gebhart/patrepeval huggingface dataset:
Identifying functionally similar code in complex codebases (2016)

Identifying similar code in software systems can assist many software engineering tasks such as program understanding and software refactoring. While most approaches focus on identifying code that looks alike, some techniques aim at detecting code that functions alike. Detecting these functional clones — code that functions alike — in object oriented languages remains an open question because of the difficulty in exposing and comparing programs' functionality effectively. We propose a novel technique, In-Vivo Clone Detection, that detects functional clones in arbitrary programs by identifying and mining their inputs and outputs. The key insight is to use existing workloads to execute programs and then measure functional similarities between programs based on their inputs and outputs, which mitigates the problems in object oriented languages reported by prior work. We implement such technique in our system, HitoshiIO, which is open source and freely available. Our experimental results show that HitoshiIO detects more than 800 functional clones across a corpus of 118 projects. In a random sample of the detected clones, HitoshiIO achieves 68+% true positive rate with only 15% false positive rate.
Use of Submentoplasty to Enhance Cervical Recontouring in Face-Lift Surgery (1993)

A number of surgical techniques for recontouring the aging neck are available. Using liposuction and direct lipectomy, the surgeon can sculpt the jowl and submental contour. Posterior tightening of the ptotic platysma refines the submental area, while incisional or excisional techniques, along with midline plication, remove anterior banding. Despite these maneuvers, recurrent submental and cervical ptosis is noted in some patients. These individuals can benefit from a secondary submentoplasty, a submental tuck-up face-lift operation, usually within 6 to 18 months after their initial surgery. We have identified several reliable causes for a secondary submentoplasty. Submentoplasty as a planned second-stage surgery in certain patients allows achievement of more dramatic and long-lasting rejuvenation of the neck.
Impact and Therapeutic Potential of PPARs in Alzheimers Disease (2011)

Peroxisome proliferator activated receptors (PPARs) are well studied for their role of peripheral metabolism, but they also may be involved in the pathogenesis of various disorders of the central nervous system (CNS) including multiple sclerosis, amyotrophic lateral sclerosis, Alzheimer's and, Parkinson's disease. The observation that PPARs are able to suppress the inflammatory response in peripheral macrophages and in several models of human autoimmune diseases, lead to the idea that PPARs might be beneficial for CNS disorders possessing an inflammatory component. The neuroinflammatory response during the course of Alzheimer's disease (AD) is triggered by the deposition of the β-amyloid peptide in extracellular plaques and ongoing neurodegeneration. Non-steroidal anti-inflammatory drugs (NSAIDs) have been considered to delay the onset and reduce the risk to develop Alzheimer's disease, while they also directly activate PPARγ. This led to the hypothesis that NSAID protection in AD may be partly mediated by PPARγ. Several lines of evidence have supported this hypothesis, using AD related transgenic cellular and animal models. Stimulation of PPARγ by synthetic agonist (thiazolidinediones) inducing anti-inflammatory, anti-amyloidogenic and insulin sensitizing effects may account for the observed effects. Several clinical trials already revealed promising results using PPARγ agonists, therefore PPARγ represents an attractive therapeutic target for the treatment of AD.
.alpha.-Trifluoromethyl-destabilized cations. A route to 1-(trifluoromethyl)tetralins by trifluoroacetolysis of 5-aryl-1,1,1-trifluoropentan-2-ols and derivatives (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT.alpha.-Trifluoromethyl-destabilized cations. A route to 1-(trifluoromethyl)tetralins by trifluoroacetolysis of 5-aryl-1,1,1-trifluoropentan-2-ols and derivativesDaniele Bonnet-Delpon, Christian Cambillau, Micheline Charpentier-Morize, Roland Jacquot, Dany Mesureur, and Michele OurevitchCite this: J. Org. Chem. 1988, 53, 4, 754–759Publication Date (Print):February 1, 1988Publication History Published online1 May 2002Published inissue 1 February 1988https://pubs.acs.org/doi/10.1021/jo00239a010https://doi.org/10.1021/jo00239a010research-articleACS PublicationsRequest reuse permissionsArticle Views769Altmetric-Citations31LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Use of Crystal Structure Informatics for Defining the Conformational Space Needed for Predicting Crystal Structures of Pharmaceutical Molecules (2017)

