gebhart/patrepeval huggingface dataset:
Isolation and characterization of monoclonal antibodies directed against plant plasma membrane and cell wall epitopes: identification of a monoclonal antibody that recognizes extensin and analysis of the process of epitope biosynthesis in plant tissues and cell cultures. (1988)

Membranes from tobacco cell suspension cultures were used as antigens for the preparation of monoclonal antibodies. Use of solid phase and indirect immunofluorescence assays led to the identification of hybridomas producing antibodies directed against cell surface epitopes. One of these monoclonal antibodies (11.D2) was found to recognize a molecular species which on two-dimensional analysis (using nonequilibrium pH-gradient electrophoresis and SDS-PAGE) was found to have a high and polydisperse molecular mass and a very basic isoelectric point. This component was conspicuously labeled by [3H]proline in vivo. The monoclonal antibody cross-reacted with authentic tomato extensin, but not with potato lectin nor larch arabinogalactan. Use of the monoclonal antibody as an immunoaffinity reagent allowed the purification of a tobacco glycoprotein which was identical in amino acid composition to extensin. Finally, immunocytological analyses revealed tissue-specific patterns of labeling by the monoclonal antibody that were identical to those observed with a polyclonal antibody raised against purified extensin. We have concluded that monoclonal antibody 11.D2 recognizes an epitope that is carried exclusively by extensin. Analysis of cellular homogenates through differential and isopycnic gradient centrifugation revealed that biosynthesis of the extensin epitope was found on or within the membranes of the endoplasmic reticulum, Golgi region and plasma membrane. This result is consistent with the progressive glycosylation of the newly-synthesized extensin polypeptide during its passage through a typical eukaryotic endomembrane pathway of secretion. The 11.D2 epitope was not found in protoplasts freshly isolated from leaf tissues. However, on incubation of these protoplasts in appropriate culture media, biosynthesis of the epitope was initiated. This process was not impeded by the presence of chemicals that are reported to be inhibitors of cell wall production or of proline hydroxylation.
DNA nanowire fabrication (2005)

Deoxyribonucleic acid (DNA) has been a key building block in nanotechnology since the earliest work on what is now called DNA-templated self-assembly (Alivisatos et al 1996 Nature 382 609; Mirkin et al 1996 Nature 382 607; Braun et al 1998 Nature 391 775). A range of different nanoparticles and nanoclusters have been assembled on single DNA molecules for a variety of purposes (Braun et al 1998 Nature 391 775; Richter et al 2001 Appl. Phys. Lett. 78 536; Park et al 2002 Science 295 1503; Mirkin 2000 Inorg. Chem. 39 2258; Keren et al 2003 Science 302 1380). Electrically conductive silver (Braun et al 1998 Nature 391 775) and palladium (Richter et al 2001 Appl. Phys. Lett. 78 536) nanowires, for example, have been fabricated by DNA templating for the development of interconnection of nanoelectric elements, and field effect transistors have been built by assembly of a single carbon nanotube and DNA-templated nanowires (Keren et al 2003 Science 302 1380). DNA is well suited for nanowire assembly because of its size, well organized structure, and exquisite molecular-recognition-ability-specific base pairing. This property has been used to detect nucleic acids (Park et al 2002 Science 295 1503) and anthrax (Mirkin 2000 Inorg. Chem. 39 2258) with high sensitivity and specificity. Molecular recognition can also be used to localize nanowires in electronics. Various methods, for example molecular combing, electrophoretic stretching, and hydrodynamic stretching, have been developed to orient DNA molecules on a solid support. This review focuses on methods used to manipulate and metallize DNA in nanowire fabrication. A novel approach based on a single-stranded DNA template and molecular recognition is also discussed.
Interpreting mass spectra of multiply charged ions (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInterpreting mass spectra of multiply charged ionsMatthias. Mann, Chin Kai. Meng, and John B. FennCite this: Anal. Chem. 1989, 61, 15, 1702–1708Publication Date (Print):August 1, 1989Publication History Published online1 May 2002Published inissue 1 August 1989https://pubs.acs.org/doi/10.1021/ac00190a023https://doi.org/10.1021/ac00190a023research-articleACS PublicationsRequest reuse permissionsArticle Views3631Altmetric-Citations486LEARN 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
The aqueous extract from Artemisia capillaris Thunb. inhibits lipopolysaccharide-induced inflammatory response through preventing NF-κB activation in human hepatoma cell line and rat liver (2004)

