gebhart/patrepeval huggingface dataset:
QM/MM Simulations for Diels−Alder Reactions in Water:  Contribution of Enhanced Hydrogen Bonding at the Transition State to the Solvent Effect (2002)

Free energy profiles for Diels−Alder reactions of cyclopentadiene with acrylonitrile, methyl vinyl ketone, and 1,4-naphthoquinone have been computed in the gas phase and in aqueous solution using Monte Carlo simulations in a fully automated, mixed quantum and molecular mechanics (QM/MM) approach. The QM/MM calculations in water featured AM1 treatment for the solute in the presence of 500 TIP4P water molecules, and computation of solute−water interactions using scaled CM1A charges for the solute. Free energy perturbation calculations yielded the profiles along a reaction coordinate with all other degrees of freedom sampled. The free energies of activation are reduced on going from the gas phase to water by 1.5, 2.8, and 4.4 kcal/mol for the reactions with acrylonitrile, methyl vinyl ketone, and naphthoquinone, respectively. These values are in good agreement with the corresponding experimental results for transfer from hydrocarbon solvents to water (2.1, 3.8, and 5.0 kcal/mol). The cycloadducts are stabilized less effectively than the transition states by water in all three cases. Therefore, the retro-Diels−Alder reactions are also predicted to be accelerated in water, in accord with related experimental data. These results and consideration of variations in solvent-accessible surface area (SASA) confirm that the rate increases in water arise in part from hydrophobic association of the reactants, but predominantly from enhanced hydrogen bonding between water molecules and the polarized transition states.
Asymmetric α-oxyacylation of cyclic ketones (2012)

Reaction of cyclic ketones with chiral N-alkyl-O-acyl hydroxylamines leads to the corresponding α-oxyacylated carbonyl compound in up to 89% ee. The levels of asymmetric induction were influenced by solvent polarity, acid strength and, to a lesser extent, temperature. Increasing the steric bulk around the nitrogen atom of the hydroxylamine reagent led to increased levels of asymmetric induction, which was also found to be detrimental to the yield observed for the transformation. Examination of N- and O-substituents along with substrates revealed the scope and limitations of the procedure.
Synthesis and characterisation of an unsymmetrical, ether-linked, fluorinated bimesogen exhibiting a new polymorphism containing the NTB or ‘twist-bend’ phase (2014)

In this article we report on the liquid crystal phases and properties of the bimesogen 4-((11-((4'-fluoro-[1,1'-biphenyl]-4-yl)oxy)undecyl)oxy)-2,3-difluoro-4'-(4-propylcyclohexyl)-1,1'-biphenyl. This material was shown to exhibit an Iso Liq-N-NTB-SmA phase sequence, thereby clearly indicating that the NTB phase possesses an ordering of the constituent molecules that is between that of a conventional nematic and the smectic A phase. This compound allows us to better understand the relationship between molecular structure and the NTB phase, and we conclude it is the gross topology that dictates the incidence of this fascinating phase and not molecular properties such as dipole moment and bend angle.
Regulation and Function of Phosphorylation on VP8, the Major Tegument Protein of Bovine Herpesvirus 1 (2015)

The progression of VP8 phosphorylation over time and its function in BoHV-1 replication have not been characterized. This study demonstrates that activation of S(16) initiates further phosphorylation at S(32) by US3. Additionally, VP8 is phosphorylated by CK2 at several residues, with T(107) having the highest level of phosphorylation. Evidence for a difference in the phosphorylation status of VP8 in host cells and mature virus is presented for the first time. Phosphorylation was found to be a critical modification, which enables VP8 to attract and to redistribute PML protein in the nucleus. This might promote viral replication through interference with a PML-mediated antiviral defense. This study provides new insights into the regulation of VP8 phosphorylation and suggests a novel, phosphorylation-dependent function for VP8 in the life cycle of BoHV-1, which is important in view of the fact that VP8 is essential for virus replication in vivo.
Accelerated Aging of Tires, Part III (2005)

