gebhart/patrepeval huggingface dataset:
Substrate-Promoted Formation of a Catalytically Competent Binuclear Center and Regulation of Reactivity in a Glycerophosphodiesterase from Enterobacter aerogenes (2008)

The glycerophosphodiesterase (GpdQ) from Enterobacter aerogenes is a promiscuous binuclear metallohydrolase that catalyzes the hydrolysis of mono-, di-, and triester substrates, including some organophosphate pesticides and products of the degradation of nerve agents. GpdQ has attracted recent attention as a promising enzymatic bioremediator. Here, we have investigated the catalytic mechanism of this versatile enzyme using a range of techniques. An improved crystal structure (1.9 A resolution) illustrates the presence of (i) an extended hydrogen bond network in the active site, and (ii) two possible nucleophiles, i.e., water/hydroxide ligands, coordinated to one or both metal ions. While it is at present not possible to unambiguously distinguish between these two possibilities, a reaction mechanism is proposed whereby the terminally bound H2O/OH(-) acts as the nucleophile, activated via hydrogen bonding by the bridging water molecule. Furthermore, the presence of substrate promotes the formation of a catalytically competent binuclear center by significantly enhancing the binding affinity of one of the metal ions in the active site. Asn80 appears to display coordination flexibility that may modulate enzyme activity. Kinetic data suggest that the rate-limiting step occurs after hydrolysis, i.e., the release of the phosphate moiety and the concomitant dissociation of one of the metal ions and/or associated conformational changes. Thus, it is proposed that GpdQ employs an intricate regulatory mechanism for catalysis, where coordination flexibility in one of the two metal binding sites is essential for optimal activity.
Face and hand gesture recognition using hybrid classifiers (2002)

This paper advances the methodology of hybrid classification architectures for face and hand gesture recognition tasks and shows their feasibility through experimental studies using the FERET data base and gesture images. The hybrid architecture, consisting of an ensemble of connectionist networks-radial basis functions (RBF)-and inductive decision trees (DT), combines the merits of 'holistic' template matching with those of 'abstractive' matching using discrete features and subject to both positive and negative learning. The hybrid architecture, quite general as it applies to both face and hand gesture recognition, derives its robustness from (i) consensus using ensembles of RBF network;, and (ii) flexible matching using categorical classification via decision trees. The experimental results, proving the feasibility of our approach, yield (i) 93% accuracy, using cross validation, for contents-based image retrieval (CBIR) subject to correct ID matching tasks, such as 'find Joe Smith with/without glasses', on a data bate of 200 images, and (ii) 96% accuracy using cross validation, for forensic verification on a data base consisting of 102 images corresponding to 350 subjects (of whom 102 are duplicates). Cross validation results on the hand gesture recognition task yield a false negative rate of 3.6% and a false positive rate of 1.8%, using a data base of 750 images corresponding to 25 hand gestures.
Churg-Strauss syndrome and polyarteritis nodosa (1991)

In the past year, the major contributions to our understanding of Churg-Strauss syndrome and polyarteritis nodosa were the development of classification criteria by which to separate these from other vasculitides. The absence of granulomas in most biopsies from patients with Churg-Strauss syndrome was noted. Other reports suggested that allergic disease may be only one of the hypereosinophilic conditions that predispose to this form of vasculitis. Eosinophilia and vasculitis occurring in a patient after dietary supplementation with L-tryptophan were reported, and the prominent cardiac involvement in Churg-Strauss syndrome was reemphasized. Impressive responses of that disease to cyclophosphamide were documented in one patient. In the American College of Rheumatology Vasculitis Classification Study, polyarteritis nodosa was one of the hardest vasculitides to distinguish. Several reports reiterated the serious risk of major pulmonary hemorrhage from microscopic polyarteritis of the lung, which probably represents a forme fruste of Wegener's granulomatosis. Although no new studies of therapy in polyarteritis were reported, a review of infections in such patients indicated that exposure to more than 15 mg/d of prednisone correlated with infectious complications, and that intra-abdominal infections were particularly problematic.
Experimental determination of critical crack size for an aircraft bulkhead with oversized fastener holes (2015)

