gebhart/patrepeval huggingface dataset:
Analysis of dispersive by wave field transformation (1981)

Abstract The dispersive waves in a common-shot wave field can be transformed into images of the dispersion curves of each mode in the data. The procedure consists of two linear transformations: a slant stack of the data produces a wave field in the phase slowness-time intercept (p - tau ) plane in which phase velocities are separated. The spectral peak of the one-dimensional (1-D) Fourier transform of the p - tau wave field then gives the frequency associated with each phase velocity. Thus, the data wave field is linearly transformed from the time-distance domain into the slowness-frequency (p - omega ) domain, where dispersion curves are imaged. All the data are present throughout the transformations. Dispersion curves for the mode overtones as well as the fundamental are directly observed in the transformed wave field. In the p - omega domain, each mode is separated from the others even when its presence is not visually detectable in the untransformed data. The resolution achieved in the result is indicated in the p - omega wave field by the width and coherence of the image. The method is applied to both synthetic and real data sets.
Collocation analysis for UMLS knowledge-based word sense disambiguation (2011)

Collocations improve the performance of knowledge-based disambiguation methods, although results vary depending on the test set and method used. Generally, the AEC method is sensitive to query drift. Using AEC, just a few selected terms provide a large improvement in disambiguation performance. The MRD method handles noisy terms better but requires a larger set of terms to improve performance.
Oligomeric structure of glycoproteins in herpes simplex virus type 1 (1996)

A number of herpes simplex virus (HSV) glycoproteins are found in oligomeric states: glycoprotein E (gE)-gI and gH-gL form heterodimers, and both gB and gC have been detected as homodimers. We have further explored the organization of glycoproteins in the virion envelope by using both purified virions to quantitate glycoprotein amounts and proportions and chemical cross-linkers to detect oligomers. We purified gB, gC, gD, and gH from cells infected with HSV type 1 and used these as immunological standards. Glycoproteins present in sucrose gradient-purified preparations of two strains of HSV type 1, KOS and NS, were detected with antibodies to each of the purified proteins. From these data, glycoprotein molar ratios of 1:2:11:16 and 1:1:14:9 were calculated for gB/gC/gD/gH in KOS and NS, respectively. gL was also detected in virions, although we lacked a purified gL standard for quantitation. We then asked whether complexes of these glycoproteins could be identified, and if they existed as homo- or hetero-oligomers. Purified KOS was incubated at 4 degrees C with bis (sulfosuccinimidyl) suberate (BS3), an 11.4 A (1A = 0.1 mm) noncleavable, water-soluble cross-linker. Virus extracts were examined by Western blotting (immunoblotting), or immunoprecipitation followed by Western blotting, to assay for homo- and hetero-oligomers. Homodimers of gB, gC, and gD were detected, and hetero-oligomers containing gB cross-linked to gC, gC to gD, and gD to gB were also identified. gH and gL were detected as a hetero-oligomeric pair and could be cross-linked to gD or gC but not to gB. We conclude that these glycoproteins are capable of forming associations with one another. These studies suggest that glycoproteins are closely associated in virions and have the potential to function as oligomeric complexes.
Subtype-selective sodium channel blockers promise a new era of pain research (2007)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Transplantation of hematopoietic stem cells from the peripheral blood (2005)

Hematopoietic stem cells can be collected from the peripheral blood. These hematopoietic stem cells (HSC), or better progenitor cells, are mostly expressed as the percentage of cells than react with CD34 antibodies or that form colonies in semi-solid medium (CFU-GM). Under steady-state conditions the number of HSC is much lower in peripheral blood than in bone marrow. Mobilization with chemotherapy and/or growth factors may lead to a concentration of HSC in the peripheral blood that equals or exceeds the concentration in bone marrow. Transplantation of HSC from the peripheral blood results in faster hematologic recovery than HSC from bone marrow. This decreases the risk of infection and the need for blood-product support. For autologous stem-cell transplantation (SCT), the use of peripheral blood cells has completely replaced the use of bone marrow. For allogeneic SCT, on the other hand, the situation is more complex. Since peripheral blood contains more T-lymphocytes than bone marrow, the use of HSC from the peripheral blood increases the risk of graft-versus-host disease after allogeneic SCT. For patients with goodrisk leukemia, bone marrow is still preferred, but for patients with high-risk disease, peripheral blood SCT has become the therapy of choice.
The human ovarian surface epithelium is an androgen responsive tissue (2002)

