gebhart/patrepeval huggingface dataset:
Molecular Basis of Proteolytic Activation of Sendai Virus Infection and the Defensive Compounds for Infection (1997)

It has been proposed that the pathogenicity of Sendai virus is primarily determined by a host cellular protease(s) that activates viral infectivity by proteolytic cleavage of envelope fusion glycoproteins. We isolated a trypsin-like serine protease, tryptase Clara, localized in and secreted from Clara cells of the bronchial epithelium of rats. The enzyme specifically cleaved the precursor of fusion glycoprotein F0 of Sendai virus at residue Arg116 in the consensus cleavage motif, Gln(Glu)-X-Arg, resulting in the presentation of the membrane fusion domain in the amino-terminus of the F1 subunit. Administration of an antibody against tryptase Clara in the airway significantly inhibited the activation of progeny virus and multiple cycles of viral replication, thus reducing the mortality rate. These findings indicate that tryptase Clara in the airway is a primary determinant of Sendai virus infection and that proteolytic activation occurs extracellularly. We identified two cellular inhibitory compounds against tryptase Clara in bronchial lavage. One was a mucus protease inhibitor, a major serine protease inhibitor of granulocyte elastase in the lining fluids of the human respiratory tract, and the other was a pulmonary surfactant which may adsorb the enzyme, resulting in its inactivation. These compounds inhibited virus activation by tryptase Clara in vitro and in vivo, but did not themselves affect the hemagglutination and the infectivity of the virus. The functional domain of the mucus protease inhibitor against the enzyme, which is organized in two homologous N- and C-terminal domains, is located in the C-terminal. Administration of these compounds in the airway may be useful for preventing infection with Sendai virus.
High-intensity Nd:YAG laser accelerates bone regeneration in calvarial defect models (2013)

High-power pulsed lasers have been recently regarded to be anabolic to bone, but in vivo evidence is still lacking. This study aimed to investigate the capacity of bone repair using a high-power, Q-switched, pulsed, neodymium-doped yttrium aluminium garnet (Nd:YAG) laser, using bilateral calvarial defect models having non-critical sized, 5 mm (rat) or 8 mm (rabbit) diameter. One of the bilateral defects, which were all filled with collagen sponge or left empty, was irradiated with a Nd:YAG laser once every 2 days for 2 weeks at a constant total fluence rate (344 J/cm(2) ), output power (0.75 W), pulse repetition rate (15 pps) and wavelength (1064 nm) and examined for the laser effect. The same experimental scheme was designed using a rabbit calvarial defect model implanted with sponge, which was explored for the dose effect of output power at 0.75 and 3 W with the same quantities of the other parameters. New bone formation was evaluated by micro-computed tomography-based analysis and histological observation at 4 weeks after surgery. Laser irradiation significantly increased new bone formation by approximately 45%, not only in the sponge-filled defects of rats but also when the defects were left empty, compared to the non-irradiated group. Consistently, both doses of output power (0.75 and 3 W) enhanced new bone formation, but there was no significant difference between the two doses. This study is one of the first to demonstrate the beneficial effect of Nd:YAG lasers on the regeneration of bone defects which were left empty or filled with collagen sponge, suggesting its great potential in postoperative treatment targeting local bone healing.
Subtilisin BPN': activity on an immobilized substrate (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSubtilisin BPN': activity on an immobilized substrateP. F. Brode III and D. S. RauchCite this: Langmuir 1992, 8, 5, 1325–1329Publication Date (Print):May 1, 1992Publication History Published online1 May 2002Published inissue 1 May 1992https://pubs.acs.org/doi/10.1021/la00041a014https://doi.org/10.1021/la00041a014research-articleACS PublicationsRequest reuse permissionsArticle Views113Altmetric-Citations17LEARN 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
Syphilis: using modern approaches to understand an old disease (2011)

Syphilis is a fascinating and perplexing infection, with protean clinical manifestations and both diagnostic and management ambiguities. Treponema pallidum subsp. pallidum, the agent of syphilis, is challenging to study in part because it cannot be cultured or genetically manipulated. Here, we review recent progress in the application of modern molecular techniques to understanding the biological basis of this multistage disease and to the development of new tools for diagnosis, for predicting efficacy of treatment with alternative antibiotics, and for studying the transmission of infection through population networks.
Vaccines and Immunotherapy for Staphylococcal Infections (2005)

