gebhart/patrepeval huggingface dataset:
Crystallization and preliminary X-ray crystallographic studies of a psychrophilic subtilisin-like protease Apa1 from Antarctic<i>Pseudoalteromonas</i>sp. strain AS-11 (2005)

The psychrophilic alkaline serine protease Apa1 secreted by the Antarctic psychrotroph Pseudoalteromonas sp. strain AS-11 consists of a subtilisin-like region (293 residues) and an additional insert region (148 residues) that does not show a sequence homology to any proteins in the RCSB Protein Data Bank. Apa1 inhibited with phenylmethanesulfonyl fluoride has been crystallized and X-ray diffraction data have been collected to 1.78 A resolution. The crystals belong to space group C2, with unit-cell parameters a = 122.94, b = 138.48, c = 64.77 A, alpha = gamma = 90, beta = 97.5 degrees. A molecular-replacement solution has been found using the structure of the mesophilic counterpart subtilisin DY with 38% sequence identity to the catalytic domain of Apa1 as a search model. This is the first crystallographic study of a cold-adapted subtilisin-like protease.
Functional Replacement of a Domain in the Rubella Virus P150 Replicase Protein by the Virus Capsid Protein (2009)

The rubella virus (RUBV) capsid (C) protein rescues mutants with a lethal deletion between two in-frame NotI sites in the P150 replicase gene, a deletion encompassing nucleotides 1685 to 2192 of the RUBV genome and amino acids (aa) 548 to 717 of P150 (which has a total length of 1,301 aa). The complete domain rescuable by the C protein was mapped to aa 497 to 803 of P150. Introduction of aa 1 to 277 of the C protein (lacking the C-terminal E2 signal sequence) between the NotI sites in the P150 gene in a replicon construct yielded a viable construct that synthesized viral RNA with wild-type kinetics, indicating that C and this region of P150 share a common function. Further genetic analysis revealed that an arginine-rich motif between aa 60 and 68 of the C protein was necessary for the rescue of DeltaNotI deletion mutants and substituted for an arginine-rich motif between aa 731 and 735 of the P150 protein when the C protein was introduced into P150. Possible common functions shared by these arginine-rich motifs include RNA binding and interaction with cell proteins.
Eine neue Synthese von 2‐Acyloxyimino‐cumaranonen (1973)

Abstract Bei der Umsetzung von Acetanhydrid mit o‐Hydroxy‐β‐nitro‐acetophenon entsteht nicht 2‐Methyl‐3‐nitro‐chromon, sondern 2‐Acetyloxyimino‐cumaranon (2‐Acetyloxyimino‐3‐oxo‐2,3‐dihydro‐benzo[b]furan). Andere Säureanhydride gehen entsprechende Umsetzungen ein; 2‐Benzoyloxyimino‐, 2‐Veratroyloxyimino‐ und 2‐(3,4‐Dibenzyloxy‐benzoyloxyimino)‐cumaranon wurden synthetisiert. Ihre Abbaureaktionen und massenspektrometrischen Fragmentierungen werden diskutiert.
Millimeter-wave phase-modulated backscatter transponder for FMCW radar applications (2011)

A millimeter-wave phase-modulated backscatter transponder in the E-band for readout with a frequency-modulated continuous-wave (FMCW) system is presented in this paper. Backscatter transponders have the advantage that, while no complete radio-frequency front end hardware, including signal generation, is required, they offer the capability to establish a one-way communication between the transponder and an interrogator. As we used an FMCW radar system as an interrogator, it is possible to extract range information as well as the modulated information from the transponder. In this paper we present the system basics as well as a fabricated prototype from which we obtained measurement results.
An Improved Polynomial Neural Network Classifier Using Real-Coded Genetic Algorithm (2015)

In this paper, a novel approach is proposed to improve the classification performance of a polynomial neural network (PNN). In this approach, the partial descriptions (PDs) are generated at the first layer based on all possible combinations of two features of the training input patterns of a dataset. The set of PDs from the first layer, the set of all input features, and a bias constitute the chromosome of the real-coded genetic algorithm (RCGA). A system of equations is solved to determine the values of the real coefficients of each chromosome of the RCGA for the training dataset with the mean classification accuracy (CA) as the fitness value of each chromosome. To adjust these values for unknown testing patterns, the RCGA is iterated in the usual manner using simple selection, crossover, mutation, and elitist selection. The method is tested extensively with the University of California, Irvine benchmark datasets by utilizing tenfold cross validation of each dataset, and the performance is compared with various well-known state-of-the-art techniques. The results obtained from the proposed method in terms of CA are superior and outperform other known methods on various datasets.
Control over Nanostructures and Associated Mesomorphic Properties of Doped Self‐Assembled Triarylamine Liquid Crystals (2014)

