gebhart/patrepeval huggingface dataset:
Parameter effects on binding chemistry in crowded media using a two-dimensional stochastic off-lattice model (2009)

The intracellular environment imposes a variety of constraints on biochemical reaction systems that can substantially change reaction rates and equilibria relative to an ideal solution-based environment. One of the most notable features of the intracellular environment is its dense macromolecular crowding, which, among many other effects, tends to strongly enhance binding and assembly reactions. Despite extensive study of biochemistry in crowded media, it remains extremely difficult to predict how crowding will quantitatively affect any given reaction system due to the dependence of the crowding effect on numerous assumptions about the reactants and crowding agents involved. We previously developed a two dimensional stochastic off-lattice model of binding reactions based on the Green's function reaction dynamics method in order to create a versatile simulation environment in which one can explore interactions among many parameters of a crowded assembly system. In the present work, we examine interactions among several critical parameters for a model dimerization system: the total concentration of reactants and inert particles, the binding probability upon a collision between two reactant monomers, the mean time of dissociation reactions, and the diffusion coefficient of the system. Applying regression models to equilibrium constants across parameter ranges shows that the effect of the total concentration is approximately captured by a low-order nonlinear polynomial model, while the other three parameter effects are each accurately captured by a linear model. Furthermore, validation on tests with multi-parameter variations reveals that the effects of these parameters are separable from one another over a broad range of variation in all four parameters. The simulation work suggests that predictive models of crowding effects can accommodate a wider variety of parameter variations than prior theoretical models have so far achieved.
<i>N</i>‐methyl‐d‐aspartate Receptor Responses Are Differentially Modulated by Noncompetitive Receptor Antagonists and Ethanol in Inbred Long‐Sleep and Short‐Sleep Mice: Behavior and Electrophysiology (2000)

Differential ethanol- and MK-801-induced behavioral activation in ILS and ISS mice was not associated with differences in NMDAR number. Nonetheless, pharmacological differences in hippocampal NMDAR responsiveness suggest that ISS mice express NMDARs that have a greater sensitivity to noncompetitive, but not competitive, NMDAR antagonists. These differences, which may reflect differences in NMDAR subunit composition, could underlie the differential responsiveness to low doses of ethanol in ILS and ISS mice.
L‐band sea surface emissivity: Preliminary results of the WISE‐2000 campaign and its application to salinity retrieval in the SMOS mission (2003)

Soil moisture and ocean salinity at surface level can be measured by passive microwave remote sensing at L‐band. To provide global coverage data of soil moisture and ocean salinity with three‐day revisit time, the Earth Explorer Opportunity Mission SMOS (Soil Moisture and Ocean Salinity) was selected by ESA (European Space Agency) in May 1999. SMOS' single payload is a Y‐shaped 2‐D aperture synthesis interferometric radiometer called MIRAS (Microwave Imaging Radiometer by Aperture Synthesis). SMOS presents some particular imaging peculiarities: variation of incidence and azimuth angles, different radiometric sensitivity and accuracy at each direction (pixels), and geometric polarization mixing. Therefore, the accuracy of the geophysical parameter retrieval depends on the knowledge of the angular dependence of the emissivity over a wide range of incidence and azimuth angles. The accuracy of the sea surface salinity retrievals depends on our capability to correct the wind‐induced variation of the brightness temperatures. To better understand wind effects, ESA sponsored the WInd and Salinity Experiment 2000 (WISE‐2000) from November 15, 2000, to January 16, 2001, in the Casablanca oil rig, at 40 km off the coast of Tarragona (Spain). This paper is divided into two parts. First, it presents the derived sensitivities of the brightness temperatures at vertical and horizontal polarizations with wind speed, and compares to Hollinger's measurements and numerical simulations. Second, these results are applied to the SMOS sea surface salinity (SSS) retrieval problem for different tracks within the swath. It is shown that, except for low SSS and sea surface temperature (SST), the retrieved SSS has a RMS error of approximately 1 psu in one satellite pass.
Long-term productive human cytomegalovirus infection of a human neuroblastoma cell line (1996)

