gebhart/patrepeval huggingface dataset:
Syntheses and Opioid Receptor Binding Affinities of 8-Amino-2,6-methano-3-benzazocines (2003)

8-Amino-2,6-methano-3-benzazocine derivatives have been made using Pd-catalyzed amination procedures, and their affinities for opioid receptors were assessed. The 8-amino group was hypothesized to be a replacement for the prototypic 8-OH substituent for 2,6-methano-3-benzazocines and related opiates. This OH group is generally required for binding yet is implicated in unfavorable pharmacokinetic characteristics such as low oral bioavailability and rapid clearance via O-glucuronidation. The core structures in which the 8-OH group was replaced were cyclazocine and its enantiomers, ethylketocyclazocine and its enantiomers, ketocyclazocine, and Mr2034. Many new analogues had high affinity for opioid receptors with several in the subnanomolar range. Highest affinity was seen in analogues with secondary 8-(hetero)arylamino appendages. Binding to opioid receptors was enantioselective with the (2R,6R,11R)-configuration preferred and high selectivity for mu and kappa over delta opioid receptors was observed within the series. Several derivatives were shown to have intrinsic opioid-receptor-mediated activity in [(35)S]GTPgammaS assays.
Automatic Generation of Fast and Certified Code for Polynomial Evaluation (2011)

Designing an efficient floating-point implementation of a function based on polynomial evaluation requires being able to find an accurate enough evaluation code, exploiting at most the target architecture features. This article introduces CGPE, a tool dealing with the generation of fast and certified codes for the evaluation of bivariate polynomials. First we discuss the issue underlying the evaluation scheme combinatorics before giving an overview of the CGPE tool. The approach we propose consists in two steps: the generation of evaluation schemes by using some heuristics so as to quickly find some of low latency, and the selection that mainly consists in automatically checking their scheduling on the given target and validating their accuracy. Then, we present on-going development and ideas for possible improvements of the whole process. Finally, we illustrate the use of CGPE on some examples, and show how it allows us to generate fast and certified codes in a few seconds and thus to reduce the development time of libms like FLIP.
Boundary Detection Benchmarking: Beyond F-Measures (2013)

For an ill-posed problem like boundary detection, human labeled datasets play a critical role. Compared with the active research on finding a better boundary detector to refresh the performance record, there is surprisingly little discussion on the boundary detection benchmark itself. The goal of this paper is to identify the potential pitfalls of today's most popular boundary benchmark, BSDS 300. In the paper, we first introduce a psychophysical experiment to show that many of the "weak" boundary labels are unreliable and may contaminate the benchmark. Then we analyze the computation of f-measure and point out that the current benchmarking protocol encourages an algorithm to bias towards those problematic "weak" boundary labels. With this evidence, we focus on a new problem of detecting strong boundaries as one alternative. Finally, we assess the performances of 9 major algorithms on different ways of utilizing the dataset, suggesting new directions for improvements.
Interplay between Sb flux and growth temperature during the formation of GaSb islands on GaP (2012)

We investigate the influence of the Sb flux on the growth of GaSb islands on a highly mismatched (001) GaP substrate. Between low and medium Sb flux values, standard kinetics drives the GaSb island formation and their relaxation is progressively favored by 90° misfit dislocations at the GaSb/GaP interface. However, under high Sb flux, the GaSb islands are elongated in the [110] direction and their density decreases. Further experiments varying the growth temperature at fixed Sb flux confirm this finding. We relate this observation to an enhancement of Ga diffusion when the effective Sb flux on the surface is increased. This behavior is qualitatively explained by the large cohesive energy of Sb-Sb bonds present on the surface, which impede the Ga adatom incorporation.
Short-current pulse-based maximum-power-point tracking method for multiple photovoltaic-and-converter module system (2002)