The pathogenesis of epithelial ovarian cancer remains unclear. From epidemiological studies raised levels of androgens have been implicated to increase the risk of developing the disease. The purpose of this study was to determine the responses of normal human ovarian surface epithelium to androgens. We have established primary cultures of human ovarian surface epithelium from patients undergoing oophorectomy for benign disease. Total RNA was isolated from these cultures and expression of mRNA encoding for the androgen receptor was demonstrated using reverse transcriptase polymerase chain reaction. The presence of androgen receptor in sections of normal ovary was also investigated using an antibody against androgen receptor. The effects of androgens on DNA synthesis and cell death were determined. Eight out of eight (100%) cultures expressed mRNA encoding the androgen receptor. The presence of androgen receptor in ovarian surface epithelium of sections of normal ovaries was demonstrated in all sections. Mibolerone, a synthetic androgen, caused a significant stimulation of DNA synthesis in 5 out of 9 (55%) cultures when used at a concentration of 1 nM. Mibolerone also caused a significant decrease in cell death in 2 out of 5 (40%) cultures tested. We have demonstrated that the ovarian surface epithelium is an androgen responsive tissue and that androgens can cause an increase in proliferation and a decrease in cell death. These findings have important implications for the pathophysiology of ovarian carcinogenesis.
Yield and Metal Composition of Lettuce and Wheat Grown on Soils Amended with Sewage Sludge Enriched with Cadmium, Copper, Nickel, and Zinc (1978)

Abstract Lettuce ( Lactuca sativa L. vat. longifolia ) and wheat ( Triticum aestivum L. ‘Inia’) were grown under greenhouse conditions on an acid and a calcareous soil amended with sewage sludge enriched with Cd, Cu, Ni, or Zn to determine relative toxicities of the metals and uptake characteristics of the test plants. While the order of toxicities was not the same for all soil and plant‐species combinations, Cd was, in general, most toxic followed by Ni, Cu, and Zn. The latter three metals were about equally toxic to wheat grown in the calcareous soil; in the acid soil, Cu was about four times and Ni about six times more toxic to wheat than was Zn. Yield results indicated strong soil and plant species effects. Nickel was more phytotoxic to lettuce and wheat grown in the acid than in the calcareous soil, whereas Cd, Cu, and Zn toxicity depended on plant species and metal‐concentration range. At relatively low soil treatments, Cu and Cd were more toxic to lettuce grown in the calcareous than in the acid soil. Both DTPA and water‐soluble metal concentrations were significantly correlated with metal uptake by plants. Water‐soluble concentrations of Cd, Cu, and Ni better predicted plant uptake of these metals while Zn uptake was more closely correlated with DTPA‐soluble Zn.
Interspecies variability and drug interactions of clozapine metabolism by microsomes (1999)

