gebhart/patrepeval huggingface dataset:
Crystal Structures of Escherichia coli Topoisomerase IV ParE Subunit (24 and 43 Kilodaltons): a Single Residue Dictates Differences in Novobiocin Potency against Topoisomerase IV and DNA Gyrase (2004)

Topoisomerase IV and DNA gyrase are related bacterial type II topoisomerases that utilize the free energy from ATP hydrolysis to catalyze topological changes in the bacterial genome. The essential function of DNA gyrase is the introduction of negative DNA supercoils into the genome, whereas the essential function of topoisomerase IV is to decatenate daughter chromosomes following replication. Here, we report the crystal structures of a 43-kDa N-terminal fragment of Escherichia coli topoisomerase IV ParE subunit complexed with adenylyl-imidodiphosphate at 2.0-A resolution and a 24-kDa N-terminal fragment of the ParE subunit complexed with novobiocin at 2.1-A resolution. The solved ParE structures are strikingly similar to the known gyrase B (GyrB) subunit structures. We also identified single-position equivalent amino acid residues in ParE (M74) and in GyrB (I78) that, when exchanged, increased the potency of novobiocin against topoisomerase IV by nearly 20-fold (to 12 nM). The corresponding exchange in gyrase (I78 M) yielded a 20-fold decrease in the potency of novobiocin (to 1.0 micro M). These data offer an explanation for the observation that novobiocin is significantly less potent against topoisomerase IV than against DNA gyrase. Additionally, the enzyme kinetic parameters were affected. In gyrase, the ATP K(m) increased approximately 5-fold and the V(max) decreased approximately 30%. In contrast, the topoisomerase IV ATP K(m) decreased by a factor of 6, and the V(max) increased approximately 2-fold from the wild-type values. These data demonstrate that the ParE M74 and GyrB I78 side chains impart opposite effects on the enzyme's substrate affinity and catalytic efficiency.
Emerging role of MAP kinase pathways as therapeutic targets in COPD (2006)

Studies examining the cellular mechanisms of inflammation and protease production in the lung tissue and airways of COPD patients have shed light on the important role of kinase-based signaling cascades. These pathways can be activated by environmental stimuli such as tobacco smoke, and by endogenous signals such as cytokines, growth factors, and inflammation-derived oxidants. The three most widely characterized cascades are those directed by the classical mitogen activated protein (MAP) kinase (ERK1/2), stress activated protein kinase/c-Jun N-terminal protein kinase, and p38 enzymes. These phosphorylation cascades transmit and amplify extracellular, receptor-mediated signals through the cytoplasm of the cell to activate nuclear transcription factors which bind and induce expression of target genes. The result is tight control of diverse cellular events, and rapid responses to external stimuli. However, recent research suggests that constitutive or aberrant activation of MAP kinases contributes to several COPD-associated phenotypes, including mucus overproduction and secretion, inflammation, cytokine expression, apoptosis, T cell activation, matrix metalloproteinase production, and fibrosis. This review explores the biological functions of the MAP kinase pathways in the pathogenesis of COPD, their activation by cigarette smoke, and discusses the potential role of MAP kinase inhibitors in COPD therapy.
Peanut hull flavonoids: their relationship with peanut maturity (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPeanut hull flavonoids: their relationship with peanut maturityD. J. Daigle, E. J. Conkerton, T. H. Sanders, and A. C. MixonCite this: J. Agric. Food Chem. 1988, 36, 6, 1179–1181Publication Date (Print):November 1, 1988Publication History Published online1 May 2002Published inissue 1 November 1988https://pubs.acs.org/doi/10.1021/jf00084a013https://doi.org/10.1021/jf00084a013research-articleACS PublicationsRequest reuse permissionsArticle Views299Altmetric-Citations24LEARN 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 seven-span transmembrane receptor CD97 has a cellular ligand (CD55, DAF). (1996)

