gebhart/patrepeval huggingface dataset:
Evaluation and Optimization of Mass Spectrometric Settings during Data-dependent Acquisition Mode: Focus on LTQ-Orbitrap Mass Analyzers (2013)

Mass-spectrometry-based proteomics has evolved as the preferred method for the analysis of complex proteomes. Undoubtedly, recent advances in mass spectrometry instrumentation have greatly enhanced proteomic analysis. A popular instrument platform in proteomics research is the LTQ-Orbitrap mass analyzer. In this tutorial, we discuss the significance of evaluating and optimizing mass spectrometric settings on the LTQ-Orbitrap during CID data-dependent acquisition (DDA) mode to improve protein and peptide identification rates. We focus on those MS and MS/MS parameters that have been systematically examined and evaluated by several researchers and are commonly used during DDA. More specifically, we discuss the effect of mass resolving power, preview mode for FTMS scan, monoisotopic precursor selection, signal threshold for triggering MS/MS events, number of microscans per MS/MS scan, number of MS/MS events, automatic gain control target value (ion population) for MS and MS/MS, maximum ion injection time for MS/MS, rapid and normal scan rate, and prediction of ion injection time. We furthermore present data from the latest generation LTQ-Orbitrap system, the Orbitrap Elite, along with recommended MS and MS/MS parameters. The Orbitrap Elite outperforms the Orbitrap Classic in terms of scan speed, sensitivity, dynamic range, and resolving power and results in higher identification rates. Several of the optimized MS parameters determined on the LTQ-Orbitrap Classic and XL were easily transferable to the Orbitrap Elite, whereas others needed to be reevaluated. Finally, the Q Exactive and HCD are briefly discussed, as well as sample preparation, LC-optimization, and bioinformatics analysis. We hope this tutorial will serve as guidance for researchers new to the field of proteomics and assist in achieving optimal results.
Hydrophobic amino acid residues in peptide antigens determine the genetic control of immune responses. (1992)

The ability to respond to an antigen is generally controlled by the activation of T helper cells. These cells are required for the initiation of immune responses including the activation of T effector cells in cell-mediated immunity and for the production of antibodies by B cells. Major histocompatibility complex (MHC) molecules present antigenic fragments to helper T cells, and recent studies suggest antigen binds to MHC molecules during this process. Both the composition and the structure of the peptide antigen and its ability to interact with MHC molecules determine the genetic responsiveness of an individual. We used a panel of synthetic polypeptide antigens with the repeating sequence Glu-X-Ala to determine the role that individual amino acid residues play in the recognition of antigens by T cells. The aromatic hydrophobic residues Tyr and Phe in polypeptide antigens Poly EYA, Poly EFA, and Poly EYAEFA were found to determine the genetic control of immune responses. Mice of H-2b,d haplotypes are high responders to Poly EYA, mice of H-2p,q haplotypes are high responders to Poly EFA and mice of H-2b,d,p,q strains are high responders to Poly EYAEFA. Mice of H-2k haplotype were nonresponders to all of these antigens. The antigen Poly ESA containing the hydrophilic residues (Ser), on the other hand, was found to be nonimmunogenic. Animals which are nonresponders to Poly EYA or Poly EFA, when primed with Poly EYAEFA, produce both T cells and antibodies which crossreact with Poly EYA and Poly EFA.(ABSTRACT TRUNCATED AT 250 WORDS)
Up-regulation of Interleukin-8, Interleukin-10, Monocyte Chemotactic Protein-1, and Monocyte Chemotactic Protein-3 in Peripheral Blood Monocytes in Stable Lung Transplant Recipients: Are Immunosuppression Regimens Working? (2005)

Because MCP-3 is a major chemoattractant for leukocytes to sites of antigenic challenge and is a natural ligand for MCP-1 receptor, this novel finding has important implications for the pathogenesis of lung transplant rejection. We now provide evidence that current immunosuppression protocols have a limited effect on monocyte inflammatory cytokine production and do not adequately suppress monocyte IL-8, MCP-1, and MCP-3 chemokine production. Drugs that modulate the action of these chemokines may improve current protocols for reducing graft rejection. Intracellular chemokine and cytokine analysis with flow cytometry may be a more accurate indicator of immunosuppression than drug levels in these patients.
Expression of the influenza A virus M2 protein is restricted to apical surfaces of polarized epithelial cells (1992)

