gebhart/patrepeval huggingface dataset:
Evolutionary analysis of variants of hepatitis C virus found in South-East Asia: comparison with classifications based upon sequence similarity (1996)

Variants of hepatitis C virus (HCV) have been classified by nucleotide sequence comparisons in different regions of the genome. Many investigators have defined the ranges of sequence similarity values or evolutionary distances corresponding to divisions of HCV into types, subtypes and isolates. Using these criteria, novel variants of HCV from Vietnam, Thailand and Indonesia have been classified as types 7, 8, 9, 10 and 11, many of which can be further subdivided into between two to four subtypes. In this study, this distance-based method of virus classification was compared with phylogenetic analysis and statistical measures to establish the confidence of the groupings. Using bootstrap resampling of phylogenetic trees in several subgenomic regions (core, E1, NS5) and with complete genomic sequences, we found that one set of novel HCV variants ('types 7, 8, 9 and 11') consistently grouped together into a single clade that also contained type 6a, while 'type 10a' grouped with type 3. In contrast, no robust higher-order groupings were observed between any of the other five previously described HCV genotypes (types 1-5). In each subgenomic region, the distribution of pairwise distances between members of the type 6 clade were consistently bi-modal and therefore provided no justification for classification of these variants into the three proposed categories (type, subtype, isolate). Based on these results, we propose that a more useful classification would regard all these variants as subtypes of type 6 or type 3, even though the level of sequence diversity within the clade was greater than observed for other genotypes. Classification by phylogenetic relatedness rules out simple sequence similarity measurements as a method for assigning HCV genotypes, but provides a more appropriate description of the evolutionary and epidemiological history of a virus.
Conjugal plasmid transfer (pAM beta 1) in Lactobacillus plantarum (1986)

The streptococcal plasmid pAM beta 1 (erythromycin resistance) was transferred via conjugation from Streptococcus faecalis to Lactobacillus plantarum and was transferred among L. plantarum strains. Streptococcus sanguis Challis was transformed with pAM beta 1 isolated from these transconjugants, and transformants harboring intact pAM beta 1 could conjugate the plasmid back to L. plantarum.
Highly heterogeneous nature of δ-aminolevulinate dehydratase (ALAD) deficiencies in ALAD porphyria (2001)

The properties of 9 delta-aminolevulinate dehydratase (ALAD) mutants from patients with ALAD porphyria (ADP) were examined by bacterial expression of their complementary DNAs and by enzymologic and immunologic assays. ALADs were expressed as glutathione-S-transferase (GST) fusion proteins in Escherichia coli and purified by glutathione-affinity column chromatography. The GST-ALAD fusion proteins were recognized by anti-ALAD antibodies and were enzymatically active as ALAD. The enzymatic activities of 3 ALAD mutants, K59N, A274T, and V153M, were 69.9%, 19.3%, and 41.0% of that of the wild-type ALAD, respectively, whereas 6 mutants, G133R, K59N/G133R, F12L, R240W, V275M, and delTC, showed little activity (< 8%). These variations generally reflect the phenotype of ALAD in vivo in patients with ADP and indicate that GST-ALAD fusion protein is indeed useful for predicting of the phenotype of ALAD mutants. The location of F12L mutation in the enzyme's molecular structure indicates that its disturbance of the quaternary contact of the ALAD dimer appears to have a significant influence on the enzymatic activity. Mouse monoclonal antibodies to human ALAD were developed that specifically recognized a carboxy terminal portion of ALAD, or other regions in the enzyme. This study represents the first complete analysis of 9 mutants of ALAD identified in ADP and indicates the highly heterogeneous nature of mutations in this disorder.
Members of CRF Family and their Receptors: From Past to Future (2011)

