gebhart/patrepeval huggingface dataset:
Isolation and characterization of a putative collagen receptor from Staphylococcus aureus strain Cowan 1 (1989)

In a previous study we demonstrated that cells of Staphylococcus aureus strain Cowan bind 125I-collagen in a receptor-ligand type of interaction (Speziale, P., Raucci, G., Visai, L., Switalski, L.M., Timpl, R., and Höök, M. (1986) J. Bacteriol. 167, 77-81). In the present communication we report on the isolation and preliminary characterization of a putative collagen receptor from a lysate of S. aureus strain Cowan. Antibodies raised against a collagen receptor positive strain inhibit the binding of 125I-collagen to bacterial cells, whereas antibodies raised against a collagen receptor negative strain were without effect. Solubilized cell surface components did not exhibit any measurable affinity for collagen-Sepharose. However, the inhibitory effect of the antibodies against bacterial cells was neutralized by the lysate from a receptor-positive but not receptor-negative strain. A collagen receptor assay was designed based on this observation and used to develop a receptor purification protocol involving anion exchange chromatography, ammonium sulfate precipitation, and gel chromatography. Using this procedure a protein with an apparent Mr of 135,000 was purified. This protein which was present on a collagen receptor-positive strain but not on a receptor-negative strain could completely neutralize the inhibitory activity of the antibodies raised against S. aureus strain Cowan. Furthermore, antibodies raised against the 135-kDa protein inhibited the binding of collagen to bacteria, and this protein is tentatively identified as a collagen receptor.
High-dose methotrexate is beneficial in parenchymal brain masses of uncertain origin suspicious for primary CNS lymphoma (2007)

In patients with parenchymal brain masses of uncertain origin responsive to corticosteroids, primary CNS lymphoma (PCNSL) should be considered. PCNSL is a rare but aggressive brain tumor that is highly sensitive to high-dose methotrexate (HDMTX)-based chemotherapy. We report a series of six patients with brain masses without histologic confirmation suspicious for PCNSL based on clinical and radiomorphologic criteria after exclusion of some infectious conditions. All patients were treated with HDMTX. We observed two complete responses, two partial responses, and one stable disease. One patient had progressive disease and received rescue whole-brain irradiation. All patients were alive without disease progression 12-48 months after HDMTX start. No symptoms of late neurotoxicity have occurred so far. The response and survival data in this small series of patients are encouraging and suggest a benefit for patients with suspected PCNSL after initial treatment with HDMTX.
Interleukin-17-induced Gene Expression in Articular Chondrocytes Is Associated with Activation of Mitogen-activated Protein Kinases and NF-κB (1998)

This study examines intracellular signaling events associated with the activation of chondrocytes by the cytokine interleukin-17 (IL-17). Stimulation of normal human articular chondrocytes with IL-17 induced nitric oxide (NO) production, concomitant with an increase in transcripts and de novo translation products of the inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) genes. Several other genes associated with inflammation and cartilage degradation, such as IL-1beta, IL-6, and stromelysin, were also up-regulated in IL-17-treated chondrocytes. Among signaling events displaying early response to IL-17 in chondrocytes were the mitogen-activated protein (MAP) kinases ERK1, ERK2, JNK, and p38. DNA binding activity of NF-kappaB was also significantly induced. IL-17 effects on NO release, as well as iNOS, COX-2, and IL-6 protein expression, were inhibited by the anti-inflammatory drug dexamethasone. Importantly, dexamethasone blunted IL-17-dependent activation of MAP kinases, suggesting a mechanistic relationship between these activities and the aforementioned gene expression responses. Similar effects of a lesser extent were observed with the p38-specific inhibitor SB203580. These results suggest that IL-17 activation of chondrocytes is associated with and depends at least in part on the activation of MAP kinases and NF-kappaB.
An Information-Maximization Approach to Blind Separation and Blind Deconvolution (1995)