Abstract The purpose of this research is to determine the conditions whereby a new tire can be artificially aged in an accelerated manner, in order to duplicate the actual mechanism of chemical aging observed in field-aged tires. The ultimate goal of the study is to age tires to a desired level, say equivalent to 4 years old, and then test the tires in durability, high speed, and performance tests. The previous paper described various oven aging methodologies and the data analysis techniques used. This paper will build on the previously described data analysis techniques developed for elongation at break measurements and apply them to swelling ratio data and peel strength data. By utilizing the method initially developed by Gillen and modified by this laboratory for use with tires, it has been shown that the skim rubber of tires oxidatively ages at oven temperatures between 40 °C and 70 °C when mounted and inflated with either air or a blend of 50/50 N 2 /O 2 . The methodology has been successfully extended from elongation at break data to peel strength and swelling ratio data. The calculation of the Arrhenius activation energy for diffusion of oxygen through new and aged rubber was also determined. The effect of aging on permeability is to reduce the permeability of oxygen and increase the activation energy. These results have important implications when attempting to model the diffusional aging characteristics of inflated tires. The effect of changing the partial pressure of oxygen and its concomitant effect on the acceleration of aging was also investigated. The results indicate that by doubling the partial pressure of oxygen, the rate of oxidation is increased by approximately 1.5 times. This result is entirely consistent with the theory of diffusion limited oxidation.
Low dose rate space estimates for integrated circuits using real time measurements and linear system theory (1992)

From real-time response measurements of the supply currents for some CMOS integrated circuits at various constant dose rates, it was possible to extrapolate time to failure back to spacelike low dose rates. Linear systems theory and convolution combine to give a quantitative way of characterizing the response of a device to radiation at various dose rates. No detailed knowledge of the damage mechanisms is required. Real-time responses during and after radiation provide the necessary information for each dose rate measurement. Reasonably successful extrapolations from accurate generalized response functions can be made to lower dose rates. Proton measurements of the low dose rate response for the ADSP2100 digital signal processor and a SEEQ EEPROM indicate increased survivability.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Scalable Wavelength-Converting Crossbar Switches (2004)

We report scalable low-power wavelength-converting crossbar switches that monolithically integrate two-dimensional compact arrays of surface-normal photodiodes with quantum-well waveguide modulators. We demonstrate proof-of-concept, electrically reconfigurable 2/spl times/2 crossbars that perform unconstrained wavelength conversion across 35 nm in the C-band (1530-1565 nm), using only <4.3-mW absorbed input optical power, and with 10-dB extinction ratio at 1.25 Gb/s. Such wavelength-converting crossbars provide complete flexibility to selectively convert any of the input wavelengths to any of the output wavelengths at high data bit rates in telecommunication, with the input and output wavelengths being arbitrarily chosen within the C-band.
Role of Microstructure in Oxygen Induced Photodegradation of Methylammonium Lead Triiodide Perovskite Films (2017)

Abstract This paper investigates the impact of microstructure on the degradation rate of methylammonium lead triiodide (MAPbI 3 ) perovskite films upon exposure to light and oxygen. By comparing the oxygen induced degradation of perovskite films of different microstructure–fabricated using either a lead acetate trihydrate precursor or a solvent engineering technique–it is demonstrated that films with larger and more uniform grains and better electronic quality show a significantly reduced degradation compared to films with smaller, more irregular grains. The effect of degradation on the optical, compositional, and microstructural properties of the perovskite layers is characterized and it is demonstrated that oxygen induced degradation is initiated at the layer surface and grain boundaries. It is found that under illumination, irreversible degradation can occur at oxygen levels as low as 1%, suggesting that degradation can commence already during the device fabrication stage. Finally, this work establishes that improved thin‐film microstructure, with large uniform grains and a low density of defects, is a prerequisite for enhanced stability necessary in order to make MAPbI 3 a promising long lived and low cost alternative for future photovoltaic applications.
Securing Processors Against Insider Attacks: A Circuit-Microarchitecture Co-Design Approach (2013)

Modification to traditional SoC design flow can enable effective protection against maliciously inserted rogue functionality during design and fabrication. This article presents a joint circuit-architecture-level design approach that helps in preventing or detecting Trojan attacks.
Evaluation of the Sparton Tight-Tolerance AXBT (1993)

