gebhart/patrepeval huggingface dataset:
Quantification of Oligodeoxynucleotides in Human Plasma with a Novel Hybridization Assay Offers Greatly Enhanced Sensitivity over Capillary Gel Electrophoresis (2005)

Capillary gel electrophoresis using UV detection (CGE-UV) has been used to quantify oligodeoxynucleotides (ODN) in human plasma. Although the sensitivity of this method is adequate to detect antisense ODN, which are administered in daily doses up to 10 mg/kg, CGE-UV is not sensitive enough to detect the much lower quantities of ODN administered for other purposes, such as immune stimulation by CpG ODN. We have developed a very sensitive colorimetric hybridization assay that increases the sensitivity of detection by more than four logs compared with CGE-UV. The hybridization assay uses sequence-specific capture and detection ODN probes complementary to portions of the ODN sequence. Herein we provide a prototype for assay development and validation using a 24- mer immunostimulatory phosphorothioate ODN. Probes were locked nucleic acids (LNA), resulting in increased sensitivity and specificity. The linear range of the assay is 7.8-1000 pg/ml, with a 7.8 pg/ml lower limit of quantification (LLOQ) and a detection limit of 2.8 pg/ml. This translates to detection of 40 attamoles. Intraassay and interassay precision were < or =5.0% CV and < or =12.9% CV, respectively, for quality control samples. The assay is suitable for a variety of matrices, including monkey and rat plasma, allowing application to toxicokinetic samples. The methodology is highly specific, with the ability to distinguish almost all single-base mismatched ODN. The assay detects 100% of the parent as well as some metabolites up to N-4, which are known to be the primary metabolites forming in the first hours after in vivo administration and are physiologically active with in vitro assays.
Synthesis, Characterization, X-ray Crystal Structure, DFT Calculations, and Catalytic Properties of a Dioxidovanadium(V) Complex Derived from Oxamohydrazide and Pyridoxal: A Model Complex of Vanadate-Dependent Bromoperoxidase (2014)

A vanadium(V) complex with the formula [Et3NH][V(V)O2(sox-pydx)] with a new tridentate ligand 2-[2-[[3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl]methylene]hydrazinyl]-2-oxoacetamide (soxH-pydxH), obtained by condensation of oxamohydrazide and pyridoxal (one of the forms of vitamin B6), has been synthesized. The compound was characterized by various analytical and spectroscopic methods, and its structure was determined by single-crystal X-ray diffraction technique. Density functional theory (DFT) and time-dependent DFT calculations were used to understand the electronic structure of the complex and nature of the electronic transitions observed in UV-vis spectra. In the complex, vanadium(V) is found to be pentacoordinated with two oxido ligands and a bianionic tridentate ONO-donor ligand. The vanadium center has square-pyramidal geometry with an axial oxido ligand, and the equatorial positions are occupied by another oxido ligand and a phenolato oxygen, an imine nitrogen, and a deprotonated amide oxygen of the hydrazone ligand. A DFT-optimized structure of the complex shows very similar metrical parameters as determined by X-ray crystallography. The O4N coordination environment of vanadium and the hydrogen-bonding abilities of the pendant amide moiety have a strong resemblance with the vanadium center in bromoperoxidase enzyme. Bromination experiments using H2O2 as the oxidizing agent, with model substrate phenol red, and the vanadium complex as a catalyst show a remarkably high value of kcat equal to 26,340 h(-1). The vanadium compound also efficiently catalyzes bromination of phenol and salicylaldehyde as well as oxidation of benzene to phenol by H2O2.
Structural and functional characterization of a putative de novo gene in Drosophila (2020)

