gebhart/patrepeval huggingface dataset:
Cloning and Characterization of the Promoter Region of a Gene Encoding a 67-kDa Glycoprotein (1997)

A rat genomic library constructed in lambda-EMBL3 (SP6/T7) vector () was screened using 32P-labeled rat p67 cDNA. A clone containing a segment of 5'-upstream region of p67 genomic DNA was obtained. The DNA (about 1.7 kilobase pairs) was isolated and characterized. Sequence analysis of this DNA fragment showed that the 898 base pairs at the 5'-end of the upstream region was identical to several long interspersed nucleotide sequences. One hundred forty-eight base pairs at the 3'-end contained the beginning of the first exon including the ATG initiator codon. The remaining 652 base pairs in between contained two AT-rich regions and several regulatory sequences. The mRNA initiation site was identified at 89 base pairs upstream from the translation start codon. The DNA fragment was also analyzed by transient transfection. When linked to a firefly luciferase reporter gene, this fragment enhanced transcription in a rat hepatoma cell line (KRC-7). Using a series of deletions in the DNA, the minimum essential promoter region (from -177 to -60) was identified. The promoter activity was also enhanced by treatment with phorbol 13-myristate 12-acetate (PMA). This enhancement required an AP-1 sequence (-298 to -292; 5'-TGACTCA-3') and a similar sequence (-97 to -88; 5'-ATGACATCAT-3'). Deletion of either of these sequences significantly reduced PMA enhancement. Deletion of both of these sequences almost completely eliminated PMA enhancement.
New therapies for familial hypercholesterolemia (2006)

The development of cholesterol-lowering drugs, including a variety of statins, bile acid binding resins and recently discovered inhibitors of cholesterol absorption has expanded the options for cardiovascular disease prevention. However, existing approaches to the treatment of familial hypercholesterolemia (FH) are still ineffective in halting the progression of coronary artery disease (CAD) in some patients despite combination therapies. Homozygous FH (and many heterozygous FH subjects) are resistant to conventional drug treatment and remain at high-risk for development and progression of atherosclerotic cardiovascular disease, therefore alternative approaches are needed. Novel agents that include inhibitors of the apical sodium-dependent bile acid transporter, cholesteryl ester transfer protein, microsomal triglyceride transfer protein and squalene synthase may play a future role in combination with statins. It is possible that with improvements in vector technology, liver-directed somatic gene therapy would be an effective approach for this disorder.
Transcriptional activation of integrin β6 during the epithelial-mesenchymal transition defines a novel prognostic indicator of aggressive colon carcinoma (2005)

We used a spheroid model of colon carcinoma to analyze integrin dynamics as a function of the epithelial-mesenchymal transition (EMT), a process that provides a paradigm for understanding how carcinoma cells acquire a more aggressive phenotype. This EMT involves transcriptional activation of the β6 integrin subunit and a consequent induction of αvβ6 expression. This integrin enhances the tumorigenic properties of colon carcinoma, including activation of autocrine TGF-β and migration on interstitial fibronectin. Importantly, this study validates the clinical relevance of the EMT. Kaplan-Meier analysis of β6 expression in 488 colorectal carcinomas revealed a striking reduction in median survival time of patients with high β6 expression. Elevated receptor expression did not simply reflect increasing tumor stage, since log-rank analysis showed a more significant impact on the survival of patients with early-stage, as opposed to late-stage, disease. Cox regression analysis confirmed that this integrin is an independent variable for these tumors. These findings define the αvβ6 integrin as an important risk factor for early-stage disease and a novel therapeutic candidate for colorectal cancer.
Salt tolerance of barley induced by the root endophytePiriformospora indicais associated with a strong increase in antioxidants (2008)

The root endophytic basidiomycete Piriformospora indica has been shown to increase resistance against biotic stress and tolerance to abiotic stress in many plants. Biochemical mechanisms underlying P. indica-mediated salt tolerance were studied in barley (Hordeum vulgare) with special focus on antioxidants. Physiological markers for salt stress, such as metabolic activity, fatty acid composition, lipid peroxidation, ascorbate concentration and activities of catalase, ascorbate peroxidase, dehydroascorbate reductase, monodehydroascorbate reductase and glutathione reductase enzymes were assessed. Root colonization by P. indica increased plant growth and attenuated the NaCl-induced lipid peroxidation, metabolic heat efflux and fatty acid desaturation in leaves of the salt-sensitive barley cultivar Ingrid. The endophyte significantly elevated the amount of ascorbic acid and increased the activities of antioxidant enzymes in barley roots under salt stress conditions. Likewise, a sustained up-regulation of the antioxidative system was demonstrated in NaCl-treated roots of the salt-tolerant barley cultivar California Mariout, irrespective of plant colonization by P. indica. These findings suggest that antioxidants might play a role in both inherited and endophyte-mediated plant tolerance to salinity.
Expression of cytokines and cytokine receptors in human Schwann cells (2008)

