gebhart/patrepeval huggingface dataset:
Engineering of a novel thioether bridge and role of modified residues in the lantibiotic Pep5 (1996)

Pep5 is a 34-amino-acid antimicrobial peptide, produced by Staphylococcus epidermidis 5, that contains the thioether amino acids lanthionine and methyllanthionine, which form three intramolecular ring structures. In addition, two didehydrobutyrines are present in the central part of the lantibiotic and an oxobutyryl residue is located at the N terminus. All rare amino acids are introduced by posttranslational modifications of a ribosomally made precursor peptide. To elucidate the function of the modified residues for the antimicrobial action of Pep5, mutant peptides, in which single modified residues had been eliminated, were produced by site-directed mutagenesis. All of these peptides showed a reduced antimicrobial activity. In addition, those peptides from which the ring structures had been deleted became susceptible to proteolytic digest. This demonstrates that the ring structures serve as stabilizers of conformations essential for activity, e.g., amphiphilicity, as well as for protecting Pep5 against proteases of the producing strains. In addition, residues that could serve as precursors of new modified amino acids in lantibiotics were introduced into the Pep5 precursor peptide. This way, a novel methyllanthionine and a didehydroalanine were inserted into the flexible central part of Pep5, demonstrating that biosynthesis of modified amino acids is feasible by protein engineering and use of the lantibiotic modification system.
Enzymic formation of sesquiterpenes (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnzymic formation of sesquiterpenesDavid E. CaneCite this: Chem. Rev. 1990, 90, 7, 1089–1103Publication Date (Print):November 1, 1990Publication History Published online1 May 2002Published inissue 1 November 1990https://pubs.acs.org/doi/10.1021/cr00105a002https://doi.org/10.1021/cr00105a002research-articleACS PublicationsRequest reuse permissionsArticle Views2069Altmetric-Citations408LEARN 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
The avian retroviral integration protein cleaves the terminal sequences of linear viral DNA at the in vivo sites of integration (1989)

The purified integration protein (IN) of avian myeloblastosis virus is shown to nick double-stranded oligodeoxynucleotide substrates that mimic the ends of the linear form of viral DNA. In the presence of Mg2+, nicks are created 2 nucleotides from the 3' OH ends of both the U5 plus strand and the U3 minus strand. Similar cleavage is observed in the presence of Mn2+ but only when the extent of the reaction is limited. Neither the complementary strands nor sequences representing the termini of human immunodeficiency virus type 1 DNA were cleaved at analogous positions. Analysis of a series of substrates containing U5 base substitutions has defined the sequence requirements for site-selective nicking; nucleotides near the cleavage site are most critical for activity. The minimum substrate size required to demonstrate significant activity corresponds to the nearly perfect 15-base terminal inverted repeat. This in vitro activity of IN thus produces viral DNA ends that are joined to host DNA in vivo and corresponds to an expected early step in the integrative recombination reaction. These results provide the first enzymatic support using purified retroviral proteins for a linear DNA precursor to the integrated provirus.
A Cutting Concentration Calculation Model of a Vertical Wellbore Annulus in Deep-Water Drilling Operation and its Application (2011)

Cutting transport is a big problem in a wellbore in deep-water drilling specially with a long and large diameter riser. And proper cutting concentration is the key parameter of controlling wellbore pressure and ECD. In this study, a cutting concentration model of a vertical wellbore annulus in deep-water drilling operation has been developed. The model is solved numerically to predict the proportion respectively in each interval of the deep-water well and the rule of proportion changed with time. It is applied in the calculation of cutting concentration in the oil field and a good effect has been achieved.
Synthesis and Biological Activity of Bile Acid-Derived HMG-CoA Reductase Inhibitors. The Role of 21-Methyl in Recognition of HMG-CoA Reductase and the Ileal Bile Acid Transport System (1994)

