gebhart/patrepeval huggingface dataset:
Modulation of IL-1α, IL-1β, and 25K Mr Non-IL-1 Activity Released by Human Mononuclear Cells (1989)

To determine if the release of IL-1 alpha and IL-1 beta by cultured PBMC could be independently modulated by different exogenous stimuli, we examined the effect of LPS, IFN gamma, latex beads, and indomethacin on the release of IL-1 alpha and IL-1 beta. PBMC culture supernatants were fractionated by Sephacryl-S-200 column chromatography or HPLC (TSK G3000SW), and each fraction was tested for thymocyte mitogenic activity in the presence or absence of preincubation with anti-IL-1 alpha or anti IL-1 beta monoclonal antibody (mAb) and for the presence of IL-1 alpha or IL-1 beta protein by ELISA. In all experiments, thymocyte mitogenic activity not neutralizable by anti-IL-1 alpha or anti-IL-1 beta mAb was detected in the 25K Mr range, which ranged from 12 to 50% of the total thymocyte mitogenic activity released, depending on the stimuli. Cultured PBMC from 95% of individuals release thymocyte mitogenic activity in the absence of exogenous stimuli, which was increased 1.3-to 7-fold by lopopolysaccharide (LPS) (25-50 micrograms/ml). All of this increased activity was due to increased release of IL-1 beta and non-IL-1 thymocyte mitogenic activity, with no change in the total amount of IL-1 alpha released. Indomethacin (0.1 microgram/ml) induced release of increased thymocyte mitogenic activity of 1.3- to 1.4-fold over unstimulated cultures. All of this increased activity was due to increased release of IL-1 alpha and non-IL-1 activity with a concomitant decrease in IL-1 beta release. Interferon gamma (40-100 U/ml) increased the amount of IL-1 alpha and decreased IL-1 beta and non-IL-1 activity released, resulting in no overall change in the total amount of thymocyte mitogenic activity. Molecular weight fractionation of the PBMC culture supernatants revealed that thymocyte mitogenic activity eluting in the 25K Mr range was not due to IL-1 alpha or IL-1 beta. With certain culture conditions, thymocyte mitogenic activity was detected in the 30-40K Mr range. PBMC cultured with LPS and latex beads in the absence of serum released 30-40K Mr IL-1 alpha, as well as 17K Mr IL-1 alpha and 17K Mr IL-1 beta. PBMC cultured in 2% fetal calf serum (FCS) alone from some donors released only 30-40K Mr thymocyte mitogenic activity. Both IL-1 alpha and IL-1 beta protein was detected by ELISA in this Mr range but only the IL-1 alpha was bioactive.(ABSTRACT TRUNCATED AT 250 WORDS)
The surface protein HvgA mediates group B streptococcus hypervirulence and meningeal tropism in neonates (2010)

Streptococcus agalactiae (group B streptococcus; GBS) is a normal constituent of the intestinal microflora and the major cause of human neonatal meningitis. A single clone, GBS ST-17, is strongly associated with a deadly form of the infection called late-onset disease (LOD), which is characterized by meningitis in infants after the first week of life. The pathophysiology of LOD remains poorly understood, but our epidemiological and histopathological results point to an oral route of infection. Here, we identify a novel ST-17-specific surface-anchored protein that we call hypervirulent GBS adhesin (HvgA), and demonstrate that its expression is required for GBS hypervirulence. GBS strains that express HvgA adhered more efficiently to intestinal epithelial cells, choroid plexus epithelial cells, and microvascular endothelial cells that constitute the blood-brain barrier (BBB), than did strains that do not express HvgA. Heterologous expression of HvgA in nonadhesive bacteria conferred the ability to adhere to intestinal barrier and BBB-constituting cells. In orally inoculated mice, HvgA was required for intestinal colonization and translocation across the intestinal barrier and the BBB, leading to meningitis. In conclusion, HvgA is a critical virulence trait of GBS in the neonatal context and stands as a promising target for the development of novel diagnostic and antibacterial strategies.
Formal Methods for the Analysis of Authentication Protocols (1993)

In this paper, we examine current approaches and the state of the art in the application of formal methods to the analysis of authentication protocols. We use Meadows&amp;apos; classification of analysis techniques into four types. The Type I approach models and verifies a protocol using specification languages and verification tools not specifically developed for the analysis of cryptographic protocols. In the Type II approach, a protocol designer develops expert systems to create and examine different scenarios, from which he may draw conclusions about the security of the protocols being studied. The Type III approach models the requirements of a protocol family using logics developed specifically for the analysis of knowledge and belief. Finally, the Type IV approach develops a formal model based on the algebraic term-rewriting properties of cryptographic systems. The majority of research and the most interesting results are in the Type III approach, including reasoning systems such as the B...
Peptide siderophores (1998)