The expression of cytokines and cytokine receptors was investigated in enriched populations of human fetal Schwann cells by reverse transcribed-PCR and enzyme-linked immunosorbent assay. Human fetal Schwann cells constitutively expressed mRNA of IL-1beta, IL-6, IL-8, IL-11, IL-12, IL-15 and TGF-beta, and also cytokine receptors for IL-1, IL-4, IL-6, IL-8, IL-13, tissue necrosis factor and gp130. The expression of IL-1beta, IL-6 and IL-15 was upregulated following treatment with IL-1beta or TGF-beta. The protein levels of IL-6 were increased with IL-1beta treatment, but were decreased with IFN-gamma treatment. Human Schwann cells may respond to cytokine signals in the nerve injury sites and modify the pathological conditions by secreting cytokines. The secreted cytokines may play a role in leukocyte recruitment and exacerbation of axonal injury process.
Genetics of multidrug resistance: relationship of a cloned gene to the complete multidrug resistant phenotype. (1987)

Resistance to multiple chemotherapeutic agents remains the major cause of failure in cancer chemotherapy. Multidrug resistant cell lines developed in vitro have provided a useful model for analyzing this phenomenon. We describe a complementary DNA, lambda DR11, which is present in normal cells and overexpressed in multidrug resistant cell lines. We have placed this complementary DNA in an expression vector which uses the beta-actin promoter to drive transcription and introduced this vector via transfection into drug sensitive cells. Cells expressing increased levels of lambda DR11 are resistant to the same broad spectrum of chemotherapeutic agents which characterize the multidrug resistant phenotype. The expression of this complementary DNA in transfected clones is dependent upon the number of copies of lambda DR11 integrated in the genome as well as the amount of selective pressure placed on the clone during selection of the clone. Furthermore, the number of copies of lambda DR11 in the genome and the expression of lambda DR11 can be modulated by releasing an individual clone from selective pressure or by increasing the selective pressure on the clone. The endogenous sequences encoding the multidrug resistance gene are not amplified in transfected drug resistant clones. Finally, the drug resistant phenotype is reversed in the transfected clones by verapamil just as drug resistance is reversed in multidrug resistant cell lines.
A study on conformationally restricted sangivamycins and their inhibitory abilities of protein kinases. (1992)

Conformational restrictions of sangivamycin, a rather selective inhibitor of PKC, could be achieved by the use of the steric effect and the gauche effect of the substituents on the ribofuranose moiety. The conformational deviations obtained by these methods were found to nicely correlate with the inhibitory ability of PKC.
Identification of ZCCHC8 as fusion partner of ROS1 in a case of congenital glioblastoma multiforme with a t(6;12)(q21;q24.3) (2016)

Congenital gliobastoma multiforme (GBM) is rare and little is known about the molecular defects underlying the initiation and progression of this tumor type. We present a case of congenital GBM analyzed by conventional cytogenetics, fluorescence in situ hybridization, array comparative genomic hybridization and next generation sequencing. On cytogenetic analysis we detected a reciprocal translocation t(6;12)(q21;q24.3). By sequencing, the translocation was shown to form a fusion between the 5' region of ZCCHC8 and the 3' region of ROS1. RT-PCR analyses confirmed the existence of an in-frame fusion transcript with ZCCHC8 exons 1-3 joined to ROS1 exons 36-43. In addition to the ZCCHC8-ROS1 fusion, we detected a deletion in the short arm of chromosome 9, including homozygous loss of the CDKN2A/2B locus in 9p21.3 and heterozygous deletion of the HAUS6 gene in 9p22.1. The latter encodes a protein involved in faithful chromosome segregation by regulating microtubule nucleation and its deletion might be associated with the marked subclonal changes of ploidy observed in the tumor. This report adds the ZCCHC8-ROS1 fusion as oncogenic driver in GBM and supports the role of ROS1 activation in the pathogenesis of a subset of GBM. © 2016 Wiley Periodicals, Inc.
Signaling and Circuitry of Multiple MAPK Pathways Revealed by a Matrix of Global Gene Expression Profiles (2000)

