gebhart/patrepeval huggingface dataset:
On finding duplication and near-duplication in large software systems (2002)

This paper describes how a program called dup can be used to locate instances of duplication or near-duplication in a software system. Dup reports both textually identical sections of code and sections that are the same textually except for systematic substitution of one set of variable names and constants for another. Further processing locates longer sections of code that are the same except for other small modifications. Experimental results from running dup on millions of lines from two large software systems show dup to be both effective at locating duplication and fast. Applications could include identifying sections of code that should be replaced by procedures, elimination of duplication during reengineering of the system, redocumentation to include references to copies, and debugging.
The Transformation of Jervine into 18-Functional D-Homo-C-norsteroids. IV. The Transformation of Jervine into (20R)-18,20β-Epoxy-3β-hydroxy-17β-ethyletiojervan-18-one 3-Acetate via (20R)-18,20β-Epoxy-3β-hydroxy-12α,17β-ethyletiojervan-11-one 3-Acetate (1981)

Abstract Catalytic hydrogenation of (22S,25S)-N-acetyl-3β,23β-dihydroxyveratra-5,13(17)-dien-11-one 3-acetate over rhodium-platinum catalyst in acetic acid gave (22S,25S)-N-acetyl-3β,23β-dihydroxyveratranin-11 -one 3-acetate (2) in ca 70% yield, together with two minor products. Irradiation of 2 in benzene containing mercury(II) oxide and iodine gave 20-formyl-3β-hydroxy-12α,17β-ethyletiojervan-11-one 3-acetate (5) in 43% yield, accompanied by the 17-epimer of (22S,23R,25S)-N-acetyl-3β-hydroxy-5α-jervanin-11-one 3-acetate (4%). Aldehyde 5 was transformed into 3β-hydroxy-12α,17β-ethyletiojervane-11,20-dione 3-acetate (15) (79% yield) by photo- or coppercatalysed oxygenation of the corresponding enamine. Reduction of 15 with sodium borohydride gave 3β,20β-dihydroxy-12α,17β-ethyletiojervan-11-one 3-acetate (17) as a major product (69%), together with the 20-epimer. The hypoiodite reaction of 17 gave 18,20β-epoxy-3β-hydroxy-17β-ethyl-12α-etiojervan-11-one 3-acetate (19) in 92% yield. Hydrolysis of 19 resulted in the isomerization of the C/D ring junction to give 18,20β-epoxy-3β-hydroxy-17β-ethyletiojervan-11 -one (20), the first 18-functional C/D trans D-homo-C-norsteroid ever prepared. Wolff-Kishner reduction of 20 gave the corresponding 11-deoxo compound; its acetylation followed by oxidation yielded 18,20β-epoxy-3β-hydroxy-17β-ethyletiojervan-18-one 3-acetate. The 11-oxo function of 19 can be reduced quite easily with lithium aluminum hydride to give the corresponding 11β-ol.
Intelligent email: aiding users with AI (2008)

Email occupies a central role in the modern workplace. This has led to a vast increase in the number of email messages that users are expected to handle daily. Further-more, email is no longer simply a tool for asynchronous online communication—email is now used for task man-agement, personal archiving, as well both synchronous and asynchronous online communication (Whittaker and Sidner 1996). This explosion can lead to “email overload”—many users are overwhelmed by the large quantity of informa-tion in their mailboxes. In the human–computer interaction community, there has been much research on tackling email overload. Recently, similar efforts have emerged in the ar-tificial intelligence (AI) and machine learning communities to form an area of research known as intelligent email. In this paper, we take a user-oriented approach to applying AI to email. We identify enhancements to email user in-terfaces and employ machine learning techniques to support these changes. We focus on three tasks—summary keyword generation, reply prediction and attachment prediction—and summarize recent work in these areas. Keyword Summarization Email inboxes typically display a limited amount of infor-mation about each email, usually the subject, sender and date. Users are then expected to perform email triage— the process of making decisions about how to handle these emails—based on this information. In practice, such limited information is often insufficient to perform good triage and can lead to missed messages or wasted time. Additional con-cise and relevant information about each message can speed up the decision-making process and reduce errors. Muresan, Tzoukermann, and Klavans (2001) introduced the
Pharmacokinetics and Metabolism in Drug Design. Methods and Principles in Medicinal Chemistry. Volume 31. Second Revised Edition By Dennis A. Smith, Han van de Waterbeemd, and Don K. Walker. Wiley-VCH, Weinheim, Germany. 2006. xix + 187 pp. 17.5 × 24.5 cm. ISBN 3527313680. $125.00. (2006)