Forty-six near-simultaneous pairs of conductivity-temperature-depth (CTD) and Sparton “tight tolerance” air expendable bathythermograph (AXBT) temperature profiles were obtained in summer 1991 from a location in the Sargasso Sea. The data were analyzed to assess the temperature and depth accuracies of the Sparton AXBTs. The tight-tolerance criterion was not achieved using the manufacturer's equations but may have been achieved using customized equations computed from the CTD data. The temperature data from the customized equations had a one standard deviation error of 0.13°C. A customized elapsed fall time-to-depth conversion equation was found to be z = 1.620t−2.2384 × 10−4 t2 + 1.291 × 10−7 t3, with z the depth in meters and t the elapsed fall time after probe release in seconds. The standard deviation of the depth error was about 5 m; a rule of thumb for estimating maximum bounds on the depth error below 100 m could be expressed as +12% of depth or +10 m, whichever is greater. This equation gave greater depth accuracy than either the manufacturer's supplied equation or the navy standard equation.
Discovery of the Clinical Candidate MAK683: An EED-Directed, Allosteric, and Selective PRC2 Inhibitor for the Treatment of Advanced Malignancies (2022)

Polycomb Repressive Complex 2 (PRC2) plays an important role in transcriptional regulation during animal development and in cell differentiation, and alteration of PRC2 activity has been associated with cancer. On a molecular level, PRC2 catalyzes methylation of histone H3 lysine 27 (H3K27), resulting in mono-, di-, or trimethylated forms of H3K27, of which the trimethylated form H3K27me3 leads to transcriptional repression of polycomb target genes. Previously, we have shown that binding of the low-molecular-weight compound EED226 to the H3K27me3 binding pocket of the regulatory subunit EED can effectively inhibit PRC2 activity in cells and reduce tumor growth in mouse xenograft models. Here, we report the stepwise optimization of the tool compound EED226 toward the potent and selective EED inhibitor MAK683 (compound <b>22</b>) and its subsequent preclinical characterization. Based on a balanced PK/PD profile, efficacy, and mitigated risk of forming reactive metabolites, MAK683 has been selected for clinical development.
DISPLACED SENSOR ARRAY FOR IMPROVED SIGNAL DETECTION UNDER GRAZING INCIDENCE CONDITIONS (2007)

This paper proposes a displaced sensor array (DSA) configuration for estimating the angles of arrival of narrowband sources arriving at grazing incidence directions. Unlike the conventional uniform linear array (ULA) where all the array elements are aligned along one axis, the proposed DSA configuration comprises two displaced ULAs aligned on two parallel axes in the vertical plane. The steering vectors of the two parallel arrays differ from each other by only two multiplicative phase terms that represent the space factors due to the vertical separation and horizontal displacement of the two arrays. This makes the computational load of using MUSIC algorithm with the proposed DSA configuration identical to that of ULA yet the accuracy is much higher especially for cases involving narrowband sources arriving at grazing incidence angles. Simulation results obtained show that the proposed DSA configuration outperforms the conventional ULA in terms numerical accuracy and angular resolution.
Preliminary Development and Validation of an Atlas-Based Finite Element Brain Model. (2015)

Traumatic brain injury (TBI) is a leading cause of disability and injury-related death, accounting for nearly one third of all injury-related deaths. To prevent and understand these types of injuries, finite element models can be employed. In this study, an anatomically accurate finite element model was developed from the International Consortium for Brain Mapping (ICBM) using a voxel-based mesh generation approach. The aim of this study was to compare relative brain displacement of the atlas-based brain model (ABM) to cadaveric data. In these experiments, neutral density targets (NDTs) were implanted in the brain and their relative motion with respect to the skull was recorded. The same boundary conditions were applied to ABM and the relative displacements of the nodes nearest to the physical location of each NDT were computed. Initial simulation and validation show good agreement with experimental data. The data obtained in this study and further development of this model will help us understand the biomechanics of head injury as well as provide a tool to predict and prevent brain injury.
Characterization of Two Types of Silanol Groups on Fused-Silica Surfaces Using Evanescent-Wave Cavity Ring-Down Spectroscopy (2007)

