gebhart/patrepeval huggingface dataset:
Purification and characterization of a novel deoxyinosine-specific enzyme, deoxyinosine 3' endonuclease, from Escherichia coli. (1994)

We have purified a novel endonuclease from Escherichia coli that recognizes deoxyinosine, a deamination product of deoxyadenosine in DNA. This activity, which we named deoxyinosine 3' endonuclease, is different from the known hypoxanthine DNA N-glycosylases which have been partially characterized in E. coli and other organisms. The enzyme was purified 24,800-fold to apparent homogeneity. SDS- and activity PAGE analyses indicate that the enzyme has an apparent molecular mass of 25 kDa. Deoxyinosine 3' endonuclease recognized deoxyinosine in both single- and double-stranded DNA but exhibited a 4-fold preference for double stranded over single-stranded DNA. In addition to deoxyinosine, the enzyme recognized urea residues and AP sites. Deoxyinosine 3' endonuclease has an obligatory requirement for Mg2+, but other cations such as Co2+ and Mn2+ could partially replace Mg2+. The optimal pH for deoxyinosine 3' endonuclease was around 7.5. In contrast to most of the known repair enzymes, deoxyinosine 3' endonuclease makes an incision at the second phosphodiester bond 3' to a deoxyinosine or AP site, leaving behind the intact lesion on the nicked DNA. Therefore, deoxyinosine 3' endonuclease recognizes, but does not remove, the lesion from the DNA molecule. The biological significance of this novel activity is discussed with reference to other repair activities in E. coli.
Driving skill classification in curve driving scenes using machine learning (2016)

Driver support and infotainment systems can be adapted to the specific needs of individual drivers by assessing driver skill and state. In this paper, we present a machine learning approach to classifying the skill at maneuvering by drivers using both longitudinal and lateral controls in a vehicle. Conceptually, a model of drivers is constructed on the basis of sensor data related to the driving environment, the drivers’ behaviors, and the vehicles’ responses to the environment and behavior together. Once the model is built, the driving skills of an unknown driver can be classified automatically from the driving data. In this paper, we demonstrate the feasibility of using the proposed method to assess driving skill from the results of a driving simulator. We experiment with curve driving scenes, using both full curve and segmented curve scenarios. Six curves with different radii and angular changes were set up for the experiment. In the full curve driving scene, principal component analysis and a support vector machine-based method accurately classified drivers in 95.7 % of cases when using driving data about high- and low/average-skilled driver groups. In the cases with segmented curves, classification accuracy was 89 %.
Elliptic Grid Control on a Discrete Level (1999)

Considering a grid cell with a single central point the solution of the discretized Laplace equation may be conceived as a weighted average of points on the cell boundary. Our grid control method is based on a local perturbation of the numerical solution to the Laplace equation by specifying line-wise central target points relative to the orientation of and the distance from the cell's bounding faces. Simple one-dimensional weighting functions allow to extend the overall control of grid line spacing and direction from the boundaries into the field.
Demonstration of inhibition of mediator release from human mast cells by azatadine base. In vivo and in vitro evaluation (1986)

