gebhart/patrepeval huggingface dataset:
Hepatocyte growth factor/scatter factor mediates angiogenesis through positive VEGF and negative thrombospondin 1 regulation (2003)

Hepatocyte growth factor/scatter factor (HGF/SF), acting through the Met receptor, plays an important role in most human solid tumors, and inappropriate expression of this ligand-receptor pair is often associated with poor prognosis. The molecular basis for the malignant potential of the HGF/SF-Met signal in cancer cells has mostly been attributed to its mitogenic and invasive properties. However, HGF/SF also induces angiogenesis, but the signaling mechanism has not been fully explained, nor has this activity been directly associated with HGF/SF-Met-mediated tumorigenesis. It is known that HGF/SF induces in vitro expression of vascular endothelial growth factor (VEGF), a key agonist of tumor angiogenesis; by contrast, thrombospondin 1 (TSP-1) is a negative regulator of angiogenesis. Here, we show that, in the very same tumor cells, in addition to inducing VEGF expression, HGF/SF dramatically down-regulates TSP-1 expression. We show that TSP-1 shut-off plays an important, extrinsic role in HGF/SF-mediated tumor development, because ectopic expression of TSP-1 markedly inhibits tumor formation through the suppression of angiogenesis. Interestingly, although VEGF-induced expression is sensitive to inhibitors of several pathways, including mitogen-activated protein kinase, phosphoinositide 3-kinase, and signal transducer and activator of transcription 3, TSP-1 shut-off by HGF/SF is prevented solely by inhibiting mitogen-activated protein kinase activation. These studies identify HGF/SF as a key switch for turning on angiogenesis. They suggest that TSP-1 is a useful antagonist to tumor angiogenesis and that it may have therapeutic value when used in conjunction with inhibitors of VEGF.
A Distributed Framework for NLP-Based Keyword and Keyphrase Extraction From Web Pages and Documents (2015)

The recent growth of the World Wide Web at increasing rate and speed and the number of online available resources populating Internet represent a massive source of knowledge for various research and business interests. Such knowledge is, for the most part, embedded in the textual content of web pages and documents, which is largely represented as unstructured natural language formats. In order to automatically ingest and process such huge amounts of data, single-machine, non-distributed architectures are proving to be inefficient for tasks like Big Data mining and intensive text processing and analysis. Current Natural Language Processing (NLP) systems are growing in complexity, and computational power needs have been significantly increased, requiring solutions such as distributed frameworks and parallel computing programming paradigms. This paper presents a distributed framework for executing NLP related tasks in a parallel environment. This has been achieved by integrating the APIs of the widespread GATE open source NLP platform in a multi-node cluster, built upon the open source Apache Hadoop file system. The proposed framework has been evaluated against a real corpus of web pages and documents.
Crystal and Molecular Structure of an Iodo‐derivative of the Cyclic Undecapeptide Cyclosporin A (1976)

Abstract The crystal structure of an iodo‐derivative of cyclosporin A has been determined in order to elucidate the constitution of this cyclic undecapeptide. Crystals of iodocyclosporin A are monoclinic, a = 10.475(5), b = 19.60(1), c = 21.04(1) Å, β 99.35(2)°, space group P 2 1 (C , No. 4). The structure was solved by the heavy atom method and refined by block‐diagonal least‐squares analysis to a final R ‐factor of 0.135 with hydrogen atoms in calculated positions. The cyclic peptide has a conformation which is partly β‐pleated sheet and partly open loop. The structure analysis demonstrates for the first time the reality of a new type of dipeptide hydrogen‐bonding, predicted by Pullman from MO calculations and leading to a conformation described by him as C .
Joint optimization of wrapper generation and template detection (2007)

