gebhart/patrepeval huggingface dataset:
Solution structure of a small protein containing a fluorinated side chain in the core (2006)

We report the first high-resolution structure for a protein containing a fluorinated side chain. Recently we carried out a systematic evaluation of phenylalanine to pentafluorophenylalanine (Phe --> F(5)-Phe) mutants for the 35-residue chicken villin headpiece subdomain (c-VHP), the hydrophobic core of which features a cluster of three Phe side chains (residues 6, 10, and 17). Phe --> F(5)-Phe mutations are interesting because aryl-perfluoroaryl interactions of optimal geometry are intrinsically more favorable than either aryl-aryl or perfluoroaryl-perfluoroaryl interactions, and because perfluoroaryl units are more hydrophobic than are analogous aryl units. Only one mutation, Phe10 --> F(5)-Phe, was found to provide enhanced tertiary structural stability relative to the native core (by approximately 1 kcal/mol, according to guanidinium chloride denaturation studies). The NMR structure of this mutant, described here, reveals very little variation in backbone conformation or side chain packing relative to the wild type. Thus, although Phe --> F(5)-Phe mutations offer the possibility of greater tertiary structural stability from side chain-side chain attraction and/or side chain desolvation, the constraints associated with the native c-VHP fold apparently prevent the modified polypeptide from taking advantage of this possibility. Our findings are important because they complement several studies that have shown that fluorination of saturated side chain carbon atoms can provide enhanced conformational stability.
Composition, geometry and polarization influences on spectroscopic properties of Yb-doped LLnB (Ln= Y, Gd) monoclinic crystals (2014)

Characterizations of linear spectroscopic properties in polarized light have been performed for the highly-concentrated Yb-doped borate family Li6Ln(BO<sub>3</sub>)<sub>3</sub> (with Ln: Gd, Y, and labeled Yb:LLnB), in order to start to evaluate their potentiality for high-power laser applications. Modifications in spectral distributions and intensities are reported with respect to crystal orientation and polarization. Chemical composition and crystal shaping are discussed, pointing strong possible dependence with experimental conditions, which has to be considered so as to take sufficient precautions regarding the prediction of potential laser properties in such anisotropic laser crystals.
T cell activation induces proteasomal degradation of argonaute and rapid remodeling of the microRNA repertoire - eScholarship (2013)

Activation induces extensive changes in the gene expression program of naive CD4+ T cells, promoting their differentiation into helper T cells that coordinate immune responses. MicroRNAs (miRNAs) play a critical role in this process, and miRNA expression a
Cross-Slotted Waveguide Array With Dual Circularly Polarized Radiation at W-Band (2021)

This article discusses the design of a cross-slotted waveguide array structure to be adopted for W-band communication between 84 and 86 GHz. Each array waveguide element contains 16 cross-slots along the broad wall to enable circularly polarized radiation behavior with a gain reaching up to 14 dBi and a cross-polarization isolation of more than 20 dB in the elevation plane. The design of the cross-slots is implemented with bent arms in order to accommodate them at an offset position from the waveguide narrow wall. Such position ensures the radiation of a circularly polarized wave. A waveguide-based feeding network with serpentine-shaped transitions is implemented to feed the eight-element cross-slotted array topology. The design of the feeding network ensures an equal power split and in-phase distribution between the eight elements with a phase deviation that does not exceed 20°. The overall cross-slotted waveguide array is prototyped as a proof of concept. The measured results show a maximum gain of 24.5 dBi for both polarization schemes. The measured half power beamwidth (HPBW) is 8° in the elevation plane and 12° in the azimuthal plane. The measured cross-polarization between the two circularly polarized schemes at both ports reaches a level of more than 26 dB. The comparison between the simulation and measurement results proves the validity of the proposed approach in achieving a high-gain dual circularly polarized structure for millimeter-wave communication.
Multi-task Deep Reinforcement Learning with Evolutionary Algorithm and Policy Gradients Method in 3D Control Tasks (2019)

