specific to tuberous sclerosis complex that require consideration before diagnosing an autism spectrum disorder. Identifying distinct profiles of autism spectrum disorder in tuberous sclerosis complex can help optimize treatment across the life span. © The Author(s) 2015.

Comparative evaluation of humic substances in oral drug delivery

PubMed Central

Mirza, Mohd. Aamir; Ahmad, Niyaz; Agarwal, Suraj Prakash; Mahmood, Danish; Khalid Anwer, M.; Iqbal, Z.

2011-01-01

Major and biologically most explored components of natural organic matter (NOM) are humic acid (HA) and fulvic acid (FA). We have explored rock shilajit as a source of NOM. On the other hand carbamazepine (CBZ) is a well known anticonvulsant drug and has a limited accessibility to brain. Bioavailability and pharmacokinetic profiles of CBZ have been improved by complexation and different techniques also. Present study has assessed the comparative abilities of FA and HA as complexing agent for CBZ in order to enhance pharmacokinetic profile of CBZ and accessibility to the brain. These two complexing agents have been compared on various indices such as their abilities to cause complexation and enhance solubility, permeability and dissolution. The present study also compared pharmacodynamic and biochemical profiles after oral administration of complexes. With the help of various pharmaceutical techniques such as freeze drying, physical mixture, kneading and solvent evaporation, two molar ratios (1:1 and 1:2) were selected for complexation and evaluated for conformational analysis (molecular modeling). Complex formed was further characterized by differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FT-IR), mass spectroscopy and X-ray diffraction (XRD). Preclinical study on rodents with CBZ–HA and CBZ–FA has yielded appreciable results in terms of their anticonvulsant and antioxidants activities. However, CBZ–HA (1:2) demonstrated better result than any other complex. PMID:25755978

Computer aided design of extrusion forming tools for complex geometry profiles

NASA Astrophysics Data System (ADS)

Goncalves, Nelson Daniel Ferreira

In the profile extrusion, the experience of the die designer is crucial for obtaining good results. In industry, it is quite usual the need of several experimental trials for a specific extrusion die before a balanced flow distribution is obtained. This experimental based trial-and-error procedure is time and money consuming, but, it works, and most of the profile extrusion companies rely on such method. However, the competition is forcing the industry to look for more effective procedures and the design of profile extrusion dies is not an exception. For this purpose, computer aided design seems to be a good route. Nowadays, the available computational rheology numerical codes allow the simulation of complex fluid flows. This permits the die designer to evaluate and to optimize the flow channel, without the need to have a physical die and to perform real extrusion trials. In this work, a finite volume based numerical code was developed, for the simulation of non-Newtonian (inelastic) fluid and non-isothermal flows using unstructured meshes. The developed code is able to model the forming and cooling stages of profile extrusion, and can be used to aid the design of forming tools used in the production of complex profiles. For the code verification three benchmark problems were tested: flow between parallel plates, flow around a cylinder, and the lid driven cavity flow. The code was employed to design two extrusion dies to produce complex cross section profiles: a medical catheter die and a wood plastic composite profile for decking applications. The last was experimentally validated. Simple extrusion dies used to produced L and T shaped profiles were studied in detail, allowing a better understanding of the effect of the main geometry parameters on the flow distribution. To model the cooling stage a new implicit formulation was devised, which allowed the achievement of better convergence rates and thus the reduction of the computation times. Having in mind the solution of large dimension problems, the code was parallelized using graphics processing units (GPUs). Speedups of ten times could be obtained, drastically decreasing the time required to obtain results.

Genetic influences on human body odor: from genes to the axillae.

PubMed

Preti, George; Leyden, James J

2010-02-01

Several groups have identified the characteristic axillary odorants and how they arrive on the skin surface, pre-formed, bound to water-soluble odorless precursors in apocrine secretions. In the current issue, Martin et al., (2010) describe the relationship between the production of axillary odorants and variants in the ABCC11 gene. Individuals who are homozygotic for a SNP (538G>A) were found to have significantly less of the characteristic axillary odorants than either individuals who were heterozygotic for this change or those who had the wild-type gene. The 538G>A SNP predominates in Asians who have nearly complete loss of typical body odor. ABCC11 is expressed and localized in apocrine sweat glands. These findings are remarkably similar to the ethnic distribution and expression patterns for apocrine apoD, a previously identified carrier of a characteristic axillary odorant.

Extreme AO coronagraphy laboratory demonstration in the context of SPHERE

NASA Astrophysics Data System (ADS)

Martinez, P.; Aller Carpentier, E.; Kasper, M.

2010-10-01

The exoplanetary science through direct imaging and spectroscopy will largely expand with the very soon raise of new instruments at the VLT (SPHERE), Gemini (GPI), and Subaru (HiCIAO) observatories. All these ground-based adaptive optics instruments include extremely high performance adaptive optics (XAO) system, advanced starlight cancellation techniques (e.g. coronagraphy), and speckle calibration techniques (e.g. spectral, angular, or polarimetry). In this context we report laboratory results obtained with the High-Order Test bench (HOT), the adaptive optics facility at the European Southern Observatory headquarters. Under 0.5 arcsec dynamical seeing, efficiently corrected by an XAO system delivering H-band Strehl ratio above 90%, we discuss contrast levels obtained with an apodized pupil Lyot coronagraph using differential imaging techniques (spectral and polarimetric). Accounting for system differences (e.g. deformable mirror actuator number), we demonstrate a good agreement between experimental results and expectations for SPHERE, or GPI, while we already met HiCIAO contrast goals.

Computation of a spectrum from a single-beam fourier-transform infrared interferogram.

PubMed

Ben-David, Avishai; Ifarraguerri, Agustin

2002-02-20

A new high-accuracy method has been developed to transform asymmetric single-sided interferograms into spectra. We used a fraction (short, double-sided) of the recorded interferogram and applied an iterative correction to the complete recorded interferogram for the linear part of the phase induced by the various optical elements. Iterative phase correction enhanced the symmetry in the recorded interferogram. We constructed a symmetric double-sided interferogram and followed the Mertz procedure [Infrared Phys. 7,17 (1967)] but with symmetric apodization windows and with a nonlinear phase correction deduced from this double-sided interferogram. In comparing the solution spectrum with the source spectrum we applied the Rayleigh resolution criterion with a Gaussian instrument line shape. The accuracy of the solution is excellent, ranging from better than 0.1% for a blackbody spectrum to a few percent for a complicated atmospheric radiance spectrum.

Research on ground-based LWIR hyperspectral imaging remote gas detection

NASA Astrophysics Data System (ADS)

Yang, Zhixiong; Yu, Chunchao; Zheng, Weijian; Lei, Zhenggang; Yan, Min; Yuan, Xiaochun; Zhang, Peizhong

2015-10-01

The new progress of ground-based long-wave infrared remote sensing is presented, which describes the windowing spatial and temporal modulation Fourier spectroscopy imaging in details. The prototype forms the interference fringes based on the corner-cube of spatial modulation of Michelson interferometer, using cooled long-wave infrared photovoltaic staring FPA (focal plane array) detector. The LWIR hyperspectral imaging is achieved by the process of collection, reorganization, correction, apodization, FFT etc. from data cube. Noise equivalent sensor response (NESR), which is the sensitivity index of CHIPED-1 LWIR hyperspectral imaging prototype, can reach 5.6×10-8W/(cm-1.sr.cm2) at single sampling. Hyperspectral imaging is used in the field of organic gas VOC infrared detection. Relative to wide band infrared imaging, it has some advantages. Such as, it has high sensitivity, the strong anti-interference ability, identify the variety, and so on.

Astrophysics Source Code Library

NASA Astrophysics Data System (ADS)

Allen, A.; DuPrie, K.; Berriman, B.; Hanisch, R. J.; Mink, J.; Teuben, P. J.

2013-10-01

The Astrophysics Source Code Library (ASCL), founded in 1999, is a free on-line registry for source codes of interest to astronomers and astrophysicists. The library is housed on the discussion forum for Astronomy Picture of the Day (APOD) and can be accessed at http://ascl.net. The ASCL has a comprehensive listing that covers a significant number of the astrophysics source codes used to generate results published in or submitted to refereed journals and continues to grow. The ASCL currently has entries for over 500 codes; its records are citable and are indexed by ADS. The editors of the ASCL and members of its Advisory Committee were on hand at a demonstration table in the ADASS poster room to present the ASCL, accept code submissions, show how the ASCL is starting to be used by the astrophysics community, and take questions on and suggestions for improving the resource.

Real-time ultrasound-tagging to track the 2D motion of the common carotid artery wall in vivo

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

Zahnd, Guillaume, E-mail: g.zahnd@erasmusmc.nl; Salles, Sébastien; Liebgott, Hervé

2015-02-15

Purpose: Tracking the motion of biological tissues represents an important issue in the field of medical ultrasound imaging. However, the longitudinal component of the motion (i.e., perpendicular to the beam axis) remains more challenging to extract due to the rather coarse resolution cell of ultrasound scanners along this direction. The aim of this study is to introduce a real-time beamforming strategy dedicated to acquire tagged images featuring a distinct pattern in the objective to ease the tracking. Methods: Under the conditions of the Fraunhofer approximation, a specific apodization function was applied to the received raw channel data, in real-time duringmore » image acquisition, in order to introduce a periodic oscillations pattern along the longitudinal direction of the radio frequency signal. Analytic signals were then extracted from the tagged images, and subpixel motion tracking of the intima–media complex was subsequently performed offline, by means of a previously introduced bidimensional analytic phase-based estimator. Results: The authors’ framework was applied in vivo on the common carotid artery from 20 young healthy volunteers and 6 elderly patients with high atherosclerosis risk. Cine-loops of tagged images were acquired during three cardiac cycles. Evaluated against reference trajectories manually generated by three experienced analysts, the mean absolute tracking error was 98 ± 84 μm and 55 ± 44 μm in the longitudinal and axial directions, respectively. These errors corresponded to 28% ± 23% and 13% ± 9% of the longitudinal and axial amplitude of the assessed motion, respectively. Conclusions: The proposed framework enables tagged ultrasound images of in vivo tissues to be acquired in real-time. Such unconventional beamforming strategy contributes to improve tracking accuracy and could potentially benefit to the interpretation and diagnosis of biomedical images.« less

MicroRNA expression profile in bovine cumulus–oocyte complexes: Possible role of let-7 and miR-106a in the development of bovine oocytes

USDA-ARS?s Scientific Manuscript database

The expression of microRNAs (miRs) in bovine cumulus-oocyte complexes (COCs) during late oogenesis was profiled to determine the potential for regulation of maternal mRNAs by this class of small RNAs. A cDNA cloning and sequencing strategy resulted in 1812 putative miR sequences, representing 72 di...

Super-massive binary black holes and emission lines in active galactic nuclei

NASA Astrophysics Data System (ADS)

Popović, Luka Č.

2012-02-01

It is now agreed that mergers play an essential role in the evolution of galaxies and therefore that mergers of supermassive black holes (SMBHs) must have been common. We see the consequences of past supermassive binary black holes (SMBs) in the light profiles of so-called 'core ellipticals' and a small number of SMBs have been detected. However, the evolution of SMBs is poorly understood. Theory predicts that SMBs should spend a substantial amount of time orbiting at velocities of a few thousand kilometers per second. If the SMBs are surrounded by gas observational effects might be expected from accretion onto one or both of the SMBHs. This could result in a binary Active Galactic Nucleus (AGN) system. Like a single AGN, such a system would emit a broad band electromagnetic spectrum and broad and narrow emission lines. The broad emission spectral lines emitted from AGNs are our main probe of the geometry and physics of the broad line region (BLR) close to the SMBH. There is a group of AGNs that emit very broad and complex line profiles, showing two displaced peaks, one blueshifted and one redshifted from the systemic velocity defined by the narrow lines, or a single such peak. It has been proposed that such line shapes could indicate an SMB system. We discuss here how the presence of an SMB will affect the BLRs of AGNs and what the observational consequences might be. We review previous claims of SMBs based on broad line profiles and find that they may have non-SMB explanations as a consequence of a complex BLR structure. Because of these effects it is very hard to put limits on the number of SMBs from broad line profiles. It is still possible, however, that unusual broad line profiles in combination with other observational effects (line ratios, quasi-periodical oscillations, spectropolarimetry, etc.) could be used for SMBs detection. Some narrow lines (e.g., [O III]) in some AGNs show a double-peaked profile. Such profiles can be caused by streams in the Narrow Line Region (NLR), but may also indicate the presence of a kilo-parsec scale mergers. A few objects indicated as double-peaked narrow line emitters are confirmed as kpc-scale margers, but double-peaked narrow line profiles are mostly caused by the complex NLR geometry. We briefly discuss the expected line profile of broad Fe Kα that probably originated in the accretion disk(s) around SMBs. This line may also be very complex and indicate the complex disk geometry or/and an SMB presence. Finally we consider rare configurations where a SMB system might be gravitationally lensed by a foreground galaxy, and discuss the expected line profiles in these systems.

Validation of SmartRank: A likelihood ratio software for searching national DNA databases with complex DNA profiles.

PubMed

Benschop, Corina C G; van de Merwe, Linda; de Jong, Jeroen; Vanvooren, Vanessa; Kempenaers, Morgane; Kees van der Beek, C P; Barni, Filippo; Reyes, Eusebio López; Moulin, Léa; Pene, Laurent; Haned, Hinda; Sijen, Titia

2017-07-01

Searching a national DNA database with complex and incomplete profiles usually yields very large numbers of possible matches that can present many candidate suspects to be further investigated by the forensic scientist and/or police. Current practice in most forensic laboratories consists of ordering these 'hits' based on the number of matching alleles with the searched profile. Thus, candidate profiles that share the same number of matching alleles are not differentiated and due to the lack of other ranking criteria for the candidate list it may be difficult to discern a true match from the false positives or notice that all candidates are in fact false positives. SmartRank was developed to put forward only relevant candidates and rank them accordingly. The SmartRank software computes a likelihood ratio (LR) for the searched profile and each profile in the DNA database and ranks database entries above a defined LR threshold according to the calculated LR. In this study, we examined for mixed DNA profiles of variable complexity whether the true donors are retrieved, what the number of false positives above an LR threshold is and the ranking position of the true donors. Using 343 mixed DNA profiles over 750 SmartRank searches were performed. In addition, the performance of SmartRank and CODIS were compared regarding DNA database searches and SmartRank was found complementary to CODIS. We also describe the applicable domain of SmartRank and provide guidelines. The SmartRank software is open-source and freely available. Using the best practice guidelines, SmartRank enables obtaining investigative leads in criminal cases lacking a suspect. Copyright © 2017 Elsevier B.V. All rights reserved.

Self-adaptive difference method for the effective solution of computationally complex problems of boundary layer theory

NASA Technical Reports Server (NTRS)

Schoenauer, W.; Daeubler, H. G.; Glotz, G.; Gruening, J.

1986-01-01

An implicit difference procedure for the solution of equations for a chemically reacting hypersonic boundary layer is described. Difference forms of arbitrary error order in the x and y coordinate plane were used to derive estimates for discretization error. Computational complexity and time were minimized by the use of this difference method and the iteration of the nonlinear boundary layer equations was regulated by discretization error. Velocity and temperature profiles are presented for Mach 20.14 and Mach 18.5; variables are velocity profiles, temperature profiles, mass flow factor, Stanton number, and friction drag coefficient; three figures include numeric data.

Flexible micro-OCT endobronchial probe for imaging of mucociliary transport (Conference Presentation)

NASA Astrophysics Data System (ADS)

Cui, Dongyao; Chu, Kengyeh K.; Unglert, Carolin I.; Ford, Tim N.; Carruth, Robert W.; Hyun, Daryl; Singh, Kanwarpal; Birket, Susan E.; Solomon, George M.; Rowe, Steve M.; Tearney, Guillermo J.

2016-03-01

Mucociliary clearance (MCC) plays a significant role in maintaining the health of human respiratory system by eliminating foreign particles trapped within mucus. Failure of this mechanism in diseases such as cystic fibrosis and chronic obstructive pulmonary disease (COPD) leads to airway blockage and lung infection, causing morbidity and mortality. The volume of airway mucus and the periciliary liquid encapsulating the cilia, in addition to ciliary beat frequency and velocity of mucociliary transport, are vital parameters of airway health. However, the diagnosis of disease pathogenesis and advances of novel therapeutics are hindered by the lack of tools for visualization of ciliary function in vivo. Our laboratory has previously developed a 1-µm resolution optical coherence tomography method, termed Micro-OCT, which is capable of visualizing mucociliary transport and quantitatively capturing epithelial functional metrics. We have also miniaturized Micro-OCT optics in a first-generation rigid 4mm Micro-OCT endoscope utilizing a common-path design and an apodizing prism configuration to produce an annular profile sample beam, and reported the first in vivo visualization of mucociliary transport in swine. We now demonstrate a flexible 2.5 mm Micro-OCT probe that can be inserted through the instrument channel of standard flexible bronchoscopes, allowing bronchoscopic navigation to smaller airways and greatly improving clinical utility. Longitudinal scanning over a field of view of more than 400 µm at a frame rate of 40 Hz was accomplished with a driveshaft transduced by a piezo-electric stack motor. We present characterization and imaging results from the flexible micro-OCT probe and progress towards clinical translation. The ability of the bronchoscope-compatible micro-OCT probe to image mucus clearance and epithelial function will enable studies of cystic fibrosis pathogenesis in small airways, provide diagnosis of mucociliary clearance disorders, and allow individual responses to treatments to be monitored.

Gene Expression Profiling in Rodent Models for Schizophrenia

PubMed Central

Schijndel, Jessica E. Van; Martens, Gerard J.M

2010-01-01

The complex neurodevelopmental disorder schizophrenia is thought to be induced by an interaction between predisposing genes and environmental stressors. In order to get a better insight into the aetiology of this complex disorder, animal models have been developed. In this review, we summarize mRNA expression profiling studies on neurodevelopmental, pharmacological and genetic animal models for schizophrenia. We discuss parallels and contradictions among these studies, and propose strategies for future research. PMID:21629445

Brightness analysis of an electron beam with a complex profile

NASA Astrophysics Data System (ADS)

Maesaka, Hirokazu; Hara, Toru; Togawa, Kazuaki; Inagaki, Takahiro; Tanaka, Hitoshi

2018-05-01

We propose a novel analysis method to obtain the core bright part of an electron beam with a complex phase-space profile. This method is beneficial to evaluate the performance of simulation data of a linear accelerator (linac), such as an x-ray free electron laser (XFEL) machine, since the phase-space distribution of a linac electron beam is not simple, compared to a Gaussian beam in a synchrotron. In this analysis, the brightness of undulator radiation is calculated and the core of an electron beam is determined by maximizing the brightness. We successfully extracted core electrons from a complex beam profile of XFEL simulation data, which was not expressed by a set of slice parameters. FEL simulations showed that the FEL intensity was well remained even after extracting the core part. Consequently, the FEL performance can be estimated by this analysis without time-consuming FEL simulations.

On Machine Capacitance Dimensional and Surface Profile Measurement System

NASA Technical Reports Server (NTRS)

Resnick, Ralph

1993-01-01

A program was awarded under the Air Force Machine Tool Sensor Improvements Program Research and Development Announcement to develop and demonstrate the use of a Capacitance Sensor System including Capacitive Non-Contact Analog Probe and a Capacitive Array Dimensional Measurement System to check the dimensions of complex shapes and contours on a machine tool or in an automated inspection cell. The manufacturing of complex shapes and contours and the subsequent verification of those manufactured shapes is fundamental and widespread throughout industry. The critical profile of a gear tooth; the overall shape of a graphite EDM electrode; the contour of a turbine blade in a jet engine; and countless other components in varied applications possess complex shapes that require detailed and complex inspection procedures. Current inspection methods for complex shapes and contours are expensive, time-consuming, and labor intensive.

Defense Profiles in Adaptation Process to Sport Competition and Their Relationships with Coping, Stress and Control

PubMed Central

Nicolas, Michel; Martinent, Guillaume; Drapeau, Martin; Chahraoui, Khadija; Vacher, Philippe; de Roten, Yves

2017-01-01

The purpose of this study was to identify the potentially distinct defense profiles of athletes in order to provide insight into the complex associations that can exist between defenses and other important variables tied to performance in sports (e.g., coping, perceived stress and control) and to further our understanding of the complexity of the adaptation process in sports. Two hundred and ninety-six (N = 296) athletes participated in a naturalistic study that involved a highly stressful situation: a sports competition. Participants were assessed before and after the competition. Hierarchical cluster analysis and a series of MANOVAs with post hoc comparisons indicated two stable defense profiles (high and low defense profiles) of athletes both before and during sport competition. These profiles differed with regards to coping, stress and control. Athletes with high defense profiles reported higher levels of coping strategies, perceived stress and control than athletes with low defense profiles. This study confirmed that defenses are involved in the psychological adaptation process and that research and intervention should not be based only on coping, but rather must include defense mechanisms in order to improve our understanding of psychological adaptation in competitive sports. PMID:29312070

Defense Profiles in Adaptation Process to Sport Competition and Their Relationships with Coping, Stress and Control.

PubMed

Nicolas, Michel; Martinent, Guillaume; Drapeau, Martin; Chahraoui, Khadija; Vacher, Philippe; de Roten, Yves

2017-01-01

The purpose of this study was to identify the potentially distinct defense profiles of athletes in order to provide insight into the complex associations that can exist between defenses and other important variables tied to performance in sports (e.g., coping, perceived stress and control) and to further our understanding of the complexity of the adaptation process in sports. Two hundred and ninety-six ( N = 296) athletes participated in a naturalistic study that involved a highly stressful situation: a sports competition. Participants were assessed before and after the competition. Hierarchical cluster analysis and a series of MANOVAs with post hoc comparisons indicated two stable defense profiles (high and low defense profiles) of athletes both before and during sport competition. These profiles differed with regards to coping, stress and control. Athletes with high defense profiles reported higher levels of coping strategies, perceived stress and control than athletes with low defense profiles. This study confirmed that defenses are involved in the psychological adaptation process and that research and intervention should not be based only on coping, but rather must include defense mechanisms in order to improve our understanding of psychological adaptation in competitive sports.

Generative complexity of Gray-Scott model

NASA Astrophysics Data System (ADS)

Adamatzky, Andrew

2018-03-01

In the Gray-Scott reaction-diffusion system one reactant is constantly fed in the system, another reactant is reproduced by consuming the supplied reactant and also converted to an inert product. The rate of feeding one reactant in the system and the rate of removing another reactant from the system determine configurations of concentration profiles: stripes, spots, waves. We calculate the generative complexity-a morphological complexity of concentration profiles grown from a point-wise perturbation of the medium-of the Gray-Scott system for a range of the feeding and removal rates. The morphological complexity is evaluated using Shannon entropy, Simpson diversity, approximation of Lempel-Ziv complexity, and expressivity (Shannon entropy divided by space-filling). We analyse behaviour of the systems with highest values of the generative morphological complexity and show that the Gray-Scott systems expressing highest levels of the complexity are composed of the wave-fragments (similar to wave-fragments in sub-excitable media) and travelling localisations (similar to quasi-dissipative solitons and gliders in Conway's Game of Life).

Vertical profiles of urban aerosol complex refractive index in the frame of ESQUIF airborne measurements

NASA Astrophysics Data System (ADS)

Raut, J.-C.; Chazette, P.

2007-07-01

A synergy between lidar, sunphotometer and in situ measurements has been applied to airborne observations performed during the Etude et Simulation de la QUalité de l'air en Ile-de-France (ESQUIF), enabling the retrieval of vertical profiles for the aerosol complex refractive index (ACRI) and single-scattering albedo with a vertical resolution of 200 m over Paris area. The averaged value over the entire planetary boundary layer (PBL) for the ACRI is close to 1.51(±0.02)-i0.017(±0.003) at 532 nm. The single-scattering albedo of the corresponding aerosols is found to be ~0.9 at the same wavelength. A good agreement is found with previous studies for urban aerosols. A comparison of vertical profiles of ACRI with simulations combining in situ measurements and relative humidity (RH) profiles has highlighted a modification in aerosol optical properties linked to their history and the origin of the air mass. The determination of ACRI in the atmospheric column enabled to retrieve vertical profiles of extinction coefficient in accordance with lidar profiles measurements.

Vertical profiles of urban aerosol complex refractive index in the frame of ESQUIF airborne measurements

NASA Astrophysics Data System (ADS)

Raut, J.-C.; Chazette, P.

2008-02-01

A synergy between lidar, sunphotometer and in situ measurements has been applied to airborne observations performed during the Etude et Simulation de la QUalité de l'air en Ile-de-France (ESQUIF), enabling the retrieval of vertical profiles for the aerosol complex refractive index (ACRI) and single-scattering albedo with a vertical resolution of 200 m over Paris area. The averaged value over the entire planetary boundary layer (PBL) for the ACRI is close to 1.51(±0.02)-i0.017(±0.003) at 532 nm. The single-scattering albedo of the corresponding aerosols is found to be ~0.9 at the same wavelength. A good agreement is found with previous studies for urban aerosols. A comparison of vertical profiles of ACRI with simulations combining in situ measurements and relative humidity (RH) profiles has highlighted a modification in aerosol optical properties linked to their history and the origin of the air mass. The determination of ACRI in the atmospheric column enabled to retrieve vertical profiles of extinction coefficient in accordance with lidar profiles measurements.

Regulators of alternative polyadenylation operate at the transition from mitosis to meiosis.

PubMed

Shan, Lingjuan; Wu, Chan; Chen, Di; Hou, Lei; Li, Xin; Wang, Lixia; Chu, Xiao; Hou, Yifeng; Wang, Zhaohui

2017-02-20

In the sexually reproductive organisms, gametes are produced by meiosis following a limited mitotic amplification. However, the intrinsic program switching cells from mitotic to meiotic cycle is unclear. Alternative polyadenylation (APA) is a highly conserved means of gene regulation and is achieved by the RNA 3'-processing machinery to generate diverse 3'UTR profiles. In Drosophila spermatogenesis, we observed distinct profiles of transcriptome-wide 3'UTR between mitotic and meiotic cells. In mutant germ cells stuck in mitosis, 3'UTRs of hundreds of genes were consistently shifted. Remarkably, altering the levels of multiple 3'-processing factors disrupted germline's progression to meiosis, indicative of APA's active role in this transition. An RNA-binding protein (RBP) Tut could directly bind 3'UTRs of 3'-processing factors whose expressions were repressed in the presence of Tut-containing complex. Further, we demonstrated that this RBP complex could execute the repression post-transcriptionally by recruiting CCR4/Twin of deadenylation complex. Thus, we propose that an RBP complex regulates the dynamic APA profile to promote the mitosis-to-meiosis transition. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Zebrafish Behavioral Profiling Links Drugs to Biological Targets and Rest/Wake Regulation

PubMed Central

Rihel, Jason; Prober, David A.; Arvanites, Anthony; Lam, Kelvin; Zimmerman, Steven; Jang, Sumin; Haggarty, Stephen J.; Kokel, David; Rubin, Lee L.; Peterson, Randall T.; Schier, Alexander F.

2010-01-01

A major obstacle for the discovery of psychoactive drugs is the inability to predict how small molecules will alter complex behaviors. We report the development and application of a high-throughput, quantitative screen for drugs that alter the behavior of larval zebrafish. We found that the multi-dimensional nature of observed phenotypes enabled the hierarchical clustering of molecules according to shared behaviors. Behavioral profiling revealed conserved functions of psychotropic molecules and predicted the mechanisms of action of poorly characterized compounds. In addition, behavioral profiling implicated new factors such as ether-a-go-go-related gene (ERG) potassium channels and immunomodulators in the control of rest and locomotor activity. These results demonstrate the power of high-throughput behavioral profiling in zebrafish to discover and characterize psychotropic drugs and to dissect the pharmacology of complex behaviors. PMID:20075256

Approximate Stokes Drift Profiles in Deep Water

NASA Astrophysics Data System (ADS)

Breivik, Øyvind; Janssen, Peter A. E. M.; Bidlot, Jean-Raymond

2014-09-01

A deep-water approximation to the Stokes drift velocity profile is explored as an alternative to the monochromatic profile. The alternative profile investigated relies on the same two quantities required for the monochromatic profile, viz the Stokes transport and the surface Stokes drift velocity. Comparisons with parametric spectra and profiles under wave spectra from the ERA-Interim reanalysis and buoy observations reveal much better agreement than the monochromatic profile even for complex sea states. That the profile gives a closer match and a more correct shear has implications for ocean circulation models since the Coriolis-Stokes force depends on the magnitude and direction of the Stokes drift profile and Langmuir turbulence parameterizations depend sensitively on the shear of the profile. The alternative profile comes at no added numerical cost compared to the monochromatic profile.

Comprehensive analysis of the transcriptional profile of the Mediator complex across human cancer types.

PubMed

Syring, Isabella; Klümper, Niklas; Offermann, Anne; Braun, Martin; Deng, Mario; Boehm, Diana; Queisser, Angela; von Mässenhausen, Anne; Brägelmann, Johannes; Vogel, Wenzel; Schmidt, Doris; Majores, Michael; Schindler, Anne; Kristiansen, Glen; Müller, Stefan C; Ellinger, Jörg; Shaikhibrahim, Zaki; Perner, Sven

2016-04-26

The Mediator complex is a key regulator of gene transcription and several studies demonstrated altered expressions of particular subunits in diverse human diseases, especially cancer. However a systematic study deciphering the transcriptional expression of the Mediator across different cancer entities is still lacking.We therefore performed a comprehensive in silico cancer vs. benign analysis of the Mediator complex subunits (MEDs) for 20 tumor entities using Oncomine datasets. The transcriptional expression profiles across almost all cancer entities showed differentially expressed MEDs as compared to benign tissue. Differential expression of MED8 in renal cell carcinoma (RCC) and MED12 in lung cancer (LCa) were validated and further investigated by immunohistochemical staining on tissue microarrays containing large numbers of specimen. MED8 in clear cell RCC (ccRCC) associated with shorter survival and advanced TNM stage and showed higher expression in metastatic than primary tumors. In vitro, siRNA mediated MED8 knockdown significantly impaired proliferation and motility in ccRCC cell lines, hinting at a role for MED8 to serve as a novel therapeutic target in ccRCC. Taken together, our Mediator complex transcriptome proved to be a valid tool for identifying cancer-related shifts in Mediator complex composition, revealing that MEDs do exhibit cancer specific transcriptional expression profiles.

Characterisation of the chemical profiles of Brazilian and Andean morphotypes belonging to the Anastrepha fraterculus complex (Diptera, Tephritidae)

PubMed Central

Vaníčková, Lucie; Břízová, Radka; Pompeiano, Antonio; Ferreira, Luana Lima; de Aquino, Nathaly Costa; Tavares, Raphael de Farias; Rodriguez, Laura D.; Mendonça, Adriana de Lima; Canal, Nelson Augusto; do Nascimento, Ruth Rufino

2015-01-01

Abstract Fruit fly sexual behaviour is directly influenced by chemical and non-chemical cues that play important roles in reproductive isolation. The chemical profiles of pheromones and cuticular hydrocarbons (CHs) of eight fruit fly populations of the Andean, Brazilian-1 and Brazilian-3 morphotypes of the Anastrepha fraterculus cryptic species complex originating from Colombia (four populations) and Brazil (four populations) were analysed using two-dimensional gas chromatography with mass spectrometric detection. The resulting chemical diversity data were studied using principal component analyses. Andean morphotypes could be discriminated from the Brazilian-1 and Brazilian-3 morphotypes by means of male-borne pheromones and/or male and female CH profiles. The Brazilian-1 and Brazilian-3 morphotypes were found to be monophyletic. The use of chemical profiles as species- and sex-specific signatures for cryptic species separations is discussed. PMID:26798260

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

Janjusic, Tommy; Kartsaklis, Christos

Application analysis is facilitated through a number of program profiling tools. The tools vary in their complexity, ease of deployment, design, and profiling detail. Specifically, understand- ing, analyzing, and optimizing is of particular importance for scientific applications where minor changes in code paths and data-structure layout can have profound effects. Understanding how intricate data-structures are accessed and how a given memory system responds is a complex task. In this paper we describe a trace profiling tool, Glprof, specifically aimed to lessen the burden of the programmer to pin-point heavily involved data-structures during an application's run-time, and understand data-structure run-time usage.more » Moreover, we showcase the tool's modularity using additional cache simulation components. We elaborate on the tool's design, and features. Finally we demonstrate the application of our tool in the context of Spec bench- marks using the Glprof profiler and two concurrently running cache simulators, PPC440 and AMD Interlagos.« less

Numerical Study of the Complex Temporal Pattern of Spontaneous Oscillation in Bullfrog Saccular Hair Cells

NASA Astrophysics Data System (ADS)

Roongthumskul, Yuttana; Fredrickson-Hemsing, Lea; Kao, Albert; Bozovic, Dolores

2011-11-01

Hair bundles of the bullfrog sacculus display spontaneous oscillations that show complex temporal profiles. Quiescent intervals are typically interspersed with oscillations, analogous to bursting behavior observed in neural systems. By introducing slow calcium dynamics into the theoretical model of bundle mechanics, we reproduce numerically the multi-mode oscillations and explore the effects of internal parameters on the temporal profiles and the frequency tuning of their linear response functions. We also study the effects of mechanical overstimulation on the oscillatory behavior.

Profiles of Motor Laterality in Young Athletes' Performance of Complex Movements: Merging the MOTORLAT and PATHoops Tools

PubMed Central

Castañer, Marta; Andueza, Juan; Hileno, Raúl; Puigarnau, Silvia; Prat, Queralt; Camerino, Oleguer

2018-01-01

Laterality is a key aspect of the analysis of basic and specific motor skills. It is relevant to sports because it involves motor laterality profiles beyond left-right preference and spatial orientation of the body. The aim of this study was to obtain the laterality profiles of young athletes, taking into account the synergies between the support and precision functions of limbs and body parts in the performance of complex motor skills. We applied two instruments: (a) MOTORLAT, a motor laterality inventory comprising 30 items of basic, specific, and combined motor skills, and (b) the Precision and Agility Tapping over Hoops (PATHoops) task, in which participants had to perform a path by stepping in each of 14 hoops arranged on the floor, allowing the observation of their feet, left-right preference and spatial orientation. A total of 96 young athletes performed the PATHoops task and the 30 MOTORLAT items, allowing us to obtain data about limb dominance and spatial orientation of the body in the performance of complex motor skills. Laterality profiles were obtained by means of a cluster analysis and a correlational analysis and a contingency analysis were applied between the motor skills and spatial orientation actions performed. The results obtained using MOTORLAT show that the combined motor skills criterion (for example, turning while jumping) differentiates athletes' uses of laterality, showing a clear tendency toward mixed laterality profiles in the performance of complex movements. In the PATHoops task, the best spatial orientation strategy was “same way” (same foot and spatial wing) followed by “opposite way” (opposite foot and spatial wing), in keeping with the research assumption that actions unfolding in a horizontal direction in front of an observer's eyes are common in a variety of sports. PMID:29930527

K-band observations of boxy bulges - I. Morphology and surface brightness profiles

NASA Astrophysics Data System (ADS)

Bureau, M.; Aronica, G.; Athanassoula, E.; Dettmar, R.-J.; Bosma, A.; Freeman, K. C.

