gebhart/patrepeval huggingface dataset:
DNA-Vaccine Platform Development Against H1N1 Subtype of Swine Influenza A Viruses (2012)

Swine influenza virus (SIV) is an important viral pathogen in pig populations. However, commercial vaccines cannot provide complete protection with induced humoral immunity only, and require frequent updates to fight against current isolates. DNA vaccination is an effective means of eliciting both arms of the immune system, the humoral and cellular immune responses. In this study, DNA vector pcDNA3.1 was inserted with a chimeric intron downstream of the CMV promoter region followed by a Kozak sequence to enhance the expression of gene inserts. The C-terminal of the VP22 gene (VP22c), encoding the tegument protein of bovine herpesvirus-1, was fused separately to the N-terminal of four quadruplicated epitopes: two B-cell epitopes (HA91-108 and M2e), and two T-cell epitopes (NP366-374 and NP380-393), which were conserved, at least among the three SIV subtypes prevailing in pig populations in North America. Linker -KK- was used to space between each copy of the two B-cell epitopes, and -RVKR- was used for the two T-cell epitopes, in order to enhance the presentation of epitopes to the immune system. The expression of epitopes was confirmed in in vitro transfection of 293FT cells, and higher percentages of epitope-positive cells were achieved from the plasmids containing VP22c than those without. After the DNA plasmids were administered to mice intramuscularly in combination or separately, or boosted with recombinant proteins of quadruplicated epitopes fused to VP22c, the vaccine stimulated the desired epitope-specific humoral immunity to the two B-cell epitopes, and cellular immunity to the epitope NP380-393. Our results indicate that plasmids with quadruplicated epitopes fused to the VP22c may be a potential vehicle in developing epitopes as vaccines against SIV.
Ultrasonic Dynamic Vector Stress Sensor (1992)

Stress inferred from measurements in specimens rather than in bonded gauges. Ultrasonic dynamic vector stress sensor (UDVSS) measures changes in dynamic directional stress occurring in material or structure at location touched by device when material or structure put under cyclic load. Includes phase-locked loop, synchronous amplifier, and contact probe. Useful among manufacturers of aerospace and automotive structures for stress testing and evaluation of designs.
Preferential Hydration of Bovine Serum Albumin in Polyhydric Alcohol-Water Mixtures1 (1981)

The preferential solvent interaction with bovine serum albumin in aqueous solution of polyhydric alcohols (ethylene glycol, glycerol, xylitol, sorbitol, mannitol, and inositol) was investigated by a densimetric method with the application of multicomponent theory. This proteins was preferentially hydrated in all solvent systems examined: the extent depended on the number and the steric configuration of the hydroxyl groups of alcohols. The absolute interactions of these alcohols with the protein were estimated by assuming that the amount of hydration of protein at every solvent composition used is identical with that in pure water. The preferential hydration of the protein in 30% aqueous solutions of glycerol and sorbitol was found to decrease as the temperature was increased, indicating that the increase in chemical potential of protein on transferring it from water to both aqueous solvents is generated by a large positive enthalpy change, sufficient to compensate for the positive entropy change in the transfer process. On the basis of these results, and mechanism of stabilization of protein structure by these alcohols was discussed from the viewpoint of the solvation of protein.
Shallow boron junctions and preamorphization for deep submicron silicon technology (1993)

In this study, shallow p+-n junction diodes were formed by implanting BF+2 ions into single-crystal silicon or silicon preamorphized by either Si or Ge implantation. BF+2 implantation at energies of 20 or 25 keV and a dose of 1×1015 cm−2 was followed by furnace annealing at 600 °C in nitrogen ambient. Most samples received a further nitrogen-ambient anneal at 850 °C, with various periods of time. Secondary ion mass spectroscopy was used to measure the B profiles. Cross-sectional transmission electron microscopy was used to study the amorphous layers and the defects remaining after annealing. Electrical characterization of the diodes is described. In preamorphized samples, the residual defect density decreases, and the defect band located at the original amorphous-crystalline interface becomes sharper, as the mass of the amorphizing ion species is increased. Ideal low-leakage shallow junctions can be made following either Si or Ge preamorphization and furnace annealing, without removing all the defects induced by preamorphization. This is achieved by containing the implanted B profile completely within the amorphous layer, and by containing the defect band completely within the final biased junction. However, even without a preamorphization step, ideal low-leakage shallow junctions were obtained after BF+2 implantation and 600 °C furnace annealing. This suggests that preamorphization may not ultimately be needed for practical engineering of shallow junctions.
Antisense oligonucleotides, exon skipping and the dystrophin gene transcript. (2005)