The M2 protein of influenza A virus is a small, nonglycosylated transmembrane protein that is expressed on surfaces of virus-infected cells. A monoclonal antibody specific for the M2 protein was used to investigate its expression in polarized epithelial cells infected with influenza virus or a recombinant vaccinia virus that expresses M2. The expression of M2 on the surfaces of influenza virus-infected cells was found to be restricted to the apical surface, closely paralleling that of the influenza virus hemagglutinin (HA). Membrane domain-specific immunoprecipitation indicated that the M2 protein was inserted directly into the apical membrane with transport kinetics similar to those of HA. In polarized cells infected with a recombinant vaccinia virus that expresses M2, we found that 86 to 93% of surface M2 was restricted to the apical domain compared with 88 to 90% of HA in a similar assay. These results indicate that the M2 protein undergoes directional transport in the absence of other influenza virus proteins and that M2 contains the structural features required for apical transport in polarized epithelial cells. The ultrastructural localization of the M2 protein in influenza virus-infected MDCK cells was investigated by immunoelectron microscopy using M2 antibody and a gold conjugate. In cells in which extensive virus budding was occurring, the apical cell membrane was labeled with gold particles evenly distributed between microvilli and the surrounding membrane. In addition, a significant fraction of the M2 label was apparently associated with virions. A monoclonal antibody specific for HA demonstrated a similar labeling pattern. These results indicate that M2 is localized in close proximity to budding and assembled virions.
Routing in modular fault tolerant multiprocessor systems (2003)

The authors consider a class of modular multiprocessor architectures in which spares are added to each module to cover for faulty nodes within that module, thus forming a fault tolerant basic block (FTBB). The goal is to preserve the logical adjacency between active nodes by means of a routing algorithm which delivers messages successfully to their destinations. Two phase routing strategies are introduced that route messages first to their destination FTBB, and then to the destination nodes within the destination FTBB. This strategy may be applied to a variety of architectures including binary hypercubes and 3-D tori. In the presence of f faults in these systems. It is shown that the worst case length of the message route is max( sigma +f, (K+1) sigma )+M, where sigma is the shortest path in the absence of faults, and M and K are the numbers of primary nodes and spare nodes in a FTBB, respectively. The average routing overhead is much lower than the worst case overhead.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Ursolic Acid from<i>Plantago</i><i>major</i>, a Selective Inhibitor of Cyclooxygenase-2 Catalyzed Prostaglandin Biosynthesis (1998)

A hexane extract of Plantago major was investigated by bioactivity-directed fractionation, using an in vitro cyclooxygenase-2 (COX-2) catalyzed prostaglandin biosynthesis inhibition assay, and resulted in the isolation of ursolic acid (1). This triterpenoid showed a significant COX-2 inhibitory effect, directly on the enzyme activity, with an IC50 value of 130 microM and a COX-2/COX-1 selectivity ratio of 0.6. The structural isomer oleanolic acid (2) was found to be less active than 1, with an IC50 value of 295 microM, but showed a similar selectivity ratio (0.8). Furthermore, no significant inhibition on COX-2 or COX-1 was observed by the triterpenoid, 18beta-glycyrrhetinic acid (3). The direct inhibitory effect of 1 and 2 on COX-2 catalyzed prostaglandin biosynthesis increased with preincubation, indicating a time-dependent inhibition, while the effect on COX-1 was found to be independent of preincubation time.
A curved‐field reflectron for improved energy focusing of product ions in time‐of‐flight mass spectrometry (1993)

A new type of curved-field reflectron has been developed for the energy focusing of ions formed after initial acceleration in time-of-flight (TOF) mass spectrometers. These include ions generated in the dissociation region of a tandem TOF, as well as metastable decay products formed in the field-free drift region prior to their reflection. Unlike conventional linear-field reflectrons, which focus product ions to different focal lengths that are proportional to the mass (energy) of the fragment, the new curved-field reflectron energy focuses all ions to within a small region near the exit of the reflectron. Thus, the collection of resolved fragment peaks is possible without scanning or stepping the potential gradient of the reflectron, enabling faster acquisition of the production spectrum and, more importantly, true multiplex recording of the spectra from each ionization event. Theoretical considerations of the design are discussed along with an evaluation of collision-induced dissociation data, demonstrating the performance of the new reflectron in a tandem TOF instrument.
Temperature dependence of radiation effects in polyethylene: Cross‐linking and gas evolution (1999)

High-density polyethylene (HDPE) and low-density polyethylene (LDPE) were irradiated in vacuo at 30–220 and 30–360°C, respectively, with γ-rays at doses of 10–400 kGy. Temperature dependence of cross-linking and gas evolution was investigated. It was found that cross-linking was the predominant process up to 300°C and the gel point decreased smoothly with temperature. The increase of G(x) with temperature was likely attributed to the temperature effect on addition of radicals to the double bonds present in the polymer. Above 300°C, the gel fraction at a given dose decreased remarkably with temperature and turned to zero at 360°C. The molecular weight variation determined with gel permeation chromatography (GPC) indicated the enhanced degradation at 360°C by radiation. G-values of H2 increased with temperature and varied with dose. The compositions of the C1–C4 hydrocarbons evolved depended on the structures of side branches. Raising the temperature favored the formation of unsaturated hydrocarbons, and the yield of unsaturated relative to saturated hydrocarbons decreased with dose. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 1541–1548, 1999
Replication and mobility (2003)

