gebhart/patrepeval huggingface dataset:
Analysis of the Fragments from Collision-Induced Dissociation of Electrospray-Produced Peptide Ions Using a Quadrupole Ion Trap Storage/Reflectron Time-of-Flight Mass Spectrometer (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAnalysis of the Fragments from Collision-Induced Dissociation of Electrospray-Produced Peptide Ions Using a Quadrupole Ion Trap Storage/Reflectron Time-of-Flight Mass SpectrometerBenjamin M. Chien and David M. LubmanCite this: Anal. Chem. 1994, 66, 10, 1630–1636Publication Date (Print):May 15, 1994Publication History Published online1 May 2002Published inissue 15 May 1994https://pubs.acs.org/doi/10.1021/ac00082a006https://doi.org/10.1021/ac00082a006research-articleACS PublicationsRequest reuse permissionsArticle Views108Altmetric-Citations11LEARN 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
Frequency-selective contrast on variably doped p-type silicon with a scanning microwave microscope (2012)

We report on frequency-dependent contrast in d(S11)/dV measurements of a variably doped p-type silicon sample in the frequency range from 2 GHz to 18 GHz. The measurements were conducted with a scanning microwave microscope. The measurements were done at selected frequencies while varying the DC tip voltage. The measured d(S11)/dV signal shows a maximum for doping concentrations (NA) of 1015 cm−3−1016 cm−3 at 2.3 GHz. As the microscope operating frequency is increased, this maximum sequentially “switches” through the regions of increasing dopant concentration, displaying a maximum for NA of 1017 cm−3−1018 cm−3 at 17.9 GHz. The frequency dependent “switching” is attributed to the physics of tip-to-sample interaction, particularly as related to the frequency-dependent local surface resistance and the depletion capacitance that control the RC time constant of tip-to-sample interaction. This provides a unique platform for local, frequency-selective, spatially resolved microwave spectroscopy of semiconducting materials.
Epitope analysis of the F4 (K88) fimbrial antigen complex of enterotoxigenic Escherichia coli by using monoclonal antibodies (1990)

So far, three subtypes of the F4 (K88) fimbrial antigen of porcine enterotoxigenic Escherichia coli, F4ab, F4ac, and F4ad, have been distinguished by using polyclonal antisera in agglutination and precipitation tests. The a factor represents one or more common epitopes, whereas each of the b, c, and d factors represents one or more subtype-specific epitopes. We further characterized the F4 antigen complex by using a panel of 40 F4-specific monoclonal antibodies (MAbs). The specificity of all MAbs was proven by enzyme-linked immunosorbent assays, agglutination and radioimmunoprecipitation tests, and immunoelectron microscopy. The MAbs either reacted with all F4 subtypes, reacted with two subtypes, or were subtype specific. Epitope analysis by competition enzyme-linked immunosorbent assays revealed at least 11 epitope clusters on the F4 antigen complex, designated a1 to a7, b1, b2, c, and d. The following antigenic formulas were found for the F4 subtypes: F4ab, a1a2a3a4a5a6b1b2; F4ac, a1a2a3(a4)a5a6a7c; and F4ad, a1a2a3a4a7d. All MAbs were directed against conformational epitopes located on the 27,500-dalton major fimbrial subunits. Consequences for the replacement of polyclonal antisera by MAbs in diagnostic tests are discussed.
Bombesin protects against bacterial translocation induced by three commercially available liquid enteral diets: A prospective, randomized, multigroup trial (1994)

Three different liquid diets induced bacterial translocation to the mesenteric lymph node. Since bombesin was effective in reducing bacterial translocation, it appears that bacterial translocation induced by these liquid diets can be modulated hormonally.
Kinetics of palm oil transesterification in a batch reactor (2000)

