gebhart/patrepeval huggingface dataset:
Comprehending Object-Oriented Software Frameworks API Through Dynamic Analysis (2007)

AbstractA common practice followed by many application developers is to use existing framework appli-cations as a guide to understand how to implement a framework-provided concept of interest. Un-fortunately, ﬂnding the code that implements the concept of interest might be very di–cult since thecode might be scattered across and tangled with code implementing other concepts. To address thisissue, this report presents an approach called FUDA ( Framework API Understanding through DynamicAnalysis ). The main idea of this approach is to extract implementation recipes of a given concept fromruntime information collected when that concept is invoked in a number of diﬁerent sample applica-tions. For this purpose, we introduce a novel dynamic slicing approach named concept trace slicing and combine it with clustering and data mining techniques. The experimental evaluation of FUDAsuggests that this approach is eﬁective in producing useful implementation recipes for a given conceptwith few false positives and false negatives.
Performance Evaluation of VIDAS® Diagnostic Assays Detecting Anti-Chikungunya Virus IgM and IgG Antibodies: An International Study (2023)

Chikungunya (CHIK) is a debilitating mosquito-borne disease with an epidemiology and early clinical symptoms similar to those of other arboviruses-triggered diseases such as dengue or Zika. Accurate and rapid diagnosis of CHIK virus (CHIKV) infection is therefore challenging. This international study evaluated the performance of the automated VIDAS<sup>®</sup> anti-CHIKV IgM and IgG assays compared to that of manual competitor IgM and IgG ELISA for the detection of anti-CHIKV IgM and IgG antibodies in 660 patients with suspected CHIKV infection. Positive and negative agreements of the VIDAS<sup>®</sup> CHIKV assays with ELISA ranged from 97.5% to 100.0%. The sensitivity of the VIDAS<sup>®</sup> CHIKV assays evaluated in patients with a proven CHIKV infection confirmed reported kinetics of anti-CHIKV IgM and IgG response, with a positive detection of 88.2-100.0% for IgM ≥ 5 days post symptom onset and of 100.0% for IgG ≥ 11 days post symptom onset. Our study also demonstrated the superiority of ELISA and VIDAS<sup>®</sup> assays over rapid diagnostic IgM/IgG tests. The analytical performance of VIDAS<sup>®</sup> anti-CHIKV IgM and IgG assays was excellent, with a high precision (coefficients of variation ≤ 7.4%) and high specificity (cross-reactivity rate ≤ 2.9%). This study demonstrates the suitability of the automated VIDAS<sup>®</sup> anti-CHIKV IgM and IgG assays to diagnose CHIKV infections and supports its applicability for epidemiological surveillance and differential diagnosis in regions endemic for CHIKV.
Tin-Free Direct C–H Arylation Polymerization for High Photovoltaic Efficiency Conjugated Copolymers (2016)

A new and highly regioselective direct C-H arylation polymerization (DARP) methodology enables the reproducible and sustainable synthesis of high-performance π-conjugated photovoltaic copolymers. Unlike traditional Stille polycondensation methods for producing photovoltaic copolymers, this DARP protocol eliminates the need for environmentally harmful, toxic organotin compounds. This DARP protocol employs low loadings of commercially available catalyst components, Pd<sub>2</sub>(dba)<sub>3</sub>·CHCl<sub>3</sub> (0.5 mol%) and P(2-MeOPh)<sub>3</sub> (2 mol%), sterically tuned carboxylic acid additives, and an environmentally friendly solvent, 2-methyltetrahydrofuran. Using this DARP protocol, several representative copolymers are synthesized in excellent yields and high molecular masses. The DARP-derived copolymers are benchmarked versus Stille-derived counterparts by close comparison of optical, NMR spectroscopic, and electrochemical properties, all of which indicate great chemical similarity and no significant detectable structural defects in the DARP copolymers. The DARP- and Stille-derived copolymer and fullerene blend microstructural properties and morphologies are characterized with AFM, TEM, and XRD and are found to be virtually indistinguishable. Likewise, the charge generation, recombination, and transport characteristics of the fullerene blend films are found to be identical. For the first time, polymer solar cells fabricated using DARP-derived copolymers exhibit solar cell performances rivalling or exceeding those achieved with Stille-derived materials. For the DARP copolymer PBDTT-FTTE, the power conversion efficiency of 8.4% is a record for a DARP copolymer.
Low incidence of new biochemical and clinical hypogonadism following hypofractionated stereotactic body radiation therapy (SBRT) monotherapy for low- to intermediate-risk prostate cancer (2011)

