gebhart/patrepeval huggingface dataset:
Comparison of whole genome sequences of Chlamydia pneumoniae J138 from Japan and CWL029 from USA (2000)

Chlamydia pneumoniae is a widespread pathogen of humans causing pneumonia and bronchitis. There are many reports of an association between C.PNEUMONIAE: infection and atherosclerosis. We determined the whole genome sequence of C.PNEUMONIAE: strain J138 isolated in Japan in 1994 and compared it with the sequence of strain CWL029 isolated in the USA before 1987. The J138 circular chromosome consists of 1 226 565 nt (40.7% G+C) with 1072 likely protein-coding genes that is 3665 nt shorter than the CWL029 genome. Plasmids, phage- or transposon-like sequences were not identified. The overall genomic organization, gene order and predicted proteomes of the two strains are very similar, suggesting a high level of structural and functional conservation between the two unrelated isolates. The most conspicuous differences in the J138 genome relative to the CWL029 genome are the absence of five DNA segments, ranging in size from 89 to 1649 nt, and the presence of three DNA segments, ranging from 27 to 84 nt. The complex organization of these 'different zones' may be attributable to a unique system of recombination.
Optimal allocation of virtual optical networks for the future internet (2012)

Optical network infrastructures can be partitioned into multiple parallel, dedicated virtual networks for a physical infrastructure sharing purpose. However, different transport technologies may impact in both the amount and the characteristics of the different virtual instances that can be built on top of a single physical infrastructure. To analyse the impact of the transport technology in this regard, we present exact Integer Linear Programming (ILP) formulations that address the off-line problem of optimally allocate a set of virtual networks in two kind of substrates: wavelength switching and spectrum switching. Both formulations serve the purpose to provide opaque transport services from the virtual network point of view, where electronic terminations are assumed in the virtual network nodes. We carry out a series of experiments to validate the presented formulations and determine which is the impact of both substrates in the number of virtual networks that can be optimally allocated in the transport network.
Discovery of a novel class of orally active, non-peptide angiotensin II antagonists (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiscovery of a novel class of orally active, non-peptide angiotensin II antagonistsB. De, M. Winn, T. M. Zydowsky, D. J. Kerkman, J. F. DeBernardis, J. Lee, S. Buckner, R. Warner, M. Brune, and Cite this: J. Med. Chem. 1992, 35, 20, 3714–3717Publication Date (Print):October 1, 1992Publication History Published online1 May 2002Published inissue 1 October 1992https://pubs.acs.org/doi/10.1021/jm00098a018https://doi.org/10.1021/jm00098a018research-articleACS PublicationsRequest reuse permissionsArticle Views366Altmetric-Citations37LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Tat‐expressing Jurkat cells show an increased resistance to different apoptotic stimuli, including acute human immunodeficiency virus‐type 1 (HIV ‐1) infection (1995)

Human CD4+ T lymphoblastoid Jurkat cells were stably transfected with two different plasmid vectors containing the cDNA of human immunodeficiency virus-type 1 (HIV-1) tat gene under the control of either the promoter of simian virus 40 (pRPneo/tat) or the long terminal repeat region of SL3 murine leukaemia virus (pRPneo/SL3/tat). Both pRPneo/tat and pRPneo/SL3/tat Jurkat cell lines showed a constant and high production of bioactive Tat in transient co-transfection assays with an HIV-1 long terminal repeat (LTR)-chloramphenicol acetyltransferase (CAT) reporter plasmid. Tat-positive and mock-transfected Jurkat cells were cultured with various cytotoxic agents, which have been associated to the progressive loss of CD4 T-lymphocytes characteristic of HIV-1 disease. In the presence of recombinant tumour necrosis factor-alpha (TNF-alpha), anti-fas antibody, Leu3a anti-CD4 antibody, the percentage of apoptosis, evaluated in a 24-72 h short-term assay, was lower (P < 0.05) in tat-positive Jurkat cells than in mock-transfected controls. The low susceptibility to the cytotoxic activity of TNF-alpha and anti-fas antibody of tat-transfected cells was confirmed by counting viable cells up to 15 d of culture. Also, recombinant Tat protein was able to prevent the increase of apoptosis induced in mock-transfected Jurkat by TNF-alpha. Of note, tat-expressing cells showed a better survival with respect to mock-transfected control cells even when acutely infected with high doses (500,000 cpm of reverse transcriptase) of HIV-1 (strain IIIB) or treated with heat-inactivated HIV-1. These data demonstrate that the expression of the regulatory HIV-1 Tat protein is able to rescue Jurkat lymphoblastoid cells from apoptosis induced by a variety of cytotoxic agents. Since Tat protein expression is restricted to the initial phases of an active HIV-1 replication, the anti-apoptotic effect of Tat could have the physiological significance of selectively protecting HIV-1 producing cells from death, at least for the time necessary to allow virus production and spreading.
Nicotine metabolite ratio as an index of cytochrome P450 2A6 metabolic activity*1 (2004)

