gebhart/patrepeval huggingface dataset:
Synthesis of poly(L‐lactide)‐block‐polyisobutylene‐block‐poly(L‐lactide), a new biodegradable thermoplastic elastomer (1995)

Abstract The anionic ring‐opening polymerization of L‐lactide was initiated by dipotassium‐poly‐isobutylene‐alcoholate telechelic polymer to yield poly( L ‐lactide)‐ block ‐polyisobutylene‐ block ‐poly( L ‐lactide) triblock copolymer, a partially biodegradable thermoplastic elastomer. The pure triblock copolymer was obtained by gradient column chromatography on silica gel. The molar mass and molar mass distribution of the block copolymer was ascertained by SEC and quantitative 1 H NMR spectroscopy. It showed two glass transitions and microphase separation.
Quality Control and Peak Finding for Proteomics Data Collected from Nipple Aspirate Fluid by Surface-Enhanced Laser Desorption and Ionization (2003)

Mahalanobis distance in principal component space provides a method for assessing the reproducibility of proteomics spectra that is robust, effective, easily computed, and statistically sound.
Exploring the folding landscape of a structured RNA (2001)

Structured RNAs achieve their active states by traversing complex, multidimensional energetic landscapes. Here we probe the folding landscape of the Tetrahymena ribozyme by using a powerful approach: the folding of single ribozyme molecules is followed beginning from distinct regions of the folding landscape. The experiments, combined with small-angle x-ray scattering results, show that the landscape contains discrete folding pathways. These pathways are separated by large free-energy barriers that prevent interconversion between them, indicating that the pathways lie in deep channels in the folding landscape. Chemical protection and mutagenesis experiments are then used to elucidate the structural features that determine which folding pathway is followed. Strikingly, a specific long-range tertiary contact can either help folding or hinder folding, depending on when it is formed during the process. Together these results provide an unprecedented view of the topology of an RNA folding landscape and the RNA structural features that underlie this multidimensional landscape.
Demonstration of a capsule plasmid in Bacillus anthracis (1985)

Virulent and certain avirulent strains of Bacillus anthracis harbor a plasmid, designated pXO2, which is involved in the synthesis of capsules. Two classes of rough, noncapsulated (Cap-) variants were isolated from the capsule-producing (Cap+) Pasteur vaccine strains ATCC 6602 and ATCC 4229. One class was cured of pXO2, and the other class still carried it. Reversion to Cap+ was demonstrable only in rough variants which had retained pXO2. Proof that pXO2 is involved in capsule synthesis came from experiments in which the plasmid was transferred by CP-51-mediated transduction and by a mating system in which plasmid transfer is mediated by a Bacillus thuringiensis fertility plasmid, pXO12. Cells of Bacillus cereus and a previously noncapsulated (pXO2-) strain of B. anthracis produced capsules after the acquisition of pXO2.
Interferon alpha (IFN alpha 2a) therapy for herpes virus-associated inflammatory bowel disease (ulcerative colitis and Crohn's disease). (1998)

For herpesvirus-associated ulcerative colitis and Crohn's disease, interferon alpha 2a treatment should be started as early as possible to prevent disease becoming chronic. Whether this kind of antiviral treatment will be as effective in the long term, and whether malignant transformation (herpes viruses are potential tumor inducers) will be delayed or prevented, are questions that can be answered only by future long-term studies.
Biofunctionalized Phospholipid-Capped Mesoporous Silica Nanoshuttles for Targeted Drug Delivery: Improved Water Suspensibility and Decreased Nonspecific Protein Binding (2010)