Evanescent-wave cavity ring-down spectroscopy has been applied to a planar fused-silica surface covered with crystal violet (CV+) cations to characterize the silanol groups indirectly. A radiation-polarization dependence of the adsorption isotherm of CV+ at the CH3CN/silica interface is measured and fit to a two-site Langmuir equation to determine the relative populations of two different types of isolated silanol groups. CV+ binding at type I sites yields a free energy of adsorption of -29.9 +/- 0.2 kJ/mol and a saturation surface density of (7.4 +/- 0.5) x 10(12) cm(-2), whereas the values of -17.9 +/- 0.4 kJ/mol and (3.1 +/- 0.4) x 10(13) cm(-2) are obtained for the type II sites. The CV+ cations, each with a planar area of approximately 120 A2, seem to be aligned randomly while lying over the SiO- type I sites, thereby suggesting that this type of site may be surrounded by a large empty surface area (>480 A2). In contrast, the CV+ cations on a type II sites are restricted with an average angle of approximately 40 degrees tilted off the surface normal, suggesting that the CV+ cations on these sites are grouped closely together. The average tilt angle increases with increasing concentration of crystal violet so that CV+ cations may be separated from each other to minimize the repulsion of nearby CV+ and SiOH sites.
Separation of vitamin E (tocopherol, tocotrienol, and tocomonoenol) in palm oil (2004)

Previous reports showed that vitamin E in palm oil consists of various isomers of tocopherols and tocotrienols [alpha-tocopherol (alpha-T), alpha-tocotrienol, gamma-tocopherol, gamma-tocotrienol, and delta-tocotrienol), and this is normally analyzed using silica column HPLC with fluorescence detection. In this study, an HPLC-fluorescence method using a C30 silica stationary phase was developed to separate and analyze the vitamin E isomers present in palm oil. In addition, an alpha-tocomonoenol (alpha-T1) isomer was quantified and characterized by MS and NMR. (alpha-T1 constitutes about 3-4% (40+/-5 ppm) of vitamin E in crude palm oil (CPO) and is found in the phytonutrient concentrate (350+/-10 ppm) from palm oil, whereas its concentration in palm fiber oil (PFO) is about 11% (430+/-6 ppm). The relative content of each individual vitamin E isomer before and after interesterification/transesterification of CPO to CPO methyl esters, followed by vacuum distillation of CPO methyl esters to yield the residue, remained the same except for alpha-T and gamma-T3. Whereas alpha-T constitutes about 36% of the total vitamin E in CPO, it is present at a level of 10% in the phytonutrient concentrate. On the other hand, the composition of gamma-T3 increases from 31% in CPO to 60% in the phytonutrient concentrate. Vitamin is present at 1160+/-43 ppm, and its concentrations in PFO and the phytonutrient concentrate are 4,040+/-41 and 13,780+/-65 ppm, respectively. The separation and quantification of alpha-T1 in palm oil will lead to more in-depth knowledge of the occurrence of vitamin E in palm oil.
Molecular specificity of two commercial enzyme linked immunosorbent assays for human immunodeficiency virus antigens. (1991)

Only "fair" agreement has been shown between the Abbott and DuPont enzyme linked immunosorbent assays when used for the detection of human immunodeficiency virus (HIV) antigen in serum samples from asymptomatic HIV antibody positive homosexual men. To investigate the discrepancies between the two ELISA results, further experiments were performed. The rabbit detector antibody solutions of both tests were western blotted and showed that the DuPont test was specific for p24; the Abbott detector antibody had bands for p18, p41-43, gp120 as well as p24. By using dilutions of a known amount of HIV antigen, the Abbott test could detect 20 pg/ml p24; the DuPont test could detect 30 pg/ml p24. The DuPont test was also more sensitive than the Abbott test at detecting a synthetic 104mer peptide of p24. Within the 104mer sequence two regions (294-318, 334-348 amino acids) inhibited the binding of the DuPont detector antibody, but no blocking was observed with the Abbott antibody. Although the Abbott test was slightly more sensitive at detecting HIV protein than the DuPont test, the major difference between the tests was in the molecular specificity, in that the Abbott test detected proteins other than p24. This may not be important for detecting antigen in cell culture, but it may affect the detection of antigenaemia in patients' sera.
Simulating Uranium(VI) Diffusion in Sodium-Montmorillonite as a Function of Chemical Solution Conditions (2019)