2006-08-01

In this first paper of a series on the structure of boxy and peanut-shaped (B/PS) bulges, Kn-band observations of a sample of 30 edge-on spiral galaxies are described and discussed. Kn-band observations best trace the dominant luminous galactic mass and are minimally affected by dust. Images, unsharp-masked images, as well as major-axis and vertically summed surface brightness profiles are presented and discussed. Galaxies with a B/PS bulge tend to have a more complex morphology than galaxies with other bulge types, more often showing centred or off-centred X structures, secondary maxima along the major-axis and spiral-like structures. While probably not uniquely related to bars, those features are observed in three-dimensional N-body simulations of barred discs and may trace the main bar orbit families. The surface brightness profiles of galaxies with a B/PS bulge are also more complex, typically containing three or more clearly separated regions, including a shallow or flat intermediate region (Freeman Type II profiles). The breaks in the profiles offer evidence for bar-driven transfer of angular momentum and radial redistribution of material. The profiles further suggest a rapid variation of the scaleheight of the disc material, contrary to conventional wisdom but again as expected from the vertical resonances and instabilities present in barred discs. Interestingly, the steep inner region of the surface brightness profiles is often shorter than the isophotally thick part of the galaxies, itself always shorter than the flat intermediate region of the profiles. The steep inner region is also much more prominent along the major-axis than in the vertically summed profiles. Similarly to other recent work but contrary to the standard `bulge + disc' model (where the bulge is both thick and steep), we thus propose that galaxies with a B/PS bulge are composed of a thin concentrated disc (a disc-like bulge) contained within a partially thick bar (the B/PS bulge), itself contained within a thin outer disc. The inner disc likely formed secularly through bar-driven processes and is responsible for the steep inner region of the surface brightness profiles, traditionally associated with a classic bulge, while the bar is responsible for the flat intermediate region of the surface brightness profiles and the thick complex morphological structures observed. Those components are strongly coupled dynamically and are formed mostly of the same (disc) material, shaped by the weak but relentless action of the bar resonances. Any competing formation scenario for galaxies with a B/PS bulge, which represent at least 45 per cent of the local disc galaxy population, must explain equally well and self-consistently the above morphological and photometric properties, the complex gas and stellar kinematics observed, and the correlations between them.

Antibody profiling sensitivity through increased reporter antibody layering

DOEpatents

Apel, William A.; Thompson, Vicki S.

2013-02-26

A method for analyzing a biological sample by antibody profiling for identifying forensic samples or for detecting the presence of an analyte. In an embodiment of the invention, the analyte is a drug, such as marijuana, Cocaine (crystalline tropane alkaloid), methamphetamine, methyltestosterone, or mesterolone. The method comprises attaching antigens to a surface of a solid support in a preselected pattern to form an array wherein locations of the antigens are known; contacting the array with the biological sample such that a portion of antibodies in the sample reacts with and binds to the antigens in the array to form immune complexes; washing away antibodies that do form immune complexes; and detecting the immune complexes, to form an antibody profile. Forensic samples are identified by comparing a sample from an unknown source with a sample from a known source. Further, an assay, such as a test for illegal drug use, can be coupled to a test for identity such that the results of the assay can be positively correlated to the subject's identity.

Antibody profiling sensitivity through increased reporter antibody layering

DOEpatents

Apel, William A.; Thompson, Vicki S.

2017-03-28

A method for analyzing a biological sample by antibody profiling for identifying forensic samples or for detecting the presence of an analyte. In an embodiment of the invention, the analyte is a drug, such as marijuana, Cocaine (crystalline tropane alkaloid), methamphetamine, methyltestosterone, or mesterolone. The method comprises attaching antigens to a surface of a solid support in a preselected pattern to form an array wherein locations of the antigens are known; contacting the array with the biological sample such that a portion of antibodies in the sample reacts with and binds to the antigens in the array to form immune complexes; washing away antibodies that do form immune complexes; and detecting the immune complexes, to form an antibody profile. Forensic samples are identified by comparing a sample from an unknown source with a sample from a known source. Further, an assay, such as a test for illegal drug use, can be coupled to a test for identity such that the results of the assay can be positively correlated to the subject's identity.

Saccharification efficiencies of multi-enzyme complexes produced by aerobic fungi.

PubMed

Badhan, Ajay; Huang, Jiangli; Wang, Yuxi; Abbott, D Wade; Di Falco, Marcos; Tsang, Adrian; McAllister, Tim

2018-05-24

In the present study, we have characterized high molecular weight multi-enzyme complexes in two commercial enzymes produced by Trichoderma reesei (Spezyme CP) and Penicillium funiculosum (Accellerase XC). We successfully identified 146-1000 kDa complexes using Blue native polyacrylamide gel electrophoresis (BN-PAGE) to fractionate the protein profile in both preparations. Identified complexes dissociated into lower molecular weight constituents when loaded on SDS PAGE. Unfolding of the secondary structure of multi-enzyme complexes with trimethylamine (pH >10) suggested that they were not a result of unspecific protein aggregation. Cellulase (CMCase) profiles of extracts of BN-PAGE fractionated protein bands confirmed cellulase activity within the multi-enzyme complexes. A microassay was used to identify protein bands that promoted high levels of glucose release from barley straw. Those with high saccharification yield were subjected to LC-MS analysis to identify the principal enzymatic activities responsible. The results suggest that secretion of proteins by aerobic fungi leads to the formation of high molecular weight multi-enzyme complexes that display activity against carboxymethyl cellulose and barley straw. Copyright © 2018. Published by Elsevier B.V.

Spectral and Temporal Properties of the Alpha and Beta Subunits and (alpha Beta) Monomer Isolated from Nostoc SP. Using Picosecond Laser Spectroscopy.

NASA Astrophysics Data System (ADS)

Dagen, Aaron J.

1985-12-01

The fluorescence decay profiles, relative quantum yield and transmission of the (alpha), (beta) and ((alpha)(beta)) complexes from phycoerythrin isolated from the photosynthetic antenna system of Nostoc sp. and measured by single picosecond laser spectroscopic techniques is studied. The fluorescence decay profiles of all three complexes are found to be intensity independent for the intensity range investigated ((TURN)4 x 10('13) to (TURN)4 x 10('15) photons-cm('-2) per pulse). The apparent decrease in the relative quantum yield of all three complexes as intensity increases is offset by a corresponding increase in the relative transmission. This evidence, along with the intensity independent fluorescence kinetics, suggests that exciton annihilation is absent in these complexes. The decay profiles are fit to models assuming energy transfer amongst fluorescing chromophores. The intraprotein transfer rate is found to be 100 ps in the (alpha) subunit, 666 ps in the (beta) subunit. Constraining these rates to be identical in the monomer results in explaining the monomer kinetics by an increase in the nonradiative rate of the f(,(beta)) chromophore, an apparent result of aggregation effects.

Spectral and temporal properties of the alpha and beta subunits and (alpha beta) monomer isolated from Nostoc sp. using picosecond laser spectroscopy

NASA Astrophysics Data System (ADS)

Dagen, A. J.

1985-12-01

The fluorescence decay profiles, relative quantum yield and transmission of the alpha, beta and (alpha beta) complexes from phycoerythrin isolated from the photosynthetic antenna system of Nostoc sp. and measured by single picosecond laser spectroscopic techniques is studied. The fluorescence decay profiles of all three complexes are found to be intensity independent for the intensity range investigated (approx. 4x10 to the 13th power to 4x10 to the 15th power photons/sq cm per pulse). The apparent decrease in the relative quantum yield of all three complexes as intensity increases is offset by a corresponding increase in the relative transmission. This evidence, along with the intensity independent fluorescence kinetics, suggests that exciton annihilation is absent in these complexes. The decay profiles are fit to models assuming energy transfer amongst fluorescing chromophores. The intraprotein transfer rate is found to be 100 ps in the alpha subunit, 666 ps in the beta subunit. Constraining these rates to be identical in the monomer results in explaining the monomer kinetics by an increase in the nonradiative rate of the f beta chromophore, an apparent result of aggregation effects.

Mixed bilayer containing dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylserine: lipid complexation, ion binding, and electrostatics.

PubMed

Pandit, Sagar A; Bostick, David; Berkowitz, Max L

2003-11-01

Two mixed bilayers containing dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylserine at a ratio of 5:1 are simulated in NaCl electrolyte solutions of different concentration using the molecular dynamics technique. Direct NH.O and CH.O hydrogen bonding between lipids was observed to serve as the basis of interlipid complexation. It is deduced from our results and previous studies that dipalmitoylphosphatidylcholine alone is less likely to form interlipid complexes than in the presence of bound ions or other bilayer "impurities" such as dipalmitoylphosphatidylserine. The binding of counterions is observed and quantitated. Based upon the calculated ion binding constants, the Gouy-Chapman surface potential (theta) is calculated. In addition we calculated the electrostatic potential profile (Phi) by twice integrating the system charge distribution. A large discrepancy between and the value of Phi at the membrane surface is observed. However, at "larger" distance from the bilayer surface, a qualitative similarity in the z-profiles of Phi and psi(GC) is seen. The discrepancy between the two potential profiles near the bilayer surface is attributed to the discrete and nonbulk-like nature of water in the interfacial region and to the complex geometry of this region.

[Preparation of coated tablets of glycyrrhetic acid-HP-beta-cyclodextrin tablets for colon-specific release].

PubMed

Cui, Qi-Hua; Cui, Jing-Hao; Zhang, Jin-Jin

2008-10-01

To prepare coated tablets of glycyrrhetinic acid and hydroxypropyl-beta-cyclodextrin (GTA-HP-beta-CYD) inclusion complex tablets for colon-specific release. In order to improve the solubility of GTA, the GTA-HP-beta-CYD inclusion complex was prepared by ultrasonic-lyophilization technique and its formation were characterized by X-ray powder diffraction profiles and infrared spectrometry. The effects of inclusion condition on the inclusion efficiency and stability coefficient of inclusion complex were investigated, respectively. After prepared GTA-HP-beta-CYD tablets by powder direct compression, the pH dependant polymer Eudragit III and/or mixed with Eudragit II were used for further coating materials in fluid-bed coater. The influences of coating weight on the GTA release in different pH conditions were evaluated to establish the method for prepering colon specific delivery tablets with pulsed release properties. The formation of inclusion complexes were proved by X-ray powder diffraction profile and phase solubility curve. The effect of pH value of solvent was played critical role on the preparation of GTA- HP-beta-CYD inclusion complex. And the inclusion efficiency of GTA was 9. 3% and the solubility was increased to 54. 6 times at optimized method. The Eudragit III coated GTA- HP-beta-CYD tablets with coating weight 10% and 16% were showed pH dependant colon specific release profiles with slow release rate. The release profile of tablets coated with the mixture of Eudragit II and Eudragit III (1:2) were indicated typical pH dependant colon specific and pulsed release properties while the coating weight was 17%. The preliminary method for preparation of colon specific release tablets containing glycyrrhetinic acid with improved solubility was established for further in vivo therapeutic experiment.

Evaluation of various processes for simultaneous complexation and granulation to incorporate drug-cyclodextrin complexes into solid dosage forms.

PubMed

Gyanani, Vijay; Siddalingappa, Basavaraj; Betageri, Guru V

2015-01-01

Insoluble drugs often formulated with various excipients to enhance the dissolution. Cyclodextrins (CDs) are widely used excipients to improve dissolution profile of poorly soluble drugs. Drug-CD complexation process is complex and often requires multiple processes to produce solid dosage form. Hence, this study explored commonly used granulation processes for simultaneous complexation and granulation. Poorly soluble drugs ibuprofen and glyburide were selected as experimental drugs. Co-evaporation of drug:CD mixture from a solvent followed by wet granulation with water was considered as standard process for comparison. Spray granulation and fluid bed processing (FBP) using drug:CD solution in ethanol were evaluated as an alternative processes. The dissolution data of glyburide tablets indicated that tablets produced by spray granulation, FBP and co-evaporation-granulation have almost identical dissolution profile in water and 0.1% SLS (>70% in water and >60% in SLS versus 30 and 34%, respectively for plain tablet, in 120 min). Similarly, ibuprofen:CD tablets produced by co-evaporation-granulation and FBP displayed similar dissolution profile in 0.01 M HCl (pH 2.0) and buffer pH 5.5 (>90 and 100% versus 44 and 80% respectively for plain tablets, 120 min). Results of this study demonstrated that spray granulation is simple and cost effective process for low dose poorly soluble drugs to incorporate drug:CD complex into solid dosage form, whereas FBP is suitable for poorly soluble drugs with moderate dose.

Predicting the spatial distribution of soil profile in Adapazari/Turkey by artificial neural networks using CPT data

NASA Astrophysics Data System (ADS)

Arel, Ersin

2012-06-01

The infamous soils of Adapazari, Turkey, that failed extensively during the 46-s long magnitude 7.4 earthquake in 1999 have since been the subject of a research program. Boreholes, piezocone soundings and voluminous laboratory testing have enabled researchers to apply sophisticated methods to determine the soil profiles in the city using the existing database. This paper describes the use of the artificial neural network (ANN) model to predict the complex soil profiles of Adapazari, based on cone penetration test (CPT) results. More than 3236 field CPT readings have been collected from 117 soundings spread over an area of 26 km2. An attempt has been made to develop the ANN model using multilayer perceptrons trained with a feed-forward back-propagation algorithm. The results show that the ANN model is fairly accurate in predicting complex soil profiles. Soil identification using CPT test results has principally been based on the Robertson charts. Applying neural network systems using the chart offers a powerful and rapid route to reliable prediction of the soil profiles.

Identifying Dynamic Protein Complexes Based on Gene Expression Profiles and PPI Networks

PubMed Central

Li, Min; Chen, Weijie; Wang, Jianxin; Pan, Yi

2014-01-01

Identification of protein complexes from protein-protein interaction networks has become a key problem for understanding cellular life in postgenomic era. Many computational methods have been proposed for identifying protein complexes. Up to now, the existing computational methods are mostly applied on static PPI networks. However, proteins and their interactions are dynamic in reality. Identifying dynamic protein complexes is more meaningful and challenging. In this paper, a novel algorithm, named DPC, is proposed to identify dynamic protein complexes by integrating PPI data and gene expression profiles. According to Core-Attachment assumption, these proteins which are always active in the molecular cycle are regarded as core proteins. The protein-complex cores are identified from these always active proteins by detecting dense subgraphs. Final protein complexes are extended from the protein-complex cores by adding attachments based on a topological character of “closeness” and dynamic meaning. The protein complexes produced by our algorithm DPC contain two parts: static core expressed in all the molecular cycle and dynamic attachments short-lived. The proposed algorithm DPC was applied on the data of Saccharomyces cerevisiae and the experimental results show that DPC outperforms CMC, MCL, SPICi, HC-PIN, COACH, and Core-Attachment based on the validation of matching with known complexes and hF-measures. PMID:24963481

Acute, 28days sub acute and genotoxic profiling of Quercetin-Magnesium complex in Swiss albino mice.

PubMed

Ghosh, Nilanjan; Sandur, Rajendra; Ghosh, Deepanwita; Roy, Souvik; Janadri, Suresh

2017-02-01

Quercetin-Magnesium complex is one of the youngest alkaline rare earth metal (Magnesium) complexes with flavonoids (Quercetin) in organo-metalic family. Earlier studies describe the details of the complex formation, characterization and antioxidant study of the complex but toxicity profile is still under darkness. The present study was taken up to investigate the oral acute toxicity, 28days repeated oral sub-acute toxicity study and genotoxicity study of Quercetin-Magnesium complex in Swiss albino mice. Quercetin-Magnesium complex showed mortality at a dose of 185mg/kg in the Swiss albino mice. In 28days repeated oral toxicity study, Quercetin-Magnesium complex was administered to both sex of Swiss albino mice at dose levels of 150, 130 and 100mg/kg body weight respectively. Where 150mg/kg dose shows increased levels of white blood cells and changes in total protein, serum creatinine and blood urea nitrogen. Histopathological study of Quercetin-Magnesium complex shows minor structural alteration in kidney at 150mg/kg dose. No observed toxic level found in 130mg/kg or below doses. No genotoxic effect found in any doses of the complex. Therefore 130mg/kg or below dose level could be better for further study. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

(PS)2: protein structure prediction server version 3.0.

PubMed

Huang, Tsun-Tsao; Hwang, Jenn-Kang; Chen, Chu-Huang; Chu, Chih-Sheng; Lee, Chi-Wen; Chen, Chih-Chieh

2015-07-01

Protein complexes are involved in many biological processes. Examining coupling between subunits of a complex would be useful to understand the molecular basis of protein function. Here, our updated (PS)(2) web server predicts the three-dimensional structures of protein complexes based on comparative modeling; furthermore, this server examines the coupling between subunits of the predicted complex by combining structural and evolutionary considerations. The predicted complex structure could be indicated and visualized by Java-based 3D graphics viewers and the structural and evolutionary profiles are shown and compared chain-by-chain. For each subunit, considerations with or without the packing contribution of other subunits cause the differences in similarities between structural and evolutionary profiles, and these differences imply which form, complex or monomeric, is preferred in the biological condition for the subunit. We believe that the (PS)(2) server would be a useful tool for biologists who are interested not only in the structures of protein complexes but also in the coupling between subunits of the complexes. The (PS)(2) is freely available at http://ps2v3.life.nctu.edu.tw/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Efficient state initialization by a quantum spectral filtering algorithm

NASA Astrophysics Data System (ADS)

Fillion-Gourdeau, François; MacLean, Steve; Laflamme, Raymond

2017-04-01

An algorithm that initializes a quantum register to a state with a specified energy range is given, corresponding to a quantum implementation of the celebrated Feit-Fleck method. This is performed by introducing a nondeterministic quantum implementation of a standard spectral filtering procedure combined with an apodization technique, allowing for accurate state initialization. It is shown that the implementation requires only two ancilla qubits. A lower bound for the total probability of success of this algorithm is derived, showing that this scheme can be realized using a finite, relatively low number of trials. Assuming the time evolution can be performed efficiently and using a trial state polynomially close to the desired states, it is demonstrated that the number of operations required scales polynomially with the number of qubits. Tradeoffs between accuracy and performance are demonstrated in a simple example: the harmonic oscillator. This algorithm would be useful for the initialization phase of the simulation of quantum systems on digital quantum computers.

The longitudinal offset technique for apodization of coupled resonator optical waveguide devices: concept and fabrication tolerance analysis.

PubMed

Doménech, José David; Muñoz, Pascual; Capmany, José

2009-11-09

In this paper, a novel technique to set the coupling constant between cells of a coupled resonator optical waveguide (CROW) device, in order to tailor the filter response, is presented. The technique is demonstrated by simulation assuming a racetrack ring resonator geometry. It consists on changing the effective length of the coupling section by applying a longitudinal offset between the resonators. On the contrary, the conventional techniques are based in the transversal change of the distance between the ring resonators, in steps that are commonly below the current fabrication resolution step (nm scale), leading to strong restrictions in the designs. The proposed longitudinal offset technique allows a more precise control of the coupling and presents an increased robustness against the fabrication limitations, since the needed resolution step is two orders of magnitude higher. Both techniques are compared in terms of the transmission esponse of CROW devices, under finite fabrication resolution steps.

Stochastic parallel gradient descent based adaptive optics used for a high contrast imaging coronagraph

NASA Astrophysics Data System (ADS)

Dong, Bing; Ren, De-Qing; Zhang, Xi

2011-08-01

An adaptive optics (AO) system based on a stochastic parallel gradient descent (SPGD) algorithm is proposed to reduce the speckle noises in the optical system of a stellar coronagraph in order to further improve the contrast. The principle of the SPGD algorithm is described briefly and a metric suitable for point source imaging optimization is given. The feasibility and good performance of the SPGD algorithm is demonstrated by an experimental system featured with a 140-actuator deformable mirror and a Hartmann-Shark wavefront sensor. Then the SPGD based AO is applied to a liquid crystal array (LCA) based coronagraph to improve the contrast. The LCA can modulate the incoming light to generate a pupil apodization mask of any pattern. A circular stepped pattern is used in our preliminary experiment and the image contrast shows improvement from 10-3 to 10-4.5 at an angular distance of 2λ/D after being corrected by SPGD based AO.

Development of a high-performance noise-reduction filter for tomographic reconstruction

NASA Astrophysics Data System (ADS)

Kao, Chien-Min; Pan, Xiaochuan

2001-07-01

We propose a new noise-reduction method for tomographic reconstruction. The method incorporates a priori information on the source image for allowing the derivation of the energy spectrum of its ideal sinogram. In combination with the energy spectrum of the Poisson noise in the measured sinogram, we are able to derive a Wiener-like filter for effective suppression of the sinogram noise. The filtered backprojection (FBP) algorithm, with a ramp filter, is then applied to the filtered sinogram to produce tomographic images. The resulting filter has a closed-form expression in the frequency space and contains a single user-adjustable regularization parameter. The proposed method is hence simple to implement and easy to use. In contrast to the ad hoc apodizing windows, such as Hanning and Butterworth filters, that are commonly used in the conventional FBP reconstruction, the proposed filter is theoretically more rigorous as it is derived by basing upon an optimization criterion, subject to a known class of source image intensity distributions.

Fully reconfigurable photonic microwave transversal filter based on digital micromirror device and continuous-wave, incoherent supercontinuum source.

PubMed

Lee, Ju Han; Chang, You Min; Han, Young-Geun; Lee, Sang Bae; Chung, Hae Yang

2007-08-01

The combined use of a programmable, digital micromirror device (DMD) and an ultrabroadband, cw, incoherent supercontinuum (SC) source is experimentally demonstrated to fully explore various aspects on the reconfiguration of a microwave filter transfer function by creating a range of multiwavelength optical filter shapes. Owing to both the unique characteristic of the DMD that an arbitrary optical filter shape can be readily produced and the ultrabroad bandwidth of the cw SC source that is 3 times larger than that of Er-amplified spontaneous emission, a multiwavelength optical beam pattern can be generated with a large number of wavelength filter taps apodized by an arbitrary amplitude window. Therefore various types of high-quality microwave filter can be readily achieved through the spectrum slicing-based photonic microwave transversal filter scheme. The experimental demonstration is performed in three aspects: the tuning of a filter resonance bandwidth at a fixed resonance frequency, filter resonance frequency tuning at a fixed resonance frequency, and flexible microwave filter shape reconstruction.

Rovibrational Constants for the ν 6 and 2ν 9 Bands of HCOOD by Fourier Transform Infrared Spectroscopy

NASA Astrophysics Data System (ADS)

Tan, T. L.; Goh, K. L.; Ong, P. P.; Teo, H. H.

1999-11-01

The Fourier transform infrared spectrum of the ν6 and 2ν9 bands of deuterated formic acid (HCOOD) was recorded with an apodized resolution of 0.004 cm-1 in the frequency range of 930-1040 cm-1. These two bands with band centers 40 cm-1 apart were mutually coupled by Coriolis and Fermi interactions. By fitting a total of 1076 infrared transitions of both ν6 and 2ν9 with a standard deviation of 0.00075 cm-1 using a Watson's A-reduced Hamiltonian in the Ir representation with the inclusion of c-type Coriolis and a Fermi-resonance term, two sets of rovibrational constants for v6 = 1, and v9 = 2 states were derived for the first time. Both ν6 and 2ν9 bands are A type with band centers at 972.8520 ± 0.0001 and 1011.6766 ± 0.0001 cm-1, respectively.

Thin-film sparse boundary array design for passive acoustic mapping during ultrasound therapy.

PubMed

Coviello, Christian M; Kozick, Richard J; Hurrell, Andrew; Smith, Penny Probert; Coussios, Constantin-C

2012-10-01

A new 2-D hydrophone array for ultrasound therapy monitoring is presented, along with a novel algorithm for passive acoustic mapping using a sparse weighted aperture. The array is constructed using existing polyvinylidene fluoride (PVDF) ultrasound sensor technology, and is utilized for its broadband characteristics and its high receive sensitivity. For most 2-D arrays, high-resolution imagery is desired, which requires a large aperture at the cost of a large number of elements. The proposed array's geometry is sparse, with elements only on the boundary of the rectangular aperture. The missing information from the interior is filled in using linear imaging techniques. After receiving acoustic emissions during ultrasound therapy, this algorithm applies an apodization to the sparse aperture to limit side lobes and then reconstructs acoustic activity with high spatiotemporal resolution. Experiments show verification of the theoretical point spread function, and cavitation maps in agar phantoms correspond closely to predicted areas, showing the validity of the array and methodology.

Photon sieve telescope

NASA Astrophysics Data System (ADS)

Andersen, Geoff; Tullson, Drew

2006-06-01

In designing next-generation, ultra-large (>20m) apertures for space, many current concepts involve compactable, curved membrane reflectors. Here we present the idea of using a flat diffractive element that requires no out-of-plane deformation and so is much simpler to deploy. The primary is a photon sieve - a diffractive element consisting of a large number of precisely positioned holes distributed according to an underlying Fresnel Zone Plate (FZP) geometry. The advantage of the photon sieve over the FZP is that all the regions are connected, so the membrane substrate under simple tension can avoid buckling. Also, the hole distribution can be varied to generate any conic or apodization for specialized telescope requirements such as exo-solar planet detection. We have designed and tested numerous photon sieves as telescope primaries. Some of these have over 10 million holes in a 0.1 m diameter aperture and all of them give diffraction limited imaging. While photon sieves are diffractive elements and thus suffer from dispersion, we will present two successful solutions to this problem.

Enabling full-field physics-based optical proximity correction via dynamic model generation

NASA Astrophysics Data System (ADS)

Lam, Michael; Clifford, Chris; Raghunathan, Ananthan; Fenger, Germain; Adam, Kostas

2017-07-01

As extreme ultraviolet lithography becomes closer to reality for high volume production, its peculiar modeling challenges related to both inter and intrafield effects have necessitated building an optical proximity correction (OPC) infrastructure that operates with field position dependency. Previous state-of-the-art approaches to modeling field dependency used piecewise constant models where static input models are assigned to specific x/y-positions within the field. OPC and simulation could assign the proper static model based on simulation-level placement. However, in the realm of 7 and 5 nm feature sizes, small discontinuities in OPC from piecewise constant model changes can cause unacceptable levels of edge placement errors. The introduction of dynamic model generation (DMG) can be shown to effectively avoid these dislocations by providing unique mask and optical models per simulation region, allowing a near continuum of models through the field. DMG allows unique models for electromagnetic field, apodization, aberrations, etc. to vary through the entire field and provides a capability to precisely and accurately model systematic field signatures.

Theoretical investigation and optimization of fiber grating based slow light

NASA Astrophysics Data System (ADS)

Wang, Qi; Wang, Peng; Du, Chao; Li, Jin; Hu, Haifeng; Zhao, Yong

2017-07-01

On the edge of bandgap in a fiber grating, narrow peaks of high transimittivity exist at frequencies where light interferes constructively in the forward direction. In the vicinity of these transmittivity peaks, light reflects back and forth numerous times across the periodic structure and experiences a large group delay. In order to generate the extremely slow light in fiber grating for applications, in this research, the common sense of formation mechanism of slow light in fiber grating was introduced. The means of producing and operating fiber grating was studied to support structural slow light with a group index that can be in principle as high as several thousand. The simulations proceeded by transfer matrix method in the paper were presented to elucidate how the fiber grating parameters effect group refractive index. The main parameters that need to be optimized include grating length, refractive index contrast, grating period, loss coefficient, chirp and apodization functions, those can influence fiber grating characteristics.

DNA entropy reveals a significant difference in complexity between housekeeping and tissue specific gene promoters.

PubMed

Thomas, David; Finan, Chris; Newport, Melanie J; Jones, Susan

2015-10-01

The complexity of DNA can be quantified using estimates of entropy. Variation in DNA complexity is expected between the promoters of genes with different transcriptional mechanisms; namely housekeeping (HK) and tissue specific (TS). The former are transcribed constitutively to maintain general cellular functions, and the latter are transcribed in restricted tissue and cells types for specific molecular events. It is known that promoter features in the human genome are related to tissue specificity, but this has been difficult to quantify on a genomic scale. If entropy effectively quantifies DNA complexity, calculating the entropies of HK and TS gene promoters as profiles may reveal significant differences. Entropy profiles were calculated for a total dataset of 12,003 human gene promoters and for 501 housekeeping (HK) and 587 tissue specific (TS) human gene promoters. The mean profiles show the TS promoters have a significantly lower entropy (p<2.2e-16) than HK gene promoters. The entropy distributions for the 3 datasets show that promoter entropies could be used to identify novel HK genes. Functional features comprise DNA sequence patterns that are non-random and hence they have lower entropies. The lower entropy of TS gene promoters can be explained by a higher density of positive and negative regulatory elements, required for genes with complex spatial and temporary expression. Copyright © 2015 Elsevier Ltd. All rights reserved.

Vectorization of copper complexes via biocompatible and biodegradable PLGA nanoparticles.

PubMed

Courant, T; Roullin, V G; Cadiou, C; Delavoie, F; Molinari, M; Andry, M C; Gafa, V; Chuburu, F

2010-04-23

A double emulsion-solvent diffusion approach with fully biocompatible materials was used to encapsulate copper complexes within biodegradable nanoparticles, for which the release kinetics profiles have highlighted their potential use for a prolonged circulating administration.

Laser characterization of the depth profile of complex refractive index of PMMA implanted with 50 keV silicon ions

NASA Astrophysics Data System (ADS)

Stefanov, Ivan L.; Stoyanov, Hristiyan Y.; Petrova, Elitza; Russev, Stoyan C.; Tsutsumanova, Gichka G.; Hadjichristov, Georgi B.

2013-03-01

The depth profile of the complex refractive index of silicon ion (Si+) implanted polymethylmethacrylate (PMMA) is studied, in particular PMMA implanted with Si+ ions accelerated to a relatively low energy of 50 keV and at a fluence of 3.2 × 1015 cm-2. The ion-modified material with nano-clustered structure formed in the near(sub)surface layer of a thickness of about 100 nm is optically characterized by simulation based on reflection ellipsometry measurements at a wavelength of 632.8 nm (He-Ne laser). Being of importance for applications of ion-implanted PMMA in integrated optics, optoelectronics and optical communications, the effect of the index depth profile of Si+-implanted PMMA on the profile of the reflected laser beam due to laser-induced thermo-lensing in reflection is also analyzed upon illumination with a low power cw laser (wavelength 532 nm, optical power 10 - 50 mW).

Real-time feedback control of the plasma density profile on ASDEX Upgrade

NASA Astrophysics Data System (ADS)

Mlynek, A.; Reich, M.; Giannone, L.; Treutterer, W.; Behler, K.; Blank, H.; Buhler, A.; Cole, R.; Eixenberger, H.; Fischer, R.; Lohs, A.; Lüddecke, K.; Merkel, R.; Neu, G.; Ryter, F.; Zasche, D.; ASDEX Upgrade Team

2011-04-01

The spatial distribution of density in a fusion experiment is of significant importance as it enters in numerous analyses and contributes to the fusion performance. The reconstruction of the density profile is therefore commonly done in offline data analysis. In this paper, we present an algorithm which allows for density profile reconstruction from the data of the submillimetre interferometer and the magnetic equilibrium in real-time. We compare the obtained results to the profiles yielded by a numerically more complex offline algorithm. Furthermore, we present recent ASDEX Upgrade experiments in which we used the real-time density profile for active feedback control of the shape of the density profile.

C-PCM based calculation of energy profiles for proton transfer in phosphorus-containing acid- N, N-dimethylformamide complexes

NASA Astrophysics Data System (ADS)

Fedorova, I. V.; Khatuntseva, E. A.; Krest'yaninov, M. A.; Safonova, L. P.

2016-02-01

Proton transfer along the hydrogen bond in complexes of DMF with H3PO4, H3PO3, CH3H2PO3, and their dimers has been investigated by the B3LYP/6-31++G** method in combination with the C-PCM model. When the Oacid···ODMF distance ( R) in the scanning procedure is not fixed, the energy profile in all cases has a single well. When this distance is fixed, there can be a proton transfer in all of the complexes in the gas phase at R > 2.6 Å; if solvation is taken into account, proton transfer can take place at R > 2.4 Å ( R > 2.5 Å for DMF complexes with CH3H2PO3 and its dimer). The height of the energy barrier to proton transfer increases with increasing R. Proton transfer is energetically most favorable in the DMF-phosphoric acid complexes. The structural and energetic characteristics of the hydrogen-bonded complexes calculated on the basis of the solvation model are compared with the same parameters for the complexes in the gas phase.

Effective Ion Mobility Peak Width as a New Isomeric Descriptor for the Untargeted Analysis of Complex Mixtures Using Ion Mobility-Mass Spectrometry

NASA Astrophysics Data System (ADS)

Farenc, Mathilde; Paupy, Benoit; Marceau, Sabrina; Riches, Eleanor; Afonso, Carlos; Giusti, Pierre

2017-07-01

Ion mobility coupled with mass spectrometry was proven to be an efficient way to characterize complex mixtures such as petroleum samples. However, the identification of isomeric species is difficult owing to the molecular complexity of petroleum and no availability of standard molecules. This paper proposes a new simple indicator to estimate the isomeric content of highly complex mixtures. This indicator is based on the full width at half maximum (FWHM) of the extracted ion mobility peak measured in millisecond or square angstrom that is corrected for instrumental factors such as ion diffusion. This value can be easily obtained without precisely identifying the number of isomeric species under the ion mobility peaks. Considering the Boduszynski model, the ion mobility profile for a particular elemental composition is expected to be a continuum of various isomeric species. The drift time-dependent fragmentation profile was studied and confirmed this hypothesis, a continuous evolution of the fragmentation profile showing that the larger alkyl chain species were detected at higher drift time values. This new indicator was proven to be a fast and efficient method to compare vacuum gas oils for which no difference was found using other analytical techniques.

Characterization of selected cellulolytic activities of multi-enzymatic complex system from Penicillium funiculosum.

PubMed

Karboune, Salwa; Geraert, Pierre-André; Kermasha, Selim

2008-02-13

The presence of endo-1,4-beta-D-glucanase, cellobiohydrolase, and beta-glucosidase activities in a multi-enzymatic complex system from Penicillium funiculosum was investigated. The interesting feature of these enzymes is their synergistic action for the hydrolysis of the native cellulose into glucose units. Both endo-1,4-beta-D-glucanase and cellobiohydrolase showed broader pH activity profiles, with pH optima of 4.0 and 4.0-5.0, respectively. However, beta-glucosidase activity showed a narrow pH-activity profile, with an optimum pH of 4.5. The different cellulolytic activities were stable in the acidic pH range of 2.5-6.0 and showed a similar optimal temperature of 60 degrees C. Although beta-glucosidase has shown a close catalytic efficiency as that of endo-1,4-beta-D-glucanase, its thermal stability was lower. However, the thermal stability profile of cellobiohydrolase was close to that of endo-1,4-beta-D-glucanase. The results also revealed the presence of high levels of endo-1,3-1,4-beta-D-glucanase, endo-1,3-beta- d-glucanase, and pectinase activities in the multi-enzymatic cellulolytic complex system. Moreover, the investigated multi-enzymatic complex system was effective in degrading the nonstarch polysaccharides of soybean meal.

Physiological typing of Pseudallescheria and Scedosporium strains using Taxa Profile, a semi-automated, 384-well microtitre system.

PubMed

Horré, R; Schaal, K P; Marklein, G; de Hoog, G S; Reiffert, S-M

2011-10-01

During the last few decades, Pseudallescheria and Scedosporium infections in humans are noted with increasing frequency. Multi-drug resistance commonly occurring in this species complex interferes with adequate therapy. Rapid and correct identification of clinical isolates is of paramount significance for optimal treatment in the early stages of infection, while strain typing is necessary for epidemiological purposes. In view of the development of physiological diagnostic parameters, 570 physiological reactions were evaluated using the Taxa Profile Micronaut system, a semi-automatic, computer-assisted, 384-well microtitre platform. Thirty two strains of the Pseudallescheria and Scedosporium complex were analysed after molecular verification of correct species attribution. Of the compounds tested, 254 proved to be polymorphic. Cluster analysis was performed with the Micronaut profile software, which is linked to the ntsypc® program. The systemic opportunist S. prolificans was unambiguously separated from the remaining species. Within the P. boydii/P. apiosperma complex differentiation was noted at the level of individual strains, but no unambiguous parameters for species recognition were revealed. © 2011 Blackwell Verlag GmbH.

