gebhart/patrepeval huggingface dataset:
DNA polymerase III accessory proteins. II. Characterization of delta and delta' (1993)

The gamma complex subassembly (gamma delta delta' chi psi) of DNA polymerase III holoenzyme couples ATP to assemble the ring-shaped beta subunit around DNA forming a DNA sliding clamp. This beta clamp is needed for highly processive synthesis by the holoenzyme. Here, the delta and delta' subunits of the gamma complex are studied for their structural and functional interaction with each other and with the gamma subunit. Both delta and delta are monomeric in their native state, and they bind each other tightly to form a 1:1 complex. Neither delta nor delta' alone binds tightly to the gamma subunit. However, as a complex, delta delta' binds gamma tightly to form a gamma delta delta' complex. The fact that all three subunits, gamma, delta, and delta', are needed to form a tight complex correlates well with activity assays which show that gamma and delta are capable but inefficient in assembly of the beta ring onto DNA and delta' is needed for an efficient reaction.
Periodic Mesoporous Organosilica Materials Incorporating Various Organic Functional Groups:  Synthesis, Structural Characterization, and Morphology (2005)

We describe the syntheses and characterization of a series of periodic mesoporous organosilica (PMO) materials containing various organic functional groups prepared using the direct synthesis method under basic conditions. This synthetic method allows the production of mesoporous organosilicas that have large surface areas and contain several different functional groups, such as a bridged amino, vinyl, ethyl, glycidoxypropyl, and cyanopropyl units. Moreover, the type of organosilane used as a co-precursor has a great influence on the final particle shape and modulates the overall properties of the resulting materials. By changing the precursor type, along with its concentration, the particles can adopt various morphologies, including rod-shaped and wormlike particles that have different degrees of bending. We propose a plausible mechanism to explain the formation of these shapes. We have used X-ray diffraction (XRD) patterns, nitrogen sorption properties, scanning electron microscopy (SEM), transmission electron microscopy (TEM), thermogravimetric analysis (TGA), and 13C and 29S magic angle spinning (MAS) NMR spectroscopy to characterize the structures and organic functionalities present in the resulting functionalized PMO materials.
The YDp plasmids: A uniform set of vectors bearing versatile gene disruption cassettes for Saccharomyces cerevisiae (1991)

The YDp plasmids (Yeast Disruption plasmids) are pUC9 vectors bearing a set of yeast gene disruption cassettes, all uniform in structure and differing only in the selectable marker used (HIS3, LEU2, LYS2, TRP1 or URA3). The markers, surrounded by translational termination codons, are embedded in the slightly modified sequence of the pUC9 multiple cloning sites.
Adnostic: Privacy Preserving Targeted Advertising (2010)

Online behavioral advertising (OBA) refers to the practice of tracking users across web sites in order to infer user interests and preferences. These interests and preferences are then used for selecting ads to present to the user. There is great concern that behavioral advertising in its present form infringes on user privacy. The resulting public debate — which includes consumer advocacy organizations, professional associations, and government agencies — is premised on the notion that OBA and privacy are inherently in conflict. In this paper we propose a practical architecture that enables targeting without compromising user privacy. Behavioral profiling and targeting in our system takes place in the user’s browser. We discuss the effectiveness of the system as well as potential social engineering and web-based attacks on the architecture. One complication is billing; ad-networks must bill the correct advertiser without knowing which ad was displayed to the user. We propose an efficient cryptographic billing system that directly solves the problem. We implemented the core targeting system as a Firefox extension and report on its effectiveness. 1
Virus–glycopolymer conjugates by copper(i) catalysis of atom transfer radical polymerization and azide–alkyne cycloaddition (2005)

The Cu(I)-catalyzed ATRP and azide-alkyne cycloaddition reactions together provide a versatile method for the synthesis of end-functionalized glycopolymers and their attachment to a suitably modified viral protein scaffold.
Myc Is an Essential Negative Regulator of Platelet-Derived Growth Factor Beta Receptor Expression (2000)

