gebhart/patrepeval huggingface dataset:
Structure and stability of the P93G variant of ribonuclease A (1998)

The peptide bonds preceding Pro 93 and Pro 114 of bovine pancreatic ribonuclease A (RNase A) are in the cis conformation. The trans-to-cis isomerization of these bonds had been indicted as the slow step during protein folding. Here, site-directed mutagenesis was used to replace Pro 93 or Pro 114 with a glycine residue, and the crystalline structure of the P93G variant was determined by X-ray diffraction analysis to a resolution of 1.7 A. This structure is essentially identical to that of the wild-type protein, except for the 91-94 beta-turn containing the substitution. In the wild-type protein, the beta-turn is of type VIa. In the P93G variant, this turn is of type II with the peptide bond preceding Gly 93 being trans. The thermal stabilities of the P93G and P114G variants were assessed by differential scanning calorimetry and thermal denaturation experiments monitored by ultraviolet spectroscopy. The value of delta deltaGm which reports on the stability lost in the variants, is 1.5-fold greater for the P114G variant than for the P93G variant. The greater stability of the P93G variant is likely due to the relatively facile accommodation of residues 91-94 in a type II turn, which has a preference for a glycine residue in its i + 2 position.
Mixing Linear SVMs for Nonlinear Classification (2010)

In this paper, we address the problem of combining linear support vector machines (SVMs) for classification of large-scale nonlinear datasets. The motivation is to exploit both the efficiency of linear SVMs (LSVMs) in learning and prediction and the power of nonlinear SVMs in classification. To this end, we develop a LSVM mixture model that exploits a divide-and-conquer strategy by partitioning the feature space into subregions of linearly separable datapoints and learning a LSVM for each of these regions. We do this implicitly by deriving a generative model over the joint data and label distributions. Consequently, we can impose priors on the mixing coefficients and do implicit model selection in a top-down manner during the parameter estimation process. This guarantees the sparsity of the learned model. Experimental results show that the proposed method can achieve the efficiency of LSVMs in the prediction phase while still providing a classification performance comparable to nonlinear SVMs.
Grating formation in BGG31 glass by UV exposure (1999)

A three-dimensional index variation grating in bulk BGG31 glass written using neither hydrogen loading nor germanium doping is demonstrated. This material is useful for fabricating ion-exchanged waveguides, and its photosensitivity to ultraviolet (UV) radiation at 248 nm has not been previously explored. Intensity measurements of the Bragg diffracted spots indicated a maximum index variation (Δn) of ~4 × 10–5.
Association Between Endothelin Receptor B Nonsynonymous Variants and Melanoma Risk (2005)

The endothelin signaling pathway plays a crucial role in melanocyte differentiation and migration. In this study, we investigated whether germline mutations of endothelin receptor B (EDNRB), a gene involved in Hirschsprung disease (HSCR), could also predispose for malignant melanoma (MM). The coding region of EDNRB was sequenced in 137 MM patients and in 130 ethnically matched Caucasian control subjects. Six nonsynonymous EDNRB variants were found in 15 patients (11%), but only two were found in four control subjects (3%, odds ratio [OR] = 3.87, 95% confidence interval [CI] = 1.25 to 12; P = .012). Overall, 14 out of 15 MM patients carried EDNRB mutations reported in HSCR, some of which had previously been shown to lead to loss of function. In multivariable logistic regression analysis including skin type, eye and hair color, number of nevi, and dorsal lentigines (freckles), the association between EDNRB mutations and MM risk remained statistically significant (OR = 19.9, 95% CI = 1.34 to 296.2; P = .03). Our data strongly suggest that EDNRB is involved in predisposition for two different multigenic disorders, HSCR and melanoma.
Transcutaneous delivery of CpG-adjuvanted allergen via laser-generated micropores (2012)

Transcutaneous immunotherapy via laser-generated micropores provides an efficient novel platform for treatment of type I allergic diseases. Furthermore, immunomodulation with T helper 1-promoting adjuvants can prevent the risk for new sensitization.
Botulinum Toxin in the Treatment of Tics (2000)