In vitro experimentation using dispersed human lung mast cells demonstrated that azatadine base, a compound with known H<sub>1</sub>-antihistamine properties, inhibited anti-IgE-induced release of histamine and leukotriene C<sub>4</sub>by 45% and 85%, respectively. To assess the clinical relevance of these findings and to compare in vitro mast cell data with results obtained in vivo, nasally instilled azatadine was tested in a double-blind, placebo-controlled clinical trial in which nasal challenges with antigen were performed on eight allergic individuals. Pretreatment with azatadine significantly suppressed the number of sneezes following antigen challenge and inhibited the associated elevations in histamine, kinins, and enzyme(s) hydrolyzing the artificial substrate<i>N</i>-α-tosyl-L-arginine-methyl-ester in nasal secretions, whereas placebo was inactive. Hence, we showed agreement between our in vitro and in vivo experimental models of the allergic reaction. Topical application of azatadine base has the potential to become an effective antiallergic treatment. (<i>JAMA</i>1986;255:225-229)
Orally Active Non-Peptide Fibrinogen Receptor (GpIIb/IIIa) Antagonists: Identification of 4-[4-[4-(Aminoimino methyl)phenyl]-1-piperazinyl]-1- piperidineacetic Acid as a Long-Acting, Broad-Spectrum Antithrombotic Agent (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOrally Active Non-Peptide Fibrinogen Receptor (GpIIb/IIIa) Antagonists: Identification of 4-[4-[4-(Aminoimino methyl)phenyl]-1-piperazinyl]-1- piperidineacetic Acid as a Long-Acting, Broad-Spectrum Antithrombotic AgentColin D. Eldred, Brian Evans, Sean Hindley, Brian D. Judkins, Henry A. Kelly, John Kitchin, Philip Lumley, Barry Porter, Barry C. Ross, and Cite this: J. Med. Chem. 1994, 37, 23, 3882–3885Publication Date (Print):November 1, 1994Publication History Published online1 May 2002Published inissue 1 November 1994https://pubs.acs.org/doi/10.1021/jm00049a006https://doi.org/10.1021/jm00049a006research-articleACS PublicationsRequest reuse permissionsArticle Views307Altmetric-Citations41LEARN 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
In vitro and in vivo pharmacologic activities of antisense oligonucleotides. (1991)

The use of antisense oligonucleotide as pharmacologic agents is a derivative of the central dogma of molecular biology and knowledge of the physical and chemical properties that govern the structure of nucleic acids. Oligonucleotides have been reported to inhibit the growth of a large number of viruses in cell culture, as well as the expression of numerous oncogenes, a variety of normal genes and transfected reporter genes controlled by several regulatory elements. The therapeutic activity of antisense compounds in animal disease models have also been reported. This review provides some general conclusions and trends regarding the pharmacologic action of antisense oligonucleotides, that can be formulated from studies previously reported in the literature. In addition, data is highlighted for two specific examples in which antisense oligonucleotides have demonstrated activity against herpes viruses and intracellular adhesion molecule RNA targets.
Spontaneous coupling to planar and index-confined quasimodes of Fabry–Pérot microcavities (1995)

Data are presented characterizing the spontaneous coupling to both planar and index-confined quasimodes of Fabry–Pérot microcavities. Index confinement is achieved using selective conversion of AlAs–AlxOy through ‘‘wet’’ oxidation to fabricate lateral cavity sizes as small as 2 μm diam. Spectral tuning and angular radiation patterns show the increased spontaneous coupling that results from three-dimensional confinement.
P53 AND CATHEPSIN-D ARE INDEPENDENT OF ESTABLISHED PROGNOSTIC FACTORS IN BREAST-CANCER (1992)

p53 and cathepsin D expression was investigated in 300 primary breast cancers by the avidin-biotin immunoperoxidase method using two murine monoclonal antibodies: PAb1801 and anti-procathepsin D, respectively. The frequency of p53- and cathepsin D-positive cells varied widely among different tumors and most tumors (82% and 86%) at least occasionally showed positive cells. The two biological markers were unrelated to one another, to cell proliferative rate and ploidy and were differently related to other biological and pathological features. In particular, p53 was directly related to tumor size and nodal involvement and inversely related to the presence of steroid receptors. Conversely, cathepsin D was directly related only to nodal involvement.
Vaccinia Virus H2 Protein Is an Essential Component of a Complex Involved in Virus Entry and Cell-Cell Fusion (2005)

