gebhart/patrepeval huggingface dataset:
EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era (2012)

The Eukaryotic Promoter Database (EPD), available online at http://epd.vital-it.ch, is a collection of experimentally defined eukaryotic POL II promoters which has been maintained for more than 25 years. A promoter is represented by a single position in the genome, typically the major transcription start site (TSS). EPD primarily serves biologists interested in analysing the motif content, chromatin structure or DNA methylation status of co-regulated promoter subsets. Initially, promoter evidence came from TSS mapping experiments targeted at single genes and published in journal articles. Today, the TSS positions provided by EPD are inferred from next-generation sequencing data distributed in electronic form. Traditionally, EPD has been a high-quality database with low coverage. The focus of recent efforts has been to reach complete gene coverage for important model organisms. To this end, we introduced a new section called EPDnew, which is automatically assembled from multiple, carefully selected input datasets. As another novelty, we started to use chromatin signatures in addition to mRNA 5'tags to locate promoters of weekly expressed genes. Regarding user interfaces, we introduced a new promoter viewer which enables users to explore promoter-defining experimental evidence in a UCSC genome browser window.
Shot Peen Forming Sheet Metal: Finite Element Prediction of Deformed Shape (1996)

Shot peen forming is a production process used to create curved metal parts from sheet. It is commercially important despite the fact that its mechanisms are not fully understood; peen forming programmes are currently generated using experience and trial and error. The purpose of this work is to increase the predictability and range of application of the process by advancing its understanding. Finite element analysis proved to be a satisfactory procedure for studying shot peen forming. The stress distribution in a sheet arising from multiple indentations, as occur in shot peen forming, was modelled. A technique of squeezing the upper layers of a finite element model was shown to be a good simulation of the stress distributions resulting from shot peen forming, and provided a much more tractable analysis with respect to computing time and resources.
Fixed wing UAV performance flight testing (2015)

This work illustrates the realization of an experimental UAV with the aim of carrying out flight tests typical of certified manned aircraft, in view of both educational and research purposes. The final goal is to explore potential applications in the field of qualification and certification of unmanned aerial vehicles. An electric-powered model motorglider with a native on-board sensor suite has been improved with two air data booms for airspeed, angle of attack and angle of sideslip measurement and its control system, based on an commercial open source autopilot has been modified to include specific autonomous flight test modes. Wind-tunnel tests were carried out to characterize the instrumented aircraft and calibrate the new sensors, in addition to preliminary numerical studies. Autonomous flight test modes, reproducing standardized maneuvers typical of certification trials for manned aircraft, were validated and tested in a 4-day flight campaign covering stall tests, climbs, power-off glides and trimmed level conditions. Data post-processing allowed to determine aerodynamic data, stall speed and optimum climb and glide performance.
The New Inorganic Ligands TeCl<sub>2</sub> and TeBr<sub>2</sub>:  Syntheses and Crystal Structures of Re<sub>6</sub>Te<sub>6</sub>Cl<sub>6</sub>(TeCl<sub>2</sub>)<sub>2</sub> and [Re<sub>6</sub>Te<sub>8</sub>(TeBr<sub>2</sub>)<sub>6</sub>]Br<sub>2</sub> (1996)

TeBr2 and TeCl2, unstable molecules which have previously been characterized only in the gas phase, are present as ligands in the new cluster compounds Re6Te6Cl6(TeCl2)2 and [Re6Te8(TeBr2)6]Br2. In Re6Te6Cl6(TeCl2)2, the Re6 cluster core is inscribed in a cube constructed of six μ3-Te2- and two μ3-Cl- ligands. The Re3+ cations bonded to four μ3-Te2- anions are also ligated by neutral TeCl2 ligands. In [Re6Te8(TeBr2)6]2+, the Re6 cluster core is inscribed in a cube constructed of eight μ3-Te2- ligands and each Re3+ cation is terminated by a neutral TeBr2 ligand.
Distribution and diversity of phytate-mineralizing bacteria (2007)