To increase hepatoselectivity of HMG-CoA reductase inhibitors by using the specific bile acid transport systems, deoxycholic acid-derived inhibitors 9 and 11 have been synthesized, on the basis of the concept of combining in one molecule structural requirements for specific inhibition of the HMG-CoA reductase and specific recognition by the ileal bile acid transport system. The 1-methyl-3-carboxylpropyl subunit of deoxycholic acid was replaced by the 3,5-dihydroxyheptanoic acid lactone of lovastatin, and position 12-OH was esterified with 2-methylbutyric acid. Compounds 9 and 11 were evaluated for their inhibitory activity on rat liver HMG-CoA reductase, cholesterol biosynthesis in HEP G2 cells, and [3H]taurocholate uptake in rabbit brush border membrane vesicles and compared with methyl derivatives 8 and 10. The steroidal 21-CH3 group affects both activity on HMG-CoA reductase and recognition by the ileal bile acid transport system.
Multiply Doped Nanostructured Silicate Sol−Gel Thin Films:  Spatial Segregation of Dopants, Energy Transfer, and Distance Measurements (2005)

Physical and chemical strategies that place designed molecules in spatially separated regions of surfactant-templated mesostructured silicate thin films are used to prepare films containing rhodamine 6G (R6G), lanthanide complexes, and both simultaneously. Fluorescence and photoexcitation spectra of R6G in amorphous and structured thin films show that it is located inside the surfactant micelles of structured thin films. A silylated ligand that binds lanthanides condenses to form part of the silica framework and causes the lanthanide to localize in the silica. Luminescence and photoexcitation spectra show that energy transfer from the metal complex to R6G occurs in the films. R6G quenches Tb emission in a concentration-dependent manner. Energy transfer efficiency is calculated using the Tb luminescence lifetime, and this quantity is used to calculate the distance between Tb and R6G with the aid of Förster theory.
Expression of the Two Major Envelope Proteins of Equine Arteritis Virus as a Heterodimer Is Necessary for Induction of Neutralizing Antibodies in Mice Immunized with Recombinant Venezuelan Equine Encephalitis Virus Replicon Particles (2000)

RNA replicon particles derived from a vaccine strain of Venezuelan equine encephalitis virus (VEE) were used as a vector for expression of the major envelope proteins (G(L) and M) of equine arteritis virus (EAV), both individually and in heterodimer form (G(L)/M). Open reading frame 5 (ORF5) encodes the G(L) protein, which expresses the known neutralizing determinants of EAV (U. B. R. Balasuriya, J. F. Patton, P. V. Rossitto, P. J. Timoney, W. H. McCollum, and N. J. MacLachlan, Virology 232:114-128, 1997). ORF5 and ORF6 (which encodes the M protein) of EAV were cloned into two different VEE replicon vectors that contained either one or two 26S subgenomic mRNA promoters. These replicon RNAs were packaged into VEE replicon particles by VEE capsid protein and glycoproteins supplied in trans in cells that were coelectroporated with replicon and helper RNAs. The immunogenicity of individual replicon particle preparations (pVR21-G(L), pVR21-M, and pVR100-G(L)/M) in BALB/c mice was determined. All mice developed antibodies against the recombinant proteins with which they were immunized, but only the mice inoculated with replicon particles expressing the G(L)/M heterodimer developed antibodies that neutralize EAV. The data further confirmed that authentic posttranslational modification and conformational maturation of the recombinant G(L) protein occur only in the presence of the M protein and that this interaction is necessary for induction of neutralizing antibodies.
Nanozeolites:  Synthesis, Crystallization Mechanism, and Applications (2005)

This review focuses on the synthesis, crystallization mechanism, and application of colloidal zeolites. The synthesis formulations and features of different zeolite-type structures prepared in nanosized form are summarized. Special attention is paid to zeolites prepared as stable colloidal suspensions. Next, new insights into zeolite crystallization mechanism gained by using colloidal zeolites as model systems are discussed. Further, the methods for deposition of zeolite nanocrystals from suspensions onto supports of different shapes and compositions used for the fabrication of zeolite films and membranes are reviewed. The use of colloidal zeolites for the fabrication of hierarchical macrostructures is also described. Other uses of nanozeolites for the preparation of functionalized materials, for the synthesis of mesoporous silicas of improved hydrothermal stability, and as seeds for zeolite syntheses are illustrated. The emerging applications of nanozeolites in sensing, optoelectronics, and medicine constitute another topic in this review. Finally, some future trends in the area are envisaged.
Network security via reverse engineering of TCP code: vulnerability analysis and proposed solutions (1997)

