gebhart/patrepeval huggingface dataset:
The transitory complex between photoexcited rhodopsin and transducin (1989)

In the first step of the visual transduction cascade a photoexcited rhodopsin molecule, R*ret, binds to a GDP-carrying transducin molecule, TGDP. The R*-T interaction causes the opening of the nucleotide site in T and catalyzes the GDP/GTP exchange by allowing the release of the GDP. We have studied the influences on this R*-T transitory complex of the occupancies of the nucleotide site in T and the retinal site in rhodopsin. After elimination of the GDP released from the bound transducin, the complex, named R*ret-te (ret for retinal present, e for nucleotide site empty) remains stabilized almost indefinitely in a medium whose ionic composition is close to physiological. In this complex the bound Te retains a lasting ability to interact with GDP or GTP, and R*ret remains spectroscopically in the meta-II state, by contrast with free R*ret which decays to opsin and free retinal. Hence the R*-T interaction which opens the nucleotide site in T conversely blocks the retinal site in R*ret. Upon prolonged incubation in a low-ionic-strength medium the R*ret-Tc complex dissociates partially, but the liberated Te is then unable to rebind GDP or GTP, even in the presence of R*ret, it is probably denaturated. Upon treatment of the R*ret-Te complex by a high concentration of hydroxylamine, the retinal can be removed from the rhodopsin. The Re-Te complex remains stable and the complexed transducin keeps its capacity to bind GTP. TGTP then dissociates from Re. The liberated Re loses its capacity to interact with a new transducin. These data are integrated into a discussion of the development of the cascade. We stress that affinities, i.e. dissociation equilibrium constants, are insufficient to describe the flow of reactions triggered by one R*ret molecule. It depends on a few critical rapid binding and dissociation processes, and is practically insensitive to other slow ones, hence to the values of affinities that express only the ratio of kinetics constants. The effect of the R*-T interaction on the retinal site in rhodopsin is analogous to the effect of the binding of a G-protein on the apparent affinity of a receptor for its agonist.
Cytokine-endothelial interactions in inflammation, immunity, and vascular injury. (1990)

This paper reviews the evidence that cytokines induce a variety of functional and structural alterations in endothelium and that cytokine-endothelial interactions play important roles in the evolution of inflammatory and immune responses. The effect of cytokines, particularly interleukin-1 and tumor necrosis factor, on leukocyte-endothelial adhesion has led to the discovery of several endothelial adhesion molecules, and the molecular and biological characteristics of these are described. Finally, the review discusses the possible contribution of cytokine-induced activation to vascular injury in such pathological processes as septic shock, the Shwartzman reaction, delayed hypersensitivity, and immune-mediated vasculitis.
Characterization of Human Inducible Costimulator Ligand Expression and Function (2000)

The inducible costimulator (ICOS) is the newest member of the CD28/CD152 receptor family involved in regulating T cell activation. We constructed a soluble-Ig fusion protein of the extracellular domain of human ICOS and used it as a probe to characterize expression patterns of the ICOS ligand (ICOSL). ICOSIg did not bind to CD80- or CD86-transfected Chinese hamster ovary cell lines, demonstrating that ICOSL is distinct from those ligands identified for CD28/CD152. ICOSIg showed selective binding to monocytic and B cell lines, whereas binding was undetectable on unstimulated monocytes and peripheral blood T and B cells. Expression of ICOSL was induced on monocytes after integrin-dependent plastic adhesion. Pretreatment of monocytes with mAb to the beta2-integrin subunit CD18 decreased adhesion and abolished ICOSL up-regulation but had no effect on CD80/86 (CD152 ligand (CD152L)) expression. Both ICOSL and CD152L were up-regulated on monocytes by IFN-gamma but by distinct signaling pathways. Unlike CD152L expression, ICOSL expression did not change when monocytes were differentiated into dendritic cells (DCs) or after DCs were induced to mature by LPS, TNF-alpha, or CD40 ligation. Addition of ICOSIg to allogeneic MLRs between DCs and T cells reduced T cell proliferative responses but did so less efficiently than CTLA4Ig (CD152Ig) did. Similarly, ICOSIg also blocked Ag-specific T cell proliferation to tetanus toxoid. Thus, ICOSL, like CD80/86, is expressed on activated monocytes and dendritic cells but is regulated differently and delivers distinct signals to T cells that can be specifically inhibited by ICOSIg.
Optimization of vaccine responses in early life: The role of delivery systems and immunomodulators (1998)