Phytate, the most abundant organic phosphorus compound in soil, dominates the biotic phosphorus input from terrestrial runoffs into aquatic systems. Microbial mineralization of phytate by phytases is a key process for recycling phosphorus in the biosphere. Bioinformatic studies were carried out on microbial genomes and environmental metagenomes in the NCBI and the CAMERA databases to determine the distribution of the four known classes of phytase in the microbial world. The beta-propeller phytase is the only phytase family that can be found in aquatic environments and it is also distributed in soil and plant bacteria. The beta-propeller phytase-like genes can be classified into several subgroups based on their domain structure and the positions of their conserved cysteine residues. Analysis of the genetic contexts of these subgroups showed that beta-propeller phytase genes exist either as an independent gene or are closely associated with a TonB-dependent receptor-like gene in operons, suggesting that these two genes are functionally linked and thus may play an important role in the cycles of phosphorus and iron. Our work suggests that beta-propeller phytases play a major role in phytate-phosphorus cycling in both soil and aquatic microbial communities.
BACTERIAL AVIRULENCE GENES (1996)

Although more than 30 bacterial avirulence genes have been cloned and characterized, the function of the gene products in the elictitation of resistance is unknown in all cases but one. The product of avrD from Pseudomonas syringae pv. glycinea likely functions indirectly to elicit resistance in soybean, that is, evidence suggests the gene product is an enzyme involved in elicitor production. In most if not all cases, bacterial avirulence gene function is dependent on interactions with the hypersensitive response and pathogenicity (hrp) genes. Many hrp genes are similar to genes involved in delivery of pathogenicity factors in mammalian bacterial pathogens. Thus, analogies between mammalian and plant pathogens may provide needed clues to elucidate how virulence gene products control induction of resistance.
Enterococcal Cytolysin: A Novel Two Component Peptide System that Serves as a Bacterial Defense Against Eukaryotic and Prokaryotic Cells (2005)

The cytolysin is a novel, two-peptide lytic toxin produced by some strains of Enterococcus faecalis. It is toxic in animal models of enterococcal infection, and associated with acutely terminal outcome in human infection. The cytolysin exerts activity against a broad spectrum of cell types including a wide range of gram positive bacteria, eukaryotic cells such as human, bovine and horse erythrocytes, retinal cells, polymorphonuclear leukocytes, and human intestinal epithelial cells. The cytolysin likely originated as a bacteriocin involved with niche control in the complex microbial ecologies associated with eukaryotic hosts. However, additional anti-eukaryotic activities may have been selected for as enterococci adapted to eukaryotic cell predation in water or soil ecologies. Cytolytic activity requires two unique peptides that possess modifications characteristic of the lantibiotic bacteriocins, and these peptides are broadly similar in size to most cationic eukaryotic defensins. Expression of the cytolysin is tightly controlled by a novel mode of gene regulation in which the smaller peptide signals high-level expression of the cytolysin gene cluster. This complex regulation of cytolysin expression may have evolved to balance defense against eukaryotic predators with stealth.
Efficient removal of PCR inhibitors using agarose-embedded DNA preparations (1998)

The use of agarose blocks containing embedded DNA improves the PCR amplification from templates naturally contaminated with polysaccharides or humic acids, two powerful PCR inhibitors. Presumably, the difference in size between the DNA macromolecules and these contaminants allows their effective removal from the agarose blocks by diffusion during the washing steps, whereas genomic DNA remains trapped within them. In addition, agarose-embedded DNA can be directly used for PCR since low melting point agarose does not interfere with the reaction. This simple and inexpensive method is also convenient for genomic DNAs extracted by other procedures, and it is potentially useful for samples containing other kinds of soluble inhibitors, overcoming this important problem of current amplification techniques.
Stress Responses in Alfalfa (<i>Medicago sativa</i> L.) (1990)