We have synthesized a series of triarylamine-cored molecules equipped with an adjacent amide moiety and dendritic peripheral tails in a variety of modes. We show by (1) H NMR and UV/Vis spectroscopy that their supramolecular self-assembly can be promoted in solution upon light stimulation and radical initiation. In addition, we have probed their molecular arrangements and mesomorphic properties in the bulk by integrated studies on their film state by using differential scanning calorimetry (DSC), variable-temperature polarizing optical microscopy (VT-POM), variable-temperature X-ray diffraction (VT-XRD), and atomic force microscopy (AFM). Differences in the number and the disposition of the peripheral tails significantly affect their mesomorphic properties associated with their lamellar- or columnar-packed nanostructures, which are based on segregated stacks of the triphenylamine cores and the lipophilic/lipophobic periphery. Such structural tuning is of interest for implementation of these soft self-assemblies as electroactive materials from solution to mesophases.
Effect of Surfactants and Polyethylene Glycol on the Activity and Stability of a Lipase from Oilseeds of <i>Pachira aquatica</i> (2008)

Abstract Lipases from oilseeds have a great potential for commercial exploration as industrial enzymes. Lipases are used mixed with surfactants in cleaning and other formulated products, and accordingly, both components must be compatible with each other. This work presents the results of the effects of anionic, cationic and nonionic surfactants, polyethylene glycol and urea on the activity and stability of a lipase extracted of oilseeds from Pachira aquatica . The enzyme was purified and the spectrophotometric assays were done using p‐ nitrophenyl acetate ( p‐ NPA) as substrate pH 7.5 and 25 °C. The activity was significantly enhanced by the cationic surfactant CTAB. Bile salts increased the lipase activity in the tested concentration range, whereas anionic and nonionic surfactants showed an inhibitory effect. Aqueous solutions of PEG activated the lipase and maximum activation (161%) occurred in PEG 12,000. This effect on lipase that can be due to exposition of some hydrophobic residues located in the vicinity of the active site or aggregation.
Structured Korean Font Generator Using METAFONT (2016)

한글의 자소들은 몇 가지의 획으로 구성되어 있고, 완전한 글자들은 자소들의 조합으로 구성되어 있다. 획과 자소들을 조합하는 과정에서 그 구성들의 크기나 위치가 변화할 수 있으므로 폰트를 제작하는데 많은 노력이 필요하다. 이와 달리 METAFONT는 매개변수 값을 변경하면서 획과 자소의 크기와 위치를 쉽게 변환할 수 있는 시스템을 제공하여 폰트 제작 과정에 효율성을 높일 수 있다. 본 논문은 METAFONT를 기반으로 사용자가 매개변수를 수정하여 다양한 폰트를 자동으로 생성할 수 있는 구조적 한글 폰트 생성기를 제안한다. 본 논문에서 제안한 한글 폰트 생성기는 폰트 임베딩 분야와 폰트 편집기 분야에 적용할 수 있다.
Imaging electronic structure of carbon nanotubes by voltage-contrast scanning electron microscopy (2008)

We introduce voltage-contrast scanning electron microscopy (VC-SEM) for visual characterization of the electronic properties of single-walled carbon nanotubes. VC-SEM involves tuning the electronic band structure and imaging the potential profi le along the length of the nanotube. The resultant secondary electron contrast allows to distinguish between metallic and semiconducting carbon nanotubes and to follow the switching of semiconducting nanotube devices, as confi rmed by in situ electrical transport measurements. We demonstrate that high-density arrays of individual nanotube devices can be rapidly and simultaneously characterized. A leakage current model in combination with fi nite element simulations of the device electrostatics is presented in order to explain the observed contrast evolution of the nanotube and surface electrodes. This work serves to fill a void in electronic characterization of molecular device architectures.
Signaling by hepatocyte growth factor in neurons is induced by pharmacological stimulation of synaptic activity (2007)