Corticotropin releasing factor (CRF), originally isolated from the mammalian hypothalamus, is a 41 amino acid peptide that plays an important physiological role and is implicated in the pathophysiology of various diseases. In addition to CRF and its related peptides, a large number of small non-peptide CRF analogs have been recently synthesized, some currently in clinical trials having considerable therapeutic potential in the treatment of CRF-related illnesses. CRF and its related peptides exert their multiple actions by interacting with two types of plasma membrane G-protein coupled CRF receptors, the type 1 (CRF(1)) and type 2 (CRF(2)). These receptors, like all GPCRs consist of an amino-terminal extracellular region, a carboxyl-terminal intracellular tail and seven, membrane-spanning segments, connected by alternating intracellular and extracellular loops. This review describes the functional role of CRF receptors and their ligands emphasizing the structural elements that are important for their function and could potentially contribute in the development of future target-based approaches to design new CRF-related drugs which will enrich the pharmaceutical armoire against serious diseases.
Adenosine stimulates glycolytic flux in isolated perfused rat hearts by A1-adenosine receptors (1989)

This study was designed to assess the role of adenosine in the regulation of exogenous glucose utilization by myocardium. Perfusion of isolated rat hearts with buffer containing D-[3-3H]glucose and analysis of the coronary effluent for 3H2O production was used as an indicator of glycolytic flux. Initially, glycolytic flux was determined during five different conditions: 1) normoxia; 2) normoxia plus 100 microM adenosine; 3) normoxia plus 100 microM adenosine and 10 microM 8-(sulfophenyl)-theophylline (SPT), an adenosine receptor antagonist; 4) hypoxia; and 5) hypoxia plus 10 microM SPT. Both adenosine and hypoxia produced an approximate threefold increase in glycolytic flux that was attenuated by adenosine receptor blockade with SPT. Next, hearts were perfused during normoxic conditions with various concentrations of either R-phenylisopropyladenosine (PIA), an A1-adenosine receptor agonist, or 5'-N-ethylcarboxamidoadenosine (NECA), an A2-adenosine receptor agonist. Significant increases in glycolytic flux occurred with PIA, whereas NECA treatment resulted in only a marginal stimulation of glycolytic flux. These data provide evidence that: 1) exogenous adenosine stimulated glycolytic flux in the normoxic myocardium; 2) endogenous adenosine stimulated glycolytic flux during hypoxia; and 3) the effect of adenosine on glycolytic flux was mediated by interaction with A1-adenosine receptors.
Structural Determinants of Ligand and Cell Surface Binding of Insulin-like Growth Factor-binding Protein-3 (1998)

Among the well defined insulin-like growth factor (IGF)-binding proteins (IGFBPs), IGFBP-3 is characterized by its interaction with an acid-labile glycoprotein (ALS) in the presence of IGFs. To identify the structural determinants on IGFBP-3 required for ligand binding and cell association, five recombinant human IGFBP-3 variants were expressed in Chinese hamster ovary cells: deletions of amino acids 89-264, 89-184, and 185-264, and site-specific mutations 228KGRKR --> MDGEA and 253KED --> RGD. The basic carboxyl-terminal region of IGFBP-3 was required for binding to heparin. The deletion variants had greatly decreased IGF binding ability as assessed by ligand blotting and solution binding assays; affinity cross-linking indicated at least a 20-fold decrease in IGF affinity. The RGD mutant had a 4-6-fold reduced affinity for both IGFs, but the MDGEA mutant bound IGF-I with near normal affinity and IGF-II with a 3-fold reduction in affinity. The three deletion variants were incapable of binding ALS; but of the site-specific variants, the MDGEA mutant bound ALS with 90% lower affinity (Ka = 2.5 +/- 0.9 liters/nmol) than seen for rhIGFBP-3 (Ka = 24.3 +/- 5.2 liters/nmol), whereas the RGD mutation had no effect on ALS affinity (Ka = 21.7 +/- 4.5 liters/nmol). The ability of IGFBP-3 to associate with the cell surface was lost in variants lacking residues 185-264 and in the 228KGRKR --> MDGEA mutant. We conclude that residues 228-232 of IGFBP-3 are essential for cell association and are required for normal ALS binding affinity.
Multiple mouse-protective antibodies directed against group B streptococci. Special reference to antibodies effective against protein antigens. (1975)

