gebhart/patrepeval huggingface dataset:
Up-Regulation of OsBIHD1, a Rice Gene Encoding BELL Homeodomain Transcriptional Factor, in Disease Resistance Responses (2005)

In the present study, we cloned and identified a full-length cDNA of a rice gene, OsBIHD1, encoding a homeodomain type transcriptional factor. OsBIHD1 is predicted to encode a 642 amino acid protein and the deduced protein sequence of OsBIHD1 contains all conserved domains, a homeodomain, a BELL domain, a SKY box, and a VSLTLGL box, which are characteristics of the BELL type homedomain proteins. The recombinant OsBIHD1 protein expressed in Escherichia coli bound to the TGTCA motif that is the characteristic cis-element DNA sequence of the homeodomain transcriptional factors. Subcellular localization analysis revealed that the OsBIHD1 protein localized in the nucleus of the plant cells. The OsBIHD1 gene was mapped to chromosome 3 of the rice genome and is a single-copy gene with four exons and three introns. Northern blot analysis showed that expression of OsBIHD1 was activated upon treatment with benzothiadiazole (BTH), which is capable of inducing disease resistance. Expression of OsBIHD1 was also up-regulated rapidly during the first 6 h after inoculation with Magnaporthe grisea in BTH-treated rice seedlings and during the incompatible interaction between M. grisea and a resistant genotype. These results suggest that OsBIHD1 is a BELL type of homeodomain transcription factor present in the nucleus, whose induction is associated with resistance response in rice.
Enhanced bioaffinity sensing using surface plasmons, surface enzyme reactions, nanoparticles and diffraction gratings (2008)

This paper introduces a novel approach to surface bioaffinity sensing based on the adsorption of nanoparticles onto a gold diffraction grating that supports the excitation of planar surface plasmons. A surface enzymatic amplification reaction is also incorporated into the detection scheme to enhance the sensitivity and utility of the nanoparticle-enhanced diffraction grating (NEDG) sensors. As a demonstration, the detection of microRNA is described where a combination of a surface polymerase reaction and DNA-modified nanoparticles is used to detect the bioaffinity adsorption of the target onto the probe-functionalized gold grating surface. The enzymatically-amplified NEDG sensors possess a great potential for a wide range of applications including the detection of biosecurity agents, DNA and RNA viruses, biomarkers, and proteins.
Robust estimation of microbial diversity in theory and in practice (2013)

Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao's estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics ('Hill diversities'), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao's estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity.
Framework Standards: How Important are They? (Panel Abstract). (1991)

We tested the hypothesis that coronary artery blood flow is sufficient to meet myocardial requirements throughout cardiac tamponade in a conscious euvolemic canine model recovered from surgery. Seven mongrel dogs were chronically instrumented to measure ascending aortic blood flow (electromagnetic flowmeter); intrapericardial, right atrial, and aortic blood pressures; regional myocardial blood flow (radionuclide labelled microspheres); and myocardial consumption of lactate, pyruvate, and oxygen. Data were collected during progressive cardiac tamponade induced by intrapericardial saline infusion to the point of hemodynamic decompensation. Decompensated cardiac tamponade (DCT) was defined as a decline in mean aortic blood pressure to 70% of the level present when the pericardial space was drained of fluid (baseline) and was produced in all animals within 25 minutes. Cardiac tamponade caused a continuous decline in coronary artery blood flow from 1.26 +/- 0.35 (baseline, mean +/- SD) to 0.53 +/- 0.15 ml/min/g (DCT, p less than 0.01), which was associated with a decrease in myocardial oxygen consumption from 1.26 +/- 0.35 (baseline) to 0.74 +/- 0.27 ml/min/g (DCT, p less than 0.05) and a slight increase in myocardial oxygen extraction from 71 +/- 3 (baseline) to 81 +/- 4% (DCT, p less than 0.05). This change in oxygen extraction occurred because of both an increase in arterial and a decrease in coronary venous oxygen content. At all degrees of cardiac tamponade, the lactate-pyruvate ratio did not change significantly from baseline (7.56 +/- 2.31), there was no evidence of lactate production, and the normal endocardial to epicardial blood flow ratio present at baseline (1.41 +/- 0.23) was preserved.(ABSTRACT TRUNCATED AT 250 WORDS)
Serine acetyltransferase from Arabidopsis thaliana can functionally complement the cysteine requirement of a cysE mutant strain of Escherichia coli. (1995)