This paper proposes a novel maximum-power-point tracking (MPPT) method with a simple algorithm for photovoltaic (PV) power generation systems. The method is based on use of a short-current pulse of the PV to determine an optimum operating current where the maximum output power can be obtained and completely differs from conventional hill-climbing-based methods. In the proposed system, the optimum operating current is instantaneously determined simply by taking a product of the short-current pulse amplitude and a parameter k because the optimum operating current is exactly proportional to the short current under various conditions of illuminance and temperature. Also, the system offers an identification capability of k by means of fast power-versus-current curve scanning, which makes the short-current pulse-based MPPT method adaptive to disturbances such as shades partially covering the PV panels and surface contamination. The above adaptive MPPT algorithm has been introduced into a current-controlled boost chopper and a multiple power converter system composed of PV-and-chopper modules. Various operating characteristics have experimentally been examined on this multiple PV-and-chopper module system from a practical viewpoint and excellent MPPT performance has been confirmed through the tests.
Advanced optimization strategies in the Rice dHPF compiler (2002)

Abstract High‐Performance Fortran (HPF) was envisioned as a vehicle for modernizing legacy Fortran codes to achieve scalable parallel performance. To a large extent, today's commercially available HPF compilers have failed to deliver scalable parallel performance for a broad spectrum of applications because of insufficiently powerful compiler analysis and optimization. Substantial restructuring and hand‐optimization can be required to achieve acceptable performance with an HPF port of an existing Fortran application, even for regular data‐parallel applications. A key goal of the Rice dHPF compiler project has been to develop optimization techniques that enable a wide range of existing scientific applications to be ported easily to efficient HPF with minimal restructuring. This paper describes the challenges to effective parallelization presented by complex (but regular) data‐parallel applications, and then describes how the novel analysis and optimization technologies in the dHPF compiler address these challenges effectively, without major rewriting of the applications. We illustrate the techniques by describing their use for parallelizing the NAS SP and BT benchmarks. The dHPF compiler generates multipartitioned parallelizations of these codes that are approaching the scalability and efficiency of sophisticated hand‐coded parallelizations. Copyright © 2002 John Wiley &amp; Sons, Ltd.
Klotho-Dependent Role of 1,25(OH)2D3 in the Brain (2021)

The antiaging protein Klotho is encoded by the Klotho gene first identified as an 'aging suppressor', in mice. Klotho deficiency is involved in premature aging and early death, while its overexpression is related to longevity. Klotho is mostly expressed in the kidney, but also in the brain, and in other organs. Two forms of Klotho, the cell membrane and secreted form, have pleiotropic activities that include regulation of general metabolism, oxidative stress, and mineral metabolism that correlates with its effect on accelerating aging. Membrane Klotho serves as an obligate co-receptor for the fibroblast growth factor (FGF), while secreted Klotho plays its role as a humoral factor. Klotho protein participates in the regulation of several biological activities, including regulation of calcium-phosphate homeostasis and PTH as well as vitamin D metabolism. The active form of vitamin D, 1,25(OH)<sub>2</sub>D<sub>3</sub> (1,25-dihydroxy-vitamin D3 = calcitriol), acts as a neurosteroid that participates in the regulation of multiple brain functions. It provides neuroprotection and suppresses oxidative stress, inhibits inflammation and inflammatory mediators, and stimulates various neurotrophins. Calcitriol is involved in many brain-related diseases, including multiple sclerosis, Alzheimer´s disease, Parkinson´s disease, and schizophrenia. This review covers the most recent advances in Klotho research and discusses Klotho-dependent roles of calcitriol in neuro-psycho-pathophysiology.
The efficacy and safety of rituximab in patients with active rheumatoid arthritis despite methotrexate treatment: Results of a phase IIB randomized, double‐blind, placebo‐controlled, dose‐ranging trial (2006)

Both rituximab doses were effective and well tolerated when added to MTX therapy in patients with active RA. The primary end point (ACR20 response) was independent of glucocorticoids, although intravenous glucocorticoid premedication improved tolerability during the first rituximab infusion.
Ribosomal frameshifting during translation of measles virus P protein mRNA is capable of directing synthesis of a unique protein (1995)

