gebhart/patrepeval huggingface dataset:
Phase separation in binary mixtures containing polymers: A quantitative comparison of single‐chain‐in‐mean‐field simulations and computer simulations of the corresponding multichain systems (2005)

Abstract We discuss a phenomenological, coarse‐grained simulation scheme, single‐chain‐in‐mean‐field (SCMF) simulation, for investigating the kinetics of phase separation in dense polymer blends and mixtures of polymers and solvents. In the spirit of self‐consistent‐field calculations, we approximate the interacting multichain problem by that of a single chain in an external field, which, in turn, depends on the local densities of the components. To study the time evolution of the mixture, we perform an explicit Monte Carlo (MC) simulation of an ensemble of independent chains in the external field and periodically calculate the average densities and update the external field. Unlike dynamic self‐consistent‐field theory, these SCMF simulations do not assume that the chain conformations relax much more quickly than the density and incorporate the single‐chain dynamics explicitly rather than via an Onsager coefficient. This allows us to study systems with large spatial inhomogeneities and dynamic asymmetries. To assess the accuracy and limitations of the simulation scheme, we compare the results of SCMF simulations using a discretized Edwards Hamiltonian with computer simulations of the corresponding multichain system for (1) the early stages of spinodal decomposition of a symmetric binary polymer blend in response to a quench from χ N = 0.314 to χ N = 5 (where χ is the Flory–Huggins parameter and N is the number of segments), for which the growth rate of composition fluctuations is compared with MC simulations of the bond fluctuation model and alternative dynamic self‐consistent‐field calculations, and (2) the evaporation of a solvent from a low‐molecular‐weight thin polymer film, for which a comparison is made with molecular dynamics (MD) simulations of a bead‐necklace model with a monomeric solvent. In the latter case, the polymer conformations are extracted from MD simulations and modeled in the SCMF simulations by a discretized Edwards Hamiltonian augmented by a chain‐bending potential. From the MD simulations of thin polymer films in equilibrium with its vapor, phase coexistence has been determined, and the second‐ and third‐order virial coefficients in the SCMF simulations have been adjusted accordingly. Finally, MD simulations of bulk solutions of a polymer and a solvent over a range of compositions, as well as the pure solvent at various densities, have been performed to determine self‐diffusion coefficients that enter the SCMF simulations in the form of density‐dependent segmental mobilities. A comparison of the polymer and solvent profiles in a thin film as a function of time and the fraction of the solvent evaporating from a solvent‐swollen film, as obtained from MD simulations and parameterized SCMF simulations, shows satisfactory agreement for this simple mapping procedure. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 934–958, 2005
An investigation into face pose distributions (2002)

Visual perception of faces is invariant under many transformations, perhaps the most problematic of which is pose change (face rotating in depth). We use a variation of Gabor wavelet transform (GWT) as a representation framework for investigating face pose measurement. Dimensionality reduction using principal components analysis (PCA) enables pose changes to be visualised as manifolds in low-dimensional subspaces and provides a useful mechanism for investigating these changes. The effectiveness of measuring face pose with GWT representations was examined using PCA. We discuss our experimental results and draw a few preliminary conclusions.
Analyses of Ehrlichia canis and a canine granulocytic Ehrlichia infection (1992)

