gebhart/patrepeval huggingface dataset:
Isolation and characterization of a hemin-regulated gene, hemR, from Porphyromonas gingivalis (1997)

An hemR (hemin-regulated) gene from Porphyromonas gingivalis ATCC 53977 has been isolated and characterized. This gene is present downstream from the prtT gene, previously cloned in this laboratory. In addition, another putative gene, ORF1, was identified between hemR and prtT. The complete nucleotide sequences of ORF1 and hemR were determined, and the deduced amino acid sequence of ORF1 and HemR proteins corresponded to 16- and 48-kDa proteins, respectively. The amino termini of the HemR protein exhibited significant homology with iron-regulated, TonB-dependent outer membrane receptor proteins from various bacteria, while the carboxyl terminus of the HemR protein displayed almost complete identity with a P. gingivalis PrtT protease domain. PCR analyses confirmed the existence of such extensive homology between the carboxyl termini of both the prtT and hemR genes on the P. gingivalis chromosome. Northern blots indicated that ORF1 was part of a 1.0-kb mRNA and was positively regulated by hemin levels. On the other hand, the hemR gene was apparently a part of a 3.0-kb polycistronic message and was negatively regulated at the transcriptional level by hemin. Primer extension analysis of the hemR gene revealed that the transcription start site was at a C residue located within ORF1. An examination of HemR::lacZ constructs in both Escherichia coli and P. gingivalis confirmed hemin repression of hemR expression in both organisms. Moreover, the HemR protein expressed in E. coli was detected by an antiserum from a periodontitis patient heavily colonized with P. gingivalis but not by serum from a periodontally healthy patient or by antisera against hemin-grown P. gingivalis cells. Therefore, it is likely that the 48-kDa HemR protein can be expressed only under hemin-restricted conditions. These results suggest that we have isolated a hemin-regulated gene, hemR, which encodes a 48-kDa protein that may be a TonB-dependent outer membrane protein.
A Rev Protein Is Expressed in Caprine Arthritis Encephalitis Virus (CAEV)-Infected Cells and Is Required for Efficient Viral Replication (1994)

Caprine arthritis encephalitis virus (CAEV) is a lentivirus that is closely related to visna virus and more distantly related to the human lentivirus human immunodeficiency virus 1 (HIV-1). Like other lentiviruses, the genome of CAEV contains multiple small ORFs that encode viral regulatory proteins. Sequence analysis of the CAEV genome and cDNAs generated from mRNA in infected cells has suggested that one of these ORFs encodes a protein (Rev-C) that is analogous to Rev of visna virus and HIV. Antibodies generated to a carboxy-terminal peptide of the rev ORF immunoprecipitate an 18-kDa protein from cells transfected with the Rev cDNA clone. Immunoprecipitation and immunofluorescence analysis of CAEV-infected ovine primary cells show that the product of the rev ORF is expressed during infection and localizes to the nucleolus of infected cells. Also, sera from CAEV-infected goats specifically immunoprecipitates an in vitro-translated product from the full-length Rev cDNA clone as well as that from the unique second open reading frame of Rev-C which shows that the Rev-C protein is expressed during natural CAEV infection of animals. Insertion of either a mutation that creates two stop codons in the unique second open reading frame of Rev-C or a mutation in the basic domain of Rev-C into the CAEV infectious molecular clone renders the virus unable to replicate in primary goat synovial membrane cells. Analysis of the RNA and proteins produced from both Rev-deficient clones indicates that they are defective in the accumulation of structural gene mRNAs in the cytoplasm as well as in synthesis of structural proteins compared to the wild-type CAEV clone. These data indicate that CAEV encodes a Rev protein that is required for efficient viral replication in culture.
Percutaneous left atrial appendage closure: Technical aspects and prevention of periprocedural complications with the watchman device (2015)

Transcatheter closure of the left atrial appendage has been developed as an alternative to chronic oral anticoagulation for stroke prevention in patients with atrial fibrillation, and as a primary therapy for patients with contraindications to chronic oral anticoagulation. The promise of this new intervention compared with warfarin has been supported by several, small studies and two pivotal randomized trial with the Watchman Device. The results regarding risk reduction for stroke have been favourable although acute complications were not infrequent. Procedural complications, which are mainly related to transseptal puncture and device implantation, include air embolism, pericardial effusions/tamponade and device embolization. Knowledge of nature, management and prevention of complications should minimize the risk of complications and allow transcatheter left atrial appendage closure to emerge as a therapeutic option for patients with atrial fibrillation at risk for cardioembolic stroke.
Breakdown of B cell tolerance in a mouse model of systemic lupus erythematosus. (1995)

