gebhart/patrepeval huggingface dataset:
The FcγRII Receptor Triggers pp125FAK Phosphorylation in Platelets (1996)

Platelets express a single low affinity receptor for immunoglobulin, FcgammaRII, that triggers multiple cellular responses upon interaction with multivalent immune complexes. In this study we show that immobilized IgG is also a potent stimulant of platelet activation triggering adhesion, aggregation, massive dense granule secretion, and thromboxane production. Platelet adhesion to IgG was blocked by the FcgammaRII receptor-specific monoclonal antibody, IV. 3. Pretreatment of the platelets with cytochalasin D to inhibit actin polymerization similarly prevented cell binding to IgG having no effect on platelet binding to fibrinogen. Platelet adhesion to IgG also led to the induction of tyrosine phosphorylation of multiple proteins including pp125(FAK) and p72(SYK). These proteins were also tyrosine-phosphorylated in alphaIIbbeta3-deficient IgG-adherent platelets from patients with Glanzmann's thrombasthenia. These data demonstrate that FcgammaRII mediates pp125(FAK) phosphorylation and platelet adhesion to IgG independent of the integrin alphaIIbbeta3. Treatment of the platelets with bisindolylmaleimide to inhibit protein kinase C prevented phosphorylation of pp125(FAK) as well as several other proteins, but not p72(SYK) phosphorylation. This study establishes that the FcgammaRII receptor mediates pp125(FAK) phosphorylation via protein kinase C.
A methodology for developing ‘Chainlink’ converters (2009)

“Chain circuits or “Chainlink converters” include the Modular Multi-Level Converter (M2LC) [1] and the multilevel Static Compensator (StatCom) [2]. They use large numbers of identical series connected modules, each of which contains a capacitor that can be switched in or out of circuit to present a continually variable voltage at the converter terminals. The technique permits multilevel converters to be constructed without the disadvantages associated with other multilevel topologies and have created major interest for high voltage power transmission applications since complex waveforms can be constructed without the filtering associated with converters utilising PWM. The approach proposed is to operate converter topologies built up from combinations of chain circuits as sets of individual current sources. These are arranged as a matrix form so the current from the input and output terminals are able to circulate through all the chain elements in a subtractive manner. To maintain the capacitor charge level in each chain circuit the net power flow must be zero which can commonly be achieved only for AC to AC or AC to DC power conversion. Additional control is required to trim the operation of the chains to ensure average capacitor voltage in a chain is constrained to a defined level, although the simulation results presented do not include this. An example of a topology that can be derived by this approach is the Matrix Chainlink converter that can directly convert three-phase AC to three-phase AC. A second topology is proposed that will give a AC to 4 quadrant DC converter form that will yield a galvanically isolated DC to DC converter.
Performance evaluation of an off-host communications architecture (2002)

The Computer Networks Laboratory at the University of Virginia has implemented the SAFENET lightweight protocol suite on the Navy's Desktop Tactical Computer (DTC-2). One of the research questions was whether to embed XTP in the DTC-2's UNIX kernel or run XTP on an attached processor on the DTC-2's VMEbus. Both strategies were implemented and the attached processor approach proved to have somewhat higher performance. The hardware and software system environment is surveyed, the performance achieved at the media access controller (MAC), transport, and user levels is reported, and an analytic model for predicting throughput and latency as a functon of vendor-provided or easily measured system parameters is developed. The authors' conclusions identify both the advantages and performance concerns inherent to off-host protocol execution.
Solubility of Multicomponent Systems in the Biodiesel Production by Transesterification of Jatropha curcas L. Oil with Methanol (2006)

Biodiesel is manufactured by transesterification of animal fat or vegetable oil. The reactants (oil and methanol) and the products (fatty acid methyl ester and glycerol) are partially mutual soluble in the reaction process. Inter-solubility of the reaction components is essential data for the production design and process operation. In this work, the Jatropha curcas L. oil (oil) has been transesterified to give Jatropha curcas L. oil methyl ester (FAME). The inter-solubility of FAME + methanol + glycerol, oil + FAME + methanol, oil + glycerol + methanol, and oil + FAME + glycerol in the range from 298.15 K to 333.15 K has been conducted. Methanol is completely soluble in both FAME and glycerol but is not soluble in oil. With an increase in the mass fraction of FAME, the solubility of methanol in the oil + FAME phase increases. The transesterification reaction is carried out in the methanol phase, and as a result, the reaction shows an induction period. When FAME content increases to 70 %, the oil + methanol + FAME mixture becomes a homogeneous phase. Glycerol has a low solubility in both oil and FAME and, hence, is easily separated from the final product of biodiesel. The solubility is temperature insensible.
The Displacement of Viscous Oil by Associative Polymer Solutions (2009)