A main challenge in nanobiomedicine is the engineering of nanostructures or nanomaterials that can efficiently encapsulate drugs at high load, cross cell membranes, and controllably release their cargo at target sites. Although mesoporous silica nanoparticles (MSNs) are safe, versatile, and promising carrier materials for targeted drug delivery, their aggregation phenomena under physiological conditions (or salt-containing environments) and their nonspecific binding in protein-containing solutions (or serum) limit their applications in biological science and biomedicine. To address this challenge, we have developed a novel delivery system, termed a nanoshuttle, comprising a nanoscale PEGylated-phospholipid coating and 13-(chlorodimethylsilylmethyl)heptacosane-derivatized MSNs, in which therapeutic or imaging agents may be trapped and ligand-assisted targeted delivery may be achieved through surface functionalization of the phospholipids. As a proof of concept in this study, we selected fluorescein isothiocyanate and folate as the imaging tracer and targeted ligand, respectively. Relative to the bare MSNs, the lipid-capped MSNs exhibited superior suspensibility in phosphate-buffered saline and much lower nonspecific binding in vitro. Furthermore, enhanced specific cellular uptake by Hela cells occurred after administering the folate-sensitized phospholipid-capped MSNs. Our results suggest that these highly versatile multifunctional MSNs are promising vectors for nanomedicine applications.
Evaluation of the Tuberculin Gamma Interferon Assay: Potential To Replace the Mantoux Skin Test (1999)

We evaluated an in vitro test of cell-mediated immunity, the tuberculin gamma interferon assay, QuantiFERON-TB (QIFN), in 455 individuals from three groups: group I, 237 immigrants from high-risk countries; group II, 127 health care workers undergoing Mantoux testing; group III, 91 patients being investigated for possible active tuberculosis (79 patients) or Mycobacterium avium-Mycobacterium intracellulare complex infection (12 patients). The QIFN results were compared either to those of the Mantoux test or to microbiological and clinical diagnosis, as appropriate. In each group the correlation between the diameter of induration for the skin test and the magnitude of QIFN response was significant and of moderate strength (Spearman's rank correlation coefficient; rho = 0.59 to 0.61; P < 0.001). For group I, the agreement between QIFN and Mantoux results was 89% for Mantoux-negative and 64% for Mantoux-positive individuals. For group II, when >/=10-mm-diameter induration was taken as positive, the agreement was 81% for Mantoux-negative and 67% for Mantoux-positive individuals. For group III, agreement was 81% for Mantoux-negative and 86% for Mantoux-positive patients. For patients being evaluated for active tuberculosis, the performance of the Mantoux test was not statistically different from that of the QIFN assay. In patients with active tuberculosis, the assay had a sensitivity of 77%, not significantly higher for extrapulmonary than pulmonary cases (83% versus 74%). QIFN sensitivity was not significantly different for smear-negative or smear-positive cases (80% versus 71%). The QIFN assay is a potential replacement for the Mantoux test. The acceptability of these performance values and those of similar evaluations will determine the place this test will have in detecting evidence of mycobacterial infection.
Tyrosine Residues in the Cytoplasmic Domains Affect Sorting and Fusion Activity of the Nipah Virus Glycoproteins in Polarized Epithelial Cells (2010)

The highly pathogenic Nipah virus (NiV) is aerially transmitted and causes a systemic infection after entering the respiratory tract. Airway epithelia are thus important targets in primary infection. Furthermore, virus replication in the mucosal surfaces of the respiratory or urinary tract in later phases of infection is essential for virus shedding and transmission. So far, the mechanisms of NiV replication in epithelial cells are poorly elucidated. In the present study, we provide evidence that bipolar targeting of the two NiV surface glycoproteins G and F is of biological importance for fusion in polarized epithelia. We demonstrate that infection of polarized cells induces focus formation, with both glycoproteins located at lateral membranes of infected cells adjacent to uninfected cells. Supporting the idea of a direct spread of infection via lateral cell-to-cell fusion, we could identify basolateral targeting signals in the cytoplasmic domains of both NiV glycoproteins. Tyrosine 525 in the F protein is part of an endocytosis signal and is also responsible for basolateral sorting. Surprisingly, we identified a dityrosine motif at position 28/29 in the G protein, which mediates polarized targeting. A dileucine motif predicted to function as sorting signal is not involved. Mutation of the targeting signal in one of the NiV glycoproteins prevented the fusion of polarized cells, suggesting that basolateral or bipolar F and G expression facilitates the spread of NiV within epithelial cell monolayers, thereby contributing to efficient virus spread in mucosal surfaces in early and late phases of infection.
Salmonella Phages and Prophages—Genomics and Practical Aspects (2007)