Anti-DNA antibodies, specifically those that stain nuclei in a homogenous nuclear (HN) fashion, are diagnostic of systemic lupus erythematosus (SLE) and the MRL-lpr/lpr SLE murine model. We have used a heavy chain transgene that increases the frequency of anti-HN antibodies to address whether their production in SLE is the consequence of a defect in B cell tolerance. Anti-HN B cells were undetectable in nonautoimmune-prone transgenic mice, but in MRL-lpr/lpr transgenic mice their Ig was evident in the sera and they were readily retrievable as hybridomas. We conclude that nonautoimmune animals actively delete anti-HN-specific B cells, and that MRL-lpr/lpr mice are defective in this process possibly because of the lpr defect in the fas gene.
Dynamic point cloud compression for free viewpoint video (2003)

In this paper, we present a coding framework addressing the compression of dynamic 3D point clouds which represent real world objects and which result from a video acquisiton using multiple cameras. The encoding is performed as an off-line process and is not time-critical. The decoding however, must allow for real-time rendering of the dynamic 3D point cloud. We introduce a compression framework which encodes multiple attributes like depth and color of 3D video fragments into progressive streams. The reference data structure is alighned on the original camera input images and thus allows for easy view-dependent decoding. The separate encoding of the object´ s silhouette allows the use of shape-adaptive compression algorithms. A novel differential coding approach permits random access in constant time throughout the complete data set and thus enables true free viewpoint video.
The flow of a jet from a body opposing a supersonic free stream (1966)

A series of experiments is described in which a jet issues from an orifice at the nose of a body in supersonic flow to oppose the mainstream. An analytical model of the flow is developed which suggests that the aerodynamic features of a steady flow depend primarily on a jet flow-force coefficient, and the Mach number of the jet in its exit plane. A sufficient condition for steady flow is developed. The experiments are found to agree well with predictions based on the flow model. A short account is presented of some previous investigations, and some of their conclusions are re-examined in the light of the present study.
INHIBITION OF PHOSPHOLIPASE (1983)

Journal Article INHIBITION OF PHOSPHOLIPASE Get access GEOFFREY J BLACKWELL, PhD, GEOFFREY J BLACKWELL, PhD Department of Prostaglandin Research Wellcome Research Laboratories BeckenhamKent Search for other works by this author on: Oxford Academic PubMed Google Scholar RODERICK J FLOWER, PhD RODERICK J FLOWER, PhD Department of Prostaglandin Research Wellcome Research Laboratories BeckenhamKent Search for other works by this author on: Oxford Academic PubMed Google Scholar British Medical Bulletin, Volume 39, Issue 3, 1983, Pages 260–264, https://doi.org/10.1093/oxfordjournals.bmb.a071830 Published: 01 September 1983
Improvement of magnetic and R/W properties in longitudinal media by using CrX/Cr dual underlayer (2001)

The effect of in-plane lattice matching on the magnetic and read/write properties has been quantitatively studied in CoCr/sub 24/Pt/sub 12/B/sub 4/ or CoCr/sub 20/Pt/sub 8/Ta/sub 4/ media grown on Cr, CrMo/sub 20/ and CrMo/sub 20//Cr underlayer. It is found that by using CrMo/sub 20/ (5 nm)/Cr (5 nm) dual underlayer, significant improvement of magnetic and R/W properties are realized. It is clarified that: (1) the utilization of CrMo/Cr dual underlayer increases H/sub c/ mainly due to the improvement of in-plane crystallographic orientation; (2) the lattice misfit has a small effect on the improvement of in-plane crystallographic orientation. The improvement of in-plane crystallographic orientation by using CrX/Cr dual underlayer is suggested to be due to lattice strain at the interface of Cr and CrX underlayer, which enhances the grain growth of the magnetic layer.
<scp>ZFN</scp>‐mediated gene targeting of the Arabidopsis <i>protoporphyrinogen oxidase</i> gene through <i>Agrobacterium</i>‐mediated floral dip transformation (2012)