During aircraft maintenance, oversizing modification has often been undertaken to remove fatigue cracking in fastener holes. In the example considered here, multiple modifications resulted in an oversized fastener hole in a fighter aircraft centre fuselage bulkhead. The short edge distance as a result of the oversized hole may have had an adverse effect on the component's fatigue life. Therefore, there was a need to reassess the fatigue life of the affected bulkhead and to establish the critical crack size for the oversized fastener hole. In this study, an ex-service bulkhead was configured with similar oversized holes as discovered in the fleet, and then was subjected to a residual strength test in accordance with the aircraft certification structural design standard. The test results obtained were essential for the determination of new inspection intervals for fleet structural integrity management for aircraft with a similar configuration.
SYNTHÈSES D'ACIDES AMINÉS CYCLIQUES À PARTIR DE DÉRIVÉS DE L'ACIDE ADIPIQUE (1962)

The Dieckmann reaction has been reinvestigated in view of obtaining alkyl-substituted cyclopentanones. Control of the reaction during alkylation now permits either the opening of the cyclopentane ring to give, without the isolation of intermediates, substituted adipic esters in excellent yields or normal substitution on the ring.Methyl- and allyl-substituted cyclopentanones were obtained from the corresponding Dieckmann esters or from the substituted adipic acids. These ketones were transformed by the Strecker method into their corresponding spirohydantoins. In both cases, two diastereo-isomers were isolated and studied.1-Amino-2-methyl-cyclopentanecarboxylic acid and 1-amino-2-allyl-cyclopentanecarboxylic acid were prepared in good yields from the spirohydantoins and characterized.
A convenient synthesis of dicarboxylic monoesters using isopropenyl esters: synthesis of oxaunomycin derivatives (1993)

Reaction of various types of alcohols with a novel type of acylating agent, the isopropenyl esters 2a–e in the presence of a catalytic amount of conc. sulfuric acid or toluene-p-sulfonic acid followed by selective deprotection of the terminal ester gives the monoesters 5a–i in good yields.
Identification of a thymidylate synthase ribonucleoprotein complex in human colon cancer cells (1994)

Translation of thymidylate synthase (TS) mRNA is controlled by its own protein product, TS, in an autoregulatory manner. Direct binding of TS protein to two different cis-acting elements on the TS mRNA is associated with this translational regulation. In this study, an immunoprecipitation-reverse transcription-PCR technique was used to identify a TS ribonucleoprotein (RNP) complex in cultured human colon cancer cells. Using antibodies specific for TS protein, we show that TS is complexed in vivo with its own TS RNA. Furthermore, evidence demonstrating a direct interaction between the mRNA of the nuclear oncogene c-myc and TS protein is presented.
Synthesis of Protected Carbohydrate Derivatives Through Homologation of Threose and Erythrose Derivatives with Chiral .gamma.-Alkoxy Allylic Stannanes (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of Protected Carbohydrate Derivatives Through Homologation of Threose and Erythrose Derivatives with Chiral .gamma.-Alkoxy Allylic StannanesJames A. Marshall, Boris M. Seletsky, and George P. LukeCite this: J. Org. Chem. 1994, 59, 12, 3413–3420Publication Date (Print):June 1, 1994Publication History Published online1 May 2002Published inissue 1 June 1994https://pubs.acs.org/doi/10.1021/jo00091a034https://doi.org/10.1021/jo00091a034research-articleACS PublicationsRequest reuse permissionsArticle Views704Altmetric-Citations47LEARN 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
Site-Directed Mutagenesis of Human Endothelial Cell Ecto-ADPase/Soluble CD39:  Requirement of Glutamate 174 and Serine 218 for Enzyme Activity and Inhibition of Platelet Recruitment (2000)