Infant immunization is a particularly important field with multiple challenges for vaccine research and development. There is, together with a high susceptibility to infections, a lower efficacy of most vaccinations in newborns and young infants, compared to those performed later in life. In the present review, the authors focus on problems arising from the attempt to vaccinate against pathogens very early in life, and on the role of selective adjuvants (i.e. antigen delivery systems or immunomodulators) that could be used to: (i) rapidly induce strong antibody responses of the appropriate isotypes; (ii) elicit sustained antibody responses extending beyond infancy; (iii) induce efficient Th1 and CTL responses in spite of the preferential Th2 polarization of early life responses; (iv) escape from maternal antibody mediated inhibition of vaccine responses; (v) show acceptable reactogenicity in early life; and (vi) allow incorporation of several vaccine antigens into a single formulation so as to reduce the number of required injections. How such objectives might be achieved by several of the vaccine formulations currently in development is illustrated by reviewing data from experimental models and clinical studies, when available.
Sequence Finishing and Gene Mapping for Candida albicans Chromosome 7 and Syntenic Analysis Against the Saccharomyces cerevisiae GenomeThe entire chromosome 7 sequence has been deposited at DDBJ/EMBL/GenBank under the project accession no. AP006852. (2005)

The size of the genome in the opportunistic fungus Candida albicans is 15.6 Mb. Whole-genome shotgun sequencing was carried out at Stanford University where the sequences were assembled into 412 contigs. C. albicans is a diploid basically, and analysis of the sequence is complicated due to repeated sequences and to sequence polymorphism between homologous chromosomes. Chromosome 7 is 1 Mb in size and the best characterized of the 8 chromosomes in C. albicans. We assigned 16 of the contigs, ranging in length from 7309 to 267,590 bp, to chromosome 7 and determined sequences of 16 regions. These regions included four gaps, a misassembled sequence, and two major repeat sequences (MRS) of >16 kb. The length of the continuous sequence attained was 949,626 bp and provided complete coverage of chromosome 7 except for telomeric regions. Sequence analysis was carried out and predicted 404 genes, 11 of which included at least one intron. A 7-kb indel, which might be caused by a retrotransposon, was identified as the largest difference between the homologous chromosomes. Synteny analysis revealed that the degree of synteny between C. albicans and Saccharomyces cerevisiae is too weak to use for completion of the genomic sequence in C. albicans.
Pulsed electron paramagnetic resonance studies of the lysine 2,3-aminomutase substrate radical: Evidence for participation of pyridoxal 5'-phosphate in a radical rearrangement (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPulsed electron paramagnetic resonance studies of the lysine 2,3-aminomutase substrate radical: Evidence for participation of pyridoxal 5'-phosphate in a radical rearrangementMarcus D. Ballinger, Perry A. Frey, George H. Reed, and Russell LoBruttoCite this: Biochemistry 1995, 34, 31, 10086–10093Publication Date (Print):August 8, 1995Publication History Published online1 May 2002Published inissue 8 August 1995https://pubs.acs.org/doi/10.1021/bi00031a033https://doi.org/10.1021/bi00031a033research-articleACS PublicationsRequest reuse permissionsArticle Views176Altmetric-Citations33LEARN 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
Further Studies of the Neuraminidase Content of Inactivated Influenza Vaccines and the Neuraminidase Antibody Responses After Vaccination of Immunologically Primed and Unprimed Populations (1980)