Artemisia capillaris Thunb. has been used for the remedy of liver diseases such as hepatitis, jaundice and fatty liver in traditional oriental medicine. However, despite extensive pharmacological studies, the molecular mechanism of the anti-inflammatory effect of Artemisia capillaris Thunb. has hardly been studied. In the present study, we investigated the pharmacological action mechanism on LPS-induced liver inflammation in HepG2 human hepatocarcinoma cells and rat liver. Aqueous extract from Artemisia capillaris Thunb. (AEAC) inhibits expression of inflammatory proteins including iNOS, COX-2 and TNF-alpha. Also, nuclear translocation of NF-kappaB and degradation of I-kappaBalpha are blocked by AEAC pretreatment. These results suggest that the inhibitory effect of AEAC on the expression of inflammatory proteins involves suppression of NF-kappaB activation.
Efficacy of daily compared to intermittent administration of IL-1Ra for protection against bone and cartilage destruction in collagen-challenged mice. (2003)

Daily administration of recombinant IL-1Ra, injected at the same time as arthritis induction, is effective in blocking the occurrence of inflammatory as well as destructive changes in CIA. Daily bolus injections of IL-1Ra may therefore be useful for protection against joint damage following minor joint injury, whereas the maintenance of appropriate blood levels of the antagonist may be critical for its therapeutic effect on chronic inflammatory arthritis.
Copper−Diamine-Catalyzed N-Arylation of Pyrroles, Pyrazoles, Indazoles, Imidazoles, and Triazoles (2004)

This paper details the copper-catalyzed N-arylation of pi-excessive nitrogen heterocycles. The coupling of either aryl iodides or aryl bromides with common nitrogen heterocycles (pyrroles, pyrazoles, indazoles, imidazoles, and triazoles) was successfully performed in good yield with catalysts derived from diamine ligands and CuI. General conditions were found that tolerate functional groups such as aldehydes, ketones, alcohols, primary amines, and nitriles on the aryl halide or heterocycle. Hindered aryl halides or heterocycles were also found to be suitable substrates using the conditions reported herein.
Content Syndication with RSS (2003)

Originally developed by Netscape in 1999, RSS (which can stand for RDF Site Summary, Rich Site Summary, or Really Simple Syndication) is an XML-based format that allows web developers to describe and syndicate web site content. Content Syndication with RSS offers webloggers, developers, and the programmers who support them a thorough explanation of syndication in general and RSS in particular. Written for web developers who want to offer XML-based feeds of their content, as well as developers who want to use the content that other people are syndicating, the book explores and explains metadata interpretation, different forms of content syndication, and the increasing use of web services in this field. If you're interested in producing your own RSS feed, this step-by-step guide to implementation is the book you'll want in hand.
Quantitative Cascade Condensations betweeno-Phenylenediamines and 1,2-Dicarbonyl Compounds without Production of Wastes (2002)

o-Phenylenediamines 1 underwent a series of cascade condensations with 1,2-dicarbonyl compounds to afford quantitative yields (eight cases) of heterocycles in solid-state syntheses that avoided waste formation. The products were produced in pure form and did not require purifying workup. The components were ball-milled in stoichiometric ratio, or in exceptional cases they were melted together and heated in the absence of solvents (some of them giving quantitative yields). Benzils and 2-hydroxy-1,4-naphthoquinone afforded quinoxaline derivatives 3 and 5, 2-oxoglutaric acid gave a 3-oxodihydroquinoxaline 7, and oxalic acid afforded the dihydroquinoxaline-2,3-dione 9. This last condensed with 1a in the melt, to afford a mixture of bis(benzimidazolyl) 10 and fluoflavin 11. Alloxane hydrate provided a 100% yield of the 3-oxodihydroquinoxaline-2-carbonylureas 15/16 at room temperature. Parabanic acid required a melt reaction providing a 78% yield of 3-oxodihydroquinoxalinyl-2-urea 22 and side products. Despite numerous reaction steps, most of these uncatalyzed stoichiometric reactions proceeded quantitatively in the solid state to give only one product (plus water), with unsurpassed atom economy. If catalysis with HCl was tried, the results were inferior. If melt reactions were required it appeared to be advantageous to have the products crystallize directly at the reaction temperature. The synthetic results have been interpreted mechanistically and compared to some similar solution reactions that do not exhibit the benefits of the solid-state techniques. (© Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002)
Detection of PCR inhibitors in cervical specimens by using the AMPLICOR Chlamydia trachomatis assay (1996)

