gebhart/patrepeval huggingface dataset:
On the protective mechanism of the thiol-specific antioxidant enzyme against the oxidative damage of biomacromolecules. (1994)

A thiol-specific antioxidant enzyme (TSA), which provides protection against the inactivation of other enzymes by the thiol/Fe(III)/oxygen system, was previously isolated and cloned. We investigated the mechanism by which TSA protects biomolecules from oxidative damage caused by the thiol-containing oxidation system using the spin trapping method with 5,5-dimethyl-1-pyrroline N-oxide (DMPO). Thiyl radicals from dithiothreitol (.DTT) were produced by horseradish peroxidase/H2O2 under aerobic and anaerobic conditions and by the Fe(III)/oxygen system. The formation of DMPO-.DTT radical adducts were inhibited by TSA regardless of the thiyl radical-generating conditions used. The active mutant C170S also quenched the signals of the radical adduct, whereas the inactive mutant C47S did not exert any effect. It was also found that C170S has a higher rate at the initial stage of the reaction than that of the native enzyme, although C170S failed to remove DMPO-.DTT radical adducts completely. These results indicate that only active TSA can catalyze the removal of thiyl radicals, and cysteine 47 is required for this activity. In addition, thiyl radicals react with oxygen to generate unidentified thiylperoxy species. Fe.EDTA reacts with this species to generate a reactive radical that can abstract hydrogen atom from ethanol to produce a hydroxyethyl radical. This reactive thiyl-oxygen radical is believed to be responsible for causing deleterious effects on biomolecules. Together, our data indicate that TSA protects biomolecules from oxidative damage by catalyzing the removal of thiyl radicals before they generate more reactive radicals. However, presently we cannot rule out the possibility that TSA can also use other thiol-containing species as substrates.
Corneal tensile strength in fully healed radial keratotomy wounds. (1994)

The presence of an epithelial plug in a fully healed radial keratotomy incision will create a stress concentration at the incision site that may predispose the cornea to rupture. The variability in the strength measurements indicates that the increase in rupture susceptibility due to RK may be hard to predict and may depend on factors such as the size of the plug and the strength of the wound collagen.
Estrogen action via the cAMP signaling pathway: stimulation of adenylate cyclase and cAMP-regulated gene transcription. (1994)

Estrogenic hormones, believed to exert most of their effects via the direct interaction of their receptors with chromatin, are found to increase cAMP in target breast cancer and uterine cells in culture and in the intact uterus in vivo. Increases in intracellular cAMP are evoked by very low concentrations of estradiol (half maximal at 10 pM) and by other physiologically active estrogens and antiestrogens, but not by an inactive estrogen stereoisomer. These increases in cAMP result from enhanced membrane adenylate cyclase activity by a mechanism that does not involve genomic actions of the hormones (are not blocked by inhibitors of RNA and protein synthesis). The estrogen-stimulated levels of cAMP are sufficient to activate transcription from cAMP response element-containing genes and reporter plasmid constructs. Our findings document a nongenomic action of estrogenic hormones that involves the activation of an important second-messenger signaling system and suggest that estrogen regulation of cAMP may provide an additional mechanism by which this steroid hormone can alter the expression of genes.
A phase II study of lenalidomide in patients with extranodal marginal zone B-cell lymphoma of the mucosa associated lymphoid tissue (MALT lymphoma) (2012)

Mucosa associated lymphoid tissue lymphoma shares certain features with multiple myeloma. In view of this and the activity of lenalidomide in various B-cell lymphomas, we have initiated a phase II study of lenalidomide in patients with mucosa associated lymphoid tissue lymphoma. Patients with histologically verified advanced stages of this lymphoma were included in the study. Treatment consisted of oral lenalidomide 25 mg Days 1-21, with a 7-day break after each cycle. A total of 18 patients were included in the trial: 5 had gastric and 13 had extragastric mucosa associated lymphoid tissue lymphoma, but 2 discontinued therapy during the first course of therapy. In the intent to treat analysis, an overall response rate of 61% was seen (11 of 18; 6 complete and 5 partial remissions). Three patients had stable disease while 2 progressed. Side effects were manageable and included neutropenia (grade III in 3 patients) as the leading hematotoxicity. After a median follow up of 20.3 months, one patient has died from lymphoma while the remaining patients are alive and relapse-free. These data suggest activity of lenalidomide monotherapy in mucosa associated lymphoid tissue lymphoma. The study protocol had been approved by the Ethical Board of the Medical University Vienna (EK-No.: 146/09), and before opening the trial, it had been registered at www.clinicaltrials.gov. (identifier: NCT00923663).
Antisense Expression of the Peptide Transport Gene AtPTR2-B Delays Flowering and Arrests Seed Development in Transgenic Arabidopsis Plants (1997)