Purified concentrates of influenza A/USSR/90/77(H1N1)-like, A/Texas/1/77 (H3N2)-like, and B/Hong Kong/5/72-like viruses used for preparation of investigational and licensed vaccines in 1978 to 1979 were tested for their content of neuraminidase enzyme activity. Concentrates of H1N1 virus used to prepare vaccines for clinical investigations performed in the spring of 1978 had neuraminidase activity at that time which decreased during storage to almost undetectable levels (three lots) or by 50% (one lot) by the winter of 1978. Several other lots of concentrates prepared with H1N1 virus and used for vaccine formulation had no detectable neuraminidase enzyme activity when tested in the winter of 1978, at a time when they would be administered in vaccines. The range of specific activity for different lots of concentrates was about 40-fold for A/Texas/1/77, B/Hong Kong/5/72, and A/USSR/90/77 neuraminidases. Immunogenicity of investigational vaccines prepared with tested concentrates and administered between April and July 1978 was measured in volunteers aged 13 to >50 years. Frequency of neuraminidase antibody rises to two doses of H1N1-containing vaccine was 10% in unprimed subjects aged <26 years and about 18 to 36% in older persons. The frequency of neuraminidase antibody rises to one dose of H3N2-containing vaccine varied from 0 to 32% in different groups (mean, 18%). The frequencies of neuraminidase antibody responses were always much lower than the frequencies of hemagglutinin antibody responses. These observations confirm the existence of practical difficulties in achieving uniformity of the neuraminidase content in influenza vaccines and of ensuring good immunogenicity of vaccine neuraminidase even in primed populations.
High‐Capacity Anode Materials for Lithium‐Ion Batteries: Choice of Elements and Structures for Active Particles (2013)

Growing market demand for portable energy storage has triggered significant research on high‐capacity lithium‐ion (Li‐ion) battery anodes. Various elements have been utilized in innovative structures to enable these anodes, which can potentially increase the energy density and decrease the cost of Li‐ion batteries. In this review, electrode and material parameters are considered in anode fabrication. The periodic table is then used to explore how the choice of anode material affects rate performance, cycle stability, Li‐ion insertion/extraction potentials, voltage hysteresis, volumetric and specific capacities, and other critical parameters. Silicon (Si), germanium (Ge), and tin (Sn) anodes receive more attention in literature and in this review, but other elements, such as antimony (Sb), lead (Pb), magnesium (Mg), aluminum (Al), gallium (Ga), phosphorus (P), arsenic (As), bismuth (Bi), and zinc (Zn) are also discussed. Among conversion anodes focus is placed on oxides, nitrides, phosphides, and hydrides. Nanostructured carbon (C) receives separate consideration. Issues in high‐ capacity research, such as volume change, insufficient coulombic efficiency, and solid electrolyte interphase (SEI) layer stability are elucidated. Finally, advanced carbon composites utilizing carbon nanotubes (CNT), graphene, and size preserving external shells are discussed, including high mass loading (thick) electrodes and electrodes capable of providing load‐bearing properties.
A Vaccine against Nicotine for Smoking Cessation: A Randomized Controlled Trial (2008)

Swiss Medical Registry 2003DR2327; ClinicalTrials.gov NCT00369616.
Iron Chelators as Anti-Neoplastic Agents: Current Developments and Promise of the PIH Class of Chelators (2003)

The chelator currently used to treat iron (Fe) overload disease, desferrioxamine (DFO), has shown anti-proliferative activity against leukemia and neuroblastoma cells in vitro, in vivo and in clinical trials. Collectively, these studies suggest that Fe-deprivation may be a useful anti-cancer strategy. However, the efficacy of DFO is severely limited due to its poor ability to permeate cell membranes and bind intracellular Fe pools. These limitations have encouraged the development of other Fe chelators that are far more effective than DFO. One group of ligands that have been extensively investigated are those of the pyridoxal isonicotinoyl hydrazone (PIH) class. In this review the marked anti-proliferative effects of the PIH analogs are discussed with reference to their mechanisms of action and structure-activity relationships. In particular, we discuss the activity of a novel group of ligands that are "hybrid" chelators derived from our most effective PIH analogs and thiosemicarbazones. The anti-tumor activity of the PIH analogs and other chelators such as tachpyridine, O-trensox and the desferrithiocin analogs have been well characterized in vitro. However, further studies in animals are critical to evaluate their selective anti-tumor activity and potential as therapeutic agents.
Calibration-free gaze tracking using a binocular 3D eye model (2009)