We derive a new self-organizing learning algorithm that maximizes the information transferred in a network of nonlinear units. The algorithm does not assume any knowledge of the input distributions, and is defined here for the zero-noise limit. Under these conditions, information maximization has extra properties not found in the linear case (Linsker 1989). The nonlinearities in the transfer function are able to pick up higher-order moments of the input distributions and perform something akin to true redundancy reduction between units in the output representation. This enables the network to separate statistically independent components in the inputs: a higher-order generalization of principal components analysis. We apply the network to the source separation (or cocktail party) problem, successfully separating unknown mixtures of up to 10 speakers. We also show that a variant on the network architecture is able to perform blind deconvolution (cancellation of unknown echoes and reverberation in a speech signal). Finally, we derive dependencies of information transfer on time delays. We suggest that information maximization provides a unifying framework for problems in "blind" signal processing.
High Affinity Binding of Receptor-associated Protein to Heparin and Low Density Lipoprotein Receptor-related Protein Requires Similar Basic Amino Acid Sequence Motifs (2001)

The 39-kDa receptor-associated protein (RAP) is a specialized chaperone for members of the low density lipoprotein receptor gene family, which also binds heparin. Previous studies have identified a triplicate repeat sequence within RAP that appears to exhibit differential functions. Here we generated a series of truncated and site-directed RAP mutants in order to define the sites within RAP that are important for interacting with heparin and low density lipoprotein receptor-related protein (LRP). We found that high affinity binding of RAP to heparin is mediated by the carboxyl-terminal repeat of RAP, whereas both the carboxyl-terminal repeat and a combination of amino and central repeats exhibit high affinity binding to LRP. Several motifs were found to mediate the binding of RAP to heparin, and each contained a cluster of basic amino acids; among them, an intact R(282)VSR(285)SR(287)EK(289) motif is required for high affinity binding of RAP to heparin, whereas two other motifs, R(203)LR(205)R(206) and R(314)ISR(317)AR(319), also contribute to this interaction. We also found that intact motifs of both R(203)LR(205)R(206) and R(282)VSR(285)SR(287)EK(289) are required for high affinity binding of RAP to LRP, with the third motif, R(314)ISR(317)AR(319), contributing little to RAP-LRP interaction. We conclude that electrostatic interactions likely contribute significantly in the binding of RAP to both heparin and LRP and that high affinity interaction with both heparin and LRP appears to require mostly overlapping sequence motifs within RAP.
Verifiable (t, n) threshold signature scheme based on elliptic curve (2005)

Based on the difficulty of solving the ECDLP (elliptic curve discrete logarithm problem) on the finite field, we present a (t, n) threshold signature scheme and a verifible key agreement scheme without trusted party. Applying a modified clliptic curve signature equation, we get a more efficient signature scheme than the existing ECDSA (elliptic curve digital signature algorithm) from the computability and security view. Our scheme has a shorter key, faster computation, and better security. Based on the difficulty of solving the ECDLP (elliptic curve discre logarithm problem) on the finite field, we present a (t, n) threshold signature scheme and a verifiable key agreement scheme without trusted party. Applying a modified clliptic curve signature equation, we get a more efficient signature scheme than the existing ECDSA (elliptic curve digital signature algorithm) form the computability and security view. Our scheme has a shorter key, faster computation, and better security.
Phospholipase A2 engineering. 3. Replacement of lysine-56 by neutral residues improves catalytic efficiency significantly, alters substrate specificity, and clarifies the mechanism of interfacial recognition (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhospholipase A2 engineering. 3. Replacement of lysine-56 by neutral residues improves catalytic efficiency significantly, alters substrate specificity, and clarifies the mechanism of interfacial recognitionJoseph P. Noel, Tiliang Deng, Kelly J. Hamilton, and Ming Daw TsaiCite this: J. Am. Chem. Soc. 1990, 112, 9, 3704–3706Publication Date (Print):April 1, 1990Publication History Published online1 May 2002Published inissue 1 April 1990https://pubs.acs.org/doi/10.1021/ja00165a090https://doi.org/10.1021/ja00165a090research-articleACS PublicationsRequest reuse permissionsArticle Views66Altmetric-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
Flavoenzyme-Catalyzed Atropo-Selective N,C-Bipyrrole Homocoupling in Marinopyrrole Biosynthesis (2012)