Platelet-derived growth factor BB (PDGF BB) is a potent mitogen for fibroblasts as well as many other cell types. Interaction of PDGF BB with the PDGF beta receptor (PDGF-betaR) activates numerous signaling pathways and leads to a decrease in receptor expression on the cell surface. PDGF-betaR downregulation is effected at two levels, the immediate internalization of ligand-receptor complexes and the reduction in pdgf-betar mRNA expression. Our studies show that pdgf-betar mRNA suppression is regulated by the c-myc proto-oncogene. Both constitutive and inducible ectopic Myc protein can suppress pdgf-betar mRNA and protein. Suppression of pdgf-betar mRNA in response to Myc is specific, since expression of the related receptor pdgf-alphar is not affected. We further show that Myc suppresses pdgf-betar mRNA expression by a mechanism which is distinguishable from Myc autosuppression. Analysis of c-Myc-null fibroblasts demonstrates that Myc is required for the repression of pdgf-betar mRNA expression in quiescent fibroblasts following mitogen stimulation. In addition, it is evident that the Myc-mediated repression of pdgf-betar mRNA levels plays an important role in the regulation of basal pdgf-betar expression in proliferating cells. Thus, our studies suggest an essential role for Myc in a negative-feedback loop regulating the expression of the PDGF-betaR.
Origin of the Color of Cv. Rhapsody in Blue Rose and Some Other So-called “Blue” Roses (2003)

Flowers of the rose cultivar Rhapsody in Blue display unusual colors, changing as they age, from a vivid red-purple to a lighter and duller purple, which are based on tonalities corresponding to hue angles between 340 and 320° in the CIELAB scale. Unexpectedly, the chemical basis of these colors is among the simplest, featuring cyanin (cyanidin 3,5-di-O-glucoside), the most frequent anthocyanin in flowers, as the sole pigment and quercetin kaempferol glycosides as copigments at a relatively low copigment/pigment ratio (about 3/1), which usually produces magenta or red shades in roses. This color shift to bluer shades is coupled with the progressive accumulation of cyanin into vacuolar anthocyanic inclusions (AVIs), the occurrence of which increases as the petals grow older. In addition to the normal λmax of cyanin at ∼545 nm, the transmission spectra of live petals and of epidermal cells exhibit a second λmax in the 620−625 nm range, the relative importance increasing with the presence of AVIs. In petals of fully opened flowers, the only pigmented structures in the vacuoles of epidermal cells are AVIs; their intense and massive absorption in the 520−640 nm area produces a much darker and bluer color than measured for the vacuolar solution present at the very first opening stage. Cyanin is probably “trapped” into AVIs at higher concentrations than would be possible in a vacuolar solution and in quinonoidal form, appearing purple-blue because of additional absorption in the 580−630 nm area. Quite similar pigmentation features were found in very ancient rose cultivars (cv. L'Evêque or Bleu Magenta), also displaying this type of so-called “blue” color. Keywords: Blue rose; cyanin; anthocyanic vacuolar inclusions (AVI); flower color
Effect of peroxisome proliferator activated receptor (PPAR)gamma agonists on prostaglandins cascade in joint cells. (2006)

In response to inflammatory cytokines, chondrocytes and synovial fibroblasts produce high amounts of prostaglandins (PG) which self-perpetuate locally the inflammatory reaction. Prostaglandins act primarily through membrane receptors coupled to G proteins but also bind to nuclear Peroxisome Proliferator-Activated Receptors (PPARs). Amongst fatty acids, the cyclopentenone metabolite of PGD2, 15-deoxy-Delta12,14PGJ2 (15d-PGJ2), was shown to be a potent ligand of the PPARgamma isotype prone to inhibit the production of inflammatory mediators. As the stimulated synthesis of PGE2 originates from the preferential coupling of inducible enzymes, cyclooxygenase-2 (COX-2) and membrane PGE synthase-1 (mPGES-1), we investigated the potency of 15d-PGJ2 to regulate prostaglandins synthesis in rat chondrocytes stimulated with interleukin-1beta (IL-1beta). We demonstrated that 15d-PGJ2, but not the high-affinity PPARgamma ligand rosiglitazone, decreased almost completely PGE2 synthesis and mPGES-1 expression. The inhibitory potency of 15d-PGJ2 was unaffected by changes in PPARgamma expression and resulted from inhibition of NF-kappaB nuclear binding and IkappaBalpha sparing, secondary to reduced phosphorylation of IKKbeta. Consistently with 15d-PGJ2 being a putative endogenous regulator of the inflammatory reaction if synthesized in sufficient amounts, the present data confirm the variable PPARgamma-dependency of its effects in joint cells while underlining possible species and cell types specificities.
Pilot-scale Production and Viability Analysis of Freeze-Dried Probiotic Bacteria Using Different Protective Agents (2010)

