gebhart/patrepeval huggingface dataset:
Optical imaging of Renilla luciferase reporter gene expression in living mice (2001)

Imaging reporter gene expression in living subjects is a rapidly evolving area of molecular imaging research. Studies have validated the use of reporter genes with positron emission tomography (PET), single photon emission computed tomography (SPECT), MRI, fluorescence with wild-type and mutants of green fluorescent protein, as well as bioluminescence using Firefly luciferase enzyme/protein (FL). In the current study, we validate for the first time the ability to image bioluminescence from Renilla luciferase enzyme/protein (RL) by injecting the substrate coelenterazine in living mice. A highly sensitive cooled charge-coupled device camera provides images within a few minutes of photon counting. Cells, transiently expressing the Rluc were imaged while located in the peritoneum, s.c. layer, as well as in the liver and lungs of living mice tail-vein injected with coelenterazine. Furthermore, d-luciferin (a substrate for FL) does not serve as a substrate for RL, and coelenterazine does not serve as a substrate for FL either in cell culture or in living mice. We also show that both Rluc and Fluc expression can be imaged in the same living mouse and that the kinetics of light production are distinct. The approaches validated will have direct applications to various studies where two molecular events need to be tracked, including cell trafficking of two cell populations, two gene therapy vectors, and indirect monitoring of two endogenous genes through the use of two reporter genes.
Involvement of antigen-presenting cells in the enhancement of the in vitro antibody responses by cholera toxin B subunit. (1992)

The enhancing effect of cholera toxin B subunit (CTB) on primary antibody responses to keyhole limpet haemocyanin (KLH) and the cellular basis of the effect were investigated, using in vitro cultures of mouse spleen cells. CTB (1-100 ng/ml) enhanced anti-KLH IgM, IgG and IgA antibody responses in a dose-dependent manner, when added to the cultures with KLH. This immunoenhancement was antigen specific, but not due to either polyclonal activation of the spleen cells or antigenic cross-reactivity between CTB and KLH. CTB did not affect the kinetics of the anti-KLH antibody responses. Early (Days 0-1) addition of CTB to the cultures enhanced the anti-KLH antibody production, whereas late (Days 5-7) addition of CTB did not. Addition of CTB with KLH to splenic adherent cells (SAC) resulted in a dose-dependent enhancement of the anti-KLH antibody responses, when the SAC were reconstituted with unimmunized non-adherent cells. Moreover, CTB enhanced IL-1 secretion from SAC incubated with KLH. These results suggest that CTB enhances the primary anti-KLH antibody responses in vitro by acting on early events in the responses, and that antigen-presenting cells play a major role in the enhancement.
HIV-1-stimulated expression of CD11/CD18 integrins and ICAM-1: a possible mechanism for extravascular dissemination of HIV-1-infected cells. (1989)

To identify mechanisms which might facilitate emigration of HIV-1-infected cells from the circulation, we studied the effect of HIV-1 infection on T lymphocyte and monocytoid cell expression of molecules involved in adherence and translocation of leukocytes across endothelial cell barriers. CD11a, CD18, and ICAM-1 were demonstrated on up to 80% of HIV-1-infected H9 T cells by flow cytometry; these molecules were not evident on uninfected H9. CD18 mRNA was detected in HIV-infected, but not in uninfected H9 T cells. Cell surface expression of CD11a and CD18, but not ICAM-1, was increased on HIV-infected, as compared to uninfected U937 and THP1 monocytoid cells. Increased cell surface expression of the leukocyte integrins was associated with a significantly increased tendency of HIV-infected monocytoid cells to adhere to human umbilical vein endothelial cell monolayers or aggregate homotypically. Preincubating the monocytoid cells with anti-CD18 or anti-CD11a or preincubating endothelial cells with anti-ICAM-1 suppressed these cell to cell interactions. These studies suggest that HIV-1 infection stimulates cell surface expression of molecules involved in leukocyte adherence and transendothelial migration in vitro. Similar mechanisms may influence leukocyte trafficking, in vivo, and may play a role in the localization of HIV-1 infected cells in the central nervous system and other tissues.
Duodenal ulcer healing after 7-day treatment: a pilot study with lansoprazole, amoxicillin and clarithromycin. (1995)

One-week therapy with lansoprazole, amoxicillin and clarithromycin is highly effective in duodenal ulcer healing and symptom improvement. Prolonged acid suppression does not seem to be essential for duodenal ulcer treatment.
Differential Activity of the 30-kD and the 100-kD Forms of 2′-5′A n Synthetase Induced by Recombinant Human Interferon-α and Interferon-γ (1988)