Numerous bacteriophages specific to Salmonella have been isolated or identified as part of host genome sequencing projects. Phylogenetic analysis of the sequenced phages, based on related protein content using CoreGenes, reveals that these viruses fall into five groupings (P27-like, P2-like, lambdoid, P22-like, and T7-like) and three outliers (epsilon15, KS7, and Felix O1). The P27 group is only represented by ST64B; the P2 group contains Fels-2, SopEphi, and PSP3; the lambdoid Salmonella phages include Gifsy-1, Gifsy-2, and Fels-1. The P22-like viruses include epsilon34, ES18, P22, ST104, and ST64T. The only member of the T7-like group is SP6. The properties of each of these phages are discussed, along with their role as agents of genetic exchange and as therapeutic agents and their involvement in phage typing.
X.25 Interface and End-to-End Virtual Circuit Service Characteristics (1980)

Public packet switching networks around the world use CCITT Recommendation X.25, which is the standard device-independent interface between packet networks and user devices operating in the packet-mode. Since its development in 1976 and with four years of network operational experience, the X.25 interface specification has reached a high level of maturity. A revised version of X.25 has been approved by CCITT Study Group VII at its meeting in February 1980. The revised X.25 specification is more complete than its predecessor, eliminates a number of ambiguous areas which lead to network implementation differences, and has been enhanced by the addition of new capabilities both to the X.25 interface and to the end-to-end service. This paper presents a consolidated view of the end-to-end characteristics of the virtual-circuit-based services accessible through the X.25 interface. It then discusses the characteristics of the revised X.25 interface, with emphasis on areas that have been addressed in the revised Recommendation. The revised Recommendation leads the way to greater commonality among network implementations. The increased functionality of the end-to-end virtual-circuit services has impact on the relationship of X.25 to system architectures being discussed by international standards bodies.
High mobility group box 1 protein attenuates myocardial ischemia reperfusion injury via inhibition of the p38 mitogen-activated protein kinase signaling pathway (2017)

The present study aimed to determine the effects of high mobility group box 1 protein (HMGB1) on myocardial ischemia reperfusion (I/R) injury in rats following acute myocardial ischemia and investigate the underlying molecular mechanisms of these effects. Male Wistar rats were randomly divided into the following groups (n=10/group): Sham operation; I/R; HMGB50 (50 ng/kg HMGB1 before I/R); HMGB100 (100 ng/kg HMGB1 before I/R); and HMGB200 (200 ng/kg HMGB1 before I/R). Serum cardiac troponin I (cTnI), interleukin (IL)-6 and tumor necrosis factor (TNF)-α levels were subsequently measured. Myocardial levels of malondialdehyde (MDA) and superoxide dismutase (SOD) were also determined. Myocardial infarction size (IS) was determined by 2,3,5-triphenyltetrazolium chloride staining. Myocardial expression of hypoxia inducible factor (HIF)-1α and phosphorylated p38 mitogen-activated protein kinase (P-p38 MAPK) protein was measured using western blotting. The results demonstrated that HMGB1 significantly decreased serum levels of cTnI, IL-6 and TNF-α and myocardial IS in I/R rats compared with the sham group (all P<0.05). HMGB1 also significantly decreased and increased myocardial levels of MDA and SOD, respectively (both P<0.05). HMGB1 significantly increased myocardial expression of HIF-1α and decreased expression of P-p38 MAPK following I/R (both P<0.05). These effects of HMGB1 occurred in a dose-dependent manner. The results of the current study indicate that the cardioprotective effects of intravenous HMGB1 are associated with increased myocardial expression of HIF-1α via inhibition of P-p38 MAPK expression, leading to inhibition of the P-p38 MAPK signaling pathway.
Well‐defined sulfobetaine‐based statistical copolymers as potential antibioadherent coatings (2000)