Previously, we identified a peptide transport gene, AtPTR2-B, from Arabidopsis thaliana that was constitutively expressed in all plant organs, suggesting an important physiological role in plant growth and development. To evaluate the function of this transporter, transgenic Arabidopsis plants were constructed expressing antisense or sense AtPTR2-B. Genomic Southern analysis indicated that four independent antisense and three independent sense AtPTR2-B transgenic lines were obtained, which was confirmed by analysis of the segregation of the kanamycin resistance gene carried on the T-DNA. RNA blot data showed that the endogenous AtPTR2-B mRNA levels were significantly reduced in transgenic leaves and flowers, but not in transgenic roots. Consistent with this reduction in endogenous AtPTR2-B mRNA levels, all four antisense lines and one sense line exhibited significant phenotypic changes, including late flowering and arrested seed development. These phenotypic changes could be explained by a defect in nitrogen nutrition due to the reduced peptide transport activity conferred by AtPTR2-B. These results suggest that AtPTR2-B may play a general role in plant nutrition. The AtPTR2-B gene was mapped to chromosome 2, which is closely linked to the restriction fragment length polymorphism marker m246.
Analysis of cytotoxic T cell responses to dominant and subdominant epitopes during acute and chronic lymphocytic choriomeningitis virus infection (1996)

The cytotoxic T cell response against lymphocytic choriomeningitis virus (LCMV) in BALB/c (H-2d) mice is predominantly directed against a single immunodominant Ld-restricted epitope in the viral nucleoprotein (NP118-126). Here we report that the immunodominance of this peptide can be in part attributed to its very high affinity for Ld class I molecules. By employing motif searches and sensitive MHC class I binding assays, we also identified 5 Kd-binding peptides in the viral nucleoprotein and glycoprotein among 16 Kd motif-fitting peptides. The nucleoprotein and glycoprotein sequences also contained 18 Dd motif-fitting peptides, three of which bound Dd with weak affinity. Two of the Kd-binding peptides, residues 99-108 and residues 283-291 from the viral glycoprotein, are subdominant epitopes. Although these peptides did not sensitize target cells for direct ex vivo killing by primary antiviral CTL, secondary responses against these peptides were readily detected in BALB/c mice after acute LCMV infection. BALB/c mice that had cleared a long-term LCMV infection showed more sustained CTL responses against these subdominant epitopes, suggesting that subdominant responses might play a role in clearance of chronic infections. One of the subdominant epitopes, GP283-291, conferred partial protection against persistent viral infection after peptide vaccination.
Intralipid, a Clinically Safe Compound, Protects the Heart Against Ischemia-Reperfusion Injury More Efficiently Than Cyclosporine-A (2012)

Although intralipid inhibits the opening of the mitochondrial permeability transition pore as efficiently as cyclosporine-A, intralipid is more effective in reducing the infarct size and improving the cardiac functional recovery.
Heat-shock proteins in cancer vaccines: agents of antigen cross-presentation (2008)

Heat-shock proteins (HSPs) derived from tumors are capable of eliciting an anticancer immune response by facilitating antigen cross-presentation in antigen-presenting cells (APCs). This process involves the ability of such chaperones to bind tumor antigens and facilitate their uptake by APCs. Recent evidence reveals that HSP-tumor antigen complexes bind cell surface proteins on APCs that mediate complex internalization and antigen-processing events, as well as inducing an innate immune response. Binding of HSPs to surface receptors is, thus, an imposing gateway to the induction of tumor-specific immune responses. Extensive studies in animals have indicated the usefulness of such HSP-based immunotherapy in killing established tumors and causing tumor regression. Currently, one HSP, the endoplasmic reticulum stress-response protein Gp96 is undergoing clinical trials for cancer treatment and has yielded promising results, including the induction of anti-tumor immunity and some benefit for patients when administered as part of a multidose regimen. Future advances in HSP-based immunotherapy will be aided by an understanding of the mechanisms by which HSP-peptide complexes induce innate and adaptive immunity to tumor cells and target the killing of primary and metastatic cancer cells.
Metabolic flux distributions in Penicillium chrysogenum during fed‐batch cultivations (1995)