Members of the Paramyxoviridae family utilize a variety of different strategies to increase coding capacity within their P cistrons. Translation initiation at alternative 5'-proximal AUG codons is used by measles virus (MV) to express the virus-specific P and C proteins from overlapping reading frames on their mRNAs. Additional species of mRNAs are transcribed from the MV P cistron by the insertion of extra nontemplated G residues at a specific site within the P transcript. Addition of only a single nontemplated G residue results in the expression of the V protein, which contains a unique carboxyl terminus. We have used an Escherichia coli system to express MV P cistron-related mRNAs and proteins. We have found that ribosomal frameshifting on the MV P protein mRNA is capable of generating a previously unrecognized P cistron-encoded protein that we have designated R. Some ribosomes which have initiated translation of the P protein mRNA use the sequence TCC CCG AG (24 nucleotides upstream of the V protein stop codon) to slip into the -1 reading frame, thus translating the sequence as TC CCC GAG. The resulting R protein terminates five codons downstream of the frameshift site at the V protein stop codon. We have gone on to use a chloramphenicol acetyltransferase reporter system to demonstrate that this MV-specific sequence is capable of directing frameshifting during in vivo translation in eukaryotic cells. Analysis of immunoprecipitated proteins from MV-infected cells by two-dimensional gel electrophoresis allowed detection of a protein species consistent with R protein in MV-infected cells. Quantitation of this protein species allowed a rough estimation of frameshift frequency of approximately 1.8%. Significant stimulation of ribosomal frameshift frequency at this locus of the MV P mRNA was mediated by a downstream stimulator element which, although not yet fully defined, appeared to be neither a conventional stem-loop nor an RNA pseudoknot structure.
Integration of MAP Kinase Signal Transduction Pathways at the Serum Response Element (1995)

The ternary complex factor (TCF) subfamily of ETS-domain transcription factors bind with serum response factor (SRF) to the serum response element (SRE) and mediate increased gene expression. The TCF protein Elk-1 is phosphorylated by the JNK and ERK groups of mitogen-activated protein (MAP) kinases causing increased DNA binding, ternary complex formation, and transcriptional activation. Activated SRE-dependent gene expression is induced by JNK in cells treated with interleukin-1 and by ERK after treatment with phorbol ester. The Elk-1 transcription factor therefore integrates MAP kinase signaling pathways in vivo to coordinate biological responses to different extracellular stimuli.
Nonlinear analysis of surface-emitting distributed feedback lasers (1990)

An analysis of surface-emitting distributed feedback lasers under conditions above threshold is presented. The coupled-wave equations are integrated numerically using a self-consistent technique that includes the effects of gain saturation, carrier diffusion, antiguiding, and free carrier loss. The laser threshold current and slope efficiency are determined as a function of the strip length and p-layer thickness where it is found that the device efficiency can be very high. Antiguiding, which varies when the grating is mistuned with respect to the gain peak, influences the slope, threshold, and shape of the emission far field. Small variations in the longitudinal index of refraction are shown to affect the far-field intensity profile significantly.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Effects of Motion on the Performance of Pulse Oximeters in Volunteers (Revised publication) (1997)

The mechanical motions used in this study significantly affected oximeter function, particularly when the sensors were connected during motion, which requires signal acquisition during motion. The error and dropout rate performance of the Masimo was superior to that of the other two instruments during all test conditions. Masimo uses a new paradigm for oximeter signal processing, which appears to represent a significant advance in low signal-to-noise performance.
Differential accumulation of plant defense gene transcripts in a compatible and an incompatible plant-pathogen interaction. (1986)