Siderophores are low molecular weight iron chelators, produced by virtually all bacteria, fungi and some plants. They serve to deliver the essential element iron, barely soluble under aerobic conditions, into microbial cells. Siderophores are therefore important secondary metabolites which are very often based on amino acids and their derivatives. Biosynthesis, transport, regulation and chemical synthesis of natural siderophores and their analogues is of considerable interest for the protein and peptide chemist. This review gives an overview of the structural classes of peptidic siderophores, along with data on their biosynthesis. On a number of representative examples, strategies and schemes of their chemical synthesis are described. ©1998 European Peptide Society and John Wiley & Sons, Ltd.
Potential Deoxyribonucleic Acid Cross-linking Agents. 8,8'-Bispurines1,2 (1961)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPotential Deoxyribonucleic Acid Cross-linking Agents. 8,8'-Bispurines1,2HENRY G. MAUTNERCite this: J. Org. Chem. 1961, 26, 6, 1914–1917Publication Date (Print):June 1, 1961Publication History Published online1 May 2002Published inissue 1 June 1961https://pubs.acs.org/doi/10.1021/jo01065a054https://doi.org/10.1021/jo01065a054research-articleACS PublicationsRequest reuse permissionsArticle Views78Altmetric-Citations5LEARN 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
Platelet-Derived Growth Factor Receptor β–Mediated Phosphorylation of MUC1 Enhances Invasiveness in Pancreatic Adenocarcinoma Cells (2007)

MUC1 is a heterodimeric transmembrane glycoprotein that is overexpressed and aberrantly glycosylated in ductal adenocarcinomas. Differential phosphorylation of the MUC1 cytoplasmic tail (MUC1CT) has been associated with signaling events that influence the proliferation and metastasis of cancer cells. We identified a novel tyrosine phosphorylation site (HGRYVPP) in the MUC1CT by mass spectrometric analysis of MUC1 from human pancreatic adenocarcinoma cell lines. Analyses in vitro and in vivo showed that platelet-derived growth factor receptor beta (PDGFRbeta) catalyzed phosphorylation of this site and of tyrosine in the RDTYHPM site. Stimulation of S2-013.MUC1F cells with PDGF-BB increased nuclear colocalization of MUC1CT and beta-catenin. PDGF-BB stimulation had no significant effect on cell proliferation rate; however, it enhanced invasion in vitro through Matrigel and in vivo tumor growth and metastases. Invasive properties of the cells were significantly altered on expression of phosphorylation-abrogating or phosphorylation-mimicking mutations at these sites. We propose that interactions of MUC1 and PDGFRbeta induce signal transduction events that influence the metastatic properties of pancreatic adenocarcinoma.
Antibacterial Action of Oxidized Spermine (1964)

SUMMARY: Spermine oxidized by partially purified serum amine oxidase inhibited the growth of a variety of Gram-positive and Gram-negative bacteria. This inhibition of growth was not antagonized by calcium ion, and occurred over a wide pH range. Inactivation increased with time and temperature of incubation. The antibacterial action was abolished by treating oxidized spermine with sodium borohydride. Oxidized spermine inhibited protein synthesis as shown by incorporation of 14C-valine into cellular protein and by inhibition of β-galactosidase induction. Incorporation of 14C-uracil into the nucleic acids of Escherichia coli was not inhibited by oxidized spermine.
Synthesis of 18-Noranhydrocamptothecin Analogs Which Retain Topoisomerase I Inhibitory Function (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of 18-Noranhydrocamptothecin Analogs Which Retain Topoisomerase I Inhibitory FunctionLawrence Snyder, Wang Shen, William G. Bornmann, and Samuel J. DanishefskyCite this: J. Org. Chem. 1994, 59, 23, 7033–7037Publication Date (Print):November 1, 1994Publication History Published online1 May 2002Published inissue 1 November 1994https://pubs.acs.org/doi/10.1021/jo00102a030https://doi.org/10.1021/jo00102a030research-articleACS PublicationsRequest reuse permissionsArticle Views243Altmetric-Citations45LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
A new reagent for the selective, high-yield N-dealkylation of tertiary amines: improved syntheses of naltrexone and nalbuphine (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleA new reagent for the selective, high-yield N-dealkylation of tertiary amines: improved syntheses of naltrexone and nalbuphineR. A. Olofson, Jonathan T. Martz, Jean Pierre Senet, Marc Piteau, and Thierry MalfrootCite this: J. Org. Chem. 1984, 49, 11, 2081–2082Publication Date (Print):June 1, 1984Publication History Published online1 May 2002Published inissue 1 June 1984https://pubs.acs.org/doi/10.1021/jo00185a072https://doi.org/10.1021/jo00185a072research-articleACS PublicationsRequest reuse permissionsArticle Views7661Altmetric-Citations315LEARN 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
Carotenoid biosynthesis: Isolation and characterization of a bifunctional enzyme catalyzing the synthesis of phytoene (1988)

