gebhart/patrepeval huggingface dataset:
Improved adapter‐ligation‐mediated allele‐specific amplification for multiplex genotyping by using software (2008)

Adapter-ligation-mediated allele-specific amplification (ALM-ASA) is a potential method for multiplex SNPs typing at an ultra low cost. Here, we describe a kind of software, which designs allele-specific primers for ALM-ASA assay on multiplex SNPs. DNA sequences containing SNPs of interest are submitted into the software which contains various endonucleases for options. Based on the SNP sequence information and the selected endonucleases, the software is capable of automatically generating sets of information needed to perform genotyping experiments. Each set contains a suitable endonuclease, qualified allele-specific primers with orientations and melting temperatures, sizes of allele-specific amplicons, and gel electropherograms simulated according to the sizes of the allele-specific amplicons and the mobility of DNA fragments in 2% agarose gel. Seven SNPs in the arylamines N-acetyltransferase 2 (NAT2) gene, five SNPs in the BRCA1 gene, five SNPs in the COMT gene, six SNPs in the CYP2E1 gene, five SNPs in the MPO gene, and six SNPs in the NRG1 gene were selected for evaluating the software. Without extra optimization, seven SNPs in the NAT2 gene were successfully genotyped for genomic DNA samples from 127 individuals by using the first set of allele-specific primers yielded by the software. Although several steps are used in the ALM-ASA assay, the whole genotyping process can be completed within 3 h by optimizing each step. Profiting from the software, the ALM-ASA assay is easy-to-perform, labor-saving, and accurate.
Treatment of<i>Helicobacter pylori</i>infection: Meeting the challenge of antimicrobial resistance (2014)

Treatment of Helicobacter pylori (H. pylori) infection is paramount for the management of prevalent gastrointestinal disorders including peptic ulcer disease and gastric cancer. Due to the wide increase in prevalence of H. pylori resistance to antibiotics, clarithromycin-based triple therapies are not any more suitable for unconditional empiric use, and should not be recommended, unless local resistance to this antibiotic is low (< 20%). Alternative strategies have been proposed to overcome the issue of increasing clarithromycin resistance, and some of them are already implemented in clinical practice. These comprise: (1) adoption of novel, more effective, empirical treatments: bismuth quadruple, sequential, non-bismuth quadruple (concomitant), dual-concomitant (hybrid), and levofloxacin-based regimens, the latter mainly designated as second-line/rescue options; (2) perspectives for a susceptibility-guided (tailored) therapeutic approach based on culture-free molecular testing methods; and (3) adjunct use of probiotics to improve eradication rates. The present article is aimed to provide a comprehensive overview of current and emerging strategies in the treatment of H. pylori infection, focusing on the challenge of antimicrobial resistance.
Cloning and expression of a novel tissue specific 17β-hydroxysteroid dehydrogenase. (1998)

The 11beta-hydroxysteroid dehydrogenases (11betaHSD) modulate intracellular glucocorticoid levels, with 11betaHSD1 converting cortisone to cortisol mainly in the liver, and 11betaHSD2 performing the reverse reaction in sodium transporting epithelia and placenta. We have attempted to expand the 11betaHSD subfamily by isolating homologous cDNA's. Expressed Sequence Tag databases were screen with segments of the 11betaHSD1 enzyme amino acid sequence and Pan1b identified as a new member of the short chain alcohol dehydrogenase superfamily. Northern blot analysis of total RNA from human tissues showed a single band at 1.9 kb and a tissue specific pattern of expression with high levels in the liver, adrenal carcinoma, lung and small intestine, and much lower levels in the kidney, heart and placenta. Expression studies in a Chinese hamster ovary cell line (CHOP) showed that Pan1b did not metabolize glucocorticoids. However, preliminary studies on a range of substrates revealed that Pan1b acted as a dehydrogenase on 17beta-hydroxysteroids, although further kinetic analysis was confounded by large amounts of endogenous oxidoreductase activity in CHOP cells. These studies suggest the existence of a novel human 17betaHSD enzyme.
The role of polymorphism in schema evolution in an object-oriented database (1989)