Serine acetyltransferase, a key enzyme in the L-cysteine biosynthetic pathway of sulfate assimilating organisms, catalyzes the formation of O-acetylserine, the immediate precursor of L-cysteine. In higher plants, it is thought that sulfur assimilation occurs primarily in leaf chloroplasts; however, serine acetyltransferase is not localized exclusively in this tissue and organelle. At least three genes for serine acetyltransferase have been identified in the higher plant Arabidopsis thaliana. Reported here is a cDNA corresponding to one of these genes, SAT1, a 1,079 bp clone with an open reading frame predicted to encode a 34-kDa protein that is able to functionally complement a serine acetyltransferase mutant strain of Escherichia coli. The predicted amino acid sequence of SAT1 shows significant homology with bacterial serine acetyltransferases. SAT1, expressed as a recombinant protein, shows serine acetyltransferase enzyme activity and cross-reacts with an antibody against the homologous E. coli enzyme. The first 40 amino acids of the SAT1 polypeptide resembles a plastid transit peptide, but the polypeptide is probably not plastid localized. Genomic DNA blot analysis of A. thaliana showed that SAT1 is a single copy gene and RNA blot analysis revealed that SAT1 is expressed in both leaves and roots.
Effects of a novel prostaglandin, 8-epi-PGF2 alpha, in rabbit lung in situ (1992)

We determined the effects of 8-epiprostaglandin (PG) F2 alpha, a noncyclooxygenase free radical-catalyzed product of arachidonic acid, on pulmonary vascular tone, its potency, and its mechanism of action. 8-Epi-PGF2 alpha (0.5-20 micrograms) was injected into the pulmonary artery (PA) catheter of 10 rabbits whose lungs were perfused in situ with Krebs-Henseleit buffer solution with 3% bovine serum albumin. PA pressure increased from a baseline of 13.5 +/- 0.6 to 25.6 +/- 2.0 cmH2O with 20 micrograms 8-epi-PGF2 alpha. 8-Epi-PGF2 alpha caused a rapid rise in PA pressure followed by a gradual decline over 40-60 min to baseline levels. Double vascular occlusion revealed a twofold increase in arterial resistance at peak rise in PA pressure. The rise in PA pressure with 20 micrograms 8-epi-PGF2 alpha was fivefold greater than with 20 micrograms of the cyclooxygenase-derived prostaglandin PGF2 alpha. The PA pressure response to 8-epi-PGF2 alpha was not altered by either cyclooxygenase block-ade with 150 microM meclofenamate or alpha-receptor blockade with 70 microM phentolamine, but was fully prevented by 40 microM SQ 29548, a thromboxane receptor antagonist. We conclude that in rabbits 8-epi-PGF2 alpha is a potent vasoconstrictor of the pulmonary vasculature, which appears to be due to the activation of SQ 29548-responsive thromboxane receptors.
Rh-catalyzed linear hydroformylation of styrene (2012)

Usually the Rh-catalyzed hydroformylation of styrene predominantly yields the branched, chiral aldehyde. An inversion of regioselectivity can be achieved using strong π-acceptor ligands. Binaphthol-based diphosphite and bis(dipyrrolyl-phosphorodiamidite) ligands were applied in the Rh-catalyzed hydroformylation of styrene. High selectivities up to 83% of 3-phenylpropanal were obtained with 1,1-bi-2-naphthol-based bis(dipyrrolyl-phosphorodiamidite) with virtually no hydrogenation to ethyl benzene. The coordination chemistry of those ligands towards Rh(I) was investigated spectroscopically and structurally.
Manipulation of Human Pluripotent Embryonal Carcinoma Stem Cells and the Development of Neural Subtypes (2003)

There are few reliable cell systems available to study the process of human neural development. Embryonal carcinoma (EC) cells are pluripotent stem cells derived from teratocarcinomas and offer a robust culture system to research cell differentiation in a manner pertinent to embryogenesis. Here, we describe the recent development of a series of culture procedures that together can be used to induce the differentiation of human EC stem cells, resulting in the formation of either pure populations of differentiated neurons, populations of differentiated astrocytes, or populations of immature neuronal cell types. Cell-type-specific markers were used to examine the induction of EC stem cell differentiation by retinoic acid. In direct response to manipulation of the culture environment, the expression of cell type markers correlated with the differentiation and appearance of distinct neural cell types, including neurons and astrocytes. These experiments demonstrate that cultured human EC stem cells provide a robust model cell system capable of reproducibly forming neural subtypes for research purposes.
Stereochemical control in reactions of nucleophiles with oxocarbenium ions formed by intramolecular opening of activated epoxides by neighboring carbonyl groups (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereochemical control in reactions of nucleophiles with oxocarbenium ions formed by intramolecular opening of activated epoxides by neighboring carbonyl groupsChristopher H. Fotsch and A. Richard ChamberlinCite this: J. Org. Chem. 1991, 56, 13, 4141–4147Publication Date (Print):June 1, 1991Publication History Published online1 May 2002Published inissue 1 June 1991https://pubs.acs.org/doi/10.1021/jo00013a013https://doi.org/10.1021/jo00013a013research-articleACS PublicationsRequest reuse permissionsArticle Views362Altmetric-Citations44LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Preparation and properties of a linked porphyrin–cyclodextrin (1985)