Comparative genomic studies have repeatedly shown that new protein-coding genes can<br> emerge <em>de novo</em> from non-coding DNA. Still unknown is how and when the structures of<br> encoded <em>de novo</em> proteins emerge and evolve. Combining biochemical, genetic and evolu-<br> tionary analyses, we elucidate the function and structure of <em>goddard</em>, a gene which appears<br> to have evolved de novo at least 50 million years ago within the Drosophila genus.<br> Previous studies found that <em>goddard</em> is required for male fertility. Here, we show that God-<br> dard protein localizes to elongating sperm axonemes and that in its absence, elongated<br> spermatids fail to undergo individualization. Combining modelling, NMR and CD data, we<br> show that Goddard protein contains a large central α-helix, but is otherwise partially disor-<br> dered. We find similar results for Goddard’s orthologs from divergent fly species and their<br> reconstructed ancestral sequences. Accordingly, Goddard’s structure appears to have been<br> maintained with only minor changes over millions of years.
Two‐Component Molecular Materials of 2,5‐Diphenyloxazole Exhibiting Tunable Ultraviolet/Blue Polarized Emission, Pump‐enhanced Luminescence, and Mechanochromic Response (2013)

The development of π‐conjugated molecular systems with high‐efficiency generation of UV and blue light plays an important role in the fields of light‐emitting diodes, fluorescent imaging, and information storage. Herein, supramolecular construction of solid‐state UV/blue luminescent materials are assembled using 2,5‐diphenyloxazole (DPO) with four typical co‐assembled building blocks (1,4‐diiodotetrafluorobenzene, 4‐bromotetrafluorobenzene carboxylic acid, pentafluorophenol, and octafluoronaphthalene). Compared with the pristine DPO sample, the as‐prepared two‐component molecular materials feature ease of crystallization, high crystallinity, enhanced thermal stability and tunable luminescence properties (such as emissive wavelength, color, fluorescence lifetime, and photoluminescence quantum yield) as well as multicolor polarized emission in the UV/blue region. Moreover, pump‐enhanced luminescence and reversible mechanochromic fluorescence (MCF) properties can also be obtained for these molecular solids, which are absent for the pristine DPO sample. Therefore, this work provides a procedure for the facile self‐assembly of ordered two‐component molecular materials with tunable UV/blue luminescence properties, which have potential application in the areas of light‐emitting displays, polarized emission, frequency doubling, and luminescent sensors.
Stabilization of Glucocerebrosidase by Active Site Occupancy (2017)

Glucocerebrosidase (GBA) is a lysosomal β-glucosidase that degrades glucosylceramide. Its deficiency results in Gaucher disease (GD). We examined the effects of active site occupancy of GBA on its structural stability. For this, we made use of cyclophellitol-derived activity-based probes (ABPs) that bind irreversibly to the catalytic nucleophile (E340), and for comparison, we used the potent reversible inhibitor isofagomine. We demonstrate that cyclophellitol ABPs improve the stability of GBA in vitro, as revealed by thermodynamic measurements (T<sub>m</sub> increase by 21 °C), and introduce resistance to tryptic digestion. The stabilizing effect of cell-permeable cyclophellitol ABPs is also observed in intact cultured cells containing wild-type GBA, N370S GBA (labile in lysosomes), and L444P GBA (exhibits impaired ER folding): all show marked increases in lysosomal forms of GBA molecules upon exposure to ABPs. The same stabilization effect is observed for endogenous GBA in the liver of wild-type mice injected with cyclophellitol ABPs. Stabilization effects similar to those observed with ABPs were also noted at high concentrations of the reversible inhibitor isofagomine. In conclusion, we provide evidence that the increase in cellular levels of GBA by ABPs and by the reversible inhibitor is in part caused by their ability to stabilize GBA folding, which increases the resistance of GBA against breakdown by lysosomal proteases. These effects are more pronounced in the case of the amphiphilic ABPs, presumably due to their high lipophilic potential, which may promote further structural compactness of GBA through hydrophobic interactions. Our study provides further rationale for the design of chaperones for GBA to ameliorate Gaucher disease.
Apparent Founder Effect during the Early Years of the San Francisco HIV Type 1 Epidemic (1978–1979) (2000)