In deep reinforcement learning, it is difficult to converge when the exploration is insufficient or a reward is sparse. Besides, on specific tasks, the amount of exploration may be limited. Therefore, it is considered effective to learn on source tasks that were previously for promoting learning on the target tasks. Existing researches have proposed pretraining methods for learning parameters that enable fast learning on multiple tasks. However, these methods are still limited by several problems, such as sparse reward, deviation of samples, dependence on initial parameters. In this research, we propose a pretraining method to train a model that can work well on variety of target tasks and solve the above problems with an evolutionary algorithm and policy gradients method. In this method, agents explore multiple environments with a diverse set of neural networks to train a general model with evolutionary algorithm and policy gradients method. In the experiments, we assume multiple 3D control source tasks. After the model training with our method on the source tasks, we show how effective the model is for the 3D control tasks of the target tasks.
Enhancement‐Mode AlGaN/GaN Vertical Trench Metal–Insulator–Semiconductor High‐Electron‐Mobility Transistors with a High Drain Current Fabricated Using the AlGaN Regrowth Technique (2019)

Herein, the first successful fabrication of enhancement (E)‐mode AlGaN/GaN vertical trench metal–insulator–semiconductor (MIS) high‐electron‐mobility transistors (HEMTs) using n + ‐GaN/p‐GaN/n − ‐GaN epistructures on free‐standing n + substrates is reported. A trench with smooth semipolar planes (sidewalls) with angles of 45° and 135° from the c ‐plane is formed by reactive ion etching. Using metalorganic vapor‐phase epitaxy, a uniform thickness of the AlGaN layer is regrown in the trench. Devices fabricated without Mg activation treatment for p‐GaN show depletion (D)‐mode operation. The operation mode is changed from D to E when Mg activation annealing temperature exceeds 700 °C. A high drain current ( I D ) ≥ 0.8 A mm −1 is obtained in the devices with a relatively low Mg concentration (≤1 × 10 18 cm −3 ), whereas a threshold voltage ( V TH ) as high as 22 V is obtained in the devices with a high Mg concentration (5 × 10 18 cm −3 ). The poorly controlled V TH with doped Mg concentration is discussed from the viewpoint of dehydrogenation of the p‐GaN layer.
Prevalence of Antibodies to Different Avian Paramyxoviruses in Commercial Poultry in the United States (2008)

Avian paramyxoviruses (APMVs) other than Newcastle disease virus have been isolated from feral avian species and have the potential to cause clinical disease. The objective of this study was to investigate the APMV antibody prevalence in commercial poultry settings. Sera from 100 commercial, layer-type and broiler-type (broiler-breeder and broiler) chicken flocks were analyzed on a random basis. Pooled serum samples from each flock were tested for the presence of antibodies to APMV-1, -2, -3, -4, -6, -7, -8, and -9 by hemagluttination inhibition (HI) test. Reactions with HI titers > or = 1:64 were shown by APMV-1 (71%), APMV-2 (15%), APMV-3 (35%), APMV-4 (26%), APMV-6 (45%), APMV-7 (27%), APMV-8 (31%), and APMV-9 (48%). In the presence of a high HI titer for APMV-1 (1024), we obtained positive HI titers for most of the other APMV subtypes, thus implicating that sensitive techniques need to be developed to detect the prevalence of these subtypes in commercial poultry.
The origins of pressure-induced phase transformations during the surface texturing of silicon using femtosecond laser irradiation (2012)

Surface texturing of silicon using femtosecond (fs) laser irradiation is an attractive method for enhancing light trapping, but the laser-induced damage that occurs in parallel with surface texturing can inhibit device performance. In this work, we investigate the light-material interaction during the texturing of silicon by directly correlating the formation of pressure-induced silicon polymorphs, fs-laser irradiation conditions, and the resulting morphology and microstructure using scanning electron microscopy, micro-Raman spectroscopy, and transmission electron microscopy. We show that raster scanning a pulsed laser beam with a Gaussian profile enhances the formation of crystalline pressure-induced silicon polymorphs by an order of magnitude compared with stationary pulsed fs-laser irradiation. Based on these observations, we identify resolidification-induced stresses as the mechanism responsible for driving sub-surface phase transformations during the surface texturing of silicon, the understanding of which is an important first step towards reducing laser-induced damage during the texturing of silicon with fs-laser irradiation.
Mammographic compression after breast conserving therapy: Controlling pressure instead of force (2014)