The vaccinia virus H2R gene (VACWR 100) is conserved in all sequenced members of the poxvirus family and encodes a protein with a predicted transmembrane domain and four invariant cysteines. A recombinant vaccinia virus, in which expression of the H2 protein is stringently regulated, was unable to replicate without inducer. However, under nonpermissive conditions, all stages of virus morphogenesis appeared normal and extracellular virions were detected at the tips of actin tails. Nevertheless, virus did not spread to neighboring cells nor did syncytia form after low-pH treatment. Purified -H2 and +H2 virions from cells infected in the absence or presence of inducer, respectively, were indistinguishable in microscopic appearance and contained the same complement of major proteins, though only +H2 virions were infectious. The -H2 virions bound to cells, but their cores did not penetrate into the cytoplasm. In addition, exogenously added -H2 virions were unable to mediate the formation of syncytia after low-pH treatment. In contrast, virions lacking the A27 (p14) protein, which was previously considered to have an essential role in fusion, penetrated cells and induced extensive syncytia. The properties of H2, however, are very similar to those recently reported for the A28 protein. Moreover, coimmunoprecipitation experiments indicated an interaction between H2 and A28. Therefore, H2 and A28 are the only proteins presently known to be specifically required for vaccinia virus entry and are likely components of a fusion complex.
Molecular mechanisms of viral evasion from antibody-mediated virus neutralization in hepatitis C virus infection (2010)

Les hépatopathies liées au virus de l hépatite C (VHC) sont une cause majeure de transplantation hépatique (TH). La réinfection du greffon est systématique. Les mécanismes par lesquels le virus échappe à l immunité de l hôte pour réinfecter le greffon ne sont pas encore élucidés. Dans une étude longitudinale, nous avons démontré que les variants de VHC qui réinfectent le greffon sont caractérisés par une entrée virale augmentée et par l échappement à la neutralisation médiée par les anticorps présents dans le sérum autologue, comparé aux variants non détectés suite à la TH. Nous avons identifié 2 mutations adaptatives (G458S et C478R) dans les glycoprotéines d enveloppe E1E2 responsables de l entrée virale augmentée et de l échappement du variant hautement infectieux. Ces mutations augmentent l entrée virale en modulant de manière marquée la dépendance à CD81. Des études fonctionnelles utilisant un large panel d anticorps monoclonaux ont montrées que ces mutations définissaient un nouvel épitope conformationel médiant l échappement viral lors de l infection du greffon hépatique. De plus, par l étude de la neutralisation par l utilisation de sérums hétérologues de patients chroniquement infectés, nous avons pu montrer que cet épitope joue un rôle important dans l échappement viral en général. En conclusion, nos découvertes identifient les interactions entre l enveloppe virale et CD81 comme un facteur clé de l échappement du VHC lors de la réinfection du greffon hépatique et dévoilent un nouvel épitope médiant l échappement viral à la neutralisation par les anticorps autologues. Ces résultats permettent d approfondir la connaissance des mécanismes moléculaires de l échappement viral lors de l infection aigue du greffon hépatique et sont un premier pas pour le développement d une stratégie préventive anti-virale ciblant les interactions entre les glycoprotéines d enveloppe et les facteurs d entrée virale de l hôte.
Immunohistochemical study of tissue factor expression in normal intestine and idiopathic inflammatory bowel disease. (1993)

These observations are consistent with a tissue factor haemostatic barrier in the intestine: this barrier seems to be incomplete or defective in ulcerative colitis. Tissue factor expression by macrophages and endothelial cells may be important, particularly in the microvascular thrombosis and induration which are characteristic of Crohn's disease.
A host type I interferon response is induced by cytosolic sensing of the bacterial second messenger cyclic-di-GMP (2009)