Previously, we showed that ZFN-mediated induction of double-strand breaks (DSBs) at the intended recombination site enhanced the frequency of gene targeting (GT) at an artificial target locus using Agrobacterium-mediated floral dip transformation. Here, we designed zinc finger nucleases (ZFNs) for induction of DSBs in the natural protoporphyrinogen oxidase (PPO) gene, which can be conveniently utilized for GT experiments. Wild-type Arabidopsis plants and plants expressing the ZFNs were transformed via floral dip transformation with a repair T-DNA with an incomplete PPO gene, missing the 5' coding region but containing two mutations rendering the enzyme insensitive to the herbicide butafenacil as well as an extra KpnI site for molecular analysis of GT events. Selection on butafenacil yielded 2 GT events for the wild type with a frequency of 0.8 × 10⁻³ per transformation event and 8 GT events for the ZFNs expressing plant line with a frequency of 3.1 × 10⁻³ per transformation event. Molecular analysis using PCR and Southern blot analysis showed that 9 of the GT events were so-called true GT events, repaired via homologous recombination (HR) at the 5' and the 3' end of the gene. One plant line contained a PPO gene repaired only at the 5' end via HR. Most plant lines contained extra randomly integrated T-DNA copies. Two plant lines did not contain extra T-DNAs, and the repaired PPO genes in these lines were transmitted to the next generation in a Mendelian fashion.
Assessment of One- and Two-Photon Excited Luminescence for Directly Measuring O<sub>2</sub>, pH, Na<sup>+</sup>, Mg<sup>2+</sup>, or Ca<sup>2+</sup> in Optically Dense and Biologically Relevant Samples (2002)

We compare the emission spectra and analytical response profiles of several semiselective luminescent probes that are commonly used to quantify nonfluorescent analytes (ruthenium(II) tris(2,2′-bipyridyl) dication, tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dication, SNARF®-1, fluorescein, Rhodol Green™, and Sodium™, Magnesium™, and Calcium Green™) when they are excited under one- and two-photon excitation conditions in water, aqueous solutions of dyes or fluorophores, undiluted mouse or human serum, human urine, and mouse whole blood. The results from this work can be summarized as follows. First, in cases where the probes possess ground states that are composed of multiple species in equilibrium (e.g., acid and base forms of a luminophore), the analyte-dependent emission spectra can be significantly different under one- and two-photon excitation conditions due to differences in the relative one- and two-photon cross-sections associated with the individual ground-state species. Second, for those probes that exhibit one- and two-photon dependent emission spectra, an assessment of the analytical response vs. target analyte concentration profiles show that the response dynamic range can be improved by up to 100 fold, but the response sensitivity can decrease by up to 25% for two- vs. one-photon excitation. Third, two-photon excited luminescence provides a means to use these semiselective luminescent probes to quantify nonfluorescent analytes directly within optically dense mixtures, including solutions of dyes, mouse or human serum, human urine, and mouse whole blood. Finally, two-photon excited luminescence allows one to quantify nonfluorescent analytes in a spatially defined manner within complex samples.
Low complexity millimeter-wave LOS-MIMO precoding systems for uniform circular arrays (2014)

In this paper we investigate low complexity millimeter-wave communication systems for uniform circular arrays (UCAs) in line-of-sight (LOS) multiple-input multiple-output (MIMO) channels. We first demonstrate that the MIMO channel matrices for UCAs in LOS-MIMO channels are circulant matrices. Then, we show that the channel matrices can be made orthogonal by choosing the array diameters appropriately as a function of range and wavelength for the 3×3 and 4×4 UCAs. We also derive simple analytical expressions of eigenvalues as a function of array design. Finally, we propose a high performance LOS-MIMO precoding system which combines forward error correction (FEC) codes and spatial interleaver with fixed precoding matrix. Unlike the SVD based eigenmode system, the proposed precoding system does not require CSI estimation, SVD calculation and feedback of precoding matrix owing to the properties of circulant matrices. Simulation results show that the proposed low complexity system can obtain excellent performance in various link ranges.
Fast ion beam chopping system for neutron generators (2005)

