gebhart/patrepeval huggingface dataset:
Crystallographic and thermodynamic comparison of natural and synthetic ligands bound to streptavidin (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCrystallographic and thermodynamic comparison of natural and synthetic ligands bound to streptavidinP. C. Weber, J. J. Wendoloski, M. W. Pantoliano, and F. R. SalemmeCite this: J. Am. Chem. Soc. 1992, 114, 9, 3197–3200Publication Date (Print):April 1, 1992Publication History Published online1 May 2002Published inissue 1 April 1992https://pubs.acs.org/doi/10.1021/ja00035a004https://doi.org/10.1021/ja00035a004research-articleACS PublicationsRequest reuse permissionsArticle Views948Altmetric-Citations203LEARN 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 Get e-Alerts
Pairwise document similarity in large collections with MapReduce (2008)

This paper presents a MapReduce algorithm for computing pairwise document similarity in large document collections. MapReduce is an attractive framework because it allows us to decompose the inner products involved in computing document similarity into separate multiplication and summation stages in a way that is well matched to efficient disk access patterns across several machines. On a collection consisting of approximately 900,000 newswire articles, our algorithm exhibits linear growth in running time and space in terms of the number of documents.
Cytoprotective effects of nitrite during in vivo ischemia-reperfusion of the heart and liver (2005)

Nitrite represents a circulating and tissue storage form of NO whose bioactivation is mediated by the enzymatic action of xanthine oxidoreductase, nonenzymatic disproportionation, and reduction by deoxyhemoglobin, myoglobin, and tissue heme proteins. Because the rate of NO generation from nitrite is linearly dependent on reductions in oxygen and pH levels, we hypothesized that nitrite would be reduced to NO in ischemic tissue and exert NO-dependent protective effects. Solutions of sodium nitrite were administered in the setting of hepatic and cardiac ischemia-reperfusion (I/R) injury in mice. In hepatic I/R, nitrite exerted profound dose-dependent protective effects on cellular necrosis and apoptosis, with highly significant protective effects observed at near-physiological nitrite concentrations. In myocardial I/R injury, nitrite reduced cardiac infarct size by 67%. Consistent with hypoxia-dependent nitrite bioactivation, nitrite was reduced to NO, S-nitrosothiols, N-nitros-amines, and iron-nitrosylated heme proteins within 1-30 minutes of reperfusion. Nitrite-mediated protection of both the liver and the heart was dependent on NO generation and independent of eNOS and heme oxygenase-1 enzyme activities. These results suggest that nitrite is a biological storage reserve of NO subserving a critical function in tissue protection from ischemic injury. These studies reveal an unexpected and novel therapy for diseases such as myocardial infarction, organ preservation and transplantation, and shock states.
Discharge plasma treatment for nox reduction from diesel engine exhaust: a laboratory investigation (2005)

A detailed study on the removal of oxides of nitrogen (NO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x </sub> ) with and without the presence of carbonaceous soot in a stationary diesel engine exhaust was carried out using pulsed electrical discharges/catalyst/adsorbent processes. The processes were separately studied first and then the cascaded processes namely plasma-catalyst and plasma-adsorbent were examined. To investigate the effect of carbonaceous soot on the plasma treatment process, the filtered and unfiltered exhaust was treated by plasma separately. In the cascaded plasma-catalyst process, the plasma treating filtered exhaust was cascaded with a reduction catalyst V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sub> /TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2 </sub> using ammonia as reducing agent and in the cascaded plasma-adsorbent process, the plasma treating unfiltered (raw) exhaust was cascaded with adsorbents (MS-13X/activated alumina/activated charcoal). The enhanced NO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> removal efficiency of plasma process in the presence of soot is identified, possible pathways are summarized and the results of the cascaded processes are discussed in detail
InTouch 4 (4) (1999)

