gebhart/patrepeval huggingface dataset:
Appican, the Proteoglycan Form of the Amyloid Precursor Protein, Contains Chondroitin Sulfate E in the Repeating Disaccharide Region and 4-O-Sulfated Galactose in the Linkage Region (2001)

Chondroitin sulfate (CS)-D and CS-E, which are characterized by oversulfated disaccharide units, have been shown to regulate neuronal adhesion, cell migration, and neurite outgrowth. CS proteoglycans (CSPGs) consist of a core protein to which one or more CS chains are attached via a serine residue. Although several brain CSPGs, including mouse DSD-1-PG/phosphacan, have been found to contain the oversulfated D disaccharide motif, no brain CSPG has been reported to contain the oversulfated E motif. Here we analyzed the CS chain of appican, the CSPG form of the Alzheimer's amyloid precursor protein. Appican is expressed almost exclusively by astrocytes and has been reported to have brain- and astrocyte-specific functions including stimulation of both neural cell adhesion and neurite outgrowth. The present findings show that the CS chain of appican has a molecular mass of 25-50 kDa. This chain contains a significant fraction (14.3%) of the oversulfated E motif GlcUA beta 1-3GalNAc(4,6-O-disulfate). The rest of the chain consists of GlcUA beta 1-3GalNAc(4-O-sulfate) (81.2%) and minor fractions of GlcUA beta 1-3GalNAc and GlcUA beta 1-3GalNAc(6-O-sulfate). We also show that the CS chain of appican contains in its linkage region the 4-O-sulfated Gal structure. Thus, appican is the first example of a specific brain CSPG that contains the E disaccharide unit in its sugar backbone and the 4-O-sulfated Gal residue in its linkage region. The presence of the E unit is consistent with and may explain the neurotrophic activities of appican.
Influence of lyophilization, fluidized bed drying, addition of protectants, and storage on the viability of lactic acid bacteria (2009)

The influence of protectants proved to be species specific and therefore needs to be determined on a case-to-case basis. Survival rates, duration, and energy consumption appear to be the crucial parameters to evaluate the economy of production processes for industrial starter cultures.
Mammalian antifertility agents. VI. A novel sequence for the preparation of 1,2-disubstituted 3,4-dihydronaphthalenes (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMammalian antifertility agents. VI. A novel sequence for the preparation of 1,2-disubstituted 3,4-dihydronaphthalenesDaniel Lednicer, D. Edward Emmert, Stanley C. Lyster, and Gordon W. DuncanCite this: J. Med. Chem. 1969, 12, 5, 881–885Publication Date (Print):September 1, 1969Publication History Published online1 May 2002Published inissue 1 September 1969https://pubs.acs.org/doi/10.1021/jm00305a038https://doi.org/10.1021/jm00305a038research-articleACS PublicationsRequest reuse permissionsArticle Views173Altmetric-Citations30LEARN 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
Cell swelling, heat, and chemical agonists use distinct pathways for the activation of the cation channel TRPV4 (2003)

TRPV4 is a Ca(2+)- and Mg(2+)-permeable cation channel within the vanilloid receptor subgroup of the transient receptor potential (TRP) family, and it has been implicated in Ca(2+)-dependent signal transduction in several tissues, including brain and vascular endothelium. TRPV4-activating stimuli include osmotic cell swelling, heat, phorbol ester compounds, and 5',6'-epoxyeicosatrienoic acid, a cytochrome p450 epoxygenase metabolite of arachidonic acid (AA). It is presently unknown how these distinct activators converge on opening of the channel. Here, we demonstrate that blockers of phospholipase A(2) (PLA(2)) and cytochrome p450 epoxygenase inhibit activation of TRPV4 by osmotic cell swelling but not by heat and 4alpha-phorbol 12,13-didecanoate. Mutating a tyrosine residue (Tyr-555) in the N-terminal part of the third transmembrane domain to an alanine strongly impairs activation of TRPV4 by 4alpha-phorbol 12,13-didecanoate and heat but has no effect on activation by cell swelling or AA. We conclude that TRPV4-activating stimuli promote channel opening by means of distinct pathways. Cell swelling activates TRPV4 by means of the PLA(2)-dependent formation of AA, and its subsequent metabolization to 5',6'-epoxyeicosatrienoic acid by means of a cytochrome p450 epoxygenase-dependent pathway. Phorbol esters and heat operate by means of a distinct, PLA(2)- and cytochrome p450 epoxygenase-independent pathway, which critically depends on an aromatic residue at the N terminus of the third transmembrane domain.
Mouse models of diabetic nephropathy (2011)