A polymorphic object algebra for an object-oriented database model is introduced. Types of schema modification that follow naturally from this model are described. It is shown to what extent queries return identical or equivalent results when the objects in the database are modified to conform to a modified schema.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Coupled molybdenum carbide and reduced graphene oxide electrocatalysts for efficient hydrogen evolution (2016)

Electrochemical water splitting is one of the most economical and sustainable methods for large-scale hydrogen production. However, the development of low-cost and earth-abundant non-noble-metal catalysts for the hydrogen evolution reaction remains a challenge. Here we report a two-dimensional coupled hybrid of molybdenum carbide and reduced graphene oxide with a ternary polyoxometalate-polypyrrole/reduced graphene oxide nanocomposite as a precursor. The hybrid exhibits outstanding electrocatalytic activity for the hydrogen evolution reaction and excellent stability in acidic media, which is, to the best of our knowledge, the best among these reported non-noble-metal catalysts. Theoretical calculations on the basis of density functional theory reveal that the active sites for hydrogen evolution stem from the pyridinic nitrogens, as well as the carbon atoms, in the graphene. In a proof-of-concept trial, an electrocatalyst for hydrogen evolution is fabricated, which may open new avenues for the design of nanomaterials utilizing POMs/conducting polymer/reduced-graphene oxide nanocomposites.
Genetic and redox determinants of nitric oxide cytotoxicity in a Salmonella typhimurium model. (1995)

Paradoxically, nitric oxide (NO) has been found to exhibit cytotoxic, antiproliferative, or cytoprotective activity under different conditions. We have utilized Salmonella mutants deficient in antioxidant defenses or peptide transport to gain insights into NO actions. Comparison of three NO donor compounds reveals distinct and independent cellular responses associated with specific redox forms of NO. The peroxynitrite (OONO-) generator 3-morpholinosydnonimine hydrochloride mediates oxygen-dependent Salmonella killing, whereas S-nitrosoglutathione (GSNO) causes oxygen-independent cytostasis, and the NO. donor diethylenetriamine-nitric oxide adduct has no antibacterial activity. GSNO has the greatest activity for stationary cells, a characteristic relevant to latent or intracellular pathogens. Moreover, the cytostatic activity of GSNO may best correlate with antiproliferative or antimicrobial effects of NO, which are unassociated with overt cell injury. dpp mutants defective in active dipeptide transport are resistant to GSNO, implicating heterolytic NO+ transfer rather than homolytic NO. release in the mechanism of cytostasis. This transport system may provide a specific pathway for GSNO-mediated signaling in biological systems. The redox state and associated carrier molecules are critical determinants of NO activity.
Reovirus-Induced Apoptosis Requires Activation of Transcription Factor NF-κB (2000)

Reovirus infection induces apoptosis in cultured cells and in vivo. To identify host cell factors that mediate this response, we investigated whether reovirus infection alters the activation state of the transcription factor nuclear factor kappa B (NF-kappaB). As determined in electrophoretic mobility shift assays, reovirus infection of HeLa cells leads to nuclear translocation of NF-kappaB complexes containing Rel family members p50 and p65. Reovirus-induced activation of NF-kappaB DNA-binding activity correlated with the onset of NF-kappaB-directed transcription in reporter gene assays. Three independent lines of evidence indicate that this functional form of NF-kappaB is required for reovirus-induced apoptosis. First, treatment of reovirus-infected HeLa cells with a proteasome inhibitor prevents NF-kappaB activation following infection and substantially diminishes reovirus-induced apoptosis. Second, transient expression of a dominant-negative form of IkappaB that constitutively represses NF-kappaB activation significantly reduces levels of apoptosis triggered by reovirus infection. Third, mutant cell lines deficient for either the p50 or p65 subunits of NF-kappaB are resistant to reovirus-induced apoptosis compared with cells expressing an intact NF-kappaB signaling pathway. These findings indicate that NF-kappaB plays a significant role in the mechanism by which reovirus induces apoptosis in susceptible host cells.
The electrospray: Fundamentals and combustion applications (1993)