Determining the range of conformations that a flexible pharmaceutical-like molecule could plausibly adopt in a crystal structure is a key to successful crystal structure prediction (CSP) studies. We aim to use conformational information from the crystal structures in the Cambridge Structural Database (CSD) to facilitate this task. The conformations produced by the CSD Conformer Generator are reduced in number by considering the underlying rotamer distributions, an analysis of changes in molecular shape, and a minimal number of molecular ab initio calculations. This method is tested for five pharmaceutical-like molecules where an extensive CSP study has already been performed. The CSD informatics-derived set of crystal structure searches generates almost all the low-energy crystal structures previously found, including all experimental structures. The workflow effectively combines information on individual torsion angles and then eliminates the combinations that are too high in energy to be found in the solid state, reducing the resources needed to cover the solid-state conformational space of a molecule. This provides insights into how the low-energy solid-state and isolated-molecule conformations are related to the properties of the individual flexible torsion angles.
Comparison of Adaptive Control Techniques Applied to Diesel Engine Idle Speed Regulation (2002)

Two self-tuning adaptive algorithms are developed for a heavy-duty diesel engine in order to tune the idle governor to the specific parameters of a given engine. Engine parameters typically vary across engines and over time, thus causing potentially detrimental effects on engine idle speed performance. Self-tuning controllers determine the specific parameters of a given engine, and then adjust the controller algorithm accordingly. Recursive least squares is used to do the parameter identification, whose samples are synchronized with the discrete injection events of the diesel engine for good convergence. Both Minimum Variance and Pole Placement Self-Tuning Regulators are developed and simulated on the nonlinear diesel engine model. The results show successful tuning of each adaptive controller to the specific parameters of a given engine model, with parameter convergence occurring within 30 seconds.
Low haze transparent electrodes and highly conducting air dried films with ultra-long silver nanowires synthesized by one-step polyol method (2013)

Transparent electrodes made of silver nanowires (AgNWs) exhibit higher flexibility when compared to those made of tin doped indium oxide (ITO) and are expected to be applied in plastic electronics. However, these transparent electrodes composed of AgNWs show high haze because the wires cause strong light scattering in the visible range. Reduction of the wire diameter has been proposed as a way to weaken light scattering, although there have seldom been any studies focusing on the haze because of the difficulty involved in controlling the wire diameter. In this report, we show that the haze can be easily reduced by increasing the length of AgNWs with a large diameter. Ultra-long (u-long) AgNWs with lengths in the range of 20–100 μm and a maximum length of 230 μm have been successfully synthesized by adjusting the reaction temperature and the stirring speed of a one-step polyol process. Compared to typical AgNWs (with diameter and length of 70 nm and 10 μm, respectively) and ITO, a transparent electrode consisting of u-long AgNWs 91 nm in diameter demonstrated a low haze of 3.4%-1.6% and a low sheet resistance of 24–109 Ω/sq. at a transmittance of 94%–97%. Even when fabricated at room temperature without any post-treatment, the electrodes composed of u-long AgNWs achieved a sheet resistance of 19 Ω/sq. at a transmittance of 80%, which is six orders of magnitude lower than that of typical AgNWs.
Efficient Syntheses of (α-Fluoropropargyl)phosphonate Esters (1996)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTEfficient Syntheses of (α-Fluoropropargyl)phosphonate EstersFarid Benayoud, Daniel J. deMendonca, Cheryl A. Digits, George A. Moniz, Tanya C. Sanders, and Gerald B. HammondView Author Information Department of Chemistry, University of Massachusetts Dartmouth, North Dartmouth, Massachusetts 02747-2300 Cite this: J. Org. Chem. 1996, 61, 15, 5159–5164Publication Date (Web):July 26, 1996Publication History Received31 January 1996Published online26 July 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/jo9602027https://doi.org/10.1021/jo9602027brief-reportACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views554Altmetric-Citations40LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Addition reactions,Organic compounds,Organophosphorus compounds,Phosphates,Phosphorus Get e-Alerts
The Second International Symposium on Tilapia in Aquaculture (1988)

Proceedings of the symposium held in 1987 in Bangkok, Thailand, by tilapia scientists to discuss strategies for future research and development in the tilapia industry worldwide. Contains 82 full papers, 17 poster abstracts and author and species indexes. The full papers were presented under 7 sessions: culture systems, management and production; pathology; genetics and reproduction; nutrition, physiology; biology and ecology; and economics and socioeconomics.
The Role of Arginine 120 of Human Prostaglandin Endoperoxide H Synthase-2 in the Interaction with Fatty Acid Substrates and Inhibitors (1999)

