Theoretical electron-impact-ionization cross section for Fe11+ forming Fe12+

NASA Astrophysics Data System (ADS)

Kwon, Duck-Hee; Savin, Daniel Wolf

2012-08-01

We have calculated cross sections for electron impact ionization (EII) of P-like Fe11+ forming Si-like Fe12+. We have used the flexible atomic code (FAC) and a distorted-wave (DW) approximation. Particular attention has been paid to the ionization through the 3l→nl' and 2l→nl' excitation autoionization (EA) channels. We compare our results to previously published FAC DW results and recent experimental results. We find that the previous discrepancy between theory and experiment at the EII threshold can be accounted for by the 3l→nl' EA channels which were not included in the earlier calculations. At higher energies the discrepancy previously seen between theory and experiment for the magnitude of the 2l→nl'(n≥4) EA remains, though the difference has been reduced by our newer results. The resulting Maxwellian rate coefficient derived from our calculations lies within 11% of the experimentally derived rate coefficient in the temperature range where Fe11+ forms in collisional ionization equilibrium.

Experimental investigation of the Multipoint Ultrasonic Flowmeter

NASA Astrophysics Data System (ADS)

Jakub, Filipský

2018-06-01

The Multipoint Ultrasonic Flowmeter is a vector tomographic device capable of reconstructing all three components of velocity field based solely on boundary ultrasonic measurements. Computer simulations have shown the feasibility of such a device and have been published previously. This paper describes an experimental investigation of achievable accuracy of such a method. Doubled acoustic tripoles used to obtain information of the solenoidal part of vector field show extremely short differences between the Time Of Flights (TOFs) of individual sensors and are therefore sensitive to parasitic effects of TOF measurements. Sampling at 40MHz and correlation method is used to measure the TOF.

Comparison of Theoretical Stresses and Deflections of Multicell Wings with Experimental Results Obtained from Plastic Models

NASA Technical Reports Server (NTRS)

Zender, George W

1956-01-01

The experimental deflections and stresses of six plastic multicell-wing models of unswept, delta, and swept plan form are presented and compared with previously published theoretical results obtained by the electrical analog method. The comparisons indicate that the theory is reliable except for the evaluation of stresses in the vicinity of the leading edge of delta wings and the leading and trailing edges of swept wings. The stresses in these regions are questionable, apparently because of simplifications employed in idealizing the actual structure for theoretical purposes and because of local effects of concentrated loads.

Addendum to "Gluten-Free and Casein-Free Diets in Treatment of Autism Spectrum Disorders: A Systematic Review"

ERIC Educational Resources Information Center

Mulloy, Austin; Lang, Russell; O'Reilly, Mark; Sigafoos, Jeff; Lancioni, Giulio; Rispoli, Mandy

2011-01-01

Shortly after the publication of our literature review on gluten-free and casein-free (GFCF) diets in the treatment of autism spectrum disorders (ASD; Mulloy et al., 2010), Whiteley et al. (2010) published the results of experimental evaluation of a GFCF diet. To update our previous literature review, we herein provide an analysis of the Whiteley…

Improved Syntheses and Expanded Analyses of the Enantiomerically Enriched Chiral Cobalt Complexes Co(en)[subscript 3]I[subscript 3] and Co(diNOsar)Br[subscript 3

ERIC Educational Resources Information Center

McClellan, Michael J.; Cass, Marion E.

2015-01-01

This communication is a collection of additions and modifications to two previously published classic inorganic synthesis laboratory experiments. The experimental protocol for the synthesis and isolation of enantiomerically enriched ?- (or ?-)Co(en)[subscript 3]I[subscript 3] has been modified to increase reproducibility, yield, and enantiomeric…

An Experimentally Robust Model of Monomeric Apolipoprotein A-I Created from a Chimera of Two X-ray Structures and Molecular Dynamics Simulations

PubMed Central

2015-01-01

High-density lipoprotein (HDL) retards atherosclerosis by accepting cholesterol from the artery wall. However, the structure of the proposed acceptor, monomeric apolipoprotein A-I (apoA-I), the major protein of HDL, is poorly understood. Two published models for monomeric apoA-I used cross-linking distance constraints to derive best fit conformations. This approach has limitations. (i) Cross-linked peptides provide no information about secondary structure. (ii) A protein chain can be folded in multiple ways to create a best fit. (iii) Ad hoc folding of a secondary structure is unlikely to produce a stable orientation of hydrophobic and hydrophilic residues. To address these limitations, we used a different approach. We first noted that the dimeric apoA-I crystal structure, (Δ185–243)apoA-I, is topologically identical to a monomer in which helix 5 forms a helical hairpin, a monomer with a hydrophobic cleft running the length of the molecule. We then realized that a second crystal structure, (Δ1–43)apoA-I, contains a C-terminal structure that fits snuggly via aromatic and hydrophobic interactions into the hydrophobic cleft. Consequently, we combined these crystal structures into an initial model that was subjected to molecular dynamics simulations. We tested the initial and simulated models and the two previously published models in three ways: against two published data sets (domains predicted to be helical by H/D exchange and six spin-coupled residues) and against our own experimentally determined cross-linking distance constraints. We note that the best fit simulation model, superior by all tests to previously published models, has dynamic features of a molten globule with interesting implications for the functions of apoA-I. PMID:25423138

New experimental stopping power data of 4He, 16O, 40Ar, 48Ca and 84Kr projectiles in different solid materials

NASA Astrophysics Data System (ADS)

Trzaska, W. H.; Knyazheva, G. N.; Perkowski, J.; Andrzejewski, J.; Khlebnikov, S. V.; Kozulin, E. M.; Malkiewicz, T.; Mutterer, M.; Savelieva, E. O.

2018-03-01

New experimental data on energy loss of 4He, 16O, 40Ar, 48Ca and 84Kr ions in thin, self-supporting foils of C, Al, Ni, Ag, Lu, Au, Pb and Th are presented. The measurements, using the TOF-E method, were done in a very broad energy range around the stopping power maximum; typically from 0.1 to 11 MeV/u. When available, the extracted stopping power values are compared with the previously published data. The overall agreement is good although a fair comparison is difficult as the covered energy range is much larger than in previous measurements. The small error bars and a broad coverage allowed us to test the predictions of theoretical codes: PASS, CasP, and semi-empirical programs: SRIM, LET, MSTAR, and the Hubert table predictions. The deviations of PASS predictions from the experimental data do not exceed 20% for all the measured combinations. CasP predictions are within 15% from the data for heavier ions but diverge up to 40% for lighter ions. Semi-empirical approaches, including SRIM, deviate from the experimental data by less than 5% for the regions already covered by previous experiments but err by about 10-20% for the ion/target combinations that were not measured before: Ca in Lu as well as Kr in Lu, Pb, and Th.

Computational and Experimental Study of Supersonic Nozzle Flow and Shock Interactions

NASA Technical Reports Server (NTRS)

Carter, Melissa B.; Elmiligui, Alaa A.; Nayani, Sudheer N.; Castner, Ray; Bruce, Walter E., IV; Inskeep, Jacob

2015-01-01

This study focused on the capability of NASA Tetrahedral Unstructured Software System's CFD code USM3D capability to predict the interaction between a shock and supersonic plume flow. Previous studies, published in 2004, 2009 and 2013, investigated USM3D's supersonic plume flow results versus historical experimental data. This current study builds on that research by utilizing the best practices from the early papers for properly capturing the plume flow and then adding a wedge acting as a shock generator. This computational study is in conjunction with experimental tests conducted at the Glenn Research Center 1'x1' Supersonic Wind Tunnel. The comparison of the computational and experimental data shows good agreement for location and strength of the shocks although there are vertical shifts between the data sets that may be do to the measurement technique.

The cardiac muscle duplex as a method to study myocardial heterogeneity

PubMed Central

Solovyova, O.; Katsnelson, L.B.; Konovalov, P.V.; Kursanov, A.G.; Vikulova, N.A.; Kohl, P.; Markhasin, V.S.

2014-01-01

This paper reviews the development and application of paired muscle preparations, called duplex, for the investigation of mechanisms and consequences of intra-myocardial electro-mechanical heterogeneity. We illustrate the utility of the underlying combined experimental and computational approach for conceptual development and integration of basic science insight with clinically relevant settings, using previously published and new data. Directions for further study are identified. PMID:25106702

An assessment of some theoretical models used for the calculation of the refractive index of InXGa1-xAs

NASA Astrophysics Data System (ADS)

Engelbrecht, J. A. A.

2018-04-01

Theoretical models used for the determination of the refractive index of InXGa1-XAs are reviewed and compared. Attention is drawn to some problems experienced with some of the models. Models also extended to the mid-infrared region of the electromagnetic spectrum. Theoretical results in the mid-infrared region are then compared to previously published experimental results.

Long term radiocesium contamination of fruit trees following the Chernobyl accident.

PubMed

Antonopoulos-Domis, M; Clouvas, A; Gagianas, A

1996-12-01

Radiocesium contamination from the Chernobyl accident of fruits and leaves from various fruit trees was systematically studied from 1990 to 1995 on two agricultural experimentation farms in Northern Greece. The results are discussed in the framework of a previously published model describing the long-term radiocesium contamination mechanism of deciduous fruit trees after a nuclear accident. The results of the present work qualitatively verify the model predictions.

Laboratory Spectroscopy of Fluorinated Molecules for Atmospheric Physics

NASA Astrophysics Data System (ADS)

Godin, Paul Joseph

Temperature-dependent absorption cross-sections are presented for five fluorinated molecules considered to be greenhouse gases due to being radiatively active in the mid-infrared. The molecules studied are perfluorotributylamine (PFTBA), 2,2,3,3,3- pentafluoropropanol (PFPO), 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP), perfluorodecalin (PFDC), and 2H,3H-perfluoropentane (HFC-43-10mee). HFIP is a fluorinated liquid commonly used as a specialty solvent for some polar polymers and in organic synthesis. PFTBA, PFPO, and HFC-43-10mee are commonly used in electronic and industrial applications. PFDC is capable of dissolving large quantities of gases, making it useful for a variety of medical applications. Experimental absorption cross-sections were derived from Fourier transform infrared spectra recorded from 530 to 3400 cm ?1 with a resolution of 0.1 cm ?1 over a temperature range of 298 to 360 K. These results were compared to theoretical density functional theory (DFT) calculations and previously published experimental measurements made at room temperature. Theoretical DFT calculations were performed using the B3LYP method and a minimum basis set of 6-311+G(d,p). The calculations have determined the optimized geometrical configuration, infrared intensities, and wavenumbers of the harmonic frequencies for different ground-state configurations due to the presence of internal rotors. As the population of each configuration changes with temperature, changes in the experimental spectra were used to make accurate band assignments. From these band assignments, the DFT spectra were calibrated to match the experimental spectra, increasing the accuracy of the DFT prediction outside of the experimental range. Using the adjusted DFT-calculated spectra, the wavenumber range was extended beyond the experimental range to calculate radiative efficiencies and global warming potentials. When using only the experimental range, the new values agreed with previously published values. However, when the range was extended using the DFT spectra, the radiative efficiency and global warming potential were increased, suggesting that the current values are underestimating the climate impacts of these species. Additionally, work done on building a multipass White cell is presented. This new system can be used in the future to resolve weak lines to extract line parameters needed for atmospheric trace gas retrievals.

USM3D Predictions of Supersonic Nozzle Flow

NASA Technical Reports Server (NTRS)

Carter, Melissa B.; Elmiligui, Alaa A.; Campbell, Richard L.; Nayani, Sudheer N.

2014-01-01

This study focused on the NASA Tetrahedral Unstructured Software System CFD code (USM3D) capability to predict supersonic plume flow. Previous studies, published in 2004 and 2009, investigated USM3D's results versus historical experimental data. This current study continued that comparison however focusing on the use of the volume souring to capture the shear layers and internal shock structure of the plume. This study was conducted using two benchmark axisymmetric supersonic jet experimental data sets. The study showed that with the use of volume sourcing, USM3D was able to capture and model a jet plume's shear layer and internal shock structure.

A method of extracting speed-dependent vector correlations from 2 + 1 REMPI ion images.

PubMed

Wei, Wei; Wallace, Colin J; Grubb, Michael P; North, Simon W

2017-07-07

We present analytical expressions for extracting Dixon's bipolar moments in the semi-classical limit from experimental anisotropy parameters of sliced or reconstructed non-sliced images. The current method focuses on images generated by 2 + 1 REMPI (Resonance Enhanced Multi-photon Ionization) and is a necessary extension of our previously published 1 + 1 REMPI equations. Two approaches for applying the new equations, direct inversion and forward convolution, are presented. As demonstration of the new method, bipolar moments were extracted from images of carbonyl sulfide (OCS) photodissociation at 230 nm and NO 2 photodissociation at 355 nm, and the results are consistent with previous publications.

Outer region scaling using the freestream velocity for nonuniform open channel flow over gravel

NASA Astrophysics Data System (ADS)

Stewart, Robert L.; Fox, James F.

2017-06-01

The theoretical basis for outer region scaling using the freestream velocity for nonuniform open channel flows over gravel is derived and tested for the first time. Owing to the gradual expansion of the flow within the nonuniform case presented, it is hypothesized that the flow can be defined as an equilibrium turbulent boundary layer using the asymptotic invariance principle. The hypothesis is supported using similarity analysis to derive a solution, followed by further testing with experimental datasets. For the latter, 38 newly collected experimental velocity profiles across three nonuniform flows over gravel in a hydraulic flume are tested as are 43 velocity profiles previously published in seven peer-reviewed journal papers that focused on fluid mechanics of nonuniform open channel over gravel. The findings support the nonuniform flows as equilibrium defined by the asymptotic invariance principle, which is reflective of the consistency of the turbulent structure's form and function within the expanding flow. However, roughness impacts the flow structure when comparing across the published experimental datasets. As a secondary objective, we show how previously published mixed scales can be used to assist with freestream velocity scaling of the velocity deficit and thus empirically account for the roughness effects that extend into the outer region of the flow. One broader finding of this study is providing the theoretical context to relax the use of the elusive friction velocity when scaling nonuniform flows in gravel bed rivers; and instead to apply the freestream velocity. A second broader finding highlighted by our results is that scaling of nonuniform flow in gravel bed rivers is still not fully resolved theoretically since mixed scaling relies to some degree on empiricism. As researchers resolve the form and function of macroturbulence in the outer region, we hope to see the closing of this research gap.

Statistical behavior of ten million experimental detection limits

NASA Astrophysics Data System (ADS)

Voigtman, Edward; Abraham, Kevin T.

2011-02-01

Using a lab-constructed laser-excited fluorimeter, together with bootstrapping methodology, the authors have generated many millions of experimental linear calibration curves for the detection of rhodamine 6G tetrafluoroborate in ethanol solutions. The detection limits computed from them are in excellent agreement with both previously published theory and with comprehensive Monte Carlo computer simulations. Currie decision levels and Currie detection limits, each in the theoretical, chemical content domain, were found to be simply scaled reciprocals of the non-centrality parameter of the non-central t distribution that characterizes univariate linear calibration curves that have homoscedastic, additive Gaussian white noise. Accurate and precise estimates of the theoretical, content domain Currie detection limit for the experimental system, with 5% (each) probabilities of false positives and false negatives, are presented.

Pure Electron Plasmas near Thermal Equilibrium

DTIC Science & Technology

1990-11-01

I University of California, San Diego Institute of Pure and Applied Physical Sciences La Jolla, CA 92093 N 0 (V) Final Technical Report N "Pure...Research/code -..... " 1112AI. VC 1/8/91 ’ , .... i ; () -ii- r INTRODUCTION Since 1982 the plasma group at UCSD has been conducting an experimental and...scale. We have also observed an unusual I = 1 instability which the previously published theoretical literature stated unconditionally was stable. The

Utilizing the Power of Nanostructures to Their Fullest Capability in Energetic Formulations

DTIC Science & Technology

2016-02-01

aluminum-cyclopentadienyl clusters. J Phys Chem A. 2011;115(48):14100– 14109. Zeng Q, Jiang X, Yu A, Lu G. Growth mechanisms of silver nanoparticles : a...assemblies of gas generators containing nanoscale Al (conventional Al nanoparticles and Al nanoclusters) to overcome the sintering and/or oxide-formation...issues. Experimentally, a previously published hypothesis for the mechanism leading to enhanced energy release from Al nanoparticles in the presence of

Conformational analysis and global warming potentials of 1,1,1,3,3,3-hexafluoro-2-propanol from absorption spectroscopy

NASA Astrophysics Data System (ADS)

Godin, Paul J.; Le Bris, Karine; Strong, Kimberly

2017-12-01

Absorption cross-sections of 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) were derived from Fourier transform infrared spectra recorded from 530 to 3400 cm-1 with a resolution of 0.1 cm-1 over a temperature range of 300-362 K. These results were compared to previously published experimental measurements made at room temperature and to a theoretical spectrum from density functional theory (DFT) calculations. Good agreement is found between the experimentally derived results, DFT calculations, and previously published data. The only temperature dependence observed was in the amplitude of some of the absorption peaks due to the changing ratio of the stable conformations of HFIP. This temperature dependence does not result in a significant trend in integrated band strength as a function of temperature. The average value for integrated band strength is found to be (2.649 ± 0.065)x10-16 cm molecule-1 for HFIP over the spectral range of 595 to 3010 cm-1. Radiative efficiency (RE) and the global warming potential (GWP) for HFIP were also derived. A RE of 0.293 ± 0.059 Wm-2ppbv-1 is derived, which leads to a GWP100 of 188 in the range of 530 to 3000 cm-1. The DFT calculation is linearly adjusted to match the experimental spectrum. Using this adjusted DFT spectrum to expand the range below 530 to 0 cm-1 , increases the RE to 0.317 ± 0.063 Wm-2ppbv-1 and the GWP100 to 203.

An update on Experimental and Clinical Psychopharmacology: Something old, something new, something borrowed, something green?

PubMed

Stoops, William W

2018-02-01

In this editorial, the author provides an update on Experimental and Clinical Psychopharmacology in several areas. First, the journal will continue to accept original research reports and full reviews as it has in past years. The author hopes to still receive outstanding manuscripts in the journal's primary areas of strength, such as clinical research on alcohol use and cigarette smoking. The journal will also continue to publish an annual special issue on a current topic in the field. Second, the journal now accepts brief communications, brief reviews, and case reports. The authors sees these new formats as opportunities to publish cutting edge, novel findings that may not be suitable as original research reports or full reviews-such work would previously not have fit with the journal. Third, the author has borrowed an idea from colleagues who serve as editors for other journals in the field: the addition of an editorial fellowship at Experimental and Clinical Psychopharmacology . Finally, the "something green" part of the title refers to the new, bright green cover color of the print version of the journal. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Computer-aided design of liposomal drugs: In silico prediction and experimental validation of drug candidates for liposomal remote loading.

PubMed

Cern, Ahuva; Barenholz, Yechezkel; Tropsha, Alexander; Goldblum, Amiram

2014-01-10

Previously we have developed and statistically validated Quantitative Structure Property Relationship (QSPR) models that correlate drugs' structural, physical and chemical properties as well as experimental conditions with the relative efficiency of remote loading of drugs into liposomes (Cern et al., J. Control. Release 160 (2012) 147-157). Herein, these models have been used to virtually screen a large drug database to identify novel candidate molecules for liposomal drug delivery. Computational hits were considered for experimental validation based on their predicted remote loading efficiency as well as additional considerations such as availability, recommended dose and relevance to the disease. Three compounds were selected for experimental testing which were confirmed to be correctly classified by our previously reported QSPR models developed with Iterative Stochastic Elimination (ISE) and k-Nearest Neighbors (kNN) approaches. In addition, 10 new molecules with known liposome remote loading efficiency that were not used by us in QSPR model development were identified in the published literature and employed as an additional model validation set. The external accuracy of the models was found to be as high as 82% or 92%, depending on the model. This study presents the first successful application of QSPR models for the computer-model-driven design of liposomal drugs. © 2013.

Computer-aided design of liposomal drugs: in silico prediction and experimental validation of drug candidates for liposomal remote loading

PubMed Central

Cern, Ahuva; Barenholz, Yechezkel; Tropsha, Alexander; Goldblum, Amiram

2014-01-01

Previously we have developed and statistically validated Quantitative Structure Property Relationship (QSPR) models that correlate drugs’ structural, physical and chemical properties as well as experimental conditions with the relative efficiency of remote loading of drugs into liposomes (Cern et al, Journal of Controlled Release, 160(2012) 14–157). Herein, these models have been used to virtually screen a large drug database to identify novel candidate molecules for liposomal drug delivery. Computational hits were considered for experimental validation based on their predicted remote loading efficiency as well as additional considerations such as availability, recommended dose and relevance to the disease. Three compounds were selected for experimental testing which were confirmed to be correctly classified by our previously reported QSPR models developed with Iterative Stochastic Elimination (ISE) and k-nearest neighbors (kNN) approaches. In addition, 10 new molecules with known liposome remote loading efficiency that were not used in QSPR model development were identified in the published literature and employed as an additional model validation set. The external accuracy of the models was found to be as high as 82% or 92%, depending on the model. This study presents the first successful application of QSPR models for the computer-model-driven design of liposomal drugs. PMID:24184343

Quasi-experimental Studies in the Fields of Infection Control and Antibiotic Resistance, Ten Years Later: A Systematic Review.

PubMed

Alsaggaf, Rotana; O'Hara, Lyndsay M; Stafford, Kristen A; Leekha, Surbhi; Harris, Anthony D

2018-02-01

OBJECTIVE A systematic review of quasi-experimental studies in the field of infectious diseases was published in 2005. The aim of this study was to assess improvements in the design and reporting of quasi-experiments 10 years after the initial review. We also aimed to report the statistical methods used to analyze quasi-experimental data. DESIGN Systematic review of articles published from January 1, 2013, to December 31, 2014, in 4 major infectious disease journals. METHODS Quasi-experimental studies focused on infection control and antibiotic resistance were identified and classified based on 4 criteria: (1) type of quasi-experimental design used, (2) justification of the use of the design, (3) use of correct nomenclature to describe the design, and (4) statistical methods used. RESULTS Of 2,600 articles, 173 (7%) featured a quasi-experimental design, compared to 73 of 2,320 articles (3%) in the previous review (P<.01). Moreover, 21 articles (12%) utilized a study design with a control group; 6 (3.5%) justified the use of a quasi-experimental design; and 68 (39%) identified their design using the correct nomenclature. In addition, 2-group statistical tests were used in 75 studies (43%); 58 studies (34%) used standard regression analysis; 18 (10%) used segmented regression analysis; 7 (4%) used standard time-series analysis; 5 (3%) used segmented time-series analysis; and 10 (6%) did not utilize statistical methods for comparisons. CONCLUSIONS While some progress occurred over the decade, it is crucial to continue improving the design and reporting of quasi-experimental studies in the fields of infection control and antibiotic resistance to better evaluate the effectiveness of important interventions. Infect Control Hosp Epidemiol 2018;39:170-176.

Measured effects of coolant injection on the performance of a film cooled turbine

NASA Technical Reports Server (NTRS)

Mcdonel, J. D.; Eiswerth, J. E.

1977-01-01

Tests have been conducted on a 20-inch diameter single-stage air-cooled turbine designed to evaluate the effects of film cooling air on turbine aerodynamic performance. The present paper reports the results of five test configurations, including two different cooling designs and three combinations of cooled and solid airfoils. A comparison is made of the experimental results with a previously published analytical method of evaluating coolant injection effects on turbine performance.

Selecting for Function: Solution Synthesis of Magnetic Nanopropellers

PubMed Central

2013-01-01

We show that we can select magnetically steerable nanopropellers from a set of carbon coated aggregates of magnetic nanoparticles using weak homogeneous rotating magnetic fields. The carbon coating can be functionalized, enabling a wide range of applications. Despite their arbitrary shape, all nanostructures propel parallel to the vector of rotation of the magnetic field. We use a simple theoretical model to find experimental conditions to select nanopropellers which are predominantly smaller than previously published ones. PMID:24127909

Demonstrated high performance of gas-filled rugby-shaped hohlraums on Omega

NASA Astrophysics Data System (ADS)

Philippe, F.; Tassin, V.; Depierreux, S.; Gauthier, P.; Masson-Laborde, P. E.; Monteil, M. C.; Seytor, P.; Villette, B.; Lasinski, B.; Park, H. S.; Ross, J. S.; Amendt, P.; Döppner, T.; Hinkel, D. E.; Wallace, R.; Williams, E.; Michel, P.; Frenje, J.; Gatu-Johnson, M.; Li, C. K.; Petrasso, R.; Glebov, V.; Sorce, C.; Stoeckl, C.; Nikroo, A.; Giraldez, E.

2014-07-01

A direct experimental comparison of rugby-shaped and cylindrical shaped gas-filled hohlraums on the Omega laser facility demonstrates that higher coupling and minimal backscatter can be achieved in the rugby geometry, leading to significantly enhanced implosion performance. A nearly 50% increase of x-ray drive is associated with earlier bangtime and increase of neutron production. The observed drive enhancement from rugby geometry in this study is almost twice stronger than in previously published results.

Calibrated dilatometer exercise to probe thermoplastic properties of coal in pressurized CO 2

DOE PAGES

Romanov, Vyacheslav N.; Lynn, Ronald J.; Warzinski, Robert P.

2017-07-03

This research was aimed at testing a hypothesis, that at elevated CO 2 pressure coal can soften at temperatures well below those obtained in the presence of other gases. That could have serious negative implications for injection of CO 2 into deep coal seams. Here, we have examined the experimental design issues and procedures used in the previously published studies, and experimentally investigated the physical behavior of a similar coal in the presence of CO 2 as a function of pressure and temperature, using the same high-pressure micro-dilatometer refurbished and carefully calibrated for this purpose. No notable reduction in coalmore » softening temperature was observed in this study.« less

Calibrated dilatometer exercise to probe thermoplastic properties of coal in pressurized CO 2

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

Romanov, Vyacheslav N.; Lynn, Ronald J.; Warzinski, Robert P.

This research was aimed at testing a hypothesis, that at elevated CO 2 pressure coal can soften at temperatures well below those obtained in the presence of other gases. That could have serious negative implications for injection of CO 2 into deep coal seams. Here, we have examined the experimental design issues and procedures used in the previously published studies, and experimentally investigated the physical behavior of a similar coal in the presence of CO 2 as a function of pressure and temperature, using the same high-pressure micro-dilatometer refurbished and carefully calibrated for this purpose. No notable reduction in coalmore » softening temperature was observed in this study.« less

The influence of stripe width on the threshold current of double-heterojunction lasers

NASA Technical Reports Server (NTRS)

Ladany, I.

1977-01-01

Experimental measurements of the threshold current of oxide-isolated stripe laser as a function of stripe width and p-layer resistivity are presented. A calculation of the influence of carrier outdiffusion has been made, including the effect of current leakage beyond the stripe edges. The calculated threshold increase is in substantial agreement with experiment for stripe widths down to about 10 microns. The data also yield an effective diffusion length of about 7 microns for the lasers studied. Deviations between experimental and calculated thresholds occurring at stripe widths of 4-6 microns are represented by an empirical curve which is compared with previously published calculations of threshold gain.

HIV Model Parameter Estimates from Interruption Trial Data including Drug Efficacy and Reservoir Dynamics

PubMed Central

Luo, Rutao; Piovoso, Michael J.; Martinez-Picado, Javier; Zurakowski, Ryan

2012-01-01

Mathematical models based on ordinary differential equations (ODE) have had significant impact on understanding HIV disease dynamics and optimizing patient treatment. A model that characterizes the essential disease dynamics can be used for prediction only if the model parameters are identifiable from clinical data. Most previous parameter identification studies for HIV have used sparsely sampled data from the decay phase following the introduction of therapy. In this paper, model parameters are identified from frequently sampled viral-load data taken from ten patients enrolled in the previously published AutoVac HAART interruption study, providing between 69 and 114 viral load measurements from 3–5 phases of viral decay and rebound for each patient. This dataset is considerably larger than those used in previously published parameter estimation studies. Furthermore, the measurements come from two separate experimental conditions, which allows for the direct estimation of drug efficacy and reservoir contribution rates, two parameters that cannot be identified from decay-phase data alone. A Markov-Chain Monte-Carlo method is used to estimate the model parameter values, with initial estimates obtained using nonlinear least-squares methods. The posterior distributions of the parameter estimates are reported and compared for all patients. PMID:22815727

Epitaxial Relationships between Calcium Carbonate and Inorganic Substrates

PubMed Central

Yang, Taewook; Jho, Jae Young; Kim, Il Won

2014-01-01

The polymorph-selective crystallization of calcium carbonate has been studied in terms of epitaxial relationship between the inorganic substrates and the aragonite/calcite polymorphs with implication in bioinspired mineralization. EpiCalc software was employed to assess the previously published experimental results on two different groups of inorganic substrates: aragonitic carbonate crystals (SrCO3, PbCO3, and BaCO3) and a hexagonal crystal family (α-Al2O3, α-SiO2, and LiNbO3). The maximum size of the overlayer (aragonite or calcite) was calculated for each substrate based on a threshold value of the dimensionless potential to estimate the relative nucleation preference of the polymorphs of calcium carbonate. The results were in good agreement with previous experimental observations, although stereochemical effects between the overlayer and substrate should be separately considered when existed. In assessing the polymorph-selective nucleation, the current method appeared to provide a better tool than the oversimplified mismatch parameters without invoking time-consuming molecular simulation\\. PMID:25226539

Annual tendency of research papers used ICR mice as experimental animals in biomedical research fields.

PubMed

Kim, Ji Eun; Nam, Jung Hoon; Cho, Joon Young; Kim, Kil Soo; Hwang, Dae Youn

2017-06-01

Institute of Cancer Research (ICR) mice have been widely used in various research fields including toxicology, oncology, pharmacology, and pharmaceutical product safety testing for decades. However, annual tendency of research papers involving ICR mice in various biomedical fields has not been previously analyzed. In this study, we examined the numbers of papers that used ICR mice as experimental animals in the social science, natural science, engineering, medicine-pharmacy, marine agriculture-fishery, and art-kinesiology fields by analyzing big data. Numbers of ICR mouse-used papers gradually increased from 1961 to 2014, but small decreases were observed in 2015 and 2016. The largest number of ICR-used papers were published in the medicine-pharmacy field, followed by natural science and art-kinesiology fields. There were no ICR mouse-used papers in other fields. Furthermore, ICR mice have been widely employed in cell biology studies within the natural science field as well as in biochemistry and pathology in the medicine-pharmacy field. Few ICR mouse-used papers were published in exercise biochemistry and exercise nutrition in the art-kinesiology field. Regardless in most fields, the total numbers of published papers involving ICR mice were higher in 2014 than in other years, although the numbers in some fields including dentistry, veterinary science, and dermatology were high in 2016. Taken together, the present study shows that various ICR stocks, including Korl:ICR mice, are widely employed as experimental animals in various biomedical research fields.

Annual tendency of research papers used ICR mice as experimental animals in biomedical research fields

PubMed Central

Kim, Ji Eun; Nam, Jung Hoon; Cho, Joon Young; Kim, Kil Soo

2017-01-01

Institute of Cancer Research (ICR) mice have been widely used in various research fields including toxicology, oncology, pharmacology, and pharmaceutical product safety testing for decades. However, annual tendency of research papers involving ICR mice in various biomedical fields has not been previously analyzed. In this study, we examined the numbers of papers that used ICR mice as experimental animals in the social science, natural science, engineering, medicine-pharmacy, marine agriculture-fishery, and art-kinesiology fields by analyzing big data. Numbers of ICR mouse-used papers gradually increased from 1961 to 2014, but small decreases were observed in 2015 and 2016. The largest number of ICR-used papers were published in the medicine-pharmacy field, followed by natural science and art-kinesiology fields. There were no ICR mouse-used papers in other fields. Furthermore, ICR mice have been widely employed in cell biology studies within the natural science field as well as in biochemistry and pathology in the medicine-pharmacy field. Few ICR mouse-used papers were published in exercise biochemistry and exercise nutrition in the art-kinesiology field. Regardless in most fields, the total numbers of published papers involving ICR mice were higher in 2014 than in other years, although the numbers in some fields including dentistry, veterinary science, and dermatology were high in 2016. Taken together, the present study shows that various ICR stocks, including Korl:ICR mice, are widely employed as experimental animals in various biomedical research fields. PMID:28747984

Energetic particle-driven compressional Alfvén eigenmodes and prospects for ion cyclotron emission studies in fusion plasmas

NASA Astrophysics Data System (ADS)

Gorelenkov, N. N.

2016-10-01

As a fundamental plasma oscillation the compressional Alfvén waves (CAWs) are interesting for plasma scientists both academically and in applications for fusion plasmas. They are believed to be responsible for the ion cyclotron emission (ICE) observed in many tokamaks. The theory of CAW and ICE was significantly advanced at the end of 20th century in particular motivated by first DT experiments on TFTR and subsequent JET DT experimental studies. More recently, ICE theory was advanced by ST (or spherical torus) experiments with the detailed theoretical and experimental studies of the properties of each instability signal. There the instability responsible for ICE signals previously indistinguishable in high aspect ratio tokamaks became the subjects of experimental studies. We discuss further the prospects of ICE theory and its applications for future burning plasma experiments such as the ITER tokamak-reactor prototype being build in France where neutrons and gamma rays escaping the plasma create extremely challenging conditions for fusion alpha particle diagnostics. This manuscript has been authored by Princeton University under Contract Number DE-AC02-09CH11466 with the US Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes.

A 3D musculoskeletal model of the western lowland gorilla hind limb: moment arms and torque of the hip, knee and ankle.

PubMed

Goh, Colleen; Blanchard, Mary L; Crompton, Robin H; Gunther, Michael M; Macaulay, Sophie; Bates, Karl T

2017-10-01

Three-dimensional musculoskeletal models have become increasingly common for investigating muscle moment arms in studies of vertebrate locomotion. In this study we present the first musculoskeletal model of a western lowland gorilla hind limb. Moment arms of individual muscles around the hip, knee and ankle were compared with previously published data derived from the experimental tendon travel method. Considerable differences were found which we attribute to the different methodologies in this specific case. In this instance, we argue that our 3D model provides more accurate and reliable moment arm data than previously published data on the gorilla because our model incorporates more detailed consideration of the 3D geometry of muscles and the geometric constraints that exist on their lines-of-action about limb joints. Our new data have led us to revaluate the previous conclusion that muscle moment arms in the gorilla hind limb are optimised for locomotion with crouched or flexed limb postures. Furthermore, we found that bipedalism and terrestrial quadrupedalism coincided more regularly with higher moment arms and torque around the hip, knee and ankle than did vertical climbing. This indicates that the ability of a gorilla to walk bipedally is not restricted by musculoskeletal adaptations for quadrupedalism and vertical climbing, at least in terms of moment arms and torque about hind limb joints. © 2017 The Authors. Journal of Anatomy published by John Wiley & Sons Ltd on behalf of Anatomical Society.

Contributions to muscle force and EMG by combined neural excitation and electrical stimulation

PubMed Central

Crago, Patrick E; Makowski, Nathaniel S; Cole, Natalie M

2014-01-01

Objective Stimulation of muscle for research or clinical interventions is often superimposed on ongoing physiological activity, without a quantitative understanding of the impact of the stimulation on the net muscle activity and the physiological response. Experimental studies show that total force during stimulation is less than the sum of the isolated voluntary and stimulated forces, but the occlusion mechanism is not understood. Approach We develop a model of efferent motor activity elicited by superimposing stimulation during a physiologically activated contraction. The model combines action potential interactions due to collision block, source resetting, and refractory periods with previously published models of physiological motor unit recruitment, rate modulation, force production, and EMG generation in human first dorsal interosseous muscle to investigate the mechanisms and effectiveness of stimulation on the net muscle force and EMG. Main Results Stimulation during a physiological contraction demonstrates partial occlusion of force and the neural component of the EMG, due to action potential interactions in motor units activated by both sources. Depending on neural and stimulation firing rates as well as on force-frequency properties, individual motor unit forces can be greater, smaller, or unchanged by the stimulation. In contrast, voluntary motor unit EMG potentials in simultaneously stimulated motor units show progressive occlusion with increasing stimulus rate. The simulations predict that occlusion would be decreased by a reverse stimulation recruitment order. Significance The results are consistent with and provide a mechanistic interpretation of previously published experimental evidence of force occlusion. The models also predict two effects that have not been reported previously - voluntary EMG occlusion and the advantages of a proximal stimulation site. This study provides a basis for the rational design of both future experiments and clinical neuroprosthetic interventions involving either motor or sensory stimulation. PMID:25242203

Implementation of a Blowing Boundary Condition in the LAURA Code

NASA Technical Reports Server (NTRS)

Thompson, Richard a.; Gnoffo, Peter A.

2008-01-01

Preliminary steps toward modeling a coupled ablation problem using a finite-volume Navier-Stokes code (LAURA) are presented in this paper. Implementation of a surface boundary condition with mass transfer (blowing) is described followed by verification and validation through comparisons with analytic results and experimental data. Application of the code to a carbon-nosetip ablation problem is demonstrated and the results are compared with previously published data. It is concluded that the code and coupled procedure are suitable to support further ablation analyses and studies.

Gust Response Analysis of a Turbine Cascade

NASA Technical Reports Server (NTRS)

Gorla, R. S. R.; Reddy, T. S. R.; Reddy, D. R.; Kurkov, A. P.

2001-01-01

A study was made of the gust response of an annular turbine cascade using a two-dimensional Navier Stokes code. The time-marching CFD code, NPARC, was used to calculate the unsteady forces due to the fluid flow. The computational results were compared with a previously published experimental data for the annular cascade reported in the literature. Reduced frequency, Mach number and angle of incidence were varied independently and the gust velocity was sinusoidal. For the high inlet velocity case, the cascade was nearly choked.

Complex Refractive Index of Ammonium Nitrate in the 2-20 micron Spectral Range

NASA Technical Reports Server (NTRS)

Jarzembski, Maurice A.; Norman, Mark L.; Fuller, Kirk A.; Srivastava, Vandana; Cutten, Dean R.

2002-01-01

Using high resolution Fourier Transform Infrared Spectroscopy (FTIR) absorbance/transmittance spectral data for ammonium sulfate (AMS), calcium carbonate (CAC) and ammonium nitrate (AMN), comparisons were made with previously published complex refractive indices data for AMS and CAC to infer experimental parameters to determine the imaginary refractive index for AMN in the infrared wavelength range from 2 to 20 microns. Kramers-Kronig mathematical relations were applied to calculate the real refractive index for the three compositions. Excellent agreement for AMS and CAC with the published values was found, validating the complex refractive indices obtained for AMN. Backscatter calculations using a lognormal size distribution for AMS, AMN, and CAC aerosols were performed to show differences in their backscattered spectra.

TU-H-BRA-07: Design, Construction, and Installation of An Experimental Beam Line for the Development of MRI-Linac Compatible Electron Accelerator

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

Whelan, B; Keall, P; Holloway, L

Purpose: MRI guided radiation therapy (MRIgRT) is a rapidly growing field; however, Linac operation in MRI fringe fields represents an ongoing challenge. We have previously shown in-silico that Linacs could be redesigned to function in the in-line orientation with no magnetic shielding by adopting an RF-gun configuration. Other authors have also published insilico studies of Linac operation in magnetic fields; however to date no experimental validation data is published. This work details the design, construction, and installation of an experimental beam line to validate our in-silico results. Methods: An RF-gun comprising 1.5 accelerating cells and capable of generating electron energiesmore » up to 3.2MeV is used. The experimental apparatus was designed to monitor both beam current (toroid current monitor), spot size (two phosphor screens with viewports), and generate peak magnetic fields of at least 1000G (three variable current electromagnetic coils). Thermal FEM simulations were developed to ensure coil temperature remained within 100degC. Other design considerations included beam disposal, vacuum maintenance, radiation shielding, earthquake safety, and machine protection interlocks. Results: The beam line has been designed, built, and installed in a radiation shielded bunker. Water cooling, power supplies, thermo-couples, cameras, and radiation shielding have been successfully connected and tested. Interlock testing, vacuum processing, and RF processing have been successfully completed. The first beam on is expected within weeks. The coil heating simulations show that with care, peak fields of up to 1200G (320G at cathode) can be produced using 40A current, which is well within the fields expected for MRI-Linac systems. The maximum coil temperature at this current was 84degC after 6 minutes. Conclusion: An experimental beam line has been constructed and installed at SLAC in order to experimentally characterise RF gun performance in in-line magnetic fields, validate in-silico design work, and provide the first published experimental data relating to accelerator functionality for MRIgRT.« less

An experimental approach in revisiting the magnetic orientation of cattle.

PubMed

Weijers, Debby; Hemerik, Lia; Heitkönig, Ignas M A

2018-01-01

In response to the increasing number of observational studies on an apparent south-north orientation in non-homing, non-migrating terrestrial mammals, we experimentally tested the alignment hypothesis using strong neodymium magnets on the resting orientation of individual cattle in Portugal. Contrary to the hypothesis, the 34 cows in the experiment showed no directional preference, neither with, nor without a strong neodymium magnet fixed to their collar. The concurrently performed 2,428 daytime observations-excluding the hottest part of the day-of 659 resting individual cattle did not show a south-north alignment when at rest either. The preferred compass orientation of these cows was on average 130 degrees from the magnetic north (i.e., south east). Cow compass orientation correlated significantly with sun direction, but not with wind direction. In as far as we can determine, this is the first experimental test on magnetic orientation in larger, non-homing, non-migrating mammals. These experimental and observational findings do not support previously published suggestions on the magnetic south-north alignment in these mammals.

Predictive Surface Complexation Modeling

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

Sverjensky, Dimitri A.

Surface complexation plays an important role in the equilibria and kinetics of processes controlling the compositions of soilwaters and groundwaters, the fate of contaminants in groundwaters, and the subsurface storage of CO 2 and nuclear waste. Over the last several decades, many dozens of individual experimental studies have addressed aspects of surface complexation that have contributed to an increased understanding of its role in natural systems. However, there has been no previous attempt to develop a model of surface complexation that can be used to link all the experimental studies in order to place them on a predictive basis. Overall,more » my research has successfully integrated the results of the work of many experimentalists published over several decades. For the first time in studies of the geochemistry of the mineral-water interface, a practical predictive capability for modeling has become available. The predictive correlations developed in my research now enable extrapolations of experimental studies to provide estimates of surface chemistry for systems not yet studied experimentally and for natural and anthropogenically perturbed systems.« less

Optical Activity of Benzil Crystal

NASA Astrophysics Data System (ADS)

Říha, Jan; Vyšín, Ivo

2003-09-01

Optical activity of benzil as an example of optically active matter in the crystalline state only, not in solution, is studied for the wavelengths ranging from 0.320 m to 0.585 m. Previously measured experimental data are approximated by the theoretical set of formulas, which were derived by the use of the three coupled oscillators model. The earlier published formula consisting of six terms differed from the experimental data particularly in the wavelength region (0.380-0.510) m. This formula is replaced by the twelve-term formula which was computed by our specially worked computer program for the interpretation of the experimental data of optical activity based on the Marquardt-Levenberg method of the sum of least squares minimization. The possibility of molecular contribution to the resulting optical activity of benzil is mentioned. The use of Kramers-Kronig transforms for the determination of the circular dichroism curve based on the optical rotatory dispersion result is shown. The theoretically computed circular dichroism is compared with the available experimental data.

Scene-based nonuniformity correction with reduced ghosting using a gated LMS algorithm.

PubMed

Hardie, Russell C; Baxley, Frank; Brys, Brandon; Hytla, Patrick

2009-08-17

In this paper, we present a scene-based nouniformity correction (NUC) method using a modified adaptive least mean square (LMS) algorithm with a novel gating operation on the updates. The gating is designed to significantly reduce ghosting artifacts produced by many scene-based NUC algorithms by halting updates when temporal variation is lacking. We define the algorithm and present a number of experimental results to demonstrate the efficacy of the proposed method in comparison to several previously published methods including other LMS and constant statistics based methods. The experimental results include simulated imagery and a real infrared image sequence. We show that the proposed method significantly reduces ghosting artifacts, but has a slightly longer convergence time. (c) 2009 Optical Society of America

Dalton's disputed nitric oxide experiments and the origins of his atomic theory.

PubMed

Usselman, Melvyn C; Leaist, Derek G; Watson, Katherine D

2008-01-11

In 1808 John Dalton published his first general account of chemical atomic theory, a cornerstone of modern chemistry. The theory originated in his earlier studies of the properties of atmospheric gases. In 1803 Dalton discovered that oxygen combined with either one or two volumes of nitric oxide in closed vessels over water and this pioneering observation of integral multiple proportions provided important experimental evidence for his incipient atomic ideas. Previous attempts to reproduce Dalton's experiments have been unsuccessful and some commentators have concluded the results were fraudulent. We report a successful reconstruction of Dalton's experiments and provide an analysis exonerating him of any scientific misconduct. But we conclude that Dalton, already thinking atomistically, adjusted experimental conditions to obtain the integral combining proportions.

Experimental validation of 2D uncertainty quantification for DIC.

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

Reu, Phillip L.

Because digital image correlation (DIC) has become such an important and standard tool in the toolbox of experimental mechanicists, a complete uncertainty quantification of the method is needed. It should be remembered that each DIC setup and series of images will have a unique uncertainty based on the calibration quality and the image and speckle quality of the analyzed images. Any pretest work done with a calibrated DIC stereo-rig to quantify the errors using known shapes and translations, while useful, do not necessarily reveal the uncertainty of a later test. This is particularly true with high-speed applications where actual testmore » images are often less than ideal. Work has previously been completed on the mathematical underpinnings of DIC uncertainty quantification and is already published, this paper will present corresponding experimental work used to check the validity of the uncertainty equations.« less

Experimental validation of 2D uncertainty quantification for digital image correlation.

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

Reu, Phillip L.

Because digital image correlation (DIC) has become such an important and standard tool in the toolbox of experimental mechanicists, a complete uncertainty quantification of the method is needed. It should be remembered that each DIC setup and series of images will have a unique uncertainty based on the calibration quality and the image and speckle quality of the analyzed images. Any pretest work done with a calibrated DIC stereo-rig to quantify the errors using known shapes and translations, while useful, do not necessarily reveal the uncertainty of a later test. This is particularly true with high-speed applications where actual testmore » images are often less than ideal. Work has previously been completed on the mathematical underpinnings of DIC uncertainty quantification and is already published, this paper will present corresponding experimental work used to check the validity of the uncertainty equations.« less

Realization of MEMS-IC Vertical Integration Utilizing Smart Bumpless Bonding

NASA Astrophysics Data System (ADS)

Shiozaki, Masayoshi; Moriguchi, Makoto; Sasaki, Sho; Oba, Masatoshi

This paper reports fundamental technologies, properties, and new experimental results of SBB (Smart Bumpless Bonding) to realize MEMS-IC vertical integration. Although conventional bonding technologies have had difficulties integrating MEMS and its processing circuit because of their rough bonding surfaces, fragile structures, and thermal restriction, SBB technology realized the vertical integration without thermal treatment, any adhesive materials including bumps, and chemical mechanical polishing. The SBB technology bonds sealing parts for vacuum sealing and electrodes for electrical connection simultaneously as published in previous experimental study. The plasma CVD SiO2 is utilized to realize vacuum sealing as sealing material. And Au projection studs are formed on each electrode and connected electrically between two wafers by compressive plastic deformation and surface activation. In this paper, new experimental results including vacuum sealing properties, electrical improvement, IC bonding results on the described fundamental concept and properties are reported.

Prophylactic effects of humic acid-glucan combination against experimental liver injury

PubMed Central

Vetvicka, Vaclav; Garcia-Mina, Jose Maria; Yvin, Jean-Claude

2015-01-01

Aim: Despite intensive research, liver diseases represent a significant health problem and current medicine does not offer a substance able to significantly inhibit the hepatotoxicity leading to various stages of liver disease. Based on our previously published studies showing the protective effects of a glucan-humic acid (HA) combination, we focused on the hypothesis that the combination of these two natural molecules can offer prophylactic protection against experimentally induced hepatotoxicity. Materials and Methods: Lipopolysaccharide, carbon tetrachloride, and ethanol were used to experimentally damage the liver. Levels of aspartate aminotransferase, alanine transaminase, alkaline phosphatase, glutathione, superoxide dismutase, and malondialdehyde, known to correspond to the liver damage, were assayed. Results: Using three different hepatotoxins, we found that in all cases, some samples of HA and most of all the glucan-HA combination, offer strong protection against liver damage. Conclusion: Glucan-HA combination is a promising agent for use in liver protection. PMID:26401416

The Discovery of the Tau Lepton and the Changes in Elementary Particle Physics in 40 Years

DOE R&D Accomplishments Database

Perl, M.

2003-10-22

This is a history of my discovery of the tau lepton in the 1970s for which I was awarded the Nobel Prize in Physics. I have previously described some aspects of the discovery. In 1996 in my collection of papers entitled, ''Reflections on Experimental Science,'' I gave a straightforward account of the experimental method and the physics involved in the discovery as an introduction to the collection. In a 2002 paper written with Mary A. Meyer published in the journal ''Theoria et Historia Scientiarum'' I used the story of the discovery to outline my thoughts on the practice of experimental science. That 2002 paper was written primarily for young women and men who are beginning their lives in science and it was based on a lecture given at Los Alamos National Laboratory. Some of the historical material in this paper has appeared in those two earlier papers.

Improved absolute calibration of LOPES measurements and its impact on the comparison with REAS 3.11 and CoREAS simulations

NASA Astrophysics Data System (ADS)

Apel, W. D.; Arteaga-Velázquez, J. C.; Bähren, L.; Bekk, K.; Bertaina, M.; Biermann, P. L.; Blümer, J.; Bozdog, H.; Brancus, I. M.; Cantoni, E.; Chiavassa, A.; Daumiller, K.; de Souza, V.; Di Pierro, F.; Doll, P.; Engel, R.; Falcke, H.; Fuchs, B.; Gemmeke, H.; Grupen, C.; Haungs, A.; Heck, D.; Hiller, R.; Hörandel, J. R.; Horneffer, A.; Huber, D.; Huege, T.; Isar, P. G.; Kampert, K.-H.; Kang, D.; Krömer, O.; Kuijpers, J.; Link, K.; Łuczak, P.; Ludwig, M.; Mathes, H. J.; Melissas, M.; Morello, C.; Nehls, S.; Oehlschläger, J.; Palmieri, N.; Pierog, T.; Rautenberg, J.; Rebel, H.; Roth, M.; Rühle, C.; Saftoiu, A.; Schieler, H.; Schmidt, A.; Schoo, S.; Schröder, F. G.; Sima, O.; Toma, G.; Trinchero, G. C.; Weindl, A.; Wochele, J.; Zabierowski, J.; Zensus, J. A.

2016-02-01

LOPES was a digital antenna array detecting the radio emission of cosmic-ray air showers. The calibration of the absolute amplitude scale of the measurements was done using an external, commercial reference source, which emits a frequency comb with defined amplitudes. Recently, we obtained improved reference values by the manufacturer of the reference source, which significantly changed the absolute calibration of LOPES. We reanalyzed previously published LOPES measurements, studying the impact of the changed calibration. The main effect is an overall decrease of the LOPES amplitude scale by a factor of 2.6 ± 0.2, affecting all previously published values for measurements of the electric-field strength. This results in a major change in the conclusion of the paper 'Comparing LOPES measurements of air-shower radio emission with REAS 3.11 and CoREAS simulations' published by Apel et al. (2013) : With the revised calibration, LOPES measurements now are compatible with CoREAS simulations, but in tension with REAS 3.11 simulations. Since CoREAS is the latest version of the simulation code incorporating the current state of knowledge on the radio emission of air showers, this new result indicates that the absolute amplitude prediction of current simulations now is in agreement with experimental data.

Source of funding in experimental studies of mobile phone use on health: Update of systematic review

NASA Astrophysics Data System (ADS)

van Nierop, Lotte E.; Röösli, Martin; Egger, Matthias; Huss, Anke

2010-11-01

A previous review showed that among 59 studies published in 1995-2005, industry-funded studies were least likely to report effects of controlled exposure to mobile phone radiation on health-related outcomes. We updated literature searches in 2005-2009 and extracted data on funding, conflicts of interest and results. Of 75 additional studies 12% were industry-funded, 44% had public and 19% mixed funding; funding was unclear in 25%. Previous findings were confirmed: industry-sponsored studies were least likely to report results suggesting effects. Interestingly, the proportion of studies indicating effects declined in 1995-2009, regardless of funding source. Source of funding and conflicts of interest are important in this field of research.

Using experimental human influenza infections to validate a viral dynamic model and the implications for prediction.

PubMed

Chen, S C; You, S H; Liu, C Y; Chio, C P; Liao, C M

2012-09-01

The aim of this work was to use experimental infection data of human influenza to assess a simple viral dynamics model in epithelial cells and better understand the underlying complex factors governing the infection process. The developed study model expands on previous reports of a target cell-limited model with delayed virus production. Data from 10 published experimental infection studies of human influenza was used to validate the model. Our results elucidate, mechanistically, the associations between epithelial cells, human immune responses, and viral titres and were supported by the experimental infection data. We report that the maximum total number of free virions following infection is 10(3)-fold higher than the initial introduced titre. Our results indicated that the infection rates of unprotected epithelial cells probably play an important role in affecting viral dynamics. By simulating an advanced model of viral dynamics and applying it to experimental infection data of human influenza, we obtained important estimates of the infection rate. This work provides epidemiologically meaningful results, meriting further efforts to understand the causes and consequences of influenza A infection.

Assessment of the neutron dose field around a biomedical cyclotron: FLUKA simulation and experimental measurements.

PubMed

Infantino, Angelo; Cicoria, Gianfranco; Lucconi, Giulia; Pancaldi, Davide; Vichi, Sara; Zagni, Federico; Mostacci, Domiziano; Marengo, Mario

2016-12-01

In the planning of a new cyclotron facility, an accurate knowledge of the radiation field around the accelerator is fundamental for the design of shielding, the protection of workers, the general public and the environment. Monte Carlo simulations can be very useful in this process, and their use is constantly increasing. However, few data have been published so far as regards the proper validation of Monte Carlo simulation against experimental measurements, particularly in the energy range of biomedical cyclotrons. In this work a detailed model of an existing installation of a GE PETtrace 16.5MeV cyclotron was developed using FLUKA. An extensive measurement campaign of the neutron ambient dose equivalent H ∗ (10) in marked positions around the cyclotron was conducted using a neutron rem-counter probe and CR39 neutron detectors. Data from a previous measurement campaign performed by our group using TLDs were also re-evaluated. The FLUKA model was then validated by comparing the results of high-statistics simulations with experimental data. In 10 out of 12 measurement locations, FLUKA simulations were in agreement within uncertainties with all the three different sets of experimental data; in the remaining 2 positions, the agreement was with 2/3 of the measurements. Our work allows to quantitatively validate our FLUKA simulation setup and confirms that Monte Carlo technique can produce accurate results in the energy range of biomedical cyclotrons. Copyright © 2016 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Magnetic and Electrical Characteristics of Permalloy Thin Tape Bobbin Cores

NASA Technical Reports Server (NTRS)

Schwarze, Gene E.; Wieserman, William R.; Niedra, Janis M.

2005-01-01

The core loss, that is, the power loss, of a soft ferromagnetic material is a function of the flux density, frequency, temperature, excitation type (voltage or current), excitation waveform (sine, square, etc.) and lamination or tape thickness. In previously published papers we have reported on the specific core loss and dynamic B-H loop results for several polycrystalline, nanocrystalline, and amorphous soft magnetic materials. In this previous research we investigated the effect of flux density, frequency, temperature, and excitation waveform for voltage excitation on the specific core loss and dynamic B-H loop. In this paper, we will report on an experimental study to investigate the effect of tape thicknesses of 1, 1/2, 1/4, and 1/8-mil Permalloy type magnetic materials on the specific core loss. The test cores were fabricated by winding the thin tapes on ceramic bobbin cores. The specific core loss tests were conducted at room temperature and over the frequency range of 10 kHz to 750 kHz using sine wave voltage excitation. The results of this experimental investigation will be presented primarily in graphical form to show the effect of tape thickness, frequency, and magnetic flux density on the specific core loss. Also, the experimental results when applied to power transformer design will be briefly discussed.

The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus

PubMed Central

Scannell, Devin R.; Zill, Oliver A.; Rokas, Antonis; Payen, Celia; Dunham, Maitreya J.; Eisen, Michael B.; Rine, Jasper; Johnston, Mark; Hittinger, Chris Todd

2011-01-01

High-quality, well-annotated genome sequences and standardized laboratory strains fuel experimental and evolutionary research. We present improved genome sequences of three species of Saccharomyces sensu stricto yeasts: S. bayanus var. uvarum (CBS 7001), S. kudriavzevii (IFO 1802T and ZP 591), and S. mikatae (IFO 1815T), and describe their comparison to the genomes of S. cerevisiae and S. paradoxus. The new sequences, derived by assembling millions of short DNA sequence reads together with previously published Sanger shotgun reads, have vastly greater long-range continuity and far fewer gaps than the previously available genome sequences. New gene predictions defined a set of 5261 protein-coding orthologs across the five most commonly studied Saccharomyces yeasts, enabling a re-examination of the tempo and mode of yeast gene evolution and improved inferences of species-specific gains and losses. To facilitate experimental investigations, we generated genetically marked, stable haploid strains for all three of these Saccharomyces species. These nearly complete genome sequences and the collection of genetically marked strains provide a valuable toolset for comparative studies of gene function, metabolism, and evolution, and render Saccharomyces sensu stricto the most experimentally tractable model genus. These resources are freely available and accessible through www.SaccharomycesSensuStricto.org. PMID:22384314

The MIXED framework: A novel approach to evaluating mixed-methods rigor.

PubMed

Eckhardt, Ann L; DeVon, Holli A

2017-10-01

Evaluation of rigor in mixed-methods (MM) research is a persistent challenge due to the combination of inconsistent philosophical paradigms, the use of multiple research methods which require different skill sets, and the need to combine research at different points in the research process. Researchers have proposed a variety of ways to thoroughly evaluate MM research, but each method fails to provide a framework that is useful for the consumer of research. In contrast, the MIXED framework is meant to bridge the gap between an academic exercise and practical assessment of a published work. The MIXED framework (methods, inference, expertise, evaluation, and design) borrows from previously published frameworks to create a useful tool for the evaluation of a published study. The MIXED framework uses an experimental eight-item scale that allows for comprehensive integrated assessment of MM rigor in published manuscripts. Mixed methods are becoming increasingly prevalent in nursing and healthcare research requiring researchers and consumers to address issues unique to MM such as evaluation of rigor. © 2017 John Wiley & Sons Ltd.

Folding cooperativity in a three-stranded beta-sheet model.

PubMed

Roe, Daniel R; Hornak, Viktor; Simmerling, Carlos

2005-09-16

The thermodynamic behavior of a previously designed three-stranded beta-sheet was studied via several microseconds of standard and replica exchange molecular dynamics simulations. The system is shown to populate at least four thermodynamic minima, including two partially folded states in which only a single hairpin is formed. Simulated melting curves show different profiles for the C and N-terminal hairpins, consistent with differences in secondary structure content in published NMR and CD/FTIR measurements, which probed different regions of the chain. Individual beta-hairpins that comprise the three-stranded beta-sheet are observed to form cooperatively. Partial folding cooperativity between the component hairpins is observed, and good agreement between calculated and experimental values quantifying this cooperativity is obtained when similar analysis techniques are used. However, the structural detail in the ensemble of conformations sampled in the simulations permits a more direct analysis of this cooperativity than has been performed on the basis of experimental data. The results indicate the actual folding cooperativity perpendicular to strand direction is significantly larger than the lower bound obtained previously.

Folding cooperativity in a 3-stranded β-sheet model

PubMed Central

Roe, Daniel R.; Hornak, Viktor

2015-01-01

Summary The thermodynamic behavior of a previously designed three-stranded β-sheet was studied via several µs of standard and replica exchange molecular dynamics simulations. The system is shown to populate at least four thermodynamic minima, including 2 partially folded states in which only a single hairpin is formed. Simulated melting curves show different profiles for the C and N-terminal hairpins, consistent with differences in secondary structure content in published NMR and CD/FTIR measurements, which probed different regions of the chain. Individual β-hairpins that comprise the 3-stranded β-sheet are observed to form cooperatively. Partial folding cooperativity between the component hairpins is observed, and good agreement between calculated and experimental values quantifying this cooperativity is obtained when similar analysis techniques are used. However, the structural detail in the ensemble of conformations sampled in the simulations permits a more direct analysis of this cooperatively than has been performed based on experimental data. The results indicate the actual folding cooperativity perpendicular to strand direction is significantly larger than the lower bound obtained previously. PMID:16095612

An accurate fatigue damage model for welded joints subjected to variable amplitude loading

NASA Astrophysics Data System (ADS)

Aeran, A.; Siriwardane, S. C.; Mikkelsen, O.; Langen, I.

2017-12-01

Researchers in the past have proposed several fatigue damage models to overcome the shortcomings of the commonly used Miner’s rule. However, requirements of material parameters or S-N curve modifications restricts their practical applications. Also, application of most of these models under variable amplitude loading conditions have not been found. To overcome these restrictions, a new fatigue damage model is proposed in this paper. The proposed model can be applied by practicing engineers using only the S-N curve given in the standard codes of practice. The model is verified with experimentally derived damage evolution curves for C 45 and 16 Mn and gives better agreement compared to previous models. The model predicted fatigue lives are also in better correlation with experimental results compared to previous models as shown in earlier published work by the authors. The proposed model is applied to welded joints subjected to variable amplitude loadings in this paper. The model given around 8% shorter fatigue lives compared to Eurocode given Miner’s rule. This shows the importance of applying accurate fatigue damage models for welded joints.

Origin matters: diversity affects the performance of alien invasive species but not of native species.

PubMed

Sun, Yan; Müller-Schärer, Heinz; Maron, John L; Schaffner, Urs

2015-06-01

At local scales, it has often been found that invasibility decreases with increasing resident plant diversity. However, whether resident community diversity similarly resists invasion by alien versus native species is seldom studied. We examined this issue by invading constructed native plant assemblages that varied in species and functional richness with invasive alien or native Asteraceae species. Assemblages were also invaded with spotted knapweed, Centaurea stoebe, a native European aster that has been previously used in diversity-invasibility experiments in North America. We also conducted a field survey to explore the generality of the patterns generated from our experimental study. Both experimental and observational work revealed that increasing diversity reduced the performance of alien but not native invaders. Centaurea stoebe invading its native community performed poorly regardless of resident diversity, whereas in a parallel, previously published study conducted in North America, C. stoebe easily invaded low-diversity but not high-diversity assemblages. Our results suggest that diversity is an attribute of resident communities that makes them more or less susceptible to invasion by novel invasive alien but not native plant species.

A literature review of blood concentrations of new psychoactive substances classified as phenethylamines, aminoindanes, arylalkylamines, arylcyclohexylamines, and indolalkylamines.

PubMed

Karinen, Ritva; Høiseth, Gudrun

2017-07-01

Interpretation of blood concentrations of new psychoactive substances (NPS) requires comparison of the results to previously published case reports; as only a few experimental studies for these substances exist. A large number of articles representing single or multiple cases have been published for a great number of substances, making a unified overview difficult. In this review we have collected all published blood concentrations from the NPS groups classified as phenethylamines, aminoindanes, arylalkylamines, arylcyclohexylamines, and indolalkylamines, and also included unpublished results for MPA, MXE, 4-FMA, 4-FA and 4-MA analyzed in our laboratory. In total, 71 publications on 35 different drugs were summarized. For most of the drugs, the total number of reported cases was very low (≤5). For some of the synthetic drugs, however, a higher number of blood concentrations are now available; especially for 5-IT (32 reported cases in total), MPA (31 reported cases in total) and MXE (36 reported cases in total), thus the published results are more substantial. The present compilation could be a helpful tool for forensic toxicologists when blood concentrations of NPS are assessed. Copyright © 2017. Published by Elsevier B.V.

Validation of light water reactor calculation methods and JEF-1-based data libraries by TRX and BAPL critical experiments

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

Paratte, J.M.; Pelloni, S.; Grimm, P.

1991-04-01

This paper analyzes the capability of various code systems and JEF-1-based nuclear data libraries to compute light water reactor lattices by comparing calculations with results from thermal reactor benchmark experiments TRX and BAPL and with previously published values. With the JEF-1 evaluation, eigenvalues are generally well predicted within 8 mk (1 mk = 0.001) or less by all code systems, and all methods give reasonable results for the measured reaction rate ratios within, or not too far from, the experimental uncertainty.

Publishing Single-Case Research Design Studies That Do Not Demonstrate Experimental Control

ERIC Educational Resources Information Center

Tincani, Matt; Travers, Jason

2018-01-01

Demonstration of experimental control is considered a hallmark of high-quality single-case research design (SCRD). Studies that fail to demonstrate experimental control may not be published because researchers are unwilling to submit these papers for publication and journals are unlikely to publish negative results (i.e., the file drawer effect).…

Non-goal-directed recall of specific events in apes after long delays.

PubMed

Lewis, Amy; Call, Josep; Berntsen, Dorthe

2017-07-12

We examined if apes spontaneously remember one-time, distinctive events across long delays when probed by discriminant cues. Apes witnessed an experimenter hide a cache of food, which they could then retrieve. They retrieved one of two food types; one more distinctive than the other. Two, 10 or 50 weeks later, the apes returned to the same enclosure and found a piece of the previously hidden food on the ground. An experimenter who had not hidden the food was also present. Apes immediately searched the location where the food was previously hidden (no food was here), showing recall of the event. One week later, apes returned to the same enclosure, with the same food on the ground, but now the experimenter that had hidden the food was present. Again, apes immediately searched the hiding location. Apes that had not witnessed the hiding event did not search. There was no significant effect of food type, and retention declined from exposure to the two-week delay, then levelled, consistent with the forgetting curve in humans (Ebbinghaus, H. 1964 Memory: a contribution to experimental psychology (transl. H.A. Ruger & C.E. Bussenvis). New York, NY: Dover. (Original work published 1885.)). This is the first study to show apes can recall a one-time, non-goal-directed event longer than two weeks ago and that apes' recall declines in accordance with a standard retention function. © 2017 The Author(s).

Deciphering assumptions about stepped wedge designs: the case of Ebola vaccine research.

PubMed

Doussau, Adélaïde; Grady, Christine

2016-12-01

Ethical concerns about randomising persons to a no-treatment arm in the context of Ebola epidemic led to consideration of alternative designs. The stepped wedge (SW) design, in which participants or clusters are randomised to receive an intervention at different time points, gained popularity. Common arguments in favour of using this design are (1) when an intervention is likely to do more good than harm, (2) all participants should receive the experimental intervention at some time point during the study and (3) the design might be preferable for practical reasons. We examine these assumptions when considering Ebola vaccine research. First, based on the claim that a stepped wedge design is indicated when it is likely that the intervention will do more good than harm, we reviewed published and ongoing SW trials to explore previous use of this design to test experimental drugs or vaccines, and found that SW design has never been used for trials of experimental drugs or vaccines. Given that Ebola vaccines were all experimental with no prior efficacy data, the use of a stepped wedge design would have been unprecedented. Second, we show that it is rarely true that all participants receive the intervention in SW studies, but rather, depending on certain design features, all clusters receive the intervention. Third, we explore whether the SW design is appealing for feasibility reasons and point out that there is significant complexity. In the setting of the Ebola epidemic, spatiotemporal variation may have posed problematic challenges to a stepped wedge design for vaccine research. Finally, we propose a set of points to consider for scientific reviewers and ethics committees regarding proposals for SW designs. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Cardiorespiratory adaptation to breath-holding in air: Analysis via a cardiopulmonary simulation model.

PubMed

Albanese, Antonio; Limei Cheng; Ursino, Mauro; Chbat, Nicolas W

2015-01-01

Apnea via breath-holding (BH) in air induces cardiorespiratory adaptation that involves the activation of several reflex mechanisms and their complex interactions. Hence, the effects of BH in air on cardiorespiratory function can become hardly predictable and difficult to be interpreted. Particularly, the effect on heart rate is not yet completely understood because of the contradicting results of different physiological studies. In this paper we apply our previously developed cardiopulmonary model (CP Model) to a scenario of BH with a twofold intent: (1) further validating the CP Model via comparison against experimental data; (2) gaining insights into the physiological reasoning for such contradicting experimental results. Model predictions agreed with published experimental animal and human data and indicated that heart rate increases during BH in air. Changes in the balance between sympathetic and vagal effects on heart rate within the model proved to be effective in inverting directions of the heart rate changes during BH. Hence, the model suggests that intra-subject differences in such sympatho-vagal balance may be one of the reasons for the contradicting experimental results.