Phenylalanine ammonia-lyase and chalcone synthase catalyze the first reaction of phenylpropanoid biosynthesis and the first reaction of a branch pathway specific for flavonoid-isoflavonoid biosynthesis, respectively. These enzymes are key control elements in the synthesis of kievitone, phaseollin, and related isoflavonoid-derived phytoalexins. RNA blot hybridization with 32P-labeled cDNA sequences was used to demonstrate marked accumulation of phenylalanine ammonia-lyase and chalcone synthase mRNAs in excision-wounded hypocotyls of Phaseolus vulgaris L. (dwarf French bean) and during race-cultivar-specific interactions between hypocotyls of P. vulgaris and the partially biotrophic fungus Colletotrichum lindemuthianum, the causal agent of anthracnose. In an incompatible interaction (host resistant), early concomitant accumulation of phenylalanine ammonia-lyase and chalcone synthase mRNAs, localized mainly but not entirely in tissue adjacent to the site of infection, was observed prior to the onset of phytoalexin accumulation and expression of localized, hypersensitive resistance. In contrast, in a compatible interaction (host susceptible) there was no early accumulation of these transcripts; instead, there was a delayed widespread response associated with phytoalexin accumulation during attempted lesion limitation. Two-dimensional gel electrophoresis of [35S]methionine-labeled polypeptides synthesized in vitro by translation of isolated polysomal RNA demonstrated stimulation of the synthesis of characteristic sets of phenylalanine ammonia-lyase and chalcone synthase isopolypeptides in directly infected tissue and distant, hitherto uninfected tissue in both compatible and incompatible interactions. Our data show that specific accumulation of plant defense gene transcripts is a key early component in the sequence of events leading to expression of defense responses in wounded tissue and in infected tissue during race-cultivar-specific interactions and that an elicitation signal is transmitted intercellularly in response to infection.
Activation and repolarization of the normal human heart under complete physiological conditions (2006)

Knowledge of normal human cardiac excitation stems from isolated heart or intraoperative mapping studies under nonphysiological conditions. Here, we use a noninvasive imaging modality (electrocardiographic imaging) to study normal activation and repolarization in intact unanesthetized healthy adults under complete physiological conditions. Epicardial potentials, electrograms, and isochrones were noninvasively reconstructed. The normal electrophysiological sequence during activation and repolarization was imaged in seven healthy subjects (four males and three females). Electrocardiographic imaging depicted salient features of normal ventricular activation, including timing and location of the earliest right ventricular (RV) epicardial breakthrough in the anterior paraseptal region, subsequent RV and left ventricular (LV) breakthroughs, apex-to-base activation of posterior LV, and late activation of LV base or RV outflow tract. The repolarization sequence was unaffected by the activation sequence, supporting the hypothesis that in normal hearts, local action potential duration (APD) determines local repolarization time. Mean activation recovery interval (ARI), reflecting local APD, was in the typical human APD range (235 ms). Mean LV apex-to-base ARI dispersion was 42 ms. Average LV ARI exceeded RV ARI by 32 ms. Atrial images showed activation spreading from the sinus node to the rest of the atria, ending at the left atrial appendage. This study provides previously undescribed characterization of human cardiac activation and repolarization under normal physiological conditions. A common sequence of activation was identified, with interindividual differences in specific patterns. The repolarization sequence was determined by local repolarization properties rather than by the activation sequence, and significant dispersion of repolarization was observed between RV and LV and from apex to base.
Production Potential and Strategies for Coalbed Methane in the Central Appalachian Basin (1988)

ABSTRACT A regional geologic assessment of the Lower Pennsylvanian age formations in the Central Appalachian Basin has indicated that the coalbeds of the Pocahontas and Lee/New River formations have a high potential for gas production. This study, sponsored by the Gas Research Institute, has established an in-place gas resource estimate of over 5 trillion cubic feet for the six primary coalbeds in the targeted east central portion of the basin. Using a production simulator designed specifically for the unique reservoir characteristics of coalbeds, estimates of gas production under varying geographic and reservoir conditions were made. The many thin, discontinuous coalbeds of the basin suggest that gas production from multiple coal seams within a single wellbore will be the optimal completion technique.
Development of basic visual functions (1989)