Activity-dependent signaling by growth factors is hypothesized to link synaptic activity to structural and functional modifications of neurons. The receptor tyrosine kinase Met and its ligand, hepatocyte growth factor (HGF), are clustered at excitatory synapses and may regulate aspects of excitatory synaptic function, as HGF increases expression of excitatory synaptic proteins, enhances their clustering at sites along dendrites, and increases current through the NMDA receptor. In this article, we test for secretion or activation of HGF and for activation of Met in response to pharmacological stimulation of synaptic activity. Stimulation of dissociated hippocampal neuron cultures with glutamate caused increased immunocytochemical staining against HGF on nonpermeabilized cells. Glutamate treatment also decreased the amount of pro HGF and increased the amount of the proteolytically-activated HGF in immunoblots of neuron culture lysates, and increased the levels of activated HGF in culture media. Stimulation of neuron cultures with glutamate or bicuculline induced autophosphorylation of Met on dendrites and the soma of neurons. Pretreatment of neurons with glutamate receptor inhibitors prior to glutamate treatment blocked autophosphorylation of Met. These results suggest that HGF can participate in activity-dependent signaling in neurons.
Antifibrinolytic drugs and perioperative hemostasis (1997)

Although excessive bleeding is widely recognized as a common complication of cardiac surgery, the recent success of antifibrinolytic drugs as prophylactic hemostatic agents has received little attention outside the surgical literature. The etiology of the coagulopathy following cardiac surgery is clearly multifactorial; however, the success of antifibrinolytic drugs as hemostatic agents suggests that fibrinolysis contributes to bleeding in this setting. Increasingly widespread administration of these drugs necessitates increased awareness of the risks and benefits posed by perioperative antifibrinolytic therapy. The objectives of this review are to understand the mechanisms of action of antifibrinolytic drugs in the context of the normal hemostatic response and to review evidence pertaining to the efficacy and safety of antifibrinolytic drugs as hemostatic agents during cardiac surgery.
Mixed Surfactant Template Method for Preparation of Nanometer Selenium (2009)

Selenium nanoparticles have been synthesized in an aqueous solution by using sodium dodecyl sulfate and polyvinyl alcohol as a soft template. The factors on synthesis, such as reaction time, concentration of reactants and ultrasonic irradiation were studied. The uniform stable selenium nanospheres were obstained in the conditions of 1.0 (mass fraction) sodium dodecyl sulfate, 1.0 (mass fraction) polyvinyl alcohol, n(Vc):n(H 2 SeO 3 )=7:1 and 7 minutes after the initiation of the reaction at room temperature. The average particle size of selenium is about 30 nm. The product was characterized by UV and TEM. Finally the applications of the red element nanometer selenium in anti‐older cosmetics are presented.
A Class of Numerical Methods for the Computation of Pythagorean Sums (1983)

Moler and Morrison have described an iterative algorithm for the computation of the Pythagorean sum (a <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> + b <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">½</sup> of two real numbers a and b. This algorithm is immune to unwarranted floating-point overflows, has a cubic rate of convergence, and is easily transportable. This paper, which shows that the algorithm is essentially Halley's method applied to the computation of square roots, provides a generalization to any order of convergence. Formulas of orders 2 through 9 are illustrated with numerical examples. The generalization keeps the number of floating-point divisions constant and should be particularly useful for computation in high-precision floating-point arithmetic.
Unique interpretation of Talbot Bands and Fourier domain white light interferometry (2007)

A theoretical model is developed to interpret the output of the diffraction grating spectrometer used to analyze the channelled spectrum produced by a low coherence interferometer set-up. This model leads to an unique interpretation which covers both cases (i) of Talbot bands and (ii) of a Michelson interferometer used in most spectral interferometry set-ups for sensing as well as for Fourier domain optical coherence tomography (FDOCT). Explanation of Talbot bands visibility as well as the decay of sensitivity with depth, characteristic for FDOCT, is explained by considering the extension of the two wavetrains diffracted by the diffraction grating in the spectrometer.
Ethylene is an endogenous stimulator of cell division in the cambial meristem of <i>Populus</i> (2009)

The plant hormone ethylene is an important signal in plant growth responses to environmental cues. In vegetative growth, ethylene is generally considered as a regulator of cell expansion, but a role in the control of meristem growth has also been suggested based on pharmacological experiments and ethylene-overproducing mutants. In this study, we used transgenic ethylene-insensitive and ethylene-overproducing hybrid aspen (Populus tremula x tremuloides) in combination with experiments using an ethylene perception inhibitor [1-methylcyclopropene (1-MCP)] to demonstrate that endogenous ethylene produced in response to leaning stimulates cell division in the cambial meristem. This ethylene-controlled growth gives rise to the eccentricity of Populus stems that is formed in association with tension wood.
Long‐ and short‐term responses of leaf carbohydrate levels and photosynthesis to decreased sink demand in soybean (1996)