Two molecular weight variants of the interferon (IFN)-induced intracellular enzyme 2',5'-oligoadenylate (2-5A) synthetase have been described recently; a 100-kD (cytoplasmic) and a 30-kD (intranuclear) form of the enzyme. The 30-kD form has been located primarily in the nucleus, while the 100-kD enzyme was found mainly in the cytoplasm. We examined 2-5A synthetase activity in extracts of human melanoma (Hs294t) cells treated with either recombinant (r) IFN-alpha A or rIFN-gamma to determine the differential regulation of these enzyme subtypes by treatment with the two types of IFN. Cells were treated (continuous exposure) with doses of rIFN-alpha A (1,000 U/ml) or rIFN-gamma (5,000 U/ml), each of which reduced the number of viable cells to 50% of control values (ED50) by day 3 of treatment. At equieffective doses, the maximal increase in 2-5A synthetase occurred at 48 h for both rIFN-alpha A and rIFN-gamma continuous exposure. The maximal 2-5A intracellular activities at 48 h were 800 +/- 40 and 160 +/- 15 nmoles/mg protein for rIFN-alpha A and rIFN-gamma treatment, respectively. High-performance gel permeation chromatography of cell lysates resolved the 2-5A activity into both 100-kD and 30-kD fractions. At 48 h after treatment with rIFN-alpha A, the activity of the 30-kD synthetase was approximately twofold greater than that of the 100-kD enzyme. In contrast, the activity of both 30- and 100-kD enzymes were equivalent 48 h after treatment with rIFN-gamma.(ABSTRACT TRUNCATED AT 250 WORDS)
CD163 is the macrophage scavenger receptor for native and chemically modified hemoglobins in the absence of haptoglobin (2005)

CD163 mediates the internalization of hemoglobin-haptoglobin (Hb-Hp) complexes by macrophages. Because Hp binding capacity is exhausted during severe hemolysis, an Hp-independent Hb-clearance pathway is presumed to exist. We demonstrate that Hb interacts efficiently with CD163 in the absence of Hp. Not only is Hb internalized into an endosomal compartment by CD163 as a result of active receptor-dependent endocytosis; it also inhibits the uptake of Hb-Hp complexes, suggesting a common receptor-binding site. Free Hb further induces heme oxygenase mRNA expression in CD163+ HEK293 cells, but not in CD163- cells. Additional evidence for Hp-independent Hb-CD163 interaction is provided by the demonstration that CD163 mediates the uptake of alpha alpha-DBBF crosslinked Hb, a chemically modified Hb that forms minimal Hp complexes. Moreover, certain modifications to Hb, such as polymerization or the attachment of specific functional groups (3 lysyl residues) to the beta-Cys93 can reduce or enhance this pathway of uptake. In human macrophages, Hp-complex formation critically enhances Hb uptake at low (1 microg/mL), but not at high (greater than 100 microg/mL), ligand concentrations, lending support for a concentration-dependent biphasic model of macrophage Hb-clearance. These results identify CD163 as a scavenger receptor for native Hb and small-molecular-weight Hb-based blood substitutes after Hp depletion.
Factor × Roma: a congenital factor × variant defective at different degrees in the intrinsic and the extrinsic activation (1988)

A factor X molecular variant was identified in a 13-year-old girl affected by a bleeding tendency. Factor X antigen levels and activation by Russel's viper venom (tested both by clotting and amidolytic assays) were normal. Factor X crossed immunoelectrophoresis was found to be identical to that of the control plasma. Factor X functional activity was low (3% of the normal) if tested by PTT-derived assays, whereas it was found at intermediate levels (about 30-50% of the normal) if measured by prothrombin time-derived assays. The defect in the extrinsic activation was more clearly disclosed using as activating agent thromboplastin from ox brain. The factor X of the patient was completely adsorbed by aluminum hydroxide. The parents of the propositus (first degree cousins) showed factor X functional levels compatible with a condition of heterozygosity for the abnormality. This factor X molecular variant appears different from the other ones so far described and was named 'Factor X Roma'.
An integrated approach to epitope analysis I: Dimensional reduction, visualization and prediction of MHC binding using amino acid principal components and regression approaches (2010)

