gebhart/patrepeval huggingface dataset:
Learning from mistakes (2008)

The reality of multi-core hardware has made concurrent programs pervasive. Unfortunately, writing correct concurrent programs is difficult. Addressing this challenge requires advances in multiple directions, including concurrency bug detection, concurrent program testing, concurrent programming model design, etc. Designing effective techniques in all these directions will significantly benefit from a deep understanding of real world concurrency bug characteristics.This paper provides the first (to the best of our knowledge) comprehensive real world concurrency bug characteristic study. Specifically, we have carefully examined concurrency bug patterns, manifestation, and fix strategies of 105 randomly selected real world concurrency bugs from 4 representative server and client open-source applications (MySQL, Apache, Mozilla and OpenOffice). Our study reveals several interesting findings and provides useful guidance for concurrency bug detection, testing, and concurrent programming language design.Some of our findings are as follows: (1) Around one third of the examined non-deadlock concurrency bugs are caused by violation to programmers' order intentions, which may not be easily expressed via synchronization primitives like locks and transactional memories; (2) Around 34% of the examined non-deadlock concurrency bugs involve multiple variables, which are not well addressed by existing bug detection tools; (3) About 92% of the examined concurrency bugs canbe reliably triggered by enforcing certain orders among no more than 4 memory accesses. This indicates that testing concurrent programs can target at exploring possible orders among every small groups of memory accesses, instead of among all memory accesses; (4) About 73% of the examinednon-deadlock concurrency bugs were not fixed by simply adding or changing locks, and many of the fixes were not correct at the first try, indicating the difficulty of reasoning concurrent execution by programmers.
Delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine synthetase from Aspergillus nidulans. Molecular characterization of the acvA gene encoding the first enzyme of the penicillin biosynthetic pathway (1991)

The Aspergillus nidulans gene (acvA) encoding the first catalytic steps of penicillin biosynthesis that result in the formation of delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine (ACV), has been positively identified by matching a 15-amino acid segment of sequence obtained from an internal CNBr fragment of the purified amino-terminally blocked protein with that predicted from the DNA sequence. acvA is transcribed in the opposite orientation to ipnA (encoding isopenicillin N synthetase), with an intergenic region of 872 nucleotides. The gene has been completely sequenced at the nucleotide level and found to encode a protein of 3,770 amino acids (molecular mass, 422,486 Da). Both fast protein liquid chromatography and native gel estimates of molecular mass are consistent with this predicted molecular weight. The enzyme was identified as a glycoprotein by means of affinity blotting with concanavalin A. No evidence for the presence of introns within the acvA gene has been found. The derived amino acid sequence of ACV synthetase (ACVS) contains three homologous regions of about 585 residues, each of which displays areas of similarity with (i) adenylate-forming enzymes such as parsley 4-coumarate-CoA ligase and firefly luciferase and (ii) several multienzyme peptide synthetases, including bacterial gramicidin S synthetase 1 and tyrocidine synthetase 1. Despite these similarities, conserved cysteine residues found in the latter synthetases and thought to be essential for the thiotemplate mechanism of peptide biosynthesis have not been detected in the ACVS sequence. These observations, together with the occurrence of putative 4'-phosphopantetheine-attachment sites and a putative thioesterase site, are discussed with reference to the reaction sequence leading to production of the ACV tripeptide. We speculate that each of the homologous regions corresponds to a functional domain that recognizes one of the three substrate amino acids.
Programmable bacteria detect and record an environmental signal in the mammalian gut (2014)

Significance The human microbiota represents the trillions of bacteria that live on the skin, in the oral, nasal, and aural cavities, and throughout the gastrointestinal tract. The species that live in the gastrointestinal tract, the gut microbiota, closely interact with host cells and have a profound impact on health. To develop tools to effectively monitor the gut microbiota and ultimately help in disease diagnosis, we have engineered Escherichia coli to sense and record environmental stimuli, and demonstrated that E. coli with such memory systems can survive and function in the mammalian gut. This work demonstrates that E. coli can be engineered into living diagnostics capable of nondestructively probing the mammalian gut.
Moisture sorption isotherm characteristics and Taguchi analysis of rice bran extraction parameters (2016)