HIV-1 envelope sequence variants were RT-PCR amplified from serum samples cryopreserved in San Francisco in 1978-1979. The HIV-1 subtype B env V3-V5 sequences from four homosexual men clustered phylogenetically, with a median nucleotide distance of 2.8%, reflecting a recent common origin. These early U.S. HIV-1 env variants mapped close to the phylogenetic root of the subtype B tree while env variants collected in the United States throughout the 1980s and 1990s showed, on average, increasing genetic diversity and divergence from the subtype B consensus sequence. These results indicate that the majority of HIV-1 currently circulating in the United States may be descended from an initial introduction and rapid spread during the mid- to late 1970s of subtype B viruses with limited variability (i.e., a founder effect). As expected from the starburst-shaped phylogeny of HIV-1 subtype B, contemporary U.S. strains were, on average, more closely related at the nucleic acid and amino acid levels to the earlier 1978-1979 env variants than to each other. The growing levels of HIV-1 genetic diversity, one of multiple obstacles in designing a protective vaccine, may therefore be mitigated by using epidemic founding variants as antigenic strains for protection against contemporary strains.
Composite and Core-Shell Cluster assemblies Prepared with Two Cluster Sources (2004)

A plasma-gas condensation cluster deposition system with two sources has been applied for preparing Co/Si clusters assemblies. When a separation plate is inserted between two glow-discharge-rooms, a mixture of Co and Si clusters is obtained: small Co clusters are distributed at random, while the Si clusters are aggregated to form large secondary particles. Without a separation plate, on the other hand, core-shell clusters are obtained: a Co core is covered by small Si crystallites. The magnetization measurement at 5 K shows that the magnetic coercive force of Co/Si cluster assemblies is much smaller than that of Co cluster assemblies. Since the Si shell prevents Co cluster surfaces from their oxidation, such core-shell clusters will be used as building blocks for novel nano-structure-controlled materials.
Effect of naloxone on tooth pulp‐evoked jaw‐opening reflex in the barbiturate‐anaesthetized cat (1988)

The threshold of the tooth pulp-evoked jaw-opening reflex was uninfluenced by administration of 0.5 or 5.0 mg kg-1, i.v. naloxone, a specific opioid antagonist, in the barbiturate-anaesthetized cat. Furthermore, facilitatory or inhibitory interactions between two successive tooth pulp-evoked jaw reflex responses were not influenced by naloxone. It is concluded that naloxone-sensitive opioid receptor-mediated mechanisms do not contribute to the modulation of tooth pulp-evoked reflexes by conditioning dental stimuli. Also they do not exert a tonic inhibition on the sensory or motor part of the tooth pulp-driven reflexes. Experiments performed for comparison showed that the non-nociceptive polysynaptic reflex discharge in the flexo-motor neurons of the limb was not influenced by naloxone either.
Parallel Performance of Domain-Decomposed Preconditioned Krylov Methods for PDEswith Locally Uniform Refinement (1992)

Preconditioners based on domain decomposition appear natural for the Krylov solution of implicitly discretized partial differential equations (PDEs) on parallel computers. Two-scale preconditioners (involving a global coarse-grid solve, independent solves over interfaces connecting the coarse-grid points, and independent subdomain solves) have been known since the early 1980s to be “near optimal” in the sense of ensuring a bounded, or at most logarithmically growing, iteration count as the mesh is refined. As a result, the refinement of the mesh can be chosen locally on the basis of truncation error, and the granularity of the domain decomposition can be chosen globally on the basis of parallel computing considerations with only mild effects on the convergence rate of the algorithm. However, overall computational complexity depends not only on the algebraic convergence rate, but also on the operation counts of the components of the preconditioner that must be applied at each iteration. The costs of solving the subdomain systems and the crosspoint system show superlinear growth in their respective (and inversely related) sizes. On the subdomains, the superlinear terms arise from arithmetic only; in the crosspoint system the cost of nonlocal data exchange is also superlinear. These factors make the preconditioner granularity and the choice of its components problem- and machine-dependent compromises. The tradeoffs involved are illustrated through numerical experiments on both shared- and distributed-memory computers for convection-diffusion problems. Because of the development of boundary layers, these problems benefit from local mesh refinement, which is straightforward to accommodate within the domain decomposition framework in a locally uniform sense, but which introduces load balancing as a further consideration in selecting the granularity of the preconditioner. In spite of the tradeoffs, cumulative speedups are obtainable out to at least medium-scale granularity (up to 64 processors in our tests). The largest problems involve $\mathcal{O}(10^5 )$ unknowns partitioned into $\mathcal{O}(10^3 )$ subdomains and converge in $\mathcal{O}(10)$ iterations requiring $\mathcal{O}(1)$ seconds on the Intel iPSC/860.
Les structures et les hommes (2003)