Human neuroblastoma cell line UKF-NB-4 persistently infected with human cytomegalovirus (HCMV) strain AD169 was established to study the effects of long-term HCMV infection on virus production and phenotypic characteristics of tumour cells. The cells designated UKF-NB-4AD169 were subcultured (80 subcultures) over a period of more than 2 years after initiation of infection. UKF-NB-4AD169 cells continued to produce infectious virus in successive passages, with a titre ranging from 9 x 10(3) to 1 x 10(5) and from 2 x 10(1) to 2 x 10(2) plaque-forming units per 10(6) cells and 1 ml culture medium, respectively; 10-20% of the cells produced HCMV-specific antigens, while 6-13% produced infectious virus progeny. The number of HCMV-specific DNA copies ranged from 9 x 10(4) to 9 x 10(6) per 10(6) cells. Transmission electron microscopy confirmed the productive nature of HCMV infection. UKF-NB-4AD169 cultures proliferated, with population doubling time ranging from 24.5 to 26.6 hr (19.5 to 20.3 hr for UKF-NB-4) and cell viability from 79% to 85% (91-96% for UKF-NB-4). Significantly lower amounts of tyrosine hydroxylase and decreased activity for dopamine-beta-hydroxylase than in uninfected cells were observed in UKF-NB-4AD169 cells. However, the expression of N-myc oncoprotein was significantly increased in persistently infected cultures. Our results show that long-term productive HCMV infection of UKF-NB-4 cell line is associated with the modulation of phenotypic properties, which may be related to the biological behaviour of neuroblastoma cells.
CD46 (membrane cofactor protein) associates with multiple β1 integrins and tetraspans (2000)

The tetraspans associate with a large number of surface molecules, including a subset of beta1 integrins and, indirectly through CD19, with the complement receptor CD21. To further characterize the tetraspan complexes we have raised and selected monoclonal antibodies (mAb) for their ability to immunoprecipitate a molecule associated with CD9. A unique mAb was identified which recognizes the complement regulator CD46 (membrane cofactor protein). CD46 associated in part with several tetranspans and with all beta1 integrins that were tested (CD29/CD49a, CD29/CD49b, CD29/CD49c, CD29/CD49e, CD29/CD49f) but not with beta4 integrins. These data, together with cross-linking experiments showing the existence in living cells of CD46/integrin complexes, suggest that CD46 associates directly with beta1 integrins and indirectly with tetraspans. CD46 also acts as a receptor for measles virus; however, mAb to various integrins and tetraspans did not modify the virus fusion entry step.
Mapping of Sequence-Tagged Sites in Rice by Single Strand Conformation Polymorphism (1994)

The conditions for efficient single-strand conformation polymorphism (SSCP) detection were examined for its application to mapping of DNA regions in the rice genome. Temperature for electrophoresis and glycerol concentrations in gel affected SSCP patterns significantly. The optimal detection conditions for SSCP also depends on the nucleotide sequences of fragments analyzed. Fragments over 300 bp show complicated patterns depending on their nucleotide sequences and were not suitable for SSCP analysis. Seventy primer pairs were designed from the sequence data available to amplify DNA regions as sequence tagged sites (STSs), and 39 of these STSs were found to generate SSCP between japonica rice (Nipponbare) and indica rice (Kasalath) in at least one of the experimental conditions. The maps of DNA fragments amplified from 186 F2-plant DNAs with 17 primer pairs were successfully determined. This direct mapping method of the amplified DNA fragments with PCR is simple and quite sensitive, and can be used to set markers in the gap regions of a genetic linkage map.
Cation Vacancies in MnO2 and Their Influence on Electrochemical Reactivity (1988)

Two types of protons must be distinguished in the cation‐deficient lattice: localized (Ruetschi) protons, associated with vacancies, and mobile (Coleman) protons, associated with electrons forming Mn3+ ions. The localized protons provide "proton bridges" for chain‐type proton transfer. Thermogravimetric experiments reveal that the cation vacancy fraction remains invariant during proton (plus electron) insertion and that the cation‐deficient lattice becomes increasingly unstable with increasing degree of (topotactical) reduction. The activation energy of proton (plus electron) diffusion is of similar magnitude as the activation energy of electronic conductivity, while the activation energy of cation (vacancy) diffusion is several times larger.
Bone mineral density and metabolism in children with congenital hypothyroidism after prolonged <scp>l</scp>‐thyroxine therapy (1997)

