gebhart/patrepeval huggingface dataset:
Pyrrolo[2,3-d]pyrimidine nucleoside antibiotics. Total synthesis and structure of toyocamycin, unamycin B, vengicide, antibiotic E-212, and sangivamycin (BA-90912) (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPyrrolo[2,3-d]pyrimidine nucleoside antibiotics. Total synthesis and structure of toyocamycin, unamycin B, vengicide, antibiotic E-212, and sangivamycin (BA-90912)Richard L. Tolman, Roland K. Robins, and Leroy B. TownsendCite this: J. Am. Chem. Soc. 1968, 90, 2, 524–526Publication Date (Print):January 1, 1968Publication History Published online1 May 2002Published inissue 1 January 1968https://pubs.acs.org/doi/10.1021/ja01004a076https://doi.org/10.1021/ja01004a076research-articleACS PublicationsRequest reuse permissionsArticle Views378Altmetric-Citations40LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
APPLICATION OF THE REVERSED ISLAND FLAP BASED ON SURAL NEUROVASCUALR PEDICLE (2001)

Objective To report the method for repair of the heel and ankle.Method On the basis of applied anatomy,the reversed island flap based on sural neurovascular pedicle has been designed for repair of heel and ankle defects.Results The flaps have been used in 14 cases,the maximum size 9 cm×15 cm,and all flaps were survival compeletely except partial necrosis in one flap.Conclusion The blood supply of the flap is good.The length of pedicle can reach 12 cm.It is an effective method for repair of heel and ankle defects.
Generalized Gradient Approximation Made Simple (1996)

Generalized gradient approximations (GGA's) for the exchange-correlation energy improve upon the local spin density (LSD) description of atoms, molecules, and solids. We present a simple derivation of a simple GGA, in which all parameters (other than those in LSD) are fundamental constants. Only general features of the detailed construction underlying the Perdew-Wang 1991 (PW91) GGA are invoked. Improvements over PW91 include an accurate description of the linear response of the uniform electron gas, correct behavior under uniform scaling, and a smoother potential.
Chemoselective Addition of Halomethyllithiums to Functionalized Isatins:A Straightforward Access to Spiro‐Epoxyoxindoles (2016)

Abstract An efficient, chemoselective approach to spiro‐epoxyoxindoles via the addition of chloromethyllithium followed by ring‐closure of the intermediate alkoxide is reported. Chemoselectivity is fully preserved in the presence of different electrophilic sites. The synthetic potential of selected spiro‐epoxyindoles has been exploited in the copper(I)‐catalyzed intramolecular oxyarylation of an alkyne and in the formation of N,N ‐dimethylisoindigo via the addition of dihalocarbenoids. magnified image
Acetate and Formate Stress: Opposite Responses in the Proteome of Escherichia coli (2001)

Acetate and formate are major fermentation products of Escherichia coli. Below pH 7, the balance shifts to lactate; an oversupply of acetate or formate retards growth. E. coli W3110 was grown with aeration in potassium-modified Luria broth buffered at pH 6.7 in the presence or absence of added acetate or formate, and the protein profiles were compared by two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Acetate increased the steady-state expression levels of 37 proteins, including periplasmic transporters for amino acids and peptides (ArtI, FliY, OppA, and ProX), metabolic enzymes (YfiD and GatY), the RpoS growth phase regulon, and the autoinducer synthesis protein LuxS. Acetate repressed 17 proteins, among them phosphotransferase (Pta). An ackA-pta deletion, which nearly eliminates interconversion between acetate and acetyl-coenzyme A (acetyl-CoA), led to elevated basal levels of 16 of the acetate-inducible proteins, including the RpoS regulon. Consistent with RpoS activation, the ackA-pta strain also showed constitutive extreme-acid resistance. Formate, however, repressed 10 of the acetate-inducible proteins, including the RpoS regulon. Ten of the proteins with elevated basal levels in the ackA-pta strain were repressed by growth of the mutant with formate; thus, the formate response took precedence over the loss of the ackA-pta pathway. The similar effects of exogenous acetate and the ackA-pta deletion, and the opposite effect of formate, could have several causes; one possibility is that the excess buildup of acetyl-CoA upregulates stress proteins but excess formate depletes acetyl-CoA and downregulates these proteins.
Fractured Reservoir Simulation (1983)