Abstract This work determined the moisture sorption isotherm of rice bran and investigated the effects of the pre‐treatment method, solvent type, solid–liquid ratio and soaping temperature on extract yield, total phenolic content, 2,2‐diphenyl‐1‐picrylhydrazyl radical‐scavenging activity assay and 2,2′‐azino‐bis antioxidant capacity assay of rice bran extract. The Taguchi method and L9 (3 4 ) orthogonal array were employed in this study. The sorption isotherms of rice bran showed a sigmoidal pattern and displayed type II of van der Waals adsorption. Adsorption and desorption data on rice bran were best fitted using the Henderson model among the six models tested at three temperatures. The net isosteric heat of desorption was higher than the net isosteric heat of adsorption. Based on the analysis of the signal‐to‐noise ratio, solvent selection effected the largest contribution to the overall performance. Confirmation experiments showed that the optimal combination that contained the four quality attributes was appropriate (error margin &lt;5%) and reproducible. © 2016 Curtin University of Technology and John Wiley &amp; Sons, Ltd.
The neo-epitope specific PRO-C3 ELISA measures true formation of type III collagen associated with liver and muscle parameters. (2013)

The developed neo-epitope specific serum ELISA for type III procollagen (PRO-C3) reflects true formation as it is specific for the propeptide cleaved off the intact collagen molecule. In a clinical and in a rodent study we showed that this marker was highly related to liver fibrosis and muscle mass.
Lithium effectively complements vasopressin V2 receptor antagonist in the treatment of hyponatraemia of SIADH rats (2006)

Although the single effect of therapeutic dose of lithium was weak, it effectively and safely compensated for the therapeutic limitations of a low dose of AVP V(2) receptor antagonist for SIADH by reducing AQP2 expression.
Hydrogen sulphide, a novel gasotransmitter involved in guard cell signalling (2010)

Hydrogen sulphide (H(2) S) has been proposed as the third gasotransmitter. In animal cells, H(2) S has been implicated in several physiological processes. H(2) S is endogenously synthesized in both animals and plants by enzymes with l-Cys desulphydrase activity in the conversion of l-Cys to H(2) S, pyruvate and ammonia. The participation of H(2) S in both stomatal movement regulation and abscisic acid (ABA)-dependent induction of stomatal closure was studied in epidermal strips of three plant species (Vicia faba, Arabidopsis thaliana and Impatiens walleriana). The effect of H(2) S on stomatal movement was contrasted with leaf relative water content (RWC) measurements of whole plants subjected to water stress. In this work we report that exogenous H(2) S induces stomatal closure and this effect is impaired by the ATP-binding cassette (ABC) transporter inhibitor glibenclamide; scavenging H(2) S or inhibition of the enzyme responsible for endogenous H(2) S synthesis partially blocks ABA-dependent stomatal closure; and H(2) S treatment increases RWC and protects plants against drought stress. Our results indicate that H(2) S induces stomatal closure and participates in ABA-dependent signalling, possibly through the regulation of ABC transporters in guard cells.
Possible involvement of the OKT4 molecule in T cell recognition of class II HLA antigens. Evidence from studies of cytotoxic T lymphocytes specific for SB antigens. (1982)