The synthesis of the linked porphyrin–cyclodextrin 3 and its zinc complex 4 is described and their characterization by 1 H nmr, l3 C nmr, circular dichroism, ultraviolet, and infrared spectroscopy is reported. The linked porphyrin–cyclodextrin compounds exhibited perturbed electronic absorption and emission spectra which are consistent with their adopting two conformations, one extended with little interaction between the porphyrin and cyclodextrin, and the other folded with the cyclodextrin weakly complexed to the porphyrin. Quenching of the porphyrin excited state of 3 by benzoquinone was examined by measurement of the fluorescence lifetime as a function of quinone concentration; the results suggest that the porphyrin excited state can be quenched intermolecularly by benzoquinone and also intramolecularly by quinone complexed within the cyclodextrin cavity.
Fiber ribbon in slotted core (1987)

Fiber ribbon structure based on UV materials offers great advantages In making not only an economical cable manufacturing process but is a practical splicing possibility for high-count fiber cables.1 Protection of these fiber ribbons has been studied with preference for the slotted core design. It would be the most practical cable design of a wide range of applications where a different number of fibers is required.
The human gastric pathogen <i>Helicobacter pylori</i> has a gene encoding an enzyme first classified as a mucinase in <i>Vibrio cholerae</i> (1994)

The human bacterial pathogen Helicobacter pylori has been suggested to be the causative agent of the most common chronic infection of man. Since its first isolation in 1982, H. pylori has been associated with gastric and duodenal ulcer disease, and more recently, gastric cancer. The proteolytic digestion of gastric mucus by this microorganism has been suggested as an important mechanism by which its pathogenicity is at least partly exerted. Here we report the detection of protease activity in H. pylori total-cell and supernatant extracts. On the basis that zinc metalloproteases are common microbial pathogenicity factors, we identified a single protein in H. pylori protein extracts with antibodies to the Pseudomonas aeruginosa elastase (a secreted zinc metalloprotease). This same protein was identified by pooled serum from patients infected with H. pylori. We used the functional and immunological relationship between the P. aeruginosa elastase and the Vibrio cholerae haemagglutinin/protease (HAP) to clone the H. pylori hap gene, which was over 99% similar to the V. cholerae hap gene in the coding region. A 4 kb DNA fragment containing the entire cloned gene was highly unstable in Escherichia coli and Bacillus subtilis cloning vectors. We also demonstrated that a hap-like gene sequence is present in all nine Helicobacter species so far discovered. The V. cholerae HAP was first classified on the basis of its mucinase activity.
Challenges in sleep transistor design and implementation in low-power designs (2006)

Optimum power gating sleep transistor design and implementation are critical to a successful low-power design. This paper describes important considerations for the sleep transistor design and implementation including header or footer switch selection, sleep transistor distribution choices and sleep transistor gate length, width and body bias optimization for area, leakage and efficiency. It also investigated various power-on current rush control methods for the sleep transistor implementation.
Induction of tolerance after establishment of peanut allergy by the food allergy herbal formula‐2 is associated with up‐regulation of interferon‐γ (2007)

FAHF-2 treatment established PN tolerance in this model, which persisted for at least 4-week post-treatment. This result was associated with modulation of intestinal T helper type 1 cell (Th1) and Th2 cytokine production, and with increased numbers of mesenteric IFN-gamma-producing CD8+ cells.
Optimal Graph-Theoretic Approach to 3D Anatomical Tree Matching (2006)

High resolution three-dimensional (3D) images are readily produced by many imaging scanners. This paper describes a novel optimal method for matching the anatomical trees contained in such 3D images. Our method explicitly describes a set of valid candidate matches between two input trees by considering topological deformations known to occur during the tree definition process, evaluates these candidate matches using a cost function that compares corresponding branch and branchpoint attributes measured from the 3D image data, and locates a globally optimal match with respect to the cost function using an efficient dynamic programming algorithm. We present matching results for human airway trees. The method is a part of a complete computer-based system for 3D tree analysis
Novel Techniques for Corner Joints Using Friction Stir Welding (2011)

This chapter contains sections titled: Introduction Corner SSFSW Joints Corner Fillet SSFSW Joints Corner AdStir Fillet SSFSW Joints Summary Patents Acknowledgements
Evaluation of Diesel Oxidation Catalyst Conversion of Hydrocarbons and Particulate Matter from Premixed Low Temperature Combustion of Biodiesel (2011)