An experimental approach in revisiting the magnetic orientation of cattle

PubMed Central

Weijers, Debby; Hemerik, Lia; Heitkönig, Ignas M. A.

2018-01-01

In response to the increasing number of observational studies on an apparent south-north orientation in non-homing, non-migrating terrestrial mammals, we experimentally tested the alignment hypothesis using strong neodymium magnets on the resting orientation of individual cattle in Portugal. Contrary to the hypothesis, the 34 cows in the experiment showed no directional preference, neither with, nor without a strong neodymium magnet fixed to their collar. The concurrently performed 2,428 daytime observations—excluding the hottest part of the day—of 659 resting individual cattle did not show a south-north alignment when at rest either. The preferred compass orientation of these cows was on average 130 degrees from the magnetic north (i.e., south east). Cow compass orientation correlated significantly with sun direction, but not with wind direction. In as far as we can determine, this is the first experimental test on magnetic orientation in larger, non-homing, non-migrating mammals. These experimental and observational findings do not support previously published suggestions on the magnetic south-north alignment in these mammals. PMID:29641517

Evidence Base Update for Autism Spectrum Disorder.

PubMed

Smith, Tristram; Iadarola, Suzannah

2015-01-01

This evidence base update examines the level of empirical support for interventions for children with autism spectrum disorder (ASD) younger than 5 years old. It focuses on research published since a previous review in this journal (Rogers & Vismara, 2008 ). We identified psychological or behavioral interventions that had been manualized and evaluated in either (a) experimental or quasi-experimental group studies or (b) systematic reviews of single-subject studies. We extracted data from all studies that met these criteria and were published after the previous review. Interventions were categorized across two dimensions. First, primary theoretical principles included applied behavior analysis (ABA), developmental social-pragmatic (DSP), or both. Second, practice elements included scope (comprehensive or focused), modality (individual intervention with the child, parent training, or classrooms), and intervention targets (e.g., spoken language or alternative and augmentative communication). We classified two interventions as well-established (individual, comprehensive ABA and teacher-implemented, focused ABA + DSP), 3 as probably efficacious (individual, focused ABA for augmentative and alternative communication; individual, focused ABA + DSP; and focused DSP parent training), and 5 as possibly efficacious (individual, comprehensive ABA + DSP; comprehensive ABA classrooms; focused ABA for spoken communication; focused ABA parent training; and teacher-implemented, focused DSP). The evidence base for ASD interventions has grown substantially since 2008. An increasing number of interventions have some empirical support; others are emerging as potentially efficacious. Priorities for future research include improving outcome measures, developing interventions for understudied ASD symptoms (e.g., repetitive behaviors), pinpointing mechanisms of action in interventions, and adapting interventions for implementation with fidelity by community providers.

78 FR 41129 - Market Test of Experimental Product - International Merchandise Return Service-Non-Published Rates

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-09

...--Non-Published Rates AGENCY: U.S. Postal Service\\TM\\. ACTION: Notice. SUMMARY: The Postal Service hereby gives notice of a market test for International Merchandise Return Service--Non-Published Rates in... Return Service (IMRS) Non-published Rate (NPR) experimental product on August 15, 2013. The Postal...

True detection limits in an experimental linearly heteroscedastic system.. Part 2

NASA Astrophysics Data System (ADS)

Voigtman, Edward; Abraham, Kevin T.

2011-11-01

Despite much different processing of the experimental fluorescence detection data presented in Part 1, essentially the same estimates were obtained for the true theoretical Currie decision levels ( YC and XC) and true Currie detection limits ( YD and XD). The obtained experimental values, for 5% probability of false positives and 5% probability of false negatives, were YC = 56.0 mV, YD = 125. mV, XC = 0.132 μg/mL and XD = 0.293 μg/mL. For 5% probability of false positives and 1% probability of false negatives, the obtained detection limits were YD = 158 . mV and XD = 0.371 μg/mL. Furthermore, by using bootstrapping methodology on the experimental data for the standards and the analytical blank, it was possible to validate previously published experimental domain expressions for the decision levels ( yC and xC) and detection limits ( yD and xD). This was demonstrated by testing the generated decision levels and detection limits for their performance in regard to false positives and false negatives. In every case, the obtained numbers of false negatives and false positives were as specified a priori.

Discovery and validation of information theory-based transcription factor and cofactor binding site motifs.

PubMed

Lu, Ruipeng; Mucaki, Eliseos J; Rogan, Peter K

2017-03-17

Data from ChIP-seq experiments can derive the genome-wide binding specificities of transcription factors (TFs) and other regulatory proteins. We analyzed 765 ENCODE ChIP-seq peak datasets of 207 human TFs with a novel motif discovery pipeline based on recursive, thresholded entropy minimization. This approach, while obviating the need to compensate for skewed nucleotide composition, distinguishes true binding motifs from noise, quantifies the strengths of individual binding sites based on computed affinity and detects adjacent cofactor binding sites that coordinate with the targets of primary, immunoprecipitated TFs. We obtained contiguous and bipartite information theory-based position weight matrices (iPWMs) for 93 sequence-specific TFs, discovered 23 cofactor motifs for 127 TFs and revealed six high-confidence novel motifs. The reliability and accuracy of these iPWMs were determined via four independent validation methods, including the detection of experimentally proven binding sites, explanation of effects of characterized SNPs, comparison with previously published motifs and statistical analyses. We also predict previously unreported TF coregulatory interactions (e.g. TF complexes). These iPWMs constitute a powerful tool for predicting the effects of sequence variants in known binding sites, performing mutation analysis on regulatory SNPs and predicting previously unrecognized binding sites and target genes. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Poverty, inequality, and increased consumption of high calorie food: Experimental evidence for a causal link.

PubMed

Bratanova, Boyka; Loughnan, Steve; Klein, Olivier; Claassen, Almudena; Wood, Robert

2016-05-01

Rising obesity represents a serious, global problem. It is now well established that obesity is associated with poverty and wealth inequality, suggesting that these factors may promote caloric intake. Whereas previous work has examined these links from an epidemiological perspective, the current paper examined them experimentally. In Study 1 we found that people experimentally induced to view themselves as poor (v. wealthy) exhibited increased calorie intake. In Study 2, participants who believed that they were poorer or wealthier than their interaction partners exhibited higher levels of anxiety compared to those in an equal partners condition; this anxiety in turn led to increased calorie consumption for people who had a strong need to belong. The findings provide causal evidence for the poverty-intake and inequality-intake links. Further, we identify social anxiety and a strong need to belong as important social psychological factors linking inequality to increased calorie intake. Copyright © 2016. Published by Elsevier Ltd.

From Ion Current to Electroosmotic Flow Rectification in Asymmetric Nanopore Membranes

PubMed Central

Wu, Xiaojian

2017-01-01

Asymmetrically shaped nanopores have been shown to rectify the ionic current flowing through pores in a fashion similar to a p-n junction in a solid-state diode. Such asymmetric nanopores include conical pores in polymeric membranes and pyramidal pores in mica membranes. We review here both theoretical and experimental aspects of this ion current rectification phenomenon. A simple intuitive model for rectification, stemming from previously published more quantitative models, is discussed. We also review experimental results on controlling the extent and sign of rectification. It was shown that ion current rectification produces a related rectification of electroosmotic flow (EOF) through asymmetric pore membranes. We review results that show how to measure and modulate this EOF rectification phenomenon. Finally, EOF rectification led to the development of an electroosmotic pump that works under alternating current (AC), as opposed to the currently available direct current EOF pumps. Experimental results on AC EOF rectification are reviewed, and advantages of using AC to drive EOF are discussed. PMID:29240676

From Ion Current to Electroosmotic Flow Rectification in Asymmetric Nanopore Membranes.

PubMed

Experton, Juliette; Wu, Xiaojian; Martin, Charles R

2017-12-14

Asymmetrically shaped nanopores have been shown to rectify the ionic current flowing through pores in a fashion similar to a p-n junction in a solid-state diode. Such asymmetric nanopores include conical pores in polymeric membranes and pyramidal pores in mica membranes. We review here both theoretical and experimental aspects of this ion current rectification phenomenon. A simple intuitive model for rectification, stemming from previously published more quantitative models, is discussed. We also review experimental results on controlling the extent and sign of rectification. It was shown that ion current rectification produces a related rectification of electroosmotic flow (EOF) through asymmetric pore membranes. We review results that show how to measure and modulate this EOF rectification phenomenon. Finally, EOF rectification led to the development of an electroosmotic pump that works under alternating current (AC), as opposed to the currently available direct current EOF pumps. Experimental results on AC EOF rectification are reviewed, and advantages of using AC to drive EOF are discussed.

Statistical reporting inconsistencies in experimental philosophy

PubMed Central

Colombo, Matteo; Duev, Georgi; Nuijten, Michèle B.; Sprenger, Jan

2018-01-01

Experimental philosophy (x-phi) is a young field of research in the intersection of philosophy and psychology. It aims to make progress on philosophical questions by using experimental methods traditionally associated with the psychological and behavioral sciences, such as null hypothesis significance testing (NHST). Motivated by recent discussions about a methodological crisis in the behavioral sciences, questions have been raised about the methodological standards of x-phi. Here, we focus on one aspect of this question, namely the rate of inconsistencies in statistical reporting. Previous research has examined the extent to which published articles in psychology and other behavioral sciences present statistical inconsistencies in reporting the results of NHST. In this study, we used the R package statcheck to detect statistical inconsistencies in x-phi, and compared rates of inconsistencies in psychology and philosophy. We found that rates of inconsistencies in x-phi are lower than in the psychological and behavioral sciences. From the point of view of statistical reporting consistency, x-phi seems to do no worse, and perhaps even better, than psychological science. PMID:29649220

Unraveling the Semiconducting/Metallic Discrepancy in Ni 3(HITP) 2

DOE PAGES

Foster, Michael E.; Sohlberg, Karl; Allendorf, Mark D.; ...

2018-01-10

Here, Ni 3(2,3,6,7,10,11-hexaiminotriphenylene) 2 is a π-stacked layered metal–organic framework material with extended π-conjugation that is analogous to graphene. Published experimental results indicate that the material is semiconducting, but all theoretical studies to date predict the bulk material to be metallic. Given that previous experimental work was carried out on specimens containing complex nanocrystalline microstructures and the tendency for internal interfaces to introduce transport barriers, we apply DFT to investigate the influence of internal interface defects on the electronic structure of Ni 3(HITP) 2. The results show that interface defects can introduce a transport barrier by breaking the π-conjugation and/ormore » decreasing the dispersion of the electronic bands near the Fermi level. We demonstrate that the presence of defects can open a small gap, in the range of 15–200 meV, which is consistent with the experimentally inferred hopping barrier.« less

Investigation on the neutral and anionic BxAlyH2 (x + y = 7, 8, 9) clusters using density functional theory combined with photoelectron spectroscopy.

PubMed

Ding, Li-Ping; Shao, Peng; Lu, Cheng; Zhang, Fang-Hui; Ding, Lei; Yuan, Tao Li

2016-08-17

The structure and bonding nature of neutral and negatively charged BxAlyH2 (x + y = 7, 8, 9) clusters are investigated with the aid of previously published experimental photoelectron spectra combined with the present density functional theory calculations. The comparison between the experimental photoelectron spectra and theoretical simulated spectra helps to identify the ground state structures. The accuracy of the obtained ground state structures is further verified by calculating their adiabatic electron affinities and vertical detachment energies and comparing them against available experimental data. The results show that the structures of BxAlyH2 transform from three-dimensional to planar structures as the number of boron atoms increases. Moreover, boron atoms tend to bind together forming Bn units. The hydrogen atoms prefer to bind with boron atoms rather than aluminum atoms. The analyses of the molecular orbital on the ground state structures further support the abovementioned results.

Molecular dynamics study of lipid bilayers modeling the plasma membranes of mouse hepatocytes and hepatomas.

PubMed

Andoh, Yoshimichi; Aoki, Noriyuki; Okazaki, Susumu

2016-02-28

Molecular dynamics (MD) calculations of lipid bilayers modeling the plasma membranes of normal mouse hepatocytes and hepatomas in water have been performed under physiological isothermal-isobaric conditions (310.15 K and 1 atm). The changes in the membrane properties induced by hepatic canceration were investigated and were compared with previous MD calculations included in our previous study of the changes in membrane properties induced by murine thymic canceration. The calculated model membranes for normal hepatocytes and hepatomas comprised 23 and 24 kinds of lipids, respectively. These included phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, sphingomyelin, lysophospholipids, and cholesterol. We referred to previously published experimental values for the mole fraction of the lipids adopted in the present calculations. The calculated structural and dynamic properties of the membranes such as lateral structure, order parameters, lateral self-diffusion constants, and rotational correlation times all showed that hepatic canceration causes plasma membranes to become more ordered laterally and less fluid. Interestingly, this finding contrasts with the less ordered structure and increased fluidity of plasma membranes induced by thymic canceration observed in our previous MD study.

Molecular dynamics study of lipid bilayers modeling the plasma membranes of mouse hepatocytes and hepatomas

NASA Astrophysics Data System (ADS)

Andoh, Yoshimichi; Aoki, Noriyuki; Okazaki, Susumu

2016-02-01

Molecular dynamics (MD) calculations of lipid bilayers modeling the plasma membranes of normal mouse hepatocytes and hepatomas in water have been performed under physiological isothermal-isobaric conditions (310.15 K and 1 atm). The changes in the membrane properties induced by hepatic canceration were investigated and were compared with previous MD calculations included in our previous study of the changes in membrane properties induced by murine thymic canceration. The calculated model membranes for normal hepatocytes and hepatomas comprised 23 and 24 kinds of lipids, respectively. These included phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, sphingomyelin, lysophospholipids, and cholesterol. We referred to previously published experimental values for the mole fraction of the lipids adopted in the present calculations. The calculated structural and dynamic properties of the membranes such as lateral structure, order parameters, lateral self-diffusion constants, and rotational correlation times all showed that hepatic canceration causes plasma membranes to become more ordered laterally and less fluid. Interestingly, this finding contrasts with the less ordered structure and increased fluidity of plasma membranes induced by thymic canceration observed in our previous MD study.

LEPER: Library of Experimental PhasE Relations

NASA Astrophysics Data System (ADS)

Davis, F.; Gordon, S.; Mukherjee, S.; Hirschmann, M.; Ghiorso, M.

2006-12-01

The Library of Experimental PhasE Relations (LEPER) seeks to compile published experimental determinations of magmatic phase equilibria and provide those data on the web with a searchable and downloadable interface. Compiled experimental data include the conditions and durations of experiments, the bulk compositions of experimental charges, and the identity, compositions and proportions of phases observed, and, where available, estimates of experimental and analytical uncertainties. Also included are metadata such as the type of experimental device, capsule material, and method(s) of quantitative analysis. The database may be of use to practicing experimentalists as well as the wider Earth science community. Experimentalists may find the data useful for planning new experiments and will easily be able to compare their results to the full body of previous experimentnal data. Geologists may use LEPER to compare rocks sampled in the field with experiments performed on similar bulk composition or with experiments that produced similar-composition product phases. Modelers may use LEPER to parameterize partial melting of various lithologies. One motivation for compiling LEPER is for calibration of updated and revised versions of MELTS, however, it is hoped that the availability of LEPER will facilitate formulation and calibration of additional thermodynamic or empirical models of magmatic phase relations and phase equilibria, geothermometers and more. Data entry for LEPER is occuring presently: As of August, 2006, >6200 experiments have been entered, chiefly from work published between 1997 and 2005. A prototype web interface has been written and beta release on the web is anticipated in Fall, 2006. Eventually, experimentalists will be able to submit their new experimental data to the database via the web. At present, the database contains only data pertaining to the phase equilibria of silicate melts, but extension to other experimental data involving other fluids or sub-solidus phase equilibria may be contemplated. Also, the data are at present limited to natural or near-natural systems, but in the future, extension to synthetic (i.e., CMAS, etc.) systems is also possible. Each would depend in part on whether there is community demand for such databases. A trace element adjunct to LEPER is presently in planning stages.

Indoleamine Hallucinogens in Cluster Headache: Results of the Clusterbusters Medication Use Survey.

PubMed

Schindler, Emmanuelle A D; Gottschalk, Christopher H; Weil, Marsha J; Shapiro, Robert E; Wright, Douglas A; Sewell, Richard Andrew

2015-01-01

Cluster headache is one of the most debilitating pain syndromes. A significant number of patients are refractory to conventional therapies. The Clusterbusters.org medication use survey sought to characterize the effects of both conventional and alternative medications used in cluster headache. Participants were recruited from cluster headache websites and headache clinics. The final analysis included responses from 496 participants. The survey was modeled after previously published surveys and was available online. Most responses were chosen from a list, though others were free-texted. Conventional abortive and preventative medications were identified and their efficacies agreed with those previously published. The indoleamine hallucinogens, psilocybin, lysergic acid diethylamide, and lysergic acid amide, were comparable to or more efficacious than most conventional medications. These agents were also perceived to shorten/abort a cluster period and bring chronic cluster headache into remission more so than conventional medications. Furthermore, infrequent and non-hallucinogenic doses were reported to be efficacious. Findings provide additional evidence that several indoleamine hallucinogens are rated as effective in treating cluster headache. These data reinforce the need for further investigation of the effects of these and related compounds in cluster headache under experimentally controlled settings.

Validation of Laser-Induced Fluorescent Photogrammetric Targets on Membrane Structures

NASA Technical Reports Server (NTRS)

Jones, Thomas W.; Dorrington, Adrian A.; Shortis, Mark R.; Hendricks, Aron R.

2004-01-01

The need for static and dynamic characterization of a new generation of inflatable space structures requires the advancement of classical metrology techniques. A new photogrammetric-based method for non-contact ranging and surface profiling has been developed at NASA Langley Research Center (LaRC) to support modal analyses and structural validation of this class of space structures. This full field measurement method, known as Laser-Induced Fluorescence (LIF) photogrammetry, has previously yielded promising experimental results. However, data indicating the achievable measurement precision had not been published. This paper provides experimental results that indicate the LIF-photogrammetry measurement precision for three different target types used on a reflective membrane structure. The target types were: (1) non-contact targets generated using LIF, (2) surface attached retro-reflective targets, and (3) surface attached diffuse targets. Results from both static and dynamic investigations are included.

Measurement of fracture properties of concrete at high strain rates

PubMed Central

Cendón, D. A.; Sánchez-Gálvez, V.; Gálvez, F.

2017-01-01

An analysis of the spalling technique of concrete bars using the modified Hopkinson bar was carried out. A new experimental configuration is proposed adding some variations to previous works. An increased length for concrete specimens was chosen and finite-element analysis was used for designing a conic projectile to obtain a suitable triangular impulse wave. The aim of this initial work is to establish an experimental framework which allows a simple and direct analysis of concrete subjected to high strain rates. The efforts and configuration of these primary tests, as well as the selected geometry and dimensions for the different elements, have been focused to achieve a simple way of identifying the fracture position and so the tensile strength of tested specimens. This dynamic tensile strength can be easily compared with previous values published in literature giving an idea of the accuracy of the method and technique proposed and the possibility to extend it in a near future to obtain other mechanical properties such as the fracture energy. The tests were instrumented with strain gauges, accelerometers and high-speed camera in order to validate the results by different ways. Results of the dynamic tensile strength of the tested concrete are presented. This article is part of the themed issue ‘Experimental testing and modelling of brittle materials at high strain rates’. PMID:27956510

Are Children the Better Placebo Analgesia Responders? An Experimental Approach.

PubMed

Wrobel, Nathalie; Fadai, Tahmine; Sprenger, Christian; Hebebrand, Johannes; Wiech, Katja; Bingel, Ulrike

2015-10-01

There is little information regarding changes in placebo responsiveness with age, although first predictors of placebo responders such as psychological and physiological processes have been identified. Reviews and meta-analyses indicate that placebo response rates in randomized controlled trials (RCTs) are higher in children and adolescents compared with adults. As these studies cannot control for age-dependent differences in the natural course of the disease, biases might contribute to different placebo rates in RCTs. To avoid these biases, this study investigated age-related differences in placebo responsiveness between children and adults in a well-established experimental model of placebo analgesia combining classic conditioning and expectation. Our data confirm placebo analgesic responses in children, which did not differ in magnitude from those of adults. The influence of previous experience on subsequent treatment outcome was stronger in children than in adults, indicating an increased relevance of learning processes for treatment outcomes in children. Further studies are needed to understand the influence of treatment-related learning processes in children and adolescents, which might critically determine treatment responsiveness during adulthood. This study is the first to experimentally explore placebo analgesia and influences of previous experience on placebo responses in children compared with adults. We found comparable placebo responses in both groups and an increased relevance of learning processes for treatment outcomes in children. Copyright © 2015 American Pain Society. Published by Elsevier Inc. All rights reserved.

Comment on "Hydrogen Balmer beta: The separation between line peaks for plasma electron density diagnostics and self-absorption test"

NASA Astrophysics Data System (ADS)

Gautam, Ghaneshwar; Surmick, David M.; Parigger, Christian G.

2015-07-01

In this letter, we present a brief comment regarding the recently published paper by Ivković et al., J Quant Spectrosc Radiat Transf 2015;154:1-8. Reference is made to previous experimental results to indicate that self absorption must have occurred; however, when carefully considering error propagation, both widths and peak-separation predict electron densities within the error margins. Yet the diagnosis method and the presented details on the use of the hydrogen beta peak separation are viewed as a welcomed contribution in studies of laser-induced plasma.

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

Detrixhe, M.; Besson, D.; Frankenfeld, C.

We have conducted a search for extended energy deposition trails left by ultrarelativistic magnetic monopoles interacting in Antarctic ice. The nonobservation of any satisfactory candidates in the 31 days of accumulated ANITA-II (Antarctic Impulsive Transient Antenna) flight data results in an upper limit on the diffuse flux of relativistic monopoles. We obtain a 90% C.L. limit of order 10{sup -19} (cm{sup 2} s sr){sup -1} for values of Lorentz factor, {gamma}, 10{sup 10{<=}{gamma}} at the anticipated energy E{sub tot}=10{sup 16} GeV. This bound is stronger than all previously published experimental limits for this kinematic range.

Functional Assessment of the Vanderbilt Multigrasp Myoelectric Hand: A Continuing Case Study

PubMed Central

Dalley, Skyler A.; Bennett, Daniel A.; Goldfarb, Michael

2015-01-01

This paper presents a case study involving the functional assessment of the Vanderbilt Multigrasp (VMG) hand prosthesis on a single transradial amputee subject. In particular, a transradial amputee subject performed the Southampton Hand Assessment Procedure (SHAP) using the hand prosthesis and multigrasp myoelectric controller in a series of experimental sessions occurring over a multi-week time span. The subject’s index of function (IoF) improved with each session, although essentially plateaued after the fourth session, resulting in a IoF score of 87, which compares favorably to SHAP scores published in previous studies. PMID:25571412

Measurement of effective air diffusion coefficients for trichloroethene in undisturbed soil cores.

PubMed

Bartelt-Hunt, Shannon L; Smith, James A

2002-06-01

In this study, we measure effective diffusion coefficients for trichloroethene in undisturbed soil samples taken from Picatinny Arsenal, New Jersey. The measured effective diffusion coefficients ranged from 0.0053 to 0.0609 cm2/s over a range of air-filled porosity of 0.23-0.49. The experimental data were compared to several previously published relations that predict diffusion coefficients as a function of air-filled porosity and porosity. A multiple linear regression analysis was developed to determine if a modification of the exponents in Millington's [Science 130 (1959) 100] relation would better fit the experimental data. The literature relations appeared to generally underpredict the effective diffusion coefficient for the soil cores studied in this work. Inclusion of a particle-size distribution parameter, d10, did not significantly improve the fit of the linear regression equation. The effective diffusion coefficient and porosity data were used to recalculate estimates of diffusive flux through the subsurface made in a previous study performed at the field site. It was determined that the method of calculation used in the previous study resulted in an underprediction of diffusive flux from the subsurface. We conclude that although Millington's [Science 130 (1959) 100] relation works well to predict effective diffusion coefficients in homogeneous soils with relatively uniform particle-size distributions, it may be inaccurate for many natural soils with heterogeneous structure and/or non-uniform particle-size distributions.

Energy thresholds of discrete breathers in thermal equilibrium and relaxation processes.

PubMed

Ming, Yi; Ling, Dong-Bo; Li, Hui-Min; Ding, Ze-Jun

2017-06-01

So far, only the energy thresholds of single discrete breathers in nonlinear Hamiltonian systems have been analytically obtained. In this work, the energy thresholds of discrete breathers in thermal equilibrium and the energy thresholds of long-lived discrete breathers which can remain after a long time relaxation are analytically estimated for nonlinear chains. These energy thresholds are size dependent. The energy thresholds of discrete breathers in thermal equilibrium are the same as the previous analytical results for single discrete breathers. The energy thresholds of long-lived discrete breathers in relaxation processes are different from the previous results for single discrete breathers but agree well with the published numerical results known to us. Because real systems are either in thermal equilibrium or in relaxation processes, the obtained results could be important for experimental detection of discrete breathers.

New Wnt/β-catenin target genes promote experimental metastasis and migration of colorectal cancer cells through different signals.

PubMed

Qi, Jingjing; Yu, Yong; Akilli Öztürk, Özlem; Holland, Jane D; Besser, Daniel; Fritzmann, Johannes; Wulf-Goldenberg, Annika; Eckert, Klaus; Fichtner, Iduna; Birchmeier, Walter

2016-10-01

We have previously identified a 115-gene signature that characterises the metastatic potential of human primary colon cancers. The signature included the canonical Wnt target gene BAMBI, which promoted experimental metastasis in mice. Here, we identified three new direct Wnt target genes from the signature, and studied their functions in epithelial-mesenchymal transition (EMT), cell migration and experimental metastasis. We examined experimental liver metastases following injection of selected tumour cells into spleens of NOD/SCID mice. Molecular and cellular techniques were used to identify direct transcription target genes of Wnt/β-catenin signals. Microarray analyses and experiments that interfered with cell migration through inhibitors were performed to characterise downstream signalling systems. Three new genes from the colorectal cancer (CRC) metastasis signature, BOP1, CKS2 and NFIL3, were identified as direct transcription targets of β-catenin/TCF4. Overexpression and knocking down of these genes in CRC cells promoted and inhibited, respectively, experimental metastasis in mice, EMT and cell motility in culture. Cell migration was repressed by interfering with distinct signalling systems through inhibitors of PI3K, JNK, p38 mitogen-activated protein kinase and/or mTOR. Gene expression profiling identified a series of migration-promoting genes, which were induced by BOP1, CKS2 and NFIL3, and could be repressed by inhibitors that are specific to these pathways. We identified new direct Wnt/β-catenin target genes, BOP1, CKS2 and NFIL3, which induced EMT, cell migration and experimental metastasis of CRC cells. These genes crosstalk with different downstream signalling systems, and activate migration-promoting genes. These pathways and downstream genes may serve as therapeutic targets in the treatment of CRC metastasis. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Kinetic modelling of a diesel-polluted clayey soil bioremediation process.

PubMed

Fernández, Engracia Lacasa; Merlo, Elena Moliterni; Mayor, Lourdes Rodríguez; Camacho, José Villaseñor

2016-07-01

A mathematical model is proposed to describe a diesel-polluted clayey soil bioremediation process. The reaction system under study was considered a completely mixed closed batch reactor, which initially contacted a soil matrix polluted with diesel hydrocarbons, an aqueous liquid-specific culture medium and a microbial inoculation. The model coupled the mass transfer phenomena and the distribution of hydrocarbons among four phases (solid, S; water, A; non-aqueous liquid, NAPL; and air, V) with Monod kinetics. In the first step, the model simulating abiotic conditions was used to estimate only the mass transfer coefficients. In the second step, the model including both mass transfer and biodegradation phenomena was used to estimate the biological kinetic and stoichiometric parameters. In both situations, the model predictions were validated with experimental data that corresponded to previous research by the same authors. A correct fit between the model predictions and the experimental data was observed because the modelling curves captured the major trends for the diesel distribution in each phase. The model parameters were compared to different previously reported values found in the literature. Pearson correlation coefficients were used to show the reproducibility level of the model. Copyright © 2016. Published by Elsevier B.V.

Measurement and modeling of CO₂ solubility in natural and synthetic formation brines for CO₂ sequestration.

PubMed

Zhao, Haining; Dilmore, Robert; Allen, Douglas E; Hedges, Sheila W; Soong, Yee; Lvov, Serguei N

2015-02-03

CO2 solubility data in the natural formation brine, synthetic formation brine, and synthetic NaCl+CaCl2 brine were collected at the pressures from 100 to 200 bar, temperatures from 323 to 423 K. Experimental results demonstrate that the CO2 solubility in the synthetic formation brines can be reliably represented by that in the synthetic NaCl+CaCl2 brines. We extended our previously developed model (PSUCO2) to calculate CO2 solubility in aqueous mixed-salt solution by using the additivity rule of the Setschenow coefficients of the individual ions (Na(+), Ca(2+), Mg(2+), K(+), Cl(-), and SO4(2-)). Comparisons with previously published models against the experimental data reveal a clear improvement of the proposed PSUCO2 model. Additionally, the path of the maximum gradient of the CO2 solubility contours divides the P-T diagram into two distinct regions: in Region I, the CO2 solubility in the aqueous phase decreases monotonically in response to increased temperature; in region II, the behavior of the CO2 solubility is the opposite of that in Region I as the temperature increases.

The impact of pedestrian countdown signals on pedestrian-motor vehicle collisions: a reanalysis of data from a quasi-experimental study.

PubMed

Richmond, Sarah A; Willan, Andrew R; Rothman, Linda; Camden, Andi; Buliung, Ron; Macarthur, Colin; Howard, Andrew

2014-06-01

To perform a more sophisticated analysis of previously published data that advances the understanding of the efficacy of pedestrian countdown signal (PCS) installation on pedestrian-motor vehicle collisions (PMVCs), in the city of Toronto, Canada. This is an updated analysis of the same dataset from Camden et al. A quasi-experimental design was used to evaluate the effect of PCS on PMVC. A Poisson regression analysis, using a one-group comparison of PMVC, pre-PCS installation to post-PCS installation was used, controlling for season and temporal effects. The outcome was the frequency of reported PMVC (January 2000-December 2009). Similar models were used to analyse specific types of collisions defined by age of pedestrian, injury severity, and pedestrian and vehicle action. Incidence rate ratios with 95% CI are presented. This analysis included 9262 PMVC, 2760 during or after PCS installation, at 1965 intersections. There was a 26% increase in the rate of collisions, pre to post-PCS installation (incidence rate ratio=1.26, 95% CI 1.11 to 1.42). The installation of PCS at 1965 signalised intersections in the city of Toronto resulted in an increase in PMVC rates post-PCS installation. PCSs may have an unintended consequence of increasing pedestrian-motor vehicle collisions in some settings. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Radiation hydrodynamics modeling of the highest compression inertial confinement fusion ignition experiment from the National Ignition Campaign

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

Clark, D. S.; Marinak, M. M.; Weber, C. R.

2015-02-15

The recently completed National Ignition Campaign (NIC) on the National Ignition Facility (NIF) showed significant discrepancies between post-shot simulations of implosion performance and experimentally measured performance, particularly in thermonuclear yield. This discrepancy between simulation and observation persisted despite concerted efforts to include all of the known sources of performance degradation within a reasonable two-dimensional (2-D), and even three-dimensional (3-D), simulation model, e.g., using measured surface imperfections and radiation drives adjusted to reproduce observed implosion trajectories [Clark et al., Phys. Plasmas 20, 056318 (2013)]. Since the completion of the NIC, several effects have been identified that could explain these discrepancies andmore » that were omitted in previous simulations. In particular, there is now clear evidence for larger than anticipated long-wavelength radiation drive asymmetries and a larger than expected perturbation seeded by the capsule support tent. This paper describes an updated suite of one-dimensional (1-D), 2-D, and 3-D simulations that include the current best understanding of these effects identified since the NIC, as applied to a specific NIC shot. The relative importance of each effect on the experimental observables is compared. In combination, these effects reduce the simulated-to-measured yield ratio from 125:1 in 1-D to 1.5:1 in 3-D, as compared to 15:1 in the best 2-D simulations published previously. While the agreement with the experimental data remains imperfect, the comparison to the data is significantly improved and suggests that the largest sources for the previous discrepancies between simulation and experiment are now being included.« less

Evaluation of the PCR method for identification of Bifidobacterium species.

PubMed

Youn, S Y; Seo, J M; Ji, G E

2008-01-01

Bifidobacterium species are known for their beneficial effects on health and their wide use as probiotics. Although various polymerase chain reaction (PCR) methods for the identification of Bifidobacterium species have been published, the reliability of these methods remains open to question. In this study, we evaluated 37 previously reported PCR primer sets designed to amplify 16S rDNA, 23S rDNA, intergenic spacer regions, or repetitive DNA sequences of various Bifidobacterium species. Ten of 37 experimental primer sets showed specificity for B. adolescentis, B. angulatum, B. pseudocatenulatum, B. breve, B. bifidum, B. longum, B. longum biovar infantis and B. dentium. The results suggest that published Bifidobacterium primer sets should be re-evaluated for both reproducibility and specificity for the identification of Bifidobacterium species using PCR. Improvement of existing PCR methods will be needed to facilitate identification of other Bifidobacterium strains, such as B. animalis, B. catenulatum, B. thermophilum and B. subtile.

PISA: Federated Search in P2P Networks with Uncooperative Peers

NASA Astrophysics Data System (ADS)

Ren, Zujie; Shou, Lidan; Chen, Gang; Chen, Chun; Bei, Yijun

Recently, federated search in P2P networks has received much attention. Most of the previous work assumed a cooperative environment where each peer can actively participate in information publishing and distributed document indexing. However, little work has addressed the problem of incorporating uncooperative peers, which do not publish their own corpus statistics, into a network. This paper presents a P2P-based federated search framework called PISA which incorporates uncooperative peers as well as the normal ones. In order to address the indexing needs for uncooperative peers, we propose a novel heuristic query-based sampling approach which can obtain high-quality resource descriptions from uncooperative peers at relatively low communication cost. We also propose an effective method called RISE to merge the results returned by uncooperative peers. Our experimental results indicate that PISA can provide quality search results, while utilizing the uncooperative peers at a low cost.

From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics

PubMed Central

Zhao, Jun; Avila-Garcia, Maria Susana; Roos, Marco; Thompson, Mark; van der Horst, Eelke; Kaliyaperumal, Rajaram; Luo, Ruibang; Lee, Tin-Lap; Lam, Tak-wah; Edmunds, Scott C.; Sansone, Susanna-Assunta

2015-01-01

Motivation Reproducing the results from a scientific paper can be challenging due to the absence of data and the computational tools required for their analysis. In addition, details relating to the procedures used to obtain the published results can be difficult to discern due to the use of natural language when reporting how experiments have been performed. The Investigation/Study/Assay (ISA), Nanopublications (NP), and Research Objects (RO) models are conceptual data modelling frameworks that can structure such information from scientific papers. Computational workflow platforms can also be used to reproduce analyses of data in a principled manner. We assessed the extent by which ISA, NP, and RO models, together with the Galaxy workflow system, can capture the experimental processes and reproduce the findings of a previously published paper reporting on the development of SOAPdenovo2, a de novo genome assembler. Results Executable workflows were developed using Galaxy, which reproduced results that were consistent with the published findings. A structured representation of the information in the SOAPdenovo2 paper was produced by combining the use of ISA, NP, and RO models. By structuring the information in the published paper using these data and scientific workflow modelling frameworks, it was possible to explicitly declare elements of experimental design, variables, and findings. The models served as guides in the curation of scientific information and this led to the identification of inconsistencies in the original published paper, thereby allowing its authors to publish corrections in the form of an errata. Availability SOAPdenovo2 scripts, data, and results are available through the GigaScience Database: http://dx.doi.org/10.5524/100044; the workflows are available from GigaGalaxy: http://galaxy.cbiit.cuhk.edu.hk; and the representations using the ISA, NP, and RO models are available through the SOAPdenovo2 case study website http://isa-tools.github.io/soapdenovo2/. Contact: philippe.rocca-serra@oerc.ox.ac.uk and susanna-assunta.sansone@oerc.ox.ac.uk. PMID:26154165

Pre-existing central nervous system lesions negate cytokine requirements for regional experimental autoimmune encephalomyelitis development.

PubMed

Li, Xin; Lees, Jason R

2013-03-01

In region-specific forms of experimental autoimmune encephalomyelitis (EAE), lesion initiation is regulated by T-cell-produced interferon-γ (IFN-γ) resulting in spinal cord disease in the presence of IFN-γ and cerebellar disease in the absence of IFN-γ. Although this role for IFN-γ in regional disease initiation is well defined, little is known about the consequences of previous tissue inflammation on subsequent regional disease, information vital to the development of therapeutics in established disease states. This study addressed the hypothesis that previous establishment of regional EAE would determine subsequent tissue localization of new T-cell invasion and associated symptoms regardless of the presence or absence of IFN-γ production. Serial transfer of optimal or suboptimal doses of encephalitogenic IFN-γ-sufficient or -deficient T-cell lines was used to examine the development of new clinical responses associated with the spinal cord and cerebellum at various times after EAE initiation. Previous inflammation within either cerebellum or spinal cord allowed subsequent T-cell driven inflammation within that tissue regardless of IFN-γ presence. Further, T-cell IFN-γ production after initial lesion formation exacerbated disease within the cerebellum, suggesting that IFN-γ plays different roles at different stages of cerebellar disease. For the spinal cord, IFN-γ-deficient cells (that are ordinarily cerebellum disease initiators) were capable of driving new spinal-cord-associated clinical symptoms more than 60 days after the initial acute EAE resolution. These data suggest that previous inflammation modulates the molecular requirements for new neuroinflammation development. © 2012 Blackwell Publishing Ltd.

Experimental investigation of alternative transmission functions: Quantitative evidence for the importance of nonlinear transmission dynamics in host-parasite systems.

PubMed

Orlofske, Sarah A; Flaxman, Samuel M; Joseph, Maxwell B; Fenton, Andy; Melbourne, Brett A; Johnson, Pieter T J

2018-05-01

Understanding pathogen transmission is crucial for predicting and managing disease. Nonetheless, experimental comparisons of alternative functional forms of transmission remain rare, and those experiments that are conducted are often not designed to test the full range of possible forms. To differentiate among 10 candidate transmission functions, we used a novel experimental design in which we independently varied four factors-duration of exposure, numbers of parasites, numbers of hosts and parasite density-in laboratory infection experiments. We used interactions between amphibian hosts and trematode parasites as a model system and all candidate models incorporated parasite depletion. An additional manipulation involving anaesthesia addressed the effects of host behaviour on transmission form. Across all experiments, nonlinear transmission forms involving either a power law or a negative binomial function were the best-fitting models and consistently outperformed the linear density-dependent and density-independent functions. By testing previously published data for two other host-macroparasite systems, we also found support for the same nonlinear transmission forms. Although manipulations of parasite density are common in transmission studies, the comprehensive set of variables tested in our experiments revealed that variation in density alone was least likely to differentiate among competing transmission functions. Across host-pathogen systems, nonlinear functions may often more accurately represent transmission dynamics and thus provide more realistic predictions for infection. © 2017 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.

[The topical problems of the car accident injury emerging from the materials of the articles published in the journal "Sudebno-meditsinskaya ekspertiza" during the period from 1958 to 2012].

PubMed

Fetisov, V A; Smirenin, S A; Nesterov, A V; Khabova, Z S

2014-01-01

The authors undertook the scientometric analysis of the articles published in the journal "Sudebno-meditsinskaya ekspertiza" during the last 55 years (from 1958 to 2012) with special reference to the information support of research and practical activities of forensic medical experts in this country concerning the topical problems of the car accident injury. The search for relevant information revealed a total of 111 articles that were categorized into several groups for their further systematization and analysis with the view for improving the effectiveness of research and experimental studies in the framework of the principal activities of the State Sanitary and Epidemiological Department of the Russian Federation. This article is an extension of previous publications of the authors concerning the main aspects of the car accident injury. The forthcoming reports to be published in the journal "Sudebno-meditsinskaya ekspertiza" will present the results of the further in-depth scientometric analysis of the data on road accidents in this country.

Interaction between the C-terminal domains of measles virus nucleoprotein and phosphoprotein: a tight complex implying one binding site.

PubMed

Blocquel, David; Habchi, Johnny; Costanzo, Stéphanie; Doizy, Anthony; Oglesbee, Michael; Longhi, Sonia

2012-10-01

The intrinsically disordered C-terminal domain (N(TAIL) ) of the measles virus (MeV) nucleoprotein undergoes α-helical folding upon binding to the C-terminal X domain (XD) of the phosphoprotein. The N(TAIL) region involved in binding coupled to folding has been mapped to a conserved region (Box2) encompassing residues 489-506. In the previous studies published in this journal, we obtained experimental evidence supporting a K(D) for the N(TAIL) -XD binding reaction in the nM range and also showed that an additional N(TAIL) region (Box3, aa 517-525) plays a role in binding to XD. In striking contrast with these data, studies published in this journal by Kingston and coworkers pointed out a much less stable complex (K(D) in the μM range) and supported lack of involvement of Box3 in complex formation. The objective of this study was to critically re-evaluate the role of Box3 in N(TAIL) -XD binding. Since our previous studies relied on N(TAIL) -truncated forms possessing an irrelevant Flag sequence appended at their C-terminus, we, herein, generated an N(TAIL) devoid of Box3 and any additional C-terminal residues, as well as a form encompassing only residues 482-525. We then used isothermal titration calorimetry to characterize the binding reactions between XD and these N(TAIL) forms. Results effectively argue for the presence of a single XD-binding site located within Box2, in agreement with the results by Kingston et al., while providing clear experimental support for a high-affinity complex. Altogether, the present data provide mechanistic insights into the replicative machinery of MeV and clarify a hitherto highly debated point. Copyright © 2012 The Protein Society.

Interaction between the C-terminal domains of measles virus nucleoprotein and phosphoprotein: A tight complex implying one binding site

PubMed Central

Blocquel, David; Habchi, Johnny; Costanzo, Stéphanie; Doizy, Anthony; Oglesbee, Michael; Longhi, Sonia

2012-01-01

The intrinsically disordered C-terminal domain (NTAIL) of the measles virus (MeV) nucleoprotein undergoes α-helical folding upon binding to the C-terminal X domain (XD) of the phosphoprotein. The NTAIL region involved in binding coupled to folding has been mapped to a conserved region (Box2) encompassing residues 489–506. In the previous studies published in this journal, we obtained experimental evidence supporting a KD for the NTAIL–XD binding reaction in the nM range and also showed that an additional NTAIL region (Box3, aa 517–525) plays a role in binding to XD. In striking contrast with these data, studies published in this journal by Kingston and coworkers pointed out a much less stable complex (KD in the μM range) and supported lack of involvement of Box3 in complex formation. The objective of this study was to critically re-evaluate the role of Box3 in NTAIL–XD binding. Since our previous studies relied on NTAIL-truncated forms possessing an irrelevant Flag sequence appended at their C-terminus, we, herein, generated an NTAIL devoid of Box3 and any additional C-terminal residues, as well as a form encompassing only residues 482–525. We then used isothermal titration calorimetry to characterize the binding reactions between XD and these NTAIL forms. Results effectively argue for the presence of a single XD-binding site located within Box2, in agreement with the results by Kingston et al., while providing clear experimental support for a high-affinity complex. Altogether, the present data provide mechanistic insights into the replicative machinery of MeV and clarify a hitherto highly debated point. PMID:22887965

The prediction of cyclic proximal humerus fracture fixation failure by various bone density measures.

PubMed

Varga, Peter; Grünwald, Leonard; Windolf, Markus

2018-02-22

Fixation of osteoporotic proximal humerus fractures has remained challenging, but may be improved by careful pre-operative planning. The aim of this study was to investigate how well the failure of locking plate fixation of osteoporotic proximal humerus fractures can be predicted by bone density measures assessed with currently available clinical imaging (realistic case) and a higher resolution and quality modality (theoretical best-case). Various density measures were correlated to experimentally assessed number of cycles to construct failure of plated unstable low-density proximal humerus fractures (N = 18). The influence of density evaluation technique was investigated by comparing local (peri-implant) versus global evaluation regions; HR-pQCT-based versus clinical QCT-based image data; ipsilateral versus contralateral side; and bone mineral content (BMC) versus bone mineral density (BMD). All investigated density measures were significantly correlated with the experimental cycles to failure. The best performing clinically feasible parameter was the QCT-based BMC of the contralateral articular cap region, providing significantly better correlation (R 2  = 0.53) compared to a previously proposed clinical density measure (R 2  = 0.30). BMC had consistently, but not significantly stronger correlations with failure than BMD. The overall best results were obtained with the ipsilateral HR-pQCT-based local BMC (R 2  = 0.74) that may be used for implant optimization. Strong correlations were found between the corresponding density measures of the two CT image sources, as well as between the two sides. Future studies should investigate if BMC of the contralateral articular cap region could provide improved prediction of clinical fixation failure compared to previously proposed measures. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

Mitochondrial Mutation Rate, Spectrum and Heteroplasmy in Caenorhabditis elegans Spontaneous Mutation Accumulation Lines of Differing Population Size.

PubMed

Konrad, Anke; Thompson, Owen; Waterston, Robert H; Moerman, Donald G; Keightley, Peter D; Bergthorsson, Ulfar; Katju, Vaishali

2017-06-01

Mitochondrial genomes of metazoans, given their elevated rates of evolution, have served as pivotal markers for phylogeographic studies and recent phylogenetic events. In order to determine the dynamics of spontaneous mitochondrial mutations in small populations in the absence and presence of selection, we evolved mutation accumulation (MA) lines of Caenorhabditis elegans in parallel over 409 consecutive generations at three varying population sizes of N = 1, 10, and 100 hermaphrodites. The N =1 populations should have a minimal influence of natural selection to provide the spontaneous mutation rate and the expected rate of neutral evolution, whereas larger population sizes should experience increasing intensity of selection. New mutations were identified by Illumina paired-end sequencing of 86 mtDNA genomes across 35 experimental lines and compared with published genomes of natural isolates. The spontaneous mitochondrial mutation rate was estimated at 1.05 × 10-7/site/generation. A strong G/C→A/T mutational bias was observed in both the MA lines and the natural isolates. This suggests that the low G + C content at synonymous sites is the product of mutation bias rather than selection as previously proposed. The mitochondrial effective population size per worm generation was estimated to be 62. Although it was previously concluded that heteroplasmy was rare in C. elegans, the vast majority of mutations in this study were heteroplasmic despite an experimental regime exceeding 400 generations. The frequencies of frameshift and nonsynonymous mutations were negatively correlated with population size, which suggests their deleterious effects on fitness and a potent role for selection in their eradication. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Contributions to muscle force and EMG by combined neural excitation and electrical stimulation

NASA Astrophysics Data System (ADS)

Crago, Patrick E.; Makowski, Nathaniel S.; Cole, Natalie M.

2014-10-01

Objective. Stimulation of muscle for research or clinical interventions is often superimposed on ongoing physiological activity without a quantitative understanding of the impact of the stimulation on the net muscle activity and the physiological response. Experimental studies show that total force during stimulation is less than the sum of the isolated voluntary and stimulated forces, but the occlusion mechanism is not understood. Approach. We develop a model of efferent motor activity elicited by superimposing stimulation during a physiologically activated contraction. The model combines action potential interactions due to collision block, source resetting, and refractory periods with previously published models of physiological motor unit recruitment, rate modulation, force production, and EMG generation in human first dorsal interosseous muscle to investigate the mechanisms and effectiveness of stimulation on the net muscle force and EMG. Main results. Stimulation during a physiological contraction demonstrates partial occlusion of force and the neural component of the EMG, due to action potential interactions in motor units activated by both sources. Depending on neural and stimulation firing rates as well as on force-frequency properties, individual motor unit forces can be greater, smaller, or unchanged by the stimulation. In contrast, voluntary motor unit EMG potentials in simultaneously stimulated motor units show progressive occlusion with increasing stimulus rate. The simulations predict that occlusion would be decreased by a reverse stimulation recruitment order. Significance. The results are consistent with and provide a mechanistic interpretation of previously published experimental evidence of force occlusion. The models also predict two effects that have not been reported previously—voluntary EMG occlusion and the advantages of a proximal stimulation site. This study provides a basis for the rational design of both future experiments and clinical neuroprosthetic interventions involving either motor or sensory stimulation.

A systematic review of financial incentives for dietary behavior change.

PubMed

Purnell, Jason Q; Gernes, Rebecca; Stein, Rick; Sherraden, Margaret S; Knoblock-Hahn, Amy

2014-07-01

In light of the obesity epidemic, there is growing interest in the use of financial incentives for dietary behavior change. Previous reviews of the literature have focused on randomized controlled trials and found mixed results. The purpose of this systematic review is to update and expand on previous reviews by considering a broader range of study designs, including randomized controlled trials, quasi-experimental, observational, and simulation studies testing the use of financial incentives to change dietary behavior and to inform both dietetic practice and research. The review was guided by theoretical consideration of the type of incentive used based on the principles of operant conditioning. There was further examination of whether studies were carried out with an institutional focus. Studies published between 2006 and 2012 were selected for review, and data were extracted regarding study population, intervention design, outcome measures, study duration and follow-up, and key findings. Twelve studies meeting selection criteria were reviewed, with 11 finding a positive association between incentives and dietary behavior change in the short term. All studies pointed to more specific information on the type, timing, and magnitude of incentives needed to motivate individuals to change behavior, the types of incentives and disincentives most likely to affect the behavior of various socioeconomic groups, and promising approaches for potential policy and practice innovations. Limitations of the studies are noted, including the lack of theoretical guidance in the selection of incentive structures and the absence of basic experimental data. Future research should consider these factors, even as policy makers and practitioners continue to experiment with this potentially useful approach to addressing obesity. Copyright © 2014 Academy of Nutrition and Dietetics. Published by Elsevier Inc. All rights reserved.

Laboratory preparation questionnaires as a tool for the implementation of the Just in Time Teaching in the Physics I laboratories: Research training

NASA Astrophysics Data System (ADS)

Miranda, David A.; Sanchez, Melba J.; Forero, Oscar M.

2017-06-01

The implementation of the JiTT (Just in Time Teaching) strategy is presented to increase the previous preparation of students enrolled in the subject Physics Laboratory I offered at the Industrial University of Santander (UIS), Colombia. In this study, a laboratory preparation questionnaire (CPL) was applied as a tool for the implementation of JiTT combined with elements of mediated learning. It was found that the CPL allows to improve the students’ experience regarding the preparation of the laboratory and the development of the experimental session. These questionnaires were implemented in an academic manager (Moodle) and a web application (lab.ciencias.uis.edu.co) was used to publish the contents essential for the preparation of the student before each practical session. The most significant result was that the students performed the experimental session with the basic knowledge to improve their learning experience.

Absolute partial photoionization cross sections of ethylene

NASA Astrophysics Data System (ADS)

Grimm, F. A.; Whitley, T. A.; Keller, P. R.; Taylor, J. W.

1991-07-01

Absolute partial photoionization cross sections for ionization out of the first four valence orbitals to the X 2B 3u, A 2B 3g, B 2A g and C 2B 2u states of the C 2H 4+ ion are presented as a function of photon energy over the energy range from 12 to 26 eV. The experimental results have been compared to previously published relative partial cross sections for the first two bands at 18, 21 and 24 eV. Comparison of the experimental data with continuum multiple scattering Xα calculations provides evidence for extensive autoionization to the X 2B 3u state and confirms the predicted shape resonances in ionization to the A 2B 3g and B 2A g states. Identification of possible transitions for the autoionizing resonances have been made using multiple scattering transition state calculations on Rydberg excited states.

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

Perl, M.

This is a history of my discovery of the tau lepton in the 1970s for which I was awarded the Nobel Prize in Physics. I have previously described some aspects of the discovery. In 1996 in my collection of papers entitled, ''Reflections on Experimental Science,'' I gave a straightforward account of the experimental method and the physics involved in the discovery as an introduction to the collection. In a 2002 paper written with Mary A. Meyer published in the journal ''Theoria et Historia Scientiarum'' I used the story of the discovery to outline my thoughts on the practice of experimentalmore » science. That 2002 paper was written primarily for young women and men who are beginning their lives in science and it was based on a lecture given at Los Alamos National Laboratory. Some of the historical material in this paper has appeared in those two earlier papers.« less

Prediction of drug-packaging interactions via molecular dynamics (MD) simulations.

PubMed

Feenstra, Peter; Brunsteiner, Michael; Khinast, Johannes

2012-07-15

The interaction between packaging materials and drug products is an important issue for the pharmaceutical industry, since during manufacturing, processing and storage a drug product is continuously exposed to various packaging materials. The experimental investigation of a great variety of different packaging material-drug product combinations in terms of efficacy and safety can be a costly and time-consuming task. In our work we used molecular dynamics (MD) simulations in order to evaluate the applicability of such methods to pre-screening of the packaging material-solute compatibility. The solvation free energy and the free energy of adsorption of diverse solute/solvent/solid systems were estimated. The results of our simulations agree with experimental values previously published in the literature, which indicates that the methods in question can be used to semi-quantitatively reproduce the solid-liquid interactions of the investigated systems. Copyright © 2012 Elsevier B.V. All rights reserved.

Bistable behavior of the lac operon in E. coli when induced with a mixture of lactose and TMG.

PubMed

Díaz-Hernández, Orlando; Santillán, Moisés

2010-01-01

In this work we investigate multistability in the lac operon of Escherichia coli when it is induced by a mixture of lactose and the non-metabolizable thiomethyl galactoside (TMG). In accordance with previously published experimental results and computer simulations, our simulations predict that: (1) when the system is induced by TMG, the system shows a discernible bistable behavior while, (2) when the system is induced by lactose, bistability does not disappear but excessively high concentrations of lactose would be required to observe it. Finally, our simulation results predict that when a mixture of lactose and TMG is used, the bistability region in the extracellular glucose concentration vs. extracellular lactose concentration parameter space changes in such a way that the model predictions regarding bistability could be tested experimentally. These experiments could help to solve a recent controversy regarding the existence of bistability in the lac operon under natural conditions.

A theoretical and experimental investigation of cylindrical electrostatic probes at arbitrary incidence in flowing plasma

NASA Technical Reports Server (NTRS)

Jenkins, R. V.; Jones, W. L., Jr.

1974-01-01

The theory for calculating the current collected by a negatively biased cylindrical electrostatic probe at an arbitrary angle of attack in a weakley ionized flowing plasma is presented. The theory was constructed by considering both random and directed motion simultaneous with dynamic coupling of the flow properties and of the electric field of the probe. This direct approach yielded a theory that is more general than static plasma theories modified to account for flow. Theoretical calculations are compared with experimental electrostatic probe data obtained in the free stream of an arc-heated hypersonic wind tunnel. The theoretical calculations are based on flow conditions and plasma electron densities measured by an independent microwave interferometer technique. In addition, the theory is compared with laboratory and satellite data previously published by other investigators. In each case the comparison gives good agreement.

Repair of traumatized mammalian hair cells via sea anemone repair proteins.

PubMed

Tang, Pei-Ciao; Smith, Karen Müller; Watson, Glen M

2016-08-01

Mammalian hair cells possess only a limited ability to repair damage after trauma. In contrast, sea anemones show a marked capability to repair damaged hair bundles by means of secreted repair proteins (RPs). Previously, it was found that recovery of traumatized hair cells in blind cavefish was enhanced by anemone-derived RPs; therefore, the ability of anemone RPs to assist recovery of damaged hair cells in mammals was tested here. After a 1 h incubation in RP-enriched culture media, uptake of FM1-43 by experimentally traumatized murine cochlear hair cells was restored to levels comparable to those exhibited by healthy controls. In addition, RP-treated explants had significantly more normally structured hair bundles than time-matched traumatized control explants. Collectively, these results indicate that anemone-derived RPs assist in restoring normal function and structure of experimentally traumatized hair cells of the mouse cochlea. © 2016. Published by The Company of Biologists Ltd.

Elaphomyces species (Elaphomycetaceae, Eurotiales) from Bartlett Experimental Forest, New Hampshire, USA.

PubMed

Castellano, Michael A; Stephens, Ryan B

2017-06-01

We describe five new species of Elaphomyces from Bartlett Experimental Forest, New Hampshire, USA ( E. americanus , E. bartlettii , E. macrosporus , E. oreoides , and E. remickii ) and revise the description of a sixth previously published species ( E. verruculosus ). Of the five new species, E. bartlettii and E. remickii are only known from New Hampshire whereas E. americanus, E. macrosporus, and E. oreoides are widely distributed in eastern North America. Elaphomyces verruculosus is the most widespread and abundant Elaphomyces species in eastern North America with a distribution extending from eastern Canada south to northeastern Mexico. All six Elaphomyces species are putatively associated with Tsuga canadensis , a tree species in regional decline. For five of the six Elaphomyces species, we report partially consumed ascomata or rodent fecal samples containing spores, indicating that small mammals play a key role in dispersing these Elaphomyces species and that the Elaphomyces are an important part of the small mammals' diet.

Experimental study on the impact of temperature on the dissipation process of supersaturated total dissolved gas.

PubMed

Shen, Xia; Liu, Shengyun; Li, Ran; Ou, Yangming

2014-09-01

Water temperature not only affects the solubility of gas in water but can also be an important factor in the dissipation process of supersaturated total dissolved gas (TDG). The quantitative relationship between the dissipation process and temperature has not been previously described. This relationship affects the accurate evaluation of the dissipation process and the subsequent biological effects. This article experimentally investigates the impact of temperature on supersaturated TDG dissipation in static and turbulent conditions. The results show that the supersaturated TDG dissipation coefficient increases with the temperature and turbulence intensity. The quantitative relationship was verified by straight flume experiments. This study enhances our understanding of the dissipation of supersaturated TDG. Furthermore, it provides a scientific foundation for the accurate prediction of the dissipation process of supersaturated TDG in the downstream area and the negative impacts of high dam projects on aquatic ecosystems. Copyright © 2014. Published by Elsevier B.V.

Proton, muon and ¹³C hyperfine coupling constants of C₆₀X and C₇₀X (X = H, Mu).

PubMed

Brodovitch, Jean-Claude; Addison-Jones, Brenda; Ghandi, Khashayar; McKenzie, Iain; Percival, Paul W

2015-01-21

The reaction of H atoms with fullerene C70 has been investigated by identifying the radical products formed by addition of the atom muonium (Mu) to the fullerene in solution. Four of the five possible radical isomers of C70Mu were detected by avoided level-crossing resonance (μLCR) spectroscopy, using a dilute solution of enriched (13)C70 in decalin. DFT calculations were used to predict muon and (13)C isotropic hyperfine constants as an aid to assigning the observed μLCR signals. Computational methods were benchmarked against previously published experimental data for (13)C60Mu in solution. Analysis of the μLCR spectrum resulted in the first experimental determination of (13)C hyperfine constants in either C70Mu or C70H. The large number of values confirms predictions that the four radical isomers have extended distributions of unpaired electron spin.

An in-depth analysis of temperature effect on DIBL in UTBB FD SOI MOSFETs based on experimental data, numerical simulations and analytical models

NASA Astrophysics Data System (ADS)

Pereira, A. S. N.; de Streel, G.; Planes, N.; Haond, M.; Giacomini, R.; Flandre, D.; Kilchytska, V.

2017-02-01

The Drain Induced Barrier Lowering (DIBL) behavior in Ultra-Thin Body and Buried oxide (UTBB) transistors is investigated in details in the temperature range up to 150 °C, for the first time to the best of our knowledge. The analysis is based on experimental data, physical device simulation, compact model (SPICE) simulation and previously published models. Contrary to MASTAR prediction, experiments reveal DIBL increase with temperature. Physical device simulations of different thin-film fully-depleted (FD) devices outline the generality of such behavior. SPICE simulations, with UTSOI DK2.4 model, only partially adhere to experimental trends. Several analytic models available in the literature are assessed for DIBL vs. temperature prediction. Although being the closest to experiments, Fasarakis' model overestimates DIBL(T) dependence for shortest devices and underestimates it for upsized gate lengths frequently used in ultra-low-voltage (ULV) applications. This model is improved in our work, by introducing a temperature-dependent inversion charge at threshold. The improved model shows very good agreement with experimental data, with high gain in precision for the gate lengths under test.

Electron capture by Ne3+ ions from atomic hydrogen

NASA Astrophysics Data System (ADS)

Rejoub, R.; Bannister, M. E.; Havener, C. C.; Savin, D. W.; Verzani, C. J.; Wang, J. G.; Stancil, P. C.

2004-05-01

Using the Oak Ridge National Laboratory ion-atom merged-beam apparatus, absolute total electron-capture cross sections have been measured for collisions of Ne3+ ions with hydrogen (deuterium) atoms at energies between 0.07 and 826 eV/u . Comparison to previous measurements shows large discrepancies between 50 and 400 eV/u . Previously published molecular-orbital close-coupling (MOCC) calculations were performed over limited energy ranges, but show good agreement with the present measurements. Here MOCC calculations are presented for energies between 0.01 and 1000 eV/u for collisions with both H and D. For energies below ˜1 eV/u , an enhancement in the magnitude of both the experimental and theoretical cross sections is observed which is attributed to the ion-induced dipole attraction between the reactants. Below ˜4 eV/u , the present calculations show a significant target isotope effect.

Validating and improving a zero-dimensional stack voltage model of the Vanadium Redox Flow Battery

NASA Astrophysics Data System (ADS)

König, S.; Suriyah, M. R.; Leibfried, T.

2018-02-01

Simple, computationally efficient battery models can contribute significantly to the development of flow batteries. However, validation studies for these models on an industrial-scale stack level are rarely published. We first extensively present a simple stack voltage model for the Vanadium Redox Flow Battery. For modeling the concentration overpotential, we derive mass transfer coefficients from experimental results presented in the 1990s. The calculated mass transfer coefficient of the positive half-cell is 63% larger than of the negative half-cell, which is not considered in models published to date. Further, we advance the concentration overpotential model by introducing an apparent electrochemically active electrode surface which differs from the geometric electrode area. We use the apparent surface as fitting parameter for adapting the model to experimental results of a flow battery manufacturer. For adapting the model, we propose a method for determining the agreement between model and reality quantitatively. To protect the manufacturer's intellectual property, we introduce a normalization method for presenting the results. For the studied stack, the apparent electrochemically active surface of the electrode is 41% larger than its geometrical area. Hence, the current density in the diffusion layer is 29% smaller than previously reported for a zero-dimensional model.

A comparative analysis of experimental selection on the stickleback pelvis.

PubMed

Miller, S E; Barrueto, M; Schluter, D

2017-06-01

Mechanisms of natural selection can be identified using experimental approaches. However, such experiments often yield nonsignificant effects and imprecise estimates of selection due to low power and small sample sizes. Combining results from multiple experimental studies might produce an aggregate estimate of selection that is more revealing than individual studies. For example, bony pelvic armour varies conspicuously among stickleback populations, and predation by vertebrate and insect predators has been hypothesized to be the main driver of this variation. Yet experimental selection studies testing these hypotheses frequently fail to find a significant effect. We experimentally manipulated length of threespine stickleback (Gasterosteus aculeatus) pelvic spines in a mesocosm experiment to test whether prickly sculpin (Cottus asper), an intraguild predator of stickleback, favours longer spines. The probability of survival was greater for stickleback with unclipped pelvic spines, but this effect was noisy and not significant. We used meta-analysis to combine the results of our mesocosm experiment with previously published experimental studies of selection on pelvic armour. We found evidence that fish predation indeed favours increased pelvic armour, with a moderate effect size. The same approach found little evidence that insect predation favours reduced pelvic armour. The causes of reduced pelvic armour in many stickleback populations remain uncertain. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

E00-110 experiment at Jefferson Lab Hall A: Deeply virtual Compton scattering off the proton at 6 GeV

DOE PAGES

Defurne, M.; Amaryan, M.; Aniol, K. A.; ...

2015-11-03

We present final results on the photon electroproduction (more » $$\\vec{e}p\\rightarrow ep\\gamma$$) cross section in the deeply virtual Compton scattering (DVCS) regime and the valence quark region from Jefferson Lab experiment E00-110. Results from an analysis of a subset of these data were published before, but the analysis has been improved which is described here at length, together with details on the experimental setup. Furthermore, additional data have been analyzed resulting in photon electroproduction cross sections at new kinematic settings, for a total of 588 experimental bins. Results of the $Q^2$- and $$x_B$$-dependences of both the helicity-dependent and helicity-independent cross sections are discussed. The $Q^2$-dependence illustrates the dominance of the twist-2 handbag amplitude in the kinematics of the experiment, as previously noted. Thanks to the excellent accuracy of this high luminosity experiment, it becomes clear that the unpolarized cross section shows a significant deviation from the Bethe-Heitler process in our kinematics, compatible with a large contribution from the leading twist-2 DVCS$^2$ term to the photon electroproduction cross section. The necessity to include higher-twist corrections in order to fully reproduce the shape of the data is also discussed. The DVCS cross sections in this study represent the final set of experimental results from E00-110, superseding the previous publication.« less

Vibrations of cantilevered circular cylindrical shells Shallow versus deep shell theory

NASA Technical Reports Server (NTRS)

Lee, J. K.; Leissa, A. W.; Wang, A. J.

1983-01-01

Free vibrations of cantilevered circular cylindrical shells having rectangular planforms are studied in this paper by means of the Ritz method. The deep shell theory of Novozhilov and Goldenveizer is used and compared with the usual shallow shell theory for a wide range of shell parameters. A thorough convergence study is presented along with comparisons to previously published finite element solutions and experimental results. Accurately computed frequency parameters and mode shapes for various shell configurations are presented. The present paper appears to be the first comprehensive study presenting rigorous comparisons between the two shell theories in dealing with free vibrations of cantilevered cylindrical shells.

Mathematical Description of Dendrimer Structure

NASA Technical Reports Server (NTRS)

Majoros, Istvan J.; Mehta, Chandan B.; Baker, James R., Jr.

2004-01-01

Characteristics of starburst dendrimers can be easily attributed to the multiplicity of the monomers used to synthesize them. The molecular weight, degree of polymerization, number of terminal groups and branch points for each generation of a dendrimer can be calculated using mathematical formulas incorporating these variables. Mathematical models for the calculation of degree of polymerization, molecular weight, and number of terminal groups and branching groups previously published were revised and elaborated on for poly(amidoamine) (PAMAM) dendrimers, and introduced for poly(propyleneimine) (POPAM) dendrimers and the novel POPAM-PAMAM hybrid, which we call the POMAM dendrimer. Experimental verification of the relationship between theoretical and actual structure for the PAMAM dendrimer was also established.

In situ spectroscopic study of the plastic deformation of amorphous silicon under nonhydrostatic conditions induced by indentation

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

Gerbig, Yvonne B.; Michaels, C. A.; Bradby, Jodie E.

Indentation-induced plastic deformation of amorphous silicon (a-Si) thin films was studied by in situ Raman imaging of the deformed contact region of an indented sample, employing a Raman spectroscopy-enhanced instrumented indentation technique (IIT). The occurrence and evolving spatial distribution of changes in the a-Si structure caused by processes, such as polyamorphization and crystallization, induced by indentation loading were observed. Furthermore, the obtained experimental results are linked with previously published work on the plastic deformation of a-Si under hydrostatic compression and shear deformation to establish a model for the deformation behavior of a-Si under indentation loading.

Dissociation rate of bromine diatomics in an argon heat bath

NASA Technical Reports Server (NTRS)

Razner, R.; Hopkins, D.

1973-01-01

The evolution of a collection of 300 K bromine diatomics embedded in a heat bath of argon atoms at 1800 K was studied by computer, and a dissociation-rate constant for the reaction Br2 + BR + Ar yields Br + Ar was determined. Previously published probability distributions for energy and angular momentum transfers in classical three-dimensional Br2-Ar collisions were used in conjunction with a newly developed Monte Carlo scheme for this purpose. Results are compared with experimental shock-tube data and the predictions of several other theoretical models. A departure from equilibrium is obtained which is significantly greater than that predicted by any of these other theories.