This paper presents a calibration-free method for estimating the point of gaze (POG) on a display by using two pairs of stereo cameras. By using one pair of cameras and two light sources, the optical axis of the eye and the position of the center of the cornea can be estimated. This estimation is carried out by using a spherical model of the cornea. One pair of cameras is used for the estimation of the optical axis of the left eye, and the other pair is used for the estimation of the optical axis of the right eye. The point of intersection of optical axis with the display is termed the point of the optical axis (POA). The POG is approximately estimated as the midpoint of the line joining POAs of both the eyes with the display. We have developed a prototype system based on this method and demonstrated that the midpoint of POAs was closer to the fiducial point that the user gazed at than each POA.
Sperm Motility Development in the Epididymis is Associated with Decreased Glycogen Synthase Kinase-3 and Protein Phosphatase 1 Activity1 (1996)

Immotile bovine caput epididymal sperm contain levels of protein phosphatase activity twofold higher than do mature motile caudal sperm. Comparison of the inhibition profiles of endogenous phosphatase activities detected by okadaic acid (OA) and calyculin A (CA) revealed a pattern consistent with the predominance of a type 1 protein phosphatase (PP1). Immunoblot analysis identified PP1 gamma 2 (the testis-specific isoform of PP1) as the only PP1 isoform in sperm and showed little protein phosphatase 2A (PP2A). In addition, of the known PP1 inhibitors, i.e., DARPP-32, inhibitor 1 (I1), and inhibitor 2 (I2), only I2-like activity was detected in sperm. Inhibition of PP1 by the heat-stable I2-like activity purified from sperm could be reversed with purified glycogen synthase kinase-3 (GSK-3). Furthermore, sperm extracts contain an inactive complex of PP1 and I2 (termed PP1I) that could also be activated by purified GSK-3. The presence of GSK-3 in sperm was demonstrated by activation of purified PP1I, and quantitation revealed that immotile caput sperm contained sixfold higher GSK-3 activity than motile caudal sperm. Immunoblot analysis confirmed the expression of GSK-3 in sperm and revealed the occurrence of both the alpha and beta isoforms. Our findings suggest that the higher PP1 activity measured in immotile sperm, presumably due to higher GSK-3 activity, is responsible for holding motility in check. This conclusion was supported by the observation that the phosphatase inhibitors OA and CA, at micromolar and nanomolar levels, respectively, were able to induce motility in completely immotile bovine caput epididymal sperm and to stimulate the kinetic activity of mature caudal sperm. The intrasperm levels of cAMP, pH, and calcium were unaltered by treatment with these inhibitors. The results suggest a biochemical basis for the development and regulation of sperm motility and a possible physiological role for the PP1/I2/GSK-3 system.
Calcium-dependent homotypic adhesion through leukocyte function- associated antigen-1/intracellular adhesion molecule-1 induces interleukin-1 and parathyroid hormone-related protein production on adult T-cell leukemia cells in vitro (1995)

Adult T-cell leukemia (ATL) is a human T-cell leukemia virus type I (HTLV-I)-infected lymphoproliferative disorder that shows a characteristic nodular infiltration into various tissues, hypercalcemia, and subsequent rapid increase of peripheral ATL cell number. ATL cells and HTLV-I-infected T-cell lines also make cluster formation rapidly after the non-stimulative culture. However, the mechanism of the acute proliferation of ATL cells remains to be understood. We report the following novel features of homotypic adhesion via leukocyte function-associated antigen-1 (LFA-1)/intracellular adhesion molecule-1 (ICAM-1) pathway that suggest a role for it in cytokine production and rapid proliferation of ATL cells: (1) ATL cells show clustering in a calcium dependent manner, even at the higher concentration; (2) ATL cells consistently and highly express ICAM-1 and an active form of LFA-1, whereas integrin expression, except for LFA-1, is rather lower compared with that of normal CD4+ T cells; (3) ATL cells make conjugate formation within 6 minutes and clustering within 48 hours, both of which are inhibited by the addition of monoclonal antibodies (MoAbs) against LFA-1 and ICAM-1; (4) spontaneous mRNA transcription and protein secretion of both interleukin-1 and parathyroid hormone-related protein are observed consistently in ATL cells, and these productions are inhibited by anti-LFA-1 and anti-ICAM-1 MoAbs but are markedly increased by cross-linking of LFA-1 and ICAM-1 by the immobilized specific MoAbs; and (5) proliferative responses of ATL cells are also inhibited by these MoAbs. We propose that ATL cells proliferate in sequential events: the homotypic and calcium-dependent adhesion through LFA-1/ICAM-1, the signal transduction through these adhesion molecules, the production of cytokines, and the proliferation.
Zur Reaktion von Cyclopropenonen mit Ketenacetalen, III1) Thermische Umwandlung der labilen 1:1‐Addukte aus Diphenylcyclopropenon bzw. Diphenylcyclopropenthion und Ketenacetalen2, 3) (1976)