As opposed to the highly constrained user-interaction paradigms of web-server approaches, local computational approaches enable interactive analysis and visualization of complex multidimensional data using robust mathematical tools. Our work shows that prediction tools such as these can be constructed on the widely available JMP® platform, can operate in a spreadsheet environment on a desktop computer, and are capable of handling proteome-scale analysis with high throughput.
Catalytic Hydroxylation of Benzene to Phenol by Dioxygen with an NADH Analogue (2016)

Hydroxylation of benzene by molecular oxygen (O2 ) occurs efficiently with 10-methyl-9,10-dihydroacridine (AcrH2 ) as an NADH analogue in the presence of a catalytic amount of Fe(ClO4 )3 or Fe(ClO4 )2 with excess trifluoroacetic acid in a solvent mixture of benzene and acetonitrile (1:1 v/v) to produce phenol, 10-methylacridinium ion and hydrogen peroxide (H2 O2 ) at 298 K. The catalytic oxidation of benzene by O2 with AcrH2 in the presence of a catalytic amount of Fe(ClO4 )3 is started by the formation of H2 O2 from AcrH2 , O2 , and H(+) . Hydroperoxyl radical (HO2 (.) ) is produced from H2 O2 with the redox pair of Fe(3+) /Fe(2+) by a Fenton type reaction. The rate-determining step in the initiation is the proton-coupled electron transfer from Fe(2+) to H2 O2 to produce HO(.) and H2 O. HO(.) abstracts hydrogen rapidly from H2 O2 to produce HO2 (.) and H2 O. The Fe(3+) produced was reduced back to Fe(2+) by H2 O2 . HO2 (.) reacts with benzene to produce the radical adduct, which abstracts hydrogen from AcrH2 to give the corresponding hydroperoxide, accompanied by generation of acridinyl radical (AcrH(.) ) to constitute the radical chain reaction. Hydroperoxyl radical (HO2 (.) ), which was detected by using the spin trap method with EPR analysis, acts as a chain carrier for the two radical chain pathways: one is the benzene hydroxylation with O2 and the second is oxidation of an NADH analogue with O2 to produce H2 O2 .
Purification and Characterization of β-Mannosidase from Human Placenta1 (1989)

Lysosomal beta-mannosidase was purified almost 10,000-fold from human placenta. The final preparation showed several protein bands on polyacrylamide gel electrophoresis. Its molecular mass was estimated to be 110 kDa, the optimal pH was 4.5, the Km was 0.56 mM, and the isoelectric point was 4.7. The enzyme was found to bind completely to Con A-Sepharose, and the pI was not changed after neuraminidase treatment. These results indicate that the purified enzyme represents a lysosomal form which contains high mannose type oligosaccharide chains and only a few sialic acids, if any.
Location, location, location: advancing veto cell therapies (2013)

In this issue of Blood , Ophir et al have identified and characterized refined conditions in which the immunoregulatory promise of veto cells, as a cellular therapy, may finally be realized.[1][1]

Veto cells have long been a somewhat obscure immunoregulatory cell type, with seemingly mysterious
<title>Fast encryption methods for audiovisual data confidentiality</title> (2001)

Two methodologies for efficient audiovisual data encryption are studied in this research, i.e. selective encryption and MHT (multiple-Huffman-table). We first discuss benefits and limitations of selective encryption, and propose a selective encryption scheme for ITU G.723.1 speech coding. A review of all cryptanalysis work of selective encryption algorithms in the literature is given, our cryptanalysis for the JPEG/MPEG sign-bit encryption scheme is presented, and two rules to determine whether selective encryption for a compression system is suitable are concluded. Then, we investigate another encryption methodology via the manipulation of Huffman coding tables of multimedia coding systems. The MHT scheme chooses several different Huffman tables from a vast number of possible candidates, and uses them alternatively to encode multimedia data. The choice of Huffman tables and the order that they are used are kept secret as the key. This method requires very little computational overhead, and can be applied to the encryption of MPEG audio, MPEG video and JPEG/JPEG2000 images.
Generation and Transport of a Low-Energy Intense Ion Beam (2004)

This paper describes experiments on the formation and transport, in vacuum and plasma, of a low-energy (70-120 keV), high-intensity (10-30 A/cm/sup 2/), long-pulse (0.5-1/spl mu/s) H/sup +/ ion beam. The beam was generated in a magnetically insulated diode with an applied radial B-field and active hydrogen-puff plasma source at the anode. The combination of a ballistic focusing large area anode (250 cm/sup 2/) with a post-cathode toroidal magnetic lens and straight transport solenoid section provided beam transport to a distance of >1 m with an overall efficiency of /spl ges/ 50%. Two-dimensional single-particle computer simulations of the ion's trajectory in the lens/solenoid system supported optimization of the lens and solenoid parameters.
Phase chemistries in a precipitation-strengthened superalloy (1983)