ADVERTISEMENT RETURN TO ISSUEPREVBook ReviewNEXTPharmacokinetics and Metabolism in Drug Design. Methods and Principles in Medicinal Chemistry. Volume 31. Second Revised Edition By Dennis A. Smith, Han van de Waterbeemd, and Don K. Walker. Wiley-VCH, Weinheim, Germany. 2006. xix + 187 pp. 17.5 × 24.5 cm. ISBN 3527313680. $125.00.James T. DaltonView Author Information College of Pharmacy, Parks Hall The Ohio State University Columbus, Ohio 43210Cite this: J. Med. Chem. 2006, 49, 25, 7556–7557Publication Date (Web):November 14, 2006Publication History Published online14 November 2006Published inissue 1 December 2006https://pubs.acs.org/doi/10.1021/jm068041ehttps://doi.org/10.1021/jm068041ebook-reviewACS PublicationsCopyright © 2006 American Chemical SocietyRequest reuse permissionsArticle Views263Altmetric-Citations-LEARN 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:Absorption,Drug discovery,Metabolism,Pharmaceuticals,Pharmacokinetics Get e-Alerts
Characterization of system L and system y+ amino acid transport activity in cultured vascular smooth muscle cells (1993)

The uptake of L-leucine and L-lysine into vascular smooth muscle cells cultured from the aortas of rats has been investigated. Both amino acids are taken up by saturable systems that are independent of the presence of a Na+ gradient and can be stimulated in trans by neutral bulky amino acids for leucine and cationic amino acids for lysine. Leucine uptake is inhibited competitively in cis by several neutral amino acids, whereas lysine uptake is inhibited strongly by other cationic amino acids but also significantly by neutral amino acids such as leucine. The leucine inhibition is noncompetitive. Cells preloaded with leucine and lysine could also export these amino acids and the rate of efflux was stimulated by the presence of appropriate amino acids in trans. These data are all consistent with leucine being transported largely if not entirely by System L and lysine by the System y+ transporter.
Amyloid precursor protein processing is stimulated by metabotropic glutamate receptors. (1995)

Stimulation of muscarinic m1 or m3 receptors can, by generating diacylglycerol and activating protein kinase C, accelerate the breakdown of the amyloid precursor protein (APP) to form soluble, nonamyloidogenic derivatives (APPs), as previously shown. This relationship has been demonstrated in human glioma and neuroblastoma cells, as well as in transfected human embryonic kidney 293 cells and PC-12 cells. We now provide evidence that stimulation of metabotropic glutamate receptors (mGluRs), which also are coupled to phosphatidylinositol 4,5-bisphosphate hydrolysis, similarly accelerates processing of APP into nonamyloidogenic APPs. This process is demonstrated both in hippocampal neurons derived from fetal rats and in human embryonic kidney 293 cells transfected with cDNA expression constructs encoding the mGluR 1 alpha subtype. In hippocampal neurons, both an mGluR antagonist, L-(+)-2-amino-3-phosphonopropionic acid, and an inhibitor of protein kinase C, GF 109203X, blocked the APPs release evoked by glutamate receptor stimulation. Ionotropic glutamate agonists, N-methyl-D-aspartate or S(-)-5-fluorowillardiine, failed to affect APPs release. These data show that selective mGluR agonists that initiate signal-transduction events can regulate APP processing in bona fide primary neurons and transfected cells. As glutamatergic neurons in the cortex and hippocampus are damaged in Alzheimer disease, amyloid production in these regions may be enhanced by deficits in glutamatergic neurotransmission.
A 54 Mbps (3,6)-regular FPGA LDPC decoder (2003)