Modelling and simulation of a pervaporation process using tubular module for production of anhydrous ethanol

NASA Astrophysics Data System (ADS)

Hieu, Nguyen Huu

2017-09-01

Pervaporation is a potential process for the final step of ethanol biofuel production. In this study, a mathematical model was developed based on the resistance-in-series model and a simulation was carried out using the specialized simulation software COMSOL Multiphysics to describe a tubular type pervaporation module with membranes for the dehydration of ethanol solution. The permeance of membranes, operating conditions, and feed conditions in the simulation were referred from experimental data reported previously in literature. Accordingly, the simulated temperature and density profiles of pure water and ethanol-water mixture were validated based on existing published data.

Hierarchical Traces for Reduced NSM Memory Requirements

NASA Astrophysics Data System (ADS)

Dahl, Torbjørn S.

This paper presents work on using hierarchical long term memory to reduce the memory requirements of nearest sequence memory (NSM) learning, a previously published, instance-based reinforcement learning algorithm. A hierarchical memory representation reduces the memory requirements by allowing traces to share common sub-sequences. We present moderated mechanisms for estimating discounted future rewards and for dealing with hidden state using hierarchical memory. We also present an experimental analysis of how the sub-sequence length affects the memory compression achieved and show that the reduced memory requirements do not effect the speed of learning. Finally, we analyse and discuss the persistence of the sub-sequences independent of specific trace instances.

Resistive method for measuring the disintegration speed of Prince Rupert's drops

NASA Astrophysics Data System (ADS)

Bochkov, Mark; Gusenkova, Daria; Glushkov, Evgenii; Zotova, Julia; Zhabin, S. N.

2016-09-01

We have successfully applied the resistance grid technique to measure the disintegration speed in a special type of glass objects, widely known as Prince Rupert's drops. We use a fast digital oscilloscope and a simple electrical circuit, glued to the surface of the drops, to detect the voltage changes, corresponding to the breaks in the specific parts of the drops. The results obtained using this method are in good qualitative and quantitative agreement with theoretical predictions and previously published data. Moreover, the proposed experimental setup does not include any expensive equipment (such as a high-speed camera) and can therefore be widely used in high schools and universities.

Densities of liquids and vapors in boiling NaCl-H2O solutions: a PVTx summary from 300° to 500°C

USGS Publications Warehouse

Bischoff, James L.

1991-01-01

Experimental data for densities of liquids and vapors on the two-phase surface of the system NaCl-H2O were compiled and evaluated to provide a complete summary between 300° and 500°C. The results are added to a previously published PTx summary compiled in the same manner to provide a PVTx summary of the present state of knowledge. Results are in table form of use to the understanding of two-phase behaviour in boiling hydrothermal systems and to theoretical modeling of this important system. 

Absolute Equation-of-State Measurement for Polystyrene from 25 - 60 Mbar Using a Spherically Converging Shock Wave

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

Glenzer, Siegfried

We have developed an experimental platform for the National Ignition Facility (NIF) that uses spherically converging shock waves for absolute equation of state (EOS) measurements along the principal Hugoniot. In this Letter we present radiographic compression measurements for polystyrene that were taken at shock pressures reaching 60 Mbar (6 TPa). This significantly exceeds previously published results obtained on the Nova laser [Cauble et al., Phys. Rev. Lett. 80, 1248 (1998)] at strongly improved precision, allowing to discriminate between different EOS models. We find excellent agreement with Kohn-Sham Density Functional Theory based molecular dynamics simulations.

In situ spectroscopic study of the plastic deformation of amorphous silicon under nonhydrostatic conditions induced by indentation

DOE PAGES

Gerbig, Yvonne B.; Michaels, C. A.; Bradby, Jodie E.; ...

2015-12-17

Indentation-induced plastic deformation of amorphous silicon (a-Si) thin films was studied by in situ Raman imaging of the deformed contact region of an indented sample, employing a Raman spectroscopy-enhanced instrumented indentation technique (IIT). The occurrence and evolving spatial distribution of changes in the a-Si structure caused by processes, such as polyamorphization and crystallization, induced by indentation loading were observed. Furthermore, the obtained experimental results are linked with previously published work on the plastic deformation of a-Si under hydrostatic compression and shear deformation to establish a model for the deformation behavior of a-Si under indentation loading.

A rabbit ventricular action potential model replicating cardiac dynamics at rapid heart rates.

PubMed

Mahajan, Aman; Shiferaw, Yohannes; Sato, Daisuke; Baher, Ali; Olcese, Riccardo; Xie, Lai-Hua; Yang, Ming-Jim; Chen, Peng-Sheng; Restrepo, Juan G; Karma, Alain; Garfinkel, Alan; Qu, Zhilin; Weiss, James N

2008-01-15

Mathematical modeling of the cardiac action potential has proven to be a powerful tool for illuminating various aspects of cardiac function, including cardiac arrhythmias. However, no currently available detailed action potential model accurately reproduces the dynamics of the cardiac action potential and intracellular calcium (Ca(i)) cycling at rapid heart rates relevant to ventricular tachycardia and fibrillation. The aim of this study was to develop such a model. Using an existing rabbit ventricular action potential model, we modified the L-type calcium (Ca) current (I(Ca,L)) and Ca(i) cycling formulations based on new experimental patch-clamp data obtained in isolated rabbit ventricular myocytes, using the perforated patch configuration at 35-37 degrees C. Incorporating a minimal seven-state Markovian model of I(Ca,L) that reproduced Ca- and voltage-dependent kinetics in combination with our previously published dynamic Ca(i) cycling model, the new model replicates experimentally observed action potential duration and Ca(i) transient alternans at rapid heart rates, and accurately reproduces experimental action potential duration restitution curves obtained by either dynamic or S1S2 pacing.

Study of PRIMAVERA steel samples by a positron annihilation spectroscopy technique

NASA Astrophysics Data System (ADS)

Grafutin, V.; Ilyukhina, O.; Krsjak, V.; Burcl, R.; Hähner, P.; Erak, D.; Zeman, A.

2010-11-01

In the present article, a positron annihilation spectroscopy investigation of VVER-440/230 weld materials is discussed. Important characteristics of metals such as Fermi energy, concentration of electrons in the conduction band, size and concentration of defects were experimentally determined for three model materials with higher level of copper (0.16 wt.%) and phosphorus (0.027-0.038 wt.%). The impact of neutron irradiation and subsequent annealing on crystal lattice parameters was investigated. The experiments with the angular correlation of positron annihilation radiation (ACAR) complement the published positron annihilation spectroscopy (PAS) studies of the radiation treated VVER materials as well as previous experiments on PRIMAVERA materials. The availability of the experimental reactor to prepare strong 64Cu positron sources provided for unique experimental conditions, such as good resolution of spectra (0.4 mrad) and reasonable short time of measurement (36 h). The present paper aims to contribute to further understanding of RPV (reactor pressure vessel) steels behaviour under irradiation conditions as well as annealing recovery procedures, which have already been applied at several VVER NPP units in Europe.

Validation of columnar CsI x-ray detector responses obtained with hybridMANTIS, a CPU-GPU Monte Carlo code for coupled x-ray, electron, and optical transport.

PubMed

Sharma, Diksha; Badano, Aldo

2013-03-01

hybridMANTIS is a Monte Carlo package for modeling indirect x-ray imagers using columnar geometry based on a hybrid concept that maximizes the utilization of available CPU and graphics processing unit processors in a workstation. The authors compare hybridMANTIS x-ray response simulations to previously published MANTIS and experimental data for four cesium iodide scintillator screens. These screens have a variety of reflective and absorptive surfaces with different thicknesses. The authors analyze hybridMANTIS results in terms of modulation transfer function and calculate the root mean square difference and Swank factors from simulated and experimental results. The comparison suggests that hybridMANTIS better matches the experimental data as compared to MANTIS, especially at high spatial frequencies and for the thicker screens. hybridMANTIS simulations are much faster than MANTIS with speed-ups up to 5260. hybridMANTIS is a useful tool for improved description and optimization of image acquisition stages in medical imaging systems and for modeling the forward problem in iterative reconstruction algorithms.

Dynamic flux balancing elucidates NAD(P)H production as limiting response to furfural inhibition in Saccharomyces cerevisiae.

PubMed

Pornkamol, Unrean; Franzen, Carl J

2015-08-01

Achieving efficient and economical lignocellulose-based bioprocess requires a robust organism tolerant to furfural, a major inhibitory compound present in lignocellulosic hydrolysate. The aim of this study was to develop a model that could generate quantitative descriptions of cell metabolism for elucidating the cell's adaptive response to furfural. Such a modelling tool could provide strategies for the design of more robust cells. A dynamic flux balance (dFBA) model of Saccharomyces cerevisiae was created by coupling a kinetic fermentation model with a previously published genome-scale stoichiometric model. The dFBA model was used for studying intracellular and extracellular flux responses to furfural perturbations under steady state and dynamic conditions. The predicted effects of furfural on dynamic flux profiles agreed well with previously published experimental results. The model showed that the yeast cell adjusts its metabolism in response to furfural challenge by increasing fluxes through the pentose phosphate pathway, TCA cycle, and proline and serine biosynthesis in order to meet the high demand of NAD(P)H cofactors. The model described here can be used to aid in systematic optimization of the yeast, as well as of the fermentation process, for efficient lignocellulosic ethanol production. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

FELASA recommendations for the health monitoring of mouse, rat, hamster, guinea pig and rabbit colonies in breeding and experimental units.

PubMed

Mähler Convenor, M; Berard, M; Feinstein, R; Gallagher, A; Illgen-Wilcke, B; Pritchett-Corning, K; Raspa, M

2014-07-01

The microbiological quality of experimental animals can critically influence animal welfare and the validity and reproducibility of research data. It is therefore important for breeding and experimental facilities to establish a laboratory animal health monitoring (HM) programme as an integrated part of any quality assurance system. FELASA has published recommendations for the HM of rodent and rabbit colonies in breeding and experimental units (Nicklas et al. Laboratory Animals, 2002), with the intention of harmonizing HM programmes. As stated in the preamble, these recommendations need to be adapted periodically to meet current developments in laboratory animal medicine. Accordingly, previous recommendations have been revised and shall be replaced by the present recommendations. These recommendations are aimed at all breeders and users of laboratory mice, rats, Syrian hamsters, guinea pigs and rabbits as well as diagnostic laboratories. They describe essential aspects of HM, such as the choice of agents, selection of animals and tissues for testing, frequency of sampling, commonly used test methods, interpretation of results and HM reporting. Compared with previous recommendations, more emphasis is put on the role of a person with sufficient understanding of the principles of HM, opportunistic agents, the use of sentinel animals (particularly under conditions of cage-level containment) and the interpretation and reporting of HM results. Relevant agents, testing frequencies and literature references are updated. Supplementary information on specific agents and the number of animals to be monitored and an example of a HM programme description is provided in the appendices. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Gas-Phase Lithium Cation Basicity: Revisiting the High Basicity Range by Experiment and Theory

NASA Astrophysics Data System (ADS)

Mayeux, Charly; Burk, Peeter; Gal, Jean-Francois; Kaljurand, Ivari; Koppel, Ilmar; Leito, Ivo; Sikk, Lauri

2014-09-01

According to high level calculations, the upper part of the previously published FT-ICR lithium cation basicity (LiCB at 373 K) scale appeared to be biased by a systematic downward shift. The purpose of this work was to determine the source of this systematic difference. New experimental LiCB values at 373 K have been measured for 31 ligands by proton-transfer equilibrium techniques, ranging from tetrahydrofuran (137.2 kJ mol-1) to 1,2-dimethoxyethane (202.7 kJ mol-1). The relative basicities (ΔLiCB) were included in a single self-consistent ladder anchored to the absolute LiCB value of pyridine (146.7 kJ mol-1). This new LiCB scale exhibits a good agreement with theoretical values obtained at G2(MP2) level. By means of kinetic modeling, it was also shown that equilibrium measurements can be performed in spite of the formation of Li+ bound dimers. The key feature for achieving accurate equilibrium measurements is the ion trapping time. The potential causes of discrepancies between the new data and previous experimental measurements were analyzed. It was concluded that the disagreement essentially finds its origin in the estimation of temperature and the calibration of Cook's kinetic method.

Electron mean free path dependence of the vortex surface impedance

DOE PAGES

Checchin, M.; Martinello, M.; Grassellino, A.; ...

2017-01-17

In the present study the radio-frequency complex response of trapped vortices in superconductors is calculated and compared to experimental data previously published. The motion equation for a magnetic flux line is solved assuming a bi-dimensional and mean-free-path-dependent Lorentzian-shaped pinning potential. The resulting surface resistance shows the unprecedented bell-shaped trend as a function of the mean-free-path observed in our previous experimental work. We demonstrate that such bell-shaped trend of the surface resistance as a function of the mean-free-path may be described as the interplay of the two limiting regimes of the surface resistance, for low and large mean-free-path values: pinning andmore » flux-flow regimes respectively. Since the possibility of defining the pinning potential at different locations from the surface and with different strengths, we discuss how the surface resistance is affected by different configurations of pinning sites. By tackling the frequency dependence of the surface resistance, we also demonstrate that the separation between pinning- and flux-flow-dominated regimes cannot be determined only by the depinning frequency. As a result, the dissipation regime can be tuned either by acting on the frequency or on the mean-free-path value.« less

Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design.

PubMed

Thyme, Summer B; Baker, David; Bradley, Philip

2012-06-08

Combinatorial sequence optimization for protein design requires libraries of discrete side-chain conformations. The discreteness of these libraries is problematic, particularly for long, polar side chains, since favorable interactions can be missed. Previously, an approach to loop remodeling where protein backbone movement is directed by side-chain rotamers predicted to form interactions previously observed in native complexes (termed "motifs") was described. Here, we show how such motif libraries can be incorporated into combinatorial sequence optimization protocols and improve native complex recapitulation. Guided by the motif rotamer searches, we made improvements to the underlying energy function, increasing recapitulation of native interactions. To further test the methods, we carried out a comprehensive experimental scan of amino acid preferences in the I-AniI protein-DNA interface and found that many positions tolerated multiple amino acids. This sequence plasticity is not observed in the computational results because of the fixed-backbone approximation of the model. We improved modeling of this diversity by introducing DNA flexibility and reducing the convergence of the simulated annealing algorithm that drives the design process. In addition to serving as a benchmark, this extensive experimental data set provides insight into the types of interactions essential to maintain the function of this potential gene therapy reagent. Published by Elsevier Ltd.

Electron mean free path dependence of the vortex surface impedance

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

Checchin, M.; Martinello, M.; Grassellino, A.

In the present study the radio-frequency complex response of trapped vortices in superconductors is calculated and compared to experimental data previously published. The motion equation for a magnetic flux line is solved assuming a bi-dimensional and mean-free-path-dependent Lorentzian-shaped pinning potential. The resulting surface resistance shows the unprecedented bell-shaped trend as a function of the mean-free-path observed in our previous experimental work. We demonstrate that such bell-shaped trend of the surface resistance as a function of the mean-free-path may be described as the interplay of the two limiting regimes of the surface resistance, for low and large mean-free-path values: pinning andmore » flux-flow regimes respectively. Since the possibility of defining the pinning potential at different locations from the surface and with different strengths, we discuss how the surface resistance is affected by different configurations of pinning sites. By tackling the frequency dependence of the surface resistance, we also demonstrate that the separation between pinning- and flux-flow-dominated regimes cannot be determined only by the depinning frequency. As a result, the dissipation regime can be tuned either by acting on the frequency or on the mean-free-path value.« less

A comparison of untagged gamma-ray and tagged-neutron yields from 241AmBe and 238PuBe sources.

PubMed

Scherzinger, J; Al Jebali, R; Annand, J R M; Fissum, K G; Hall-Wilton, R; Koufigar, S; Mauritzson, N; Messi, F; Perrey, H; Rofors, E

2017-09-01

Untagged gamma-ray and tagged-neutron yields from 241 AmBe and 238 PuBe mixed-field sources have been measured. Gamma-ray spectroscopy measurements from 1 to 5MeV were performed in an open environment using a CeBr 3 detector and the same experimental conditions for both sources. The shapes of the distributions are very similar and agree well with previous data. Tagged-neutron measurements from 2 to 6MeV were performed in a shielded environment using a NE-213 liquid-scintillator detector for the neutrons and a YAP(Ce) detector to tag the 4.44MeVgamma-rays associated with the de-excitation of the first-excited state of 12 C. Again, the same experimental conditions were used for both sources. The shapes of these distributions are also very similar and agree well with previous data, each other, and the ISO recommendation. Our 238 PuBe source provides approximately 2.6 times more 4.44MeVgamma-rays and 2.4 times more neutrons over the tagged-neutron energy range, the latter in reasonable agreement with the original full-spectrum source-calibration measurements performed at the time of their acquisition. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Experimental Investigations of the Internal Energy of Molecules Evaporated via Laser-induced Acoustic Desorption into a Fourier-transform Ion Cyclotron Resonance Mass Spectrometer (LIAD/FT-ICR)

PubMed Central

Shea, Ryan C.; Petzold, Christopher J.; Liu, Ji-ang; Kenttämaa, Hilkka I.

2008-01-01

The internal energy of neutral gas-phase organic and biomolecules, evaporated by means of laser-induced acoustic desorption (LIAD) into a Fourier-transform ion cyclotron resonance mass spectrometer (FT-ICR), was investigated through several experimental approaches. The desorbed molecules were demonstrated not to undergo degradation during the desorption process by collecting LIAD-evaporated molecules and subjecting them to analysis by electrospray ionization/quadrupole ion trap mass spectrometry. Previously established gas-phase basicity (GB) values were remeasured for LIAD-evaporated organic molecules and biomolecules with the use of the bracketing method. No endothermic reactions were observed. The remeasured basicity values are in close agreement with the values reported in the literature. The amount of internal energy deposited during LIAD is concluded to be less than a few kcal/mol. Chemical ionization with a series of proton transfer reagents was employed to obtain a breakdown curve for a protonated dipeptide, val-pro, evaporated by LIAD. Comparison of this breakdown curve with a previously published analogous curve obtained by using substrate-assisted laser desorption (SALD) to evaporate the peptide suggests that the molecules evaporated via LIAD have less internal energy than those evaporated via SALD. PMID:17263513

Spinodal decomposition in amorphous metal-silicate thin films: Phase diagram analysis and interface effects on kinetics

NASA Astrophysics Data System (ADS)

Kim, H.; McIntyre, P. C.

2002-11-01

Among several metal silicate candidates for high permittivity gate dielectric applications, the mixing thermodynamics of the ZrO2-SiO2 system were analyzed, based on previously published experimental phase diagrams. The driving force for spinodal decomposition was investigated in an amorphous silicate that was treated as a supercooled liquid solution. A subregular model was used for the excess free energy of mixing of the liquid, and measured invariant points were adopted for the calculations. The resulting simulated ZrO2-SiO2 phase diagram matched the experimental results reasonably well and indicated that a driving force exists for amorphous Zr-silicate compositions between approx40 mol % and approx90 mol % SiO2 to decompose into a ZrO2-rich phase (approx20 mol % SiO2) and SiO2-rich phase (>98 mol % SiO2) through diffusional phase separation at a temperature of 900 degC. These predictions are consistent with recent experimental reports of phase separation in amorphous Zr-silicate thin films. Other metal-silicate systems were also investigated and composition ranges for phase separation in amorphous Hf, La, and Y silicates were identified from the published bulk phase diagrams. The kinetics of one-dimensional spinodal decomposition normal to the plane of the film were simulated for an initially homogeneous Zr-silicate dielectric layer. We examined the effects that local stresses and the capillary driving force for component segregation to the interface have on the rate of spinodal decomposition in amorphous metal-silicate thin films.

Chinchilla laniger can be used as an experimental model for Taenia solium taeniasis.

PubMed

Maravilla, Pablo; Garza-Rodriguez, Adriana; Gomez-Diaz, Benjamin; Jimenez-Gonzalez, Diego Emiliano; Toral-Bastida, Elizabeth; Martinez-Ocaña, Joel; West, Brett; Molina, Nadia; Garcia-Cortes, Ramon; Kawa-Karasik, Simon; Romero-Valdovinos, Mirza; Avila-Ramirez, Guillermina; Flisser, Ana

2011-12-01

Chinchilla laniger has been reported as an experimental definitive host for Taenia solium; however no information about its suitability and yield of gravid tapeworm proglottids containing viable and infective eggs has been published. In total 55 outbred female chinchillas were infected with 4 cysticerci each; hosts were immunodeppressed with 6 or 8 mg of methyl-prednisolone acetate every 14 days starting the day of infection and their discomfort was followed. Kinetics of coproantigen ELISA or expelled proglottids was used to define the infection status. Efficiency of tapeworm establishment was 21% and of parasite gravidity was 8%; chinchillas showed some degree of suffering along the infection. Viability of eggs obtained from gravid proglottids was tested comparing methods previously published, our results showed 62% viability with propidium iodide, 54% with trypan blue, 34% with neutral red, 30% by oncosphere activation and 7% with bromide 3-(4,5-dimetil-tiazol-2-il)-2,5-difenil-tetrazolio (MTT) reduction; no statistical differences were obtained between most techniques, except activation. Four piglets were infected with 50,000 eggs each, necropsy was performed 3 months later and, after counting the number of cysticerci recovered, the percentage of infection was similar to data obtained with T. solium eggs recovered from humans. Our results demonstrate that the experimental model of T. solium taeniasis in C. laniger is a good alternative for providing eggs and adult tapeworms to be used in different types of experiments; optimization of the model probably depends on the use of inbred hosts and on the reduction of infected animals' suffering. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Semi-physiologic model validation and bioequivalence trials simulation to select the best analyte for acetylsalicylic acid.

PubMed

Cuesta-Gragera, Ana; Navarro-Fontestad, Carmen; Mangas-Sanjuan, Victor; González-Álvarez, Isabel; García-Arieta, Alfredo; Trocóniz, Iñaki F; Casabó, Vicente G; Bermejo, Marival

2015-07-10

The objective of this paper is to apply a previously developed semi-physiologic pharmacokinetic model implemented in NONMEM to simulate bioequivalence trials (BE) of acetyl salicylic acid (ASA) in order to validate the model performance against ASA human experimental data. ASA is a drug with first-pass hepatic and intestinal metabolism following Michaelis-Menten kinetics that leads to the formation of two main metabolites in two generations (first and second generation metabolites). The first aim was to adapt the semi-physiological model for ASA in NOMMEN using ASA pharmacokinetic parameters from literature, showing its sequential metabolism. The second aim was to validate this model by comparing the results obtained in NONMEM simulations with published experimental data at a dose of 1000 mg. The validated model was used to simulate bioequivalence trials at 3 dose schemes (100, 1000 and 3000 mg) and with 6 test formulations with decreasing in vivo dissolution rate constants versus the reference formulation (kD 8-0.25 h (-1)). Finally, the third aim was to determine which analyte (parent drug, first generation or second generation metabolite) was more sensitive to changes in formulation performance. The validation results showed that the concentration-time curves obtained with the simulations reproduced closely the published experimental data, confirming model performance. The parent drug (ASA) was the analyte that showed to be more sensitive to the decrease in pharmaceutical quality, with the highest decrease in Cmax and AUC ratio between test and reference formulations. Copyright © 2015 Elsevier B.V. All rights reserved.

Application of New Partition Coefficients to Modeling Plagioclase

NASA Technical Reports Server (NTRS)

Fagan, A. L.; Neal, C. R.; Rapp, J. F.; Draper, D. S.; Lapen, T. J.

2017-01-01

Previously, studies that determined the partition coefficient for an element, i, between plagioclase and the residual basaltic melt (Di plag) have been conducted using experimental conditions dissimilar from the Moon, and thus these values are not ideal for modeling plagioclase fractionation in a lunar system. However, recent work [1] has determined partition coefficients for plagioclase at lunar oxygen fugacities, and resulted in plagioclase with Anorthite contents =An90; these are significantly more calcic than plagioclase in previous studies, and the An content has a profound effect on partition coefficient values [2,3]. Plagioclase D-values, which are dependent on the An content of the crystal [e.g., 2-6], can be determined using published experimental data and the correlative An contents. Here, we examine new experimental data from [1] to ascertain their effect on the calculation of equilibrium liquids from Apollo 16 sample 60635,2. This sample is a coarse grained, subophitic impact melt composed of 55% plagioclase laths with An94.4-98.7 [7,8], distinctly more calcic than of previous partition coefficient studies (e.g., [3-6, 9-10]). Sample 60635,2 is notable as having several plagioclase trace element analyses containing a negative Europium anomaly (-Eu) in the rare-earth element (REE) profile, rather than the typical positive Eu anomaly (+Eu) [7-8] (Fig. 1). The expected +Eu is due to the similarity in size and charge with Ca2+, thereby allowing Eu2+ to be easily taken up by the plagioclase crystal structure, in contrast to the remaining REE3+. Some 60635,2 plagioclase crystals only have +Eu REE profiles, some only have -Eu REE profiles, and some +Eu and -Eu analyses in different areas on a single crystal [7, 8]. Moreover, there does not seem to be any core-rim association with the +Eu or -Eu analyses, nor does there appear to be a correlation between the size, shape, or location of a particular crystal within the sample and the sign of its Eu anomaly, which suggests a complex evolution. In order to investigate this sample further, we can calculate the equilibrium liquids, but with An contents distinct from previous experimental studies, we must calculate the appropriate partition coefficients for each trace element analysis.

Using semantics for representing experimental protocols.

PubMed

Giraldo, Olga; García, Alexander; López, Federico; Corcho, Oscar

2017-11-13

An experimental protocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas, e.g. biology, genetics, immunology, neurosciences, virology. Protocols often include references to equipment, reagents, descriptions of critical steps, troubleshooting and tips, as well as any other information that researchers deem important for facilitating the reusability of the protocol. Although experimental protocols are central to reproducibility, the descriptions are often cursory. There is the need for a unified framework with respect to the syntactic structure and the semantics for representing experimental protocols. In this paper we present "SMART Protocols ontology", an ontology for representing experimental protocols. Our ontology represents the protocol as a workflow with domain specific knowledge embedded within a document. We also present the S ample I nstrument R eagent O bjective (SIRO) model, which represents the minimal common information shared across experimental protocols. SIRO was conceived in the same realm as the Patient Intervention Comparison Outcome (PICO) model that supports search, retrieval and classification purposes in evidence based medicine. We evaluate our approach against a set of competency questions modeled as SPARQL queries and processed against a set of published and unpublished protocols modeled with the SP Ontology and the SIRO model. Our approach makes it possible to answer queries such as Which protocols use tumor tissue as a sample. Improving reporting structures for experimental protocols requires collective efforts from authors, peer reviewers, editors and funding bodies. The SP Ontology is a contribution towards this goal. We build upon previous experiences and bringing together the view of researchers managing protocols in their laboratory work. Website: https://smartprotocols.github.io/ .

An Automated, Experimenter-Free Method for the Standardised, Operant Cognitive Testing of Rats

PubMed Central

Rivalan, Marion; Munawar, Humaira; Fuchs, Anna; Winter, York

2017-01-01

Animal models of human pathology are essential for biomedical research. However, a recurring issue in the use of animal models is the poor reproducibility of behavioural and physiological findings within and between laboratories. The most critical factor influencing this issue remains the experimenter themselves. One solution is the use of procedures devoid of human intervention. We present a novel approach to experimenter-free testing cognitive abilities in rats, by combining undisturbed group housing with automated, standardized and individual operant testing. This experimenter-free system consisted of an automated-operant system (Bussey-Saksida rat touch screen) connected to a home cage containing group living rats via an automated animal sorter (PhenoSys). The automated animal sorter, which is based on radio-frequency identification (RFID) technology, functioned as a mechanical replacement of the experimenter. Rats learnt to regularly and individually enter the operant chamber and remained there for the duration of the experimental session only. Self-motivated rats acquired the complex touch screen task of trial-unique non-matching to location (TUNL) in half the time reported for animals that were manually placed into the operant chamber. Rat performance was similar between the two groups within our laboratory, and comparable to previously published results obtained elsewhere. This reproducibility, both within and between laboratories, confirms the validity of this approach. In addition, automation reduced daily experimental time by 80%, eliminated animal handling, and reduced equipment cost. This automated, experimenter-free setup is a promising tool of great potential for testing a large variety of functions with full automation in future studies. PMID:28060883

A novel approach to parasite population genetics: experimental infection reveals geographic differentiation, recombination and host-mediated population structure in Pasteuria ramosa, a bacterial parasite of Daphnia.

PubMed

Andras, J P; Ebert, D

2013-02-01

The population structure of parasites is central to the ecology and evolution of host-parasite systems. Here, we investigate the population genetics of Pasteuria ramosa, a bacterial parasite of Daphnia. We used natural P. ramosa spore banks from the sediments of two geographically well-separated ponds to experimentally infect a panel of Daphnia magna host clones whose resistance phenotypes were previously known. In this way, we were able to assess the population structure of P. ramosa based on geography, host resistance phenotype and host genotype. Overall, genetic diversity of P. ramosa was high, and nearly all infected D. magna hosted more than one parasite haplotype. On the basis of the observation of recombinant haplotypes and relatively low levels of linkage disequilibrium, we conclude that P. ramosa engages in substantial recombination. Isolates were strongly differentiated by pond, indicating that gene flow is spatially restricted. Pasteuria ramosa isolates within one pond were segregated completely based on the resistance phenotype of the host-a result that, to our knowledge, has not been previously reported for a nonhuman parasite. To assess the comparability of experimental infections with natural P. ramosa isolates, we examined the population structure of naturally infected D. magna native to one of the two source ponds. We found that experimental and natural infections of the same host resistance phenotype from the same source pond were indistinguishable, indicating that experimental infections provide a means to representatively sample the diversity of P. ramosa while reducing the sampling bias often associated with studies of parasite epidemics. These results expand our knowledge of this model parasite, provide important context for the large existing body of research on this system and will guide the design of future studies of this host-parasite system. © 2012 Blackwell Publishing Ltd.

Nuclear Data Sheets for A = 61

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

Zuber, Kazimierz; Singh, Balraj

2015-03-15

The evaluated spectroscopic data are presented for known nuclides of mass 61 (Sc,Ti,V,Cr,Mn,Fe,Co,Ni, Cu,Zn,Ga,Ge). Excited-state data are nonexistent for {sup 61}Sc, {sup 61}Ti, {sup 61}V, and {sup 61}Ge. Significant amounts of new data have been added since the previous NDS evaluation of A=61 nuclides (1999Bh04). {sup 61}Sc nuclide is now experimentally known, but without any knowledge of its half-life. The ground state half-lives of {sup 61}Ti and {sup 61}V are now determined. Excited-state data have become available for {sup 61}Cr, {sup 61}Mn and {sup 61}Ga, while for {sup 61}Ge, five excited states were erroneously assigned in the previous evaluation, thesemore » have been omitted here. Improved and extensive high-spin excitations are available for {sup 61}Fe, {sup 61}Cu and {sup 61}Zn, including several new superdeformed structures in {sup 61}Cu and {sup 61}Zn. Thermal neutron capture γ-ray data are available in detail from 2004Ra23. The radioactive decay schemes of {sup 61}Sc and {sup 61}Ti are not known, while those for {sup 61}V, {sup 61}Fe and {sup 61}Ge are poorly known. This work benefited from the earlier full evaluations of A=61 published by 1999Bh04, 1983Ek01 and 1975Au05 and the one published in an ‘update’ mode by 1992Zh31. The data and conclusions presented in the current work supersede those in all the previous evaluations.« less

A method to investigate the diffusion properties of nuclear calcium.

PubMed

Queisser, Gillian; Wittum, Gabriel

2011-10-01

Modeling biophysical processes in general requires knowledge about underlying biological parameters. The quality of simulation results is strongly influenced by the accuracy of these parameters, hence the identification of parameter values that the model includes is a major part of simulating biophysical processes. In many cases, secondary data can be gathered by experimental setups, which are exploitable by mathematical inverse modeling techniques. Here we describe a method for parameter identification of diffusion properties of calcium in the nuclei of rat hippocampal neurons. The method is based on a Gauss-Newton method for solving a least-squares minimization problem and was formulated in such a way that it is ideally implementable in the simulation platform uG. Making use of independently published space- and time-dependent calcium imaging data, generated from laser-assisted calcium uncaging experiments, here we could identify the diffusion properties of nuclear calcium and were able to validate a previously published model that describes nuclear calcium dynamics as a diffusion process.

A Cross-Sectional Analysis of Publication Types in Quality Improvement Journals.

PubMed

Wong, Christopher J; White, Andrew A; Merel, Susan E; Brock, Douglas M; Staiger, Thomas O

2016-07-01

Despite widespread engagement in quality improvement activities, little is known about the designs of studies currently published in quality improvement journals. This study's goal is to establish the prevalence of the types of research conducted in articles published in journals dedicated to quality improvement. A cross-sectional analysis was performed of 145 research articles published in 11 quality improvement journals in 2011. The majority of study designs were considered pre-experimental (95%), with a small percentage of quasi-experimental and experimental designs. Of the studies that reported the results of an intervention (n = 60), the most common research designs were pre-post studies (33%) and case studies (25%). There were few randomized controlled trials or quasi-experimental study designs (12% of intervention studies). These results suggest that there are opportunities for increased use of quasi-experimental study designs. © The Author(s) 2015.

Simulation of an Isolated Tiltrotor in Hover with an Unstructured Overset-Grid RANS Solver

NASA Technical Reports Server (NTRS)

Lee-Rausch, Elizabeth M.; Biedron, Robert T.

2009-01-01

An unstructured overset-grid Reynolds Averaged Navier-Stokes (RANS) solver, FUN3D, is used to simulate an isolated tiltrotor in hover. An overview of the computational method is presented as well as the details of the overset-grid systems. Steady-state computations within a noninertial reference frame define the performance trends of the rotor across a range of the experimental collective settings. Results are presented to show the effects of off-body grid refinement and blade grid refinement. The computed performance and blade loading trends show good agreement with experimental results and previously published structured overset-grid computations. Off-body flow features indicate a significant improvement in the resolution of the first perpendicular blade vortex interaction with background grid refinement across the collective range. Considering experimental data uncertainty and effects of transition, the prediction of figure of merit on the baseline and refined grid is reasonable at the higher collective range- within 3 percent of the measured values. At the lower collective settings, the computed figure of merit is approximately 6 percent lower than the experimental data. A comparison of steady and unsteady results show that with temporal refinement, the dynamic results closely match the steady-state noninertial results which gives confidence in the accuracy of the dynamic overset-grid approach.

Evolution of divergent female mating preference in response to experimental sexual selection.

PubMed

Debelle, Allan; Ritchie, Michael G; Snook, Rhonda R

2014-09-01

Sexual selection is predicted to drive the coevolution of mating signals and preferences (mating traits) within populations, and could play a role in speciation if sexual isolation arises due to mating trait divergence between populations. However, few studies have demonstrated that differences in mating traits between populations result from sexual selection alone. Experimental evolution is a promising approach to directly examine the action of sexual selection on mating trait divergence among populations. We manipulated the opportunity for sexual selection (low vs. high) in populations of Drosophila pseudoobscura. Previous studies on these experimental populations have shown that sexual selection manipulation resulted in the divergence between sexual selection treatments of several courtship song parameters, including interpulse interval (IPI) which markedly influences male mating success. Here, we measure female preference for IPI using a playback design to test for preference divergence between the sexual selection treatments after 130 generations of experimental sexual selection. The results suggest that female preference has coevolved with male signal, in opposite directions between the sexual selection treatments, providing direct evidence of the ability of sexual selection to drive the divergent coevolution of mating traits between populations. We discuss the implications in the context sexual selection and speciation. © 2014 The Authors. Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Experimental investigation of commercial small diameter dental implants in porcine mandibular segments.

PubMed

Hasan, Istabrak; Heinemann, Friedhelm; Schwegmann, Monika; Keilig, Ludger; Stark, Helmut; Bourauel, Christoph

2017-02-01

Small diameter (mini) dental implants have become more popular in recent years as alternatives to classical implant treatment in clinical cases with critical bony situations. However, an in-depth scientific analysis of the mechanical and biomechanical effects of small diameter implants has not yet been published. The aim of the present study was to investigate experimentally different commercial mini implants by measuring their displacements under immediate loading. Twelve commercially available mini implants were measured. Implants were inserted into porcine mandibular segments and loaded by means of a predefined displacement of 0.5 mm of the loading system. The implants were loaded at an angle of 30° to the implant long axis using the self-developed biomechanical hexapod measurement system. Implant displacements were registered. The experimental results were compared to the numerical ones from a previous study. Measured implant displacements were within the range of 39-194 μm. A large variation in the displacements was obtained among the different implant systems due to the different designs and thread profiles. Comparing experimental and numerical results, the displacements that were obtained numerically were within the range of 79-347 μm. The different commercial mini implants showed acceptable primary stability and could be loaded immediately after their insertion.

Reference Accuracy among Research Articles Published in "Research on Social Work Practice"

ERIC Educational Resources Information Center

Wilks, Scott E.; Geiger, Jennifer R.; Bates, Samantha M.; Wright, Amy L.

2017-01-01

Objective: The objective was to examine reference errors in research articles published in Research on Social Work Practice. High rates of reference errors in other top social work journals have been noted in previous studies. Methods: Via a sampling frame of 22,177 total references among 464 research articles published in the previous decade, a…

EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments.

PubMed

Zhou, Bailing; Zhao, Huiying; Yu, Jiafeng; Guo, Chengang; Dou, Xianghua; Song, Feng; Hu, Guodong; Cao, Zanxia; Qu, Yuanxu; Yang, Yuedong; Zhou, Yaoqi; Wang, Jihua

2018-01-04

Long non-coding RNAs (lncRNAs) play important functional roles in various biological processes. Early databases were utilized to deposit all lncRNA candidates produced by high-throughput experimental and/or computational techniques to facilitate classification, assessment and validation. As more lncRNAs are validated by low-throughput experiments, several databases were established for experimentally validated lncRNAs. However, these databases are small in scale (with a few hundreds of lncRNAs only) and specific in their focuses (plants, diseases or interactions). Thus, it is highly desirable to have a comprehensive dataset for experimentally validated lncRNAs as a central repository for all of their structures, functions and phenotypes. Here, we established EVLncRNAs by curating lncRNAs validated by low-throughput experiments (up to 1 May 2016) and integrating specific databases (lncRNAdb, LncRANDisease, Lnc2Cancer and PLNIncRBase) with additional functional and disease-specific information not covered previously. The current version of EVLncRNAs contains 1543 lncRNAs from 77 species that is 2.9 times larger than the current largest database for experimentally validated lncRNAs. Seventy-four percent lncRNA entries are partially or completely new, comparing to all existing experimentally validated databases. The established database allows users to browse, search and download as well as to submit experimentally validated lncRNAs. The database is available at http://biophy.dzu.edu.cn/EVLncRNAs. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

A general panel sizing computer code and its application to composite structural panels

NASA Technical Reports Server (NTRS)

Anderson, M. S.; Stroud, W. J.

1978-01-01

A computer code for obtaining the dimensions of optimum (least mass) stiffened composite structural panels is described. The procedure, which is based on nonlinear mathematical programming and a rigorous buckling analysis, is applicable to general cross sections under general loading conditions causing buckling. A simplified method of accounting for bow-type imperfections is also included. Design studies in the form of structural efficiency charts for axial compression loading are made with the code for blade and hat stiffened panels. The effects on panel mass of imperfections, material strength limitations, and panel stiffness requirements are also examined. Comparisons with previously published experimental data show that accounting for imperfections improves correlation between theory and experiment.

Ab initio calculation of the shear viscosity of neon in the liquid and hypercritical state over a wide pressure and temperature range

NASA Astrophysics Data System (ADS)

Eggenberger, Rolf; Gerber, Stefan; Huber, Hanspeter; Searles, Debra; Welker, Marc

1992-08-01

The shear viscosity is calculated ab initio for the liquid and hypercritical state, i.e. a previously published potential for Ne 2, obtained from ab initio calculations including electron correlation, is used in classical equilibrium molecular dynamics simulations to obtain the shear viscosity from a Green-Kubo integral. The quality of the results is quite uniform over a large pressure range up to 1000 MPa and a wide temperature range from 26 to 600 K. In most cases the calculated shear viscosity deviates by less than 10% from the experimental value, in general the error being only a few percent.

Tables of nuclear cross sections for galactic cosmic rays: Absorption cross sections

NASA Technical Reports Server (NTRS)

Townsend, L. W.; Wilson, J. W.

1985-01-01

A simple but comprehensive theory of nuclear reactions is presented. Extensive tables of nucleon, deuteron, and heavy-ion absorption cross sections over a broad range of energies are generated for use in cosmic ray shielding studies. Numerous comparisons of the calculated values with available experimental data show agreement to within 3 percent for energies above 80 MeV/nucleon and within approximately 10 percent for energies as low as 30 MeV/nucleon. These tables represent the culmination of the development of the absorption cross section formalism and supersede the preliminary absorption cross sections published previously in NASA TN D-8107, NASA TP-2138, and NASA TM-84636.

Generalisation of the identity method for determination of high-order moments of multiplicity distributions with a software implementation

NASA Astrophysics Data System (ADS)

Maćkowiak-Pawłowska, Maja; Przybyła, Piotr

2018-05-01

The incomplete particle identification limits the experimentally-available phase space region for identified particle analysis. This problem affects ongoing fluctuation and correlation studies including the search for the critical point of strongly interacting matter performed on SPS and RHIC accelerators. In this paper we provide a procedure to obtain nth order moments of the multiplicity distribution using the identity method, generalising previously published solutions for n=2 and n=3. Moreover, we present an open source software implementation of this computation, called Idhim, that allows one to obtain the true moments of identified particle multiplicity distributions from the measured ones provided the response function of the detector is known.

Cesium alignment produced by pumping with unpolarized light★

NASA Astrophysics Data System (ADS)

Shi, Yongqi; Weis, Antoine

2018-04-01

We demonstrate optical pumping on the four hyperfine components of the Cs D 1 transition by unpolarized (UPL) resonant laser light. The evidence is based on the reduction of the absorption coefficients κ 0 with increasing light power P in an uncoated Cs vapor cell with isotropic spin relaxation. For comparison we perform the same quantitative κ 0( P) measurements with linearly-polarized light (LPL) and circularly-polarized light (CPL). We find that our previously published algebraic expressions give an excellent description of all experimentally recorded induced transparency signals. Based on this we can make reliable absolute predictions for the power dependence of the spin orientation and alignment produced by pumping with LPL, CPL and UPL.

Characteristics of cesium iodide for use as a particle discriminator for high energy cosmic rays

NASA Technical Reports Server (NTRS)

Crannell, C. J.; Kurz, R. J.; Viehmann, W.

1973-01-01

The possible use of CsI to discriminate between high energy cosmic ray electrons and interacting protons has been investigated. The pulse-shape properties as a function of ionization density, temperature, and spectral response are presented for thallium-activated CsI and as a function of ionization density for sodium-activated CsI. The results are based on previously published data and on corroborative measurements from the present work. Experimental results on the response of CsI to electron-induced electromagnetic cascades and to interacting hadrons are described. Bibliographies of publications dealing with the properties of CsI and with pulse-shape discrimination techniques are presented.

Absolute Photoionization Cross Section for Fe6+ to Fe10+ Ions in the Photon Energy Region of the 2p–3d Resonance Lines

NASA Astrophysics Data System (ADS)

Blancard, C.; Cubaynes, D.; Guilbaud, S.; Bizau, J.-M.

2018-01-01

Resonant single photoionization cross sections of Fen+ (n = 6 to 10) ions have been measured in absolute values using a merged-beams setup at the SOLEIL synchrotron radiation facility. Photon energies were between about 710 and 780 eV, covering the range of the 2p–3d transitions. The experimental cross sections are compared to calculations we performed using a multi-configuration Dirac–Fock code and the OPAS code dedicated to radiative opacity calculations. Comparisons are also done with the Chandra X-ray observatory NGC 3783 spectra and with the results of previously published calculations.

Empirical retrocausality: Testing physics hypotheses with parapsychological experiments

NASA Astrophysics Data System (ADS)

Dobyns, York

2017-05-01

In 2011, Daryl Bem published a report of nine parapsychological experiments showing evidence of retrocausal information transfer. Earlier in 2016, the team of Bem, Tressoldi, Rabeyron, and Duggan published the results of a meta-analysis containing 81 independent replications of the original Bem experiments (total of 90 with the originals).[1] This much larger database continues to show positive results of generally comparable effect size, thus demonstrating that the effects claimed by Bem can be replicated by independent researchers and greatly strengthening the case for empirically observed retrocausation. Earlier (2011) work by this author showed how a modification of one of Bem's original experiments could be used to test the mechanism implicitly proposed by Echeverria, Klinkhammer, and Thorne to explain how retrocausal phenomena can exist without any risk of self-contradictory event sequences (time paradoxes). In light of the new publication and new evidence, the current work generalizes the previous analysis which was restricted to only one of Bem's experimental genres (precognitive approach and avoidance). The current analysis shows how minor modifications can be made in Bem's other experimental genres of retroactive priming, retroactive habituation, and retroactive facilitation of recall to test the EKT anti-paradox mechanism. If the EKT hypothesis is correct, the modified experiments, while continuing to show replicable retrocausal phenomena, will also show a characteristic pattern of distortion in the statistics of the random selections used to drive the experiments.

Quasi-experimental study designs series-paper 5: a checklist for classifying studies evaluating the effects on health interventions-a taxonomy without labels.

PubMed

Reeves, Barnaby C; Wells, George A; Waddington, Hugh

2017-09-01

The aim of the study was to extend a previously published checklist of study design features to include study designs often used by health systems researchers and economists. Our intention is to help review authors in any field to set eligibility criteria for studies to include in a systematic review that relate directly to the intrinsic strength of the studies in inferring causality. We also seek to clarify key equivalences and differences in terminology used by different research communities. Expert consensus meeting. The checklist comprises seven questions, each with a list of response items, addressing: clustering of an intervention as an aspect of allocation or due to the intrinsic nature of the delivery of the intervention; for whom, and when, outcome data are available; how the intervention effect was estimated; the principle underlying control for confounding; how groups were formed; the features of a study carried out after it was designed; and the variables measured before intervention. The checklist clarifies the basis of credible quasi-experimental studies, reconciling different terminology used in different fields of investigation and facilitating communications across research communities. By applying the checklist, review authors' attention is also directed to the assumptions underpinning the methods for inferring causality. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Intense Pulsed Neutron Source: Progress report 1991--1996. 15. Anniversary edition -- Volume 2

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

NONE

1996-05-01

The 15th Anniversary Edition of the IPNS Progress Report is being published in recognition of the Intense Pulsed Neutron Source`s first 15 years of successful operation as a user facility. To emphasize the importance of this milestone, the author shave made the design and organization of the report significantly different from previous IPNS Progress Reports. This report consists of two volumes. For Volume 1, authors were asked to prepare articles that highlighted recent scientific accomplishments at IPNS, from 1991 to present; to focus on and illustrate the scientific advances achieved through the unique capabilities of neutron studies performed by IPNSmore » users; to report on specific activities or results from an instrument; or to focus on a body of work encompassing different neutron-scattering techniques. Articles were also included on the accelerator system, instrumentation, computing, target, and moderators. A list of published and ``in press` articles in journals, books, and conference proceedings, resulting from work done at IPNS since 1991, was compiled. This list is arranged alphabetically according to first author. Publication references in the articles are listed by last name of first author and year of publication. The IPNS experimental reports received since 1991 are compiled in Volume 2. Experimental reports referenced in the articles are listed by last name of first author, instrument designation, and experiment number.« less

Intense Pulsed Neutron Source: Progress report 1991--1996. 15. Anniversary edition -- Volume 1

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

Marzec, B.

1996-05-01

The 15th Anniversary Edition of the IPNS Progress Report is being published in recognition of the Intense Pulsed Neutron Source`s first 15 years of successful operation as a user facility. To emphasize the importance of this milestone, the authors have made the design and organization of the report significantly different from previous IPNS Progress Reports. This report consists of two volumes. For Volume 1, authors were asked to prepare articles that highlighted recent scientific accomplishments at IPNS, from 1991 to present; to focus on and illustrate the scientific advances achieved through the unique capabilities of neutron studies performed by IPNSmore » users; to report on specific activities or results from an instrument; or to focus on a body of work encompassing different neutron-scattering techniques. Articles were also included on the accelerator system, instrumentation, computing, target, and moderators. A list of published and ``in press` articles in journals, books, and conference proceedings, resulting from work done at IPNS since 1991, was compiled. This list is arranged alphabetically according to first author. Publication references in the articles are listed by last name of first author and year of publication. The IPNS experimental reports received since 1991 are compiled in Volume 2. Experimental reports referenced in the articles are listed by last name of first author, instrument designation, and experiment number.« less

Snake fangs: 3D morphological and mechanical analysis by microCT, simulation, and physical compression testing.

PubMed

du Plessis, Anton; Broeckhoven, Chris; le Roux, Stephan G

2018-01-01

This Data Note provides data from an experimental campaign to analyse the detailed internal and external morphology and mechanical properties of venomous snake fangs. The aim of the experimental campaign was to investigate the evolutionary development of 3 fang phenotypes and investigate their mechanical behaviour. The study involved the use of load simulations to compare maximum Von Mises stress values when a load is applied to the tip of the fang. The conclusions of this study have been published elsewhere, but in this data note we extend the analysis, providing morphological comparisons including details such as curvature comparisons, thickness, etc. Physical compression results of individual fangs, though reported in the original paper, were also extended here by calculating the effective elastic modulus of the entire snake fang structure including internal cavities for the first time. This elastic modulus of the entire fang is significantly lower than the locally measured values previously reported from indentation experiments, highlighting the possibility that the elastic modulus is higher on the surface than in the rest of the material. The micro-computed tomography (microCT) data are presented both in image stacks and in the form of STL files, which simplifies the handling of the data and allows its re-use for future morphological studies. These fangs might also serve as bio-inspiration for future hypodermic needles. © The Author 2017. Published by Oxford University Press.

Nuclear Data Sheets for A=164

NASA Astrophysics Data System (ADS)

Singh, Balraj; Chen, Jun

2018-01-01

Experimental nuclear structure data for the known A=164 isobaric nuclides (Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, Hf, Ta, W, Re, Os, Ir) have been evaluated, and presented together with Adopted properties of level energies, and associated γ rays. The decay data for these nuclides have also been evaluated, providing Adopted values of γ and β radiations, and log ft values. No excited states are known in 164Eu, 164Tb, and 164Ir. Information for 164Gd, 164Re and 164Os is limited due to insufficient experimental data. For radioactive nuclides, decay schemes of 164Sm, 164Gd and 164Re are not known, and those of 164W, 164Tb, 164Lu, 164Hf, 164Ta and 164W are incomplete. The decay schemes of 164Ho and the two activities of 164Tm seem fairly complete. The decay scheme of 164Yb presents a major problem that the Q(ε) value of 887 keV 29 recommended in 2017Wa10 is in disagreement with the population of levels at 928, 952 and 1060 keV in the daughter nucleus. This decay scheme, which so far has been mainly reported in a secondary reference (1982AdZZ) needs further investigation. Also the masses of 164Yb and 164Tm need either new measurements or a re-evaluation to resolve discrepancy of about 220 keV in the Q value of 164Yb decay to 164Tm. The reactions and decays for which no new experimental information has become available since the 2001 update have undergone revisions to incorporate conversion coefficients from BrIcc code, and evaluated Q values from 2017Wa10, but the essential content of such datasets may have remained the same as in previous evaluations. In this respect the present work greatly benefited from all the previous NDS evaluations (2001Si27,1992Sh07, 1986Sh03,1974Bu30), but at the same time data presented herein supersede all the previous published evaluations.

Complex refractive index measurements for BaF 2 and CaF 2 via single-angle infrared reflectance spectroscopy

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

Kelly-Gorham, Molly Rose K.; DeVetter, Brent M.; Brauer, Carolyn S.

We have re-investigated the optical constants n and k for the homologous series of inorganic salts barium fluoride (BaF2) and calcium fluoride (CaF2) using a single-angle near-normal incidence reflectance device in combination with a calibrated Fourier transform infrared (FTIR) spectrometer. Our results are in good qualitative agreement with most previous works. However, certain features of the previously published data near the reststrahlen band exhibit distinct differences in spectral characteristics. Notably, our measurements of BaF2 do not include a spectral feature in the ~250 cm-1 reststrahlen band that was previously published. Additionally, CaF2 exhibits a distinct wavelength shift relative to themore » model derived from previously published data. We confirmed our results with recently published works that use significantly more modern instrumentation and data reduction techniques« less

Ion cyclotron emission studies: Retrospects and prospects

DOE PAGES

Gorelenkov, N. N.

2016-06-05

Ion cyclotron emission (ICE) studies emerged in part from the papers by A.B. Mikhailovskii published in the 1970s. Among the discussed subjects were electromagnetic compressional Alfv,nic cyclotron instabilities with the linear growth rate similar ~ √(n α/n e) driven by fusion products, -particles which draw a lot of attention to energetic particle physics. The theory of ICE excited by energetic particles was significantly advanced at the end of the 20th century motivated by first DT experiments on TFTR and subsequent JET experimental studies which we highlight. Recently ICE theory was advanced by detailed theoretical and experimental studies on spherical torusmore » (ST) fusion devices where the instability signals previously indistinguishable in high aspect ratio tokamaks due to high toroidal magnetic field became the subjects of experiments. Finally, we discuss prospects of ICE theory applications for future burning plasma (BP) experiments such as those to be conducted in ITER device in France, where neutron and gamma rays escaping the plasma create extremely challenging conditions fusion alpha particle diagnostics.« less

Stress dependence of microstructures in experimentally deformed calcite

NASA Astrophysics Data System (ADS)

Platt, John P.; De Bresser, J. H. P.

2017-12-01

Optical measurements of microstructural features in experimentally deformed Carrara marble help define their dependence on stress. These features include dynamically recrystallized grain size (Dr), subgrain size (Sg), minimum bulge size (Lρ), and the maximum scale length for surface-energy driven grain-boundary migration (Lγ). Taken together with previously published data Dr defines a paleopiezometer over the range 15-291 MPa and temperature over the range 500-1000 °C, with a stress exponent of -1.09 (CI -1.27 to -0.95), showing no detectable dependence on temperature. Sg and Dr measured in the same samples are closely similar in size, suggesting that the new grains did not grow significantly after nucleation. Lρ and Lγ measured on each sample define a relationship to stress with an exponent of approximately -1.6, which helps define the boundary between a region of dominant strain-energy-driven grain-boundary migration at high stress, from a region of dominant surface-energy-driven grain-boundary migration at low stress.

The anomalous demagnetization behaviour of chondritic meteorites

NASA Astrophysics Data System (ADS)

Morden, S. J.

1992-06-01

Alternating field (AF) demagnetization of chondritic samples often shows anomalous results such as large directional and intensity changes; 'saw-tooth' intensity vs. demagnetizing field curves are also prevalent. An attempt to explain this behaviour is presented, using a computer model in which individual 'mineral grains' can be 'magnetized' in a variety of different ways. A simulated demagnetization can then be carried out to examine the results. It was found that the experimental behaviour of chondrites can be successfully mimicked by loading the computer model with a series of randomly orientated and sized vectors. The parameters of the model can be changed to reflect different trends seen in experimental data. Many published results can be modelled using this method. A known magnetic mineralogy can be modelled, and an unknown mineralogy deduced from AF demagnetization curves. Only by comparing data from mutually orientated samples can true stable regions for palaeointensity measurements be identified, calling into question some previous estimates of field strength from meteorites.

Modelling the effect of GRP78 on anti-oestrogen sensitivity and resistance in breast cancer

PubMed Central

Parmar, Jignesh H.; Cook, Katherine L.; Shajahan-Haq, Ayesha N.; Clarke, Pamela A. G.; Tavassoly, Iman; Clarke, Robert; Tyson, John J.; Baumann, William T.

2013-01-01

Understanding the origins of resistance to anti-oestrogen drugs is of critical importance to many breast cancer patients. Recent experiments show that knockdown of GRP78, a key gene in the unfolded protein response (UPR), can re-sensitize resistant cells to anti-oestrogens, and overexpression of GRP78 in sensitive cells can cause them to become resistant. These results appear to arise from the operation and interaction of three cellular systems: the UPR, autophagy and apoptosis. To determine whether our current mechanistic understanding of these systems is sufficient to explain the experimental results, we built a mathematical model of the three systems and their interactions. We show that the model is capable of reproducing previously published experimental results and some new data gathered specifically for this paper. The model provides us with a tool to better understand the interactions that bring about anti-oestrogen resistance and the effects of GRP78 on both sensitive and resistant breast cancer cells. PMID:24511377

Classical continuum theory limits to determine the size-dependency of mechanical properties of GaN NWs

NASA Astrophysics Data System (ADS)

Zamani Kouhpanji, Mohammad Reza; Behzadirad, Mahmoud; Busani, Tito

2017-12-01

We used the stable strain gradient theory including acceleration gradients to investigate the classical and nonclassical mechanical properties of gallium nitride (GaN) nanowires (NWs). We predicted the static length scales, Young's modulus, and shear modulus of the GaN NWs from the experimental data. Combining these results with atomic simulations, we also found the dynamic length scale of the GaN NWs. Young's modulus, shear modulus, static, and dynamic length scales were found to be 318 GPa, 131 GPa, 8 nm, and 8.9 nm, respectively, usable for demonstrating the static and dynamic behaviors of GaN NWs having diameters from a few nm to bulk dimensions. Furthermore, the experimental data were analyzed with classical continuum theory (CCT) and compared with the available literature to illustrate the size-dependency of the mechanical properties of GaN NWs. This practice resolves the previous published discrepancies that happened due to the limitations of CCT used for determining the mechanical properties of GaN NWs and their size-dependency.

Bistable Behavior of the Lac Operon in E. Coli When Induced with a Mixture of Lactose and TMG

PubMed Central

Díaz-Hernández, Orlando; Santillán, Moisés

2010-01-01

In this work we investigate multistability in the lac operon of Escherichia coli when it is induced by a mixture of lactose and the non-metabolizable thiomethyl galactoside (TMG). In accordance with previously published experimental results and computer simulations, our simulations predict that: (1) when the system is induced by TMG, the system shows a discernible bistable behavior while, (2) when the system is induced by lactose, bistability does not disappear but excessively high concentrations of lactose would be required to observe it. Finally, our simulation results predict that when a mixture of lactose and TMG is used, the bistability region in the extracellular glucose concentration vs. extracellular lactose concentration parameter space changes in such a way that the model predictions regarding bistability could be tested experimentally. These experiments could help to solve a recent controversy regarding the existence of bistability in the lac operon under natural conditions. PMID:21423364

Relationships between lattice energies of inorganic ionic solids

NASA Astrophysics Data System (ADS)

Kaya, Savaş

2018-06-01

Lattice energy, which is a measure of the stabilities of inorganic ionic solids, is the energy required to decompose a solid into its constituent independent gaseous ions. In the present work, the relationships between lattice energies of many diatomic and triatomic inorganic ionic solids are revealed and a simple rule that can be used for the prediction of the lattice energies of inorganic ionic solids is introduced. According to this rule, the lattice energy of an AB molecule can be predicted with the help of the lattice energies of AX, BY and XY molecules in agreement with the experimental data. This rule is valid for not only diatomic molecules but also triatomic molecules. The lattice energy equations proposed in this rule provides compatible results with previously published lattice energy equations by Jenkins, Kaya, Born-Lande, Born-Mayer, Kapustinskii and Reddy. For a large set of tested molecules, calculated percent standard deviation values considering experimental data and the results of the equations proposed in this work are in general between %1-2%.

Experimental result analysis for scaled model of UiTM tailless blended wing-body (BWB) Baseline 7 unmanned aerial vehicle (UAV)

NASA Astrophysics Data System (ADS)

Nasir, R. E. M.; Ahmad, A. M.; Latif, Z. A. A.; Saad, R. M.; Kuntjoro, W.

2017-12-01

Blended wing-body (BWB) aircraft having planform configuration similar to those previously researched and published by other researchers does not guarantee that an efficient aerodynamics in term of lift-to-drag ratio can be achieved. In this wind tunnel experimental study, BWB half model is used. The model is also being scaled down to 71.5% from the actual size. Based on the results, the maximum lift coefficient is found to be 0.763 when the angle is at 27.5° after which the model starts to stall. The minimum drag coefficient is 0.014, measured at zero angle of attack. The corrected lift-to-drag ratio (L/D) is 15.9 at angle 7.8°. The scaled model has a big flat surface that surely gives an inaccurate data but the data obtained shall give some insights for future perspective towards the BWB model being tested.

Ion cyclotron emission studies: Retrospects and prospects

NASA Astrophysics Data System (ADS)

Gorelenkov, N. N.

2016-05-01

Ion cyclotron emission (ICE) studies emerged in part from the papers by A.B. Mikhailovskii published in the 1970s. Among the discussed subjects were electromagnetic compressional Alfvénic cyclotron instabilities with the linear growth rate √ {n_α /n_e } driven by fusion products, -particles which draw a lot of attention to energetic particle physics. The theory of ICE excited by energetic particles was significantly advanced at the end of the 20th century motivated by first DT experiments on TFTR and subsequent JET experimental studies which we highlight. More recently ICE theory was advanced by detailed theoretical and experimental studies on spherical torus (ST) fusion devices where the instability signals previously indistinguishable in high aspect ratio tokamaks due to high toroidal magnetic field became the subjects of experiments. We discuss further prospects of ICE theory applications for future burning plasma (BP) experiments such as those to be conducted in ITER device in France, where neutron and gamma rays escaping the plasma create extremely challenging conditions fusion alpha particle diagnostics.

A Categorical Content Analysis of Highly Cited Literature Related to Trends and Issues in Special Education.

PubMed

Arden, Sarah V; Pentimonti, Jill M; Cooray, Rochana; Jackson, Stephanie

2017-07-01

This investigation employs categorical content analysis processes as a mechanism to examine trends and issues in a sampling of highly cited (100+) literature in special education journals. The authors had two goals: (a) broadly identifying trends across publication type, content area, and methodology and (b) specifically identifying articles with disaggregated outcomes for students with learning disabilities (LD). Content analyses were conducted across highly cited (100+) articles published during a 20-year period (1992-2013) in a sample ( n = 3) of journals focused primarily on LD, and in one broad, cross-categorical journal recognized for its impact in the field. Results indicated trends in the article type (i.e., commentary and position papers), content (i.e., reading and behavior), and methodology (i.e., small proportions of experimental and quasi-experimental designs). Results also revealed stability in the proportion of intervention research studies when compared to previous analyses and a decline in the proportion of those that disaggregated data specifically for students with LD.

MMA-EoS: A Computational Framework for Mineralogical Thermodynamics

NASA Astrophysics Data System (ADS)

Chust, T. C.; Steinle-Neumann, G.; Dolejš, D.; Schuberth, B. S. A.; Bunge, H.-P.

2017-12-01

We present a newly developed software framework, MMA-EoS, that evaluates phase equilibria and thermodynamic properties of multicomponent systems by Gibbs energy minimization, with application to mantle petrology. The code is versatile in terms of the equation-of-state and mixing properties and allows for the computation of properties of single phases, solution phases, and multiphase aggregates. Currently, the open program distribution contains equation-of-state formulations widely used, that is, Caloric-Murnaghan, Caloric-Modified-Tait, and Birch-Murnaghan-Mie-Grüneisen-Debye models, with published databases included. Through its modular design and easily scripted database, MMA-EoS can readily be extended with new formulations of equations-of-state and changes or extensions to thermodynamic data sets. We demonstrate the application of the program by reproducing and comparing physical properties of mantle phases and assemblages with previously published work and experimental data, successively increasing complexity, up to computing phase equilibria of six-component compositions. Chemically complex systems allow us to trace the budget of minor chemical components in order to explore whether they lead to the formation of new phases or extend stability fields of existing ones. Self-consistently computed thermophysical properties for a homogeneous mantle and a mechanical mixture of slab lithologies show no discernible differences that require a heterogeneous mantle structure as has been suggested previously. Such examples illustrate how thermodynamics of mantle mineralogy can advance the study of Earth's interior.

Widespread occurrence of organelle genome-encoded 5S rRNAs including permuted molecules.

PubMed

Valach, Matus; Burger, Gertraud; Gray, Michael W; Lang, B Franz

2014-12-16

5S Ribosomal RNA (5S rRNA) is a universal component of ribosomes, and the corresponding gene is easily identified in archaeal, bacterial and nuclear genome sequences. However, organelle gene homologs (rrn5) appear to be absent from most mitochondrial and several chloroplast genomes. Here, we re-examine the distribution of organelle rrn5 by building mitochondrion- and plastid-specific covariance models (CMs) with which we screened organelle genome sequences. We not only recover all organelle rrn5 genes annotated in GenBank records, but also identify more than 50 previously unrecognized homologs in mitochondrial genomes of various stramenopiles, red algae, cryptomonads, malawimonads and apusozoans, and surprisingly, in the apicoplast (highly derived plastid) genomes of the coccidian pathogens Toxoplasma gondii and Eimeria tenella. Comparative modeling of RNA secondary structure reveals that mitochondrial 5S rRNAs from brown algae adopt a permuted triskelion shape that has not been seen elsewhere. Expression of the newly predicted rrn5 genes is confirmed experimentally in 10 instances, based on our own and published RNA-Seq data. This study establishes that particularly mitochondrial 5S rRNA has a much broader taxonomic distribution and a much larger structural variability than previously thought. The newly developed CMs will be made available via the Rfam database and the MFannot organelle genome annotator. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Single-Case Experimental Designs: A Systematic Review of Published Research and Current Standards

ERIC Educational Resources Information Center

Smith, Justin D.

2012-01-01

This article systematically reviews the research design and methodological characteristics of single-case experimental design (SCED) research published in peer-reviewed journals between 2000 and 2010. SCEDs provide researchers with a flexible and viable alternative to group designs with large sample sizes. However, methodological challenges have…

Experimental artifacts influencing polarization sensitive magneto-Raman spectroscopy

NASA Astrophysics Data System (ADS)

Thirunavukkuarasu, K.; Lu, Z.; Su, L.; Yu, Y.; Cao, L.; Ballotin, M. V.; Christianen, P. C. M.; Zhang, Y.; Smirnov, D.

Since the discovery of graphene, there has been an explosion of research on 2D layered materials such as transition metal dichalcogenides (TMDs). Among several experimental techniques utilized for studying these materials, Raman spectroscopy has proven to be a very powerful tool due to it's sensitivity to layer numbers, interlayer coupling etc. Layered MoS2, member of TMD family, is a typical example with promising applications in nano-optoelectronics. A recent magneto-Raman investigations on MoS2 published by J. Ji etal reported an observation of giant magneto-optical effect. In this work, the intensity of Raman modes exhibited dramatic change in intensities and was attributed to field-induced broken symmetry on Raman scattering cross-section. Due to the ambiguous nature of the interpretation presented in this publication, we performed further Raman studies on MoS2 at high magnetic fields to illustrate the experimental factors overlooked by the previous study. It is highly important to consider the magnetic field-induced rotation of the polarization of the light and its effect on the Raman active phonon modes in anisotropic materials. A detailed report of our magneto-Raman experiments and their outcomes will be presented.