While there are many murine models of mesangial matrix expansion in the setting of diabetes, few progress to develop advanced diabetic lesions. Mice with eNOS deficiency, OVE26 mice, and the recently described BTBR ob/ob mouse currently appear to be the best murine models of advanced disease. A model that allows testing of interventions that modulate podocyte loss and regeneration, such as the BTBR ob/ob mouse, may be of particular benefit in developing therapeutics for diabetic nephropathy.
Cysteinyl-tRNA synthetase is not essential for viability of the archaeon Methanococcus maripaludis (2001)

The methanogenic archaea Methanocaldococcus jannaschii and Methanothermobacter thermautotrophicus contain a dual-specificity prolyl-tRNA synthetase (ProCysRS) that accurately forms both prolyl-tRNA (Pro-tRNA) and cysteinyl-tRNA (Cys-tRNA) suitable for in vivo translation. This intriguing enzyme may even perform its dual role in organisms that possess a canonical single-specificity cysteinyl-tRNA synthetase (CysRS), raising the question as to whether this latter aminoacyl-tRNA synthetase is indeed required for cell viability. To test the postulate that all synthetase genes are essential, we disrupted the cysS gene (encoding CysRS) of Methanococcus maripaludis. The knockout strain was viable under normal growth conditions. Biochemical analysis showed that the pure M. maripaludis ProCysRS was capable of forming Cys-tRNA, implying that the dual-specificity enzyme compensates in vivo for the loss of CysRS. The canonical CysRS has a higher affinity for cysteine than ProCysRS, a reason why M. maripaludis may have acquired cysS by a late lateral gene transfer. These data challenge the notion that all twenty aminoacyl-tRNA synthetases are essential for the viability of a cell.
Complement-Induced Release of Monocyte Chemotactic Protein-1 From Human Smooth Muscle Cells (1996)

Increasing evidence suggests that complement activation might represent an important mechanism in early atherogenesis. Thus, complement components, in particular the membrane attack complex (MAC) C5b-9(m), have been isolated from human atherosclerotic lesions. Furthermore, complement activation is known to occur in atherosclerotic lesions induced in experimental animals, and the severity of cholesterol-induced plaques is markedly reduced in complement-deficient animals. During atherogenesis monocytes are recruited into the arterial wall, and a potent chemoattractant for monocytes, monocyte chemotactic protein-1 (MCP-1), is expressed by vascular smooth muscle cells (SMCs). We hypothesized that generation of MACs on SMCs during the activation of complement might lead to the release of MCP-1 and hence to monocyte recruitment. In this study, MACs were generated on human SMCs in vitro by sequential addition of the purified complement components C5b6, C7, C8, and C9. This supernatant of the culture was chemotactic for freshly isolated peripheral blood monocytes in a modified Boyden chamber. The chemotactic activity of the supernatant was abolished by anti-MCP-1 blocking antibodies but not by an isotype-matched antibody against an irrelevant antigen. The release of chemotactic activity was dependent on the dose of MAC formed on SMCs and was demonstrated within 10 minutes of exposure of the cells. The data support the hypothesis that complement-mediated release of MCP-1 from SMCs might be important in the recruitment of monocytes into the developing atherosclerotic lesion and could be an important initiating event in atherogenesis.
Choosing GLP-1 Receptor Agonists or DPP-4 Inhibitors: Weighing the Clinical Trial Evidence (2012)