The functional food industry requires an improvement of probiotic strain stability during storage, especially when they are stored at room temperature. In this study, the viability of freeze-dried Lactobacillus rhamnosus IMC 501(®) and Lactobacillus paracasei IMC 502(®) using different protective agents (i.e., glycerine, mannitol, sorbitol, inulin, dextrin, Crystalean(®)) was determined and compared with semi skimmed milk (SSM) control. No significant differences were observed between the tested protectants and the control (SSM) during storage at refrigerated conditions. During storage at room temperature, only glycerine was found to stabilize viability better than other tested substances.
Two-Year Angiographic and Intravascular Ultrasound Follow-Up After Implantation of Sirolimus-Eluting Stents in Human Coronary Arteries (2003)

This study demonstrates the safety and efficacy of sirolimus-eluting Bx Velocity stents 2 years after implantation in humans. In-stent lumen dimensions remained essentially unchanged at 2-year follow-up in the 2 groups, although angiographic lumen loss was slightly higher in the FR group. Restenosis "catch-up" was not found in our patient population.
Contributions of cloned type I interferon receptor subunits to differential ligand binding1 (1997)

The human type I interferons, including at least 12 IFN-alphas, IFN-beta and IFN-omega, bind to a receptor (IFNAR) composed of at least two transmembrane subunits, IFNAR-1 and IFNAR-2. The contributions of the receptor subunits to ligand binding were investigated by measuring the binding properties of IFNAR-1 or IFNAR-2 alone, or when co-expressed. The affinity of IFNAR-2 for IFN-alpha2 was increased by the co-expression of IFNAR-1, which itself binds ligand very weakly. Most type I IFNs inhibited the binding of IFN-alpha2 to IFNAR-2 alone with IC50 values of 2-20 nM. For cells co-expressing IFNAR-1 and IFNAR-2, the IC50 values decreased 3-20-fold for various ligands, relative to their values on IFNAR-2 alone. Thus, while IFNAR-2 plays the major role in affinity determination and differential recognition of type I IFNs, IFNAR-1 modulates both the ligand affinity and selectivity of the IFNAR-1/IFNAR-2 receptor complex.
POTENTIAL OF BAMBOO (BAMBUSA VULGARIS) AS A SOURCE OF RAW MATERIAL FOR PULP AND PAPER IN GHANA (1994)

Laboratory studies were carried out to determine the pulping characteristics of a local variety of Bambusa vulgaris. The fibre length of 2.65mm and Runkel Ratio of 1.03 suggest that bamboo fibres might be suitable for pulp and paper-making. The bamboo with a lignin content of 26.8% and cellulose of 61.2% was cooked with 18% active alkali for 90mins to obtain a yield of 54.2% and kappa number of 48~2%. The pulp evaluations showed that it is not necessary to separate the node from the internode during pulping. The physical and strength properties of the pulp produced also showed that the bamboo can make good papers.
Overproduction of a Functional Fatty Acid Biosynthetic Enzyme Blocks Fatty Acid Synthesis in Escherichia coli (1998)