Mobility of users and services and its impact on data replication and migration will be one of the main technical problems to be resolved. In fact, the authors view mobility as probably the most challenging new issue facing distributed systems of the future. The distinct new element which mobility brings into the issues of data replication is system's uncertainty about its own state (meaning primarily location). Thus the cost of communication between two mobile users is dependent not only on the distance between them but also on the cost of search necessary to determine the exact value of location. The authors address some of the questions, by proposing an adaptive replication scheme for mobile data.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Mycobacterium tuberculosis-Induced Polarization of Human Macrophage Orchestrates the Formation and Development of Tuberculous Granulomas In Vitro (2015)

The tuberculous granuloma is an elaborately organized structure and one of the main histological hallmarks of tuberculosis. Macrophages, which are important immunologic effector and antigen-presenting cells, are the main cell type found in the tuberculous granuloma and have high plasticity. Macrophage polarization during bacterial infection has been elucidated in numerous recent studies; however, macrophage polarization during tuberculous granuloma formation and development has rarely been reported. It remains to be clarified whether differences in the activation status of macrophages affect granuloma formation. In this study, the variation in macrophage polarization during the formation and development of tuberculous granulomas was investigated in both sections of lung tissues from tuberculosis patients and an in vitro tuberculous granuloma model. The roles of macrophage polarization in this process were also investigated. Mycobacterium tuberculosis (M. tuberculosis) infection was found to induce monocyte-derived macrophage polarization. In the in vitro tuberculous granuloma model, macrophage transformation from M1 to M2 was observed over time following M. tuberculosis infection. M2 macrophages were found to predominate in both necrotic and non-necrotic granulomas from tuberculosis patients, while both M1 and M2 polarized macrophages were found in the non-granulomatous lung tissues. Furthermore, it was found that M1 macrophages promote granuloma formation and macrophage bactericidal activity in vitro, while M2 macrophages inhibit these effects. The findings of this study provide insights into the mechanism by which M. tuberculosis circumvents the host immune system as well as a theoretical foundation for the development of novel tuberculosis therapies based on reprogramming macrophage polarization.
Logic (1995)

In this chapter, we will introduce the study of logic from a mathematical point of view. Mathematical logic finds applications in many areas of computing. The laws of logic are employed in the design of the digital circuitry in a computer. Logical expressions occur as conditions in the control structures in algorithms and computer programs, and in the commands used for querying databases. Expert systems employing knowledge-based software use rules of logical inference to draw conclusions from known facts. Formal specification documents, which state in a precise way what computer systems are required to do, are written in specification languages, such as Z, which use the theory and notation of symbolic logic.
A Java/CORBA based universal framework for super server user-end integrated environments (2003)

Integrating super server side tools and applications to the user's desktop in an easily used manner over the Internet is a challenging problem. This paper outlines a software framework DMUE, that is an ongoing project for making Dawning super server (one of the National Hi-Tech 863 Projects in China) with single-processor or SMP nodes cluster architecture available to end users, who may be situated anywhere and using any platform through the Internet. The DMUE chose the 3-tier client/server distributed objects style architecture proposed by CORBA. The key part of the DMUE is its middle tier JC-Glue, which must meet the requirements for interacting with the implement logic of the parallel tool and application objects on the super server side and the client side visual objects serving as user interface. Our case study, parallel and distributed debugging over the Internet, made us feel confident of that the industry standard middleware system CORBA coupled with the platform independence of Java language, provided innovative and viable technology to realize the usability of parallel computers.
Lythraceae Alkaloids. I. Isolation and Structural Studies of the Alkaloids of Decodon verticillatus (L.) Ell.<sup>1</sup> (1962)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLythraceae Alkaloids. I. Isolation and Structural Studies of the Alkaloids of Decodon verticillatus (L.) Ell.1James P. FerrisCite this: J. Org. Chem. 1962, 27, 9, 2985–2990Publication Date (Print):September 1, 1962Publication History Published online1 May 2002Published inissue 1 September 1962https://pubs.acs.org/doi/10.1021/jo01056a005https://doi.org/10.1021/jo01056a005research-articleACS PublicationsRequest reuse permissionsArticle Views196Altmetric-Citations33LEARN 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
Single Particle Spectroscopy Study of Metal-Film-Induced Tuning of Silver Nanoparticle Plasmon Resonances (2010)