Abstract This paper describes the development of a three-dimensional (3D), three-phase model for simulating the flow of water, oil, and gas in a naturally fractured reservoir. A dual porosity system is used to describe the fluids present in the fractures and matrix blocks. Primary flow in the reservoir occurs within the fractures with local exchange of fluids between the fracture system and matrix blocks. The matrix/fracture transfer function is based on an extension of the equation developed by Warren and Root and accounts for capillary pressure, gravity, and viscous forces. Both the fracture flow equations and matrix/fracture flow are solved implicitly for pressure, water saturation, gas saturation, and saturation pressure. We present example problems to demonstrate the utility of the model. These include a comparison of our results with previous results: comparisons of individual block matrix/fracture transfers obtained using a detailed 3D grid with results using the fracture model's matrix/fracture transfer function; and 3D field-scale simulations of two- and three-phase flow. The three-phase example illustrates the effect of free gas saturation on oil recovery by waterflooding.
Role of DNA repair enzymes in the cellular resistance to oxidative stress. (1996)

Oxidative stress occurs in cells when the equilibrium between prooxidant and antioxidant species is broken in favor of the prooxidant state. It is due to reactive oxygen species (ROS) generated either by the cellular metabolism such as phagocytosis, mitochondrial respiration, xenobiotic detoxification, or by exogenous factors such as ionizing radiation or chemical compounds performing red-ox reactions. Some ROS are extremely reactive and interact with all the macromolecules including lipids, nucleic acids and proteins. Cells have numerous defence systems to counteract the deleterious effects of ROS. Proteins and small molecules specifically eliminate ROS when they are formed. There are three species of superoxyde dismutases which transform the superoxyde anion O2- in hydrogen peroxyde H2O2 which in turn will be destroyed by peroxysomal catalase or by various peroxydases. There are numerous small molecules in the cell such as glutathion, alpha-tocopherol, vitamines A and C, melanine, etc. which are antioxydant molecules. ROS escaping destruction generate various lesions in DNA such as base modifications, degradation products of deoxyribose, chain breaks. These various lesions have been characterized and it is possible to quantitate them in the DNA of cells which have been irradiated or treated by free radical generating systems. The biological properties of the bases modified by ROS have been established. For example C8-hydroxyguanine (8-oxoG) is promutagenic since, if present in DNA during replication, it leads to incorporation of dAMP residues, leading to transversion mutation (GC-->TA). Purines whose imidazole ring is opened (Fapy residues) are stops for the DNA polymerase during DNA replication and are therefore potentially lethal lesions for the cell. Oxidized pyrimidines have comparable coding properties. Efficient DNA repair mechanisms remove these oxidized bases. In Escherichia coli cells, endonuclease III (NTH protein) and endonuclease VIII (NEI protein) excise many oxidized pyrimidines, whereas the FPG protein (formamidopyrimidine-DNA-glycosylase) eliminates 8-oxoG and Fapy lesions. Besides its DNA glycosylase activity, the protein FPG has a beta-lyase activity incising DNA at abasic site by a beta-delta elimination mechanism, and a dRPase activity. The FPG protein has a zinc finger motive which is mandatory for the recognition of its substrate. Mammalian cells have similar DNA repair proteins and it should be emphazized that there is conservation of the different functions and in most cases a remarquable homology of the amino acids sequences from E. coli to man.
Finite‐Size, Fully Addressable DNA Tile Lattices Formed by Hierarchical Assembly Procedures (2005)