Abstract Methyl esters were produced by transesterification of palm oil with methanol in the presence of a catalyst (KOH). The rate of transesterification in a batch reactor increased with temperature up to 60°C. Higher temperatures did not reduce the time to reach maximal conversion. The conversion of triglycerides (TG), diglycerides (DG), and monoglycerides (MG) appeared to be second order up to 30 min of reaction time. Reaction rate constants for TG, DG, and MG hydrolysis reactions were 0.018–0.191 (wt%·min) −1 , and were higher at higher temperatures and higher for the MG reaction than for TG hydrolysis. Activation energies were 14.7, 14.2, and 6.4 kcal/mol for the TG, DG, and MG hydrolysis reactions, respectively. The optimal catalyst concentration was 1% KOH.
Evidence of Preferential Protein Targets for Age‐Related Modifications in Peripheral Blood Lymphocytes (2004)

Oxidatively modified proteins have been analyzed in aging human peripheral blood lymphocytes since protein modification by oxidation and other related pathways are believed to contribute to the intracellular age-related accumulation of damaged proteins, a process that has been associated with the cellular functional deficits that occur with age. Advanced glycation end products (AGE) were quantified and the pattern of glycated proteins analyzed by two-dimensional gel electrophoresis followed by Western blotting using an anti-AGE antibody raised against glycated RNAse. The protein silver stain and the immunoblot patterns were not superimposable, indicating that glycoxidative modifications are targeting only a restricted set of proteins. Modification of proteins with the lipid peroxidation product 4-hydroxy-2-nonenal has also been studied. The patterns of modified proteins have been analyzed using two- dimensional gel electrophoresis followed by Western blotting with an antibody recognizing 4-hydroxy-2-nonenal protein adducts using the same proteomic approach as for glycoxidative modifications. Specific protein targets for these modifications, that might serve as biomarkers of aging lymphocytes, are currently characterized and identified by mass spectrometry.
Characterization of side-population cells in human normal endometrium (2007)

SP cells in the human endometrium can function as progenitor cells. This is the first report of the phenotype of SP cells from normal human endometrial cells.
The MacIntosh Prosthesis (1975)

Thirty-seven knees that had undergone plateau reconstruction with the Macintosh prosthesis were evaluated on a prospective basis for 24 items of history and physical examination. It was found that the procedure did not significantly improve either the gait characteristics of the knee or the ability to perform activities of daily living. Valgus deformity and laxity of the lateral collateral structures, when present, predisposed to a poor result. Patellofemoral arthritis was detrimental to those activities that required using the loaded knee in a flexed position. The primary benefit of this procedure was the partial relief of pain. The study has provided a method and basis for evaluation of other types of implants in the rheumatoid knee.
A growing role for mTOR in promoting anabolic metabolism (2013)

mTOR [mammalian (or mechanistic) target of rapamycin] is a protein kinase that, as part of mTORC1 (mTOR complex 1), acts as a critical molecular link between growth signals and the processes underlying cell growth. Although there has been intense interest in the upstream mechanisms regulating mTORC1, the full repertoire of downstream molecular events through which mTORC1 signalling promotes cell growth is only recently coming to light. It is now recognized that mTORC1 promotes cell growth and proliferation in large part through the activation of key anabolic processes. Through a variety of downstream targets, mTORC1 alters cellular metabolism to drive the biosynthesis of building blocks and macromolecules fundamentally essential for cell growth, including proteins, lipids and nucleic acids. In the present review, we focus on the metabolic functions of mTORC1 as they relate to the control of cell growth and proliferation. As mTORC1 is aberrantly activated in a number of tumour syndromes and up to 80% of human cancers, we also discuss the importance of this mTORC1-driven biosynthetic programme in tumour growth and progression.
DNA Helicase Activity of the Hepatitis C Virus Nonstructural Protein 3 (1997)