The 3HC/COT ratio derived from nicotine either administered as a probe drug or from tobacco use, measured in either plasma or saliva, is highly correlated with the oral clearance of nicotine. The ratio appears to be a useful noninvasive marker of the rate of nicotine metabolism (which is important in studying nicotine addiction and smoking behavior), as well as a general marker of CYP2A6 activity (which is important in studying drug and toxin metabolism).
Molecular cloning, sequence, and expression of a human GDP-L-fucose:beta-D-galactoside 2-alpha-L-fucosyltransferase cDNA that can form the H blood group antigen. (1990)

We have previously used a gene-transfer scheme to isolate a human genomic DNA fragment that determines expression of a GDP-L-fucose:beta-D-galactoside 2-alpha-L-fucosyltransferase [alpha(1,2)FT; EC 2.4.1.69]. Although this fragment determined expression of an alpha(1,2)FT whose kinetic properties mirror those of the human H blood group alpha(1,2)FT, their precise nature remained undefined. We describe here the molecular cloning, sequence, and expression of a human cDNA corresponding to these human genomic sequences. When expressed in COS-1 cells, this cDNA directs expression of cell surface H structures and a cognate alpha(1,2)FT activity with properties analogous to the human H blood group alpha(1,2)FT. The cDNA sequence predicts a 365-amino acid polypeptide characteristic of a type II transmembrane glycoprotein with a domain structure analogous to that of other glycosyltransferases but without significant primary sequence similarity to these or other known proteins. To directly demonstrate that the cDNA encodes an alpha(1,2)FT, the COOH-terminal domain predicted to be Golgi-resident was expressed in COS-1 cells as a catalytically active, secreted, and soluble protein A fusion peptide. Southern blot analysis showed that this cDNA identifies DNA sequences syntenic to the human H locus on chromosome 19. These results strongly suggest that this cloned alpha(1,2)FT cDNA represents the product of the human H blood group locus.
A RAPID METHOD FOR THE DETERMINATION OF DIASTATIC POWER (1984)

A rapid method for the determination of diastatic power is described. The enzyme extraction and starch hydrolysis steps have been shortened to 10 min each and a colorimetric method involving the use of p-hydroxybenzoic acid hydrazide has been used for the determination of reducing sugars. The method avoids some sources of error associated with previous methods. The sensitivity of the method allows the use of small samples making it suitable for the measurement of diastatic power in barley breeding.
Facile Regio- and Stereoselective Carbon−Carbon Coupling of Phenol Derivatives with Aryl Aziridines (2006)

A chemo-, regio-, and stereoselective direct carbon-carbon coupling of readily available aryl borates with N-protected aryl aziridines provides a method for the synthesis of new 2-(o-hydroxyaryl)-2-aryl ethylamines which can be used, in a novel annulation sequence, to give stereodefined substituted 3-aryl indolines. [reaction: see text]
Foodborne Disease Control: A Transnational Challenge (1997)

