gebhart/patrepeval huggingface dataset:
Staphylococcus aureus -Derived Staphopain B, a Potent Cysteine Protease Activator of Plasma Chemerin (2007)

Chemerin is an attractant for cells that express the serpentine receptor CMKLR1, which include immature plasmacytoid dendritic cells (pDC) and macrophages. Chemerin circulates in the blood where it exhibits low biological activity, but upon proteolytic cleavage of its C terminus, it is converted to a potent chemoattractant. Enzymes that contribute to this conversion include host serine proteases of the coagulation, fibrinolytic, and inflammatory cascades, and it has been postulated that recruitment of pDC and macrophages by chemerin may serve to balance local tissue immune and inflammatory responses. In this work, we describe a potent, pathogen-derived proteolytic activity capable of chemerin activation. This activity is mediated by staphopain B (SspB), a cysteine protease secreted by Staphylococcus aureus. Chemerin activation is triggered by growth medium of clinical isolates of SspB-positive S. aureus, but not by that of a SspB(null) mutant. C-terminal processing by SspB generates a chemerin isoform identical with the active endogenous attractant isolated from human ascites fluid. Interestingly, SspB is a potent trigger of chemerin even in the presence of plasma inhibitors. SspB may help direct the recruitment of specialized host cells, including immunoregulatory pDC and/or macrophages, contributing to the ability of S. aureus to elicit and maintain a chronic inflammatory state.
A new inhibitor of metalloproteinases from chicken: ChIMP-3. A third member of the TIMP family. (1992)

We report cDNA cloning and primary structure of a new metalloproteinase inhibitor (ChIMP-3) produced by chicken embryo fibroblasts. ChIMP-3, formerly called the 21-kDa protein, is one of five ChIMPs (Chicken Inhibitor of MetalloProteinases). In this paper, we report that of the three most abundant ChIMPs, ChIMP-3 and ChIMP-a are extracellular matrix components, whereas ChIMP-2 is found in the media conditioned by the cells. Treatment of ChIMP-3 and ChIMP-a with N-glycosidase-F indicates that ChIMP-a is N-glycosylated whereas ChIMP-3 is not. The deduced amino acid sequence of ChIMP-3 predicts a protein whose properties are consistent with experimental measurements. Analysis of sequence alignments with the two previously described members of the TIMP (tissue inhibitor of metalloproteinases) family, TIMP-1 and TIMP-2, from various species indicates that ChIMP-3 is a related but distinct protein. This conclusion is supported by lack of significant binding with anti-TIMP-1 and anti-TIMP-2 antibodies. Based on these data, its unusual solubility properties, and its exclusive location in the matrix, we propose that ChIMP-3 is a new member of this family of metalloproteinase inhibitors, a TIMP-3.
Interior Surface Modification of Bacteriophage MS2 (2004)

An efficient strategy for the interior surface functionalization of MS2 viral capsids is reported, featuring a new hetero-Diels-Alder bioconjugation reaction. After virus isolation, the RNA genome was removed from the spherical particles by exposure to pH 11.8 conditions for a period of 4 h. Following this, 180 tyrosine residues on the interior surface of each "empty" capsid shell were modified by using a site-selective diazonium-coupling reaction. To attach additional functionality, the azo conjugate was reduced with Na2S2O4 to afford an ortho-amino tyrosine derivative. Oxidation of this moiety with NaIO4 produced an o-iminoquinone on the protein surface, which was found to undergo an efficient hetero-Diels-Alder reaction with N-(4-aminophenyl)acrylamide. This four-step procedure can be carried out in under 4 h, reaches high levels of conversion, and yields the desired conjugates in >60% overall yield.
奎因、怀曼与布里丹：本体论约定的三种方法 (2012)

本文对本体论约定（ontological commitment）问题的三种根本不同方法进行了比较。认为尽管它们具有表面上的相似性，但中世纪晚期的唯名论哲学家布里丹（约1300—1361）的方法，是比以迈农和奎因为代表的其他两种被普遍认同的现代方法更具吸引力的第三种选择。本文同时指出，只有基于其关于真与逻辑有效性的语义观念的截然不同的前现代方法。布里丹的方法才是可能的。
Melanoma Antigen Gene Protein-A11 (MAGE-11) F-box Links the Androgen Receptor NH2-terminal Transactivation Domain to p160 Coactivators (2009)