CD97 is an activation-induced antigen on leukocytes with a seven-span transmembrane (7-TM) region homologous to the secretin receptor superfamily. However, in contrast to this group of peptide hormone receptors, CD97 has an extended extracellular region with three EGF domains at the NH2 terminus, two of them with a calcium binding site. By demonstrating that lymphocytes and erythrocytes specifically adhere to CD97-transfected COS cells we here show that CD97 in parallel with its molecular evolution has acquired the ability to bind cellular ligands. A mAb selected on its capacity to block the adhesion between CD97 transfectants and red cells was found to be directed to the NH2-terminal short consensus repeat (SCR) of decay accelerating factor (DAF, CD55), a regulatory protein of the complement cascade. The specificity of the interaction of CD97 with CD55 was established by the observation that erythrocytes that lack CD55, obtained from patients with paroxysmal nocturnal hemoglobinuria (PNH) or the CD55, phenotype Inab, failed to adhere to CD97 transfectants. This is the first demonstration of a cellular ligand for a 7-TM receptor.
Cytosine methylation profiling of cancer cell lines (2008)

DNA-methylation changes in human cancer are complex and vary between the different types of cancer. Capturing this epigenetic variability in an atlas of DNA-methylation changes will be beneficial for basic research as well as translational medicine. Hypothesis-free approaches that interrogate methylation patterns genome-wide have already generated promising results. However, these methods are still limited by their quantitative accuracy and the number of CpG sites that can be assessed individually. Here, we use a unique approach to measure quantitative methylation patterns in a set of >400 candidate genes. In this high-resolution study, we employed a cell-line model consisting of 59 cancer cell lines provided by the National Cancer Institute and six healthy control tissues for discovery of methylation differences in cancer-related genes. To assess the effect of cell culturing, we validated the results from colon cancer cell lines by using clinical colon cancer specimens. Our results show that a large proportion of genes (78 of 400 genes) are epigenetically altered in cancer. Although most genes show methylation changes in only one tumor type (35 genes), we also found a set of genes that changed in many different forms of cancer (seven genes). This dataset can easily be expanded to develop a more comprehensive and ultimately complete map of quantitative methylation changes. Our methylation data also provide an ideal starting point for further translational research where the results can be combined with existing large-scale datasets to develop an approach that integrates epigenetic, transcriptional, and mutational findings.
Gene Therapy for Hemophilia B: Host Immunosuppression Prolongs the Therapeutic Effect of Adenovirus-Mediated Factor IX Expression (1995)

Hemophilia B is caused by a deficiency of blood clotting factor IX (FIX). Previous studies have shown that the delivery of a recombinant adenoviral vector expressing canine FIX (cFIX) resulted in a complete correction of hemophilia B in FIX-deficient dogs, but that cFIX expression decreased to only about 1-2% of normal levels 3 weeks after treatment. In the present study, therapeutic levels of cFIX expression capable of producing a partial correction of hemophilia B were maintained for at least 6 months after the coadministration of the cFIX-expressing adenovirus and the immunosuppressive agent cyclosporin A (CsA). These findings support a recent report (Yang et al., 1994) that host T-cell-mediated immunity against virally transduced cells is a major contributing factor to the transient nature of adenovirus-mediated gene expression in immunocompetent animals. Although a second administration of the cFIX-expressing adenovirus 6 months after the first infusion had only a minimal effect on plasma FIX levels in a dog that had been continuously treated with CsA, the prolonged expression of the transgene indicates that immunosuppression may be applicable in attaining long-term treatment of clinically relevant disorders.
Novel molecular mechanisms of dendritic cell-induced T cell activation (2000)