Liquid fuel dispersion in practical systems is typically achieved by spraying the fuel into a polydisperse distribution of droplets evaporating and burning in a turbulent gaseous environment. In view of the nearly unsurmountable difficulties of this two-phase flow, it would be useful to use an experimental arrangement that allow a systematic study of spray evolution and burning in configurations of gradually increasing levels of complexity, starting from laminar sprays to fully turbulent ones. An Electrostatic Spray (ES) of charged droplets lends itself to this type of combustion experiments under well-defined conditions and can be used to synthesize gradually more complex spray environments. In its simplest configuration, a liquid is fed into a small metal tube maintained at several kilovolts relative to a ground electrode few centimeters away. Under the action of the electric field, the liquid meniscus at the outlet of the capillary takes a conical shape, with a thin jet emerging from the cone tip. This jet breaks up farther downstream into a fine spray of charged droplets. Several advantages distinguish the electrospray from alternative atomization techniques: the self-dispersion property of the spray due to coulombic repulsion; the absence of droplet coalescence; the potential control of the trajectories of charged droplets by suitable disposition of electrostatic fields; and the decoupling of atomization, which is strictly electrostatic, from gas flow processes. Furthermore, as recently shown in our laboratory, the electrospray can produce quasi-monodisperse droplets over a very broad size range (1-100 microns). The ultimate objective of this research project is to study the formation and burning of electrosprays of liquid fuels first in laminar regimes and then in turbulent ones. Combustion will eventually be investigated in conditions of three-dimensional droplet-droplet interaction, for which experimental studies have been limited to either qualitative observations in sprays or more quantitative observations on simplified systems consisting of a small number of droplets or droplet arrays. The compactness and potential controllability of this spray generaiton system makes it appealing for studies to be undertaken in the next two years on electrospray combustion in reduced-gravity environments such as those achievable at NASA microgravity test facilities.
Protein Kinase C and Prostate Carcinogenesis: Targeting the Cell Cycle and Apoptotic Mechanisms (2004)

A series of both genetic and epigenetic factors have been implicated in the genesis and progression of prostate cancer. Recent evidence revealed that protein kinase C (PKC) isozymes play a crucial role in the control of cell proliferation and apoptosis in prostate cancer models, as well as in the transition from an androgen-dependent to an androgen-independent status. Indeed, PKCalpha and PKCdelta promote apoptosis in androgen-dependent prostate cancer cells. Due to the relevance of PKC isozymes in the control of cell cycle, both in G1/S and G2/M, the elucidation of such complex intracellular networks using cellular and animal models has become of outmost importance. In this review, we present the current knowledge on the regulation of apoptosis and tumorigenicity by PKC isozymes and the functional roles of cell cycle regulators in prostate carcinogenesis. The development of animal models where overexpression of discrete PKCs or cell cycle regulators is targeted to the prostate will greatly contribute to the understanding of the molecular basis of the disease, and more importantly, it will have profound implications for the development of novel strategies for prostate cancer therapy.
Effect of cationic surfactants on biofilm removal and mechanical stability (2004)

In this study, a methodology is proposed to evaluate the mechanical stability of biofilms, by using a stainless steel rotating device where biofilms formed by Pseudomonas fluorescens were allowed to grow for 7 days at 300 rmp. Those biofilms were afterwards submitted to the joined action of chemical agents and mechanical cleaning. Two cationic surfactants (cetyltrimethyl ammonium bromide - CTAB and benzalkonium chloride - BC) were the agents tested. Mechanical cleaning was performed by the variation of the rotation speeds of the rotating device. The following conclusions can be drawn: the biofilm has an inherent mechanical stability; the increase in the rotation speed increased the biofilm removal, but total biofilm removal was not found for the surfactants. BC promoted the increase in the biofilm mechanical stability while CTAB promoted the weakening in the biofilm mechanical stability. From this study, it can be stated that the chemical treatment is far from being a tool that induces massive biofilm detachment and even the synergistic chemical and mechanical treatment did not promoted total biofilm removal.
Prediction of in-situ acoustic and elastic properties of marine sediments (1971)