<div class="section abstract"><div class="htmlview paragraph">Premixed low temperature combustion (LTC) in diesel engines simultaneously reduces soot and NO<sub>x</sub> at the expense of increased hydrocarbon (HC) and CO emissions. The use of biodiesel in the LTC regime has been shown to produce lower HC emissions than petroleum diesel; however, unburned methyl esters from biodiesel are more susceptible to particulate matter (PM) formation following atmospheric dilution due to their low volatility. In this study, the efficacy of a production-type diesel oxidation catalyst (DOC) for the conversion of light hydrocarbons species and heavier, semi-volatile species like those in unburned fuel is examined. Experimental data were taken from a high speed direct-injection diesel engine operating in a mid-load, late injection partially premixed LTC mode on ultra-low sulfur diesel (ULSD) and neat soy-based biodiesel (B100). Gaseous emissions were recorded using a conventional suite of analyzers and individual light HCs were measured using an FT-IR analyzer. PM emissions data were collected from filter samples taken before and after the DOC using gravimetric analysis, Soxhlet extraction with speciation of extracted HCs, and total organic versus elemental carbon (OCEC) analysis. The previous results were confirmed with LTC of B100 resulting in over an order of magnitude increase in engine-out PM. It was found in the experimental study that 76% of the unburned fuel species responsible for this increase can be converted by a production-type DOC with an inlet temperature of 240°C and gas hourly space velocity (GHSV) of 85,000 hr<sup>-₁</sup>. Unfortunately, the remaining unburned biodiesel left unconverted by the DOC still contributed significantly to the PM following dilution. Methyl esters from biodiesel were found to be the primary species contributing to the higher total organic fraction (≻95%) on the PM for biodiesel LTC following a DOC.</div></div>
Ferroelectric switching and fatigue behavior for PZT/YBCO thin film heterostructures (1994)

Abstract The dielectric and ferroelectric properties for Au/Pb(Zr,Ti)O3/YBa2Cu3O7−x heterostructures at low temperatures are reported. The fatigue behavior and the ferroelectric switching effect for the structures are also investigated. The PZT/YBCO thin film heterostructures were deposited on MgO(100) substrates by laser ablation. The ferroelectric and dielectric properties and optical response of the oriented PZT films with different thicknesses have been studied over the temperature range from 20 K to 300 K. The dielectric loss of the structure was found to decrease by an order of magnitude when the YBCO bottom electrode became superconducting. A very low fatigue rate of the structure has also been obtained below T c of YBCO layer.
The Promise of the Sharing Economy among Disadvantaged Communities (2015)

The digital-sharing economy presents opportunities for individuals to find temporary employment, generate extra income, increase reciprocity, enhance social interaction, and access resources not otherwise attainable. Although the sharing economy is profitable, little is known about its use among the unemployed or those struggling financially. This paper describes the results of a participatory-design based workshop to investigate the perception and feasibility of finding temporary employment and sharing spare resources using sharing-economy applications. Specifically, this study included 20 individuals seeking employment in a U.S. city suffering economic decline. We identify success factors of the digital-sharing economy to these populations, identify shortcomings and propose mitigation strategies based on prior research related to trust, social capital and theories of collective efficacy. Finally, we contribute new principles that may foster collaborative consumption within this population and identify new concepts for practical employment applications among these populations.
Polymer-noble metal nanocomposites: Review (2011)

Polymer-noble metal nanocomposites have been extensively investigated due to their potential ability to provide materials with novel mechanical, electronic or chemical behaviour for technological applications. Many preparative procedures have been proposed and detailed characterizations have been carried out on conducting polymer-noble metal nanocomposites; thanks to the rapid improvement in analytical techniques on surface and nanoscale materials. This review focuses on the preparation, characterization of polymer-noble metal nanocomposites and some potential areas for applications such as sensors, batteries (fuel cells) and capacitors.

	 

	Key words: Polymer, noble metal, nanocomposites, preparation, characterization.
Phase Microscopy with Vertical Illumination* (1948)

Phase microscopy has been adapted for observing specularly reflecting specimens with the vertical illuminator. The specimen is illuminated by light, preferably monochromatic, issuing from an annular opening in a diaphragm placed at the entrance pupil of an optical system consisting of the field lens, the microscope objective, and the reflecting surface of the specimen. The diaphragm is imaged on a diffraction plate placed at the exit pupil of this optical system. Stray light and illumination losses are minimized by locating the exit pupil between the beam splitter and the eyepiece. The method can be used advantageously to examine those surface irregularities which give rise to small differences in optical path or in phase between the reflected-ray bundles. Both bright and dark contrast with excellent definition may be obtained by the use of suitable diffraction plates. The advantage of this method disappears when the specimen diffuses the incident light.