Phytoene is the first C(40) intermediate in the biogenesis of carotenoids. It is formed by two enzyme activities, catalyzing (i) the coupling of two molecules of geranylgeranyl diphosphate to yield prephytoene diphosphate and (ii) the conversion of prephytoene diphosphate into phytoene. We show now, with Capsicum chromoplast stroma, that the overall activity resides in a single protein, which has been purified to homogeneity by affinity chromatography. The monomeric structure and the molecular size (M(r) 47,500) were demonstrated by NaDodSO(4)/PAGE and glycerol gradient centrifugation. Further characterization was achieved by using specific antibodies which allowed immunofractionation and immunoprecipitation of the enzymatic activity from chromoplast stroma. The two reactions followed conventional Michaelis-Menten kinetics, with K(m) values of 0.30 muM and 0.27 muM, respectively, for geranylgeranyl diphosphate and prephytoene diphosphate. The activity of the enzyme depends strictly upon the presence of Mn(2+). This selectivity may be one of the factors regulating the competition with potentially rival enzymes converting geranylgeranyl diphosphate into other plastid terpenoids. The two enzymatic reactions were inhibited by inorganic pyrophosphate and by the arginine-specific reagent hydroxyphenylglyoxal. In no instance were the two reactions kinetically uncoupled. These properties strongly suggest that the same enzyme catalyzes the two consecutive reactions, and we propose to name it phytoene synthase.
Demonstration of thyromimetic effects of 3,5,3'-triiodothyronine sulfate (T3S) in euthyroid rats. (1996)

We have previously demonstrated that T3 sulfate (T3S) exhibits thyromimetic effects in hypothyroid rats and that, on a molar basis, its activity approximates 20% that of T3. Since T3S is avidly deiodinated by 5'-deiodinase, type I (5'-DI) and 5'-DI activity is markedly reduced in hypothyroidism, it seemed possible that T3S is active only in hypothyroidism and not in the euthyroid state wherein normal tissue 5'-DI activity will rapidly degrade T3S and little T3S will be left for metabolism (desulfation) to biologically active T3. This study was undertaken to test this possibility. We studied the effect of T3S (4.6, 14, or 42 nmol/day for 7 days, ip) and T3 (1.0, 3.0 or 9.0 nmol/day for 7 days, ip) in groups of male Sprague-Dawley rats (5-6/group); the control group was treated with saline ip. Treatment with both T3 and T3S caused a significant (p < 0.05) increase in hepatic and renal 5'-DI. Similarly, both treatments caused a significant reduction in serum total T4 and TSH levels. In these effects, T3S was approximately one-fifth as potent as T3 on a molar basis. Interestingly, changes in body weight during treatment with T3 and T3S suggested that at doses that caused a comparable tissue or pituitary effect, T3S treatment permitted a significantly greater weight gain than treatment with T3. We conclude that T3S exhibits thyromimetic effects in euthyroid rats in a manner comparable to that in hypothyroid rats. The biological effects of T3S may be due to T3 generated in tissues by desulfation of T3S.
A 56nm CMOS 99mm2 8Gb Multi-level NAND Flash Memory with 10MB/s Program Throughput (2006)

Fabricated in 56nm CMOS technology, an 8Gb multi-level NAND Flash memory occupies 98.8mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , with a memory cell size of 0.0075mum/b. The 10MB/s programming and 93ms block copy are also realized by introducing 8kB page, noise-cancellation circuits, external page copy and the dual V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DD</sub> scheme enabling efficient use of 1MB blocks
A context-free markup language for semi-structured text (2010)

An ad hoc data format is any nonstandard, semi-structured data format for which robust data processing tools are not easily available. In this paper, we present ANNE, a new kind of markup language designed to help users generate documentation and data processing tools for ad hoc text data. More specifically, given a new ad hoc data source, an ANNE programmer edits the document to add a number of simple annotations, which serve to specify its syntactic structure. Annotations include elements that specify constants, optional data, alternatives, enumerations, sequences, tabular data, and recursive patterns. The ANNE system uses a combination of user annotations and the raw data itself to extract a context-free grammar from the document. This context-free grammar can then be used to parse the data and transform it into an XML parse tree, which may be viewed through a browser for analysis or debugging purposes. In addition, the ANNE system generates a PADS/ML description, which may be saved as lasting documentation of the data format or compiled into a host of useful data processing tools.
Harpin, Elicitor of the Hypersensitive Response Produced by the Plant Pathogen Erwinia amylovora (1992)