Based on a review of the Penicillium chrysogenum biochemistry a stoichiometric model has been set up. The model considers 61 internal fluxes and there are 49 intracellular metabolites which are assumed to be in pseudo-steady state. In addition to the intracellular fluxes the model considers the uptake of 21 amino acids. From the stoichiometric model the maximum theoretical yield of penicillin V is calculated to 0.43 mol/mol glucose. If biosynthesis of cysteine is by direct sulfhydrylation rather than by transsulfuration, the maximum theoretical yield is about 20% higher, i.e., 0.50 mol/mol glucose. The theoretical yield decreases substantially if alpha-aminoadipate is converted to 6-oxo-piperidine-2-carboxylic acid (OPC). If only 40% of the alpha-aminoadipate is recycled, the maximum theoretical yield is 0.31 mol/mol glucose. The uptake rates of glucose, lactate, gamma-aminobutyrate, and 21 amino acids were measured during fed-batch cultivations. The rates of formation of penicillin V, delta-(L-alpha)-aminoadipyl-L-cysteinyl-D-valine (ACV), OPC, and the pool of isopenicillin N, 6-APA, and 8-HPA were also measured. Finally the synthesis rates of the biomass constituents RNA/DNA, protein, lipid, carbohydrate, and amino carbohydrate were measured. From these measured rates and the stoichiometric model the metabolic fluxes through the different intracellular pathways are calculated. The calculations show that penicillin formation is accompanied by a large flux through the pentose phosphate (PP) pathway due to a large requirement for nicotinamide-adenine dinucleotide phosphate (NADPH) used in the biosynthesis of cysteine. If cysteine is added to the medium, the flux through the PP pathway decreases. From the stoichiometric model Y(xATP) is calculated to 87 mmol adenosine triphosphate (ATP)/g dry weight (DW), and from the flux calculations m(ATP) is found to 3 mmol ATP/g DW/h. (c) 1995 John Wiley & Sons, Inc.
Aqueous Suspension and Characterization of Chemically Modified Graphene Sheets (2008)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTAqueous Suspension and Characterization of Chemically Modified Graphene SheetsSungjin Park†, Jinho An†, Richard D. Piner†, Inhwa Jung†, Dongxing Yang†, Aruna Velamakanni†, SonBinh T. Nguyen‡, and Rodney S. Ruoff*†View Author Information Department of Mechanical Engineering, University of Texas at Austin, One University Station C2200, Austin, Texas, 78712-0292, and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3111* To whom correspondence should be addressed. E-mail: [email protected]†University of Texas at Austin.‡Northwestern University.Cite this: Chem. Mater. 2008, 20, 21, 6592–6594Publication Date (Web):October 22, 2008Publication History Received16 July 2008Revised26 September 2008Published online23 October 2008Published inissue 11 November 2008https://pubs.acs.org/doi/10.1021/cm801932uhttps://doi.org/10.1021/cm801932urapid-communicationACS PublicationsCopyright © 2008 American Chemical SocietyRequest reuse permissionsArticle Views16862Altmetric-Citations883LEARN 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 SUBJECTS:Ions,Oxides,Oxygen,Suspensions,Two dimensional materials Get e-Alerts
Quasi-TE00 singlemode optical waveguides for electro-optical modulation at 1.3 µm using standard SIMOX material (1997)

A standard SIMOX substrate with 0.2 µm silicon film can be used for integrated optics. A lateral P+–I–N+ structure in the silicon film is proposed to obtain electro-optical phase modulation by carrier injection. Field confinement is ensured by a rib-loaded geometry. Simulations have been performed to estimate waveguide losses for such 2D-guiding structures suitable for phase modulation. Quasi-singlemode propagation with low losses in the doped regions and low additional loss under injection conditions is predicted.
Nucleotide sequence and expression of kerA, the gene encoding a keratinolytic protease of Bacillus licheniformis PWD-1 (1995)