Nosocomial or hospital-acquired infections are associated with prolonged hospitalizations and increased healthcare costs. Infections associated with surgical implants are becoming more difficult and more costly to manage, as they require repeated surgical procedures and a longer period of time to treat patients. Continued advances in the use of medical devices, an increase in the number of immunocompromised patients, and a steady rise in the prevalence of antibiotic-resistant organisms has renewed interest in the development of novel therapies that can be used to prevent and treat nosocomial infections. This review provides an overview of bacterial adhesins and focuses on novel immunological therapies developed to treat staphylococcal infections.
Structural basis for recognition ofS-adenosylhomocysteine by riboswitches (2010)

S-adenosyl-(L)-homocysteine (SAH) riboswitches are regulatory elements found in bacterial mRNAs that up-regulate genes involved in the S-adenosyl-(L)-methionine (SAM) regeneration cycle. To understand the structural basis of SAH-dependent regulation by RNA, we have solved the structure of its metabolite-binding domain in complex with SAH. This structure reveals an unusual pseudoknot topology that creates a shallow groove on the surface of the RNA that binds SAH primarily through interactions with the adenine ring and methionine main chain atoms and discriminates against SAM through a steric mechanism. Chemical probing and calorimetric analysis indicate that the unliganded RNA can access bound-like conformations that are significantly stabilized by SAH to direct folding of the downstream regulatory switch. Strikingly, we find that metabolites bearing an adenine ring, including ATP, bind this aptamer with sufficiently high affinity such that normal intracellular concentrations of these compounds may influence regulation of the riboswitch.
Urokinase Expression by Tumor Suppressor Protein p53 (2008)

Lung carcinoma (H1299) cells deficient in p53 (p53(-/-)) express large amounts of urokinase-type plasminogen activator (uPA) protein and uPA mRNA, and exhibit slower degradation of uPA mRNA than that of p53-expressing nonmalignant Beas2B human airway epithelial cells. Expression of p53 protein in H1299 cells, upon transfection with p53 cDNA, suppressed basal as well as uPA-induced expression of uPA protein in both conditioned media and cell lysates, and decreased the level of steady-state uPA mRNA primarily due to increased uPA mRNA turnover. Inhibition of p53 expression by RNA silencing (SiRNA) in Beas2B cells enhanced basal and uPA-mediated uPA protein and mRNA expression with stabilization of uPA mRNA. Purified p53 binds to the uPA mRNA 3' untranslated region (UTR) in a sequence-specific manner and endogenous uPA mRNA associates with p53 protein isolated from Beas2B cytosolic extracts. p53 binds to a 35-nucleotide uPA 3'UTR sequence and insertion of this sequence into beta-globin mRNA accelerates degradation of otherwise stable beta-globin mRNA. These observations confirm a new role for p53 as a uPA mRNA binding protein that down-regulates uPA mRNA stability and decreases cellular uPA expression.
RELEASE OF ENDOTOXIN IN THE FORM OF CELL WALL BLEBS DURING IN VITRO GROWTH OF NEISSERIA MENINGITIDIS (1973)

Multiple cell wall blebs were observed on the surface of three strains of N. meningitidis taken from log phase cultures. The blebs originated as evaginations of the outer layer of the cell wall. Bleb production was noted on both defined or complex media either as broth or a solid medium. The addition of 10% normal bovine serum to the various media did not affect the production and release of these surface blebs. However, as broth cultures progressed into the stationary phase of growth, the blebs disappeared from the surface of the cells. Blebs were present in substantial quantities in culture supernatant fluids and on cell surfaces and were readily isolated by ultracentrifugation. Analysis for 2-keto-3-deoxyoctonate in cultures revealed that 18% of the total endotoxin of log phase cultures was present in blebs from the cell wall.
Kinetic Control of Interparticle Spacing in Au Colloid-Based Surfaces:  Rational Nanometer-Scale Architecture (1996)