Hypofractionated SBRT offers the radiobiological benefit of a large fraction size and is well-tolerated by men with low- to intermediate-risk prostate cancer. Early results are encouraging with an excellent biochemical response. The rate of new biochemical and clinical hypogonadism was low one year after treatment.
Multiple re-focusing of ultrashort laser pulse propagating in condensed matter (2003)

We focused a 38 fs laser pulse, which is spatially filtered, into a glass cell containing a very dilute solution of coumarin 440 in methanol. Via three photons fluorescence of coumarin, up to 6 re-focusing filaments were observed along one straight line. This is the first evidence showing a way to control multiple filamentation.
Pathologically Node-Positive Prostate Cancer (2020)

The postoperative management of men with lymph node involved prostate cancer (pN+) remains a challenge as there is a general lack of randomized trial data and a range of management strategies. Retrospective studies suggest a variable clinic course for patients with pN+ prostate cancer. Some men progress rapidly to metastatic disease despite further therapies, whereas other men can have a period of prolonged quiescence without adjuvant androgen deprivation therapy (ADT) or radiation therapy (RT). For men who have undergone radical prostatectomy, randomized trial data indicate that the addition of ADT in pN+ disease extends metastasis-free, prostate cancer-specific, and overall survival. Additional retrospective studies suggest that adding RT is potentially beneficial in this setting, improving overall and cancer-specific survival especially in men with certain pathologic parameters. Conversely, men with lower disease burden in their lymph nodes have longer times to progression and may be candidates for observation and salvage therapy as opposed to adjuvant ADT/RT.
ICONE23-1600 DEVELOPMENT OF FUEL DEBRIS CUTTING TECHNIQUE BY LASER GOUGING (2015)

Development of damaged fuel debris cutting technique in Fukushima Daiichi nuclear plant is one of the important issues for the defueling operations such as removing from the reactor, handling and storage, and so on. Previous knowledge in the Three Mile Island Unit 2 (TMI-2) nuclear plant accident is reported that fuel debris was made of uranium oxides, stainless steel, zircaloy and so on. Therefore, it is difficult to cut fuel debris by machine processing. Laser cutting is convenient to cut complex materials. However, it is difficult to know the thickness of fuel debris in advance, so it is hard to apply the conventional laser cutting method. In this study, we have been developed the cutting technique for fuel debris by using laser gouging method. Test pieces that simulate fuel debris ware fabricated by embedding ceramic pellet on stainless steel. Laser gouging test was performed by cutting surface of the test pieces with high power fiber laser, whose maximum irradiation power was 10kW. According to the test result, laser gouging process has the ability to grind the simulated fuel debris under atmospheric condition. In addition, same kind of cutting effect could be performed underwater.
Progress in growth, fabrication, and characterization of semiconductor photonic crystal nanocavities [Phys. Status Solidi B 248, No. 4, 892–896 (2011)] (2012)

Abstract An error was made in the calculation of the photonic crystal mode volume. Fixing this error increases our mode volume by a factor of 2 and makes our claim of highest Q / V invalid.
Practical Quantizer Design for Half-Duplex Estimate-and-Forward Relaying (2010)