This is a newsletter of the World Bank country office Manila. This issue features: LOGOFIND: strengthening local government units. World Development Report launched. Global poverty issues discussed at WB-IMF meetings 1999. Prospects for East Asia. Update on the Philippine country assistance strategy. WB news: 2 NGOs receive grants for FY 1999. Joint Japan/World Bank graduate scholarship program for Year 2000. Bank, Asian Institute Management enhance Department of Social Work Development capability in procurement management. WB publications.
Dielectrophoresis and electrohydrodynamics-mediated fluidic assembly of silicon resistors (2003)

In this letter, we present techniques, utilizing dielectrophoresis and electrohydrodynamics, which can be used for assembling single-crystal silicon devices suspended in a solution onto a binding site on a heterogeneous substrate. Silicon resistors with gold/chromium layers located at the end of the resistors and silicon blocks without metal were fabricated on bonded and etched-backed silicon-on-insulator wafers and successfully released into deionized water. The devices were subsequently assembled on a different substrate at specific binding sites by dielectrophoretic and electrohydrodynamic forces with submicron precision. Current–voltage measurements of the assembled resistors exhibited low contact resistance after the solution was completely evaporated and the contacts were annealed.
The role of Syk/CARD9 coupled C‐type lectins in antifungal immunity (2010)

Fungal infections are affecting an increasing number of people, and the failure of current therapies in treating systemic infection has resulted in an unacceptably high mortality rate. It is therefore of importance that we understand immune mechanisms operating during fungal infections, in order to facilitate development of adjunctive immunotherapies for the treatment of these diseases. C-type lectin receptors (CLRs) are pattern recognition receptors (PRRs) that are critical for immune responses to fungi. Many of these receptors are coupled to Syk kinase, which allows these receptors to signal via CARD9 leading to NF-κB activation, which in turn contributes to the induction of both innate and adaptive immunity. Dectin-1, Dectin-2 and Mincle are all CLRs that share this common signalling mechanism and have been shown to play key roles in antifungal immunity. This review aims to update existing paradigms and summarise the most recent findings on these CLRs, their signal transduction mechanisms and the collaborations between these CLRs and other PRRs.
Alpha-2 Adrenergic Receptor Agonists: A Review of Current Clinical Applications (2015)

The α-2 adrenergic receptor agonists have been used for decades to treat common medical conditions such as hypertension; attention-deficit/hyperactivity disorder; various pain and panic disorders; symptoms of opioid, benzodiazepine, and alcohol withdrawal; and cigarette craving. (1) However, in more recent years, these drugs have been used as adjuncts for sedation and to reduce anesthetic requirements. This review will provide an historical perspective of this drug class, an understanding of pharmacological mechanisms, and an insight into current applications in clinical anesthesiology.
Diversity and junction residues as hotspots of binding energy in an antibody neutralizing the dengue virus (2005)

Dengue is a re-emerging viral disease, affecting approx. 100 million individuals annually. The monoclonal antibody mAb4E11 neutralizes the four serotypes of the dengue virus, but not other flaviviruses. Its epitope is included within the highly immunogenic domain 3 of the envelope glycoprotein E. To understand the favorable properties of recognition between mAb4E11 and the virus, we recreated the genetic events that led to mAb4E11 during an immune response and performed an alanine scanning mutagenesis of its third hypervariable loops (H-CDR3 and L-CDR3). The affinities between 16 mutant Fab fragments and the viral antigen (serotype 1) were measured by a competition ELISA in solution and their kinetics of interaction by surface plasmon resonance. The diversity and junction residues of mAb4E11 (D segment; V(H)-D, D-J(H) and V(L)-J(L) junctions) constituted major hotspots of interaction energy. Two residues from the D segment (H-Trp96 and H-Glu97) provided > 85% of the free energy of interaction and were highly accessible to the solvent in a three-dimensional model of mAb4E11. Changes of residues (L-Arg90 and L-Pro95) that statistically do not participate in the contacts between antibodies and antigens but determine the structure of L-CDR3, decreased the affinity between mAb4E11 and its antigen. Changes of L-Pro95 and other neutral residues strongly decreased the rate of association, possibly by perturbing the topology of the electrostatic field of the antibody. These data will help to improve the properties of mAb4E11 for therapeutic applications and map its epitope precisely.
C-Type Natriuretic Peptide Stimulates Ovarian Follicle Development (2012)