The effect of long-term L-thyroxine (LT4) replacement therapy on bone mineral density and on biochemical markers of bone turnover were studied in children with congenital hypothyroidism (CH). Forty-four children and adolescents (mean age 8.5 +/- 3.5 years) with primary CH who began LT4 replacement therapy within the first month of life were studied. Bone mineral density (BMD) of the lumbar vertebrae and the upper femoral bone was measured by dual energy X-ray absorptiometry. Serum osteocalcin (OC) and bone alkaline phosphatase were measured as markers of bone formation and urinary deoxypyridinoline was taken as a marker of bone resorption. Bone mineral densities of CH children were not different from those in age-matched controls. The biochemical markers of bone turnover were normal except for the serum OC levels which were found to be higher than in controls and positively correlated with the free thyroid hormone levels (for FT4 r = 0.42, p = 0.02). Eight CH children demonstrated low BMD values (below -1 SDS) at -2 +/- 0.7 SDS for the lumbar spine and -1.6 +/- 0.5 SDS for the femoral site. These eight children showed lower mean weight (p < 0.05) and their dietary calcium intake tended to be less (p <0.06) than that seen in the normal BMD group. In conclusion, our results show that LT4 replacement therapy for 8 years is not detrimental to the skeletal mineralization of CH children. As in a healthy population, weight and current intake of calcium seem to be major determinants of bone density. Dietary recommendations, especially when calcium intake is below the recommended dietary allowance, may have to be reconsidered.
The Marshall Grazing Incidence X-ray Spectrometer (2017)

The Marshall Grazing Incidence X-ray Spectrometer (MaGIXS) is a NASA sounding rocket instrument designed to obtain spatially resolved soft X-ray spectra of the solar atmosphere in the 6–24 Å (0.5–2.0 keV) range. The instrument consists of a single shell Wolter Type-I telescope, a slit, and a spectrometer comprising a matched pair of grazing incidence parabolic mirrors and a planar varied-line space diffraction grating. The instrument is designed to achieve a 50 mÅ spectral resolution and 5 arcsecond spatial resolution along a ±4-arcminute long slit, and launch is planned for 2019. We report on the status and our approaches for fabrication and alignment for this novel optical system. The telescope and spectrometer mirrors are replicated nickel shells, and are currently being fabricated at the NASA Marshall Space Flight Center. The diffraction grating is currently under development by the Massachusetts Institute of Technology (MIT); because of the strong line spacing variation across the grating, it will be fabricated through e-beam lithography.
ACTIVATION ENERGIES FOR CREEP OF CADMIUM, INDIUM, AND TIN. Technical Report No. 36 (1954)

The cerebral cortex is divided into many functionally distinct areas. The emergence of these areas during neural development is dependent on the expression patterns of several genes. Along the anterior-posterior axis, gradients of Fgf8, Emx2, Pax6, Coup-tfi, and Sp8 play a particularly strong role in specifying areal identity. However, our understanding of the regulatory interactions between these genes that lead to their confinement to particular spatial patterns is currently qualitative and incomplete. We therefore used a computational model of the interactions between these five genes to determine which interactions, and combinations of interactions, occur in networks that reproduce the anterior-posterior expression patterns observed experimentally. The model treats expression levels as Boolean, reflecting the qualitative nature of the expression data currently available. We simulated gene expression patterns created by all possible networks containing the five genes of interest. We found that only of these networks were able to reproduce the experimentally observed expression patterns. These networks all lacked certain interactions and combinations of interactions including auto-regulation and inductive loops. Many higher order combinations of interactions also never appeared in networks that satisfied our criteria for good performance. While there was remarkable diversity in the structure of the networks that perform well, an analysis of the probability of each interaction gave an indication of which interactions are most likely to be present in the gene network regulating cortical area development. We found that in general, repressive interactions are much more likely than inductive ones, but that mutually repressive loops are not critical for correct network functioning. Overall, our model illuminates the design principles of the gene network regulating cortical area development, and makes novel predictions that can be tested experimentally.
Multiple stressors in aquatic environments may profile biomarker baseline responses: a case study in Dreissena polymorpha at the population scale (2012)

International audience
Nature of the Peroxo Intermediate of the W48F/D84E Ribonucleotide Reductase Variant:  Implications for O<sub>2</sub> Activation by Binuclear Non-Heme Iron Enzymes (2004)