ABSTRACT Axillary buds and the apical portion of shoots of soybean [ Glycine max (L.) Merr. cultivar Turchina] plants were trimmed to investigate long‐term regulation of photosynthesis by sink demand at ambient CO 2 and 22 °C. Also, in intact and trimmed shoots, the CO 2 level was increased to 660 μmol mol −1 and temperature was lowered to 5°C to examine the superimposed short‐term responses of photosynthesis to low sink demand. Under growth conditions, trimming the shoots increased leaf photosynthesis and the levels of sucrose, glucose‐6‐phosphate (G6P) and 3‐phosphoglycerate (PGA), as well as the G6P/fructose‐6‐phosphate (F6P) and sucrose/starch ratios, while it decreased the level of starch and the triose‐phosphate (glyceraldehyde 3‐phosphate and dihydroxyacetone phosphate, TP)/PGA ratio. Photosynthesis enhancement was accompanied by increased chlorophyll contents and ribulose‐l,5‐bisphosphate carboxylase oxygenase (Rubisco) activity. Sink removal consistently increased photosynthesis measured under a variety of conditions (growth CO 2 or a short‐term change to 660 μmol mol ‐1 CO 2 ; growth temperature or a short‐term change to 5 °C), except when low temperature was combined with ambient CO 2 ; the increase in photosynthesis was higher under short‐term elevated CO 2 than at ambient CO 2 . In contrast with its effect at ambient CO 2 , shoot trimming increased the levels of TP and ribulose‐1,5‐bisphosphate (RuBP) and the TP/PGA ratio under high‐CO 2 conditions.
Open fixed dose trial of fluoxetine in the treatment of obsessive compulsive disorder (1990)

Abstract Twelve non‐depressed DSM‐III obsessive compulsive disorder (OCD) patients were treated with fluoxetine in a 12 week open fixed dose study. After a 2 week washout period, patients were treated with 20 mg/day of fluoxetine for 1 week. The dosage was then raised to 40 mg/day for the remainder of the study. The Yale‐Brown Obsessive Compulsive Scale (Y‐BOCS) score (mean ± SD) decreased from 25.8 ± 4.5 to 15.4 ± 7.0 ( P < 0.01) and the Symptom Check List‐90‐Obsessive Compulsive Subscale (SCL‐90‐OC) score (mean ± SD) also showed a decrease from 2.4 ± 0.8 to 1.3 ± 0.9 ( P < 0.005). The results suggest that fluoxetine is effective in non‐depressed OCD patients. Our results also show that a 40 mg/day dosage is effective in contrast to previous studies that used 80 mg/day. Our finding of a significant treatment reduction in the SCL‐90‐OC is also in contrast to a previous OCD study in which the SCL‐58‐OC was not significantly reduced.
Characterization of a Protease-resistant Domain of the Cytosolic Portion of Sarcoplasmic Reticulum Ca2+-ATPase (1998)

Treatment of rabbit sarcoplasmic reticulum Ca 2 -ATPase with a variety of proteases, including elastase, proteinase K, and endoproteinases Asp-N and Glu-C, results in accumulation of soluble fragments starting close to the ATPase phosphorylation site Asp 351 and ending in the Lys 605 -Arg 615 region, well before the conserved sequences generally described as constituting the "hinge" region of this P-type ATPase (residues 670 -760). These fragments, designated as p29/30, presumably originate from a relatively compact domain of the cytoplasmic head of the ATPase. They retain two structural characteristics of intact Ca 2 -ATPase as follows: high sensitivity of peptidic bond Arg 505 -Ala 506 to trypsin cleavage, and high reactivity of lysine residue Lys 515 toward the fluorescent label fluorescein 5-isothiocyanate. Regarding functional properties, these fragments retain the ability to bind nucleotides, although with reduced affinity compared with intact Ca 2 -ATPase. The fragments also bind Nd 3 ions, leaving open the possibility that these fragments could contain the metal-binding site(s) responsible for the inhibitory effect of lanthanide ions on ATPase activity. The p29/30 soluble domain, like similar proteolytic fragments that can be obtained from other P-type ATPases, may be useful for obtaining threedimensional structural information on the cytosolic portion of these ATPases, with or without bound nucleotides. From our findings we infer that a real hinge region with conformational flexibility is located at the C-terminal boundary of p29/30 (rather than in the conserved region of residues 670 -760); we also propose that the ATP-binding cleft is mainly located within the p29/30 domain, with the phosphorylation site strategically located at the N-terminal border of this domain.
The exon quantification pipeline (EQP): a comprehensive approach to the quantification of gene, exon and junction expression from RNA-seq data (2016)