Identifying technical aliases in SELDI mass spectra of complex mixtures of proteins

PubMed Central

2013-01-01

Background Biomarker discovery datasets created using mass spectrum protein profiling of complex mixtures of proteins contain many peaks that represent the same protein with different charge states. Correlated variables such as these can confound the statistical analyses of proteomic data. Previously we developed an algorithm that clustered mass spectrum peaks that were biologically or technically correlated. Here we demonstrate an algorithm that clusters correlated technical aliases only. Results In this paper, we propose a preprocessing algorithm that can be used for grouping technical aliases in mass spectrometry protein profiling data. The stringency of the variance allowed for clustering is customizable, thereby affecting the number of peaks that are clustered. Subsequent analysis of the clusters, instead of individual peaks, helps reduce difficulties associated with technically-correlated data, and can aid more efficient biomarker identification. Conclusions This software can be used to pre-process and thereby decrease the complexity of protein profiling proteomics data, thus simplifying the subsequent analysis of biomarkers by decreasing the number of tests. The software is also a practical tool for identifying which features to investigate further by purification, identification and confirmation. PMID:24010718

Antibody profiling sensitivity through increased reporter antibody layering

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

Apel, William A.; Thompson, Vicki S

A method for analyzing a biological sample by antibody profiling for identifying forensic samples or for detecting the presence of an analyte. In an embodiment of the invention, the analyte is a drug, such as marijuana, Cocaine (crystalline tropane alkaloid), methamphetamine, methyltestosterone, or mesterolone. The method comprises attaching antigens to a surface of a solid support in a preselected pattern to form an array wherein locations of the antigens are known; contacting the array with the biological sample such that a portion of antibodies in the sample reacts with and binds to the antigens in the array to form immunemore » complexes; washing away antibodies that do form immune complexes; and detecting the immune complexes, to form an antibody profile. Forensic samples are identified by comparing a sample from an unknown source with a sample from a known source. Further, an assay, such as a test for illegal drug use, can be coupled to a test for identity such that the results of the assay can be positively correlated to the subject's identity.« less

Analytical aspects of plant metabolite profiling platforms: current standings and future aims.

PubMed

Seger, Christoph; Sturm, Sonja

2007-02-01

Over the past years, metabolic profiling has been established as a comprehensive systems biology tool. Mass spectrometry or NMR spectroscopy-based technology platforms combined with unsupervised or supervised multivariate statistical methodologies allow a deep insight into the complex metabolite patterns of plant-derived samples. Within this review, we provide a thorough introduction to the analytical hard- and software requirements of metabolic profiling platforms. Methodological limitations are addressed, and the metabolic profiling workflow is exemplified by summarizing recent applications ranging from model systems to more applied topics.

Reconstruction Of The Permittivity Profile Of A Stratified Dielectric Layer

NASA Astrophysics Data System (ADS)

Vogelzang, E.; Ferwerda, H. A.; Yevick, D.

1985-03-01

A numerical procedure is given for the reconstruction of the permittivity profile of a dielectric slab on a perfect conductor. Profiles not supporting guided modes are reconstructed from the complex reflection amplitude for TE-polarized, monochromatic plane waves incident from different directions using the Marchenko theory. The contribution of guided modes is incorporated in the reconstruction procedure through the Gelfand-Levitan equations. An advantage of our approach is that a unique solution for the permittivity profile is obtained without the use of complicated regularization techniques. Some illustrative numerical examples are presented.

Unravelling the Chemical Complexity of Biomass Burning VOC Emissions via H3O+ ToF-CIMS: Separation of High- and Low-temperature Pyrolysis Products

NASA Astrophysics Data System (ADS)

Sekimoto, K.; Koss, A.; Gilman, J.; Selimovic, V.; Coggon, M.; Zarzana, K. J.; Yuan, B.; Lerner, B. M.; Brown, S. S.; Warneke, C.; Yokelson, R. J.; De Gouw, J. A.

2017-12-01

Biomass burning is a large source of volatile organic compounds (VOCs) and many other trace species to the atmosphere. These VOCs can act as precursors to formation of secondary pollutants such as ozone and fine particles, and some VOCs can also have direct effects on human and ecosystem health. Multiple different and complex processes take place in biomass burning, e.g., distillation, flaming, and smoldering combustion processes. In a given fire, most of these processes occur simultaneously, but the relative importance of each can change over the course of a fire. This gives rise to some of the variability in VOC emissions between different fires. To study gas-phase emissions from biomass burning, an H3O+ ToF-CIMS was deployed during the FIREX 2016 laboratory intensive at the US Forest Service Fire Sciences Laboratory in Missoula, Montana. This instrument has a fast time response and the measurements in stack burns show the varying gas-phase emissions as the mix of distillation, flaming, and smoldering varies. We used positive matrix factorization (PMF) to reduce and explain the observed chemical complexity in the gas phase. Despite the complexity and variability of emissions, we found that a solution including just two emission profiles explained on average 85% of the VOC emissions across 15 different fuel types including pines, firs, spruce, grass, shrubs, chaparrals, and wood wool. We identified the two profiles as resulting from high-temperature and low-temperature pyrolysis processes, and found that the profiles were remarkably similar (correlation coefficient r > 0.9) across nearly all the fuel types described above. Some of the remaining differences in VOC emission profiles between fuel types, and exceptions to the two-profile solution, can be explained by differences in the chemical composition of the fuels.

Organizational Agility Model and Simulation

DTIC Science & Technology

2011-06-01

and response profile. Also, compensatory, anticipatory , adaptive, and learning behaviours (methods) are employed to modify stiffness and resistance...The hypothetical profile in Figure 1b shows some complexity changes for a major sporting event or...classical motion tracking problem using compensatory, anticipatory , adaptive, and learning behaviours. These behaviours modify the size, resistance, and

Complex Sentence Profiles in Children with Specific Language Impairment: Are They Really Atypical?

ERIC Educational Resources Information Center

Riches, Nick G.

2017-01-01

Children with Specific Language Impairment (SLI) have language difficulties of unknown origin. Syntactic profiles are atypical, with poor performance on non-canonical structures, e.g. object relatives, suggesting a localized deficit. However, existing analyses using ANOVAs are problematic because they do not systematically address unequal…

Simple & Rapid Generation of Complex DNA Profiles for the Undergraduate Laboratory

ERIC Educational Resources Information Center

Kass, David H.

2007-01-01

Deoxyribonucleic acid (DNA) profiles can be generated by a variety of techniques incorporating different types of DNA markers. Simple methods are commonly utilized in the undergraduate laboratory, but with certain drawbacks. In this article, the author presents an advancement of the "Alu" dimorphism technique involving two tetraplex polymerase…

Reconstruction of refractive index profile of a stratified medium

NASA Astrophysics Data System (ADS)

Vogelzang, E.; Ferwerda, H. A.; Yevick, D.

In this paper, a method for determining the permittivity profile of a stratified medium terminated by a perfect conductor from the (complex) reflectivity is presented. The calculations are based on the Gelfand-Levitan and the Marchenko equations. The bound modes of the system are explicitly taken into account.

Difference in volatile profile between pericarp tissue and locular gel in tomato fruit

USDA-ARS?s Scientific Manuscript database

Aroma, a complex mixture of volatile compounds, plays an important role in the perception and acceptability of tomato products by consumers. Numerous studies have reported volatile profiles in tomatoes based on measurement of the whole fruit or pericarp tissue, however, little is understood regardin...

Rethinking the longitudinal stream temperature paradigm: region-wide comparison of thermal infrared imagery reveals unexpected complexity of river temperatures

EPA Science Inventory

We used an extensive dataset of remotely sensed summertime river temperature to compare longitudinal profiles (temperature versus distance) for 54 rivers in the Pacific Northwest. We evaluated (1) how often profiles fit theoretical expectations of asymptotic downstream warming, a...

Modeling and Simulation of Lab-on-a-Chip Systems

DTIC Science & Technology

2005-08-12

complex chip geometries (including multiple turns). Variations of sample concentration profiles in laminar diffusion-based micromixers are also derived...CHAPTER 6 MODELING OF LAMINAR DIFFUSION-BASED COMPLEX ELECTROKINETIC PASSIVE MICROMIXERS ...140 6.4.4 Multi-Stream (Inter-Digital) Micromixers

The viscosity and temperature dependence of 1H T1-NMRD of the Gd(H 2O) 83+ complex

NASA Astrophysics Data System (ADS)

Zhou, Xiangzhi; Westlund, Per-Olof

2005-11-01

Water proton T1-NMRD profiles of the Gd(H 2O) 83+ complex have been recorded at three temperatures and at four concentrations of glycerol. The analysis is performed using both the generalized Solomon-Bloembergen-Morgan (GSBM) theory [J. Magn. Reson. 167(2004), 147-160], and the stochastic Liouville approach (SLA). The GSBM approach uses a two processes dynamic model of the zero-field splitting (ZFS) correlation function whereas SLA uses a single process model. Both models reproduce the proton T1-NMRD profiles well. However, the model parameters extracted from the two analyses, yield different ESR X-band spectra which moreover do not reproduce the experimental ESR spectra. It is shown that the analyses of the proton T1-NMRD profiles recorded for a solution Gd(H 2O) 83+ ions are relatively insensitive to the slow modulation part of dynamic model of the ZFS interaction correlation function. The description of the electron spin system results in a very small static ZFS, while recent ESR lineshape analysis indicates that the contribution from the static ZFS is important. Analysis of proton T1-NMRD profiles of Gd(H 2O) 83+ complex do result in a description of the electron spin system but these microscopic parameters are uncertain unless they also are tested in a ESR-lineshape analysis.

Plasma Exosome Profiling of Cancer Patients by a Next Generation Systems Biology Approach.

PubMed

Domenyuk, Valeriy; Zhong, Zhenyu; Stark, Adam; Xiao, Nianqing; O'Neill, Heather A; Wei, Xixi; Wang, Jie; Tinder, Teresa T; Tonapi, Sonal; Duncan, Janet; Hornung, Tassilo; Hunter, Andrew; Miglarese, Mark R; Schorr, Joachim; Halbert, David D; Quackenbush, John; Poste, George; Berry, Donald A; Mayer, Günter; Famulok, Michael; Spetzler, David

2017-02-20

Technologies capable of characterizing the full breadth of cellular systems need to be able to measure millions of proteins, isoforms, and complexes simultaneously. We describe an approach that fulfils this criterion: Adaptive Dynamic Artificial Poly-ligand Targeting (ADAPT). ADAPT employs an enriched library of single-stranded oligodeoxynucleotides (ssODNs) to profile complex biological samples, thus achieving an unprecedented coverage of system-wide, native biomolecules. We used ADAPT as a highly specific profiling tool that distinguishes women with or without breast cancer based on circulating exosomes in their blood. To develop ADAPT, we enriched a library of ~10 11 ssODNs for those associating with exosomes from breast cancer patients or controls. The resulting 10 6 enriched ssODNs were then profiled against plasma from independent groups of healthy and breast cancer-positive women. ssODN-mediated affinity purification and mass spectrometry identified low-abundance exosome-associated proteins and protein complexes, some with known significance in both normal homeostasis and disease. Sequencing of the recovered ssODNs provided quantitative measures that were used to build highly accurate multi-analyte signatures for patient classification. Probing plasma from 500 subjects with a smaller subset of 2000 resynthesized ssODNs stratified healthy, breast biopsy-negative, and -positive women. An AUC of 0.73 was obtained when comparing healthy donors with biopsy-positive patients.

Plasma Exosome Profiling of Cancer Patients by a Next Generation Systems Biology Approach

PubMed Central

Domenyuk, Valeriy; Zhong, Zhenyu; Stark, Adam; Xiao, Nianqing; O’Neill, Heather A.; Wei, Xixi; Wang, Jie; Tinder, Teresa T.; Tonapi, Sonal; Duncan, Janet; Hornung, Tassilo; Hunter, Andrew; Miglarese, Mark R.; Schorr, Joachim; Halbert, David D.; Quackenbush, John; Poste, George; Berry, Donald A.; Mayer, Günter; Famulok, Michael; Spetzler, David

2017-01-01

Technologies capable of characterizing the full breadth of cellular systems need to be able to measure millions of proteins, isoforms, and complexes simultaneously. We describe an approach that fulfils this criterion: Adaptive Dynamic Artificial Poly-ligand Targeting (ADAPT). ADAPT employs an enriched library of single-stranded oligodeoxynucleotides (ssODNs) to profile complex biological samples, thus achieving an unprecedented coverage of system-wide, native biomolecules. We used ADAPT as a highly specific profiling tool that distinguishes women with or without breast cancer based on circulating exosomes in their blood. To develop ADAPT, we enriched a library of ~1011 ssODNs for those associating with exosomes from breast cancer patients or controls. The resulting 106 enriched ssODNs were then profiled against plasma from independent groups of healthy and breast cancer-positive women. ssODN-mediated affinity purification and mass spectrometry identified low-abundance exosome-associated proteins and protein complexes, some with known significance in both normal homeostasis and disease. Sequencing of the recovered ssODNs provided quantitative measures that were used to build highly accurate multi-analyte signatures for patient classification. Probing plasma from 500 subjects with a smaller subset of 2000 resynthesized ssODNs stratified healthy, breast biopsy-negative, and -positive women. An AUC of 0.73 was obtained when comparing healthy donors with biopsy-positive patients. PMID:28218293

Controlled loading of cryoprotectants (CPAs) to oocyte with linear and complex CPA profiles on a microfluidic platform.

PubMed

Heo, Yun Seok; Lee, Ho-Joon; Hassell, Bryan A; Irimia, Daniel; Toth, Thomas L; Elmoazzen, Heidi; Toner, Mehmet

2011-10-21

Oocyte cryopreservation has become an essential tool in the treatment of infertility by preserving oocytes for women undergoing chemotherapy. However, despite recent advances, pregnancy rates from all cryopreserved oocytes remain low. The inevitable use of the cryoprotectants (CPAs) during preservation affects the viability of the preserved oocytes and pregnancy rates either through CPA toxicity or osmotic injury. Current protocols attempt to reduce CPA toxicity by minimizing CPA concentrations, or by minimizing the volume changes via the step-wise addition of CPAs to the cells. Although the step-wise addition decreases osmotic shock to oocytes, it unfortunately increases toxic injuries due to the long exposure times to CPAs. To address limitations of current protocols and to rationally design protocols that minimize the exposure to CPAs, we developed a microfluidic device for the quantitative measurements of oocyte volume during various CPA loading protocols. We spatially secured a single oocyte on the microfluidic device, created precisely controlled continuous CPA profiles (step-wise, linear and complex) for the addition of CPAs to the oocyte and measured the oocyte volumetric response to each profile. With both linear and complex profiles, we were able to load 1.5 M propanediol to oocytes in less than 15 min and with a volumetric change of less than 10%. Thus, we believe this single oocyte analysis technology will eventually help future advances in assisted reproductive technologies and fertility preservation.

Significant effect of topographic normalization of airborne LiDAR data on the retrieval of plant area index profile in mountainous forests

NASA Astrophysics Data System (ADS)

Liu, Jing; Skidmore, Andrew K.; Heurich, Marco; Wang, Tiejun

2017-10-01

As an important metric for describing vertical forest structure, the plant area index (PAI) profile is used for many applications including biomass estimation and wildlife habitat assessment. PAI profiles can be estimated with the vertically resolved gap fraction from airborne LiDAR data. Most research utilizes a height normalization algorithm to retrieve local or relative height by assuming the terrain to be flat. However, for many forests this assumption is not valid. In this research, the effect of topographic normalization of airborne LiDAR data on the retrieval of PAI profile was studied in a mountainous forest area in Germany. Results show that, although individual tree height may be retained after topographic normalization, the spatial arrangement of trees is changed. Specifically, topographic normalization vertically condenses and distorts the PAI profile, which consequently alters the distribution pattern of plant area density in space. This effect becomes more evident as the slope increases. Furthermore, topographic normalization may also undermine the complexity (i.e., canopy layer number and entropy) of the PAI profile. The decrease in PAI profile complexity is not solely determined by local topography, but is determined by the interaction between local topography and the spatial distribution of each tree. This research demonstrates that when calculating the PAI profile from airborne LiDAR data, local topography needs to be taken into account. We therefore suggest that for ecological applications, such as vertical forest structure analysis and modeling of biodiversity, topographic normalization should not be applied in non-flat areas when using LiDAR data.

Local sensitivity to stimulus orientation and spatial frequency within the receptive fields of neurons in visual area 2 of macaque monkeys

PubMed Central

Tao, X.; Zhang, B.; Smith, E. L.; Nishimoto, S.; Ohzawa, I.

2012-01-01

We used dynamic dense noise stimuli and local spectral reverse correlation methods to reveal the local sensitivities of neurons in visual area 2 (V2) of macaque monkeys to orientation and spatial frequency within their receptive fields. This minimized the potentially confounding assumptions that are inherent in stimulus selections. The majority of neurons exhibited a relatively high degree of homogeneity for the preferred orientations and spatial frequencies in the spatial matrix of facilitatory subfields. However, about 20% of all neurons showed maximum orientation differences between neighboring subfields that were greater than 25 deg. The neurons preferring horizontal or vertical orientations showed less inhomogeneity in space than the neurons preferring oblique orientations. Over 50% of all units also exhibited suppressive profiles, and those were more heterogeneous than facilitatory profiles. The preferred orientation and spatial frequency of suppressive profiles differed substantially from those of facilitatory profiles, and the neurons with suppressive subfields had greater orientation selectivity than those without suppressive subfields. The peak suppression occurred with longer delays than the peak facilitation. These results suggest that the receptive field profiles of the majority of V2 neurons reflect the orderly convergence of V1 inputs over space, but that a subset of V2 neurons exhibit more complex response profiles having both suppressive and facilitatory subfields. These V2 neurons with heterogeneous subfield profiles could play an important role in the initial processing of complex stimulus features. PMID:22114163

The complexity of gene expression dynamics revealed by permutation entropy

PubMed Central

2010-01-01

Background High complexity is considered a hallmark of living systems. Here we investigate the complexity of temporal gene expression patterns using the concept of Permutation Entropy (PE) first introduced in dynamical systems theory. The analysis of gene expression data has so far focused primarily on the identification of differentially expressed genes, or on the elucidation of pathway and regulatory relationships. We aim to study gene expression time series data from the viewpoint of complexity. Results Applying the PE complexity metric to abiotic stress response time series data in Arabidopsis thaliana, genes involved in stress response and signaling were found to be associated with the highest complexity not only under stress, but surprisingly, also under reference, non-stress conditions. Genes with house-keeping functions exhibited lower PE complexity. Compared to reference conditions, the PE of temporal gene expression patterns generally increased upon stress exposure. High-complexity genes were found to have longer upstream intergenic regions and more cis-regulatory motifs in their promoter regions indicative of a more complex regulatory apparatus needed to orchestrate their expression, and to be associated with higher correlation network connectivity degree. Arabidopsis genes also present in other plant species were observed to exhibit decreased PE complexity compared to Arabidopsis specific genes. Conclusions We show that Permutation Entropy is a simple yet robust and powerful approach to identify temporal gene expression profiles of varying complexity that is equally applicable to other types of molecular profile data. PMID:21176199

The Mesozoic-Cenozoic igneous intrusions and related sediment-dominated hydrothermal activities in the South Yellow Sea Basin, the Western Pacific continental margin

NASA Astrophysics Data System (ADS)

Yumao, Pang; Xunhua, Zhang; Guolin, Xiao; Luning, Shang; Xingwei, Guo; Zhenhe, Wen

2018-04-01

Various igneous complexes were identified in multi-channel seismic reflection profiles from the South Yellow Sea Basin. It is not rare that magmatic intrusions in sedimentary basins cause strong thermal perturbations and hydrothermal activities. Some intrusion-related hydrothermal vent complexes have been identified and they are considered to originate from the deep sedimentary contact aureole around igneous intrusions and terminate in upper vents structures, and are linked by a vertical conduit system. The upper vent complexes are usually eye-shaped, dome-shaped, fault-related, crater-shaped or pock-shaped in seismic profiles. A schematic model was proposed to illustrate the structures of different types of hydrothermal vent complexes. A conceptual conduit model composed of an upper pipe-like part and a lower branching part was also derived. Hydrothermal vent complexes mainly developed during the Middle-Late Cretaceous, which is coeval with, or shortly after the intrusion. The back-arc basin evolution of the area which is related to the subduction of the Paleo-Pacific plate during the Mesozoic-Cenozoic may be the principal factor for voluminous igneous complexes and vent complexes in this area. It is significant to study the characteristics of igneous complexes and related hydrothermal vent complexes, which will have implications for the future study of this area.

Searching and Extracting Data from the EMBL-EBI Complex Portal.

PubMed

Meldal, Birgit H M; Orchard, Sandra

2018-01-01

The Complex Portal ( www.ebi.ac.uk/complexportal ) is an encyclopedia of macromolecular complexes. Complexes are assigned unique, stable IDs, are species specific, and list all participating members with links to an appropriate reference database (UniProtKB, ChEBI, RNAcentral). Each complex is annotated extensively with its functions, properties, structure, stoichiometry, tissue expression profile, and subcellular location. Links to domain-specific databases allow the user to access additional information and enable data searching and filtering. Complexes can be saved and downloaded in PSI-MI XML, MI-JSON, and tab-delimited formats.

Real-Time Measurement of Host Bioenergetics During Mycobacterium Tuberculosis Infection

DTIC Science & Technology

2015-05-01

antimycobacterial drugs on Mtb bioenergetics. We focused on Clofazimine (CFZ, targets Complex I), Bedaquiline (BDQ/TMC207, targets Complex V) and Q203 (targets... Complex III). Firstly we investigated the effect of CFZ and BDQ on the OCR profiles of Mtb mc2 6230 (Figure 3). These experiments were done in...addition with of CFZ. The decrease in OCR is consistent with ETC complex inhibition. BDQ caused a very surprising concentration-depended increase

Challenges in assessing college students' conception of duality: the case of infinity

NASA Astrophysics Data System (ADS)

Babarinsa-Ochiedike, Grace Olutayo

Interpreting students' views of infinity posits a challenge for researchers due to the dynamic nature of the conception. There is diversity and variation among students' process-object perceptions. The fluctuations between students' views however reveal an undeveloped duality conception. This study examined college students' conception of duality in understanding and representing infinity with the intent to design strategies that could guide researchers in categorizing students' views of infinity into different levels. Data for the study were collected from N=238 college students enrolled in Calculus sequence courses (Pre-Calculus, Calculus I through Calculus III) at one of the southwestern universities in the U.S. using self-report questionnaires and semi-structured individual task-based interviews. Data was triangulated using multiple measures analyzed by three independent experts using self-designed coding sheets to assess students' externalization of the duality conception of infinity. Results of this study reveal that college students' experiences in traditional Calculus sequence courses are not supportive of the development of duality conception. On the contrary, it strengthens the singularity perspective on fundamental ideas of mathematics such as infinity. The study also found that coding and assessing college students' conception of duality is a challenging and complex process due to the dynamic nature of the conception that is task-dependent and context-dependent. Practical significance of the study is that it helps to recognize misconceptions and starts addressing them so students will have a more comprehensive view of fundamental mathematical ideas as they progress through the Calculus coursework sequence. The developed duality concept development framework called Action-Process-Object-Duality (APOD) adapted from the APOS theory could guide educators and researchers as they engage in assessing students' conception of duality. The results of this study could serve as a facilitating instrument to further analyze cognitive obstacles in college students' understanding of the infinity concept.

First Year of WFIRST/AFTA Coronagraph Technology Development: Testbed Progress Update

NASA Astrophysics Data System (ADS)

Poberezhskiy, Ilya; Poberezhskiy, Ilya; Zhao, Feng; An, Xin; Balasubramanian, Kunjithapatham; Belikov, Rus; Cady, Eric; Diaz, Rosemary; Gordon, Brian; Guyon, Olivier; Kasdin, N. Jeremy; Kern, Brian; Kuhnert, Andreas; Moody, Dwight; Muller, Richard; Nemati, Bijan; Patterson, Keith; Riggs, A. J.; Ryan, Daniel; Seo, Byoung-Joon; Sidick, Erkin; Shi, Fang; Tang, Hong; Trauger, John; Wallace, Kent; Wang, Xu; Wilson, Daniel; White, Victor; Yee, Karl; Zhou, Hanying; Zimmerman, Neil

2015-01-01

NASA's WFIRST/AFTA mission study includes the first high-contrast stellar coronagraph in space. This coronagraph will be capable of imaging and spectrally characterizing giant exoplanets similar to Neptune and Jupiter and possibly super-Earths, as well as circumstellar disks. After a transparent and rigorous downselect process, NASA chose in December of 2013 a primary design called an Occulting Mask Coronagraph (OMC) that combines two technical approaches, Shaped Pupil and Hybrid Lyot, in one instrument. The Phase-Induced Amplitude Apodization Complex Mask Coronagraph was selected as the backup design.The OMC coronagraph technologies were assessed to have the highest likelihood of passing the WFIRST/AFTA flight readiness gates and the ability to produce compelling science by working with the existing 2.4-meter telescope 'as is,' including its central obscuration, expected thermal drift, and the observatory pointing jitter. NASA set us the objective of maturing the WFIRST/AFTA coronagraph to Technology Readiness Level (TRL) 5 by October 1, 2016. A set of technical milestones was agreed upon to track the progress toward achieving TRL 5.Substantial advances in WFIRST/AFTA coronagraph technology have been made during 2014, and the OMC progress is currently running ahead of the schedule laid out by the milestones. Our poster will present some of these key recent results to the community, including:(1) Fabrication and characterization of WFIRST/AFTA coronagraph pupil plane and focal plane masks designed to work with the existing 2.4 telescope.(2) Experimental results demonstrating high contrast achieved on a coronagraph testbed in narrowband and broadband light - first such results obtained with an obscured pupil.(3) Progress in the development of the low-order wavefront sensing and control subsystem that will use rejected starlight to sense and correct both high frequency pointing jitter and slow varying low order aberrations. This subsystem will be integrated with the OMC coronagraph in mid-2015 for the next phase of starlight suppression experiments with dynamic input wavefront.

Three dimensional full-wave nonlinear acoustic simulations: Applications to ultrasound imaging

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

Pinton, Gianmarco

Characterization of acoustic waves that propagate nonlinearly in an inhomogeneous medium has significant applications to diagnostic and therapeutic ultrasound. The generation of an ultrasound image of human tissue is based on the complex physics of acoustic wave propagation: diffraction, reflection, scattering, frequency dependent attenuation, and nonlinearity. The nonlinearity of wave propagation is used to the advantage of diagnostic scanners that use the harmonic components of the ultrasonic signal to improve the resolution and penetration of clinical scanners. One approach to simulating ultrasound images is to make approximations that can reduce the physics to systems that have a low computational cost.more » Here a maximalist approach is taken and the full three dimensional wave physics is simulated with finite differences. This paper demonstrates how finite difference simulations for the nonlinear acoustic wave equation can be used to generate physically realistic two and three dimensional ultrasound images anywhere in the body. A specific intercostal liver imaging scenario for two cases: with the ribs in place, and with the ribs removed. This configuration provides an imaging scenario that cannot be performed in vivo but that can test the influence of the ribs on image quality. Several imaging properties are studied, in particular the beamplots, the spatial coherence at the transducer surface, the distributed phase aberration, and the lesion detectability for imaging at the fundamental and harmonic frequencies. The results indicate, counterintuitively, that at the fundamental frequency the beamplot improves due to the apodization effect of the ribs but at the same time there is more degradation from reverberation clutter. At the harmonic frequency there is significantly less improvement in the beamplot and also significantly less degradation from reverberation. It is shown that even though simulating the full propagation physics is computationally challenging it is necessary to quantify ultrasound image quality and its sources of degradation.« less

Modeling and life prediction methodology for Titanium Matrix Composites subjected to mission profiles

NASA Technical Reports Server (NTRS)

Mirdamadi, M.; Johnson, W. S.

1994-01-01

Titanium matrix composites (TMC) are being evaluated as structural materials for elevated temperature applications in future generation hypersonic vehicles. In such applications, TMC components are subjected to complex thermomechanical loading profiles at various elevated temperatures. Therefore, thermomechanical fatigue (TMF) testing, using a simulated mission profile, is essential for evaluation and development of life prediction methodologies. The objective of the research presented in this paper was to evaluate the TMF response of the (0/90)2s SCS-6/Timetal-21S subjected to a generic hypersonic flight profile and its portions with a temperature ranging from -130 C to 816 C. It was found that the composite modulus, prior to rapid degradation, had consistent values for all the profiles tested. A micromechanics based analysis was used to predict the stress-strain response of the laminate and of the constituents in each ply during thermomechanical loading conditions by using only constituent properties as input. The fiber was modeled as elastic with transverse orthotropic and temperature dependent properties. The matrix was modeled using a thermoviscoplastic constitutive relation. In the analysis, the composite modulus degradation was assumed to result from matrix cracking and was modeled by reducing the matrix modulus. Fatigue lives of the composite subjected to the complex generic hypersonic flight profile were well correlated using the predicted stress in 0 degree fibers.

Clonal spread and accumulation of β-lactam resistance determinants in Enterobacter aerogenes and Enterobacter cloacae complex isolates from infection and colonization in patients at a public hospital in Recife, Pernambuco, Brazil.

PubMed

Cabral, Adriane Borges; Maciel, Maria Amélia Vieira; Barros, Josineide Ferreira; Antunes, Marcelo Maranhão; Barbosa de Castro, Célia Maria Machado; Lopes, Ana Catarina Souza

2017-01-01

Enterobacter aerogenes and Enterobacter cloacae complex are the two species of this genus most involved in healthcare-associated infections that are ESBL and carbapenemase producers. This study characterized, phenotypically and genotypically, 51 isolates of E. aerogenes and E. cloacae complex originating from infection or colonization in patients admitted to a public hospital in Recife, Pernambuco, Brazil, by antimicrobial susceptibility profile, analysis of β-lactamase genes (blaTEM, blaSHV, blaCTX-M, blaKPC, blaVIM, blaIMP and blaSPM), PCR and DNA sequencing, plasmid profile and ERIC-PCR. In both species, the genes blaTEM, blaCTX-M and blaKPC were detected. The DNA sequencing confirmed the variants blaTEM-1, blaCTX-M-15 and blaKPC-2 in isolates. More than one gene conferring resistance in the isolates, including the detection of the three previously cited genes in strains isolated from infection sites, was observed. The detection of blaCTX-M was more frequent in isolates from infection sites than from colonization. The gene blaKPC predominated in E. cloacae complex isolates obtained from infections; however, in E. aerogenes isolates, it predominated in samples obtained from colonization. A clonal relationship among all of E. aerogenes isolates was detected by ERIC-PCR. The majority of E. cloacae complex isolates presented the same ERIC-PCR pattern. Despite the clonal relation presented by the isolates using ERIC-PCR, different plasmid and resistance profiles and several resistance genes were observed. The clonal dissemination and the accumulation of β-lactam resistance determinants presented by the isolates demonstrated the ability of E. aerogenes and E. cloacae complex, obtained from colonization and infection, to acquire and maintain different resistance genes.

Approximate Stokes Drift Profiles and their use in Ocean Modelling

NASA Astrophysics Data System (ADS)

Breivik, O.; Biblot, J.; Janssen, P. A. E. M.

2016-02-01

Deep-water approximations to the Stokes drift velocity profile are explored as alternatives to the monochromatic profile. The alternative profiles investigated rely on the same two quantities required for the monochromatic profile, viz the Stokes transport and the surface Stokes drift velocity. Comparisons with parametric spectra and profiles under wave spectra from the ERA-Interim reanalysis and buoy observations reveal much better agreement than the monochromatic profile even for complex sea states. That the profiles give a closer match and a more correct shear has implications for ocean circulation models since the Coriolis-Stokes force depends on the magnitude and direction of the Stokes drift profile and Langmuir turbulence parameterizations depend sensitively on the shear of the profile. The NEMO general circulation ocean model was recently extended to incorporate the Stokes-Coriolis force along with two other wave-related effects. I will show some results from the coupled atmosphere-wave-ocean ensemble forecast system of ECMWF where these wave effects are now included in the ocean model component.

The Atmospheric Chemistry Suite (ACS) of Three Spectrometers for the ExoMars 2016 Trace Gas Orbiter

NASA Astrophysics Data System (ADS)

Korablev, O.; Montmessin, F.; Trokhimovskiy, A.; Fedorova, A. A.; Shakun, A. V.; Grigoriev, A. V.; Moshkin, B. E.; Ignatiev, N. I.; Forget, F.; Lefèvre, F.; Anufreychik, K.; Dzuban, I.; Ivanov, Y. S.; Kalinnikov, Y. K.; Kozlova, T. O.; Kungurov, A.; Makarov, V.; Martynovich, F.; Maslov, I.; Merzlyakov, D.; Moiseev, P. P.; Nikolskiy, Y.; Patrakeev, A.; Patsaev, D.; Santos-Skripko, A.; Sazonov, O.; Semena, N.; Semenov, A.; Shashkin, V.; Sidorov, A.; Stepanov, A. V.; Stupin, I.; Timonin, D.; Titov, A. Y.; Viktorov, A.; Zharkov, A.; Altieri, F.; Arnold, G.; Belyaev, D. A.; Bertaux, J. L.; Betsis, D. S.; Duxbury, N.; Encrenaz, T.; Fouchet, T.; Gérard, J.-C.; Grassi, D.; Guerlet, S.; Hartogh, P.; Kasaba, Y.; Khatuntsev, I.; Krasnopolsky, V. A.; Kuzmin, R. O.; Lellouch, E.; Lopez-Valverde, M. A.; Luginin, M.; Määttänen, A.; Marcq, E.; Martin Torres, J.; Medvedev, A. S.; Millour, E.; Olsen, K. S.; Patel, M. R.; Quantin-Nataf, C.; Rodin, A. V.; Shematovich, V. I.; Thomas, I.; Thomas, N.; Vazquez, L.; Vincendon, M.; Wilquet, V.; Wilson, C. F.; Zasova, L. V.; Zelenyi, L. M.; Zorzano, M. P.

2018-02-01

The Atmospheric Chemistry Suite (ACS) package is an element of the Russian contribution to the ESA-Roscosmos ExoMars 2016 Trace Gas Orbiter (TGO) mission. ACS consists of three separate infrared spectrometers, sharing common mechanical, electrical, and thermal interfaces. This ensemble of spectrometers has been designed and developed in response to the Trace Gas Orbiter mission objectives that specifically address the requirement of high sensitivity instruments to enable the unambiguous detection of trace gases of potential geophysical or biological interest. For this reason, ACS embarks a set of instruments achieving simultaneously very high accuracy (ppt level), very high resolving power (>10,000) and large spectral coverage (0.7 to 17 μm—the visible to thermal infrared range). The near-infrared (NIR) channel is a versatile spectrometer covering the 0.7-1.6 μm spectral range with a resolving power of ˜20,000. NIR employs the combination of an echelle grating with an AOTF (Acousto-Optical Tunable Filter) as diffraction order selector. This channel will be mainly operated in solar occultation and nadir, and can also perform limb observations. The scientific goals of NIR are the measurements of water vapor, aerosols, and dayside or night side airglows. The mid-infrared (MIR) channel is a cross-dispersion echelle instrument dedicated to solar occultation measurements in the 2.2-4.4 μm range. MIR achieves a resolving power of >50,000. It has been designed to accomplish the most sensitive measurements ever of the trace gases present in the Martian atmosphere. The thermal-infrared channel (TIRVIM) is a 2-inch double pendulum Fourier-transform spectrometer encompassing the spectral range of 1.7-17 μm with apodized resolution varying from 0.2 to 1.3 cm-1. TIRVIM is primarily dedicated to profiling temperature from the surface up to ˜60 km and to monitor aerosol abundance in nadir. TIRVIM also has a limb and solar occultation capability. The technical concept of the instrument, its accommodation on the spacecraft, the optical designs as well as some of the calibrations, and the expected performances for its three channels are described.