beta-Ketoacyl-acyl carrier protein (ACP) synthetase II (KAS II) is one of three Escherichia coli isozymes that catalyze the elongation of growing fatty acid chains by condensation of acyl-ACP with malonyl-ACP. Overexpression of this enzyme has been found to be extremely toxic to E. coli, much more so than overproduction of either of the other KAS isozymes, KAS I or KAS III. The immediate effect of KAS II overproduction is the cessation of phospholipid synthesis, and this inhibition is specifically due to the blockage of fatty acid synthesis. To determine the cause of this inhibition, we examined the intracellular pools of ACP, coenzyme A (CoA), and their acyl thioesters. Although no significant changes were detected in the acyl-ACP pools, the CoA pools were dramatically altered by KAS II overproduction. Malonyl-CoA increased to about 40% of the total cellular CoA pool upon KAS II overproduction from a steady-state level of around 0.5% in the absence of KAS II overproduction. This finding indicated that the conversion of malonyl-CoA to fatty acids had been blocked and could be explained if either the conversion of malonyl-CoA to malonyl-ACP and/or the elongation reactions of fatty acid synthesis had been blocked. Overproduction of malonyl-CoA:ACP transacylase, the enzyme catalyzing the conversion of malonyl-CoA to malonyl-ACP, partially relieved the toxicity of KAS II overproduction, consistent with a model in which high levels of KAS II blocks access of the other KAS isozymes to malonyl-CoA:ACP transacylase.
Preparation of Microemulsions Using Polyglycerol Fatty Acid Esters as Surfactant for the Delivery of Protein Drugs (1996)

Phase diagrams containing the microemulsion region were constructed for pseudo-ternary systems composed for polyglycerol fatty acid ester/cosurfactant/Captex 300/water. It was found necessary to add ethanol, 1-propanol, 1-butanol as cosurfactant to produce microemulsions. The results also demonstrated microemulsions were only able to form when employing polyglycerol fatty acid esters with hydrophile-lipophile balances (HLBs) between 8 and 13, such as MO500, MO750, SO750, and ML310. Most microemulsions were determined to be Winsor type IV by dilution and dye solubility tests. Microemulsions stored at ambient temperature maintained constant viscosity, indicating that the system was thermodynamically stable for long periods. Further, several microemulsion formulations were demonstrated to be promising for oral delivery of insulin based on the results of stability tests and acid-protection efficiency.
A blood biomarker for monitoring response to anti-EGFR therapy (2018)

Our results show that changes in serum PRDX6 during the course of gefitinib treatment of xenograft models provide insight into tumor response and such an approach offers several advantages over imaging-based strategies for monitoring response to anti-EGFR agents.
The PRINTS Database of Protein Fingerprints:  A Novel Information Resource for Computational Molecular Biology (1997)

PRINTS is a compendium of protein motif fingerprints derived from the OWL composite sequence database. Fingerprints are groups of motifs within sequence alignments whose conserved nature allows them to be used as signatures of family membership. Fingerprints inherently offer improved diagnostic reliability over single motif methods by virtue of the mutual context provided by motif neighbors. To date, 650 fingerprints have been constructed and stored in PRINTS, the size of which has doubled in the last 2 years. The current version, 14.0, encodes 3500 motifs, covering a range of globular and membrane proteins, modular polypeptides, and so on. The database is now accessible via the UCL Bioinformatics Server on http:@ www.biochem.ucl.ac.uk/bsm/dbbrowser/. We describe here progress with the database, its compilation and interrogation software, and its Web interface.
Acrylamide in French Fries:  Influence of Free Amino Acids and Sugars (2004)

The free amino acid profile and sugar (fructose, glucose, and sucrose) composition were determined in potato samples selected to give a large range of variation (a total of 66 samples). From these samples French fries were produced in a laboratory-scale simulation of an industrial process followed by a finish fry at 180 degrees C for 3.5 min using a restaurant fryer. The final product was blast frozen and analyzed for acrylamide. Acrylamide was detected in all samples, but its concentration varied significantly from 50 to 1800 ng/g. For isotope dilution (13C3) acrylamide analysis, samples were extracted with water, cleaned up on HLB Oasis polymeric and Accucat mixed mode anion and cation exchange SPE columns, and analyzed by LC-MS/MS. Statistical analysis of the data indicates that the effect of sugars and asparagine on the concentration of acrylamide in French fries is positive and significant (p < 0.001). It appears that one of the ways acrylamide formation in French fries can be effectively controlled is by the use of raw products with low sugar (and to a lesser degree, asparagine) content.
Quantitative methods for developing Fc mutants with extended half‐lives (2005)