After BCT, women have hardly any choice in avoiding an annual follow-up mammogram. Model estimations show that a 10 kPa pressure-controlled protocol has the potential to reduce pain and severe pain particularly for these women. The results highly motivate conducting further research in larger subject groups.
Simple synthetic routes to ruthenium–indenylidene olefin metathesis catalysts (2011)

An efficient synthetic protocol involving reactions between the free carbene and [RuCl(2)(PPh(3))(2)(Ind)] followed by addition of pyridine leads to the isolation of olefin metathesis active [RuCl(2)(L)(Py)(Ind)] (L = SIMes and SIPr) complexes. This novel approach circumvents the use of costly tricyclohexylphosphine.
Enhancement of Distributed Temperature Sensitivity Using Al-Coated Fiber in OFDR (2018)

We present a distributed optical-fiber temperature sensor with enhanced sensitivity based on an Al-coated fiber using the Rayleigh backscattering spectra (RBS) shift in optical frequency-domain reflectometry (OFDR). The Al-coated sensing fiber with a higher thermal expansion coefficient compared to silica produces a strain-coupled shift in the RBS under an increase in temperature. This effect leads to an enhanced temperature sensitivity of the distributed measurement scheme. Our results revealed that the temperature sensitivity obtained using the Al-coated fiber in OFDR was ~56% higher relative to that of a single-mode fiber. Moreover, the minimum measurable temperature recorded was 1 &amp;deg;C with a spatial resolution of 5 cm.
Mineral Intake in Urban Pregnant Women from Base Diet, Fortified Foods, and Food Supplements: Focus on Calcium, Iron, and Zinc. (2016)

In the Chinese national nutrition surveys, fortified foods were not investigated separately from the base diet, and the contribution of fortified foods to micronutrients intake is not very clear. This study investigated the diet, including fortified foods and food supplements, of urban pregnant women and analyzed the intake of calcium, iron, and zinc to assess the corresponding contributions of fortified foods, food supplements, and the base diet. The results demonstrated that the base diet was the major source of calcium, iron, and zinc, and was recommended to be the first choice for micronutrients intake. Furthermore, consumption of fortified foods and food supplements offered effective approaches to improve the dietary intake of calcium, iron, and zinc in Chinese urban pregnant women.
Study of trans-2-tert-Butylcyclopropylcarbene by Laser Flash Photolysis and Chemical Analysis1 (1998)

Laser flash photolysis (LFP) of trans-2-tert-butylcyclopropyldiazirine (4) produces trans-2-tert-butylcyclopropylcarbene (5). Carbene 5 can be trapped with pyridine to form ylide 6. The rate of formation of ylide 6 was resolved and found to be linearly dependent on the concentration of pyridine. The lifetime of carbene 5 was determined to be 22 ns (pentane), 18 ns (acetonitrile and CF2ClCFCl2), 15 ns (cyclohexane), and 27 ns (cyclohexane-d12) at ambient temperature. The lifetime of carbene 5 in solution, at ambient temperature, is controlled substantially by reaction with solvent and only to a minor extent by rearrangement to cyclobutene 7. Photolysis of 4 (350 nm) in Freon-113 produces 3-tert-butylcyclobutene (7) along with products derived from attack of the carbene on solvent. Photolysis of 4 in the presence of trapping agents (tetramethylethylene, cyclopentene, propylamine, trifluoroethanol) produces adducts with little or no corresponding decrease in the yield of 7. The preferred interpretation is that cyclobutene 7 is formed by a rearrangement of the excited state of the diazirine (diazirinyl biradical), and not by a carbenic process at 0 °C and lower temperatures. This mechanism is supported by product analysis of a non-nitrogenous cyclopropylcarbene precursor. At ambient temperature, cyclobutene 7 is formed by both diazirine excited state (diazirinyl biradical) and carbene rearrangement.
IntegraGen SA (2005)