Bioinformatic detection of E47, E2F1 and SREBP1 transcription factors as potential regulators of genes associated to acquisition of endometrial receptivity

PubMed Central

2011-01-01

Background The endometrium is a dynamic tissue whose changes are driven by the ovarian steroidal hormones. Its main function is to provide an adequate substrate for embryo implantation. Using microarray technology, several reports have provided the gene expression patterns of human endometrial tissue during the window of implantation. However it is required that biological connections be made across these genomic datasets to take full advantage of them. The objective of this work was to perform a research synthesis of available gene expression profiles related to acquisition of endometrial receptivity for embryo implantation, in order to gain insights into its molecular basis and regulation. Methods Gene expression datasets were intersected to determine a consensus endometrial receptivity transcript list (CERTL). For this cluster of genes we determined their functional annotations using available web-based databases. In addition, promoter sequences were analyzed to identify putative transcription factor binding sites using bioinformatics tools and determined over-represented features. Results We found 40 up- and 21 down-regulated transcripts in the CERTL. Those more consistently increased were C4BPA, SPP1, APOD, CD55, CFD, CLDN4, DKK1, ID4, IL15 and MAP3K5 whereas the more consistently decreased were OLFM1, CCNB1, CRABP2, EDN3, FGFR1, MSX1 and MSX2. Functional annotation of CERTL showed it was enriched with transcripts related to the immune response, complement activation and cell cycle regulation. Promoter sequence analysis of genes revealed that DNA binding sites for E47, E2F1 and SREBP1 transcription factors were the most consistently over-represented and in both up- and down-regulated genes during the window of implantation. Conclusions Our research synthesis allowed organizing and mining high throughput data to explore endometrial receptivity and focus future research efforts on specific genes and pathways. The discovery of possible new transcription factors orchestrating the CERTL opens new alternatives for understanding gene expression regulation in uterine function. PMID:21272326

Methods and tools for profiling and control of distributed systems

NASA Astrophysics Data System (ADS)

Sukharev, R.; Lukyanchikov, O.; Nikulchev, E.; Biryukov, D.; Ryadchikov, I.

2018-02-01

This article is devoted to the topic of profiling and control of distributed systems. Distributed systems have a complex architecture, applications are distributed among various computing nodes, and many network operations are performed. Therefore, today it is important to develop methods and tools for profiling distributed systems. The article analyzes and standardizes methods for profiling distributed systems that focus on simulation to conduct experiments and build a graph model of the system. The theory of queueing networks is used for simulation modeling of distributed systems, receiving and processing user requests. To automate the above method of profiling distributed systems the software application was developed with a modular structure and similar to a SCADA-system.

Try Out a New OD Approach: Measuring Climate and Communication with the Organizational Communication Profile.

ERIC Educational Resources Information Center

Peterson, Brent D.; Pace, R. Wayne

The Organizational Communication Profile (OCP) provides a way to survey organization member attitudes, perceptions, expectations, and degree of satisfaction with the manner in which information is handled within the organization. Although the OCP is relatively easy to administer and interpret, the instrument has a complex design and provides…

Time scale variation of NV resonance line profiles of HD203064

NASA Astrophysics Data System (ADS)

Strantzalis, A.

2012-01-01

Hot emission star, such as Be and Oe, present many spectral lines with very complex and peculiar profiles. Therefore, we cannot find a classical distribution to fit theoretically those physical line profiles. So, many physical parameters of the regions, where spectral lines are created, are difficult to estimate. Here, in this poster paper we study the UV NV (λλ 1238.821, 1242.804 A) resonance lines of the Be star HD203064 at three different dates. We using the Gauss-Rotation model, that proposed the idea that these complex profiles consist of a number of independent Discrete or Satellite Absorption Components (DACs, SACs). Our purpose is to calculate the values of a group of physical parameters as the apparent rotational, radial, and random velocities of the thermal motions of the ions. Also the Full Width at Half Maximum (FWHM) and the column density, as well as the absorbed energy of the independent regions of matter, which produce the main and the satellite components of the studied spectral lines. In addition, we determine the time scale variations of the above physical parameters.

Analytical Scheme Leading to Integrated High-Sensitivity Profiling of Glycosphingolipids Together with N- and O-Glycans from One Sample

NASA Astrophysics Data System (ADS)

Benktander, John D.; Gizaw, Solomon T.; Gaunitz, Stefan; Novotny, Milos V.

2018-05-01

Glycoconjugates are directly or indirectly involved in many biological processes. Due to their complex structures, the structural elucidation of glycans and the exploration of their role in biological systems have been challenging. Glycan pools generated through release from glycoprotein or glycolipid mixtures can often be very complex. For the sake of procedural simplicity, many glycan profiling studies choose to concentrate on a single class of glycoconjugates. In this paper, we demonstrate it feasible to cover glycosphingolipids, N-glycans, and O-glycans isolated from the same sample. Small volumes of human blood serum and ascites fluid as well as small mouse brain tissue samples are sufficient to profile sequentially glycans from all three classes of glycoconjugates and even positively identify some mixture components through MALDI-MS and LC-ESI-MS. The results show that comprehensive glycan profiles can be obtained from the equivalent of 500-μg protein starting material or possibly less. These methodological improvements can help accelerating future glycomic comprehensive studies, especially for precious clinical samples.

Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates

PubMed Central

Skerker, Jeffrey M; Leon, Dacia; Price, Morgan N; Mar, Jordan S; Tarjan, Daniel R; Wetmore, Kelly M; Deutschbauer, Adam M; Baumohl, Jason K; Bauer, Stefan; Ibáñez, Ana B; Mitchell, Valerie D; Wu, Cindy H; Hu, Ping; Hazen, Terry; Arkin, Adam P

2013-01-01

The efficient production of biofuels from cellulosic feedstocks will require the efficient fermentation of the sugars in hydrolyzed plant material. Unfortunately, plant hydrolysates also contain many compounds that inhibit microbial growth and fermentation. We used DNA-barcoded mutant libraries to identify genes that are important for hydrolysate tolerance in both Zymomonas mobilis (44 genes) and Saccharomyces cerevisiae (99 genes). Overexpression of a Z. mobilis tolerance gene of unknown function (ZMO1875) improved its specific ethanol productivity 2.4-fold in the presence of miscanthus hydrolysate. However, a mixture of 37 hydrolysate-derived inhibitors was not sufficient to explain the fitness profile of plant hydrolysate. To deconstruct the fitness profile of hydrolysate, we profiled the 37 inhibitors against a library of Z. mobilis mutants and we modeled fitness in hydrolysate as a mixture of fitness in its components. By examining outliers in this model, we identified methylglyoxal as a previously unknown component of hydrolysate. Our work provides a general strategy to dissect how microbes respond to a complex chemical stress and should enable further engineering of hydrolysate tolerance. PMID:23774757

Deciphering the Dynamic Interaction Profile of an Intrinsically Disordered Protein by NMR Exchange Spectroscopy.

PubMed

Delaforge, Elise; Kragelj, Jaka; Tengo, Laura; Palencia, Andrés; Milles, Sigrid; Bouvignies, Guillaume; Salvi, Nicola; Blackledge, Martin; Jensen, Malene Ringkjøbing

2018-01-24

Intrinsically disordered proteins (IDPs) display a large number of interaction modes including folding-upon-binding, binding without major structural transitions, or binding through highly dynamic, so-called fuzzy, complexes. The vast majority of experimental information about IDP binding modes have been inferred from crystal structures of proteins in complex with short peptides of IDPs. However, crystal structures provide a mainly static view of the complexes and do not give information about the conformational dynamics experienced by the IDP in the bound state. Knowledge of the dynamics of IDP complexes is of fundamental importance to understand how IDPs engage in highly specific interactions without concomitantly high binding affinity. Here, we combine rotating-frame R 1ρ , Carr-Purcell-Meiboom Gill relaxation dispersion as well as chemical exchange saturation transfer to decipher the dynamic interaction profile of an IDP in complex with its partner. We apply the approach to the dynamic signaling complex formed between the mitogen-activated protein kinase (MAPK) p38α and the intrinsically disordered regulatory domain of the MAPK kinase MKK4. Our study demonstrates that MKK4 employs a subtle combination of interaction modes in order to bind to p38α, leading to a complex displaying significantly different dynamics across the bound regions.

Glycobiotechnology of the Insect Cell-Baculovirus Expression System Technology.

PubMed

Palomares, Laura A; Srivastava, Indresh K; Ramírez, Octavio T; Cox, Manon M J

2018-06-10

The insect cell-baculovirus expression system technology (BEST) has a prominent role in producing recombinant proteins to be used as research and diagnostic reagents and vaccines. The glycosylation profile of proteins produced by the BEST is composed predominantly of terminal mannose glycans, and, in Trichoplusia ni cell lines, core α3 fucosylation, a profile different to that in mammals. Insects contain all the enzymatic activities needed for complex N- and O-glycosylation and sialylation, although few reports of complex glycosylation and sialylation by the BEST exist. The insect cell line and culture conditions determine the glycosylation profile of proteins produced by the BEST. The promoter used, dissolved oxygen tension, presence of sugar precursors, bovine serum or hemolymph, temperature, and the time of harvest all influence glycosylation, although more research is needed. The lack of activity of glycosylation enzymes possibly results from the transcription regulation and stress imposed by baculovirus infection. To solve this limitation, the glycosylation pathway of insect cells has been engineered to produce complex sialylated glycans and to eliminate α3 fucosylation, either by generating transgenic cell lines or by using baculovirus vectors. These strategies have been successful. Complex glycosylation, sialylation, and inhibition of α3 fucosylation have been achieved, although the majority of glycans still have terminal mannose residues. The implication of insect glycosylation in the proteins produced by the BEST is discussed. Graphical Abstract.

The development of a vocabulary for PEEPS-SE-profiles of early expressive phonological skills for Swedish.

PubMed

Marklund, Ulrika; Lacerda, Francisco; Persson, Anna; Lohmander, Anette

2018-04-10

This paper describes the development of a vocabulary for Profiles of Early Expressive Phonological Skills for Swedish (PEEPS-SE), a tool for assessment of expressive phonology in Swedish-learning children in the age range of 18-36 months. PEEPS-SE is the Swedish version of the original PEEPS, Profiles of Early Expressive Phonological Skills, which uses two age-adequate word lists-a basic word list (BWL) for the assessment of 18-24-month-old children, to which an expanded word list (EWL) is added for assessment of 24-36-month-old children, or children with more than 250 words in their expressive vocabulary. The selection of words in PEEPS-SE is based on two types of criteria: age of acquisition and phonological complexity. The words also need to be easy to elicit in a natural way in test situations. Vocabulary data previously collected with the Swedish Early Communicative Development Inventory are used for selection of age-adequate words, where the BWL contains words acquired earlier compared to the additional words in the EWL. The latter also contains words that are more phonologically complex compared to those in the BWL. Word complexity was determined by the Swedish version of word complexity measure. PEEPS-SE has made an attempt to match the original version of PEEPS in terms of both assessment method and word selection.

Global minimum profile error (GMPE) - a least-squares-based approach for extracting macroscopic rate coefficients for complex gas-phase chemical reactions.

PubMed

Duong, Minh V; Nguyen, Hieu T; Mai, Tam V-T; Huynh, Lam K

2018-01-03

Master equation/Rice-Ramsperger-Kassel-Marcus (ME/RRKM) has shown to be a powerful framework for modeling kinetic and dynamic behaviors of a complex gas-phase chemical system on a complicated multiple-species and multiple-channel potential energy surface (PES) for a wide range of temperatures and pressures. Derived from the ME time-resolved species profiles, the macroscopic or phenomenological rate coefficients are essential for many reaction engineering applications including those in combustion and atmospheric chemistry. Therefore, in this study, a least-squares-based approach named Global Minimum Profile Error (GMPE) was proposed and implemented in the MultiSpecies-MultiChannel (MSMC) code (Int. J. Chem. Kinet., 2015, 47, 564) to extract macroscopic rate coefficients for such a complicated system. The capability and limitations of the new approach were discussed in several well-defined test cases.

Distributed acoustic sensing: how to make the best out of the Rayleigh-backscattered energy?

NASA Astrophysics Data System (ADS)

Eyal, A.; Gabai, H.; Shpatz, I.

2017-04-01

Coherent fading noise (also known as speckle noise) affects the SNR and sensitivity of Distributed Acoustic Sensing (DAS) systems and makes them random processes of position and time. As in speckle noise, the statistical distribution of DAS SNR is particularly wide and its standard deviation (STD) roughly equals its mean (σSNR/ ≍ 0.89). Trading resolution for SNR may improve the mean SNR but not necessarily narrow its distribution. Here a new approach to achieve both SNR improvement (by sacrificing resolution) and narrowing of the distribution is introduced. The method is based on acquiring high resolution complex backscatter profiles of the sensing fiber, using them to compute complex power profiles of the fiber which retain phase variation information and filtering of the power profiles. The approach is tested via a computer simulation and demonstrates distribution narrowing up to σSNR/ < 0.2.

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

PubMed Central

Gao, Jianjiong; Aksoy, Bülent Arman; Dogrusoz, Ugur; Dresdner, Gideon; Gross, Benjamin; Sumer, S. Onur; Sun, Yichao; Jacobsen, Anders; Sinha, Rileen; Larsson, Erik; Cerami, Ethan; Sander, Chris; Schultz, Nikolaus

2014-01-01

The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal reduces molecular profiling data from cancer tissues and cell lines into readily understandable genetic, epigenetic, gene expression, and proteomic events. The query interface combined with customized data storage enables researchers to interactively explore genetic alterations across samples, genes, and pathways and, when available in the underlying data, to link these to clinical outcomes. The portal provides graphical summaries of gene-level data from multiple platforms, network visualization and analysis, survival analysis, patient-centric queries, and software programmatic access. The intuitive Web interface of the portal makes complex cancer genomics profiles accessible to researchers and clinicians without requiring bioinformatics expertise, thus facilitating biological discoveries. Here, we provide a practical guide to the analysis and visualization features of the cBioPortal for Cancer Genomics. PMID:23550210

Conference on Complex Turbulent Flows: Comparison of Computation and Experiment, Stanford University, Stanford, CA, September 14-18, 1981, Proceedings. Volume 2 - Taxonomies, reporters' summaries, evaluation, and conclusions

NASA Technical Reports Server (NTRS)

Kline, S. J. (Editor); Cantwell, B. J. (Editor); Lilley, G. M.

1982-01-01

Computational techniques for simulating turbulent flows were explored, together with the results of experimental investigations. Particular attention was devoted to the possibility of defining a universal closure model, applicable for all turbulence situations; however, conclusions were drawn that zonal models, describing localized structures, were the most promising techniques to date. The taxonomy of turbulent flows was summarized, as were algebraic, differential, integral, and partial differential methods for numerical depiction of turbulent flows. Numerous comparisons of theoretically predicted and experimentally obtained data for wall pressure distributions, velocity profiles, turbulent kinetic energy profiles, Reynolds shear stress profiles, and flows around transonic airfoils were presented. Simplifying techniques for reducing the necessary computational time for modeling complex flowfields were surveyed, together with the industrial requirements and applications of computational fluid dynamics techniques.

New procyanidin B3-human salivary protein complexes by mass spectrometry. Effect of salivary protein profile, tannin concentration, and time stability.

PubMed

Perez-Gregorio, Maria Rosa; Mateus, Nuno; De Freitas, Victor

2014-10-15

Several factors could influence the tannin-protein interaction such as the human salivary protein profile, the tannin tested, and the tannin/protein ratio. The goal of this study aims to study the effect of different salivas (A, B, and C) and different tannin concentrations (0.5 and 1 mg/mL) on the interaction process as well as the complex's stability over time. This study is focused on the identification of new procyanidin B3-human salivary protein complexes. Thus, 48 major B3-human salivary protein aggregates were identified regardless of the saliva and tannin concentration tested. A higher number of aggregates was found at lower tannin concentration. Moreover, the number of protein moieties involved in the aggregation process was higher when the tannin concentration was also higher. The selectivity of the different groups of proteins to bind tannin was also confirmed. It was also verified that the B3-human salivary protein complexes formed evolved over time.

Complexity in pH-Dependent Ribozyme Kinetics: Dark pKa Shifts and Wavy Rate-pH Profiles.

PubMed

Frankel, Erica A; Bevilacqua, Philip C

2018-02-06

Charged bases occur in RNA enzymes, or ribozymes, where they play key roles in catalysis. Cationic bases donate protons and perform electrostatic catalysis, while anionic bases accept protons. We previously published simulations of rate-pH profiles for ribozymes in terms of species plots for the general acid and general base that have been useful for understanding how ribozymes respond to pH. In that study, we did not consider interaction between the general acid and general base or interaction with other species on the RNA. Since that report, diverse small ribozyme classes have been discovered, many of which have charged nucleobases or metal ions in the active site that can either directly interact and participate in catalysis or indirectly interact as "influencers". Herein, we simulate experimental rate-pH profiles in terms of species plots in which reverse protonated charged nucleobases interact. These analyses uncover two surprising features of pH-dependent enzyme kinetics. (1) Cooperativity between the general acid and general base enhances population of the functional forms of a ribozyme and manifests itself as hidden or "dark" pK a shifts, real pK a shifts that accelerate the reaction but are not readily observed by standard experimental approaches, and (2) influencers favorably shift the pK a s of proton-transferring nucleobases and manifest themselves as "wavy" rate-pH profiles. We identify parallels with the protein enzyme literature, including reverse protonation and wavelike behavior, while pointing out that RNA is more prone to reverse protonation. The complexities uncovered, which arise from simple pairwise interactions, should aid deconvolution of complex rate-pH profiles for RNA and protein enzymes and suggest veiled catalytic devices for promoting catalysis that can be tested by experiment and calculation.

Comprehensive chemical characterization of industrial PM2.5 from steel industry activities

NASA Astrophysics Data System (ADS)

Sylvestre, Alexandre; Mizzi, Aurélie; Mathiot, Sébastien; Masson, Fanny; Jaffrezo, Jean L.; Dron, Julien; Mesbah, Boualem; Wortham, Henri; Marchand, Nicolas

2017-03-01

Industrial sources are among the least documented PM (Particulate Matter) source in terms of chemical composition, which limits our understanding of their effective impact on ambient PM concentrations. We report 4 chemical emission profiles of PM2.5 for multiple activities located in a vast metallurgical complex. Emissions profiles were calculated as the difference of species concentrations between an upwind and a downwind site normalized by the absolute PM2.5 enrichment between both sites. We characterized the PM2.5 emissions profiles of the industrial activities related to the cast iron (complex 1) and the iron ore conversion processes (complex 2), as well as 2 storage areas: a blast furnace slag area (complex 3) and an ore terminal (complex 4). PM2.5 major fractions (Organic Carbon (OC) and Elemental Carbon (EC), major ions), organic markers as well as metals/trace elements are reported for the 4 industrial complexes. Among the trace elements, iron is the most emitted for the complex 1 (146.0 mg g-1 of PM2.5), the complex 2 (70.07 mg g-1) and the complex 3 (124.4 mg g-1) followed by Al, Mn and Zn. A strong emission of Polycyclic Aromatic Hydrocarbons (PAH), representing 1.3% of the Organic Matter (OM), is observed for the iron ore transformation complex (complex 2) which merges the activities of coke and iron sinter production and the blast furnace processes. In addition to unsubstituted PAHs, sulfur containing PAHs (SPAHs) are also significantly emitted (between 0.011 and 0.068 mg g-1) by the complex 2 and could become very useful organic markers of steel industry activities. For the complexes 1 and 2 (cast iron and iron ore converters), a strong fraction of sulfate ranging from 0.284 to 0.336 g g-1) and only partially neutralized by ammonium, is observed indicating that sulfates, if not directly emitted by the industrial activity, are formed very quickly in the plume. Emission from complex 4 (Ore terminal) are characterized by high contribution of Al (125.7 mg g-1 of PM2.5) but also, in a lesser extent, of Fe, Mn, Ti and Zn. We also highlighted high contribution of calcium ranging from 0.123 to 0.558 g g-1 for all of the industrial complexes under study. Since calcium is also widely used as a proxy of the dust contributions in source apportionment studies, our results suggest that this assumption should be reexamined in environments impacted by industrial emissions.

Spectroscopic and Statistical Techniques for Information Recovery in Metabonomics and Metabolomics

NASA Astrophysics Data System (ADS)

Lindon, John C.; Nicholson, Jeremy K.

2008-07-01

Methods for generating and interpreting metabolic profiles based on nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), and chemometric analysis methods are summarized and the relative strengths and weaknesses of NMR and chromatography-coupled MS approaches are discussed. Given that all data sets measured to date only probe subsets of complex metabolic profiles, we describe recent developments for enhanced information recovery from the resulting complex data sets, including integration of NMR- and MS-based metabonomic results and combination of metabonomic data with data from proteomics, transcriptomics, and genomics. We summarize the breadth of applications, highlight some current activities, discuss the issues relating to metabonomics, and identify future trends.

Spectroscopic and statistical techniques for information recovery in metabonomics and metabolomics.

PubMed

Lindon, John C; Nicholson, Jeremy K

2008-01-01

Methods for generating and interpreting metabolic profiles based on nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), and chemometric analysis methods are summarized and the relative strengths and weaknesses of NMR and chromatography-coupled MS approaches are discussed. Given that all data sets measured to date only probe subsets of complex metabolic profiles, we describe recent developments for enhanced information recovery from the resulting complex data sets, including integration of NMR- and MS-based metabonomic results and combination of metabonomic data with data from proteomics, transcriptomics, and genomics. We summarize the breadth of applications, highlight some current activities, discuss the issues relating to metabonomics, and identify future trends.

Observation of atmospheric time variation of Mira stars using Interferometry

NASA Astrophysics Data System (ADS)

Lacour, S.; Perrin, G.; Haubois, X.; Meimon, S.; Monnier, J.; Berger, J. P.; Traub, W.; Schuller, P.

2006-08-01

Interferometric data of Mira type stars in the near-infrared have already produce radial visibility curves with a shape far from simple limb darkening profile. The measured visibilities as a function of wavelength revealed the presence in K band of a close ( at a ~ 1 stellar radius distance above the photosphere ) molecular layer. However, thanks to the phase closure and telescope mobility of the IOTA interferometer, we have now access to the two dimensional complex visibility profile. We will present the u-v plane of different Mira stars at different epochs, and we will discuss the problems and advantages of analyzing complex objects in the Fourier domain.

Mycobacterium tuberculosis RsdA provides a conformational rationale for selective regulation of σ-factor activity by proteolysis

PubMed Central

Jaiswal, Ravi K.; Prabha, Tangirala Surya; Manjeera, Gowravaram; Gopal, Balasubramanian

2013-01-01

The relative levels of different σ factors dictate the expression profile of a bacterium. Extracytoplasmic function σ factors synchronize the transcriptional profile with environmental conditions. The cellular concentration of free extracytoplasmic function σ factors is regulated by the localization of this protein in a σ/anti-σ complex. Anti-σ factors are multi-domain proteins with a receptor to sense environmental stimuli and a conserved anti-σ domain (ASD) that binds a σ factor. Here we describe the structure of Mycobacterium tuberculosis anti-σD (RsdA) in complex with the -35 promoter binding domain of σD (σD4). We note distinct conformational features that enable the release of σD by the selective proteolysis of the ASD in RsdA. The structural and biochemical features of the σD/RsdA complex provide a basis to reconcile diverse regulatory mechanisms that govern σ/anti-σ interactions despite high overall structural similarity. Multiple regulatory mechanisms embedded in an ASD scaffold thus provide an elegant route to rapidly re-engineer the expression profile of a bacterium in response to an environmental stimulus. PMID:23314154

An assessment of the information content of likelihood ratios derived from complex mixtures.

PubMed

Marsden, Clare D; Rudin, Norah; Inman, Keith; Lohmueller, Kirk E

2016-05-01

With the increasing sensitivity of DNA typing methodologies, as well as increasing awareness by law enforcement of the perceived capabilities of DNA typing, complex mixtures consisting of DNA from two or more contributors are increasingly being encountered. However, insufficient research has been conducted to characterize the ability to distinguish a true contributor (TC) from a known non-contributor (KNC) in these complex samples, and under what specific conditions. In order to investigate this question, sets of six 15-locus Caucasian genotype profiles were simulated and used to create mixtures containing 2-5 contributors. Likelihood ratios were computed for various situations, including varying numbers of contributors and unknowns in the evidence profile, as well as comparisons of the evidence profile to TCs and KNCs. This work was intended to illustrate the best-case scenario, in which all alleles from the TC were detected in the simulated evidence samples. Therefore the possibility of drop-out was not modeled in this study. The computer program DNAMIX was then used to compute LRs comparing the evidence profile to TCs and KNCs. This resulted in 140,000 LRs for each of the two scenarios. These complex mixture simulations show that, even when all alleles are detected (i.e. no drop-out), TCs can generate LRs less than 1 across a 15-locus profile. However, this outcome was rare, 7 of 140,000 replicates (0.005%), and associated only with mixtures comprising 5 contributors in which the numerator hypothesis includes one or more unknown contributors. For KNCs, LRs were found to be greater than 1 in a small number of replicates (75 of 140,000 replicates, or 0.05%). These replicates were limited to 4 and 5 person mixtures with 1 or more unknowns in the numerator. Only 5 of these 75 replicates (0.004%) yielded an LR greater than 1,000. Thus, overall, these results imply that the weight of evidence that can be derived from complex mixtures containing up to 5 contributors, under a scenario in which no drop-out is required to explain any of the contributors, is remarkably high. This is a useful benchmark result on top of which to layer the effects of additional factors, such as drop-out, peak height, and other variables. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Geoarchaeological research of the mid-age Ilyas Bey complex buildings with ground penetrating radar in Miletus, Aydin, Western Anatolia, Turkey

NASA Astrophysics Data System (ADS)

Kadioğlu, S.; Kadioğlu, Y. K.; Akyol, A. A.

2008-07-01

The ancient Miletus which were one of the most important city of ancient Iona, are today of great value from cultural standpoint of Turkey. Miletus, situated near the village of Balat in the present district of Soke was founded on a peninsula, approximately 2.5 km long. In the Byzantine period, the city boundaries were quite reduced. In 1424 Miletus was taken inside of the Ottoman Empire and was completely abandoned in the 17th century. Ancient Miletus excavation studies were first begun in 1899 by in Berlin Museum and interrupted during the World War I. At present, the extensive restoration works in Ilyas Bey Complex has applied as a project since 2006. Ilyas Bey Complex that includes Mosque, Medresah and baths situated on the archaeological area in ancient Miletus. Impressive Mosque built in 1404 by Ilyas Bey, Emir of Menteseogullari founded in 1279 and the complex was named after him, is one of the most remarkable buildings of mid-age Miletus. There are two main purposes of the study are (1) to determine archaeological remains of the study area underneath Ilyas Bey Complex and (2) to define the nature of main rock unit and their sources in the vicinity or Aegean region. After preliminary archaeometrical studies, acquired GPR profile data paralleled each other in Ilyas Bey Mosque and its around, Medresah Courtyard and inner Courtyard of the Mosque. After processing 2D parallel GPR profiles, we constructed 3D data volume by lining processed 2D profiles up to correlate remain signatures from each profile for each studied area. It was obtained transparent 3D visualisation of GPR data by assigning a new colour scale for the amplitude range and by constructing a new opacity function instead of the linear opacity function. Therefore we could successfully image the archaeological remains in an interactive transparent 3D volume and its sub-volumes, starting at different depth levels or limited profiles. The archaeometrical (geological and mineralogical, petrographical) studies reveal that the main bulding rock units of Ilyas Bey Mosque are mainly composed of 4 main units these are marble, metalimestone, mica gneiss and granodiorite. The marble, metalimestone with the mica gneiss were obtained from Menderes Massif in Western Anatolia. The granodiorite columns might be obtained from Kozak Pluton in the north of Bergama-Izmir line of western Anatolia.

Dissociation free-energy profiles of specific and nonspecific DNA-protein complexes.

PubMed

Yonetani, Yoshiteru; Kono, Hidetoshi

2013-06-27

DNA-binding proteins recognize DNA sequences with at least two different binding modes: specific and nonspecific. Experimental structures of such complexes provide us a static view of the bindings. However, it is difficult to reveal further mechanisms of their target-site search and recognition only from static information because the transition process between the bound and unbound states is not clarified by static information. What is the difference between specific and nonspecific bindings? Here we performed adaptive biasing force molecular dynamics simulations with the specific and nonspecific structures of DNA-Lac repressor complexes to investigate the dissociation process. The resultant free-energy profiles showed that the specific complex has a sharp, deep well consistent with tight binding, whereas the nonspecific complex has a broad, shallow well consistent with loose binding. The difference in the well depth, ~5 kcal/mol, was in fair agreement with the experimentally obtained value and was found to mainly come from the protein conformational difference, particularly in the C-terminal tail. Also, the free-energy profiles were found to be correlated with changes in the number of protein-DNA contacts and that of surface water molecules. The derived protein spatial distributions around the DNA indicate that any large dissociation occurs rarely, regardless of the specific and nonspecific sites. Comparison of the free-energy barrier for sliding [~8.7 kcal/mol; Furini J. Phys. Chem. B 2010, 114, 2238] and that for dissociation (at least ~16 kcal/mol) calculated in this study suggests that sliding is much preferred to dissociation.

Anxiety is not enough to drive me away: A latent profile analysis on math anxiety and math motivation.

PubMed

Wang, Zhe; Shakeshaft, Nicholas; Schofield, Kerry; Malanchini, Margherita

2018-01-01

Mathematics anxiety (MA) and mathematics motivation (MM) are important multi-dimensional non-cognitive factors in mathematics learning. While the negative relation between global MA and MM is well replicated, the relations between specific dimensions of MA and MM are largely unexplored. The present study utilized latent profile analysis to explore profiles of various aspects of MA (including learning MA and exam MA) and MM (including importance, self-perceived ability, and interest), to provide a more holistic understanding of the math-specific emotion and motivation experiences. In a sample of 927 high school students (13-21 years old), we found 8 distinct profiles characterized by various combinations of dimensions of MA and MM, revealing the complexity in the math-specific emotion-motivation relation beyond a single negative correlation. Further, these profiles differed on mathematics learning behaviors and mathematics achievement. For example, the highest achieving students reported modest exam MA and high MM, whereas the most engaged students were characterized by a combination of high exam MA and high MM. These results call for the need to move beyond linear relations among global constructs to address the complexity in the emotion-motivation-cognition interplay in mathematics learning, and highlight the importance of customized intervention for these heterogeneous groups.

Anxiety is not enough to drive me away: A latent profile analysis on math anxiety and math motivation

PubMed Central

Shakeshaft, Nicholas; Schofield, Kerry; Malanchini, Margherita

2018-01-01

Mathematics anxiety (MA) and mathematics motivation (MM) are important multi-dimensional non-cognitive factors in mathematics learning. While the negative relation between global MA and MM is well replicated, the relations between specific dimensions of MA and MM are largely unexplored. The present study utilized latent profile analysis to explore profiles of various aspects of MA (including learning MA and exam MA) and MM (including importance, self-perceived ability, and interest), to provide a more holistic understanding of the math-specific emotion and motivation experiences. In a sample of 927 high school students (13–21 years old), we found 8 distinct profiles characterized by various combinations of dimensions of MA and MM, revealing the complexity in the math-specific emotion-motivation relation beyond a single negative correlation. Further, these profiles differed on mathematics learning behaviors and mathematics achievement. For example, the highest achieving students reported modest exam MA and high MM, whereas the most engaged students were characterized by a combination of high exam MA and high MM. These results call for the need to move beyond linear relations among global constructs to address the complexity in the emotion-motivation-cognition interplay in mathematics learning, and highlight the importance of customized intervention for these heterogeneous groups. PMID:29444137

Lung tumor diagnosis and subtype discovery by gene expression profiling.

PubMed

Wang, Lu-yong; Tu, Zhuowen

2006-01-01

The optimal treatment of patients with complex diseases, such as cancers, depends on the accurate diagnosis by using a combination of clinical and histopathological data. In many scenarios, it becomes tremendously difficult because of the limitations in clinical presentation and histopathology. To accurate diagnose complex diseases, the molecular classification based on gene or protein expression profiles are indispensable for modern medicine. Moreover, many heterogeneous diseases consist of various potential subtypes in molecular basis and differ remarkably in their response to therapies. It is critical to accurate predict subgroup on disease gene expression profiles. More fundamental knowledge of the molecular basis and classification of disease could aid in the prediction of patient outcome, the informed selection of therapies, and identification of novel molecular targets for therapy. In this paper, we propose a new disease diagnostic method, probabilistic boosting tree (PB tree) method, on gene expression profiles of lung tumors. It enables accurate disease classification and subtype discovery in disease. It automatically constructs a tree in which each node combines a number of weak classifiers into a strong classifier. Also, subtype discovery is naturally embedded in the learning process. Our algorithm achieves excellent diagnostic performance, and meanwhile it is capable of detecting the disease subtype based on gene expression profile.

High-resolution proteomic profiling of spider venom: expanding the toxin diversity of Phoneutria nigriventer venom.

PubMed

Liberato, Tarcísio; Troncone, Lanfranco Ranieri Paolo; Yamashiro, Edson T; Serrano, Solange M T; Zelanis, André

2016-03-01

Here we present a proteomic characterization of Phoneutria nigriventer venom. A shotgun proteomic approach allowed the identification, for the first time, of O-glycosyl hydrolases (chitinases) in P. nigriventer venom. The electrophoretic profiles under nonreducing and reducing conditions, and protein identification by mass spectrometry, indicated the presence of oligomeric toxin structures in the venom. Complementary proteomic approaches allowed for a qualitative and semi-quantitative profiling of P. nigriventer venom complexity, expanding its known venom proteome diversity.

Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles

PubMed Central

Brender, Jeffrey R.; Zhang, Yang

2015-01-01

The formation of protein-protein complexes is essential for proteins to perform their physiological functions in the cell. Mutations that prevent the proper formation of the correct complexes can have serious consequences for the associated cellular processes. Since experimental determination of protein-protein binding affinity remains difficult when performed on a large scale, computational methods for predicting the consequences of mutations on binding affinity are highly desirable. We show that a scoring function based on interface structure profiles collected from analogous protein-protein interactions in the PDB is a powerful predictor of protein binding affinity changes upon mutation. As a standalone feature, the differences between the interface profile score of the mutant and wild-type proteins has an accuracy equivalent to the best all-atom potentials, despite being two orders of magnitude faster once the profile has been constructed. Due to its unique sensitivity in collecting the evolutionary profiles of analogous binding interactions and the high speed of calculation, the interface profile score has additional advantages as a complementary feature to combine with physics-based potentials for improving the accuracy of composite scoring approaches. By incorporating the sequence-derived and residue-level coarse-grained potentials with the interface structure profile score, a composite model was constructed through the random forest training, which generates a Pearson correlation coefficient >0.8 between the predicted and observed binding free-energy changes upon mutation. This accuracy is comparable to, or outperforms in most cases, the current best methods, but does not require high-resolution full-atomic models of the mutant structures. The binding interface profiling approach should find useful application in human-disease mutation recognition and protein interface design studies. PMID:26506533

The influence of temperament and character profiles on specialty choice and well-being in medical residents

PubMed Central

Sievert, Martin; Zwir, Igor; Cloninger, Kevin M.; Lester, Nigel; Rozsa, Sandor

2016-01-01

Background Multiple factors influence the decision to enter a career in medicine and choose a specialty. Previous studies have looked at personality differences in medicine but often were unable to describe the heterogeneity that exists within each specialty. Our study used a person-centered approach to characterize the complex relations between the personality profiles of resident physicians and their choice of specialty. Methods 169 resident physicians at a large Midwestern US training hospital completed the Temperament and Character Inventory (TCI) and the Satisfaction with Life Scale (SWLS). Clusters of personality profiles were identified without regard to medical specialty, and then the personality clusters were tested for association with their choice of specialty by co-clustering analysis. Life satisfaction was tested for association with personality traits and medical specialty by linear regression and analysis of variance. Results We identified five clusters of people with distinct personality profiles, and found that these were associated with particular medical specialties Physicians with an “investigative” personality profile often chose pathology or internal medicine, those with a “commanding” personality often chose general surgery, “rescuers” often chose emergency medicine, the “dependable” often chose pediatrics, and the “compassionate” often chose psychiatry. Life satisfaction scores were not enhanced by personality-specialty congruence, but were related strongly to self-directedness regardless of specialty. Conclusions The personality profiles of physicians were strongly associated with their medical specialty choices. Nevertheless, the relationships were complex: physicians with each personality profile went into a variety of medical specialties, and physicians in each medical specialty had variable personality profiles. The plasticity and resilience of physicians were more important for their life satisfaction than was matching personality to the prototype of a particular specialty. PMID:27651982

Old worries and new anxieties: behavioral symptoms and mild cognitive impairment in a population study.

PubMed

Andreescu, Carmen; Teverovsky, Esther; Fu, Bo; Hughes, Tiffany F; Chang, Chung-Chou H; Ganguli, Mary

2014-03-01

To disentangle the complex associations of depression and anxiety with mild cognitive impairment (MCI) at the population level. We examined subgroups of anxiety symptoms and depression symptom profiles in relation to MCI, which we defined using both cognitive and functional approaches. We used an epidemiologic, cross-sectional study with an age-stratified, random, population-based sample of 1,982 individuals aged 65 years and over. Three definitions of MCI were used: 1) a purely cognitive classification into amnestic and nonamnestic MCI, 2) a combined cognitive-functional definition by International Working Group (IWG) criteria, and 3) a purely functional definition by the Clinical Dementia Rating (CDR) of 0.5. Three depression profiles were identified by factor analysis of the modified Center for Epidemiological Studies-Depression Scale: core mood, self-esteem/interpersonal, and apathy/neurovegetative profiles. Three anxiety groups, chronic mild worry, chronic severe anxiety, and recent-onset anxiety, were based on screening questions. Recent-onset anxiety was associated with MCI by nonamnestic and IWG criteria, chronic severe anxiety was associated with MCI by all definitions, and chronic mild worry was associated with none. Of the depression profiles, the core mood profile was associated with CDR-defined MCI, the apathy/neurovegetative profile was associated with MCI by amnestic, IWG, and CDR definitions, and the self-esteem/interpersonal profile was associated with none. In this population-based sample, subgroups with different anxiety and depression profiles had different relationships with cognitive and functional definitions of MCI. Anxiety, depression, and MCI are all multidimensional entities, interacting in complex ways that may shed light on underlying neural mechanisms. Copyright © 2014 American Association for Geriatric Psychiatry. Published by Elsevier Inc. All rights reserved.

Measurements of thermal updraft intensity over complex terrain using American white pelicans and a simple boundary-layer forecast model

USGS Publications Warehouse

Shannon, H.D.; Young, G.S.; Yates, M.; Fuller, Mark R.; Seegar, W.

2003-01-01

An examination of boundary-layer meteorological and avian aerodynamic theories suggests that soaring birds can be used to measure the magnitude of vertical air motions within the boundary layer. These theories are applied to obtain mixed-layer normalized thermal updraft intensity over both flat and complex terrain from the climb rates of soaring American white pelicans and from diagnostic boundary-layer model-produced estimates of the boundary-layer depth zi and the convective velocity scale w*. Comparison of the flatland data with the profiles of normalized updraft velocity obtained from previous studies reveals that the pelican-derived measurements of thermal updraft intensity are in close agreement with those obtained using traditional research aircraft and large eddy simulation (LES) in the height range of 0.2 to 0.8 zi. Given the success of this method, the profiles of thermal vertical velocity over the flatland and the nearby mountains are compared. This comparison shows that these profiles are statistically indistinguishable over this height range, indicating that the profile for thermal updraft intensity varies little over this sample of complex terrain. These observations support the findings of a recent LES study that explored the turbulent structure of the boundary layer using a range of terrain specifications. For terrain similar in scale to that encountered in this study, results of the LES suggest that the terrain caused less than an 11% variation in the standard deviation of vertical velocity.

Near-surface structure of the Central Scandinavian Caledonides in northern Trøndelag, Norway, from correlation of seismic and MT profiles using gravity and magnetic data

NASA Astrophysics Data System (ADS)

Ebbing, J.; Goerigk, L.; Nasuti, A.; Roberts, D.; Korja, T. J.; Smirnov, M.

2014-12-01

The deep geology of northern Trøndelag is somewhat speculative as the Central Scandinavian Caledonides are intersected by the Møre-Trøndelag Fault Complex (MTFC) and only a few depth-penetrating geophysical profiles exist. Here, we correlate the mapped geological units and faults between a seismic-reflection profile and a MT profile. The seismic-reflection data were acquired in 5 segments over the period 1986-1990. The westernmost section of the seismic profile is dominated by a complex pattern of reflections and diffractions. This type of pattern is typical of polydeformed terranes with a mixture of contrasting felsic and mafic lithologies. The two steeply-dipping strands of the MTFC (Hitra-Snåsa and Verran faults) that transect the profile do not show any distinctive signature in the seismic data. The MT data were acquired in 2007 from the Swedish border to the Norwegian coast. The conductivity profile shows some distinct vertical changes as well as changes from the near-surface to shallow depths. The strands of the MTFC show especially a distinctive change in conductivity. The two profiles are almost parallel but separated by 100 km. To correlate the structures seen on both profiles, we have applied lineament analysis and 3D modelling of the gravity and magnetic field. The tilt derivative of the magnetic and isostatic gravity anomaly clearly allows us to identify and link the main geological boundaries between the profiles and to trace the strands of the MTFC from one profile to the other. This trend analysis indicates that at least the Verran Fault visibly modifies the pattern of seismic reflections. However, the main change in crustal lithology occurs farther to the west, almost at the coast where the Tarva Fault intersects the MT profile. This integrated analysis shows the benefit of combining gravity and magnetic interpretations with MT and seismic data to enable us to understand the near-surface geology and structure in more detail.

A Latent Profile Analysis of Math Achievement, Numerosity, and Math Anxiety in Twins

ERIC Educational Resources Information Center

Hart, Sara A.; Logan, Jessica A. R.; Thompson, Lee; Kovas, Yulia; McLoughlin, Gráinne; Petrill, Stephen A.

2016-01-01

Underperformance in math is a problem with increasing prevalence, complex etiology, and severe repercussions. This study examined the etiological heterogeneity of math performance in a sample of 264 pairs of 12-year-old twins assessed on measures of math achievement, numerosity, and math anxiety. Latent profile analysis indicated 5 groupings of…

Profile-Likelihood Approach for Estimating Generalized Linear Mixed Models with Factor Structures

ERIC Educational Resources Information Center

Jeon, Minjeong; Rabe-Hesketh, Sophia

2012-01-01

In this article, the authors suggest a profile-likelihood approach for estimating complex models by maximum likelihood (ML) using standard software and minimal programming. The method works whenever setting some of the parameters of the model to known constants turns the model into a standard model. An important class of models that can be…

Nonstandard Career Paths and Profiles of Commitment to Life Roles: A Complex Relation

ERIC Educational Resources Information Center

Fournier, Genevieve; Lachance, Lise; Bujold, Charles

2009-01-01

The career paths (ascending, interesting, uninteresting, descending) of 124 White Canadian francophones (62 men, 62 women) who had experienced nonstandard and precarious work for the last three years were examined in relation to the participants' profiles of commitment to three life roles (work, family, and duality, that is, investment in both…

Electro-Optical Design for Efficient Visual Communication

NASA Technical Reports Server (NTRS)

Huck, Friedrich O.; Fales, Carl L.; Jobson, Daniel J.; Rahman, Zia-Ur

1995-01-01

Visual communication, in the form of telephotography and television, for example, can be regarded as efficient only if the amount of information that it conveys about the scene to the observer approaches the maximum possible and the associated cost approaches the minimum possible. Elsewhere we have addressed the problem of assessing the end to end performance of visual communication systems in terms of their efficiency in this sense by integrating the critical limiting factors that constrain image gathering into classical communications theory. We use this approach to assess the electro-optical design of image gathering devices as a function of the f number and apodization of the objective lens and the aperture size and sampling geometry of the phot-detection mechanism. Results show that an image gathering device that is designed to optimize information capacity performs similarly to the human eye. For both, the performance approaches the maximum possible, in terms of the efficiency with which the acquired information can be transmitted as decorrelated data, and the fidelity, sharpness, and clearity with which fine detail can be restored.

An active coronagraph using a liquid crystal array for exoplanet imaging: principle and testing

NASA Astrophysics Data System (ADS)

Zhang, Xi; Ren, De-Qing; Zhu, Yong-Tian; Dou, Jiang-Pei

2012-05-01

High-contrast imaging coronagraphs, used for the detection of exoplanets, have always adopted passive coronagraph optical components. It is therefore impossible to actively optimize the coronagraphs to achieve their best performance. To solve this problem, we propose a novel high-contrast imaging coronagraph which combines a liquid crystal array (LCA) for active pupil apodization and a deformable mirror (DM) for phase correction. The LCA we use is an amplitude-only spatial light modulator. The LCA is well calibrated and compensates for its amplitude non-uniformity and nonlinear intensity responsivity. We measured the imaging contrasts of the coronagraph system with the LCA only and without the DM deployed. Imaging contrasts of 10-4 and 10-5 can be reached at an inner working angular distance of 2.5 and 5λ/D, respectively. A simulation shows that the phase errors on the coronagraph pupil limit the contrast performance. The contrast could be further improved if a DM is deployed to correct the phase errors induced by the LCA and coronagraph optics.

Defocus-corrected analysis of the foveal Stiles-Crawford effect of the first kind across the visible spectrum

NASA Astrophysics Data System (ADS)

Lochocki, Benjamin; Vohnsen, Brian

2013-12-01

The Stiles-Crawford effect of the first kind describes a gradually diminished visibility of light that enters the eye towards the pupil rim. Although of retinal origin, it is commonly described by a Gaussian pupil apodization whose width is determined by a directionality parameter that depends on retinal eccentricity, wavelength and spatial coherence of the light. As the measurements are done psychophysically they are prone to subjective variations and difficult to obtain across the visible spectrum. In this work, requirements for accurate refractive correction when determining the directionality parameter at any given wavelength are discussed and we show that a current-controlled tunable liquid-polymer lens provides a convenient means to accomplish this without requiring mechanical readjustments. This may be the most convenient way to combat defocus across the visible spectrum in the analysis of the Stiles-Crawford effect as demonstrated through experiments and with a detailed Zemax eye-and-system analysis. The results obtained are discussed in relation to myopia and a reduced directionality for highly myopic eyes.

Cloud cover typing from environmental satellite imagery. Discriminating cloud structure with Fast Fourier Transforms (FFT)

NASA Technical Reports Server (NTRS)

Logan, T. L.; Huning, J. R.; Glackin, D. L.

1983-01-01

The use of two dimensional Fast Fourier Transforms (FFTs) subjected to pattern recognition technology for the identification and classification of low altitude stratus cloud structure from Geostationary Operational Environmental Satellite (GOES) imagery was examined. The development of a scene independent pattern recognition methodology, unconstrained by conventional cloud morphological classifications was emphasized. A technique for extracting cloud shape, direction, and size attributes from GOES visual imagery was developed. These attributes were combined with two statistical attributes (cloud mean brightness, cloud standard deviation), and interrogated using unsupervised clustering amd maximum likelihood classification techniques. Results indicate that: (1) the key cloud discrimination attributes are mean brightness, direction, shape, and minimum size; (2) cloud structure can be differentiated at given pixel scales; (3) cloud type may be identifiable at coarser scales; (4) there are positive indications of scene independence which would permit development of a cloud signature bank; (5) edge enhancement of GOES imagery does not appreciably improve cloud classification over the use of raw data; and (6) the GOES imagery must be apodized before generation of FFTs.

Design and performance evaluation of a dispersion compensation unit using several chirping functions in a tanh apodized FBG and comparison with dispersion compensation fiber.

PubMed

Mohammed, Nazmi A; Solaiman, Mohammad; Aly, Moustafa H

2014-10-10

In this work, various dispersion compensation methods are designed and evaluated to search for a cost-effective technique with remarkable dispersion compensation and a good pulse shape. The techniques consist of different chirp functions applied to a tanh fiber Bragg grating (FBG), a dispersion compensation fiber (DCF), and a DCF merged with an optimized linearly chirped tanh FBG (joint technique). The techniques are evaluated using a standard 10 Gb/s optical link over a 100 km long haul. The linear chirp function is the most appropriate choice of chirping function, with a pulse width reduction percentage (PWRP) of 75.15%, lower price, and poor pulse shape. The DCF yields an enhanced PWRP of 93.34% with a better pulse quality; however, it is the most costly of the evaluated techniques. Finally, the joint technique achieved the optimum PWRP (96.36%) among all the evaluated techniques and exhibited a remarkable pulse shape; it is less costly than the DCF, but more expensive than the chirped tanh FBG.

Comparative analysis of imaging configurations and objectives for Fourier microscopy.

PubMed

Kurvits, Jonathan A; Jiang, Mingming; Zia, Rashid

2015-11-01

Fourier microscopy is becoming an increasingly important tool for the analysis of optical nanostructures and quantum emitters. However, achieving quantitative Fourier space measurements requires a thorough understanding of the impact of aberrations introduced by optical microscopes that have been optimized for conventional real-space imaging. Here we present a detailed framework for analyzing the performance of microscope objectives for several common Fourier imaging configurations. To this end, we model objectives from Nikon, Olympus, and Zeiss using parameters that were inferred from patent literature and confirmed, where possible, by physical disassembly. We then examine the aberrations most relevant to Fourier microscopy, including the alignment tolerances of apodization factors for different objective classes, the effect of magnification on the modulation transfer function, and vignetting-induced reductions of the effective numerical aperture for wide-field measurements. Based on this analysis, we identify an optimal objective class and imaging configuration for Fourier microscopy. In addition, the Zemax files for the objectives and setups used in this analysis have been made publicly available as a resource for future studies.

Electromagnetic Design of a Magnetically-Coupled Spatial Power Combiner

NASA Technical Reports Server (NTRS)

Bulcha, B.; Cataldo, G.; Stevenson, T. R.; U-Yen, K.; Moseley, S. H.; Wollack, E. J.

2017-01-01

The design of a two-dimensional beam-combining network employing a parallel-plate superconducting waveguide with a mono-crystalline silicon dielectric is presented. This novel beam-combining network structure employs an array of magnetically coupled antenna elements to achieve high coupling efficiency and full sampling of the intensity distribution while avoiding diffractive losses in the multi-mode region defined by the parallel-plate waveguide. These attributes enable the structures use in realizing compact far-infrared spectrometers for astrophysical and instrumentation applications. When configured with a suitable corporate-feed power-combiner, this fully sampled array can be used to realize a low-sidelobe apodized response without incurring a reduction in coupling efficiency. To control undesired reflections over a wide range of angles in the finite-sized parallel-plate waveguide region, a wideband meta-material electromagnetic absorber structure is implemented. This adiabatic structure absorbs greater than 99 of the power over the 1.7:1 operational band at angles ranging from normal (0 degree) to near parallel (180 degree) incidence. Design, simulations, and application of the device will be presented.

Optimal apodization design for medical ultrasound using constrained least squares part I: theory.

PubMed

Guenther, Drake A; Walker, William F

2007-02-01

Aperture weighting functions are critical design parameters in the development of ultrasound systems because beam characteristics affect the contrast and point resolution of the final output image. In previous work by our group, we developed a metric that quantifies a broadband imaging system's contrast resolution performance. We now use this metric to formulate a novel general ultrasound beamformer design method. In our algorithm, we use constrained least squares (CLS) techniques and a linear algebra formulation to describe the system point spread function (PSF) as a function of the aperture weightings. In one approach, we minimize the energy of the PSF outside a certain boundary and impose a linear constraint on the aperture weights. In a second approach, we minimize the energy of the PSF outside a certain boundary while imposing a quadratic constraint on the energy of the PSF inside the boundary. We present detailed analysis for an arbitrary ultrasound imaging system and discuss several possible applications of the CLS techniques, such as designing aperture weightings to maximize contrast resolution and improve the system depth of field.

Rovibrational Analysis of ν 2 and 2ν 5 Bands of DCOOH by High Resolution FTIR Spectroscopy

NASA Astrophysics Data System (ADS)

Tan, T. L.; Goh, K. L.; Ong, P. P.; Teo, H. H.

1999-12-01

The infrared absorption spectrum of the ν2 band of deuterated formic acid (DCOOH) was recorded using a Bomem DA3.002 Fourier transform spectrometer in the wavenumber region 2130-2300 cm-1 with an apodized resolution of 0.004 cm-1. A total of 1024 transitions were assigned to this band which is hybrid type A and B, centered at 2219.6896 ± 0.0002 cm-1. As expected, the ν2 band is coupled to 2ν5 by a c-type Coriolis interaction. Both perturbed and unperturbed transitions were assigned and fitted to give seven rovibrational constants for the ν2 = 1 state with a standard deviation of 0.00094 cm-1 using Watson's A-reduced Hamiltonian in the Ir representation. A c-type Coriolis interaction term between ν2 and 2ν5 was derived from the rovibrational analysis. The ratio of the transition moments, ‖μb/μa‖, was found to be 1.42 ± 0.10 for the hybrid band.

Using redundancy of round-trip ultrasound signal for non-continuous arrays: Application to gap and blockage compensation.

PubMed

Robert, Jean-Luc; Erkamp, Ramon; Korukonda, Sanghamithra; Vignon, François; Radulescu, Emil

2015-11-01

In ultrasound imaging, an array of elements is used to image a medium. If part of the array is blocked by an obstacle, or if the array is made from several sub-arrays separated by a gap, grating lobes appear and the image is degraded. The grating lobes are caused by missing spatial frequencies, corresponding to the blocked or non-existing elements. However, in an active imaging system, where elements are used both for transmitting and receiving, the round trip signal is redundant: different pairs of transmit and receive elements carry similar information. It is shown here that, if the gaps are smaller than the active sub-apertures, this redundancy can be used to compensate for the missing signals and recover full resolution. Three algorithms are proposed: one is based on a synthetic aperture method, a second one uses dual-apodization beamforming, and the third one is a radio frequency (RF) data based deconvolution. The algorithms are evaluated on simulated and experimental data sets. An application could be imaging through ribs with a large aperture.

Electro-optical design for efficient visual communication

NASA Astrophysics Data System (ADS)

Huck, Friedrich O.; Fales, Carl L.; Jobson, Daniel J.; Rahman, Zia-ur

1995-03-01

Visual communication, in the form of telephotography and television, for example, can be regarded as efficient only if the amount of information that it conveys about the scene to the observer approaches the maximum possible and the associated cost approaches the minimum possible. Elsewhere we have addressed the problem of assessing the end-to-end performance of visual communication systems in terms of their efficiency in this sense by integrating the critical limiting factors that constrain image gathering into classical communication theory. We use this approach to assess the electro-optical design of image-gathering devices as a function of the f number and apodization of the objective lens and the aperture size and sampling geometry of the photodetection mechanism. Results show that an image-gathering device that is designed to optimize information capacity performs similarly to the human eye. For both, the performance approaches the maximum possible, in terms of the efficiency with which the acquired information can be transmitted as decorrelated data, and the fidelity, sharpness, and clarity with which fine detail can be restored.

Jovian Planet Finder optical system

NASA Astrophysics Data System (ADS)

Krist, John E.; Clampin, Mark; Petro, Larry; Woodruff, Robert A.; Ford, Holland C.; Illingworth, Garth D.; Ftaclas, Christ

2003-02-01

The Jovian Planet Finder (JPF) is a proposed NASA MIDEX mission to place a highly optimized coronagraphic telescope on the International Space Station (ISS) to image Jupiter-like planets around nearby stars. The optical system is an off-axis, unobscured telescope with a 1.5 m primary mirror. A classical Lyot coronagraph with apodized occulting spots is used to reduce diffracted light from the central star. In order to provide the necessary contrast for detection of a planet, scattered light from mid-spatial-frequency errors is reduced by using super-smooth optics. Recent advances in polishing optics for extreme-ultraviolet lithography have shown that a factor of >30 reduction in midfrequency errors relative to those in the Hubble Space Telescope is possible (corresponding to a reduction in scattered light of nearly 1000x). The low level of scattered and diffracted light, together with a novel utilization of field rotation introduced by the alt-azimuth ISS telescope mounting, will provide a relatively low-cost facility for not only imaging extrasolar planets, but also circumstellar disks, host galaxies of quasars, and low-mass substellar companions such as brown dwarfs.

Intercomparison of 7 Planetary Boundary-Layer/Surface-Layer Physics Schemes over Complex Terrain for Battlefield Situational Awareness

DTIC Science & Technology

This study considers the performance of 7 of the Weather Research and Forecast model boundary-layer (BL) parameterization schemes in a complex...schemes performed best. The surface parameters, planetary BL structure, and vertical profiles are important for US Army Research Laboratory

Determination of ground structures of the Suleymaniye complex and the Selimiye madrasa with GPR in Damaskus-Syria

NASA Astrophysics Data System (ADS)

Kadioglu, Selma; Kadioglu, Yusuf K.

2010-05-01

Suleymaniye complex located on the banks of the Barada River was built by Sultan Suleyman I of the Ottoman Empire or Suleiman the Magnificent (1520-1566) between 1554 and 1560, locally known as the Takiyya. This complex represents a direct implantation of architectural style of the Ottoman capital, Istanbul, in the plan of its buildings with their exterior configurations and decorative features. Its main part composes of a mosque, caravanserai, public kitchen and hospice, was designed by Sinan (the 'Great Architect Sinan'), In 1566 a madrasa including a mosque called Selimiye Madrasa was added to the East of the group of buildings by Selim II (1566-1574) of the Ottoman Empire and was linked to the Suleymaniye complex by a souk (arasta). Basic elements of architectural iconography of the complex and the madrasa are hemispherical lead-covered dome, cylindrical minaret, domed portico, courtyard, a large regtangular pool in the courtyard. First restoration was done in the mosque during French occupation in Syria. But then the dome was inclined about 56 cm in 1920. The second restoration was done and the colons were fastened by hawsers to avoid collapsing of the dome in 1928. The network of the drainage around the complex has been changed 25 years ago. After 5 years passed, according to the Syrian engineers saying, the first subsidence deformations have started on the courtyards and the porticos surface and some fractures have been occupied on the wall of the buildings of the madrasa and the Suleymaniye complex. Now these subsidences threaten the madrasa. The aim of the study was to determine the reason of the subsidences in the courtyards especially in the madrasa. Therefore ground penetrating radar (GPR) method was used to reveal ground structure of the whole complex, to determine buried drainage locations, and In addition to research basement of the Suleymaniye mosque. Two dimensional (2D) GPR data were acquired on the parallel GPR profiles on the courtyards around of the pools in the Selimiye madrasa and Suleymaniye complex, arasta, and some special areas around the complex using 500 MHz shielded antennas. Secondly, the GPR data measurements were also carried out on spaced 1 m parallel profiles in the Suleymaniye mosque. The results showed that the first very shallow ductile layer was approximately 1 m thick and included some water pipes or drain pipes. The second layer was until 2.5 m depth and included buried human made structures in the Suleymaniye courtyard. They could be restoration traces in the early time or could be archaeological remains. The third layer was a more compact layer seen until the end of profile sections. However, it was seen on the profile section that third layer included more effective vertical fracture groups and some of them reached to the surface in the courtyard and the portico of the Selimiye madrasa. This result could be the reason of the deformation in the courtyard and the portico. There was no important anomaly in the profile sections of the Suleymaniye mosque to find the reason of the fractures on its dome. This study were supported by Turkish International Cooperation and Development Acency (TIKA) and Earth Sciences Application and Research Center of Ankara University (YEBIM).

Ray Meta: scalable de novo metagenome assembly and profiling

PubMed Central

2012-01-01

Voluminous parallel sequencing datasets, especially metagenomic experiments, require distributed computing for de novo assembly and taxonomic profiling. Ray Meta is a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers. It can accurately assemble and profile a three billion read metagenomic experiment representing 1,000 bacterial genomes of uneven proportions in 15 hours with 1,024 processor cores, using only 1.5 GB per core. The software will facilitate the processing of large and complex datasets, and will help in generating biological insights for specific environments. Ray Meta is open source and available at http://denovoassembler.sf.net. PMID:23259615

Nutritional metabolomics: Progress in addressing complexity in diet and health

PubMed Central

Jones, Dean P.; Park, Youngja; Ziegler, Thomas R.

2013-01-01

Nutritional metabolomics is rapidly maturing to use small molecule chemical profiling to support integration of diet and nutrition in complex biosystems research. These developments are critical to facilitate transition of nutritional sciences from population-based to individual-based criteria for nutritional research, assessment and management. This review addresses progress in making these approaches manageable for nutrition research. Important concept developments concerning the exposome, predictive health and complex pathobiology, serve to emphasize the central role of diet and nutrition in integrated biosystems models of health and disease. Improved analytic tools and databases for targeted and non-targeted metabolic profiling, along with bioinformatics, pathway mapping and computational modeling, are now used for nutrition research on diet, metabolism, microbiome and health associations. These new developments enable metabolome-wide association studies (MWAS) and provide a foundation for nutritional metabolomics, along with genomics, epigenomics and health phenotyping, to support integrated models required for personalized diet and nutrition forecasting. PMID:22540256

Patterns of neighborhood environment attributes in relation to children's physical activity.

PubMed

Kurka, Jonathan M; Adams, Marc A; Todd, Michael; Colburn, Trina; Sallis, James F; Cain, Kelli L; Glanz, Karen; Frank, Lawrence D; Saelens, Brian E

2015-07-01

Characterizing neighborhood environments in relation to physical activity is complex. Latent profiles of parents' perceptions of neighborhood characteristics were examined in relation to accelerometer-measured moderate-to-vigorous physical activity (MVPA) among 678 children (ages 6-12) in two US regions. Neighborhood environment profiles derived from walkability, transit access, aesthetics, crime and traffic safety, pedestrian infrastructure, and recreation/park access were created for each region. The San Diego County profile lowest on walkability and recreation/park access was associated with an average of 13 fewer min/day of children's out-of-school MVPA compared to profiles higher on walkability and recreation/park access. Seattle/King County profiles did not differ on children's MVPA. Neighborhood environment profiles were associated with children's MVPA in one region, but results were inconsistent across regions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Growth mechanisms of MgO nanocrystals via a sol-gel synthesis using different complexing agents

PubMed Central

2014-01-01

In the preparation of nanostructured materials, it is important to optimize synthesis parameters in order to obtain the desired material. This work investigates the role of complexing agents, oxalic acid and tartaric acid, in the production of MgO nanocrystals. Results from simultaneous thermogravimetric analysis (STA) show that the two different synthesis routes yield precursors with different thermal profiles. It is found that the thermal profiles of the precursors can reveal the effects of crystal growth during thermal annealing. X-ray diffraction confirms that the final products are pure, single phase and of cubic shape. It is also found that complexing agents can affect the rate of crystal growth. The structures of the oxalic acid and tartaric acid as well as the complexation sites play very important roles in the formation of the nanocrystals. The complexing agents influence the rate of growth which affects the final crystallite size of the materials. Surprisingly, it is also found that oxalic acid and tartaric acid act as surfactants inhibiting crystal growth even at a high temperature of 950°C and a long annealing time of 36 h. The crystallite formation routes are proposed to be via linear and branched polymer networks due to the different structures of the complexing agents. PMID:24650322

Make It Short and Easy: Username Complexity Determines Trustworthiness Above and Beyond Objective Reputation

PubMed Central

Silva, Rita R.; Chrobot, Nina; Newman, Eryn; Schwarz, Norbert; Topolinski, Sascha

2017-01-01

Can the mere name of a seller determine his trustworthiness in the eye of the consumer? In 10 studies (total N = 608) we explored username complexity and trustworthiness of eBay seller profiles. Name complexity was manipulated through variations in username pronounceability and length. These dimensions had strong, independent effects on trustworthiness, with sellers with easy-to-pronounce or short usernames being rated as more trustworthy than sellers with difficult-to-pronounce or long usernames, respectively. Both effects were repeatedly found even when objective information about seller reputation was available. We hypothesized the effect of name complexity on trustworthiness to be based on the experience of high vs. low processing fluency, with little awareness of the underlying process. Supporting this, participants could not correct for the impact of username complexity when explicitly asked to do so. Three alternative explanations based on attributions of the variations in name complexity to seller origin (ingroup vs. outgroup), username generation method (seller personal choice vs. computer algorithm) and age of the eBay profiles (10 years vs. 1 year) were tested and ruled out. Finally, we show that manipulating the ease of reading product descriptions instead of the sellers’ names also impacts the trust ascribed to the sellers. PMID:29312062

Solubility profiles, hydration and desolvation of curcumin complexed with γ-cyclodextrin and hydroxypropyl-γ-cyclodextrin

NASA Astrophysics Data System (ADS)

Shityakov, Sergey; Salmas, Ramin Ekhteiari; Durdagi, Serdar; Roewer, Norbert; Förster, Carola; Broscheit, Jens

2017-04-01

In this study, we investigated curcumin (CUR) solubility profiles and hydration/desolvation effects of this substance formulated with γ-cyclodextrin (γ-CD) and hydroxypropyl-γ-cyclodextrin (HP-γ-CD) excipients. The CUR/HP-γ-CD complex was found to be more stable in solution with the highest apparent stability constant for CUR/HP-γ-CD (Kc = 1.58*104 M-1) as the more soluble form in distilled water. The in silico calculations, including molecular docking, Monte Carlo (MC), and molecular dynamics (MD) simulations, indicated that water molecules play an important role in host-guest complexation mediating the CUR binding to cyclodextrins via hydrogen bond formations. The CUR hydration/desolvation effects contributed to the complex formation by elevating the CUR binding affinity to both CDs. The CUR/HP-γ-CD complex after the CUR hydration was determined with a minimal Gibbs free energy of binding (ΔGbind = -9.93 kcal*mol-1) due to the major hydrophobic (vdW) forces. Overall, the results of this study can aid a development of cyclodextrin-based drug delivery vectors, signifying the importance of water molecules during the formulation processes.

Approximate Stokes Drift Profiles and their use in Ocean Modelling

NASA Astrophysics Data System (ADS)

Breivik, Oyvind; Bidlot, Jea-Raymond; Janssen, Peter A. E. M.; Mogensen, Kristian

2016-04-01

Deep-water approximations to the Stokes drift velocity profile are explored as alternatives to the monochromatic profile. The alternative profiles investigated rely on the same two quantities required for the monochromatic profile, viz the Stokes transport and the surface Stokes drift velocity. Comparisons against parametric spectra and profiles under wave spectra from the ERA-Interim reanalysis and buoy observations reveal much better agreement than the monochromatic profile even for complex sea states. That the profiles give a closer match and a more correct shear has implications for ocean circulation models since the Coriolis-Stokes force depends on the magnitude and direction of the Stokes drift profile and Langmuir turbulence parameterizations depend sensitively on the shear of the profile. Of the two Stokes drift profiles explored here, the profile based on the Phillips spectrum is by far the best. In particular, the shear near the surface is almost identical to that influenced by the f-5 tail of spectral wave models. The NEMO general circulation ocean model was recently extended to incorporate the Stokes-Coriolis force along with two other wave-related effects. The ECWMF coupled atmosphere-wave-ocean ensemble forecast system now includes these wave effects in the ocean model component (NEMO).

Oral sustained-release suspension based on a lauryl sulfate salt/complex.

PubMed

Kasashima, Yuuki; Uchida, Shinya; Yoshihara, Keiichi; Yasuji, Takehiko; Sako, Kazuhiro; Namiki, Noriyuki

2016-12-30

The objective of this study was to evaluate the feasibility of lauryl sulfate (LS) salt/complex as a novel carrier in oral sustained-release suspensions. Mirabegron, which has a pH-dependent solubility, was selected as the model drug. Sodium lauryl sulfate (SLS) was bound to mirabegron in a stoichiometric manner to form an LS salt/complex. LS salt/complex formulation significantly reduced the solubility of mirabegron and helped mirabegron achieve sustained-release over a wide range of pH conditions. Microparticles containing the LS salt/complex were prepared by spray drying with the aqueous dispersion of ethylcellulose (Aquacoat ® ECD). The diameter of the microparticles was less than 200μm, which will help avoid a gritty taste. In vitro results indicated the microparticles had slower dissolution profiles than the LS salt/complex. The dissolution rate could be controlled flexibly by changing the amount of Aquacoat ® ECD. The microparticle suspension retained the desired sustained-release property and dissolution profile after being stored for 30days at 40°C. In addition, the suspension displayed sustained-release behavior in dogs without a pronounced C max peak, which will help prevent side effects. These results suggest that microparticles containing LS salt/complex may be useful as a novel sustained-release suspension for oral delivery. Copyright © 2016 Elsevier B.V. All rights reserved.

Signal enhancement based on complex curvelet transform and complementary ensemble empirical mode decomposition

NASA Astrophysics Data System (ADS)

Dong, Lieqian; Wang, Deying; Zhang, Yimeng; Zhou, Datong

2017-09-01

Signal enhancement is a necessary step in seismic data processing. In this paper we utilize the complementary ensemble empirical mode decomposition (CEEMD) and complex curvelet transform (CCT) methods to separate signal from random noise further to improve the signal to noise (S/N) ratio. Firstly, the original data with noise is decomposed into a series of intrinsic mode function (IMF) profiles with the aid of CEEMD. Then the IMFs with noise are transformed into CCT domain. By choosing different thresholds which are based on the noise level difference of each IMF profile, the noise in original data can be suppressed. Finally, we illustrate the effectiveness of the approach by simulated and field datasets.

Development of a Software-Defined Radar

DTIC Science & Technology

2017-10-01

waveform to the widest available (unoccupied) instantaneous bandwidth in real time. Consequently, the radar range resolution and target detection are...LabVIEW The matched filter range profile is calculated in real time using fast Fourier transform (FFT) operations to perform a cross-correlation...between the transmitted waveform and the received complex data. Figure 4 demonstrates the block logic used to achieve real -time range profile

Custom E-Learning Experiences: Working with Profiles for Multiple Content Sources Access and Adaptation

ERIC Educational Resources Information Center

Ferretti, Stefano; Roccetti, Marco; Salomoni, Paola; Mirri, Silvia

2009-01-01

It is a common belief that the problem of extracting learners' profiles to be used for delivering custom learning experiences is a closed case. Yet, practical solutions do not completely cope with the complex issue of capturing all the features of users, especially those of heterogeneous learners, who may have special needs or characteristics…

Identifying Demographic and Language Profiles of Children with a Primary Diagnosis of Attention Deficit Hyperactivity Disorder

ERIC Educational Resources Information Center

Walsh, Irene P.; Scullion, Mary; Burns, Sarah; MacEvilly, Deirdre; Brosnan, Geraldine

2014-01-01

As the language presentation of children with attention deficit (hyperactivity) disorder (ADHD) is highly complex, this study aims to delineate the profile of a cohort of 40 children with ADHD, aged between 9 and 12 years, attending a child and adolescent mental health service (CAMHS). Speech and language therapists (SLTs) assessed the children on…

Shade avoidance components and pathways in adult plants revealed by phenotypic profiling.