This paper details the kinetic aspects of covalent self-assembly of colloidal Au particles from solution onto immobilized organosilane polymers. On glass substrates, surface formation can be monitored using UV−vis spectroscopy and field emission scanning electron microscopy (FE-SEM). Correlation of these data allows the effect of nanostructure on bulk optical properties to be evaluated. At short derivatization times, particle coverage is proportional to (time)1/2. The particle sticking probability p, defined as the ratio of bound particles to the number of particles reaching the surface in a given time period, can be determined from a knowledge of the particle radius, solution concentration, temperature, and solution viscosity; for surfaces derivatized with (3-mercaptopropyl)trimethoxysilane (MPTMS), p ≈ 1. At longer derivatization times, interparticle repulsions result in a “saturation” coverage at ≈30% of a close-packed monolayer. Two approaches for modulating the rate of surface formation are described: electrochemical potential control on organosilane-modified SnO2 electrodes and charge screening by organic adsorbates. Self-assembly of colloidal Au particles onto functionalized substrate surfaces is a reproducible phenomenon, as evidenced by UV−vis and surface enhanced Raman scattering (SERS) measurements on identically prepared substrates.
C-Reactive Protein Is an Independent Predictor of Mortality in Women With HIV-1 Infection (2003)

The relationship of C-reactive protein (CRP) to mortality was assessed in 209 HIV-1-infected women after adjusting for age, body mass index (BMI), serum albumin, CD4 cell lymphocyte count, and HIV-1 RNA. During the follow-up period of up to 5 years (median = 45 months) there were 49 deaths. CRP at study enrollment was measured using a low sensitivity assay. CRP levels were only weakly correlated (Pearson correlation coefficient r < .2) with other predictors of mortality. CRP was a powerful predictor of mortality (p < .01) after adjusting for age, BMI, serum albumin, CD4 cell lymphocytes, and HIV-1 RNA. The relative hazard associated with an elevated CRP level, independent of the covariates noted above, varied from 3.4- to 13.6-fold depending on how CRP values were grouped. CRP may be a useful and inexpensive predictor of HIV disease mortality in women.
Microfluidic Device for Single-Cell Analysis (2003)

We have developed a novel microfluidic device constructed from poly(dimethylsiloxane) using multilayer soft lithography technology for the analysis of single cells. The microfluidic network enables the passive and gentle separation of a single cell from the bulk cell suspension, and integrated valves and pumps enable the precise delivery of nanoliter volumes of reagents to that cell. Various applications are demonstrated, including cell viability assays, ionophore-mediated intracellular Ca2+ flux measurements, and multistep receptor-mediated Ca2+ measurements. These assays, and others, are achieved with significant improvements in reagent consumption, analysis time, and temporal resolution over macroscale alternatives.
Structure and expression of the human cystatin C gene (1990)

The structural organization of the gene for the human cysteine-proteinase inhibitor cystatin C was studied. Restriction-endonuclease digests of human genomic DNA hybridized with human cystatin C cDNA and genomic probes produced patterns consistent with a single cystatin C gene and, also, the presence of six closely related sequences in the human genome. A 30 kb restriction map covering the genomic region of the cystatin C gene was constructed. The positions of three polymorphic restriction sites, found at examination of digests of genomic DNA from 79 subjects, were localized in the flanking regions of the gene. The gene was cloned and the nucleotide sequence of a 7.3 kb genomic segment was determined, containing the three exons of the cystatin C structural gene as well as 1.0 kb of 5'-flanking and 2.0 kb of 3'-flanking sequences. Northern-blot experiments revealed that the cystatin C gene is expressed in every human tissue examined, including kidney, liver, pancreas, intestine, stomach, antrum, lung and placenta. The highest cystatin C expression was seen in seminal vesicles. The apparently non-tissue-specific expression of this cysteine-proteinase inhibitor gene is discussed with respect to the structure of its 5'-flanking region, which shares several features with those of housekeeping genes.
Histological analysis of forelimb regeneration in the California newt Taricha granulosa. (1992)

The regenerative ability of the forelimbs of the California rough-skinned newt, Taricha granulosa was determined and compared to the same ability of the adult Mexican axolotl, Ambystoma mexicanum. Forelimbs were amputated distally at the wrist and limbs removed at 1, 2, 3, 4, 5 and 6 weeks post-amputation were examined by histological analysis. Since vitamin A and its derivatives cause extreme changes in pattern formation in the regenerating amphibian limb, we decided to study the ability of retinoic acid to proximalize the distal amputation. Animals injected with RA displayed apparent proximalization of the distal amputation.
Vincristine treatment of advanced cancer: a cooperative study of 392 cases. (1973)