IntegraGen SA is at the stage of commercializing a series of innovative IntegraTests™ to position itself as a leader within the rapidly growing market of predictive medicine. By applying its proprietary gene-mapping technology GenomeHIP™ (Genome Hybrid Identity Profiling) in premier patient collections, IntegraGen has rapidly discovered novel genes and genetic markers associated with a variety of complex, multifactorial diseases to use in its IntegraTests - a new class of personalized medicine diagnostics. IntegraTests provide prediction, prevention, detailed diagnosis and tailored treatment of complex diseases. Depending on the disease and the applied set of genetic markers, these tests can calculate the personal risk for acquiring the disease, define the various subforms of complex diseases, predict susceptibility to severe comorbidities, and help to define a personalized health management program. Focusing on metabolic syndrome and neuropsychiatric disorders, IntegraGen will launch its first tests in Europe in 2005.
Spatial hole burning effects in distributed feedback lasers (1989)

The effects of spatial hole burning in a steady-state distributed feedback (DFB) laser are examined by numerically solving the coupled mode equations that describe the system. An approximate solution for the gain above threshold is derived and compared to the exact solution. It is shown that the self-induced grating that arises due to spatial hole burning significantly reduces the mode discrimination of index-coupled DFB lasers. This makes it difficult for these lasers to maintain single-longitudinal-mode behavior above threshold. However, it is found in addition that bulk-modulated (gain-coupled) DFB lasers do not lose their mode selectivity above threshold, indicating that these lasers may be better choices for narrow-linewidth operation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Circulatory levels of catecholamines, serotonin and lipids in attention deficit hyperactivity diiorder (1999)

Attention deficit hyperactivity disorder (ADHD) may be associated with a dysregulation of the catecholaminergic and serotonergic systems. Furthermore, ADHD is frequently complicated by aggressive impulsive behaviour, which is suggested to be related to low serum cholesterol levels. We examined the relationship between blood serotonin, norepinephrine, dopa and lipid levels and the degree of hyperactivity, impulsiveness, lack of concentration, and aggressiveness in boys with ADHD of low and high severity as determined by a specially designed formulated scale based on the DSM-IV criteria for ADHD. No differences were noted between the groups in any of the peripheral biological parameters except blood serotonin, for which a tendency (P=0.08) towards lower levels was observed in the children with more severe disorder. We conclude that children with severe ADHD may have a different serotonin turnover compared to children with mild ADHD. These results may have implications for our understanding of the pathogenesis of ADHD, at least the more severe type.
Stereoelectronic and steric effects in side chains preorganize a protein main chain (2009)

Preorganization is shown to endow a protein with extraordinary conformational stability. This preorganization is achieved by installing side-chain substituents that impose stereoelectronic and steric effects that restrict main-chain torsion angles. Replacing proline residues in (ProProGly)(7) collagen strands with 4-fluoroproline and 4-methylproline leads to the most stable known triple helices, having T ( m ) values that are increased by > 50 degrees C. Differential scanning calorimetry data indicate an entropic basis to the hyperstability, as expected from an origin in preorganization. Structural data at a resolution of 1.21 A reveal a prototypical triple helix with insignificant deviations to its main chain, even though 2/3 of the residues are nonnatural. Thus, preorganization of a main chain by subtle changes to side chains can confer extraordinary conformational stability upon a protein without perturbing its structure.
A Low-Protein Diet Protects Uremic Rats against the Negative Sequelae of Metabolic Acidosis (1990)

Metabolic acidosis is a common finding in uremia. The metabolic consequences, however, are poorly understood. Thus, the aim of our study was to assess the effect of chronic metabolic acidosis in 5/6-nephrectomized male Sprague-Dawley rats given a normal (18%; n = 19) and a low-protein diet (8%; n = 23). Each of these groups was sequentially given CaCO3 and CaCl2 in the drinking water for a fortnight each. The animals were randomly assigned to start either with CaCO3 or CaCl2 (random cross-over design). The blood pH decreased significantly in both CaCl2 groups (18% protein: CaCO3 7.18 vs. CaCl2 7.11; 8% protein: CaCO3 7.26 vs. CaCl2 7.09) as did standardized base excess (18% protein: CaCO3-5.9 vs. CaCl2-9.7; 8% protein: CaCO3-3.6 vs. CaCl2-12.6). Food intake declined during acidosis in both groups, but more in the 18% protein group. The same occurred with body weight (g) in the 18% group, which decreased dramatically (8% protein: CaCO3 389 vs. CaCl2 390; 18% protein: CaCO3 413 vs. CaCl2 366). The change in body weight was reflected in the urinary urea excretion (mg/24 h/g food) (8% protein: CaCO3 0.9 vs. CaCl2 1.0; 18% protein: CaCO3 2.2 vs. CaCl2 30.8). There was a significant increase in proteinuria (mg/24 h) in the 8% group (CaCO3 10 vs. CaCl2 15), while in the 18% group no real change occurred (CaCO3 24 vs. CaCl2 18). Factoring the proteinuria for food intake, however, also resulted in a tendency towards an increased proteinuria in the 18% group.(ABSTRACT TRUNCATED AT 250 WORDS)
Reinforcement determines the timing dependence of corticostriatal synaptic plasticity in vivo (2017)