To determine that susceptibility of AMPLICOR Chlamydia trachomatis PCR to inhibitory factors possibly present in cervical specimens, we obtained cervical specimens from 200 gynecology patients attending our outpatient clinic. The prevalence of C. trachomatis infection was 4.1%, as determined by cell culture. All AMPLICOR specimens were tested in one procedure as described by the manufacturer, and after the specimen was spiked with C. trachomatis, several other pretreatment protocols were used. Complete inhibition of the PCR was observed in 38 (19%) cervical specimens. Heat treatment at 95 degrees C, freeze-thawing, or 10-fold dilution of the samples reduced the initial inhibition to 9, 16, or 9%, respectively. A combination of heat treatment and 10-fold dilution reduced the inhibition to 4% of the samples. A second specimen type (swabs inoculated in 0.2 M sucrose phosphate buffer [2SP]) was also evaluated. A 10-fold dilution of the spiked 2SP specimen resulted in an inhibition rate of 6%, which was comparable to that obtained by centrifugation of the 2SP specimen prior to processing. Furthermore, it was shown that the inhibition was not correlated with blood contamination. Processing the specimens on the day of collection or the day after resulted in a higher inhibition rate than did delayed processing (27.6 versus 15.5%, respectively). An inverse correlation was found between the concentration of C. trachomatis added to the sample and the rate of inhibition observed. The inhibition was partly correlated with the pH of the cervical mucosa. Decreased inhibition was found at pH values of > or = 7.5. The effects of blood, pH, and delay in processing were all evaluated by using the AMPLICOR specimen. We conclude that the susceptibility of AMPLICOR C. trachomatis PCR to inhibiting factors in cervical specimens can be significantly reduced if the pretreatment procedure includes heat treatment or the use of 2SP transport medium. Also, a 10-fold dilution of the clinical specimen followed by heat treatment will largely prevent the inhibition of this PCR.
Inhibition of coagulation and thrombin-induced platelet activities by a synthetic dodecapeptide modeled on the carboxy-terminus of hirudin (1990)

A synthetic, tyrosine-sulfated, dodecapeptide (BG8865) modeled on residues 53–64 of hirudin was found to elevate the activated partial thromboplastin time (APTT), prothrombin time (PT), and thrombin time (TT) of human plasma in a dose-dependent manner. The most sensitive assay was the TT, which was prolonged 2 and 3 times control values at 2.2 and 4.1 micrograms/mL hirudin peptide, respectively. The sulfated dodecapeptide exhibited no dependency on antithrombin III as monitored by the APTT in the presence of sheep anti-human antithrombin III antibodies, and its activity was not neutralized by platelet releasates or platelet factor 4. In studies of thrombin-induced platelet activation, the hirudin peptide was found to block aggregation, serotonin release and thromboxane A2 generation. At thrombin concentrations of 0.25 U/mL, the IC50 (concentration resulting in 50% inhibition) for inhibition of platelet aggregation was 0.72 micrograms/mL peptide. Inhibition of TXA2 generation and serotonin release correlated closely with inhibition of aggregation. Using platelets from patients with clinically documented heparin-induced thrombocytopenia anticoagulant doses of heparin were found to induce platelet aggregation and thromboxane A2 generation. In sharp contrast, anticoagulant-equivalent doses of hirudin peptide had no effect on patient platelets, as evidenced by a lack of platelet aggregation and thromboxane A2 generation. These data provide compelling in vitro evidence that the hirudin peptide has several potential advantages over heparin, namely effective inhibition of thrombin-induced platelet activities, co-factor independence, insensitivity to endogenous heparin- neutralizing factors, and an apparent lack of direct or immune-mediated platelet stimulating properties.
Articular cartilage: degeneration and osteoarthritis, repair, regeneration, and transplantation. (1998)

