gebhart/patrepeval huggingface dataset:
Polarized phase shift mask: concept, design, and potential advantages to photolithography process and physical design (2002)

In this paper we introduce the concept and design of a novel phase shift mask technology, Polarized Phase Shift Mask (P:PSM). The P:PSM technology utilizes non-interference between orthogonally polarized light sources to avoid undesired destructive interference seen in conventional two-phase shift mask technology. Hence P:PSM solves the well-known 'phase edge' or 'phase conflict' problem. By obviating the 2nd exposure and 2nd mask in current Complementary Phase Shift Mask (C:PSM) technology, this single mask/single exposure technology offers significant advantages towards photolithography process as well as pattern design. We use examples of typical design and process difficulties associated with the C:PSM technology to illustrate the advantages of the P:PSM technology. We present preliminary aerial image simulation results that support the potential of this new reticle technology for enhanced design flexibility. We also propose possible mask structures and manufacturing methods for building a P:PSM.
The TREC Spoken Document Retrieval Track: A Success Story. (1999)

This paper describes work within the NIST Text REtrieval Conference (TREC) over the last three years in designing and implementing evaluations of Spoken Document Retrieval (SDR) technology within a broadcast news domain. SDR involves the search and retrieval of excerpts from spoken audio recordings using a combination of automatic speech recognition and information retrieval technologies. The TREC SDR Track has provided an infrastructure for the development and evaluation of SDR technology and a common forum for the exchange of knowledge between the speech recognition and information retrieval research communities. The SDR Track can be declared a success in that it has provided objective, demonstrable proof that this technology can be successfully applied to realistic audio collections using a combination of existing technologies and that it can be objectively evaluated. The design and implementation of each of the SDR evaluations are presented and the results are summarized. Plans for...
The Purification of Human Prothrombin (1966)

Summary A method has been presented for the preparation of human prothrombin. The product is apparently homogenous by chromatographic, ultracentrifugal, electrophoretic and immunochemical analysis. It contains less than 1 part in 107 of thrombin and has a specific activity of 1560 u/mg dry weight. Problems related to the variability in specific activity of prothrombin preparations reported in the literature have been critically reviewed.
Terminating substrates of DNA polymerases: synthesis and functional study. (1987)

In order to study the mechanisms of DNA biosynthesis a number of modified nucleoside - substrates of DNA polymerases was synthesized. The absence of hydroxyl at 3'-position of ribose results in terminating properties of DNA biosynthesis of these analogues. A single step synthesis of triphosphates and alpha-thiotriphosphates of natural and 3'-modified 2'-deoxynucleosides is described.
Bootstrapping an Infrastructure (1998)

When deploying and administering systems infrastructures it is still common to think in terms of individual machines rather than view an entire infrastructure as a combined whole. This standard practice creates many problems, including labor-intensive administration, high cost of ownership, and limited generally available knowledge or code usable for administering large infrastructures. The model we describe treats an infrastructure as a single large distributed virtual machine. We found that this model allowed us to approach the problems of large infrastructures more effectively. This model was developed during the course of four years of mission-critical rollouts and administration of global financial trading floors. The typical infrastructure size was 300-1000 machines, but the principles apply equally as well to much smaller environments. Added together these infrastructures totaled about 15,000 hosts. Further refinements have been added since then, based on experiences ...
Eine flexible Synthese von 4-Oxobutansäure- methylestern und deren Derivaten (1990)

A Flexible Synthesis of Methyl 4-Oxobutanoates and Their Derivatives Ring cleavage of several methyl 2-trimethylsiloxycyclopropanecarboxylates 3 provides rather sensitive methyl 4-oxobutanoates (ß-formyl esters) 4 in excellent yields. Siloxycyclopropanes 3 are easily available either directly from the corresponding silyl enol ethers 2 and methyl diazoacetate or by alkylation of deprotonated cyclopropanes 3. A highly efficient one-pot procedure affords methyl 4,4-dimethoxybutanoates 5, which can be converted into protected 4-hydroxybutanals 7 and 8 by standard methods.
Expression Cloning and Production of Human Heavy-Chain-Only Antibodies from Murine Transgenic Plasma Cells (2016)