An internally consistent pressure calibration of geobarometers applicable to the Earth’s upper mantle using in situ XRD

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

Beyer, Christopher; Rosenthal, Anja; Myhill, Robert

We have performed an experimental cross calibration of a suite of mineral equilibria within mantle rock bulk compositions that are commonly used in geobarometry to determine the equilibration depths of upper mantle assemblages. Multiple barometers were compared simultaneously in experimental runs, where the pressure was determined using in-situ measurements of the unit cell volumes of MgO, NaCl, Re and h-BN between 3.6 and 10.4 GPa, and 1250 and 1500 °C. The experiments were performed in a large volume press (LVPs) in combination with synchrotron X-ray diffraction. Noble metal capsules drilled with multiple sample chambers were loaded with a range ofmore » bulk compositions representative of peridotite, eclogite and pyroxenite lithologies. By this approach, we simultaneously calibrated the geobarometers applicable to different mantle lithologies under identical and well determined pressure and temperature conditions. We identified discrepancies between the calculated and experimental pressures for which we propose simple linear or constant correction factors to some of the previously published barometric equations. As a result, we establish internally-consistent cross-calibrations for a number of garnet-orthopyroxene, garnet-clinopyroxene, Ca-Tschermaks-in-clinopyroxene and majorite geobarometers.« less

Validation of columnar CsI x-ray detector responses obtained with hybridMANTIS, a CPU-GPU Monte Carlo code for coupled x-ray, electron, and optical transport

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

Sharma, Diksha; Badano, Aldo

2013-03-15

Purpose: hybridMANTIS is a Monte Carlo package for modeling indirect x-ray imagers using columnar geometry based on a hybrid concept that maximizes the utilization of available CPU and graphics processing unit processors in a workstation. Methods: The authors compare hybridMANTIS x-ray response simulations to previously published MANTIS and experimental data for four cesium iodide scintillator screens. These screens have a variety of reflective and absorptive surfaces with different thicknesses. The authors analyze hybridMANTIS results in terms of modulation transfer function and calculate the root mean square difference and Swank factors from simulated and experimental results. Results: The comparison suggests thatmore » hybridMANTIS better matches the experimental data as compared to MANTIS, especially at high spatial frequencies and for the thicker screens. hybridMANTIS simulations are much faster than MANTIS with speed-ups up to 5260. Conclusions: hybridMANTIS is a useful tool for improved description and optimization of image acquisition stages in medical imaging systems and for modeling the forward problem in iterative reconstruction algorithms.« less

Meta-analyses of animal studies: an introduction of a valuable instrument to further improve healthcare.

PubMed

Hooijmans, Carlijn R; IntHout, Joanna; Ritskes-Hoitinga, Merel; Rovers, Maroeska M

2014-01-01

In research aimed at improving human health care, animal studies still play a crucial role, despite political and scientific efforts to reduce preclinical experimentation in laboratory animals. In animal studies, the results and their interpretation are not always straightforward, as no single study is executed perfectly in all steps. There are several possible sources of bias, and many animal studies are replicates of studies conducted previously. Use of meta-analysis to combine the results of studies may lead to more reliable conclusions and a reduction of unnecessary duplication of animal studies. In addition, due to the more exploratory nature of animal studies as compared to clinical trials, meta-analyses of animal studies have greater potential in exploring possible sources of heterogeneity. There is an abundance of literature on how to perform meta-analyses on clinical data. Animal studies, however, differ from clinical studies in some aspects, such as the diversity of animal species studied, experimental design, and study characteristics. In this paper, we will discuss the main principles and practices for meta-analyses of experimental animal studies. © The Author 2014. Published by Oxford University Press.

Experimental approach for thermal parameters estimation during glass forming process

NASA Astrophysics Data System (ADS)

Abdulhay, B.; Bourouga, B.; Alzetto, F.; Challita, C.

2016-10-01

In this paper, an experimental device designed and developedto estimate thermal conditions at the Glass / piston contact interface is presented. This deviceis made of two parts: the upper part contains the piston made of metal and a heating device to raise the temperature of the piston up to 500 °C. The lower part is composed of a lead crucible and a glass sample. The assembly is provided with a heating system, an induction furnace of 6 kW for heating the glass up to 950 °C.The developed experimental procedure has permitted in a previous published study to estimate the Thermal Contact ResistanceTCR using the inverse technique developed by Beck [1]. The semi-transparent character of the glass has been taken into account by an additional radiative heat flux and an equivalent thermal conductivity. After the set-up tests, reproducibility experiments for a specific contact pressure have been carried outwith a maximum dispersion that doesn't exceed 6%. Then, experiments under different conditions for a specific glass forming process regarding the application (Packaging, Buildings and Automobile) were carried out. The objective is to determine, experimentallyfor each application,the typical conditions capable to minimize the glass temperature loss during the glass forming process.

Computer modeling of obesity links theoretical energetic measures with experimental measures of fuel use for lean and obese men.

PubMed

Rossow, Heidi A; Calvert, C Chris

2014-10-01

The goal of this research was to use a computational model of human metabolism to predict energy metabolism for lean and obese men. The model is composed of 6 state variables representing amino acids, muscle protein, visceral protein, glucose, triglycerides, and fatty acids (FAs). Differential equations represent carbohydrate, amino acid, and FA uptake and output by tissues based on ATP creation and use for both lean and obese men. Model parameterization is based on data from previous studies. Results from sensitivity analyses indicate that model predictions of resting energy expenditure (REE) and respiratory quotient (RQ) are dependent on FA and glucose oxidation rates with the highest sensitivity coefficients (0.6, 0.8 and 0.43, 0.15, respectively, for lean and obese models). Metabolizable energy (ME) is influenced by ingested energy intake with a sensitivity coefficient of 0.98, and a phosphate-to-oxygen ratio by FA oxidation rate and amino acid oxidation rate (0.32, 0.24 and 0.55, 0.65 for lean and obese models, respectively). Simulations of previously published studies showed that the model is able to predict ME ranging from 6.6 to 9.3 with 0% differences between published and model values, and RQ ranging from 0.79 to 0.86 with 1% differences between published and model values. REEs >7 MJ/d are predicted with 6% differences between published and model values. Glucose oxidation increases by ∼0.59 mol/d, RQ increases by 0.03, REE increases by 2 MJ/d, and heat production increases by 1.8 MJ/d in the obese model compared with lean model simulations. Increased FA oxidation results in higher changes in RQ and lower relative changes in REE. These results suggest that because fat mass is directly related to REE and rate of FA oxidation, body fat content could be used as a predictor of RQ. © 2014 American Society for Nutrition.

Book review: The Wilderness Debate Rages On: Continuing the Great New Wilderness Debate

Treesearch

Peter Landres

2009-01-01

The Wilderness Debate Rages On is a collection of mostly previously published papers about the meaning, value, and role of wilderness and continues the discussion that was propelled by the editors' previous book The Great New Wilderness Debate (also a collection of papers) published in 1998. The editors state that this sequel to their previous book is mandated...

Hydrodynamic and Chemical Factors in Clogging by Montmorillonite in Porous Media

PubMed Central

Mays, David C.; Hunt, James R.

2008-01-01

Clogging by colloid deposits is important in water treatment filters, groundwater aquifers, and petroleum reservoirs. The complexity of colloid deposition and deposit morphology preclude models based on first principles, so this study extends an empirical approach to quantify clogging using a simple, one-parameter model. Experiments were conducted with destabilized suspensions of sodium- and calcium-montmorillonite to quantify the hydrodynamic and chemical factors important in clogging. Greater clogging is observed at slower fluid velocity, consistent with previous investigations. However, calcium-montmorillonite causes one order of magnitude less clogging per mass of deposited particles compared to sodium-montmorillonite or a previously published summary of clogging in model granular media. Steady state conditions, in which the permeability and the quantity of deposited material are both constant, were not observed, even though the experimental conditions were optimized for that purpose. These results indicate that hydrodynamic aspects of clogging by these natural materials are consistent with those of simplified model systems, and they demonstrate significant chemical effects on clogging for fully destabilized montmorillonite clay. PMID:17874771

Thermal Rate Coefficients for the Astrochemical Process C + CH+ → C2+ + H by Ring Polymer Molecular Dynamics.

PubMed

Rampino, Sergio; Suleimanov, Yury V

2016-12-22

Thermal rate coefficients for the astrochemical reaction C + CH + → C 2 + + H were computed in the temperature range 20-300 K by using novel rate theory based on ring polymer molecular dynamics (RPMD) on a recently published bond-order based potential energy surface and compared with previous Langevin capture model (LCM) and quasi-classical trajectory (QCT) calculations. Results show that there is a significant discrepancy between the RPMD rate coefficients and the previous theoretical results that can lead to overestimation of the rate coefficients for the title reaction by several orders of magnitude at very low temperatures. We argue that this can be attributed to a very challenging energy profile along the reaction coordinate for the title reaction, not taken into account in extenso by either the LCM or QCT approximation. In the absence of any rigorous quantum mechanical or experimental results, the computed RPMD rate coefficients represent state-of-the-art estimates to be included in astrochemical databases and kinetic networks.

Hydrodynamic and chemical factors in clogging by montmorillonite in porous media.

PubMed

Mays, David C; Hunt, James R

2007-08-15

Clogging by colloid deposits is important in water treatment filters, groundwater aquifers, and petroleum reservoirs. The complexity of colloid deposition and deposit morphology preclude models based on first principles, so this study extends an empirical approach to quantify clogging using a simple, one-parameter model. Experiments were conducted with destabilized suspensions of sodium- and calcium-montmorillonite to quantify the hydrodynamic and chemical factors important in clogging. Greater clogging is observed at slower fluid velocity, consistent with previous investigations. However, calcium-montmorillonite causes 1 order of magnitude less clogging per mass of deposited particles compared to sodium-montmorillonite or a previously published summary of clogging in model granular media. Steady-state conditions, in which the permeability and the quantity of deposited material are both constant, were not observed, even though the experimental conditions were optimized for that purpose. These results indicate that hydrodynamic aspects of clogging by these natural materials are consistent with those of simplified model systems, and they demonstrate significant chemical effects on clogging for fully destabilized montmorillonite clay.

Simplified and economical 2D IR spectrometer design using a dual acousto-optic modulator

PubMed Central

Skoff, David R.; Laaser, Jennifer E.; Mukherjee, Sudipta S.; Middleton, Chris T.; Zanni, Martin T.

2012-01-01

Over the last decade two-dimensional infrared (2D IR) spectroscopy has proven to be a very useful extension of infrared spectroscopy, yet the technique remains restricted to a small group of specialized researchers because of its experimental complexity and high equipment cost. We report on a spectrometer that is compact, mechanically robust, and is much less expensive than previous designs because it uses a single pixel MCT detector rather than an array detector. Moreover, each axis of the spectrum can be collected in either the time or frequency domain via computer programming. We discuss pulse sequences for scanning the probe axis, which were not previously possible. We present spectra on metal carbonyl compounds at 5 µm and a model peptide at 6 µm. Data collection with a single pixel MCT takes longer than using an array detector, but publishable quality data are still achieved with only a few minutes of averaging. PMID:24659850

Resting-state functional connectivity assessed with two diffuse optical tomographic systems.

PubMed

Niu, Haijing; Khadka, Sabin; Tian, Fenghua; Lin, Zi-Jing; Lu, Chunming; Zhu, Chaozhe; Liu, Hanli

2011-04-01

Functional near-infrared spectroscopy (fNIRS) is recently utilized as a new approach to assess resting-state functional connectivity (RSFC) in the human brain. For any new technique or new methodology, it is necessary to be able to replicate similar experiments using different instruments in order to establish its liability and reproducibility. We apply two different diffuse optical tomographic (DOT) systems (i.e., DYNOT and CW5), with various probe arrangements to evaluate RSFC in the sensorimotor cortex by utilizing a previously published experimental protocol and seed-based correlation analysis. Our results exhibit similar spatial patterns and strengths in RSFC between the bilateral motor cortexes. The consistent observations are obtained from both DYNOT and CW5 systems, and are also in good agreement with the previous fNIRS study. Overall, we demonstrate that the fNIRS-based RSFC is reproducible by various DOT imaging systems among different research groups, enhancing the confidence of neuroscience researchers and clinicians to utilize fNIRS for future applications.

Review of Research Reporting Guidelines for Radiology Researchers.

PubMed

Cronin, Paul; Rawson, James V

2016-05-01

Prior articles have reviewed reporting guidelines and study evaluation tools for clinical research. However, only some of the many available accepted reporting guidelines at the Enhancing the QUAlity and Transparency Of health Research Network have been discussed in previous reports. In this paper, we review the key Enhancing the QUAlity and Transparency Of health Research reporting guidelines that have not been previously discussed. The study types include diagnostic and prognostic studies, reliability and agreement studies, observational studies, analytical and descriptive, experimental studies, quality improvement studies, qualitative research, health informatics, systematic reviews and meta-analyses, economic evaluations, and mixed methods studies. There are also sections on study protocols, and statistical analyses and methods. In each section, there is a brief overview of the study type, and then the reporting guideline(s) that are most applicable to radiology researchers including radiologists involved in health services research are discussed. Copyright © 2016 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

Comparison of the thermal stabilization of proteins by oligosaccharides and monosaccharide mixtures: Measurement and analysis in the context of excluded volume theory.

PubMed

Beg, Ilyas; Minton, Allen P; Islam, Asimul; Hassan, Md Imtaiyaz; Ahmad, Faizan

2018-06-01

The thermal stability of apo α-lactalbumin (α-LA) and lysozyme was measured in the presence of mixtures of glucose, fructose, and galactose. Mixtures of these monosaccharides in the appropriate stoichiometric ratio were found to have a greater stabilizing effect on each of the two proteins than equal weight/volume concentrations of di- tri- and tetrasaccharides with identical subunit composition (sucrose, trehalose, raffinose, and stachyose). The excluded volume model for the effect of a single saccharide on the stability of a protein previously proposed by Beg et al. [Biochemistry 54 (2015) 3594] was extended to treat the case of saccharide mixtures. The extended model predicts quantitatively the stabilizing effect of all monosaccharide mixtures on α-LA and lysozyme reported here, as well as previously published results obtained for ribonuclease A [Biophys. Chem. 138 (2008) 120] to within experimental uncertainty. Copyright © 2018 Elsevier B.V. All rights reserved.

Pathway Activity Profiling (PAPi): from the metabolite profile to the metabolic pathway activity.

PubMed

Aggio, Raphael B M; Ruggiero, Katya; Villas-Bôas, Silas Granato

2010-12-01

Metabolomics is one of the most recent omics-technologies and uses robust analytical techniques to screen low molecular mass metabolites in biological samples. It has evolved very quickly during the last decade. However, metabolomics datasets are considered highly complex when used to relate metabolite levels to metabolic pathway activity. Despite recent developments in bioinformatics, which have improved the quality of metabolomics data, there is still no straightforward method capable of correlating metabolite level to the activity of different metabolic pathways operating within the cells. Thus, this kind of analysis still depends on extremely laborious and time-consuming processes. Here, we present a new algorithm Pathway Activity Profiling (PAPi) with which we are able to compare metabolic pathway activities from metabolite profiles. The applicability and potential of PAPi was demonstrated using a previously published data from the yeast Saccharomyces cerevisiae. PAPi was able to support the biological interpretations of the previously published observations and, in addition, generated new hypotheses in a straightforward manner. However, PAPi is time consuming to perform manually. Thus, we also present here a new R-software package (PAPi) which implements the PAPi algorithm and facilitates its usage to quickly compare metabolic pathways activities between different experimental conditions. Using the identified metabolites and their respective abundances as input, the PAPi package calculates pathways' Activity Scores, which represents the potential metabolic pathways activities and allows their comparison between conditions. PAPi also performs principal components analysis and analysis of variance or t-test to investigate differences in activity level between experimental conditions. In addition, PAPi generates comparative graphs highlighting up- and down-regulated pathway activity. These datasets are available in http://www.4shared.com/file/hTWyndYU/extra.html and http://www.4shared.com/file/VbQIIDeu/intra.html. PAPi package is available in: http://www.4shared.com/file/s0uIYWIg/PAPi_10.html s.villas-boas@auckland.ac.nz Supplementary data are available at Bioinformatics online.

Milk-derived or recombinant transforming growth factor-beta has effects on immunological outcomes: a review of evidence from animal experimental studies.

PubMed

Oddy, W H; McMahon, R J

2011-06-01

Identified factors from milk have been shown to improve health outcomes. One specific factor, transforming growth factor-Beta (TGF)-β, has been identified previously as having the potential to impact on immunological outcomes in the newborn offspring. The primary objective of this review was to examine the published studies that have considered TGF-β in association with immunological outcomes of experimental models. We hypothesized that oral administration of TGF-β (through human milk, cow's milk, infant formula) or recombinant TGF-β delivered via gavage, may down-regulate immune activation in newborn offspring. Animal experimental studies were identified through MEDLINE, CAB Abstracts, Biological Abstracts and Scopus. Selection criteria included well-described animal populations, sample and study design, source of TGF-β, age and immunological outcomes measured and effect size. The findings were summarized temporally in tabular format, giving an overall measure of effect based on the literature available since 1994. Animal experimental studies (n=13) were included in the review to determine an association between maternal TGF-β and immunological outcomes. Overall 92% of these studies (12/13) showed a positive association with TGF-β1 or TGF-β2, demonstrating protection against immunologically related outcomes in early life in an animal model. TGF-β is important in developing and maintaining appropriate immune responses in the offspring. TGF-β delivered orally to neonatal animals provides protection against adverse immunological outcomes, corroborating and supporting findings from human studies. Animal studies provide important clues to the pathogenesis and therapeutics of immune activation and allergy in early childhood. TGF-βs are important growth factors involved in maintaining homeostasis in the intestine, regulating inflammation and allergy development and promoting oral tolerance in infants. Thus, taken as a whole, these and our other findings suggest that this cytokine in milk may influence the development of immunological outcomes in offspring. © 2011 Blackwell Publishing Ltd.

Integrated computational model of the bioenergetics of isolated lung mitochondria

PubMed Central

Zhang, Xiao; Jacobs, Elizabeth R.; Camara, Amadou K. S.; Clough, Anne V.

2018-01-01

Integrated computational modeling provides a mechanistic and quantitative framework for describing lung mitochondrial bioenergetics. Thus, the objective of this study was to develop and validate a thermodynamically-constrained integrated computational model of the bioenergetics of isolated lung mitochondria. The model incorporates the major biochemical reactions and transport processes in lung mitochondria. A general framework was developed to model those biochemical reactions and transport processes. Intrinsic model parameters such as binding constants were estimated using previously published isolated enzymes and transporters kinetic data. Extrinsic model parameters such as maximal reaction and transport velocities were estimated by fitting the integrated bioenergetics model to published and new tricarboxylic acid cycle and respirometry data measured in isolated rat lung mitochondria. The integrated model was then validated by assessing its ability to predict experimental data not used for the estimation of the extrinsic model parameters. For example, the model was able to predict reasonably well the substrate and temperature dependency of mitochondrial oxygen consumption, kinetics of NADH redox status, and the kinetics of mitochondrial accumulation of the cationic dye rhodamine 123, driven by mitochondrial membrane potential, under different respiratory states. The latter required the coupling of the integrated bioenergetics model to a pharmacokinetic model for the mitochondrial uptake of rhodamine 123 from buffer. The integrated bioenergetics model provides a mechanistic and quantitative framework for 1) integrating experimental data from isolated lung mitochondria under diverse experimental conditions, and 2) assessing the impact of a change in one or more mitochondrial processes on overall lung mitochondrial bioenergetics. In addition, the model provides important insights into the bioenergetics and respiration of lung mitochondria and how they differ from those of mitochondria from other organs. To the best of our knowledge, this model is the first for the bioenergetics of isolated lung mitochondria. PMID:29889855

Integrated computational model of the bioenergetics of isolated lung mitochondria.

PubMed

Zhang, Xiao; Dash, Ranjan K; Jacobs, Elizabeth R; Camara, Amadou K S; Clough, Anne V; Audi, Said H

2018-01-01

Integrated computational modeling provides a mechanistic and quantitative framework for describing lung mitochondrial bioenergetics. Thus, the objective of this study was to develop and validate a thermodynamically-constrained integrated computational model of the bioenergetics of isolated lung mitochondria. The model incorporates the major biochemical reactions and transport processes in lung mitochondria. A general framework was developed to model those biochemical reactions and transport processes. Intrinsic model parameters such as binding constants were estimated using previously published isolated enzymes and transporters kinetic data. Extrinsic model parameters such as maximal reaction and transport velocities were estimated by fitting the integrated bioenergetics model to published and new tricarboxylic acid cycle and respirometry data measured in isolated rat lung mitochondria. The integrated model was then validated by assessing its ability to predict experimental data not used for the estimation of the extrinsic model parameters. For example, the model was able to predict reasonably well the substrate and temperature dependency of mitochondrial oxygen consumption, kinetics of NADH redox status, and the kinetics of mitochondrial accumulation of the cationic dye rhodamine 123, driven by mitochondrial membrane potential, under different respiratory states. The latter required the coupling of the integrated bioenergetics model to a pharmacokinetic model for the mitochondrial uptake of rhodamine 123 from buffer. The integrated bioenergetics model provides a mechanistic and quantitative framework for 1) integrating experimental data from isolated lung mitochondria under diverse experimental conditions, and 2) assessing the impact of a change in one or more mitochondrial processes on overall lung mitochondrial bioenergetics. In addition, the model provides important insights into the bioenergetics and respiration of lung mitochondria and how they differ from those of mitochondria from other organs. To the best of our knowledge, this model is the first for the bioenergetics of isolated lung mitochondria.

Experimental Study of the Richtmyer-Meshkov Instability of Incompressible Fluids

NASA Technical Reports Server (NTRS)

Niederhaus, Charles; Jacobs, Jeffrey W.

2002-01-01

The Richtmyer-Meshkov instability of a low Atwood number, miscible, two-liquid system is investigated experimentally. The initially stratified fluids are contained within a rectangular tank mounted to a sled that rides on a vertical set of rails. The instability is generated by dropping the sled onto a coil spring, producing a nearly impulsive upward acceleration. The subsequent freefall that occurs as the container travels upward and then downward on the rails allows the instability to evolve in the absence of gravity. The interface separating the two liquids initially has a well-defined, sinusoidal perturbation that quickly inverts and then grows in amplitude after undergoing the impulsive acceleration. Disturbance amplitudes are measured and compared to theoretical predictions. Linear stability theory gives excellent agreement with the measured initial growth rate, a(sub 0), for single-mode perturbations with the predicted amplitudes differing by less than 10% from experimental measurements up to a nondimensional time ka(sub 0)t = 0.7, where k is the wavenumber. Linear stability theory also provides excellent agreement for the individual mode amplitudes of multi-mode initial perturbations up until the interface becomes multi-valued. Comparison with previously published weakly nonlinear single-mode models shows good agreement up to ka(sub 0)t = 3, while published nonlinear single-mode models provide good agreement up to ka(sub 0)t = 30. The effects of Reynolds number on the vortex core evolution and overall growth rate of the interface are also investigated. Measurements of the overall amplitude are found to be unaffected by the Reynolds number for the range of values studied here. However, experiments carried out at lower values of Reynolds numbers were found to have decreased vortex core rotation rates. In addition, an instability in the vortex cores is observed.

Single subject controlled experiments in aphasia: The science and the state of the science

PubMed Central

Thompson, Cynthia K.

2007-01-01

This paper discusses the use of single subject controlled experimental designs for investigating the effect of treatment for aphasia. A brief historical perspective is presented, followed by discussions of the advantages and disadvantages of single subject and group approaches, the basic requirements of single subject experimental research, and crucial considerations in design selection. In the final sections, results of reviews of published single subject controlled experiments are discussed, with emphasis on internal validity issues, the number of participants enrolled in published studies, operational specification of the dependent and independent variables, and reliability of measurement. Learning outcomes As a result of reading this paper, the participant will: (1) understand the mechanisms required for demonstration of internal and external validity using single subject controlled experimental designs, (2) become familiar with the basic requirements of single subject controlled experimental research, (3) understand the types of single subject controlled experimental designs that are the most appropriate for studying the effects of treatment for aphasia, and (4) become familiar with trends in the published aphasia treatment literature in which single subject controlled experimental designs have been used. PMID:16635494

Effects of linking a soil-water-balance model with a groundwater-flow model

USGS Publications Warehouse

Stanton, Jennifer S.; Ryter, Derek W.; Peterson, Steven M.

2013-01-01

A previously published regional groundwater-flow model in north-central Nebraska was sequentially linked with the recently developed soil-water-balance (SWB) model to analyze effects to groundwater-flow model parameters and calibration results. The linked models provided a more detailed spatial and temporal distribution of simulated recharge based on hydrologic processes, improvement of simulated groundwater-level changes and base flows at specific sites in agricultural areas, and a physically based assessment of the relative magnitude of recharge for grassland, nonirrigated cropland, and irrigated cropland areas. Root-mean-squared (RMS) differences between the simulated and estimated or measured target values for the previously published model and linked models were relatively similar and did not improve for all types of calibration targets. However, without any adjustment to the SWB-generated recharge, the RMS difference between simulated and estimated base-flow target values for the groundwater-flow model was slightly smaller than for the previously published model, possibly indicating that the volume of recharge simulated by the SWB code was closer to actual hydrogeologic conditions than the previously published model provided. Groundwater-level and base-flow hydrographs showed that temporal patterns of simulated groundwater levels and base flows were more accurate for the linked models than for the previously published model at several sites, particularly in agricultural areas.

The Traditional Scholarly Journal Publishers Legitimize the Web.

ERIC Educational Resources Information Center

Peek, Robin; Pomerantz, Jeffrey; Paling, Stephen

1998-01-01

Examines the entry of the major academic publishing houses into World Wide Web publishing. Suggests that early experimentation in Web publishing began unevenly with areas that needed improvement. Concludes with a discussion about the implications of the traditional academic publisher's presence on the Web. (Author/AEF)

Developments in the field of allergy in 2011 through the eyes of Clinical and Experimental Allergy.

PubMed

Arshad, S H; Dharmage, S C; Ferreira, F; Fixman, E D; Gadermaier, G; Hauser, M; Sampson, A P; Teran, L M; Wallner, M; Wardlaw, A J

2012-12-01

As in previous years, we felt it would be of value to our readership to summarize the new information provided by the authors who have published in Clinical and Experimental Allergy in 2011 and set this in the context of recent advances in our understanding of the pathogenesis and management of allergic disease in all its many manifestations. In 2011, about 210 articles were published in Clinical and Experimental Allergy including editorials, reviews, opinion articles, guidelines, letters, book reviews and of course at the heart of the journal, papers containing original data. As before, this review is divided into sections based on the way the journal is structured, although this year we have grouped together all the papers dealing with mechanisms of allergic disease, whether they involve patients (clinical mechanisms), pure in vitro studies (basic mechanisms) or animal models (experimental models), as we felt this was a more coherent way to deal with the subject. In the field of asthma and rhinitis, the relationship between airway inflammation and airway dysfunction was of perennial interest to investigators, as were phenotypes and biomarkers. Aspirin hypersensitivity appeared in studies in several papers and there was new interest in asthma in the elderly. The mechanisms involved in allergic disease describe advances in our understanding of T cell responses, the relationship between inflammation and disease, mast cell and basophil activation, steroid resistance and novel therapies. In the section dealing with epidemiology, studies seeking to identify risk factors for allergic disease including vitamin D are prominent, as once again are studies investigating gene-environment interactions. The clinical allergy section focuses on drug allergy, food allergy and immunotherapy. The area of oral immunotherapy for food allergy is well covered and we were grateful to Stephen Durham for guest editing an outstanding special issue on immunotherapy in the centenary year of Leonard Noon's pioneering work. Lastly, in the field of allergens, the interest in component-resolved diagnosis continues to grow and there are also articles describing important novel cultivars and the effect of food processing on the allergenic properties of foods. Another terrific year, full of important and high-quality work,which the journal has been proud to bring to the allergy community. © 2012 Blackwell Publishing Ltd.

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach.

PubMed

Henriques, David; Rocha, Miguel; Saez-Rodriguez, Julio; Banga, Julio R

2015-09-15

Systems biology models can be used to test new hypotheses formulated on the basis of previous knowledge or new experimental data, contradictory with a previously existing model. New hypotheses often come in the shape of a set of possible regulatory mechanisms. This search is usually not limited to finding a single regulation link, but rather a combination of links subject to great uncertainty or no information about the kinetic parameters. In this work, we combine a logic-based formalism, to describe all the possible regulatory structures for a given dynamic model of a pathway, with mixed-integer dynamic optimization (MIDO). This framework aims to simultaneously identify the regulatory structure (represented by binary parameters) and the real-valued parameters that are consistent with the available experimental data, resulting in a logic-based differential equation model. The alternative to this would be to perform real-valued parameter estimation for each possible model structure, which is not tractable for models of the size presented in this work. The performance of the method presented here is illustrated with several case studies: a synthetic pathway problem of signaling regulation, a two-component signal transduction pathway in bacterial homeostasis, and a signaling network in liver cancer cells. Supplementary data are available at Bioinformatics online. julio@iim.csic.es or saezrodriguez@ebi.ac.uk. © The Author 2015. Published by Oxford University Press.

Novel de novo variant in EBF3 is likely to impact DNA binding in a patient with a neurodevelopmental disorder and expanded phenotypes: patient report, in silico functional assessment, and review of published cases.

PubMed

Blackburn, Patrick R; Barnett, Sarah S; Zimmermann, Michael T; Cousin, Margot A; Kaiwar, Charu; Pinto E Vairo, Filippo; Niu, Zhiyv; Ferber, Matthew J; Urrutia, Raul A; Selcen, Duygu; Klee, Eric W; Pichurin, Pavel N

2017-05-01

Pathogenic variants in EBF3 were recently described in three back-to-back publications in association with a novel neurodevelopmental disorder characterized by intellectual disability, speech delay, ataxia, and facial dysmorphisms. In this report, we describe an additional patient carrying a de novo missense variant in EBF3 (c.487C>T, p.(Arg163Trp)) that falls within a conserved residue in the zinc knuckle motif of the DNA binding domain. Without a solved structure of the DNA binding domain, we generated a homology-based atomic model and performed molecular dynamics simulations for EBF3, which predicted decreased DNA affinity for p.(Arg163Trp) compared with wild-type protein and control variants. These data are in agreement with previous experimental studies of EBF1 showing the paralogous residue is essential for DNA binding. The conservation and experimental evidence existing for EBF1 and in silico modeling and dynamics simulations to validate comparable behavior of multiple variants in EBF3 demonstrates strong support for the pathogenicity of p.(Arg163Trp). We show that our patient presents with phenotypes consistent with previously reported patients harboring EBF3 variants and expands the phenotypic spectrum of this newly identified disorder with the additional feature of a bicornuate uterus.

Modeling As(III) oxidation and removal with iron electrocoagulation in groundwater.

PubMed

Li, Lei; van Genuchten, Case M; Addy, Susan E A; Yao, Juanjuan; Gao, Naiyun; Gadgil, Ashok J

2012-11-06

Understanding the chemical kinetics of arsenic during electrocoagulation (EC) treatment is essential for a deeper understanding of arsenic removal using EC under a variety of operating conditions and solution compositions. We describe a highly constrained, simple chemical dynamic model of As(III) oxidation and As(III,V), Si, and P sorption for the EC system using model parameters extracted from some of our experimental results and previous studies. Our model predictions agree well with both data extracted from previous studies and our observed experimental data over a broad range of operating conditions (charge dosage rate) and solution chemistry (pH, co-occurring ions) without free model parameters. Our model provides insights into why higher pH and lower charge dosage rate (Coulombs/L/min) facilitate As(III) removal by EC and sheds light on the debate in the recent published literature regarding the mechanism of As(III) oxidation during EC. Our model also provides practically useful estimates of the minimum amount of iron required to remove 500 μg/L As(III) to <50 μg/L. Parameters measured in this work include the ratio of rate constants for Fe(II) and As(III) reactions with Fe(IV) in synthetic groundwater (k(1)/k(2) = 1.07) and the apparent rate constant of Fe(II) oxidation with dissolved oxygen at pH 7 (k(app) = 10(0.22) M(-1)s(-1)).

Inelastic neutron scattering spectrum of cyclotrimethylenetrinitramine: a comparison with solid-state electronic structure calculations.

PubMed

Ciezak, Jennifer A; Trevino, S F

2006-04-20

Solid-state geometry optimizations and corresponding normal-mode analysis of the widely used energetic material cyclotrimethylenetrinitramine (RDX) were performed using density functional theory with both the generalized gradient approximation (BLYP and BP functionals) and the local density approximation (PWC and VWN functionals). The structural results were found to be in good agreement with experimental neutron diffraction data and previously reported calculations based on the isolated-molecule approximation. The vibrational inelastic neutron scattering (INS) spectrum of polycrystalline RDX was measured and compared with simulated INS constructed from the solid-state calculations. The vibrational frequencies calculated from the solid-state methods had average deviations of 10 cm(-1) or less, whereas previously published frequencies based on an isolated-molecule approximation had deviations of 65 cm(-1) or less, illustrating the importance of including crystalline forces. On the basis of the calculations and analysis, it was possible to assign the normal modes and symmetries, which agree well with previous assignments. Four possible "doorway modes" were found in the energy range defined by the lattice modes, which were all found to contain fundamental contributions from rotation of the nitro groups.

Quantifying sources of methane using light alkanes in the Los Angeles basin, California

NASA Astrophysics Data System (ADS)

Peischl, J.; Ryerson, T. B.; Brioude, J.; Aikin, K. C.; Andrews, A. E.; Atlas, E.; Blake, D.; Daube, B. C.; de Gouw, J. A.; Dlugokencky, E.; Frost, G. J.; Gentner, D. R.; Gilman, J. B.; Goldstein, A. H.; Harley, R. A.; Holloway, J. S.; Kofler, J.; Kuster, W. C.; Lang, P. M.; Novelli, P. C.; Santoni, G. W.; Trainer, M.; Wofsy, S. C.; Parrish, D. D.

2013-05-01

Methane (CH4), carbon dioxide (CO2), carbon monoxide (CO), and C2-C5 alkanes were measured throughout the Los Angeles (L.A.) basin in May and June 2010. We use these data to show that the emission ratios of CH4/CO and CH4/CO2 in the L.A. basin are larger than expected from population-apportioned bottom-up state inventories, consistent with previously published work. We use experimentally determined CH4/CO and CH4/CO2 emission ratios in combination with annual State of California CO and CO2 inventories to derive a yearly emission rate of CH4 to the L.A. basin. We further use the airborne measurements to directly derive CH4 emission rates from dairy operations in Chino, and from the two largest landfills in the L.A. basin, and show these sources are accurately represented in the California Air Resources Board greenhouse gas inventory for CH4. We then use measurements of C2-C5 alkanes to quantify the relative contribution of other CH4 sources in the L.A. basin, with results differing from those of previous studies. The atmospheric data are consistent with the majority of CH4 emissions in the region coming from fugitive losses from natural gas in pipelines and urban distribution systems and/or geologic seeps, as well as landfills and dairies. The local oil and gas industry also provides a significant source of CH4 in the area. The addition of CH4 emissions from natural gas pipelines and urban distribution systems and/or geologic seeps and from the local oil and gas industry is sufficient to account for the differences between the top-down and bottom-up CH4 inventories identified in previously published work.

Impact of intervention on breastfeeding outcomes and determinants based on theory of planned behavior.

PubMed

Zhu, Yu; Zhang, Zhihong; Ling, Yun; Wan, Hongwei

2017-04-01

Breastfeeding knowledge, attitude, subjective norm, and perceived control are significant determinants of breastfeeding, according to the theory of planned behavior (TPB). However, evidence concerning the effectiveness of the TPB-based intervention in breastfeeding promotion is sparse. Meanwhile, the changes of these determinants with time have not been examined in previous studies. To investigate the effectiveness of the TPB-based intervention program in improving exclusive breastfeeding, and the interaction of time and intervention on these determinants of breastfeeding. 285 primiparous mothers were included, with 157 mothers in the experimental group and 128 mothers in the control group. The experimental group received the TPB-based intervention program delivered during 6 weeks postpartum, while both the experimental and control groups received the standard obstetric care. Scores of breastfeeding knowledge, attitude and breastfeeding control increased with time from baseline to 6 weeks postpartum, while breastfeeding subjective norm decreased at 6 weeks both in the experimental and the control groups. Besides, scores of the four determinants were significantly higher in the experimental group than these in the control group at 3days and 6 weeks, except for breastfeeding control at 6 weeks, which resulted in the higher exclusive breastfeeding rates at 3days and 6 weeks in the experimental group than the control group. The TPB-based intervention was effective in promoting exclusive breastfeeding during 6 weeks postpartum. Future interventions are recommended to adjust intervention strategies with time, and give more focus on providing continued breastfeeding support after discharge. Copyright © 2016 Australian College of Midwives. Published by Elsevier Ltd. All rights reserved.

Experimental conformational energy maps of proteins and peptides.

PubMed

Balaji, Govardhan A; Nagendra, H G; Balaji, Vitukudi N; Rao, Shashidhar N

2017-06-01

We have presented an extensive analysis of the peptide backbone dihedral angles in the PDB structures and computed experimental Ramachandran plots for their distributions seen under a various constraints on X-ray resolution, representativeness at different sequence identity percentages, and hydrogen bonding distances. These experimental distributions have been converted into isoenergy contour plots using the approach employed previously by F. M. Pohl. This has led to the identification of energetically favored minima in the Ramachandran (ϕ, ψ) plots in which global minima are predominantly observed either in the right-handed α-helical or the polyproline II regions. Further, we have identified low energy pathways for transitions between various minima in the (ϕ,ψ) plots. We have compared and presented the experimental plots with published theoretical plots obtained from both molecular mechanics and quantum mechanical approaches. In addition, we have developed and employed a root mean square deviation (RMSD) metric for isoenergy contours in various ranges, as a measure (in kcal.mol -1 ) to compare any two plots and determine the extent of correlation and similarity between their isoenergy contours. In general, we observe a greater degree of compatibility with experimental plots for energy maps obtained from molecular mechanics methods compared to most quantum mechanical methods. The experimental energy plots we have investigated could be helpful in refining protein structures obtained from X-ray, NMR, and electron microscopy and in refining force field parameters to enable simulations of peptide and protein structures that have higher degree of consistency with experiments. Proteins 2017; 85:979-1001. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Are C-reps contextual representations? A reply to Brewin and Burgess.

PubMed

Pearson, David G

2014-03-01

Brewin and Burgess (2013) argue that our recent papers investigating the role of contextual representations in intrusive memories do not pose a challenge to dual-representation theory as originally claimed (Pearson, 2012; Pearson, Ross, & Webster, 2012). Here I point out that their alternative explanation for our results can be rejected using data already published in both papers. I also argue that their definition of what constitutes a contextual representation renders their revised dual-representation theory incompatible with experimental results that have previously been argued in the literature to support it. Valuable though their contribution is, it does not impact on our main conclusion that abstract contextual representations serve to increase intrusive memories for traumatic material. Copyright © 2013 Elsevier Ltd. All rights reserved.

Polynomial dual energy inverse functions for bone Calcium/Phosphorus ratio determination and experimental evaluation.

PubMed

Sotiropoulou, P; Fountos, G; Martini, N; Koukou, V; Michail, C; Kandarakis, I; Nikiforidis, G

2016-12-01

An X-ray dual energy (XRDE) method was examined, using polynomial nonlinear approximation of inverse functions for the determination of the bone Calcium-to-Phosphorus (Ca/P) mass ratio. Inverse fitting functions with the least-squares estimation were used, to determine calcium and phosphate thicknesses. The method was verified by measuring test bone phantoms with a dedicated dual energy system and compared with previously published dual energy data. The accuracy in the determination of the calcium and phosphate thicknesses improved with the polynomial nonlinear inverse function method, introduced in this work, (ranged from 1.4% to 6.2%), compared to the corresponding linear inverse function method (ranged from 1.4% to 19.5%). Copyright © 2016 Elsevier Ltd. All rights reserved.

Short-bearing approximation for full journal bearings

NASA Technical Reports Server (NTRS)

Ocvirk, F W

1952-01-01

A short-bearing approximation of pressure distribution in the oil film is presented which is an extension of the pressure-distribution function of Michell and Cardullo and includes end-leakage effects. Equations giving applied load, attitude angle, location and magnitude of peak film pressure, friction, and required oil flow rate as functions of the eccentricity ratio are also given. The capacity number, a basic non dimensional quantity resulting from this analysis is the product of the Sommerfeld number and the square of the length-diameter ratio. Curves determined by this analysis are compared with previously published experimental data and theoretical curves of Sommerfeld and Cameron and Wood. Conclusions reached indicate that this approximation is of practical value for analysis of short bearings.

Singular observation of the polarization-conversion effect for a gammadion-shaped metasurface

PubMed Central

Lin, Chu-En; Yen, Ta-Jen; Yu, Chih-Jen; Hsieh, Cheng-Min; Lee, Min-Han; Chen, Chii-Chang; Chang, Cheng-Wei

2016-01-01

In this article, the polarization-conversion effects of a gammadion-shaped metasurface in transmission and reflection modes are discussed. In our experiment, the polarization-conversion effect of a gammadion-shaped metasurface is investigated because of the contribution of the phase and amplitude anisotropies. According to our experimental and simulated results, the polarization property of the first-order transmitted diffraction is dominated by linear anisotropy and has weak depolarization; the first-order reflected diffraction exhibits both linear and circular anisotropies and has stronger depolarization than the transmission mode. These results are different from previously published research. The Mueller matrix ellipsometer and polar decomposition method will aid in the investigation of the polarization properties of other nanostructures. PMID:26915332

Modelling toehold-mediated RNA strand displacement.

PubMed

Šulc, Petr; Ouldridge, Thomas E; Romano, Flavio; Doye, Jonathan P K; Louis, Ard A

2015-03-10

We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand previously bound to a complementary substrate strand, is an essential mechanism in active nucleic acid nanotechnology and has also been hypothesized to occur in vivo. We study the rate of displacement reactions as a function of the length of the toehold and temperature and make two experimentally testable predictions: that the displacement is faster if the toehold is placed at the 5' end of the substrate; and that the displacement slows down with increasing temperature for longer toeholds. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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

AlKhaldi, Mashaal Q.; Wehlitz, Ralf, E-mail: rwehlitz@gmail.com

We have experimentally investigated the double-photoionization process in C{sub 6}BrF{sub 5} using monochromatized synchrotron radiation. We compare our results with previously published data for partially deuterated benzene (C{sub 6}H{sub 3}D{sub 3}) over a wide range of photon energies from threshold to 270 eV. A broad resonance in the ratio of doubly to singly charged parent ions at about 65 eV appears shifted in energy compared to benzene data. This shift is due to the difference in the bond lengths in two molecules. A simple model can explain the shape of this resonance. At higher photon energies, we observe another broadmore » resonance that can be explained as a second harmonic of the first resonance.« less

Case report: Long-standing complex regional pain syndrome relieved by a cephalosporin antibiotic.

PubMed

Ware, Mark A; Bennett, Gary J

2014-07-01

We describe a young woman who had had treatment-refractory complex regional pain syndrome (CRPS) for 6 years before receiving antibiotic treatment with cefadroxil (a cephalosporin derivative) for a minor infection. Cefadroxil reduced the patient's pain and motor dysfunction (dystonia and impaired voluntary movement) within days; the pain and motor disorder returned when cefadroxil was discontinued; and both again abated when cefadroxil was re-instituted. The patient has now had symptom relief for more than 3 years on continuing cefadroxil therapy. We discuss this case in the context of previous reports of antibiotic treatment relieving neuropathic pain in experimental animals. Copyright © 2014 International Association for the Study of Pain. Published by Elsevier B.V. All rights reserved.

15 CFR 10.10 - Review of published standards.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false Review of published standards. 10.10... DEVELOPMENT OF VOLUNTARY PRODUCT STANDARDS § 10.10 Review of published standards. (a) Each standard published... considered until a replacement standard is published. (b) Each standard published under these or previous...

From Fibrils to Toughness: Multi-Scale Mechanics of Fibrillating Interfaces in Stretchable Electronics

PubMed Central

van der Sluis, Olaf; Vossen, Bart; Geers, Marc

2018-01-01

Metal-elastomer interfacial systems, often encountered in stretchable electronics, demonstrate remarkably high interface fracture toughness values. Evidently, a large gap exists between the rather small adhesion energy levels at the microscopic scale (‘intrinsic adhesion’) and the large measured macroscopic work-of-separation. This energy gap is closed here by unravelling the underlying dissipative mechanisms through a systematic numerical/experimental multi-scale approach. This self-containing contribution collects and reviews previously published results and addresses the remaining open questions by providing new and independent results obtained from an alternative experimental set-up. In particular, the experimental studies on Cu-PDMS (Poly(dimethylsiloxane)) samples conclusively reveal the essential role of fibrillation mechanisms at the micro-meter scale during the metal-elastomer delamination process. The micro-scale numerical analyses on single and multiple fibrils show that the dynamic release of the stored elastic energy by multiple fibril fracture, including the interaction with the adjacent deforming bulk PDMS and its highly nonlinear behaviour, provide a mechanistic understanding of the high work-of-separation. An experimentally validated quantitative relation between the macroscopic work-of-separation and peel front height is established from the simulation results. Finally, it is shown that a micro-mechanically motivated shape of the traction-separation law in cohesive zone models is essential to describe the delamination process in fibrillating metal-elastomer systems in a physically meaningful way. PMID:29393908

Modelling solute dispersion in periodic heterogeneous porous media: Model benchmarking against intermediate scale experiments

NASA Astrophysics Data System (ADS)

Majdalani, Samer; Guinot, Vincent; Delenne, Carole; Gebran, Hicham

2018-06-01

This paper is devoted to theoretical and experimental investigations of solute dispersion in heterogeneous porous media. Dispersion in heterogenous porous media has been reported to be scale-dependent, a likely indication that the proposed dispersion models are incompletely formulated. A high quality experimental data set of breakthrough curves in periodic model heterogeneous porous media is presented. In contrast with most previously published experiments, the present experiments involve numerous replicates. This allows the statistical variability of experimental data to be accounted for. Several models are benchmarked against the data set: the Fickian-based advection-dispersion, mobile-immobile, multirate, multiple region advection dispersion models, and a newly proposed transport model based on pure advection. A salient property of the latter model is that its solutions exhibit a ballistic behaviour for small times, while tending to the Fickian behaviour for large time scales. Model performance is assessed using a novel objective function accounting for the statistical variability of the experimental data set, while putting equal emphasis on both small and large time scale behaviours. Besides being as accurate as the other models, the new purely advective model has the advantages that (i) it does not exhibit the undesirable effects associated with the usual Fickian operator (namely the infinite solute front propagation speed), and (ii) it allows dispersive transport to be simulated on every heterogeneity scale using scale-independent parameters.

A Decade of Literacy Research in the "Journal of Experimental Education."

ERIC Educational Resources Information Center

Knudson, Ruth E.; Theurer, Joan Leikam; Onofrey, Karen A.

This study examined various trends that exist among the 246 refereed articles published in the "Journal of Experimental Education" between 1990 and 1999. The study's results showed that 39 (16%) of the Journal articles published during this 9-year span focused on literacy. Information was categorized for each article with respect to authors'…

A New Method of Constructing a Drug-Polymer Temperature-Composition Phase Diagram Using Hot-Melt Extrusion.

PubMed

Tian, Yiwei; Jones, David S; Donnelly, Conor; Brannigan, Timothy; Li, Shu; Andrews, Gavin P

2018-04-02

Current experimental methodologies used to determine the thermodynamic solubility of an API within a polymer typically involves establishing the dissolution/melting end point of the crystalline API within a physical mixture or through the use of the glass transition temperature measurement of a demixed amorphous solid dispersion. The measurable "equilibrium" points for solubility are normally well above the glass transition temperature of the system, meaning extrapolation is required to predict the drug solubility at pharmaceutically relevant temperatures. In this manuscript, we argue that the presence of highly viscous polymers in these systems results in experimental data that exhibits an under or overestimated value relative to the true thermodynamic solubility. In previous work, we demonstrated the effects of experimental conditions and their impact on measured and predicted thermodynamic solubility points. In light of current understanding, we have developed a new method to limit error associated with viscosity effects for application in small-scale hot-melt extrusion (HME). In this study, HME was used to generate an intermediate (multiphase) system containing crystalline drug, amorphous drug/polymer-rich regions as well as drug that was molecularly dispersed in polymer. An extended annealing method was used together with high-speed differential scanning calorimetry to accurately determine the upper and lower boundaries of the thermodynamic solubility of a model drug-polymer system (felodipine and Soluplus). Compared to our previously published data, the current results confirmed our hypothesis that the prediction of the liquid-solid curve using dynamic determination of dissolution/melting end point of the crystalline API physical mixture presents an underestimation relative to the thermodynamic solubility point. With this proposed method, we were able to experimentally measure the upper and lower boundaries of the liquid-solid curve for the model system. The relationship between inverse temperature and drug-polymer solubility parameter (χ) remained linear at lower drug loadings. Significantly higher solubility and miscibility between the felodipine-Soluplus system were derived from the new χ values.

Studies of the electron density in the highest occupied molecular orbitals of PH 3, PF 3 and P(CH 3) 3 by electron momentum spectroscopy and Hartree-Fock, MRSD-CI and DFT calculations

NASA Astrophysics Data System (ADS)

Rolke, J.; Brion, C. E.

1996-06-01

The spherically averaged momentum profiles for the highest occupied molecular orbitals of PF 3 and P(CH 3) 3 have been obtained by electron momentum spectroscopy. The measurements provide a stringent test of basis set effects and the quality of ab-initio methods in the description of these larger molecular systems. As in previous work on the methyl-substituted amines, intuitive arguments fail to predict the correct amount of s- and p-type contributions to the momentum profile while delocalized molecular orbital concepts provide a more adequate description of the HOMOs. The experimental momentum profiles have been compared with theoretical momentum profiles calculated at the level of the target Hartree-Fock approximation with a range of basis sets. New Hartree-Fock calculations are also presented for the HOMO of PH 3 and compared to previously published experimental and theoretical momentum profiles. The experimental momentum profiles have further been compared to calculations at the level of the target Kohn-Sham approximation using density functional theory with the local density approximation and also with gradient corrected (non-local) exchange correlation potentials. In addition, total energies and dipole moments have been calculated for all three molecules by the various theoretical methods and compared to experimental values. Calculated 'density difference maps' show the regions where the HOMO momentum and position electron densities of PF 3 and P(CH 3) 3 change relative to the corresponding HOMO density of PH 3. The results suggest that methyl groups have an electron-attracting effect (relative to H) on the HOMO charge density in trimethyl phosphines. These conclusions are supported by a consideration of dipole moments and the 31P NMR chemical shifts for PH 3, PF 3 and P(CH 3) 3.

Can small field diode correction factors be applied universally?

PubMed

Liu, Paul Z Y; Suchowerska, Natalka; McKenzie, David R

2014-09-01

Diode detectors are commonly used in dosimetry, but have been reported to over-respond in small fields. Diode correction factors have been reported in the literature. The purpose of this study is to determine whether correction factors for a given diode type can be universally applied over a range of irradiation conditions including beams of different qualities. A mathematical relation of diode over-response as a function of the field size was developed using previously published experimental data in which diodes were compared to an air core scintillation dosimeter. Correction factors calculated from the mathematical relation were then compared those available in the literature. The mathematical relation established between diode over-response and the field size was found to predict the measured diode correction factors for fields between 5 and 30 mm in width. The average deviation between measured and predicted over-response was 0.32% for IBA SFD and PTW Type E diodes. Diode over-response was found to be not strongly dependent on the type of linac, the method of collimation or the measurement depth. The mathematical relation was found to agree with published diode correction factors derived from Monte Carlo simulations and measurements, indicating that correction factors are robust in their transportability between different radiation beams. Copyright © 2014. Published by Elsevier Ireland Ltd.

Cryptic Translocation Identification in Human and Mouse using Several Telomeric Multiplex FISH (TM-FISH) Strategies

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

Henegariu, O; Artan, S; Greally, J M

2003-08-19

Experimental data published in recent years showed that up to 10% of all cases with mild to severe idiopathic mental retardation may result from small rearrangements of the subtelomeric regions of human chromosomes. To detect such cryptic translocations, we developed a ''telomeric'' multiplex FISH assay, using a set of previously published and commercially available subtelomeric probes. This set of probes includes 41 cosmid/PAC/P1 clones located from less than 100kb to about 1 Mb from the end of the chromosomes. Similarly, a published mouse probe set, comprised of BACs hybridizing to the closest known marker toward the centromere and telomere ofmore » each mouse chromosome, was used to develop a mouse-specific ''telomeric'' M-FISH. Three different combinatorial labeling strategies were used to simultaneously detect all human sub-telomeric regions on one slide. The simplest approach uses only three fluors, and can be performed in laboratories lacking sophisticated imaging equipment or personnel highly trained in cytogenetics. A standard fluorescence microscope equipped with only three filters is sufficient. Fluor-dUTPs and labeled probes can be custom-made, thus dramatically reducing costs. Images can be prepared using generic imaging software (Adobe Photoshop), and analysis performed by simple visual inspection.« less

The bias of experimental design, including strain background, in the determination of critical Streptococcus suis serotype 2 virulence factors

PubMed Central

Auger, Jean-Philippe; Chuzeville, Sarah; Roy, David; Mathieu-Denoncourt, Annabelle; Xu, Jianguo; Grenier, Daniel

2017-01-01

Streptococcus suis serotype 2 is an important porcine bacterial pathogen and emerging zoonotic agent mainly responsible for sudden death, septic shock, and meningitis. However, serotype 2 strains are genotypically and phenotypically heterogeneous. Though a multitude of virulence factors have been described for S. suis serotype 2, the lack of a clear definition regarding which ones are truly “critical” has created inconsistencies that have only recently been highlighted. Herein, the involvement of two factors previously described as being critical for S. suis serotype 2 virulence, whether the dipeptidyl peptidase IV and autolysin, were evaluated with regards to different ascribed functions using prototype strains belonging to important sequence types. Results demonstrate a lack of reproducibility with previously published data. In fact, the role of the dipeptidyl peptidase IV and autolysin as critical virulence factors could not be confirmed. Though certain in vitro functions may be ascribed to these factors, their roles are not unique for S. suis, probably due to compensation by other factors. As such, variations and discrepancies in experimental design, including in vitro assays, cell lines, and animal models, are an important source of differences between results. Moreover, the use of different sequence types in this study demonstrates that the role attributed to a virulence factor may vary according to the S. suis serotype 2 strain background. Consequently, it is necessary to establish standard experimental designs according to the experiment and purpose in order to facilitate comparison between laboratories. Alongside, studies should include strains of diverse origins in order to prevent erroneous and biased conclusions that could affect future studies. PMID:28753679

Mathematical modeling of white adipocyte exocytosis predicts adiponectin secretion and quantifies the rates of vesicle exo- and endocytosis.

PubMed

Brännmark, Cecilia; Lövfors, William; Komai, Ali M; Axelsson, Tom; El Hachmane, Mickaël F; Musovic, Saliha; Paul, Alexandra; Nyman, Elin; Olofsson, Charlotta S

2017-12-08

Adiponectin is a hormone secreted from white adipocytes and takes part in the regulation of several metabolic processes. Although the pathophysiological importance of adiponectin has been thoroughly investigated, the mechanisms controlling its release are only partly understood. We have recently shown that adiponectin is secreted via regulated exocytosis of adiponectin-containing vesicles, that adiponectin exocytosis is stimulated by cAMP-dependent mechanisms, and that Ca 2+ and ATP augment the cAMP-triggered secretion. However, much remains to be discovered regarding the molecular and cellular regulation of adiponectin release. Here, we have used mathematical modeling to extract detailed information contained within our previously obtained high-resolution patch-clamp time-resolved capacitance recordings to produce the first model of adiponectin exocytosis/secretion that combines all mechanistic knowledge deduced from electrophysiological experimental series. This model demonstrates that our previous understanding of the role of intracellular ATP in the control of adiponectin exocytosis needs to be revised to include an additional ATP-dependent step. Validation of the model by introduction of data of secreted adiponectin yielded a very close resemblance between the simulations and experimental results. Moreover, we could show that Ca 2+ -dependent adiponectin endocytosis contributes to the measured capacitance signal, and we were able to predict the contribution of endocytosis to the measured exocytotic rate under different experimental conditions. In conclusion, using mathematical modeling of published and newly generated data, we have obtained estimates of adiponectin exo- and endocytosis rates, and we have predicted adiponectin secretion. We believe that our model should have multiple applications in the study of metabolic processes and hormonal control thereof. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Thermonuclear 19F(p, {{\\boldsymbol{\\alpha }}}_{0})16O reaction rate

NASA Astrophysics Data System (ADS)

He, Jian-Jun; Lombardo, Ivano; Dell'Aquila, Daniele; Xu, Yi; Zhang, Li-Yong; Liu, Wei-Ping

2018-01-01

The thermonuclear 19F(p, {{{α }}}0)16O reaction rate in the temperature region 0.007-10 GK has been derived by re-evaluating the available experimental data, together with the low-energy theoretical R-matrix extrapolations. Our new rate deviates by up to about 30% compared to the previous results, although all rates are consistent within the uncertainties. At very low temperature (e.g. 0.01 GK) our reaction rate is about 20% lower than the most recently published rate, because of a difference in the low energy extrapolated S-factor and a more accurate estimate of the reduced mass used in the calculation of the reaction rate. At temperatures above ˜1 GK, our rate is lower, for instance, by about 20% around 1.75 GK, because we have re-evaluated the previous data (Isoya et al., Nucl. Phys. 7, 116 (1958)) in a meticulous way. The present interpretation is supported by the direct experimental data. The uncertainties of the present evaluated rate are estimated to be about 20% in the temperature region below 0.2 GK, and are mainly caused by the lack of low-energy experimental data and the large uncertainties in the existing data. Asymptotic giant branch (AGB) stars evolve at temperatures below 0.2 GK, where the 19F(p, {{α }})16O reaction may play a very important role. However, the current accuracy of the reaction rate is insufficient to help to describe, in a careful way, the fluorine over-abundances observed in AGB stars. Precise cross section (or S factor) data in the low energy region are therefore needed for astrophysical nucleosynthesis studies. Supported by National Natural Science Foundation of China (11490562, 11490560, 11675229) and National Key Research and Development Program of China (2016YFA0400503)

Injury tolerance and moment response of the knee joint to combined valgus bending and shear loading.

PubMed

Bose, Dipan; Bhalla, Kavi S; Untaroiu, Costin D; Ivarsson, B Johan; Crandall, Jeff R; Hurwitz, Shepard

2008-06-01

Valgus bending and shearing of the knee have been identified as primary mechanisms of injuries in a lateral loading environment applicable to pedestrian-car collisions. Previous studies have reported on the structural response of the knee joint to pure valgus bending and lateral shearing, as well as the estimated injury thresholds for the knee bending angle and shear displacement based on experimental tests. However, epidemiological studies indicate that most knee injuries are due to the combined effects of bending and shear loading. Therefore, characterization of knee stiffness for combined loading and the associated injury tolerances is necessary for developing vehicle countermeasures to mitigate pedestrian injuries. Isolated knee joint specimens (n=40) from postmortem human subjects were tested in valgus bending at a loading rate representative of a pedestrian-car impact. The effect of lateral shear force combined with the bending moment on the stiffness response and the injury tolerances of the knee was concurrently evaluated. In addition to the knee moment-angle response, the bending angle and shear displacement corresponding to the first instance of primary ligament failure were determined in each test. The failure displacements were subsequently used to estimate an injury threshold function based on a simplified analytical model of the knee. The validity of the determined injury threshold function was subsequently verified using a finite element model. Post-test necropsy of the knees indicated medial collateral ligament injury consistent with the clinical injuries observed in pedestrian victims. The moment-angle response in valgus bending was determined at quasistatic and dynamic loading rates and compared to previously published test data. The peak bending moment values scaled to an average adult male showed no significant change with variation in the superimposed shear load. An injury threshold function for the knee in terms of bending angle and shear displacement was determined by performing regression analysis on the experimental data. The threshold values of the bending angle (16.2 deg) and shear displacement (25.2 mm) estimated from the injury threshold function were in agreement with previously published knee injury threshold data. The continuous knee injury function expressed in terms of bending angle and shear displacement enabled injury prediction for combined loading conditions such as those observed in pedestrian-car collisions.

Developing a mailed phantom to implement a local QA program in Egypt radiotherapy centers

NASA Astrophysics Data System (ADS)

Soliman, H. A.; Aletreby, M.

2016-07-01

In this work, a simple method that differs from the IAEA/WHO Thermoluminescent dosimeters (TLD) postal quality assurance (QA) program is developed. A small perspex; polymethyl methacrylate (PMMA), phantom measured 50 mm × 50 mm × 50 mm is constructed to be used for absorbed dose verification of high-energy photon beams in some major radiotherapy centers in Egypt. The phantom weighted only 140.7 g with two buildup covers weighted 14.8 and 43.19 g for the Cobalt-60 and the 6-MV X-ray beams, respectively. This phantom is aimed for use in the future's external audit/QA services in Egypt for the first time. TLD-700 chips are used for testing and investigating a convenient and national dosimetry QA program. Although the used methodology is comparable to previously introduced but new system; it has smaller size, less weight, and different more available material. Comparison with the previous similar designs is introduced. Theoretical calculations were done by the commercial Eclipse treatment planning system, implementing the pencil beam convolution algorithm to verify the accuracy of the experimental calculation of the dose conversion factor of water to the perspex phantom. The new constructed small phantom and methodology was applied in 10 participating radiotherapy centers. The absorbed dose was verified under the reference conditions for both 60Co and 6-MV high-energy photon beams. The checked beams were within the 5% limit except for four photon beams. There was an agreement of 0.2% between our experimental data and those previously published confirming the validity of the applied method in verifying radiotherapy absorbed dose.

The epidermal Ca(2+) gradient: Measurement using the phasor representation of fluorescent lifetime imaging.

PubMed

Celli, A; Sanchez, S; Behne, M; Hazlett, T; Gratton, E; Mauro, T

2010-03-03

Ionic gradients are found across a variety of tissues and organs. In this report, we apply the phasor representation of fluorescence lifetime imaging data to the quantitative study of ionic concentrations in tissues, overcoming technical problems of tissue thickness, concentration artifacts of ion-sensitive dyes, and calibration across inhomogeneous tissue. We used epidermis as a model system, as Ca(2+) gradients in this organ have been shown previously to control essential biologic processes of differentiation and formation of the epidermal permeability barrier. The approach described here allowed much better localization of Ca(2+) stores than those used in previous studies, and revealed that the bulk of free Ca(2+) measured in the epidermis comes from intracellular Ca(2+) stores such as the Golgi and the endoplasmic reticulum, with extracellular Ca(2+) making a relatively small contribution to the epidermal Ca(2+) gradient. Due to the high spatial resolution of two-photon microscopy, we were able to measure a marked heterogeneity in average calcium concentrations from cell to cell in the basal keratinocytes. This finding, not reported in previous studies, calls into question the long-held hypothesis that keratinocytes increase intracellular Ca(2+), cease proliferation, and differentiate passively in response to changes in extracellular Ca(2+). The experimental results obtained using this approach illustrate the power of the experimental and analytical techniques outlined in this report. Our approach can be used in mechanistic studies to address the formation, maintenance, and function of the epidermal Ca(2+) gradient, and it should be broadly applicable to the study of other tissues with ionic gradients. 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Multimodal Emotion Recognition Is Resilient to Insufficient Sleep: Results From Cross-Sectional and Experimental Studies.

PubMed

Holding, Benjamin C; Laukka, Petri; Fischer, Håkan; Bänziger, Tanja; Axelsson, John; Sundelin, Tina

2017-11-01

Insufficient sleep has been associated with impaired recognition of facial emotions. However, previous studies have found inconsistent results, potentially stemming from the type of static picture task used. We therefore examined whether insufficient sleep was associated with decreased emotion recognition ability in two separate studies using a dynamic multimodal task. Study 1 used a cross-sectional design consisting of 291 participants with questionnaire measures assessing sleep duration and self-reported sleep quality for the previous night. Study 2 used an experimental design involving 181 participants where individuals were quasi-randomized into either a sleep-deprivation (N = 90) or a sleep-control (N = 91) condition. All participants from both studies were tested on the same forced-choice multimodal test of emotion recognition to assess the accuracy of emotion categorization. Sleep duration, self-reported sleep quality (study 1), and sleep deprivation (study 2) did not predict overall emotion recognition accuracy or speed. Similarly, the responses to each of the twelve emotions tested showed no evidence of impaired recognition ability, apart from one positive association suggesting that greater self-reported sleep quality could predict more accurate recognition of disgust (study 1). The studies presented here involve considerably larger samples than previous studies and the results support the null hypotheses. Therefore, we suggest that the ability to accurately categorize the emotions of others is not associated with short-term sleep duration or sleep quality and is resilient to acute periods of insufficient sleep. © Sleep Research Society 2017. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For permissions, please e-mail journals.permissions@oup.com.

[Trends in nursing research in Korea: research trends for studies published from the inaugural issue to 2010 in the Journal of Korean Academy of Nursing and the journals published by member societies under Korean Academy of Nursing Science].

PubMed

Choe, Myoung Ae; Kim, Nam Cho; Kim, Kyung Mi; Kim, Sung Jae; Park, Kyung Sook; Byeon, Young Soon; Shin, Sung Rae; Yang, Soo; Lee, Kyung Sook; Lee, Eun Hyun; Lee, In Sook; Lee, Tae Wha; Cho, Myung Ok; Kim, Jin Hak

2014-10-01

The purpose of this study was to identify trends for studies published in the Journal of Korean Academy of Nursing and journals published by member societies from inaugural issues to 2010. A total of 6890 studies were analyzed using descriptive statistics. Quantitative studies accounted for 83.6% while qualitative studies accounted for 14.4%. Most frequently used research designs were quasi-experimental (91.1%) for experimental research and survey (85.2%) for non-experimental research. Most frequent study participants were healthy people (35.8%), most frequent nursing interventions, nursing skills (53.5%), and 39.8% used knowledge, attitude and behavior outcomes for dependent variables. Most frequently used keyword was elderly. Survey studies decreased from 1991 to 2010 by approximately 50%, while qualitative studies increased by about 20%. True experimental research (1.2%) showed no significant changes. Studies focusing on healthy populations increased from 2001-2005 (37.5%) to 2006-2010 (41.0%). From 1970 to 2010, studies using questionnaire accounted for over 50% whereas physiological measurement, approximately 5% only. Experimental studies using nursing skill interventions increased from 1970-1980 (30.4%) to 2006-2010 (64.0%). No significant changes were noted in studies using knowledge, attitude and behavior (39.9%) as dependent variables. The results suggest that further expansion of true experimental, qualitative studies and physiological measurements are needed.

Computational Analysis of Epidermal Growth Factor Receptor Mutations Predicts Differential Drug Sensitivity Profiles toward Kinase Inhibitors.

PubMed

Akula, Sravani; Kamasani, Swapna; Sivan, Sree Kanth; Manga, Vijjulatha; Vudem, Dashavantha Reddy; Kancha, Rama Krishna

2018-05-01

A significant proportion of patients with lung cancer carry mutations in the EGFR kinase domain. The presence of a deletion mutation in exon 19 or L858R point mutation in the EGFR kinase domain has been shown to cause enhanced efficacy of inhibitor treatment in patients with NSCLC. Several less frequent (uncommon) mutations in the EGFR kinase domain with potential implications in treatment response have also been reported. The role of a limited number of uncommon mutations in drug sensitivity was experimentally verified. However, a huge number of these mutations remain uncharacterized for inhibitor sensitivity or resistance. A large-scale computational analysis of clinically reported 298 point mutants of EGFR kinase domain has been performed, and drug sensitivity profiles for each mutant toward seven kinase inhibitors has been determined by molecular docking. In addition, the relative inhibitor binding affinity toward each drug as compared with that of adenosine triphosphate was calculated for each mutant. The inhibitor sensitivity profiles predicted in this study for a set of previously characterized mutants correlated well with the published clinical, experimental, and computational data. Both the single and compound mutations displayed differential inhibitor sensitivity toward first- and next-generation kinase inhibitors. The present study provides predicted drug sensitivity profiles for a large panel of uncommon EGFR mutations toward multiple inhibitors, which may help clinicians in deciding mutant-specific treatment strategies. Copyright © 2018 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.

Application of SEAWAT to select variable-density and viscosity problems

USGS Publications Warehouse

Dausman, Alyssa M.; Langevin, Christian D.; Thorne, Danny T.; Sukop, Michael C.

2010-01-01

SEAWAT is a combined version of MODFLOW and MT3DMS, designed to simulate three-dimensional, variable-density, saturated groundwater flow. The most recent version of the SEAWAT program, SEAWAT Version 4 (or SEAWAT_V4), supports equations of state for fluid density and viscosity. In SEAWAT_V4, fluid density can be calculated as a function of one or more MT3DMS species, and optionally, fluid pressure. Fluid viscosity is calculated as a function of one or more MT3DMS species, and the program also includes additional functions for representing the dependence of fluid viscosity on temperature. This report documents testing of and experimentation with SEAWAT_V4 with six previously published problems that include various combinations of density-dependent flow due to temperature variations and/or concentration variations of one or more species. Some of the problems also include variations in viscosity that result from temperature differences in water and oil. Comparisons between the results of SEAWAT_V4 and other published results are generally consistent with one another, with minor differences considered acceptable.