Bacillus licheniformis PWD-1 (ATCC 53757) secretes keratinase, a proteolytic enzyme which is active on whole feathers. By amino acid sequence similarity and phenylmethylsulfonyl fluoride inhibition, the keratinase was demonstrated to be a serine protease. The entire nucleotide sequence of the coding and flanking regions of the keratinase structure gene, kerA, was determined. A fixed oligonucleotide primer derived from the N-terminal sequence of the purified enzyme and a second random oligonucleotide primer were used in a procedure called PCR walking, which was developed to amplify and sequence the upstream and downstream regions of kerA. Another method, PCR screening, was conducted with a lambda phage vector with inserted PWD-1 genomic DNA fragments as templates and with the known sequences of the vector arms and the N-terminal sequence of the enzyme as primers. PCR amplification and sequence analysis of the lambda library completed the entire kerA sequence and established a set of gene deletions. The kerA gene shares a 97% sequence identity with the gene encoding subtilisin Carlsberg from B. licheniformis NCIMB 6816. The putative promoters, ribosome binding sites, and transcriptional terminators are also similar in these two bacteria. The deduced amino acid sequences indicate only three amino acid differences between the two mature proteases. Northern (RNA) analysis demonstrates that transcriptional regulation controls kerA expression on different growth media.
The Sensitivity of G0‐State Haemopoietic Spleen Colony‐Forming Cells to A Stimulus For Proliferation (1986)

Haemopoietic spleen colony-forming units (CFU-s) close to the axis (axial CFU-s) of the long bones have a high probability of self-renewal. They are pluripotent cells and are largely in a G0-State. By contrast, CFU-s close to the bone surface (marginal CFU-s) have a lower probability of self-renewal and are probably more mature, though still pluripotent. Most CFU-s proliferation arises in this zone. As a consequence, marginal CFU-s tend to have shorter G0 histories than do axial CFU-s. Femoral marrow was, therefore, divided into axial and marginal populations and the sensitivity of the CFU-s to an endogenous CFU-s-specific proliferation-stimulating factor was assessed and compared by the tritiated thymidine suicide technique. It was found that axial CFU-s are considerably more resistant to stimulation than are marginal CFU-s in that larger doses for longer periods of exposure are required to increase the proliferative activity of the cells. This behaviour is consistent with the suggestion that cells with a low division probability exist in deeper levels of the quiescent G0-state. Although this hypothesis was developed from the behaviour of cells maintained in culture under sub-optimal physiological conditions, this phenomenon appears, in vivo, to be a characteristic of the stem cell population of haemopoietic tissue; their high resistance to stimulation maintaining the axial CFU-s in a quiescent state.
Engineered Streptomyces quorum‐sensing components enable inducible siRNA‐mediated translation control in mammalian cells and adjustable transcription control in mice (2004)

As exemplified by Q-ON technology, bacterial quorum-sensing regulons may represent a near-infinite source for the design of mammalian gene control systems compatible with molecular interventions relevant to future gene therapy and tissue engineering scenarios.
Bone Marrow-Derived Macrophages (BMM): Isolation and Applications (2008)

INTRODUCTIONBone marrow-derived macrophages (BMM) are primary macrophage cells, derived from bone marrow cells in vitro in the presence of growth factors. Macrophage colony-stimulating factor (M-CSF) is a lineage-specific growth factor that is responsible for the proliferation and differentiation of committed myeloid progenitors into cells of the macrophage/monocyte lineage. Mice lacking functional M-CSF are deficient in macrophages and osteoclasts and suffer from osteopetrosis. In this protocol, bone marrow cells are grown in culture dishes in the presence of M-CSF, which is secreted by L929 cells and is used in the form of L929-conditioned medium. Under these conditions, the bone marrow monocyte/macrophage progenitors will proliferate and differentiate into a homogenous population of mature BMMs. The efficiency of the differentiation is assessed using fluorescence-activated cell sorting (FACS) analysis of Mac-1 and 4/80 surface antigen expression. Once differentiated, the BMMs are suitable for numerous types of experimental manipulations, including morphological, gene expression, and physiological studies. For example, phagocytic cells such as macrophages have a unique ability to ingest microbes. We describe a test for the phagocytic efficiency of BMMs by exposing them to fluorescently labeled yeast zymosan bioparticles. Also, a method to deliver DNA or small interfering RNAs (siRNAs) into these hard-to-transfect cells is described. Finally, the proliferation of the BMMs is assayed using carboxyfluorescein succinimidyl ester (CFSE), a fluorescein derivative that partitions equally between daughter cells after cell division.
Novel Reporter Mouse Reveals Constitutive and Inflammatory Expression of IFN-β In Vivo (2009)