Botulinum toxin A injections are an effective and well-tolerated treatment of tics. In addition to improving the motor component of tics, BTX also provides relief of premonitory sensations. Arch Neurol. 2000;57:1190-1193
Humoral control of airway tone. (1996)

Publisher Summary Circulating hormones and vasoactive peptides play a minor role in the physiological regulation of airway tone in normal individuals. Adrenaline is the only hormone known to influence bronchomotor tone, and it is only during strenuous exercise that concentrations are elevated sufficiently to cause bronchodilation. Circulating hormones play a more important role in the regulation of airway tone in diseased states of the airways, such as asthma, and possibly in other disorders, such as cor pulmonale, congestive cardiac failure, respiratory failure, and thyroid diseases. Circulating adrenaline has a role in the maintenance of resting airway tone in asthma, particularly in those patients in whom resting airway caliber is already reduced. The elevated adrenaline and atrial natriuretic peptide concentrations achieved after vigorous exercise may act to counteract exercise-induced asthma. Airway tone and reactivity are influenced by oxygen levels, although the precise effects of oxygen tension on airway function in health and airway disease are not clearly established.
Antigenic characterization of flavivirus structural proteins separated by isoelectric focusing (1977)

Isoelectrofocusing of nonionic-detergent-disrupted flaviviruses separated the envelope glycoprotein of 53,000 to 58,000 daltons and the nucleocapsid protein of 14,000 daltons. The envelope protein and nucleocapsid protein were isolated at isoelectric points of pI 7.8 and 10.3, respectively. The antigenic determinants of St. Louis encephalitis, Japanese encephalitis, and dengue virus envelope and nucleocapsid proteins were examined by solid-phase competition radioimmunoassay. By the appropriate selection of antiserum and competing proteins, it was possible to distinguish type-specific, complex-reactive and flavivirus group-reactive antigenic determinants. The envelope glycoproteins of St. Louis encephalitis, Japanese encephalitis, and dengue viruses were found to contain each of these three classes of antigenic determinants. Most of the determinants on the envelope protein were type specific, some were complex reactive, and a small fraction were flavivirus group reactive. The nucleocapsid protein contained only flavivirus group-reactive antigenic determinants.
Unconventional Applications in Pacemaker Therapy (2001)

Since its inception, the principal application of permanent pacing has been for the correction of symptomatic bradycardia. During the past 3 decades, pacemaker therapy indications have evolved, through scientific research and through advances in technology, beyond conduction system disorders and sinus node dysfunction. This article presents recent progress in the application of permanent pacing in hypertrophic obstructive cardiomyopathy, dilated cardiomyopathy, paroxysmal atrial fibrillation, neurocardiogenic syncope, and in long-QT syndrome. In each clinical entity, certain pacing parameters are crucial for achieving the therapeutic goal. Advanced practice clinicians will encounter these patients in practice and are urged to recognize the therapeutic goal and optimal function of the device.
Genetic diversity of human immunodeficiency virus type 2: evidence for distinct sequence subtypes with differences in virus biology (1994)

The virulence properties of human immunodeficiency virus type 2 (HIV-2) are known to vary significantly and to range from relative attenuation in certain individuals to high-level pathogenicity in others. These differences in clinical manifestations may, at least in part, be determined by genetic differences among infecting virus strains. Evaluation of the full spectrum of HIV-2 genetic diversity is thus a necessary first step towards understanding its molecular epidemiology, natural history of infection, and biological diversity. In this study, we have used nested PCR techniques to amplify viral sequences from the DNA of uncultured peripheral blood mononuclear cells from 12 patients with HIV-2 seroreactivity. Sequence analysis of four nonoverlapping genomic regions allowed a comprehensive analysis of HIV-2 phylogeny. The results revealed (i) the existence of five distinct and roughly equidistant evolutionary lineages of HIV-2 which, by analogy with HIV-1, have been termed sequence subtypes A to E; (ii) evidence for a mosaic HIV-2 genome, indicating that coinfection with genetically divergent strains and recombination can occur in HIV-2-infected individuals; and (iii) evidence supporting the conclusion that some of the HIV-2 subtypes may have arisen from independent introductions of genetically diverse sooty mangabey viruses into the human population. Importantly, only a subset of HIV-2 strains replicated in culture: all subtype A viruses grew to high titers, but attempts to isolate representatives of subtypes C, D, and E, as well as the majority of subtype B viruses, remained unsuccessful. Infection with all five viral subtypes was detectable by commercially available serological (Western immunoblot) assays, despite intersubtype sequence differences of up to 25% in the gag, pol, and env regions. These results indicate that the genetic and biological diversity of HIV-2 is far greater than previously appreciated and suggest that there may be subtype-specific differences in virus biology. Systematic natural history studies are needed to determine whether this heterogeneity has clinical relevance and whether the various HIV-2 subtypes differ in their in vivo pathogenicity.
Detection and molecular characterisation of thyroid cancer precursor lesions in a specific subset of Hashimoto's thyroiditis (2004)