In the globalized political economy of the late 20th century, increasing social, political, and economic interdependence is occurring as a result of the rapid movement of people, images, values, and financial transactions across national borders. Another consequence of the increase in transnational trade, travel, and migration is the greater risk of cross-border transmission of infectious diseases. As the world becomes more interconnected, diseases spread more rapidly and effectively. With more than one million people crossing international borders every day, and with the globalization of food production, manufacturing, and marketing, the risk of infectious disease transmission is greater. Economic globalization has also increased the need for governmental budget austerity, and consequent national preparedness has been eroded. The emergence of new infectious diseases, as well as the reemergence of old ones, thus represents a crucial transnational policy issue. These problems cannot be resolved by national governments alone; they require international cooperation. This article analyzes the role of foodborne disease surveillance programs, nationally and internationally, in the control of foodborne diseases.
The Role of Outer-Sphere Surface Acidity in Alkene Epoxidation Catalyzed by Calixarene−Ti(IV) Complexes (2007)

Cooperativity between Brønsted acidic defect sites on oxide surfaces and Lewis acid catalyst sites consisting of grafted calixarene-Ti(IV) complexes is investigated for controlling epoxidation catalysis. Materials are synthesized that, regardless of the surface or calixarene substituent, demonstrate nearly identical UV-visible ligand-to-metal charge-transfer bands and Ti K-edge X-ray absorption near edge spectral features consistent with site-isolated, coordinatively unsaturated Ti(IV) atoms. Despite similar Ti frontier orbital energies demonstrated by these spectra, replacing a homogeneous triphenylsilanol ligand with a silanol on a SiO2 surface increases cyclohexene epoxidation rates with tert-butyl hydroperoxide 20-fold per Ti site. Supporting calixarene-Ti active sites on fully hydroxylated Al2O3 or TiO2, which possess lower average surface hydroxyl pKa than that of SiO2, reduces catalytic rates 50-fold relative to SiO2. These effects are consistent with SiO2 surfaces balancing two competing factors that control epoxidation rates-equilibrated hydroperoxide binding at Ti, disfavored by stronger surface Brønsted acidity, and rate-limiting oxygen transfer from this intermediate to alkenes, favored by strongly H-bonding intermediates. These observations also imply that Ti-OSi rather than Ti-OCalix bonds are broken upon hydroperoxide binding to Ti in kinetically relevant steps, which is verified by the lack of a calixarene upper-rim substituent effect on epoxidation rate. The pronounced sensitivity of observed epoxidation rates to the support oxide, in the absence of changes to the Ti coordination environment, provides experimental evidence for the importance of outer-sphere H-bonding interactions for the exceptional epoxidation reactivity of titanium silicalite and related catalysts.
U-shaped PN junctions for efficient silicon Mach-Zehnder and microring modulators in the O-band (2017)

We demonstrate U-shaped silicon PN junctions for energy efficient Mach-Zehnder modulators and ring modulators in the O-band. This type of junction has an improved modulation efficiency compared to existing PN junction geometries, has low losses, and supports high-speed operation. The U-shaped junctions were fabricated in an 8" silicon photonics platform, and they were incorporated in travelling-wave Mach-Zehnder modulators and microring modulators. For the high-bandwidth Mach-Zehnder modulator, the DC V<sub>π</sub>L at -0.5 V bias was 4.6 V·mm. It exhibited a 3dB bandwidth of 13 GHz, and eye patterns at up to 24 Gb/s were observed. A V<sub>π</sub>L as low as ~2.6 V·mm at a -0.5 V bias was measured in another device. The ring modulator tuning efficiency was 40 pm·V<sup>-1</sup> between 0 V and -0.5 V bias. It had a 3-dB bandwidth of 13.5 GHz and open eye patterns at up to 13 Gb/s were measured. This type of PN junctions can be easily fabricated without extra masks and can be incorporated into generic silicon photonics platforms.
Dynamics of laser-induced cavitation bubbles near an elastic boundary (2001)

