gebhart/patrepeval huggingface dataset:
Localization of the heparin-binding site on complement factor H. (1991)

Factor H is a regulator of complement activation and, in this capacity, it prevents activation of the alternative pathway on host cells and tissues when it recognizes markers on these surfaces. This report describes the binding characteristics and location of the site on factor H that is responsible for host recognition. Factor H was found to bind a variety of polyanions, including heparin, heparan sulfate, dextran sulfate, and clusters of sialic acid. In heparin-agarose binding assays it exhibited an affinity for heparin only 2-fold weaker than that of antithrombin III. Factor H exhibited little or no affinity for polyaspartic acid or bacterial colominic acid (polysialic acid). Factor H (Mr 150,000 with approximate dimensions of 30 x 600 A) is composed of 20 highly homologous domains (SCRs) that are arranged as beads on a string. Polyanions were found to block a tryptic cleavage site in domain 15, and a photoaffinity-tagged heparin probe labeled the region between domains 12 and 15. Affinity chromatography of tryptic fragments on heparin-Sepharose confirmed that this region contained the heparin-binding site. CNBr cleavage at Met787 located between SCRs 13 and 14 split the photoaffinity-tagged region. Sequence analysis strongly suggests that domain 13 contains the primary site of polyanion binding. Factor H expresses its complement regulatory function through a site located in domains 4-6 where C3b binds. Thus, the polyanion-binding site that regulates the affinity of factor H for C3b appears to reside more than 200 A away from the C3b-binding site.
A Single Gene (tts) Located outside the cap Locus Directs the Formation of Streptococcus pneumoniae Type 37 Capsular Polysaccharide (1999)

The molecular aspects of the type 37 pneumococcal capsular biosynthesis, a homopolysaccharide composed of sophorosyl units (beta-d-Glc-(1-->2)-beta-d-Glc) linked by beta-1,3 bonds, have been studied. Remarkably, the biosynthesis of the type 37 capsule is driven by a single gene (tts) located far apart from the cap locus responsible for capsular formation in all of the types characterized to date in Streptococcus pneumoniae. However, a cap37 locus virtually identical to the cap33f cluster has been found in type 37 strains, although some of its genes are inactivated by mutations. The tts gene has been sequenced and its transcription start point determined. Tts shows sequence motifs characteristic of cellulose synthases and other beta-glycosyltransferases. Insertion of the tts gene into the pneumococcal DNA causes a noticeable genome reorganization in such a way that genes normally separated by more than 350 kb in the chromosome are located together in clinical isolates of type 37. Encapsulated pneumococcal strains belonging to 10 different serotypes (or serogroups) transformed with tts synthesized type 37 polysaccharide, leading to the formation of strains that display the binary type of capsule. Type 37 pneumococcus constitutes the first case of a natural, genetically binary strain and represents a novel alternative to the mechanisms of intertype transformation.
Reactive Extraction of Levulinic Acid by Amberlite LA-2 Extractant (2009)

The production of organic acids at relatively low concentrations in aqueous solutions is typical of both electrochemical and biochemical syntheses. The recovery of these solute species can be achieved by solvent extraction, and the reactive recovery of carboxylic acids from aqueous solutions has received increasing attention. In this study the reactive extraction of levulinic acid was done at 298.15 K, and all experiments were reported on the extraction of levulinic acid by Amberlite LA-2 dissolved in five different esters (dimethyl phthalate, dimethyl adipate, dimethyl succinate, dimethyl glutarate, and diethyl carbonate), five different alcohols (isoamyl alcohol, hexan-1-ol, octan-1-ol, nonan-1-ol, and decan-1-ol) and two different ketones (diisobutyl ketone (DIBK) and methyl isobutyl ketone (MIBK)). Furthermore, single pure solvents (not containing Amberlite LA-2) were used for physical extraction. Experimental results of batch extraction experiments were calculated and reported as distribution coefficients (KD), loading factors (TT), stoichiometric loading factors (TS), separation factors (Sf) and extraction efficiencies (E). The isoamyl alcohol was found to be the most effective solvent with a maximum distribution value (KD) of 68.017. According to the data determined from the experiments, a linear solvation energy relationship (LSER) model equation was found to calculate loading factors (TT) for the alcohols with an R2 value of 0.98.
Postsynthetic modification of mixed-linker metal–organic frameworks for ethylene oligomerization (2014)