Hashimoto's thyroiditis (HT) represents the most common cause of hypothyroidism and nonendemic goiter, but its clinical and pathological heterogeneity opens the question if this disease should be more properly considered as a spectrum of different thyroid conditions rather than as a single nosological entity. In this study, we analysed 133 cases of HT for the expression of galectin-3, a lectin molecule involved in malignant transformation, apoptosis and cell cycle control. An unexpected expression of galectin-3 was demonstrated in a subset of HT together with the presence of HBME-1, c-met and cyclin-D1 that are also involved in malignant transformation and deregulated cell growth. Furthermore, a loss of allelic heterozygosity in a specific cancer-related chromosomal region was demonstrated in some HT harbouring galectin-3-positive follicular cells, by using laser capture microdissection. On the basis of the morphological and molecular findings we identified four subsets of HT: (a) HT with classic features of chronic autoimmune thyroiditis; (b) HT associated to hyperplastic/adenomatous lesions; (c) HT harbouring thyroid cancer precursors; (d) HT associated to unequivocal thyroid microcarcinomas. Our findings provide a well-substantiated morphological and molecular demonstration that HT may include a spectrum of different thyroid conditions ranging from chronic autoimmune thyroiditis to thyroiditis triggered by specific immune-response to cancer-related antigens.
Detection of 2-Hydroxyglutarate in IDH -Mutated Glioma Patients by In Vivo Spectral-Editing and 2D Correlation Magnetic Resonance Spectroscopy (2012)

Mutations in the gene isocitrate dehydrogenase 1 (IDH1) are present in up to 86% of grade II and III gliomas and secondary glioblastoma. Arginine 132 (R132) mutations in the enzyme IDH1 result in excess production of the metabolite 2-hydroxyglutarate (2HG), which could be used as a biomarker for this subset of gliomas. Here, we use optimized in vivo spectral-editing and two-dimensional (2D) correlation magnetic resonance spectroscopy (MRS) methods to unambiguously detect 2HG noninvasively in glioma patients with IDH1 mutations. By comparison, fitting of conventional 1D MR spectra can provide false-positive readouts owing to spectral overlap of 2HG and chemically similar brain metabolites, such as glutamate and glutamine. 2HG was also detected using 2D high-resolution magic angle spinning MRS performed ex vivo on a separate set of glioma biopsy samples. 2HG detection by in vivo or ex vivo MRS enabled detailed molecular characterization of a clinically important subset of human gliomas. This has implications for diagnosis as well as monitoring of treatments targeting mutated IDH1.
Pro-alpha 1(XI) collagen. Structure of the amino-terminal propeptide and expression of the gene in tumor cell lines. (1990)

We have determined the nucleotide sequence of several overlapping cDNA clones encoding the amino-terminal portion of human alpha 1(XI) procollagen. These experiments have revealed that this domain of the pro-alpha(XI) chain displays structural features common to other fibrillar procollagen molecules, such as a putative amino-terminal proteinase cleavage site and an interrupted collagenous segment. In the latter, structural similarities were noted when alpha 1(XI) was compared with alpha 1(II) and alpha 2(V) procollagens. Overall, however, the amino-terminal region of pro-alpha 1(XI) differs greatly in composition and size from that of other fibrillar chains. Nearly three-fourths of this domain is in fact composed of a 383-amino acid globular region in which a 3-cysteine cluster signals the transition to a long and highly acidic carboxyl-terminal segment. Finally, the unrestricted expression of this cartilage-specific collagen gene has been confirmed by the finding of high levels of pro-alpha 1(XI) mRNA in two human rhabdomyosarcoma cell lines.
Hyaluronan and sulphated hyaluronan micropatterns: effect of chemical and topographic cues on lymphatic endothelial cell alignment and proliferation. (2005)