In this study we have re-examined the molecular mechanisms involved in activation of T cells by dendritic cells (DC). Human peripheral blood DC (PBDC) were derived by 2 h adhesion followed by 7 day culture in a combination of granulocyte macrophage colony stimulating factor and IL-4, and depletion of residual T and B cells. These PBDC were used to induce autologous T cell proliferation in a CD3-dependent response, and antibodies against CD11a/18 and CD86 were used as control inhibitors of accessory function. Antibodies against five of the cell surface molecules that we have recently identified on the surface of DC, CD13, CD87, CD98, CD147 and CD148, and an antibody which recognizes a molecule that has not as yet been identified, all inhibited the CD3-induced T cell proliferation. These findings were observed not only when antibodies were present throughout the culture, but also when they were prepulsed on to the surface of the DC, suggesting the inhibition was mediated via the antigen-presenting cells rather than the T cell. The same set of antibodies also inhibited an allospecific mixed lymphocyte reaction, confirming that the inhibitory effect was not dependent on the use of a CD3 antibody as the stimulating agent. All the antibodies of known specificity inhibited both CD4 and CD8 T cells equally. Unlike CD87, CD98 and CD147 antibodies, which inhibited activation of both CD45RA (naive) T cells and CD45RO (memory) T cells, CD13 and CD148 appeared to be involved in activation of naive cells only. The molecules identified in this study have not previously been demonstrated to play a role as accessory molecules on DC, the cells that are pivotal for immune induction. Therefore they may provide new potential targets for modulation of the immune response at the APC level.
Censoring of self-reactive B cells with a range of receptor affinities in transgenic mice expressing heavy chains for a lysozyme-specific antibody (1994)

Transgenic mice carrying a rearranged Ig gene encoding the H chain of a lysozyme-specific antibody were used to examine the effect of antigen binding affinity on elimination of self-reactive B cells. In H chain transgenic mice, B cells expressed surface IgM and IgD composed of lysozyme-specific H chains and many different possible L chains from endogenous L chain genes. Immunofluorescent staining and flow cytometry revealed a distinct subset comprising approximately 1% of spleen B cells that bound lysozyme with a high affinity comparable with the original lysozyme-specific antibody. Additional subsets accounting for a total of 5-6% of spleen B cells bound lysozyme more weakly, with the weakest requiring 10,000-fold higher concentrations of monomeric hen egg lysozyme to attain 50% receptor saturation. When the various B cell subpopulations were allowed to develop in animals expressing lysozyme as a membrane-bound antigen on autologous cells, both low and high affinity lysozyme-binding B cells were undetectable in peripheral lymphoid organs. These findings demonstrate the efficacy with which low affinity self-reactive B cells can be eliminated in vivo, consistent with the notion that this cellular mechanism accounts for the absence of natural IgM antibodies against self antigens on the surface of blood cells. The data also illustrate the potential use of Ig transgenic mice for analyzing and selecting novel receptor-ligand interactions.
Mrgprd-Expressing Polymodal Nociceptive Neurons Innervate Most Known Classes of Substantia Gelatinosa Neurons (2009)

The Mas-related G-protein-coupled receptor D (Mrgprd) marks a distinct subset of sensory neurons that transmit polymodal nociceptive information from the skin epidermis to the substantia gelatinosa (SG, lamina II) of the spinal cord. Moreover, Mrgprd-expressing (Mrgprd(+)) neurons are required for the full expression of mechanical but not thermal nociception. While such anatomical and functional specificity suggests Mrgprd(+) neurons might synapse with specific postsynaptic targets in the SG, precisely how Mrgprd(+) neurons interface with spinal circuits is currently unknown. To study circuit connectivity, we genetically targeted the light-activated ion channel Channelrhodopsin-2-Venus (ChR2-Venus) to the Mrgprd locus. In these knock-in mice, ChR2-Venus was localized to nonpeptidergic Mrgprd(+) neurons and axons, while peptidergic CGRP(+) neurons were not significantly labeled. Dissociated Mrgprd(+) DRG neurons from mice expressing one or two copies of ChR2-Venus could be activated in vitro as evidenced by light-evoked currents and action potentials. In addition, illumination of Mrgprd-ChR2-Venus(+) axon terminals in spinal cord slices evoked EPSCs in half of all SG neurons. Within this subset, Mrgprd(+) neurons were monosynaptically connected to most known classes of SG neurons, including radial, tonic central, transient central, vertical, and antenna cells. This cellular diversity ruled out the possibility that Mrgprd(+) neurons innervate a dedicated class of SG neuron. Our findings set broad constraints on the types of spinal neurons that process afferent input from Mrgprd(+) polymodal nociceptors.
Steroidogenic Enzyme AKR1C3 Is a Novel Androgen Receptor-Selective Coactivator that Promotes Prostate Cancer Growth (2013)