Hepatitis C virus (HCV) nonstructural protein 3 (NS3) is a known RNA helicase, an enzyme that unwinds RNA x DNA and RNA x RNA duplexes. We have now deciphered the biochemical characteristics of the HCV NS3 DNA helicase activity. Recombinant NS3 was expressed in Escherichia coli, purified to near homogeneity, and tested for DNA helicase activity. The optimal conditions for DNA unwinding (for example, the preferred pH and magnesium ion concentration) were similar to those for RNA unwinding. The DNA helicase activity was very sensitive to potassium ion concentration, while DNA binding and DNA-stimulated ATPase activities were not. The direction of DNA unwinding was determined to be 3' to 5'. All four ribonucleoside triphosphates (ATP, GTP, CTP, UTP) and deoxynucleoside triphosphates (dATP, dGTP, dCTP, dTTP) could serve as energy sources, but GTP and dGTP were less efficient than the others. When nucleotide analog inhibitors were added to the DNA helicase reaction, the overall order of inhibitory capacity was: adenosine 5'-O-(3-thiotriphosphate) > adenylyl-imidodiphosphate and adenylyl-(beta,gamma-methylene)-diphosphate > AMP. DNA helicase activity was inhibited strongly by ssDNA and ssRNA, but was little affected by dsDNA. The ATPase activity was stimulated greatly by ssDNA and ssRNA, but not by dsDNA. The NS3 protein could unwind up to 500 base pairs of duplex DNA. The possible multifunctional nature of the NS3 protein is discussed and compared with that of Simian virus 40 large T antigen.
Cardiac Bodies: A Novel Culture Method for Enrichment of Cardiomyocytes Derived from Human Embryonic Stem Cells (2006)

Human embryonic stem (hES) cell-derived cardiomyocytes hold great promise for cardiovascular regenerative medicine. However, this application faces a number of challenges, including generating cardiomyocytes of adequate purity. With current protocols being used by several laboratories, cardiomyocyte differentiation from hES cells occurs at low frequency and results in a mixture of differentiated cells. Here we describe a novel method for enrichment of cardiomyocytes. Cardiomyocytes were isolated from embryoid body (EB) outgrowths by Percoll separation and then enriched by culturing the aggregates of cells (termed cardiac bodies, CBs) in suspension. The majority of CBs showed contractility after 1 week in culture and were positive for multiple cardiomyocyte- associated proteins. Enrichment of cardiomyocytes was evident by the increase in the expression of cardiac alpha and beta myosin heavy chains (alpha and betaMHC) in CBs in suspension culture compared to unpurified EB outgrowths. Flow cytometry analysis showed that 35-66% of the cells in CBs were positive for sarcomeric myosin heavy chain (sMHC) or cardiac troponin T (cTnT) expression. In addition, dissociated CBs were capable of reassociating into contracting aggregates in suspension and recovering contractility after the individual cells were replated onto matrix-coated surfaces. These data suggest that the CB method is a useful approach for the generation of cardiomyocytes at an adequate purity for cardiovascular therapies.
Five New Labdane-Type Diterpenes from Excoecaria agallocha. IV. (1998)

Five new labdane-type diterpenes were isolated from the resinous wood of Excoecaria agallocha. The structures of these compounds were established as ent-13-epi-8, 13-epoxy-2-hydroxylabda-1, 14-dien-3-one (1), ent-13-epi-8, 13-epoxy-14S, 15-dohydroxylabdan-3-one (2), ent-13-epi-8, 13-epoxy-2, 3-secolabd-14-ene-2, 3-dioic acid (3), ent-13-epi-8, 13-epoxy-2, 3-secolabd-14-ene-2, 3-dioic acid 3-methyl ester (4) and ent-13-epi-8, 13-epoxy-2-oxa-3-oxolabd-14-ene-1R-carboxylic acid (5).
Plant Farnesyltransferase Can Restore Yeast Ras Signaling and Mating (1997)

Farnesyltransferase (FTase) is a heterodimeric enzyme that modifies a group of proteins, including Ras, in mammals and yeasts. Plant FTase alpha and beta subunits were cloned from tomato and expressed in the yeast Saccharomyces cerevisiae to assess their functional conservation in farnesylating Ras and a-factor proteins, which are important for cell growth and mating. The tomato FTase beta subunit (LeFTB) alone was unable to complement the growth defect of ram1 delta mutant yeast strains in which the chromosomal FTase beta subunit gene was deleted, but coexpression of LeFTB with the plant alpha subunit gene (LeFTA) restored normal growth, Ras membrane association, and mating. LeFTB contains a novel 66-amino-acid sequence domain whose deletion reduces the efficiency of tomato FTase to restore normal growth to yeast ram1 delta strains. Coexpression of LeFTA and LeFTB in either yeast or insect cells yielded a functional enzyme that correctly farnesylated CaaX-motif-containing peptides. Despite their low degree of sequence homology, yeast and plant FTases shared similar in vivo and in vitro substrate specificities, demonstrating that this enzymatic modification of proteins with intermediates from the isoprenoid biosynthesis pathway is conserved in evolutionarily divergent eukaryotes.
Intestinal colonization of laboratory rats with Oxalobacter formigenes (1987)