Endothelial cell CD39/ecto-ADPase plays a major role in vascular homeostasis. It rapidly metabolizes ADP released from stimulated platelets, thereby preventing further platelet activation and recruitment. We recently developed a recombinant, soluble form of human CD39, solCD39, with enzymatic and biological properties identical to CD39. To identify amino acids essential for enzymatic/biological activity, we performed site-directed mutagenesis within the four highly conserved apyrase regions of solCD39. Mutation of glutamate 174 to alanine (E174A) and serine 218 to alanine (S218A) resulted in complete and approximately 90% loss of solCD39 enzymatic activity, respectively. Furthermore, compared to wild-type, S57A exhibited a 2-fold increase in ADPase activity without change in ATPase activity, while the tyrosine 127 to alanine (Y127A) mutant lost 50-60% of both ADPase and ATPase activity. The ADPase activity of wild-type solCD39 and each mutant, except for R135A, was greater with calcium as the required divalent cation than with magnesium, but for ATPase activity generally no such preference was observed. Y127A demonstrated the highest calcium/magnesium ADPase activity ratio, 2.8-fold higher than that of wild-type, even though its enzyme activity was greatly reduced. SolCD39 mutants were further characterized by correlating enzymatic with biological activity in an in vitro platelet aggregation system. Each solCD39 mutant was similar to wild-type in reversing platelet aggregation, except for E174A and S218A. E174A, completely devoid of enzymatic activity, failed to inhibit platelet responsiveness, as anticipated. S218A, with 91% loss of ADPase activity, could still reverse platelet aggregation, albeit much less effectively than wild-type solCD39. Thus, glutamate 174 and serine 218 are essential for both the enzymatic and biological activity of solCD39.
Methods for identifying versioned and plagiarized documents (2003)

Abstract The widespread use of on‐line publishing of text promotes storage of multiple versions of documents and mirroring of documents in multiple locations, and greatly simplifies the task of plagiarizing the work of others. We evaluate two families of methods for searching a collection to find documents that are coderivative, that is, are versions or plagiarisms of each other. The first, the ranking family, uses information retrieval techniques; extending this family, we propose the identity measure, which is specifically designed for identification of coderivative documents. The second, the fingerprinting family, uses hashing to generate a compact document description, which can then be compared to the fingerprints of the documents in the collection. We introduce a new method for evaluating the effectiveness of these techniques, and demonstrate it in practice. Using experiments on two collections, we demonstrate that the identity measure and the best fingerprinting technique are both able to accurately identify coderivative documents. However, for fingerprinting parameters must be carefully chosen, and even so the identity measure is clearly superior.
Functional expression of the alpha-hemolysin of Staphylococcus aureus in intact Escherichia coli and in cell lysates. Deletion of five C-terminal amino acids selectively impairs hemolytic activity. (1992)

The alpha-hemolysin gene from Staphylococcus aureus, excluding the 5' region encoding the hydrophobic leader sequence, was amplified from genomic DNA. The identity of the disputed C terminus has been confirmed and revisions made to the internal sequence. The hemolysin is expressed at high levels in Escherichia coli and has been purified to homogeneity from this source. In addition, active [35S-Met]alpha-hemolysin of high specific radioactivity can be generated in an E. coli transcription-translation system. By criteria based on protein chemistry, and biological and electrophysiological assays, the recombinant polypeptide is closely similar to the staphylococcal polypeptide ruling out the possibility of functionally important posttranslational modifications in S. aureus. Convenient new assays utilizing the 35S-labeled polypeptide to measure erythrocyte binding, oligomer formation in detergent and on target cells, and hemolysis have been developed. They have been used to demonstrate that a deletion mutant of alpha-hemolysin, in which five C-terminal amino acids are absent, is severely compromised in its ability both to oligomerize and to lyse rabbit erythrocytes. The mutant polypeptide nevertheless binds tightly to erythrocytes as a monomer, strengthening the idea that oligomerization is required for cell lysis.
Insights into Long-Range Structural Effects on the Stereochemistry of Aldol Condensations:  A Practical Total Synthesis of Desoxyepothilone F (2001)