Axially chiral biaryl compounds are frequently encountered in nature where they exhibit diverse biological properties. Many are biphenols that have C-C or C-O linkages installed by cytochrome P450 oxygenases that control the regio- and stereoselectivity of the intermolecular coupling reaction. In contrast, bipyrrole-coupling enzymology has not been observed. Marinopyrroles, produced by a marine-derived streptomycete, are the first 1,3'-bipyrrole natural products. On the basis of marinopyrrole's unusual bipyrrole structure, we explored its atropo-selective biosynthesis in Streptomyces sp. CNQ-418 in order to elucidate the N,C-bipyrrole homocoupling enzymology. Through a series of genetic experiments involving the discovery and heterologous expression of marinopyrrole biosynthesis genes, we report that two flavin-dependent halogenases catalyze the unprecedented homocoupling reaction.
A balanced approach towards healthy eating in autism (1998)

Background: This audit was undertaken to investigate the dietary intake and food‐related behaviour of children diagnosed within the autistic spectrum continuum. It was hoped to understand the difficulties faced by parents and carers and to offer a holistic service. Method: Parents of 17 autistic children aged 42–117 months were interviewed and data collected by 3‐day dietary recall and food frequency questionnaire. Weight and height measurements for each child were obtained. South Derbyshire Ethics Committee approval was given. Results: Nutrient intakes on analysis fell below reference nutrient intake (RNI) levels for 53% (nine) children in one or more of the following nutrients: vitamin C, iron, vitamin D, niacin, riboflavin, vitamin B 6 , calcium and zinc. One child fell below the lower reference nutrient intake (LRNI) for iron and three children aged under 4 years did not meet the LRNI for vitamin D from dietary sources. Excessive milk consumption in 13 children raised calcium intake to levels above 200% of RNI levels. Conclusion: Eating habits were extremely prescriptive. Food preferences were specific for ‘dry’ or ‘wet’ forms, colour, shaped retail products and even brand packaging. Food refusal and introduction of new foods were cited as the most difficult problems faced by parents. Oral sensitivity, poor oral motor movements and difficult eating behaviours were identified and an integrated service involving dietitian, speech therapist and paediatric clinical psychologist was advocated.
Focused-Ion-Beam Fabrication of Slanted Grating Couplers in Silicon-on-Insulator Waveguides (2007)

We have designed and fabricated an efficient grating coupler for coupling light between optical fibers and silicon-on-insulator waveguides. The coupler consists of 88-nm-wide slits, etched at an angle of 58deg to the surface normal. They are defined by direct etching with a focused ion beam, using iodine gas and an alumina hard mask. The measured efficiency is 46%
Effect of amorphous calcium phosphate and silver nanocomposites on dental plaque microcosm biofilms (2012)

A dental composite containing amorphous calcium phosphate nanoparticles (NACP) was developed that released calcium (Ca) and phosphate (PO(4)) ions and possessed acid-neutralization capability. There has been little study on incorporation of antibacterial agents into calcium phosphate composites. The objective of this study was to investigate the effect of silver nanoparticle (NAg) mass fraction in NACP nanocomposite on mechanical properties and dental plaque microcosm biofilm for the first time. NACP nanoparticles of 116 nm were synthesized via a spray-drying technique. NAg nanoparticles were synthesized using Ag 2-ethylhexanoate and 2-(tert-butylamino)ethyl methacrylate, yielding NAg of particle size of 2.7 nm that were well-dispersed in the resin. Five NACP nanocomposites were fabricated with NAg mass fractions of 0, 0.028, 0.042, 0.088, and 0.175%, respectively. Mechanical properties of NACP nanocomposites containing 0-0.042% of NAg matched those of a commercial composite without antibacterial activity. Live/dead assay of dental plaque microcosm biofilms showed complete coverage with live bacteria on commercial composite. However, there were increasingly more dead bacteria with higher NAg content in the NACP nanocomposite. Colony-forming unit (CFU) counts for total microorganisms, total streptococci, and mutans streptococci for NACP nanocomposite with 0.042% NAg were about 1/4 those of commercial composite. Lactic acid production on NACP nanocomposite with 0.042% NAg was 1/3 that on commercial composite. In conclusion, novel NACP-NAg nanocomposites were developed which possessed good mechanical properties and potent antibacterial properties, with substantially reduced biofilm viability and lactic acid production. Hence, the NACP-NAg nanocomposites are promising for dental restorations with remineralizing and antibacterial capabilities.
Automatic presentation of multimedia documents using relational grammars (1994)