MOFs-containing nickel catalysts have been synthesized through postsynthetic modification of mixed-linker MOFs (Zn<sub>4</sub>O(BDC)<sub>x</sub>(ABDC)<sub>3−x</sub>) and used for ethylene oligomerization.
The 47-kD lens-specific protein phakinin is a tailless intermediate filament protein and an assembly partner of filensin. (1993)

In previous studies we have characterized a lens-specific intermediate filament (IF) protein, termed filensin. Filensin does not self-assemble into regular IFs but is known to associate with another 47-kD lens-specific protein which has been suggested to represent its assembly partner. To address this possibility, we cloned and sequenced the cDNA coding for the bovine 47-kD protein which we have termed phakinin (from the greek phi alpha kappa omicron sigma = phakos = lens). The predicted sequence comprises 406 amino acids and shows significant similarity (31.3% identity over 358 residues) to type I cytokeratins. Phakinin possesses a 95-residue, non-helical domain (head) and a 311 amino acid long alpha-helical domain punctuated with heptad repeats (rod). Similar to cytokeratin 19, phakinin lacks a COOH-terminal tail domain and it therefore represents the second known example of a naturally tailless IF protein. Confocal microscopy on frozen lens sections reveals that phakinin colocalizes with filensin and is distributed along the periphery of the lens fiber cells. Quantitative immunoblotting with whole lens fiber cell preparations and fractions of washed lens membranes suggest that the natural stoichiometry of phakinin to filensin is approximately 3:1. Under in vitro conditions, phakinin self-assembles into metastable filamentous structures which tend to aggregate into thick bundles. However, mixing of phakinin and filensin at an optimal ratio of 3:1 yields stable 10-nm filaments which have a smooth surface and are ultrastructurally indistinguishable from "mainstream" IFs. Immunolabeling with specific antibodies shows that these filaments represent phakinin/filensin heteropolymers. Despite its homology to the cytokeratins, phakinin does not coassemble with acidic (type I), or basic (type II) cytokeratins. From these data we conclude that filensin and phakinin are obligate heteropolymers which constitute a new membrane-associated, lens-specific filament system related to, but distinct from the known classes of IFs.
Stable V/f control system with unity power factor for PMSM drives (2012)

This paper develops a scalar V/f control system for permanent magnet synchronous motor (PMSM) drives with two stabilizing feedback corrections: i) a voltage-vector speed correction using active power variation, in action only in transient states, and ii) a voltage amplitude correction based on unity power-factor regulation loop, employing reactive power. Motor/generator operating mode is allowed using the active power sign information. The proposed solution, inherent for sensorless control, is simple, requires reduced computation time, thus it is competitive for very-high variable speed PMSM drives like fans, pumps, micro gas-turbine generators, etc. Significant simulation results prove good performance for the proposed control structure in steady and transient states, for fast speed references and step rated load torque.
Temperature‐dependent transmembrane potential changes in cells infected with a temperature‐sensitive moloney sarcoma virus (1984)

Normal rat kidney cells (NRK) infected with the temperature-sensitive (ts) transformation mutant of Moloney murine sarcoma virus yielded a clone of cells, 6m2, that exhibited a transformed morphology at 33 degrees C and a normal morphology at 39 degrees C. Transmembrane potential (Em) was measured fluorometrically using a cyanine dye diS-C3-(5). Fluorescence was inversely correlated with Em. Cells at 33 degrees C had lower Em. Em changes were recorded within 15 minutes of temperature shift from 33 degrees C to 39 degrees C in both directions, increasing in the 33 degrees C to 39 degrees C direction and decreasing in the 39 degrees C to 33 degrees C direction. Uninfected NRK cells when shifted under the same condition exhibited small fluorescence changes in the 33 degrees C to 39 degrees C direction. Shifting from 39 degrees C to 33 degrees C resulted in Em changes similar to those in 6m2 cells. Also studied was a cell line infected with a spontaneous revertant of the ts mutant, designated 54-5A4; it was transformed at both temperatures. Shifting from 33 degrees C to 39 degrees C in both directions yielded small changes. Transmembrane potential changes in 6m2 cells precede other transformation-specific changes that occur after a temperature shift.
Short Communication: Interferon-α Response to Swine Arterivirus (PoAV), the Porcine Reproductive and Respiratory Syndrome Virus (1998)