C-type natriuretic peptide (CNP) encoded by the NPPC (Natriuretic Peptide Precursor C) gene expressed in ovarian granulosa cells inhibits oocyte maturation by activating the natriuretic peptide receptor (NPR)B (NPRB) in cumulus cells. RT-PCR analyses indicated increased NPPC and NPRB expression during ovarian development and follicle growth, associated with increases in ovarian CNP peptides in mice. In cultured somatic cells from infantile ovaries and granulosa cells from prepubertal animals, treatment with CNP stimulated cGMP production. Also, treatment of cultured preantral follicles with CNP stimulated follicle growth whereas treatment of cultured ovarian explants from infantile mice with CNP, similar to FSH, increased ovarian weight gain that was associated with the development of primary and early secondary follicles to the late secondary stage. Of interest, treatment with FSH increased levels of NPPC, but not NPRB, transcripts in ovarian explants. In vivo studies further indicated that daily injections of infantile mice with CNP for 4 d promoted ovarian growth, allowing successful ovulation induction by gonadotropins. In prepubertal mice, CNP treatment alone also promoted early antral follicle growth to the preovulatory stage, leading to efficient ovulation induction by LH/human chorionic gonadotropin. Mature oocytes retrieved after CNP treatment could be fertilized in vitro and developed into blastocysts, allowing the delivery of viable offspring. Thus, CNP secreted by growing follicles is capable of stimulating preantral and antral follicle growth. In place of FSH, CNP treatment could provide an alternative therapy for female infertility.
Variables affecting convection-enhanced delivery to the striatum: a systematic examination of rate of infusion, cannula size, infusate concentration, and tissue—cannula sealing time (1999)

Rate of infusion and cannula size can significantly affect convective distribution of molecules, whereas preinfusion sealing time and variations in infusate concentration have no effect in this small animal model. Understanding the parameters that influence convective delivery within the CNS can be used to enhance delivery of potentially therapeutic agents in an experimental setting and to indicate the variables that will need to be considered for optimum use of this approach for drug delivery in the clinical setting.
Influence of the Axial Dispersion on the Performance of Tubular Reactors during the Noncatalytic Supercritical Transesterification of Triglycerides (2006)

Transesterification of fats and oils by methanol is known to proceed by a three-step consecutive reaction mechanism in which the formation of the diglyceride is the rate-limiting step. At low conversion values (<25−35%), the system has mass transfer limitations due to the immiscibility of the oil−methanol system. Noncatalytic transesterication in supercritical methanol overcomes this problem by forming a one-phase reacting system. The implementation of this reaction mode in the continuous tubular reactor is needed for the evaluation of the effect of the backmixing that appears when methanol acquires a gaslike mobility in the supercritical state. Such a study was performed here, and it was found that supercritical transesterification reactors must be operated at an axial Péclet number equal or higher than 1000 in order to limit backmixing effects to a minimum and achieve batchlike conversions at residence times of 1 h or less. High conversion values at low Péclet numbers can only be obtained by working at inconveniently high temperatures and high methanol-to-oil ratios.
Classical Swine Fever Virus E rns Deletion Mutants: trans -Complementation and Potential Use as Nontransmissible, Modified, Live-Attenuated Marker Vaccines (2000)