Several technologies have been developed to isolate human antibodies against different target antigens as a source of potential therapeutics, including hybridoma technology, phage and yeast display systems. For conventional antibodies, this involves either random pairing of VH and variable light (VL) domains in combinatorial display libraries or isolation of cognate pairs of VH and VL domains from human B cells or from transgenic mice carrying human immunoglobulin loci followed by single-cell sorting, single-cell RT-PCR, and bulk cloning of isolated natural VH-VL pairs. Heavy-chain-only antibodies (HCAbs) that naturally occur in camelids require only heavy immunoglobulin chain cloning. Here, we present an automatable novel, high-throughput technology for rapid direct cloning and production of fully human HCAbs from sorted population of transgenic mouse plasma cells carrying a human HCAb locus. Utility of the technique is demonstrated by isolation of diverse sets of sequence unique, soluble, high-affinity influenza A strain X-31 hemagglutinin-specific HCAbs.
Automated Conversion of Chemical Substance Names to Atom-Bond Connection Tables (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAutomated Conversion of Chemical Substance Names to Atom-Bond Connection TablesG. G. Vander Stouw, P. M. Elliott, and A. C. IsenbergCite this: J. Chem. Doc. 1974, 14, 4, 185–193Publication Date (Print):November 1, 1974Publication History Published online1 May 2002Published inissue 1 November 1974https://pubs.acs.org/doi/10.1021/c160055a009https://doi.org/10.1021/c160055a009research-articleACS PublicationsRequest reuse permissionsArticle Views95Altmetric-Citations17LEARN 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 options Get e-Alerts
Evaluation of antimicrobial effect of hops extracts on intramacrophages Brucella abortus and B. melitensis (2011)

Introduction and objective: Brucellosis is a zoonosis disease among animal and human, and has been endemic in Iran. The most important virulence factors of Brucella are related to their capability of intraphagocytic survival. Because of the side effects of brucellosis treatment regime, it is necessary to find new antimicrobial agents. The hop plant (Humulus lupulus) extract reported as having antimicrobial effects. The present study evaluated the antimicrobial activity of hops extracts against Brucella abortus 544 and B. melitensis 16M. Materials and methods: Hops extracts were prepared in water, acetone and ethanol. Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) for two strains of Brucella determined by broth macrodilution and agar well diffusion methods. Effect of extracts on intramacrophge surviving of Brucella strains studied on cell culture of mouse peritoneal macrophages. Results: Results indicated that MIC for aqueous extract was 1:80 (0.625mg/ml) and for acetonic and ethanolic extracts was 1:160 (0.05mg/ml). MBC for aquatic extract was 1:40 (1.2mg/ml) and for two other extracts was 1:80 (0.1mg/ml). In cell culture results indicated that all of extracts were effective and eradicated intramacrophage Brucella strains in 1:40 (1.2mg/ml for aqueous and 0.2mg/ml for ethanolic and acetonic extracts), 1:80 (0.625mg/ml for aqueous and 0.1mg/ml for ethanolic and acetonic extracts) and 1:160 (0.312mg/ml for aqueous and 0.05mg/ml for ethanolic and acetonic extracts) of extracts dilutions after 24h. Conclusion: Overall this study indicated that aquatic, acetonic and ethanolic extracts of hops showed antimicrobial effect against B. abortus and B. melitensis, therefore, they are useful in the treatment of brucellosis.
tRNA transfers to the limelight (2003)

￻tRNA has a central role in biology as the adaptor between mRNA and protein, in which anticodon interactions with the mRNA codon at one end of the L-shaped tRNA allow an attached amino acid at the other end of the tRNA to condense with the peptide chain on a second tRNA through the action of the ribosome. This familiar role of tRNA requires mature tRNAs to be recognized by the aminoacyl tRNA synthetase to add the amino acid to its 3 end, by EF1 to form a ternary complex with the aminoacylated tRNA and GTP, and by elements of the ribosome and associated components to allow binding, peptide synthesis, and translocation. Before fulfilling this role, all tRNA transcripts have to be extensively processed. Maturation of tRNAs requires five major steps: (1) removal of the 5 leader by RNase P,
Electrogenerated Chemiluminescence from Phosphorescent Molecules Used in Organic Light-Emitting Diodes (2002)