The degeneration of articular cartilage as part of the clinical syndrome of osteoarthritis is one of the most common causes of pain and disability in middle-aged and older people. The strong correlation between increasing age and the prevalence of osteoarthritis, and recent evidence of important age-related changes in the function of chondrocytes, suggest that age-related changes in articular cartilage can contribute to the development and progression of osteoarthritis. Although the mechanisms responsible for osteoarthritis remain poorly understood lifelong moderate use of normal joints does not increase the risk. Thus, the degeneration of normal articular cartilage is not simply the result of aging and mechanical wear. However, high-impact and torsional loads may increase the risk of degeneration of normal joints, and individuals who have an abnormal joint anatomy, joint instability, disturbances of joint or muscle innervation, or inadequate muscle strength or endurance probably have a greater risk of degenerative joint disease. Recent work has shown the potential for the restoration of an articular surface. Currently, surgeons frequently debride joints and penetrate subchondral bone as well as perform osteotomies, with the intent of decreasing symptoms and restoring or maintaining a functional articular surface. The results of these procedures vary considerably among patients. Clinical and experimental work has shown the important influence of loading and motion on the healing of articular cartilage and joints. Experimental studies have revealed that transplantation of chondrocytes and mesenchymal stem cells; use of periosteal and perichondrial grafts, synthetic matrices, and growth factors: and other methods have the potential to stimulate the formation of a new articular surface. The long-term follow-up of small series of patients has shown that the transplantation of osteochondral autologous grafts and allografts can be effective for the treatment of focal defects of articular cartilage in selected patients. Thus far, none of these methods has been shown to predictably restore a durable articular surface to an osteoarthritic joint, and it is unlikely that any one of them will be uniformly successful. Rather, the available clinical and experimental evidence indicates that future optimum methods for the restoration of articular surfaces will begin with a detailed analysis of the structural and functional abnormalities of the involved joint and the patient's expectations for future use of the joint. On the basis of this analysis, the surgeon will develop a treatment plan that potentially combines correction of mechanical abnormalities (including malalignment, instability, and intra-articular causes of mechanical dysfunction), debridement that may or may not include hunted penetration of subchondral bone, and applications of growth factors of implants that may consist of a synthetic matrix that incorporates cells or growth factors or use of transplants followed by a postoperative course of controlled loading and motion.
Fc-Binding Ligands of Immunoglobulin G: An Overview of High Affinity Proteins and Peptides (2016)

The rapidly increasing application of antibodies has inspired the development of several novel methods to isolate and target antibodies using smart biomaterials that mimic the binding of Fc-receptors to antibodies. The Fc-binding domain of antibodies is the primary binding site for e.g., effector proteins and secondary antibodies, whereas antigens bind to the Fab region. Protein A, G, and L, surface proteins expressed by pathogenic bacteria, are well known to bind immunoglobulin and have been widely exploited in antibody purification strategies. Several difficulties are encountered when bacterial proteins are used in antibody research and application. One of the major obstacles hampering the use of bacterial proteins is sample contamination with trace amounts of these proteins, which can invoke an immune response in the host. Many research groups actively develop synthetic ligands that are able to selectively and strongly bind to antibodies. Among the reported ligands, peptides that bind to the Fc-domain of antibodies are attractive tools in antibody research. Besides their use as high affinity ligands in antibody purification chromatography, Fc-binding peptides are applied e.g., to localize antibodies on nanomaterials and to increase the half-life of proteins in serum. In this review, recent developments of Fc-binding peptides are presented and their binding characteristics and diverse applications are discussed.
Oxoammonium cation intermediate in the nitroxide-catalyzed dismutation of superoxide. (1992)

Dismutation of superoxide has been shown previously to be catalyzed by stable nitroxide compounds. In the present study, the mechanism of superoxide (.O2-) dismutation by various five-membered ring and six-membered ring nitroxides was studied by electron paramagnetic resonance spectrometry, UV-visible spectrophotometry, cyclic voltammetry, and bulk electrolysis. Electron paramagnetic resonance signals from the carbocyclic nitroxide derivatives (piperidinyl, pyrrolidinyl, and pyrrolinyl) were unchanged when exposed to enzymatically generated .O2-, whereas, in the presence of .O2- and reducing agents such as NADH and NADPH, the nitroxides underwent reduction to their respective hydroxylamines. The reaction of 4-hydroxy-2,2,6,6-tetramethyl-1-hydroxypiperidine (Tempol-H) with .O2- was measured and, in agreement with earlier reports on related compounds, the rate was found to be too slow to be consistent with a mechanism of .O2- dismutation involving the hydroxylamine as an intermediate. Voltammetric analyses of the carbocyclic nitroxide derivatives revealed a reversible one-electron redox couple at positive potentials. In contrast, oxazolidine derivatives were irreversibly oxidized. At negative potentials, all of the nitroxides studied exhibited a broad, irreversible reductive wave. The rate of .O2- dismutation correlated with the reversible midpoint redox potential. Bulk electrolysis at positive potentials was found to generate a metastable oxidized form of the nitroxide. The results indicate that the dismutation of .O2- is catalyzed by the oxoammonium/nitroxide redox couple for carbocyclic nitroxide derivatives. In addition to the one-electron mitochondrial reduction pathway, the present results suggest the possibility that cellular bioreduction by a two-electron pathway may occur subsequent to oxidation of stable nitroxides. Furthermore, the cellular destruction of persistent spin adduct nitroxides might also be facilitated by a primary univalent oxidation.