Ehrlichia canis and canine granulocytic Ehrlichia sp. (CGE) infect canine monocytes and granulocytes, respectively. E. canis has been cultured in vitro and used to develop an immunofluorescence assay. CGE has not been cultured, and a serologic assay is not available. The sera of dogs infected with CGE were reported to react with E. canis by immunofluorescence. In this study, the temporal response of immunoglobulin G (IgG) was determined by an enzyme-linked immunosorbent assay (ELISA) with purified E. canis antigen in four dogs experimentally infected with E. canis, in two dogs experimentally infected with CGE, and in one dog infected with E. canis and subsequently infected with CGE. E. canis-infected dogs developed an IgG ELISA result of 1.5 or greater for the optical density signal/noise ratio by 2 months postinfection. CGE challenge of a dog with a previous E. canis infection induced an anamnestic increase in the IgG ELISA result; however, CGE infection alone did not induce a significant IgG ELISA response. Western immunoblot analysis showed that dogs infected with E. canis developed antibodies initially that reacted with low-molecular-mass proteins (30, 24, and 21 kDa) and subsequently with higher-molecular-mass proteins (160, 100, 78, 64, 47, and 40 kDa). In contrast, CGE-infected dogs showed reactions with the same higher-molecular-mass proteins of E. canis but, unlike E. canis-infected dogs, not with the low-molecular-mass proteins of E. canis. Of 10 serum samples collected in the field of Indonesia from dogs with tropical canine pancytopenia, all had an optical density signal minus noise value of 2.54 or greater in the IgG ELISA and reacted with E. canis antigen in a pattern similar to that of serum samples from dogs experimentally infected with E. canis in Western immunoblotting. This study suggests that the IgG ELISA and Western immunoblotting with purified E. canis as the antigen are useful in distinguishing between E. canis and CGE infections in dogs.
Molecular interactions and metal binding in the theophylline-binding core of an RNA aptamer (2000)

An RNA aptamer containing a 15-nt binding site shows high affinity and specificity for the bronchodilator theophylline. A variety of base modifications or 2' deoxyribose substitutions in binding-site residues were tested for theophyllinebinding affinity and the results were compared with the previously determined three-dimensional structure of the RNA-theophylline complex. The RNA-theophylline complex contains a U6-A28-U23 base triple, and disruption of this A28-U23 Hoogsteen-pair by a 7-deaza, 2'-deoxy A28 mutant reduces theophylline binding >45-fold at 25 degrees C. U24 is part of a U-turn in the core of the RNA, and disruption of this U-turn motif by a 2'-deoxy substitution of U24 also reduces theophylline binding by >90-fold. Several mutations outside the "conserved core" of the RNA aptamer showed reduced binding affinity, and these effects could be rationalized by comparison with the three-dimensional structure of the complex. Divalent ions are absolutely required for high-affinity theophylline binding. High-affinity binding was observed with 5 mM Mg2+, Mn2+, or Co2+ ions, whereas little or no significant binding was observed for other divalent or lanthanide ions. A metal-binding site in the core of the complex was revealed by paramagnetic Mn2+-induced broadening of specific RNA resonances in the NMR spectra. When caffeine is added to the aptamer in tenfold excess, the NMR spectra show no evidence for binding in the conserved core and instead the drug stacks on the terminal helix. The lack of interaction between caffeine and the theophylline-binding site emphasizes the extreme molecular discrimination of this RNA aptamer.
Glutamate and astrocytes—Key players in human mesial temporal lobe epilepsy? (2008)

Approximately one-third of all patients with epilepsy continue to suffer from seizures even after appropriate treatment with antiepileptic drugs. Medically refractory epilepsies are associated with considerable morbidity and mortality, and more efficacious therapies against these disorders are clearly needed. However, the discovery of better therapies has been lagging due to an incomplete understanding of the mechanisms underlying the development of epilepsy (epileptogensis) and seizures (ictogenesis) in humans. An increasing number of studies have suggested that an abnormal amplification of glutamatergic activity--often referred to as the "glutamate hypothesis"--is involved in the pathophysiology of seizures and certain types of medically refractory epilepsies. For example, elevated levels of extracellular glutamate in hyperexcitable areas of the brain, up-regulation of glutamate receptors, and loss of the glutamate-metabolizing enzyme, glutamine synthetase (GS), have all been reported in patients with mesial temporal lobe epilepsy (MTLE). Moreover, it appears that glial cells, particularly the astrocyte, may play a key role in the glutamate overflow in MTLE. Proliferation of astrocytes is a hallmark of the epileptogenic focus in MTLE, and the proliferated cells are characterized by several unique features that are permissive for the excessive accumulation and release of astrocytic glutamate. Here, we assess recent data regarding the glutamate excess in epilepsy, review the role of glutamine synthetase, and discuss the implications of astrocytes in the pathophysiology of MTLE.
Geraniol and Geranial Dehydrogenases Induced in Anaerobic Monoterpene Degradation by Castellaniella defragrans (2012)