While tissue engineered blood vessels have entered surgical practice, the construction of artificial lymphatic vessels has never been attempted due to the small dimensions and fragility of lymphatic vessels. A possible alternative would be to obtain a new growth of interrupted lymphatic vessels. We have previously reported that lymphatic endothelial cells align when cultured on striped micropatterns of hyaluronan (Hyal) and aminosilanized glass. We here report a comparative study in which lymphatic endothelial cells have been plated on micropatterns with stripes of different width and height obtained by the photoimmobilization of Hyal and its sulphated derivative (HyalS) on aminosilanized glass to verify whether their response correlated with surface-chemistry andlor topography. On Hyal micropatterns, cells adhered to aminosilanized glass, avoiding Hyal stripes and molding their shape in accordance to the micropattern topography. Stress fibers, integrins and focal adhesion kinase organized accordingly. HyalS micropatterns with the same topography were unable to guide cell response, cells randomly adhered to HyalS and glass stripes, and polarization was attained only by increasing stripe height. These data indicate that surface chemistry is the main cue responsible for lymphatic endothelial cell guidance. When surface chemistry of stripes promotes cell adhesion as well as that of the substrate, topographical parameters become prevalent. Micropatterns with defined chemical and topographical properties may contribute to the design of new platforms for controlled cell growth in tissue engineering of lymphatic vessels.
A molecular mechanism for gas hydrate nucleation from ice (1991)

Abstract Induction phenomena are explained that exist in the only two reproducible sets of kinetic data in the literature for gas hydrate formation from an agitated ice surface. The previously unexplained data are interpreted using recent crystal diffraction results. The induction explanation is validated through cyclopropane hydrate kinetic experiments. The induction reasoning forms the basis of an hypothesis for a molecular mechanism of hydrate formation from ice. The hypothesized mechanism is quantified and given physical interpretation. The hypothesis may have significant implications for inhibiting hydrate formation.
Design of Low Molecular Weight Hematoregulatory Agents from the Structure−Activity Relationship of a Dimeric Pentapeptide (1997)

We report herein, a new class of simple hematoregulatory semipeptides, formally derived from the cystine-dimerized peptide pGlu-Glu-Asp-Cys-Lys-OH, where the disulfide bond has been replaced by an isosteric dicarba bridge. The structure-activity relationship (SAR) of a series of analogues incorporating replacements at positions 1 and 2 of peptide 1 led to the design of active conformationally constrained cyclic peptides (12, 13). Ring closure was achieved by cyclization of the N-terminal amino groups at position 2 of peptide 2 using pyrazine-2,3-dicarboxylic acid. Subsequent excision of the putative C-terminal scaffold domain from the active cyclic peptides resulted in the discovery of a new class of low molecular weight hematoregulatory agents exemplified by compound 16. This semipeptide analogue, comprising two D-Ser residues connected via amide bonds to the acid groups of pyrazine-2,3-dicarboxylic acid, had comparable biological activity to the lead peptide 1. The stereochemical requirements for the observed biological activity of these novel compounds were examined. Furthermore, the hematopoietic synergistic activity induced by compound 16 in stromal cell cultures was blocked by an antibody known to neutralize the hematoregulatory effect of 1, indicating a common mechanistic end point. Compounds of the class typified by 16 may form the basis for the development of novel therapeutic agents within the area of immunoregulation.
Efficiency enhancement of a tunable RF power amplifier by second harmonic manipulation using thin-film BST varactor (2010)