Abstract This is one of several interrelated reports concerning sound velocity, elasticity, and related properties of marine sediments from several major environments in the North Pacific and adjacent areas. Previous reports were concerned with methods, measured properties (e.g., compressional-wave velocity, density, porosity), environmental control, empirical relationships, elastic models for saturated, porous marine sediments, and the computation of elastic moduli. These measured and computed properties were referred to 1 atmosphere pressure and 23 degrees C; all samples were from the sediment surface (0 to 30 cm). This report is concerned with the correction of laboratory values to in-situ values, and the prediction of in-situ values in the absence of any sediment data. Although the samples and values are related to the North Pacific and adjacent areas, the methods and techniques of prediction are applicable to other areas and sediments. The sediments were assigned to three general sedimentary environments associated with three great physiographic provinces: continental terrace (shelf and slope), deep-water abyssal plains, and abyssal hills. The sediment types and their properties in the latter two environments can be predicted with some confidence; detailed sediment charts are required for continental shelf areas. The keys to prediction of in-situ properties of marine sediments are knowledge of (1) general physiographic provinces and their associated sediments, (2) sedimentary processes within these environments, (3) laboratory or in-situ values of properties of the principal sediment types within the environments, and (4) methods of correcting laboratory values to in-situ values. Sound velocity in deep-sea areas can be predicted within about 1 to 2 percent for the sediment surface; velocity should be predicted directly rather than predicting porosity or another property, from which velocity is predicted. Laboratory values of velocity can be corrected to in-situ conditions by multiplying the bottom-water velocity by the velocity ratio (velocity in sediment/velocity in water); this ratio is the same in the laboratory as in situ. Sediment porosity can be considered to be the same in the laboratory as in situ, provided a correction is made to the apparent laboratory porosity to allow for salts evaporated from pore water and weighed with the mineral grains during laboratory analyses. This correction amounts to an increment to porosity of 0.5 to 1.0 percent. Density in situ is slightly greater than in the laboratory because of more dense water in pore spaces; the correction, at a depth of 6000 m, amounts to about 0.025 gm/cm 3 and can usually be disregarded. Using measured values of density and compressional-wave velocity (corrected to in-situ values), plus a computed value of the bulk modulus, we can compute the other elastic constants; these include compressibility, rigidity (shear) modulus, Poisson's ratio, and velocity of shear waves. Numerical examples are given of all computations.
YscP and YscU Regulate Substrate Specificity of the<i>Yersinia</i>Type III Secretion System (2003)

Pathogenic Yersinia species use a type III secretion system to inhibit phagocytosis by eukaryotic cells. At 37 degrees C, the secretion system is assembled, forming a needle-like structure on the bacterial cell surface. Upon eukaryotic cell contact, six effector proteins, called Yops, are translocated into the eukaryotic cell cytosol. Here, we show that a yscP mutant exports an increased amount of the needle component YscF to the bacterial cell surface but is unable to efficiently secrete effector Yops. Mutations in the cytoplasmic domain of the inner membrane protein YscU suppress the yscP phenotype by reducing the level of YscF secretion and increasing the level of Yop secretion. These results suggest that YscP and YscU coordinately regulate the substrate specificity of the Yersinia type III secretion system. Furthermore, we show that YscP and YscU act upstream of the cell contact sensor YopN as well as the inner gatekeeper LcrG in the pathway of substrate export regulation. These results further strengthen the strong evolutionary link between flagellar biosynthesis and type III synthesis.
Alternative Medicine (1997)

associate editor of ACSM's Health & Fitness I Journal, is a leader in preventive health ' and fitness. He was selected as one of only 120 Americans to he recognized as a Heathy American Fitness Leader by the U.S. Junior Chamber of Commerce.
Dual marching cubes (2005)

We present the definition and computational algorithms for a new class of surfaces which are dual to the isosurface produced by the widely used marching cubes (MC) algorithm. These new isosurfaces have the same separating properties as the MC surfaces but they are comprised of quad patches that tend to eliminate the common negative aspect of poorly shaped triangles of the MC isosurfaces. Based upon the concept of this new dual operator, we describe a simple, but rather effective iterative scheme for producing smooth separating surfaces for binary, enumerated volumes which are often produced by segmentation algorithms. Both the dual surface algorithm and the iterative smoothing scheme are easily implemented.
Vertical optical ring resonators fully integrated with nanophotonic waveguides on silicon-on-insulator substrates (2015)