Thermochemical conversion of biomass in smouldering combustion across scales: The roles of heterogeneous kinetics, oxygen and transport phenomena.

PubMed

Huang, Xinyan; Rein, Guillermo

2016-05-01

The thermochemical conversion of biomass in smouldering combustion is investigated here by combining experiments and modeling at two scales: matter (1mg) and bench (100g) scales. Emphasis is put on the effect of oxygen (0-33vol.%) and oxidation reactions because these are poorly studied in the literature in comparison to pyrolysis. The results are obtained for peat as a representative biomass for which there is high-quality experimental data published previously. Three kinetic schemes are explored, including various steps of drying, pyrolysis and oxidation. The kinetic parameters are found using the Kissinger-Genetic Algorithm method, and then implemented in a one-dimensional model of heat and mass transfer. The predictions are validated with thermogravimetric and bench-scale experiments and then analyzed to unravel the role of heterogeneous reaction. This is the first time that the influence of oxygen on biomass smouldering is explained in terms of both chemistry and transport phenomena across scales. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Simulation of Low-Intensity Ultrasound Propagating in a Beagle Dog Dentoalveolar Structure to Investigate the Relations between Ultrasonic Parameters and Cementum Regeneration.

PubMed

Vafaeian, Behzad; Al-Daghreer, Saleh; El-Rich, Marwan; Adeeb, Samer; El-Bialy, Tarek

2015-08-01

The therapeutic effect of low-intensity pulsed ultrasound on orthodontically induced inflammatory root resorption is believed to be brought about through mechanical signals induced by the low-intensity pulsed ultrasound. However, the stimulatory mechanism triggering dental cell response has not been clearly identified yet. The aim of this study was to evaluate possible relations between the amounts of new cementum regeneration and ultrasonic parameters such as pressure amplitude and time-averaged energy density. We used the finite-element method to simulate the previously published experiment on ultrasonic wave propagation in the dentoalveolar structure of beagle dogs. Qualitative relations between the thickness of the regenerated cementum in the experiment and the ultrasonic parameters were observed. Our results indicated that the areas of the root surface with greater ultrasonic pressure were associated with larger amounts of cementum regeneration. However, the establishment of reliable quantitative correlations between ultrasound parameters and cementum regeneration requires more experimental data and simulations. Copyright © 2015 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Accurate expressions for solar cell fill factors including series and shunt resistances

NASA Astrophysics Data System (ADS)

Green, Martin A.

2016-02-01

Together with open-circuit voltage and short-circuit current, fill factor is a key solar cell parameter. In their classic paper on limiting efficiency, Shockley and Queisser first investigated this factor's analytical properties showing, for ideal cells, it could be expressed implicitly in terms of the maximum power point voltage. Subsequently, fill factors usually have been calculated iteratively from such implicit expressions or from analytical approximations. In the absence of detrimental series and shunt resistances, analytical fill factor expressions have recently been published in terms of the Lambert W function available in most mathematical computing software. Using a recently identified perturbative relationship, exact expressions in terms of this function are derived in technically interesting cases when both series and shunt resistances are present but have limited impact, allowing a better understanding of their effect individually and in combination. Approximate expressions for arbitrary shunt and series resistances are then deduced, which are significantly more accurate than any previously published. A method based on the insights developed is also reported for deducing one-diode fits to experimental data.

Towards an acoustic model-based poroelastic imaging method: II. experimental investigation.

PubMed

Berry, Gearóid P; Bamber, Jeffrey C; Miller, Naomi R; Barbone, Paul E; Bush, Nigel L; Armstrong, Cecil G

2006-12-01

Soft biological tissue contains mobile fluid. The volume fraction of this fluid and the ease with which it may be displaced through the tissue could be of diagnostic significance and may also have consequences for the validity with which strain images can be interpreted according to the traditional idealizations of elastography. In a previous paper, under the assumption of frictionless boundary conditions, the spatio-temporal behavior of the strain field inside a compressed cylindrical poroelastic sample was predicted (Berry et al. 2006). In this current paper, experimental evidence is provided to confirm these predictions. Finite element modeling was first used to extend the previous predictions to allow for the existence of contact friction between the sample and the compressor plates. Elastographic techniques were then applied to image the time-evolution of the strain inside cylindrical samples of tofu (a suitable poroelastic material) during sustained unconfined compression. The observed experimental strain behavior was found to be consistent with the theoretical predictions. In particular, every sample studied confirmed that reduced values of radial strain advance with time from the curved cylindrical surface inwards towards the axis of symmetry. Furthermore, by fitting the predictions of an analytical model to a time sequence of strain images, parametric images of two quantities, each related to one or more of three poroelastic material constants were produced. The two parametric images depicted the Poisson's ratio (nu(s)) of the solid matrix and the product of the aggregate modulus (H(A)) of the solid matrix with the permeability (k) of the solid matrix to the pore fluid. The means of the pixel values in these images, nu(s) = 0.088 (standard deviation 0.023) and H(A)k = 1.449 (standard deviation 0.269) x 10(-7) m(2) s(-1), were in agreement with values derived from previously published data for tofu (Righetti et al. 2005). The results provide the first experimental detection of the fluid-flow-induced characteristic diffusion-like behavior of the strain in a compressed poroelastic material and allow parameters related to the above material constants to be determined. We conclude that it may eventually be possible to use strain data to detect and measure characteristics of diffusely distributed mobile fluid in tissue spaces that are too small to be imaged directly.

How Song Experience Affects Female Mate-Choice, Male Song, and Monoaminergic Activity in the Auditory Telencephalon in Lincoln's Sparrows.

PubMed

Sockman, Keith W; Lyons, Susan M

2017-10-01

A sexual signal can indicate not only the signaler's attractiveness as a potential mate but also the signaler's competitiveness relative to rivals. As the attractiveness or competitiveness of the prevailing signaling environment increases, individuals prospecting for mates should change their choice threshold, whereas competing individuals should shift resources toward elevating their own competitiveness. Previous studies show that experimental elevations of song competition increase male competitive behavior in Lincoln's sparrows (Melospiza lincolnii) and European starlings (Sturnus vulgaris). Through a series of experimental manipulations using laboratory-housed Lincoln's sparrows, we have also discovered that females change the strength of their song preferences depending on the attractiveness of the song environment to which they have recently been exposed; compared to a less-attractive environment, a highly-attractive environment elevates the threshold for releasing phonotaxis behavior toward male song. These behavioral adjustments are associated with changes in forebrain monoaminergic activity that are triggered by experimental manipulations of the quality of the song environment. Findings from these studies suggest possible neural mechanisms for the regulation of adaptive behavioral plasticity associated with dynamic sexual signaling environments. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions.

PubMed

Chou, Chih-Hung; Shrestha, Sirjana; Yang, Chi-Dung; Chang, Nai-Wen; Lin, Yu-Ling; Liao, Kuang-Wen; Huang, Wei-Chi; Sun, Ting-Hsuan; Tu, Siang-Jyun; Lee, Wei-Hsiang; Chiew, Men-Yee; Tai, Chun-San; Wei, Ting-Yen; Tsai, Tzi-Ren; Huang, Hsin-Tzu; Wang, Chung-Yu; Wu, Hsin-Yi; Ho, Shu-Yi; Chen, Pin-Rong; Chuang, Cheng-Hsun; Hsieh, Pei-Jung; Wu, Yi-Shin; Chen, Wen-Liang; Li, Meng-Ju; Wu, Yu-Chun; Huang, Xin-Yi; Ng, Fung Ling; Buddhakosai, Waradee; Huang, Pei-Chun; Lan, Kuan-Chun; Huang, Chia-Yen; Weng, Shun-Long; Cheng, Yeong-Nan; Liang, Chao; Hsu, Wen-Lian; Huang, Hsien-Da

2018-01-04

MicroRNAs (miRNAs) are small non-coding RNAs of ∼ 22 nucleotides that are involved in negative regulation of mRNA at the post-transcriptional level. Previously, we developed miRTarBase which provides information about experimentally validated miRNA-target interactions (MTIs). Here, we describe an updated database containing 422 517 curated MTIs from 4076 miRNAs and 23 054 target genes collected from over 8500 articles. The number of MTIs curated by strong evidence has increased ∼1.4-fold since the last update in 2016. In this updated version, target sites validated by reporter assay that are available in the literature can be downloaded. The target site sequence can extract new features for analysis via a machine learning approach which can help to evaluate the performance of miRNA-target prediction tools. Furthermore, different ways of browsing enhance user browsing specific MTIs. With these improvements, miRTarBase serves as more comprehensively annotated, experimentally validated miRNA-target interactions databases in the field of miRNA related research. miRTarBase is available at http://miRTarBase.mbc.nctu.edu.tw/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Experimental characterization of the AFIT neutron facility. Master's thesis

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

Lessard, O.J.

1993-09-01

AFIT's Neutron Facility was characterized for room-return neutrons using a (252)Cf source and a Bonner sphere spectrometer with three experimental models, the shadow shield, the Eisenhauer, Schwartz, and Johnson (ESJ), and the polynomial models. The free-field fluences at one meter from the ESJ and polynomial models were compared to the equivalent value from the accepted experimental shadow shield model to determine the suitability of the models in the AFIT facility. The polynomial model behaved erratically, as expected, while the ESJ model compared to within 4.8% of the shadow shield model results for the four Bonner sphere calibration. The ratio ofmore » total fluence to free-field fluence at one meter for the ESJ model was then compared to the equivalent ratio obtained by a Monte Cario Neutron-Photon transport code (MCNP), an accepted computational model. The ESJ model compared to within 6.2% of the MCNP results. AFIT's fluence ratios were compared to equivalent ratios reported by three other neutron facilities which verified that AFIT's results fit previously published trends based on room volumes. The ESJ model appeared adequate for health physics applications and was chosen was chosen for calibration of the AFIT facility. Neutron Detector, Bonner Sphere, Neutron Dosimetry, Room Characterization.« less

Destabilization of Human Serum Albumin by Ionic Liquids Studied Using Enhanced Molecular Dynamics Simulations.

PubMed

Jaeger, Vance W; Pfaendtner, Jim

2016-12-01

Ionic liquid (IL) containing solvents can change the structure, dynamics, function, and stability of proteins. In order to investigate the mechanisms by which ILs induce structural changes in a large multidomain protein, we study the interactions of human serum albumin (HSA) with two different ILs, 1-butyl-3-methylimidazolium tetrafluoroborate and choline dihydrogen phosphate. Root mean square deviation and fluctuation calculations indicate that high concentrations of ILs in mixtures with water lead to protein structures that remain close to their crystallographic structures on time scales of hundreds of nanoseconds. To overcome potential time scale limitations due to the high viscosity of the solvent, we employed enhanced sampling techniques to estimate the free energy of an experimentally determined important transition within the protein structure. Metadynamics simulations show that the free energy landscape of the unfolding of loop 1 of domain I is different in the presence of ILs than it is in water, consistent with previously published experimental evidence. We then apply essential dynamics coarse graining to systematically predict differences in the dynamics of proteins solvated in IL-water mixtures versus pure water systems. We also demonstrate that the presence of ionic liquids changes the distribution of intermolecular distances among several ligands, indicating that the protein structure swells in the presence of certain ILs, consistent with experimental evidence.

RAID v2.0: an updated resource of RNA-associated interactions across organisms.

PubMed

Yi, Ying; Zhao, Yue; Li, Chunhua; Zhang, Lin; Huang, Huiying; Li, Yana; Liu, Lanlan; Hou, Ping; Cui, Tianyu; Tan, Puwen; Hu, Yongfei; Zhang, Ting; Huang, Yan; Li, Xiaobo; Yu, Jia; Wang, Dong

2017-01-04

With the development of biotechnologies and computational prediction algorithms, the number of experimental and computational prediction RNA-associated interactions has grown rapidly in recent years. However, diverse RNA-associated interactions are scattered over a wide variety of resources and organisms, whereas a fully comprehensive view of diverse RNA-associated interactions is still not available for any species. Hence, we have updated the RAID database to version 2.0 (RAID v2.0, www.rna-society.org/raid/) by integrating experimental and computational prediction interactions from manually reading literature and other database resources under one common framework. The new developments in RAID v2.0 include (i) over 850-fold RNA-associated interactions, an enhancement compared to the previous version; (ii) numerous resources integrated with experimental or computational prediction evidence for each RNA-associated interaction; (iii) a reliability assessment for each RNA-associated interaction based on an integrative confidence score; and (iv) an increase of species coverage to 60. Consequently, RAID v2.0 recruits more than 5.27 million RNA-associated interactions, including more than 4 million RNA-RNA interactions and more than 1.2 million RNA-protein interactions, referring to nearly 130 000 RNA/protein symbols across 60 species. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Role of non-native electrostatic interactions in the coupled folding and binding of PUMA with Mcl-1

PubMed Central

Chu, Wen-Ting; Clarke, Jane; Shammas, Sarah L.; Wang, Jin

2017-01-01

PUMA, which belongs to the BH3-only protein family, is an intrinsically disordered protein (IDP). It binds to its cellular partner Mcl-1 through its BH3 motif, which folds upon binding into an α helix. We have applied a structure-based coarse-grained model, with an explicit Debye—Hückel charge model, to probe the importance of electrostatic interactions both in the early and the later stages of this model coupled folding and binding process. This model was carefully calibrated with the experimental data on helical content and affinity, and shown to be consistent with previously published experimental data on binding rate changes with respect to ionic strength. We find that intramolecular electrostatic interactions influence the unbound states of PUMA only marginally. Our results further suggest that intermolecular electrostatic interactions, and in particular non-native electrostatic interactions, are involved in formation of the initial encounter complex. We are able to reveal the binding mechanism in more detail than is possible using experimental data alone however, and in particular we uncover the role of non-native electrostatic interactions. We highlight the potential importance of such electrostatic interactions for describing the binding reactions of IDPs. Such approaches could be used to provide predictions for the results of mutational studies. PMID:28369057

Chlorination kinetics of glyphosate and its by-products: modeling approach.

PubMed

Brosillon, Stephan; Wolbert, Dominique; Lemasle, Marguerite; Roche, Pascal; Mehrsheikh, Akbar

2006-06-01

Chlorination reactions of glyphosate, glycine, and sodium cyanate were conducted in well-agitated reactors to generate experimental kinetic measurements for the simulation of chlorination kinetics under the conditions of industrial water purification plants. The contribution of different by-products to the overall degradation of glyphosate during chlorination has been identified. The kinetic rate constants for the chlorination of glyphosate and its main degradation products were either obtained by calculation according to experimental data or taken from published literature. The fit of the kinetic constants with experimental data allowed us to predict consistently the concentration of the majority of the transitory and terminal chlorination products identified in the course of the glyphosate chlorination process. The simulation results conducted at varying aqueous chlorine/glyphosate molar ratios have shown that glyphosate is expected to degrade in fraction of a second under industrial aqueous chlorination conditions. Glyphosate chlorination products are not stable under the conditions of drinking water chlorination and are degraded to small molecules common to the degradation of amino acids and other naturally occurring substances in raw water. The kinetic studies of the chlorination reaction of glyphosate, together with calculations based on kinetic modeling in conditions close to those at real water treatment plants, confirm the reaction mechanism that we have previously suggested for glyphosate chlorination.

Efficacy of imidocarb dipropionate in eliminating Theileria equi from experimentally infected horses.

PubMed

Grause, Juanita F; Ueti, Massaro W; Nelson, Jeffrey T; Knowles, Donald P; Kappmeyer, Lowell S; Bunn, Thomas O

2013-06-01

Theileria equi, one of the causative agents of equine piroplasmosis, is endemic in many regions of the world but is considered a 'foreign' animal disease in the USA. In an effort to prevent the importation of T. equi, stringent serological screening of horses is practiced prior to entry to the USA. Current regulatory options available where horses are found to be infected include permanent quarantine with or without chemotherapy, repatriation, or euthanasia. Chemotherapeutics that eliminate infection and subsequently transmission risk are critical in the management of infected horses. In this study, the efficacy of the drug imidocarb dipropionate against experimental T. equi infection was assessed. Of nine horses experimentally inoculated with T. equi isolated from an animal previously imported from Peru, six were treated with imidocarb dipropionate after the resolution of the acute phase of the disease. Elimination of the parasite was demonstrated in 5/6 by nested PCR, blood transfusions to naïve horses, and reversion to seronegative status. The findings support the use of this drug as a potential treatment option in controlling outbreaks of T. equi, and also suggest that 'combination testing' using both serological and PCR detection methods are necessary to demonstrate clearance of infection. Published by Elsevier Ltd.

Effect of Profilin on Actin Critical Concentration: A Theoretical Analysis

PubMed Central

Yarmola, Elena G.; Dranishnikov, Dmitri A.; Bubb, Michael R.

2008-01-01

To explain the effect of profilin on actin critical concentration in a manner consistent with thermodynamic constraints and available experimental data, we built a thermodynamically rigorous model of actin steady-state dynamics in the presence of profilin. We analyzed previously published mechanisms theoretically and experimentally and, based on our analysis, suggest a new explanation for the effect of profilin. It is based on a general principle of indirect energy coupling. The fluctuation-based process of exchange diffusion indirectly couples the energy of ATP hydrolysis to actin polymerization. Profilin modulates this coupling, producing two basic effects. The first is based on the acceleration of exchange diffusion by profilin, which indicates, paradoxically, that a faster rate of actin depolymerization promotes net polymerization. The second is an affinity-based mechanism similar to the one suggested in 1993 by Pantaloni and Carlier although based on indirect rather than direct energy coupling. In the model by Pantaloni and Carlier, transformation of chemical energy of ATP hydrolysis into polymerization energy is regulated by direct association of each step in the hydrolysis reaction with a corresponding step in polymerization. Thus, hydrolysis becomes a time-limiting step in actin polymerization. In contrast, indirect coupling allows ATP hydrolysis to lag behind actin polymerization, consistent with experimental results. PMID:18835900

Multi-omics approach identifies molecular mechanisms of plant-fungus mycorrhizal interaction

DOE PAGES

Larsen, Peter E.; Sreedasyam, Avinash; Trivedi, Geetika; ...

2016-01-19

In mycorrhizal symbiosis, plant roots form close, mutually beneficial interactions with soil fungi. Before this mycorrhizal interaction can be established however, plant roots must be capable of detecting potential beneficial fungal partners and initiating the gene expression patterns necessary to begin symbiosis. To predict a plant root – mycorrhizal fungi sensor systems, we analyzed in vitro experiments of Populus tremuloides (aspen tree) and Laccaria bicolor (mycorrhizal fungi) interaction and leveraged over 200 previously published transcriptomic experimental data sets, 159 experimentally validated plant transcription factor binding motifs, and more than 120-thousand experimentally validated protein-protein interactions to generate models of pre-mycorrhizal sensormore » systems in aspen root. These sensor mechanisms link extracellular signaling molecules with gene regulation through a network comprised of membrane receptors, signal cascade proteins, transcription factors, and transcription factor biding DNA motifs. Modeling predicted four pre-mycorrhizal sensor complexes in aspen that interact with fifteen transcription factors to regulate the expression of 1184 genes in response to extracellular signals synthesized by Laccaria. Predicted extracellular signaling molecules include common signaling molecules such as phenylpropanoids, salicylate, and, jasmonic acid. Lastly, this multi-omic computational modeling approach for predicting the complex sensory networks yielded specific, testable biological hypotheses for mycorrhizal interaction signaling compounds, sensor complexes, and mechanisms of gene regulation.« less

Multi-omics approach identifies molecular mechanisms of plant-fungus mycorrhizal interaction

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

Larsen, Peter E.; Sreedasyam, Avinash; Trivedi, Geetika

In mycorrhizal symbiosis, plant roots form close, mutually beneficial interactions with soil fungi. Before this mycorrhizal interaction can be established however, plant roots must be capable of detecting potential beneficial fungal partners and initiating the gene expression patterns necessary to begin symbiosis. To predict a plant root – mycorrhizal fungi sensor systems, we analyzed in vitro experiments of Populus tremuloides (aspen tree) and Laccaria bicolor (mycorrhizal fungi) interaction and leveraged over 200 previously published transcriptomic experimental data sets, 159 experimentally validated plant transcription factor binding motifs, and more than 120-thousand experimentally validated protein-protein interactions to generate models of pre-mycorrhizal sensormore » systems in aspen root. These sensor mechanisms link extracellular signaling molecules with gene regulation through a network comprised of membrane receptors, signal cascade proteins, transcription factors, and transcription factor biding DNA motifs. Modeling predicted four pre-mycorrhizal sensor complexes in aspen that interact with fifteen transcription factors to regulate the expression of 1184 genes in response to extracellular signals synthesized by Laccaria. Predicted extracellular signaling molecules include common signaling molecules such as phenylpropanoids, salicylate, and, jasmonic acid. Lastly, this multi-omic computational modeling approach for predicting the complex sensory networks yielded specific, testable biological hypotheses for mycorrhizal interaction signaling compounds, sensor complexes, and mechanisms of gene regulation.« less

Enhancing photocurrent transient spectroscopy by electromagnetic modeling.

PubMed

Diesinger, H; Panahandeh-Fard, M; Wang, Z; Baillargeat, D; Soci, C

2012-05-01

The shape and duration of photocurrent transients generated by a photoconductive switch depend on both the intrinsic response of the active material and the geometry of the transmission line structure. The present electromagnetic model decouples both shape forming contributions. In contrast to previously published work, it accounts for the particular operating mode of transient spectroscopy. The objective is to increase the time resolution by two approaches, by optimizing structural response and by deconvolving it from experimental data. The switch structure is represented by an effective transimpedance onto which the active material acts as current generator. As proof of concept, the response of a standard microstrip switch is modeled and deconvolved from experimental data acquired in GaAs, yielding a single exponential material response and hence supporting the validity of the approach. Beyond compensating for the response deterioration by the structure, switch architectures can be a priori optimized with respect to frequency response. As an example, it is shown that a microstrip gap that can be deposited on materials incompatible with standard lithography reduces pulse broadening by an order of magnitude if it is provided with transitions to coplanar access lines.

General correlation for prediction of critical heat flux ratio in water cooled channels

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

Pernica, R.; Cizek, J.

1995-09-01

The paper present the general empirical Critical Heat Flux Ration (CHFR) correlation which is valid for vertical water upflow through tubes, internally heated concentric annuli and rod bundles geometries with both wide and very tight square and triangular rods lattices. The proposed general PG correlation directly predicts the CHFR, it comprises axial and radial non-uniform heating, and is valid in a wider range of thermal hydraulic conditions than previously published critical heat flux correlations. The PG correlation has been developed using the critical heat flux Czech data bank which includes more than 9500 experimental data on tubes, 7600 data onmore » rod bundles and 713 data on internally heated concentric annuli. Accuracy of the CHFR prediction, statistically assessed by the constant dryout conditions approach, is characterized by the mean value nearing 1.00 and the standard deviation less than 0.06. Moverover, a subchannel form of the PG correlations is statistically verified on Westinghouse and Combustion Engineering rod bundle data bases, i.e. more than 7000 experimental CHF points of Columbia University data bank were used.« less

The Atomic Mass Evaluation (AME2012): Status and Perspectives

NASA Astrophysics Data System (ADS)

Kondev, F. G.; Audi, G.; Wang, M.; Xu, X.; Wapstra, A. H.; MacCormick, M.; Pfeiffer, B.

2013-10-01

The atomic mass is a fundamental property of the nucleus that has wide applications in natural sciences and technology. The new evaluated mass table, AME2012, has been recently published as a collaborative effort between scientists from China, Europe and USA, under the leadership of G. Audi. It represents a significant update of the previous AME2003 evaluation by considering a large number of precise experimental results obtained at existing Penning Trap and Storage Ring facilities, thus expending the region of experimentally known masses towards exotic neutron- and proton-rich nuclei. Since the presence of isomers plays an important role in determining the masses of many nuclei, a complementary database, NUBASE2012, that contains the isomer-level properties for all nuclei was also developed. This presentation will briefly review recent achievements of the collaboration, present on-going activities, and reflect on ideas for future developments and challenges in the field of evaluation of atomic masses. The work at ANL was supported by the U.S. Department of Energy, Office of Nuclear Physics, under Contract No. DE-AC02-06CH11357.

In silico assessment of the conduction mechanism of the Ryanodine Receptor 1 reveals previously unknown exit pathways.

PubMed

Heinz, Leonard P; Kopec, Wojciech; de Groot, Bert L; Fink, Rainer H A

2018-05-02

The ryanodine receptor 1 is a large calcium ion channel found in mammalian skeletal muscle. The ion channel gained a lot of attention recently, after multiple independent authors published near-atomic cryo electron microscopy data. Taking advantage of the unprecedented quality of structural data, we performed molecular dynamics simulations on the entire ion channel as well as on a reduced model. We calculated potentials of mean force for Ba 2+ , Ca 2+ , Mg 2+ , K + , Na + and Cl - ions using umbrella sampling to identify the key residues involved in ion permeation. We found two main binding sites for the cations, whereas the channel is strongly repulsive for chloride ions. Furthermore, the data is consistent with the model that the receptor achieves its ion selectivity by over-affinity for divalent cations in a calcium-block-like fashion. We reproduced the experimental conductance for potassium ions in permeation simulations with applied voltage. The analysis of the permeation paths shows that ions exit the pore via multiple pathways, which we suggest to be related to the experimental observation of different subconducting states.

DMSO-Li2O2 Interface in the Rechargeable Li-O2 Battery Cathode: Theoretical and Experimental Perspectives on Stability.

PubMed

Schroeder, Marshall A; Kumar, Nitin; Pearse, Alexander J; Liu, Chanyuan; Lee, Sang Bok; Rubloff, Gary W; Leung, Kevin; Noked, Malachi

2015-06-03

One of the greatest obstacles for the realization of the nonaqueous Li-O2 battery is finding a solvent that is chemically and electrochemically stable under cell operating conditions. Dimethyl sulfoxide (DMSO) is an attractive candidate for rechargeable Li-O2 battery studies; however, there is still significant controversy regarding its stability on the Li-O2 cathode surface. We performed multiple experiments (in situ XPS, FTIR, Raman, and XRD) which assess the stability of the DMSO-Li2O2 interface and report perspectives on previously published studies. Our electrochemical experiments show long-term stable cycling of a DMSO-based operating Li-O2 cell with a platinum@carbon nanotube core-shell cathode fabricated via atomic layer deposition, specifically with >45 cycles of 40 h of discharge per cycle. This work is complemented by density functional theory calculations of DMSO degradation pathways on Li2O2. Both experimental and theoretical evidence strongly suggests that DMSO is chemically and electrochemically stable on the surface of Li2O2 under the reported operating conditions.

Use Of Zernike Polynomials And Interferometry In The Optical Design And Assembly Of Large Carbon-Dioxide Laser Systems

NASA Astrophysics Data System (ADS)

Viswanathan, V. K.

1982-02-01

This paper describes the need for non-raytracing schemes in the optical design and analysis of large carbon-dioxide lasers like the Gigawatt,1 Gemini, 2 and Helios3 lasers currently operational at Los Alamos, and the Antares 4 laser fusion system under construction. The scheme currently used at Los Alamos involves characterizing the various optical components with a Zernike polynomial sets obtained by the digitization6 of experimentally produced interferograms of the components. A Fast Fourier Transform code then propagates the complex amplitude and phase of the beam through the whole system and computes the optical parameters of interest. The analysis scheme is illustrated through examples of the Gigawatt, Gemini, and Helios systems. A possible way of using the Zernike polynomials in optical design problems of this type is discussed. Comparisons between the computed values and experimentally obtained results are made and it is concluded that this appears to be a valid approach. As this is a review article, some previously published results are also used where relevant.

Physiological and biochemical changes associated with acute experimental dehydration in the desert adapted mouse, Peromyscus eremicus.

PubMed

Kordonowy, Lauren; Lombardo, Kaelina D; Green, Hannah L; Dawson, Molly D; Bolton, Evice A; LaCourse, Sarah; MacManes, Matthew D

2017-03-01

Characterizing traits critical for adaptation to a given environment is an important first step in understanding how phenotypes evolve. How animals adapt to the extreme heat and aridity commonplace to deserts is an exceptionally interesting example of these processes, and has been the focus of study for decades. In contrast to those studies, where experiments are conducted on either wild animals or captive animals held in non-desert conditions, the study described here leverages a unique environmental chamber that replicates desert conditions for captive Peromyscus eremicus (cactus mouse). Here, we establish baseline values for daily water intake and for serum electrolytes, as well as the response of these variables to acute experimental dehydration. In brief, P   eremicus daily water intake is very low. Its serum electrolytes are distinct from many previously studied animals, and its response to acute dehydration is profound, though not suggestive of renal impairment, which is atypical of mammals. © 2017 The Authors. Physiological Reports published by Wiley Periodicals, Inc. on behalf of The Physiological Society and the American Physiological Society.

Measuring the flexoelectric coefficient of bulk barium titanate from a shock wave experiment

NASA Astrophysics Data System (ADS)

Hu, Taotao; Deng, Qian; Liang, Xu; Shen, Shengping

2017-08-01

In this paper, a phenomenon of polarization introduced by shock waves is experimentally studied. Although this phenomenon has been reported previously in the community of physics, this is the first time to link it to flexoelectricity, the coupling between electric polarization and strain gradients in dielectrics. As the shock waves propagate in a dielectric material, electric polarization is thought to be induced by the strain gradient at the shock front. First, we control the first-order hydrogen gas gun to impact and generate shock waves in unpolarized bulk barium titanate (BT) samples. Then, a high-precision oscilloscope is used to measure the voltage generated by the flexoelectric effect. Based on experimental results, strain elastic wave theory, and flexoelectric theory, a longitudinal flexoelectric coefficient of the bulk BT sample is calculated to be μ 11 = 17.33 × 10 - 6 C/m, which is in accord with the published transverse flexoelectric coefficient. This method effectively suppresses the majority of drawbacks in the quasi-static and low frequency dynamic techniques and provides more reliable results of flexoelectric behaviors.

Numerical investigation of potential stratification caused by a cryogenic helium spill inside a tunnel

NASA Astrophysics Data System (ADS)

Sinclair, Cameron; Malecha, Ziemowit; Jedrusyna, Artur

2018-04-01

The sudden release of cryogenic fluid into an accelerator tunnel can pose a significant health and safety risk. For this reason, it is important to evaluate the consequences of such a spill. Previous publications concentrated on either Oxygen Deficiency Hazard or the evaluation of mathematical models using experimental data. No studies to date have focussed on the influence of cryogen inlet conditions on flow development. In this paper, the stratification behaviour of low-temperature helium released into an air-filled accelerator tunnel is investigated for varying helium inlet diameters. A numerical model was constructed using the OpenFOAM Toolbox of a generalised 3D geometry, with similar hydraulic characteristics to the CERN and SLAC tunnels. This model has been validated against published experimental and numerical data. A dimensionless parameter, based on Bakke number, was then determined for the onset of stratification, taking into account the helium inlet diameter; a dimensionless parameter for the degree of stratification was also employed. The simulated flow behaviour is described in terms of these dimensionless parameters, as well as the temperature and oxygen concentration at various heights throughout the tunnel.

Plasma rate coefficients for electron-impact ionization of Xeq+ ions (q = 8, …, 17)

NASA Astrophysics Data System (ADS)

Borovik, A., Jr.; Gharaibeh, M. F.; Schippers, S.; Müller, A.

2015-02-01

Plasma rate coefficients (PRCs) for electron-impact single ionization of ground-state Xeq+ ions (q=8,\\ldots ,17) in the temperature range 2 × 105 - 2 × 107 K have been derived from a combination of experimental cross-section data and results of distorted-wave calculations. For Xe8+ and Xe9+ new measurements were performed and thoroughly analyzed with respect to the contributions from different ionization mechanisms and the effects of long-lived excited states in the parent ion beams that had been employed in the experiments. In the same manner, previously published experimental data for the higher charge states were analyzed to extract the ground-configuration ionization cross sections and to derive the associated PRCs. The resulting temperature-dependent PRC functions were parameterized and the associated parameters are provided in tabular form. With the exception of Xe8+ the absolute uncertainties of the inferred rate coefficients are estimated to be +/- 10%. For Xe8+ the uncertainties are +/- 25% due to the necessary correction for strong metastable-ion contributions to the measured cross sections.

Protein kinase C is involved with upstream signaling of methyl farnesoate for photoperiod-dependent sex determination in the water flea Daphnia pulex.

PubMed

Toyota, Kenji; Sato, Tomomi; Tatarazako, Norihisa; Iguchi, Taisen

2017-02-15

Sex determination of Daphnia pulex is decided by environmental conditions. We established a suitable experimental system for this study using D. pulex WTN6 strain, in which the sex of the offspring can be controlled by photoperiod. Long-day conditions induced females and short-day conditions induced males. Using this system, we previously found that methy farnesoate (MF), which is a putative innate juvenile hormone molecule in daphnids, is necessary for male sex determination and that protein kinase C (PKC) is a candidate factor of male sex determiner. In this study, we demonstrated that a PKC inhibitor [bisindolylmaleimide IV (BIM)] application strongly suppressed male offspring induction in the short-day condition. Moreover, co-treatment of BIM with MF revealed that PKC signaling acts upstream of MF signaling for male sex determination. This is the first experimental evidence that PKC is involved in the male sex determination process associated with methyl farnesoate signaling in daphnid species. © 2017. Published by The Company of Biologists Ltd.

The Molecular Basis for Dual Fatty Acid Amide Hydrolase (FAAH)/Cyclooxygenase (COX) Inhibition.

PubMed

Palermo, Giulia; Favia, Angelo D; Convertino, Marino; De Vivo, Marco

2016-06-20

The design of multitarget-directed ligands is a promising strategy for discovering innovative drugs. Here, we report a mechanistic study that clarifies key aspects of the dual inhibition of the fatty acid amide hydrolase (FAAH) and the cyclooxygenase (COX) enzymes by a new multitarget-directed ligand named ARN2508 (2-[3-fluoro-4-[3-(hexylcarbamoyloxy)phenyl]phenyl]propanoic acid). This potent dual inhibitor combines, in a single scaffold, the pharmacophoric elements often needed to block FAAH and COX, that is, a carbamate moiety and the 2-arylpropionic acid functionality, respectively. Molecular modeling and molecular dynamics simulations suggest that ARN2508 uses a noncovalent mechanism of inhibition to block COXs, while inhibiting FAAH via the acetylation of the catalytic Ser241, in line with previous experimental evidence for covalent FAAH inhibition. This study proposes the molecular basis for the dual FAAH/COX inhibition by this novel hybrid scaffold, stimulating further experimental studies and offering new insights for the rational design of novel anti-inflammatory agents that simultaneously act on FAAH and COX. © 2015 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Externalities and article citations: experience of a national public health journal (Gaceta Sanitaria).

PubMed

Ruano-Ravina, Alberto; Álvarez-Dardet, Carlos; Domínguez-Berjón, M Felicitas; Fernández, Esteve; García, Ana M; Borrell, Carme

2016-01-01

The purpose of the study was to analyze the determinants of citations such as publication year, article type, article topic, article selected for a press release, number of articles previously published by the corresponding author, and publication language in a Spanish journal of public health. Observational study including all articles published in Gaceta Sanitaria during 2007-2011. We retrieved the number of citations from the ISI Web of Knowledge database in June 2013 and also information on other variables such as number of articles published by the corresponding author in the previous 5 years (searched through PubMed), selection for a press release, publication language, article type and topic, and others. We included 542 articles. Of these, 62.5% were cited in the period considered. We observed an increased odds ratio of citations for articles selected for a press release and also with the number of articles published previously by the corresponding author. Articles published in English do not seem to increase their citations. Certain externalities such as number of articles published by the corresponding author and being selected for a press release seem to influence the number of citations in national journals. Copyright © 2016 Elsevier Inc. All rights reserved.

Structure-property relations and modeling of small crack fatigue behavior of various magnesium alloys

NASA Astrophysics Data System (ADS)

Bernard, Jairus Daniel

Lightweight structural components are important to the automotive and aerospace industries so that better fuel economy can be realized. Magnesium alloys in particular are being examined to fulfill this need due to their attractive stiffness- and strength-to-weight ratios when compared to other materials. However, when introducing a material into new roles, one needs to properly characterize its mechanical properties. Fatigue behavior is especially important considering aerospace and automotive component applications. Therefore, quantifying the structure-property relationships and accurately predicting the fatigue behavior for these materials are vital. This study has two purposes. The first is to quantify the structure-property relationships for the fatigue behavior in an AM30 magnesium alloy. The second is to use the microstructural-based MultiStage Fatigue (MSF) model in order to accurately predict the fatigue behavior of three magnesium alloys: AM30, Elektron 21, and AZ61. While some studies have previously quantified the MSF material constants for several magnesium alloys, detailed research into the fatigue regimes, notably the microstructurally small crack (MSC) region, is lacking. Hence, the contribution of this work is the first of its kind to experimentally quantify the fatigue crack incubation and MSC regimes that are used for the MultiStage Fatigue model. Using a multi-faceted experimental approach, these regimes were explored with a replica method that used a dual-stage silicone based compound along with previously published in situ fatigue tests. These observations were used in calibrating the MultiStage Fatigue model.

Optimization and experimental validation of electrostatic adhesive geometry

NASA Astrophysics Data System (ADS)

Ruffatto, D.; Shah, J.; Spenko, M.

This paper introduces a method to optimize the electrode geometry of electrostatic adhesives for robotic gripping, attachment, and manipulation applications. Electrostatic adhesion is achieved by applying a high voltage potential, on the order of kV, to a set of electrodes, which generates an electric field. The electric field polarizes the substrate material and creates an adhesion force. Previous attempts at creating electro-static adhesives have shown them to be effective, but researchers have made no effort to optimize the electrode configuration and geometry. We have shown that by optimizing the geometry of the electrode configuration, the electric field strength, and therefore the adhesion force, is enhanced. To accomplish this, Comsol Multiphysics was utilized to evaluate the average electric field generated by a given electrode geometry. Several electrode patterns were evaluated, including parallel conductors, concentric circles, Hilbert curves (a fractal geometry) and spirals. The arrangement of the electrodes in concentric circles with varying electrode widths proved to be the most effective. The most effective sizing was to use the smallest gap spacing allowable coupled with a variable electrode width. These results were experimentally validated on several different surfaces including drywall, wood, tile, glass, and steel. A new manufacturing process allowing for the fabrication of thin, conformal electro-static adhesive pads was utilized. By combining the optimized electrode geometry with the new fabrication process we are able to demonstrate a marked improvement of up to 500% in shear pressure when compared to previously published values.

Performance Evaluation of Advanced Retrofit Roof Technologies Using Field-Test Data Phase Three Final Report, Volume 2

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

Biswas, Kaushik; Childs, Phillip W.; Atchley, Jerald Allen

2015-01-01

This article presents some miscellaneous data from two low-slope and two steep-slope experimental roofs. The low-slope roofs were designed to compare the performance of various roof coatings exposed to natural weatherization. The steep-slope roofs contained different combinations of phase change material, rigid insulation, low emittance surface and above-sheathing ventilation, with standing-seam metal panels on top. The steep-slope roofs were constructed on a series of adjacent attics separated at the gables using thick foam insulation. This article describes phase three (3) of a study that began in 2009 to evaluate the energy benefits of a sustainable re-roofing technology utilizing standing-seam metalmore » roofing panels combined with energy efficient features like above-sheathing-ventilation (ASV), phase change material (PCM) and rigid insulation board. The data from phases 1 and 2 have been previously published and reported [Kosny et al., 2011; Biswas et al., 2011; Biswas and Childs, 2012; Kosny et al., 2012]. Based on previous data analyses and discussions within the research group, additional test roofs were installed in May 2012, to test new configurations and further investigate different components of the dynamic insulation systems. Some experimental data from phase 3 testing from May 2012 to December 2013 and some EnergyPlus modeling results have been reported in volumes 1 and 3, respectively, of the final report [Biswas et al., 2014; Biswas and Bhandari, 2014].« less

Gaseous Sulfate Solubility in Glass: Experimental Method

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

Bliss, Mary

2013-11-30

Sulfate solubility in glass is a key parameter in many commercial glasses and nuclear waste glasses. This report summarizes key publications specific to sulfate solubility experimental methods and the underlying physical chemistry calculations. The published methods and experimental data are used to verify the calculations in this report and are expanded to a range of current technical interest. The calculations and experimental methods described in this report will guide several experiments on sulfate solubility and saturation for the Hanford Waste Treatment Plant Enhanced Waste Glass Models effort. There are several tables of sulfate gas equilibrium values at high temperature tomore » guide experimental gas mixing and to achieve desired SO3 levels. This report also describes the necessary equipment and best practices to perform sulfate saturation experiments for molten glasses. Results and findings will be published when experimental work is finished and this report is validated from the data obtained.« less

Rapid experimental measurements of physicochemical properties to inform models and testing.

PubMed

Nicolas, Chantel I; Mansouri, Kamel; Phillips, Katherine A; Grulke, Christopher M; Richard, Ann M; Williams, Antony J; Rabinowitz, James; Isaacs, Kristin K; Yau, Alice; Wambaugh, John F

2018-05-02

The structures and physicochemical properties of chemicals are important for determining their potential toxicological effects, toxicokinetics, and route(s) of exposure. These data are needed to prioritize the risk for thousands of environmental chemicals, but experimental values are often lacking. In an attempt to efficiently fill data gaps in physicochemical property information, we generated new data for 200 structurally diverse compounds, which were rigorously selected from the USEPA ToxCast chemical library, and whose structures are available within the Distributed Structure-Searchable Toxicity Database (DSSTox). This pilot study evaluated rapid experimental methods to determine five physicochemical properties, including the log of the octanol:water partition coefficient (known as log(K ow ) or logP), vapor pressure, water solubility, Henry's law constant, and the acid dissociation constant (pKa). For most compounds, experiments were successful for at least one property; log(K ow ) yielded the largest return (176 values). It was determined that 77 ToxPrint structural features were enriched in chemicals with at least one measurement failure, indicating which features may have played a role in rapid method failures. To gauge consistency with traditional measurement methods, the new measurements were compared with previous measurements (where available). Since quantitative structure-activity/property relationship (QSAR/QSPR) models are used to fill gaps in physicochemical property information, 5 suites of QSPRs were evaluated for their predictive ability and chemical coverage or applicability domain of new experimental measurements. The ability to have accurate measurements of these properties will facilitate better exposure predictions in two ways: 1) direct input of these experimental measurements into exposure models; and 2) construction of QSPRs with a wider applicability domain, as their predicted physicochemical values can be used to parameterize exposure models in the absence of experimental data. Published by Elsevier B.V.

DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions.

PubMed

Vlachos, Ioannis S; Paraskevopoulou, Maria D; Karagkouni, Dimitra; Georgakilas, Georgios; Vergoulis, Thanasis; Kanellos, Ilias; Anastasopoulos, Ioannis-Laertis; Maniou, Sofia; Karathanou, Konstantina; Kalfakakou, Despina; Fevgas, Athanasios; Dalamagas, Theodore; Hatzigeorgiou, Artemis G

2015-01-01

microRNAs (miRNAs) are short non-coding RNA species, which act as potent gene expression regulators. Accurate identification of miRNA targets is crucial to understanding their function. Currently, hundreds of thousands of miRNA:gene interactions have been experimentally identified. However, this wealth of information is fragmented and hidden in thousands of manuscripts and raw next-generation sequencing data sets. DIANA-TarBase was initially released in 2006 and it was the first database aiming to catalog published experimentally validated miRNA:gene interactions. DIANA-TarBase v7.0 (http://www.microrna.gr/tarbase) aims to provide for the first time hundreds of thousands of high-quality manually curated experimentally validated miRNA:gene interactions, enhanced with detailed meta-data. DIANA-TarBase v7.0 enables users to easily identify positive or negative experimental results, the utilized experimental methodology, experimental conditions including cell/tissue type and treatment. The new interface provides also advanced information ranging from the binding site location, as identified experimentally as well as in silico, to the primer sequences used for cloning experiments. More than half a million miRNA:gene interactions have been curated from published experiments on 356 different cell types from 24 species, corresponding to 9- to 250-fold more entries than any other relevant database. DIANA-TarBase v7.0 is freely available. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Reproducible model development in the cardiac electrophysiology Web Lab.

PubMed

Daly, Aidan C; Clerx, Michael; Beattie, Kylie A; Cooper, Jonathan; Gavaghan, David J; Mirams, Gary R

2018-05-26

The modelling of the electrophysiology of cardiac cells is one of the most mature areas of systems biology. This extended concentration of research effort brings with it new challenges, foremost among which is that of choosing which of these models is most suitable for addressing a particular scientific question. In a previous paper, we presented our initial work in developing an online resource for the characterisation and comparison of electrophysiological cell models in a wide range of experimental scenarios. In that work, we described how we had developed a novel protocol language that allowed us to separate the details of the mathematical model (the majority of cardiac cell models take the form of ordinary differential equations) from the experimental protocol being simulated. We developed a fully-open online repository (which we termed the Cardiac Electrophysiology Web Lab) which allows users to store and compare the results of applying the same experimental protocol to competing models. In the current paper we describe the most recent and planned extensions of this work, focused on supporting the process of model building from experimental data. We outline the necessary work to develop a machine-readable language to describe the process of inferring parameters from wet lab datasets, and illustrate our approach through a detailed example of fitting a model of the hERG channel using experimental data. We conclude by discussing the future challenges in making further progress in this domain towards our goal of facilitating a fully reproducible approach to the development of cardiac cell models. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

The neural bases of feeling understood and not understood.

PubMed

Morelli, Sylvia A; Torre, Jared B; Eisenberger, Naomi I

2014-12-01

Past research suggests that feeling understood enhances both personal and social well-being. However, little research has examined the neurobiological bases of feeling understood and not understood. We addressed these gaps by experimentally inducing felt understanding and not understanding as participants underwent functional magnetic resonance imaging. The results demonstrated that feeling understood activated neural regions previously associated with reward and social connection (i.e. ventral striatum and middle insula), while not feeling understood activated neural regions previously associated with negative affect (i.e. anterior insula). Both feeling understood and not feeling understood activated different components of the mentalizing system (feeling understood: precuneus and temporoparietal junction; not feeling understood: dorsomedial prefrontal cortex). Neural responses were associated with subsequent feelings of social connection and disconnection and were modulated by individual differences in rejection sensitivity. Thus, this study provides insight into the psychological processes underlying feeling understood (or not) and may suggest new avenues for targeted interventions that amplify the benefits of feeling understood or buffer individuals from the harmful consequences of not feeling understood. © The Author (2014). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Identification and quantification of glucosinolate and flavonol compounds in rocket salad (Eruca sativa, Eruca vesicaria and Diplotaxis tenuifolia) by LC-MS: highlighting the potential for improving nutritional value of rocket crops.

PubMed

Bell, Luke; Oruna-Concha, Maria Jose; Wagstaff, Carol

2015-04-01

Liquid chromatography mass spectrometry (LC-MS) was used to obtain glucosinolate and flavonol content for 35 rocket accessions and commercial varieties. 13 glucosinolates and 11 flavonol compounds were identified. Semi-quantitative methods were used to estimate concentrations of both groups of compounds. Minor glucosinolate composition was found to be different between accessions; concentrations varied significantly. Flavonols showed differentiation between genera, with Diplotaxis accumulating quercetin glucosides and Eruca accumulating kaempferol glucosides. Several compounds were detected in each genus that have only previously been reported in the other. We highlight how knowledge of phytochemical content and concentration can be used to breed new, nutritionally superior varieties. We also demonstrate the effects of controlled environment conditions on the accumulations of glucosinolates and flavonols and explore the reasons for differences with previous studies. We stress the importance of consistent experimental design between research groups to effectively compare and contrast results. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Does dishonesty really invite third-party punishment? Results of a more stringent test.

PubMed

Konishi, Naoki; Ohtsubo, Yohsuke

2015-05-01

Many experiments have demonstrated that people are willing to incur cost to punish norm violators even when they are not directly harmed by the violation. Such altruistic third-party punishment is often considered an evolutionary underpinning of large-scale human cooperation. However, some scholars argue that previously demonstrated altruistic third-party punishment against fairness-norm violations may be an experimental artefact. For example, envy-driven retaliatory behaviour (i.e. spite) towards better-off unfair game players may be misidentified as altruistic punishment. Indeed, a recent experiment demonstrated that participants ceased to inflict third-party punishment against an unfair player once a series of key methodological problems were systematically controlled for. Noticing that a previous finding regarding apparently altruistic third-party punishment against honesty-norm violations may have been subject to methodological issues, we used a different and what we consider to be a more sound design to evaluate these findings. Third-party punishment against dishonest players withstood this more stringent test. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Molecular dynamics equation of state for nonpolar geochemical fluids

NASA Astrophysics Data System (ADS)

Duan, Zhenhao; Møller, Nancy; Wears, John H.

1995-04-01

Remarkable agreement between molecular dynamics simulations and experimental measurements has been obtained for methane for a large range of intensive variables, including those corresponding to liquid/vapor coexistence. Using a simple Lennard-Jones potential the simulations not only predict the PVT properties up to 2000°C and 20,000 bar with errors less than 1.5%, but also reproduce phase equilibria well below 0°C with accuracy close to experiment. This two-parameter molecular dynamics equation of state (SOS) is accurate for a much larger range of temperatures and pressures than our previously published EOS with a total fifteen parameters or that of Angus et al. (1978) with thirty-three parameters. By simple scaling, it is possible to predict PVT and phase equilibria of other nonpolar and weakly polar species.

A representation of an NTCP function for local complication mechanisms

NASA Astrophysics Data System (ADS)

Alber, M.; Nüsslin, F.

2001-02-01

A mathematical formalism was tailored for the description of mechanisms complicating radiation therapy with a predominantly local component. The functional representation of an NTCP function was developed based on the notion that it has to be robust against population averages in order to be applicable to experimental data. The model was required to be invariant under scaling operations of the dose and the irradiated volume. The NTCP function was derived from the model assumptions that the complication is a consequence of local tissue damage and that the probability of local damage in a small reference volume is independent of the neighbouring volumes. The performance of the model was demonstrated with an animal model which has been published previously (Powers et al 1998 Radiother. Oncol. 46 297-306).

Determination of the global recombination rate coefficient for the ISX-B Tokamak

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

Langley, R.A.; Howe, H.C.

1983-01-01

The global recombination rate coefficient for hydrogen has been measured for the ISX-B tokamak vacuum vessel for various surface conditions. The measurements were performed by observing the rate of decrease of gas pressure in the vessel during a glow discharge. The parameters of the glow discharge and the complete experimental method are described. Previously published analytic and numerical models are used for data analysis. The effects of surface contamination on the results are described. For ''unclean'' wall conditions sigmak/sub r/ = 1.8 x 10/sup -28/ cm/sup 4//atom.s at 296 K and increases to sigmak/sub r/ = 4.4 x 10/sup -28/more » cm/sup 4//atoms.s for ''clean'' conditions and remains constant until subsequent exposure to air.« less

Dynamical effects in x-ray absorption spectra of graphene and monolayered h -BN on Ni(111)

NASA Astrophysics Data System (ADS)

Rusz, J.; Preobrajenski, A. B.; Ng, May Ling; Vinogradov, N. A.; Mårtensson, N.; Wessely, O.; Sanyal, B.; Eriksson, O.

2010-02-01

We present first-principles calculations of x-ray absorption spectra of graphene and hexagonal BN monolayer on the Ni(111) substrate. Including dynamical core-hole screening effects according to the theory of Mahan-Nozières-de Dominics (MND) results in an overall good agreement with previously published experimental data and our new observations. This approach provides a unified first-principles description of the electronic structure and core excitations in the sp2 -bonded materials on metal surfaces and a better insight into the dynamics of screening effects. We demonstrate in particular that the observed spectral features of graphene and hexagonal BN can be well reproduced with the MND theory, and that they are determined by a delicate balance between initial and final-state effects.

Ab initio non-adiabatic study of the 4pσ B'' 1Σ+u state of H2

NASA Astrophysics Data System (ADS)

Glass-Maujean, M.; Schmoranzer, H.

2018-05-01

Fully ab initio non-adiabatic multichannel quantum defect calculations of the 4pσ B'' 1∑u+ energy levels, line intensities and widths, based on the latest quantum-chemical clamped-nuclei calculations of Wolniewicz and collaborators are presented for H2. The B″ state corresponds to the inner well of the ? state. The B'' v ≥ 1 levels are rapidly predissociated through vibrational coupling with the 3pσ B' 1Σ+u continuum so that coupled-equation calculations become unstable. Multichannel quantum defect theory, on the other hand, is demonstrated to be particularly suited to this situation. Experimental data as level energies, line intensities and dissociation widths were revisited and corrected. Reinvestigating previously published spectra, several new lines were assigned.

Generalized Effective Medium Theory for Particulate Nanocomposite Materials

PubMed Central

Siddiqui, Muhammad Usama; Arif, Abul Fazal M.

2016-01-01

The thermal conductivity of particulate nanocomposites is strongly dependent on the size, shape, orientation and dispersion uniformity of the inclusions. To correctly estimate the effective thermal conductivity of the nanocomposite, all these factors should be included in the prediction model. In this paper, the formulation of a generalized effective medium theory for the determination of the effective thermal conductivity of particulate nanocomposites with multiple inclusions is presented. The formulated methodology takes into account all the factors mentioned above and can be used to model nanocomposites with multiple inclusions that are randomly oriented or aligned in a particular direction. The effect of inclusion dispersion non-uniformity is modeled using a two-scale approach. The applications of the formulated effective medium theory are demonstrated using previously published experimental and numerical results for several particulate nanocomposites. PMID:28773817

The AMP-activated protein kinase beta 1 subunit modulates erythrocyte integrity.

PubMed

Cambridge, Emma L; McIntyre, Zoe; Clare, Simon; Arends, Mark J; Goulding, David; Isherwood, Christopher; Caetano, Susana S; Reviriego, Carmen Ballesteros; Swiatkowska, Agnieszka; Kane, Leanne; Harcourt, Katherine; Adams, David J; White, Jacqueline K; Speak, Anneliese O

2017-01-01

Failure to maintain a normal in vivo erythrocyte half-life results in the development of hemolytic anemia. Half-life is affected by numerous factors, including energy balance, electrolyte gradients, reactive oxygen species, and membrane plasticity. The heterotrimeric AMP-activated protein kinase (AMPK) is an evolutionarily conserved serine/threonine kinase that acts as a critical regulator of cellular energy balance. Previous roles for the alpha 1 and gamma 1 subunits in the control of erythrocyte survival have been reported. In the work described here, we studied the role of the beta 1 subunit in erythrocytes and observed microcytic anemia with compensatory extramedullary hematopoiesis together with splenomegaly and increased osmotic resistance. Copyright © 2016 ISEH - International Society for Experimental Hematology. Published by Elsevier Inc. All rights reserved.

Arbitrary amplitude ion-acoustic solitary waves in electronegative plasmas with electrons featuring Tsallis distribution

NASA Astrophysics Data System (ADS)

Ghebache, Siham; Tribeche, Mouloud

2017-10-01

The problem of arbitrary amplitude ion-acoustic solitary waves (IASWs), which accompany electronegative plasmas having positive ions, negative ions, and nonextensive electrons is addressed. The energy integral equation with a new Sagdeev potential is analyzed to examine the existence regions of the IASWs. Different types of electronegative plasmas inspired from the experimental studies of Ichiki et al. (2001) are discussed. Our results show that in such plasmas IASWs, the amplitude and nature of which depend sensitively on the mass and density ratio of the positive and negative ions as well as the q-nonextensive parameter, can exist. Interestingly, one finds that our plasma model supports the coexistence of smooth rarefactive and spiky compressive IASWs. Our results complement and provide new insights on previously published findings on this problem.

Ichthyophonus-induced cardiac damage: a mechanism for reduced swimming stamina in salmonids

USGS Publications Warehouse

Kocan, R.; LaPatra, S.; Gregg, J.; Winton, J.; Hershberger, P.

2006-01-01

Swimming stamina, measured as time-to-fatigue, was reduced by approximately two-thirds in rainbow trout experimentally infected with Ichthyophonus. Intensity of Ichthyophonus infection was most severe in cardiac muscle but multiple organs were infected to a lesser extent. The mean heart weight of infected fish was 40% greater than that of uninfected fish, the result of parasite biomass, infiltration of immune cells and fibrotic (granuloma) tissue surrounding the parasite. Diminished swimming stamina is hypothesized to be due to cardiac failure resulting from the combination of parasite-damaged heart muscle and low myocardial oxygen supply during sustained aerobic exercise. Loss of stamina in Ichthyophonus-infected salmonids could explain the poor performance previously reported for wild Chinook and sockeye salmon stocks during their spawning migration. ?? 2006 Blackwell Publishing Ltd.

Methane emission by adult ostriches (Struthio camelus).

PubMed

Frei, Samuel; Dittmann, Marie T; Reutlinger, Christoph; Ortmann, Sylvia; Hatt, Jean-Michel; Kreuzer, Michael; Clauss, Marcus

2015-02-01

Ostriches (Struthio camelus) are herbivorous birds with a digestive physiology that shares several similarities with that of herbivorous mammals. Previous reports, however, claimed a very low methane emission from ostriches, which would be clearly different from mammals. If this could be confirmed, ostrich meat would represent a very attractive alternative to ruminant-and generally mammalian-meat by representing a particularly low-emission agricultural form of production. We individually measured, by chamber respirometry, the amount of oxygen consumed as well as carbon dioxide and methane emitted from six adult ostriches (body mass 108.3±8.3 kg) during a 24-hour period when fed a pelleted lucerne diet. While oxygen consumption was in the range of values previously reported for ostriches, supporting the validity of our experimental setup, methane production was, at 17.5±3.2 L d(-1), much higher than previously reported for this species, and was of the magnitude expected for similar-sized, nonruminant mammalian herbivores. These results suggest that methane emission is similar between ostriches and nonruminant mammalian herbivores and that the environmental burden of these animals is comparable. The findings furthermore indicate that it appears justified to use currently available scaling equations for methane production of nonruminant mammals in paleo-reconstructions of methane production of herbivorous dinosaurs. Copyright © 2014. Published by Elsevier Inc.

The Impact of Guided Notes on Post-Secondary Student Achievement: A Meta-Analysis

ERIC Educational Resources Information Center

Larwin, Karen H.; Larwin, David A.

2013-01-01

The common practice of using of guided notes in the post-secondary classroom is not fully appreciated or understood. In an effort to add to the existing research about this phenomenon, the current investigation expands on previously published research and one previously published meta-analysis that examined the impact of guided notes on…

50 CFR 648.12 - Experimental fishing.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 10 2011-10-01 2011-10-01 false Experimental fishing. 648.12 Section 648... Experimental fishing. Link to an amendment published at 76 FR 60649, Sept. 29, 2011. The Regional Administrator... part for the conduct of experimental fishing beneficial to the management of the resources or fishery...

Manipulation strategies for massive space payloads

NASA Technical Reports Server (NTRS)

Book, Wayne J.

1989-01-01

Control for the bracing strategy is being examined. It was concluded earlier that trajectory planning must be improved to best achieve the bracing motion. Very interesting results were achieved which enable the inverse dynamics of flexible arms to be calculated for linearized motion in a more efficient manner than previously published. The desired motion of the end point beginning at t=0 and ending at t=t sub f is used to calculate the required torque at the joint. The solution is separated into a causal function that is zero for t is less than 0 and an accusal function which is zero for t is greater than t sub f. A number of alternative end point trajectories were explored in terms of the peak torque required, the amount of anticipatory action, and other issues. The single link case is the immediate subject and an experimental verification of that case is being performed. Modeling with experimental verification of closed chain dynamics continues. Modeling effort has pointed out inaccuracies that result from the choice of numerical techniques used to incorporate the closed chain constraints when modeling our experimental prototype RALF (Robotic Arm Large and Flexible). Results were compared to TREETOPS, a multi body code. The experimental verification work is suggesting new ways to make comparisons with systems having structural linearity and joint and geometric nonlinearity. The generation of inertial forces was studied with a small arm that will damp the large arm's vibration.

Experimental sheep BSE prions generate the vCJD phenotype when serially passaged in transgenic mice expressing human prion protein.

PubMed

Joiner, Susan; Asante, Emmanuel A; Linehan, Jacqueline M; Brock, Lara; Brandner, Sebastian; Bellworthy, Susan J; Simmons, Marion M; Hope, James; Collinge, John; Wadsworth, Jonathan D F

2018-03-15

The epizootic prion disease of cattle, bovine spongiform encephalopathy (BSE), causes variant Creutzfeldt-Jakob disease (vCJD) in humans following dietary exposure. While it is assumed that all cases of vCJD attributed to a dietary aetiology are related to cattle BSE, sheep and goats are susceptible to experimental oral challenge with cattle BSE prions and farmed animals in the UK were undoubtedly exposed to BSE-contaminated meat and bone meal during the late 1980s and early 1990s. Although no natural field cases of sheep BSE have been identified, it cannot be excluded that some BSE-infected sheep might have entered the European human food chain. Evaluation of the zoonotic potential of sheep BSE prions has been addressed by examining the transmission properties of experimental brain isolates in transgenic mice that express human prion protein, however to-date there have been relatively few studies. Here we report that serial passage of experimental sheep BSE prions in transgenic mice expressing human prion protein with methionine at residue 129 produces the vCJD phenotype that mirrors that seen when the same mice are challenged with vCJD prions from patient brain. These findings are congruent with those reported previously by another laboratory, and thereby strongly reinforce the view that sheep BSE prions could have acted as a causal agent of vCJD within Europe. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Adaptability and reproducibility of a memory disruption rTMS protocol in the PharmaCog IMI European project.

PubMed

Martin-Trias, Pablo; Lanteaume, Laura; Solana, Elisabeth; Cassé-Perrot, Catherine; Fernández-Cabello, Sara; Babiloni, Claudio; Marzano, Nicola; Junqué, Carme; Rossini, Paolo Maria; Micallef, Joëlle; Truillet, Romain; Charles, Estelle; Jouve, Elisabeth; Bordet, Régis; Santamaria, Joan; Jovicich, Jorge; Rossi, Simone; Pascual-Leone, Alvaro; Blin, Olivier; Richardson, Jill; Bartrés-Faz, David

2018-06-19

Transcranial magnetic stimulation (TMS) can interfere with cognitive processes, such as transiently impairing memory. As part of a multi-center European project, we investigated the adaptability and reproducibility of a previously published TMS memory interfering protocol in two centers using EEG or fMRI scenarios. Participants were invited to attend three experimental sessions on different days, with sham repetitive TMS (rTMS) applied on day 1 and real rTMS on days 2 and 3. Sixty-eight healthy young men were included. On each experimental day, volunteers were instructed to remember visual pictures while receiving neuronavigated rTMS trains (20 Hz, 900 ms) during picture encoding at the left dorsolateral prefrontal cortex (L-DLPFC) and the vertex. Mixed ANOVA model analyses were performed. rTMS to the L-DLPFC significantly disrupted recognition memory on experimental day 2. No differences were found between centers or between fMRI and EEG recordings. Subjects with lower baseline memory performances were more susceptible to TMS disruption. No stability of TMS-induced memory interference could be demonstrated on day 3. Our data suggests that adapted cognitive rTMS protocols can be implemented in multi-center studies incorporating standardized experimental procedures. However, our center and modality effects analyses lacked sufficient statistical power, hence highlighting the need to conduct further studies with larger samples. In addition, inter and intra-subject variability in response to TMS might limit its application in crossover or longitudinal studies.

Proceedings, phenomenology and applications of high temperature superconductors

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

Bedell, K.S.

1991-01-01

Phenomenology and Applications of High Temperature Superconductors, The Los Alamos Symposium: 1991, was sponsored by the Los Alamos National Laboratory, Center for Materials Science, the Advanced Studies Program on High Temperature Superconductivity Theory (ASP) and the Exploratory Research and Development Center. This is the second symposium in the series. High Temperature Superconductivity, The Los Alamos Symposium: 1989, also published by Addison Wesley, focused on the cutting-edge theoretical and experimental issues in high temperature superconductors. This symposium, with its focus on the phenomenology and applications of high temperature superconductors, gives a complementary review of the aspects of the field closely relatedmore » to the impact of high temperature superconductors on technology. The objective of ASP is to advance the field on a broad front with no specific point of view by bringing a team of leading academic theorists into a joint effort with the theoretical and experimental scientists of a major DOE national laboratory. The ASP consisted of fellows led by Robert Schrieffer (UCSB and now FSU) joined by David Pines (University of illinois), Elihu Abrahams (Rutgers), Sebastian Doniach (Stanford), and Maurice Rice (ETH, Zurich) and theoretical and experimental staff of Los Alamos National Laboratory. This synergism of academic, laboratory, theoretical and experimental research produced a level of interaction and excitement that would not be possible otherwise. This publication and the previous one in the series are just examples of how this approach to advancing science can achieve significant contributions.« less

Proceedings, phenomenology and applications of high temperature superconductors

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

Bedell, K.S.

1991-12-31

Phenomenology and Applications of High Temperature Superconductors, The Los Alamos Symposium: 1991, was sponsored by the Los Alamos National Laboratory, Center for Materials Science, the Advanced Studies Program on High Temperature Superconductivity Theory (ASP) and the Exploratory Research and Development Center. This is the second symposium in the series. High Temperature Superconductivity, The Los Alamos Symposium: 1989, also published by Addison Wesley, focused on the cutting-edge theoretical and experimental issues in high temperature superconductors. This symposium, with its focus on the phenomenology and applications of high temperature superconductors, gives a complementary review of the aspects of the field closely relatedmore » to the impact of high temperature superconductors on technology. The objective of ASP is to advance the field on a broad front with no specific point of view by bringing a team of leading academic theorists into a joint effort with the theoretical and experimental scientists of a major DOE national laboratory. The ASP consisted of fellows led by Robert Schrieffer (UCSB and now FSU) joined by David Pines (University of illinois), Elihu Abrahams (Rutgers), Sebastian Doniach (Stanford), and Maurice Rice (ETH, Zurich) and theoretical and experimental staff of Los Alamos National Laboratory. This synergism of academic, laboratory, theoretical and experimental research produced a level of interaction and excitement that would not be possible otherwise. This publication and the previous one in the series are just examples of how this approach to advancing science can achieve significant contributions.« less

Validating internet research: a test of the psychometric equivalence of internet and in-person samples.

PubMed

Meyerson, Paul; Tryon, Warren W

2003-11-01

This study evaluated the psychometric equivalency of Web-based research. The Sexual Boredom Scale was presented via the World-Wide Web along with five additional scales used to validate it. A subset of 533 participants that matched a previously published sample (Watt & Ewing, 1996) on age, gender, and race was identified. An 8 x 8 correlation matrix from the matched Internet sample was compared via structural equation modeling with a similar 8 x 8 correlation matrix from the previously published study. The Internet and previously published samples were psychometrically equivalent. Coefficient alpha values calculated on the matched Internet sample yielded reliability coefficients almost identical to those for the previously published sample. Factors such as computer administration and uncontrollable administration settings did not appear to affect the results. Demographic data indicated an overrepresentation of males by about 6% and Caucasians by about 13% relative to the U.S. Census (2000). A total of 2,230 participants were obtained in about 8 months without remuneration. These results suggest that data collection on the Web is (1) reliable, (2) valid, (3) reasonably representative, (4) cost effective, and (5) efficient.

Rotational spectrum of 13C{2}-methyl formate (HCOO13CH{3}) and detection of the two 13C-methyl formate in Orion

NASA Astrophysics Data System (ADS)

Carvajal, M.; Margulès, L.; Tercero, B.; Demyk, K.; Kleiner, I.; Guillemin, J. C.; Lattanzi, V.; Walters, A.; Demaison, J.; Wlodarczak, G.; Huet, T. R.; Møllendal, H.; Ilyushin, V. V.; Cernicharo, J.