Antisense oligonucleotide induced exon skipping has recently emerged as a potential therapy to by-pass the consequences of many, but not all dystrophin mutations that lead to Duchenne muscular dystrophy. Targeted removal of one or more exons, to restore a disrupted reading frame, or omit a nonsense mutation, could lessen the consequences of an estimated 80% of dystrophin gene mutations. Promising in vitro and in vivo experiments in animal models of dystrophinopathies, as well as demonstration of induced exon skipping in cultured human myogenic cells have prompted considerable enthusiasm. Furthermore, advances in antisense oligonucleotide chemistries have resulted in the development of more stable and less toxic compounds, some of which are currently in Phase III clinical trials for selected antiviral applications. This review will summarize developments in induced exon skipping that have paved the way to clinical trials and some of the challenges and possible limitations.
Effectiveness of Animation in Trend Visualization (2008)

Animation has been used to show trends in multi-dimensional data. This technique has recently gained new prominence for presentations, most notably with Gapminder Trendalyzer. In Trendalyzer, animation together with interesting data and an engaging presenter helps the audience understand the results of an analysis of the data. It is less clear whether trend animation is effective for analysis. This paper proposes two alternative trend visualizations that use static depictions of trends: one which shows traces of all trends overlaid simultaneously in one display and a second that uses a small multiples display to show the trend traces side-by-side. The paper evaluates the three visualizations for both analysis and presentation. Results indicate that trend animation can be challenging to use even for presentations; while it is the fastest technique for presentation and participants find it enjoyable and exciting, it does lead to many participant errors. Animation is the least effective form for analysis; both static depictions of trends are significantly faster than animation, and the small multiples display is more accurate.
Lower prevalence of Chlamydia pneumoniae DNA compared with Chlamydia trachomatis DNA in synovial tissue of arthritis patients (1999)

DNA of C pneumoniae is present in synovial specimens from some arthritis patients. The prevalence of this organism in the joints was lower than that of C trachomatis, and synovial presence of the organism was not associated with any distinct clinical syndrome. Widely disseminated nucleic acids such as those of C. pneumoniae might have some role in the pathogenesis of several arthritides, since the organism was not found in the ST from normal control individuals.
New Visco-Elastic Surfactant Formulations Extend Simultaneous Gravel-Packing and Cake-Cleanup Technique to Higher-Pressure and Higher-Temperature Horizontal Open-Hole Completions: Laboratory Development and a Field Case History From the North Sea. (2002)

Abstract Filter-cake cleanup in open-hole gravel-pack completions has traditionally involved several stages: gravel-packing, pulling out of the hole with the work string, running in hole with production tubing, running in hole with coiled tubing, circulating the excess carrier fluid from inside the base pipe and spotting a breaker solution. Furthermore, in cases where removal of both the polymeric components and the CaCO3 bridging agents is necessary, an enzyme or an oxidizer soak has typically been followed by an acid treatment. This process is time consuming and costly, in addition to being non-optimal in terms of uniform cake-cleanup in long open-hole completions, due to rapid reaction between acid and CaCO3 particles. Recently proposed simultaneous gravel-packing and cake-cleanup method incorporating breakers into the gravel-pack carrier fluid have been demonstrated to be an efficient technique through more than a dozen field applications, as evidenced by higher productivity compared to offset wells completed with conventional techniques. Because of the inherent risk in simultaneous gravel-packing and cake-cleanup with water-packing technique, carrier fluids containing breakers for filtercake removal have been used in conjunction with shunt-packing, which has been demonstrated through both field applications and large-scale yard testing not to rely on either the filter-cake or the formation properties. However, because shunt technique relies on viscosity for gravel placement, application of the simultaneous gravel-packing and cake-cleanup technique with polymer-free visco-elastic-surfactant (VES) carrier fluids has been limited to wells requiring a density of about 9.8 ppg (for circulating packs) and a bottom hole circulating temperature less than 200°F. In this paper, we present new surfactant formulations, which have unique chemistry that allows them to form visco-elastic surfactant solutions in high-density brines and remain stable at elevated temperatures. Densities up to 13.8 ppg with a rheological profile suitable for shunt-packing at bottom hole circulating temperatures exceeding 250°F are achievable with this new surfactant, covering a large majority of the gravel-pack applications. It is further demonstrated that this new surfactant system does not only allow the use of certain chemicals that can be used for CaCO3 dissolution in conjunction with a gravel-pack process, but also requires these chemicals as co-surfactants in order to develop a visco-elastic structure. In addition to discussion of the unique chemistry of this VES formulation, data pertaining to proposed gravel-pack applications are presented. These include rheology, gravel suspension properties, filtercake dissolution characteristics, and retained permeabilities. A field case history utilizing the new VES fluid incorporating filter-cake cleanup chemicals is also detailed.
A Robust Background Subtraction and Shadow Detection (1999)