We demonstrate full integration of vertical optical ring resonators with silicon nanophotonic waveguides on silicon-on-insulator substrates to accomplish a significant step toward 3D photonic integration. The on-chip integration is realized by rolling up 2D differentially strained TiO(2) nanomembranes into 3D microtube cavities on a nanophotonic microchip. The integration configuration allows for out-of-plane optical coupling between the in-plane nanowaveguides and the vertical microtube cavities as a compact and mechanically stable optical unit, which could enable refined vertical light transfer in 3D stacks of multiple photonic layers. In this vertical transmission scheme, resonant filtering of optical signals at telecommunication wavelengths is demonstrated based on subwavelength thick-walled microcavities. Moreover, an array of microtube cavities is prepared, and each microtube cavity is integrated with multiple waveguides, which opens up interesting perspectives toward parallel and multi-routing through a single-cavity device as well as high-throughput optofluidic sensing schemes.
Ammonius, Teacher of Origen (1993)

Porphyry and Eusebius, antagonistic witnesses, agree that one of Origcn’s early tutors was called Ammonius. This was also the name of the tutor of Origen’s younger contemporary Plot in us, and it. has long been the fashion to argue or assume that they were pupils of the same man. Heinrich Dörrie perhaps remains alone in his view that the two men called Ammonius were distinct, a view for which I shall argue in this article, though not entirely on Döme’s grounds. In the first part I shall present the available evidence, and in the second use it to defend Döme’s position against its detractors; in the third part I shall argue that the confusion of the two began in the early Christian centuries, through a mixture of knowledge and pardonable ignorance, and finally I shall advance another candidate, whose credentials for the position of Origen’s tutor have not been adequately examined in modern discussion.
A New Route for the Preparation of Pyrazolo[4,3-<i>c</i>]pyridines (1973)

Abstract The anhydride (II) of 4-carboxy-1,5-diphenylpyrazole-3-acetic acid (I) has been prepared. The reactions of II with primary amines resulted in the formation of the monoamides IIIa–c. 2,3-Diphenylpyrazolo[4,3-c]pyridine-(5H,7H)-4,6-dione (VIIa), has been obtained by heating the ammonium salt of I in a vacuum at 220 °C. The ring closure of IIIc with acetyl chloride in benzene afforded VIIb. Compound VIIb was coupled with benzenediazonium chloride to give the 7-phenylazo derivative (XII) and also condensed with aromatic aldehydes giving 7-arylidene derivatives (XV).
Computer simulations in the Gibbs ensemble (1989)

In this article we demonstrate that the Gibbs ensemble and the canonical ensemble are equivalent in the thermodynamic limit. Furthermore, we discuss some interesting aspects of the method when applied close to the critical point. We show that for a finite number of particles the Gibbs ensemble leads to a lower value of the critical temperature of the finite system than that obtained by standard N,V,T simulations with the same number of particles. This is due to entropic considerations. Simulations in the Gibbs ensemble, because it allows for fluctuations in the number of particles and in the volume of the sub-systems, may lead to a better estimate of the critical temperature of the infinite system.
Is zinc the link between compromises of brain perfusion (excitotoxicity) and Alzheimer's disease? (2005)

Prior brain injury is a major risk factor in the development of Alzheimer's disease. This is true for traumatic brain injury, stroke or ischemic brain injury, and (more speculatively) for brain injury resulting from the hypo-perfusion-reperfusion in cardiac arrest or cardiac bypass surgery and even hypo- or hypertension. Here we propose that the release of excess, toxic, "floods" of free zinc into the brain that occurs during and after all excitotoxic brain injury is a key factor that sets the stage for the later development of Alzheimer's disease. Rapid and aggressive administration of zinc buffering compounds to patients suffering brain injury may therefore not only ameliorate the acute injury but might also reduce the risk of subsequent development of Alzheimer's disease.