International audience
Numerical Study on a Thermal Response of the Jet Vane System in a Rocket Nozzle (2004)

The analysis of the heat transfer characteristics on the surface of jet vane needs to know ablation mechanism in a rocket engine. In this study, the distribution of heat transfer coefficient on the vane surface is calculated by means of the thermal boundary layer analysis for two dimension jet vane model. This method is only needed to get the free stream information around a vane and not required many fine meshes with large calculation time. User defined functions are inserted into a numerical code (FLUENT) for calculation of thermal boundary conditions. Some properties such as density, Mach number and heat transfer coefficient are plotted along the vane surface for different attack angles and several time steps. Also, the temperature contour inside vane is represented during the operation time. Finally, the heat transfer coefficient calculated by boundary layer integral method compares to that of using FLUENT solver itself.
The Structural Gene for a T7 Endonuclease Essential for Phage DNA Synthesis (1970)

Infection of Escherichia coli with bacteriophage T7 results in the appearance of an endonuclease activity capable of hydrolyzing both double-and single-stranded DNA. Treatment with chloramphenicol prevents the induction of the endonuclease. Amber mutants of phage T7 defective in gene 3 are unable to produce the enzyme after infection of the nonpermissive host, and mutants that produce a heat-labile endonuclease were found, indicating that this gene is the structural gene for the enzyme. Gene 3 mutants synthesize only a limited amount of DNA. In addition, they are defective in carrying out the degradation of host DNA, suggesting that the gene 3 endonuclease is involved in this function.
Local Gray Component Replacement Using Image Analysis (2011)

In printing, ink is one of the most important cost factors, which accounts for approximately 25-30% of the cost per page; therefore, reducing ink consumption is of great interest. The traditional approach to this problem is to modify the ICC profile to increase the use of black ink instead of the combination of cyan, yellow, and magenta; this approach is known as the gray component replacement (GCR). While this strategy reduces ink consumption, it often results in visually grainy images in otherwise smooth regions, and is therefore of limited use or even unacceptable for many applications, such as photoprinting.In this work, we propose a novel, context sensitive and spatially variant GCR method, which yields ink consumption figures that are similar to an aggressive GCR, but in contrast produces perfectly acceptable print quality results. Our approach is based on the visual masking effect: image areas with high activity level, such as high contrast textures, mask the increased graininess, and other inaccuracies such as (small) color shifts. Therefore, we propose to dynamically vary the amount of gray replacement across the image as a function of the local &#x201C;activity&#x201D; of the image. In lighter, smoother regions, less aggressive GCR is applied, and the image quality is preserved, while in more active regions where the change is not visible, more aggressive GCR is applied.The performance of the proposed method is tested on images randomly chosen from several photo collections. The initial results indicate about 15% reduction in overall ink consumption with perfectly acceptable print quality.
Hydrothermally Grown In-doped ZnO Nanorods on p-GaN Films for Color-tunable Heterojunction Light-emitting-diodes (2015)

The incorporation of doping elements in ZnO nanostructures plays an important role in adjusting the optical and electrical properties in optoelectronic devices. In the present study, we fabricated 1-D ZnO nanorods (NRs) doped with different In contents (0% ~ 5%) on p-GaN films using a facile hydrothermal method, and investigated the effect of the In doping on the morphology and electronic structure of the NRs and the electrical and optical performances of the n-ZnO NRs/p-GaN heterojunction light emitting diodes (LEDs). As the In content increased, the size (diameter and length) of the NRs increased, and the electrical performance of the LEDs improved. From the electroluminescence (EL) spectra, it was found that the broad green-yellow-orange emission band significantly increased with increasing In content due to the increased defect states (oxygen vacancies) in the ZnO NRs, and consequently, the superposition of the emission bands centered at 415 nm and 570 nm led to the generation of white-light. These results suggest that In doping is an effective way to tailor the morphology and the optical, electronic, and electrical properties of ZnO NRs, as well as the EL emission property of heterojunction LEDs.