Decorated tiles: Self-assembling DNA nanostructures can be used to form addressable, size-controlled nanoarrays with a variety of programmed patterns. Arrays of DNA cross-shaped tiles were decorated with pixels of individual protein molecules. The letters “D”, “N”, and “A” on self-assembled 4×4 arrays (<80-nm square, see picture) were prepared by a minimal-depth strategy. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2006/z503797_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Persistence of the .alpha.-helix stop signal in the S-peptide in trifluoroethanol solutions (1989)

alpha-Helix formation in the S-peptide (residues 1-19 of ribonuclease A) was studied in detail by use of two-dimensional 1H nuclear magnetic resonance to monitor the effects of 2,2,2-trifluoroethanol (TFE) at 0 degrees C and pH* 2.07. TFE stabilizes the S-peptide alpha-helix. Helix formation by a particular amino acid was monitored by the chemical shifts of the C alpha, C beta, and C gamma protons while increasing the concentration of TFE: large changes in chemical shift of a particular residue indicate that it is induced to go helical, whereas small chemical shift changes indicate little helix formation. Residues Thr-3 to Met-13 undergo chemical shift changes consistent with helix formation, whereas the other residues do not. Earlier work [Kim, P. S., & Baldwin, R. L. (1984) Nature 307, 329-334] reported that residues Thr-3 to His-12 become helical in aqueous solution. The existence of a "helix stop signal" was inferred from this behavior. We thus conclude that this helix stop signal persists in TFE solutions.
Effect of protein tyrosine phosphatase 1B expression on transformation by the human neu oncogene. (1992)

Many oncogenes encode proteins with a tyrosine kinase activity that appears to be directly involved in the process of transformation. Because these kinases are themselves activated for transformation by tyrosine phosphorylation, proteins which remove phosphate from tyrosine residues, protein tyrosine phosphatases (also termed phosphotyrosine phosphatases and protein phosphotyrosyl phosphatases), are intuitive candidate transformation suppressors. The human PTP1B gene, previously cloned in our laboratory and encoding the low molecular weight protein tyrosine phosphatase PTPase 1B, was introduced into NIH 3T3 cells. Subsequent transformation of these PTPase 1B-expressing cells by an oncogenic form of the human neu gene was suppressed relative to control NIH 3T3 cells. This suppression of transformation was observed in assays for focus formation, anchorage-independent growth, and tumorigenicity. Tumorigenicity assays indicated a complex effect of PTPase 1B expression on transformation.
A Fundamental Assumption about OH- Attack in Phosphate Ester Hydrolysis Is Not Fully Justified (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTA Fundamental Assumption about OH- Attack in Phosphate Ester Hydrolysis Is Not Fully JustifiedJan Florián and Arieh WarshelView Author Information Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062Cite this: J. Am. Chem. Soc. 1997, 119, 23, 5473–5474Publication Date (Web):June 11, 1997Publication History Received12 December 1996Published online11 June 1997Published inissue 1 June 1997https://pubs.acs.org/doi/10.1021/ja964270mhttps://doi.org/10.1021/ja964270mrapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views760Altmetric-Citations97LEARN 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:Alkyls,Free energy,Hydrolysis,Kinetic parameters,Phosphates Get e-Alerts
Protein design: novel metal-binding sites (1995)

In natural proteins, metal ions play a variety of roles, including nucleophilic catalysis, electron transfer and the stabilization of protein structure. The de novo design of metal-binding sites is therefore an attractive means by which to impart proteins with novel properties and activities.
Short-channel effects in contact-passivated nanotube chemical sensors (2003)

We report a design for carbon nanotube field-effect transistors which tests the nanotube depletion length. In this design, the metal contacts and adjacent nanotubes were coated with impermeable silicon oxide, while the central region of nanotubes was exposed. We tested the devices by measuring sensitivity to NH3 and poly(ethylene imine). NH3 caused similar responses in passivated devices and in normal, nonpassivated devices. Thus, the device design passivates the metal-nanotube contacts while preserving chemical sensor characteristics. Poly(ethylene imine) produced negative threshold shifts of tens of volts, despite being in contact with only the center region of devices. Based on the observed device characteristics, we conclude that the length scale of the covered nanotubes in our structure is comparable to the decay length of the depletion charge in nanotube transistors.
Adjuvant systemic therapy for resectable breast cancer. (1985)