An SK6 cell line (SK6c26) which constitutively expressed the glycoprotein E(rns) of classical swine fever virus (CSFV) was used to rescue CSFV E(rns) deletion mutants based on the infectious copy of CSFV strain C. The biochemical properties of E(rns) from this cell line were indistinguishable from those of CSFV E(rns). Two E(rns) deletion mutants were constructed, virus Flc23 and virus Flc22. Virus Flc23 encoded only the utmost N- and C-terminal amino acids of E(rns) (deletion of 215 amino acids) to retain the original protease cleavage sites. Virus Flc22 is not recognized by a panel of E(rns) antibodies, due to a deletion of 66 amino acids in E(rns). The E(rns) deletion mutants Flc22 and Flc23 could be rescued in vitro only on the complementing SK6c26 cells. These rescued viruses could infect and replicate in SK6 cells but did not yield infectious virus. Virus neutralization by E(rns)-specific antibodies was similar for the wild-type virus and the recombinant viruses, indicating that E(rns) from SK6c26 cells was incorporated in the viral particles. Pigs vaccinated with Flc22 or Flc23 were protected against a challenge with a lethal dose of CSFV strain Brescia. This is the first demonstration of trans-complementation of defective pestivirus RNA with a pestiviral structural protein and opens new ways to develop nontransmissible modified live pestivirus vaccines. In addition, the absence of (the antigenic part of) E(rns) in the recombinant viral particles can be used to differentiate between infected and vaccinated animals.
Effects of eicosapentaenoic acid (EPA) on prostacyclin production in diabetics: GC/MS analysis of PGI2 and PGI3 levels. (1997)

The enzymatic metabolites, 6-keto-PGF1 alpha and delta 17-6-keto-PGF1 alpha, were measured by gas chromatography/high resolution-selected ion monitoring (GC/HR-SIM) as markers of prostaglandin I2 (PGI2) and prostacyclin (PGI3) production in human sera. Eicosapentaenoic acid (EPA) ethyl ester (1.8 g/day) was administered to 12 noninsulin-dependent diabetes mellitus (NIDDM) patients for 2 weeks. Forty patients with similar NIDDM were followed as a control group. PGI3 production in sera was significantly increased in the EPA intake group in comparison with the control group. These findings suggest that EPA intake prevents complications of diabetes mellitus, such as microangiopathy and vaso-occlusive diseases.
Turbo codes for nonuniform memoryless sources over noisy channels (2002)

This work addresses the problem of designing turbo codes for nonuniform binary memoryless or independent and identically distributed (i.i.d.) sources over noisy channels. The extrinsic information in the decoder is modified to exploit the source redundancy in the form of nonuniformity; furthermore, the constituent encoder structure is optimized for the considered nonuniform i.i.d. source to further enhance the system performance. Some constituent encoders are found to substantially outperform Berrou's (1996) (37, 21) encoder. Indeed, it is shown that the bit error rate (BER) performance of the newly designed turbo codes is greatly improved as significant coding gains are obtained.
Some additional suggestions for an intervertebral disc prosthesis (1985)

The paper, which refers to previous original papers on the subject, gives suggestions indicating four intervertebral disc prostheses, one utilizing bone cement for fixation to the bony substance of the motion segment. In the paper a modification of this inter-vertebral disc prosthesis offers a possibility for fixation of the prosthesis by osteointegration.
Identification of a Novel Inhibitor of Mitogen-activated Protein Kinase Kinase (1998)

The compound U0126 (1,4-diamino-2,3-dicyano-1, 4-bis[2-aminophenylthio]butadiene) was identified as an inhibitor of AP-1 transactivation in a cell-based reporter assay. U0126 was also shown to inhibit endogenous promoters containing AP-1 response elements but did not affect genes lacking an AP-1 response element in their promoters. These effects of U0126 result from direct inhibition of the mitogen-activated protein kinase kinase family members, MEK-1 and MEK-2. Inhibition is selective for MEK-1 and -2, as U0126 shows little, if any, effect on the kinase activities of protein kinase C, Abl, Raf, MEKK, ERK, JNK, MKK-3, MKK-4/SEK, MKK-6, Cdk2, or Cdk4. Comparative kinetic analysis of U0126 and the MEK inhibitor PD098059 (Dudley, D. T., Pang, L., Decker, S. J., Bridges, A. J., and Saltiel, A. R. (1995) Proc. Natl. Acad. Sci U. S. A. 92, 7686-7689) demonstrates that U0126 and PD098059 are noncompetitive inhibitors with respect to both MEK substrates, ATP and ERK. We further demonstrate that the two compounds bind to deltaN3-S218E/S222D MEK in a mutually exclusive fashion, suggesting that they may share a common or overlapping binding site(s). Quantitative evaluation of the steady state kinetics of MEK inhibition by these compounds reveals that U0126 has approximately 100-fold higher affinity for deltaN3-S218E/S222D MEK than does PD098059. We further tested the effects of these compounds on the activity of wild type MEK isolated after activation from stimulated cells. Surprisingly, we observe a significant diminution in affinity of both compounds for wild type MEK as compared with the deltaN3-S218E/S222D mutant enzyme. These results suggest that the affinity of both compounds is mediated by subtle conformational differences between the two activated MEK forms. The MEK affinity of U0126, its selectivity for MEK over other kinases, and its cellular efficacy suggest that this compound will serve as a powerful tool for in vitro and cellular investigations of mitogen-activated protein kinase-mediated signal transduction.
Soluble Plant Cell Signals Induce the Expression of the Type III Secretion System of Pseudomonas syringae and Upregulate the Production of Pilus Protein HrpA (2009)