The majority of Ni-base superalloys are strengthened by precipitation of the γ' phase, which has a coherent ordered Ll 2 structure based on Ni 3 (Al,Ti). However, a few superalloys, most notably Inconel 718, are strengthened instead by a γ" phase, which is a metastable coherent ordered DO 22 precipitate with a tetragonal unit cell and nominal stoichiometry Ni 3 (Nb,Ta). The γ' phase generally precipitates homogeneously in the form of spheres or cubes, whereas the γ" phase occurs as disks with the (001) γ" plane parallel to one of the {100} planes of the cubic matrix. Thus, three variants of γ" are possible. The γ" phase is generally metastable and is replaced on extended aging by the δ phase, which is also Ni 3 (Nb,Ta) but which has a Cu 3 Ti-ordered orthorhombic structure. It has been shown that the type of precipitate formed in Ni-base alloys is a sensitive function of overall alloy chemistry. In particular, the Ti+Al/Nb+Ta ratio has a strong effect, with increases in this ratio favoring γ and decreases γ'.
Benign and Malignant Thyroid Nodules: US Differentiation—Multicenter Retrospective Study (2008)

Shape, margin, echogenicity, and presence of calcification are helpful criteria for the discrimination of malignant from benign nodules; the diagnostic accuracy of US criteria is dependent on tumor size.
Discourse structure and language technology (2011)

Abstract An increasing number of researchers and practitioners in Natural Language Engineering face the prospect of having to work with entire texts, rather than individual sentences. While it is clear that text must have useful structure, its nature may be less clear, making it more difficult to exploit in applications. This survey of work on discourse structure thus provides a primer on the bases of which discourse is structured along with some of their formal properties. It then lays out the current state-of-the-art with respect to algorithms for recognizing these different structures, and how these algorithms are currently being used in Language Technology applications. After identifying resources that should prove useful in improving algorithm performance across a range of languages, we conclude by speculating on future discourse structure-enabled technology.
Care of a case of Haemophius aphrophilus endocarditis with a combination of fosfomycin and gentamicin (1986)

Journal Article Care of a case of Haemophius aphrophilus endocarditis with a combination of fosfomycin and gentamicin Get access S. MORENO, S. MORENO Unidad de Enfermedades Infecciosas. Servicio de Microbiologia, Centro Especial ‘Ramón y Cajal’Madrid, Spain Search for other works by this author on: Oxford Academic PubMed Google Scholar C. EZPELETA, C. EZPELETA Unidad de Enfermedades Infecciosas. Servicio de Microbiologia, Centro Especial ‘Ramón y Cajal’Madrid, Spain Search for other works by this author on: Oxford Academic PubMed Google Scholar F. PARRAS, F. PARRAS Unidad de Enfermedades Infecciosas. Servicio de Microbiologia, Centro Especial ‘Ramón y Cajal’Madrid, Spain Search for other works by this author on: Oxford Academic PubMed Google Scholar C. BARROS, C. BARROS Unidad de Enfermedades Infecciosas. Servicio de Microbiologia, Centro Especial ‘Ramón y Cajal’Madrid, Spain Search for other works by this author on: Oxford Academic PubMed Google Scholar J. MARTINEZ BELTRÁN, J. MARTINEZ BELTRÁN Unidad de Enfermedades Infecciosas. Servicio de Microbiologia, Centro Especial ‘Ramón y Cajal’Madrid, Spain Search for other works by this author on: Oxford Academic PubMed Google Scholar L. BUZÓN L. BUZÓN Unidad de Enfermedades Infecciosas. Servicio de Microbiologia, Centro Especial ‘Ramón y Cajal’Madrid, Spain Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Antimicrobial Chemotherapy, Volume 18, Issue 6, December 1986, Pages 771–772, https://doi.org/10.1093/jac/18.6.771-a Published: 01 December 1986
Evaluation of normal and neoplastic human mast cells for expression of CD172a (SIRPα), CD47, and SHP-1 (2005)