We propose a quantizer design method for practical half-duplex estimate-and-forward (EF) relaying. First, we identify the regime in which EF relaying yields substantial gains where the SNR is low and the relay-destination link is strong. Then we discover design simplifications that reduce complexity with little loss in the above regime. For relay quantizer design, we first consider mean-squared distortion minimization. To illustrate the unsuitability of the approach, we present an example with AWGN links and a BPSK source where the quantizer with worst mean squared distortion in a given set maximizes achievable rate. A distortion-minimizing quantizer attempts to preserve the received signal at the relay. The quantizer should instead preserve source information. In information theoretical terms, the quantizer should maximize the mutual information between the source transmission and the quantizer output conditioned on the side information at the destination subject to a rate constraint. The above conclusion, derived from information theoretical principles, is then translated to a quantizer design method for the low SNR regime. Using LDPC codes of blocklength 100000, BPSK modulation, and quantizers designed using the proposed criterion, we observe performance less than a decibel away from the achievable rate at a BER of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-4</sup> .
Discovery of BMS-986339, a Pharmacologically Differentiated Farnesoid X Receptor Agonist for the Treatment of Nonalcoholic Steatohepatitis (2022)

While several farnesoid X receptor (FXR) agonists under clinical investigation for the treatment of nonalcoholic steatohepatitis (NASH) have shown beneficial effects, adverse effects such as pruritus and elevation of plasma lipids have limited their clinical efficacy and approvability. Herein, we report the discovery and preclinical evaluation of compound <b>32</b> (BMS-986339), a nonbile acid FXR agonist with a pharmacologically distinct profile relative to our previously reported agonist BMS-986318. Compound <b>32</b> exhibited potent in vitro and in vivo activation of FXR, albeit with a context-dependent profile that resulted in tissue-selective effects in vivo. To our knowledge, this is the first report that demonstrates differential induction of <i>Fgf15</i> in the liver and ileum by FXR agonists in vivo. Compound <b>32</b> demonstrated robust antifibrotic efficacy despite reduced activation of certain genes in the liver, suggesting that the additional pharmacology of BMS-986318 does not further benefit efficacy, possibly presenting an opportunity for reduced adverse effects. Further evaluation in humans is warranted to validate this hypothesis.
Characterization of Na-based phospate as electrode materials for electrochemical cells (2011)

International audience
Tailoring the Thickness‐Dependent Optical Properties of Conducting Nitrides and Oxides for Epsilon‐Near‐Zero‐Enhanced Photonic Applications (2022)

The unique properties of the emerging photonic materials, conducting nitrides and oxides, especially their tailorability, large damage thresholds, and, importantly, the so-called epsilon-near-zero (ENZ) behavior, have enabled novel photonic phenomena spanning optical circuitry, tunable metasurfaces, and nonlinear optical devices. This work explores direct control of the optical properties of polycrystalline titanium nitride (TiN) and aluminum-doped zinc oxide (AZO) by tailoring the film thickness, and their potential for ENZ-enhanced photonic applications. This study demonstrates that TiN-AZO bilayers support Ferrell-Berreman modes using the thickness-dependent ENZ resonances in the AZO films operating in the telecom wavelengths spanning from 1470 to 1750 nm. The bilayer stacks also act as strong light absorbers in the ultraviolet regime using the radiative ENZ modes and the Fabry-Perot modes in the constituent TiN films. The studied Berreman resonators exhibit optically induced reflectance modulation of 15% with picosecond response time. Together with the optical response tailorability of conducting oxides and nitrides, using the field enhancement near the tunable ENZ regime can enable a wide range of nonlinear optical phenomena, including all-optical switching, time refraction, and high-harmonic generation.
Chief cells possess somatostatin receptors regulated by secretagogues acting through the calcium or cAMP pathway (1994)