IN BRIEF Comparative trials show that there are important differences between and among the glucagon-like peptide-1 (GLP-1) receptor agonists and dipeptidyl peptidase-4 (DPP-4) inhibitors with respect to glycemic lowering, weight effects, and effects on systolic blood pressure and the lipid profile. Nausea, diarrhea, headaches, and dizziness are common with both of the available GLP-1 receptor agonists. Upper respiratory tract infections, nasopharyngitis, and headaches are common with the DPP-4 inhibitors. Ongoing safety evaluations should provide a clear picture regarding long-term safety.
Mechanical properties and biodegradability of crosslinked soy protein isolate/waterborne polyurethane composites (2004)

Abstract With anionic waterborne polyurethane (WPU) as a plasticizer and ethylene glycol diglycidyl ether (EGDE) as a crosslinker, we successfully prepared crosslinked soy protein isolate (SPI) plastics. Anionic WPU was mixed with SPI and EGDE in an aqueous dispersion at room temperature. The mixed aqueous dispersion was cast and cured, and the obtained material was pickled and hot‐pressed to produce the crosslinked SPI/WPU sheets. The resulting sheets containing about 60 wt % SPI were characterized with infrared spectroscopy, scanning electron microscopy, atomic force microscopy, dynamic mechanical analysis, and tensile testing, and biodegradation testing of the sheets was performed in a mineral salt medium containing microorganisms. The results revealed that the crosslinked SPI/WPU plastics with EGDE concentrations of 2–4 wt % possessed high miscibility, good mechanical properties, and water resistivity. In addition, the crosslinked sheets could be biodegraded, and the half‐life of the biodegradation for a sheet crosslinked with 3 wt % EGDE was calculated to be less than 1 month. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 95: 465–473, 2005
Analysis of the spatial and temporal characteristics of platelet-delivered factor VIII–based clots (2008)

Normally factor (F) VIII is not expressed in megakaryocytes, but when human FVIII was transgenically expressed in murine megakaryocytes, it was stored in platelet alpha-granules and released at sites of injury. This platelet FVIII (pFVIII) is effective in correcting hemostasis, even in the presence of circulating inhibitors, so it offers a potential gene therapy strategy for hemophilia A. To understand clot development by pFVIII, we have examined clot response to laser injury in both cremaster arterioles and venules in FVIII(null) mice either infused with FVIII or transgenic for pFVIII. In both sets of vessels, pFVIII is at least as effective as infused FVIII. However, there are temporal and spatial differences in fibrin and platelet accumulation within clots depending on how FVIII is delivered. These differences may be related to the temporal and spatial distribution of the alpha-granular-released FVIII within the developing clot, and may explain the increased frequency and size of embolic events seen with pFVIII. These observations may not only have implications for the use of pFVIII in gene therapy for hemophilia A, but may also have physiologic consequences, explaining why many procoagulant factors are delivered both in the plasma and in platelet alpha-granules.
The Remote Control of Multiplexed Telecine Chains (1971)

The remote control of telecine equipment of various manufacturers, in various combinations, is complicated by the nonstandard control circuits and command signals in use. By using a standard interface unit between the projectors and the remote control system, standardized command signals and consistent status indications can be used, the remote control panels can be kept simple, and telecine modifications are minimal. Automated switching systems can be incorporated into the remote control path at any time. The problem of handling both digital and analog controls is discussed, and the use of hard-wired and coded control systems are compared; a description of a typical installation is included, together with recommendations for future designs.
Coherent quantum control of multiphoton transitions by shaped ultrashort optical pulses (1999)

Multiphoton transitions can be reached by many routes through a continuum of virtual levels. We show that the transition probability of two-photon and multiphoton processes can be controlled by tailoring the shape of an ultrashort excitation pulse, so that the many paths leading to the final state interfere to give a desired probability amplitude. We analyze the effect of pulse shapes on N-photon absorption as well as on Raman transitions. We show theoretically that certain tailored dark pulses do not excite the system at all, while other shaped pulses induce transitions as effectively as transform limited pulses, even when their peak amplitudes are greatly reduced. These results are confirmed experimentally for two-photon transitions in atomic cesium.
Crystallization and preliminary X‐ray analysis of the 9 kDa protein of the mouse signal recognition particle and the selenomethionyl‐SRP9 (1996)