The quantification of transcriptomic features is the basis of the analysis of RNA-seq data. We present an integrated alignment workflow and a simple counting-based approach to derive estimates for gene, exon and exon-exon junction expression. In contrast to previous counting-based approaches, EQP takes into account only reads whose alignment pattern agrees with the splicing pattern of the features of interest. This leads to improved gene expression estimates as well as to the generation of exon counts that allow disambiguating reads between overlapping exons. Unlike other methods that quantify skipped introns, EQP offers a novel way to compute junction counts based on the agreement of the read alignments with the exons on both sides of the junction, thus providing a uniformly derived set of counts. We evaluated the performance of EQP on both simulated and real Illumina RNA-seq data and compared it with other quantification tools. Our results suggest that EQP provides superior gene expression estimates and we illustrate the advantages of EQP's exon and junction counts. The provision of uniformly derived high-quality counts makes EQP an ideal quantification tool for differential expression and differential splicing studies. EQP is freely available for download at https://github.com/Novartis/EQP-cluster.
ChemInform Abstract: Studies on Fluorine‐Containing Heterocyclic Compounds. Part 3. Reactions of 3,5‐Dinitro‐2‐chlorobenzotrifluoride and 3,5‐Dinitro‐4‐chlorobenzotrifluoride with Sulfur‐ and Nitrogen‐Containing Nucleophiles. (1988)

Abstract The chlorodinitrobenzotrifluorides (I) and (IV) mentioned in the title react with methyl thioglycolate (II) and triethylamine at room temperature, forming the benzothiazole N‐oxides (III) or (V).
A 12-bit 50-MS/s 3.3-mW SAR ADC with background digital calibration (2012)

This paper describes a background digital calibration technique based on bitwise correlation (BWC) to correct the capacitive digital-to-analog converter (DAC) mismatch error in successive-approximation-register (SAR) analog-to-digital converters (ADC's). Aided by a single-bit pseudorandom noise (PN) injected to the ADC input, the calibration engine extracts all bit weights simultaneously to facilitate a digital-domain correction. The analog overhead associated with this technique is negligible and the conversion speed is fully retained (in contrast to [1] in which the ADC throughput is halved). A prototype 12bit 50-MS/s SAR ADC fabricated in 90-nm CMOS measured a 66.5-dB peak SNDR and an 86.0-dB peak SFDR with calibration, while occupying 0.046 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and dissipating 3.3 mW from a 1.2-V supply. The calibration logic is estimated to occupy 0.072 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> with a power consumption of 1.4 mW in the same process.
NiAl powder alloys: I. Production of NiAl powders (2011)

The influence of five methods of production of Ni50Al50 powder alloys on the processes occurring during reactive alloy formation of nickel monoaluminide during heating is considered. It is shown that, when powder mixtures obtained by agitation in ball mills and cladded composite powders with a low level of internal stresses are used, it is possible to produce a material with a nearly equilibrium phase composition in the course of reactive sintering due to an exothermic effect with the participation of a liquid phase (aluminum melt) in the reaction. The sintered material is porous and has an island structure. Mechanical alloying in a high-energy ball mill (attritor) results in the formation of layered Ni/Al granules with a developed interface and a high level of internal stresses and defects, which makes it possible to decrease the temperatures of initiation of reactive interaction by ∼300°C. This interaction develops in the solid phase according to a slow diffusive mechanism leading to the formation of intermediate nickel aluminides and hindering the achievement of equilibrium phase composition. The microingot granules (∼80 wt % particles 100–400 μm in size) produced by melt spraying by gases (N, Ar) has the composition of the melt, but grain boundaries are depleted of aluminum in comparison with the volume. The NiAl powders (∼90 wt % particles <40 μm in size) produced by combined hydride-calcium reduction are characterized by a highly homogeneous nickel and aluminum distribution, and their composition is close to equilibrium. These two types of powders are selected as the initial material for investigating the compacting and production of NiAl-based alloys.