Applying a joint code and decoder design methodology, we develop a high-speed (3, k)-regular LDPC code partly parallel decoder architecture, based on which a 9216-bit, rate-1/2 (3,6)-regular LDPC code decoder is implemented on an Xilinx FPGA device. When performing maximum 18 iterations for each code block decoding, this partly parallel decoder supports a maximum symbol throughput of 54 Mbps and achieves BER 10/sup -6/ at 2 dB over an AWGN channel.
A novel approach for the construction of multiple shRNA expression vectors (2007)

The application of RNA interference (RNAi) as a research and therapeutic tool depends on its ability to silence genes in a sequence-specific manner. Recent studies have reported that the effective knockdown of genes can be achieved by multiple short hairpin RNAs (shRNAs) in a single vector. Moreover, this approach can depress several genes simultaneously. However, current methods for the construction of multiple shRNA vectors often suffer from vector instability and are time-consuming. Here, we describe a simple, quick and low-cost approach to construct a single vector expressing four shRNA sequences driven by four different promoters. Using this vector, we were able to improve the gene silencing efficiency and make it possible to silence four different genes simultaneously, further expanding the application spectrum of RNAi, both in functional studies and therapeutic strategies.
The effect of pore size on tissue ingrowth and neovascularization in porous bioceramics of controlled architecturein vivo (2011)

The purpose of this study was to investigate the role of pore size on tissue ingrowth and neovascularization in porous bioceramics under the accurate control of the pore parameters. For that purpose, β-tricalcium phosphate (β-TCP) cylinders with four different macropore sizes (300-400, 400-500, 500-600 and 600-700 µm) but the same interconnection size (120 µm) and unchangeable porosity were implanted into fascia lumbodorsalis in rabbits. The fibrous tissues and blood vessels formed in scaffolds were observed histologically and histomorphometrically. The vascularization of the porous bioceramics was analyzed by single-photon emission computed tomography (SPECT). It is found that pore size as an important parameter of a porous structure plays an important role in tissue infiltration into porous biomaterial scaffolds. The amount of fibrous tissue ingrowth increases with the decrease of the pore size. In four kinds of scaffolds with different macropore sizes (300-400, 400-500, 500-600 and 600-700 µm) and a constant interconnection size of 120 µm, the areas of fibrous tissue (%) were 60.5%, 52.2%, 41.3% and 37.3%, respectively, representing a significant decrease at 4 weeks (P < 0.01). The pore size of a scaffold is closely related to neovascularization of macroporous biomaterials implanted in vivo. A large pore size is beneficial for the growth of blood vessels, and the diameter of a pore smaller than 400 µm limits the growth of blood vessels and results in a smaller blood vessel diameter.
Primary structure of human preangiotensinogen deduced from the cloned cDNA sequence (1984)

Cloned cDNA sequences for human preangiotensinogen have been isolated from a human liver cDNA library by hybridization with a restriction fragment derived from a previously cloned cDNA for rat preangiotensinogen. Analyses by nucleotide sequence determination, S1 nuclease mapping, and RNA blot hybridization indicate that human preangiotensinogen is encoded by two mRNAs that differ only in the length of the 3'-untranslated region. The deduced amino acid sequence shows that the mature angiotensinogen consists of 452 amino acid residues with the angiotensin sequence at its amino-terminal portion. Two potential initiation sites have been discussed. These are the methionine codon located at the position exactly corresponding to the initiation site of rat preangiotensinogen mRNA and an additional methionine codon positioned nearest the 5' end of the mRNA. The amino acid sequences starting at either of the initiation sites and preceding the angiotensin sequence constitute a large number of hydrophobic amino acid residues, thus representing the signal peptide characteristic of the secretory proteins. Human and rat preangiotensinogens show that 63.6% of the amino acid positions of the two proteins are identical. However, the amino-terminal portions directly distal to angiotensin I diverge markedly between the two proteins and differ in their possible glycosylation sites. These structural differences may contribute to the known species specificity exhibited by renin.
Selective expression of the murine homologue of the G-protein-coupled receptor BLR1 in B cell differentiation, B cell neoplasia and defined areas of the cerebellum. (1994)