A proteinaceous elicitor of the plant defense reaction known as the hypersensitive response was isolated from Erwinia amylovora, the bacterium that causes fire blight of pear, apple, and other rosaceous plants. The elicitor, named harpin, is an acidic, heat-stable, cell-envelope-associated protein with an apparent molecular weight of 44 kilodaltons. Harpin caused tobacco leaf lamina to collapse and caused an increase in the pH of bathing solutions of suspension-cultured tobacco cells. The gene encoding harpin (hrpN) was located in the 40-kilobase hrp gene cluster of E. amylovora, sequenced, and mutated with Tn5tac1. The hrpN mutants were not pathogenic to pear, did not elicit the hypersensitive response, and did not produce harpin.
Longitudinal Assessment of Tau Pathology in Patients with Alzheimer’s Disease Using [18F]THK-5117 Positron Emission Tomography (2015)

The formation of neurofibrillary tangles is believed to contribute to the neurodegeneration observed in Alzheimer's disease (AD). Postmortem studies have shown strong associations between the neurofibrillary pathology and both neuronal loss and the severity of cognitive impairment. However, the temporal changes in the neurofibrillary pathology and its association with the progression of the disease are not well understood. Tau positron emission tomography (PET) imaging is expected to be useful for the longitudinal assessment of neurofibrillary pathology in the living brain. Here, we performed a longitudinal PET study using the tau-selective PET tracer [18F]THK-5117 in patients with AD and in healthy control subjects. Annual changes in [18F]THK-5117 binding were significantly elevated in the middle and inferior temporal gyri and in the fusiform gyrus of patients with AD. Compared to patients with mild AD, patients with moderate AD showed greater changes in the tau load that were more widely distributed across the cortical regions. Furthermore, a significant correlation was observed between the annual changes in cognitive decline and regional [18F]THK-5117 binding. These results suggest that the cognitive decline observed in patients with AD is attributable to the progression of neurofibrillary pathology. Longitudinal assessment of tau pathology will contribute to the assessment of disease progression and treatment efficacy.
Enzymatic Reduction of Arsenic Compounds in Mammalian Systems:  The Rate-Limiting Enzyme of Rabbit Liver Arsenic Biotransformation Is MMAV Reductase (1999)

A unique enzyme, MMA(V) reductase, has been partially purified from rabbit liver by using DEAE-cellulose, carboxymethylcellulose, and red dye ligand chromatography. The enzyme is unique since it is the rate-limiting enzyme in the biotransformation of inorganic arsenite in rabbit liver. The K(m) and V(max) values were 2.16 x 10(-)(3) M and 10.3 micromol h(-)(1) (mg of protein)(-)(1). When DMA(V) or arsenate was tested as a substrate, the K(m) was 20.9 x 10(-)(3) or 109 x 10(-)(3) M, respectively. The enzyme has an absolute requirement for GSH. Other thiols such as DTT or L-cysteine were inactive alone. At a pH below the physiological pH, GSH carried out this reduction, but this GSH reduction in the absence of the enzyme had little if any value at pH 7.4. When the K(m) values of rabbit liver arsenite methyltransferase (5.5 x 10(-)(6) M) and MMA(III) methyltransferase (9.2 x 10(-)(6)) were compared to that of MMA(V) reductase (2.16 x 10(-)(3) M), it can be concluded that MMA(V) reductase was the rate-limiting enzyme of inorganic arsenite biotransformation. MMA(V) reductase was also present in surgically removed human liver.
The A2 Subunit of Factor VIIIa Modulates the Active Site of Factor IXa (1998)

Factor VIIIa, the protein cofactor for factor IXa, is comprised of A1, A2, and A3-C1-C2 subunits. Isolated subunits of factor VIIIa were examined for their ability to accelerate the factor IXa-catalyzed activation of factor X. The A2 subunit enhanced the kcat for this conversion by 100-fold whereas the Km for factor X was unaffected. The apparent Kd for the interaction of A2 subunit with factor IXa was approximately 300 nM. Similar results were obtained using purified A2 expressed as the isolated domain in Chinese hamster ovary cells, although this material was less stable than the factor VIIIa-derived material. Isolated A1 and A3-C1-C2 subunits showed no effect on the rate of factor X conversion. A2 subunit increased the fluorescence anisotropy of fluorescein-Phe-Phe-Arg-factor IXa (Deltar = 0.015) and markedly increased anisotropy in the presence of factor X (Deltar = 0.057), suggesting that it contributes to the orientation of the factor IXa active site and its relation to substrate. A synthetic peptide to A2 residues 558-565 inhibited the A2-dependent enhancement of factor X activation with an IC50 = 40 microM, a value similar to its Ki for inhibition of the intrinsic factor Xase (105 microM). These results indicate that the isolated A2 subunit modulates the active site of factor IXa and identifies a functional role for this subunit in factor VIIIa.