Type I IFN is a major player in innate and adaptive immune responses. Besides, it is involved in organogenesis and tumor development. Generally, IFN responses are amplified by an autocrine loop with IFN-beta as the priming cytokine. However, due to the lack of sensitive detection systems, where and how type I IFN is produced in vivo is still poorly understood. In this study, we describe a luciferase reporter mouse, which allows tracking of IFN-beta gene induction in vivo. Using this reporter mouse, we reveal strong tissue-specific induction of IFN-beta following infection with influenza or La Crosse virus. Importantly, this reporter mouse also allowed us to visualize that IFN-beta is expressed constitutively in several tissues. As suggested before, low amounts of constitutively produced IFN might maintain immune cells in an activated state ready for a timely response to pathogens. Interestingly, thymic epithelial cells were the major source of IFN-beta under noninflammatory conditions. This relatively high constitutive expression was controlled by the NF Aire and might influence induction of tolerance or T cell development.
Extracellular Signal-Regulated Kinases Regulate Leukotriene C4 Generation, But Not Histamine Release or IL-4 Production from Human Basophils (1999)

Human basophils secrete histamine and leukotriene C4 (LTC4) in response to various stimuli, such as Ag and the bacterial product, FMLP. IgE-mediated stimulation also results in IL-4 secretion. However, the mechanisms of these three classes of secretion are unknown in human basophils. The activation of extracellular signal-regulated kinases (ERKs; ERK-1 and ERK-2) during IgE- and FMLP-mediated stimulation of human basophils was examined. Following FMLP stimulation, histamine release preceded phosphorylation of ERKs, whereas phosphorylation of cytosolic phospholipase A2 (cPLA2), and arachidonic acid (AA) and LTC4 release followed phosphorylation of ERKs. The phosphorylation of ERKs was transient, decreasing to baseline levels after 15 min. PD98059 (MEK inhibitor) inhibited the phosphorylation of ERKs and cPLA2 without inhibition of several other tyrosine phosphorylation events, including phosphorylation of p38 MAPK. PD98059 also inhibited LTC4 generation (IC50 = approximately 2 microM), but not histamine release. Stimulation with anti-IgE Ab resulted in the phosphorylation of ERKs, which was kinetically similar to both histamine and LTC4 release and decreased toward resting levels by 30 min. Similar to FMLP, PD98059 inhibited anti-IgE-mediated LTC4 release (IC50, approximately 2 microM), with only a modest effect on histamine release and IL-4 production at higher concentrations. Taken together, these results suggest that ERKs might selectively regulate the pathway leading to LTC4 generation by phosphorylating cPLA2, but not histamine release or IL-4 production, in human basophils.
The Radio-Frequency Single-Electron Transistor (RF-SET): A Fast and Ultrasensitive Electrometer (1998)

A new type of electrometer is described that uses a single-electron transistor (SET) and that allows large operating speeds and extremely high charge sensitivity. The SET readout was accomplished by measuring the damping of a 1.7-gigahertz resonant circuit in which the device is embedded, and in some ways is the electrostatic "dual" of the well-known radio-frequency superconducting quantum interference device. The device is more than two orders of magnitude faster than previous single-electron devices, with a constant gain from dc to greater than 100 megahertz. For a still-unoptimized device, a charge sensitivity of 1.2 x 10(-5) e/hertz was obtained at a frequency of 1.1 megahertz, which is about an order of magnitude better than a typical, 1/f-noise-limited SET, and corresponds to an energy sensitivity (in joules per hertz) of about 41 Planck's over 2pi.