The Burkitt's lymphoma receptor 1 (BLR1) identified initially in Burkitt lymphoma cells has been the first member of the superfamily of G-protein-coupled receptors with a lymphocyte specific expression pattern. BLR1 shows significant relationship to receptors for chemokines (IL-8, MIP-1 beta) and neuropeptides. The gene encoding the murine homologue of the human BLR1 receptor was isolated and used to study its tissue-specific expression. Blr-1 consists of two exons encoding a protein of 374 amino acid residues which shows 83% identity with the human homologue. Screening of normal tissues of adult BALB/c mice revealed that blr-1-specific RNA is detected consistently at low levels in secondary lymphatic organs. The blr-1 gene is expressed regularly and strongly in lymphomas of mature B cells but not in plasmacytomas. SCID mice deficient in the development of mature B cells have strongly reduced levels of blr-1-specific RNA in the spleen. Cytokine mediated induction (IL4, IL6) of terminal differentiation of resting B cells towards Ig-secreting plasma cells completely downregulates expression of blr-1. RNA in situ hybridization using brain sections demonstrates blr 1 transcription in the granule and Purkinje cell layer of the cerebellum. The precise delineation of the restricted expression pattern of the blr-1 gene will support the identification of its ligand and may provide a clue to understand how BLR1 exerts its biological function within the immune and nervous system.
Inferential control for rolling mills (2000)

A robust inferential controller is developed for hot strip rolling mill tension control. Tension cannot be measured, therefore a nonlinear model is used to infer the tension from the looper angle. The model uses constant physical parameters while the actual physical system will be uncertain, therefore quantitative feedback theory is used to design a tension controller, which will provide robust performance despite uncertainty from both the physical system and the inference model or soft sensor.
NO Disproportionation at a Mononuclear Site-Isolated Fe2+ Center in Fe2+-MOF-5 (2015)

The weak-field ligand environments at the metal nodes of metal-organic frameworks (MOFs) mimic the electronic environment of metalloenzyme active sites, but little is known about the reactivity of MOF nodes toward small molecules of biological relevance. Here, we report that the ferrous ions in Fe(2+)-exchanged MOF-5 disproportionate nitric oxide to produce nitrous oxide and a ferric nitrito complex. Although mechanistic studies of N-N bond forming transformations often invoke a hyponitrite species, as in nitric oxide reductase and NOx reduction catalysis, little is known about this intermediate in its monoanionic state. Together with the first report of N-N coupling between NO molecules in a MOF, we present evidence for a species that is consistent with a ferric hyponitrite radical, whose isolation is enabled by the spatial constraints of the MOF matrix.
Photonic-Crystal Fibers (2006)

The history, fabrication, theory, numerical modeling, optical properties, guidance mechanisms, and applications of photonic-crystal fibers are reviewed
Evolution of Zidovudine Resistance-Associated Genotypes in Human Immunodeficiency Virus Type 1-Infected Patients (1996)

Substantial differences have been described in the response of individual patients to zidovudine (ZDV) therapy, both in the clinical impact and in virus load. Genotypic changes associated with the appearance of drug resistance may also be different or occur at different rates. We have obtained the nucleotide sequence of the RT domain of individual HIV-1 genomes extracted from 10 plasma and peripheral blood mononuclear cell (PBMC) samples donated by two haemophiliac patients before, during, and after long-term ZDV therapy. Although the plasma virus load was similar throughout, the order and timing of appearance of resistance-associated substitutions differed in the two patients. In patient p74, K70R appeared after 4 months, T215Y at 5.5 months, and M41L at 13 months. In p87, K70R also appeared at 4 months, but T215Y and K219Q were not observed until 18 months and M41L not at all. Much greater sequence change overall occurred in p74. The evolution of the viral population in that patient was dominated by the unique appearance of T215Y and subsequently M41L, with all sequences from the last time point being descended by a single path from the pretreatment samples. However, in p87, several different lineages of RT sequences were found to persist throughout treatment. We propose that these differences in outcome may be determined by differences in genetic background at sites other than the five generally considered to be associated with ZDV sensitivity.
Studies on a Serum Substitute for Mammalian Cells in Culture I. Biological Efficacy of Whole and Fractionated Peptone Dialysate (1972)