The potential use of novel poly(sulfobetaine) copolymers as antibioadherent coatings was investigated using Pseudomonas aeruginosa as a model microorganism and human macrophages and 3T3 mouse embryonic fibroblasts. Two well-defined statistical copolymers with narrow molecular weight distributions were prepared by group transfer copolymerization of n-butyl methacrylate (nBuMA) with either 10 or 30 mol % 2-(dimethylamino)ethyl methacrylate (DMAEMA). Sulfobetainized nBuMA-DMAEMA copolymers (poly[sulfobetaine-stat-nBuMA]) were obtained by treating these precursor polymers with 1,3-propanesultone under mild conditions. Both proton NMR spectroscopy and elemental microanalyses indicated that essentially all the DMAEMA residues were derivatized in both copolymers. Poly(methyl methacrylate) (PMMA) discs were coated with the sulfobetainized nBuMA-DMAEMA copolymers and the bioadherent properties of these coated materials were compared with those of PMMA. Statistically significantly fewer (p<.05) bacteria, macrophages, and fibroblasts adhered to the poly(sulfobetaine-stat-nBuMA)-coated PMMA than to the uncoated PMMA. The poly(sulfobetaine-stat-nBuMA) copolymer containing the higher proportion (30 mol %) sulfobetainized DMAEMA residues proved to be the more effective antibioadherent coating. The antibioadherent properties of these coating materials may allow the cost-effective production of dirt-resistant, easy to clean work surfaces, bioinert coatings for medical devices, and antifouling coatings for marine, agricultural, and industrial applications.
Interfocal heterogeneity of PTEN/MMAC1 gene alterations in multiple metastatic prostate cancer tissues. (1998)

The long arm of chromosome 10 is frequently affected by allelic loss in prostate cancer. PTEN/MMAC1, a candidate tumor suppressor gene located at 10q23.3, a region commonly deleted in prostate cancer, was recently identified and found to be deleted or mutated in cancer cell lines derived from a variety of human tissues including prostate. To examine the role of PTEN/MMAC1 in the progression of prostate cancer, we screened a unique set of 50 metastatic prostate cancer tissues from 19 cancer-death patients for alterations in the PTEN/MMAC1 gene, using single-strand conformational polymorphism analysis and direct sequencing to identify sequence changes and microsatellite analysis to examine allelic loss in the vicinity of PTEN/MMAC1. Overall, gene alterations (deletions or point mutations) were observed in at least 1 metastatic site in 12 of the 19 patients studied. Two cases had homozygous deletions that were confirmed by fluorescence in situ hybridization analysis. Four patients harbored point mutations, with one mutation being found in all four tumors (a primary lesion and three different metastases) from the same patient. The remaining three mutations were detected in only one of multiple metastases. Loss of heterozygosity was found in 10 of 18 informative cases, with 1 case showing a unique pattern of microsatellite instability in each of six different metastases examined. Loss of the same allele was found in all metastases in a given patient in 9 of 10 cases. These results indicate that PTEN/MMAC1 gene alterations occur frequently in lethal prostate cancer, although a substantial amount of mutational heterogeneity is found among different metastatic sites within the same patient. These latter findings emphasize the potentially complex genetic relationship that can exist between various clonal lineages of prostate cancer cells as they evolve during the metastatic process and suggest a molecular basis for phenotypic heterogeneity of different prostate cancer foci in patients with disseminated disease.
An Interactive Machine Translation System with Online Learning (2011)

State-of-the-art Machine Translation (MT) systems are still far from being perfect. An alternative is the so-called Interactive Machine Translation (IMT) framework, where the knowledge of a human translator is combined with the MT system. We present a statistical IMT system able to learn from user feedback by means of the application of online learning techniques. These techniques allow the MT system to update the parameters of the underlying models in real time. According to empirical results, our system outperforms the results of conventional IMT systems. To the best of our knowledge, this online learning capability has never been provided by previous IMT systems. Our IMT system is implemented in C++, JavaScript, and ActionScript; and is publicly available on the Web. 1
Silver-Mediated Synthesis of Heterocycles (2008)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTSilver-Mediated Synthesis of HeterocyclesMíriam Álvarez-Corral, Manuel Muñoz-Dorado, and Ignacio Rodríguez-García*View Author Information Dpt. Química Orgánica, Universidad de Almería, 04120 Almería, Spain* To whom correspondence should be addressed. E-mail: [email protected]. Phone: +34 950 015610. Fax: +34 950 015481.Cite this: Chem. Rev. 2008, 108, 8, 3174–3198Publication Date (Web):July 17, 2008Publication History Received14 December 2007Published online17 July 2008Published inissue 1 August 2008https://pubs.acs.org/doi/10.1021/cr078361lhttps://doi.org/10.1021/cr078361lreview-articleACS PublicationsCopyright © 2008 American Chemical SocietyRequest reuse permissionsArticle Views9377Altmetric-Citations539LEARN 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 SUBJECTS:Addition reactions,Cyclization,Hydrocarbons,Organic compounds,Silver Get e-Alerts
α,β-Unsaturated Ketone Is a Core Moiety of Natural Ligands for Covalent Binding to Peroxisome Proliferator-activated Receptor γ (2005)