Article Tools Article Tools OPTIONS & TOOLS Export Citation Track Citation Add To Favorites Rights & Permissions COMPANION ARTICLES No companion articles ARTICLE CITATION DOI: 10.1200/JCO.1985.3.2.259 Journal of Clinical Oncology - published online before print September 22, 2016 PMID: 3881562 Adjuvant systemic therapy for resectable breast cancer. G BonadonnaxG BonadonnaSearch for articles by this author , P ValagussaxP ValagussaSearch for articles by this author https://doi.org/10.1200/JCO.1985.3.2.259 First Page PDF © 1985 by American Society of Clinical Oncology
Th2 Cells Are Required for the Schistosoma mansoni Egg-Induced Granulomatous Response (1998)

The development of Schistosoma mansoni ova-induced granulomas is regulated by cytokines secreted by distinct Th cell subsets. To determine the importance of Th1 and Th2 cells in granuloma formation, we have studied the immune response to S. mansoni ova in Stat4- and Stat6-deficient mice, which lack Th1 and Th2 cells, respectively. Lymphocytes from both naive and infected Stat6-deficient mice produced minimal levels of Th2 cell cytokines and Ag-specific IgG1 and IgE, but showed enhanced production of IFN-gamma and Ag-specific IgG2a and IgG2b following schistosome egg injection. This shift away from a Th2 cell-mediated immune response was coupled with the development of pulmonary and hepatic granulomas that were greatly decreased in size compared with those in control littermates. Hepatic granulomas in Stat6-deficient mice were composed of predominantly mononuclear cells with very sparse appearance of eosinophils, and their diminished size was accompanied by decreased amounts of liver hydroxyproline content as a measure of collagen deposition. In contrast, lymphocytes from infected Stat4-deficient mice produced Th2 cell cytokines in amounts comparable to those produced by control littermates, but low levels of IFN-gamma. While infected Stat4-deficient mice developed pulmonary granulomas following schistosome egg injection that were modestly impaired in size, the granuloma size and amount of collagen deposition in the liver were equivalent to those seen in control littermates. These studies demonstrate that Th2 cells are required for the full development of the granulomas and tissue-destructive fibrotic pathology associated with the immune response to S. mansoni ova.
Inhibition of Quorum Sensing in Pseudomonas aeruginosa by N -Acyl Cyclopentylamides (2007)

N-octanoyl cyclopentylamide (C8-CPA) was found to moderately inhibit quorum sensing in Pseudomonas aeruginosa PAO1. To obtain more powerful inhibitors, a series of structural analogs of C8-CPA were synthesized and examined for their ability to inhibit quorum sensing in P. aeruginosa PAO1. The lasB-lacZ and rhlA-lacZ reporter assays revealed that the chain length and the ring structure were critical for C8-CPA analogs to inhibit quorum sensing. N-decanoyl cyclopentylamide (C10-CPA) was found to be the strongest inhibitor, and its concentrations required for half-maximal inhibition for lasB-lacZ and rhlA-lacZ expression were 80 and 90 microM, respectively. C10-CPA also inhibited production of virulence factors, including elastase, pyocyanin, and rhamnolipid, and biofilm formation without affecting growth of P. aeruginosa PAO1. C10-CPA inhibited induction of both lasI-lacZ by N-(3-oxododecanoyl)-L-homoserine lactone (PAI1) and rhlA-lacZ by N-butanoyl-L-homoserine lactone (PAI2) in the lasI rhlI mutant of P. aeruginosa PAO1, indicating that C10-CPA interferes with the las and rhl quorum-sensing systems via inhibiting interaction between their response regulators (LasR and RhlR) and autoinducers.
Predimerization of Recombinant Platelet-Derived Growth Factor Receptor Extracellular Domains Increases Antagonistic Potency (2000)