Two different crystal forms of the 9 kDa protein of the signal recognition particle (SRP9) have been prepared by the hanging drop vapor diffusion technique using 28% (w/v) PEG8000 or 28% saturated ammonium sulphate as precipitant. The crystals are hexagonal bipyramids with average dimensions of 0.2 X 0.1 X 0.1 mm(3) and they diffract to a resolution of 2.3 Angstroms. They belong to the space groups P6(2)22/P6(4)22 or P3(1)21/P3(2)21 with cell dimensions a = b = 63.0 Angstroms, and c = 111.5 Angstroms. Crystals have also been grown from the selenomethionyl protein and multiwavelength data sets have been collected.
Recognition of platinum-induced DNA damage by nuclear proteins: screening for mechanisms. (1994)

The association of high mobility group (HMG) proteins with cisplatin-damaged DNA has attracted considerable interest because of a possible relationship with drug-acquired resistance and the repair of DNA damage caused by this important chemotherapeutic agent. We have further characterized the binding of HMG proteins to cisplatin-damaged DNA using a modification of the damaged DNA affinity precipitation assay (DDAP) and proteins isolated from the nuclei of V79 cells. HMG proteins recognized cisplatin adducts only in double-stranded DNA sequences. Pre-treatment of cells with cisplatin (1 microM) prior to protein extraction decreased the apparent yield of HMG proteins. However, the pre-treatment of isolated protein did not prevent recognition of the DNA adducts. To investigate the possible role of HMG proteins in toxicity and resistance, we have extended the DDAP method to study other platinum agents, some of which are active in cisplatin-resistant cells. A comparison of trans- and cis-[PtCl2(NH3)quinoline] is presented as an example. HMG proteins recognized DNA damage caused by the cis, but not the trans isomer. However, the trans isomer is known to be significantly more toxic and is highly active in cisplatin-resistant cells, suggesting a mechanism of action different from cisplatin. Therefore, the toxicity of trans-[PtCl2(NH3)quinoline] appears to be unrelated to the recognition of damage by HMG proteins. The DDAP assay may provide an additional screen for new mechanisms of cytotoxic platinum agents.
<title>Fast texture database retrieval using extended fractal features</title> (1997)

The increase in the number of multimedia databases consisting of images has created a need for a quick method to search these databases for a particular type of image. An image retrieval system will output images from the database similar to the query image in terms of shape, color, and texture. For the scope of our work, we study the performance of multiscale Hurst parameters as texture features for database image retrieval over a database consisting of homogeneous textures. These extended Hurst features represent a generalization of the Hurst parameter for fractional Brownian motion (fBm) where the extended parameters quantize the texture roughness of an image at various scales. We compare the retrieval performance of the extended parameters against traditional Hurst features and features obtained from the Gabor wavelet. Gabor wavelets have previously been suggested for image retrieval applications because they can be tuned to obtain texture information for a number of different scales and orientations. In our experiments, we form a database combining textures from the Bonn, Brodatz, and MIT VisTex databases. Over the hybrid database, the extended fractal features were able to retrieve a higher percentage of similar textures than the Gabor features. Furthermore, the fractal features are faster to compute than the Gabor features.
Refined crystal structure of DsRed, a red fluorescent protein from coral, at 2.0-Å resolution (2001)