Many websites have large collections of pages generated dynamically from an underlying structured source like a database. The data of a category are typically encoded into similar pages by a common script or template. In recent years, some value-added services, such as comparison shopping and vertical search in a specific domain, have motivated the research of extraction technologies with high accuracy. Almost all previous works assume that input pages of a wrapper induction system conform to a common template and they can be easily identified in terms of a common schema of URL. However, we observed that it is hard to distinguish different templates using dynamic URLs today. Moreover, since extraction accuracy heavily depends on how consistent input pages are, we argue that it is risky to determine whether pages share a common template solely based on URLs. Instead, we propose a new approach that utilizes similarity between pages to detect templates. Our approach separates pages with notable inner differences and then generates wrappers, respectively. Experimental results show that our proposed approach is feasible and effective for improving extraction accuracy.
Palladium(0)-based approach to functionalized C-glycopyranosides (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPalladium(0)-based approach to functionalized C-glycopyranosidesMohamed Brakta, Paul Lhoste, and Denis SinouCite this: J. Org. Chem. 1989, 54, 8, 1890–1896Publication Date (Print):April 1, 1989Publication History Published online1 May 2002Published inissue 1 April 1989https://pubs.acs.org/doi/10.1021/jo00269a026https://doi.org/10.1021/jo00269a026research-articleACS PublicationsRequest reuse permissionsArticle Views454Altmetric-Citations79LEARN 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
Comparison of Normal and CLL Lymphocyte Surface Ig Determinants Using Peroxidase-labeled Antibodies. I. Detection and Quantitation of Light Chain Determinants (1974)

Abstract Chronic lymphocytic leukemia (CLL) and normal human blood lymphocytes were investigated with regard to their membrane-associated light (L) chains. Peroxidase-labeled anti-kappa or anti-lambda antibodies were used to visualize by light microscopy the cells bearing L chain determinants. In addition, the activity of the enzyme coupled to the antibody was measured spectrophotometricly in order to determine the number of antigenic determinants on each positive cell. The results demonstrated that 16%-25% of lymphocytes from six normal control subjects were positive for kappa chains, and 4%-10% were positive for lambda chains. The average number of antigenic sites on the surface of each positive cell was calculated to be 90,000. Lymphocytes of each of the 14 CLL patients studied carried either kappa or lambda antigenic determinants on their surface, but not both; 50%-70% of the lymphocytes were stained. The average number of antigenic sites per positive CLL was calculated to be 9000. These results confirm previously reported studies indicating that CLL is a monoclonal proliferative disease. In addition, the quantitative results demonstrate that the CLL lymphocyte surface membrane bears, on the average, only 10% of the L chain determinants present on the normal lymphocyte.
Parkinson's Disease (2009)

Accumulating evidence suggests that sporadic Parkinson's disease (sPD) has a long prodromal period during which several nonmotor features develop; in particular, impairment of olfaction, vagal dysfunction, and sleep disorder. Early sites of Lewy pathology are the olfactory bulb and enteric plexuses of the foregut. We propose that a neurotropic pathogen, probably viral, enters the brain via two routes: (a) nasal, with anterograde progression into the temporal lobe; and (b) gastric, secondary to swallowing of nasal secretions in saliva. These secretions might contain a neurotropic pathogen that, after penetration of the epithelial lining, could enter axons of the Meissner's plexus and via transsynaptic transmission reach the preganglionic parasympathetic motor neurons of the vagus nerve. This would allow retrograde transport into the medulla and from here into the pons and midbrain until the substantia nigra is reached and typical aspects of disease commence. Evidence for this theory from the perspective of olfactory and autonomic dysfunction is reviewed and the possible routes of pathogenic invasion are considered. It is concluded that the most parsimonious explanation for the initial events of sPD is pathogenic access to the brain through the foregut and nose-hence the term "dual hit."
A model to enable application-scoped access control as a service for IoT using OAuth 2.0 (2017)