Castellaniella defragrans is a Betaproteobacterium capable of coupling the oxidation of monoterpenes with denitrification. Geraniol dehydrogenase (GeDH) activity was induced during growth with limonene in comparison to growth with acetate. The N-terminal sequence of the purified enzyme directed the cloning of the corresponding open reading frame (ORF), the first bacterial gene for a GeDH (geoA, for geraniol oxidation pathway). The C. defragrans geraniol dehydrogenase is a homodimeric enzyme that affiliates with the zinc-containing benzyl alcohol dehydrogenases in the superfamily of medium-chain-length dehydrogenases/reductases (MDR). The purified enzyme most efficiently catalyzes the oxidation of perillyl alcohol (k(cat)/K(m) = 2.02 × 10(6) M(-1) s(-1)), followed by geraniol (k(cat)/K(m) = 1.57 × 10(6) M(-1) s(-1)). Apparent K(m) values of <10 μM are consistent with an in vivo toxicity of geraniol above 5 μM. In the genetic vicinity of geoA is a putative aldehyde dehydrogenase that was named geoB and identified as a highly abundant protein during growth with phellandrene. Extracts of Escherichia coli expressing geoB demonstrated in vitro a geranial dehydrogenase (GaDH) activity. GaDH activity was independent of coenzyme A. The irreversible formation of geranic acid allows for a metabolic flux from β-myrcene via linalool, geraniol, and geranial to geranic acid.
Local Expression of Interleukin-17a is Correlated with Nasal Eosinophilia and Clinical Severity in Allergic Rhinitis (2014)

Interleukin (IL)-17A is a major cytokine produced by Th17 cells, which are associated with chronic inflammations. The local expression of IL-17A in allergic rhinitis (AR) remains to be characterized. We sought to determine the role of IL-17A expression in human inferior turbinate mucosa in the pathophysiology of AR. Inferior turbinate mucosa was sampled from medical treatment-resistant, surgery-required patients with perennial AR (PAR, n = 21), nonallergic rhinitis with eosinophilia syndrome (NARES, n = 7), and nonallergic hypertrophic rhinitis (HR, n = 13). IL-17A expression was determined with immunohistochemical staining. The mean number of IL-17A(+) cells and eosinophils per field were counted. Total serum immunoglobulin E (IgE) levels, blood eosinophil count, and forced expiratory volume in 1 second (FEV1)/forced vital capacity (FVC) ratio were also examined in each patient. IL-17A was primarily expressed in infiltrating inflammatory cells. The number of IL-17A(+) cells in nasal mucosa was significantly higher in the PAR group compared with HR (p = 0.002) and NARES (p = 0.021) groups. There was a significant and positive correlation between the number of IL-17A(+) cells and total nasal symptom score (rho = 0.403; p = 0.011), especially sneezing score (rho = 0.471; p = 0.003). The number of IL-17A(+) cells was significantly and positively correlated with the degree of eosinophil infiltration (rho = 0.623; p < 0.001), but not with total serum IgE levels (rho = 0.284; p = 0.098), blood eosinophil counts (rho = 0.302; p = 0.056), or FEV1/FVC ratio (rho = 0.092; p = 0.569). The present study provides evidence that IL-17A expression in the nasal mucosa is associated with the pathophysiology of AR, including disease severity and nasal eosinophilia.
Component customization for object-oriented distributed real-time software development (2002)