Inhibition both in vivo and in vitro of pepsinogen secretion by somatostatin (SS) and the histological demonstration that fundic D-cells contain long cytoplasmic processes extending to chief cells suggest a possible direct effect of SS on chief cell function. The aim of the present study was to determine whether SS interacts directly with receptors on isolated gastric chief cells and, if so, how SS alters cell function. Binding of 125I-[Tyr11]SS14 to chief cells was saturable, time and temperature dependent, and was inhibited by both SS14 (Ki 1.6 nM) and SS28 (Ki 5.2 nM). SMS-201-995 was 1,300-fold less potent than SS14. Calcium-mobilizing secretagogues reduced binding of 125I-[Tyr11]SS14 with efficacies of cholecystokinin octapeptide (CCK-8) > carbachol > gastrin. Adenosine 3',5'-cyclic monophosphate (cAMP)-activating secretagogues also inhibited binding with efficacies of secretin > vasoactive intestinal polypeptide (VIP). 12-O-tetradecanoylphorbol 13-acetate (TPA) or A-23187 also decreased binding. Analyses demonstrated that CCK-8 and TPA were decreasing the affinity of SS receptors for 125I-[Tyr11]SS14 without affecting their binding capacity. Both SS14 and SS28 at a maximally effective concentration inhibited cAMP production caused by VIP or secretin (20-30%) but did not alter cytosolic calcium ([Ca2+]i), inositol phosphates, or pepsinogen release. We conclude that chief cells possess SS receptors with a high affinity for both SS14 and SS28 but low affinity for SMS-201-995 and thus resemble the SSB receptors described in the rat cerebral cortex. Although occupation of these receptors by SS has no effect on pepsinogen release induced by secretagogues acting through either the calcium or the cAMP pathway, SS receptor occupation is regulated by agents activating phospholipase C, adenylate cyclase, protein kinase C, and [Ca2]i.
Phase-sensitive frequency-modulation noise spectroscopy with a diode laser (1996)

We have demonstrated phase-sensitive FM noise spectroscopy, using the frequency noise of a diode laser. We obtained the reference signal for this experiment by sending part of the diode-laser beam through a Mach-Zehnder interferometer, which acted as a frequency discriminator. Both the reference beam (prepared with an interferometer) and the probe beam (which probed a Fabry-Perot cavity) carried amplitude noise converted from the intrinsic frequency noise. Mixing the two noise signals allowed us to measure the absorptive and dispersive responses of the sample. This method may provide a simple and sensitive spectroscopic tool.
Mutation of peptide binding site in transmembrane region of a G protein-coupled receptor accounts for endothelin receptor subtype selectivity. (1994)

The molecular basis for endothelin (ET) isopeptide selectivity between ETA and ETB receptors was studied by examining ligand binding to several site-specific mutants of the human ETA receptor. Based on a computer-built three-dimensional model of the ETA receptor, five non-conserved amino acids, clustered around the putative ligand binding site, were targeted for mutation to alanine. Expression of the wild-type and mutant ETA receptors in COS-7 cells revealed that the binding profile of one of the ETA mutants, Tyr129-->Ala, was characteristic of the ETB receptor. In the Tyr129-->Ala ETA receptor mutant the affinity of two ETB-selective agonists, endothelin-3 and sarafotoxin S6c, was increased 10-200-fold, whereas that for two ETA-selective antagonists, BQ-123 and BMS-182874, was reduced 350-2,000-fold. Thus, mutation of a single amino acid in the second transmembrane region of the wild-type ETA receptor results in subtype conversion. In addition, these data represent the first example of peptide interactions with a transmembrane region of a G protein-coupled receptor and indicate that Tyr129, located in the second transmembrane region of the ETA receptor, is a critical component for determination of endothelin receptor subtype-selective ligand binding.
Association between Lower Body Temperature and Increased Tau Pathology in Cognitively Normal Older Adults (2021)

Abstract The authors have requested that this preprint be removed from Research Square.
Adaptive control of two robot arms carrying an unknown object (2002)

We deal with the control of two robot manipulators carrying an unknown object. We consider the uncertainties in mass, inertia and center of mass of the object. A dynamic model is obtained for the combined system. An adaptive scheme is proposed to track the desired motion trajectory of the object in the presence of uncertainties. A feedforward plus PI type force controller is designed for internal force control. A Lyapunov based stability analysis is conducted for the proposed scheme. In the adaptive motion control scheme for the combined system we cannot specify the individual torques of the manipulators uniquely. To obtain a set of individual torques an optimal control problem is formulated by minimizing a cost function.
On Material Models for Static Sizing of Compression Driven Airframe Structure (2002)