The crystal structure of DsRed, a red fluorescent protein from a corallimorpharian, has been determined at 2.0-A resolution by multiple-wavelength anomalous dispersion and crystallographic refinement. Crystals of the selenomethionine-substituted protein have space group P2(1) and contain a tetramer with 222 noncrystallographic symmetry in the asymmetric unit. The refined model has satisfactory stereochemistry and a final crystallographic R factor of 0.162. The protein, which forms an obligatory tetramer in solution and in the crystal, is a squat rectangular prism comprising four protomers whose fold is extremely similar to that of the Aequorea victoria green fluorescent protein despite low ( approximately 23%) amino acid sequence homology. The monomer consists of an 11-stranded beta barrel with a coaxial helix. The chromophores, formed from the primary sequence -Gln-Tyr-Gly- (residues 66-68), are arranged in a approximately 27 x 34-A rectangular array in two approximately antiparallel pairs. The geometry at the alpha carbon of Gln-66 (refined without stereochemical restraints) is consistent with an sp(2) hybridized center, in accord with the proposal that red fluorescence is because of an additional oxidation step that forms an acylimine extension to the chromophore [Gross, L. A., Baird, G. S., Hoffman, R. C., Baldridge, K. K. & Tsien, R. Y. (2000) Proc. Natl. Acad. Sci. USA 87, 11990-11995]. The carbonyl oxygen of Phe-65 is almost 90 degrees out of the plane of the chromophore, consistent with theoretical calculations suggesting that this is the minimum energy conformation of this moiety despite the conjugation of this group with the rest of the chromophore.
Effect of Different Extraction Methods on Fatty Acids, Volatile Compounds, and Physical and Chemical Properties of Avocado (Persea americana Mill.) Oil (2003)

Because Mexico is the number one producer of avocados in the world, this fruit has potential as a source for oil extraction. It is appropriate to further investigate the detailed changes that the oil undergoes when different extraction methods are applied. This research paper presents the study of the physical and chemical changes, the fatty acids profile, the trans fatty acid content, and the identification of volatile compounds of the oils from avocado pulp (Persea americana Mill.), obtained by four different extraction methods. The method with the greatest extraction yield was the combined microwave-hexane method. The amount of trans fatty acids produced in the microwave-squeezing treatment was <0.5 g/100 g. On the other hand, the amounts of trans fatty acids produced with the hexane and acetone treatments were 0.52 and 0.87 g/100 g, respectively. The method that caused the slightest modification to the oil quality was a novel combined extraction method of microwave-squeezing proposed by the authors.
pp60c-src activation in human colon carcinoma. (1989)

We measured the in vitro protein-tyrosine kinase activity of pp60c-src from human colon carcinoma cell lines and tumors. The activity of pp60c-src from six of nine carcinoma cell lines was higher (on average, fivefold as measured by enolase phosphorylation, or eightfold as measured by autophosphorylation) than that of pp60c-src from normal colonic mucosal cells, or human or rodent fibroblasts. Similarly, the activity of pp60c-src from 13 of 21 primary colon carcinomas was five- or sevenfold higher than that of pp60c-src from normal colonic mucosa adjacent to the tumor. The increased pp60c-src activity did not result solely from an increase in the level of pp60c-src protein, suggesting the specific activity of the pp60c-src kinase is elevated in the tumor cells. pp60c-src from colon carcinoma cells and normal colonic mucosal cells was phosphorylated at similar sites. We used immunoblotting with antibodies to phosphotyrosine to identify substrates of protein-tyrosine kinases in colonic cells. Three phosphotyrosine-containing proteins were detected at significantly higher levels in most colon carcinoma cell lines than in normal colonic mucosal cells or human or rat fibroblasts. All colon carcinoma cell lines with elevated pp60c-src in vitro kinase activity, showed increased phosphorylation of proteins on tyrosine in vivo, suggesting the presence of an activated protein-tyrosine kinase(s).
Expression of matrix metalloproteinase-9 (MMP-9) and blood vessel density in laryngeal squamous cell carcinomas (2010)

MMP-9 was detected in inflammatory cells. Positivity for MMP-9 correlated significantly with the grade of differentiation (p = 0.025). Expression of MMP-9 was not correlated with T stage, nodal metastasis, or tumor recurrence. The mean blood vessel density was 51.4 vessels/mm². Specimens were more likely to exhibit higher density of blood vessels when MMP-9 expression was also present (p = 0.014).