The data presented in this paper establish the finding that multiple specific protective antibodies exist in rabbits in response to immunization with Group B streptococci. The summary in Table I indicates the serological types into which Group B streptococci have been divided on the basis of their antigenic composition. This classification is dependent upon passive protection of mice with antibodies directed against the specific antigens, and types are defined in these terms. Heretofore, it was thought that type-specific polysaccharides accounted for all such protection in Group B streptococci. Certain exceptions of cross-protection between types due to minor polysaccharide determinants soon appeared; cross-protection reactions based on protein determinants in at least two types were also discovered. The present experiments show that specific antibodies directed to either polysaccharide or protein antigens of a single strain can be protective against infection with streptococci containing these antigens.
Human helper T cell factor(s). IV. Demonstration of a human late-acting B cell differentiation factor acting on Staphylococcus aureus Cowan I-stimulated B cells. (1984)

At least two distinct B cell stimulatory factors (BSF) were found to be involved in the differentiation of Staphylococcus aureus Cowan I (SAC)-stimulated human B cells to IgG-producing cells. A factor tentatively called B cell differentiation factor I (BCDF I) was found in one fraction, and a second factor, BCDF II was found in another fraction. The BCDF I fraction alone induces IgG-production in SAC-stimulated B cells, but the BCDF II fraction does not. The BCDF II fraction enhances IgG production in SAC-stimulated B cells in the presence of the BCDF I fraction. Studies concerning the time-course of the action of the BCDF II fraction revealed that it contains a late-acting differentiation factor that acts on B cells most effectively when it is added to the SAC-stimulated B cell culture after the addition of BCDF I fraction; it induces IgG plaque-forming cells within 1 day. The pI value of a late-acting BCDF was in the range of 5 to 6; this pI range is different from that of BCDF I but similar to that of BCDF II, which was shown in our previous studies to be able to induce IgG production in Epstein Barr Virus-transformed B lymphoblastoid cell lines. In addition, the m.w. of a late-acting BCDF were about 35,000 and 20,000, which are the same as those of BCDF II, and thus its identity with BCDF II was suggested.
Purification and characterisation of phospholipase A2 from human epidermis (1991)

Conference Article| April 01 1991 Purification and characterisation of phospholipase A2 from human epidermis MICHAEL J FINNEN; MICHAEL J FINNEN 1Department of Dermatology, Royal United Hospital, Combe Park, Bath, Avon, BA1 3NG, U.K. Search for other works by this author on: This Site PubMed Google Scholar CHRISTOPHER R LOVELL CHRISTOPHER R LOVELL 1Department of Dermatology, Royal United Hospital, Combe Park, Bath, Avon, BA1 3NG, U.K. Search for other works by this author on: This Site PubMed Google Scholar Author and article information Publisher: Portland Press Ltd Online ISSN: 1470-8752 Print ISSN: 0300-5127 © 1991 Biochemical Society1991 Biochem Soc Trans (1991) 19 (2): 91S. https://doi.org/10.1042/bst019091s Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation MICHAEL J FINNEN, CHRISTOPHER R LOVELL; Purification and characterisation of phospholipase A2 from human epidermis. Biochem Soc Trans 1 April 1991; 19 (2): 91S. doi: https://doi.org/10.1042/bst019091s Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1991 Biochemical Society1991 Article PDF first page preview Close Modal You do not currently have access to this content.
Rapid Detection and Identification ofCandida,Aspergillus, andFusariumSpecies in Ocular Samples Using Nested PCR (2000)

A protocol for the rapid detection of fungal DNA in ocular samples, derived from three species, Candida albicans, Aspergillus fumigatus, and Fusarium solani, has been developed. Two novel panfungal primers complementary to 18S rRNA sequences present in all three species were designed. Panfungal PCR was followed by three nested PCRs utilizing species-specific primers. PCR sensitivity ranged from 50 to 100 fg of free DNA and between one and two C. albicans organisms. In addition, we also developed a rapid and reliable DNA extraction protocol. This protocol minimized DNA loss during extraction, whilst removing compounds from vitreous and aqueous fluids that have previously been shown to have inhibitory effects on PCR. Preliminary results obtained after testing the protocol on three patient samples support culture results and medical history. However, one patient was PCR positive but culture negative, suggesting that the sensitivity of this protocol may exceed that of traditional culture techniques. This system, therefore, constitutes an additional protocol that may significantly aid patient management in cases where fungal endophthalmitis is suspected.
Electroluminescence from heterostructures of poly(phenylene vinylene) and inorganic CdSe nanocrystals (1998)