Protoplasts derived from cell suspensions of alfalfa (Medicago sativa L.) responded to treatment with fungal elicitor (FE) by an increase in endogenous chalcone synthase (CHS) activity but were unresponsive to reduced glutathione (GSH). Preexposure of protoplasts to polyethylene glycol and electroporation resulted in strong responsiveness to GSH but little change in responsiveness to FE. Protoplasts from suspension cultures which had been subcultured more than 12 times lost responsiveness to GSH, but not FE, as assessed by measuring expression of a chimeric gene containing a bean CHS promoter linked to a bacterial chloramphenicol acetyltransferase (CAT) reporter gene. In protoplasts in which putative cis-acting CHS promoter sequences had been coelectroporated in trans with the intact CHS promoter-CAT construct, the extent of CAT expression depended upon the elicitor used (FE or GSH), the age (number of times subcultured) of the cells from which the protoplasts were isolated, and the nature of the coelectroporated CHS promoter sequence. For example, a region of the CHS promoter from -326 to -141 behaved as a trans-activator when coelectroporated with the CAT construct into unelicited protoplasts isolated from newly initiated cell suspensions, but the same region acted as a trans-silencer in the same protoplasts in the presence of FE. This silencer activity was much reduced in GSH-treated protoplasts. The results suggest that there are differences in the signal transduction pathways for elicitation of CHS transcription by FE and GSH, which involve previously indentified cis-elements in the CHS promoter.
Imagerie du sein multispectrale avec injection de produit de contraste (2008)

Durant le developpement du cancer du sein, de nouveaux vaisseaux sanguins se forment autour des tumeurs afin de soutenir leur croissance. L’imagerie du sein avec injection de produit de contraste est une nouvelle technique basee sur ce phenomene appele angiogenese tumorale, permettant potentiellement une detection et une caracterisation precoces des tumeurs. Ces travaux s’interessent aux methodes multispectrales, qui consistent a combiner des images acquises avec des spectres d’energies differentes pour generer des images fonctionnelles de la neovascularisation des tumeurs. Cette these a pour objectif de developper les applications d’imagerie du sein multispectrale avec injection de produit de contraste, et plus specifiquement, celles d’angiomammographie et d’angiotomosynthese double-energie. Dans un premier temps, nous presentons une modelisation du systeme d’imagerie, ainsi que la methode de combinaison permettant d’obtenir des images de neovascularisation. Ensuite, nous nous interessons a l’optimisation des spectres d’acquisition afin de maximiser la visibilite du produit de contraste vis-a-vis de la dose a la patiente. Nous etudions egalement la quantification du produit de contraste sur les images, en analysant l’influence du rayonnement diffuse, de la variation d’epaisseur du sein et la resolution limitee en Z pour la tomosynthese, et en proposant des premieres approches de correction. Enfin, nous presentons les resultats d’une etude clinique sur l’angiomammographie double-energie menee en collaboration avec l’Institut Gustave Roussy et l’Institut Curie, avec une premiere comparaison de l’angiomammographie avec la mammographie et l’echographie.
Interfacial tension in high-pressure carbon dioxide mixtures (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInterfacial tension in high-pressure carbon dioxide mixturesByung-Soo Chun and Gordon T. WilkinsonCite this: Ind. Eng. Chem. Res. 1995, 34, 12, 4371–4377Publication Date (Print):December 1, 1995Publication History Published online1 May 2002Published inissue 1 December 1995https://pubs.acs.org/doi/10.1021/ie00039a029https://doi.org/10.1021/ie00039a029research-articleACS PublicationsRequest reuse permissionsArticle Views1756Altmetric-Citations197LEARN 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
Ultraviolet emission intensity, visible luminance, and electrical characteristics of small arrays of Al∕Al2O3 microcavity plasma devices operating in Ar∕N2 or Ne at high-power loadings (2006)

Small arrays (3×3→10×10) of microcavity plasma devices, having a two-stage structure comprising multilayer stacks of nanostructured Al2O3 grown on Al foil with cylindrical microcavities 100–300μm in diameter, produce intense ultraviolet (UV) and visible emission when operated in Ar∕3% N2 gas mixtures or Ne and excited by a sinusoidal ac voltage wave form. Near-UV (300–400nm) intensities emitted into a solid angle of ∼10−2sr above 30 mW per cm2 of radiating area are measured for Ar∕N2 gas mixture pressures of 400–800Torr, an excitation frequency of 15kHz, and an average current ⩾20mA (rms). Two or more conjoined cylindrical microcavities of differing diameters allow for the confinement of the plasma to progressively smaller volumes as the power deposited is increased (thereby decreasing the Debye length and the spatial extent of the cathode fall region) and provides a convenient tool with which the luminosity of an array can be modulated. The transition of a microplasma from confinement in a 200-μm-diam cavity into an adjacent 100-μm-diam microcavity is accompanied by an order-of-magnitude increase in the luminance of Ne plasmas in a 3×3 array as the rms current is increased by ∼1mA.
Scan-Rate-Dependent Current Rectification of Cone-Shaped Silica Nanopores in Quartz Nanopipettes (2010)