Analysis of the spectroscopic signatures of the R2-W48F/D84E biferric peroxo intermediate identifies a cis mu-1,2 peroxo coordination geometry. DFT geometry optimizations on both R2-W48F/D84E and R2-wild-type peroxo intermediate models including constraints imposed by the protein also identify the cis mu-1,2 peroxo geometry as the most stable peroxo intermediate structure. This study provides significant insight into the electronic structure and reactivity of the R2-W48F/D84E peroxo intermediate, structurally related cis mu-1,2 peroxo model complexes, and other enzymatic biferric peroxo intermediates.
Oscillatory behaviour of the transport properties in PbTe quantum wells (2002)

Oscillatory behaviour was detected in the dependences of the transport properties (electrical conductivity, Hall coefficient, charge carrier mobility, Seebeck coefficient and thermoelectric power factor) on the PbTe layer thickness d (d = 2–200 nm) in (001) KCl/PbTe/EuS quantum well (QW) structures at room temperature. The non-monotonic character of these dependences is attributed to quantum size effects, which manifest themselves in PbTe QWs at sufficiently small values of d. The positions of the extrema in the thickness dependences of the transport properties shift with changing electron concentration in PbTe QWs.
Comparison of different polymers and printing technologies for realizing flexible optical waveguide Bragg grating strain sensor foils (2019)

Waveguides with Bragg gratings realized on a flat polymer foil are promising candidates for advanced strain sensors since such a planar approach allows precise positioning of multiple sensors in various well-defined directions, in the same foil. As such, an optical version of an electrical strain gage can be realized. Herein, several parameters are discussed which define the behaviour of such sensor foils, in particular the grating design, including the wavelength of operation and mechanical and optical properties of the used polymers. Epoxy and Ormocer®-based Bragg grating sensors operating at 850 nm and 1550 nm wavelength were realized using nano-imprint lithography and laser direct-write lithography and their strain and temperature sensitivities were compared. Finally, it is demonstrated that optical strain gage rosettes can be realized by multiplexing 3 angularly displaced sensors in the same waveguide on a single foil.
Kinetics of CH<SUB>4</SUB>, H<SUB>2</SUB>S and SO<SUB>2</SUB> oxidation on precious metal catalysts under stagnation point flow conditions (2006)

A new methodology which combines reactor experiments and numerical modelling to derive kinetic rates of solid-gas heterogeneous reactions in a stagnation point flow reactor (SPFR) is developed and used to investigate the effects of small concentrations of H 2 S and SO 2 on the lean catalytic combustion of methane on precious metal catalysts. The activity of polycrystalline Pt foil, then Pt, Rh and Pd-containing washcoats supported on stainless steel foils are investigated in the SPFR, where the washcoat consisted of a thin layer of -Alumina or ceria/-alumina. The porous washcoats supported on steel foil were more active than the equivalent flat surface of pure precious metal (case of Pt) with pre-exponential factors of 7.410 5 cm s -1 and 4.910 4 cm s -1 respectively. Repeated use of the washcoated catalyst add the effect of pore opening given rise to a change in the pre-exponential factor from 7.410 5 cm s -1 to 1.110 9 cm s -1 for Pt. The high temperature activity behaviour of Pt in presence of sulphur species in the feed was however superior to that of Pd, due to the changing nature of the active site in CH 4 oxidation (PdO/Pd), as is consistent with the literature based on other type of reactor studies. Methane combustion was enhanced by both H 2 S and SO 2 on the Pt catalysts as opposed to the Pd and Rh catalysts, which saw a decrease in the methane conversion.
Globalizáció, individualizáció, modernizáció, urbanizáció és lakásmód Magyarországon (2005)