The Transmission Control Protocol/Internet Protocol (TCP/IP) suite is widely employed to interconnect computing facilities in today's network environments. However, there exist several security vulnerabilities in the TCP specification and additional weaknesses in a number of its implementations. These vulnerabilities may allow an intruder to "attack" TCP-based systems, enabling him/her to "hijack" a TCP connection or cause denial of service to legitimate users. The authors analyze the TCP code via a "reverse engineering" technique called "program slicing" to identify several of these vulnerabilities, especially those that are related to the TCP state-transition diagram. They discuss many of the flaws present in the TCP implementation of many widely used operating systems, such as SUNOS 4.1.3, SVR4, and ULTRIX 4.3. The corresponding TCP attack "signatures" (including the well-known 1994 Christmas Day Mitnick Attack) are described, and recommendations are provided to improve the security state of a TCP-based system (e.g., incorporation of a "timer escape route" from every TCP state). Also, it is anticipated that wide dissemination of this article's results may not only lead to vendor patches to TCP code to plug security holes, but also raise awareness of how program slicing may be used to analyze other networking software and how future designs of TCP and other software can be improved.
Surface Chemistry and Electrochemistry of Supported Zerovalent Iron Nanoparticles in the Remediation of Aqueous Metal Contaminants (2001)

The microstructure, physical characteristics, corrosion behavior, and reactivity of zerovalent iron nanoparticles synthesized on a support (primarily a nonporous, hydrophobic polymer resin) were studied. The remediation of groundwater by zerovalent iron in in situ permeable reactive barriers relies on the redox reaction between metallic iron and a reducible contaminant. Decreasing the size of the iron particles and dispersing them on a support increases the specific surface area of the iron, as well as the ratio of surface to bulk iron atoms, and should thereby increase both the reaction rate and the fraction of iron atoms available for the reaction. Borohydride reduction of aqueous ferrous sulfate gives supported iron nanoparticles, 10−30 nm in diameter, which consist of 85% zerovalent iron by weight. These materials (“ferragels”) are stable in air and have corrosion behavior comparable to iron filings. Interestingly, the presence or absence of a support, as well as the boron remaining from the borohydride reduction process, influences the electrochemical corrosion rate of the composite materials. Supported and unsupported zerovalent iron nanoparticles are superior to iron filings in both terms of initial rates of reduction and total moles of contaminants (Cr(VI), Pb(II), TcO4-) reduced per mole of iron. The enhanced reactivity and passive corrosion behavior of these materials should make them good candidates for use in permeable reactive barriers.
Fabrication of 0.2 μm large scale integrated circuits using synchrotron radiation x-ray lithography (1995)

In the last few years, we have made dramatic improvements in the key components of synchrotron radiation x-ray lithography including a high-brightness and compact synchrotron radiation source, high-accuracy steppers, precise masks, and highly sensitive chemically amplified resists. These advances have been used in the test fabrication of complementary metal–oxide–semiconductor large scale integrated circuits using separation by implanted oxygen technology in the 0.2 μm regime. Synchrotron radiation lithography was used at the active, gate, contact, and four-level metallization levels or at the gate level only. Fabricated gate array large scale integrated circuits, including a 48×48 bit multiplier, have excellent and fully functional characteristics. This article describes lithographic performance under device fabrication conditions, demonstrating an excellent critical dimension control of 0.02 μm (3σ), an overall overlay better than 0.15 μm (3σ) (including metallization levels), and a throughput of 12 wafers (6 in.) per hour.
High efficiency DC-DC converter chip size module with integrated soft ferrite (2004)