Here we report the voltammetric behavior of cone-shaped silica nanopores in quartz nanopipettes in aqueous solutions as a function of the scan rate, v. Current rectification behavior for silica nanopores with diameters in the range 4-25 nm was studied. The rectification behavior was found to be strongly dependent on the scan rate. At low scan rates (e.g., v < 1 V/s), the rectification ratio was found to be at its maximum and relatively independent of v. At high scan rates (e.g., v > 200 V/s), a nearly linear current-voltage response was obtained. In addition, the initial voltage was shown to play a critical role in the current-voltage response of cone-shaped nanopores at high scan rates. We explain this v-dependent current-voltage response by ionic redistribution in the vicinity of the nanopore mouth.
Imaging Immune Response <i>In vivo</i>: Cytolytic Action of Genetically Altered T Cells Directed to Glioblastoma Multiforme (2008)

The present study indicates the feasibility of MRI to visualize different phases of immune response when IL-13Ralpha2-specific CTLs are administered directly to the glioma tumor bed. This will further the aim of better predicting clinical outcome following immunotherapy.
Novel Approach to Reduce Source/Drain Series and Contact Resistance in High-Performance UTSOI CMOS Devices Using Selective Electrodeless CoWP or CoB Process (2007)

This letter reports a selective metal deposition process using an electrodeless technique for MOSFETs fabricated in an ultrathin silicon-on-insulator (UTSOI) substrate. A layer of metal (CoWP or CoB) is formed on the source and drain nickel and cobalt silicides without depositing on the dielectric spacers. Leakage current information, which is an indication of selectivity of the process, is presented in this letter. The shortest channel length of the UTSOI NMOSFETs is 20 nm, and the SOI thickness is 10 nm. The data show that excellent selectivity is achieved without increasing the leakage current of the transistors.
2-Ethynylbenzenealkanamines. A new class of calcium entry blockers (1988)

A series of 2-(aryl- or alkylethynyl)benzenealkanamines were synthesized. They exhibit antihypertensive activity in spontaneously hypertensive rats and coronary vasodilator activity with minimal negative inotropic activity in the "Langendorff" guinea pig heart in vitro. They have been shown to exert their activity by inhibition of Ca2+ influx across cell membranes. Optimal activity is found among the N-(arylethyl)-5-methoxy-alpha-methyl-2-(phenylethynyl)ben zeneethanamines and -propanamines.
The film property and deposition process of TSV inside for 3D interconnection (2008)

This investigation was performed in order to study the properties of deposition and layers by Silicon Dioxide, SiO2, as dielectric onto Via and Trench which have high Aspect Ratio (AR). Thus, in order to confirm these properties, three types of CVD, which were PECVD, PETEOS, and ALD, were selected. On the experiment each of the property sections was estimated that step overage of PECVD: by /1cycle, was prominently lower than PETEOS, which had the deposition rate of /min. Since electric film requires at least thicknesses, ALD was not suitable for the deposition rate. which is the most important component in a practical use. Therefore, in this particular study, PETEOS was evaluated to be the most suitable recipe.
Extracting Global 3D Scattering Center Model of Radar Target from Multiple HRR Profiles (2007)