This paper presents a novel algorithm for detecting moving objects from a static background scene that contains shading and shadows using color images. Although the background subtraction technique has been used for years in many vision systems as a preprocessing step for object detection and tracking, most of these algorithms are susceptible to both global and local illumination changes such as shadows and highlights. These cause the consequent processes, e.g. tracking, recognition, etc., to fail. This problem is the underlying motivation of our work. We develop a robust and efficiently computed background subtraction algorithm that is able to cope with local illumination change problems, such as shadows and highlights, as well as global illumination changes. Experimental results, which demonstrate the system’s performance, are also shown. Ã�ÝÛÓÖ�× � segmentation, color model, background subtraction, shadow detection. 1
The Insulin Receptor and Its Cellular Targets1 (2001)

The pleiotropic actions of insulin are mediated by a single receptor tyrosine kinase. Structure/function relationships of the insulin receptor have been conclusively established, and the early steps of insulin signaling are known in some detail. A generally accepted paradigm is that insulin receptors, acting through insulin receptor substrates, stimulate the lipid kinase activity of phosphatidylinositol 3-kinase. The rapid rise in Tris-phosphorylated inositol (PIP(3)) that ensues triggers a cascade of PIP(3)-dependent serine/threonine kinases. Among the latter, Akt (a product of the akt protooncogene) and atypical protein kinase C isoforms are thought to be involved in insulin regulation of glucose transport and oxidation; glycogen, lipid, and protein synthesis; and modulation of gene expression. The presence of multiple insulin-regulated, PIP(3)-dependent kinases is consistent with the possibility that different pathways are required to regulate different biological actions of insulin. Additional work remains to be performed to understand the distal components of insulin signaling. Moreover, there exists substantial evidence for insulin receptor substrate- and/or phosphatidylinositol 3-kinase-independent pathways of insulin action. The ultimate goal of these investigations is to provide clues to the pathogenesis and treatment of the insulin resistant state that is characteristic of type 2 diabetes.
A Review of Research in Revising Instructional Text (1991)

School textbooks are commonly criticized. This article reviews research in revising instructional text by examining multidisciplinary research in readability, text structure, text interestingness, expert revisers' strategies, and readers' comprehension strategies. Findings are that much of this research is limited by a simplistic view of reading, the use of experimentally contrived texts and contexts, and a dependency on recall as a measure of comprehension. A promising line of recent research uses readers' verbal protocols to guide revision and develop revision principles. Further research needs to: (a) develop other innovative ways of measuring comprehension, (b) focus on subject specific concerns, and (c) examine classroom contexts of textbook use.
Phase 1 trial and assay of rubidazone (NSC 164011) in patients with advanced solid tumors. (1979)

A new high-pressure liquid chromatographic method was developed for the simultaneous determination of rubidazone and daunorubicin in human plasma at concentrations as low as 60 ng/ml. Clinical toxicity and the stability of rubidazone were studied in nine patients with advanced solid tumors. Rubidazone was administered by i.v. infusion over 1 hr on a single day every 4 weeks. Moderate leukopenia was the dose-limiting toxicity in four of six patients treated at 150 mg sq/m. Assay of rubidazone in plasma samples obtained after administration of rubidazone showed that the drug was stable for at least 7 hr.
DNA-metal binding by antitumor-active metallocene dichlorides from inductively coupled plasma spectroscopy analysis: titanocene dichloride forms DNA-Cp2Ti or DNA-CpTi adducts depending on pH (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDNA-metal binding by antitumor-active metallocene dichlorides from inductively coupled plasma spectroscopy analysis: titanocene dichloride forms DNA-Cp2Ti or DNA-CpTi adducts depending on pHMark L. McLaughlin, John M. Cronan Jr., Tamara R. Schaller, and Ronald D. SnellingCite this: J. Am. Chem. Soc. 1990, 112, 24, 8949–8952Publication Date (Print):November 1, 1990Publication History Published online1 May 2002Published inissue 1 November 1990https://pubs.acs.org/doi/10.1021/ja00180a046https://doi.org/10.1021/ja00180a046research-articleACS PublicationsRequest reuse permissionsArticle Views453Altmetric-Citations76LEARN 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
Reverse transcriptase from human immunodeficiency virus: a single template-primer binding site serves two physically separable catalytic functions (1991)