Platelet-derived growth factor (PDGF) is a dimeric growth factor acting through tyrosine kinase alpha- and beta-receptors. In both receptors, the extracellular parts are composed of five Ig-like domains. Functional mapping of the extracellular part of the receptors have shown that ligand-binding occurs to Ig-like domains 2 and 3 and that Ig-like domain 4 is involved in receptor-receptor interactions. Recombinant GST-fusion proteins of PDGF alpha-receptor Ig-like domains 1-4 and beta-receptor Ig-like domains 1-3 (alphaRD1-4-GST and betaRD1-3-GST) were generated and compared with their cleaved counterparts (alphaRD1-4 and betaRD1-3) with regard to their ability to block PDGF binding to cell surface receptors. In the case of both the alpha- and the beta-receptors, 100-1000-fold lower concentrations of the GST-fusion proteins were required, as compared to the cleaved forms, for inhibition of PDGF binding to cell surface receptors. alphaRD1-4-GST and betaRD1-3-GST, in contrast to alphaRD1-4 and betaRD1-3, were shown to occur as ligand independent dimers. Covalently cross-linked alphaRD1-4 dimers displayed a 50-fold increased potency as compared to alphaRD1-4. We thus conclude that the dimeric nature of alphaRD1-4-GST and betaRD1-3-GST is responsible for the high antagonistic potency of the fusion proteins.
A Novel Pharmacological Approach to Treating Cardiac Ischemia (2000)

Adenosine released during cardiac ischemia exerts a potent, protective effect in the heart via activation of A(1) or A(3) receptors. However, the interaction between the two cardioprotective adenosine receptors and the question of which receptor is the more important anti-ischemic receptor remain largely unexplored. The objective of this study was to test the hypothesis that activation of both receptors exerted a cardioprotective effect that was significantly greater than activation of either receptor individually. This was accomplished by using a novel design in which new binary conjugates of adenosine A(1) and A(3) receptor agonists were synthesized and tested in a novel cardiac myocyte model of adenosine-elicited cardioprotection. Binary drugs having mixed selectivity for both A(1) and A(3) receptors were created through the covalent linking of functionalized congeners of adenosine agonists, each being selective for either the A(1) or A(3) receptor subtype. MRS 1740 and MRS 1741, thiourea-linked, regioisomers of a binary conjugate, were highly potent and selective in radioligand binding assays for A(1) and A(3) receptors (K(i) values of 0.7-3.5 nm) versus A(2A) receptors. The myocyte models utilized cultured chick embryo cells, either ventricular cells expressing native adenosine A(1) and A(3) receptors, or engineered atrial cells, in which either human A(3) receptors alone or both human A(1) and A(3) receptors were expressed. The binary agonist MRS 1741 coactivated A(1) and A(3) receptors simultaneously, with full cardioprotection (EC(50) approximately 0.1 nm) dependent on expression of both receptors. Thus, co-activation of both adenosine A(1) and A(3) receptors by the binary A(1)/A(3) agonists represents a novel general cardioprotective approach for the treatment of myocardial ischemia.
A survey of simulation optimization techniques and procedures (2002)

Discrete event simulation optimization is a problem of significant interest to practitioners interested in extracting useful information about an actual (or yet to be designed) system that can be modeled using discrete event simulation. This paper presents a brief survey of the literature on discrete event simulation optimization over the past decade (1988 to the present). Swisher et al. (2000) provides a more comprehensive review of this topic while Jacobson and Schruben (1989) covers the literature preceding 1988. Optimization of both discrete and continuous input parameters are examined. The continuous input parameter case is separated into gradient and non-gradient based optimization procedures. The discrete input parameter case differentiates techniques appropriate for small and for large numbers of feasible input parameter values.