To apply the component-based approach to distributed real-time software development, it is necessary to identify components based on both functional and real-time requirements. Since a component may be acquired from external sources, it becomes necessary during integration to ensure that a component satisfies the real-time requirements of the target application software. Since these requirements vary, customizable so that during integration it can adapt itself to the specific real-time requirements of the target-distributed software. To facilitate such activities, it is preferable to have components that are capable of performing self-customization using a set of built-in services. In this paper, an object-oriented real-time component framework and two built-in customization services are presented to address the specified issues.
Increasing the tolerance of organophosphorus hydrolase to bleach (1999)

Organophosphorus hydrolase (OPH) has been incorporated within polyurethane foams during polymer synthesis as a means of reducing the enzyme's environmental sensitivity to alterations in pH and bleach-induced enzyme denaturation. Unfavorable losses of enzyme activity upon altered pH are reduced by covalently incorporating OPH within polyurethane matrices. Also, the stability of the immobilized enzyme under alkaline conditions is significantly enhanced. The bleach compatibility of OPH is also increased upon enzyme polymerization. Although a fraction of the increased bleach compatibility results from polyurethane oxidation, the covalent linkages between OPH and polyurethane directly enhance enzyme stability in buffered solutions of calcium hypochlorite bleach. Copyright 1999 John Wiley & Sons, Inc.
Preferential Hydrolysis of Aberrant Intermediates by the Type II Thioesterase in Escherichia coli Nonribosomal Enterobactin Synthesis: Substrate Specificities and Mutagenic Studies on the Active-Site Residues (2009)

The type II thioesterase EntH is a hotdog fold protein required for optimal nonribosomal biosynthesis of enterobactin in Escherichia coli. Its proposed proofreading activity in the biosynthesis is confirmed by its efficient restoration of enterobactin synthesis blocked in vitro by analogs of the cognate precursor 2,3-dihydroxybenzoate. Steady-state kinetic studies show that EntH recognizes the phosphopantetheine group and the pattern of hydroxylation in the aryl moiety of its thioester substrates. Remarkably, it is able to distinguish aberrant intermediates from the normal one in the enterobactin assembly line by demonstrating at least 10-fold higher catalytic efficiency toward thioesters derived from aberrant aryl precursors without a para-hydroxyl group, such as salicylate. By structural comparison and site-directed mutagenesis, the thioesterase is found to possess an active site closely resembling that of the 4-hydroxybenzoyl-CoA thioesterase from Arthrobacter sp. strain SU and to involve an acidic residue (glutamate-63) as the catalytic base or nucleophile like all other hotdog thioesterases. In addition, the EntH specificities toward the substrate hydroxylation pattern are found to depend on the active-site histidine-54, threonine-64, serine-67, and methionine-68 with the selectivity significantly reduced or even reversed when they are individually replaced by alanine. These residues are likely responsible for differential interaction of the enzyme with the substrates which leads to distinction between the normal and aberrant precursors in the enterobactin assembly line. These results show that the type II thioesterase evolves its distinctive ability to recognize the aberrant intermediates from the versatile catalytic platform of hotdog proteins and suggests an active search mechanism for type II thioesterases in nonribosomal peptide synthesis.
Lexical Entrainment in Written Discourse: Is Experts' Word Use Adapted to the Addressee? (2008)

Overlaps with one's interlocutor in the choice of words are called lexical entrainment. This article looks at accounts for these overlaps in word use. The question addressed is the extent to which the word use of the addressee, as opposed to available words from other sources, has a special impact on experts' choice of words. A laboratory experiment was conducted that addresses this question in the domain of online health advice. Eighty advanced medical students responded to a fictitious patient inquiry via e-mail. Results indicate that the mere availability of words (whether they were used by the addressee or not) accounts for experts' word use. Nonetheless, an analysis of experts' reflections on the patient's knowledge also indicated a metacognitive awareness of the specific word choice of the addressee.
The evaluation of prooxidant and antioxidant state of two variants of lewis lung carcinoma: a comparative study. (2010)