SUMMARY Vincristine was studied in a series of dose levels in 392 patients with advanced cancer. It produced tumor regres sions in a substantial proportion of patients with advanced lymphosarcoma, reticulum cell sarcoma, Hodgkin's dis ease, breast cancer, bladder cancer, and carcinomas of un known primary site. Response occurred about as frequently at 25 jug/kg/week as at higher doses. Maximum response rates occurred in those patients who sustained moderate toxicity as contrasted to those with only mild or no toxic effects or to those with severe manifestations of drug effect on normal tissues. Dose-related sensory, motor, and auto nomie neuropathy and central nervous system dysfunc tions were observed. Leukopenia and thrombocytopenia were observed. The frequency of responses achieved and their duration were modified by good- or poor-risk status of the patients. Prediction of survival was rather accurate as determined by comparison of prognostication and actual survival times. Responders survived longer than nonresponders. In pa tients with breast cancer, the survival extension beyond prediction cannot be explained as due solely to vincristineinduced remission time. In some other diseases, therapeu tic response to vincristine was able to overbalance a poor prognosis and apparently to increase survival beyond that predicted.
Expression and Function of the Mouse Collagen Receptor Glycoprotein VI Is Strictly Dependent on Its Association with the FcRγ Chain (2000)

Platelet glycoprotein (GP) VI has been proposed as the major collagen receptor for activation of human platelets. Human GPVI belongs to the immunoglobulin superfamily and is noncovalently associated with the FcRgamma chain that is involved in signaling through the receptor. In mice, similar mechanisms seem to exist as platelets from FcRgamma chain-deficient mice do not aggregate in response to collagen. However, the activating collagen receptor on mouse platelets has not been definitively identified. In the current study we examined the function and in vivo expression of GPVI in control and FcRgamma chain-deficient mice with the first monoclonal antibody against GPVI (JAQ1). On wild type platelets, JAQ1 inhibited platelet aggregation induced by collagen but not PMA or thrombin. Cross-linking of bound JAQ1, on the other hand, induced aggregation of wild type but not FcRgamma chain-deficient platelets. JAQ1 stained platelets and megakaryocytes from wild type but not FcRgamma chain-deficient mice. Furthermore, JAQ1 recognized GPVI (approximately 60 kDa) in immunoprecipitation and Western blot experiments with wild type but not FcRgamma chain-deficient platelets. These results strongly suggest that GPVI is the collagen receptor responsible for platelet activation in mice and demonstrate that the association with the FcRgamma chain is critical for its expression and function.
Self-Assembly of Ordered Microporous Materials from Rod-Coil Block Copolymers (1999)

Rod-coil diblock copolymers in a selective solvent for the coil-like polymer self-organize into hollow spherical micelles having diameters of a few micrometers. Long-range, close-packed self-ordering of the micelles produced highly iridescent periodic microporous materials. Solution-cast micellar films consisted of multilayers of hexagonally ordered arrays of spherical holes whose diameter, periodicity, and wall thickness depended on copolymer molecular weight and composition. Addition of fullerenes into the copolymer solutions also regulated the microstructure and optical properties of the microporous films. These results demonstrate the potential of hierarchical self-assembly of macromolecular components for engineering complex two- and three-dimensional periodic and functional mesostructures.
Separation and quantitation of subclasses of human plasma high density lipoproteins by a simple precipitation procedure (1982)