Type III protein secretion is essential for the pathogenicity of Pseudomonas syringae on its host plants. Expression of HrpA, a major component of the type III secretion system (T3SS)-associated pilus, was studied both in plant leaves and in vitro using reporter genes. We found that induction of the hrpA promoter was stronger in plants than in vitro, and that the induction was enhanced by both host and nonhost plants of P. syringae pv. tomato. In vitro, the expression was enhanced by cell-free exudates from plant cell suspension cultures, added into the minimal medium. Further analysis of the plant-cell-derived, hrpA-inducing factors showed that they were small and water-soluble compounds, which could signal P. syringae the proximity of living plant cells. We also studied the production and secretion of native HrpA protein in vitro, and detected a plant-signal-dependent increase in HrpA secretion. In contrast to HrpA, the intracellular accumulation or secretion of the other T3SS-dependent proteins were not significantly increased, despite the presence of plant cell-derived, promoter-inducing factors. Thus, the accumulation of HrpA pilin seems to be subjected to a distinct post-transcriptional regulation.
Scheduling heavy-tailed data traffic over the wireless Internet (2003)

We propose new concepts in quality of service (QoS) and scheduling for the wireless Internet that account for the following key observations: (a) Internet traffic is long range dependent, or heavy-tailed, but the conventional approach of handling this via more conservative resource provisioning is unattractive in relatively low bandwidth wireless networks; (b) flat rate charging is an attractive paradigm for data applications, in which case the network's objective becomes to satisfy as many users as possible, rather than be fair in a traditional sense. The QoS framework consists of guaranteeing a certain bandwidth, with high probability, to the transactions on the network, where a transaction might be interpreted, for example, as a TCP connection, or a group of TCP connections, for a given source-destination pair. The lengths of these transactions can vary widely, ranging from a large file transfer to a short E-mail or Web page download, and follows a heavy-tailed distribution. We demonstrate that much fewer network resources are required to satisfy a given QoS guarantee using scheduling strategies that implicitly or explicitly penalize long transactions, compared to a "fair" strategy such as round robin. For multiple users that see channels of different capacities on a shared wireless medium, we modify our QoS framework to be consistent with the proportional fairness criterion. We show that schedulers that discriminate against long transactions, while providing roughly equal "air time" to the users, work much better than conventional round robin based scheduling.
Analysis and Suppression of DNA Polymerase Pauses Associated with a Trinucleotide Consensus (1996)

We have studied a novel class of DNA sequences that cause DNA polymerases to pause. These sequences have the central consensus Py-G-C and are not necessarily adjacent to hairpins in the DNA template. Since most consensus sequences do not cause pauses under standard conditions, additional template features must exist that make it difficult to incorporate nucleotides at these positions. We believe that these pauses result from constraints that make the conformation change involved in nucleotide selection more difficult. These pauses can obscure parts of DNA sequencing ladders and prevent DNA amplification by the polymerase chain reaction. The addition of betaine, and some related compounds, relieves these pauses.
World's Youth Connect through Global Nomads Group: An Interview with GNG's David Macquart. (2006)

David Macquart [DM