Résumé Les chiffres parlent d’eux-mêmes. Ils mettent en évidence l’accroissement du travail quotidien des secteurs et des psychiatres malgré le manque de moyens matériels par fermeture des lits d’hospitalisation et le peu de création en structures alternatives à l’hospitalisation, mais aussi malgré la baisse tragique de la démographie du corps de métier infirmier et médical, notamment dans cette spécialité.
Plasminogen Activator Inhibitor-1 and the Circadian Clock in Metabolic Disorders (2009)

Plasma PAI-1 levels robustly fluctuate in a circadian manner and consequently contribute to hypofibrinolysis during the early morning. The circadian expression of PAI-1 gene is thought to be directly regulated by the circadian clock proteins such as CLOCK and BMAL1/BMAL2 which drive the endogenous biological clock. Plasma PAI-1 levels are increased in the beginning of the active phase in both diurnal humans and in nocturnal rodents, suggesting that the rhythmic PAI-1 expression is commonly indispensable for organisms. A series of our recent studies revealed that circadian clock proteins are important for hypofibrinolysis induced by metabolic disorders such as obesity and diabetes.
Size and Shape Controlled Growth of Molecular Nanostructures on Silicon Oxide Templates (2004)

A new process for nanoscale fabrication of ordered monolayer films of conjugated organic molecules is presented. The process makes it possible to grow sexithiophene monolayers (T6) at precise locations on a silicon substrate with a high degree of order while preserving the orientation of growth. The process is based on the integration of local oxidation nanolithography of the substrate and template growth of the molecular thin film. The former is used to fabricate silicon oxide arrays of parallel lines of 30−50 nm in width and several microns in length. Template growth arises from the interplay between kinetic growth parameters and preferential interactions with the patterned surface. The result is a monolayer film of organic molecules that conformally mimicks the features of the fabricated motives. This approach could be used to connect molecular domains of well-defined size between metallic electrodes.
Haplotype analysis of the RYR1 gene in Malignant Hyperthermia and Central Core Disease (1995)

Conference Article| May 01 1995 Haplotype analysis of the RYR1 gene in Malignant Hyperthermia and Central Core Disease KATHLEEN A. QUANE; KATHLEEN A. QUANE 1Department of Biochemistry, University College, Cork, Ireland Search for other works by this author on: This Site PubMed Google Scholar KATHERINE E. KEATING; KATHERINE E. KEATING 1Department of Biochemistry, University College, Cork, Ireland Search for other works by this author on: This Site PubMed Google Scholar JM SANDRA. HEALY; JM SANDRA. HEALY 1Department of Biochemistry, University College, Cork, Ireland Search for other works by this author on: This Site PubMed Google Scholar JAMES JA. HEFFRON; JAMES JA. HEFFRON 1Department of Biochemistry, University College, Cork, Ireland Search for other works by this author on: This Site PubMed Google Scholar MARY LEHANE; MARY LEHANE 1Department of Anaesthetics, University College, Cork, Ireland Search for other works by this author on: This Site PubMed Google Scholar RENEE KRIVOSIC-HORBER; RENEE KRIVOSIC-HORBER 2Malignant Hyperthermia Unit, Hospital B - CHRU Lille 59037, France Search for other works by this author on: This Site PubMed Google Scholar LUC HEYTENS; LUC HEYTENS 3Department of Intensive Care, University Hospital of Antwerp, Wilrijkstraat 10, B2650 Edegem, Belgium Search for other works by this author on: This Site PubMed Google Scholar TOMMIE V. MCCARTHY TOMMIE V. MCCARTHY 1Department of Biochemistry, University College, Cork, Ireland Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1995) 23 (2): 372S. https://doi.org/10.1042/bst023372s Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation KATHLEEN A. QUANE, KATHERINE E. KEATING, JM SANDRA. HEALY, JAMES JA. HEFFRON, MARY LEHANE, RENEE KRIVOSIC-HORBER, LUC HEYTENS, TOMMIE V. MCCARTHY; Haplotype analysis of the RYR1 gene in Malignant Hyperthermia and Central Core Disease. Biochem Soc Trans 1 May 1995; 23 (2): 372S. doi: https://doi.org/10.1042/bst023372s Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: CCD, central core disease, MH, malignant hyperthermia, MHS, malignant hyperthermia susceptible, RYR1, ryanodine receptor gene, SSCP, single stranded conformation polymorphism © 1995 Biochemical Society1995 Article PDF first page preview Close Modal You do not currently have access to this content.
Blind equalization of multichannel IIR system using second order statistics (2002)