Fast deuterium (D+) and tritium (T+) ion beam pulses are needed in some neutron-based imaging systems. A compact, integrated fast ion beam extraction and chopping system has been developed and tested at the Lawrence Berkeley National Laboratory for these applications, and beam pulses with 15ns full width at half maximum have been achieved. Computer simulations together with experimental tests indicate that even faster pulses are achievable by shortening the chopper voltage rise time. This chopper arrangement will be implemented in a coaxial neutron generator, in which a small point-like neutron source is created by multiple 120keV D+ ion beams hitting a titanium target at the center of the source.
Effect of initial moisture content and chip size on the bioconversion efficiency of softwood lignocellulosics (2004)

Previous optimization strategies for the bioconversion of lignocellulosics by steam explosion technologies have focused on the effects of temperature, pH, and treatment time, but have not accounted for changes in severity brought about by properties inherent in the starting feedstock. Consequently, this study evaluated the effects of chip properties, feedstock size (40-mesh, 1.5 x 1.5 cm, 5 x 5 cm), and moisture content (12% and 30%) on the overall bioconversion process, and more specifically on the efficacy of removal of recalcitrant lignin from the lignocellulosic substrates following steam explosion. Increasing chip size resulted in an improvement in the solids recovery, with concurrent increases in the water soluble, hemicellulose-derived sugar recovery (7.5%). This increased recovery is a result of a decrease in the "relative severity" of the pretreatment as chip size increases. Additionally, the decreased relative severity minimized the condensation of the recalcitrant residual lignin and therefore increased the efficacy of peroxide fractionation, where a 60% improvement in lignin removal was possible with chips of larger initial size. Similarly, increased initial moisture content reduced the relative severity of the pretreatment, generating improved solids and hemicellulose-derived carbohydrate recovery. Both increased chip size and higher initial moisture content results in a substrate that performs better during peroxide delignification, and consequently enzymatic hydrolysis. Furthermore, a post steam-explosion refining step increased hemicellulose-derived sugar recovery and was most effectively delignified (to as low as 6.5%). The refined substrate could be enzymatically hydrolyzed to very high levels (98%) and relatively fast rates (1.23 g/L/h).
Chemical enhancement of tumor immunogenicity. (1980)

C57BL/6 spleen cells immunized in vitro against syngeneic methylcholanthrene-induced sarcoma cells(MC-1 cells) modified with various chemical reagents show cytotoxic activity against unmodified MC-1 cells in a short-term 51Cr release assay, whereas unmodified MC-1 cells are nonimmunogenic. The effector cells cross-react widely with many other fibroblastic and epithelioid tumors, even those that are not H-2 matched, as well as with some nonneoplastic cells. Priming mice in vivo with a hapten leads to enhanced anti-tumor cytotoxicity developed by spleen cells from these mice immunized in vitro against tumor cells modified with the same hapten. Cytotoxic activity is largely, but not completely, removed by treatment with anti-theta serum and C. The existence of suppressor cells that can inhibit an anti-tumor response is demonstrasted in in vitro immunizations of mixtures of spleen cells from normal mice and mice primed with mitomyhcin-treated tumor cells, the latter suppressing the former.
Xeno-Cannibalism: A Survival “Escamotage” (2007)

Several lines of evidence have demonstrated that self-cannibalism (macroautophagy) is a well regulated process of cell repair as well as of molecule and organelle recycling that allows the cells to survive. However, autophagic activity also represents a cell death pathway characterized by specific features that differentiate autophagy from other cell death processes. We found that cells that are able to exert intense autophagic activity were also able to engulf and digest entire cell siblings. This phenomenon represents a sort of xeno-cannibalism. We wonder whether these two phenomena, self and xeno-cannibalism, could be related the latter being an exacerbation of the first and providing a further survival option to the cells.
Self-Assembled Gyroidal Mesoporous Polymer-Derived High Temperature Ceramic Monoliths (2016)