This paper presents an idea of efficiency enhancement of a tunable class-AB radio frequency power amplifier (RF PA) utilizing a tunable resonant circuit along with tunable matching at the output using barium-strontium-titanate (BST) varactors. It is demonstrated that application of appropriate bias voltages across tunable output 2nd harmonic termination as well as matching network, comprising of BST varactors, results in continuously tunable performance of RF PA. Power added efficiency (PAE) along with other performance parameters such as gain and output power, are shown to be adapted as the RF PA is tuned for multiband operation from 1.8 to 2.0 GHz. For class-AB operation, an improvement of up to 8% in PAE and up to 0.5 dBm in output power were observed in saturated output power range provided the output harmonics are properly terminated.
Identification of a region in the human vasoactive intestinal polypeptide gene responsible for regulation by cyclic AMP. (1987)

Transcription of the vasoactive intestinal polypeptide (VIP) gene is regulated by cAMP. To identify the nucleotide sequences in the human VIP gene responsible for this regulation, we constructed chimeric genes containing different portions of the 5'-flanking region of the human VIP gene fused to the structural sequence encoding the bacterial reporter enzyme chloramphenicol acetyltransferase (CAT). The transcriptional activities of the fusion genes introduced into the rat pheochromocytoma cell line PC12 were assayed by measuring CAT activity in the cell lysates. Forskolin, an adenylate cyclase-activating agent, stimulated the expression of VIP-CAT fusion genes. Deletional analysis demonstrated that a region between -86 and -70 nucleotides upstream from the transcriptional origin of the human VIP gene was responsible for stimulation by forskolin. This region was able to confer cAMP-responsiveness to a gene that is not normally regulated by cAMP. Two copies of a 5 base pair motif, 5'-CGTCA-3', are required for activity of the VIP cAMP regulatory region. This motif is also present in the cAMP regulatory region of several other eukaryotic genes.
Controlled/“Living” Radical Polymerization. Kinetics of the Homogeneous Atom Transfer Radical Polymerization of Styrene (1997)

The homogeneous atom transfer radical polymerization (ATRP) of styrene using solubilizing 4,4'-dialkyl substituted 2,2'-bipyridines yielded well-defined polymers with Mw/Mn ≤ 1.10. The polymerizations exhibited an increase in molecular weight in direct proportion to the ratio of the monomer consumed to the initial initiator concentration and also exhibited internal first-order kinetics with respect to monomer concentration. The optimum ratio of ligand-to-copper(I) halide for these polymerizations was found to be 2:1, which tentatively indicates that the coordination sphere of the active copper(I) center contains two bipyridine ligands. The exclusive role for this copper(I) complex in ATRP is atom transfer, since at typical concentrations that occur for these polymerizations (≈10-7−10-8 M), polymeric radicals were found not to react with the copper(I) center in any manner that enhanced or detracted from the observed control. ATRP also exhibited first-order kinetics with respect to both initiator and copper(I) halide concentration; however, the polymerization kinetics were not simple inverse first-order with respect to the initial copper(II) halide concentration. The latter observation was found to be due to the persistent radical effect, which resulted in an increase in copper(II) concentration during the initial stages of the polymerization. This phenomenon also has the effect of regulating the polymerization by ensuring that the rate of radical combination and/or disproportionation is sufficiently less than the rate of propagation.
Carbonyl olefination reaction using silyl-substituted organometallic compounds (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCarbonyl olefination reaction using silyl-substituted organometallic compoundsDonald John PetersonCite this: J. Org. Chem. 1968, 33, 2, 780–784Publication Date (Print):February 1, 1968Publication History Published online1 May 2002Published inissue 1 February 1968https://doi.org/10.1021/jo01266a061RIGHTS & PERMISSIONSArticle Views5599Altmetric-Citations682LEARN 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 InReddit PDF (713 KB) Get e-Alerts Get e-Alerts
Environmental Applications of Semiconductor Photocatalysis (1995)

The civilian, commercial, and defense sectors of most advanced industrialized nations are faced with a tremendous set of environmental problems related to the remediation of hazardous wastes, contaminated groundwaters, and the control of toxic air contaminants. For example, the slow pace of hazardous waste remediation at military installations around the world is causing a serious delay in conversion of many of these facilities to civilian uses. Over the last 10 years problems related to hazardous waste remediation have emerged as a high national and international priority.