Fc mutants with increased binding affinity for the neonatal receptor, FcRn, exhibit increased half-lives in vivo, and represent an attractive means for extending the half-lives of therapeutic antibodies. The half-lives of other therapeutic molecules (e.g., proteins) may also be extended by conjugating them to Fc fragments, thus decreasing the frequency of patient injections and allowing the administration of low and potentially nontoxic concentrations of the therapeutics. To investigate the possibility for further increasing the half-life of Fc, a pair of quantitative methods is presented to complement combinatorial screening and in vivo testing. Specifically, a simple molecular modeling procedure was developed to predict relative Gibbs free energies of binding values (DeltaDeltaGbind) between Fc and FcRn across different mutants and species. This procedure was found to reasonably reproduce experimental DeltaDeltaGbind values from our experiments and the literature, and may be used as an initial screen to explore Fc sequence space more fully prior to experimental testing. In addition, a mathematical model of Fc trafficking was formulated and combined with a cell-level pulse-chase assay to obtain a quantitative recycling parameter in human T84 cells. This Fc recycling parameter was found to be correlated with binding affinity, but captures the pH dependent nature of the interaction between Fc and FcRn and may serve as an additional screen following combinatorial experiments.
Design Constraints of Photonic-Lantern Spatial Multiplexer Based on Laser-Inscribed 3-D Waveguide Technology (2014)

Laser-inscribed 3-D waveguide (3DW) technology has been applied to realize photonic-lantern spatial multiplexer (SMUX), which potentially enables lossless mode (de)multiplexing. However, the index contrast Δn between the transparent substrate and the spatially-inscribed waveguides by femto-second laser pulses is generally smaller than <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math>$6 \times 10^{-3}$</tex-math></inline-formula> . It is simulated that a 3DW SMUX with <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math>$\Delta {\rm n} &lt; 6 \times 10^{-3}$</tex-math></inline-formula> is able to provide a low mode-dependent loss (MDL) and coupler insertion loss (CIL) when coupling to a three-mode few-mode fiber (FMF). However, in six- and 15-mode cases, to guide all supermodes, few-mode region created by coupled or merged waveguides at the FMF side of the 3DW SMUX cannot be very small. This results in mode-profile mismatch between the 3DW SMUX and a low differential-group-delay FMF, which is generally with Δn around <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math>$1 \times 10^{-2}$ </tex-math></inline-formula> . Instead of employing bulky imaging optics, uptapering FMF is proposed to enlarge the modes of the FMF for minimizing the mode-profile mismatch. Simulation shows MDL and CIL enhancement can be achieved by the uptapering solution. It also points out that as mode number increases to 15, although uptapering FMF still improves coupling performance, low MDL < 1dB cannot be acquired with <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math>$\Delta {\rm n} &lt; = 6 \times 10^{-3}$</tex-math></inline-formula> . In order to achieve a lossless mode (de)multiplexing for 15 spatial modes, <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math>$\Delta {\rm n} = 1 \times 10^{-2} $</tex-math></inline-formula> is required for a 15-core 3DW SMUX. Moreover, a fully-packaged dual-channel 3DW coupling circuit including two six-mode SMUXes is introduced and experimentally demonstrated. <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math>${\rm MDL = 7\; dB}$</tex-math> </inline-formula> and CIL < 8 dB is achieved in a loop through measurement with the two SMUXes. Mode-profile mismatch due to the limited Δn of the 3DW device is solved by uptapering FMF with a factor of 1.4.
Human leukocyte and porcine pancreatic elastase: x-ray crystal structures, mechanism, substrate specificity, and mechanism-based inhibitors (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHuman leukocyte and porcine pancreatic elastase: x-ray crystal structures, mechanism, substrate specificity, and mechanism-based inhibitorsWolfram Bode, Edgar Meyer, Jr., and James C. PowersCite this: Biochemistry 1989, 28, 5, 1951–1963Publication Date (Print):March 7, 1989Publication History Published online1 May 2002Published inissue 7 March 1989https://pubs.acs.org/doi/10.1021/bi00431a001https://doi.org/10.1021/bi00431a001research-articleACS PublicationsRequest reuse permissionsArticle Views1200Altmetric-Citations302LEARN 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