We studied the interferon-alpha (IFN-alpha) system in relation to the porcine arterivirus (PoAV), porcine reproductive and respiratory syndrome virus (PRRSV). Recombinant porcine IFN-alpha inhibited the growth of this virus in alveolar macrophage cultures. When pigs were challenged intranasally with PoAV, their serum contained IFN-alpha in relatively low concentrations on the second day after challenge and up to 5 days at the latest. Most animals had no IFN-alpha in their lung secretions, even though PoAV replicates in the respiratory tract. In vitro, PoAV replicates in alveolar macrophages, but neither these nor peripheral blood mononuclear cells (PBMC) produced IFN-alpha in response to infection. This may be because PoAV suppresses IFN-alpha production. When macrophages treated with PoAV were superinfected with swine transmissible gastroenteritis virus (TGEV), a known good inducer of IFN, no IFN-alpha was detected. This suppressive effect was lost when the virus was inactivated by UV light. Our results suggest that downregulation of IFN-alpha production may play an important part in enabling PoAV to replicate in cell cultures and in pigs.
The Sch9 protein kinase in the yeast Saccharomyces cerevisiae controls cAPK activity and is required for nitrogen activation of the fermentable-growth-medium-induced (FGM) pathway (1997)

In cells of the yeast Saccharomyces cerevisiae, trehalase activation, repression of CTT1 (catalase), SSA3 (Hsp70) and other STRE-controlled genes, feedback inhibition of cAMP synthesis and to some extent induction of ribosomal protein genes is controlled by the Ras-adenylate cyclase pathway and by the fermentable-growth-medium-induced pathway (FGM pathway). When derepressed cells are shifted from a non-fermentable carbon source to glucose, the Ras-adenylate cyclase pathway is transiently activated while the FGM pathway triggers a more lasting activation of the same targets when the cells become glucose-repressed. Activation of the FGM pathway is not mediated by cAMP but requires catalytic activity of cAMP-dependent protein kinase (cAPK; Tpk1, 2 or 3). This study shows that elimination of Sch9, a protein kinase with homology to the catalytic subunits of cAPK, affects all target systems in derepressed cells in a way consistent with higher activity of cAPK in vivo. In vitro measurements with trehalase and kemptide as substrates confirmed that elimination of sch9 enhances cAPK activity about two- to threefold, in both the absence and presence of cAMP. In vivo it similarly affected the basal and final level but not the extent of the glucose-induced responses in derepressed cells. The reduction in growth rate caused by deletion of SCH9 is unlikely to be responsible for the increase in cAPK activity since reduction of growth rate generally leads to lower cAPK activity in yeast. On the other hand, deletion of SCH9 abolished the responses of the protein kinase A targets in glucose-repressed cells. Re-addition of nitrogen to cells starved for nitrogen in the presence of glucose failed to trigger activation of trehalase, caused strongly reduced and aberrant repression of CTT1 and SSA3, and failed to induce the upshift in RPL25 expression. From these results three conclusions can be drawn: (1) Sch9 either directly or indirectly reduces the activity of protein kinase A; (2) Sch9 is not required for glucose-induced activation of the Ras-adenylate cyclase pathway; and (3) Sch9 is required for nitrogen-induced activation of the FGM pathway. The latter indicates that Sch9 might be the target of the FGM pathway rather than cAPK itself.
Defining the Residual Vision in Leber Congenital Amaurosis Caused byRPE65Mutations (2009)