SummaryA biological titration of whole peptone dialysate (PD) demonstrated a broad concentration range over which large cell populations were obtained. Sephadex G-10 chromatography of PD resulted in six UV-absorbing fractions, three of which were recovered in sufficient quantities for biological analysis. Fractions G-10(I) and G-10(II) supported proliferation and survival, whereas fraction G-10(III) maintained cell populations at their seed inoculum level. Greater cell populations were observed in cultures supplemented with fraction G-10(II) than in those to which fraction G-10(I) was added.
Photoluminescence studies of Si (100) doped with low-energy (100–1000 eV) B+ ions during molecular beam epitaxy (1990)

Temperature-dependent photoluminescence (PL) measurements have been used to characterize 5-μm-thick Si(100) epitaxial layers doped in situ during molecular beam epitaxial growth with low-energy (100, 500, and 1000 eV) 11 B+ ions at growth temperatures of 500, 650, and 800 °C. Moderate doping (NB ∼1017 cm−3) yielded PL features comprised of both sharp and broad peaks in the boron bound exciton (B-BE) region. At 4.2 K a broad B-BE feature near 1086 meV dominated, although the sharp transverse optical phonon-assisted B-BE peak (B1TO ) at 1092.5 meV was resolvable for NB&amp;lt;1017 cm−3. Increasing the PL sample temperature above 4.2 K caused a rapid decay of the broad B-BE peak intensity, thus permitting comparison of B1TO intensity for a range of ion energies and growth temperatures. At 10 K, a bulk-like spectrum containing a sharp B1TO peak with weaker multiexciton peaks B2TO and B3TO was observed for the film growth at the highest temperature and lowest ion energy (800 °C and 100 eV). However, the intensity of the B1TO peak decreased with decreasing growth temperature (constant ion energy) and with increasing ion energy (constant growth temperature). Samples grown at the lowest temperature (500 °C) displayed very different PL spectra with much weaker line emission, a rising PL background, and additional lines near 1040 meV due to ion-induced residual lattice defects. Quenching of B1TO and the other sharp B-BE peaks was accompanied by an increase in the N1 peak at 745.7 meV.
IL-18 Is Induced and IL-18 Receptor α Plays a Critical Role in the Pathogenesis of Cigarette Smoke-Induced Pulmonary Emphysema and Inflammation (2007)

Th1 inflammation and remodeling characterized by local tissue destruction coexist in pulmonary emphysema and other diseases. To test the hypothesis that IL-18 plays an important role in these responses, we characterized the regulation of IL-18 in lungs from cigarette smoke (CS) and room air-exposed mice and characterized the effects of CS in wild-type mice and mice with null mutations of IL-18Ralpha (IL-18Ralpha(-/-)). CS was a potent stimulator and activator of IL-18 and caspases 1 and 11. In addition, although CS caused inflammation and emphysema in wild-type mice, both of these responses were significantly decreased in IL-18Ralpha(-/-) animals. CS also induced epithelial apoptosis, activated effector caspases and stimulated proteases and chemokines via IL-18Ralpha-dependent pathways. Importantly, the levels of IL-18 and its targets, cathepsins S and B, were increased in pulmonary macrophages from smokers and patients with chronic obstructive lung disease. Elevated levels of circulating IL-18 were also seen in patients with chronic obstructive lung disease. These studies demonstrate that IL-18 and the IL-18 pathway are activated in CS-exposed mice and man. They also demonstrate, in a murine modeling system, that IL-18R signaling plays a critical role in the pathogenesis of CS-induced inflammation and emphysema.