The role of triplet states in the electrogenerated chemiluminescence (ECL) of organic light-emitting diode (OLED) materials was investigated. The spectroscopic, electrochemical, and electrochemiluminescent properties of two phosphorescent materials, platinum(II) octaethylporphyrin (PtOEP) and tris(2-phenylpyridine)iridium(II) are described. Radical cations and anions of PtOEP were generated in solution and recombined to produce ECL. The ECL from PtOEP was less than a 9,10-diphenylanthracene (DPA) standard. could be electro-oxidized and reduced in acetonitrile to produced ECL that was brighter than DPA. The light from both of these compounds was stable, and their emission spectra were the same as those reported for OLEDs based on these compounds. © 2002 The Electrochemical Society. All rights reserved.
The role of the mast cell in asthma: a reassessment (2003)

The development of potent and specific inhibitors of mast cell secretion, which remain active when administered long term to asthmatic airways, should offer a novel approach to the treatment of asthma.
Kinetic analysis of amyloid fibril polymerization in vitro. (1991)

We investigated the polymerization kinetics of murine senile amyloid fibrils (fASSAM) in vitro. When sonicated murine senile amyloid fibrils was incubated with its constituent monomer protein, the extension of amyloid fibrils was observed in an electron microscopic analysis. Quantitative fluorometric analysis with thioflavine T (Naiki H, Higuchi K, Hosokawa M, Takeda T: Anal Biochem 177:244, 1989) revealed that (a) extension of amyloid fibrils occurred by a pseudo-first-order exponential increase in the fluorescence of thioflavine T; (b) the rate of extension was maximal around pH 7.5, and was inhibited with the increase in KCl or NaCl concentration in the reaction mixture; (c) the rate of polymerization was proportional to the product of the murine senile amyloid fibrils number concentration and the constituent monomer protein concentration; (d) the net rate of extension was the sum of the rates of polymerization and depolymerization with the equilibrium association constant K of 5 x 10(7) M-1. These results show that amyloid fibril formation can apparently be explained by a first-order kinetic model: that is, extension of amyloid fibrils proceeds by consecutive association of precursor proteins onto the ends of existing fibrils.
Identification of Highly Reactive Sequences For PLP-Mediated Bioconjugation Using a Combinatorial Peptide Library (2010)

Chemical reactions that facilitate the attachment of synthetic groups to proteins are useful tools for the field of chemical biology and enable the incorporation of proteins into new materials. We have previously reported a pyridoxal 5'-phosphate (PLP)-mediated reaction that site-specifically oxidizes the N-terminal amine of a protein to afford a ketone. This unique functional group can then be used to attach a reagent of choice through oxime formation. Since its initial report, we have found that the N-terminal sequence of the protein can significantly influence the overall success of this strategy. To obtain short sequences that lead to optimal conversion levels, an efficient method for the evaluation of all possible N-terminal amino acid combinations was needed. This was achieved by developing a generalizable combinatorial peptide library screening platform suitable for the identification of sequences that display high levels of reactivity toward a desired bioconjugation reaction. In the context of N-terminal transamination, a highly reactive alanine-lysine motif emerged, which was confirmed to promote the modification of peptide substrates with PLP. This sequence was also tested on two protein substrates, leading to substantial increases in reactivity relative to their wild-type termini. This readily encodable tripeptide thus appears to provide a significant improvement in the reliability with which the PLP-mediated bioconjugation reaction can be used. This study also provides an important first example of how synthetic peptide libraries can accelerate the discovery and optimization of protein bioconjugation strategies.
Viral oncoprotein-induced mislocalization of select PDZ proteins disrupts tight junctions and causes polarity defects in epithelial cells (2005)