Abstract About half of world oil production results from waterflooding. The remaining resources, however, are more viscous and less amenable to waterflood as conventional oil reserves are produced. In offshore and Arctic environments improved methods of cold production for viscous oil are needed because the introduction of heat to thin viscous oil appears to be unlikely. Unfavorable mobility ratio and sweep is modified by use of polymer solutions. Of the various EOR polymer formulations, newly developed associative polymers show special promise. We investigate pore and pore network scales because polymer solutions ultimately flow through the pore space of rock to displace oil. We conduct and monitor optically water/oil and polymer solution/oil displacements in a two-dimensional etched-silicon micromodel. The micromodel has the geometrical and topological characteristics of sandstone. Conventional hydrolyzed polyacrylamide solutions and newly developed associative polymer solutions with concentrations ranging from 500 ppm to 2500 ppm were tested. The crude oil had a viscosity of 210 cP at test conditions. Our results provide new insight regarding the ability of polymer to stabilize multiphase flow. At zero and low polymer concentrations, relatively long and wide fingers of injectant developed, leading to early water breakthrough and low recoveries. At increased polymer concentration, a much greater number of relatively fine fingers formed. The width to length ratio of these fingers was quite small and the absolute length of fingers decreased. At a larger scale of observation, the displacement front appears to be stabilized; hence, recovery efficiency improved remarkably. Above a concentration of 1500 ppm, plugging of the micromodel by polymer and lower oil recovery was observed for both polymer types. For tertiary polymer injection that begins at breakthrough of water, the severe fingers resulting from water injection are modified significantly. Fingers become wider and grow in the direction normal to flow as polymer solution replaces water. Apparently, improved sweep efficiency of viscous oils is possible (at this scale of investigation) even after water flooding. The associative and conventional polymer solutions improved oil recovery by about the same amount. The associative polymers, however, showed more stable fronts in comparison to conventional polymer solutions.
Netscape Navigator Gold (1997)

All the Preliminaries: What's a Web Page. Introducing the Navigator Gold Editor. Creating Your First Web Page with Netscape Page Wizard. Evaluating What You've Created. The Basics of Web Document Design: Titling Your Web Page. Using Backgrounds, Font Colors, Graphics. Inserting a Hyperlink. Adding Numbered and Bulleted Lists. Evaluating. Gaining Confidence and Control: Understanding Background Properties. Adding and Inserting Hyperlinks with Drag and Drop. Aligning Text, Graphics, Spacing Text. Linking to Internal Targets. Using Character Emphases. Revising, Reformatting and Evaluating. Creating Tables: Inserting a Table. Adding Information, Columns, Rows. Controlling Table Spacing. Choosing Options and Evaluating. Creating Dynamic Web Presentations: Why Create a Multi-Document Presentation? Looking at Winning Multi-Document Presentations. Designing Your Welcome Page. Creating Navigation Aids. Adding Links to an Image Map. Multimedia File Formats. Publishing Your Presentation. Adding Interactive Forms. Planning Your Form. Adding Drop Down List Box. Adding Text Entry Area. Option Buttons, And Check Boxes. Evaluating. Making Things Happen with Javascript: Understanding How to Add Javascript Snippets. Making Sound Play When Your Page Is Accessed. Dealing with Data from Forms. Evaluating.
Neoglycoproteins as Carriers for Receptor‐Mediated Drug Targeting in the Treatment of Experimental Visceral Leishmaniasis (1990)