This paper describes an approach to the automatic presentation of multimedia documents based on parsing and syntax-directed translation using Relational Grammars. This translation is followed by a constraint solving mechanism to create the final layout. Grammatical rules provide the mechanism for mapping from a representation of the content of a presentation to forms that specify the media objects to be realized. These realization forms include sets of spatial and temporal constraints between elements of the presentation. Individual grammars encapsulate the “look and feel” of a presentation and can be used as generators of that style. By making the grammars sensitive to the requirements of the output medium, parsing can introduce flexibility into the information realization process.
Eosinophilic granulomatosis with polyangiitis (Churg–Strauss): state of the art (2013)

Eosinophilic granulomatosis with polyangiitis (Churg-Strauss, EGPA) is a systemic small-vessel vasculitis associated with asthma and eosinophilia. Histology of EGPA shows tissue eosinophilia, necrotizing vasculitis, and eosinophil-rich granulomatous inflammation. EGPA commonly presents with upper airway tract and lung involvement, peripheral neuropathy, cardiac and skin lesions. Antineutrophil cytoplasmic antibodies (ANCA) are positive in ~40% of the cases and more often in patients with clinical manifestations due to small-vessel vasculitis. The pathogenesis of EGPA is multifactorial: the disease can be triggered by exposure to allergens or drugs, but a genetic background has also been recognized, particularly an association with HLA-DRB4. Th2 responses are prominent, with up-regulation of IL-4, IL-13, and IL-5; however, Th1 and Th17 responses are not negligible. Eosinophils are activated, have a prolonged lifespan and probably cause tissue damage by releasing their granule proteins; their tissue recruitment can be regulated by chemokines such as eotaxin-3 and CCL17. Humoral immunity is also dysregulated, as demonstrated by prominent IgG4 and IgE responses. EGPA promptly responds to glucocorticoid therapy, although combinations of glucocorticoids and immunosuppressants (e.g., cyclophosphamide, azathioprine) are eventually required in most cases. Newer therapeutic options include the anti-IL5 antibody mepolizumab, whose efficacy has been described in small clinical trials, and the B-cell-depleting agent rituximab, reported in several case series.
Trypsin IV, a Novel Agonist of Protease-activated Receptors 2 and 4 (2004)

Certain serine proteases signal to cells by cleaving protease-activated receptors (PARs) and thereby regulate hemostasis, inflammation, pain and healing. However, in many tissues the proteases that activate PARs are unknown. Although pancreatic trypsin may be a physiological agonist of PAR(2) and PAR(4) in the small intestine and pancreas, these receptors are expressed by cells not normally exposed pancreatic trypsin. We investigated whether extrapancreatic forms of trypsin are PAR agonists. Epithelial cells lines from prostate, colon, and airway and human colonic mucosa expressed mRNA encoding PAR(2), trypsinogen IV, and enteropeptidase, which activates the zymogen. Immunoreactive trypsinogen IV was detected in vesicles in these cells. Trypsinogen IV was cloned from PC-3 cells and expressed in CHO cells, where it was also localized to cytoplasmic vesicles. We expressed trypsinogen IV with an N-terminal Igkappa signal peptide to direct constitutive secretion and allow enzymatic characterization. Treatment of conditioned medium with enteropeptidase reduced the apparent molecular mass of trypsinogen IV from 36 to 30 kDa and generated enzymatic activity, consistent with formation of trypsin IV. In contrast to pancreatic trypsin, trypsin IV was completely resistant to inhibition by polypeptide inhibitors. Exposure of cell lines expressing PAR(2) and PAR(4) to trypsin IV increased [Ca(2+)](i) and strongly desensitized cells to PAR agonists, whereas there were no responses in cells lacking these receptors. Thus, trypsin IV is a potential agonist of PAR(2) and PAR(4) in epithelial tissues where its resistance to endogenous trypsin inhibitors may permit prolonged signaling.
Enzymatic- and renal-dependent catabolism of the intestinotropic hormone glucagon-like peptide-2 in rats (2000)