Androgen-dependent transcriptional activity by the androgen receptor (AR) and its coregulators is required for male reproductive development and function. In humans and other primates, melanoma antigen gene protein-A11 (MAGE-11) is an AR selective coregulator that increases AR transcriptional activity. Here we show that the interaction between AR and MAGE-11 is mediated by AR NH(2)-terminal FXXLF motif binding to a highly conserved MAGE-11 F-box in the MAGE homology domain, and is modulated by serum stimulation of mitogen-activated protein kinase phosphorylation of MAGE-11 Ser-174. The MAGE-11-dependent increase in AR transcriptional activity is mediated by a direct interaction between MAGE-11 and transcriptional intermediary factor 2 (TIF2) through the NH(2)-terminal region of TIF2, and by a MAGE-11 FXXIF motif interaction with an F-box-like region in activation domain 1 of TIF2. The results suggest that MAGE-11 functions as a bridging factor to recruit AR coactivators through a novel FXX(L/I)F motif-F-box interaction paradigm.
PIM2 inhibition as a rational therapeutic approach in B-cell lymphoma (2011)

PIM serine/threonine kinases are overexpressed, translocated, or amplified in multiple B-cell lymphoma types. We have explored the frequency and relevance of PIM expression in different B-cell lymphoma types and investigated whether PIM inhibition could be a rational therapeutic approach. Increased expression of PIM2 was detected in subsets of mantle cell lymphoma, diffuse large B-cell lymphoma (DLBLC), follicular lymphoma, marginal zone lymphoma-mucosa-associated lymphoid tissue type, chronic lymphocytic leukemia, and nodal marginal zone lymphoma cases. Increased PIM2 protein expression was associated with an aggressive clinical course in activated B-like-DLBCL patients. Pharmacologic and genetic inhibition of PIM2 revealed p4E-BP1(Thr37/46) and p4E-BP1(Ser65) as molecular biomarkers characteristic of PIM2 activity and indicated the involvement of PIM2 kinase in regulating mammalian target of rapamycin complex 1. The simultaneous genetic inhibition of all 3 PIM kinases induced changes in apoptosis and cell cycle. In conclusion, we show that PIM2 kinase inhibition is a rational approach in DLBCL treatment, identify appropriate biomarkers for pharmacodynamic studies, and provide a new marker for patient stratification.
An adaptive filtering algorithm using an orthogonal projection to an affine subspace and its properties (1984)

Abstract The LMS algorithm and learning identification, which presently are typical adaptive algorithms, have a problem in that the speed of convergence may decrease greatly depending on the property of the input signal. To avoid this problem, this paper presents a geometrical discussion as to the origin of that defect, and proposes a new adaptive algorithm based on the result of the investigation. Comparing the convergence speeds of the proposed algorithm and the learning identification by numerical experiment by computer, great improvement was verified. The algorithm is extended to a group of algorithms which includes the original algorithm and the learning identification, which are called APA (affine projection algorithm). It is shown that APA has some desirable properties, such as, the coefficient vector approaches the true value monotonically and the convergence speed is independent of the amplitude of the input signal. Clear conclusions are also obtained for the problem as to what noise is included in the output signal when an external disturbance is impressed or the degree of the adaptive filter is not sufficient.
Actinomycin D induced DNase I cleavage enhancement caused by sequence specific propagation of an altered DNA structure (1988)

Two DNA hexadecamers containing one central 5'-GC-3' base step have been examined by footprinting methodology in the presence and absence of actinomycin D. The results of these studies, coupled with imino proton NMR measurements indicate that the antitumor drug causes a change in DNA conformation at a distance from the actinomycin intercalation site in a molecule of sequence d[ATATATAGCTATATAT] that does not occur in d[AAAAAAAGCTTTTTTT]. The experiments demonstrate that DNase I rate enhancements associated with actinomycin D binding are caused by ligand alteration of equilibrium DNA structure.
Electrochemical behaviour of dopamine at covalent modified glassy carbon electrode with l-cysteine: preliminary results (2009)