Methotrexate (MTX) coupled to mannosyl bovine serum albumin (BSA) was taken up efficiently through the mannosyl receptors present on macrophages. Binding experiments indicate that conjugation does not decrease the affinity of the neoglycoprotein for its cell surface receptor. The drug conjugate eliminated intracellular amastigotes of Leishmania donovani in mouse peritoneal macrophages about 100 times more efficiently than free drug on the basis of 50% inhibitory dose. Inhibitory effect of the conjugate was directly proportional to the density of sugar on the neoglycoprotein carrier. Colchicine and monensin, inhibitors of receptor-mediated endocytosis, can prevent the leishmanicidal effect of the conjugate. Antileishmanial effect of the conjugate can be competitively inhibited by mannose-BSA and mannan. In a murine model of experimental visceral leishmaniasis the drug conjugate reduced the spleen parasite burden by more than 85% in a 30-day model whereas the same concentration of free drug caused little effect. These results indicate that MTX-neoglycoprotein conjugate binds specifically to macrophages, and is internalized and degraded in lysosomes releasing the active drug to act on Leishmania parasites. These results also represent the potential for a general approach to intracellular targeting of clinical agents for macrophage-associated disorders.
Unipro UGENE: a unified bioinformatics toolkit (2012)

UGENE binaries are freely available for MS Windows, Linux and Mac OS X at http://ugene.unipro.ru/download.html. UGENE code is licensed under the GPLv2; the information about the code licensing and copyright of integrated tools can be found in the LICENSE.3rd_party file provided with the source bundle.
Lipid domains of mycobacteria studied with fluorescent molecular probes (1999)

The complex mycobacterial cell envelope is recognized as a critical factor in our failure to control tuberculosis, leprosy and other non-tuberculous pathogens. Although its composition has been extensively determined, many details regarding the organization of the envelope remain uncertain. This is particularly so for the non-covalently bound lipids, whose natural distribution may be disrupted by conventional biochemical or cytological techniques. In order to study the native organization of lipid domains in the mycobacterial envelope, we have applied a range of fluorescent lipophilic probes to live mycobacteria, including Mycobacterium smegmatis, Mycobacterium tuberculosis, Mycobacterium avium, Mycobacterium gadium and Mycobacterium aurum, and analysed the resultant signals by fluorescence microscopy and digital image processing. Five key features were observed: (i) the presence of both envelope and intracellular lipid domains; (ii) differential localization of probes into these domains influenced predominantly by their hydrophobicity, as modelled by their calculated octanol:water partition coefficients and by their amphiphilicities; (iii) uneven distribution of lipophilic material in the envelope; (iv) selective labelling of septal regions of the envelope; and (v) modification of labelling patterns by additional treatments such as fluorescence quenching antibodies, detergents and solvents. Using this last approach, a coherent cell envelope lipid domain was demonstrated outside the cytoplasmic membrane and, for the first time, the proposed covalently linked mycolyl-arabinogalactan-peptidoglycan macromolecular complex was imaged directly. The use of fluorescent probes and high-resolution fluorescence microscopy has enabled us to obtain a coherent view of distinct lipid domains in mycobacteria. Further application of this approach will facilitate understanding of the role of lipids in the physiology of these organisms.
Charade (1993)

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Topology of the Membrane Domain of Human Erythrocyte Anion Exchange Protein, AE1 (1999)

Anion exchanger 1 (AE1) is the chloride/bicarbonate exchange protein of the erythrocyte membrane. By using a combination of introduced cysteine mutants and sulfhydryl-specific chemistry, we have mapped the topology of the human AE1 membrane domain. Twenty-seven single cysteines were introduced throughout the Leu708-Val911 region of human AE1, and these mutants were expressed by transient transfection of human embryonic kidney cells. On the basis of cysteine accessibility to membrane-permeant biotin maleimide and to membrane-impermeant lucifer yellow iodoacetamide, we have proposed a model for the topology of AE1 membrane domain. In this model, AE1 is composed of 13 typical transmembrane segments, and the Asp807-His834 region is membrane-embedded but does not have the usual alpha-helical conformation. To identify amino acids that are important for anion transport, we analyzed the anion exchange activity for all introduced cysteine mutants, using a whole cell fluorescence assay. We found that mutants G714C, S725C, and S731C have very low transport activity, implying that this region has a structurally and/or catalytically important role. We measured the residual anion transport activity after mutant treatment with the membrane-impermeant, cysteine-directed compound, sodium (2-sulfonatoethyl)methanethiosulfonate) (MTSES). Only two mutants, S852C and A858C, were inhibited by MTSES, indicating that these residues may be located in a pore-lining region.
The roles of ASK family proteins in stress responses and diseases (2009)