Access Control is crucial for security management, but in the context of the Internet of Things it cannot be implemented the same way as traditional systems do. Indeed, devices that make the Internet of Things impose some constraints that encourage the design of new access control mechanisms, which should provide flexibility of configuration, as well as support several authorization scopes at the same time, yet being computationally light, dynamic and scalable in order to be ready for the forthcoming Cloud Computing paradigm. In this paper we propose an authorization model that is based on the OAuth 2.0 protocol. From the point of view of the identity provider, this model allows managing roles and permissions for an application-scoped authorization, to enable more flexible scenarios in which multiple tenants take part. With regard to devices, the OAuth 2.0 makes authorization extremely light, because all the required information is provided with a token. Considering all this, authorization management is completely delegated to an external system, so that an as-a-service access control mechanism is provided. The proposed model complies with the security, flexibility and performance requirements that are needed in the Internet of Things paradigm.
Glycoengineered Pichia produced anti-HER2 is comparable to trastuzumab in preclinical study (2011)

Mammalian cell culture systems are used predominantly for the production of therapeutic monoclonal antibody (mAb) products. A number of alternative platforms, such as Pichia engineered with a humanized N-linked glycosylation pathway, have recently been developed for the production of mAbs. The glycosylation profiles of mAbs produced in glycoengineered Pichia are similar to those of mAbs produced in mammalian systems. This report presents for the first time the comprehensive characterization of an anti-human epidermal growth factor receptor 2 (HER2) mAb produced in a glycoengineered Pichia, and a study comparing the anti-HER2 from Pichia, which had an amino acid sequence identical to trastuzumab, with trastuzumab. The comparative study covered a full spectrum of preclinical evaluation, including bioanalytical characterization, in vitro biological functions, in vivo anti-tumor efficacy and pharmacokinetics in both mice and non-human primates. Cell signaling and proliferation assays showed that anti-HER2 from Pichia had antagonist activities comparable to trastuzumab. However, Pichia-produced material showed a 5-fold increase in binding affinity to FcγIIIA and significantly enhanced antibody dependant cell-mediated cytotoxicity (ADCC) activity, presumably due to the lack of fucose on N-glycans. In a breast cancer xenograft mouse model, anti-HER2 was comparable to trastuzumab in tumor growth inhibition. Furthermore, comparable pharmacokinetic profiles were observed for anti-HER2 and trastuzumab in both mice and cynomolgus monkeys. We conclude that glycoengineered Pichia provides an alternative production platform for therapeutic mAbs and may be of particular interest for production of antibodies for which ADCC is part of the clinical mechanism of action.
Plasminogen Activation Is Stimulated by Prion Protein and Regulated in a Copper-Dependent Manner (2002)

Prion diseases are associated with the conversion of the normal prion protein, PrP(C), to the infectious disease form PrP(Sc). Discrimination between these isoforms would significantly enhance diagnosis of these diseases, and it has recently been reported that PrP(Sc) is specifically recognized by the serine protease zymogen plasminogen (Fischer et al. (2000) Nature 408, 479). Here we have tested the hypothesis that PrP is a regulator of the plasminogen activation system. The effect of recombinant PrP, either containing copper (holo-PrP) or devoid of it (apo-PrP), on plasminogen activation by both uPA and tPA was determined. PrP had no effect on plasminogen activation by uPA. By contrast, the activity of tPA was stimulated by up to 280-fold. This was observed only with the apo-PrP isoforms. The copper-binding octapeptide repeat region of PrP was involved in the effects, as a mutant lacking this region failed to stimulate plasminogen activation, although a synthetic peptide corresponding to this region was unable to stimulate tPA activity. Competition experiments demonstrated that, in addition to plasminogen binding, the stimulation required a high-affinity interaction between tPA and PrP (K(d) < 2.5 nM). Kinetic analysis revealed a template mechanism for the stimulation, suggesting independent binding sites for tPA and plasminogen. Lack of copper-binding may be an early event in the conversion of PrP(C) to PrP(Sc), and our data therefore suggest that tPA-catalyzed plasminogen activation may provide the basis for a sensitive detection system for the early stages of prion diseases and also play a role in the pathogenesis of these diseases.
Object Detection Free Instance Segmentation With Labeling Transformations (2016)