The surface of glassy carbon (GC) electrode has been modified by oxidation of L-cysteine. The covalent modified GC electrode with L-Cysteine has been studied, according the supporting electrolyte used. Favourable interactions between the L-cysteine film and DA enhance the current response compared to that at the Nafion GC and bare GC electrodes, achieving better performances than those other electrodes. This behaviour was as result of the adsorption of the cysteine layer film, compact and uniform formation; depending on L-cysteine solution (phosphate buffer or chloridric acid supporting electrolyte) used for modifying GC surface. In cyclic voltammetric measurements, modified electrodes can successfully separate the oxidation/reduction DA peaks in different buffer solutions, but an evident dependence in the response was obtained as function of pH and modified electrode. The modified electrode prepared with L-cysteine/HCl solution was used to obtain the calibration curve and it exhibited a stable and sensitive response to DA. The results are described and discussed in the light of the existing literature.
The Spectrum of Symptoms and QT Intervals in Carriers of the Gene for the Long-QT Syndrome (1992)

In families affected by the long-QT syndrome, measurement of the QTc interval may not permit an accurate diagnosis. DNA markers make it possible to make a genetic diagnosis in some families, but not all gene carriers have symptoms.
Facile synthesis of 8-substituted quinolines (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFacile synthesis of 8-substituted quinolinesJ. William Suggs and G. D. N. PearsonCite this: J. Org. Chem. 1980, 45, 8, 1514–1515Publication Date (Print):April 1, 1980Publication History Published online1 May 2002Published inissue 1 April 1980https://pubs.acs.org/doi/10.1021/jo01296a035https://doi.org/10.1021/jo01296a035research-articleACS PublicationsRequest reuse permissionsArticle Views1706Altmetric-Citations25LEARN 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
Combined Effect of Arginine, Valine, and Serine on Exercise-Induced Fatigue in Healthy Volunteers: A Randomized, Double-Blinded, Placebo-Controlled Crossover Study (2019)

Although several kinds of amino acids (AAs) are known to affect physiological actions during exercise, little is known about the combined effects of a mixture of several AAs on fatigue during exercise. The aim of the present study was to investigate the effect of an AA mixture supplement containing arginine, valine, and serine on exercise-induced fatigue in healthy volunteers. These AAs were selected because they were expected to reduce fatigue during exercise by acting the positive effects synergistically. A randomized, double-blinded, placebo-controlled crossover trial was conducted. Thirty-nine males ingested an AA mixture containing 3600 mg of arginine, 2200 mg of valine, and 200 mg of serine or a placebo each day for 14 days. On the 14th day, the participants completed an exercise trial on a cycle ergometer at 50% of VO<sub>2</sub>max for 120 min. After the two-week washout period, the participants repeated the same trial with the other test sample. The participant's feeling of fatigue based on a visual analog scale (VAS) and a rating of perceived exertion (RPE), as well as blood and physical parameters were evaluated. The feeling of fatigue based on VAS and RPE were significantly improved in AA compared to those in placebo. In the blood analysis, the increase in serum total ketone bodies during exercise and plasma tryptophan/branched-chain amino acids were significantly lower in AA than those in placebo. The present study demonstrated that supplementation with an AA mixture containing arginine, valine, and serine reduced the feeling of fatigue during exercise. The AA mixture also changed several blood parameters, which may contribute to the anti-fatigue effect.
Thiocyanate and chloride as competing substrates for myeloperoxidase (1997)