Európa keleti felén a globalizáció folyamata együtt zajlott/zajlik a modernizáció, az urbanizáció, az individualizáció és a (re)kapitalizáció folyamatával. Mindezen folyamatok már régen megkezdődtek, de a rendszerváltás radikálisan felgyorsította őket. Ez az időszak számos területen kiváló lehetőséget nyújt e folyamatok megnyilvánulásainak elemzésére. A szemiotikai elemzésben érdemes különválasztani ezeket a folyamatokat, van, amit elsősorban értékrendszeri változásként, van, amit a haladás/konzervativizmus metszetben, ismét más jelenségeket elsősorban új szimbólumok megjelenéseként érdemes elemezni. A fent jelzett szocio-kulturális változásokat mi elsősorban a lakásmód (különösen a középosztályi lakásmód) változásaiban vizsgáltuk. Az utóbbi évtized változásai közül elsősorban az alábbiakat elemeztük: a multikulturalizáció jelei és lépcsőfokai a tárgykultúrában (különösen az észak-amerikai és a távol-keleti jelek és szimbólumok beáramlása); az individualizáció jelei a lakás egyes helyiségeinek (fürdőszoba, gyerekszoba, hálószoba) jellegváltozásaiban; a komputerhasználat szerepe az új lakásmódban mint modernizáció-szimbólum; az erkélyek és kertek megváltozott használatmódja és ennek összefüggése a nyilvánossághoz való viszony változásával; illetve a könyvek szerepének változása és ennek összefüggése a szűkebb értelemben vett kultúra szerepváltozásával - mint a rendszerváltás következményei; a „látványlakások” divatja; az urbanizáció (és modernizáció) jelei a falusi életmódban és az értelmiségi ellen-irányzat: törekvés a falvak revitalizálására (és ennek összefüggése a globalizáció negatív hatásaival szembeni ellenállással).
Cyclohexane dehydrogenation kinetics on a platinum‐rhenium/aluminium oxide catalyst with hydrogen and inert diluents (1980)

Abstract The dehydrogenation of cyclohexane to benzene on a platinum‐rhenium/aluminium oxide (Pt‐Re/Al 2 O 3 ) catalyst was investigated using both pulse and continuous flow techniques with hydrogen and inert (N 2 , He, Ar) diluents at the following conditions: 1 and 4 atm (1 atm = 101 kPa) total pressure and 432–623 K. Experiments performed with hydrogen as a carrier in the pulse mode showed anomalous behaviour as cyclohexane conversion was observed to increase with pulse size/pulse width and decrease with temperature and contact time. The dehydrogenation reaction was first‐order with respect to cyclohexane for both the pulse and continuous flow experiments. Lower activation energies were observed for the inert carriers; activation energies were between 37.7–54.4 kJ mol< −1 for inert diluents. With a hydrogen carrier, the activation energies were found to be 87.9 and 121.3 kJ mol −1 for T <553 K and <553 K, respectively. The difference in activation energy between hydrogen and the inert carriers was attributed to a change in mechanism on the coked catalyst surface. Surface conversion of cyclohexane to adsorbed cyclohexane was the slowest step in a hydrogen carrier. For the inert carriers, it was postulated that surface diffusion of adsorbed intermediate for for subsequent conversion was rate determining.
Synthesis of chemicals from glycerol with gold-based catalysts (2011)

Glycerol is a bio-renewable resource that can be useful in the synthesis of many useful chemical intermediates. For example, glycerol can be oxidized in high selectivity to glyceric acid using supported gold catalysts. By controlling the reaction conditions very high selectivities to glyceric acid can be obtained. Additionally, the reaction of glycerol with urea to form glycerol carbonate is a very attractive reaction which utilises two inexpensive and readily available raw materials. Typically homogeneous catalysts based on metal sulfates have been found to be effective catalysts and it is recognised that a heterogeneous catalysts would be preferred. We have now found that supported gold catalysts are very effective heterogeneous catalysts for this reaction. In this presentation these reactions will be discussed.
Effect of pressure and timing of contraction on human diaphragm fatigue (1982)

The relationship between the mean transdiaphragmatic pressure swing developed with each inspiration (Pdi) and the fraction of the breathing cycle time spent in inspiration (TI/Ttot) (Pdi X TI/Ttot) was related to the maximal time that such a run could be sustained (Tlim). Four normal subjects breathed with a constant breathing pattern for 45 min or until Pdi could no longer be sustained, whichever came first. The breathing patterns included Pdi of 0.15-0.90 of Pdimax and TI/Ttot of 0.15-1.0. Pdi was obtained by adjusting an inspiratory resistance, and the timing by monitoring tidal volume with time base from an oscilloscope. The Tlim of a run was found to be inversely related to both Pdi and TI/Ttot and hence inversely related to their product, following a quadratic hyperbole function. Pdi X TI/Ttot represents an index of the tension time of the diaphragm (TTdi). The breathing pattern that could be sustained more than 45 min was found to have a TTdi of about 0.15, which was termed critical TTdi. Above that value Tlim decreased as a function of TTdi. The results are consistent with Tlim being related to diaphragmatic blood flow limitation.