Residual rod as well as cone function is detectable in RPE65-LCA. The finding of different regional patterns of visual loss in these patients suggests that the optimal retinal site(s) for subretinal gene delivery to achieve efficacy are likely to change with disease progression.
(R,R,R)-2,5-Diaminocylohexanecarboxylic Acid, a Building Block for Water-Soluble, Helix-Forming β-Peptides (2000)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXT(R,R,R)-2,5-Diaminocylohexanecarboxylic Acid, a Building Block for Water-Soluble, Helix-Forming β-PeptidesDaniel H. Appella, Paul R. LePlae, Tami L. Raguse, and Samuel H. GellmanView Author Information Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706-1396 [email protected]Cite this: J. Org. Chem. 2000, 65, 15, 4766–4769Publication Date (Web):June 23, 2000Publication History Received29 February 2000Published online23 June 2000Published inissue 1 July 2000https://pubs.acs.org/doi/10.1021/jo000277hhttps://doi.org/10.1021/jo000277hbrief-reportACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views639Altmetric-Citations33LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Alcohols,Azides,Conformation,Hydrolysis,Pharmaceuticals Get e-Alerts
Relationship between the Optimal Temperature for Oxidative Refolding and the Thermal Stability of Refolded State of Hen Lysozyme Three-Disulfide Derivatives (1994)

The temperature dependence of the efficiency of oxidative refolding was examined for hen lysozyme three-disulfide derivatives produced in Escherichia coli. Each derivative was designed to lack one of the four disulfide bridges in authentic lysozyme: delta 1 (Cys6-->Ser, Cys127-->Ser), delta 2 (Cys30-->Ser, Cys115-->Ser), delta 3 (Cys64-->Ser, Cys80-->Ser), delta 4 (Cys76-->Ser, Cys94-->Ser), delta 2Ala (Cys30-->Ala, Cys115-->Ala), and delta 4Ala (Cys76-->Ala, Cys94-->Ala). The optimal refolding temperature was lowest for delta 1 (19 degrees C) and highest for delta 4Ala (30 degrees C). The chromatographically purified, completely refolded three-disulfide species were not stable above the optimal refolding temperature in the presence of glutathione. The stability of each of them was determined from the far-UV CD thermal denaturation measurement at pH 3.9 in the absence of glutathione, where the denaturation was reversible. The transition temperature was lowest for delta 1 and highest for delta 4Ala. Precise values of difference in the transition temperature among the three-disulfide derivatives were found to correlate with those in the optimal refolding temperature. Next, the effect of glycerol, which has been shown to increase the refolding efficiency [Sawano et al. (1992) FEBS Lett. 303, 11-14], was examined for delta 1 in detail. The optimal temperature for refolding increased by 3-4 degrees C with the increase in glycerol concentration by 10%. The amount of increase in the optimal refolding temperature was nearly equal to the amount of the increase in thermal stability in the presence of glycerol of refolded and purified delta 1.(ABSTRACT TRUNCATED AT 250 WORDS)
Genetic and Biochemical Characterization of the Phosphoenolpyruvate:Glucose/Mannose Phosphotransferase System ofStreptococcus thermophilus (2003)

In most streptococci, glucose is transported by the phosphoenolpyruvate (PEP):glucose/mannose phosphotransferase system (PTS) via HPr and IIAB(Man), two proteins involved in regulatory mechanisms. While most strains of Streptococcus thermophilus do not or poorly metabolize glucose, compelling evidence suggests that S. thermophilus possesses the genes that encode the glucose/mannose general and specific PTS proteins. The purposes of this study were to determine (i) whether these PTS genes are expressed, (ii) whether the PTS proteins encoded by these genes are able to transfer a phosphate group from PEP to glucose/mannose PTS substrates, and (iii) whether these proteins catalyze sugar transport. The pts operon is made up of the genes encoding HPr (ptsH) and enzyme I (EI) (ptsI), which are transcribed into a 0.6-kb ptsH mRNA and a 2.3-kb ptsHI mRNA. The specific glucose/mannose PTS proteins, IIAB(Man), IIC(Man), IID(Man), and the ManO protein, are encoded by manL, manM, manN, and manO, respectively, which make up the man operon. The man operon is transcribed into a single 3.5-kb mRNA. To assess the phosphotransfer competence of these PTS proteins, in vitro PEP-dependent phosphorylation experiments were conducted with purified HPr, EI, and IIAB(Man) as well as membrane fragments containing IIC(Man) and IID(Man). These PTS components efficiently transferred a phosphate group from PEP to glucose, mannose, 2-deoxyglucose, and (to a lesser extent) fructose, which are common streptococcal glucose/mannose PTS substrates. Whole cells were unable to catalyze the uptake of mannose and 2-deoxyglucose, demonstrating the inability of the S. thermophilus PTS proteins to operate as a proficient transport system. This inability to transport mannose and 2-deoxyglucose may be due to a defective IIC domain. We propose that in S. thermophilus, the general and specific glucose/mannose PTS proteins are not involved in glucose transport but might have regulatory functions associated with the phosphotransfer properties of HPr and IIAB(Man).
Enzymic Methylation of Arsenic Compounds: Assay, Partial Purification, and Properties of Arsenite Methyltransferase and Monomethylarsonic Acid Methyltransferase of Rabbit Liver (1995)