PubMed

Nozue, Kazunari; Tat, An V; Kumar Devisetty, Upendra; Robinson, Matthew; Mumbach, Maxwell R; Ichihashi, Yasunori; Lekkala, Saradadevi; Maloof, Julin N

2015-04-01

Shade from neighboring plants limits light for photosynthesis; as a consequence, plants have a variety of strategies to avoid canopy shade and compete with their neighbors for light. Collectively the response to foliar shade is called the shade avoidance syndrome (SAS). The SAS includes elongation of a variety of organs, acceleration of flowering time, and additional physiological responses, which are seen throughout the plant life cycle. However, current mechanistic knowledge is mainly limited to shade-induced elongation of seedlings. Here we use phenotypic profiling of seedling, leaf, and flowering time traits to untangle complex SAS networks. We used over-representation analysis (ORA) of shade-responsive genes, combined with previous annotation, to logically select 59 known and candidate novel mutants for phenotyping. Our analysis reveals shared and separate pathways for each shade avoidance response. In particular, auxin pathway components were required for shade avoidance responses in hypocotyl, petiole, and flowering time, whereas jasmonic acid pathway components were only required for petiole and flowering time responses. Our phenotypic profiling allowed discovery of seventeen novel shade avoidance mutants. Our results demonstrate that logical selection of mutants increased success of phenotypic profiling to dissect complex traits and discover novel components.

Metabolome and proteome profiling of complex I deficiency induced by rotenone.

PubMed

Gielisch, Ina; Meierhofer, David

2015-01-02

Complex I (CI; NADH dehydrogenase) deficiency causes mitochondrial diseases, including Leigh syndrome. A variety of clinical symptoms of CI deficiency are known, including neurodegeneration. Here, we report an integrative study combining liquid chromatography-mass spectrometry (LC-MS)-based metabolome and proteome profiling in CI deficient HeLa cells. We report a rapid LC-MS-based method for the relative quantification of targeted metabolome profiling with an additional layer of confidence by applying multiple reaction monitoring (MRM) ion ratios for further identity confirmation and robustness. The proteome was analyzed by label-free quantification (LFQ). More than 6000 protein groups were identified. Pathway and network analyses revealed that the respiratory chain was highly deregulated, with metabolites such as FMN, FAD, NAD(+), and ADP, direct players of the OXPHOS system, and metabolites of the TCA cycle decreased up to 100-fold. Synthesis of functional iron-sulfur clusters, which are of central importance for the electron transfer chain, and degradation products like bilirubin were also significantly reduced. Glutathione metabolism on the pathway level, as well as individual metabolite components such as NADPH, glutathione (GSH), and oxidized glutathione (GSSG), was downregulated. Overall, metabolome and proteome profiles in CI deficient cells correlated well, supporting our integrated approach.

A novel multi-tiered experimental approach unfolding the mechanisms behind cyclodextrin-vitamin inclusion complexes for enhanced vitamin solubility and stability.

PubMed

Braithwaite, Miles C; Kumar, Pradeep; Choonara, Yahya E; du Toit, Lisa C; Tomar, Lomas K; Tyagi, Charu; Pillay, Viness

2017-10-30

This study was conducted to provide a mechanistic account for understanding the synthesis, characterization and solubility phenomena of vitamin complexes with cyclodextrins (CD) for enhanced solubility and stability employing experimental and in silico molecular modeling strategies. New geometric, molecular and energetic analyses were pursued to explicate experimentally derived cholecalciferol complexes. Various CD molecules (α-, β-, γ-, and hydroxypropyl β-) were complexed with three vitamins: cholecalciferol, ascorbic acid and α-tocopherol. The Inclusion Efficiency (IE%) was computed for each CD-vitamin complex. The highest IE% achieved for a cholecalciferol complex was for 'βCDD 3 -8', after utilizing a unique CD:cholecalciferol molar synthesis ratio of 2.5:1, never before reported as successful. 2HPβCD-cholecalciferol, γCD-cholecalciferol and α-tocopherol inclusion complexes (IC's) reached maximal IE% with a CD:vitamin molar ratio of 5:1. The results demonstrate that IE%, thermal stability, concentration, carrier solubility, molecular mechanics and intended release profile are key factors to consider when synthesizing vitamin-CD complexes. Phase-solubility data provided insights into the design of formulations with IC's that may provide analogous oral vitamin release profiles even when hydrophobic and hydrophilic vitamins are co-incorporated. Static lattice atomistic simulations were able to validate experimentally derived cholecalciferol IE phenomena and are invaluable parameters when approaching formulation strategies using CD's for improved solubility and efficacy of vitamins. Copyright © 2017 Elsevier B.V. All rights reserved.

Aeolian sand transport over complex intertidal bar-trough beach topography

NASA Astrophysics Data System (ADS)

Anthony, Edward J.; Ruz, Marie-Hélène; Vanhée, Stéphane

2009-04-01

Aeolian sand transport on macrotidal beaches with complex intertidal bar-trough topography (ridge-and-runnel beaches) was assessed from experiments in northern France that involved measurements of wind speed, saltation, surface moisture contents, and rates of sand trapping across surveyed portions of the upper beach profile. Beaches exhibiting intertidal bars and troughs are much more complex, topographically, than simple reflective or dissipative beaches. Furthermore, the intertidal bar-trough morphology commonly exhibits strong cross-shore variations in the moisture contents of the beach surface and in patterns of bedform development. The results of four 30-minute experiments, conducted along topographically surveyed portions of the upper beach-dune toe profile, show that troughs act as extremely efficient sand interceptors, because of their permanently saturated state, which also inhibits sand mobilisation. Troughs, thus, limit or segment the dry fetch during conditions of intermittent saltation. Flow lines, inferred from the wind profiles, suggest that complex interactions at the boundary layer are generated by the bar-trough topography. Troughs systematically appear to be characterised by air expansion, while bar faces generate ramp wind acceleration for onshore winds, and sometimes immediate downwind deceleration for offshore winds. These effects may also contribute to cross-shore variations in the rates of sand trapping. Finally, a simple conceptual model of effective fetch development, integrating the effects of the spring-neap tidal range and of gross bar-trough morphological variability over time, is proposed for bar-trough beaches. The model highlights the key theme of fetch segmentation induced by cross-shore differentiation in the moisture contents of the beach surface hinged on the complex topography of multiple bars and troughs.

Multilevel analysis of the influence of patients' and general practitioners' characteristics on patented versus multiple-sourced statin prescribing in France.

PubMed

Pichetti, Sylvain; Sermet, Catherine; Godman, Brian; Campbell, Stephen M; Gustafsson, Lars L

2013-06-01

The French National Health Insurance and the Ministry of Health have introduced multiple reforms in recent years to increase prescribing efficiency. These include guidelines, academic detailing, financial incentives for the prescribing and dispensing of generics drugs as well as a voluntary pay-for-performance programme. However, the quality and efficiency of prescribing could be enhanced potentially if there was better understanding of the dynamics of prescribing behaviour in France. To analyse the patient and general practitioner characteristics that influence patented versus multiple-sourced statin prescribing in France. Statistical analysis was performed on the statin prescribing habits from 341 general practitioners (GPs) that were included in the IMS-Health Permanent Survey on Medical Prescription in France, which was conducted between 2009 and 2010 and involved 14,360 patients. Patient characteristics included their age and gender as well as five medical profiles that were constructed from the diagnoses obtained during consultations. These were (1) disorders of lipoprotein metabolism, (2) heart disease, (3) diabetes, (4) complex profiles and (5) profiles based on other diagnoses. Physician characteristics included their age, gender, solo or group practice, weekly workload and payment scheme. Patient age had a statistically significant impact on statin prescribing for patients in profile 1 (disorders of lipoprotein metabolism) and profile 3 (complex profiles) with a greater number of patented statins being prescribed for the youngest patients. For instance, patients older than 76 years with a complex profile were prescribed fewer patented statins than patients aged 68-76 years old with the same medical profile (coefficient: -0.225; p = 0.0008). By contrast, regardless of the patient's age, the medical profile did not affect the probability of prescribing a patented statin except in young patients with heart diseases who were prescribed a greater number of patented statins (coefficient: 0.3992; p = 0.0007). Prescribing was also statistically influenced by physician features, e.g., older male physicians were more likely to prescribe patented statins (coefficient: 0.245; p = 0.0417) and GPs practicing in groups were more likely to prescribe multiple sourced statins (coefficient: -0.178; p = 0.0338), which is an important finding of the study. GPs with a lower workload prescribed a greater number of patented statins. There is significant variability in the prescribing of different statins among patient and physician profiles as well as between solo and group practices. Consequently, there are opportunities to target demand-side measures to enhance the prescribing of multiple-sourced statins. Further studies are warranted, in particular in other therapeutic classes, to provide a counter-balance to the considerable marketing activities of pharmaceutical companies.

Ruminant Rhombencephalitis-Associated Listeria monocytogenes Alleles Linked to a Multilocus Variable-Number Tandem-Repeat Analysis Complex ▿ †

PubMed Central

Balandyté, Lina; Brodard, Isabelle; Frey, Joachim; Oevermann, Anna; Abril, Carlos

2011-01-01

Listeria monocytogenes is among the most important food-borne pathogens and is well adapted to persist in the environment. To gain insight into the genetic relatedness and potential virulence of L. monocytogenes strains causing central nervous system (CNS) infections, we used multilocus variable-number tandem-repeat analysis (MLVA) to subtype 183 L. monocytogenes isolates, most from ruminant rhombencephalitis and some from human patients, food, and the environment. Allelic-profile-based comparisons grouped L. monocytogenes strains mainly into three clonal complexes and linked single-locus variants (SLVs). Clonal complex A essentially consisted of isolates from human and ruminant brain samples. All but one rhombencephalitis isolate from cattle were located in clonal complex A. In contrast, food and environmental isolates mainly clustered into clonal complex C, and none was classified as clonal complex A. Isolates of the two main clonal complexes (A and C) obtained by MLVA were analyzed by PCR for the presence of 11 virulence-associated genes (prfA, actA, inlA, inlB, inlC, inlD, inlE, inlF, inlG, inlJ, and inlC2H). Virulence gene analysis revealed significant differences in the actA, inlF, inlG, and inlJ allelic profiles between clinical isolates (complex A) and nonclinical isolates (complex C). The association of particular alleles of actA, inlF, and newly described alleles of inlJ with isolates from CNS infections (particularly rhombencephalitis) suggests that these virulence genes participate in neurovirulence of L. monocytogenes. The overall absence of inlG in clinical complex A and its presence in complex C isolates suggests that the InlG protein is more relevant for the survival of L. monocytogenes in the environment. PMID:21984240

The Dispositions, Abilities and Behaviours (DAB) Framework for Profiling Learners' Sustainability Competencies in Higher Education

ERIC Educational Resources Information Center

Besong, Frida; Holland, Charlotte

2015-01-01

The concepts of sustainability and sustainability competence are controversial, complex, difficult to define and measure, and have varied meanings for different people and practices. Given the complex nature of sustainability, there is limited availability of paradigmatic frameworks to guide educators in assessing sustainability competencies. This…

Modelling gene expression profiles related to prostate tumor progression using binary states

PubMed Central

2013-01-01

Background Cancer is a complex disease commonly characterized by the disrupted activity of several cancer-related genes such as oncogenes and tumor-suppressor genes. Previous studies suggest that the process of tumor progression to malignancy is dynamic and can be traced by changes in gene expression. Despite the enormous efforts made for differential expression detection and biomarker discovery, few methods have been designed to model the gene expression level to tumor stage during malignancy progression. Such models could help us understand the dynamics and simplify or reveal the complexity of tumor progression. Methods We have modeled an on-off state of gene activation per sample then per stage to select gene expression profiles associated to tumor progression. The selection is guided by statistical significance of profiles based on random permutated datasets. Results We show that our method identifies expected profiles corresponding to oncogenes and tumor suppressor genes in a prostate tumor progression dataset. Comparisons with other methods support our findings and indicate that a considerable proportion of significant profiles is not found by other statistical tests commonly used to detect differential expression between tumor stages nor found by other tailored methods. Ontology and pathway analysis concurred with these findings. Conclusions Results suggest that our methodology may be a valuable tool to study tumor malignancy progression, which might reveal novel cancer therapies. PMID:23721350

How do cuticular hydrocarbons evolve? Physiological constraints and climatic and biotic selection pressures act on a complex functional trait

PubMed Central

Blaimer, Bonnie B.; Schmitt, Thomas

2017-01-01

Cuticular hydrocarbons (CHCs) cover the cuticles of virtually all insects, serving as a waterproofing agent and as a communication signal. The causes for the high CHC variation between species, and the factors influencing CHC profiles, are scarcely understood. Here, we compare CHC profiles of ant species from seven biogeographic regions, searching for physiological constraints and for climatic and biotic selection pressures. Molecule length constrained CHC composition: long-chain profiles contained fewer linear alkanes, but more hydrocarbons with disruptive features in the molecule. This is probably owing to selection on the physiology to build a semi-fluid cuticular layer, which is necessary for waterproofing and communication. CHC composition also depended on the precipitation in the ants' habitats. Species from wet climates had more alkenes and fewer dimethyl alkanes than those from drier habitats, which can be explained by different waterproofing capacities of these compounds. By contrast, temperature did not affect CHC composition. Mutualistically associated (parabiotic) species possessed profiles highly distinct from non-associated species. Our study is, to our knowledge, the first to show systematic impacts of physiological, climatic and biotic factors on quantitative CHC composition across a global, multi-species dataset. We demonstrate how they jointly shape CHC profiles, and advance our understanding of the evolution of this complex functional trait in insects. PMID:28298343

Observing Consistency in Online Communication Patterns for User Re-Identification.

PubMed

Adeyemi, Ikuesan Richard; Razak, Shukor Abd; Salleh, Mazleena; Venter, Hein S

2016-01-01

Comprehension of the statistical and structural mechanisms governing human dynamics in online interaction plays a pivotal role in online user identification, online profile development, and recommender systems. However, building a characteristic model of human dynamics on the Internet involves a complete analysis of the variations in human activity patterns, which is a complex process. This complexity is inherent in human dynamics and has not been extensively studied to reveal the structural composition of human behavior. A typical method of anatomizing such a complex system is viewing all independent interconnectivity that constitutes the complexity. An examination of the various dimensions of human communication pattern in online interactions is presented in this paper. The study employed reliable server-side web data from 31 known users to explore characteristics of human-driven communications. Various machine-learning techniques were explored. The results revealed that each individual exhibited a relatively consistent, unique behavioral signature and that the logistic regression model and model tree can be used to accurately distinguish online users. These results are applicable to one-to-one online user identification processes, insider misuse investigation processes, and online profiling in various areas.

Assessment of complex dissociative disorder patients and simulated dissociation in forensic contexts.

PubMed

Brand, Bethany L; Webermann, Aliya R; Frankel, A Steven

Few assessors receive training in assessing dissociation and complex dissociative disorders (DDs). Potential differential diagnoses include anxiety, mood, psychotic, substance use, and personality disorders, as well as exaggeration and malingering. Individuals with DDs typically elevate on many clinical and validity scales on psychological tests, yet research indicates that they can be distinguished from DD simulators. Becoming informed about the testing profiles of DD individuals and DD simulators can improve the accuracy of differential diagnoses in forensic settings. In this paper, we first review the testing profiles of individuals with complex DDs and contrast them with DD simulators on assessment measures used in forensic contexts, including the Minnesota Multiphasic Personality Inventory-2 (MMPI-2), Personality Assessment Inventory (PAI), and the Structured Inventory of Reported Symptoms (SIRS), as well as dissociation-specific measures such as the Dissociative Experiences Scale (DES) and Structured Clinical Interview for DSM-IV Dissociative Disorders (SCID-D-R). We then provide recommendations for assessing complex trauma and dissociation through the aforementioned assessments. Copyright © 2016 Elsevier Ltd. All rights reserved.

Gravity profiles across the Uyaijah Ring structure, Kingdom of Saudi Arabia

USGS Publications Warehouse

Gettings, M.E.; Andreasen, G.E.

1987-01-01

The resulting structural model, based on profile fits to gravity responses of three-dimensional models and excess-mass calculations, gives a depth estimate to the base of the complex of 4.75 km. The contacts of the complex are inferred to be steeply dipping inward along the southwest margin of the structure. To the north and east, however, the basal contact of the complex dips more gently inward (about 30 degrees). The ring structure appears to be composed of three laccolith-shaped plutons; two are granitic in composition and make up about 85 percent of the volume of the complex, and one is granodioritic and comprises the remaining 15 percent. The source area for the plutons appears to be in the southwest quadrant of the Uyaijah ring structure. A northwest-trending shear zone cuts the northern half of the structure and contains mafic dikes that have a small but identifiable gravity-anomaly response. The structural model agrees with models derived from geological interpretation except that the estimated depth to which the structure extends is decreased considerably by the gravity results.

Utilization of supercritical carbon dioxide for complex formation of ibuprofen and methyl-beta-cyclodextrin.

PubMed

Charoenchaitrakool, M; Dehghani, F; Foster, N R

2002-06-04

The dissolution rate of a drug into the biological environment can be enhanced by forming complexes with cyclodextrins and their derivatives. In this study, ibuprofen-methyl-beta-cyclodextrin complexes were prepared successfully by passing ibuprofen-laden CO(2) through a methyl-beta-cyclodextrin packed bed. The maximum drug loading obtained in this work was 10.8 wt.%, which was comparable to that of a 1:1 complex (13.6 wt.% of ibuprofen). The complex exhibited instantaneous dissolution profiles in water solution. The enhanced dissolution rate was attributed to the amorphous character and improved wettability of the product.

Beam property measurement of a 300-kV ion source test stand for a 1-MV electrostatic accelerator

NASA Astrophysics Data System (ADS)

Park, Sae-Hoon; Kim, Dae-Il; Kim, Yu-Seok

2016-09-01

The KOMAC (Korea Multi-purpose Accelerator Complex) has been developing a 300-kV ion source test stand for a 1-MV electrostatic accelerator for industrial purposes. A RF ion source was operated at 200 MHz with its matching circuit. The beam profile and emittance were measured behind an accelerating column to confirm the beam property from the RF ion source. The beam profile was measured at the end of the accelerating tube and at the beam dump by using a beam profile monitor (BPM) and wire scanner. An Allison-type emittance scanner was installed behind the beam profile monitor (BPM) to measure the beam density in phase space. The measurement results for the beam profile and emittance are presented in this paper.

A Profile of Patients With Traumatic Brain Injury Within Home Care, Long-Term Care, Complex Continuing Care, and Institutional Mental Health Settings in a Publicly Insured Population.

PubMed

Colantonio, Angela; Hsueh, Jayden; Petgrave, Josian; Hirdes, John P; Berg, Katherine

2015-01-01

To describe the sociodemographic and clinical profile of people with traumatic brain injury (TBI) in home care, nursing homes, and complex continuing care settings in a national sample. Cross-sectional study using available Resident Assessment Instrument (RAI 2.0 and RAI Home Care [HC]) national databases in Canada from 1996 to 2011. The profile of people with TBI was compared with patients with and without prespecified neurological conditions within each setting. Adults 18 years and older identified with TBI (n = 10 878) and adult patients with other neurological (n = 422 300) and non-neurological (n = 571 567) conditions. Demographic and clinical characteristics, functional characteristics, mood and behavior, and treatment and medication variables. Data from Canadian home care (RAI-HC), mental health (RAI-MH), nursing home, and complex continuing care facilities (RAI Minimum Data Set 2.0). Patients with TBI were significantly different on almost all items. They were among the youngest in care settings, and psychotropic drug use by this population was among the highest in at least 2 settings. These data can inform the planning for appropriate care and resources for patients with TBI in a range of settings.

Small-angle neutron scattering study of specific interaction and coordination structure formed by mono-acetyl-substituted dibenzo-20-crown-6-ether and cesium ions

DOE PAGES

Motokawa, Ryuhei; Kobayashi, Tohru; Endo, Hitoshi; ...

2015-10-26

This study uses small-angle neutron scattering (SANS) to elucidate the coordination structure of the complex of mono-acetyl-substituted dibenzo-20-crown-6-ether (ace-DB20C6) with cesium ions (Cs +). SANS profiles obtained for the complex of ace-DB20C6 and Cs + (ace-DB20C6/Cs) in deuterated dimethyl sulfoxide indicated that Cs + coordination resulted in a more compact structure than the free ace-DB20C6. The data were fitted well with SANS profiles calculated using Debye function for scattering on an absolute scattering intensity scale. For this theoretical calculation of the scattering profiles, the coordination structure proposed based on density functional theory calculation was used. Furthermore, we conclude that themore » SANS analysis experimentally supports the proposed coordination structure of ace-DB20C6/Cs and suggests the following: (1) the complex of ace-DB20C6 and Cs + is formed with an ace-DB20C6/Cs molar ratio of 1/1 and (2) the two benzene rings of ace-DB20C6 fold around Cs + above the center of the crown ether ring of ace-DB20C6.« less

Small-angle neutron scattering study of specific interaction and coordination structure formed by mono-acetyl-substituted dibenzo-20-crown-6-ether and cesium ions

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

Motokawa, Ryuhei; Kobayashi, Tohru; Endo, Hitoshi

This study uses small-angle neutron scattering (SANS) to elucidate the coordination structure of the complex of mono-acetyl-substituted dibenzo-20-crown-6-ether (ace-DB20C6) with cesium ions (Cs +). SANS profiles obtained for the complex of ace-DB20C6 and Cs + (ace-DB20C6/Cs) in deuterated dimethyl sulfoxide indicated that Cs + coordination resulted in a more compact structure than the free ace-DB20C6. The data were fitted well with SANS profiles calculated using Debye function for scattering on an absolute scattering intensity scale. For this theoretical calculation of the scattering profiles, the coordination structure proposed based on density functional theory calculation was used. Furthermore, we conclude that themore » SANS analysis experimentally supports the proposed coordination structure of ace-DB20C6/Cs and suggests the following: (1) the complex of ace-DB20C6 and Cs + is formed with an ace-DB20C6/Cs molar ratio of 1/1 and (2) the two benzene rings of ace-DB20C6 fold around Cs + above the center of the crown ether ring of ace-DB20C6.« less

Study of Equatorial Ionospheric irregularities and Mapping of Electron Density Profiles and Ionograms

DTIC Science & Technology

2012-03-09

equation is a product of a complex basis vector in Jackson and a linear combination of plane wave functions. We convert both the amplitudes and the...wave function arguments from complex scalars to complex vectors . This conversion allows us to separate the electric field vector and the imaginary...magnetic field vector , because exponentials of imaginary scalars convert vectors to imaginary vectors and vice versa, while ex- ponentials of imaginary

Application of denaturing high-performance liquid chromatography (DHPLC) for the identification of fish: a new way to determine the composition of processed food containing multiple species.

PubMed

Le Fresne, Sophie; Popova, Milena; Le Vacon, Françoise; Carton, Thomas

2011-12-14

The identification of fish species in transformed food products is difficult because the existing methods are not adapted to heat-processed products containing more than one species. Using a common to all vertebrates region of the cytochrome b gene, we have developed a denaturing high-performance liquid chromatography (DHPLC) fingerprinting method, which allowed us to identify most of the species in commercial crab sticks. Whole fish and fillets were used for the creation of a library of referent DHPLC profiles. Crab sticks generated complex DHPLC profiles in which the number of contained fish species can be estimated by the number of major fluorescence peaks. The identity of some of the species was predicted by comparison of the peaks with the referent profiles, and others were identified after collection of the peak fractions, reamplification, and sequencing. DHPLC appears to be a quick and efficient method to analyze the species composition of complex heat-processed fish products.

First density profile measurements using frequency modulation of the continuous wave reflectometry on JETa)

NASA Astrophysics Data System (ADS)

Meneses, L.; Cupido, L.; Sirinelli, A.; Manso, M. E.; Jet-Efds Contributors

2008-10-01

We present the main design options and implementation of an X-mode reflectometer developed and successfully installed at JET using an innovative approach. It aims to prove the viability of measuring density profiles with high spatial and temporal resolution using broadband reflectometry operating in long and complex transmission lines. It probes the plasma with magnetic fields between 2.4 and 3.0 T using the V band [~(0-1.4)×1019 m-3]. The first experimental results show the high sensitivity of the diagnostic when measuring changes in the plasma density profile occurring ITER relevant regimes, such as ELMy H-modes. The successful demonstration of this concept motivated the upgrade of the JET frequency modulation of the continuous wave (FMCW) reflectometry diagnostic, to probe both the edge and core. This new system is essential to prove the viability of using the FMCW reflectometry technique to probe the plasma in next step devices, such as ITER, since they share the same waveguide complexity.

Deciphering Late-Pleistocence landscape evolution: linking proxies by combining pedo-stratigraphy and luminescence dating

NASA Astrophysics Data System (ADS)

Kreutzer, Sebastian; Meszner, Sascha; Faust, Dominik; Fuchs, Markus

2014-05-01

Interpreting former landscape evolution asks for understanding the processes that sculpt such landforms by means of deciphering complex systems. For reconstructing terrestrial Quaternary environments based on loess archives this might be considered, at least, as a three step process: (1) Identifying valuable records in appropriate morphological positions in a previously defined research area, (2) analysing the profiles by field work and laboratory methods and finally (3) linking the previously considered pseudo-isolated systems to set up a comprehensive picture. Especially the first and the last step might bring some pitfalls, as it is tempting to specify single records as pseudo-isolated, closed systems. They might be, with regard to their preservation in their specific morphological position, but in fact they are part of a complex, open system. Between 2008 and 2013, Late-Pleistocene loess archives in Saxony have been intensively investigated by field and laboratory methods. Linking pedo- and luminescence dating based chronostratigraphies, a composite profile for the entire Saxonian Loess Region has been established. With this, at least, two-fold approach we tried to avoid misinterpretations that might appear when focussing on one standard profile in an open morphological system. Our contribution focuses on this multi-proxy approach to decipher the Late-Pleistocene landscape evolution in the Saxonian Loess Region. Highlighting the challenges and advantages of combining different methods, we believe that (1) this multi-proxy approach is without alternative, (2) the combination of different profiles may simplify the more complex reality, but it may be a useful generalisation to understand and reveal the stratigraphical significance of the landscape evolution in this region.

Spatiotemporal profiles of receptive fields of neurons in the lateral posterior nucleus of the cat LP-pulvinar complex.

PubMed

Piché, Marilyse; Thomas, Sébastien; Casanova, Christian

2015-10-01

The pulvinar is the largest extrageniculate thalamic visual nucleus in mammals. It establishes reciprocal connections with virtually all visual cortexes and likely plays a role in transthalamic cortico-cortical communication. In cats, the lateral posterior nucleus (LP) of the LP-pulvinar complex can be subdivided in two subregions, the lateral (LPl) and medial (LPm) parts, which receive a predominant input from the striate cortex and the superior colliculus, respectively. Here, we revisit the receptive field structure of LPl and LPm cells in anesthetized cats by determining their first-order spatiotemporal profiles through reverse correlation analysis following sparse noise stimulation. Our data reveal the existence of previously unidentified receptive field profiles in the LP nucleus both in space and time domains. While some cells responded to only one stimulus polarity, the majority of neurons had receptive fields comprised of bright and dark responsive subfields. For these neurons, dark subfields' size was larger than that of bright subfields. A variety of receptive field spatial organization types were identified, ranging from totally overlapped to segregated bright and dark subfields. In the time domain, a large spectrum of activity overlap was found, from cells with temporally coinciding subfield activity to neurons with distinct, time-dissociated subfield peak activity windows. We also found LP neurons with space-time inseparable receptive fields and neurons with multiple activity periods. Finally, a substantial degree of homology was found between LPl and LPm first-order receptive field spatiotemporal profiles, suggesting a high integration of cortical and subcortical inputs within the LP-pulvinar complex. Copyright © 2015 the American Physiological Society.

Heterogeneous fractionation profiles of meta-analytic coactivation networks.

PubMed

Laird, Angela R; Riedel, Michael C; Okoe, Mershack; Jianu, Radu; Ray, Kimberly L; Eickhoff, Simon B; Smith, Stephen M; Fox, Peter T; Sutherland, Matthew T

2017-04-01

Computational cognitive neuroimaging approaches can be leveraged to characterize the hierarchical organization of distributed, functionally specialized networks in the human brain. To this end, we performed large-scale mining across the BrainMap database of coordinate-based activation locations from over 10,000 task-based experiments. Meta-analytic coactivation networks were identified by jointly applying independent component analysis (ICA) and meta-analytic connectivity modeling (MACM) across a wide range of model orders (i.e., d=20-300). We then iteratively computed pairwise correlation coefficients for consecutive model orders to compare spatial network topologies, ultimately yielding fractionation profiles delineating how "parent" functional brain systems decompose into constituent "child" sub-networks. Fractionation profiles differed dramatically across canonical networks: some exhibited complex and extensive fractionation into a large number of sub-networks across the full range of model orders, whereas others exhibited little to no decomposition as model order increased. Hierarchical clustering was applied to evaluate this heterogeneity, yielding three distinct groups of network fractionation profiles: high, moderate, and low fractionation. BrainMap-based functional decoding of resultant coactivation networks revealed a multi-domain association regardless of fractionation complexity. Rather than emphasize a cognitive-motor-perceptual gradient, these outcomes suggest the importance of inter-lobar connectivity in functional brain organization. We conclude that high fractionation networks are complex and comprised of many constituent sub-networks reflecting long-range, inter-lobar connectivity, particularly in fronto-parietal regions. In contrast, low fractionation networks may reflect persistent and stable networks that are more internally coherent and exhibit reduced inter-lobar communication. Copyright © 2017 Elsevier Inc. All rights reserved.

Heterogeneous fractionation profiles of meta-analytic coactivation networks

PubMed Central

Laird, Angela R.; Riedel, Michael C.; Okoe, Mershack; Jianu, Radu; Ray, Kimberly L.; Eickhoff, Simon B.; Smith, Stephen M.; Fox, Peter T.; Sutherland, Matthew T.

2017-01-01

Computational cognitive neuroimaging approaches can be leveraged to characterize the hierarchical organization of distributed, functionally specialized networks in the human brain. To this end, we performed large-scale mining across the BrainMap database of coordinate-based activation locations from over 10,000 task-based experiments. Meta-analytic coactivation networks were identified by jointly applying independent component analysis (ICA) and meta-analytic connectivity modeling (MACM) across a wide range of model orders (i.e., d = 20 to 300). We then iteratively computed pairwise correlation coefficients for consecutive model orders to compare spatial network topologies, ultimately yielding fractionation profiles delineating how “parent” functional brain systems decompose into constituent “child” sub-networks. Fractionation profiles differed dramatically across canonical networks: some exhibited complex and extensive fractionation into a large number of sub-networks across the full range of model orders, whereas others exhibited little to no decomposition as model order increased. Hierarchical clustering was applied to evaluate this heterogeneity, yielding three distinct groups of network fractionation profiles: high, moderate, and low fractionation. BrainMap-based functional decoding of resultant coactivation networks revealed a multi-domain association regardless of fractionation complexity. Rather than emphasize a cognitive-motor-perceptual gradient, these outcomes suggest the importance of inter-lobar connectivity in functional brain organization. We conclude that high fractionation networks are complex and comprised of many constituent sub-networks reflecting long-range, inter-lobar connectivity, particularly in fronto-parietal regions. In contrast, low fractionation networks may reflect persistent and stable networks that are more internally coherent and exhibit reduced inter-lobar communication. PMID:28222386

Flow over Canopies with Complex Morphologies

NASA Astrophysics Data System (ADS)

Rubol, S.; Ling, B.; Battiato, I.

2017-12-01

Quantifying and predicting how submerged vegetation affects the velocity profile of riverine systems is crucial in ecohydraulics to properly assess the water quality and ecological functions or rivers. The state of the art includes a plethora of models to study the flow and transport over submerged canopies. However, most of them are validated against data collected in flume experiments with rigid cylinders. With the objective of investigating the capability of a simple analytical solution for vegetated flow to reproduce and predict the velocity profile of complex shaped flexible canopies, we use the flow model proposed by Battiato and Rubol [WRR 2013] as the analytical approximation of the mean velocity profile above and within the canopy layer. This model has the advantages (i) to threat the canopy layer as a porous medium, whose geometrical properties are associated with macroscopic effective permeability and (ii) to use input parameters that can be estimated by remote sensing techniques, such us the heights of the water level and the canopy. The analytical expressions for the average velocity profile and the discharge are tested against data collected across a wide range of canopy morphologies commonly encountered in riverine systems, such as grasses, woody vegetation and bushes. Results indicate good agreement between the analytical expressions and the data for both simple and complex plant geometry shapes. The rescaled low submergence velocities in the canopy layer followed the same scaling found in arrays of rigid cylinders. In addition, for the dataset analyzed, the Darcy friction factor scaled with the inverse of the bulk Reynolds number multiplied by the ratio of the fluid to turbulent viscosity.

A transform from absorption to Raman excitation profile. A time-dependent approach

NASA Astrophysics Data System (ADS)

Lee, Soo-Y.; Yeo, Robert C. K.

1994-04-01

An alternative time-frame approach, which is canonically conjugate to the energy-frame approach, for implementing the transform relations for calculating Raman excitation profiles directly from the optical absorption spectrum is presented. Practical and efficient fast Fourier transformation in the time frame replaces the widely used Chan and Page algorithm for evaluating the Hilbert transform in the energy frame. The time-frame approach is applied to: (a) a two-mode model which illustrates the missing mode effect in both absorption and Raman excitation profiles, (b) carotene, in which both the absorption spectrum and the Raman excitation profile show vibrational structure and (c) hexamethylbenzene: TCNE electron donor—acceptor complex where the same spectra are structureless and the Raman excitation profile for the 168 cm -1 mode poses a problem for the energy-frame approach. A similar time-frame approach can be used for the inverse transform from the Raman excitation profile to the optical absorption spectrum.

Application of genetic algorithm in the evaluation of the profile error of archimedes helicoid surface

NASA Astrophysics Data System (ADS)

Zhu, Lianqing; Chen, Yunfang; Chen, Qingshan; Meng, Hao

2011-05-01

According to minimum zone condition, a method for evaluating the profile error of Archimedes helicoid surface based on Genetic Algorithm (GA) is proposed. The mathematic model of the surface is provided and the unknown parameters in the equation of surface are acquired through least square method. Principle of GA is explained. Then, the profile error of Archimedes Helicoid surface is obtained through GA optimization method. To validate the proposed method, the profile error of an Archimedes helicoid surface, Archimedes Cylindrical worm (ZA worm) surface, is evaluated. The results show that the proposed method is capable of correctly evaluating the profile error of Archimedes helicoid surface and satisfy the evaluation standard of the Minimum Zone Method. It can be applied to deal with the measured data of profile error of complex surface obtained by three coordinate measurement machines (CMM).

Profiling protein function with small molecule microarrays

PubMed Central

Winssinger, Nicolas; Ficarro, Scott; Schultz, Peter G.; Harris, Jennifer L.