The development of human cancers is frequently associated with a failure of epithelial cells to form tight junctions and to establish proper apicobasal polarity. Interestingly, the oncogenic potential of the adenovirus E4-ORF1 protein correlates with its binding to the cellular PDZ proteins MUPP1, MAGI-1, ZO-2 and SAP97, the first three of which assemble protein complexes at tight junctions. Given that E4-ORF1 sequesters these three PDZ proteins in the cytoplasm of fibroblasts, we postulated that E4-ORF1 would inhibit tight junction formation in epithelial cells. Providing further support for this idea, we identified MUPP1-related PATJ, a key component of the tight junction-associated CRB3-PALS1-PATJ polarity complex, as a new PDZ-protein target for both the E4-ORF1 and high-risk human papillomavirus type 18 E6 oncoproteins. Moreover, in epithelial cells, E4-ORF1 blocked the tight junction localization of PATJ and ZO-2, as well as their interacting partners, and disrupted both the tight junction barrier and apicobasal polarity. These significant findings expose a direct link between the tumorigenic potential of E4-ORF1 and inactivation of cellular PDZ proteins involved in tight junction assembly and polarity establishment.
Adenovirus Serotype 5 Fiber Shaft Influences In Vivo Gene Transfer in Mice (2003)

Adenoviral vectors used in gene therapy are predominantly derived from adenovirus serotype 5 (Ad5), which infects a broad range of cells. Ad5 cell entry involves interactions with the coxsackie-adenovirus receptor (CAR) and integrins. To assess these receptors in vivo, we mutated amino acid residues in fiber and penton that are involved in receptor interaction and showed that CAR and integrins play a minor role in hepatic transduction but that integrins can influence gene delivery to other tissues. These data suggest that an alternative entry pathway exists for hepatocyte transduction in vivo that is more important than CAR or integrins. In vitro data suggest a role for heparan sulfate glycosaminoglycans (HSG) in adenovirus transduction. The role of the fiber shaft in liver uptake was examined by introducing specific amino acid changes into a putative HSG-binding motif contained within the shaft or by preparing fiber shaft chimeras between Ad5 and Ad35 fibers. Results were obtained that demonstrate that the Ad5 fiber shaft can influence gene transfer both in vitro and to the liver in vivo. These observations indicate that the currently accepted two-step entry pathway, which involves CAR and integrins, described for adenoviral infection in vitro, is not used for hepatic gene transfer in vivo. In contrast, alpha(v) integrins influence gene delivery to the lung, spleen, heart, and kidney. The detargeted vector constructs described here may provide a foundation for the development of targeted adenoviral vectors.
N-glycoprotein biosynthesis in plants: recent developments and future trends. (1998)

N-glycosylation is a major modification of proteins in plant cells. This process starts in the endoplasmic reticulum by the co-translational transfer of a precursor oligosaccharide to specific asparagine residues of the nascent polypeptide chain. Processing of this oligosaccharide into high-mannose-type, paucimannosidic-type, hybrid-type or complex-type N-glycans occurs in the secretory pathway as the glycoprotein moves from the endoplasmic reticulum to its final destination. At the end of their maturation, some plant N-glycans have typical structures that differ from those found in their mammalian counterpart by the absence of sialic acid and the presence of beta(1,2)-xylose and alpha( 1,3)-fucose residues. Glycosidases and glycosyltransferases that respectively catalyse the stepwise trimming and addition of sugar residues are generally considered as working in a co-ordinated and highly ordered fashion to form mature N-glycans. On the basis of this assembly line concept, fast progress is currently made by using N-linked glycan structures as milestones of the intracellular transport of proteins along the plant secretory pathway. Further developments of this approach will need to more precisely define the topological distribution of glycosyltransferases within a plant Golgi stack. In contrast with their acknowledged role in the targeting of lysosomal hydrolases in mammalian cells, N-glycans have no specific function in the transport of glycoproteins into the plant vacuole. However, the presence of N-glycans, regardless of their structures, is necessary for an efficient secretion of plant glycoproteins. In the biotechnology field, transgenic plants are rapidly emerging as an important system for the production of recombinant glycoproteins intended for therapeutic purposes, which is a strong motivation to speed up research in plant glycobiology. In this regard, the potential and limits of plant cells as a factory for the production of mammalian glycoproteins will be illustrated.
A Randomized Clinical Trial of an Inactivated Avian Influenza A (H7N7) Vaccine (2012)

ClinicalTrials.gov NCT00546585.
Mapping of the C3d Ligand Binding Site on Complement Receptor 2 (CR2/CD21) Using Nuclear Magnetic Resonance and Chemical Shift Analysis (2009)