Six strains of Oxalobacter formigenes (anaerobic oxalate-degrading bacteria) were examined for their ability to colonize the gastrointestinal tracts of adult laboratory rats. These rats did not harbor O. formigenes. Strain OxCR6, isolated from the cecal contents of a laboratory rat that was naturally colonized by oxalate-degrading bacteria, colonized the ceca and colons of adult rats fed a diet that contained 4.5% sodium oxalate. Five days after rats were inoculated intragastrically with 10(9) viable cells of strain OxCR6, oxalate degradation rates in cecal and colonic contents increased by 19 and 40 times, respectively. Viable counts of strain OxCR6 from these rats averaged 10(8)/g (dry weight) of cecal contents. Strain OxCR6 was not detected in the cecal contents of inoculated rats fed diets that contained less than 3.0% sodium oxalate. Strains of O. formigenes isolated from the cecal contents of swine, guinea pigs, and wild rats and from human feces also colonized the ceca of laboratory rats; a ruminal strain failed to colonize the rat cecum.
Heterotrinuclear Carboxylates of Chromium(III) and Iron(III): Mixtures or Pure Compounds? (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHeterotrinuclear Carboxylates of Chromium(III) and Iron(III): Mixtures or Pure Compounds?John B. VincentCite this: Inorg. Chem. 1994, 33, 24, 5604–5606Publication Date (Print):November 1, 1994Publication History Published online1 May 2002Published inissue 1 November 1994https://pubs.acs.org/doi/10.1021/ic00102a041https://doi.org/10.1021/ic00102a041research-articleACS PublicationsRequest reuse permissionsArticle Views123Altmetric-Citations18LEARN 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
Preferential Localization of Effector Memory Cells in Nonlymphoid Tissue (2001)

Many intracellular pathogens infect a broad range of host tissues, but the importance of T cells for immunity in these sites is unclear because most of our understanding of antimicrobial T cell responses comes from analyses of lymphoid tissue. Here, we show that in response to viral or bacterial infection, antigen-specific CD8 T cells migrated to nonlymphoid tissues and were present as long-lived memory cells. Strikingly, CD8 memory T cells isolated from nonlymphoid tissues exhibited effector levels of lytic activity directly ex vivo, in contrast to their splenic counterparts. These results point to the existence of a population of extralymphoid effector memory T cells poised for immediate response to infection.
Syntheses and antifolate activity of 5-methyl-5-deaza analogs of aminopterin, methotrexate, folic acid, and N10-methylfolic acid (1986)