Apoptosis signal-regulating kinase 1 (ASK1) is a member of the mitogen-activated protein kinase kinase kinase family, which activates c-Jun N-terminal kinase and p38 in response to a diverse array of stresses such as oxidative stress, endoplasmic reticulum stress and calcium influx. In the past decade, various regulatory mechanisms of ASK1 have been elucidated, including its oxidative stress-dependent activation. Recently, it has emerged that ASK family proteins play key roles in cancer, cardiovascular diseases and neurodegenerative diseases. In this review, we summarize the recent findings on ASK family proteins and their implications in various diseases.
Evaluating some computer enhancement algorithms that improve the visibility of cometary morphology (1991)

The observed morphology of cometary comae is determined by ejection circumstances and the interaction of the ejected material with the local environment. Anisotropic emission can provide useful information on such things as orientation of the nucleus, location of active areas on the nucleus, and the formation of ion structure near the nucleus. However, discrete coma features are usually diffuse, of low amplitude, and superimposed on a steep intensity gradient radial to the nucleus. To improve the visibility of these features, a variety of digital enhancement algorithms were employed with varying degrees of success. They usually produce some degree of spatial filtering, and are chosen to optimize visibility of certain detail. Since information in the image is altered, it is important to understand the effects of parameter selection and processing artifacts can have on subsequent interpretation. Using the criteria that the ideal algorithm must enhance low contrast features while not introducing misleading artifacts (or features that cannot be seen in the stretched, unprocessed image), the suitability of various algorithms that aid cometary studies were assessed. The strong and weak points of each are identified in the context of maintaining positional integrity of features at the expense of photometric information.
Mesenchymal stem cells attenuate cardiac fibroblast proliferation and collagen synthesis through paracrine actions (2007)

Mesenchymal stem cells (MSC) transplantation has been shown to decrease fibrosis in the heart; however, whether MSC directly influence the function of cardiac fibroblasts (CFB) remains unknown. MSC-conditioned medium significantly attenuated proliferation of CFB compared with CFB-conditioned medium. MSC-conditioned medium upregulated antiproliferation-related genes such as elastin, myocardin and DNA-damage inducible transcript 3, whereas CFB-conditioned medium upregulated proliferation-related genes such as alpha-2-macroglobulin and v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog. MSC-conditioned medium significantly downregulated type I and III collagen expression, and significantly suppressed type III collagen promoter activity. MSC may exert paracrine anti-fibrotic effects at least in part through regulation of CFB proliferation and collagen synthesis.
Normal cellular and transformation-associated abl proteins share common sites for protein kinase C phosphorylation. (1987)

Viral transduction and chromosomal translocations of the c-abl gene result in the synthesis of abl proteins with structurally altered amino termini. These altered forms of the abl protein, but not the c-abl proteins, are detectably phosphorylated on tyrosine in vivo. In contrast, all forms of the abl protein are phosphorylated on serine following in vivo labeling with Pi. Treatment of NIH-3T3 cells with protein kinase C activators resulted in a four- to eightfold increase in the phosphorylation of murine c-abl due to modification of two serines on the c-abl protein. Purified protein kinase C phosphorylated all abl proteins at the same two sites. Both sites are precisely conserved in murine and human abl proteins. The sites on the abl proteins were found near the carboxy terminus. In contrast, for the epidermal growth factor receptor (T. Hunter, N. Ling, and J. A. Cooper, Nature [London] 311:480-483, 1984) and pp60src (K. L. Gould, J. R. Woodgett, J. A. Cooper, J. E. Buss, D. Shalloway, and T. Hunter, Cell 42:849-857, 1985), the sites of protein kinase C phosphorylation are amino-terminal to the kinase domain. The abl carboxy-terminal region is not necessary for the tyrosine kinase activity or transformation potential of the viral abl protein and may represent a regulatory domain. Using an in vitro immune complex kinase assay, we were not able to correlate reproducible changes in c-abl activity with phosphorylation by protein kinase C. However, the high degree of conservation of the phosphorylation sites for protein kinase C between human and mouse abl proteins suggests an important functional role.
Mannitol transport in Streptococcus mutans (1975)