The neutrophil enzyme myeloperoxidase uses H2O2 to oxidize chloride, bromide, iodide and thiocyanate to their respective hypohalous acids. Chloride is considered to be the physiological substrate. However, a detailed kinetic study of its substrate preference has not been undertaken. Our aim was to establish whether myeloperoxidase oxidizes thiocyanate in the presence of chloride at physiological concentrations of these substrates. We determined this by measuring the rate of H2O2 loss in reactions catalysed by the enzyme at various concentrations of each substrate. The relative specificity constants for chloride, bromide and thiocyanate were 1:60:730 respectively, indicating that thiocyanate is by far the most favoured substrate for myeloperoxidase. In the presence of 100 mM chloride, myeloperoxidase catalysed the production of hypothiocyanite at concentrations of thiocyanate as low as 25 microM. With 100 microM thiocyanate, about 50% of the H2O2 present was converted into hypothiocyanite, and the rate of hypohalous acid production equalled the sum of the individual rates obtained when each of these anions was present alone. The rate of H2O2 loss catalysed by myeloperoxidase in the presence of 100 mM chloride doubled when 100 microM thiocyanate was added, and was maximal with 1mM thiocyanate. This indicates that at plasma concentrations of thiocyanate and chloride, myeloperoxidase is far from saturated. We conclude that thiocyanate is a major physiological substrate of myeloperoxidase, regardless of where the enzyme acts. As a consequence, more consideration should be given to the oxidation products of thiocyanate and to the role they play in host defence and inflammation.
Magnetic Resonance Imaging Characteristics Predict Epidermal Growth Factor Receptor Amplification Status in Glioblastoma (2005)

Mean T2/T1 was 4.7 for EGFR-amplified glioblastomas, greater than that of TP53-mutated glioblastomas (2.3) or non-TP53/non-EGFR glioblastomas (2.6; P<0.00005). All four tumors with T2/T1>7.2 were EGFR-amplified; 0 of 15 with T2/T1<4.7 underwent gross total resection. The mean T2 BSC of EGFR-amplified glioblastomas was 33.7, less sharp (P<0.0000005) than TP53-mutated (72.2) and non-TP53/non-EGFR glioblastomas (81.2). All 15 glioblastomas with T2 BSC<30.8 were EGFR-amplified. Percentage necrosis and T1 BSC did not differ between glioblastoma subtypes. The increased T2/T1 ratio and decreased T2 BSC in EGFR-overexpressing tumors are the first radiographic distinctions described between glioblastoma molecular subtypes. These findings may reflect increased angiogenesis, edema, and/or invasion in EGFR-overexpressing tumors.
A Monomeric Uncleaved Respiratory Syncytial Virus F Antigen Retains Prefusion-Specific Neutralizing Epitopes (2014)

Respiratory syncytial virus (RSV) is the leading infectious cause of severe respiratory disease in infants and a major cause of respiratory illness in the elderly. There remains an unmet vaccine need despite decades of research. Insufficient potency, homogeneity, and stability of previous RSV fusion protein (F) subunit vaccine candidates have hampered vaccine development. RSV F and related parainfluenza virus (PIV) F proteins are cleaved by furin during intracellular maturation, producing disulfide-linked F1 and F2 fragments. During cell entry, the cleaved Fs rearrange from prefusion trimers to postfusion trimers. Using RSV F constructs with mutated furin cleavage sites, we isolated an uncleaved RSV F ectodomain that is predominantly monomeric and requires specific cleavage between F1 and F2 for self-association and rearrangement into stable postfusion trimers. The uncleaved RSV F monomer is folded and homogenous and displays at least two key RSV-neutralizing epitopes shared between the prefusion and postfusion conformations. Unlike the cleaved trimer, the uncleaved monomer binds the prefusion-specific monoclonal antibody D25 and human neutralizing immunoglobulins that do not bind to postfusion F. These observations suggest that the uncleaved RSV F monomer has a prefusion-like conformation and is a potential prefusion subunit vaccine candidate. Importance: RSV is the leading infectious cause of severe respiratory disease in infants and a major cause of respiratory illness in the elderly. Development of an RSV vaccine was stymied when a clinical trial using a formalin-inactivated RSV virus made disease, following RSV infection, more severe. Recent studies have defined the structures that the RSV F envelope glycoprotein adopts before and after virus entry (prefusion and postfusion conformations, respectively). Key neutralization epitopes of prefusion and postfusion RSV F have been identified, and a number of current vaccine development efforts are focused on generating easily produced subunit antigens that retain these epitopes. Here we show that a simple modification in the F ectodomain results in a homogeneous protein that retains critical prefusion neutralizing epitopes. These results improve our understanding of RSV F protein folding and structure and can guide further vaccine design efforts.
INFECTION-IMMUNITY IN EXPERIMENTAL SALMONELLOSIS (1966)