In this paper, we present the performance of the micro DC-DC convertor CSM. We have developed this convertor with the configuration of Chip Size Module, consisting of a high speed PWM controller IC and an integrated soft ferrite as a solenoid type thin micro inductor.
Clinicopathological and prognostic significance of sialyl Lewis X overexpression in patients with cancer: a meta-analysis (2016)

Many studies have shown that sialyl Lewis X (sLe(X)) is related to cancer prognosis and clinicopathology, but failed to provide conclusive results. We conducted the present meta-analysis to identify the association between sLe(X) overexpression and cancer prognosis. We searched studies in PubMed and Embase databases. Relative risk or hazard ratio with 95% confidence intervals were estimated with the Mantel-Haenszel random-effect method and 29 studies were included. Our meta-analysis showed that sLe(X) overexpression is significantly related to lymphatic invasion, venous invasion, T stage, N stage, M stage, tumor stage, recurrence, and overall survival. In subgroup analysis, we found that cancer type and ethnicity might be two major contributing factors to the possible presence of heterogeneity among the studies. In conclusion, sLe(X) overexpression is associated with tumor metastasis, recurrence, and overall survival in cancer patients, it plays an important role in cancer prognosis.
Properties of Paramagnetic Metals in MRI (1997)

The use of different metals in Magnetic Resonance Imaging will be briefly described.This overview will be more a qualitative description than a full paper on this topic, in other words, this paper contributes to explaining how and why some metal ions have been chosen for MRI.Paramagnetic compounds are currently used in clinical practice. The main differencesin the four gadolinium complexes come from their different chemical structures. The macrocyclic compounds display a high symmetry and rigidity and therefore a high level of stability.All these four complexes display the same efficacyon the signal in MRI. In addition, they are very well tolerated.The second main class of compounds consists of the iron oxide superparamagnetic particles. They are used in the detection of focal liver lesions. Through their action in dephasing the spin, they are used as negative enhancers.
Detection of MicroRNAs Using Target-Guided Formation of Conducting Polymer Nanowires in Nanogaps (2007)

A nanogapped microelectrode-based biosensor array is fabricated for ultrasensitive electrical detection of microRNAs (miRNAs). After peptide nucleic acid (PNA) capture probes were immobilized in nanogaps of a pair of interdigitated microelectrodes and hybridization was performed with their complementary target miRNA, the deposition of conducting polymer nanowires, polyaniline (PAn) nanowires, is carried out by an enzymatically catalyzed method, where the electrostatic interaction between anionic phosphate groups in miRNA and cationic aniline molecules is exploited to guide the formation of the PAn nanowires onto the hybridized target miRNA. The conductance of the deposited PAn nanowires correlates directly to the amount of the hybridized miRNA. Under optimized conditions, the target miRNA can be quantified in a range from 10 fM to 20 pM with a detection limit of 5.0 fM. The biosensor array is applied to the direct detection of miRNA in total RNA extracted from cancer cell lines.
Interactive texture mapping (1993)

This paper describes a new approach to texture mapping. A global method to lower the distortion of the mapped image is presented; by considering a general optimization function we view the mapping as an energy-minimization process. We have constructed an interactive texture tool, which is fast and easy to use, to manipulate atlases in texture space. We present the tool’s large set of interactive operations on mapping functions. We also introduce an algorithm which automatically generates an atlas for any type of object. These techniques allow the mapping of different textures onto the same object and handle non-continuous mapping functions, needed for complicated mapped objects. CR Categories and subject descriptors: I.3.3 [Computer Graphics] Picture/Image Generation. I.3.7 [Computer Graphics] Graphics and Realism - Color, Shading and Texture. Additional Keywords: Texture Mapping, Texture Map Distortion, Realistic Rendering, Interaction.
Macrophages Inhibit Neovascularization in a Murine Model of Age-Related Macular (2006)