Cytochrome P450 expression in liver is influenced by several factors, including species, sex and strain. We compared metabolism formation of clozapine in different species (rat, mouse, guinea-pig, dog, monkey and man) so as to choose between species to further validate interaction studies. Liver microsomes of male and female Sprague-Dawley rats, hairless rats, OF1 mice, Balb C mice and Dunkin-Hartley albino guinea-pigs, male beagle dogs, male cynomolgus monkeys and man were used to investigate in vitro metabolism of clozapine. This process was dependent on the presence of NADPH and on the presence of microsome protein. In addition, we observed the formation of desmethyl- and N-oxide metabolites, with the rate of formation of each of these compounds varying with species, sex and strain of microsomes incubated. The desmethyl- and N-oxide metabolites formed were statistically greater in male than in female rats, mice in the two strains studied, as well as for the guinea-pigs. Levels of desmethyl clozapine formed were high for the rats and no significant difference in clozapine biotransformation was observed between Sprague-Dawley and hairless rats. For man, the formation of metabolites of clozapine was comparable with guinea-pig, dog and monkey. In addition, we screened the effect of 52 molecules, representative of 11 different therapeutic classes, on the metabolism of clozapine by rat liver microsomes. We found that most of the calcium channel blockers (diltiazem, felodipine, isradipine, lacidipine, nicardipine and nitrendipine), antifungals (ketoconazole, miconazole) and two anticancer drugs (paclitaxel, teniposide) caused more than 50% inhibition of clozapine metabolism in vitro. The extent of inhibition was increased in a concentration-dependant manner. Complementary clinical and pharmacokinetic studies should be performed to confirm these results.
Generation of longer emission wavelength red fluorescent proteins using computationally designed libraries (2010)

The longer emission wavelengths of red fluorescent proteins (RFPs) make them attractive for whole-animal imaging because cells are more transparent to red light. Although several useful RFPs have been developed using directed evolution, the quest for further red-shifted and improved RFPs continues. Herein, we report a structure-based rational design approach to red-shift the fluorescence emission of RFPs. We applied a combined computational and experimental approach that uses computational protein design as an in silico prescreen to generate focused combinatorial libraries of mCherry mutants. The computational procedure helped us identify residues that could fulfill interactions hypothesized to cause red-shifts without destabilizing the protein fold. These interactions include stabilization of the excited state through H-bonding to the acylimine oxygen atom, destabilization of the ground state by hydrophobic packing around the charged phenolate, and stabilization of the excited state by a π-stacking interaction. Our methodology allowed us to identify three mCherry mutants (mRojoA, mRojoB, and mRouge) that display emission wavelengths > 630 nm, representing red-shifts of 20-26 nm. Moreover, our approach required the experimental screening of a total of ∼5,000 clones, a number several orders of magnitude smaller than those previously used to achieve comparable red-shifts. Additionally, crystal structures of mRojoA and mRouge allowed us to verify fulfillment of the interactions hypothesized to cause red-shifts, supporting their contribution to the observed red-shifts.
Synthesis and Characterization of Pseudopeptide Bradykinin B2 Receptor Antagonists Containing the 1,3,8-Triazaspiro[4.5]decan-4-one Ring System (1996)

A series of pseudopeptides containing alkyl-, cycloalkyl-, aryl-, and aralkyl-substituted 1,3,8-triazaspiro[4.5]decan-4-one-3-acetic acids as amino acid surrogates to replace the Pro2-Pro3-Gly4-Phe5 section of the peptide bradykinin B2 receptor antagonist [Pro3, Phe5]HOE 140 (D-Arg0-Arg1-Pro2-Pro3-Gly4-Phe5-Ser6-D-Tic7+ ++-Oic8-Arg9) were prepared. These psuedopeptides were examined in vitro for their B2 receptor affinities as well as for their ability to block bradykinin mediated actions in vivo. Two compounds in particular, NPC 18521 (I) and NPC 18688 (V) were quite potent in these latter assays, indicating that a significant portion of this prototypical second generation decapeptide antagonist can be replaced with a more compact nonpeptide molecule.
Structural Analysis of Metal Ion Ligation to Nucleotides and Nucleic Acids Using Pulsed EPR Spectroscopy (2002)