Salmonella enteritidis is highly virulent for the mouse causing an infection resembling mouse typhoid. Survivors of the infection are completely resistant to reinfection and eliminate a large challenge dose of virulent organisms within 72 hr. The antigenically related Salmonella gallinarum was almost avirulent for the mouse but animals vaccinated with this organism were equally capable of eliminating a lethal dose of virulent S. enteritidis. Living Salmonella pullorum, on the other hand, was quickly eliminated from the tissues of normal mice. Vaccination with this organism failed to evoke an effective bactericidal mechanism. Alcohol-killed vaccines of these three Salmonellae all produced an increase in blood clearance rate, but gave only marginal protection against S. enteritidis. Liver and spleen counts on these mice revealed a 1 to 2 day delay before any net increase in the total bacterial population could be observed. Immunization of mice with increasing doses of living Salmonella montevideo resulted in progressively greater killing of a challenge dose of S. enteritidis despite the absence of common somatic antigens between the two strains. The degree of protection varied with the size of the residual population of S. montevideo in the vaccinated mice. The significance of these findings in assessing the importance of various factors involved in the development of acquired resistance to Salmonella infections is discussed.
Water-Soluble Fullerene (C60) Derivatives as Nonviral Gene-Delivery Vectors (2008)

A new class of water-soluble C60 transfecting agents has been prepared using Hirsch-Bingel chemistry and assessed for their ability to act as gene-delivery vectors in vitro. In an effort to elucidate the relationship between the hydrophobicity of the fullerene core, the hydrophilicity of the water-solubilizing groups, and the overall charge state of the C60 vectors in gene delivery and expression, several different C60 derivatives were synthesized to yield either positively charged, negatively charged, or neutral chemical functionalities under physiological conditions. These fullerene derivatives were then tested for their ability to transfect cells grown in culture with DNA carrying the green fluorescent protein (GFP) reporter gene. Statistically significant expression of GFP was observed for all forms of the C60 derivatives when used as DNA vectors and compared to the ability of naked DNA alone to transfect cells. However, efficient in vitro transfection was only achieved with the two positively charged C60 derivatives, namely, an octa-amino derivatized C60 and a dodeca-amino derivatized C60 vector. All C60 vectors showed an increase in toxicity in a dose-dependent manner. Increased levels of cellular toxicity were observed for positively charged C60 vectors relative to the negatively charged and neutral vectors. Structural analyses using dynamic light scattering and optical microscopy offered further insights into possible correlations between the various derivatized C60 compounds, the C60 vector/DNA complexes, their physical attributes (aggregation, charge) and their transfection efficiencies. Recently, similar Gd@C60-based compounds have demonstrated potential as advanced contrast agents for magnetic resonance imaging (MRI). Thus, the successful demonstration of intracellular DNA uptake, intracellular transport, and gene expression from DNA using C60 vectors suggests the possibility of developing analogous Gd@C60-based vectors to serve simultaneously as both therapeutic and diagnostic agents.
Boundary Layer Mixture Model for a Microbubble Drag Reduction Technique (2011)

The boundary mixture model is derived to predict the performance of the microbubble drag reduction technique for a flat plate. The flat plate with a porous material microbubble injecting system and resistance-measuring system are set up to measure the frictional resistance of the flat plate without and with injected microbubbles. The tests are conducted in a water tunnel and a towing tank. The test results show that the boundary mixture model predicts the drag reduction well for the flat plate when testing with injected microbubbles in the water tunnel. However, the boundary mixture model overestimates the drag reduction effect for the flat plate tested in the towing tank. The possible mechanism for the overestimation of drag reduction effect in the towing tank may be due to the different behaviors of microbubbles in the velocity gradient of boundary layer.