A recently described HLA gene, SB, which maps between GLO and HLA-DR, codes for Ia-like molecules that are similar to but distinct from HLA-DR molecules. Cytotoxic T lymphocytes (CTL) specific for SB1, SB2, SB3, and SB4 were compared with HLA-A2-specific CTL with respect to their surface expression of the T cell differentiation antigens OKT3, OKT4, and OKT8. All CTL activity was eliminated by treatment with OKT3 and C'. The SB-specific cytotoxicity was eliminated by OKT4 plus C' but not by OKT8 plus C'. In contrast, HLA-A2-specific killing was completely susceptible to treatment with OKT8 plus C' but not with OKT4 plus C'. Cytotoxicity was analyzed in the presence of OKT8 and a series of monoclonal antibodies (OKT4A, 4B, 4C, and 4D) that react with distinct epitopes on the OKT4 molecule. SB1-, SB3-, and SB4-specific CTL were partially inhibited by OKT4A and 4B (45-75%), whereas HLA-A2-specific CTL were partially inhibited by OKT8 (48-63%) but not by OKT4. SB2-specific CTL were not inhibited (less than 26%) by OKT8 or by any of the OKT4-related antibodies. These results suggest that the OKT4 marker may be expressed on most T cells that recognize allogeneic Ia or self Ia plus foreign antigens; OKT4+ cells do not appear to be functionally homogeneous in that they can act both as helper/inducer and cytotoxic cells. Models are proposed for the functional involvement of the OKT4 molecule in T cell-Ia antigen interactions.
Primary health care in action. (1997)

In a 40-page report on the Comox Valley Nursing Centre Demonstration Project RNABC says the project showed what nurses can do when they are allowed to practice the full scope of their profession. Overall, the project was a success in making a contribution to understanding the principles of primary health care and community-based nursing practice.
Multimeric complex formation by the thyrotropin receptor in solubilized thyroid membranes. (1996)

The TSH receptor (TSHR) has a large glycosylated ectodomain comprising the amino-terminal half of the molecule (394 of 743 residues) implicated in TSH binding, as well as autoantibody recognition in Graves' disease. In this study we employed antibodies specific for the amino-terminus (Ab1), midportion (Ab2), and carboxyl-terminus (Ab3) of the TSHR-ectodomain, previously mapped using recombinant receptor proteins, to detect the natural receptor present in detergent-solubilized porcine thyroid cell membranes via immunoblotting. Several forms of the receptor were detected. In reduced samples Ab1 detected full-length holoreceptors present in both nonglycosylated and glycoslylated forms of apparent molecular masses 80 and 90 kDa, respectively, as well as apparent dimeric nonglycosylated and dimeric glycosylated holoreceptor forms resistant to reduction. Also detected by Ab1 were a glycosylated amino-terminal 47- to 52-kDa fragment of the holoreceptor (gly alpha-subunit), reduced to 42 kDa (alpha-subunit) by Endo F deglycosylation. Ab2 detected all of the same forms. Ab3 detected primarily a carboxy-terminal, nonglycosylated fragment of 35 kDa (beta-subunit). In unreduced samples, the recognition pattern was unchanged with Ab1. Ab2 detected monomeric and dimeric beta-subunits, as well as higher order complexes. The different TSHR forms present in unreduced preparations were resolved by ammonium sulfate precipitation, confirming their autonomy. The data demonstrate the presence of multiple forms of the natural TSHR. Their roles in TSH action and TSHR autoimmunity require further exploration.
Detection of Alzheimer‘S and Parkinson‘S Disease From Exhaled Breath Using Nanomaterial-Based Sensors (2012)

The breath prints that were identified with combinations of nanomaterial-based sensors have future potential as cost-effective, fast and reliable biomarkers for AD and PD.
REGULATION OFENZYMES OF THEUREACYCLE ANDARGININEMETABOLISM (2002)

The urea cycle is comprised of five enzymes but also requires other enzymes and mitochondrial amino acid transporters to function fully. The complete urea cycle is expressed in liver and to a small degree also in enterocytes. However, highly regulated expression of several enzymes present in the urea cycle occurs also in many other tissues, where these enzymes are involved in synthesis of nitric oxide, polyamines, proline and glutamate. Glucagon, insulin, and glucocorticoids are major regulators of the expression of urea cycle enzymes in liver. In contrast, the "urea cycle" enzymes in nonhepatic cells are regulated by a wide range of pro- and antiinflammatory cytokines and other agents. Regulation of these enzymes is largely transcriptional in virtually all cell types. This review emphasizes recent information regarding roles and regulation of urea cycle and arginine metabolic enzymes in liver and other cell types.
Solution phase combinatorial chemistry (1998)