Metal ions play key structural and functional roles in many nucleic acid systems, particularly as required cofactors for many catalytic RNA molecules (ribozymes). We apply the pulsed EPR technologies of electron spin-echo envelope modulation and electron spin-echo-electron nuclear double resonance to the structural analysis of the paramagnetic metal ion Mn(II) bound to nucleotides and nucleic acids. We demonstrate that pulsed EPR, supplemented with specific isotope labeling, can characterize ligation to nucleotide base nitrogens, outer-sphere interactions with phosphate groups, distances to sites of specific (2)H atom labels, and the hydration level of the metal ion. These techniques allow a comprehensive structural analysis of the mononucleotide model system MnGMP. Spectra of phenylalanine-specific transfer RNA from budding yeast and of the hammerhead ribozyme demonstrate the applicability of the methods to larger, structured RNA systems. This suite of experiments opens the way to detailed structural characterization of specifically bound metal ions in a variety of ribozymes and other nucleic acids of biological interest.
Variegate porphyria in South Africa, 1688-1996--new developments in an old disease. (1997)

Variegate porphyria, an autosomal dominant inherited trait resulting in decreased activity of protoporphyrinogen oxidase, the penultimate haem biosynthetic enzyme, is characterised clinically by photosensitive skin disease and a propensity to acute neurovisceral crises. The disease has an exceptionally high frequency in South Africa, owing to a founder effect. The specific mutation in the protoporphyrinogen oxidase gene sequence which represents this founder gene has been identified. Genetic diagnosis is therefore now possible in families in whom the gene defect is known. However, the exact nature and degree of activity of the porphyria can only be determined by detailed quantitative biochemical analysis of excreted porphyrins. The relative contributions of the acute attack and the skin disease to the total disease burden of patients with variegate porphyria is not static, and in South Africa there have been significant changes over the past 25 years, with fewer patients presenting with acute attacks, leaving a greater proportion to present with skin disease or to remain asymptomatic with the diagnosis being made in the laboratory. The most common precipitating cause of the acute attack of VP is administration of porphyrinogenic drugs. Specific suppression of haem synthesis with intravenous haem arginate is the most useful treatment of a moderate or severe acute attack. Although cutaneous lesions are limited to the sun-exposed areas, management of the skin disease of VP remains inadequate.
High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling (2006)

Human individuals differ from one another at only approximately 0.1% of nucleotide positions, but these single nucleotide differences account for most heritable phenotypic variation. Large-scale efforts to discover and genotype human variation have been limited to common polymorphisms. However, these efforts overlook rare nucleotide changes that may contribute to phenotypic diversity and genetic disorders, including cancer. Thus, there is an increasing need for high-throughput methods to robustly detect rare nucleotide differences. Toward this end, we have adapted the mismatch discovery method known as Ecotilling for the discovery of human single nucleotide polymorphisms. To increase throughput and reduce costs, we developed a universal primer strategy and implemented algorithms for automated band detection. Ecotilling was validated by screening 90 human DNA samples for nucleotide changes in 5 gene targets and by comparing results to public resequencing data. To increase throughput for discovery of rare alleles, we pooled samples 8-fold and found Ecotilling to be efficient relative to resequencing, with a false negative rate of 5% and a false discovery rate of 4%. We identified 28 new rare alleles, including some that are predicted to damage protein function. The detection of rare damaging mutations has implications for models of human disease.
Thermal decomposition of bifunctional peroxides (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThermal decomposition of bifunctional peroxidesFelicia Tang and Earl S. HuyserCite this: J. Org. Chem. 1977, 42, 12, 2160–2163Publication Date (Print):June 1, 1977Publication History Published online1 May 2002Published inissue 1 June 1977https://pubs.acs.org/doi/10.1021/jo00432a031https://doi.org/10.1021/jo00432a031research-articleACS PublicationsRequest reuse permissionsArticle Views127Altmetric-Citations13LEARN 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
A new test generation method for sequential circuits (2002)