Signal regulatory proteins (SIRPs) and tyrosine phosphatases have recently been implicated in the control of receptor tyrosine kinase (RTK)-dependent cell growth. In systemic mastocytosis (SM), neoplastic cells are driven by the RTK KIT, which is mutated at codon 816 in most patients. We examined expression of SIRPalpha, SIRPalpha ligand CD47, and Src homology 2 domain-containing protein tyrosine phosphatase-1 (SHP-1), a tyrosine phosphatase-type, negative regulator of KIT-dependent signaling, in normal human lung mast cells (HLMC) and neoplastic MC obtained from nine patients with SM. As assessed by multicolor flow cytometry, normal LMC expressed SIRPalpha, CD47, and SHP-1. In patients with SM, MC also reacted with antibodies against SIRPalpha and CD47. By contrast, the levels of SHP-1 were low or undetectable in MC in most cases. Corresponding data were obtained from mRNA analysis. In fact, whereas SIRPalpha mRNA and CD47 mRNA were detected in all samples, the levels of SHP-1 mRNA varied among donors. To demonstrate adhesive functions for SIRPalpha and CD47 on neoplastic MC, an adhesion assay was applied using the MC leukemia cell line HMC-1, which was found to bind to immobilized extracellular domains of SIRPalpha1 (SIRPalpha1ex) and CD47 (CD47ex), and binding of these cells to CD47ex was inhibited by the CD172 antibody SE5A5. In summary, our data show that MC express functional SIRPalpha and CD47 in SM, whereas expression of SHP-1 varies among donors and is low compared with LMC. It is hypothesized that CD172 and CD47 contribute to MC clustering and that the "lack" of SHP-1 in MC may facilitate KIT-dependent signaling in a subgroup of patients.
A simple and efficient method for direct gene deletion inSaccharomyces cerevisiae (1993)

Journal Article A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae Get access A. Baudin, A. Baudin Centre de Génétique Moléculaire du Centre National de la Recherche Scientifique, Laboratoire Propre Associé à I'Université Pierre-et-Marie-Curie91198 Gif-sur-Yvette Cedex, France Search for other works by this author on: Oxford Academic PubMed Google Scholar O. Ozier-Kalogeropoulos, O. Ozier-Kalogeropoulos Centre de Génétique Moléculaire du Centre National de la Recherche Scientifique, Laboratoire Propre Associé à I'Université Pierre-et-Marie-Curie91198 Gif-sur-Yvette Cedex, France Search for other works by this author on: Oxford Academic PubMed Google Scholar A. Denouel, A. Denouel Centre de Génétique Moléculaire du Centre National de la Recherche Scientifique, Laboratoire Propre Associé à I'Université Pierre-et-Marie-Curie91198 Gif-sur-Yvette Cedex, France Search for other works by this author on: Oxford Academic PubMed Google Scholar F. Lacroute, F. Lacroute Centre de Génétique Moléculaire du Centre National de la Recherche Scientifique, Laboratoire Propre Associé à I'Université Pierre-et-Marie-Curie91198 Gif-sur-Yvette Cedex, France Search for other works by this author on: Oxford Academic PubMed Google Scholar C. Cullin C. Cullin * Centre de Génétique Moléculaire du Centre National de la Recherche Scientifique, Laboratoire Propre Associé à I'Université Pierre-et-Marie-Curie91198 Gif-sur-Yvette Cedex, France *To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 21, Issue 14, 11 July 1993, Pages 3329–3330, https://doi.org/10.1093/nar/21.14.3329 Published: 11 July 1993 Article history Received: 13 April 1993 Revision received: 02 June 1993 Accepted: 02 June 1993 Published: 11 July 1993
node2vec: Scalable Feature Learning for Networks (2016)

Prediction tasks over nodes and edges in networks require careful effort in engineering features used by learning algorithms. Recent research in the broader field of representation learning has led to significant progress in automating prediction by learning the features themselves. However, present feature learning approaches are not expressive enough to capture the diversity of connectivity patterns observed in networks. Here we propose <i>node2vec</i>, an algorithmic framework for learning continuous feature representations for nodes in networks. In <i>node2vec</i>, we learn a mapping of nodes to a low-dimensional space of features that maximizes the likelihood of preserving network neighborhoods of nodes. We define a flexible notion of a node's network neighborhood and design a biased random walk procedure, which efficiently explores diverse neighborhoods. Our algorithm generalizes prior work which is based on rigid notions of network neighborhoods, and we argue that the added flexibility in exploring neighborhoods is the key to learning richer representations. We demonstrate the efficacy of <i>node2vec</i> over existing state-of-the-art techniques on multi-label classification and link prediction in several real-world networks from diverse domains. Taken together, our work represents a new way for efficiently learning state-of-the-art task-independent representations in complex networks.