Background Age-related macular degeneration (AMD) is the leading cause of blindness in people over 50 y of age in at least three continents. Choroidal neovascularization (CNV) is the process by which abnormal blood vessels develop underneath the retina. CNV develops in 10% of patients with AMD but accounts for up to 90% of the blindness from AMD. Although the precise etiology of CNV in AMD remains unknown, the macrophage component of the inflammatory response, which has been shown to promote tumor growth and support atherosclerotic plaque formation, is thought to stimulate aberrant angiogenesis in blinding eye diseases. The current theory is that macrophage infiltration promotes the development of neovascularization in CNV.
Modulation of Magainin 2−Lipid Bilayer Interactions by Peptide Charge (1997)

Magainin 2, an antimicrobial peptide from Xenopus skin, assumes an amphiphilic helix when bound to acidic phospholipids, forming a pore composed of a dynamic, peptide-lipid supramolecular complex [Matsuzaki et al. (1996) Biochemistry 35, 11361-11368]. Upon the disintegration of the pore, a fraction of the peptide molecules stochastically translocates across the bilayer (Matsuzaki, et al., 1995). In order to investigate the effects of peptide charge on the magainin 2-lipid bilayer interactions, we synthesized four magainin 2 analogs with different charges (0-6+). MG0: K10E, K11E, F12W-magainin 2. MG2+: K10E, F12W-magainin 2. MG4+: F12W-magainin 2. MG6+: F12W, E19Q-magainin 2 amide. An increase in charge resulted in a stronger binding of the peptide to the negatively charged membranes, suggesting that electrostatic attractions play a crucial role in the binding process. The helical stability in a trifluoroethanol/buffer mixture was decreased with increasing positive charge because of electrostatic repulsions between the closely spaced positive side chains, whereas the helicity in the lipid bilayer was much higher and appeared to be independent of the peptide charge. However, enhanced repulsions between the highly positively charged helices destabilized the pore. Therefore, the efficiency of the most basic peptide (MG6+) to translocate across the bilayer was the greatest by virtue of the short life span of its pore and the very tight membrane binding. The charge distribution of wild-type magainin 2 was found to be so designed as to exhibit the maximal lytic activity by simultaneously achieving a strong binding and a moderate pore stability.
Multiple PU.1 sites cooperate in the regulation ofp40phox transcription during granulocytic differentiation of myeloid cells (2002)

The p40(phox) protein, a regulatory component of the phagocyte NADPH oxidase, is preferentially expressed in cells of myeloid lineage. We investigated transcriptional regulation of the p40(phox) gene in HL-60 myeloid cells. Deletion analysis of approximately 6 kb of the 5'-flanking sequence of the gene demonstrated that the proximal 106 base pair of the promoter exhibited maximum reporter activity. This region contains 3 potential binding sites for PU.1, a myeloid-restricted member of the ets family of transcription factors. Mutation or deletion of each PU.1 site decreased promoter activity, and the level of activity mediated by each site correlated with its binding avidity for PU.1, as determined by gel shift competition assays. Mutation of all 3 sites abolished promoter activity in myeloid cells. PU.1-dependent expression was also observed in the Raji B-cell line, whereas the moderate level of promoter reporter activity in the nonmyeloid HeLa cell line was independent of PU.1. Chromatin immunoprecipitation assay demonstrated occupation of the PU.1 sites by PU.1 in vivo in HL-60 cells. Cotransfection of the pGL3-p40-106 reporter construct with a dominant-negative PU.1 mutant dramatically reduced promoter activity, whereas the overexpression of PU.1 increased promoter activity. Promoter activity and transcript levels of p40(phox) increased in HL-60 cells during dimethyl sulfoxide-induced differentiation toward the granulocyte phenotype, and this was associated with increased cellular levels of PU.1 protein. Our findings demonstrate that PU.1 binding at multiple sites is required for p40(phox) gene transcription in myeloid cells and that granulocytic differentiation is associated with the coordinated up-regulation of PU.1 and p40(phox) expression.