Instance segmentation has attracted recent attention in computer vision and existing methods in this domain mostly have an object detection stage. In this paper, we study the intrinsic challenge of the instance segmentation problem, the presence of a quotient space (swapping the labels of different instances leads to the same result), and propose new methods that are object proposal- and object detection- free. We propose three alternative methods, namely pixel-based affinity mapping, superpixel-based affinity learning, and boundary-based component segmentation, all focusing on performing labeling transformations to cope with the quotient space problem. By adopting fully convolutional neural networks (FCN) like models, our framework attains competitive results on both the PASCAL dataset (object-centric) and the Gland dataset (texture-centric), which the existing methods are not able to do. Our work also has the advantages in its transparency, simplicity, and being all segmentation based.
Electron cyclotron resonance plasma ion source for material depositions (1998)

An electron cyclotron resonance (ECR) plasma has been used in conjunction with solid metal targets for deposition of various metal and oxide compounds. A large microwave system provides dense and high-quality films at low gas pressures with a plasma generation independent on the sputtering process. The 2.45 GHz microwave power is introduced in the reactor via two separate rectangular waveguides and the plasma cross section is 20×5 cm2 in area. High plasma densities over 4×1011 cm−3 were measured by interferometry. An iron deposition rate of 2000 Å/mn has been achieved. Transparent aluminum oxide Al2O3 films with a refractive index of 1.57 were obtained under a deposition rate of 150 Å/mn. The association of several rectangular plasma chambers similar to the elementary plasma source used in this work is discussed. Direct metal ion production was also investigated in such a waveguide plasma source. Metal vaporization and ionization have been provided by energetic electrons from the ECR surface. Thus, a Zn+ ion current density of 30 mA/cm2 has been reached without support gas.
Up-Regulation of GITRL on Dendritic Cells by WGP Improves Anti-Tumor Immunity in Murine Lewis Lung Carcinoma (2012)

These findings suggest that particulate β-glucans can be used as an immunomodulator to stimulate potent T cell-mediated adaptive immunity while down-regulate suppressive immune activity via GITR/GITRL interaction, leading to a more efficient defense mechanism against tumor development.
Nucleotide sequence of cDNA encoding the catalytic subunit of phosphorylase kinase from rat soleus muscle (1988)

Phosphorylase kinase is a key enzyme of glycogenolysis, with a hexadecameric protein structure Of W0464 The -t subunit is catalytic and the others are regulatory. Two isozymes exist, w and r, disting'uished by the size of their a subunits; the other subunits are of apparently equal size in the two isozymes. Isozyme distribution in skeletal muscle is correlated with
Synthesis of Mono- and Dinuclear Vanadium Complexes and Their Reactivity toward Dehydroperoxidation of Alkyl Hydroperoxides (2017)

Several vanadium(V) complexes with either dipic-based or Schiff base ligands were synthesized. The complexes were fully characterized by elemental analysis, IR, <sup>1</sup>H, <sup>13</sup>C, and <sup>51</sup>V NMR spectroscopy, as well as mass spectrometry and X-ray diffraction. Furthermore, they were tested toward their catalytic deperoxidation behavior and a significant difference between 4-heptyl hydroperoxide and cyclohexyl hydroperoxide was observed. In the case of 4-heptyl hydroperoxide, the selectivity toward the corresponding ketone was higher than with cyclohexyl hydroperoxide. DFT calculations performed on the vanadium complex showed that selective decomposition of secondary hydroperoxides with vanadium(V) to yield the corresponding ketone and water is indeed energetically feasible. The computed catalytic path, involving cleavage of the O-O bond, hydrogen transfer, release of ketone/water, and finally addition of hydroperoxide, can proceed without the generation of radical species.
Water as a plasticizer: physico-chemical aspects of low-moisture polymeric systems (1988)