Arg-120 is located near the mouth of the hydrophobic channel that forms the cyclooxygenase active site of prostaglandin endoperoxide H synthases (PGHSs)-1 and -2. Replacement of Arg-120 of ovine PGHS-1 with a glutamine increases the apparent Km of PGHS-1 for arachidonate by 1,000-fold (Bhattacharyya, D. K., Lecomte, M., Rieke, C. J., Garavito, R. M., and Smith, W. L. (1996) J. Biol. Chem. 271, 2179-2184). This and other evidence indicate that the guanido group of Arg-120 forms an ionic bond with the carboxylate group of arachidonate and that this interaction is an important contributor to the overall strength of arachidonate binding to PGHS-1. In contrast, we report here that R120Q human PGHS-2 (hPGHS-2) and native hPGHS-2 have very similar kinetic properties, but R120L hPGHS-2 catalyzes the oxygenation of arachidonate inefficiently. Our data indicate that the guanido group of Arg-120 of hPGHS-2 interacts with arachidonate through a hydrogen bond rather than an ionic bond and that this interaction is much less important for arachidonate binding to PGHS-2 than to PGHS-1. The Km values of PGHS-1 and -2 for arachidonate are the same, and all but one of the core residues of the active sites of the two isozymes are identical. Thus, the results of our studies of Arg-120 of PGHS-1 and -2 imply that interactions involved in the binding of arachidonate to PGHS-1 and -2 are quite different and that residues within the hydrophobic cyclooxygenase channel must contribute more significantly to arachidonate binding to PGHS-2 than to PGHS-1. As observed previously with R120Q PGHS-1, flurbiprofen was an ineffective inhibitor of R120Q hPGHS-2. PGHS-2-specific inhibitors including NS398, DuP-697, and SC58125 had IC50 values for the R120Q mutant that were up to 1,000-fold less than those observed for native hPGHS-2; thus, the positively charged guanido group of Arg-120 interferes with the binding of these compounds. NS398 did not cause time-dependent inhibition of R120Q hPGHS-2, whereas DuP-697 and SC58125 were time-dependent inhibitors. Thus, Arg-120 is important for the time-dependent inhibition of hPGHS-2 by NS398 but not by DuP-697 or SC58125.
SketchHelper: Real-Time Stroke Guidance for Freehand Sketch Retrieval (2019)

Text-based retrieval systems have been popular, but content-based retrieval systems have gained widespread acceptance in recent years to directly retrieve diverse media based on their visual content, such as color, texture, and shape. Among many content-based retrieval systems, sketch-based media retrieval systems have attracted attention recently with the proliferation of tablet PCs and smart mobile devices. Sketch-based retrieval requires the user to draw a freehand sketch query, but freehand drawing can be challenging for those with limited drawing skills. This degrades retrieval performance, since successful retrieval depends on the quality of the sketch query image drawn by the user. To address this issue, we propose a real-time stroke guidance for freehand sketch retrieval that continuously displays next-stroke shadow sketches on the canvas based on the user's step-by-step partial strokes. We train a stroke guidance network that learns the mapping between the step-wise stroke relations to predict the user's next stroke. The proposed stroke guidance for freehand sketch retrieval system runs on a five step next-stroke prediction model that identifies candidate next-stroke sketches from a database of millions of sketches. The system retrieves variable number of sketch object classes at different drawing stages. During the initial sketching stage, diverse drawing possibilities are covered by retrieving multiple sketch classes; as the sketching progresses, the intended sketch class is narrowed down to one. Deep binary hashing is employed for efficient similarity matching of relevant next-stroke sketches. We extend the Google QuickDraw dataset to create a five step sketch stroke database. Qualitative and quantitative experiments are conducted to verify the effectiveness of the proposed system, which can be utilized for drawing guidance, tracing, and sketch retrieval. Tracing refers to the act of copying the shadowed line of a guiding image by drawing over its lines.
Pressure-Induced Anomalous Phase Transitions and Colossal Enhancement of Piezoelectricity in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msub><mml:mi>PbTiO</mml:mi><mml:mn>3</mml:mn></mml:msub></mml:math> (2005)

We find an unexpected tetragonal-to-monoclinic-to-rhombohedral-to-cubic phase transition sequence induced by pressure, and a morphotropic phase boundary in a pure compound using first-principles calculations. Huge dielectric and piezoelectric coupling constants occur in the transition regions, comparable to those observed in the new complex single-crystal solid-solution piezoelectrics such as Pb(Mg(1/3)Nb(2/3))O3-PbTiO3, which are expected to revolutionize electromechanical applications. Our results show that morphotropic phase boundaries and giant piezoelectric effects do not require intrinsic disorder, and open the possibility of studying this effect in simple systems.
Wound-induced ATP release and EGF receptor activation in epithelial cells (2007)