Global 3D scattering center model represents the radar target in optical region by a set of point scatterers in three dimensional space with spatial scattering patterns. Such a model is useful in scattering analysis, data compression and target recognition. R. Bhalla et al. have proposed to extract such a model from multiple 3D radar images at viewing angles on a mesh grid covering the space extent of interest. Here we propose another method to extract the model from multiple 1D radar images, i.e., high range resolution profiles. This alleviates the tremendous task of collecting enough data for 3D imaging at each viewing angle. We explore the fact that the projected 1D locations of a fixed scattering center at different viewing angles are on the same sphere and we devise a 1D-3D scatter map (OTSM) to visualize those spheres. Though OTSM gives a straightforward demonstration of the 3D scattering center model, we devise a procedure to extract the model automatically, which makes use of algorithms such as Hough transform and morphologic operation. The model we extracted contains the stable scattering centers of the target and is valid in a large space extent. It can be used to restore the target signatures such as RCS and 1D to 3D radar images at any viewing angles in this space extent and at any frequencies in or near the band of the original data. Examples using both simple and complex targets demonstrate the validity of this method.
Antigen-coated Sepharose Beads Induce Airway Eosinophilia and Airway Hyperresponsiveness in Cynomolgus Monkeys (1989)

A method of inducing sustained airway eosinophilia and airway hyperresponsiveness in primates has been developed. Our method utilizes a series of intratracheal instillations of Ascaris suum-coated sepharose 4B beads (3 x 10(5] administered once a week for four weeks. Five cynomolgus monkeys (Macaca fascicularis) demonstrating a naturally occurring skin and respiratory sensitivity to Ascaris suum extract were studied. Airway cell composition was measured by bronchoalveolar lavage (BAL), and airway responsiveness was determined as the bronchoconstrictor response to inhaled methacholine. Ascaris suum bead administration resulted in a transient increase in total cells recovered by BAL (2.4 +/- 0.4 to 8.7 +/- 2.5 x 10(5) cells/ml, p less than 0.05) and a selective increase in BAL eosinophils (17 +/- 6 to 916 +/- 158 x 10(3) cells/ml, p less than 0.05). Increases in airway responsiveness were concurrent with the increase in airway eosinophils. These observations show that airway eosinophilia is associated with airway hyperresponsiveness in primates. Furthermore, this new model is a novel experimental system in which the underlying mechanisms in the pathogenesis of airway hyperresponsiveness can be investigated.
On the noise generating behaviour of high current AC arcs and the possibility of noise reduction in electric arc furnaces by electrotechnical means (1981)

On the noise generating behaviour of high current AC arcs and the possibility of noise reduction in electric arc furnaces by electrotechnical means
Charge identification in PAMELA: preliminary results on light nuclei (2008)

The study of the light-nuclei component of the cosmic radiation is strictly connected to a better\nunderstanding of the propagation properties, which has great importance for the study of signatures\nof new physics in CRs. For example, indirect signals of dark matter pairs annihilating in the\nhalo of our Galaxy could be found in antiproton, antideuteron or positron CRs but this research is\nlimited by the uncertainties in the propagation parameters and fluxes of charged particles located\nin the whole diffusive halo. The PAMELA experiment will contribute to this issue measuring\nlight nuclei fluxes and ratios with good accuracy, also in some unexplored energy range. Some\npreliminary results on discrimination capability of the subdetectors will be presented in this work.
CREB DNA binding activity is inhibited by glycogen synthase kinase‐3β and facilitated by lithium (2001)

The regulatory influences of glycogen synthase kinase-3 beta (GSK3 beta) and lithium on the activity of cyclic AMP response element binding protein (CREB) were examined in human neuroblastoma SH-SY5Y cells. Activation of Akt (protein kinase B) with serum-increased phospho-serine-9-GSK3 beta (the inactive form of the enzyme), inhibited GSK3 beta activity, and increased CREB DNA binding activity. Inhibition of GSK3 beta by another paradigm, treatment with the selective inhibitor lithium, also increased CREB DNA binding activity. The inhibitory regulation of CREB DNA binding activity by GSK3 beta also was evident in differentiated SH-SY5Y cells, indicating that this regulatory interaction is maintained in non-proliferating cells. These results demonstrate that inhibition of GSK3 beta by serine-9 phosphorylation or directly by lithium increases CREB activation. Conversely, overexpression of active GSK3 beta to 3.5-fold the normal levels completely blocked increases in CREB DNA binding activity induced by epidermal growth factor, insulin-like growth factor-1, forskolin, and cyclic AMP. The inhibitory effects due to overexpressed GSK3 beta were reversed by treatment with lithium and with another GSK 3beta inhibitor, sodium valproate. Overall, these results demonstrate that GSK3 beta inhibits, and lithium enhances, CREB activation.