2009-06-01

Context: Laboratory measurements and analysis of the microwave and millimeter-wave spectra of potential interstellar molecules are a prerequisite for their subsequent identification by radioastronomical techniques. The spectral analysis provides spectroscopic parameters that are used in the assignment procedure of the laboratory spectra, and that also predict the frequencies of transitions not measured in the laboratory with a high degree of precision. Aims: An experimental laboratory study and its theoretical analysis is presented for 13C2-methyl formate (HCOO13CH3) allowing a search for this isotopologue in the Orion molecular cloud. The 13C1-methyl formate (H13COOCH3) molecule was also searched for in this interstellar cloud, using previously published spectroscopic data. Methods: The experimental spectra of 13C2-methyl formate were recorded in the microwave and sub-mm energy ranges (4-20 GHz, 8-80 GHz, 150-700 GHz). The spectra were analyzed using the Rho-Axis Method (RAM), which takes the CH3 internal rotation and the coupling between internal rotation and global rotation into account. Results: Twenty-seven spectroscopic constants of 13C2-methyl formate have been obtained from a fit of 936 transitions of the ground torsional state with a standard (unitless) deviation of 1.08. A prediction of line positions and intensities is also produced. This prediction allowed us to identify 230 13C2-methyl formate lines in the Orion interstellar molecular cloud. We refitted all previously published ground state transitions of the 13C1-methyl formate molecule in order to provide a prediction of its ground state spectrum. 234 lines of 13C1-methyl formate were detected in the Orion interstellar cloud using that prediction. Tables A.1-A.5 are only available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb.u-strasbg.fr/cgi-bin/qcat?J/A+A/500/1109

Observation of Weyl points

Science.gov Websites

copolymers, liquid crystals. Experimental observation of Weyl points First public annoucement on 11 Feburary Vishwanath from University of California, Berkeley. "Experimental Observation of Weyl Semimetals" ; Published by Science on 16 July, 2015. "Experimental observation of Weyl points" Featured on the

A Quantitative Comparison of the Behavior of Human Ventricular Cardiac Electrophysiology Models in Tissue

PubMed Central

Elshrif, Mohamed M.; Cherry, Elizabeth M.

2014-01-01

Numerical integration of mathematical models of heart cell electrophysiology provides an important computational tool for studying cardiac arrhythmias, but the abundance of available models complicates selecting an appropriate model. We study the behavior of two recently published models of human ventricular action potentials, the Grandi-Pasqualini-Bers (GPB) and the O'Hara-Virág-Varró-Rudy (OVVR) models, and compare the results with four previously published models and with available experimental and clinical data. We find the shapes and durations of action potentials and calcium transients differ between the GPB and OVVR models, as do the magnitudes and rate-dependent properties of transmembrane currents and the calcium transient. Differences also occur in the steady-state and S1–S2 action potential duration and conduction velocity restitution curves, including a maximum conduction velocity for the OVVR model roughly half that of the GPB model and well below clinical values. Between single cells and tissue, both models exhibit differences in properties, including maximum upstroke velocity, action potential amplitude, and minimum diastolic interval. Compared to experimental data, action potential durations for the GPB and OVVR models agree fairly well (although OVVR epicardial action potentials are shorter), but maximum slopes of steady-state restitution curves are smaller. Although studies show alternans in normal hearts, it occurs only in the OVVR model, and only for a narrow range of cycle lengths. We find initiated spiral waves do not progress to sustained breakup for either model. The dominant spiral wave period of the GPB model falls within clinically relevant values for ventricular tachycardia (VT), but for the OVVR model, the dominant period is longer than periods associated with VT. Our results should facilitate choosing a model to match properties of interest in human cardiac tissue and to replicate arrhythmia behavior more closely. Furthermore, by indicating areas where existing models disagree, our findings suggest avenues for further experimental work. PMID:24416228

Article processing charges, funding, and open access publishing at Journal of Experimental & Clinical Assisted Reproduction.

PubMed

Sills, Eric Scott; Vincent, Tina Thibault; Palermo, Gianpiero D

2005-01-13

Journal of Experimental & Clinical Assisted Reproduction is an Open Access, online, electronic journal published by BioMed Central with full contents available to the scientific and medical community free of charge to all readers. Authors maintain the copyright to their own work, a policy facilitating dissemination of data to the widest possible audience without requiring permission from the publisher. This Open Access publishing model is subsidized by authors (or their institutions/funding agencies) in the form of a single pound330 article processing charge (APC), due at the time of manuscript acceptance for publication. Payment of the APC is not a condition for formal peer review and does not apply to articles rejected after review. Additionally, this fee is waived for authors whose institutions are BioMed Central members or where genuine financial hardship exists. Considering ordinary publication fees related to page charges and reprints, the APC at Journal of Experimental & Clinical Assisted Reproduction is comparable to costs associated with publishing in some traditional print journals, and is less expensive than many. Implementation of the APC within this Open Access framework is envisioned as a modern research-friendly policy that supports networking among investigators, brings new research into reach rapidly, and empowers authors with greater control over their own scholarly publications.

Predicting crystalline lens fall caused by accommodation from changes in wavefront error

PubMed Central

He, Lin; Applegate, Raymond A.

2011-01-01

PURPOSE To illustrate and develop a method for estimating crystalline lens decentration as a function of accommodative response using changes in wavefront error and show the method and limitations using previously published data (2004) from 2 iridectomized monkey eyes so that clinicians understand how spherical aberration can induce coma, in particular in intraocular lens surgery. SETTINGS College of Optometry, University of Houston, Houston, USA. DESIGN Evaluation of diagnostic test or technology. METHODS Lens decentration was estimated by displacing downward the wavefront error of the lens with respect to the limiting aperture (7.0 mm) and ocular first surface wavefront error for each accommodative response (0.00 to 11.00 diopters) until measured values of vertical coma matched previously published experimental data (2007). Lens decentration was also calculated using an approximation formula that only included spherical aberration and vertical coma. RESULTS The change in calculated vertical coma was consistent with downward lens decentration. Calculated downward lens decentration peaked at approximately 0.48 mm of vertical decentration in the right eye and approximately 0.31 mm of decentration in the left eye using all Zernike modes through the 7th radial order. Calculated lens decentration using only coma and spherical aberration formulas was peaked at approximately 0.45 mm in the right eye and approximately 0.23 mm in the left eye. CONCLUSIONS Lens fall as a function of accommodation was quantified noninvasively using changes in vertical coma driven principally by the accommodation-induced changes in spherical aberration. The newly developed method was valid for a large pupil only. PMID:21700108

Pathophysiological mechanisms of neuropathic pain: comparison of sensory phenotypes in patients and human surrogate pain models.

PubMed

Vollert, Jan; Magerl, Walter; Baron, Ralf; Binder, Andreas; Enax-Krumova, Elena K; Geisslinger, Gerd; Gierthmühlen, Janne; Henrich, Florian; Hüllemann, Philipp; Klein, Thomas; Lötsch, Jörn; Maier, Christoph; Oertel, Bruno; Schuh-Hofer, Sigrid; Tölle, Thomas R; Treede, Rolf-Detlef

2018-06-01

As an indirect approach to relate previously identified sensory phenotypes of patients suffering from peripheral neuropathic pain to underlying mechanisms, we used a published sorting algorithm to estimate the prevalence of denervation, peripheral and central sensitization in 657 healthy subjects undergoing experimental models of nerve block (NB) (compression block and topical lidocaine), primary hyperalgesia (PH) (sunburn and topical capsaicin), or secondary hyperalgesia (intradermal capsaicin and electrical high-frequency stimulation), and in 902 patients suffering from neuropathic pain. Some of the data have been previously published. Randomized split-half analysis verified a good concordance with a priori mechanistic sensory profile assignment in the training (79%, Cohen κ = 0.54, n = 265) and the test set (81%, Cohen κ = 0.56, n = 279). Nerve blocks were characterized by pronounced thermal and mechanical sensory loss, but also mild pinprick hyperalgesia and paradoxical heat sensations. Primary hyperalgesia was characterized by pronounced gain for heat, pressure and pinprick pain, and mild thermal sensory loss. Secondary hyperalgesia was characterized by pronounced pinprick hyperalgesia and mild thermal sensory loss. Topical lidocaine plus topical capsaicin induced a combined phenotype of NB plus PH. Topical menthol was the only model with significant cold hyperalgesia. Sorting of the 902 patients into these mechanistic phenotypes led to a similar distribution as the original heuristic clustering (65% identity, Cohen κ = 0.44), but the denervation phenotype was more frequent than in heuristic clustering. These data suggest that sorting according to human surrogate models may be useful for mechanism-based stratification of neuropathic pain patients for future clinical trials, as encouraged by the European Medicines Agency.

Residual γH2AX foci after ex vivo irradiation of patient samples with known tumour-type specific differences in radio-responsiveness.

PubMed

Menegakis, Apostolos; De Colle, Chiara; Yaromina, Ala; Hennenlotter, Joerg; Stenzl, Arnulf; Scharpf, Marcus; Fend, Falko; Noell, Susan; Tatagiba, Marcos; Brucker, Sara; Wallwiener, Diethelm; Boeke, Simon; Ricardi, Umberto; Baumann, Michael; Zips, Daniel

2015-09-01

To apply our previously published residual ex vivo γH2AX foci method to patient-derived tumour specimens covering a spectrum of tumour-types with known differences in radiation response. In addition, the data were used to simulate different experimental scenarios to simplify the method. Evaluation of residual γH2AX foci in well-oxygenated tumour areas of ex vivo irradiated patient-derived tumour specimens with graded single doses was performed. Immediately after surgical resection, the samples were cultivated for 24h in culture medium prior to irradiation and fixed 24h post-irradiation for γH2AX foci evaluation. Specimens from a total of 25 patients (including 7 previously published) with 10 different tumour types were included. Linear dose response of residual γH2AX foci was observed in all specimens with highly variable slopes among different tumour types ranging from 0.69 (95% CI: 1.14-0.24) to 3.26 (95% CI: 4.13-2.62) for chondrosarcomas (radioresistant) and classical seminomas (radiosensitive) respectively. Simulations suggest that omitting dose levels might simplify the assay without compromising robustness. Here we confirm clinical feasibility of the assay. The slopes of the residual foci number are well in line with the expected differences in radio-responsiveness of different tumour types implying that intrinsic radiation sensitivity contributes to tumour radiation response. Thus, this assay has a promising potential for individualized radiation therapy and prospective validation is warranted. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Transcriptome-wide investigation of genomic imprinting in chicken.

PubMed

Frésard, Laure; Leroux, Sophie; Servin, Bertrand; Gourichon, David; Dehais, Patrice; Cristobal, Magali San; Marsaud, Nathalie; Vignoles, Florence; Bed'hom, Bertrand; Coville, Jean-Luc; Hormozdiari, Farhad; Beaumont, Catherine; Zerjal, Tatiana; Vignal, Alain; Morisson, Mireille; Lagarrigue, Sandrine; Pitel, Frédérique

2014-04-01

Genomic imprinting is an epigenetic mechanism by which alleles of some specific genes are expressed in a parent-of-origin manner. It has been observed in mammals and marsupials, but not in birds. Until now, only a few genes orthologous to mammalian imprinted ones have been analyzed in chicken and did not demonstrate any evidence of imprinting in this species. However, several published observations such as imprinted-like QTL in poultry or reciprocal effects keep the question open. Our main objective was thus to screen the entire chicken genome for parental-allele-specific differential expression on whole embryonic transcriptomes, using high-throughput sequencing. To identify the parental origin of each observed haplotype, two chicken experimental populations were used, as inbred and as genetically distant as possible. Two families were produced from two reciprocal crosses. Transcripts from 20 embryos were sequenced using NGS technology, producing ∼200 Gb of sequences. This allowed the detection of 79 potentially imprinted SNPs, through an analysis method that we validated by detecting imprinting from mouse data already published. However, out of 23 candidates tested by pyrosequencing, none could be confirmed. These results come together, without a priori, with previous statements and phylogenetic considerations assessing the absence of genomic imprinting in chicken.

δ-dependency for privacy-preserving XML data publishing.

PubMed

Landberg, Anders H; Nguyen, Kinh; Pardede, Eric; Rahayu, J Wenny

2014-08-01

An ever increasing amount of medical data such as electronic health records, is being collected, stored, shared and managed in large online health information systems and electronic medical record systems (EMR) (Williams et al., 2001; Virtanen, 2009; Huang and Liou, 2007) [1-3]. From such rich collections, data is often published in the form of census and statistical data sets for the purpose of knowledge sharing and enabling medical research. This brings with it an increasing need for protecting individual people privacy, and it becomes an issue of great importance especially when information about patients is exposed to the public. While the concept of data privacy has been comprehensively studied for relational data, models and algorithms addressing the distinct differences and complex structure of XML data are yet to be explored. Currently, the common compromise method is to convert private XML data into relational data for publication. This ad hoc approach results in significant loss of useful semantic information previously carried in the private XML data. Health data often has very complex structure, which is best expressed in XML. In fact, XML is the standard format for exchanging (e.g. HL7 version 3(1)) and publishing health information. Lack of means to deal directly with data in XML format is inevitably a serious drawback. In this paper we propose a novel privacy protection model for XML, and an algorithm for implementing this model. We provide general rules, both for transforming a private XML schema into a published XML schema, and for mapping private XML data to the new privacy-protected published XML data. In addition, we propose a new privacy property, δ-dependency, which can be applied to both relational and XML data, and that takes into consideration the hierarchical nature of sensitive data (as opposed to "quasi-identifiers"). Lastly, we provide an implementation of our model, algorithm and privacy property, and perform an experimental analysis, to demonstrate the proposed privacy scheme in practical application. Copyright © 2014. Published by Elsevier Inc.

Measurement of Contractile Stress Generated by Cultured Rat Muscle on Silicon Cantilevers for Toxin Detection and Muscle Performance Enhancement

PubMed Central

Wilson, Kerry; Das, Mainak; Wahl, Kathryn J.; Colton, Richard J.; Hickman, James

2010-01-01

Background To date, biological components have been incorporated into MEMS devices to create cell-based sensors and assays, motors and actuators, and pumps. Bio-MEMS technologies present a unique opportunity to study fundamental biological processes at a level unrealized with previous methods. The capability to miniaturize analytical systems enables researchers to perform multiple experiments in parallel and with a high degree of control over experimental variables for high-content screening applications. Methodology/Principal Findings We have demonstrated a biological microelectromechanical system (BioMEMS) based on silicon cantilevers and an AFM detection system for studying the physiology and kinetics of myotubes derived from embryonic rat skeletal muscle. It was shown that it is possible to interrogate and observe muscle behavior in real time, as well as selectively stimulate the contraction of myotubes with the device. Stress generation of the tissue was estimated using a modification of Stoney's equation. Calculated stress values were in excellent agreement with previously published results for cultured myotubes, but not adult skeletal muscle. Other parameters such as time to peak tension (TPT), the time to half relaxation (½RT) were compared to the literature. It was observed that the myotubes grown on the BioMEMS device, while generating stress magnitudes comparable to those previously published, exhibited slower TPT and ½RT values. However, growth in an enhanced media increased these values. From these data it was concluded that the myotubes cultured on the cantilevers were of an embryonic phenotype. The system was also shown to be responsive to the application of a toxin, veratridine. Conclusions/Significance The device demonstrated here will provide a useful foundation for studying various aspects of muscle physiology and behavior in a controlled high-throughput manner as well as be useful for biosensor and drug discovery applications. PMID:20548775

Development of a step-down method for altering male C57BL/6 mouse housing density and hierarchical structure: Preparations for spaceflight studies.

PubMed

Scofield, David C; Rytlewski, Jeffrey D; Childress, Paul; Shah, Kishan; Tucker, Aamir; Khan, Faisal; Peveler, Jessica; Li, Ding; McKinley, Todd O; Chu, Tien-Min G; Hickman, Debra L; Kacena, Melissa A

2018-05-01

This study was initiated as a component of a larger undertaking designed to study bone healing in microgravity aboard the International Space Station (ISS). Spaceflight experimentation introduces multiple challenges not seen in ground studies, especially with regard to physical space, limited resources, and inability to easily reproduce results. Together, these can lead to diminished statistical power and increased risk of failure. It is because of the limited space, and need for improved statistical power by increasing sample size over historical numbers, NASA studies involving mice require housing mice at densities higher than recommended in the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011). All previous NASA missions in which mice were co-housed, involved female mice; however, in our spaceflight studies examining bone healing, male mice are required for optimal experimentation. Additionally, the logistics associated with spaceflight hardware and our study design necessitated variation of density and cohort make up during the experiment. This required the development of a new method to successfully co-house male mice while varying mouse density and hierarchical structure. For this experiment, male mice in an experimental housing schematic of variable density (Spaceflight Correlate) analogous to previously established NASA spaceflight studies was compared to a standard ground based housing schematic (Normal Density Controls) throughout the experimental timeline. We hypothesized that mice in the Spaceflight Correlate group would show no significant difference in activity, aggression, or stress when compared to Normal Density Controls. Activity and aggression were assessed using a novel activity scoring system (based on prior literature, validated in-house) and stress was assessed via body weights, organ weights, and veterinary assessment. No significant differences were detected between the Spaceflight Correlate group and the Normal Density Controls in activity, aggression, body weight, or organ weight, which was confirmed by veterinary assessments. Completion of this study allowed for clearance by NASA of our bone healing experiments aboard the ISS, and our experiment was successfully launched February 19, 2017 on SpaceX CRS-10. Copyright © 2018 The Committee on Space Research (COSPAR). Published by Elsevier Ltd. All rights reserved.

Quantitative evaluation of thermodynamic parameters of Li-Sn alloys related to their use in fusion reactor

NASA Astrophysics Data System (ADS)

Krasin, V. P.; Soyustova, S. I.

2018-07-01

Along with other liquid metals liquid lithium-tin alloys can be considered as an alternative to the use of solid plasma facing components of a future fusion reactor. Therefore, parameters characterizing both the ability to retain hydrogen isotopes and those that determine the extraction of tritium from a liquid metal can be of particular importance. Theoretical correlations based on the coordination cluster model have been used to obtain Sieverts' constants for solutions of hydrogen in liquid Li-Sn alloys. The results of theoretical computations are compared with the previously published experimental values for two alloys of the Li-Sn system. The Butler equation in combination with the equations describing the thermodynamic potentials of a binary solution is used to calculate the surface composition and surface tension of liquid Li-Sn alloys.

Research and development for a ground-based hydrogen-maser system

NASA Technical Reports Server (NTRS)

1972-01-01

The results of a joint experiment aimed primarily at the determination of the frequency of the H(1) hyperfine transition are reported. The transition frequency value for Cs-133 hyperfine transition is found. The result is the mean of two independent evaluations against the cesium reference, which differ by 0.002 Hz. The one-sigma uncertainty of the value nu sub H is also estimated to be 0.002 Hz. One evaluation is based on wall shift experiments at Harvard University; the other is a result of new wall shift measurement using many storage bulbs of different sizes at the National Bureau of Standards. The experimental procedures and the applied corrections are described. Results for the wall shift and for the frequency of hydrogen are compared with previously published values, and error limits of the experiments are discussed.

Optimizing sensitivity to γ with B0→D K+π-, D →KS0π+π- double Dalitz plot analysis

NASA Astrophysics Data System (ADS)

Craik, D.; Gershon, T.; Poluektov, A.

2018-03-01

Two of the most powerful methods currently used to determine the angle γ of the CKM Unitarity Triangle exploit B+→D K+, D →KS0π+π- decays and B0→D K+π-, D →K+K-, π+π- decays. It is possible to combine the strengths of both approaches in a "double Dalitz plot" analysis of B0→D K+π-, D →KS0π+π- decays. The potential sensitivity of such an analysis is investigated in the light of recently published experimental information on the B0→D K+π- decay. The formalism is also expanded, compared to previous discussions in the literature, to allow B0→D K+π- with any subsequent D decay to be included.

Defibrotide: properties and clinical use of an old/new drug.

PubMed

Pescador, R; Capuzzi, L; Mantovani, M; Fulgenzi, A; Ferrero, M E

2013-01-01

The drug named defibrotide (DFT) has been studied for many years. It has been shown to possess many activities: profibrinolytic, antithrombotic-thrombolytic, antiischemic (heart, liver, kidney, skin, brain), antishock, antiatherosclerotic, antirejection and anti-angiogenic. The previously displayed activities, as antithrombotic, profibrinolytic and anti-inflammatory, suggested its use in vascular disorders, as in the treatment of peripheral obliterative arterial disease and in thrombophlebitis. Some years after, the use of DFT in hepatic veno-occlusive disease has been also proposed. Even if DFT was considered for long time a multi-target drug, now it could be considered on the whole as a drug able to protect endothelium against activation. The present work reviews the more important experimental and clinical studies performed to detect DFT effects. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Atom chips in the real world: the effects of wire corrugation

NASA Astrophysics Data System (ADS)

Schumm, T.; Estève, J.; Figl, C.; Trebbia, J.-B.; Aussibal, C.; Nguyen, H.; Mailly, D.; Bouchoule, I.; Westbrook, C. I.; Aspect, A.

2005-02-01

We present a detailed model describing the effects of wire corrugation on the trapping potential experienced by a cloud of atoms above a current carrying micro wire. We calculate the distortion of the current distribution due to corrugation and then derive the corresponding roughness in the magnetic field above the wire. Scaling laws are derived for the roughness as a function of height above a ribbon shaped wire. We also present experimental data on micro wire traps using cold atoms which complement some previously published measurements [CITE] and which demonstrate that wire corrugation can satisfactorily explain our observations of atom cloud fragmentation above electroplated gold wires. Finally, we present measurements of the corrugation of new wires fabricated by electron beam lithography and evaporation of gold. These wires appear to be substantially smoother than electroplated wires.

Method of measuring blood oxygenation based on spectroscopy of diffusely scattered light

NASA Astrophysics Data System (ADS)

Kleshnin, M. S.; Orlova, A. G.; Kirillin, M. Yu.; Golubyatnikov, G. Yu.; Turchin, I. V.

2017-05-01

A new approach to the measurement of blood oxygenation is developed and implemented, based on an original two-step algorithm reconstructing the relative concentration of biological chromophores (haemoglobin, water, lipids) from the measured spectra of diffusely scattered light at different distances from the radiation source. The numerical experiments and approbation of the proposed approach using a biological phantom have shown the high accuracy of the reconstruction of optical properties of the object in question, as well as the possibility of correct calculation of the haemoglobin oxygenation in the presence of additive noises without calibration of the measuring device. The results of the experimental studies in animals agree with the previously published results obtained by other research groups and demonstrate the possibility of applying the developed method to the monitoring of blood oxygenation in tumour tissues.

Alignment of cell division axes in directed epithelial cell migration

NASA Astrophysics Data System (ADS)

Marel, Anna-Kristina; Podewitz, Nils; Zorn, Matthias; Oskar Rädler, Joachim; Elgeti, Jens

2014-11-01

Cell division is an essential dynamic event in tissue remodeling during wound healing, cancer and embryogenesis. In collective migration, tensile stresses affect cell shape and polarity, hence, the orientation of the cell division axis is expected to depend on cellular flow patterns. Here, we study the degree of orientation of cell division axes in migrating and resting epithelial cell sheets. We use microstructured channels to create a defined scenario of directed cell invasion and compare this situation to resting but proliferating cell monolayers. In experiments, we find a strong alignment of the axis due to directed flow while resting sheets show very weak global order, but local flow gradients still correlate strongly with the cell division axis. We compare experimental results with a previously published mesoscopic particle based simulation model. Most of the observed effects are reproduced by the simulations.

Light Vector Meson Photoproduction off of 1H at Jefferson Lab and p-w Interference in the Leptonic Decay Channel

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

Djalali, Chaden; Paolone, Michael; Weygand, Dennis

2014-09-01

Although the phenomena of r – w interference has been studied at great length in pionic decay channel over the past 50 years, a study of the interference in a purely electromagnetic production and decay channel has never been performed on an elementary proton target until now. The only published photo-production data of the r - w leptonic decay channel was obtained in the early seventies on C and Be. An investigation of the r - w interference on a Hydrogen was recently completed at Jefferson Lab with the CLAS detector. The di-lepton spectra was fit with two inter- feringmore » relativistic Breit-Wigner functions, and the interference phase was extracted. Preliminary results will be compared to the previous experimental studies in nuclei.« less

Reply to comment by Melsen et al. on "Most computational hydrology is not reproducible, so is it really science?"

NASA Astrophysics Data System (ADS)

Hutton, Christopher; Wagener, Thorsten; Freer, Jim; Han, Dawei; Duffy, Chris; Arheimer, Berit

2017-03-01

In this article, we reply to a comment made by Melsen et al. [2017] on our previous commentary regarding reproducibility in computational hydrology. Re-executing someone else's code and workflow to derive a set of published results does not by itself constitute reproducibility. However, it forms a key part of the process: it demonstrates that all the degrees of freedom and choices made by the scientist in running the experiment are contained within that code and workflow. This does not only allow us to build and extend directly from the original work, but with full knowledge of decisions made in the original experimental setup, we can then focus our attention to the degrees of freedom of interest: those that occur in hydrological systems that are ultimately our subject of study.

A methodological analysis of chaplaincy research: 2000-2009.

PubMed

Galek, Kathleen; Flannelly, Kevin J; Jankowski, Katherine R B; Handzo, George F

2011-01-01

The present article presents a comprehensive review and analysis of quantitative research conducted in the United States on chaplaincy and closely related topics published between 2000 and 2009. A combined search strategy identified 49 quantitative studies in 13 journals. The analysis focuses on the methodological sophistication of the studies, compared to earlier research on chaplaincy and pastoral care. Cross-sectional surveys of convenience samples still dominate the field, but sample sizes have increased somewhat over the past three decades. Reporting of the validity and reliability of measures continues to be low, although reporting of response rates has improved. Improvements in the use of inferential statistics and statistical controls were also observed, compared to previous research. The authors conclude that more experimental research is needed on chaplaincy, along with an increased use of hypothesis testing, regardless of the research designs that are used.

Optimising experimental design for MEG resting state functional connectivity measurement.

PubMed

Liuzzi, Lucrezia; Gascoyne, Lauren E; Tewarie, Prejaas K; Barratt, Eleanor L; Boto, Elena; Brookes, Matthew J

2017-07-15

The study of functional connectivity using magnetoencephalography (MEG) is an expanding area of neuroimaging, and adds an extra dimension to the more common assessments made using fMRI. The importance of such metrics is growing, with recent demonstrations of their utility in clinical research, however previous reports suggest that whilst group level resting state connectivity is robust, single session recordings lack repeatability. Such robustness is critical if MEG measures in individual subjects are to prove clinically valuable. In the present paper, we test how practical aspects of experimental design affect the intra-subject repeatability of MEG findings; specifically we assess the effect of co-registration method and data recording duration. We show that the use of a foam head-cast, which is known to improve co-registration accuracy, increased significantly the between session repeatability of both beamformer reconstruction and connectivity estimation. We also show that recording duration is a critical parameter, with large improvements in repeatability apparent when using ten minute, compared to five minute recordings. Further analyses suggest that the origin of this latter effect is not underpinned by technical aspects of source reconstruction, but rather by a genuine effect of brain state; short recordings are simply inefficient at capturing the canonical MEG network in a single subject. Our results provide important insights on experimental design and will prove valuable for future MEG connectivity studies. Copyright © 2016. Published by Elsevier Inc.

Experimental and simulation characterisation of flexural vibration modes in unimorph ultrasound transducers.

PubMed

Eriksson, T J R; Ramadas, S N; Dixon, S M

2016-02-01

A unimorph flexural transducer design is proposed and tested with regard to mode shapes and frequencies. The transducers consist of a passive metal cap structure, and a thin piezoelectric disc, rigidly bonded to the inside. Extensive finite element (FE) modelling, and experimental 2D, time-resolved displacement measurements were done to characterise the transducers flexural properties, and to compare them to the analytical solutions of thin vibrating plates. Emphasis was put on characterising the passive layer of the unimorph structure, before bonding the piezoelectric element, to understand how the active element affects the behaviour of the flexing plate. A high power Nd:YAG laser was used to actuate the metal plate (non-contact), and the frequency content of the resulting displacement signal was analysed to identify the flexural modes. The non-axisymmetric modes, which are conventionally disregarded because of their unfavourable acoustic properties, were also taken into account. There was excellent agreement between the experimental results and the FE simulation data. There was good agreement with the analytical edge clamped plate model, but with some notable deviations, which have not previously been identified or commented upon. Specifically, the second axisymmetric mode is split into three separate modes, which is not explained by the traditional theory of vibrating plates. Crown Copyright © 2015. Published by Elsevier B.V. All rights reserved.

Model anodes and anode models for understanding the mechanism of hydrogen oxidation in solid oxide fuel cells.

PubMed

Bessler, Wolfgang G; Vogler, Marcel; Störmer, Heike; Gerthsen, Dagmar; Utz, Annika; Weber, André; Ivers-Tiffée, Ellen

2010-11-14

This article presents a literature review and new results on experimental and theoretical investigations of the electrochemistry of solid oxide fuel cell (SOFC) model anodes, focusing on the nickel/yttria-stabilized zirconia (Ni/YSZ) materials system with operation under H(2)/H(2)O atmospheres. Micropatterned model anodes were used for electrochemical characterization under well-defined operating conditions. Structural and chemical integrity was confirmed by ex situ pre-test and post-test microstructural and chemical analysis. Elementary kinetic models of reaction and transport processes were used to assess reaction pathways and rate-determining steps. The comparison of experimental and simulated electrochemical behaviors of pattern anodes shows quantitative agreement over a wide range of operating conditions (p(H(2)) = 8×10(2) - 9×10(4) Pa, p(H(2)O) = 2×10(1) - 6×10(4) Pa, T = 400-800 °C). Previously published experimental data on model anodes show a strong scatter in electrochemical performance. Furthermore, model anodes exhibit a pronounced dynamics on multiple time scales which is not reproduced in state-of-the-art models and which is also not observed in technical cermet anodes. Potential origin of these effects as well as consequences for further steps in model anode and anode model studies are discussed.

A method for predicting static-to-flight effects on coaxial jet noise

NASA Astrophysics Data System (ADS)

Bryce, William D.; Chinoy, Cyrus B.

2016-08-01

Previously-published work has provided a theoretical modelling of the jet noise from coaxial nozzle configurations in the form of component sources which can each be quantified in terms of modified single-stream jets. This modelling has been refined and extended to cover a wide range of the operating conditions of aircraft turbofan engines with separate exhaust flows, encompassing area ratios from 0.8 to 4. The objective has been to establish a basis for predicting the static-to-flight changes in the coaxial jet noise by applying single-stream flight effects to each of the sources comprising the modelling of the coaxial jet noise under static conditions. Relatively few experimental test points are available for validation although these do cover the full extent of the jet conditions and area ratios considered. The experimental results are limited in their frequency range by practical considerations but the static-to-flight changes in the third-octave SPLs are predicted to within a standard deviation of 0.4 dB although the complex effects of jet refraction and convection cause the errors to increase at low flight emission angles to the jet axis. The modelling also provides useful insights into the mechanisms involved in the generation of coaxial jet noise and has facilitated the identification of inadequacies in the experimental simulation of flight effects.

The Use of Virtual Reality in the Study of People's Responses to Violent Incidents.

PubMed

Rovira, Aitor; Swapp, David; Spanlang, Bernhard; Slater, Mel

2009-01-01

This paper reviews experimental methods for the study of the responses of people to violence in digital media, and in particular considers the issues of internal validity and ecological validity or generalisability of results to events in the real world. Experimental methods typically involve a significant level of abstraction from reality, with participants required to carry out tasks that are far removed from violence in real life, and hence their ecological validity is questionable. On the other hand studies based on field data, while having ecological validity, cannot control multiple confounding variables that may have an impact on observed results, so that their internal validity is questionable. It is argued that immersive virtual reality may provide a unification of these two approaches. Since people tend to respond realistically to situations and events that occur in virtual reality, and since virtual reality simulations can be completely controlled for experimental purposes, studies of responses to violence within virtual reality are likely to have both ecological and internal validity. This depends on a property that we call 'plausibility' - including the fidelity of the depicted situation with prior knowledge and expectations. We illustrate this with data from a previously published experiment, a virtual reprise of Stanley Milgram's 1960s obedience experiment, and also with pilot data from a new study being developed that looks at bystander responses to violent incidents.

The Use of Virtual Reality in the Study of People's Responses to Violent Incidents

PubMed Central

Rovira, Aitor; Swapp, David; Spanlang, Bernhard; Slater, Mel

2009-01-01

This paper reviews experimental methods for the study of the responses of people to violence in digital media, and in particular considers the issues of internal validity and ecological validity or generalisability of results to events in the real world. Experimental methods typically involve a significant level of abstraction from reality, with participants required to carry out tasks that are far removed from violence in real life, and hence their ecological validity is questionable. On the other hand studies based on field data, while having ecological validity, cannot control multiple confounding variables that may have an impact on observed results, so that their internal validity is questionable. It is argued that immersive virtual reality may provide a unification of these two approaches. Since people tend to respond realistically to situations and events that occur in virtual reality, and since virtual reality simulations can be completely controlled for experimental purposes, studies of responses to violence within virtual reality are likely to have both ecological and internal validity. This depends on a property that we call ‘plausibility’ – including the fidelity of the depicted situation with prior knowledge and expectations. We illustrate this with data from a previously published experiment, a virtual reprise of Stanley Milgram's 1960s obedience experiment, and also with pilot data from a new study being developed that looks at bystander responses to violent incidents. PMID:20076762

Detection of VEGF-A(xxx)b isoforms in human tissues.

PubMed

Bates, David O; Mavrou, Athina; Qiu, Yan; Carter, James G; Hamdollah-Zadeh, Maryam; Barratt, Shaney; Gammons, Melissa V; Millar, Ann B; Salmon, Andrew H J; Oltean, Sebastian; Harper, Steven J

2013-01-01

Vascular Endothelial Growth Factor-A (VEGF-A) can be generated as multiple isoforms by alternative splicing. Two families of isoforms have been described in humans, pro-angiogenic isoforms typified by VEGF-A165a, and anti-angiogenic isoforms typified by VEGF-A165b. The practical determination of expression levels of alternative isoforms of the same gene may be complicated by experimental protocols that favour one isoform over another, and the use of specific positive and negative controls is essential for the interpretation of findings on expression of the isoforms. Here we address some of the difficulties in experimental design when investigating alternative splicing of VEGF isoforms, and discuss the use of appropriate control paradigms. We demonstrate why use of specific control experiments can prevent assumptions that VEGF-A165b is not present, when in fact it is. We reiterate, and confirm previously published experimental design protocols that demonstrate the importance of using positive controls. These include using known target sequences to show that the experimental conditions are suitable for PCR amplification of VEGF-A165b mRNA for both q-PCR and RT-PCR and to ensure that mispriming does not occur. We also provide evidence that demonstrates that detection of VEGF-A165b protein in mice needs to be tightly controlled to prevent detection of mouse IgG by a secondary antibody. We also show that human VEGF165b protein can be immunoprecipitated from cultured human cells and that immunoprecipitating VEGF-A results in protein that is detected by VEGF-A165b antibody. These findings support the conclusion that more information on the biology of VEGF-A165b isoforms is required, and confirm the importance of the experimental design in such investigations, including the use of specific positive and negative controls.

EXACT2: the semantics of biomedical protocols

PubMed Central

2014-01-01

Background The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ensures that all information required for the replication of experimental protocols is essential to achieve reproducibility. Methods We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility. To construct EXACT2 we manually inspected hundreds of published and commercial biomedical protocols from several areas of biomedicine. After establishing a clear pattern for extracting the required information we utilized text-mining tools to translate the protocols into a machine amenable format. We have verified the utility of EXACT2 through the successful processing of previously 'unseen' (not used for the construction of EXACT2) protocols. Results The paper reports on a fundamentally new version EXACT2 that supports the semantically-defined representation of biomedical protocols. The ability of EXACT2 to capture the semantics of biomedical procedures was verified through a text mining use case. In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language. An EXACT2-based framework for the translation of biomedical protocols to a machine amenable format is proposed. Conclusions The EXACT2 ontology is sufficient to record, in a machine processable form, the essential information about biomedical protocols. EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications. It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format. PMID:25472549

The use of genetic programming to develop a predictor of swash excursion on sandy beaches

NASA Astrophysics Data System (ADS)

Passarella, Marinella; Goldstein, Evan B.; De Muro, Sandro; Coco, Giovanni

2018-02-01

We use genetic programming (GP), a type of machine learning (ML) approach, to predict the total and infragravity swash excursion using previously published data sets that have been used extensively in swash prediction studies. Three previously published works with a range of new conditions are added to this data set to extend the range of measured swash conditions. Using this newly compiled data set we demonstrate that a ML approach can reduce the prediction errors compared to well-established parameterizations and therefore it may improve coastal hazards assessment (e.g. coastal inundation). Predictors obtained using GP can also be physically sound and replicate the functionality and dependencies of previous published formulas. Overall, we show that ML techniques are capable of both improving predictability (compared to classical regression approaches) and providing physical insight into coastal processes.

Experimental and Modeling Study of the Burning of an Ethanol Droplet in Microgravity

NASA Technical Reports Server (NTRS)

Kazakov, Andrei; Conley, Jordan; Dryer, Frederick L.; Ferkul, Paul (Technical Monitor)

2000-01-01

The microgravity ethanol droplet combustion experiments were performed aboard the STS-94/MSL-1 Shuttle mission within the Fiber-Supported Droplet Combustion-2 (FSDC-2) program. The burning histories and flame standoffs for pure ethanol and ethanol/water droplets were obtained from the images recorded with two 8 mm videocameras. The obtained results show that average gasification rate is related to the initial droplet size in a manner similar to n-alkanes and methanol and consistent with the results of Hara and Kumagai and the data taken recently in the NASA-Lewis 2.2 s droptower. A transient, moving finite-element chemically reacting flow model applied previously to sphero-symmetric combustion of methanol, methanol/water, n-alkane, and n-alkane binary mixture droplets was adopted for the problem of ethanol droplet combustion. The model includes detailed description of gas-phase reaction chemistry and transport, a simplified description of liquid phase transport, and non-luminous radiative heat transfer. Gas-phase chemistry was described with the detailed reaction mechanism of Norton and Dryer, which consists of 142 reversible elementary reactions of 33 species. Another recently published reaction mechanism of high-temperature ethanol oxidation was also considered. The model predictions were found to compare favorably with the experimental data. The model analysis also indicates that water condensation in the case of ethanol has smaller effect on average droplet gasification rate as compared with previously studied methanol cases. This effect is explained by non-ideal (azeotropic) behavior of binary ethanol-water mixtures. Further analysis of computational results and ethanol droplet radiative extinction behavior will be discussed.

Novel integrated microdialysis-amperometric system for in vitro detection of dopamine secreted from PC12 cells: design, construction, and validation.

PubMed

Migheli, Rossana; Puggioni, Giulia; Dedola, Sonia; Rocchitta, Gaia; Calia, Giammario; Bazzu, Gianfranco; Esposito, Giovanni; Lowry, John P; O'Neill, Robert D; Desole, M S; Miele, Egidio; Serra, Pier A

2008-09-15

A novel dual channel in vitro apparatus, derived from a previously described design, has been coupled with dopamine (DA) microsensors for the flow-through detection of DA secreted from PC12 cells. The device, including two independent microdialysis capillaries, was loaded with a solution containing PC12 cells while a constant phosphate-buffered saline (PBS) medium perfusion was carried out using a dual channel miniaturized peristaltic pump. One capillary was perfused with normal PBS, whereas extracellular calcium was removed from extracellular fluid of the second capillary. After a first period of stabilization and DA baseline recording, KCl (75 mM) was added to the perfusion fluid of both capillaries. In this manner, a simultaneous "treatment-control" experimental design was performed to detect K+-evoked calcium-dependent DA secretion. For this purpose, self-referencing DA microsensors were developed, and procedures for making, testing, and calibrating them are described in detail. The electronic circuitry was derived from previously published schematics and optimized for dual sensor constant potential amperometry applications. The microdialysis system was tested and validated in vitro under different experimental conditions, and DA secretion was confirmed by high-performance liquid chromatography with electrochemical detection (HPLC-EC). PC12 cell viability was quantified before and after each experiment. The proposed apparatus serves as a reliable model for studying the effects of different drugs on DA secretion through the direct comparison of extracellular DA increase in treatment-control experiments performed on the same initial PC12 cell population.

Beta decay of the fission product 125Sb and a new complete evaluation of absolute gamma ray transition intensities

NASA Astrophysics Data System (ADS)

Rajput, M. U.; Ali, N.; Hussain, S.; Mujahid, S. A.; MacMahon, D.

2012-04-01

The radionuclide 125Sb is a long-lived fission product, which decays to 125Te by negative beta emission with a half-life of 1008 day. The beta decay is followed by the emission of several gamma radiations, ranging from low to medium energy, that can suitably be used for high-resolution detector calibrations, decay heat calculations and in many other applications. In this work, the beta decay of 125Sb has been studied in detail. The complete published experimental data of relative gamma ray intensities in the beta decay of the radionuclide 125Sb has been compiled. The consistency analysis was performed and discrepancies found at several gamma ray energies. Evaluation of the discrepant data was carried out using Normalized Residual and RAJEVAL methods. The decay scheme balance was carried out using beta branching ratios, internal conversion coefficients, populating and depopulating gamma transitions to 125Te levels. The work has resulted in the consistent conversion factor equal to 29.59(13) %, and determined a new evaluated set of the absolute gamma ray emission probabilities. The work has also shown 22.99% of the delayed intensity fraction as outgoing from the 58 d isomeric 144 keV energy level and 77.01% of the prompt intensity fraction reaching to the ground state from the other excited states. The results are discussed and compared with previous evaluations. The present work includes additional experimental data sets which were not included in the previous evaluations. A new set of recommended relative and absolute gamma ray emission probabilities is presented.

Preliminary Multivariable Cost Model for Space Telescopes

NASA Technical Reports Server (NTRS)

Stahl, H. Philip

2010-01-01

Parametric cost models are routinely used to plan missions, compare concepts and justify technology investments. Previously, the authors published two single variable cost models based on 19 flight missions. The current paper presents the development of a multi-variable space telescopes cost model. The validity of previously published models are tested. Cost estimating relationships which are and are not significant cost drivers are identified. And, interrelationships between variables are explored

Publication Trends in The Analysis of Verbal Behavior: 1999-2008

ERIC Educational Resources Information Center

Marcon-Dawson, Allyne; Vicars, Sara M.; Miguel, Caio F.

2009-01-01

"The Analysis of Verbal Behavior" ("TAVB") publishes experimental and theoretical papers relevant to a behavioral analysis of language. Normand, Fossa, and Poling (2000) reviewed the published studies in "TAVB" across several dimensions and found that despite the growth of the journal, most articles published in "TAVB" from 1982 to 1998 were…

The Influence of Scientific Research and Evaluation on Publishing Educational Curriculum

ERIC Educational Resources Information Center

Baughman, Marcy

2008-01-01

Prior to the No Child Left Behind (NCLB) Act, scientific research to support development of curriculum materials or to demonstrate curricular efficacy was not required. NCLB transformed the development and publishing process for K-12 educational materials by prompting publishers to increase funding for experimentally based research on educational…

Infrared spectroscopy of matrix-isolated neutral polycyclic aromatic nitrogen heterocycles: The acridine series.

PubMed

Mattioda, A L; Bauschlicher, C W; Ricca, A; Bregman, J; Hudgins, D M; Allamandola, L J

2017-06-15

The matrix-isolated, mid-infrared spectra of seven acridine-based polycyclic aromatic nitrogen heterocycles (PANHs) have been measured and compared to their non-nitrogen containing parent molecule. The acridine species investigated include acridine, benz[a]acridine, benz[c]acridine, dibenz[a,j]acridine, dibenz[c,h]acridine, dibenz[a,h]acridine and dibenz[a,c]acridine. The previously reported results for 1 and 2-azabenz[a]anthracenes are included for comparison. The experimentally determined band frequencies and intensities are compared with their B3LYP/6-31G(d) values. The overall agreement between experimental and theoretical values is good and in line with our previous investigations. Shifts, typically to the blue, are noted for the C-H out-of-plane (CH oop ) motions upon insertion of a nitrogen atom. The formation of a bay region upon addition of additional benzene rings to the anthracene/acridine structure splits the solo hydrogen motions into a bay region solo and an external solo hydrogen, with the bay region solo hydrogen coupling to the quartet hydrogen motions and the external solo hydrogen coupling with the duo hydrogen motions resulting in an extreme decrease in intensity for the CH oop solo hydrogen band when the external hydrogen is replaced by a nitrogen atom. The C-C and C-H in-plane region of this acridine series exhibits the characteristic two fold increase in intensity, noted previously for PANHs. The strong ≈1400cm -1 band, which was identified in the previous PANH study, is noted in several molecular species as well as another strong PANH feature between 1480 and 1515cm -1 for several molecules. The presence of these strong bands appear to be primarily responsible for the two-fold increase in the C-H in-plane region's (1100-1600cm -1 ) intensity. The C-H stretching region can be characterized by contributions from the solo (bay or external), duo and quartet hydrogens, similar to what was observed in the dibenzopolyacene compounds. Published by Elsevier B.V.

75 FR 43172 - Maternal, Infant, and Early Childhood Home Visiting Program

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-23

... the evaluation results have been published in a peer-reviewed journal; or (bb) quasi-experimental... design (i.e. randomized controlled trial [RCT] or quasi-experimental design [QED]), level of attrition... a quasi-experimental design as a study design in which sample members are selected for the program...

Spectroscopy of 70Kr and isospin symmetry in the T =1 f p g shell nuclei

NASA Astrophysics Data System (ADS)

Debenham, D. M.; Bentley, M. A.; Davies, P. J.; Haylett, T.; Jenkins, D. G.; Joshi, P.; Sinclair, L. F.; Wadsworth, R.; Ruotsalainen, P.; Henderson, J.; Kaneko, K.; Auranen, K.; Badran, H.; Grahn, T.; Greenlees, P.; HerzaáÅ, A.; Jakobsson, U.; Konki, J.; Julin, R.; Juutinen, S.; Leino, M.; Sorri, J.; Pakarinen, J.; Papadakis, P.; Peura, P.; Partanen, J.; Rahkila, P.; Sandzelius, M.; Sarén, J.; Scholey, C.; Stolze, S.; Uusitalo, J.; David, H. M.; de Angelis, G.; Korten, W.; Lotay, G.; Mallaburn, M.; Sahin, E.

2016-11-01

The recoil-β tagging technique has been used in conjunction with the 40Ca(32S,2 n ) reaction at a beam energy of 88 MeV to identify transitions associated with the decay of the 2+ and, tentatively, 4+ states in the nucleus 70Kr. These data are used, along with previously published data, to examine the triplet energy differences (TED) for the mass 70 isobars. The experimental TED values are compared with shell model calculations, performed with the JUN45 interaction in the f p g model space, that include a J =0 isospin nonconserving (INC) interaction with an isotensor strength of 100 keV. The agreement is found to be very good up to spin 4 and supports the expectation for analog states that all three nuclei have the same oblate shape at low-spin. The A =70 results are compared with the experimental and shell model predicted TED and mirror energy differences (MED) for the mass 66 and 74 systems. The comparisons clearly demonstrate the importance of the isotensor INC interaction in replicating the TED data in this region. Issues related to the observed MED values and their interpretation within the shell model are discussed.

Prediction of distal residue participation in enzyme catalysis.

PubMed

Brodkin, Heather R; DeLateur, Nicholas A; Somarowthu, Srinivas; Mills, Caitlyn L; Novak, Walter R; Beuning, Penny J; Ringe, Dagmar; Ondrechen, Mary Jo

2015-05-01

A scoring method for the prediction of catalytically important residues in enzyme structures is presented and used to examine the participation of distal residues in enzyme catalysis. Scores are based on the Partial Order Optimum Likelihood (POOL) machine learning method, using computed electrostatic properties, surface geometric features, and information obtained from the phylogenetic tree as input features. Predictions of distal residue participation in catalysis are compared with experimental kinetics data from the literature on variants of the featured enzymes; some additional kinetics measurements are reported for variants of Pseudomonas putida nitrile hydratase (ppNH) and for Escherichia coli alkaline phosphatase (AP). The multilayer active sites of P. putida nitrile hydratase and of human phosphoglucose isomerase are predicted by the POOL log ZP scores, as is the single-layer active site of P. putida ketosteroid isomerase. The log ZP score cutoff utilized here results in over-prediction of distal residue involvement in E. coli alkaline phosphatase. While fewer experimental data points are available for P. putida mandelate racemase and for human carbonic anhydrase II, the POOL log ZP scores properly predict the previously reported participation of distal residues. 2015 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Aminoquinolines as fluorescent labels for hydrophilic interaction liquid chromatography of oligosaccharides.

PubMed

Struwe, Weston B; Rudd, Pauline M

2012-08-01

In this study, we investigated the potential of four different aminoquinoline (AQ) compounds as fluorescent labels for glycan analysis using hydrophilic interaction liquid chromatography (HILIC) and fluorescence detection (FLD). We confirmed the optimal excitation and emission wavelengths of 3-AQ and 6-AQ conjugated to glycan standards using three-dimensional fluorescent spectral scanning. The optimal excitation and emission wavelengths for 6-AQ were confirmed at λ(ex)=355 nm and λ(em)=440 nm. We concluded that the optimal wavelengths for 3-AQ were λ(ex)=355 nm and λ(em)=420 nm, which differed considerably from the wavelengths applied in previous reports. HILIC-FLD chromatograms using experimentally determined wavelengths were similar to 2-aminobenzamide controls, but the peak capacity and resolution differed significantly when published 3-AQ λ(ex/em) values were applied. Furthermore, we found that 5-AQ and 8-AQ labeled maltohexaose did not display any fluorescent properties when used as a carbohydrate tag for HPLC analysis. Finally, we applied experimentally determined wavelengths to 3-AQ labeled N-glycans released from human IgG to illustrate changes in retention time as well as to demonstrate that AQ labeling is applicable to complex sample analysis via exoglycosidase sequencing.

Theory of optimal balance predicts and explains the amplitude and decay time of synaptic inhibition

PubMed Central

Kim, Jaekyung K.; Fiorillo, Christopher D.

2017-01-01

Synaptic inhibition counterbalances excitation, but it is not known what constitutes optimal inhibition. We previously proposed that perfect balance is achieved when the peak of an excitatory postsynaptic potential (EPSP) is exactly at spike threshold, so that the slightest variation in excitation determines whether a spike is generated. Using simulations, we show that the optimal inhibitory postsynaptic conductance (IPSG) increases in amplitude and decay rate as synaptic excitation increases from 1 to 800 Hz. As further proposed by theory, we show that optimal IPSG parameters can be learned through anti-Hebbian rules. Finally, we compare our theoretical optima to published experimental data from 21 types of neurons, in which rates of synaptic excitation and IPSG decay times vary by factors of about 100 (5–600 Hz) and 50 (1–50 ms), respectively. From an infinite range of possible decay times, theory predicted experimental decay times within less than a factor of 2. Across a distinct set of 15 types of neuron recorded in vivo, theory predicted the amplitude of synaptic inhibition within a factor of 1.7. Thus, the theory can explain biophysical quantities from first principles. PMID:28281523

Experimental and molecular dynamics simulation study of the sublimation energetics of cyclopentadienyltricarbonylmanganese (Cymantrene).

PubMed

Picciochi, Ricardo; Canongia Lopes, José N; Diogo, Hermínio P; Minas da Piedade, Manuel E

2008-10-16

The standard molar enthalpy of sublimation of monoclinic cyclopentadienyltricarbonylmanganese, Mn(eta (5)-C 5H 5)(CO) 3, at 298.15 K, was determined as Delta sub H m (o)[Mn(eta (5)-C 5H 5)(CO) 3] = 75.97 +/- 0.37 kJ x mol (-1) from Knudsen effusion and Calvet-drop microcalorimetry measurements, thus considerably improving the very large inaccuracy (>10 kJ x mol (-1)) of the published data. The obtained value was used to assess the extension of the OPLS-based all-atom force field we previously developed for iron metallocenes to manganese organometallic compounds. The modified force field was able to reproduce the volumetric properties (density and unit-cell volume) of crystalline Mn(eta (5)-C 5H 5)(CO) 3 with a deviation of 0.6% and the experimentally determined enthalpy of sublimation with an accuracy of 1 kJ x mol (-1). The interaction (epsilon) and atomic-diameter (sigma) parameters of the Lennard-Jones (12-6) potential function used to calculate dispersion contributions within the framework of the force field were found to be transferable from iron to manganese.

Simulation of an Impact Test of the All-Composite Lear Fan Aircraft

NASA Technical Reports Server (NTRS)

Stockwell, Alan E.; Jones, Lisa E. (Technical Monitor)

2002-01-01

An MSC.Dytran model of an all-composite Lear Fan aircraft fuselage was developed to simulate an impact test conducted at the NASA Langley Research Center Impact Dynamics Research Facility (IDRF). The test was the second of two Lear Fan impact tests. The purpose of the second test was to evaluate the performance of retrofitted composite energy-absorbing floor beams. A computerized photogrammetric survey was performed to provide airframe geometric coordinates, and over 5000 points were processed and imported into MSC.Patran via an IGES file. MSC.Patran was then used to develop the curves and surfaces and to mesh the finite element model. A model of the energy-absorbing floor beams was developed separately and then integrated into the Lear Fan model. Structural responses of components such as the wings were compared with experimental data or previously published analytical data wherever possible. Comparisons with experimental results were used to guide structural model modifications to improve the simulation performance. This process was based largely on qualitative (video and still camera images and post-test inspections) rather than quantitative results due to the relatively few accelerometers attached to the structure.

Synthesis, characterization and modelling of zinc and silicate co-substituted hydroxyapatite.

PubMed

Friederichs, Robert J; Chappell, Helen F; Shepherd, David V; Best, Serena M

2015-07-06

Experimental chemistry and atomic modelling studies were performed here to investigate a novel ionic co-substitution in hydroxyapatite (HA). Zinc, silicate co-substituted HA (ZnSiHA) remained phase pure after heating to 1100 °C with Zn and Si amounts of 0.6 wt% and 1.2 wt%, respectively. Unique lattice expansions in ZnSiHA, silicate Fourier transform infrared peaks and changes to the hydroxyl IR stretching region suggested Zn and silicate co-substitution in ZnSiHA. Zn and silicate insertion into HA was modelled using density functional theory (DFT). Different scenarios were considered where Zn substituted for different calcium sites or at a 2b site along the c-axis, which was suspected in singly substituted ZnHA. The most energetically favourable site in ZnSiHA was Zn positioned at a previously unreported interstitial site just off the c-axis near a silicate tetrahedron sitting on a phosphate site. A combination of experimental chemistry and DFT modelling provided insight into these complex co-substituted calcium phosphates that could find biomedical application as a synthetic bone mineral substitute. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Experimental Myocardial Infarction Upregulates Circulating Fibroblast Growth Factor‐23

PubMed Central

Andrukhova, Olena; Slavic, Svetlana; Odörfer, Kathrin I; Erben, Reinhold G

2015-01-01

ABSTRACT Myocardial infarction (MI) is a major cause of death worldwide. Epidemiological studies have linked vitamin D deficiency to MI incidence. Because fibroblast growth factor‐23 (FGF23) is a master regulator of vitamin D hormone production and has been shown to be associated with cardiac hypertrophy per se, we explored the hypothesis that FGF23 may be a previously unrecognized pathophysiological factor causally linked to progression of cardiac dysfunction post‐MI. Here, we show that circulating intact Fgf23 was profoundly elevated, whereas serum vitamin D hormone levels were suppressed, after induction of experimental MI in rat and mouse models, independent of changes in serum soluble Klotho or serum parathyroid hormone. Both skeletal and cardiac expression of Fgf23 was increased after MI. Although the molecular link between the cardiac lesion and circulating Fgf23 concentrations remains to be identified, our study has uncovered a novel heart–bone–kidney axis that may have important clinical implications and may inaugurate the new field of cardio‐osteology. © 2015 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research (ASBMR). PMID:25858796

The usefulness of systematic reviews of animal experiments for the design of preclinical and clinical studies.

PubMed

de Vries, Rob B M; Wever, Kimberley E; Avey, Marc T; Stephens, Martin L; Sena, Emily S; Leenaars, Marlies

2014-01-01

The question of how animal studies should be designed, conducted, and analyzed remains underexposed in societal debates on animal experimentation. This is not only a scientific but also a moral question. After all, if animal experiments are not appropriately designed, conducted, and analyzed, the results produced are unlikely to be reliable and the animals have in effect been wasted. In this article, we focus on one particular method to address this moral question, namely systematic reviews of previously performed animal experiments. We discuss how the design, conduct, and analysis of future (animal and human) experiments may be optimized through such systematic reviews. In particular, we illustrate how these reviews can help improve the methodological quality of animal experiments, make the choice of an animal model and the translation of animal data to the clinic more evidence-based, and implement the 3Rs. Moreover, we discuss which measures are being taken and which need to be taken in the future to ensure that systematic reviews will actually contribute to optimizing experimental design and thereby to meeting a necessary condition for making the use of animals in these experiments justified. © The Author 2014. Published by Oxford University Press.

Fas Promotes T Helper 17 Cell Differentiation and Inhibits T Helper 1 Cell Development by Binding and Sequestering Transcription Factor STAT1.

PubMed

Meyer Zu Horste, Gerd; Przybylski, Dariusz; Schramm, Markus A; Wang, Chao; Schnell, Alexandra; Lee, Youjin; Sobel, Raymond; Regev, Aviv; Kuchroo, Vijay K

2018-03-20

The death receptor Fas removes activated lymphocytes through apoptosis. Previous transcriptional profiling predicted that Fas positively regulates interleukin-17 (IL-17)-producing T helper 17 (Th17) cells. Here, we demonstrate that Fas promoted the generation and stability of Th17 cells and prevented their differentiation into Th1 cells. Mice with T-cell- and Th17-cell-specific deletion of Fas were protected from induced autoimmunity, and Th17 cell differentiation and stability were impaired. Fas-deficient Th17 cells instead developed a Th1-cell-like transcriptional profile, which a new algorithm predicted to depend on STAT1. Experimentally, Fas indeed bound and sequestered STAT1, and Fas deficiency enhanced IL-6-induced STAT1 activation and nuclear translocation, whereas deficiency of STAT1 reversed the transcriptional changes induced by Fas deficiency. Thus, our computational and experimental approach identified Fas as a regulator of the Th17-to-Th1 cell balance by controlling the availability of opposing STAT1 and STAT3 to have a direct impact on autoimmunity. Copyright © 2018. Published by Elsevier Inc.

Modeling tuberculosis pathogenesis through ex vivo lung tissue infection.

PubMed

Carranza-Rosales, Pilar; Carranza-Torres, Irma Edith; Guzmán-Delgado, Nancy Elena; Lozano-Garza, Gerardo; Villarreal-Treviño, Licet; Molina-Torres, Carmen; Villarreal, Javier Vargas; Vera-Cabrera, Lucio; Castro-Garza, Jorge

2017-12-01

Tuberculosis (TB) is one of the top 10 causes of death worldwide. Several in vitro and in vivo experimental models have been used to study TB pathogenesis and induction of immune response during Mycobacterium tuberculosis infection. Precision cut lung tissue slices (PCLTS) is an experimental model, in which all the usual cell types of the organ are found, the tissue architecture and the interactions amongst the different cells are maintained. PCLTS in good physiological conditions, monitored by MTT assay and histology, were infected with either virulent Mycobacterium tuberculosis strain H37Rv or the TB vaccine strain Mycobacterium bovis BCG. Histological analysis showed that bacilli infecting lung tissue slices were observed in the alveolar septa, alveolar light spaces, near to type II pneumocytes, and inside macrophages. Mycobacterial infection of PCLTS induced TNF-α production, which is consistent with previous M. tuberculosis in vitro and in vivo studies. This is the first report of using PCLTS as a system to study M. tuberculosis infection. The PCLTS model provides a useful tool to evaluate the innate immune responses and other aspects during the early stages of mycobacterial infection. Copyright © 2017. Published by Elsevier Ltd.

NLSdb-major update for database of nuclear localization signals and nuclear export signals.

PubMed

Bernhofer, Michael; Goldberg, Tatyana; Wolf, Silvana; Ahmed, Mohamed; Zaugg, Julian; Boden, Mikael; Rost, Burkhard

2018-01-04

NLSdb is a database collecting nuclear export signals (NES) and nuclear localization signals (NLS) along with experimentally annotated nuclear and non-nuclear proteins. NES and NLS are short sequence motifs related to protein transport out of and into the nucleus. The updated NLSdb now contains 2253 NLS and introduces 398 NES. The potential sets of novel NES and NLS have been generated by a simple 'in silico mutagenesis' protocol. We started with motifs annotated by experiments. In step 1, we increased specificity such that no known non-nuclear protein matched the refined motif. In step 2, we increased the sensitivity trying to match several different families with a motif. We then iterated over steps 1 and 2. The final set of 2253 NLS motifs matched 35% of 8421 experimentally verified nuclear proteins (up from 21% for the previous version) and none of 18 278 non-nuclear proteins. We updated the web interface providing multiple options to search protein sequences for NES and NLS motifs, and to evaluate your own signal sequences. NLSdb can be accessed via Rostlab services at: https://rostlab.org/services/nlsdb/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Theory of optimal balance predicts and explains the amplitude and decay time of synaptic inhibition

NASA Astrophysics Data System (ADS)

Kim, Jaekyung K.; Fiorillo, Christopher D.

2017-03-01

Synaptic inhibition counterbalances excitation, but it is not known what constitutes optimal inhibition. We previously proposed that perfect balance is achieved when the peak of an excitatory postsynaptic potential (EPSP) is exactly at spike threshold, so that the slightest variation in excitation determines whether a spike is generated. Using simulations, we show that the optimal inhibitory postsynaptic conductance (IPSG) increases in amplitude and decay rate as synaptic excitation increases from 1 to 800 Hz. As further proposed by theory, we show that optimal IPSG parameters can be learned through anti-Hebbian rules. Finally, we compare our theoretical optima to published experimental data from 21 types of neurons, in which rates of synaptic excitation and IPSG decay times vary by factors of about 100 (5-600 Hz) and 50 (1-50 ms), respectively. From an infinite range of possible decay times, theory predicted experimental decay times within less than a factor of 2. Across a distinct set of 15 types of neuron recorded in vivo, theory predicted the amplitude of synaptic inhibition within a factor of 1.7. Thus, the theory can explain biophysical quantities from first principles.

Evolutionary Instability of Symbiotic Function in Bradyrhizobium japonicum

PubMed Central

Sachs, Joel L.; Russell, James E.; Hollowell, Amanda C.

2011-01-01

Bacterial mutualists are often acquired from the environment by eukaryotic hosts. However, both theory and empirical work suggest that this bacterial lifestyle is evolutionarily unstable. Bacterial evolution outside of the host is predicted to favor traits that promote an independent lifestyle in the environment at a cost to symbiotic function. Consistent with these predictions, environmentally-acquired bacterial mutualists often lose symbiotic function over evolutionary time. Here, we investigate the evolutionary erosion of symbiotic traits in Bradyrhizobium japonicum, a nodulating root symbiont of legumes. Building on a previous published phylogeny we infer loss events of nodulation capability in a natural population of Bradyrhizobium, potentially driven by mutation or deletion of symbiosis loci. Subsequently, we experimentally evolved representative strains from the symbiont population under host-free in vitro conditions to examine potential drivers of these loss events. Among Bradyrhizobium genotypes that evolved significant increases in fitness in vitro, two exhibited reduced symbiotic quality, but no experimentally evolved strain lost nodulation capability or evolved any fixed changes at six sequenced loci. Our results are consistent with trade-offs between symbiotic quality and fitness in a host free environment. However, the drivers of loss-of-nodulation events in natural Bradyrhizobium populations remain unknown. PMID:22073160

A multiscale strength model for tantalum over an extended range of strain rates

NASA Astrophysics Data System (ADS)

Barton, N. R.; Rhee, M.

2013-09-01

A strength model for tantalum is developed and exercised across a range of conditions relevant to various types of experimental observations. The model is based on previous multiscale modeling work combined with experimental observations. As such, the model's parameterization includes a hybrid of quantities that arise directly from predictive sub-scale physics models and quantities that are adjusted to align the model with experimental observations. Given current computing and experimental limitations, the response regions for sub-scale physics simulations and detailed experimental observations have been largely disjoint. In formulating the new model and presenting results here, attention is paid to integrated experimental observations that probe strength response at the elevated strain rates where a previous version of the model has generally been successful in predicting experimental data [Barton et al., J. Appl. Phys. 109(7), 073501 (2011)].

An automated parallel crystallisation search for predicted crystal structures and packing motifs of carbamazepine.

PubMed

Florence, Alastair J; Johnston, Andrea; Price, Sarah L; Nowell, Harriott; Kennedy, Alan R; Shankland, Norman

2006-09-01

An automated parallel crystallisation search for physical forms of carbamazepine, covering 66 solvents and five crystallisation protocols, identified three anhydrous polymorphs (forms I-III), one hydrate and eight organic solvates, including the single-crystal structures of three previously unreported solvates (N,N-dimethylformamide (1:1); hemi-furfural; hemi-1,4-dioxane). Correlation of physical form outcome with the crystallisation conditions demonstrated that the solvent adopts a relatively nonspecific role in determining which polymorph is obtained, and that the previously reported effect of a polymer template facilitating the formation of form IV could not be reproduced by solvent crystallisation alone. In the accompanying computational search, approximately half of the energetically feasible predicted crystal structures exhibit the C=O...H--N R2(2)(8)dimer motif that is observed in the known polymorphs, with the most stable correctly corresponding to form III. Most of the other energetically feasible structures, including the global minimum, have a C=O...H--N C(4) chain hydrogen bond motif. No such chain structures were observed in this or any other previously published work, suggesting that kinetic, rather than thermodynamic, factors determine which of the energetically feasible crystal structures are observed experimentally, with the kinetics apparently favouring nucleation of crystal structures based on the CBZ-CBZ R2(2)(8) motif. (c) 2006 Wiley-Liss, Inc. and the American Pharmacists Association.

Absolute protein-protein association rate constants from flexible, coarse-grained Brownian dynamics simulations: the role of intermolecular hydrodynamic interactions in barnase-barstar association.

PubMed

Frembgen-Kesner, Tamara; Elcock, Adrian H

2010-11-03

Theory and computation have long been used to rationalize the experimental association rate constants of protein-protein complexes, and Brownian dynamics (BD) simulations, in particular, have been successful in reproducing the relative rate constants of wild-type and mutant protein pairs. Missing from previous BD studies of association kinetics, however, has been the description of hydrodynamic interactions (HIs) between, and within, the diffusing proteins. Here we address this issue by rigorously including HIs in BD simulations of the barnase-barstar association reaction. We first show that even very simplified representations of the proteins--involving approximately one pseudoatom for every three residues in the protein--can provide excellent reproduction of the absolute association rate constants of wild-type and mutant protein pairs. We then show that simulations that include intermolecular HIs also produce excellent estimates of association rate constants, but, for a given reaction criterion, yield values that are decreased by ∼35-80% relative to those obtained in the absence of intermolecular HIs. The neglect of intermolecular HIs in previous BD simulation studies, therefore, is likely to have contributed to the somewhat overestimated absolute rate constants previously obtained. Consequently, intermolecular HIs could be an important component to include in accurate modeling of the kinetics of macromolecular association events. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Psychoeducation and cognitive-behavioral therapy for patients with refractory bipolar disorder: a 5-year controlled clinical trial.

PubMed

González Isasi, A; Echeburúa, E; Limiñana, J M; González-Pinto, A

2014-03-01

The aim of this research, which represents an additional and longer follow-up to a previous trial, was to evaluate a 5-year follow-up study of a combined treatment (pharmacological+psychoeducational and cognitive-behavioral therapy) as compared with a standard pharmacological treatment in patients with refractory bipolar disorder. Forty patients were randomly assigned to either an Experimental group-under combined treatment - or a Control group - under pharmacological treatment. Data were analyzed by analysis of variance (ANOVA), with repeated measures at different evaluation time points. Between-group differences were significant at all evaluation time points after treatment. Experimental group had less hospitalization events than Control group in the 12-month evaluation (P=0.015). The Experimental group showed lower depression and anxiety in the 6-month (P=0.006; P=0.019), 12-month (P=0.001; P<0.001) and 5-year (P<0.001, P<0.001) evaluation time points. Significant differences emerged in mania and misadjustment already in the post-treatment evaluation (P=0.009; P<0.001) and were sustained throughout the study (6-month: P=0.006, P<0.001; 12-month: P<0.001, P<0.001; 5-year: P=0.004, P<0.001). After 5-year follow-up, 88.9% of patients in the Control group and 20% of patients in the Experimental group showed persistent affective symptoms and/or difficulties in social-occupational functioning. A combined therapy is long-term effective for patients with refractory bipolar disorder. Suggestions for future research are commented. Published by Elsevier Masson SAS.