Abstract Bei höherer Temperatur setzen sich Diphenylcyclopropenon (1) und Diphenylcyclopropenthion (2) mit Ketenacetalen 3 bzw. 7 zu stabilen 1:1‐Addukten um, denen die Konstitution von cis‐2,4‐Pentadienamiden 6 bzw. 8 zukommt. Die früher beschriebenen thermolabilen 1:1‐Addukte (2‐Azoniabicyclo[3.1.0]hex‐3‐en‐3‐olate bzw. ‐thiolate) sind Zwischenprodukte der Reaktion. Die Konstitution 6 wird durch Hydrolyse‐, Ozonolyse‐ und Hydrierungsreaktionen bewiesen. In zwei Fällen unterliegen die cis ‐2,4‐Pentadienamide 6 thermischen cis‐trans ‐Isomerisierungen zu 9 .
Tumour MHC class I downregulation and immunotherapy (Review) (2003)

MHC class I downregulation is an important mechanism of tumour escape from T cell-mediated immune responses. Approximately 40-90% of human tumours derived from various MHC class I+ tissues were reported to be MHC class I deficient. Decreased or absent MHC class I expression is frequently associated with the invasive and metastatic tumour phenotype. Altered MHC class I antigen expression involves total loss, loss of haplotype, locus downregulation, allelic loss or downregulation, and combinations. Description of partial or complete losses of MHC class I molecules in tumour cells as mechanisms of immune escape often fails to consider an increased susceptibility to NK cell-mediated lysis, which is a direct consequence of such losses. A low MHC class I level favours NK cells as effectors, whereas a high level of MHC class I favours T cells as effectors. The microheterogeneity of MHC class I expression in tumour cell populations, the balance of the MHC-restricted and MHC-unrestricted defence as well as the selective pressure of antigen-specific (CTL) and antigen non-specific (NK) effector mechanisms decide the final outcome of the MHC class I expression in the primary tumour and its metastases as well as the final outcome of the tumour defence reaction. Despite the MHC class I molecule deficiency and the resulting absence of the CD8+ T cell-mediated immunity, the tumour hosts were found to be capable of being immunized against MHC class I- tumours. The purpose of this review is to discuss the positive results of MHC class I- tumour treatment obtained with immunomodulatory cytokines and tumour vaccines, as well as the prospects and limitations of such therapy.
In vitro oligosaccharide synthesis using intact yeast cells that display glycosyltransferases at the cell surface through cell wall-anchored protein Pir (2002)

A glycosyltransferase was fused to the yeast cell wall protein Pir, which forms the Pir1-4 protein family and is incorporated into the cell wall by an unknown linkage to be displayed at the yeast cell surface. We first expressed the PIR1-HA-gma12+ fusion, in which gma12+ encodes alpha-1,2-galactosyltransferase from the fission yeast Schizosaccharomyces pombe under the Saccharomyces cerevisiae GAPDH promoter. The alpha-1,2-galactosyltransferase activity was detected at the surface of the intact cells that produce Pir1-HA-Gma12 fusion. To further demonstrate sequential oligosaccharide synthesis, two plasmids containing PIR1-HA-KRE2 and PIR2-FLAG-MNN1 fusion genes were constructed in which KRE2 and MNN1 encode alpha-1,2-mannosyltransferase and alpha-1,3-mannosyltransferase from S. cerevisiae, respectively. The intact yeast cells transformed with these two plasmids added mannoses initially with an alpha-1,2 linkage and subsequently with an alpha-1,3 linkage to the alpha-1,2-mannobiose acceptor in the presence of a GDP-mannose donor, demonstrating that Pir1 and Pir2 can be used as anchors to simultaneously immobilize several glycosyltransferases at the yeast cell surface. Based on the high acceptor specificity of glycosyltransferases, we propose a simple in vitro method for oligosaccharide synthesis using the yeast intact cell as a biocatalyst.