The book provides detailed up to date and authoritative accounts of major areas of infant development.
Nondegenerate two-photon absorption in zinc blende semiconductors (1992)

An algorithm is presented for the calculation of the nondegenerate two-photon absorption coefficient by using second-order perturbation theory and a Kane band-structure model, including the effects of nonparabolicity and nonzone-center wave functions. The polarization dependence is included by correctly accounting for the symmetry of the electronic wave functions. A comparison is made with degenerate two-photon absorption data in various zinc blende semiconductors, and excellent agreement is found without the use of fitting parameters. Comparisons are also made with nondegenerate two-photon absorption spectra measured in ZnSe and ZnS by using a picosecond continuum and with some polarization-dependent measurements obtained by a two-color Z-scan measurement.
Parameters optimization for a scalable multiple description coding scheme based on spatial subsampling (2008)

In this work, we design a multiple description coding (MDC) system for video streams moving from the concept of spatial MDC and introducing an efficient algorithm to obtain sub-streams that exploits some form of scalability. We first generate four subsequences by sub-sampling, then, from these four
Contact imaging in the atomic force microscope using a higher order flexural mode combined with a new sensor (1996)

Using an atomic force microscope (AFM) with a silicon cantilever partially covered with a layer of zinc oxide (ZnO), we have imaged in the constant force mode by employing the ZnO as both a sensor and actuator. The cantilever deflection is determined by driving the ZnO at the second mechanical resonance while the tip is in contact with the sample. As the tip-sample force varies, the mechanical boundary condition of the oscillating cantilever is altered, and the ZnO electrical admittance is changed. Constant force is obtained by offsetting the ZnO drive so that the admittance remains constant. We have also used the ZnO as an actuator and sensor for imaging in the intermittent contact mode. In both modes, images produced by using the ZnO as a sensor are compared to images acquired with a piezoresistive sensor.
Inspirations from nature. New reactions, new therapeutic leads, and new drug delivery systems (2003)

Abstract Studies in our laboratory focus on problems in chemistry (new reactions and synthesis), biology (novel modes of action), and medicine (new therapeutic leads and drug delivery systems). These interconnected and often synergistic activities are inspired by an interest in novel structures, frequently from nature, that possess unique modes of action and significant clinical potential. Described herein are some examples of recent work from our laboratory that have led to new transition metal-catalyzed reactions, a new and remarkably potent therapeutic lead, and new drug delivery systems that are in clinical trials.
Review of the female Duroc/Yorkshire pig model of human fibroproliferative scarring (2007)

Hypertrophic scarring after burns is an unsolved problem and remains as devastating today as it was in the 40s and it may be that the main reason for this is the lack of an accepted, useful animal model. The female, red Duroc pig was described as a model of hypertrophic scarring nearly 30 years ago but then vanished from the literature. This seemed strange since the authors reported that 12 of 12 pigs developed thick scar. In the mid 90s we explored the model and found that, indeed, the red Duroc pig does make thick scar. Other authors have established that the Yorkshire pig does not heal in this fashion so there is the possibility of a same species control. We have continued to explore the Duroc/Yorkshire model and herein describe our experiences. Is it a perfect model of hypertrophic scarring? No. Is it a useful model of hypertrophic scarring? Time will tell. We have now obtained gene expression data from the Duroc/Yorkshire model and analysis is underway.
Tracking hackers on IRC (1999)

Few hackers are motivated purely by knowledge, science and curiosity. Hackers continue to break into systems long after they become familiar with the technology. Instead, many continue to hack simply because of the social status it brings. For many, hacking is a social activity. Hackers meet online to discuss the latest hacking tools, their hacking conquests, and their personal lives. To be truly effective, system administrator and security professionals must become familiar with the social culture in which hackers dwell.