The interaction of a laser-induced cavitation bubble with an elastic boundary and its dependence on the distance between bubble and boundary are investigated experimentally. The elastic boundary consists of a transparent polyacrylamide (PAA) gel with 80% water concentration with elastic modulus E = 0.25 MPa. At this E -value, the deformation and rebound of the boundary is very pronounced providing particularly interesting features of bubble dynamics. It is shown by means of high-speed photography with up to 5 million frames s −1 that bubble splitting, formation of liquid jets away from and towards the boundary, and jet-like ejection of the boundary material into the liquid are the main features of this interaction. The maximum liquid jet velocity measured was 960 m s −1 . Such high-velocity jets penetrate the elastic boundary even through a water layer of 0.35 mm thickness. The jetting behaviour arises from the interaction between the counteracting forces induced by the rebound of the elastic boundary and the Bjerknes attraction force towards the boundary. General principles of the formation of annular and axial jets are discussed which allow the interpretation of the complex dynamics. The concept of the Kelvin impulse is examined with regard to bubble migration and jet formation. The results are discussed with respect to cavitation erosion, collateral damage in laser surgery, and cavitation-mediated enhancement of pulsed laser ablation of tissue.
Naturally occurring rhodopsin mutation in the dog causes retinal dysfunction and degeneration mimicking human dominant retinitis pigmentosa (2002)

Rhodopsin is the G protein-coupled receptor that is activated by light and initiates the transduction cascade leading to night (rod) vision. Naturally occurring pathogenic rhodopsin (RHO) mutations have been previously identified only in humans and are a common cause of dominantly inherited blindness from retinal degeneration. We identified English Mastiff dogs with a naturally occurring dominant retinal degeneration and determined the cause to be a point mutation in the RHO gene (Thr4Arg). Dogs with this mutant allele manifest a retinal phenotype that closely mimics that in humans with RHO mutations. The phenotypic features shared by dog and man include a dramatically slowed time course of recovery of rod photoreceptor function after light exposure and a distinctive topographic pattern to the retinal degeneration. The canine disease offers opportunities to explore the basis of prolonged photoreceptor recovery after light in RHO mutations and determine whether there are links between the dysfunction and apoptotic retinal cell death. The RHO mutant dog also becomes the large animal needed for preclinical trials of therapies for a major subset of human retinopathies.
Insect Cuticle Tanning (1991)

Insects periodically secrete and stabilize a cuticular exoskeleton to allow for growth and differentiation during development to the adult stage. Sclerotization or tanning is a vital process in which specific regions of the newly secreted cuticle are stabilized by the formation of cross-links between biopolymers such as protein and chitin. Solid state NMR analysis of pupal cuticle has detected covalent bonding between aromatic or aliphatic carbons of catecholamines and protein nitrogen. Weaker secondary bonding and dehydration may also occur as phenolic content increases. The tanning agents are electrophilic derivatives (o-quinones and ρ-quinone methides or free radicals) of catecholamines that may be involved in both sclerotization and pigmentation. Phenoloxidases such as laccases and tyrosinases and other types of enzymes such as isomerases catalyze the formation of reactive tanning agents from N-acylcatecholamines. Understanding the chemistry of insect cuticular sclerotization could lead to the development of new insecticides.
Establishment of a Pancreatic β Cell Line That Retains Glucose-Inducible Insulin Secretion: Special Reference to Expression of Glucose Transporter Isoforms* (1990)

Two cell lines have been established from insulinomas obtained by targeted expression of the simian virus 40 T antigen gene in transgenic mice. These cell lines, designated MIN6 and MIN7, produce insulin and T antigen and have morphological characteristics of pancreatic beta cells. MIN6 cells exhibit glucose-inducible insulin secretion comparable with cultured normal mouse islet cells, whereas MIN7 cells do not. Both cell lines produce liver-type glucose transporter (GT) mRNA at high level. Brain-type GT mRNA is also present at considerable level in MIN7 cells, but is barely detectable in MIN6 cells, suggesting that exclusive expression of the liver-type GT is related to glucose-inducible insulin secretion. MIN6 cells do not express either major histocompatibility (MHC) class I or class II antigens on the cell surface. However, treatment with interferon-gamma induces high levels of MHC class I antigens, and a combination of interferon-gamma and tumor necrosis factor-alpha induces a MHC class II antigen on the cell surface. These results emphasize that the MIN6 cell line retains physiological characteristics of normal beta cells. The MIN6 cell line will be especially useful to analyze the molecular mechanisms by which beta cells regulate insulin secretion in response to extracellular glucose concentrations. We discuss a possible role of GT isoforms in glucose sensing by beta cells.
Integrating power devices into silicon roadmaps (2006)