Comparison of numerical and experimental results of the flow in the U9 Kaplan turbine model

NASA Astrophysics Data System (ADS)

Petit, O.; Mulu, B.; Nilsson, H.; Cervantes, M.

2010-08-01

The present work compares simulations made using the OpenFOAM CFD code with experimental measurements of the flow in the U9 Kaplan turbine model. Comparisons of the velocity profiles in the spiral casing and in the draft tube are presented. The U9 Kaplan turbine prototype located in Porjus and its model, located in Älvkarleby, Sweden, have curved inlet pipes that lead the flow to the spiral casing. Nowadays, this curved pipe and its effect on the flow in the turbine is not taken into account when numerical simulations are performed at design stage. To study the impact of the inlet pipe curvature on the flow in the turbine, and to get a better overview of the flow of the whole system, measurements were made on the 1:3.1 model of the U9 turbine. Previously published measurements were taken at the inlet of the spiral casing and just before the guide vanes, using the laser Doppler anemometry (LDA) technique. In the draft tube, a number of velocity profiles were measured using the LDA techniques. The present work extends the experimental investigation with a horizontal section at the inlet of the draft tube. The experimental results are used to specify the inlet boundary condition for the numerical simulations in the draft tube, and to validate the computational results in both the spiral casing and the draft tube. The numerical simulations were realized using the standard k-e model and a block-structured hexahedral wall function mesh.

Writing and Publishing Handbook.

ERIC Educational Resources Information Center

Hansen, William F., Ed.

Intended to provide guidance in academic publishing to faculty members, especially younger faculty members, this handbook is a compilation of four previously published essays by different authors. Following a preface and an introduction, the four essays and their authors are as follows: (1) "One Writer's Secrets" (Donald M. Murray); (2)…

Constructing experimental designs for discrete-choice experiments: report of the ISPOR Conjoint Analysis Experimental Design Good Research Practices Task Force.

PubMed

Reed Johnson, F; Lancsar, Emily; Marshall, Deborah; Kilambi, Vikram; Mühlbacher, Axel; Regier, Dean A; Bresnahan, Brian W; Kanninen, Barbara; Bridges, John F P

2013-01-01

Stated-preference methods are a class of evaluation techniques for studying the preferences of patients and other stakeholders. While these methods span a variety of techniques, conjoint-analysis methods-and particularly discrete-choice experiments (DCEs)-have become the most frequently applied approach in health care in recent years. Experimental design is an important stage in the development of such methods, but establishing a consensus on standards is hampered by lack of understanding of available techniques and software. This report builds on the previous ISPOR Conjoint Analysis Task Force Report: Conjoint Analysis Applications in Health-A Checklist: A Report of the ISPOR Good Research Practices for Conjoint Analysis Task Force. This report aims to assist researchers specifically in evaluating alternative approaches to experimental design, a difficult and important element of successful DCEs. While this report does not endorse any specific approach, it does provide a guide for choosing an approach that is appropriate for a particular study. In particular, it provides an overview of the role of experimental designs for the successful implementation of the DCE approach in health care studies, and it provides researchers with an introduction to constructing experimental designs on the basis of study objectives and the statistical model researchers have selected for the study. The report outlines the theoretical requirements for designs that identify choice-model preference parameters and summarizes and compares a number of available approaches for constructing experimental designs. The task-force leadership group met via bimonthly teleconferences and in person at ISPOR meetings in the United States and Europe. An international group of experimental-design experts was consulted during this process to discuss existing approaches for experimental design and to review the task force's draft reports. In addition, ISPOR members contributed to developing a consensus report by submitting written comments during the review process and oral comments during two forum presentations at the ISPOR 16th and 17th Annual International Meetings held in Baltimore (2011) and Washington, DC (2012). Copyright © 2013 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

Studies on absorption coefficient near edge of multi elements

NASA Astrophysics Data System (ADS)

Eisa, M. H.; Shen, H.; Yao, H. Y.; Mi, Y.; Zhou, Z. Y.; Hu, T. D.; Xie, Y. N.

2005-12-01

X-ray absorption near edge structure (XANES) was used to study the near edge mass-absorption coefficients of seven elements, such as, Ti, V, Fe, Co, Ni, Cu and Zn. It is well known that, on the near edge absorption of element, when incident X-ray a few eV change can make the absorption coefficient an order magnitude alteration. So that, there are only a few points mass-absorption coefficient at the near edge absorption and that always average value in published table. Our results showed a wide range of data, the total measured data of mass-absorption coefficient of the seven elements was about 505. The investigation confirmed that XANES is useful technique for multi-element absorption coefficient measurement. Details of experimental methods and results are given and discussed. The experimental work has been performed at Beijing Synchrotron Radiation Facility. The measured values were compared with the published data. Good agreement between experimental results and published data is obtained.

Dermal uptake of phthalates from clothing: Comparison of model to human participant results.

PubMed

Morrison, G C; Weschler, C J; Bekö, G

2017-05-01

In this research, we extend a model of transdermal uptake of phthalates to include a layer of clothing. When compared with experimental results, this model better estimates dermal uptake of diethylphthalate and di-n-butylphthalate (DnBP) than a previous model. The model predictions are consistent with the observation that previously exposed clothing can increase dermal uptake over that observed in bare-skin participants for the same exposure air concentrations. The model predicts that dermal uptake from clothing of DnBP is a substantial fraction of total uptake from all sources of exposure. For compounds that have high dermal permeability coefficients, dermal uptake is increased for (i) thinner clothing, (ii) a narrower gap between clothing and skin, and (iii) longer time intervals between laundering and wearing. Enhanced dermal uptake is most pronounced for compounds with clothing-air partition coefficients between 10 4 and 10 7 . In the absence of direct measurements of cotton cloth-air partition coefficients, dermal exposure may be predicted using equilibrium data for compounds in equilibrium with cellulose and water, in combination with computational methods of predicting partition coefficients. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Experimental and Theoretical Studies of the Pure Rotational Spectra of Lead Halides: PbF and PbCl

NASA Astrophysics Data System (ADS)

Norman, Spencer; Dawes, Richard; Grubbs, G. S., II; Cooke, S. A.; Long, B. E.; Dewberry, Chris

2014-06-01

The pure rotational spectrum of lead monochloride, PbCl, has been measured and analyzed using chirped pulse and cavity Fourier transform microwave (CP-FTMW and FTMW) spectrometers equipped with an ablation source. Refined parameters of an effective Hamiltonian including fine and hyperfine interactions similar to those previously reported by Fink et al. [1] were determined. Dynamically-weighted, explicitly-correlated MRCI-F12 calculations [2] were performed for both PbF and the valence isoelectronic PbCl to predict potential energy curves (PEC). Spin-orbit coupling was included in the calculations, which is known to split the X12Π1/2 and X22Π3/2 components of the ground electronic state by roughly 8280 wn in both lead halide systems. Calculated rotational levels were obtained using the PECs and compared with experiment including previously published results for PbF [3]. References: 1- K. Ziebarth, K. D. Setzer, O. Shestakov,1 and E. H. Fink, J. Mol. Spec. 191, 108 (1998). 2- B. J. Barker et al. J. Chem. Phys. 137, 214313 (2012). 3- R. J. Mawhorter et al. Phys. Rev. A 84, 022508 (2011).

Federating heterogeneous datasets to enhance data sharing and experiment reproducibility

NASA Astrophysics Data System (ADS)

Prieto, Juan C.; Paniagua, Beatriz; Yatabe, Marilia S.; Ruellas, Antonio C. O.; Fattori, Liana; Muniz, Luciana; Styner, Martin; Cevidanes, Lucia

2017-03-01

Recent studies have demonstrated the difficulties to replicate scientific findings and/or experiments published in past.1 The effects seen in the replicated experiments were smaller than previously reported. Some of the explanations for these findings include the complexity of the experimental design and the pressure on researches to report positive findings. The International Committee of Medical Journal Editors (ICMJE) suggests that every study considered for publication must submit a plan to share the de-identified patient data no later than 6 months after publication. There is a growing demand to enhance the management of clinical data, facilitate data sharing across institutions and also to keep track of the data from previous experiments. The ultimate goal is to assure the reproducibility of experiments in the future. This paper describes Shiny-tooth, a web based application created to improve clinical data acquisition during the clinical trial; data federation of such data as well as morphological data derived from medical images; Currently, this application is being used to store clinical data from an osteoarthritis (OA) study. This work is submitted to the SPIE Biomedical Applications in Molecular, Structural, and Functional Imaging conference.

Optics-Only Calibration of a Neural-Net Based Optical NDE Method for Structural Health Monitoring

NASA Technical Reports Server (NTRS)

Decker, Arthur J.

2004-01-01

A calibration process is presented that uses optical measurements alone to calibrate a neural-net based NDE method. The method itself detects small changes in the vibration mode shapes of structures. The optics-only calibration process confirms previous work that the sensitivity to vibration-amplitude changes can be as small as 10 nanometers. A more practical value in an NDE service laboratory is shown to be 50 nanometers. Both model-generated and experimental calibrations are demonstrated using two implementations of the calibration technique. The implementations are based on previously published demonstrations of the NDE method and an alternative calibration procedure that depends on comparing neural-net and point sensor measurements. The optics-only calibration method, unlike the alternative method, does not require modifications of the structure being tested or the creation of calibration objects. The calibration process can be used to test improvements in the NDE process and to develop a vibration-mode-independence of damagedetection sensitivity. The calibration effort was intended to support NASA s objective to promote safety in the operations of ground test facilities or aviation safety, in general, by allowing the detection of the gradual onset of structural changes and damage.

Impact of doping on the density of states and the mobility in organic semiconductors

NASA Astrophysics Data System (ADS)

Zuo, Guangzheng; Abdalla, Hassan; Kemerink, Martijn

2016-06-01

We experimentally investigated conductivity and mobility of poly(3-hexylthiophene) (P3HT) doped with tetrafluorotetracyanoquinodimethane (F4TCNQ ) for various relative doping concentrations ranging from ultralow (10-5) to high (10-1) and various active layer thicknesses. Although the measured conductivity monotonously increases with increasing doping concentration, the mobilities decrease, in agreement with previously published work. Additionally, we developed a simple yet quantitative model to rationalize the results on basis of a modification of the density of states (DOS) by the Coulomb potentials of ionized dopants. The DOS was integrated in a three-dimensional (3D) hopping formalism in which parameters such as energetic disorder, intersite distance, energy level difference, and temperature were varied. We compared predictions of our model as well as those of a previously developed model to kinetic Monte Carlo (MC) modeling and found that only the former model accurately reproduces the mobility of MC modeling in a large part of the parameter space. Importantly, both our model and MC simulations are in good agreement with experiments; the crucial ingredient to both is the formation of a deep trap tail in the Gaussian DOS with increasing doping concentration.

Vaccination and reduced cohort duration can drive virulence evolution: Marek's disease virus and industrialized agriculture.

PubMed

Atkins, Katherine E; Read, Andrew F; Savill, Nicholas J; Renz, Katrin G; Islam, A F M Fakhrul; Walkden-Brown, Stephen W; Woolhouse, Mark E J

2013-03-01

Marek's disease virus (MDV), a commercially important disease of poultry, has become substantially more virulent over the last 60 years. This evolution was presumably a consequence of changes in virus ecology associated with the intensification of the poultry industry. Here, we assess whether vaccination or reduced host life span could have generated natural selection, which favored more virulent strains. Using previously published experimental data, we estimated viral fitness under a range of cohort durations and vaccine treatments on broiler farms. We found that viral fitness maximized at intermediate virulence, as a result of a trade-off between virulence and transmission previously reported. Our results suggest that vaccination, acting on this trade-off, could have led to the evolution of increased virulence. By keeping the host alive, vaccination prolongs infectious periods of virulent strains. Improvements in host genetics and nutrition, which reduced broiler life spans below 50 days, could have also increased the virulence of the circulating MDV strains because shortened cohort duration reduces the impact of host death on viral fitness. These results illustrate the dramatic impact anthropogenic change can potentially have on pathogen virulence. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Is email a reliable means of contacting authors of previously published papers? A study of the Emergency Medicine Journal for 2001.

PubMed

O'Leary, F

2003-07-01

To determine whether it is possible to contact authors of previously published papers via email. A cross sectional study of the Emergency Medicine Journal for 2001. 118 articles were included in the study. The response rate from those with valid email addresses was 73%. There was no statistical difference between the type of email address used and the address being invalid (p=0.392) or between the type of article and the likelihood of a reply (p=0.197). More responses were obtained from work addresses when compared with Hotmail addresses (86% v 57%, p=0.02). Email is a valid means of contacting authors of previously published articles, particularly within the emergency medicine specialty. A work based email address may be a more valid means of contact than a Hotmail address.

Gist of Dr. Katsusaburo Yamagiwa's papers entitled "Experimental study on the pathogenesis of epithelial tumors" (I to VI reports).

PubMed

Fujiki, Hirota

2014-02-01

The concept of cancer and inflammation has a long history. Virchow's irritation theory based on human cancer engendered the essential role of inflammation in carcinogenesis. Drs. Yamagiwa and Ichikawa first published a comprehensive paper entitled "Experimental study on the pathogenesis of epithelial tumors" (I report) in 1915 in German, and went on to publish five more reports (1915-1924) under the same title. They succeeded in demonstrating that inflammation is an important carcinogenic factor, and the mechanisms are now being investigated by numerous scientists all over the world. In order to introduce Yamagiwa's work to modern cancer researchers, the essentials of their six reports have been translated into English as a short review. Scientists' comments on Yamagiwa's contribution are attached by way of introduction. © 2013 The Authors. Cancer Science published by Wiley Publishing Asia Pty Ltd on behalf of Japanese Cancer Association.

Consequences of common data analysis inaccuracies in CNS trauma injury basic research.

PubMed

Burke, Darlene A; Whittemore, Scott R; Magnuson, David S K

2013-05-15

The development of successful treatments for humans after traumatic brain or spinal cord injuries (TBI and SCI, respectively) requires animal research. This effort can be hampered when promising experimental results cannot be replicated because of incorrect data analysis procedures. To identify and hopefully avoid these errors in future studies, the articles in seven journals with the highest number of basic science central nervous system TBI and SCI animal research studies published in 2010 (N=125 articles) were reviewed for their data analysis procedures. After identifying the most common statistical errors, the implications of those findings were demonstrated by reanalyzing previously published data from our laboratories using the identified inappropriate statistical procedures, then comparing the two sets of results. Overall, 70% of the articles contained at least one type of inappropriate statistical procedure. The highest percentage involved incorrect post hoc t-tests (56.4%), followed by inappropriate parametric statistics (analysis of variance and t-test; 37.6%). Repeated Measures analysis was inappropriately missing in 52.0% of all articles and, among those with behavioral assessments, 58% were analyzed incorrectly. Reanalysis of our published data using the most common inappropriate statistical procedures resulted in a 14.1% average increase in significant effects compared to the original results. Specifically, an increase of 15.5% occurred with Independent t-tests and 11.1% after incorrect post hoc t-tests. Utilizing proper statistical procedures can allow more-definitive conclusions, facilitate replicability of research results, and enable more accurate translation of those results to the clinic.

Gradient retention prediction of acid-base analytes in reversed phase liquid chromatography: a simplified approach for acetonitrile-water mobile phases.

PubMed

Andrés, Axel; Rosés, Martí; Bosch, Elisabeth

2014-11-28

In previous work, a two-parameter model to predict chromatographic retention of ionizable analytes in gradient mode was proposed. However, the procedure required some previous experimental work to get a suitable description of the pKa change with the mobile phase composition. In the present study this previous experimental work has been simplified. The analyte pKa values have been calculated through equations whose coefficients vary depending on their functional group. Forced by this new approach, other simplifications regarding the retention of the totally neutral and totally ionized species also had to be performed. After the simplifications were applied, new prediction values were obtained and compared with the previously acquired experimental data. The simplified model gave pretty good predictions while saving a significant amount of time and resources. Copyright © 2014 Elsevier B.V. All rights reserved.

77 FR 61375 - Endangered and Threatened Wildlife and Plants; 12-Month Finding on Petitions To List the Mexican...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-09

... 15915). We published a final rule, ``Establishment of a Nonessential Experimental Population of the... Mexican Wolf Experimental Population Area in central Arizona and New Mexico and designated the reintroduced population as a nonessential experimental population under section 10(j) of the Act. In March of...

Low Cost Gas Turbine Off-Design Prediction Technique

NASA Astrophysics Data System (ADS)

Martinjako, Jeremy

This thesis seeks to further explore off-design point operation of gas turbines and to examine the capabilities of GasTurb 12 as a tool for off-design analysis. It is a continuation of previous thesis work which initially explored the capabilities of GasTurb 12. The research is conducted in order to: 1) validate GasTurb 12 and, 2) predict off-design performance of the Garrett GTCP85-98D located at the Arizona State University Tempe campus. GasTurb 12 is validated as an off-design point tool by using the program to predict performance of an LM2500+ marine gas turbine. Haglind and Elmegaard (2009) published a paper detailing a second off-design point method and it includes the manufacturer's off-design point data for the LM2500+. GasTurb 12 is used to predict off-design point performance of the LM2500+ and compared to the manufacturer's data. The GasTurb 12 predictions show good correlation. Garrett has published specification data for the GTCP85-98D. This specification data is analyzed to determine the design point and to comment on off-design trends. Arizona State University GTCP85-98D off-design experimental data is evaluated. Trends presented in the data are commented on and explained. The trends match the expected behavior demonstrated in the specification data for the same gas turbine system. It was originally intended that a model of the GTCP85-98D be constructed in GasTurb 12 and used to predict off-design performance. The prediction would be compared to collected experimental data. This is not possible because the free version of GasTurb 12 used in this research does not have a module to model a single spool turboshaft. This module needs to be purchased for this analysis.

Benefits of smoking bans on preterm and early-term births: a natural experimental design in Switzerland.

PubMed

Vicedo-Cabrera, Ana M; Schindler, Christian; Radovanovic, Dragana; Grize, Leticia; Witassek, Fabienne; Dratva, Julia; Röösli, Martin; Perez, Laura

2016-12-01

Birth outcomes are relevant for future children's heath. Capitalising on a natural experimental design in Switzerland, we evaluated how regional smoking bans introduced at different time points affected birth outcomes, including preterm and early-term births. We used birth registry data of all singleton neonates born in Switzerland (2007-2012). We developed canton-specific interrupted time-series followed by random meta-analysis to evaluate the benefits of smoking bans on preterm (<37 gestational weeks) and early-term (37-38 gestational weeks) births. Heterogeneity across type of ban and contextual characteristics was explored through metaregression. A time-to-event approach was used for evaluating duration of pregnancy under the smoking bans and effects, taking into account individual maternal factors. We observed a decrease in the risk of preterm birth of 3.6% (95% CI, -9.3% to 2.5%), and early-term birth of 5.0% (95% CI -7.5% to -2.5%). Results showed a clear dose-response relationship. Greater risk reductions were obtained for preterm births in areas with more comprehensive bans (-6.8%; 95% CI -12.1% to 0.1%), and for pregnancies with the longest gestational time under smoking bans (HR, 0.991; 95% CI 0.984 to 0.997 per 10% increase in duration). Benefits were unequal across outcomes and characteristics of cantons and mothers. Smoking bans resulted in improved birth outcomes in Switzerland with cantons that adopted more comprehensive smoking bans achieving greater benefits. Early-term births constitute a previously ignored though important group. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Eutectic melting in the MgO-SiO2 system and its implication to Earth's lower mantle evolution

NASA Astrophysics Data System (ADS)

Baron, M. A.; Lord, O. T.; Myhill, R.; Thomson, A.; Wang, W.; Tronnes, R. G.; Walter, M. J.

2017-12-01

Eutectic melting curves in the system MgO-SiO2 have been experimentally studied at lower mantle pressures using laser-heated diamond anvil cell (LH-DAC) techniques. We investigated eutectic melting of bridgmanite plus periclase in the MgO-MgSiO3 binary and bridgmanite plus stishovite in the MgSiO3-SiO2 sub-system as the simplest models of natural peridotite and basalt. The eutectic melting have been detected on the basis of the thermal perturbations (i.e. melting plateau) during the experiment but also post-experimental textural and chemical analyses of the recovered samples. We also performed a suite of sub-solidus experiments in order to compare and bracket the eutectic melting experiments. The melting curve of model basalt occurs at lower temperatures, has a shallower dT/dP slope and slightly less curvature than the model peridotitic melting curve. Overall, melting temperatures detected in this study are in good agreement with previous experiments and ab initio simulations at 25 GPa (Liebske and Frost, 2012; de Koker et al., 2013). However, at higher pressures the measured eutectic melting curves are systematically lower in temperature than curves extrapolated on the basis of thermodynamic modelling of low-pressure experimental data, and those calculated from atomistic simulations. In turn, when comparing with previously published solidus curves obtained for natural basalt and peridotite (e.g. Fiquet et al., 2010; Andrault et al. 2011; Nomura et al. 2014; Hirose et al. 1999; Andrault et al. 2014 and Pradhan et al. 2015) the melting curves from this study are higher. However, the difference in temperature is less significant than previously though. Based on the comparison of the curvature of the model peridotite eutectic relative to an MgSiO3 melt adiabat we infer that crystallization in a global magma ocean would begin at 100 GPa rather than at the bottom of the mantle, allowing for an early basal melt layer. The model peridotite melting curve lies 500 K above the mantle geotherm at the core-mantle boundary, indicating that it will not be molten. The model basalt melting curve intersects the geotherm at the base of the mantle, and partial melting of subducted oceanic crust is therefore expected.

Exploring the effects of transducer models when training convolutional neural networks to eliminate reflection artifacts in experimental photoacoustic images

NASA Astrophysics Data System (ADS)

Allman, Derek; Reiter, Austin; Bell, Muyinatu

2018-02-01

We previously proposed a method of removing reflection artifacts in photoacoustic images that uses deep learning. Our approach generally relies on using simulated photoacoustic channel data to train a convolutional neural network (CNN) that is capable of distinguishing sources from artifacts based on unique differences in their spatial impulse responses (manifested as depth-based differences in wavefront shapes). In this paper, we directly compare a CNN trained with our previous continuous transducer model to a CNN trained with an updated discrete acoustic receiver model that more closely matches an experimental ultrasound transducer. These two CNNs were trained with simulated data and tested on experimental data. The CNN trained using the continuous receiver model correctly classified 100% of sources and 70.3% of artifacts in the experimental data. In contrast, the CNN trained using the discrete receiver model correctly classified 100% of sources and 89.7% of artifacts in the experimental images. The 19.4% increase in artifact classification accuracy indicates that an acoustic receiver model that closely mimics the experimental transducer plays an important role in improving the classification of artifacts in experimental photoacoustic data. Results are promising for developing a method to display CNN-based images that remove artifacts in addition to only displaying network-identified sources as previously proposed.

75 FR 12003 - Investing in Innovation Fund

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-12

..., Proposed Practice, Strategy, or implemented experimental implemented strategy, or program, Program. study or well-designed experimental or quasi- or one similar to it, and well-implemented experimental study, has been attempted quasi-experimental with small sample sizes previously, albeit on a study; or (2...

A Computational Model of the Rainbow Trout Hypothalamus-Pituitary-Ovary-Liver Axis

PubMed Central

Gillies, Kendall; Krone, Stephen M.; Nagler, James J.; Schultz, Irvin R.

2016-01-01

Reproduction in fishes and other vertebrates represents the timely coordination of many endocrine factors that culminate in the production of mature, viable gametes. In recent years there has been rapid growth in understanding fish reproductive biology, which has been motivated in part by recognition of the potential effects that climate change, habitat destruction and contaminant exposure can have on natural and cultured fish populations. New approaches to understanding the impacts of these stressors are being developed that require a systems biology approach with more biologically accurate and detailed mathematical models. We have developed a multi-scale mathematical model of the female rainbow trout hypothalamus-pituitary-ovary-liver axis to use as a tool to help understand the functioning of the system and for extrapolation of laboratory findings of stressor impacts on specific components of the axis. The model describes the essential endocrine components of the female rainbow trout reproductive axis. The model also describes the stage specific growth of maturing oocytes within the ovary and permits the presence of sub-populations of oocytes at different stages of development. Model formulation and parametrization was largely based on previously published in vivo and in vitro data in rainbow trout and new data on the synthesis of gonadotropins in the pituitary. Model predictions were validated against several previously published data sets for annual changes in gonadotropins and estradiol in rainbow trout. Estimates of select model parameters can be obtained from in vitro assays using either quantitative (direct estimation of rate constants) or qualitative (relative change from control values) approaches. This is an important aspect of mathematical models as in vitro, cell-based assays are expected to provide the bulk of experimental data for future risk assessments and will require quantitative physiological models to extrapolate across biological scales. PMID:27096735

A Computational Model of the Rainbow Trout Hypothalamus-Pituitary-Ovary-Liver Axis.

PubMed

Gillies, Kendall; Krone, Stephen M; Nagler, James J; Schultz, Irvin R

2016-04-01

Reproduction in fishes and other vertebrates represents the timely coordination of many endocrine factors that culminate in the production of mature, viable gametes. In recent years there has been rapid growth in understanding fish reproductive biology, which has been motivated in part by recognition of the potential effects that climate change, habitat destruction and contaminant exposure can have on natural and cultured fish populations. New approaches to understanding the impacts of these stressors are being developed that require a systems biology approach with more biologically accurate and detailed mathematical models. We have developed a multi-scale mathematical model of the female rainbow trout hypothalamus-pituitary-ovary-liver axis to use as a tool to help understand the functioning of the system and for extrapolation of laboratory findings of stressor impacts on specific components of the axis. The model describes the essential endocrine components of the female rainbow trout reproductive axis. The model also describes the stage specific growth of maturing oocytes within the ovary and permits the presence of sub-populations of oocytes at different stages of development. Model formulation and parametrization was largely based on previously published in vivo and in vitro data in rainbow trout and new data on the synthesis of gonadotropins in the pituitary. Model predictions were validated against several previously published data sets for annual changes in gonadotropins and estradiol in rainbow trout. Estimates of select model parameters can be obtained from in vitro assays using either quantitative (direct estimation of rate constants) or qualitative (relative change from control values) approaches. This is an important aspect of mathematical models as in vitro, cell-based assays are expected to provide the bulk of experimental data for future risk assessments and will require quantitative physiological models to extrapolate across biological scales.

Retracted articles in surgery journals. What are surgeons doing wrong?

PubMed

Cassão, Bruna Dell'Acqua; Herbella, Fernando A M; Schlottmann, Francisco; Patti, Marco G

2018-06-01

Retraction of previously published scientific articles is an important mechanism to preserve the integrity of scientific work. This study analyzed retractions of previously published articles from surgery journals. We searched for retracted articles in the 100 surgery journals with the highest SJR2 indicator grades. We found 130 retracted articles in 49 journals (49%). Five or more retracted articles were published in 8 journals (8%). The mean time between publication and retraction was 26 months (range 1 to 158 months). The United States, China, Germany, Japan, and the United Kingdom accounted for more than 3 out of 4 of the retracted articles. The greatest number of retractions came from manuscripts about orthopedics and traumatology, general surgery, anesthesiology, cardiothoracic surgery, and plastic surgery. Nonsurgeons were responsible for 16% of retractions in these surgery journals. The main reasons for retraction were duplicate publication (42%), plagiarism (16%), absence of proven integrity of the study (14%), incorrect data (13%), data published without authorization (12%), violation of research ethics (11%), documented fraud (11%), request of an author(s) (5%), and unknown (3%). In 25% of the retracted articles, other publications by the same authors also had been retracted. Retraction of published articles does not occur frequently in surgery journals. Some form of scientific misconduct was present in the majority of retractions, especially duplication of publication and plagiarism. Retractions of previously published articles were most frequent from countries with the greatest number of publications; some authors showed recidivism. Copyright © 2018 Elsevier Inc. All rights reserved.

Mutual coupling effects in antenna arrays, volume 1

NASA Technical Reports Server (NTRS)

Collin, R. E.

1986-01-01

Mutual coupling between rectangular apertures in a finite antenna array, in an infinite ground plane, is analyzed using the vector potential approach. The method of moments is used to solve the equations that result from setting the tangential magnetic fields across each aperture equal. The approximation uses a set of vector potential model functions to solve for equivalent magnetic currents. A computer program was written to carry out this analysis and the resulting currents were used to determine the co- and cross-polarized far zone radiation patterns. Numerical results for various arrays using several modes in the approximation are presented. Results for one and two aperture arrays are compared against published data to check on the agreement of this model with previous work. Computer derived results are also compared against experimental results to test the accuracy of the model. These tests of the accuracy of the program showed that it yields valid data.

Understanding and controlling plasmon-induced convection

NASA Astrophysics Data System (ADS)

Roxworthy, Brian J.; Bhuiya, Abdul M.; Vanka, Surya P.; Toussaint, Kimani C.

2014-01-01

The heat generation and fluid convection induced by plasmonic nanostructures is attractive for optofluidic applications. However, previously published theoretical studies predict only nanometre per second fluid velocities that are inadequate for microscale mass transport. Here we show both theoretically and experimentally that an array of plasmonic nanoantennas coupled to an optically absorptive indium-tin-oxide (ITO) substrate can generate >micrometre per second fluid convection. Crucially, the ITO distributes thermal energy created by the nanoantennas generating an order of magnitude increase in convection velocities compared with nanoantennas on a SiO2 base layer. In addition, the plasmonic array alters absorption in the ITO, causing a deviation from Beer-Lambert absorption that results in an optimum ITO thickness for a given system. This work elucidates the role of convection in plasmonic optical trapping and particle assembly, and opens up new avenues for controlling fluid and mass transport on the micro- and nanoscale.

Theoretical study of the crystal-field energy levels and two-photon absorption intensities of Tb3+ in cubic host lattices.

PubMed

Duan, Chang-Kui; Tanner, Peter A

2011-03-17

Published two photon excitation (TPE) intensities for the cubic elpasolite systems Cs(2)NaTbX(6) (X = Cl, F) have been simulated by a calculation of two photon absorption (TPA) intensities which takes into account electric dipole transitions involving the detailed crystal-field structure of 4f(7)5d intermediate states, as well as the interactions of the 4f(7) core with the d-electron. The intensity calculation employed parameters from an energy level calculation which not only presented an accurate fit, but also yielded parameters consistent with those from other lanthanide ions. The calculated intensities were used to confirm or adjust the previous assignments of energy levels, resulting in some minor revisions. Generally, the TPA intensity simulations were in better agreement with experimental data for the fluoride, rather than the chloride, system and possible reasons for this are given.

Refractive index and birefringence of 2H silicon carbide.

NASA Technical Reports Server (NTRS)

Powell, J. A.

1972-01-01

Measurement of the refractive indices of 2H SiC over the wavelength range from 435.8 to 650.9 nm by the method of minimum deviation. A curve fit of the experimental data to the Cauchy dispersion equation yielded, for the ordinary index, n sub zero = 2.5513 + 25,850/lambda squared + 8.928 x 10 to the 8th power/lambda to the 4th power and, for the extraordinary index, n sub e = 2.6161 + 28,230/lambda squared + 11.490 x 10 to the 8th power/lambda to the 4th power when lambda is expressed in nm. The estimated error (standard deviation) in these values is plus or minus 0.0006 for n sub zero and plus or minus 0.0009 for n sub e. The birefringence calculated from these expressions is about 20% less than previously published values.

Discrete Roughness Effects on Shuttle Orbiter at Mach 6

NASA Technical Reports Server (NTRS)

Berry, Scott A.; Hamilton, H. Harris, II

2002-01-01

Discrete roughness boundary layer transition results on a Shuttle Orbiter model in the NASA Langley Research Center 20-Inch Mach 6 Air Tunnel have been reanalyzed with new boundary layer calculations to provide consistency for comparison to other published results. The experimental results were previously obtained utilizing the phosphor thermography system to monitor the status of the boundary layer via global heat transfer images of the Orbiter windward surface. The size and location of discrete roughness elements were systematically varied along the centerline of the 0.0075-scale model at an angle of attack of 40 deg and the boundary layer response recorded. Various correlative approaches were attempted, with the roughness transition correlations based on edge properties providing the most reliable results. When a consistent computational method is used to compute edge conditions, transition datasets for different configurations at several angles of attack have been shown to collapse to a well-behaved correlation.

Thermodynamic prediction of protein neutrality.

PubMed

Bloom, Jesse D; Silberg, Jonathan J; Wilke, Claus O; Drummond, D Allan; Adami, Christoph; Arnold, Frances H

2005-01-18

We present a simple theory that uses thermodynamic parameters to predict the probability that a protein retains the wild-type structure after one or more random amino acid substitutions. Our theory predicts that for large numbers of substitutions the probability that a protein retains its structure will decline exponentially with the number of substitutions, with the severity of this decline determined by properties of the structure. Our theory also predicts that a protein can gain extra robustness to the first few substitutions by increasing its thermodynamic stability. We validate our theory with simulations on lattice protein models and by showing that it quantitatively predicts previously published experimental measurements on subtilisin and our own measurements on variants of TEM1 beta-lactamase. Our work unifies observations about the clustering of functional proteins in sequence space, and provides a basis for interpreting the response of proteins to substitutions in protein engineering applications.

Thermodynamic prediction of protein neutrality

PubMed Central

Bloom, Jesse D.; Silberg, Jonathan J.; Wilke, Claus O.; Drummond, D. Allan; Adami, Christoph; Arnold, Frances H.

2005-01-01

We present a simple theory that uses thermodynamic parameters to predict the probability that a protein retains the wild-type structure after one or more random amino acid substitutions. Our theory predicts that for large numbers of substitutions the probability that a protein retains its structure will decline exponentially with the number of substitutions, with the severity of this decline determined by properties of the structure. Our theory also predicts that a protein can gain extra robustness to the first few substitutions by increasing its thermodynamic stability. We validate our theory with simulations on lattice protein models and by showing that it quantitatively predicts previously published experimental measurements on subtilisin and our own measurements on variants of TEM1 β-lactamase. Our work unifies observations about the clustering of functional proteins in sequence space, and provides a basis for interpreting the response of proteins to substitutions in protein engineering applications. PMID:15644440

Heat transfer in the turbulent boundary layer with a short strip of surface roughness

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

Taylor, R.P.; Chakroun, W.M.

1992-01-01

The effects of a short strip of surface roughness on heat transfer and fluid flow in the turbulent boundary layer are investigated experimentally. This is done by measuring Stanton number and skin friction distributions and mean velocity, turbulence intensity, and mean temperature profiles in a turbulent boundary layer where the first 0.7 m length is smooth, the next 0.2 m is roughened with 1.27 mm hemispheres spaced 2 base diameters apart and the final 1.5 m is smooth. These results are compared with previously published data from experiments wiht a rough leading portion and smooth final portion and from experimentsmore » on an all-smooth surface. The influence of the roughness is large in the neighborhood of the rough strip, but the Stanton number and skin friction distributions are seen to quickly recover smooth-wall behavior downstream of the rough strip. 19 refs.« less

Extended evolution: A conceptual framework for integrating regulatory networks and niche construction

PubMed Central

Renn, Jürgen

2015-01-01

ABSTRACT This paper introduces a conceptual framework for the evolution of complex systems based on the integration of regulatory network and niche construction theories. It is designed to apply equally to cases of biological, social and cultural evolution. Within the conceptual framework we focus especially on the transformation of complex networks through the linked processes of externalization and internalization of causal factors between regulatory networks and their corresponding niches and argue that these are an important part of evolutionary explanations. This conceptual framework extends previous evolutionary models and focuses on several challenges, such as the path‐dependent nature of evolutionary change, the dynamics of evolutionary innovation and the expansion of inheritance systems. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 565–577, 2015. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution published by Wiley Periodicals, Inc. PMID:26097188

In-situ characterization of laser-powder interaction and cooling rates through high-speed imaging of powder bed fusion additive manufacturing

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

Scipioni Bertoli, Umberto; Guss, Gabe; Wu, Sheldon

We report detailed understanding of the complex melt pool physics plays a vital role in predicting optimal processing regimes in laser powder bed fusion additive manufacturing. In this work, we use high framerate video recording of Selective Laser Melting (SLM) to provide useful insight on the laser-powder interaction and melt pool evolution of 316 L powder layers, while also serving as a novel instrument to quantify cooling rates of the melt pool. The experiment was performed using two powder types – one gas- and one water-atomized – to further clarify how morphological and chemical differences between these two feedstock materialsmore » influence the laser melting process. Finally, experimentally determined cooling rates are compared with values obtained through computer simulation, and the relationship between cooling rate and grain cell size is compared with data previously published in the literature.« less

Interfacial charge transfer absorption: Application to metal molecule assemblies

NASA Astrophysics Data System (ADS)

Creutz, Carol; Brunschwig, Bruce S.; Sutin, Norman

2006-05-01

Optically induced charge transfer between adsorbed molecules and a metal electrode was predicted by Hush to lead to new electronic absorption features, but has been only rarely observed experimentally. Interfacial charge transfer absorption (IFCTA) provides information concerning the barriers to charge transfer between molecules and the metal/semiconductor and the magnitude of the electronic coupling and could thus provide a powerful tool for understanding interfacial charge-transfer kinetics. Here, we utilize a previously published model [C. Creutz, B.S. Brunschwig, N. Sutin, J. Phys. Chem. B 109 (2005) 10251] to predict IFCTA spectra of metal-molecule assemblies and compare the literature observations to these predictions. We conclude that, in general, the electronic coupling between molecular adsorbates and the metal levels is so small that IFCTA is not detectable. However, few experiments designed to detect IFCTA have been done. We suggest approaches to optimizing the conditions for observing the process.

How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity

NASA Technical Reports Server (NTRS)

Fox, G. E.; Wisotzkey, J. D.; Jurtshuk, P. Jr

1992-01-01

16S rRNA (genes coding for rRNA) sequence comparisons were conducted with the following three psychrophilic strains: Bacillus globisporus W25T (T = type strain) and Bacillus psychrophilus W16AT, and W5. These strains exhibited more than 99.5% sequence identity and within experimental uncertainty could be regarded as identical. Their close taxonomic relationship was further documented by phenotypic similarities. In contrast, previously published DNA-DNA hybridization results have convincingly established that these strains do not belong to the same species if current standards are used. These results emphasize the important point that effective identity of 16S rRNA sequences is not necessarily a sufficient criterion to guarantee species identity. Thus, although 16S rRNA sequences can be used routinely to distinguish and establish relationships between genera and well-resolved species, very recently diverged species may not be recognizable.

A Comparison of Measured and Predicted XV-15 Tiltrotor Surface Acoustic Pressures

NASA Technical Reports Server (NTRS)

Lyle, Karen H.; Burley, Casey L.; Prichard, Devon S.

1997-01-01

Predicted XV-15 exterior surface acoustic pressures are compared with previously published experimental data. Surface acoustic pressure transducers were concentrated near the tip-path-plane of the rotor in airplane mode. The comparison emphasized cruise conditions which are of interest for tiltrotor interior noise - level flight for speeds ranging from 72 m/s to 113 m/s. The predictions were produced by components of the NASA Langley Tiltrotor Aeroacoustic Code (TRAC) system of computer codes. Comparisons between measurements and predictions were made in both the time and frequency domains, as well as overall sound pressure levels. In general, the predictions replicated the measured data well. Discrepancies between measurements and predictions were noted. Some of the discrepancies were due to poor correlation of the measured data with the rotor tach signal. In other cases limitations of the predictive methodology have been indicated.

The study of 'microsurfaces' using thermal desorption spectroscopy

NASA Technical Reports Server (NTRS)

Thomas, M. E.; Poppa, H.; Pound, G. M.

1979-01-01

The use of a newly combined ultrahigh vacuum technique for studying continuous and particulate evaporated thin films using thermal desorption spectroscopy (TDS), transmission electron microscopy (TEM), and transmission electron diffraction (TED) is discussed. It is shown that (1) CO thermal desorption energies of epitaxially deposited (111) Ni and (111) Pd surfaces agree perfectly with previously published data on bulk (111) single crystal, (2) contamination and surface structural differences can be detected using TDS as a surface probe and TEM as a complementary technique, and (3) CO desorption signals from deposited metal coverages of one-thousandth of a monolayer should be detectable. These results indicate that the chemisorption properties of supported 'microsurfaces' of metals can now be investigated with very high sensitivity. The combined use of TDS and TEM-TED experimental methods is a very powerful technique for fundamental studies in basic thin film physics and in catalysis.

Excitation cross sections for the ns 2S yields np 2P resonance transitions in Mg(+) (n = 3) and Zn(+) (n = 4) using electron-energy-loss and merged-beams methods

NASA Technical Reports Server (NTRS)

Smith, Steven J.; Chutjian, A.; Mitroy, J.; Tayal, S. S.; Henry, Ronald J. W.; Man, K.-F.; Mawhorter, R. J.; Williams, I. D.

1993-01-01

Electron-excitation cross sections are reported for the 3s 2S yields 3p 2P(h, k) resonance transition in Mg(+) at energies from threshold (4.43 eV) to approximately 9 times threshold (40.0 eV). The electron-energy-loss merged-beams technique used in these measurements is described in detail. In addition, the method of separating contributions of the elastically scattered (Coulomb) and the inelastically scattered electrons in the present Mg(+) case and previously reported Zn(+) results is described. Comparisons in the experimental energy range are made for Mg(+) with the two five-state close-coupling theoretical calculations carried out herein, and with other published close-coupling, distorted-wave, and semiempirical calculations. The present Mg(+) cross sections and Zn(+) cross sections from earlier measurements are tabulated.

Refractive-index measurement and inverse correction using optical coherence tomography.

PubMed

Stritzel, Jenny; Rahlves, Maik; Roth, Bernhard

2015-12-01

We describe a novel technique for determination of the refractive index of hard biological tissue as well as nonopaque technical samples based on optical coherence tomography (OCT). Our method relies on an inverse refractive-index correction (I-RIC), which matches a measured feature geometry distorted due to refractive-index boundaries to its real geometry. For known feature geometry, the refractive index can be determined with high precision from the best match between the distorted and corrected images. We provide experimental data for refractive-index measurements on a polymethylmethacrylate (PMMA) and on an ex vivo porcine cranial-bone, which are compared to reference measurements and previously published data. Our method is potentially capable of in vivo measurements on rigid biological tissue such as bone as, for example, is required to improve guidance in robot-aided surgical interventions and also for retrieving complex refractive-index profiles of compound materials.

Airfoil self-noise and prediction

NASA Technical Reports Server (NTRS)

Brooks, Thomas F.; Pope, D. Stuart; Marcolini, Michael A.

1989-01-01

A prediction method is developed for the self-generated noise of an airfoil blade encountering smooth flow. The prediction methods for the individual self-noise mechanisms are semiempirical and are based on previous theoretical studies and data obtained from tests of two- and three-dimensional airfoil blade sections. The self-noise mechanisms are due to specific boundary-layer phenomena, that is, the boundary-layer turbulence passing the trailing edge, separated-boundary-layer and stalled flow over an airfoil, vortex shedding due to laminar boundary layer instabilities, vortex shedding from blunt trailing edges, and the turbulent vortex flow existing near the tip of lifting blades. The predictions are compared successfully with published data from three self-noise studies of different airfoil shapes. An application of the prediction method is reported for a large scale-model helicopter rotor, and the predictions compared well with experimental broadband noise measurements. A computer code of the method is given.

Quantification of volatile organic compounds in smoke from prescribed burning and comparison with occupational exposure limits

NASA Astrophysics Data System (ADS)

Romagnoli, E.; Barboni, T.; Santoni, P.-A.; Chiaramonti, N.

2014-05-01

Prescribed burning represents a serious threat to personnel fighting fires due to smoke inhalation. The aim of this study was to investigate exposure by foresters to smoke from prescribed burning, focusing on exposure to volatile organic compounds (VOCs). The methodology for smoke sampling was first evaluated. Potentially dangerous compounds were identified among the VOCs emitted by smoke fires at four prescribed burning plots located around Corsica. The measured mass concentrations for several toxic VOCs were generally higher than those measured in previous studies due to the experimental framework (short sampling distance between the foresters and the flame, low combustion, wet vegetation). In particular, benzene, phenol and furfural exceeded the legal short-term exposure limits published in Europe and/or the United States. Other VOCs such as toluene, ethybenzene or styrene remained below the exposure limits. In conclusion, clear and necessary recommendations were made for protection of personnel involved in fighting fires.

Aluminum binding by humus

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

Benedetti, M.F.; Hiemstra, T.; Riemsdijk, W. van

The need for qualitative and quantitative description of the chemical speciation of Al, in particular and other metal ions in general, is stressed by the increased mobilization of metal ions in water and soils due to acid rain deposition. In this paper we present new data of Al binding to two humic acids. These new data sets and the some previously published data will be analyzed with the NICA-Donnan model using one set of parameters to describe the Al binding to the different humic substances. Once the experimental data is described with the NICA-Donnan approach, we will show the effectmore » of Ca on Al binding and surface speciation as well as the effect of Al on the charge of the humic particles. The parameters derived from the laboratory experiments will be used to describe the variation of the field based Al partition coefficient.« less

Comment on "A convenient method for preparation of 2-amino-4,6-diphenylnicotinonitrile using HBF4 as an efficient catalyst via an anomeric based oxidation: A joint experimental and theoretical study" [J. Mol. Struct. 1137 (2017) 674-680

NASA Astrophysics Data System (ADS)

Salehzadeh, Sadegh; Maleki, Farahnaz

2018-02-01

The title paper contains two types of calculations that are in disagreement with some basic concepts of chemistry. The first one is calculating a macroscopic amount of energy difference between one pair of enantiomers that is not correct. The second one is that the different bond orders for R and S stereoisomers and for different pathways of hyperconjugation/electron delocalization have been reported that both are impossible. In addition, the term electron transfer has been wrongly used for donor-acceptor orbital interactions inside one molecule where nothing is oxidized or reduced. Furthermore, the paper has missed some necessary comparisons with a previously published work of authors. There are also some technical problems in the title paper that are discussed in the present comment article.

Outdoor air pollution and asthma

PubMed Central

Guarnieri, Michael; Balmes, John R.

2015-01-01

Traffic and power generation are the main sources of urban air pollution. The idea that outdoor air pollution can cause exacerbations of pre-existing asthma is supported by an evidence base that has been accumulating for several decades, with several studies suggesting a contribution to new-onset asthma as well. In this Series paper, we discuss the effects of particulate matter (PM), gaseous pollutants (ozone, nitrogen dioxide, and sulphur dioxide), and mixed traffic-related air pollution. We focus on clinical studies, both epidemiological and experimental, published in the previous 5 years. From a mechanistic perspective, air pollutants probably cause oxidative injury to the airways, leading to inflammation, remodelling, and increased risk of sensitisation. Although several pollutants have been linked to new-onset asthma, the strength of the evidence is variable. We also discuss clinical implications, policy issues, and research gaps relevant to air pollution and asthma. PMID:24792855

The extent of lunar regolith mixing

NASA Technical Reports Server (NTRS)

Nishiizumi, K.; Imamura, M.; Kohl, C. P.; Murrell, M. T.; Arnold, J. R.; Russ, G. P., III

1979-01-01

The activity of solar cosmic-ray-produced Mn-53 measured as a function of depth in the upper 100 g/sq cm of lunar cores 60009-60010 and 12025-12028 is discussed. Analyses of samples from the Apollo 15 and 16 drill stems together with authors' previously published results (1974, 1976), and the Battelle Na-22 and Al-26 data, indicate that in three of the four cases studied the regolith was measurably disturbed within the last 10 m.y. Activities measured in the uppermost 2 g/sq cm indicate frequent mixing within this depth range. The Monte Carlo gardening model of Arnold (1975) was used to derive profiles for the gardened moon-wide average of Mn-53 and Al-26 as a function of depth. The Mn-53 and Al-26 experimental results agreed with theoretical predictions, but the calculated depths of disturbance appeared too low.

Comparative analysis of the modified enclosed energy metric for self-focusing holograms from digital lensless holographic microscopy.

PubMed

Trujillo, Carlos; Garcia-Sucerquia, Jorge

2015-06-01

A comparative analysis of the performance of the modified enclosed energy (MEE) method for self-focusing holograms recorded with digital lensless holographic microscopy is presented. Notwithstanding the MEE analysis previously published, no extended analysis of its performance has been reported. We have tested the MEE in terms of the minimum axial distance allowed between the set of reconstructed holograms to search for the focal plane and the elapsed time to obtain the focused image. These parameters have been compared with those for some of the already reported methods in the literature. The MEE achieves better results in terms of self-focusing quality but at a higher computational cost. Despite its longer processing time, the method remains within a time frame to be technologically attractive. Modeled and experimental holograms have been utilized in this work to perform the comparative study.

Single image super-resolution based on approximated Heaviside functions and iterative refinement

PubMed Central

Wang, Xin-Yu; Huang, Ting-Zhu; Deng, Liang-Jian

2018-01-01

One method of solving the single-image super-resolution problem is to use Heaviside functions. This has been done previously by making a binary classification of image components as “smooth” and “non-smooth”, describing these with approximated Heaviside functions (AHFs), and iteration including l1 regularization. We now introduce a new method in which the binary classification of image components is extended to different degrees of smoothness and non-smoothness, these components being represented by various classes of AHFs. Taking into account the sparsity of the non-smooth components, their coefficients are l1 regularized. In addition, to pick up more image details, the new method uses an iterative refinement for the residuals between the original low-resolution input and the downsampled resulting image. Experimental results showed that the new method is superior to the original AHF method and to four other published methods. PMID:29329298

In-situ characterization of laser-powder interaction and cooling rates through high-speed imaging of powder bed fusion additive manufacturing

DOE PAGES

Scipioni Bertoli, Umberto; Guss, Gabe; Wu, Sheldon; ...

2017-09-21

We report detailed understanding of the complex melt pool physics plays a vital role in predicting optimal processing regimes in laser powder bed fusion additive manufacturing. In this work, we use high framerate video recording of Selective Laser Melting (SLM) to provide useful insight on the laser-powder interaction and melt pool evolution of 316 L powder layers, while also serving as a novel instrument to quantify cooling rates of the melt pool. The experiment was performed using two powder types – one gas- and one water-atomized – to further clarify how morphological and chemical differences between these two feedstock materialsmore » influence the laser melting process. Finally, experimentally determined cooling rates are compared with values obtained through computer simulation, and the relationship between cooling rate and grain cell size is compared with data previously published in the literature.« less

Pedestrian headways - Reflection of territorial social forces

NASA Astrophysics Data System (ADS)

Krbálek, Milan; Hrabák, Pavel; Bukáček, Marek

2018-01-01

The aim of the article is to give a more detailed insight into territorial social forces acting between pedestrians by means of headway distribution and spectral rigidity. Probabilistic distribution of time headways between consecutive pedestrians is studied theoretically and experimentally. Several original experiments/empirical observations are presented and compared to data obtained from previously published experiments. The study is restricted to an unidirectional one-lane motion where overtaking is forbidden. The main stress is put on natural choices of mutual interaction represented by logarithmic and hyperbolic potentials leading to gamma and generalized inverse Gaussian distribution respectively. We show that the time headway distribution does not sufficiently reflect the differences between such distributions. The tools related to spectral rigidity and compressibility are chosen instead so as to predict the territorial social forces more accurately. Surprisingly, pedestrian flow seems to show a higher level of synchronization (lower compressibility) than vehicular flow.

Percolation behaviour in the magnetic permeability and electrical conductivity in conducting magnetic - Insulating non magnetic binary composites

NASA Astrophysics Data System (ADS)

McLachlan, David S.; Doyle, Terence B.; Sauti, Godfrey

2018-07-01

Experimental results of the complex magnetic permeability (μ) and the electrical conductivity (σ) of a granular paramagnetic Gadolinium Gallium Garnet (GGG: 0.3-26 vol%) and Teflon (PTFE) system are presented and discussed in relation to previously published (conductivity) and unpublished (permeability) studies on granular Fe3O4 - talc and Ni - talc wax systems. In these systems plots of the real conductivity (σm‧) against the volume fraction (φ) lie on characteristic sigmoid curves that when fitted to the Two Exponent Phenomenological Percolation Equation (TEPPE) confirm the existence of "percolation microstructures" with critical volume fractions (φc). The plots of the real and imaginary permeability (μm‧) and (μm″) satisfactorily fit to the TEPPE using the φc obtained in each case from the "conductivity" measurements. In all three cases the conductivity results gave the exponent t > 2, and the permeability results gave t < 1.

Electromigration model for the prediction of lifetime based on the failure unit statistics in aluminum metallization

NASA Astrophysics Data System (ADS)

Park, Jong Ho; Ahn, Byung Tae

2003-01-01

A failure model for electromigration based on the "failure unit model" was presented for the prediction of lifetime in metal lines.The failure unit model, which consists of failure units in parallel and series, can predict both the median time to failure (MTTF) and the deviation in the time to failure (DTTF) in Al metal lines. The model can describe them only qualitatively. In our model, both the probability function of the failure unit in single grain segments and polygrain segments are considered instead of in polygrain segments alone. Based on our model, we calculated MTTF, DTTF, and activation energy for different median grain sizes, grain size distributions, linewidths, line lengths, current densities, and temperatures. Comparisons between our results and published experimental data showed good agreements and our model could explain the previously unexplained phenomena. Our advanced failure unit model might be further applied to other electromigration characteristics of metal lines.

Brain correlates of subjective freedom of choice.

PubMed

Filevich, Elisa; Vanneste, Patricia; Brass, Marcel; Fias, Wim; Haggard, Patrick; Kühn, Simone

2013-12-01

The subjective feeling of free choice is an important feature of human experience. Experimental tasks have typically studied free choice by contrasting free and instructed selection of response alternatives. These tasks have been criticised, and it remains unclear how they relate to the subjective feeling of freely choosing. We replicated previous findings of the fMRI correlates of free choice, defined objectively. We introduced a novel task in which participants could experience and report a graded sense of free choice. BOLD responses for conditions subjectively experienced as free identified a postcentral area distinct from the areas typically considered to be involved in free action. Thus, the brain correlates of subjective feeling of free action were not directly related to any established brain correlates of objectively-defined free action. Our results call into question traditional assumptions about the relation between subjective experience of choosing and activity in the brain's so-called voluntary motor areas. Copyright © 2013. Published by Elsevier Inc.

A combined computational and structural model of the full-length human prolactin receptor

PubMed Central

Bugge, Katrine; Papaleo, Elena; Haxholm, Gitte W.; Hopper, Jonathan T. S.; Robinson, Carol V.; Olsen, Johan G.; Lindorff-Larsen, Kresten; Kragelund, Birthe B.

2016-01-01

The prolactin receptor is an archetype member of the class I cytokine receptor family, comprising receptors with fundamental functions in biology as well as key drug targets. Structurally, each of these receptors represent an intriguing diversity, providing an exceptionally challenging target for structural biology. Here, we access the molecular architecture of the monomeric human prolactin receptor by combining experimental and computational efforts. We solve the NMR structure of its transmembrane domain in micelles and collect structural data on overlapping fragments of the receptor with small-angle X-ray scattering, native mass spectrometry and NMR spectroscopy. Along with previously published data, these are integrated by molecular modelling to generate a full receptor structure. The result provides the first full view of a class I cytokine receptor, exemplifying the architecture of more than 40 different receptor chains, and reveals that the extracellular domain is merely the tip of a molecular iceberg. PMID:27174498

Dose Schedule Optimization and the Pharmacokinetic Driver of Neutropenia

PubMed Central

Patel, Mayankbhai; Palani, Santhosh; Chakravarty, Arijit; Yang, Johnny; Shyu, Wen Chyi; Mettetal, Jerome T.

2014-01-01

Toxicity often limits the utility of oncology drugs, and optimization of dose schedule represents one option for mitigation of this toxicity. Here we explore the schedule-dependency of neutropenia, a common dose-limiting toxicity. To this end, we analyze previously published mathematical models of neutropenia to identify a pharmacokinetic (PK) predictor of the neutrophil nadir, and confirm this PK predictor in an in vivo experimental system. Specifically, we find total AUC and Cmax are poor predictors of the neutrophil nadir, while a PK measure based on the moving average of the drug concentration correlates highly with neutropenia. Further, we confirm this PK parameter for its ability to predict neutropenia in vivo following treatment with different doses and schedules. This work represents an attempt at mechanistically deriving a fundamental understanding of the underlying pharmacokinetic drivers of neutropenia, and provides insights that can be leveraged in a translational setting during schedule selection. PMID:25360756

Integrative strategies to identify candidate genes in rodent models of human alcoholism.

PubMed

Treadwell, Julie A

2006-01-01

The search for genes underlying alcohol-related behaviours in rodent models of human alcoholism has been ongoing for many years with only limited success. Recently, new strategies that integrate several of the traditional approaches have provided new insights into the molecular mechanisms underlying ethanol's actions in the brain. We have used alcohol-preferring C57BL/6J (B6) and alcohol-avoiding DBA/2J (D2) genetic strains of mice in an integrative strategy combining high-throughput gene expression screening, genetic segregation analysis, and mapping to previously published quantitative trait loci to uncover candidate genes for the ethanol-preference phenotype. In our study, 2 genes, retinaldehyde binding protein 1 (Rlbp1) and syntaxin 12 (Stx12), were found to be strong candidates for ethanol preference. Such experimental approaches have the power and the potential to greatly speed up the laborious process of identifying candidate genes for the animal models of human alcoholism.

Nuclear Data Sheets for A = 152

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

Martin, M.J.

2013-11-15

Detailed level schemes, decay schemes, and the experimental data on which they are based are presented for all nuclei with mass number A=152. The experimental data are evaluated; inconsistencies and discrepancies are noted; and adopted values for level and γ–ray energies, γ intensities, as well as for other nuclear properties are given. This evaluation replaces the A=152 evaluation published by Agda Artna–Cohen in Nuclear Data Sheets 79, 1 (1996) and the evaluation for 152Dy prepared by Balraj Singh and published in Nuclear Data Sheets 95, 995 (2002)

Continuation of a Postdoctoral Research Associateship Program

DTIC Science & Technology

1998-12-01

ODRS and LPO can be alleviated by nitric oxide. Rsearch in Progress: The experimental part of the research has been completed. The experimental ... Rsearch in Progress: The experimental part of the research has been completed. The experimental results have been published, or prepared for...construed as an official Department of the Army position, policy or decision unless so designated by other documentation. •*•*«, 19990521 029 fPII

Experimental Demonstration of the Microscopic Origin of Circular Dichroism in Two dimensional Metamaterials

DTIC Science & Technology

2016-06-22

ARTICLE Received 16 Sep 2015 | Accepted 25 May 2016 | Published 22 Jun 2016 Experimental demonstration of the microscopic origin of circular...dissipation of the constituent metamolecules. Because such dissipation occurs on a nanoscale, this effect has never been experimentally probed and...never been experimentally verified because of the challenge of measuring non-radiative loss on the nanoscale. In this study we use a combination of

Systematic Analysis of Theses in the Field of Emergency Medicine in Turkey.

PubMed

Cevik, Erdem; Karakus Yilmaz, Banu; Acar, Yahya Ayhan; Dokur, Mehmet

2015-03-01

The aim of this study is to systematically evaluate the theses in the field of emergency medicine in Turkey and to determine whether they were published as a scientific paper. This is a retrospective observational study. Theses in the field of emergency medicine between 1998 and 2013 were browsed from the internet database of National Thesis Center (Council of Higher Education). Study type, both if it was in the field of emergency, or if it was published and the journal's scope of published studies were assessed and recorded in the study chart. 579 theses were included in the study. 27.1% of them were published and 14.9% of them were published in SCI/SCI-E journals. Advisors of theses were emergency medicine specialists in 67.6% of theses and 493 (85.1%) of them were in the field of emergency medicine. 77.4% of theses were observational and 20.9% were experimental study. Most of the experimental studies (72.7%, n=88) were animal studies. It was concluded that very few theses in the field of emergency medicine were published in journals that were indexed in SCI/SCI-E.

37 CFR 381.10 - Cost of living adjustment.

Code of Federal Regulations, 2011 CFR

2011-07-01

... determined by the Consumer Price Index (all consumers, all items) during the period from the most recent Index published prior to December 1, 2006, to the most recent Index published prior to December 1, 2007... the cost of living during the period from the most recent index published prior to the previous notice...

37 CFR 253.10 - Cost of living adjustment.

Code of Federal Regulations, 2013 CFR

2013-07-01

... determined by the Consumer Price Index (all consumers, all items) during the period from the most recent Index published prior to December 1, 2002, to the most recent Index published prior to December 1, 2003... cost of living during the period from the most recent index published prior to the previous notice, to...

37 CFR 381.10 - Cost of living adjustment.

Code of Federal Regulations, 2013 CFR

2013-07-01

... determined by the Consumer Price Index (all consumers, all items) during the period from the most recent Index published prior to December 1, 2012, to the most recent Index published prior to December 1, 2013... change in the cost of living during the period from the most recent index published prior to the previous...

37 CFR 381.10 - Cost of living adjustment.

Code of Federal Regulations, 2010 CFR

2010-07-01

... determined by the Consumer Price Index (all consumers, all items) during the period from the most recent Index published prior to December 1, 2006, to the most recent Index published prior to December 1, 2007... the cost of living during the period from the most recent index published prior to the previous notice...

37 CFR 381.10 - Cost of living adjustment.

Code of Federal Regulations, 2014 CFR

2014-07-01

... determined by the Consumer Price Index (all consumers, all items) during the period from the most recent Index published prior to December 1, 2012, to the most recent Index published prior to December 1, 2013... change in the cost of living during the period from the most recent index published prior to the previous...

37 CFR 253.10 - Cost of living adjustment.

Code of Federal Regulations, 2014 CFR

2014-07-01

... determined by the Consumer Price Index (all consumers, all items) during the period from the most recent Index published prior to December 1, 2002, to the most recent Index published prior to December 1, 2003... cost of living during the period from the most recent index published prior to the previous notice, to...

37 CFR 253.10 - Cost of living adjustment.

Code of Federal Regulations, 2011 CFR

2011-07-01

... determined by the Consumer Price Index (all consumers, all items) during the period from the most recent Index published prior to December 1, 2002, to the most recent Index published prior to December 1, 2003... cost of living during the period from the most recent index published prior to the previous notice, to...

37 CFR 253.10 - Cost of living adjustment.

Code of Federal Regulations, 2012 CFR

2012-07-01

... determined by the Consumer Price Index (all consumers, all items) during the period from the most recent Index published prior to December 1, 2002, to the most recent Index published prior to December 1, 2003... cost of living during the period from the most recent index published prior to the previous notice, to...

37 CFR 381.10 - Cost of living adjustment.

Code of Federal Regulations, 2012 CFR

2012-07-01

... determined by the Consumer Price Index (all consumers, all items) during the period from the most recent Index published prior to December 1, 2006, to the most recent Index published prior to December 1, 2007... the cost of living during the period from the most recent index published prior to the previous notice...

"Experimental Оncology" is the Best Scientific Journal in Ukraine according to SCOPUS!

PubMed

2016-06-01

International scientific journal "Experimental Оncology" (Publishing House "MORION LLC", Kyiv, Ukraine - R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology of the NAS of Ukraine, Kyiv, Ukraine) earned high global recognition, receiving the prestigious international award "SCOPUS Awards Ukraine" as a winner in the category "The Best Journal".

Articles Published in Four School Psychology Journals from 2000 to 2005: An Analysis of Experimental/Intervention Research

ERIC Educational Resources Information Center

Bliss, Stacy L.; Skinner, Christopher H.; Hautau, Briana; Carroll, Erin E.

2008-01-01

Using an experimenter-developed system, articles from four school psychology journals for the years 2000-2005 (n = 929) were classified. Results showed that 40% of the articles were narrative, 29% correlational, 16% descriptive, 8% causal-experimental, 4% causal-comparative, and 2% were meta-analytic. Further analysis of the causal-experimental…

The Validity of Communication Experiments Using Human Subjects: A Review

ERIC Educational Resources Information Center

Rossiter, Charles M.

1976-01-01

Reviews sixty-eight experiments published in various journals in 1973 and 1974 and concludes that communication experimentation may be severely limited by the nature of the subjects studied and the inappropriate handling of experimental reactivity. (MH)

Standard of reporting animal-based experimental research in Indian Journal of Pharmacology.

PubMed

Aiman, Umme; Rahman, Syed Ziaur

2015-01-01

The objective of present study was to survey and determine the reporting standards of animal studies published during three years from 2012 to 2014 in the Indian Journal of Pharmacology (IJP). All issues of IJP published in the year 2012, 2013 and 2014 were reviewed to identify animal studies. Each animal study was searched for 15 parameters specifically designed to review standards of animal experimentation and research methodology. All published studies had clearly defined aims and objectives while a statement on ethical clearance about the study protocol was provided in 97% of papers. Information about animal strain and sex was given in 91.8% and 90% of papers respectively. Age of experimental animals was mentioned by 44.4% papers while source of animals was given in 50.8% papers. Randomization was reported by 37.4% while 9.9% studies reported blinding. Only 3.5% studies mentioned any limitations of their work. Present study demonstrates relatively good reporting standards in animal studies published in IJP. The items which need to be improved are randomization, blinding, sample size calculation, stating the limitations of study, sources of support and conflict of interest. The knowledge shared in the present paper could be used for better reporting of animal based experiments.

Modeling of aluminum/gallium interdiffusion in aluminum gallium arsenide/gallium arsenide heterostructure materials

NASA Astrophysics Data System (ADS)

Tai, Cheng-Yu

There is considerable interest in interdiffusion in III-IV based structures, such as AlGaAs/GaAs heterojunctions and superlattices (SL). This topic is of practical and fundamental interest since it relates to the stability of devices based on superlattices and heterojunctions, as well as to fundamental diffusion theory. The main goals of this study are to obtain the Al/Ga interdiffusivity, to understand Al/Ga interdiffusion behavior, and to understand how Si doping enhances the diffusion in AlGaAs/GaAs structures. Our first approach entails experimental studies of Al/Ga interdiffusion using Molecular Beam Epitaxy (MBE) samples of AlGaAs/GaAs structures, with or without Si doping. SUPREM-IV.GS was used to model the Fermi-level dependencies and extract the diffusivities. The experimental results show that Al/Ga interdiffusion in undoped AlGaAs/GaAs structures is small, but can be greatly enhanced in doped materials. The extracted Al/Ga interdiffusivity values match well with the Al/Ga interdiffusivity values reported by other groups, and they appear to be composition-independent. The interdiffusivity values are smaller than published Ga self-diffusivity values which are often mistakenly assumed to be equivalent to the interdiffusivity. Another set of Al/Ga interdiffusion experiments using AlAs/GaAs SL were performed to study Al/Ga interdiffusion. The experimental results are consistent with the previously discussed heterostructure results. Using Darken's analysis and treating the AlAs/GaAs SL material as a non-ideal solution, ALAMODE was used to model our SL disordering results explicitly. Assuming that the Al/Ga interdiffusivity is different from the Ga and Al self-diffusivities, we extracted the Al self-diffusivity and the Al activity coefficient as a function of composition using published Ga self-diffusivity values. The simulation results fit well with the experimental results. The extracted Al self-diffusivity value is close to the extracted Al/Ga interdiffusivity but different from the Ga self-diffusivity. The last part of this thesis focuses on modeling localized Al/Ga disordering in AlGaAs/GaAs devices. We present a localized disordering process as a solution to controlling the lateral oxidation process in AlGaAs/GaAs materials. SUPREM can predict these localized disordering results and can help to design an annealing process corresponding to the required aperture size in devices.

Novel ITS1 Fungal Primers for Characterization of the Mycobiome

PubMed Central

Usyk, Mykhaylo; Zolnik, Christine P.; Patel, Hitesh; Levi, Michael H.