A processable total synthesis of a potent antitumor agent, desoxyepothilone F (dEpoF, 21-hydroxy-12,13-desoxyepothilone B, 21-hydroxyepothilone D), has been accomplished. The route is highly convergent. The new technology has also been applied to a total synthesis of 12,13-desoxyepothilone (dEpoB). The crucial point of departure from previous syntheses of dEpoB and dEpoF involves presentation of the C1-C11 sector for Suzuki coupling with C3 in reduced form. Hitherto, the required S stereochemistry at C3 had been implemented via reduction of a keto function after Suzuki coupling. Whereas that chemistry worked quite well in a synthesis of dEpoB, it was not transferable to a high-yielding synthesis of dEpoF. The reduction of the keto group at C3 via a Noyori protocol after Suzuki coupling had proved to be very difficult. In our current approach, two consecutive aldol reactions are used to fashion the acyl sector. In the first aldol condensation, C6 becomes attached to C7. Following protection at C7, a two-carbon acetate equivalent is used to join C2 and C3 with very high asymmetric induction at C3. Only after this center has been implemented is the Suzuki reaction conducted. This major advance allowed us to synthesize dEpoF in a straightforward fashion. These findings found ready application in the total synthesis of dEpoB. Another part of the study involved analysis of the factors associated with aldol condensations joining C6 to C7. In the work described herein, the consequences of the status of C3 in promoting the C6-C7 aldol coupling are probed in detail. Dramatic stereochemical long-range effects uncovered during the study are described, and a working model to explain these effects has emerged.
Low power laser irradiation alters gene expression of olfactory ensheathing cells in vitro (2005)

These results demonstrate that low and high dosages of PBM alter OEC activity, including upregulation of a number of neurotrophic growth factors and extracellular matrix proteins known to support neurite outgrowth. Therefore, the application of PBM in conjunction with OEC transplantation warrants consideration as a potential combination therapy for spinal cord injury.
BISMA - Fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences (2010)

BISMA works highly automated but still provides the user full control over all steps of the analysis. The BISMA software is freely available as an online tool for academic purposes for the analysis of bisulfite sequencing data from both unique and repetitive sequences http://biochem.jacobs-university.de/BDPC/BISMA/.
Inhibition of Nitric Oxide Synthesis Increases Focal Ischemic Infarction in Rat (1992)

We investigated whether inhibition of nitric oxide (NO) biosynthesis with N-omega-nitro-L-arginine (NNA), a competitive inhibitor of NO synthase (NOS), would modify the volume of the focal ischemic infarction produced by occlusion of the middle cerebral artery (MCA) in spontaneously hypertensive rats. NNA was infused for 1 h (2.4 mg/kg/h) immediately following occlusion of the MCA. NNA increased lesion volume 24 h later by 32% over controls (150.8 +/- 16.6 to 199.2 +/- 17.4 mm3; p less than 0.001, n = 6). This effect was antagonized by co-infusion of L- but not D-arginine. The antihypertensive rilmenidine (0.75 mg/kg) reduced the lesion by 27% (p less than 0.05, n = 4). Changes in lesion size were confined to the penumbra. NNA increased arterial pressure (AP) (118 +/- 8.9 to 149 +/- 16.0 mm Hg; p less than 0.01, n = 3) but did not change regional CBF. However, elevation of AP did not change the lesion volume or distribution. We conclude that inhibition of the constitutive form of NOS in vivo increases the volume of focal ischemic infarction as a consequence of reduced NO biosynthesis. The absence of NO availability may extend lesion formation by inhibition of reactive hyperemia, platelet disaggregation, and/or release of neuroprotective neuromodulators in the penumbra, which may counteract and override any of its neurotoxic actions.
Production of stable cytolytic T‐cell clones directed against autologous human melanoma (1987)

We have attempted to optimize the production of stable human cytolytic T lymphocyte clones directed against autologous melanoma cell lines. MLTC were restimulated every week with irradiated melanoma cells in medium containing human serum and IL-2. After 21 to 35 days, in 5 out of 6 patients, these cultures expressed a preferential cytolytic activity against the autologous melanoma cells, as compared to autologous EBV-B cells or NK target K562. Limiting dilution of MLTC responder cells was performed at times varying from days 7 to 28, in medium containing IL-2 and allogeneic EBV-B cells as feeders. Approximately 1% of these responder cells gave rise to CTL clones that lysed the autologous melanoma cells, but did not lyse K562 or autologous B cells. It was possible to maintain in culture for several months a large number of CTL clones that retained this specificity with high activity, and multiplied more than 5-fold every week. Some of these CTL clones were dependent on the presence of the autologous melanoma cells for their growth. With one melanoma, the use of autologous CTL clones made it possible to identify 3 different antigens on the tumor cells.
Molecular biology of prions causing infectious and genetic encephalopathies of humans as well as scrapie of sheep and BSE of cattle. (1991)