Although silicon roadmaps have had a major impact on the progress of semiconductor technology, roadmap emphasis has largely been in the digital arena. Integration of high-voltage and high-current devices into chip designs has tended to follow the original roadmap with a delay of a year or more owing to both economic and technological factors. The resulting ‘mixed-signal’ roadmaps tend to be less structured company-to-company, since more opportunities exist for a variety of approaches. To aid in the understanding of mixed-signal roadmaps, this paper summarises some of the requirements for including power devices into an existing BiCMOS technology. Some of the principles that determine the integration process are described.
Different Strategies for Formation of PEGylated EGF-Conjugated PEI/DNA Complexes for Targeted Gene Delivery (2001)

With the aim of generating gene delivery systems for tumor targeting, we have synthesized a conjugate consisting of polyethylenimine (PEI) covalently modified with epidermal growth factor (EGF) peptides. Transfection efficiency of the conjugate was evaluated and compared to native PEI in three tumor cell lines: KB epidermoid carcinoma cells, CMT-93 rectum carcinoma cells, and Renca-EGFR renal carcinoma cells. Depending on the tumor cell line, incorporation of EGF resulted in an up to 300-fold increased transfection efficiency. This ligand-mediated enhancement and competition with free EGF strongly suggested uptake of the complexes through the EGF receptor-mediated endocytosis pathway. Shielded particles being crucial for systemic gene delivery, we studied the effect of covalent surface modification of EGF-PEI/DNA complexes with a poly(ethylene glycol) (PEG) derivative. An alternative way for the formation of PEGylated EGF-containing complexes was also evaluated where EGF was projected away from PEI/DNA core complexes through a PEG linker. Both strategies led to shielded particles still able to efficiently transfect tumor cells in a receptor-dependent fashion. These PEGylated EGF-containing complexes were 10- to 100-fold more efficient than PEGylated complexes without EGF.
Ovulation-Induced DNA Damage in Ovarian Surface Epithelial Cells of Ewes: Prospective Regulatory Mechanisms of Repair/Survival and Apoptosis1 (2001)

Oxidative base (8-oxoguanine) damage, DNA fragmentation, and apoptosis occurred among ovarian surface epithelial cells within the formative site of ovulation in sheep. The incidence of 8-oxoguanine adducts in surviving antiapoptotic Bcl-2/base excision repair polymerase beta-positive cells at the margins of ruptured follicles (which avoid the focal point of the ovulatory assault) was intermediate between apoptotic and outlying healthy epithelium. Cells containing perturbations to DNA expressed the tumor suppressor p53. Localized reactions of DNA injury and programmed cellular death were averted by ovulation blockade with indomethacin. Progesterone enhanced the biosynthesis of polymerase beta in ovarian surface epithelial cells exposed in vitro to a sublethal concentration of H(2)O(2). Ovulation is a putative etiological factor in common epithelial ovarian cancer. A genetically altered progenitor cell, with unrepaired DNA, but not committed to death, could give rise to a transformed phenotype that is hence propagated upon healing of the ovulatory wound; it appears that this incongruity is normally reconciled by up-regulation of the base excision repair pathway during the ensuing luteal phase.
The monoclonal antibody DCGM4 recognizes Langerin, a protein specific of Langerhans cells, and is rapidly internalized from the cell surface (1999)

We generated monoclonal antibody (mAb) DCGM4 by immunization with human dendritic cells (DC) from CD34+ progenitors cultured with granulocyte-macrophage colony-stimulating factor and TNF-alpha. mAb DCGM4 was selected for its reactivity with a cell surface epitope present only on a subset of DC. Reactivity was strongly enhanced by the Langerhans cell (LC) differentiation factor TGF-beta and down-regulated by CD40 ligation. mAb DCGM4 selectively stained LC, hence we propose that the antigen be termed Langerin. mAb DCGM4 also stained intracytoplasmically, but neither colocalized with MHC class II nor with lysosomal LAMP-1 markers. Notably, mAb DCGM4 was rapidly internalized at 37 degrees C, but did not gain access to MHC class II compartments. Finally, Langerin was immunoprecipitated as a 40-kDa protein with a pI of 5.2 - 5.5. mAb DCGM4 will be useful to further characterize Langerin, an LC-restricted molecule involved in routing of cell surface material in immature DC.