A hexitol-inducible, phosphoenolpyruvate-dependent phosphotransferase system was demonstrated in Streptococcus mutans. Cell-free extracts obtained from mannitol-grown cells from a representative strain of each of the five S. mutans serotypes (AHT, BHT, C-67-1, 6715, and LM7) were capable of converting mannitol to mannitol-1-phosphate by a reaction which required phosphoenolpyruvate and Mg2+. Mannitol and sorbitol phosphotransferase activities were found in cell-free extracts prepared from cells grown on the respective substrate, but neither hexitol phosphotransferase activity was present in extracts obtained from cells grown on other substrates examined. A heat-stable, low-molecular-weight component was partially purified from glucose-grown cells and found to stimulate the mannitol phosphotransferase system. Divalent cations Mn2+ and Ca2+ partially replaced Mg2+, while Zn2+ was found to be highly inhibitory.
N-Acetylated and deacetylated 4'-fluoro-4-aminobiphenyl and 4-aminobiphenyl adducts differ in their ability to inhibit DNA replication of single-stranded M13 in vitro and of single-stranded φX174 in Escherichia coli (1992)

Calf thymus single-stranded (ss) DNA was modified with the N-sulfate conjugate of N-hydroxy-2-acetylaminofluorene (N-OH-AAF), N-hydroxy-4'-fluoro-4-acetylaminobiphenyl (N-OH-FAABP) or N-hydroxy-4-acetylaminobiphenyl (N-OH-AABP) to yield predominantly N-acetylated adducts of 2-aminofluorene, 4-aminobiphenyl and 4'-fluoro-4-amino-biphenyl respectively to C8 of deoxyguanosine (dG-C8-AAF, dG-C8-AABP and dG-C8-FAABP). The modified DNAs were used as templates for in vitro DNA synthesis. DNA replication on the randomly primed template was inhibited as compared to control (unmodified) DNA to the same extent by all three types of adducts, irrespective of whether polymerization was performed by Escherichia coli DNA polymerase I, modified T7 DNA polymerase or Thermus aquaticus (Taq) DNA polymerase. In addition, all three types of adducts completely blocked replication of ss phi X174 in an E. coli host: on average one adduct per DNA molecule was sufficient to inactivate the bacteriophage. Polyacrylamide gel electrophoresis of DNA fragments synthesized by E. coli DNA polymerase I on FAABP- and AABP-modified ss M13mp9 DNA templates, showed that termination occurred predominantly one nucleotide before (and occasionally opposite) a modified deoxyguanosine in the template. However, the deacetylated adducts, dG-C8-AF, dG-C8-ABP and dG-C8-FABP (obtained by reacting DNA with their N-trifluoroacetyl-N-acetoxy esters) were frequently bypassed during replication of ss phi X174 in E. coli, though with different efficiencies: 1 out 7, 1 out of 2 and 1 out of 3 adducts on average respectively caused bacteriophage inactivation. Polyacrylamide gel electrophoresis showed that termination of DNA synthesis occurred at least as frequently opposite as 3' to a modified deoxyguanosine in the template.
Push or Pull? Proton Responsive Ligand Effects in Rhenium Tricarbonyl CO2 Reduction Catalysts (2015)

Proton responsive ligands offer control of catalytic reactions through modulation of pH-dependent properties, second coordination sphere stabilization of transition states, or by providing a local proton source for multiproton, multielectron reactions. Two fac-[Re(I)(α-diimine)(CO)3Cl] complexes with α-diimine = 4,4'- (or 6,6'-) dihydroxy-2,2'-bipyridine (4DHBP and 6DHBP) have been prepared and analyzed as electrocatalysts for the reduction of carbon dioxide. Consecutive electrochemical reduction of these complexes yields species identical to those obtained by chemical deprotonation. An energetically feasible mechanism for reductive deprotonation is proposed in which the bpy anion is doubly protonated followed by loss of H2 and 2H(+). Cyclic voltammetry reveals a two-electron, three-wave system owing to competing EEC and ECE pathways. The chemical step of the ECE pathway might be attributed to the reductive deprotonation but cannot be distinguished from chloride dissociation. The rate obtained by digital simulation is approximately 8 s(-1). Under CO2, these competing reactions generate a two-slope catalytic waveform with onset potential of -1.65 V vs Ag/AgCl. Reduction of CO2 to CO by the [Re(I)(4DHBP-2H(+))(CO)3](-) suggests the interaction of CO2 with the deprotonated species or a third reduction followed by catalysis. Conversely, the reduced form of [Re(6DHBP)(CO)3Cl] converts CO2 to CO with a single turnover.