Combinatorial chemistry and parallel array synthesis techniques are now used extensively in the drug discovery process. Although published literature has been dominated by solid phase chemistry approaches, the use of solution phase techniques has also been widely explored. This review considers the advantages and disadvantages of choosing solution phase approaches in the various stages of drug discovery and optimisation, and assesses the practical issues related to these approaches. The uses of standard solution chemistry, the related liquid phase approach, and of supported materials to enhance solution phase chemistry are all illustrated by a comprehensive review of the published literature over the past three years.
Phospholipid polymer hydrogel formed by the photodimerization of cinnamoyl groups in the polymer side chain (2007)

Abstract We synthesized new polymers with both photocrosslinkability and biocompatibility by a random copolymerization of 4‐(4‐methoxycinnamoyl)phenyl methacrylate and 2‐methacryloyloxyethyl phosphorylcholine. These polymers were used as prepolymers to make a hydrogel by photoirradiation. Gelation began with 5 s of photoirradiation and reached an equilibrium state after 360 s of photoirradiation. The absorption maximum at 347 nm, attributed to the cinnamoyl group, disappeared with the photoirradiation time. That is, dimerization between cinnamoyl groups in the polymer proceeded and formed a hydrogel. The equilibrium water concentration of the hydrogels was more than 90%. Moreover, we succeeded in making a microshape hydrogel on glass by photoirradiation through a photomask. The window shape of the photomask was transferred to the hydrogel that was formed. We concluded that these photocrosslinkable polymers could be useful in preparing microfluidic devices for separating or immobilizing biomolecules and cells. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 104: 44–50, 2007
A Non-cryogenic Method for the Preparation of 2-(Indolyl) Borates, Silanes, and Silanols (2002)

2-Indolyl borates are prepared via addition of LDA to a mixture of N-Boc-indole and triisopropyl borate at 0-5 degrees C. Following acidic hydrolysis, the boronic acids are isolated by crystallization in good to excellent yield (73-99%). The method is quite general, tolerating a wide range of functional groups, and also provides access to 2-silyl derivatives (80-91%).
Novel Orthogonal Strategy toward Solid-Phase Synthesis of 1,3,5-Substituted Triazines (2003)

[reaction: see text] To improve upon the previous orthogonal method for synthesis of a triazine library, an alternative strategy has been developed via oxidation-activation of the thioether to the sulfone. Through a comparison between these two methods, the sulfone strategy was demonstrated as an enhanced method in the generation of highly pure triazine library compounds.
In vivo phosphorylation of regulatory light chain of myosin II during mitosis of cultured cells (1994)

Phosphorylation of the regulatory light chain of myosin II (MLC) controls the contractility of actomyosin in nonmuscle and muscle cells. It has been reported that cdc2 phosphorylates MLC in vitro at Ser-1 or Ser-2 and Thr-9 which protein kinase C phosphorylates (Satterwhite, L. L., M. J. Lohka, K. L. Wilson, T. Y. Scherson, L. K. Cisek, J. L. Corden, and T. D. Pollard. 1992 J. Cell Biol. 118:595-605). We have examined in vivo phosphorylation of MLC during mitosis and after the release of mitotic arrest. Phosphate incorporation of MLC in mitotic cells is found to be 6-12 times greater than that in nonmitotic cells. Phosphopeptide maps have revealed that the MLC from mitotic cells is phosphorylated at Ser-1 and/or Ser-2 (Ser-1/2), but not at Thr-9. MLC is also phosphorylated to a much lesser extent at Ser-19 which myosin light chain kinase phosphorylates. On the other hand, MLC of nonmitotic cells is phosphorylated at Ser-19 but not at Ser-1/2. The extent of phosphate incorporation is doubled at 30 min after the release of mitotic arrest when some cells start cytokinesis. Phosphopeptide analyses have revealed that the phosphorylation at Ser-19 is increased 20 times, while the phosphorylation at Ser-1/2 is decreased by half. This high extent of MLC phosphorylation at Ser-19 is maintained for another 30 min and gradually decreased to near the level of interphase cells as cells complete spreading at 180 min. On the other hand, phosphorylation at Ser-1/2 is decreased to 18% at 60 min, and is practically undetectable at 180 min after the release of mitotic arrest. The stoichiometry of MLC phosphorylation has been determined by quantitation of phosphorylated and unphosphorylated forms of MLC separated on 2D gels. The molar ratio of phosphorylated MLC to total MLC is found to be 0.16 +/- 0.06 and 0.31 +/- 0.05 in interphase and mitotic cells, respectively. The ratio is increased to 0.49 +/- 0.05 at 30 min after the release of mitotic arrest. These results suggest that the change in the phosphorylation site from Ser-1/2 to Ser-19 plays an important role in signaling cytokinesis.
Photodynamic therapy of high‐grade cervical intraepithelial neoplasia with 5‐aminolevulinic acid (2002)