2017-01-01

ABSTRACT Studies of the human microbiome frequently omit characterization of fungal communities (the mycobiome), which limits our ability to investigate how fungal communities influence human health. The internal transcribed spacer 1 (ITS1) region of the eukaryotic ribosomal cluster has features allowing for wide taxonomic coverage and has been recognized as a suitable barcode region for species-level identification of fungal organisms. We developed custom ITS1 primer sets using iterative alignment refinement. Primer performance was evaluated using in silico testing and experimental testing of fungal cultures and human samples. Using an expanded novel reference database, SIS (18S-ITS1-5.8S), the newly designed primers showed an average in silico taxonomic coverage of 79.9% ± 7.1% compared to a coverage of 44.6% ± 13.2% using previously published primers (P = 0.05). The newly described primer sets recovered an average of 21,830 ± 225 fungal reads from fungal isolate culture samples, whereas the previously published primers had an average of 3,305 ± 1,621 reads (P = 0.03). Of note was an increase in the taxonomic coverage of the Candida genus, which went from a mean coverage of 59.5% ± 13% to 100.0% ± 0.0% (P = 0.0015) comparing the previously described primers to the new primers, respectively. The newly developed ITS1 primer sets significantly improve general taxonomic coverage of fungal communities infecting humans and increased read depth by an order of magnitude over the best-performing published primer set tested. The overall best-performing primer pair in terms of taxonomic coverage and read recovery, ITS1-30F/ITS1-217R, will aid in advancing research in the area of the human mycobiome. IMPORTANCE The mycobiome constitutes all the fungal organisms within an environment or biological niche. The fungi are eukaryotes, are extremely heterogeneous, and include yeasts and molds that colonize humans as part of the microbiome. In addition, fungi can also infect humans and cause disease. Characterization of the bacterial component of the microbiome was revolutionized by 16S rRNA gene fragment amplification, next-generation sequencing technologies, and bioinformatics pipelines. Characterization of the mycobiome has often not been included in microbiome studies because of limitations in amplification systems. This report revisited the selection of PCR primers that amplify the fungal ITS1 region. We have identified primers with superior identification of fungi present in the database. We have compared the new primer sets against those previously used in the literature and show a significant improvement in read count and taxon identification. These primers should facilitate the study of fungi in human physiology and disease states. PMID:29242834

Shock compression response of cold-rolled Ni/Al multilayer composites

DOE PAGES

Specht, Paul E.; Weihs, Timothy P.; Thadhani, Naresh N.

2017-01-06

Uniaxial strain, plate-on-plate impact experiments were performed on cold-rolled Ni/Al multilayer composites and the resulting Hugoniot was determined through time-resolved measurements combined with impedance matching. The experimental Hugoniot agreed with that previously predicted by two dimensional (2D) meso-scale calculations. Additional 2D meso-scale simulations were performed using the same computational method as the prior study to reproduce the experimentally measured free surface velocities and stress profiles. Finally, these simulations accurately replicated the experimental profiles, providing additional validation for the previous computational work.

REMARK checklist elaborated to improve tumor prognostician

Cancer.gov

Experts have elaborated on a previously published checklist of 20 items -- including descriptions of design, methods, and analysis -- that researchers should address when publishing studies of prognostic markers. These markers are indicators that enable d

Viability of Cross-Flow Fan with Helical Blades for Vertical Take-off and Landing Aircraft

DTIC Science & Technology

2012-09-01

fluid dynamics (CFD) software, ANSYS - CFX , a three-dimensional (3-D) straight-bladed model was validated against previous study’s experimental results...computational fluid dynamics software (CFD), ANSYS - CFX , a three-dimensional (3-D) straight-bladed model was validated against previous study’s experimental...37 B. SIZING PARAMETERS AND ILLUSTRATION ................................. 37 APPENDIX B. ANSYS CFX PARAMETERS

Estimation and uncertainty analysis of dose response in an inter-laboratory experiment

NASA Astrophysics Data System (ADS)

Toman, Blaza; Rösslein, Matthias; Elliott, John T.; Petersen, Elijah J.

2016-02-01

An inter-laboratory experiment for the evaluation of toxic effects of NH2-polystyrene nanoparticles on living human cancer cells was performed with five participating laboratories. Previously published results from nanocytoxicity assays are often contradictory, mostly due to challenges related to producing a reliable cytotoxicity assay protocol for use with nanomaterials. Specific challenges include reproducibility preparing nanoparticle dispersions, biological variability from testing living cell lines, and the potential for nano-related interference effects. In this experiment, such challenges were addressed by developing a detailed experimental protocol and using a specially designed 96-well plate layout which incorporated a range of control measurements to assess multiple factors such as nanomaterial interference, pipetting accuracy, cell seeding density, and instrument performance. Detailed data analysis of these control measurements showed that good control of the experiments was attained by all participants in most cases. The main measurement objective of the study was the estimation of a dose response relationship between concentration of the nanoparticles and metabolic activity of the living cells, under several experimental conditions. The dose curve estimation was achieved by imbedding a three parameter logistic curve in a three level Bayesian hierarchical model, accounting for uncertainty due to all known experimental conditions as well as between laboratory variability in a top-down manner. Computation was performed using Markov Chain Monte Carlo methods. The fit of the model was evaluated using Bayesian posterior predictive probabilities and found to be satisfactory.

Near L-edge Single and Multiple Photoionization of Singly Charged Iron Ions

NASA Astrophysics Data System (ADS)

Schippers, Stefan; Martins, Michael; Beerwerth, Randolf; Bari, Sadia; Holste, Kristof; Schubert, Kaja; Viefhaus, Jens; Savin, Daniel Wolf; Fritzsche, Stephan; Müller, Alfred

2017-11-01

Absolute cross-sections for m-fold photoionization (m=1, \\ldots , 6) of Fe+ by a single photon were measured employing the photon-ion merged-beams setup PIPE at the PETRA III synchrotron light source, operated by DESY in Hamburg, Germany. Photon energies were in the range 680-920 eV, which covers the photoionization resonances associated with 2p and 2s excitation to higher atomic shells as well as the thresholds for 2p and 2s ionization. The corresponding resonance positions were measured with an uncertainty of ±0.2 eV. The cross-section for Fe+ photoabsorption is derived as the sum of the individually measured cross-sections for m-fold ionization. Calculations of the Fe+ absorption cross-sections were carried out using two different theoretical approaches, Hartree-Fock including relativistic extensions and fully relativistic multiconfiguration Dirac-Fock. Apart from overall energy shifts of up to about 3 eV, the theoretical cross-sections are in good agreement with each other and with the experimental results. In addition, the complex de-excitation cascades after the creation of inner-shell holes in the Fe+ ion were tracked on the atomic fine-structure level. The corresponding theoretical results for the product charge-state distributions are in much better agreement with the experimental data than previously published configuration-average results. The present experimental and theoretical results are valuable for opacity calculations and are expected to pave the way to a more accurate determination of the iron abundance in the interstellar medium.

An integrated physiology model to study regional lung damage effects and the physiologic response

PubMed Central

2014-01-01

Background This work expands upon a previously developed exercise dynamic physiology model (DPM) with the addition of an anatomic pulmonary system in order to quantify the impact of lung damage on oxygen transport and physical performance decrement. Methods A pulmonary model is derived with an anatomic structure based on morphometric measurements, accounting for heterogeneous ventilation and perfusion observed experimentally. The model is incorporated into an existing exercise physiology model; the combined system is validated using human exercise data. Pulmonary damage from blast, blunt trauma, and chemical injury is quantified in the model based on lung fluid infiltration (edema) which reduces oxygen delivery to the blood. The pulmonary damage component is derived and calibrated based on published animal experiments; scaling laws are used to predict the human response to lung injury in terms of physical performance decrement. Results The augmented dynamic physiology model (DPM) accurately predicted the human response to hypoxia, altitude, and exercise observed experimentally. The pulmonary damage parameters (shunt and diffusing capacity reduction) were fit to experimental animal data obtained in blast, blunt trauma, and chemical damage studies which link lung damage to lung weight change; the model is able to predict the reduced oxygen delivery in damage conditions. The model accurately estimates physical performance reduction with pulmonary damage. Conclusions We have developed a physiologically-based mathematical model to predict performance decrement endpoints in the presence of thoracic damage; simulations can be extended to estimate human performance and escape in extreme situations. PMID:25044032

Genomic Sequence and Experimental Tractability of a New Decapod Shrimp Model, Neocaridina denticulata

PubMed Central

Kenny, Nathan J.; Sin, Yung Wa; Shen, Xin; Zhe, Qu; Wang, Wei; Chan, Ting Fung; Tobe, Stephen S.; Shimeld, Sebastian M.; Chu, Ka Hou; Hui, Jerome H. L.

2014-01-01

The speciose Crustacea is the largest subphylum of arthropods on the planet after the Insecta. To date, however, the only publically available sequenced crustacean genome is that of the water flea, Daphnia pulex, a member of the Branchiopoda. While Daphnia is a well-established ecotoxicological model, previous study showed that one-third of genes contained in its genome are lineage-specific and could not be identified in any other metazoan genomes. To better understand the genomic evolution of crustaceans and arthropods, we have sequenced the genome of a novel shrimp model, Neocaridina denticulata, and tested its experimental malleability. A library of 170-bp nominal fragment size was constructed from DNA of a starved single adult and sequenced using the Illumina HiSeq2000 platform. Core eukaryotic genes, the mitochondrial genome, developmental patterning genes (such as Hox) and microRNA processing pathway genes are all present in this animal, suggesting it has not undergone massive genomic loss. Comparison with the published genome of Daphnia pulex has allowed us to reveal 3750 genes that are indeed specific to the lineage containing malacostracans and branchiopods, rather than Daphnia-specific (E-value: 10−6). We also show the experimental tractability of N. denticulata, which, together with the genomic resources presented here, make it an ideal model for a wide range of further aquacultural, developmental, ecotoxicological, food safety, genetic, hormonal, physiological and reproductive research, allowing better understanding of the evolution of crustaceans and other arthropods. PMID:24619275

Impaired Inhibitory Force Feedback in Fixed Dystonia.

PubMed

Mugge, Winfred; Schouten, Alfred C; van Hilten, Jacobus J; van der Helm, Frans C T

2016-04-01

Complex regional pain syndrome (CRPS) is a multifactorial disorder associated with an aberrant host response to tissue injury. About 25% of CRPS patients suffer poorly understood involuntary sustained muscle contractions associated with dysfunctional reflexes that result in abnormal postures (fixed dystonia). A recent modeling study simulated fixed dystonia (FD) caused by aberrant force feedback. The current study aims to validate this hypothesis by experimentally recording the modulation of reflexive force feedback in patients with FD. CRPS patients with and without FD, patients with FD but without CRPS, as well as healthy controls participated in the experiment. Three task instructions and three perturbation characteristics were used to evoke a wide range of responses to force perturbations. During position tasks ("maintain posture"), healthy subjects as well as patients resisted the perturbations, becoming more stiff than when being relaxed (i.e., the relax task). Healthy subjects and CRPS patients without FD were both more compliant during force tasks ("maintain force") than during relax tasks, meaning they actively gave way to the imposed forces. Remarkably, the patients with FD failed to do so. A neuromuscular model was fitted to the experimental data to separate the distinct contributions of position, velocity and force feedback, as well as co-contraction to the motor behavior. The neuromuscular modeling indicated that inhibitory force feedback is deregulated in patients with FD, for both CRPS and non-CRPS patients. From previously published simulation results and the present experimental study, it is concluded that aberrant force feedback plays a role in fixed dystonia.

Elucidating Molecular Motion through Structural and Dynamic Filters of Energy-Minimized Conformer Ensembles

PubMed Central

2015-01-01

Complex RNA structures are constructed from helical segments connected by flexible loops that move spontaneously and in response to binding of small molecule ligands and proteins. Understanding the conformational variability of RNA requires the characterization of the coupled time evolution of interconnected flexible domains. To elucidate the collective molecular motions and explore the conformational landscape of the HIV-1 TAR RNA, we describe a new methodology that utilizes energy-minimized structures generated by the program “Fragment Assembly of RNA with Full-Atom Refinement (FARFAR)”. We apply structural filters in the form of experimental residual dipolar couplings (RDCs) to select a subset of discrete energy-minimized conformers and carry out principal component analyses (PCA) to corroborate the choice of the filtered subset. We use this subset of structures to calculate solution T1 and T1ρ relaxation times for 13C spins in multiple residues in different domains of the molecule using two simulation protocols that we previously published. We match the experimental T1 times to within 2% and the T1ρ times to within less than 10% for helical residues. These results introduce a protocol to construct viable dynamic trajectories for RNA molecules that accord well with experimental NMR data and support the notion that the motions of the helical portions of this small RNA can be described by a relatively small number of discrete conformations exchanging over time scales longer than 1 μs. PMID:24479561

Bias against foreign-born or foreign-trained doctors: experimental evidence.

PubMed

Louis, Winnifred R; Lalonde, Richard N; Esses, Victoria M

2010-12-01

Bias against foreign-born or -trained medical students and doctors is not well understood, despite its documented impact on recruitment, integration and retention. This research experimentally examines the interaction of location of medical education and nationality in evaluations of doctors' competence and trustworthiness. A convenience sample of prospective patients evaluated fictitious candidates for a position as a doctor in community practice at a new local health clinic. All applicants were described as having the same personality profile, legal qualifications to practise, a multi-degree education and relevant work experience. The location of medical education (the candidate's home country or the UK) and national background (Australia or Pakistan) of the applicants were independently experimentally manipulated. Consistent with previous research on skills discounting and bias, foreign-born candidates were evaluated less favourably than native-born candidates, despite their comparable education level, work experience and personality. However, overseas medical education obtained in the First World both boosted evaluations (of competence and trustworthiness) and attenuated bias based on nationality. The present findings demonstrate the selective discounting of foreign-born doctors' credentials. The data show an interaction of location of medical education and birth nationality in bias against foreign doctors. On an applied level, the data document that the benefits of medical education obtained in the First World can extend beyond its direct outcomes (high-quality training and institutional recognition) to the indirect benefit of the attenuation of patient bias based on nationality. © Blackwell Publishing Ltd 2010.

Enhancing Scientific Foundations to Ensure Reproducibility: A New Paradigm.

PubMed

Hsieh, Terry; Vaickus, Max H; Remick, Daniel G

2018-01-01

Progress in science is dependent on a strong foundation of reliable results. The publish or perish paradigm in research, coupled with an increase in retracted articles from the peer-reviewed literature, is beginning to erode the trust of both the scientific community and the public. The NIH is combating errors by requiring investigators to follow new guidelines addressing scientific premise, experimental design, biological variables, and authentication of reagents. Herein, we discuss how implementation of NIH guidelines will help investigators proactively address pitfalls of experimental design and methods. Careful consideration of the variables contributing to reproducibility helps ensure robust results. The NIH, investigators, and journals must collaborate to ensure that quality science is funded, explored, and published. Copyright © 2018 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

New Issues for New Methods: Ethical and Editorial Challenges for an Experimental Philosophy.

PubMed

Polonioli, Andrea

2017-08-01

This paper examines a constellation of ethical and editorial issues that have arisen since philosophers started to conduct, submit and publish empirical research. These issues encompass concerns over responsible authorship, fair treatment of human subjects, ethicality of experimental procedures, availability of data, unselective reporting and publishability of research findings. This study aims to assess whether the philosophical community has as yet successfully addressed such issues. To do so, the instructions for authors, submission process and published research papers of 29 main journals in philosophy have been considered and analyzed. In light of the evidence reported here, it is argued that the philosophical community has as yet failed to properly tackle such issues. The paper also delivers some recommendations for authors, reviewers and editors in the field.

Reduced vergence adaptation is associated with a prolonged output of convergence accommodation in convergence insufficiency.

PubMed

Sreenivasan, Vidhyapriya; Bobier, William R

2014-07-01

Convergence insufficiency (CI) is a developmental visual anomaly defined clinically by a reduced near point of convergence, a reduced capacity to view through base-out prisms (fusional convergence); coupled with asthenopic symptoms typically blur and diplopia. Experimental studies show reduced vergence parameters and tonic adaptation. Based upon current models of accommodation and vergence, we hypothesize that the reduced vergence adaptation in CI leads to excessive amounts of convergence accommodation (CA). Eleven CI participants (mean age=17.4±2.3 years) were recruited with reduced capacity to view through increasing magnitudes of base out (BO) prisms (mean fusional convergence at 40 cm=12±0.9Δ). Testing followed our previous experimental design for (n=11) binocularly normal adults. Binocular fixation of a difference of Gaussian (DoG) target (0.2 cpd) elicited CA responses during vergence adaptation to a 12Δ BO. Vergence and CA responses were obtained at 3 min intervals over a 15 min period and time course were quantified using exponential decay functions. Results were compared to previously published data on eleven binocular normals. Eight participants completed the study. CI's showed significantly reduced magnitude of vergence adaptation (CI: 2.9Δ vs. normals: 6.6Δ; p=0.01) and CA reduction (CI=0.21 D, Normals=0.55 D; p=0.03). However, the decay time constants for adaptation and CA responses were not significantly different. CA changes were not confounded by changes in tonic accommodation (Change in TA=0.01±0.2D; p=0.8). The reduced magnitude of vergence adaptation found in CI patients resulting in higher levels of CA may potentially explain their clinical findings of reduced positive fusional vergence (PFV) and the common symptom of blur. Copyright © 2014 Elsevier B.V. All rights reserved.

The protective effects of free wheel-running against cocaine psychomotor sensitization persist after exercise cessation in C57BL/6J mice.

PubMed

Lespine, L-F; Tirelli, E

2015-12-03

Previous literature suggests that free access to a running wheel can attenuate the behavioral responsiveness to addictive drugs in rodents. In a few studies, wheel-running cessation accentuated drug responsiveness. Here, we tested whether free wheel-running cessation is followed by (1) an accentuation or (2) an attenuation of cocaine psychomotor sensitization, knowing that no cessation of (continuous) wheel-running is associated with an attenuation of cocaine responsiveness. Male C57BL/6J mice, aged 35 days, were housed singly either with (exercising mice) or without (non-exercising mice) a running wheel. At the end of a period of 36 days, half of the exercising mice were deprived of their wheel whereas the other half of exercising mice kept their wheel until the end of experimentation (which lasted 85 days). The non-exercising mice were housed without wheel throughout experimentation. Testing took place 3 days after exercise cessation. After 2 once-daily drug-free test sessions, mice were tested for initiation of psychomotor sensitization over 13 once-daily injections of 8 mg/kg cocaine. Post-sensitization conditioned activation (saline challenge) and long-term expression of sensitization were assessed 2 or 30 days after the last sensitizing injection (same treatments as for initiation of sensitization), respectively. Exercising mice and mice undergoing wheel-running cessation exhibited comparable degrees of attenuation of all cocaine effects in comparison with the continuously non-exercising mice, which showed the greatest effects. Thus, the efficaciousness of wheel-running at attenuating cocaine sensitization not only resisted to exercise cessation but was also unambiguously persistent (an important effect rarely reported in previous literature). Copyright © 2015 IBRO. Published by Elsevier Ltd. All rights reserved.

A Systematic Review of Financial Incentives for Dietary Behavior Change

PubMed Central

Purnell, Jason Q.; Gernes, Rebecca; Stein, Rick; Sherraden, Margaret S.; Knoblock-Hahn, Amy

2014-01-01

In light of the obesity epidemic, there is growing interest in the use of financial incentives for dietary behavior change. Previous reviews of the literature have focused on randomized, controlled trials and found mixed results. The purpose of this systematic review is to update and expand upon previous reviews by considering a broader range of study designs, including RCTs, quasi-experimental, observational, and simulation studies testing the use of financial incentives to change dietary behavior and to inform both dietetic practice and research. The review was guided by theoretical consideration of the type of incentive used based upon the principles of operant conditioning. There was further examination of whether studies were carried out with an institutional focus and whether incentives took the form of assets or savings. Studies published between 2006 and 2012 were selected for review, and data were extracted regarding study population, intervention design, outcome measures, study duration and follow-up, and key findings. Twelve studies meeting selection criteria were reviewed, with eleven finding a positive association between incentives and dietary behavior change in the short-term. All studies pointed to more specific information on the type, timing, and magnitude of incentives needed to motivate individuals to change behavior, the types of incentives and disincentives most likely to affect the behavior of various socioeconomic groups, and promising approaches for potential policy and practice innovations. Limitations of studies are noted, including the lack of theoretical guidance in the selection of incentive structures and the absence of basic experimental data. Future research should consider these factors even as policymakers and practitioners continue to experiment with this potentially useful approach to addressing obesity. PMID:24836967

Accurate electrostatic and van der Waals pull-in prediction for fully clamped nano/micro-beams using linear universal graphs of pull-in instability

NASA Astrophysics Data System (ADS)

Tahani, Masoud; Askari, Amir R.

2014-09-01

In spite of the fact that pull-in instability of electrically actuated nano/micro-beams has been investigated by many researchers to date, no explicit formula has been presented yet which can predict pull-in voltage based on a geometrically non-linear and distributed parameter model. The objective of present paper is to introduce a simple and accurate formula to predict this value for a fully clamped electrostatically actuated nano/micro-beam. To this end, a non-linear Euler-Bernoulli beam model is employed, which accounts for the axial residual stress, geometric non-linearity of mid-plane stretching, distributed electrostatic force and the van der Waals (vdW) attraction. The non-linear boundary value governing equation of equilibrium is non-dimensionalized and solved iteratively through single-term Galerkin based reduced order model (ROM). The solutions are validated thorough direct comparison with experimental and other existing results reported in previous studies. Pull-in instability under electrical and vdW loads are also investigated using universal graphs. Based on the results of these graphs, non-dimensional pull-in and vdW parameters, which are defined in the text, vary linearly versus the other dimensionless parameters of the problem. Using this fact, some linear equations are presented to predict pull-in voltage, the maximum allowable length, the so-called detachment length, and the minimum allowable gap for a nano/micro-system. These linear equations are also reduced to a couple of universal pull-in formulas for systems with small initial gap. The accuracy of the universal pull-in formulas are also validated by comparing its results with available experimental and some previous geometric linear and closed-form findings published in the literature.

Thermodynamic data of lawsonite and zoisite in the system CaO-Al2O3-SiO2-H2O based on experimental phase equilibria and calorimetric work

NASA Astrophysics Data System (ADS)

Grevel, Klaus-Dieter; Schoenitz, Mirko; Skrok, Volker; Navrotsky, Alexandra; Schreyer, Werner

2001-08-01

The enthalpy of drop-solution in molten 2PbO.B2O3 of synthetic and natural lawsonite, CaAl2(Si2O7)(OH)2.H2O, was measured by high-temperature oxide melt calorimetry. The enthalpy of formation determined for the synthetic material is ΔfHOxides=-168.7+/-3.4 kJ mol-1, or ΔfH0298=-4,872.5+/-4.0 kJ mol-1. These values are in reasonable agreement with previously published data, although previous calorimetric work yielded slightly more exothermic data and optimisation methods resulted in slightly less exothermic values. The equilibrium conditions for the dehydration of lawsonite to zoisite, kyanite and quartz/coesite at pressures and temperatures up to 5 GPa and 850 °C were determined by piston cylinder experiments. These results, other recent phase equilibrium data, and new calorimetric and thermophysical data for lawsonite and zoisite, Ca2Al3(SiO4)(Si2O7)O(OH), were used to constrain a mathematical programming analysis of the thermodynamic data for these two minerals in the chemical system CaO-Al2O3-SiO2-H2O (CASH). The following data for lawsonite and zoisite were obtained: ΔfH0298 (lawsonite)=-4,865.68 kJ mol-1 , S0298 (lawsonite)=229.27 J K-1 mol-1 , ΔfH0298 (zoisite)=-6,888.99 kJ mol-1 , S0298 (zoisite)=297.71 J K-1 mol-1 . Additionally, a recalculation of the bulk modulus of lawsonite yielded K=120.7 GPa, which is in good agreement with recent experimental work.

Oxygen as a critical determinant of bone fracture healing-a multiscale model.

PubMed

Carlier, Aurélie; Geris, Liesbet; van Gastel, Nick; Carmeliet, Geert; Van Oosterwyck, Hans

2015-01-21

A timely restoration of the ruptured blood vessel network in order to deliver oxygen and nutrients to the fracture zone is crucial for successful bone healing. Indeed, oxygen plays a key role in the aerobic metabolism of cells, in the activity of a myriad of enzymes as well as in the regulation of several (angiogenic) genes. In this paper, a previously developed model of bone fracture healing is further improved with a detailed description of the influence of oxygen on various cellular processes that occur during bone fracture healing. Oxygen ranges of the cell-specific oxygen-dependent processes were established based on the state-of-the art experimental knowledge through a rigorous literature study. The newly developed oxygen model is compared with previously published experimental and in silico results. An extensive sensitivity analysis was also performed on the newly introduced oxygen thresholds, indicating the robustness of the oxygen model. Finally, the oxygen model was applied to the challenging clinical case of a critical sized defect (3mm) where it predicted the formation of a fracture non-union. Further model analyses showed that the harsh hypoxic conditions in the central region of the callus resulted in cell death and disrupted bone healing thereby indicating the importance of a timely vascularization for the successful healing of a large bone defect. In conclusion, this work demonstrates that the oxygen model is a powerful tool to further unravel the complex spatiotemporal interplay of oxygen delivery, diffusion and consumption with the several healing steps, each occurring at distinct, optimal oxygen tensions during the bone repair process. Copyright © 2014 Elsevier Ltd. All rights reserved.

Photo-ignition process of multiwall carbon nanotubes and ferrocene by continuous wave Xe lamp illumination.

PubMed

Visconti, Paolo; Primiceri, Patrizio; Longo, Daniele; Strafella, Luciano; Carlucci, Paolo; Lomascolo, Mauro; Cretì, Arianna; Mele, Giuseppe

2017-01-01

This work aims to investigate and characterize the photo-ignition phenomenon of MWCNT/ferrocene mixtures by using a continuous wave (CW) xenon (Xe) light source, in order to find the power ignition threshold by employing a different type of light source as was used in previous research (i.e., pulsed Xe lamp). The experimental photo-ignition tests were carried out by varying the weight ratio of the used mixtures, luminous power, and wavelength range of the incident Xe light by using selective optical filters. For a better explanation of the photo-induced ignition process, the absorption spectra of MWCNT/ferrocene mixtures and ferrocene only were obtained. The experimental results show that the luminous power (related to the entire spectrum of the Xe lamp) needed to trigger the ignition of MWCNT/ferrocene mixtures decreases with increasing metal nanoparticles content according to previously published results when using a different type of light source (i.e., pulsed vs CW Xe light source). Furthermore, less light power is required to trigger photo-ignition when moving towards the ultraviolet (UV) region. This is in agreement with the measured absorption spectra, which present higher absorption values in the UV-vis region for both MWCNT/ferrocene mixtures and ferrocene only diluted in toluene. Finally, a chemo-physical interpretation of the ignition phenomenon is proposed whereby ferrocene photo-excitation, due to photon absorption, produces ferrocene itself in its excited form and is thus capable of promoting electron transfer to MWCNTs. In this way, the resulting radical species, FeCp2 +∙ and MWCNT - , easily react with oxygen giving rise to the ignition of MWCNT/ferrocene samples.

Experimental investigations of ablation stream interaction dynamics in tungsten wire arrays: Interpenetration, magnetic field advection, and ion deflection

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

Swadling, G. F.; Lebedev, S. V.; Hall, G. N.

2016-05-01

Experiments have been carried out to investigate the collisional dynamics of ablation streams produced by cylindrical wire array z-pinches. A combination of laser interferometric imaging, Thomson scattering, and Faraday rotation imaging has been used to make a range of measurements of the temporal evolution of various plasma and flow parameters. Our paper presents a summary of previously published data, drawing together a range of different measurements in order to give an overview of the key results. The paper focuses mainly on the results of experiments with tungsten wire arrays. Early interferometric imaging measurements are reviewed, then more recent Thomson scatteringmore » measurements are discussed; these measurements provided the first direct evidence of ablation stream interpenetration in a wire array experiment. Combining the data from these experiments gives a view of the temporal evolution of the tungsten stream collisional dynamics. In the final part of the paper, we present new experimental measurements made using an imaging Faraday rotation diagnostic. Our experiments investigated the structure of magnetic fields near the array axis directly; the presence of a magnetic field has previously been inferred based on Thomson scattering measurements of ion deflection near the array axis. Although the Thomson and Faraday measurements are not in full quantitative agreement, the Faraday data do qualitatively supports the conjecture that the observed deflections are induced by a static toroidal magnetic field, which has been advected to the array axis by the ablation streams. It is likely that detailed modeling will be needed in order to fully understand the dynamics observed in the experiment.« less

Experimental investigations of ablation stream interaction dynamics in tungsten wire arrays: Interpenetration, magnetic field advection, and ion deflection

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

Swadling, G. F.; Lebedev, S. V.; Hall, G. N.

2016-05-15

Experiments have been carried out to investigate the collisional dynamics of ablation streams produced by cylindrical wire array z-pinches. A combination of laser interferometric imaging, Thomson scattering, and Faraday rotation imaging has been used to make a range of measurements of the temporal evolution of various plasma and flow parameters. This paper presents a summary of previously published data, drawing together a range of different measurements in order to give an overview of the key results. The paper focuses mainly on the results of experiments with tungsten wire arrays. Early interferometric imaging measurements are reviewed, then more recent Thomson scatteringmore » measurements are discussed; these measurements provided the first direct evidence of ablation stream interpenetration in a wire array experiment. Combining the data from these experiments gives a view of the temporal evolution of the tungsten stream collisional dynamics. In the final part of the paper, we present new experimental measurements made using an imaging Faraday rotation diagnostic. These experiments investigated the structure of magnetic fields near the array axis directly; the presence of a magnetic field has previously been inferred based on Thomson scattering measurements of ion deflection near the array axis. Although the Thomson and Faraday measurements are not in full quantitative agreement, the Faraday data do qualitatively supports the conjecture that the observed deflections are induced by a static toroidal magnetic field, which has been advected to the array axis by the ablation streams. It is likely that detailed modeling will be needed in order to fully understand the dynamics observed in the experiment.« less

Rapid mood-elevating effects of low field magnetic stimulation in depression.

PubMed

Rohan, Michael L; Yamamoto, Rinah T; Ravichandran, Caitlin T; Cayetano, Kenroy R; Morales, Oscar G; Olson, David P; Vitaliano, Gordana; Paul, Steven M; Cohen, Bruce M

2014-08-01

We previously reported rapid mood elevation following an experimental magnetic resonance imaging procedure in depressed patients with bipolar disorder (BPD). This prompted the design, construction, and testing of a portable electromagnetic device that reproduces only the rapidly oscillating (1 kHz, <1 V/m) electromagnetic field of the experimental procedure, called low field magnetic stimulation (LFMS). We used a randomized, double blind, sham controlled treatment protocol to study the effects of LFMS in a large group of stably medicated, depressed patients with either BPD (n = 41) or major depressive disorder (n = 22). Subjects received a single, 20-minute treatment. Change in mood was assessed immediately afterward using a visual analog scale (VAS), the 17-item Hamilton Depression Rating Scale (HDRS-17), and the Positive and Negative Affect Schedule scales. Substantial improvement (>10% of baseline) in mood was observed following LFMS treatment relative to sham treatment for both diagnostic subgroups for our primary outcomes, the VAS and the HDRS-17. These differences were not statistically significant in primary analyses stratifying by diagnosis but were significant in secondary analyses combining data across the two diagnostic groups (p = .01 VAS, p = .02 HDRS-17). Rapid improvement in mood was also observed using the Positive and Negative Affect Schedule scales as secondary measures (positive affect scale p = .02 BPD, p = .002 combined group). A finite element method calculation indicates a broad penetration of the LFMS electric field throughout the cerebral cortex. Low field magnetic stimulation may produce rapid changes in mood using a previously unexplored range of electromagnetic fields. © 2013 Society of Biological Psychiatry Published by Society of Biological Psychiatry All rights reserved.

Photo-ignition process of multiwall carbon nanotubes and ferrocene by continuous wave Xe lamp illumination

PubMed Central

Primiceri, Patrizio; Longo, Daniele; Strafella, Luciano; Carlucci, Paolo; Lomascolo, Mauro; Cretì, Arianna; Mele, Giuseppe

2017-01-01

This work aims to investigate and characterize the photo-ignition phenomenon of MWCNT/ferrocene mixtures by using a continuous wave (CW) xenon (Xe) light source, in order to find the power ignition threshold by employing a different type of light source as was used in previous research (i.e., pulsed Xe lamp). The experimental photo-ignition tests were carried out by varying the weight ratio of the used mixtures, luminous power, and wavelength range of the incident Xe light by using selective optical filters. For a better explanation of the photo-induced ignition process, the absorption spectra of MWCNT/ferrocene mixtures and ferrocene only were obtained. The experimental results show that the luminous power (related to the entire spectrum of the Xe lamp) needed to trigger the ignition of MWCNT/ferrocene mixtures decreases with increasing metal nanoparticles content according to previously published results when using a different type of light source (i.e., pulsed vs CW Xe light source). Furthermore, less light power is required to trigger photo-ignition when moving towards the ultraviolet (UV) region. This is in agreement with the measured absorption spectra, which present higher absorption values in the UV–vis region for both MWCNT/ferrocene mixtures and ferrocene only diluted in toluene. Finally, a chemo-physical interpretation of the ignition phenomenon is proposed whereby ferrocene photo-excitation, due to photon absorption, produces ferrocene itself in its excited form and is thus capable of promoting electron transfer to MWCNTs. In this way, the resulting radical species, FeCp2+∙ and MWCNT−, easily react with oxygen giving rise to the ignition of MWCNT/ferrocene samples. PMID:28144572

Effect of a Pheromone on Stress-Associated Reactivation of Feline Herpesvirus-1 in Experimentally Inoculated Kittens.

PubMed

Contreras, Elena T; Hodgkins, E; Tynes, V; Beck, A; Olea-Popelka, F; Lappin, M R

2018-01-01

Stress contributes to reactivation of feline herpesvirus-1 (FHV-1). The usage of pheromones to decrease stress in FHV-1 experimentally inoculated kittens has not previously been investigated. To determine whether a feline pheromone would lessen stress, resulting in decreased recurrence of FHV-1-associated illness in kittens. Twelve 5-month-old, purpose-bred kittens. Randomized, double-blind, placebo-controlled clinical trial. Kittens previously infected with the same dose of FHV-1 were randomized into 2 separate but identical group rooms. After a 2-week equilibration period, a diffuser containing either the pheromone or placebo was placed in each of the rooms, and the kittens acclimated for an additional 2 weeks. Every 2 weeks thereafter, for the 8-week study period, housing was alternated between kennel- and group housing. Blinded observers applied a standardized clinical and behavioral scoring rubric daily. After each 2-week period, serum cortisol concentrations and quantitative PCR for FHV-1 and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) ratios were evaluated. Clinical, behavioral, and laboratory test results were compared between groups within individual and combined study periods. Sneezing occurred more frequently in the placebo group during individual (P = 0.006) and combined study periods (P = 0.001). Sleep at the end of observation periods occurred more frequently in the pheromone group during individual (P = 0.006) and combined study periods (P < 0.001). The findings suggest that the pheromone decreased stress, and the decrease in stress response may have resulted in decreased sneezing associated with FHV-1. Copyright © 2017 The Authors. Journal of Veterinary Internal Medicine published by Wiley Periodicals, Inc. on behalf of the American College of Veterinary Internal Medicine.

Modeling and Measuring the Effects of Radiation Damage Annealing on Helium Diffusion Kinetics in Apatite

NASA Astrophysics Data System (ADS)

Willett, C. D.; Fox, M.; Shuster, D. L.

2016-12-01

Understanding helium diffusion kinetics in apatite is critical for the accurate interpretation of (U-Th)/He thermochronometric data. This problem is complicated by the observation that helium diffusivity is not a simple function of temperature, but may evolve as a function of damage to the apatite crystal lattice resulting from alpha recoil. This `radiation damage' increases as a function of the amount of radiometric parent products, or effective uranium concentration, and time, but decreases due to thermal annealing of damage, necessitating a detailed understanding of radiation damage production and annealing in cases of burial heating over geologic timescales. Published observations [1,2] suggest that annealing rates of damage caused by alpha recoil and fission tracks in apatite differ. Existing models, however, assume the diffusion kinetics resulting from the two sources of damage are identical [3], demonstrating the need for further investigation of these damage sources. We present modeling and experimental work designed to interrogate the effects of radiation damage and its annealing on helium diffusion kinetics in apatite. Using previously published results [4] that investigated the effects of annealing temperature and duration on measured helium diffusivity, we fit a set of functions that are then integrated into a numerical model that tracks the evolution of radiation damage and apparent (U-Th)/He age. We compare the results of this model calibration to existing models [3]. In addition, we present data from two suites of diffusion experiments. The first suite, intended to test the published methodology and results, uses Durango apatite, while the second uses Sierran (CA) granite as a first test to determine if apatite of varying chemistry and age responds differently to the thermal annealing of radiation damage. Ultimately, the updated model and experimental results will benefit the interpretation of the effects of radiation damage accumulation and annealing in apatite and expand the range of geologic settings that can be studied using low-temperature thermochronology. References: [1] Fox, M., Shuster, D. (2014), EPSL 397, 174-183; [2] Gautheron, C. et al. (2013), Chem. Geol. 351, 257-267; [3] Flowers, R. et al. (2009), GCA 73, 2347-2365; [4] Shuster, D., Farley, K. (2009), GCA 73, 6183-6196.

Educational attainment and obesity: a systematic review.

PubMed

Cohen, A K; Rai, M; Rehkopf, D H; Abrams, B

2013-12-01

Although previous systematic reviews considered the relationship between socioeconomic status and obesity, almost 200 peer-reviewed articles have been published since the last review on that topic, and this paper focuses specifically on education, which has different implications. The authors systematically review the peer-reviewed literature from around the world considering the association between educational attainment and obesity. Databases from public health and medicine, education, psychology, economics, and other social sciences were searched, and articles published in English, French, Portuguese and Spanish were included. This paper includes 289 articles that report on 410 populations in 91 countries. The relationship between educational attainment and obesity was modified by both gender and the country's economic development level: an inverse association was more common in studies of higher-income countries and a positive association was more common in lower-income countries, with stronger social patterning among women. Relatively few studies reported on lower-income countries, controlled for a comprehensive set of potential confounding variables and/or attempted to assess causality through the use of quasi-experimental designs. Future research should address these gaps to understand if the relationship between educational attainment and obesity may be causal, thus supporting education policy as a tool for obesity prevention. © 2013 The Authors. obesity reviews © 2013 International Association for the Study of Obesity.

Comparison of DNA preservation methods for environmental bacterial community samples.

PubMed

Gray, Michael A; Pratte, Zoe A; Kellogg, Christina A

2013-02-01

Field collections of environmental samples, for example corals, for molecular microbial analyses present distinct challenges. The lack of laboratory facilities in remote locations is common, and preservation of microbial community DNA for later study is critical. A particular challenge is keeping samples frozen in transit. Five nucleic acid preservation methods that do not require cold storage were compared for effectiveness over time and ease of use. Mixed microbial communities of known composition were created and preserved by DNAgard(™), RNAlater(®), DMSO-EDTA-salt (DESS), FTA(®) cards, and FTA Elute(®) cards. Automated ribosomal intergenic spacer analysis and clone libraries were used to detect specific changes in the faux communities over weeks and months of storage. A previously known bias in FTA(®) cards that results in lower recovery of pure cultures of Gram-positive bacteria was also detected in mixed community samples. There appears to be a uniform bias across all five preservation methods against microorganisms with high G + C DNA. Overall, the liquid-based preservatives (DNAgard(™), RNAlater(®), and DESS) outperformed the card-based methods. No single liquid method clearly outperformed the others, leaving method choice to be based on experimental design, field facilities, shipping constraints, and allowable cost. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Validation of a high-throughput real-time polymerase chain reaction assay for the detection of capripoxviral DNA.

PubMed

Stubbs, Samuel; Oura, Chris A L; Henstock, Mark; Bowden, Timothy R; King, Donald P; Tuppurainen, Eeva S M

2012-02-01

Capripoxviruses, which are endemic in much of Africa and Asia, are the aetiological agents of economically devastating poxviral diseases in cattle, sheep and goats. The aim of this study was to validate a high-throughput real-time PCR assay for routine diagnostic use in a capripoxvirus reference laboratory. The performance of two previously published real-time PCR methods were compared using commercially available reagents including the amplification kits recommended in the original publication. Furthermore, both manual and robotic extraction methods used to prepare template nucleic acid were evaluated using samples collected from experimentally infected animals. The optimised assay had an analytical sensitivity of at least 63 target DNA copies per reaction, displayed a greater diagnostic sensitivity compared to conventional gel-based PCR, detected capripoxviruses isolated from outbreaks around the world and did not amplify DNA from related viruses in the genera Orthopoxvirus or Parapoxvirus. The high-throughput robotic DNA extraction procedure did not adversely affect the sensitivity of the assay compared to manual preparation of PCR templates. This laboratory-based assay provides a rapid and robust method to detect capripoxviruses following suspicion of disease in endemic or disease-free countries. Crown Copyright © 2011. Published by Elsevier B.V. All rights reserved.

Darcy Permeability of Hollow Fiber Membrane Bundles Made from Membrana Polymethylpentene Fibers Used in Respiratory Assist Devices.

PubMed

Madhani, Shalv P; D'Aloiso, Brandon D; Frankowski, Brian; Federspiel, William J

2016-01-01

Hollow fiber membranes (HFMs) are used in blood oxygenators for cardiopulmonary bypass or in next generation artificial lungs. Flow analyses of these devices is typically done using computational fluid dynamics (CFD) modeling HFM bundles as porous media, using a Darcy permeability coefficient estimated from the Blake-Kozeny (BK) equation to account for viscous drag from fibers. We recently published how well this approach can predict Darcy permeability for fiber bundles made from polypropylene HFMs, showing the prediction can be significantly improved using an experimentally derived correlation between the BK constant (A) and bundle porosity (ε). In this study, we assessed how well our correlation for A worked for predicting the Darcy permeability of fiber bundles made from Membrana polymethylpentene (PMP) HFMs, which are increasingly being used clinically. Swatches in the porosity range of 0.4 to 0.8 were assessed in which sheets of fiber were stacked in parallel, perpendicular, and angled configurations. Our previously published correlation predicted Darcy within ±8%. A new correlation based on current and past measured permeability was determined: A = 497ε - 103; using this correlation measured Darcy permeability was within ±6%. This correlation varied from 8% to -3.5% of our prior correlation over the tested porosity range.

Darcy permeability of hollow fiber membrane bundles made from Membrana® Polymethylpentene (PMP) fibers used in respiratory assist devices

PubMed Central

Madhani, Shalv. P.; D’Aloiso, Brandon. D.; Frankowski, Brian.; Federspiel, William. J.

2016-01-01

Hollow fiber membranes (HFMs) are used in blood oxygenators for cardiopulmonary bypass or in next generation artificial lungs. Flow analyses of these devices is typically done using computational fluid dynamics (CFD) modeling HFM bundles as porous media, using a Darcy permeability coefficient estimated from the Blake – Kozeny (BK) equation to account for viscous drag from fibers. We recently published how well this approach can predict Darcy permeability for fiber bundles made from polypropylene HFMs, showing the prediction can be significantly improved using an experimentally derived correlation between the BK constant (A) and bundle porosity (ε). In this study, we assessed how well our correlation for A worked for predicting the Darcy permeability of fiber bundles made from Membrana® polymethylpentene (PMP) HFMs, which are increasingly being used clinically. Swatches in the porosity range of 0.4 to 0.8 were assessed in which sheets of fiber were stacked in parallel, perpendicular and angled configurations. Our previously published correlation predicted Darcy within ±8%. A new correlation based on current and past measured permeability was determined: A=497ε-103; using this correlation measured Darcy permeability was within ±6%. This correlation varied from 8% to −3.5% of our prior correlation over the tested porosity range. PMID:26809086

Educational attainment and obesity: A systematic review

PubMed Central

Cohen, Alison K.; Rai, Manisha; Rehkopf, David H.; Abrams, Barbara

2013-01-01

Background Although previous systematic reviews considered the relationship between socioeconomic status and obesity, almost 200 peer-reviewed articles have been published since the last review on that topic, and this paper focuses specifically on education, which has different implications. Methods The authors systematically review the peer-reviewed literature from around the world considering the association between educational attainment and obesity. Databases from public health and medicine, education, psychology, economics, and other social sciences were searched, and articles published in English, French, Portuguese, and Spanish were included. Results This paper includes 289 articles that report on 410 populations in 91 countries. The relationship between educational attainment and obesity was modified by both gender and the country's economic development level: an inverse association was more common in studies of higher-income countries and a positive association was more common in lower-income countries, with stronger social patterning among women. Relatively few studies reported on lower-income countries, controlled for a comprehensive set of potential confounding variables, and/or attempted to assess causality through the use of quasi-experimental designs. Conclusions Future research should address these gaps to understand if the relationship between educational attainment and obesity may be causal, thus supporting education policy as a tool for obesity prevention. PMID:23889851

Transcriptome-wide investigation of genomic imprinting in chicken

PubMed Central

Frésard, Laure; Leroux, Sophie; Servin, Bertrand; Gourichon, David; Dehais, Patrice; Cristobal, Magali San; Marsaud, Nathalie; Vignoles, Florence; Bed'hom, Bertrand; Coville, Jean-Luc; Hormozdiari, Farhad; Beaumont, Catherine; Zerjal, Tatiana; Vignal, Alain; Morisson, Mireille; Lagarrigue, Sandrine; Pitel, Frédérique

2014-01-01

Genomic imprinting is an epigenetic mechanism by which alleles of some specific genes are expressed in a parent-of-origin manner. It has been observed in mammals and marsupials, but not in birds. Until now, only a few genes orthologous to mammalian imprinted ones have been analyzed in chicken and did not demonstrate any evidence of imprinting in this species. However, several published observations such as imprinted-like QTL in poultry or reciprocal effects keep the question open. Our main objective was thus to screen the entire chicken genome for parental-allele-specific differential expression on whole embryonic transcriptomes, using high-throughput sequencing. To identify the parental origin of each observed haplotype, two chicken experimental populations were used, as inbred and as genetically distant as possible. Two families were produced from two reciprocal crosses. Transcripts from 20 embryos were sequenced using NGS technology, producing ∼200 Gb of sequences. This allowed the detection of 79 potentially imprinted SNPs, through an analysis method that we validated by detecting imprinting from mouse data already published. However, out of 23 candidates tested by pyrosequencing, none could be confirmed. These results come together, without a priori, with previous statements and phylogenetic considerations assessing the absence of genomic imprinting in chicken. PMID:24452801

Assessing the scientific research productivity of a leading toxicology journal: A case study of Human & Experimental Toxicology from 2003 to 2012.

PubMed

Zyoud, Sa'ed H; Al-Jabi, Samah W; Sweileh, Waleed M; Awang, Rahmat

2014-01-01

Bibliometric studies are increasingly being used for research assessments. Bibliometric indicators involve the application of statistical methods to scientific publications to obtain the bibliographics for each journal. The main objective of this study was to conduct a bibliometric evaluation of Human & Experimental Toxicology retrieved from the Scopus database. This study obtained data from Scopus published from 1 January 2003 till 31 December 2012. The keywords entered in Scopus to accomplish the objective of this study were 'Human', 'Experimental' and 'Toxicology' as 'Source Title'. Research productivity was evaluated based on a methodology developed and used in other bibliometric studies by analysing (a) total and trends in Human & Experimental Toxicology contributions in research between 2003 and 2012; (b) Human & Experimental Toxicology authorship patterns and productivity; (c) collaboration patterns; and (d) the citations received by the publications. There were 1229 research articles published in Human & Experimental Toxicology. Of the articles included, 947 (77.1%) were original articles and 104 (8.5%) were review articles. The Hirsch-index of the retrieved documents was 35. The largest number of publications in Human & Experimental Toxicology was from the United States (19.6%), followed by India (12.8%) and Turkey (10.9%). The total number of citations was 9119, with a median (interquartile range) of 3 (1-9) in 6797 documents. The highest median (interquartile range) number of citations was 8 (2.7-12.7) for France, followed by 7.5 (2-22.5) for Iran and 6 (3-13.5) for the United Kingdom. The country most often citing articles that were published in Human & Experimental Toxicology was the United States, which made citations in 1508 documents, followed by India with citations in 792 documents. The documents in Human & Experimental Toxicology focus principally on original data, with very few review articles. Review articles tend to have higher citation rates than original articles, and hence, the editors and authors of Human & Experimental Toxicology might usefully promote the submission of reviews in the future to improve the impact of the journal.

A BIBLIOGRAPHY OF BIOLOGICAL APPLICATIONS OF AUTORADIOGRAPHY, 1958 THROUGH 1959

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

Johnston, M.E.

1959-08-01

This bibliography of 281 reports and published literature references on biological applications of autoradiography is a supplement to the one published July 1958 as UCRL-8400. References previously omitted are included. (J.E. D.)

A second chance for authors of hijacked journals to publish in legitimate journals.

PubMed

Jalalian, Mehrdad

2015-01-01

This article proposes the republication of articles that have previously been published in counterfeit websites of hijacked journals. The paper also discusses the technical and ethical aspects of republishing such articles.

Publisher Correction: Measuring progress from nationally determined contributions to mid-century strategies

NASA Astrophysics Data System (ADS)

Iyer, Gokul; Ledna, Catherine; Clarke, Leon; Edmonds, James; McJeon, Haewon; Kyle, Page; Williams, James H.

2018-03-01

In the version of this Article previously published, technical problems led to the wrong summary appearing on the homepage, and an incorrect Supplementary Information file being uploaded. Both errors have now been corrected.

Modeling and Experiments with Carbon Nanotubes for Applications in High Performance Circuits

DTIC Science & Technology

2017-04-06

purchased and installed for experimental characterization of atomic layer deposited graphene on different substrates for radiation-hardened studies...72 3.6 Experimental Research in Graphene for Radiation Hardened Devices……………..73 4 Recommendations...physics for analysis and design of integrated circuits. The developed model is verified from published experimental data. Basic logic gates in

Impact of Jigsaw on the Achievement and Attitudes of Saudi Arabian Male High School Science Students

NASA Astrophysics Data System (ADS)

Alghamdi, Abdulmonem

The aim of the study is to investigate the impact of cooperative learning instruction, specifically by using the Jigsaw instructional strategy on science achievement and attitudes towards science among 11th grade students. Based upon previous research literature, it was hypothesized that significant differences existed on gains between general science achievement of experimental group and control group. The quasi-experimental design was chosen for this study. The study sample consisted of 50 students of 11th grade class who were equally distributed among experimental group and control group, matched on the basic of their annual examination at general science scores. The students' achievement was measured through the implementation of 30-item achievement test used as a pretest, as well as a posttest and deferred (follow-up) test. The experiment group was taught through cooperative learning while control group was taught through the instructions of "traditional teaching". The material was used such as lesson plans, worksheets and quizzes, designed to implement Jigsaw as a cooperative learning methodology. For the attitude scale towards science, a published 30-item Likert scale called Test of Science Related Attitudes (TOSRA) has been translated to Arabic in order to determine the students' attitudes ranging between strongly agree to strongly disagree. The data were analyzed through repeated measure analysis and multivariate analysis of variance with a .05 selected level of significance. The results of this study showed that using Jigsaw as a cooperative learning strategy has improved the students' achievement for the benefit of the experimental group. However, there was no significant change on the students' attitudes towards science for both groups, where the scores of all the attitude subscales were at or near the neutral level.

Computer Simulations of Coronary Blood Flow Through a Constriction

DTIC Science & Technology

2014-03-01

interventional procedures (e.g., stent deployment). Building off previous models that have been partially validated with experimental data, this thesis... stent deployment). Building off previous models that have been partially validated with experimental data, this thesis continues to develop the...the artery and increase blood flow. Generally a stent , or a mesh wire tube, is permanently inserted in order to scaffold open the artery wall

Communicating Uncertain Experimental Evidence

ERIC Educational Resources Information Center

Davis, Alexander L.; Fischhoff, Baruch

2014-01-01

Four experiments examined when laypeople attribute unexpected experimental outcomes to error, in foresight and in hindsight, along with their judgments of whether the data should be published. Participants read vignettes describing hypothetical experiments, along with the result of the initial observation, considered as either a possibility…

Improved determination of particulate absorption from combined filter pad and PSICAM measurements.

PubMed

Lefering, Ina; Röttgers, Rüdiger; Weeks, Rebecca; Connor, Derek; Utschig, Christian; Heymann, Kerstin; McKee, David

2016-10-31

Filter pad light absorption measurements are subject to two major sources of experimental uncertainty: the so-called pathlength amplification factor, β, and scattering offsets, o, for which previous null-correction approaches are limited by recent observations of non-zero absorption in the near infrared (NIR). A new filter pad absorption correction method is presented here which uses linear regression against point-source integrating cavity absorption meter (PSICAM) absorption data to simultaneously resolve both β and the scattering offset. The PSICAM has previously been shown to provide accurate absorption data, even in highly scattering waters. Comparisons of PSICAM and filter pad particulate absorption data reveal linear relationships that vary on a sample by sample basis. This regression approach provides significantly improved agreement with PSICAM data (3.2% RMS%E) than previously published filter pad absorption corrections. Results show that direct transmittance (T-method) filter pad absorption measurements perform effectively at the same level as more complex geometrical configurations based on integrating cavity measurements (IS-method and QFT-ICAM) because the linear regression correction compensates for the sensitivity to scattering errors in the T-method. This approach produces accurate filter pad particulate absorption data for wavelengths in the blue/UV and in the NIR where sensitivity issues with PSICAM measurements limit performance. The combination of the filter pad absorption and PSICAM is therefore recommended for generating full spectral, best quality particulate absorption data as it enables correction of multiple errors sources across both measurements.

Dual-stiffness flooring: can it reduce fracture rates associated with falls?

PubMed

Knoefel, Frank; Patrick, Louise; Taylor, Jodie; Goubran, Rafik

2013-04-01

Falls cause significant morbidity and mortality in long term care facilities. Dual-stiffness flooring (DSF) has previously shown promise in reducing such morbidity in experimental models. This study set out to measure the impact of SmartCell flooring on falls-related morbidity in a nursing home. All falls occurring at an Arizona nursing home between July 1, 2008, and December 31, 2010, were reviewed for age, sex, diagnosis of osteoporosis, number of medications, history of previous falls, type of flooring (normal vs DSF), time of day, type of injury, and resulting actions. Fall-related outcomes were compared across room types using chi-square and logistic regression methods. Eighty-two falls on the DSF were compared with 85 falls on the regular floor. There was a tendency for residents falling on DSF to have less bruising and abrasions, while having more redness and cuts. There were 2 fractures on regular flooring (2.4% fracture rate) and none on the DSF flooring (0% fracture rate). The fracture rate of 2.4% of falls on the regular floor is consistent with previous reports in the literature, whereas a 0% rate found on the DSF floor is a clinically significant improvement. This suggests that DSF may be a practical approach for institutions and consumers to reduce fall-related injuries. A larger scale controlled study to confirm these encouraging preliminary findings is warranted. Copyright © 2013 American Medical Directors Association, Inc. Published by Elsevier Inc. All rights reserved.

White-tailed deer are a biotic filter during community assembly, reducing species and phylogenetic diversity.

PubMed

Begley-Miller, Danielle R; Hipp, Andrew L; Brown, Bethany H; Hahn, Marlene; Rooney, Thomas P

2014-06-09

Community assembly entails a filtering process, where species found in a local community are those that can pass through environmental (abiotic) and biotic filters and successfully compete. Previous research has demonstrated the ability of white-tailed deer (Odocoileus virginianus) to reduce species diversity and favour browse-tolerant plant communities. In this study, we expand on our previous work by investigating deer as a possible biotic filter altering local plant community assembly. We used replicated 23-year-old deer exclosures to experimentally assess the effects of deer on species diversity (H'), richness (SR), phylogenetic community structure and phylogenetic diversity in paired browsed (control) and unbrowsed (exclosed) plots. Additionally, we developed a deer-browsing susceptibility index (DBSI) to assess the vulnerability of local species to deer. Deer browsing caused a 12 % reduction in H' and 17 % reduction in SR, consistent with previous studies. Furthermore, browsing reduced phylogenetic diversity by 63 %, causing significant phylogenetic clustering. Overall, graminoids were the least vulnerable to deer browsing based on DBSI calculations. These findings demonstrate that deer are a significant driver of plant community assembly due to their role as a selective browser, or more generally, as a biotic filter. This study highlights the importance of knowledge about the plant tree of life in assessing the effects of biotic filters on plant communities. Application of such knowledge has considerable potential to advance our understanding of plant community assembly. Published by Oxford University Press on behalf of the Annals of Botany Company.

The research evidence published in high impact nursing journals between 2000 and 2006: a quantitative content analysis.

PubMed

Mantzoukas, Stefanos

2009-04-01

Evidence-based practice has become an imperative for efficient, effective and safe practice. Furthermore, evidences emerging from published research are considered as valid knowledge sources to guiding practice. The aim of this paper is to review all research articles published in the top 10 general nursing journals for the years 2000-2006 to identify the methodologies used, the types of evidence these studies produced and the issues upon which they endeavored. Quantitative content analysis was implemented to study all published research papers of the top 10 general nursing journals for the years 2000-2006. The top 10 general nursing journals were included in the study. The abstracts of all research articles were analysed with regards the methodologies of enquiry, the types of evidence produced and the issues of study they endeavored upon. Percentages were developed as to enable conclusions to be drawn. The results for the category methodologies used were 7% experimental, 6% quasi-experimental, 39% non-experimental, 2% ethnographical studies, 7% phenomenological, 4% grounded theory, 1% action research, 1% case study, 15% unspecified, 5.5% other, 0.5% meta-synthesis, 2% meta-analysis, 5% literature reviews and 3% secondary analysis. For the category types of evidence were 4% hypothesis/theory testing, 11% evaluative, 5% comparative, 2% correlational, 46% descriptive, 5% interpretative and 27% exploratory. For the category issues of study were 45% practice/clinical, 8% educational, 11% professional, 3% spiritual/ethical/metaphysical, 26% health promotion and 7% managerial/policy. Published studies can provide adequate evidences for practice if nursing journals conceptualise evidence emerging from non-experimental and qualitative studies as relevant types of evidences for practice and develop appropriate mechanisms for assessing their validity. Also, nursing journals need to increase and encourage the publication of studies that implement RCT methodology, systematic reviews, meta-synthesis and meta-analysis methodologies. Finally, nursing journals need to encourage more high quality research evidence that derive from interpretative, theory testing and evaluative types of studies that are practice relevant.

77 FR 7609 - Policy Letter 11-01, Performance of Inherently Governmental and Critical Functions

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-13

... Regulation. The corrections below should be used in place of text previously published in the September 12, 2011 notice. All other information from the published Final Policy remains unchanged. The full text of...

Device SEE Susceptibility Update: 1996-1998

NASA Technical Reports Server (NTRS)

Coss, J. R.; Miyahira, T. F.; Swift, G. M.

1998-01-01

This eighth Compendium continues the previous work of Nichols, et al, on single event effects (SEE) first published in 1985. Because the compendium has grown so voluminous, this update only presents data not publised in previous compendia.

Shock compression response of cold-rolled Ni/Al multilayer composites

NASA Astrophysics Data System (ADS)

Specht, Paul E.; Weihs, Timothy P.; Thadhani, Naresh N.

2017-01-01

Uniaxial strain, plate-on-plate impact experiments were performed on cold-rolled Ni/Al multilayer composites and the resulting Hugoniot was determined through time-resolved measurements combined with impedance matching. The experimental Hugoniot agreed with that previously predicted by two dimensional (2D) meso-scale calculations [Specht et al., J. Appl. Phys. 111, 073527 (2012)]. Additional 2D meso-scale simulations were performed using the same computational method as the prior study to reproduce the experimentally measured free surface velocities and stress profiles. These simulations accurately replicated the experimental profiles, providing additional validation for the previous computational work.

Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum.

PubMed

Isakov, Ofer; Bordería, Antonio V; Golan, David; Hamenahem, Amir; Celniker, Gershon; Yoffe, Liron; Blanc, Hervé; Vignuzzi, Marco; Shomron, Noam

2015-07-01

The study of RNA virus populations is a challenging task. Each population of RNA virus is composed of a collection of different, yet related genomes often referred to as mutant spectra or quasispecies. Virologists using deep sequencing technologies face major obstacles when studying virus population dynamics, both experimentally and in natural settings due to the relatively high error rates of these technologies and the lack of high performance pipelines. In order to overcome these hurdles we developed a computational pipeline, termed ViVan (Viral Variance Analysis). ViVan is a complete pipeline facilitating the identification, characterization and comparison of sequence variance in deep sequenced virus populations. Applying ViVan on deep sequenced data obtained from samples that were previously characterized by more classical approaches, we uncovered novel and potentially crucial aspects of virus populations. With our experimental work, we illustrate how ViVan can be used for studies ranging from the more practical, detection of resistant mutations and effects of antiviral treatments, to the more theoretical temporal characterization of the population in evolutionary studies. Freely available on the web at http://www.vivanbioinfo.org : nshomron@post.tau.ac.il Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

BRIDGING SCALES IN THE EVOLUTION OF INFECTIOUS DISEASE LIFE HISTORIES: APPLICATION

PubMed Central

Mideo, Nicole; Nelson, William A.; Reece, Sarah E.; Bell, Andrew S.; Read, Andrew F.; Day, Troy

2014-01-01

Within- and between-host disease processes occur on the same timescales, therefore changes in the within-host dynamics of parasites, resources, and immunity can interact with changes in the epidemiological dynamics to affect evolutionary outcomes. Consequently, studies of the evolution of disease life histories, that is, infection-age-specific patterns of transmission and virulence, have been constrained by the need for a mechanistic understanding of within-host disease dynamics. In a companion paper (Day et al. 2011), we develop a novel approach that quantifies the relevant within-host aspects of disease through genetic covariance functions. Here, we demonstrate how to apply this theory to data. Using two previously published datasets from rodent malaria infections, we show how to translate experimental measures into disease life-history traits, and how to quantify the covariance in these traits. Our results show how patterns of covariance can interact with epidemiological dynamics to affect evolutionary predictions for disease life history. We also find that the selective constraints on disease life-history evolution can vary qualitatively, and that “simple” virulence-transmission trade-offs that are often the subject of experimental investigation can be obscured by trade-offs within one trait alone. Finally, we highlight the type and quality of data required for future applications. PMID:22023593

Statistical shear lag model - unraveling the size effect in hierarchical composites.

PubMed

Wei, Xiaoding; Filleter, Tobin; Espinosa, Horacio D

2015-05-01

Numerous experimental and computational studies have established that the hierarchical structures encountered in natural materials, such as the brick-and-mortar structure observed in sea shells, are essential for achieving defect tolerance. Due to this hierarchy, the mechanical properties of natural materials have a different size dependence compared to that of typical engineered materials. This study aimed to explore size effects on the strength of bio-inspired staggered hierarchical composites and to define the influence of the geometry of constituents in their outstanding defect tolerance capability. A statistical shear lag model is derived by extending the classical shear lag model to account for the statistics of the constituents' strength. A general solution emerges from rigorous mathematical derivations, unifying the various empirical formulations for the fundamental link length used in previous statistical models. The model shows that the staggered arrangement of constituents grants composites a unique size effect on mechanical strength in contrast to homogenous continuous materials. The model is applied to hierarchical yarns consisting of double-walled carbon nanotube bundles to assess its predictive capabilities for novel synthetic materials. Interestingly, the model predicts that yarn gauge length does not significantly influence the yarn strength, in close agreement with experimental observations. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Branch-point energies and the band-structure lineup at Schottky contacts and heterostrucures

NASA Astrophysics Data System (ADS)

Mönch, Winfried

2011-06-01

Empirical branch-point energies of Si, the group-III nitrides AlN, GaN, and InN, and the group-II and group-III oxides MgO, ZnO, Al2O3 and In2O3 are determined from experimental valance-band offsets of their heterostructures. For Si, GaN, and MgO, these values agree with the branch-point energies obtained from the barrier heights of their Schottky contacts. The empirical branch-point energies of Si and the group-III nitrides are in very good agreement with results of previously published calculations using quite different approaches such as the empirical tight-binding approximation and modern electronic-structure theory. In contrast, the empirical branch-point energies of the group-II and group-III oxides do not confirm the respective theoretical results. As at Schottky contacts, the band-structure lineup at heterostructures is also made up of a zero-charge-transfer term and an intrinsic electric-dipole contribution. Hence, valence-band offsets are not equal to the difference of the branch-point energies of the two semiconductors forming the heterostructure. The electric-dipole term may be described by the electronegativity difference of the two solids in contact. A detailed analysis of experimental Si Schottky barrier heights and heterostructure valence-band offsets explains and proves these conclusions.

A Weibull statistics-based lignocellulose saccharification model and a built-in parameter accurately predict lignocellulose hydrolysis performance.

PubMed

Wang, Mingyu; Han, Lijuan; Liu, Shasha; Zhao, Xuebing; Yang, Jinghua; Loh, Soh Kheang; Sun, Xiaomin; Zhang, Chenxi; Fang, Xu

2015-09-01

Renewable energy from lignocellulosic biomass has been deemed an alternative to depleting fossil fuels. In order to improve this technology, we aim to develop robust mathematical models for the enzymatic lignocellulose degradation process. By analyzing 96 groups of previously published and newly obtained lignocellulose saccharification results and fitting them to Weibull distribution, we discovered Weibull statistics can accurately predict lignocellulose saccharification data, regardless of the type of substrates, enzymes and saccharification conditions. A mathematical model for enzymatic lignocellulose degradation was subsequently constructed based on Weibull statistics. Further analysis of the mathematical structure of the model and experimental saccharification data showed the significance of the two parameters in this model. In particular, the λ value, defined the characteristic time, represents the overall performance of the saccharification system. This suggestion was further supported by statistical analysis of experimental saccharification data and analysis of the glucose production levels when λ and n values change. In conclusion, the constructed Weibull statistics-based model can accurately predict lignocellulose hydrolysis behavior and we can use the λ parameter to assess the overall performance of enzymatic lignocellulose degradation. Advantages and potential applications of the model and the λ value in saccharification performance assessment were discussed. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Periodic table-based descriptors to encode cytotoxicity profile of metal oxide nanoparticles: a mechanistic QSTR approach.

PubMed

Kar, Supratik; Gajewicz, Agnieszka; Puzyn, Tomasz; Roy, Kunal; Leszczynski, Jerzy

2014-09-01

Nanotechnology has evolved as a frontrunner in the development of modern science. Current studies have established toxicity of some nanoparticles to human and environment. Lack of sufficient data and low adequacy of experimental protocols hinder comprehensive risk assessment of nanoparticles (NPs). In the present work, metal electronegativity (χ), the charge of the metal cation corresponding to a given oxide (χox), atomic number and valence electron number of the metal have been used as simple molecular descriptors to build up quantitative structure-toxicity relationship (QSTR) models for prediction of cytotoxicity of metal oxide NPs to bacteria Escherichia coli. These descriptors can be easily obtained from molecular formula and information acquired from periodic table in no time. It has been shown that a simple molecular descriptor χox can efficiently encode cytotoxicity of metal oxides leading to models with high statistical quality as well as interpretability. Based on this model and previously published experimental results, we have hypothesized the most probable mechanism of the cytotoxicity of metal oxide nanoparticles to E. coli. Moreover, the required information for descriptor calculation is independent of size range of NPs, nullifying a significant problem that various physical properties of NPs change for different size ranges. Copyright © 2014 Elsevier Inc. All rights reserved.

Representation of Nursing Scientists from German-speaking countries in High Impact Journals. A bibliometric publication analysis

PubMed

Hirt, Julian; Buhtz, Christian; Mersdorf, Benedikt; Meyer, Gabriele

2018-02-01

Background: The frequency of publications by nursing scientists from the German-speaking area in journals with a high impact factor is an indicator for participation of the discipline in the international discourse. Previous publication analyses focused on nursing science journals only and regularly found an underrepresentation of experimental studies and clinical topics. Aim: To identify and analyse the number of publications by nursing scientists from Germany, Austria and German-speaking Switzerland in international high impact journals. Method: The Journal Citation Reports were used to identify nursing relevant categories of journals in which the highest 10 % of the years 2010 to 2014 were selected according to the 5-year Impact Factor. Inclusion of publications and data extraction were carried out by two independent persons. Results: 106939 publications from 126 journals were screened; 100 publications were identified with 229 contributions by 114 nursing scientists. 42 % of studies are observational and 11 % are experimental. The majority of studies are clinically oriented (55 %). More than 50 % have been published in the past two years. Conclusions: The number of publications by nursing scientists from the German-speaking countries in High Impact Journals is low. There is an increase throughout the observation period. In opposite to former analyses a higher proportion of clinical research has been found.