'Water is the most ubiquitous plasticizer in our world.' It has become well established that plasticization by water affects the glass-to-rubber transition temperatures (Tg) of many synthetic and natural amorphous polymers (particularly at low moisture contents), and that Tg depression can be advantageous or disadvantageous to material properties, processing, and stability. Eisenberg has stated that 'the glass transition is perhaps the most important single parameter which one needs to know before one can decide on the application of the many non-crystalline (synthetic) polymers that are now available.' Karel has noted that 'water is the most important… plasticizer for hydrophilic food components.' The physicochemical effect of water, as a plasticizer, on the Tg of starch and other amorphous or partially-crystalline (PC) polymeric food materials has been increasingly discussed in several recent reviews and reports, dating back to the pioneering doctoral research of van den Berg.
An improved iterative reconstruction algorithm for traveltime tomography (1996)

Traveltime tomography is a technique to reconstruct acoustic, seismic, or electromagnetic wave-speed distributions from first arrival traveltime data. The ray paths that should be used for tomographic techniques strongly depend on the wave-speed distribution. In this paper, a new method is proposed for finding out the ray paths from Fermat's principle, that means the traveltime of the ray path should be a minimum value. The problem of finding out the ray path is actually an optimum problem. Our new method uses the idea to find out the shortest path in a weighted directed graph to solve the problem. The ray paths found out by this method are used in the iterative reconstruction algorithm. Computer simulation result produced by this reconstruction algorithm is better than that by the conventional ones. It also shows that the new algorithm is effective with good convergency and stability.
Rapid detection of human chromosome 21 aberrations by in situ hybridization. (1988)

Plasmid clones containing up to 94 kilobases of single-copy DNA from band q22.3 of chromosome 21 and a complete pool of insert DNA from a chromosome 21 recombinant library have been used to rapidly detect numerical and structural aberrations of chromosome 21 by in situ hybridization in both metaphase and interphase cells. A trisomic karyotype, diagnostic of Down syndrome, is readily detected in nonmitotic cells because the majority of their nuclei exhibit three discrete foci of hybridization, in contrast to normal diploid cells, which show two foci. Chromosomal translocations involving chromosome 21 sequences were also detected with these probes, and the intranuclear location of 21q22.3 DNA sequences in "normal" human brain neurons was established with the plasmid DNA probe set. These results suggest that chromosome 21-specific probes may have utility in clinical diagnostics, especially by facilitating the direct analysis of interphase cells.
A Remarkably Efficient Markovnikov Hydrochlorination of Olefins and Transformation of Nitriles into Imidates by Use of AcCl and an Alcohol (2005)

Abstract HCl generated by mixing AcCl with EtOH brings about Markovnikov hydrochlorination of olefins in excellent yields. The products are isolated in states of high purity simply by removal of the volatile components under reduced pressure. Further, nitriles are transformed into imidate hydrochlorides on similar treatment with AcCl and an alcohol. This procedure for nitrile‐imidate transformation is much more efficient than that used previously, which involved continuous passing of HCl gas into the solution of a nitrile in a solvent such as Et 2 O or benzene and an alcohol until one equivalent had been absorbed. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2005)
Receptor for advanced glycation end products-binding COOH-terminal motif of amphoterin inhibits invasive migration and metastasis. (2002)

Amphoterin has been suggested to regulate invasive process extension and cell migration in tumor cells and embryonic neurons through binding to receptor for advanced glycation end products (RAGE), a multiligand transmembrane receptor belonging to the immunoglobulin superfamily. In this study, we identify a COOH-terminal motif in amphoterin (amino acids 150-183) that is responsible for RAGE binding. We show that as a surface-bound ligand, this part of amphoterin is sufficient to induce RAGE-dependent process extension, suggesting a role in the regulation of cell motility. When applied in solution, the RAGE-binding COOH-terminal motif of amphoterin efficiently inhibits process extension and transendothelial migration of tumor cells. Furthermore, in an in vivo model, the corresponding synthetic peptide significantly suppresses formation of lung metastases. Taken together, these results suggest that amphoterin binds to RAGE through a COOH-terminal motif that can be used as an efficient inhibitor to block invasive migration of tumor cells.