Peroxisome proliferator-activated receptor gamma (PPARgamma) functions in various biological processes, including macrophage and adipocyte differentiation. Several natural lipid metabolites have been shown to activate PPARgamma. Here, we report that some PPARgamma ligands, including 15-deoxy-Delta12,14-prostaglandin J2, covalently bind to a cysteine residue in the PPARgamma ligand binding pocket through a Michael addition reaction by an alpha,beta-unsaturated ketone. Using rhodamine-maleimide as well as mass spectroscopy, we showed that the binding of these ligands is covalent and irreversible. Consistently, mutation at the cysteine residue abolished abilities of these ligands to activate PPARgamma, but not of BRL49653, a non-covalent synthetic agonist, indicating that covalent binding of the alpha,beta-unsaturated ketone in the natural ligands was required for their transcriptional activities. Screening of lipid metabolites containing the alpha,beta-unsaturated ketone revealed that several other oxidized metabolites of hydroxyeicosatetraenoic acid, hydroxyeicosadecaenoic acid, and prostaglandins can also function as novel covalent ligands for PPARgamma. We propose that PPARgamma senses oxidation of fatty acids by recognizing such an alpha,beta-unsaturated ketone as a common moiety.
Swept-wavelength interferometric interrogation of fiber Rayleigh scatter for distributed sensing applications (2007)

We review recent advancements in making high resolution distributed strain and temperature measurements using swept-wavelength interferometry to observe the spectral characteristics of Rayleigh scatter in optical fibers. Current methods available for distributed strain or temperature sensing in optical fiber include techniques based on Raman, Brillouin, and Rayleigh scattering. These techniques typically employ optical time domain reflectometry and are thus limited in spatial resolution to 0.1 to 1 m. Fiber Bragg gratings can yield higher spatial resolution but are difficult to multiplex in large numbers for applications requiring wide scale coverage. Swept-wavelength interferometry allows the Rayleigh scatter amplitude and phase to be sampled with very high spatial resolution (10s of microns). The Rayleigh scatter complex amplitude can be Fourier Transformed to obtain the Rayleigh scatter optical spectrum and shifts in the spectral pattern can related to changes in strain or temperature. This technique results in distributed strain measurements with 1 &mu;&epsilon; resolution or temperature measurements with 0.1 C resolution. These measurements can be made with sub-cm spatial resolution over a 100 m measurement range or with sub-10 cm resolution over a 1 Km range. A principle advantage of this technique is that it does not require specialty fiber. Thus, measurements can be made in pre-installed single mode or multimode fibers, including those used for telecommunication networks. Applications range from fault monitoring in short range communications networks, structural health monitoring, shape sensing, pipeline and electrical transmission line monitoring, to perimeter security. Several examples are discussed in detail.
The Further Chemistry of Ellagic Acid: I. Synthesis of Tetramethylellagic Acid and Associated Polymer Precursors (2001)

Summary A quantitative method for the production of 3,3′,4,4′-tetra-O-methylellagic acid was developed. Ellagic acid was fully methylated under nitrogen and in air using dimethyl sulphate and 25% guanidinium methoxide in N -methyl- 2 -pyrrolidone. The synthesis of a range of polymer precursors derived from 3,3′,4,4′-tetra-O-methylellagic acid are outlined, including the previously unreported 2,3,4,2′,3′,4′-hexamethoxy-6,6′-diphenoyl-dichloride, 2,3,4,2′,3′,4′-hexamethoxy-6,6′-diisocyanato-diphenyl, 2,3,4, 2′,3′,4′-hexamethoxy-6,6′-diamino-diphenyl, 2,3,4,2′,3′,4′-hexamethoxy-6,6′-dihydroxymethyl-diphenyl and 2,3,4,2′,3′,4′-hexamethoxy-diphenyl-6,6′-dialdehyde.