PDT at this light and ALA dose is well tolerated but has minimal activity in the treatment of CIN 2 and CIN 3. Other doses and schedules of light and ALA or novel photosensitizers may improve efficacy.
Regiocontrolled Cyclization Reaction of N-(2-Hydroxyethyl)ureas by Transfer of Activation:  One-Pot Synthesis of 2-Imidazolidinones (1999)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTRegiocontrolled Cyclization Reaction of N-(2-Hydroxyethyl)ureas by Transfer of Activation: One-Pot Synthesis of 2-ImidazolidinonesTaek Hyeon Kim and Gue-Jae LeeView Author Information Faculty of Applied Chemistry, Chonnam National University, Kwangju 500-757, Korea Cite this: J. Org. Chem. 1999, 64, 8, 2941–2943Publication Date (Web):March 31, 1999Publication History Received7 October 1998Published online31 March 1999Published inissue 1 April 1999https://doi.org/10.1021/jo9820061Copyright © 1999 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views800Altmetric-Citations27LEARN 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 InReddit Read OnlinePDF (39 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Alcohols,Aldol reactions,Anions,Cyclization,Urea Get e-Alerts
A Comparison of Naive and Experienced Bidders in Common Value Offer Auctions: A Laboratory Analysis (1989)

Journal Article A Comparison of Naive and Experienced Bidders in Common Value Offer Auctions: A Laboratory Analysis Get access Douglas Dyer, Douglas Dyer Memphis State University Search for other works by this author on: Oxford Academic Google Scholar John H. Kagel, John H. Kagel University of Houston and University of Pittsburgh Search for other works by this author on: Oxford Academic Google Scholar Dan Levin Dan Levin University of Houston Search for other works by this author on: Oxford Academic Google Scholar The Economic Journal, Volume 99, Issue 394, 1 March 1989, Pages 108–115, https://doi.org/10.2307/2234207 Published: 01 March 1989
Alzheimer's Disease: Genes, Proteins, and Therapy (2001)

Rapid progress in deciphering the biological mechanism of Alzheimer's disease (AD) has arisen from the application of molecular and cell biology to this complex disorder of the limbic and association cortices. In turn, new insights into fundamental aspects of protein biology have resulted from research on the disease. This beneficial interplay between basic and applied cell biology is well illustrated by advances in understanding the genotype-to-phenotype relationships of familial Alzheimer's disease. All four genes definitively linked to inherited forms of the disease to date have been shown to increase the production and/or deposition of amyloid beta-protein in the brain. In particular, evidence that the presenilin proteins, mutations in which cause the most aggressive form of inherited AD, lead to altered intramembranous cleavage of the beta-amyloid precursor protein by the protease called gamma-secretase has spurred progress toward novel therapeutics. The finding that presenilin itself may be the long-sought gamma-secretase, coupled with the recent identification of beta-secretase, has provided discrete biochemical targets for drug screening and development. Alternate and novel strategies for inhibiting the early mechanism of the disease are also emerging. The progress reviewed here, coupled with better ability to diagnose the disease early, bode well for the successful development of therapeutic and preventative drugs for this major public health problem.