The intestinotropic hormone glucagon-like peptide (GLP)-2-(1-33) is cleaved in vitro to GLP-2-(3-33) by dipeptidyl peptidase IV (DP IV). To determine the importance of DP IV versus renal clearance in the regulation of circulating GLP-2-(1-33) levels in vivo, GLP-2-(1-33) or the DP IV-resistant analog [Gly(2)]GLP-2 was injected in normal or DP IV-negative rats and assayed by HPLC and RIA. Normal rats showed a steady degradation of GLP-2-(1-33) to GLP-2-(3-33) over time, whereas little or no conversion was detected for GLP-2-(1-33) in DP IV-negative rats and for [Gly(2)]GLP-2 in normal rats. To determine the role of the kidney in clearance of GLP-2-(1-33) from the circulation, normal rats were bilaterally nephrectomized, and plasma immunoreactive GLP-2 levels were measured. The slope of the disappearance curves for both GLP-2-(1-33) and [Gly(2)]GLP-2 were significantly reduced in nephrectomized compared with non-nephrectomized rats (P < 0.01). In contrast to both GLP-2-(1-33) and [Gly(2)]GLP-2, GLP-2-(3-33) did not stimulate intestinal growth in a murine assay in vivo. Thus the intestinotropic actions of GLP-2-(1-33) are determined both by the actions of DP IV and by the kidney in vivo in the rat.
Expression of cellular adhesion molecules on human prostate tumor cell lines (1995)

By flow cytometric analysis we have examined the expression of cellular adhesion molecules (CAMs) on the surface of four different human prostate tumor cell lines: DU 145, from a brain metastasis; PC 3, from a bone metastasis; LNCaP.FGC, from a lymph node metastasis; and a primary tumor cell line, ND 1. The corresponding ligands for the expressed CAMs were, by and large, extracellular matrix proteins. We detected high-level expression of ICAM-1 on three of the four prostate cell lines, whereas LNCaP cells were negative. We observed unstable, heterogeneous expression of E-cadherin in the cell lines DU 145, PC 3, and ND 1. Flow cytometric cell sorting enabled us to divide PC 3 cells into negative and bright positive subpopulations but, after several cell divisions in culture, sorted cells returned to the original heterogeneous phenotype. The laminin-specific alpha 6 beta 4 integrin was not expressed by LNCaP, and was expressed at a low level and heterogeneously on DU 145 and PC 3 cell lines. In contrast, ND 1 cells, derived from a primary tumor, showed homogeneous and high-level expression of the alpha 6 beta 4 integrin. All of the prostate cell lines expressed the RGD-dependent binding of alpha 3 beta 1 and alpha 5 beta 1 integrins and did not reveal non-RGD-dependent alpha 4 beta 1 integrin expression. This finding provides a stimulus to investigate the inhibition capacity of RGD-containing peptides on the metastatic behavior of prostate tumor cells.
ACM international workshop on interactive multimedia on mobile and portable devices (IMMPD'11) (2011)

With the mobile and portable devices become ubiquitous for people's daily life, how to design user interfaces of these products that enable natural, intuitive and fun interaction is one of the main challenges the multimedia community is facing. Following several successful events, the ACM International workshop on Interactive Multimedia on Mobile and Portable Devices (IMMPD'11) aims to bring together researchers from both academia and industry in domains including computer vision, audio and speech processing, machine learning, pattern recognition, communications, human-computer interaction, and media technology to share and discuss recent advances in interactive multimedia.
Experience with Disconnected Operation in a Mobile Computing Environment (1993)

In this paper we present qualitative and quantitative data on file access in a mobile computing environment. This information is based on actual usage experience with the Coda File System over a period of about two years. Our experience confirms the viability and effectiveness of disconnected operation. It also exposes certain deficiencies of the current implementation of Coda, and identifies new functionality that would enhance its usefulness for mobile computing. The paper concludes with a description of what we are doing to address these issues.