A novel test generation method for synchronous sequential circuits is proposed. Among the new ideas employed are: (1) efficiently maintaining path information using an extended value system in forward time processing, and (2) efficiently enumerating cubes for state justification in backward time processing. Experimental results show that the proposed method is effective in generating high coverage tests for sequential circuits.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Enzymic Reconstruction of Glycosaminoglycan Oligosaccharide Chains Using the Transglycosylation Reaction of Bovine Testicular Hyaluronidase (1995)

The reconstruction of glycosaminoglycan chains using the transglycosylation reaction of testicular hyaluronidase was investigated. First, the optimal conditions for the transglycosylation reaction catalyzed by the enzyme were determined by incubation with the enzyme, using hyaluronic acid (M(r) = 800,000) as a donor and pyridylaminated hyaluronic acid hexasaccharide having glucuronic acid at the nonreducing terminal as an acceptor. The carbohydrate chains as reaction products were determined by high performance liquid chromatography and mass spectrometry. The optimal pH for hydrolysis by the enzyme was found to be about 5.0, whereas that for the transglycosylation reaction was about 7.0. Sodium chloride in the reaction medium inhibited the transglycosylation reaction. Under the optimal conditions, the carbohydrate chains were sequentially transferred along with disaccharide units to the nonreducing terminal of the acceptor and elongated up to docosasaccharide from the acceptor, pyridylaminated hexasaccharide. Using a combination of hyaluronic acid, chondroitin, and chondroitin 4- and 6-sulfate as an acceptor and a donor, it was possible to reconstruct hybrid chains, which were natural or unnatural types of glycosaminoglycan chains. Therefore, it is highly likely that application of the transglycosylation reaction using testicular hyaluronidase would facilitate artificial reconstruction of glycosaminoglycans having some physiological functions.
An identity-authentication system using fingerprints (1997)

Fingerprint verification is an important biometric technique for personal identification. We describe the design and implementation of a prototype automatic identity-authentication system that uses fingerprints to authenticate the identity of an individual. We have developed an improved minutiae-extraction algorithm that is faster and more accurate than our earlier algorithm (1995). An alignment-based minutiae-matching algorithm has been proposed. This algorithm is capable of finding the correspondences between input minutiae and the stored template without resorting to exhaustive search and has the ability to compensate adaptively for the nonlinear deformations and inexact transformations between an input and a template. To establish an objective assessment of our system, both the Michigan State University and the National Institute of Standards and Technology NIST 9 fingerprint data bases have been used to estimate the performance numbers. The experimental results reveal that our system can achieve a good performance on these data bases. We also have demonstrated that our system satisfies the response-time requirement. A complete authentication procedure, on average, takes about 1.4 seconds on a Sun ULTRA I workstation (it is expected to run as fast or faster on a 200 HMz Pentium).
Aryl-palladium-NHC complex: efficient phosphine-free catalyst precursors for the carbonylation of aryl iodides with amines or alkynes (2014)

A series of aryl-palladium-NHC compounds was prepared according to the reported methods and their catalytic activity in the carbonylation of aryl iodides to synthesize α-keto amides and alkynones was examined. These practical aryl-palladium-NHC complexes have shown highly efficient catalyzed carbonylation and Sonogashira carbonylation reactions, with high turnover number in synthesis of α-keto amides (TON = 4300) and in synthesis of alkynones (TON = 980).
Combining phenotypic and proteomic approaches to identify membrane targets in a ‘triple negative’ breast cancer cell type (2013)

This study has demonstrated that multiple methods are required to successfully analyse the membranome of a desired cell type. It has also successfully demonstrated that phenotypic antibody screening provides a mechanism for rapidly discovering and evaluating antibody tractable targets, which can significantly accelerate the therapeutic discovery process.
Prevention of HIV-1 Infection with Early Antiretroviral Therapy (2011)

The early initiation of antiretroviral therapy reduced rates of sexual transmission of HIV-1 and clinical events, indicating both personal and public health benefits from such therapy. (Funded by the National Institute of Allergy and Infectious Diseases and others; HPTN 052 ClinicalTrials.gov number, NCT00074581.).