Considerable progress has been made in deciphering the role of an abnormal isoform of the prion protein (PrP) in scrapie of animals and Gerstmann-Sträussler syndrome (GSS) of humans. Transgenic (Tg) mice expressing both Syrian hamster (Ha) and mouse (Mo) PrP genes, which encode proteins differing at 16 residues out of 254, were used to probe the mechanism of scrapie prion replication. Four Tg lines expressing HaPrP exhibited distinct incubation times ranging from 48 to 277 days after Ha prion inoculation, which were inversely correlated with the steady-state levels of HaPrP mRNA and HaPrPc. Bioassays of brain extracts from two scrapie-infected Tg lines showed that the prion inoculum dictates which prions are synthesized de novo, even though the cells express both PrP genes. Tg mice inoculated with Ha prions had approximately 10(9) ID50 units of Ha prions per gram of brain while less than 10 units of Mo prions were found. Conversely, Tg mice inoculated with Mo prions had approximately 10(6) ID50 units of Mo prions and less than 10 units of Ha prions. Consistent with the analysis of prion synthesis, Tg mice inoculated with Ha prions exhibited neuropathologic changes characteristic of hamsters with scrapie while Mo prions produced changes similar to those in non-Tg mice with scrapie. Our results argue that species specificity of scrapie prions resides in the primary structure of PrP and formation of infectious prions is initiated by a species-specific interaction between PrPSc in the inoculum and homologous, cellular PrP. Studies on Syrian, Armenian and Chinese hamsters suggest that the domain of the PrP molecule between codons 100 and 120 controls both the length of the incubation time and the deposition of PrP in amyloid plaques. Ataxic GSS in families shows genetic linkage to a mutation in the PrP gene leading to the substitution of Leu for Pro at codon 102. Discovery of a point mutation in the PrP gene from humans with GSS established that GSS is unique among human diseases--it is both genetic and infectious. These results have revised thinking about sporadic Creutzfeldt-Jakob disease (CJD) suggesting it may arise from a somatic mutation. Pulse-chase radiolabeling experiments of scrapie-infected cultures of mouse neuroblastoma cells indicate that protease-resistant PrPSc is synthesized during the chase period with t1/2 approximately 15 h from a protease-sensitive precursor, consistent with the conclusion that PrPc and PrPSc differ due to a post-translational event.(ABSTRACT TRUNCATED AT 400 WORDS)
Development of a TODGA based Process for Partitioning of Actinides from a PUREX Raffinate Part I: Batch Extraction Optimization Studies and Stability Tests (2007)

Abstract The extractant, N,N,N′,N′‐tetraoctyl diglycolamide (TODGA) has been evaluated for the separation of actinides(III) and lanthanides(III) from a high active raffinate (HAR). The effect of oxalic acid and HEDTA complexant on the extraction of actinides(III), lanthanides(III), and important fission products (e.g. Mo, Pd, Sr, Zr, Ru etc.) from synthetic HAR has been studied with 0.2 mol/L TODGA in TPH. With an extractant mixture of TODGA and tributyl phosphate (TBP) the amount of oxalic acid can be reduced to less than 0.3 mol/L for the effective complexation of zirconium, whereas the distribution ratios of actinides(III) and lanthanides(III) are still high for the separation from HAR. Furthermore the maximum loading of lanthanides (e.g. Nd) can be significantly increased by adding TBP to the extractant. However, the extraction of oxalic acid and nitric acid also increased by the addition of TBP, which can lead to problems during back extraction of the loaded extractant. Extraction studies after radiolysis and hydrolysis reveal that the TODGA+TBP mixture is a sufficient stable extraction system suited for further process development studies.