Studies in recent years have suggested that measurement of high density lipoprotein (HDL) subclasses may provide significant information beyond that provided by measurement of total HDL. However, conventional methodology for separation of HDL subclasses involves various types of ultracentrifugation that are time-consuming, costly, and not suitable for many clinical or epidemiological studies. We have developed a simple precipitation method for the separation of HDL subclasses in human plasma. After precipitation of apoB-containing lipoproteins with heparin-Mn2+, HDL2 is precipitated by addition of dextran sulfate (mol wt 15,000). HDL2 cholesterol is calculated as the difference between total HDL cholesterol (heparin-Mn2+ supernatant) and HDL3 cholesterol (dextran sulfate supernatant). HDL2 determined by this method correlated well with results obtained by preparative ultracentrifugation (n = 295, r = 0.91) and analytical ultracentrifugation (n = 17, r = 0.92). In the original method final concentration of dextran sulfate was 0.09 g/dl; however further studies indicated that 0.13 g/dl is a more suitable concentration. The chemical compositions of HDL2 and HDL3 isolated by the precipitation method were very similar to those of HDL2 and HDL3 isolated by preparative ultracentrifugation. The concentration of HDL2 cholesterol was 40% higher in normal women than in normal men. In men with coronary heart disease, total HDL was decreased by 28%, HDL2 was decreased by 44%, while HDL3 was 19% lower. A similar pattern of change was found in women with coronary heart disease. In other conditions where total HDL either increased or decreased, the change in HDL2 was always proportionately greater than the change in total HDL. HDL3 showed relatively less change, and in some instances its concentration was unchanged. Thus HDL2 is the more variable component and may be a more meaningful index of altered HDL metabolism.
Generation of pH-sensitive liposomes: use of large unilamellar vesicles containing N-succinyldioleoylphosphatidylethanolamine (1985)

By use of a carboxylated derivative of phosphatidylethanolamine, N-succinyldioleoylphosphatidylethanolamine (COPE), pH-sensitive liposomes have been designed that have a wide range of leakage properties. The leakage rate of the vesicle contents, as determined by the release kinetics of the water-soluble fluorophore 8-aminonaphthalene-1,3,6-trisulfonic acid complexed with the quencher p-xylenebis(pyridinium) dibromide [Ellens, H., Bentz, J., & Szoka, F. C. (1984) Biochemistry 23, 1532], was found to be dependent on the lipid composition and the pH of the incubation medium. Pure COPE vesicles released their encapsulated contents at pH 7.4 but not at pH 4.0. Leakage of these vesicles appears to be due to the electrostatic interactions between the COPE molecules. A dramatic reversal of the leakage properties was observed in mixed-lipid vesicles composed of COPE containing increasing amounts of dioleoylphosphatidylethanolamine (DOPE). Unlike pure COPE vesicles, COPE/DOPE (3:7) vesicles were more leaky under acidic conditions (pH 4.0) than they were at neutral pH. Studies employing a fluorescent COPE analogue, N-succinyl-1-acyl-2-[6-[(7-nitro-2,1,3-benzoxadiazol-4-yl)amino]ca proyl]phosphatidylethanolamine, suggested that the mechanism of leakage might be a result of lipid-packing defects due to the nonbilayer properties of DOPE and protonation of the COPE molecules. Hence, the mechanism of release is different from that of other recently described pH-sensitive liposomes where either fusion or aggregation of the vesicles results in the release of vesicle contents.
Functional Replacement of the FabA and FabB Proteins of Escherichia coli Fatty Acid Synthesis by Enterococcus faecalis FabZ and FabF Homologues (2004)

The anaerobic unsaturated fatty acid synthetic pathway of Escherichia coli requires two specialized proteins, FabA and FabB. However, the fabA and fabB genes are found only in the Gram-negative alpha- and gamma-proteobacteria, and thus other anaerobic bacteria must synthesize these acids using different enzymes. We report that the Gram-positive bacterium Enterococcus faecalis encodes a protein, annotated as FabZ1, that functionally replaces the E. coli FabA protein, although the sequence of this protein aligns much more closely with E. coli FabZ, a protein that plays no specific role in unsaturated fatty acid synthesis. Therefore E. faecalis FabZ1 is a bifunctional dehydratase/isomerase, an enzyme activity heretofore confined to a group of Gram-negative bacteria. The FabZ2 protein is unable to replace the function of E. coli FabZ, although FabZ2, a second E. faecalis FabZ homologue, has this ability. Moreover, an E. faecalis FabF homologue (FabF1) was found to replace the function of E. coli FabB, whereas a second FabF homologue was inactive. From these data it is clear that bacterial fatty acid biosynthetic pathways cannot be deduced solely by sequence comparisons.