Polymer-derived ceramics (PDCs) have enabled the development of nonoxide ceramic coatings and fibers with exceptional thermo-mechanical stability. Here, we report the self-assembly based synthesis of gyroidal (space group Q230, Ia3̅d) mesoporous silicon oxynitride ceramic monoliths by pyrolysis of blends of commercially available preceramic polysilazane with a structure-directing triblock terpolymer up to temperatures of 1000 °C. Monoliths had pore diameters of 9.4 ± 1.1 nm and surface area of 160 m2/g. The three-dimensionally (3D) ordered periodic pore structure of the as-made hybrids acts to relieve stresses by allowing the escape of gases formed during ceramization. This process in turn enables the retention of smooth monoliths during ceramization under ammonia, a process that both adds nitrogen to the material and removes carbon pyrolysis products. The monoliths are appealing for high-temperature applications such as catalyst supports and microelectromechanical system (MEMS) devices including gas and pressure sensors, as well as strong, stiff, and creep-resistant scaffolds for ordered interpenetrating phase composites.
Properties of coherence-gated wavefront sensing (2007)

Coherence-gated wavefront sensing (CGWS) allows the determination of wavefront aberrations in strongly scattering tissue and their correction by adaptive optics. This allows, e.g., the restoration of the diffraction limit in light microscopy. Here, we develop a model, based on ray tracing of ballistic light scattered from a set of discrete scatterers, to characterize CGWS performance as it depends on coherence length, scatterer density, coherence-gate position, and polarization. The model is evaluated by using Monte Carlo simulation and verified against experimental measurements. We show, in particular, that all aberrations needed for adaptive wavefront restoration are correctly sensed if circularly polarized light is used.
Anticancer Activity of <i>Scutellaria baicalensis</i> and Its Potential Mechanism (2002)

Scutellaria baicalensis strongly inhibits cell growth in all cancer cell lines tested. However, prostate and breast cancer cells (PC-3, LNCaP, and MCF-7) are slightly more sensitive than other type of cancer cells. It also inhibits PGE(2) production, indicating that suppression of tumor cell growth may be due to its ability to inhibit COX-2 activity. This study supports the notion of using Scutellaria baicalensis as a novel anticancer agent to treat various cancers.
Particle Size Effect of Crumb Rubber on Rheology and Morphology of Asphalt Binders with Long-term Aging (2008)

ABSTRACT Two different particle sizes of crumb rubber at three different concentrations were mixed with two asphalts to investigate the effect of rubber particles on the fundamental internal microstructure of asphalt binders with respect to their long-term aging performance. The rheological, morphological, and chemical properties of unaged and aged unmodified and rubber modified asphalt binders were studied as a function of long-term oxidative aging. Based on the limited study, the results indicate that the amounts of rubber particles added into asphalt binder are asphalt dependent. For highly incompatible asphalt, rubber concentration has substantial effect on the long-term flow properties of asphalt binders. For compatible asphalt, addition of rubber increased the elasticity of asphalts and also reduced viscosity buildup with aging. In addition, particle size of rubber does not show significant differences in terms of its effect on the long-term aging characteristics of asphalt binder. Furthermore, results from atomic force microscopy (AFM) showed that some fractions of the rubber particles may be dissolved in the asphalt due to devulcanization of the rubber, and hence, could explain the appearance of “new” material in the AFM image of the recovered asphalt samples. KEYWORDS: Crumb RubberRheologyMorphologyCompatibilityAgingMaster Curve
Sterility caused by cooling treatment at the flowering stage in rice plants. III. Establishment of a method of in vitro pollen germination. (1989)

Rice pollen grains germinated more than 80% with low variation (standard deviation less than 10%) and their pollen tubes elongated to more than 150μm within one hour with a simple medium composed of 1% agar, 20% sucrose and 20μg·ml-1 (ppm) boric acid, using a Petri dish (4.5 cm in diameter). In addition to the composition of the medium, it is important that the incubation temperature should be around 20°C and that the pollen grains should be shed directly on the medium from the anthers as soon as the flowers begin to open. Under these conditions, their pollen grains began to germinate 2 to 3 min after shedding and attained maximum growth rate within 20 min. After that time, the length of pollen tube increased at a linear rate of ca. 7.5μm·min-1 over the next 15 min.
Cascade Molecules: 15.<sup>1</sup>Synthesis of Tris(3-substituted) Tripropylnitromethanes (1991)

Starting from 4-(3-hydroxypropyl)-4-nitro-1,7-heptanediol, a series of polyfunctional nitromethane derivatives, 1,3′,7-trisubstituted 4-nitro-4-propylheptanes, has been prepared and spectroscopically correlated; these derivatives validate methodologies for surface derivativization of specifically sized cascade polymers.