Second order statistics based solutions to blind equalization of p-inputs/q-outputs (q>p) IIR (infinite impulse response) system are presented. Many interesting results have been developed for the blind identification of single-input multiple-outputs (SIMO) FIR system. We show here, how to extend some of the existing results to the ARMA (autoregressive moving average) case. More precisely, two equalization methods, namely: (i) a linear prediction method and (ii) a noise subspace method are developed. Moreover, extension to the multi-inputs multi-outputs (MIMO) case is described for each of the two methods. Finally some simulation results are presented to compare and illustrate the effectiveness of the proposed methods.
Scanning Near-Field Raman Microscopy on Ferroelectrics (2003)

By combining scanning atomic force microscopy with micro-probed Raman scattering spectroscopy, we have developed a new type of scanning near-field Raman scattering system. A special designed cantilever with aperture of about 150 nm in diameter was used both as an illumination nano-source and a nano-detector of scattering light. Near-field Raman spectra of internal modes in TGS and GMO single crystals were observed at their cleavage surfaces at room temperature. The results are compared with those obtained by a conventional Raman microscope. Keywords: Near-fieldScanning MicroscopyRaman ScatteringInternal ModesNano-scale
The Increasing Popularity of Cosmetic Surgery Procedures: A Look at Statistics in Plastic Surgery (2000)

Dallas, Texas Rod J. Rohrich, M.D. Department of Plastic and Reconstructive Surgery UT Southwestern Medical Center 5323 Harry Hines Boulevard, Suite E7.210 Dallas, Texas 75390–9132 rod.[email protected]
Light-Induced Changes in Photoreceptor Membrane Resistance and Potential in Gecko Retinas (1974)

The time-course of light-induced changes in membrane voltage and resistance were measured in single photoreceptors in eyecup preparations of Gekko gekko. A small circular stimulus directed toward the impaled receptor produced membrane hyperpolarization. Application of a steady annular light to the receptor periphery resulted in diminution of the receptor's response to the stimulus. The effects of illumination of the surrounding receptors were isolated by directing a small, steady desensitizing light to the impaled receptor and then applying a peripheral stimulus. Brief stimuli produced a transient decrease in resistance with rapid onset and offset, a time-course similar to that of the response diminution. For some cells a depolarization that coincided with the resistance decrease was seen. During illumination with prolonged stimuli the resistance decrease was followed by a slow increase. After offset resistance rose transiently above the original value and then returned slowly to its original value. The slow resistance changes were not accompanied by changes in membrane voltage. The response diminution, resistance decrease, and depolarization were not observed in retinas treated with aspartate or hypoxia. It is therefore concluded that these effects are mediated by horizontal cells. The diminution is achieved by shunting the receptor potential and may play a role in field adaptation.
The Lithium Metal Induced Isomerization of Propenyl Derivatives of Tin, Silicon, and Germanium1 (1966)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Lithium Metal Induced Isomerization of Propenyl Derivatives of Tin, Silicon, and Germanium1Dietmar Seyferth, Reiichi Suzuki, and Lawrence G. VaughanCite this: J. Am. Chem. Soc. 1966, 88, 2, 286–291Publication Date (Print):January 1, 1966Publication History Published online1 May 2002Published inissue 1 January 1966https://pubs.acs.org/doi/10.1021/ja00954a020https://doi.org/10.1021/ja00954a020research-articleACS PublicationsRequest reuse permissionsArticle Views95Altmetric-Citations18LEARN 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