We present an experimental study of the tunability of the silver nanoparticle localized plasmon resonance in close proximity to a gold film. Broad-band tuning of the silver particle plasmon resonance from blue wavelengths into the near-IR region can be achieved due to strong electromagnetic coupling between the nanoparticle and the metal film. When the thickness of a thin silica spacer layer between the metal nanoparticle and the metal film is altered, the resonance frequency shifts. Single particle spectroscopy of over 250 isolated silver nanoparticles revealed evidence for the excitation of both horizontal and vertical plasmon modes. Distinct resonance features observed in the scattering spectra were assigned to specific modes based on a dipole-dipole interaction model. The experimental results suggest that low-loss silver nanoparticles can be used in surface-enhanced spectroscopy studies throughout the entire visible spectrum. The use of frequency-tuned spherical metal nanoparticles on solid substrates could lead to thermally stable substrates for plasmon-enhanced sensing applications, including surface-enhanced Raman scattering and refractive index based biodetection methods. © 2010 American Chemical Society.
Protective effects of IL-4, IL-10, IL-12, and IL-13 in IgG immune complex-induced lung injury: role of endogenous IL-12 (1997)

Using the IgG immune complex (BSA-anti-BSA) model of acute lung injury in rats, we have compared four intratracheally administered cytokines for their protective effects on parameters of injury (albumin leak and hemorrhage) and on neutrophil accumulation (lung content of myeloperoxidase). The descending rank order of protective effects was: IL-10 > or = IL-13 > IL-4 > > IL-12. In animals receiving an intratracheal instillation of 1.0 microg murine rIL-4, IL-10, IL-12 or IL-13, the levels of TNF-alpha in bronchoalveolar (BAL) fluids after intrapulmonary deposition of IgG immune complexes were reduced by 98, 98, 34, and 97%, respectively, implying a corresponding reduction in up-regulation of lung vascular intercellular adhesion molecule-1. The unexpected findings with IL-12 were further evaluated. In spite of reduced BAL levels of TNF-alpha in IL-12-treated animals, BAL levels of IFN-gamma were elevated sixfold, indicative of the expected biologic response to IL-12. Alveolar macrophages obtained from the same animals showed a 68% reduction in formation in vitro of NO2-/NO3-. When rats undergoing intrapulmonary deposition of IgG immune complexes were treated either i.v. or intratracheally with blocking Ab to murine IL-12, there were significant increases in lung permeability and myeloperoxidase values, suggesting that in this model intrinsic IL-12 functions in a regulatory manner. In homogenates of injured lungs, this Ab detected heterodimeric complex, consistent with rat IL-12. These data confirm the ability of certain cytokines to suppress in vivo lung inflammatory responses and underscore the unexpected anti-inflammatory activities of IL-12.
Solenolides, new antiinflammatory and antiviral diterpenoids from a marine octocoral of the genus Solenopodium (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSolenolides, new antiinflammatory and antiviral diterpenoids from a marine octocoral of the genus SolenopodiumAmiram Groweiss, Sally A. Look, and William FenicalCite this: J. Org. Chem. 1988, 53, 11, 2401–2406Publication Date (Print):May 1, 1988Publication History Published online1 May 2002Published inissue 1 May 1988https://pubs.acs.org/doi/10.1021/jo00246a001https://doi.org/10.1021/jo00246a001research-articleACS PublicationsRequest reuse permissionsArticle Views240Altmetric-Citations56LEARN 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
Preliminary results from a current mode CMOS front-end circuit for silicon photomultiplier detectors (2007)

We propose a CMOS front-end circuit suitable for Silicon Photomultiplier detectors (SiPM) based on a current buffer, as input stage, which features small input impedance and large bandwidth, thanks to the application of current feedback techniques. The current mode approach enhances the dynamic range of the front-end and does not suffer from possible voltage limitations due to deep-submicron CMOS implementation. We report the first measurement results obtained by coupling the circuit prototype to a SiPM detector excited by a blue LED light source. The measurements confirm the effectiveness of the proposed front-end approach and demonstrate its capability of managing large current signals with good linearity.
One-Step Conversion of Pyridine<i>N</i>-Oxides to Tetrazolo[1,5-<i>a</i>]pyridines (2006)

Pyridine N-oxides were converted to tetrazolo[1,5-a]pyridines in good to excellent yield by heating in the presence sulfonyl or phosphoryl azides and pyridine in the absence of solvent. Various sulfonyl and phosphoryl azides were screened for reactivity under a standard set of conditions. Diphenyl phosphorazidate was the most convenient reagent and gave high yields. Reaction optimization, scope, and scalability are discussed.