Electroluminescence (EL) and photoluminescence (PL) from heterostructure thin films made of organic poly (phenylene vinylene), PPV, and inorganic semiconductor CdSe nanocrystals are investigated. In these devices, the organic PPV structure is built next to an indium tin oxide anode, using the technique of molecular layer-by-layer sequential adsorption, and serves primarily as the hole transport layer. The inorganic layer, adjacent to an Al electrode, is made of spin cast CdSe nanocrystals, passivated with either organic groups or with a wider band gap semiconductor, e.g., ZnS in the present case. We find that the electroluminescence signal is almost exclusively generated within the inorganic layer, with a very weak contribution from the PPV layer at higher applied voltage. The performance of these heterostructure devices is influenced by the thickness of the dot layer. Lifetime tests reveal promising stability, with devices operating continuously over 50–100 h. Values of the external quantum efficiency, ηext, as high as 0.1% are reached. The quantum efficiency is not enhanced by the presence of ZnS overcoating, as opposed to the observed increase in the PL quantum yield. This reflects a difference in the efficiency of charge injection into the nanocrystals due to the ZnS overlayer.
The successful use of pronuclear embryo transfers the day following oocyte retrieval (1998)

A retrospective analysis of results from 114 initiated in-vitro fertilization cycles utilizing pronuclear embryo transfer is presented. Patients were unselected for age or infertility criteria, constituted a continuous series and were grouped according to response to stimulation (Group 1, ideal; Group 2, suboptimal) or ovarian reserve (Group 3, poor). At 16-18 h post-insemination, embryos were scored for alignment of pronuclei and nucleoli and the appearance of the cytoplasm, generating an embryo score (ES). Transfers were performed 24-26 h post-insemination using two to six embryos with the highest ES. A corrected score was calculated (total score/number of embryos; CS). A total of 114 initiated cycles resulted in 97 oocyte retrievals with 38 clinical pregnancies (39%; 15% implantation). Pregnancy rates were significantly different between the three groups; 37 pregnancies in Group 1 (55% clinical pregnancy; 20% implantation), none in Group 2 and one in Group 3 (6%; 2% implantation: P < 0.001). The ES of transferred embryos correlated with groups. There was a strong correlation between CS and implantation and delivery rates. CS >15 resulted in a 28% implantation; 65% delivery rate. CS <14 resulted in four pregnancies, one delivered. The data show that oocyte quality and pronuclear embryo morphology are related to implantation and that pronuclear embryos can be successfully selected for embryo transfer.
Tim-3/Galectin-9 Pathway: Regulation of Th1 Immunity through Promotion of CD11b+Ly-6G+ Myeloid Cells (2010)

IFN-gamma plays a central role in antitumor immunity. T cell Ig and mucin domain (Tim-3) is expressed on IFN-gamma-producing Th1 cells; on interaction with its ligand, galectin-9, Th1 immunity is terminated. In this study, we show that transgenic overexpression of Tim-3 on T cells results in an increase in CD11b(+)Ly-6G(+) cells and inhibition of immune responses. Molecular characterization of CD11b(+)Ly-6G(+) cells reveals a phenotype consistent with granulocytic myeloid-derived suppressor cells. Accordingly, we find that modulation of the Tim-3/galectin-9 (Gal-9) pathway impacts on tumor growth. Similarly, overexpression of Tim-3 ligand, Gal-9, results in an increase in CD11b(+)Ly-6G(+) cells and inhibition of immune responses. Loss of Tim-3 restores normal levels of CD11b(+)Ly-6G(+) cells and normal immune responses in Gal-9 transgenic mice. Our data uncover a novel mechanism by which the Tim-3/Gal-9 pathway regulates immune responses and identifies this pathway as a therapeutic target in diseases where myeloid-derived suppressor cells are disadvantageous.
Macromol. Chem. Phys. 3/2015 (2015)