AKR1C3 is a novel AR-selective enzymatic coactivator and may represent the first of more than 200 known nuclear hormone receptor coactivators that can be pharmacologically targeted.
Surface Analysis of Erodible Multilayered Polyelectrolyte Films:  Nanometer-Scale Structure and Erosion Profiles (2005)

Atomic force microscopy (AFM) and scanning electron microscopy (SEM) coupled with ellipsometry have been used to characterize the microscale and nanoscale structures of erodible multilayered films fabricated from degradable polyamine 1 and either sodium poly(styrene sulfonate) (SPS) or plasmid DNA. Striking differences were found in the topography, structures, and erosion profiles of these two materials upon incubation in PBS buffer at 37 degrees C. For films fabricated from SPS, AFM data are consistent with an erosion process that occurs uniformly without the generation of holes or pits over large, micrometer-scale areas. By contrast, films fabricated from plasmid DNA undergo structural rearrangements to present surface-bound particles ranging in size from 50 to 400 nm. Additional characterization of these particulate structures by SEM suggested that they are interpenetrated with or fused to underlying polyelectrolyte layers on the silicon surface, providing a potential mechanism to manipulate the adhesive forces with which these particles are bound to the surface. The erosion profile observed for polymer 1/SPS films suggests that it may be possible to design assemblies that release two film components with well-defined release kinetics. In the context of gene delivery, the presentation of condensed DNA as nanoparticles at these surfaces may be advantageous with respect to stimulating the internalization and processing of DNA by cells. A quantitative understanding of the factors influencing the fabrication, structure, and erosion profiles of these materials will be useful for the design of multilayered assemblies for specific applications in which controlled film erosion or the release of therapeutic materials is desired.
LARnet, a local access router network (1995)

A novel local access network, LARNet, is proposed and demonstrated. A multifrequency laser, whose wavelength COMB94 is matched to that of a passive waveguide router in the remote node, is used as a downstream signal source. A 1.3-μm commercially available LED provides the upstream signal. LARNet solves a major problem of WDM networks, the spectral alignment between the optical wavelengths of different channels. Furthermore. The expensive components are shared among all subscribers. Our measurements indicate that aggregate rates of 2 Gbps downstream and 155 Mbps upstream are feasible.
Monte Carlo simulations of diblock copolymer thin films confined between two homogeneous surfaces (2000)

Thin films of symmetric diblock copolymers confined between two hard, flat and homogeneous surfaces have been investigated by means of Monte Carlo simulations on a simple cubic lattice. For such simulations, the match between bulk lamellar period L0 and the simulation box size is crucial to obtain meaningful results. The simulations have been performed in an expanded grand-canonical ensemble, where the chemical potential and the temperature of the confined films are specified and the density is allowed to fluctuate. The dependence of morphology, density, and chain conformation in the confined films on the type of surfaces, surface separation, and the strength of surface-block interactions has been studied systematically. Our results are consistent with experimental findings.
Characterization of alkaliphilic laccase activity in the culture supernatant ofMyrothecium verrucaria24G-4 in comparison with bilirubin oxidase (2003)

An enzyme showing alkaliphilic laccase activity was purified from the culture supernatant of Myrothecium verrucaria 24G-4. The enzyme was highly stable under alkaline conditions, showed an optimum reaction pH of 9.0 for 4-aminoantipyrine/phenol coupling, and decolorized synthetic dyes under alkaline conditions. It showed structural and catalytic similarities with bilirubin oxidase, but preferably oxidized phenolic compounds. The enzyme catalyzed veratryl alcohol oxidation at pH 9.0 with 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) as a mediator, suggesting that the laccase mediator system functioned well under alkaline conditions.
SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments (2005)