The binding of substrates to recombinant reverse transcriptase from human immunodeficiency virus (HIV) and the natural enzyme from avian myeloblastosis virus (AMV) has been examined by analyzing both the ribonuclease H and the RNA-dependent DNA polymerase activities. With 3'-end-labeled globin mRNA hybridized to (dT)15 as the substrate in the ribonuclease H reaction, the enzymes partially deadenylated the mRNA in a distributive manner. Under these conditions, there was a rapid initial burst followed by a prolonged, but much slower, steady-state rate. The biphasic reaction made possible determinations of kinetic constants as follows: values for Km, KD, and kcat were, respectively, 27 nM, 11 nM, and 5 x 10(-3) s-1 for the HIV enzyme and 30 nM, 9 nM, and 5 x 10(-3) s-1, respectively, for the avian enzyme. These constants were used to derive other parameters: The rate of association of the template-primer with reverse transcriptase was approximately 2 x 10(5) M-1 s-1, and the rate of dissociation was approximately 2 x 10(-3) s-1, regardless of the source of the enzyme. The rate of release of the product was essentially equivalent to the value of kcat indicated above for each of the enzymes. The polymerase reaction was evaluated under processive conditions of synthesis; values of Km and kcat of approximately 6 nM and approximately 2.5 s-1, respectively, for the human enzyme, and approximately 10 nM and approximately 2 s-1, respectively, for the avian enzyme were observed. The interaction of substrates with HIV reverse transcriptase was characterized further with the aid of ribonucleoside-vanadyl complexes. These complexes inhibited the polymerase and ribonuclease H activities of the enzyme competitively with respect to globin mRNA.(dT)15. Values of Ki ranging from 1 to 3 mM were obtained. With respect to deoxyribonucleoside triphosphate substrates in the polymerase reaction, mixed inhibition was observed. Deoxyribonucleoside triphosphates had no effect on kinetic parameters governing the ribonuclease H activity of the HIV enzyme but apparently facilitated the formation of active enzyme. These data fit a model in which one template-primer binding site serves both the polymerase and the ribonuclease H catalytic sites.
Intraductal Meibomian Gland Probing Relieves Symptoms of Obstructive Meibomian Gland Dysfunction (2010)

Invasive orifice penetration and intraductal probing seems to provide lasting rapid symptom relief for patients with O-MGD. Probing findings in this study frequently included (1) mild resistance upon orifice penetration, (2) proximal duct gritty tactile and aural sensation suggestive of keratinized cellular debris, and (3) focal variable resistance deeper within the duct, which may be relieved with the probe, suggestive of fibrovascular tissue. Taken together, these findings may offer probing characteristics that may allow for a grading system for duct obstruction. The postprobing improvement of symptoms not previously appreciated supports the notion that meibomian gland disease exists subclinically.
HIV Protease Inhibitors Act as Competitive Inhibitors of the Cytoplasmic Glucose Binding Site of GLUTs with Differing Affinities for GLUT1 and GLUT4 (2011)

The clinical use of several first generation HIV protease inhibitors (PIs) is associated with the development of insulin resistance. Indinavir has been shown to act as a potent reversible noncompetitive inhibitor of zero-trans glucose influx via direct interaction with the insulin responsive facilitative glucose transporter GLUT4. Newer drugs within this class have differing effects on insulin sensitivity in treated patients. GLUTs are known to contain two distinct glucose-binding sites that are located on opposite sides of the lipid bilayer. To determine whether interference with the cytoplasmic glucose binding site is responsible for differential effects of PIs on glucose transport, intact intracellular membrane vesicles containing GLUT1 and GLUT4, which have an inverted transporter orientation relative to the plasma membrane, were isolated from 3T3-L1 adipocytes. The binding of biotinylated ATB-BMPA, a membrane impermeable bis-mannose containing photolabel, was determined in the presence of indinavir, ritonavir, atazanavir, tipranavir, and cytochalasin b. Zero-trans 2-deoxyglucose transport was measured in both 3T3-L1 fibroblasts and primary rat adipocytes acutely exposed to these compounds. PI inhibition of glucose transport correlated strongly with the PI inhibition of ATB-BMPA/transporter binding. At therapeutically relevant concentrations, ritonavir was not selective for GLUT4 over GLUT1. Indinavir was found to act as a competitive inhibitor of the cytoplasmic glucose binding site of GLUT4 with a K(I) of 8.2 µM. These data establish biotinylated ATB-BMPA as an effective probe to quantify accessibility of the endofacial glucose-binding site in GLUTs and reveal that the ability of PIs to block this site differs among drugs within this class. This provides mechanistic insight into the basis for the clinical variation in drug-related metabolic toxicity.
Human immunodeficiency virus-associated systemic lymphomas may be subdivided into two main groups according to Epstein-Barr viral latent gene expression. (1993)

Differences in EBV association and LMP-1 expression were found between a major group of HIV-associated systemic NHL with blastic cell morphology, including SNCC lymphoma and its variants, and anaplastic cell lymphomas. A proportion of immunoblastic (polymorphic) lymphomas was different in viral latent gene expression from other blastic cell systemic lymphomas. It is concluded that only a group of these lymphomas (most ALC Ki-1+ and HD cases, along with a nonnegligible fraction of immunoblastic lymphomas) seems to be linked etiopathologically to EBV.