The innate immune system responds to unique molecular signatures that are widely conserved among microbes but that are not normally present in host cells. Compounds that stimulate innate immune pathways may be valuable in the design of novel adjuvants, vaccines, and other immunotherapeutics. The cyclic dinucleotide cyclic-di-guanosine monophosphate (c-di-GMP) is a recently appreciated second messenger that plays critical regulatory roles in many species of bacteria but is not produced by eukaryotic cells. In vivo and in vitro studies have previously suggested that c-di-GMP is a potent immunostimulatory compound recognized by mouse and human cells. We provide evidence that c-di-GMP is sensed in the cytosol of mammalian cells via a novel immunosurveillance pathway. The potency of cytosolic signaling induced by c-di-GMP is comparable to that induced by cytosolic delivery of DNA, and both nucleic acids induce a similar transcriptional profile, including triggering of type I interferons and coregulated genes via induction of TBK1, IRF3, nuclear factor kappaB, and MAP kinases. However, the cytosolic pathway that senses c-di-GMP appears to be distinct from all known nucleic acid-sensing pathways. Our results suggest a novel mechanism by which host cells can induce an inflammatory response to a widely produced bacterial ligand.
Grafted cellulose strands on the surface of silica: effect of environment on reactivity (2010)

The design, synthesis and characterization of materials consisting of grafted poly(1 → 4-β-glucan) strands on silica is reported. The silanol-rich environment provided in these materials activates the glycosidic bond for hydrolysis under mild conditions.
Mechanism of electric-field-induced segregation of additives in a liquid-crystal host (2012)

The mechanism for electric-field-induced segregation of additives, containing a polar group, in a host liquid crystal is proposed. It is shown that the polarity of an applied dc electric field, or the frequency of an ac electric field, strongly influences the segregation of reactive monomers containing an ester group. An explanation of this result is offered based on the association of dissolved ions with polar groups of the reactive monomers. This association is considered to cause these types of additives to drift to the cell surface in the presence of an external electric field. The described mechanism can be applied to the segregation of a broad range of additives in a liquid-crystal host.
Enantioselective Rhodium-Catalyzed Addition of Arylboronic Acids to Alkenylheteroarenes (2010)

In the presence of a rhodium complex containing a newly developed chiral diene ligand, alkenes activated by a range of π-deficient or π-excessive heteroarenes engage in highly enantioselective conjugate additions with various arylboronic acids.
Antimicrobial Effect of Visible Light—Photoinactivation of Legionella rubrilucens by Irradiation at 450, 470, and 620 nm (2019)

Despite the high number of legionella infections, there are currently no convincing preventive measures. Photoinactivation with visible light is a promising new approach and the photoinactivation sensitivity properties of planktonic <i>Legionella rubrilucens</i> to 450, 470, and 620 nm irradiation were thus investigated and compared to existing 405 nm inactivation data for obtaining information on responsible endogenous photosensitizers. Legionella were streaked on agar plates and irradiated with different doses by light emitting diodes (LEDs) of different visible wavelengths. When irradiating bacterial samples with blue light of 450 nm, a 5-log reduction could be achieved by applying a dose of 300 J cm<sup>-</sup><sup>2</sup>, whereas at 470 nm, a comparable reduction required about 500 J cm<sup>-</sup><sup>2</sup>. For red irradiation at 620 nm, no inactivation could be observed, even at 500 J cm<sup>-</sup><sup>2</sup>. The declining photoinactivation sensitivity with an increasing wavelength is consistent with the assumption of porphyrins and flavins being among the relevant photosensitizers. These results were obtained for <i>L. rubrilucens</i>, but there is reason to believe that its inactivation behavior is similar to that of pathogenic legionella species. Therefore, this photoinactivation might lead to new future concepts for legionella reduction and prevention in technical applications or even on or inside the human body.
Studies on Fluorinated Pyrimidines. XIV. The Synthesis of Derivatives of 5-Fluoro-2'-deoxyuridine 5'-Phosphate and Related Compounds1 (1962)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies on Fluorinated Pyrimidines. XIV. The Synthesis of Derivatives of 5-Fluoro-2'-deoxyuridine 5'-Phosphate and Related Compounds1David C. Remy, A. V. Sunthankar, and Charles HeidelbergerCite this: J. Org. Chem. 1962, 27, 7, 2491–2500Publication Date (Print):July 1, 1962Publication History Published online1 May 2002Published inissue 1 July 1962https://pubs.acs.org/doi/10.1021/jo01054a046https://doi.org/10.1021/jo01054a046research-articleACS PublicationsRequest reuse permissionsArticle Views142Altmetric-Citations17LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Evaluation of a New Computer Intervention to Teach People with Autism or Asperger Syndrome to Recognize and Predict Emotions in Others (2001)