The design of large parts of the airframe is driven by compression stability requirements. This stability is generally evaluated using a Ramberg-Osgood (R-O) model of the material. The objective of the present work is to evaluate to what extent the precise shape of the stress-strain curve determines the outcome of the stability analysis. R-O-based material models with nc fitted for various ranges of plastic strain were compared to data measured both in the micro-plastic strain domain (between 0 and 0.2% strain) and conventional stress-strain data (measured between roughly 0.2 and 8%) for an AA7xxx alloy. It was observed that R-O-based models are not capable of representing all of the measured data accurately: models fitted for larger ranges of strain (e.g. 0.2 – 1%) represented the stress-strain data measured in the micro-plastic domain poorly, and vice-versa. It was verified however, that when using the material models to compute critical stresses of post-buckling designs through analytical-empirical Euler-Engesser calculations, little improvement in precision over current generally accepted practice is possible. On the other hand, detailed comparisons of post-buckling stiffened panel stability with finite element analyses (FEA) did demonstrate room for improvement of the accuracy of the analysis by using a different stress-strain fit. This was concluded to be attributable to a more accurate representation of local phenomena: The analytical-empirical methods used model the buckling of the stiffener + effective plating as if it were the collapse of an idealized column. Strains are averaged over the entire section and therefore remain small. The buckling stress is determined by the tangent modulus at this small plastic strain. The higher the strain hardening as modeled in the R-O representation, the higher the tangent modulus for small strains and therefore the higher the predicted critical stress. Elastic-plastic geometrically non-linear FEA, on the contrary, is not limited to simulating a column. All deformations, however local, are taken into account. Also, manufacturing imperfections can be simulated. For the panel configuration and perturbation practice used for these studies, the simulations lead to locally high plastic strains. Trend analysis indicated that without the correct material models, different from the ones that are used conventionally, this may lead to non-negligible imprecision in the predicted performance of a stiffened panel when using FEA.
5‐Lipoxygenase gene disruption reduces amyloid‐β pathology in a mouse model of Alzheimer's disease (2007)

5-Lipoxygenase (5LO), by producing leukotrienes, is a proinflammatory enzyme, and there is evidence suggesting that it is up-regulated with aging and may be involved in Alzheimer's disease (AD). In this paper, we studied the effect of 5LO-targeted gene disruption on the amyloid phenotype of a transgenic mouse model of AD, the Tg2576. Amyloid-beta (Abeta) deposition in the brains of Tg2576 mice lacking 5LO was reduced by 64-80% compared with Tg2576 controls. This reduction was associated with a similar significant decrease in Abeta levels measured by sandwich ELISA. Absence of 5LO did not induce any significant change in amyloid-beta precursor protein (APP) levels and processing, or Abeta catabolic pathways. Furthermore, in vitro studies showed that 5LO activation or 5LO metabolites increase, whereas 5LO inhibition decreases, Abeta formation, secondary to correspondent changes in gamma-secretase activity. These data establish for the first time a novel functional role for 5LO in the pathogenesis of AD-like amyloidosis, thereby modulating gamma-secretase activity. Our work suggests that pharmacological inhibition of 5LO could provide a novel therapeutic tool for AD.
Tabletop coherent diffractive microscopy with extreme ultraviolet light from high harmonic generation (2009)

We demonstrate lensless diffractive microscopy using a tabletop source of extreme ultraviolet (EUV) light from high harmonic generation at 29 nm and 13.5 nm. High harmonic generation has been shown to produce fully spatially coherent EUV light when the conversion process is well phase-matched in a hollow-core waveguide. We use this spatial coherence for two related diffractive imaging techniques which circumvent the need for lossy imaging optics in the EUV region of the spectrum. Holography with a reference beam gives sub-100 nm resolution in short exposure times with fast image retrieval. Application of the Guided Hybrid Input-Output phase retrieval algorithm refines the image resolution to 53 nm with 29 nm light. Initial images using the technologically important 13.5 nm wavelength give 92-nm resolution in a 10-minute exposure. Straightforward extensions of this work should also allow near-wavelength resolution with the 13.5 nm source. Diffractive imaging techniques provide eased alignment and focusing requirements as compared with zone plate or multilayer mirror imaging systems. The short-pulsed nature of the extreme ultraviolet source will allow pump-probe imaging of materials dynamics with time resolutions down to the pulse duration of the EUV.