A rapid, accurate, in vitro assay utilizing radioactive S-adenosylmethionine (SAM) has been developed for the methylation of arsenite and monomethylarsonate (MMA) by rabbit liver methyltransferases. The assay has been validated by separating, identifying, and measuring the products of the reaction using chloroform extraction, ion exchange chromatography, TLC, or HPLC. The enzymes involved in this pathway, arsenite methyltransferase and MMA methyltransferase, have been purified approximately 2000-fold from rabbit liver. After gel electrophoresis, a single band is obtained with both enzyme activities in it. The pH optima for purified arsenite methyltransferase and monomethylarsonic acid methyltransferase are 8.2 and 8.0, respectively. A thiol, S-adenosylmethionine, and arsenite are required for the partially purified arsenite methyltransferase that catalyzes the synthesis of monomethylarsonate. A different enzyme activity that catalyzes the methylation of monomethylarsonate to dimethylarsinate also requires SAM and a thiol. Even though arsenite methyltransferase and monomethylarsonate methyltransferase have different substrates, pH optima, and saturation concentrations for their substrates, whether the two activities are present on one protein molecule or different protein molecules is still uncertain. Both activities have a molecular mass of 60 kDa as determined by gel exclusion chromatography. There is no evidence at the present time for these enzyme activities being on different protein molecules. Neither arsenate, selenate, selenite, or selenide are methylated by the purified enzyme preparations. Results from the use of crude extracts, often called cytosol, to study the properties of these methyltransferases dealing with arsenic species should be viewed with caution since such crude extracts contain inhibiting and other interfering activities.
Characterization of phase and frequency instabilities in precision frequency sources: Fifteen years of progress (1978)

Precision frequency sources such as quartz oscillators, masers, and passive atomic frequency standards are affected by phase and frequency instabilities including both random and deterministic components. It is of prime importance to have a comprehensive characterization of these instabilities in order to be able to assess the potential utility of each source. For that purpose, many parameters have been proposed especially for dealing with random fluctuations. Some of them have been recommended by the IEEE Subcommittee on Frequency Stability and later by Study Group 7 on "Standard Frequencies and Time Signals" of the International Radio Consultative Committee (CCIR). Others are not so widely used but show interesting capabilities. This paper aims at giving a broad review of parameters proposed for phase and frequency instability characterization, including both classical widely used concepts and more recent less familiar approaches. Transfer functions that link frequency-domain and time-domain parameters are emphasized because they provide improved understanding of the properties of a given time-domain parameter or facilitate introducing of new parameters. As far as new approaches are concerned, an attempt has been made to demonstrate clearly their respective advantages. To this end, some developments that did not appear in the original references ate presented here, e.g, the modified three sample variance Σ <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">y</inf> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> (τ), the expressions of 〈δy <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-</sup> <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</inf> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> 〉, the intetpretation of structure functions of phase and its relations with Σ <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">y</inf> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> (τ) and the Hadamard variance. The effects of polynomial phase and frequency drifts on various parameters have also been pointed out in parallel with those of random processes modeled by power-law spectral densities.