This randomized controlled trial looked at the effect of a new computer program designed to teach people with autistic spectrum disorders to better recognize and predict emotional responses in others. Two groups of 11 children (age 12-18) with autism or Asperger syndrome at two special schools participated: one group used the computer program for 10 half-hour sessions over 2 weeks. Within-program data showed a significant reduction in errors made from first to last use. Students were assessed pre- and post-intervention using facial expression photographs, cartoons depicting emotion-laden situations, and non-literal stories. Scores were not related to age or verbal ability. The experimental group made gains relative to the control group on all three measures. Gains correlated significantly with the number of times the computer program was used and results suggest positive effects. Further research could assess whether these gains generalized into real life or improved performance on theory of mind measures.
Fabrication of scaffold-free contractile skeletal muscle tissue using magnetite-incorporated myogenic C2C12 cells (2010)

We have fabricated a functional skeletal muscle tissue using magnetite-incorporated myogenic cell line C2C12 and a magnetic field. Magnetite-incorporated C2C12 cells were patterned linearly on a monolayer of fibroblast NIH3T3 cells, using a magnetic field concentrator. After induction of differentiation, the C2C12 cells fused and formed multi-nucleated myotubes. The 3T3 layer became detached in a sheet-like manner after cultivation in differentiation medium for 5-8 days. When two separate collagen films were placed on a culture dish as tendon structures, a cylindrical construct was formed. Histological observation of the fabricated cylindrical tissue revealed the presence of multinucleate cells within it. Immunofluorescence staining of the construct showed the presence of sarcomere structures within the construct. Western blot analysis showed that muscle proteins were expressed in the construct. When the construct was stimulated with electric pulses, it exhibited active tension of approximately 1 microN. These results demonstrate that functional skeletal muscle tissue was formed through magnetic force-based tissue engineering. This is the first report of fabrication of skeletal muscle tissue with active tension-generating capability using magnetic force-based tissue engineering. The scaffold-free skeletal muscle tissue engineering technique presented in this study will be useful for regenerative medicine, drug screening or use as a bio-actuator.
Green tea extract enhances parieto-frontal connectivity during working memory processing (2014)

Our findings provide first evidence for the putative beneficial effect of green tea on cognitive functioning, in particular, on working memory processing at the neural system level by suggesting changes in short-term plasticity of parieto-frontal brain connections. Modeling effective connectivity among frontal and parietal brain regions during working memory processing might help to assess the efficacy of green tea for the treatment of cognitive impairments in psychiatric disorders such as dementia.
Inhibition of arginase by in alveolar macrophages: implications for the utilization of l‐arginine for nitric oxide synthesis (1995)

The hypothesis was investigated that the nitric oxide (NO) synthase intermediate, NG-hydroxy-L-arginine (HOArg), is an arginase inhibitor in rabbit or rat alveolar macrophages. Exogenously applied HOArg strongly inhibited the arginase activity present in these cells (IC50 > or = 15 microM), and attenuated L-[3H]arginine transport (IC50 > or = 500 microM) in rabbit alveolar macrophages. Moreover, up to 37 microM HOArg were detected in the conditioned medium, but not in the lysate, of rat alveolar macrophages exposed to bacterial lipopolysaccharide for 18 h. HOArg may thus be a potent endogenous arginase inhibitor in these cells which increases the availability of L-arginine for NO biosynthesis.
Rainbow Color Map (Still) Considered Harmful (2007)

In this article, we reiterate the characteristics that make the rainbow color map a poor choice, provide examples that clearly illustrate these deficiencies even on simple data sets, and recommend better color maps for several categories of display. The goal is to make the rainbow color map as rare in visualization as the goto statement is in programming - which complicates the task of analyzing and verifying program correctness