Footprinting is a powerful and widely used tool for characterizing the structure, thermodynamics, and kinetics of nucleic acid folding and ligand binding reactions. However, quantitative analysis of the gel images produced by footprinting experiments is tedious and time-consuming, due to the absence of informatics tools specifically designed for footprinting analysis. We have developed SAFA, a semi-automated footprinting analysis software package that achieves accurate gel quantification while reducing the time to analyze a gel from several hours to 15 min or less. The increase in analysis speed is achieved through a graphical user interface that implements a novel methodology for lane and band assignment, called "gel rectification," and an optimized band deconvolution algorithm. The SAFA software yields results that are consistent with published methodologies and reduces the investigator-dependent variability compared to less automated methods. These software developments simplify the analysis procedure for a footprinting gel and can therefore facilitate the use of quantitative footprinting techniques in nucleic acid laboratories that otherwise might not have considered their use. Further, the increased throughput provided by SAFA may allow a more comprehensive understanding of molecular interactions. The software and documentation are freely available for download at http://safa.stanford.edu.
Explicit expressions and numerical calculations for the Fréchet and second derivatives in 2.5D Helmholtz equation inversion (1999)

In order to perform resistivity imaging, seismic waveform tomography or sensitivity analysis of geophysical data, the Fréchet derivatives, and even the second derivatives of the data with respect to the model parameters, may be required. We develop a practical method to compute the relevant derivatives for 2.5D resistivity and 2.5D frequency‐domain acoustic velocity inversion. Both geophysical inversions entail the solution of a 2.5D Helmholtz equation. First, using differential calculus and the Green's functions of the 2.5D Helmholtz equation, we strictly formulate the explicit expressions for the Fréchet and second derivatives, then apply the finite‐element method to approximate the Green's functions of an arbitrary medium. Finally, we calculate the derivatives using the expressions and the numerical solutions of the Green's functions. Two model parametrization approaches, constant‐point and constant‐block, are suggested and the computational efficiencies are compared. Numerical examples of the derivatives for various electrode arrays in cross‐hole resistivity imaging and for cross‐hole seismic surveying are demonstrated. Two synthetic experiments of resistivity and acoustic velocity imaging are used to illustrate the method.
Streptococcus pneumoniae and its bacteriophages: one long argument. (2004)

Infectious diseases currently kill more than 15 million people annually, and the WHO estimates that every year 1.6 million people die from pneumococcal diseases. Streptococcus pneumoniae (pneumococcus), a bacterium with a long biological pedigree, best illustrates the rapid evolution of antibiotic resistance, which has led to major public health concern. This article discusses the molecular basis of the two main virulence factors of pneumococcus, the capsule and cell-wall hydrolases, as well as new approaches to developing medicinal weapons for preventing pneumococcal infections. In addition, current knowledge regarding pneumococcal phages as potential contributors to virulence and the use of lytic enzymes encoded by these phages as therapeutic tools is reviewed.
A simple vascular calcification score predicts cardiovascular risk in haemodialysis patients (2004)

The present vascular calcification scoring represents a simple tool for the assessment of cardiovascular risk related with vascular calcifications in chronic HD patients.
Surface-Engineered Dendrimers with a Diaminododecane Core Achieve Efficient Gene Transfection and Low Cytotoxicity (2014)

Cationic dendrimers are widely used as gene vectors; however, these materials are usually associated with unsatisfied transfection efficiency and biocompatibility. In this study, we used an aliphatic hydrocarbon-cored polyamidoamine (PAMAM) dendrimer as an alternative to traditional cationic PAMAM dendrimers in the design of efficient gene vectors. Diaminododecane-cored generation 4 (C12G4) PAMAM dendrimer showed dramatically higher efficacy in luciferase and EGFP gene transfection than diaminoethane-cored generation 4 (C2G4) and diaminohexane-cored generation 4 (C6G4) PAMAM dendrimers. The viability of cells incubated with C12G4 at transfection concentrations is above 90%. The significantly improved gene transfection efficacy of C12G4 is attributed to the hydrophobic core of C12G4 which increases the cellular uptake of dendrimer/DNA polyplexes. Further modification of C12G4 with functional ligands such as arginine, 2,4-diamino-1,3,5-triazine, and fluorine compounds significantly increase its transfection efficiency on several cell lines. These results suggest that diaminododecane-cored dendrimers can be developed as a versatile scaffold in the design of efficient gene vectors.