We have shown previously that wounding of human corneal epithelial (HCE) cells resulted in epidermal growth factor receptor (EGFR) transactivation through ectodomain shedding of heparin-binding EGF-like growth factor (HB-EGF). However, the initial signal to trigger these signaling events in response to cell injury remains elusive. In the present study, we investigated the role of ATP released from the injured cells in EGFR transactivation in HCE cells as well as in BEAS 2B cells, a bronchial epithelial cell line. Wounding of epithelial monolayer resulted in the release of ATP into the culture medium. The wound-induced rapid activation of phosphatidylinositol-3-kinase (PI3K) and extracellular signal-regulated kinase (ERK) pathways in HCE cells was attenuated by eliminating extracellular ATP, ADP and adenosine. The nonhydrolyzable ATP analog ATP-gamma-S induced rapid and sustained EGFR activation that depended on HB-EGF shedding and ADAM (a disintegrin and metalloproteinase). Targeting pathways leading to HB-EGF shedding and EGFR activation attenuated ATP-gamma-S-enhanced closure of small scratch wounds. The purinoceptor antagonist reactive blue 2 decreased wound closure and attenuated ATP-gamma-S induced HB-EGF shedding. Taken together, our data suggest that ATP, released upon epithelial injury, acts as an early signal to trigger cell responses including an increase in HB-EGF shedding, subsequent EGFR transactivation and its downstream signaling, resulting in wound healing.
The Structure of Calpain (2001)

Recent very rapid developments in genome and EST projects have identified an increasing number of gene products homologous to those that were previously identified by other methods. Calpain is no exception. At the time this review is written, 83 genes from 23 living organisms have been identified in the database to encode amino acid sequences showing significant similarities to the protease domain of "conventional" calpain, which was first purified as a homogeneous protein in 1978. Progress in genome/EST projects has occurred so quickly that there seems to be some confusion as to the identity of each calpain molecule. This review will attempt to clarify all calpain homologues, to describe the common and differing features of calpain homologues in terms of structure-function relationship, and to discuss the evolutionary process of calpain.
GPI-anchored proteins and lipid rafts. (2004)

Several proteins are anchored to membranes via a post-translational lipid modification, the glycosylphosphatidylinositol (GPI) anchor. In mammals and other vertebrates, GPI-anchored proteins have been found in almost all tissues and cells examined. Several studies have provided significant insight into the functions of this ubiquitous modification. An intriguing relevant feature of GPI-anchored proteins is their association with lipid rafts, specialized regions of elevated cholesterol and sphingolipid content, that are present within most cell membranes. In addition to the structure and biosynthesis of the GPI-anchor, recent researches have focused on its molecular interaction with lipid rafts and the biological meaning of such interaction. The aim of this review is to examine the emerging evidences of association between lipid rafts and GPI-anchored proteins, and their relationship with the modulation of important cellular functions such as protein/lipid sorting, signaling mechanisms and with human disease.
SOLID STATE CRYSTALLINITY, AMORPHOUS STATE, AND ITS IMPLICATIONS IN THE PHARMACEUTICAL PROCESS (2011)

Many drugs exist in crystalline solid form due to reasons of stability and ease of handling during the various stages of drug development. Crystalline solids can exist in the form of polymorphs, solvates or hydrates. Phase transitions such as polymorph inter-conversion, formation of hydrates, desolvation of solvates, and conversion of the crystalline to amorphous form may occur during various pharmaceutical processes. This could change the dissolution rate and transport characteristics of the drug. The current focus of research in the area is to understand the origins of polymorphism at the molecular level, and to predict and prepare the most stable polymorph of the drug. The aim of this review is to understand the recent development in the area of solid state crystallinity, amorphous state and to address the current challenges faced by pharmaceutical formulation, process development scientists and to anticipate future developments.
Solution Polymerization of Styrene (1967)

Abstract Polymers were obtained by free-radical solution polymerization of styrene, carried out by continuous feed-type polymerization. Molecular weights were determined by gel-permeation chromatography, light scattering, and osmotic pressure and viscosity measurements. A study of molecular structures indicated that polymerizations of styrene conducted in solution at relatively low temperatures and to a low degree of conversion can result in varying degrees of branching when certain initiating radicals are present.
A Fast and Accurate Segmentation Method for Ordered LiDAR Point Cloud of Large-Scale Scenes (2014)

This letter proposes an efficient two-step segmentation method for large-scale 3-D point cloud data collected by the mobile laser scanners. First, a new scan-line-based ground segmentation algorithm is designed to filter the points corresponding to the ground with high accuracy. Second, we propose a selfadaptive Euclidean clustering algorithm to further separate the off-ground points corresponding to different objects. Experiments show that our method delivers superior segmentation results on scanned data. In fact, the proposed method can be used in complex scenes including slope and bumpy road at an error rate of 0.674% and a computing throughput of over 20 million points/s.