Peer Reviewed
Bridging grafts and transient nerve growth factor infusions promote long-term central nervous system neuronal rescue and partial functional recovery. (1995)

Grafts of favorable axonal growth substrates were combined with transient nerve growth factor (NGF) infusions to promote morphological and functional recovery in the adult rat brain after lesions of the septohippocampal projection. Long-term septal cholinergic neuronal rescue and partial hippocampal reinnervation were achieved, resulting in partial functional recovery on a simple task assessing habituation but not on a more complex task assessing spatial reference memory. Control animals that received transient NGF infusions without axonal-growth-promoting grafts lacked behavioral recovery but also showed long-term septal neuronal rescue. These findings indicate that (i) partial recovery from central nervous system injury can be induced by both preventing host neuronal loss and promoting host axonal regrowth and (ii) long-term neuronal loss can be prevented with transient NGF infusions.
Shiga toxin-associated hemolytic uremic syndrome: combined cytotoxic effects of shiga toxin and lipopolysaccharide (endotoxin) on human vascular endothelial cells in vitro (1992)

This study explores the in vitro relationship between Shiga toxin-producing Shigella spp. and Escherichia coli and the development of vascular complications in humans following bacillary dysentery. We propose that lipopolysaccharide (LPS; endotoxin) may combine with Shiga toxin to facilitate vascular damage characteristic of hemolytic uremic syndrome. We have examined the direct cytotoxic effects of Shiga toxin and LPS on human umbilical vein endothelial cells (HUVEC) in culture. Shiga toxin alone was cytotoxic to HUVEC, whereas LPS was noncytotoxic at concentrations at or below 10 micrograms/ml. Combinations of LPS with Shiga toxin resulted in a synergistic cytotoxic effect. The synergistic cytotoxic response of HUVEC to Shiga toxin plus LPS was dose dependent for both agents and was maximal at 24 h of exposure. This synergistic response was enhanced by preincubation of HUVEC with LPS. LPS (1 micrograms/ml) alone depressed HUVEC protein synthesis in a transient manner and enhanced the protein synthesis-inhibiting activity of Shiga toxin. The synergistic cytotoxic activity of LPS analogs was as follows, in decreasing order: complete LPS = diphosphoryl lipid A greater than monophosphoryl lipid A greater than deacylated LPS. These results are consistent with a role for Shiga toxin and LPS in the development of hemolytic uremic syndrome at the level of the vascular endothelium in humans.
Efficacy and tolerability of the new antiepileptic drugs II: Treatment of refractory epilepsy [RETIRED] (2004)

The choice of AED depends upon seizure and/or syndrome type, patient age, concomitant medications, AED tolerability, safety, and efficacy. The results of this evidence-based assessment provide guidelines for the prescription of AEDs for patients with refractory epilepsy and identify those seizure types and syndromes where more evidence is necessary.
Supramolecular architectures from phthalocyanine building blocks (1994)

Abstract Different procedures for preparing columnar stacks and layered structures from phthalocyanine molecules are presented and discussed, including organization of the molecules by one of the following means: (i) with the help of liquid crystallinity, (ii) by using crown ether rings attached to the phthalocyanine core, (iii) by polymerization, and (iv) by Langmuir‐Blodgett film formation.
Role of Quinoids in Estrogen Carcinogenesis (1998)

ADVERTISEMENT RETURN TO ISSUEReviewNEXTRole of Quinoids in Estrogen CarcinogenesisJudy L. Bolton, Emily Pisha, Fagen Zhang, and Shengxiang QiuView Author Information Department of Medicinal Chemistry and Pharmacognosy (M/C 781), College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612-7231 Cite this: Chem. Res. Toxicol. 1998, 11, 10, 1113–1127Publication Date (Web):August 26, 1998Publication History Received7 May 1998Published online26 August 1998Published inissue 1 October 1998https://pubs.acs.org/doi/10.1021/tx9801007https://doi.org/10.1021/tx9801007review-articleACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views570Altmetric-Citations132LEARN 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:Adducts,Aromatic compounds,Genetics,Hydrocarbons,Redox reactions Get e-Alerts