Plasticity at synapses between the cortex and striatum is considered critical for learning novel actions. However, investigations of spike-timing-dependent plasticity (STDP) at these synapses have been performed largely in brain slice preparations, without consideration of physiological reinforcement signals. This has led to conflicting findings, and hampered the ability to relate neural plasticity to behavior. Using intracellular striatal recordings in intact rats, we show here that pairing presynaptic and postsynaptic activity induces robust Hebbian bidirectional plasticity, dependent on dopamine and adenosine signaling. Such plasticity, however, requires the arrival of a reward-conditioned sensory reinforcement signal within 2 s of the STDP pairing, thus revealing a timing-dependent eligibility trace on which reinforcement operates. These observations are validated with both computational modeling and behavioral testing. Our results indicate that Hebbian corticostriatal plasticity can be induced by classical reinforcement learning mechanisms, and might be central to the acquisition of novel actions.Spike timing dependent plasticity (STDP) has been studied extensively in slices but whether such pairings can induce plasticity in vivo is not known. Here the authors report an experimental paradigm that achieves bidirectional corticostriatal STDP in vivo through modulation by behaviourally relevant reinforcement signals, mediated by dopamine and adenosine signaling.
Effects of Olefin Substitution on the Ring-Closing Metathesis of Dienes (1997)

Ruthenium alkylidene 1 and molybdenum alkylidene 2 have been utilized in the ring-closing metathesis (RCM) of dienes containing gem-disubstituted olefins to yield tri- and tetrasubstituted cyclic olefins. Dienes with sterically demanding and/or electron-withdrawing substituents such as Ph, CO(2)Me, and (t)()Bu were cyclized successfully with 2, but did not cyclize with 1. Tetrasubstituted cyclic olefins could be formed with 2, but not using alkylidene 1. Dienes with allylic functional groups yielded functionalized cyclic olefins when treated with 1.
A Prospective Overview of the Essential Requirements in Molecular Modeling for Nanomedicine Design (2013)

Nanotechnology has presented many new challenges and opportunities in the area of nanomedicine design. The issues related to nanoconjugation, nanosystem-mediated targeted drug delivery, transitional stability of nanovehicles, the integrity of drug transport, drug-delivery mechanisms and chemical structural design require a pre-estimated and determined course of assumptive actions with property and characteristic estimations for optimal nanomedicine design. Molecular modeling in nanomedicine encompasses these pre-estimations and predictions of pertinent design data via interactive computographic software. Recently, an increasing amount of research has been reported where specialized software is being developed and employed in an attempt to bridge the gap between drug discovery, materials science and biology. This review provides an assimilative and concise incursion into the current and future strategies of molecular-modeling applications in nanomedicine design and aims to describe the utilization of molecular models and theoretical-chemistry computographic techniques for expansive nanomedicine design and development.
Corynebacterium diphtheriae pili: assembly, structure and function. (2014)

<title>Abstract</title> This chapter reviews current knowledge of the pilus assembly mechanism in <italic>Corynebacterium diphtheriae</italic> as well as the importance of <italic>C. diphtheriae</italic> pili as adhesive determinants. Three-dimensional structural insights into pilus assembly in <italic>C. diphtheriae</italic>, and functional features of <italic>C. diphtheriae</italic> pili are presented.