Complement receptor 2 (CR2, CD21) is a cell membrane protein, with 15 or 16 extracellular short consensus repeats (SCRs), that promotes B lymphocyte responses and bridges innate and acquired immunity. The most distally located SCRs (SCR1-2) mediate the interaction of CR2 with its four known ligands (C3d, Epstein-Barr virus gp350, interferon-alpha, and CD23). Inhibitory monoclonal antibodies against SCR1-2 block binding of all ligands. To develop ligand-specific inhibitors that would also assist in identifying residues unique to each receptor-ligand interaction, phage were selected from randomly generated libraries by panning with recombinant SCR1-2, followed by specific ligand-driven elution. Derived peptides were tested by competition ELISA. One peptide, C3dp1 (APQHLSSQYSRT) exhibited ligand-specific inhibition at midmicromolar IC(50). C3d was titrated into (15)N-labeled SCR1-2, which revealed chemical shift changes indicative of specific intermolecular interactions. With backbone assignments made, the chemical shift changes were mapped onto the crystal structure of SCR1-2. With regard to C3d, the binding surface includes regions of SCR1, SCR2, and the inter-SCR linker, specifically residues Arg(13), Tyr(16), Arg(28), Tyr(29), Ser(32), Thr(34), Lys(48), Asp(56), Lys(57), Tyr(68), Arg(83), Gly(84), Asn(101), Asn(105), and Ser(109). SCR1 and SCR2 demonstrated distinct binding modes. The CR2 binding surface incorporating SCR1 is inconsistent with a previous x-ray CR2-C3d co-crystal analysis but consistent with mutagenesis, x-ray neutron scattering, and inhibitory monoclonal antibody epitope mapping. Titration with C3dp1 yielded chemical shift changes (Arg(13), Tyr(16), Thr(34), Lys(48), Asp(56), Lys(57), Tyr(68), Arg(83), Gly(84), Asn(105), and Ser(109)) overlapping with C3d, indicating that C3dp1 interacts at the same CR2 site as C3d.
Stem cell factor influences the proliferation and erythroid differentiation of the MB-02 human erythroleukemia cell line by binding to a high-affinity c-kit receptor (1993)

Stem cell factor (SCF) acts in synergy with other growth factors such as erythropoietin (Epo), granulocyte-macrophage colony-stimulating factor (GM-CSF), or interleukin-3 (IL-3), to stimulate the growth of primitive hematopoietic cells. Because of the prominent role of CSF in the maintenance of normal erythropoiesis in vivo, we examined the effects of SCF on the Epo-inducible human erythroleukemia cell line MB- 02, and characterized the c-kit receptor in these cells. MB-02 cells cultured in serum-containing media do not survive in the absence of exogenous growth factors, but the addition of SCF, Epo, or IL-3 as a single factor enhanced MB-02 survival. Furthermore, in the presence of Epo, SCF (5 to 25 ng/mL) enhanced MB-02 proliferation in a dose- dependent manner, and increased the relative and absolute number of benzidine-positive cells generated. SCF also enhanced cell proliferation in the presence of either IL-3 or low concentrations of GM-CSF. A neutralizing anti-c-kit receptor monoclonal antibody (SR-1) blocked binding of 125I-SCF to MB-02 cells by 98%, and the effect of SCF on MB-02 growth, c-kit receptor-binding parameters were quantitated by equilibrium-binding experiments with 125I-SCF. MB-02 cells display a single class of high-affinity (50 pmol/L) c-kit receptors, with approximately 8,000 receptors per cell. The molecular weight of the c- kit receptor was determined by affinity cross-linking 125I-SCF to MB-02 cells. 125I-SCF-c-kit receptor complexes of approximately 155,000 and approximately 310,000 daltons were found, likely representing the monomeric and dimeric forms of the c-kit receptor. The binding affinity and molecular weight of the c-kit receptor on MB-02 cells are similar to those of normal human marrow cells. These results suggest that SCF synergizes with Epo to influence not only the proliferation but the erythroid differentiation of MB-02 cells. Thus, the MB-02 cell line may be a useful model in which to investigate the molecular mechanisms of SCF action.