The pool of reduced glutathione in LLC/R9 tumors is more effectively replenished with GP involvement and is used by GST for detoxification of exogenous xenobiotics compared with LLC. Lower GP activity and the tendency to decreased Cat activity is characteristic property for LLC/R9 tumors compared to LLC.
EGFR Mutations in Non–Small-Cell Lung Cancer: Analysis of a Large Series of Cases and Development of a Rapid and Sensitive Method for Diagnostic Screening With Potential Implications on Pharmacologic Treatment (2005)

Mutations in the EGFR tyrosine kinase domain define a new molecular type of lung carcinoma, more frequent in particular subsets of patients. The SSCP assay is a rapid and reliable method for the detection of EGFR kinase domain mutations in lung cancer.
Use of Laser Doppler Flowmetry for Estimation of the Depth of Burns (1998)

The trend for treatment of deep second degree burns and third degree burns is toward early excision and skin grafting. The ability to predict burn depth accurately as early as possible is important for early excision and skin grafting. This study, prospectively evaluated the ability of laser Doppler flow measurements, obtained within 72 hours after burn injury, to predict the depth of burn wounds. A Periflux system 4001 laser Doppler flowmeter was used to measure the cutaneous microflow circulation of 100 selected points of burn wounds on 44 inpatients and of 1680 selected points on 120 volunteers from March of 1993 to February of 1994. The mean value of superficial second degree burns checked by laser Doppler was 194.6 perfusion units (PU). The value of deep second degree burns was 59.7 PU, and the value of third degree burns was 5.1 PU. The mean normal cutaneous blood flow of 120 volunteers (control group) was between 4 and 9 PU, except on the head, neck, hand, and foot. Blood flow of more than 100 PU correctly predicted (90.2 percent of cases) a superficial second degree burn. Blood flow between 100 and 10 PU correctly predicted (96.2 percent of cases) a deep second degree dermal burn. That of less than 10 PU correctly predicted (100 percent of cases) a third degree burn. There was also a significant correlation between initial flow measurements and the depth of burn wounds. We conclude that laser Doppler flow measurements performed early after burn injury are useful in predicting the depth of burn wounds. Laser Doppler flowmetry has the advantage of being easy to use and noninvasive and of providing immediate results for early determination of burn depth. Laser Doppler flowmetry is useful in selecting patients for early excision and grafting of burn wounds.
The chemistry of alkyl thiosulfate esters. 8. (E,Z)-Ajoene: a potent antithrombotic agent from garlic (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe chemistry of alkyl thiosulfate esters. 8. (E,Z)-Ajoene: a potent antithrombotic agent from garlicEric Block, Saleem Ahmad, Mahendra K. Jain, Roger W. Crecely, Rafael Apitz-Castro, and Maria R. CruzCite this: J. Am. Chem. Soc. 1984, 106, 26, 8295–8296Publication Date (Print):December 1, 1984Publication History Published online1 May 2002Published inissue 1 December 1984https://pubs.acs.org/doi/10.1021/ja00338a049https://doi.org/10.1021/ja00338a049research-articleACS PublicationsRequest reuse permissionsArticle Views967Altmetric-Citations201LEARN 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
A Broadband Fast Multipole Accelerated Boundary Element Method for the 3D Helmholtz Equation (2008)

The development of a fast multipole method (FMM) accelerated iterative solution of the boundary element method (BEM) for the Helmholtz equations in 3D is described. The FMM for the Helmholtz equation is significantly different for problems with low and high kD (where k is the wavenumber and D the domain size), and for large problems the method must be switched between levels of the hierarchy. The BEM requires several approximate computations (numerical quadrature, approximations of the boundary shapes using elements), and these errors must be balanced against approximations introduced by the FMM and the convergence criterion for iterative solution. These different errors must all be chosen in a way that on the one hand excess work is not done and on the other that the error achieved by the overall computation is acceptable. Details of translation operators for low and high kD, choice of representations, and BEM quadrature schemes, all consistent with these approximations are described. A novel preconditioner using a low accuracy FMM accelerated solver as a right preconditioner is also described. Results of the developed solvers for large boundary value problems with 0.0001 kD 500 are presented and shown to perform close to theoretical expectations.