2002-01-01

The regulation of protein function through posttranslational modification, local environment, and protein–protein interaction is critical to cellular function. The ability to analyze on a genome-wide scale protein functional activity rather than changes in protein abundance or structure would provide important new insights into complex biological processes. Herein, we report the application of a spatially addressable small molecule microarray to an activity-based profile of proteases in crude cell lysates. The potential of this small molecule-based profiling technology is demonstrated by the detection of caspase activation upon induction of apoptosis, characterization of the activated caspase, and inhibition of the caspase-executed apoptotic phenotype using the small molecule inhibitor identified in the microarray-based profile. PMID:12167675

GRASP/Ada 95: Reverse Engineering Tools for Ada

NASA Technical Reports Server (NTRS)

Cross, James H., II

1996-01-01

The GRASP/Ada project (Graphical Representations of Algorithms, Structures, and Processes for Ada) has successfully created and prototyped an algorithmic level graphical representation for Ada software, the Control Structure Diagram (CSD), and a new visualization for a fine-grained complexity metric called the Complexity Profile Graph (CPG). By synchronizing the CSD and the CPG, the CSD view of control structure, nesting, and source code is directly linked to the corresponding visualization of statement level complexity in the CPG. GRASP has been integrated with GNAT, the GNU Ada 95 Translator to provide a comprehensive graphical user interface and development environment for Ada 95. The user may view, edit, print, and compile source code as a CSD with no discernible addition to storage or computational overhead. The primary impetus for creation of the CSD was to improve the comprehension efficiency of Ada software and, as a result, improve reliability and reduce costs. The emphasis has been on the automatic generation of the CSD from Ada 95 source code to support reverse engineering and maintenance. The CSD has the potential to replace traditional prettyprinted Ada source code. The current update has focused on the design and implementation of a new Motif compliant user interface, and a new CSD generator consisting of a tagger and renderer. The Complexity Profile Graph (CPG) is based on a set of functions that describes the context, content, and the scaling for complexity on a statement by statement basis. When combined graphicafly, the result is a composite profile of complexity for the program unit. Ongoing research includes the development and refinement of the associated functions, and the development of the CPG generator prototype. The current Version 5.0 prototype provides the capability for the user to generate CSDs and CPGs from Ada 95 source code in a reverse engineering as well as forward engineering mode with a level of flexibility suitable for practical application. This report provides an overview of the GRASP/Ada project with an emphasis on the current update.

A random set scoring model for prioritization of disease candidate genes using protein complexes and data-mining of GeneRIF, OMIM and PubMed records.

PubMed

Jiang, Li; Edwards, Stefan M; Thomsen, Bo; Workman, Christopher T; Guldbrandtsen, Bernt; Sørensen, Peter

2014-09-24

Prioritizing genetic variants is a challenge because disease susceptibility loci are often located in genes of unknown function or the relationship with the corresponding phenotype is unclear. A global data-mining exercise on the biomedical literature can establish the phenotypic profile of genes with respect to their connection to disease phenotypes. The importance of protein-protein interaction networks in the genetic heterogeneity of common diseases or complex traits is becoming increasingly recognized. Thus, the development of a network-based approach combined with phenotypic profiling would be useful for disease gene prioritization. We developed a random-set scoring model and implemented it to quantify phenotype relevance in a network-based disease gene-prioritization approach. We validated our approach based on different gene phenotypic profiles, which were generated from PubMed abstracts, OMIM, and GeneRIF records. We also investigated the validity of several vocabulary filters and different likelihood thresholds for predicted protein-protein interactions in terms of their effect on the network-based gene-prioritization approach, which relies on text-mining of the phenotype data. Our method demonstrated good precision and sensitivity compared with those of two alternative complex-based prioritization approaches. We then conducted a global ranking of all human genes according to their relevance to a range of human diseases. The resulting accurate ranking of known causal genes supported the reliability of our approach. Moreover, these data suggest many promising novel candidate genes for human disorders that have a complex mode of inheritance. We have implemented and validated a network-based approach to prioritize genes for human diseases based on their phenotypic profile. We have devised a powerful and transparent tool to identify and rank candidate genes. Our global gene prioritization provides a unique resource for the biological interpretation of data from genome-wide association studies, and will help in the understanding of how the associated genetic variants influence disease or quantitative phenotypes.

Evaluation of novel trans-sulfonamide platinum complexes against tumor cell lines.

PubMed

Pérez, Carlos; Díaz-García, C Vanesa; Agudo-López, Alba; del Solar, Virginia; Cabrera, Silvia; Agulló-Ortuño, M Teresa; Navarro-Ranninger, Carmen; Alemán, José; López-Martín, José A

2014-04-09

Platinum-based drugs, mainly cisplatin, are employed for the treatment of solid malignancies. However, cisplatin treatment often results in the development of chemoresistance, leading to therapeutic failure. Here, the antitumor activity of different trans-sulfonamide platinum complexes in a panel of human cell lines is presented. The cytotoxicity profiles and cell cycle analyses of these platinum sulfonamide complexes were different from those of cisplatin. These studies showed that complex 2b with cyclohexyldiamine and dansyl moieties had the best antitumoral activities. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Complex and region-specific changes in astroglial markers in the aging brain.

PubMed

Rodríguez, José J; Yeh, Chia-Yu; Terzieva, Slavica; Olabarria, Markel; Kulijewicz-Nawrot, Magdalena; Verkhratsky, Alexei

2014-01-01

Morphological aging of astrocytes was investigated in entorhinal cortex (EC), dentate gyrus (DG), and cornu ammonis 1 (CA1) regions of hippocampus of male SV129/C57BL6 mice of different age groups (3, 9, 18, and 24 months). Astroglial profiles were visualized by immunohistochemistry by using glial fibrillary acidic protein (GFAP), glutamine synthetase (GS), and s100β staining; these profiles were imaged using confocal or light microscopy for subsequent morphometric analysis. GFAP-positive profiles in the DG and the CA1 of the hippocampus showed progressive age-dependent hypertrophy, as indicated by an increase in surface, volume, and somata volume at 24 months of age compared with 3-month-old mice. In contrast with the hippocampal regions, aging induced a decrease in GFAP-positive astroglial profiles in the EC: the surface, volume, and cell body volume of astroglial cells at 24 months of age were decreased significantly compared with the 3-month group. The GS-positive astrocytes displayed smaller cellular surface areas at 24 months compared with 3-month-old animals in both areas of hippocampus, whereas GS-positive profiles remained unchanged in the EC of old mice. The morphometry of s100β-immunoreactive profiles revealed substantial increase in the EC, more moderate increase in the DG, and no changes in the CA1 area. Based on the morphological analysis of 3 astroglial markers, we conclude that astrocytes undergo a complex age-dependent remodeling in a brain region-specific manner. Copyright © 2014. Published by Elsevier Inc.

Functional protease profiling for diagnosis of malignant disease.

PubMed

Findeisen, Peter; Neumaier, Michael

2012-01-01

Clinical proteomic profiling by mass spectrometry (MS) aims at uncovering specific alterations within mass profiles of clinical specimens that are of diagnostic value for the detection and classification of various diseases including cancer. However, despite substantial progress in the field, the clinical proteomic profiling approaches have not matured into routine diagnostic applications so far. Their limitations are mainly related to high-abundance proteins and their complex processing by a multitude of endogenous proteases thus making rigorous standardization difficult. MS is biased towards the detection of low-molecular-weight peptides. Specifically, in serum specimens, the particular fragments of proteolytically degraded proteins are amenable to MS analysis. Proteases are known to be involved in tumour progression and tumour-specific proteases are released into the blood stream presumably as a result of invasive progression and metastasis. Thus, the determination of protease activity in clinical specimens from patients with malignant disease can offer diagnostic and also therapeutic options. The identification of specific substrates for tumour proteases in complex biological samples is challenging, but proteomic screens for proteases/substrate interactions are currently experiencing impressive progress. Such proteomic screens include peptide-based libraries, differential isotope labelling in combination with MS, quantitative degradomic analysis of proteolytically generated neo-N-termini, monitoring the degradation of exogenous reporter peptides with MS, and activity-based protein profiling. In the present article, we summarize and discuss the current status of proteomic techniques to identify tumour-specific protease-substrate interactions for functional protease profiling. Thereby, we focus on the potential diagnostic use of the respective approaches. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Accuracy of retrieving temperature and humidity profiles by ground-based microwave radiometry in truly complex terrain

NASA Astrophysics Data System (ADS)

Massaro, G.; Stiperski, I.; Pospichal, B.; Rotach, M. W.

2015-03-01

Within the Innsbruck Box project, a ground-based microwave radiometer (RPG-HATPRO) was operated in the Inn Valley (Austria), in very complex terrain, between September 2012 and May 2013 to obtain temperature and humidity vertical profiles of the full troposphere with a specific focus on the valley boundary layer. The profiles obtained by the radiometer with different retrieval algorithms based on different climatologies, are compared to local radiosonde data. A retrieval that is improved with respect to the one provided by the manufacturer, based on better resolved data, shows a significantly smaller root mean square error (RMSE), both for the temperature and humidity profiles. The improvement is particularly substantial at the heights close to the mountaintop level and in the upper troposphere. Lower level inversions, common in an alpine valley, are resolved to a satisfactory degree. On the other hand, upper level inversions (above 1200 m) still pose a significant challenge for retrieval. For this purpose, specialized retrieval algorithms were developed by classifying the radiosonde climatologies into specialized categories according to different criteria (seasons, daytime, nighttime) and using additional regressors (e.g., measurements from mountain stations). The training and testing on the radiosonde data for these specialized categories suggests that a classification of profiles that reproduces meaningful physical characteristics can yield improved targeted specialized retrievals. A really new and very promising method of improving the profile retrieval in a mountain region is adding further information in the retrieval, such as the surface temperature at fixed levels along a topographic slope or from nearby mountain tops.

Metabolite profiling and associated gene expression reveal two metabolic shifts during the seed-to-seedling transition in Arabidopsis thaliana.

PubMed

Silva, Anderson Tadeu; Ligterink, Wilco; Hilhorst, Henk W M

2017-11-01

Metabolic and transcriptomic correlation analysis identified two distinctive profiles involved in the metabolic preparation for seed germination and seedling establishment, respectively. Transcripts were identified that may control metabolic fluxes. The transition from a quiescent metabolic state (dry seed) to the active state of a vigorous seedling is crucial in the plant's life cycle. We analysed this complex physiological trait by measuring the changes in primary metabolism that occur during the transition in order to determine which metabolic networks are operational. The transition involves several developmental stages from seed germination to seedling establishment, i.e. between imbibition of the mature dry seed and opening of the cotyledons, the final stage of seedling establishment. We hypothesized that the advancement of growth is associated with certain signature metabolite profiles. Metabolite-metabolite correlation analysis underlined two specific profiles which appear to be involved in the metabolic preparation for seed germination and efficient seedling establishment, respectively. Metabolite profiles were also compared to transcript profiles and although transcriptional changes did not always equate to a proportional metabolic response, in depth correlation analysis identified several transcripts that may directly influence the flux through metabolic pathways during the seed-to-seedling transition. This correlation analysis also pinpointed metabolic pathways which are significant for the seed-to-seedling transition, and metabolite contents that appeared to be controlled directly by transcript abundance. This global view of the transcriptional and metabolic changes during the seed-to-seedling transition in Arabidopsis opens up new perspectives for understanding the complex regulatory mechanism underlying this transition.

Hydrodynamic Controls on Acoustical and Optical Water Properties in Tropical Reefs

DTIC Science & Technology

2012-09-30

scattering, absorption, and backscattering , shows more complex variations, with a strong diel signal , but with a tidal influence reflecting asymmetry in...Relative acoustic backscatter (ABS) profiles were derived from individual ADCP beam echo intensity correcting for range and absorption using the sonar...REFERENCES Deines K. L., 1999, Backscatter estimation using Broadband acoustic Doppler current profilers. Proceedings of the IEEE Sixth Working

Biogeochemical Typing of Paddy Field by a Data-Driven Approach Revealing Sub-Systems within a Complex Environment - A Pipeline to Filtrate, Organize and Frame Massive Dataset from Multi-Omics Analyses

PubMed Central

Ogawa, Diogo M. O.; Moriya, Shigeharu; Tsuboi, Yuuri; Date, Yasuhiro; Prieto-da-Silva, Álvaro R. B.; Rádis-Baptista, Gandhi; Yamane, Tetsuo; Kikuchi, Jun

2014-01-01

We propose the technique of biogeochemical typing (BGC typing) as a novel methodology to set forth the sub-systems of organismal communities associated to the correlated chemical profiles working within a larger complex environment. Given the intricate characteristic of both organismal and chemical consortia inherent to the nature, many environmental studies employ the holistic approach of multi-omics analyses undermining as much information as possible. Due to the massive amount of data produced applying multi-omics analyses, the results are hard to visualize and to process. The BGC typing analysis is a pipeline built using integrative statistical analysis that can treat such huge datasets filtering, organizing and framing the information based on the strength of the various mutual trends of the organismal and chemical fluctuations occurring simultaneously in the environment. To test our technique of BGC typing, we choose a rich environment abounding in chemical nutrients and organismal diversity: the surficial freshwater from Japanese paddy fields and surrounding waters. To identify the community consortia profile we employed metagenomics as high throughput sequencing (HTS) for the fragments amplified from Archaea rRNA, universal 16S rRNA and 18S rRNA; to assess the elemental content we employed ionomics by inductively coupled plasma optical emission spectroscopy (ICP-OES); and for the organic chemical profile, metabolomics employing both Fourier transformed infrared (FT-IR) spectroscopy and proton nuclear magnetic resonance (1H-NMR) all these analyses comprised our multi-omics dataset. The similar trends between the community consortia against the chemical profiles were connected through correlation. The result was then filtered, organized and framed according to correlation strengths and peculiarities. The output gave us four BGC types displaying uniqueness in community and chemical distribution, diversity and richness. We conclude therefore that the BGC typing is a successful technique for elucidating the sub-systems of organismal communities with associated chemical profiles in complex ecosystems. PMID:25330259

Biogeochemical typing of paddy field by a data-driven approach revealing sub-systems within a complex environment--a pipeline to filtrate, organize and frame massive dataset from multi-omics analyses.

PubMed

Ogawa, Diogo M O; Moriya, Shigeharu; Tsuboi, Yuuri; Date, Yasuhiro; Prieto-da-Silva, Álvaro R B; Rádis-Baptista, Gandhi; Yamane, Tetsuo; Kikuchi, Jun

2014-01-01

We propose the technique of biogeochemical typing (BGC typing) as a novel methodology to set forth the sub-systems of organismal communities associated to the correlated chemical profiles working within a larger complex environment. Given the intricate characteristic of both organismal and chemical consortia inherent to the nature, many environmental studies employ the holistic approach of multi-omics analyses undermining as much information as possible. Due to the massive amount of data produced applying multi-omics analyses, the results are hard to visualize and to process. The BGC typing analysis is a pipeline built using integrative statistical analysis that can treat such huge datasets filtering, organizing and framing the information based on the strength of the various mutual trends of the organismal and chemical fluctuations occurring simultaneously in the environment. To test our technique of BGC typing, we choose a rich environment abounding in chemical nutrients and organismal diversity: the surficial freshwater from Japanese paddy fields and surrounding waters. To identify the community consortia profile we employed metagenomics as high throughput sequencing (HTS) for the fragments amplified from Archaea rRNA, universal 16S rRNA and 18S rRNA; to assess the elemental content we employed ionomics by inductively coupled plasma optical emission spectroscopy (ICP-OES); and for the organic chemical profile, metabolomics employing both Fourier transformed infrared (FT-IR) spectroscopy and proton nuclear magnetic resonance (1H-NMR) all these analyses comprised our multi-omics dataset. The similar trends between the community consortia against the chemical profiles were connected through correlation. The result was then filtered, organized and framed according to correlation strengths and peculiarities. The output gave us four BGC types displaying uniqueness in community and chemical distribution, diversity and richness. We conclude therefore that the BGC typing is a successful technique for elucidating the sub-systems of organismal communities with associated chemical profiles in complex ecosystems.

A search for weak or complex magnetic fields in the B3V star ι Herculis

NASA Astrophysics Data System (ADS)

Wade, G. A.; Folsom, C. P.; Petit, P.; Petit, V.; Lignières, F.; Aurière, M.; Böhm, T.

2014-11-01

We obtained 128 high signal-to-noise ratio Stokes V spectra of the B3V star ι Her on five consecutive nights in 2012 with the ESPaDOnS spectropolarimeter at the Canada-France-Hawaii Telescope, with the aim of searching for the presence of weak and/or complex magnetic fields. Least-squares deconvolution (LSD) mean profiles were computed from individual spectra, averaged over individual nights and over the entire run. No Zeeman signatures are detected in any of the profiles. The longitudinal magnetic field in the grand average profile was measured to be -0.24 ± 0.32 G, as compared to -0.22 ± 0.32 G in the null profile. Our observations therefore provide no evidence for the presence of Zeeman signatures analogous to those observed in the A0V star Vega by Lignières et al. We interpret these observations in three ways. First, we compare the LSD profiles with synthetic Stokes V profiles corresponding to organized (dipolar) magnetic fields, for which we find an upper limit of about 8 G on the polar strength of any surface dipole present. Secondly, we compare the grand average profile with calculations corresponding to the random magnetic spot topologies of Kochukhov & Sudnik, inferring that spots, if present, of 2° radius with strengths of 2-4 G and a filling factor of 50 per cent should have been detected in our data. Finally, we compare the observations with synthetic V profiles corresponding to the surface magnetic maps of Vega (Petit et al.) computed for the spectral characteristics of ι Her. We conclude that while it is unlikely we would have detected a magnetic field identical to Vega's, we would have likely detected one with a peak strength of about 30 G, i.e. approximately four times as strong as that of Vega.

ComplexQuant: high-throughput computational pipeline for the global quantitative analysis of endogenous soluble protein complexes using high resolution protein HPLC and precision label-free LC/MS/MS.

PubMed

Wan, Cuihong; Liu, Jian; Fong, Vincent; Lugowski, Andrew; Stoilova, Snejana; Bethune-Waddell, Dylan; Borgeson, Blake; Havugimana, Pierre C; Marcotte, Edward M; Emili, Andrew

2013-04-09

The experimental isolation and characterization of stable multi-protein complexes are essential to understanding the molecular systems biology of a cell. To this end, we have developed a high-throughput proteomic platform for the systematic identification of native protein complexes based on extensive fractionation of soluble protein extracts by multi-bed ion exchange high performance liquid chromatography (IEX-HPLC) combined with exhaustive label-free LC/MS/MS shotgun profiling. To support these studies, we have built a companion data analysis software pipeline, termed ComplexQuant. Proteins present in the hundreds of fractions typically collected per experiment are first identified by exhaustively interrogating MS/MS spectra using multiple database search engines within an integrative probabilistic framework, while accounting for possible post-translation modifications. Protein abundance is then measured across the fractions based on normalized total spectral counts and precursor ion intensities using a dedicated tool, PepQuant. This analysis allows co-complex membership to be inferred based on the similarity of extracted protein co-elution profiles. Each computational step has been optimized for processing large-scale biochemical fractionation datasets, and the reliability of the integrated pipeline has been benchmarked extensively. This article is part of a Special Issue entitled: From protein structures to clinical applications. Copyright © 2012 Elsevier B.V. All rights reserved.

Cyclodextrin-insulin complex encapsulated polymethacrylic acid based nanoparticles for oral insulin delivery.

PubMed

Sajeesh, S; Sharma, Chandra P

2006-11-15

Present investigation was aimed at developing an oral insulin delivery system based on hydroxypropyl beta cyclodextrin-insulin (HPbetaCD-I) complex encapsulated polymethacrylic acid-chitosan-polyether (polyethylene glycol-polypropylene glycol copolymer) (PMCP) nanoparticles. Nanoparticles were prepared by the free radical polymerization of methacrylic acid in presence of chitosan and polyether in a solvent/surfactant free medium. Dynamic light scattering (DLS) experiment was conducted with particles dispersed in phosphate buffer (pH 7.4) and size distribution curve was observed in the range of 500-800 nm. HPbetaCD was used to prepare non-covalent inclusion complex with insulin and complex was analyzed by Fourier transform infrared (FTIR) and fluorescence spectroscopic studies. HPbetaCD complexed insulin was encapsulated into PMCP nanoparticles by diffusion filling method and their in vitro release profile was evaluated at acidic/alkaline pH. PMCP nanoparticles displayed good insulin encapsulation efficiency and release profile was largely dependent on the pH of the medium. Enzyme linked immunosorbent assay (ELISA) study demonstrated that insulin encapsulated inside the particles was biologically active. Trypsin inhibitory effect of PMCP nanoparticles was evaluated using N-alpha-benzoyl-L-arginine ethyl ester (BAEE) and casein as substrates. Mucoadhesive studies of PMCP nanoparticles were conducted using freshly excised rat intestinal mucosa and the particles were found fairly adhesive. From the preliminary studies, cyclodextrin complexed insulin encapsulated mucoadhesive nanoparticles appear to be a good candidate for oral insulin delivery.

Toward self-organization and complex matter.

PubMed

Lehn, Jean-Marie

2002-03-29

Beyond molecular chemistry based on the covalent bond, supramolecular chemistry aims at developing highly complex chemical systems from components interacting through noncovalent intermolecular forces. Over the past quarter century, supramolecular chemistry has grown into a major field and has fueled numerous developments at the interfaces with biology and physics. Some of the conceptual advances and future challenges are profiled here.

Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes.

PubMed

Uchikoga, Nobuyuki; Hirokawa, Takatsugu

2010-05-11

Protein-protein docking for proteins with large conformational changes was analyzed by using interaction fingerprints, one of the scales for measuring similarities among complex structures, utilized especially for searching near-native protein-ligand or protein-protein complex structures. Here, we have proposed a combined method for analyzing protein-protein docking by taking large conformational changes into consideration. This combined method consists of ensemble soft docking with multiple protein structures, refinement of complexes, and cluster analysis using interaction fingerprints and energy profiles. To test for the applicability of this combined method, various CaM-ligand complexes were reconstructed from the NMR structures of unbound CaM. For the purpose of reconstruction, we used three known CaM-ligands, namely, the CaM-binding peptides of cyclic nucleotide gateway (CNG), CaM kinase kinase (CaMKK) and the plasma membrane Ca2+ ATPase pump (PMCA), and thirty-one structurally diverse CaM conformations. For each ligand, 62000 CaM-ligand complexes were generated in the docking step and the relationship between their energy profiles and structural similarities to the native complex were analyzed using interaction fingerprint and RMSD. Near-native clusters were obtained in the case of CNG and CaMKK. The interaction fingerprint method discriminated near-native structures better than the RMSD method in cluster analysis. We showed that a combined method that includes the interaction fingerprint is very useful for protein-protein docking analysis of certain cases.

Improving the Representation of Snow Crystal Properties within a Single-Moment Microphysics Scheme

NASA Technical Reports Server (NTRS)

Molthan, Andrew L.; Petersen, Walter A.; Case, Jonathan L.; Dembek, Scott R.

2010-01-01

The assumptions of a single-moment microphysics scheme (NASA Goddard) were evaluated using a variety of surface, aircraft and radar data sets. Fixed distribution intercepts and snow bulk densities fail to represent the vertical variability and diversity of crystal populations for this event. Temperature-based equations have merit, but they can be adversely affected by complex temperature profiles that are inverted or isothermal. Column-based approaches can mitigate complex profiles of temperature but are restricted by the ability of the model to represent cloud depth. Spheres are insufficient for use in CloudSat reflectivity comparisons due to Mie resonance, but reasonable for Rayleigh scattering applications. Microphysics schemes will benefit from a greater range of snow crystal characteristics to accommodate naturally occurring diversity.

Analysis of volatile metabolites in biological fluids as indicators of prodromal disease condition

NASA Technical Reports Server (NTRS)

Zlatkis, A.

1982-01-01

The volatile profile cannot be defined as a single class of substances, rather it is a broad spectrum of materials of different polarities characterized by having a boiling-point in the low to medium range (up to approximately 300 C) and the fact that the compounds are suitable for gas chromatography without derivatization. The organic volatile profiles are very complex mixtures of metabolic byproducts, intermediates, and terminal products of enzymatic degradations composed mainly of alcohols, ketones, aldehydes, pyrazines, sulfides, isothiocyanates, pyrroles, and furans. The concentration of organic volatiles in biological fluids covers a wide range with many important components present at trace levels. The complexity of the organic volatile fraction requires the use of capillary columns for their separation.

Peak Metamorphic Temperature Profile across Eastern Belt Franciscan, Northern California Coast Ranges

NASA Astrophysics Data System (ADS)

Schmidt, W. L.; Platt, J. P.

2017-12-01

Previous work done on metamorphic temperatures across the lawsonite-albite to blueschist facies rocks of the Eastern Belt of the Franciscan accretionary complex has relied on a combination of many methods, and suggests that temperature broadly increases from west to east. The Taliaferro Metamorphic Complex is an exception to this pattern and shows higher pressures, and possibly higher temperatures, than its surroundings. The exact location and nature of the faults separating accreted packets in the Eastern Belt is somewhat controversial. A recently calibrated low-temperature laser Raman geothermometer for use on carbonaceous material provides a uniform method of estimating peak metamorphic temperature across the eastern Franciscan and is here used to identify the position of major tectonic boundaries. Temperatures were obtained from exposures in Thomes Creek, Cottonwood Creek, Grindstone Creek, and the middle fork of the Eel River. Peak T in the South Fork Mountain Schist, the highest grade and easternmost unit in the Franciscan, is 310-375°C, whereas in immediately underlying lawsonite-albite facies rocks below the Log Springs thrust, peak T is 270 - 300°C. The Taliaferro Metamorphic Complex reached a peak temperature of 336°C, whereas the surrounding lawsonite-albite facies rocks yield peak temperatures as low as 232°C. Preliminary temperature profiles clearly allow the major faults bounding the Taliaferro Metamorphic Complex and the South Fork Mountain Schist to be located. Extension of the temperature profile has the potential to reveal further detail within these units and the lower grade rocks surrounding them.

Density effects on the electronic contribution to hydrogen Lyman alpha Stark profiles

NASA Astrophysics Data System (ADS)

Motapon, O.

1998-01-01

The quantum unified theory of Stark broadening (Tran Minh et al. 1975, Feautrier et al. 1976) is used to study the density effects on the electronic contribution to the hydrogen Lyman alpha lineshape. The contribution of the first angular momenta to the total profile is obtained by an extrapolation method, and the results agree with other approaches. The comparison made with Vidal et al. (1973) shows a good agreement; and the electronic profile is found to be linear in density for | Delta lambda right | greater than 8 Angstroms for densities below 10(17) cm(-3) , while the density dependence becomes more complex for | Delta lambda right | less than 8 Angstroms. The wing profiles are calculated at various temperatures scaling from 2500 to 40000K and a polynomial fit of these profiles is given.

Lithium diffusion in polyether ether ketone and polyimide stimulated by in situ electron irradiation and studied by the neutron depth profiling method

NASA Astrophysics Data System (ADS)

Vacik, J.; Hnatowicz, V.; Attar, F. M. D.; Mathakari, N. L.; Dahiwale, S. S.; Dhole, S. D.; Bhoraskar, V. N.

2014-10-01

Diffusion of lithium from a LiCl aqueous solution into polyether ether ketone (PEEK) and polyimide (PI) assisted by in situ irradiation with 6.5 MeV electrons was studied by the neutron depth profiling method. The number of the Li atoms was found to be roughly proportional to the diffusion time. Regardless of the diffusion time, the measured depth profiles in PEEK exhibit a nearly exponential form, indicating achievement of a steady-state phase of a diffusion-reaction process specified in the text. The form of the profiles in PI is more complex and it depends strongly on the diffusion time. For the longer diffusion time, the profile consists of near-surface bell-shaped part due to Fickian-like diffusion and deeper exponential part.

Inclusion complex effect on the bioavailability of clotrimazole from poloxamer-based solid suppository.

PubMed

Balakrishnan, Prabagar; Song, Chung Kil; Cho, Hyun-Jong; Yang, Su-Geun; Kim, Dae Duk; Yong, Chul Soon; Choi, Han-Gon

2012-07-01

To study the effect of β-cyclodextrin (βCD) inclusion complex on the bioavailability of clotrimazole from poloxamer-based suppository, formulations composed of P 188, propylene glycol and different molar ratio of clotrimazole-βCD inclusion complex were prepared. Clotrimazole (1%) has been formulated in a suppository using the thermo sensitive polymer P188 (70%) together with propylene glycol (30%). To increase its aqueous solubility, clotrimazole was incorporated as its inclusion complex at various molar ratios with βCD (1:0.25, 1:0.5, 1:1, and 1:2). The inclusion complex was characterized by differential scanning calorimetry (DSC), XRD and phase solubility studies. It was observed that the complexation with βCD, particularly at high molar ratio (F3 (1:1) and F4 (1:2)) decreased the release profile of clotrimazole considerably. However, suppositories containing inclusion complex at low molar ratio (F1 (1:0.25) and F2 (1:0.5)) showed excellent release profile compared to control formulation. In vivo study in rats at 15 mg/Kg dose showed that the F1 and F2 (82.39 ± 15.40 and 67.05 ± 8.79, respectively) significantly increased the AUC compared to that of F3 (41.48 ± 11.51), F4 (23.34 ± 8.37) and control (46.7 ± 7.87) suppositories. Thus, the suppositories containing inclusion complexes prepared at low drug to βCD molar ratio (F1) could be a potential suppository formulation to increase the bioavailability of hydrophobic drugs such as clotrimazole.

The diverse density profiles of galaxy clusters with self-interacting dark matter plus baryons

NASA Astrophysics Data System (ADS)

Robertson, Andrew; Massey, Richard; Eke, Vincent; Tulin, Sean; Yu, Hai-Bo; Bahé, Yannick; Barnes, David J.; Bower, Richard G.; Crain, Robert A.; Dalla Vecchia, Claudio; Kay, Scott T.; Schaller, Matthieu; Schaye, Joop

2018-05-01

We present the first simulated galaxy clusters (M200 > 1014 M⊙) with both self-interacting dark matter (SIDM) and baryonic physics. They exhibit a greater diversity in both dark matter and stellar density profiles than their counterparts in simulations with collisionless dark matter (CDM), which is generated by the complex interplay between dark matter self-interactions and baryonic physics. Despite variations in formation history, we demonstrate that analytical Jeans modelling predicts the SIDM density profiles remarkably well, and the diverse properties of the haloes can be understood in terms of their different final baryon distributions.

A latent profile analysis of math achievement, numerosity, and math anxiety in twins

PubMed Central

Hart, Sara A.; Logan, Jessica A.R.; Thompson, Lee; Kovas, Yulia; McLoughlin, Gráinne; Petrill, Stephen A.

2015-01-01

Underperformance in math is a problem with increasing prevalence, complex etiology, and severe repercussions. This study examined the etiological heterogeneity of math performance in a sample of 264 pairs of 12-year-old twins assessed on measures of math achievement, numerosity and math anxiety. Latent profile analysis indicated five groupings of individuals representing different patterns of math achievement, numerosity and math anxiety, coupled with differing degrees of familial transmission. These results suggest that there may be distinct profiles of math achievement, numerosity and anxiety; particularly for students who struggle in math. PMID:26957650

A latent profile analysis of math achievement, numerosity, and math anxiety in twins.

PubMed

Hart, Sara A; Logan, Jessica A R; Thompson, Lee; Kovas, Yulia; McLoughlin, Gráinne; Petrill, Stephen A

2016-02-01

Underperformance in math is a problem with increasing prevalence, complex etiology, and severe repercussions. This study examined the etiological heterogeneity of math performance in a sample of 264 pairs of 12-year-old twins assessed on measures of math achievement, numerosity and math anxiety. Latent profile analysis indicated five groupings of individuals representing different patterns of math achievement, numerosity and math anxiety, coupled with differing degrees of familial transmission. These results suggest that there may be distinct profiles of math achievement, numerosity and anxiety; particularly for students who struggle in math.

Accounting for observed small angle X-ray scattering profile in the protein-protein docking server ClusPro.

PubMed

Xia, Bing; Mamonov, Artem; Leysen, Seppe; Allen, Karen N; Strelkov, Sergei V; Paschalidis, Ioannis Ch; Vajda, Sandor; Kozakov, Dima

2015-07-30

The protein-protein docking server ClusPro is used by thousands of laboratories, and models built by the server have been reported in over 300 publications. Although the structures generated by the docking include near-native ones for many proteins, selecting the best model is difficult due to the uncertainty in scoring. Small angle X-ray scattering (SAXS) is an experimental technique for obtaining low resolution structural information in solution. While not sufficient on its own to uniquely predict complex structures, accounting for SAXS data improves the ranking of models and facilitates the identification of the most accurate structure. Although SAXS profiles are currently available only for a small number of complexes, due to its simplicity the method is becoming increasingly popular. Since combining docking with SAXS experiments will provide a viable strategy for fairly high-throughput determination of protein complex structures, the option of using SAXS restraints is added to the ClusPro server. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

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

Apel, William A; Thompson, Vicki S

A method for analyzing a biological sample by antibody profiling for identifying forensic samples or for detecting the presence of an analyte. In an embodiment of the invention, the analyte is a drug, such as marijuana, Cocaine (crystalline tropane alkaloid), methamphetamine, methyltestosterone, or mesterolone. The method comprises attaching antigens to a surface of a solid support in a preselected pattern to form an array wherein locations of the antigens are known; contacting the array with the biological sample such that a portion of antibodies in the sample reacts with and binds to the antigens in the array to form immunemore » complexes; washing away antibodies that do form immune complexes; and detecting the immune complexes, to form an antibody profile. Forensic samples are identified by comparing a sample from an unknown source with a sample from a known source. Further, an assay, such as a test for illegal drug use, can be coupled to a test for identity such that the results of the assay can be positively correlated to the subject's identity.« less

Anatomy of a metamorphic core complex: seismic refraction/wide-angle reflection profiling in southeastern California and western Arizona

USGS Publications Warehouse

McCarthy, J.; Larkin, S.P.; Fuis, G.S.; Simpson, R.W.; Howard, K.A.

1991-01-01

The metamorphic core complex belt in southeastern California and western Arizona is a NW-SE trending zone of unusually large Tertiary extension and uplift. Midcrustal rocks exposed in this belt raise questions about the crustal thickness, crustal structure, and the tectonic evolution of the region. Three seismic refraction/wide-angle reflection profiles were collected to address these issues. The results presented here, which focus on the Whipple and Buckskin-Rawhide mountains, yield a consistent three-dimensiional image of this part of the metamorphic core complex belt. The final model consists of a thin veneer (<2 km) of upper plate and fractured lower plate rocks (1.5-5.5 km s-1) overlying a fairly homogeneous basement (~6.0 km s-1) and a localized high-velocity (6.4 km s -1) body situated beneath the western Whipple Mountains. A prominent midcrustal reflection is identified beneath the Whipple and Buckskin Rawhide mountains between 10 and 20km depth. -from Authors

Rapid classification of biological components

DOEpatents

Thompson, Vicki S.; Barrett, Karen B.; Key, Diane E.

2013-10-15

A method is disclosed for analyzing a biological sample by antibody profiling for identifying forensic samples or for detecting the presence of an analyte. In an illustrative embodiment of the invention, the analyte is a drug, such as marijuana, cocaine (crystalline tropane alkaloid), methamphetamine, methyltestosterone, or mesterolone. The method involves attaching antigens to a surface of a solid support in a preselected pattern to form an array wherein the locations of the antigens are known; contacting the array with the biological sample such that a portion of antibodies in the sample reacts with and binds to antigens in the array, thereby forming immune complexes; washing away antibodies that do not form immune complexes; and detecting the immune complexes, thereby forming an antibody profile. Forensic samples are identified by comparing a sample from an unknown source with a sample from a known source. Further, an assay, such as a test for illegal drug use, can be coupled to a test for identity such that the results of the assay can be positively correlated to a subject's identity.

Rapid classification of biological components

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

Thompson, Vicki S.; Barrett, Karen B.; Key, Diane E.