Evidence indicating that modifications at the 5- and 10-positions of classical folic acid antimetabolites lead to compounds with favorable differential membrane transport in tumor vs. normal proliferative tissue prompted an investigation of 5-alkyl-5-deaza analogues. 2-Amino-4-methyl-3,5-pyridinedicarbonitrile, prepared by hydrogenolysis of its known 6-chloro precursor, was treated with guanidine to give 2,4-diamino-5-methylpyrido[2,3-d]pyrimidine-6-carbonitrile which was converted via the corresponding aldehyde and hydroxymethyl compound to 6-(bromomethyl)-2,4-diamino-5-methylpyrido[2,3-d]pyrimidine. Reductive condensation of the nitrile 8 with diethyl N-(4-amino-benzoyl)-L-glutamate followed by ester hydrolysis gave 5-methyl-5-deazaaminopterin. Treatment of 12 with formaldehyde and Na(CN)BH3 afforded 5-methyl-5-deazamethotrexate, which was also prepared from 15 and dimethyl N-[(4-methylamino)benzoyl]-L-glutamate followed by ester hydrolysis. 5-Methyl-10-ethyl-5-deazaaminopterin was similarly prepared from 15. Biological evaluation of the 5-methyl-5-deaza analogues together with previously reported 5-deazaaminopterin and 5-deazamethotrexate for inhibition of dihydrofolate reductase (DHFR) isolated from L1210 cells and for their effect on cell growth inhibition, transport characteristics, and net accumulation of polyglutamate forms in L1210 cells revealed the analogues to have essentially the same properties as the appropriate parent compound, aminopterin or methotrexate (MTX), except that 20 and 21 were approximately 10 times more growth inhibitory than MTX. In in vivo tests against P388/0 and P388/MTX leukemia in mice, the analogues showed activity comparable to that of MTX, with the more potent 20 producing the same response in the P388/0 test as MTX but at one-fourth the dose; none showed activity against P388/MTX. Hydrolytic deamination of 12 and 20 produced 5-methyl-5-deazafolic acid and 5,10-dimethyl-5-deazafolic acid, respectively. In bacterial studies on the 2-amino-4-oxo analogues, 5-deazafolic acid proved to be a potent inhibitor of Lactobacillus casei DHFR and also the growth of both L. casei ATCC 7469 and Streptococcus faecium ATCC 8043. Its 5-methyl congener 22 is also inhibitory toward L. casei, but its IC50 for growth inhibition is much lower than its IC50 values for inhibition of DHFR or thymidylate synthase from L. casei, suggesting an alternate site of action.
Proteomic analysis reveals co-ordinated alterations in protein synthesis and degradation pathways in LRRK2 knockout mice (2018)

Mutations in leucine-rich repeat kinase 2 (LRRK2) segregate with familial Parkinson's disease (PD) and genetic variation around LRRK2 contributes to risk of sporadic disease. Although knockout (KO) of Lrrk2 or knock-in of pathogenic mutations into the mouse germline does not result in a PD phenotype, several defects have been reported in the kidneys of Lrrk2 KO mice. To understand LRRK2 function in vivo, we used an unbiased approach to determine which protein pathways are affected in LRRK2 KO kidneys. We nominated changes in cytoskeletal-associated proteins, lysosomal proteases, proteins involved in vesicular trafficking and in control of protein translation. Changes were not seen in mice expressing the pathogenic G2019S LRRK2 mutation. Using cultured epithelial kidney cells, we replicated the accumulation of lysosomal proteases and demonstrated changes in subcellular distribution of the cation-independent mannose-6-phosphate receptor. These results show that loss of LRRK2 leads to co-ordinated responses in protein translation and trafficking and argue against a dominant negative role for the G2019S mutation.
Antibody engineering: the use of Escherichia coli as an expression host (1992)

The hypervariable loops of an antibody molecule are supported on the relatively conserved beta-sheeted frameworks of the heavy- and light-chain variable domains (designated VH and VL domains, respectively). Residues within and flanking these loops interact with antigen and confer the specificity and affinity of antigen binding on the immunoglobulin molecule. Thus, the isolation and expression of VH and VL domain genes are of particular interest both for analysis of the determinants of antibody specificity and for generation of fragments with binding affinities for use in therapy and diagnosis. The PCR can now be used to isolate diverse repertoires of antibody VH and VL domain genes from antibody-producing cells from different species, including humans and mice. The genes can be expressed as either secreted or surface-bound Fv or Fab fragments, using Escherichia coli expression systems, and the desired antigen-binding specificity screened for or, preferably, selected. The use of E. coli as an expression host allows the required antigen-binding specificity to be isolated in clonal form in a matter of days. The VH and VL domain genes can also be hypermutated and higher-affinity variants isolated by screening or selection. Thus, the use of this technology should allow the isolation of novel binding specificities or specificities that are difficult to generate by hybridoma technology. It will also facilitate the isolation of human-derived Fv/Fab fragments that may be less immunogenic in therapy. This approach therefore has almost unlimited potential in the generation of therapeutics with binding specificities to order. The fragments can be used either alone or linked to effector functions in the form of antibody-constant domains or toxins. The new technology could prove to be a method of choice for the rapid and convenient production of designer antibodies.