A method is disclosed for analyzing a biological sample by antibody profiling for identifying forensic samples or for detecting the presence of an analyte. In an illustrative embodiment of the invention, the analyte is a drug, such as marijuana, cocaine, methamphetamine, methyltestosterone, or mesterolone. The method involves attaching antigens to the surface of a solid support in a preselected pattern to form an array wherein the locations of the antigens are known; contacting the array with the biological sample such that a portion of antibodies in the sample reacts with and binds to antigens in the array, thereby forming immunemore » complexes; washing away antibodies that do form immune complexes; and detecting the immune complexes, thereby forming an antibody profile. Forensic samples are identified by comparing a sample from an unknown source with a sample from a known source. Further, an assay, such as a test for illegal drug use, can be coupled to a test for identity such that the results of the assay can be positively correlated to the subject's identity.« less

Incorporating profile information in community detection for online social networks

NASA Astrophysics Data System (ADS)

Fan, W.; Yeung, K. H.

2014-07-01

Community structure is an important feature in the study of complex networks. It is because nodes of the same community may have similar properties. In this paper we extend two popular community detection methods to partition online social networks. In our extended methods, the profile information of users is used for partitioning. We apply the extended methods in several sample networks of Facebook. Compared with the original methods, the community structures we obtain have higher modularity. Our results indicate that users' profile information is consistent with the community structure of their friendship network to some extent. To the best of our knowledge, this paper is the first to discuss how profile information can be used to improve community detection in online social networks.

Ozone height profiles using laser heterodyne radiometer

NASA Technical Reports Server (NTRS)

Jain, S. L.

1994-01-01

The monitoring of vertical profiles of ozone and related minor constituents in the atmosphere are of great significance to understanding the complex interaction between atmospheric dynamics, chemistry and radiation budget. An ultra high spectral resolution tunable CO2 laser heterodyne radiometer has been designed, developed and set up at the National Physical Laboratory, New Delhi to obtain vertical profiles of various minor constituents the characteristic absorption lines in 9 to 11 micron spectral range. Due to its high spectral resolution the lines can be resolved completely and data obtained are inverted to get vertical profiles using an inversion technique developed by the author. In the present communication the salient features of the laser heterodyne system and the results obtained are discussed in detail.

Unmasking molecular profiles of bladder cancer.

PubMed

Piao, Xuan-Mei; Byun, Young Joon; Kim, Wun-Jae; Kim, Jayoung

2018-03-01

Precision medicine is designed to tailor treatments for individual patients by factoring in each person's specific biology and mechanism of disease. This paradigm shifted from a "one size fits all" approach to "personalized and precision care" requires multiple layers of molecular profiling of biomarkers for accurate diagnosis and prediction of treatment responses. Intensive studies are also being performed to understand the complex and dynamic molecular profiles of bladder cancer. These efforts involve looking bladder cancer mechanism at the multiple levels of the genome, epigenome, transcriptome, proteome, lipidome, metabolome etc. The aim of this short review is to outline the current technologies being used to investigate molecular profiles and discuss biomarker candidates that have been investigated as possible diagnostic and prognostic indicators of bladder cancer.

Incidence of the WAIS-R Fuld profile in HIV-1 infection.

PubMed

van Gorp, W G; Tulin, S J; Evans, G; Satz, P

1990-10-01

The incidence of a WAIS-R subtest "marker" sensitive to cholinergic dysfunction was assessed in a sample 116 homosexual males infected with HIV (Acquired Immunodeficiency Syndrome [AIDS] N = 40; AIDS Related Complex [ARC], N = 76). The incidence of positive profiles was low in the overall sample (11/116, 9%), and significantly lower than incidence rates reported for known cholinergic deficient groups (Alzheimer's disease; scopolamine). However, significantly more AIDS patients (8/40, 20%) than ARC patients (3/76, 4%) demonstrated positive profiles. These results suggest that, as a group, persons with ARC or AIDS do not show an increased incidence of the Fuld profile associated with cholinergic disruption, and offer continued support for diagnostic specificity of the Fuld formula for Alzheimer's disease.

CRISPR-cas loci profiling of Cronobacter sakazakii pathovars.

PubMed

Ogrodzki, Pauline; Forsythe, Stephen James

2016-12-01

Cronobacter sakazakii sequence types 1, 4, 8 and 12 are associated with outbreaks of neonatal meningitis and necrotizing enterocolitis infections. However clonality results in strains which are indistinguishable using conventional methods. This study investigated the use of clustered regularly interspaced short palindromic repeats (CRISPR)-cas loci profiling for epidemiological investigations. Seventy whole genomes of C. sakazakii strains from four clonal complexes which were widely distributed temporally, geographically and origin of source were profiled. All strains encoded the same type I-E subtype CRISPR-cas system with a total of 12 different CRISPR spacer arrays. This study demonstrated the greater discriminatory power of CRISPR spacer array profiling compared with multilocus sequence typing, which will be of use in source attribution during Cronobacter outbreak investigations.

Covalent small-molecule-RNA complex formation enables cellular profiling of small-molecule-RNA interactions.

PubMed

Guan, Lirui; Disney, Matthew D

2013-09-16

Won't let you go! A strategy is described to design small molecules that react with their cellular RNA targets. This approach not only improves the activity of compounds targeting RNA in cell culture by a factor of about 2500 but also enables cell-wide profiling of its RNA targets. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Central nervous system tumours profile at a referral center in the Brazilian Amazon region, 1997–2014

PubMed Central

Semblano, Aluízio Augusto Pereira; Moreira, Matheus Acácio; de Lemos, Manuela Nascimento; de Mello, Vanessa Jóia; Hamoy, Moisés; Nazareth Junior, Mario Hermes; Paschoal Junior, Fernando Mendes; Adami, Fernando

2017-01-01

Tumours of the Central Nervous System (CNS) are an important cause of mortality from cancer. Epidemiological data on neoplams affecting the CNS are scarce in Brazil, especially in the Amazon region. The study aims at describing the histopathological profile of CNS tumours cases at a high-complexity referral cancer center. This study has described a 17-year-series profile of CNS tumours, registered at a high-complexity referral cancer center in Pará state, from January 1997 until July 2014 in the Brazilian Amazon Region. Data was gathered from histopathology reports kept in the hospital’s cancer registry and 949 cases of CNS tumours were analyzed. The most common histopathology were neuroepithelial tumours (approx. 40%) and meningioma was the most frequent especific tumor histologic subtype (22.2%). Neuroepithelial tumours were more frequent in patients with ages ranging from less than a year to 19 years, whereas metastatic tumours were prevalent in patients over 40 years of age. It was not found temporal trends during the studied period. The knowledge of these tumours profile is valuable for the understanding of cancer epidemiology in the region, since its prevalence is currently underreported and more awareness on the disease is needed. PMID:28369089

A formal protocol test procedure for the Survivable Adaptable Fiber Optic Embedded Network (SAFENET)

NASA Astrophysics Data System (ADS)

High, Wayne

1993-03-01

This thesis focuses upon a new method for verifying the correct operation of a complex, high speed fiber optic communication network. These networks are of growing importance to the military because of their increased connectivity, survivability, and reconfigurability. With the introduction and increased dependence on sophisticated software and protocols, it is essential that their operation be correct. Because of the speed and complexity of fiber optic networks being designed today, they are becoming increasingly difficult to test. Previously, testing was accomplished by application of conformance test methods which had little connection with an implementation's specification. The major goal of conformance testing is to ensure that the implementation of a profile is consistent with its specification. Formal specification is needed to ensure that the implementation performs its intended operations while exhibiting desirable behaviors. The new conformance test method presented is based upon the System of Communicating Machine model which uses a formal protocol specification to generate a test sequence. The major contribution of this thesis is the application of the System of Communicating Machine model to formal profile specifications of the Survivable Adaptable Fiber Optic Embedded Network (SAFENET) standard which results in the derivation of test sequences for a SAFENET profile. The results applying this new method to SAFENET's OSI and Lightweight profiles are presented.

A transcriptome-based assessment of the astrocytic dystrophin-associated complex in the developing human brain.

PubMed

Simon, Matthew J; Murchison, Charles; Iliff, Jeffrey J

2018-02-01

Astrocytes play a critical role in regulating the interface between the cerebral vasculature and the central nervous system. Contributing to this is the astrocytic endfoot domain, a specialized structure that ensheathes the entirety of the vasculature and mediates signaling between endothelial cells, pericytes, and neurons. The astrocytic endfoot has been implicated as a critical element of the glymphatic pathway, and changes in protein expression profiles in this cellular domain are linked to Alzheimer's disease pathology. Despite this, basic physiological properties of this structure remain poorly understood including the developmental timing of its formation, and the protein components that localize there to mediate its functions. Here we use human transcriptome data from male and female subjects across several developmental stages and brain regions to characterize the gene expression profile of the dystrophin-associated complex (DAC), a known structural component of the astrocytic endfoot that supports perivascular localization of the astroglial water channel aquaporin-4. Transcriptomic profiling is also used to define genes exhibiting parallel expression profiles to DAC elements, generating a pool of candidate genes that encode gene products that may contribute to the physiological function of the perivascular astrocytic endfoot domain. We found that several genes encoding transporter proteins are transcriptionally associated with DAC genes. © 2017 Wiley Periodicals, Inc.

Genome-Wide Expression Profiling of Complex Regional Pain Syndrome

PubMed Central

Jin, Eun-Heui; Zhang, Enji; Ko, Youngkwon; Sim, Woo Seog; Moon, Dong Eon; Yoon, Keon Jung; Hong, Jang Hee; Lee, Won Hyung

2013-01-01

Complex regional pain syndrome (CRPS) is a chronic, progressive, and devastating pain syndrome characterized by spontaneous pain, hyperalgesia, allodynia, altered skin temperature, and motor dysfunction. Although previous gene expression profiling studies have been conducted in animal pain models, there genome-wide expression profiling in the whole blood of CRPS patients has not been reported yet. Here, we successfully identified certain pain-related genes through genome-wide expression profiling in the blood from CRPS patients. We found that 80 genes were differentially expressed between 4 CRPS patients (2 CRPS I and 2 CRPS II) and 5 controls (cut-off value: 1.5-fold change and p<0.05). Most of those genes were associated with signal transduction, developmental processes, cell structure and motility, and immunity and defense. The expression levels of major histocompatibility complex class I A subtype (HLA-A29.1), matrix metalloproteinase 9 (MMP9), alanine aminopeptidase N (ANPEP), l-histidine decarboxylase (HDC), granulocyte colony-stimulating factor 3 receptor (G-CSF3R), and signal transducer and activator of transcription 3 (STAT3) genes selected from the microarray were confirmed in 24 CRPS patients and 18 controls by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). We focused on the MMP9 gene that, by qRT-PCR, showed a statistically significant difference in expression in CRPS patients compared to controls with the highest relative fold change (4.0±1.23 times and p = 1.4×10−4). The up-regulation of MMP9 gene in the blood may be related to the pain progression in CRPS patients. Our findings, which offer a valuable contribution to the understanding of the differential gene expression in CRPS may help in the understanding of the pathophysiology of CRPS pain progression. PMID:24244504

Mobility and leachability of zinc in two soils treated with six organic zinc complexes.

PubMed

Alvarez, J M; Novillo, J; Obrador, A; López-Valdivia, L M

2001-08-01

A study of soil columns was conducted to evaluate Zn movement potential in two reconstructed soil profiles. Zn-phenolate, Zn-EDDHA, Zn-EDTA, Zn-lignosulfonate, Zn-polyflavonoid, and Zn-heptagluconate were applied in the upper zone of the column. The different physicochemical properties of the two soils and the micronutrient source may influence Zn leaching, the distribution of Zn among soil fractions, and the Zn available to the plant in the depth of the layers. In Aquic Haploxeralf soil, the application of six fertilizers produced little migration and very small leaching of Zn in the soil profiles. In Calcic Haploxeralf soil, Zn-EDTA migrated and was distributed throughout the soil columns. This Zn chelate produces a loss of Zn by leaching, which was 36% of the added Zn. In the latter soil, Zn leached very little with the other five fertilizer treatments. The same as for these organic Zn complexes, the retention of added Zn indicated the potential of metal accumulation in the A(p) horizons of the two soil profiles. A large portion of applied Zn was available to plants [diethylenetriaminepentaacetic acid (DTPA) and Mehlich-3 extractable Zn] in the depths reached by the different commercial formulations. The relationship between the two methods was highly significant (Mehlich-3-Zn = 1.25 + 1.13 DTPA-Zn, R(2) = 99.19%). When Zn was added as Zn-EDTA, the amounts of the most labile fractions (water-soluble plus exchangeable and organically complexed Zn) increased throughout the entire profile column in comparison with the control columns, although in the B(t) horizon of the Aquic Haploxeralf soil they increased only slightly.

Evaluation of Single-Doppler Radar Wind Retrievals in Flat and Complex Terrain

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

Newsom, Rob K.; Berg, Larry K.; Pekour, Mikhail S.

2014-08-01

The accuracy of winds derived from NEXRAD level II data is assessed by comparison with independent observations from 915 MHz radar wind profilers. The evaluation is carried out at two locations with very different terrain characteristics. One site is located in an area of complex terrain within the State Line Wind Energy Center in northeast Oregon. The other site is located in an area of flat terrain on the east-central Florida coast. The National Severe Storm Laboratory’s 2DVar algorithm is used to retrieve wind fields from the KPDT (Pendleton OR) and KMLB (Melbourne FL) NEXRAD radars. Comparisons between the 2DVarmore » retrievals and the radar profilers were conducted over a period of about 6 months and at multiple height levels at each of the profiler sites. Wind speed correlations at most observation height levels fell in the range from 0.7 to 0.8, indicating that the retrieved winds followed temporal fluctuations in the profiler-observed winds reasonably well. The retrieved winds, however, consistently exhibited slow biases in the range of1 to 2 ms-1. Wind speed difference distributions were broad with standard deviations in the range from 3 to 4 ms-1. Results from the Florida site showed little change in the wind speed correlations and difference standard deviations with altitude between about 300 and 1400 m AGL. Over this same height range, results from the Oregon site showed a monotonic increase in the wind speed correlation and a monotonic decrease in the wind speed difference standard deviation with increasing altitude. The poorest overall agreement occurred at the lowest observable level (~300 m AGL) at the Oregon site, where the effects of the complex terrain were greatest.« less

Transcriptome complexity in cardiac development and diseases--an expanding universe between genome and phenome.

PubMed

Gao, Chen; Wang, Yibin

2014-01-01

With the advancement of transcriptome profiling by micro-arrays and high-throughput RNA-sequencing, transcriptome complexity and its dynamics are revealed at different levels in cardiovascular development and diseases. In this review, we will highlight the recent progress in our knowledge of cardiovascular transcriptome complexity contributed by RNA splicing, RNA editing and noncoding RNAs. The emerging importance of many of these previously under-explored aspects of gene regulation in cardiovascular development and pathology will be discussed.

Complexity Measures, Task Type, and Analytic Evaluations of Speaking Proficiency in a School-Based Assessment Context

ERIC Educational Resources Information Center

Gan, Zhengdong

2012-01-01

This study, which is part of a large-scale study of using objective measures to validate assessment rating scales and assessment tasks in a high-profile school-based assessment initiative in Hong Kong, examined how grammatical complexity measures relate to task type and analytic evaluations of students' speaking proficiency in a classroom-based…

Comparison of protein profiles of beech bark disease-resistant or beech bark disease-susceptible American beech

Treesearch

Mary E. Mason; Marek Krasowski; Judy Loo; Jennifer. Koch

2011-01-01

Proteomic analysis of beech bark proteins from trees resistant and susceptible to beech bark disease (BBD) was conducted. Sixteen trees from eight geographically isolated stands, 10 resistant (healthy) and 6 susceptible (diseased/infested) trees, were studied. The genetic complexity of the sample unit, the sampling across a wide geographic area, and the complexity of...

Community Learning Campus: It Takes a Simple Message to Build a Complex Project

ERIC Educational Resources Information Center

Pearson, George

2012-01-01

Education Canada asked Tom Thompson, president of Olds College and a prime mover behind the Community Learning Campus (CLC): What were the lessons learned from this unusually ambitious education project? Thompson mentions six lessons he learned from this complex project which include: (1) Dream big, build small, act now; (2) Keep a low profile at…

Observing Consistency in Online Communication Patterns for User Re-Identification

PubMed Central

Venter, Hein S.

2016-01-01

Comprehension of the statistical and structural mechanisms governing human dynamics in online interaction plays a pivotal role in online user identification, online profile development, and recommender systems. However, building a characteristic model of human dynamics on the Internet involves a complete analysis of the variations in human activity patterns, which is a complex process. This complexity is inherent in human dynamics and has not been extensively studied to reveal the structural composition of human behavior. A typical method of anatomizing such a complex system is viewing all independent interconnectivity that constitutes the complexity. An examination of the various dimensions of human communication pattern in online interactions is presented in this paper. The study employed reliable server-side web data from 31 known users to explore characteristics of human-driven communications. Various machine-learning techniques were explored. The results revealed that each individual exhibited a relatively consistent, unique behavioral signature and that the logistic regression model and model tree can be used to accurately distinguish online users. These results are applicable to one-to-one online user identification processes, insider misuse investigation processes, and online profiling in various areas. PMID:27918593

Accuracy of retrieving temperature and humidity profiles by ground-based microwave radiometry in truly complex terrain

NASA Astrophysics Data System (ADS)

Massaro, G.; Stiperski, I.; Pospichal, B.; Rotach, M. W.

2015-08-01

Within the Innsbruck Box project, a ground-based microwave radiometer (RPG-HATPRO) was operated in the Inn Valley (Austria), in very complex terrain, between September 2012 and May 2013 to obtain temperature and humidity vertical profiles of the full troposphere with a specific focus on the valley boundary layer. In order to assess its performance in a deep alpine valley, the profiles obtained by the radiometer with different retrieval algorithms based on different climatologies are compared to local radiosonde data. A retrieval that is improved with respect to the one provided by the manufacturer, based on better resolved data, shows a significantly smaller root mean square error (RMSE), both for the temperature and humidity profiles. The improvement is particularly substantial at the heights close to the mountaintop level and in the upper troposphere. Lower-level inversions, common in an alpine valley, are resolved to a satisfactory degree. On the other hand, upper-level inversions (above 1200 m) still pose a significant challenge for retrieval. For this purpose, specialized retrieval algorithms were developed by classifying the radiosonde climatologies into specialized categories according to different criteria (seasons, daytime, nighttime) and using additional regressors (e.g., measurements from mountain stations). The training and testing on the radiosonde data for these specialized categories suggests that a classification of profiles that reproduces meaningful physical characteristics can yield improved targeted specialized retrievals. A novel and very promising method of improving the profile retrieval in a mountainous region is adding further information in the retrieval, such as the surface temperature at fixed levels along a topographic slope or from nearby mountaintops.

Deep sea sedimentation processes and geomorphology: Northwest Atlantic continental margin

NASA Astrophysics Data System (ADS)

Mosher, David; Campbell, Calvin; Gardner, Jim; Chaytor, Jason; Piper, David; Rebesco, Michele

2017-04-01

Deep-sea sedimentation processes impart a fundamental control on the morphology of the western North Atlantic continental margin from Blake Spur to Hudson Strait. This fact is illustrated by the variable patterns of cross-margin gradients that are based on extensive new multibeam echo-sounder data informed by subbottom profiler and seismic reflection data. Erosion by off-shelf sediment transport in turbidity currents creates gullies, canyons and channels and a steep upper slope. Amalgamation of these conduits produces singular channels and turbidite fan complexes on the lower slope, flattening slope-profile gradients. The effect is an exponentially decaying "graded" slope profile. Comparatively, sediment mass failure produces steeper upper slopes due to head scarp development and a wedging architecture to the lower slope as deposits thin in the downslope direction. This process results in either a "stepped" slope, and/or a significant downslope gradient change where MTDs pinch out. Large drift deposits created by geostrophic currents are developed all along the margin. Blake Ridge, Sackville Spur, and Hamilton Spur are large detached drifts on disparate parts of the margin. They form a linear "above grade" profile along their crests from the shelf to abyssal plain. Deeper portions of the US continental margin are dominated by the Chesapeake Drift and Hatteras Outer Ridge; both plastered elongate mounded drifts. Farther north, particularly on the Grand Banks margin, are plastered and separated drifts. These drifts form "stepped" slope profiles, where they onlap the margin. Trough-mouth fan complexes become more common along the margin with increasing latitude. Sediment deposition and retention, particularly those dominated by glacigenic debris flows, characterize these segments producing an "above grade" slope profile. Understanding these geomorphological consequences of deep sea sedimentation processes is important to extended continental shelf mapping in which gradients and gradient change is a critical metric.

Evaluating two-dimensional electrophoresis profiles of the protein phaseolin as markers of genetic differentiation and seed protein quality in common bean (Phaseolus vulgaris L.).

PubMed

López-Pedrouso, María; Bernal, Javier; Franco, Daniel; Zapata, Carlos

2014-07-23

High-resolution two-dimensional electrophoresis (2-DE) profiles of the protein phaseolin, the major seed storage protein of common bean, display great number of spots with differentially glycosylated and phosphorylated α- and β-type polypeptides. This work aims to test whether these complex profiles can be useful markers of genetic differentiation and seed protein quality in bean populations. The 2-DE phaseolin profile and the amino acid composition were examined in bean seeds from 18 domesticated and wild accessions belonging to the Mesoamerican and Andean gene pools. We found that proteomic distances based on 2-DE profiles were successful in identifying the accessions belonging to each gene pool and outliers distantly related. In addition, accessions identified as outliers from proteomic distances showed the highest levels of methionine content, an essential amino acid deficient in bean seeds. These findings suggest that 2-DE phaseolin profiles provide valuable information with potential of being used in common bean genetic improvement.

Appreciating Complexity in Adolescent Self-Harm Risk Factors: Psychological Profiling in a Longitudinal Community Sample.

PubMed

Stanford, Sarah; Jones, Michael P; Hudson, Jennifer L

2018-05-01

Past research identifies a number of risk factors for adolescent self-harm, but often fails to account for overlap between these factors. This study investigated the underlying, broader concepts by identifying different psychological profiles among adolescents. We then compared new self-harm rates over a six-month period across different psychological profiles. Australian high school students (n = 326, 68.1% female) completed a questionnaire including a broad range of psychological and socioenvironmental risk and protective factors. Non-hierarchical cluster analysis produced six groups with different psychological profiles at baseline and rate of new self-harm at follow-up. The lowest rate was 1.4% in a group that appeared psychologically healthy; the highest rate was 37.5% in a group that displayed numerous psychological difficulties. Four groups with average self-harm had varied psychological profiles including low impulsivity, anxiety, impulsivity, and poor use of positive coping strategies. Identifying multiple profiles with distinct psychological characteristics can improve detection, guide prevention, and tailor treatment.

Study of Profile Changes during Mechanical Polishing using Relocation Profilometry

NASA Astrophysics Data System (ADS)

Kumaran, S. Chidambara; Shunmugam, M. S.

2017-10-01

Mechanical polishing is a finishing process practiced conventionally to enhance quality of surface. Surface finish is improved by mechanical cutting action of abrasive particles on work surface. Polishing is complex in nature and research efforts have been focused on understanding the polishing mechanism. Study of changes in profile is a useful method of understanding behavior of the polishing process. Such a study requires tracing same profile at regular process intervals, which is a tedious job. An innovative relocation technique is followed in the present work to study profile changes during mechanical polishing of austenitic stainless steel specimen. Using special locating fixture, micro-indentation mark and cross-correlation technique, the same profile is traced at certain process intervals. Comparison of different parameters of profiles shows the manner in which metal removal takes place in the polishing process. Mass removal during process estimated by the same relocation technique is checked with that obtained using weight measurement. The proposed approach can be extended to other micro/nano finishing processes and favorable process conditions can be identified.

PROFILE user's guide

NASA Technical Reports Server (NTRS)

Collins, L.; Saunders, D.

1986-01-01

User information for program PROFILE, an aerodynamics design utility for refining, plotting, and tabulating airfoil profiles is provided. The theory and implementation details for two of the more complex options are also presented. These are the REFINE option, for smoothing curvature in selected regions while retaining or seeking some specified thickness ratio, and the OPTIMIZE option, which seeks a specified curvature distribution. REFINE uses linear techniques to manipulate ordinates via the central difference approximation to second derivatives, while OPTIMIZE works directly with curvature using nonlinear least squares techniques. Use of programs QPLOT and BPLOT is also described, since all of the plots provided by PROFILE (airfoil coordinates, curvature distributions) are achieved via the general purpose QPLOT utility. BPLOT illustrates (again, via QPLOT) the shape functions used by two of PROFILE's options. The programs were designed and implemented for the Applied Aerodynamics Branch at NASA Ames Research Center, Moffett Field, California, and written in FORTRAN and run on a VAX-11/780 under VMS.

Complex EUV imaging reflectometry: spatially resolved 3D composition determination and dopant profiling with a tabletop 13nm source

NASA Astrophysics Data System (ADS)

Porter, Christina L.; Tanksalvala, Michael; Gerrity, Michael; Miley, Galen P.; Esashi, Yuka; Horiguchi, Naoto; Zhang, Xiaoshi; Bevis, Charles S.; Karl, Robert; Johnsen, Peter; Adams, Daniel E.; Kapteyn, Henry C.; Murnane, Margaret M.

2018-03-01

With increasingly 3D devices becoming the norm, there is a growing need in the semiconductor industry and in materials science for high spatial resolution, non-destructive metrology techniques capable of determining depth-dependent composition information on devices. We present a solution to this problem using ptychographic coherent diffractive imaging (CDI) implemented using a commercially available, tabletop 13 nm source. We present the design, simulations, and preliminary results from our new complex EUV imaging reflectometer, which uses coherent 13 nm light produced by tabletop high harmonic generation. This tool is capable of determining spatially-resolved composition vs. depth profiles for samples by recording ptychographic images at multiple incidence angles. By harnessing phase measurements, we can locally and nondestructively determine quantities such as device and thin film layer thicknesses, surface roughness, interface quality, and dopant concentration profiles. Using this advanced imaging reflectometer, we can quantitatively characterize materials-sciencerelevant and industry-relevant nanostructures for a wide variety of applications, spanning from defect and overlay metrology to the development and optimization of nano-enhanced thermoelectric or spintronic devices.

Proteome-Wide Profiling of Targets of Cysteine reactive Small Molecules by Using Ethynyl Benziodoxolone Reagents.

PubMed

Abegg, Daniel; Frei, Reto; Cerato, Luca; Prasad Hari, Durga; Wang, Chao; Waser, Jerome; Adibekian, Alexander

2015-09-07

In this study, we present a highly efficient method for proteomic profiling of cysteine residues in complex proteomes and in living cells. Our method is based on alkynylation of cysteines in complex proteomes using a "clickable" alkynyl benziodoxolone bearing an azide group. This reaction proceeds fast, under mild physiological conditions, and with a very high degree of chemoselectivity. The formed azide-capped alkynyl-cysteine adducts are readily detectable by LC-MS/MS, and can be further functionalized with TAMRA or biotin alkyne via CuAAC. We demonstrate the utility of alkynyl benziodoxolones for chemical proteomics applications by identifying the proteomic targets of curcumin, a diarylheptanoid natural product that was and still is part of multiple human clinical trials as anticancer agent. Our results demonstrate that curcumin covalently modifies several key players of cellular signaling and metabolism, most notably the enzyme casein kinase I gamma. We anticipate that this new method for cysteine profiling will find broad application in chemical proteomics and drug discovery. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparison of distortions of complex aluminium sections formed in single-step and incremental roll bending

NASA Astrophysics Data System (ADS)

Farstad, Jan Magnus Granheim; Netland, Øyvind; Welo, Torgeir

2017-10-01

This paper presents the results from a second series of experiments made to study local plastic deformations of a complex, hollow aluminium extrusion formed in roll bending. The first experimental series utilizing a single step roll bending sequence has been presented at the ESAFORM 2016 conference by Farstad et. al. In this recent experimental series, the same aluminium extrusion was formed in incremental steps. The objective was to investigate local distortions of the deformed cross section as a result of different number of steps employed to arrive at the final global shape of the extrusion. Moreover, the results between the two experimental series are compared, focusing on identifying differences in both the desired and the undesired deformations taking place as a result of bending and contact stresses. The profiles formed through multiple passes had less undesirable local distortions of the cross-section than the profiles that were formed in a single pass. However, the springback effect was more pronounced, meaning that the released radii of the profiles were higher.

Studying the location of SACs and DACs regions in the environment of hot emission stars

NASA Astrophysics Data System (ADS)

Antoniou, A.; Danezis, E.; Lyratzi, E.; Popović, L. Č.; Dimitrijević, M. S.; Theodossiou, E.

Hot emission stars (Oe and Be stars) present complex spectral line profiles, which are formed by a number of DACs and/or SACs. In order to explain and reproduce theoretically these complex line profiles we use the GR model (Gauss-Rotation model). This model presupposes that the regions, where the spectral lines are created, consist of a number of independent and successive absorbing or emitting density regions of matter. Here we are testing a new approach of the GR model, which supposes that the independent density regions are not successive. We use this new approach in the spectral lines of some Oe and Be stars and we compare the results of this method with the results deriving from the classical GR model that supposes successive regions.

Energy profile of nanobody-GFP complex under force.

PubMed

Klamecka, Kamila; Severin, Philip M; Milles, Lukas F; Gaub, Hermann E; Leonhardt, Heinrich

2015-09-10

Nanobodies (Nbs)-the smallest known fully functional and naturally occuring antigen-binding fragments-have attracted a lot of attention throughout the last two decades. Exploring their potential beyond the current use requires more detailed characterization of their binding forces as those cannot be directly derived from the binding affinities. Here we used atomic force microscope to measure rupture force of the Nb-green fluorescent protein (GFP) complex in various pulling geometries and derived the energy profile characterizing the interaction along the direction of the pulling force. We found that-despite identical epitopes-the Nb binds stronger (41-56 pN) to enhanced GFP than to wild-type GFP (28-45 pN). Measured forces make the Nb-GFP pair a potent reference for investigating molecular forces in living systems both in and ex vivo.

Methods of identification employing antibody profiles

DOEpatents

Francoeur, Ann-Michele

1993-12-14

An identification method, applicable to the identification of animals or inanimate objects, is described. The method takes advantage of the set of individual-specific antibodies that are part of the unique antibody repertoire present in animals, by reacting an effective amount of such antibodies with a particular panel, of n-dimensional array (where n is typically one or two) consisting of an effective amount of many different antigens (typically greater than one thousand), to give antibody-antigen complexes. The profile or pattern formed by the antigen-antibody complexes, termed an antibody fingerprint, when revealed by an effective amount of an appropriate detector molecule, is uniquely representative of a particular individual. The method can similarly be used to distinguish genetically, or otherwise similar individuals, or their body parts containing individual-specific antibodies.

Application of Layered Perforation Profile Control Technique to Low Permeable Reservoir

NASA Astrophysics Data System (ADS)

Wei, Sun

2018-01-01

it is difficult to satisfy the demand of profile control of complex well section and multi-layer reservoir by adopting the conventional profile control technology, therefore, a research is conducted on adjusting the injection production profile with layered perforating parameters optimization. i.e. in the case of coproduction for multi-layer, water absorption of each layer is adjusted by adjusting the perforating parameters, thus to balance the injection production profile of the whole well section, and ultimately enhance the oil displacement efficiency of water flooding. By applying the relationship between oil-water phase percolation theory/perforating damage and capacity, a mathematic model of adjusting the injection production profile with layered perforating parameters optimization, besides, perforating parameters optimization software is programmed. Different types of optimization design work are carried out according to different geological conditions and construction purposes by using the perforating optimization design software; furthermore, an application test is done for low permeable reservoir, and the water injection profile tends to be balanced significantly after perforation with optimized parameters, thereby getting a good application effect on site.

An Estimation of a Nonlinear Dynamic Process Using Latent Class Extended Mixed Models: Affect Profiles After Terrorist Attacks.

PubMed

Burro, Roberto; Raccanello, Daniela; Pasini, Margherita; Brondino, Margherita

2018-01-01

Conceptualizing affect as a complex nonlinear dynamic process, we used latent class extended mixed models (LCMM) to understand whether there were unobserved groupings in a dataset including longitudinal measures. Our aim was to identify affect profiles over time in people vicariously exposed to terrorism, studying their relations with personality traits. The participants were 193 university students who completed online measures of affect during the seven days following two terrorist attacks (Paris, November 13, 2015; Brussels, March 22, 2016); Big Five personality traits; and antecedents of affect. After selecting students whose negative affect was influenced by the two attacks (33%), we analysed the data with the LCMM package of R. We identified two affect profiles, characterized by different trends over time: The first profile comprised students with lower positive affect and higher negative affect compared to the second profile. Concerning personality traits, conscientious-ness was lower for the first profile compared to the second profile, and vice versa for neuroticism. Findings are discussed for both their theoretical and applied relevance.

Comparative Activity-Based Flavin-Dependent Oxidase Profiling.

PubMed

Krysiak, Joanna; Breinbauer, Rolf

2017-01-01

Activity-based protein profiling (ABPP) has become a powerful chemoproteomic technology allowing for the dissection of complex ligand-protein interactions in their native cellular environment. One of the biggest challenges for ABPP is the extension of the proteome coverage. In this chapter a new ABPP strategy dedicated to monoamine oxidases (MAO) is presented. These enzymes are representative examples of flavin-dependent oxidases, playing a crucial role in the regulation of nervous system signaling.

Restoration of solar and star images with phase diversity-based blind deconvolution

NASA Astrophysics Data System (ADS)

Li, Qiang; Liao, Sheng; Wei, Honggang; Shen, Mangzuo

2007-04-01

The images recorded by a ground-based telescope are often degraded by atmospheric turbulence and the aberration of the optical system. Phase diversity-based blind deconvolution is an effective post-processing method that can be used to overcome the turbulence-induced degradation. The method uses an ensemble of short-exposure images obtained simultaneously from multiple cameras to jointly estimate the object and the wavefront distribution on pupil. Based on signal estimation theory and optimization theory, we derive the cost function and solve the large-scale optimization problem using a limited memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) method. We apply the method to the turbulence-degraded images generated with computer, the solar images acquired with the swedish vacuum solar telescope (SVST, 0.475 m) in La Palma and the star images collected with 1.2-m telescope in Yunnan Observatory. In order to avoid edge effect in the restoration of the solar images, a modified Hanning apodized window is adopted. The star image still can be restored when the defocus distance is measured inaccurately. The restored results demonstrate that the method is efficient for removing the effect of turbulence and reconstructing the point-like or extended objects.

Nonlinear ultrasonic imaging with X wave

NASA Astrophysics Data System (ADS)

Du, Hongwei; Lu, Wei; Feng, Huanqing

2009-10-01

X wave has a large depth of field and may have important application in ultrasonic imaging to provide high frame rate (HFR). However, the HFR system suffers from lower spatial resolution. In this paper, a study of nonlinear imaging with X wave is presented to improve the resolution. A theoretical description of realizable nonlinear X wave is reported. The nonlinear field is simulated by solving the KZK nonlinear wave equation with a time-domain difference method. The results show that the second harmonic field of X wave has narrower mainlobe and lower sidelobes than the fundamental field. In order to evaluate the imaging effect with X wave, an imaging model involving numerical calculation of the KZK equation, Rayleigh-Sommerfeld integral, band-pass filtering and envelope detection is constructed to obtain 2D fundamental and second harmonic images of scatters in tissue-like medium. The results indicate that if X wave is used, the harmonic image has higher spatial resolution throughout the entire imaging region than the fundamental image, but higher sidelobes occur as compared to conventional focus imaging. A HFR imaging method with higher spatial resolution is thus feasible provided an apodization method is used to suppress sidelobes.