Genome-wide transcript profiling was used to monitor signal transduction during yeast pheromone response. Genetic manipulations allowed analysis of changes in gene expression underlying pheromone signaling, cell cycle control, and polarized morphogenesis. A two-dimensional hierarchical clustered matrix, covering 383 of the most highly regulated genes, was constructed from 46 diverse experimental conditions. Diagnostic subsets of coexpressed genes reflected signaling activity, cross talk, and overlap of multiple mitogen-activated protein kinase (MAPK) pathways. Analysis of the profiles specified by two different MAPKs-Fus3p and Kss1p-revealed functional overlap of the filamentous growth and mating responses. Global transcript analysis reflects biological responses associated with the activation and perturbation of signal transduction pathways.
A (2′-5′)A n -Dependent Endonuclease: Tissue Distribution in BALB/c Mice and the Effects of IFN-β Treatment and Anti-IFN-α/β Immunoglobulin on the Levels of the Enzyme (1988)

A (2'-5')oligoadenylate-dependent endoribonuclease (RNase L) is an important mediator of the IFN-induced antiviral state. RNase L has been found in several different murine tissues at levels comparable to those previously observed in cultured cells. A basal level of RNase L is present in all tissues assayed. The levels of RNase L in tissues are not significantly increased in mice following treatment with interferon-beta (IFN-beta). The amount of RNase L is, however, decreased in spleen when mice are injected with rabbit antimouse IFN-alpha/beta immunoglobulin. These data suggest that relatively high levels of RNase L may be maintained in tissues by endogenous IFN-alpha/beta production.
Recombinant interleukin 1 suppresses lipoprotein lipase activity in 3T3-L1 cells. (1985)

Recombinant murine interleukin 1 (rIL 1) inhibits 3T3-L1 cell expression of lipoprotein lipase (LPL) activity when present in exceedingly dilute concentration (less than 10(-15) M). The extreme sensitivity of the adipocyte system to rIL 1 far exceeds that of the standard lymphocyte-activating factor assay. However, enzyme suppression is incomplete; even at micromolar concentrations, rIL 1 causes only about a 50% reduction in LPL activity. By contrast, cachectin (tumor necrosis factor) achieves nearly complete LPL suppression at subnanomolar concentrations. Concentrated solutions of rIL 1 are incapable of competing with radiolabeled cachectin for binding sites on 3T3-L1 cells. rIL 1-induced LPL suppression is abolished by the addition of a specific IL 1 neutralizing antiserum to the assay system. rIL 1 appears capable of influencing adipocyte expression of LPL, but apparently acts through a different mechanism than cachectin/TNF.
Dexamethasone Stimulates Luciferase Gene Expression Through the Rat Bone Sialoprotein Gene Promoter in Transgenic Mice (1996)

Bone sialoprotein (BSP) is expressed by differentiated osteoblasts during the initial formation and mineralization of bone matrix. Studies using transgenic mice harboring 2.7 kb of the rat BSP promoter linked to a luciferase reporter gene have shown luciferase activity in bone and other mineralized tissues while most soft tissues tested expressed a much lower level of the reporter gene. To study regulation of the transgene, mice were administered dexamethasone (dex) by intramuscular injection. After 4 h and 24 h, various tissues were dissected from the treated mice as well as from untreated transgenic littermates. Luciferase assays showed that dex stimulated expression of the transgene significantly. In bone tissues, dex increased the average luciferase activity 1.6- to 11-fold compared with control tissues from untreated transgenic mice. The luciferase activity in lung, liver and kidney remained at a low level and showed no increase with dex treatment. In some animals, however, the luciferase activity in brain and skin was also increased after dex administration. These experiments indicate that a transgene comprising 2.7 kb of the rat BSP promoter linked to a luciferase reporter is regulated in a tissue and developmental stage-dependent manner and that glucocorticoid-induced stimulation of BSP gene expression may be mediated within this region of the promoter.
A naming specification language for syntax-directed editors (2003)

A naming specification language, NSL, is described, which supplements existing syntax and semantics specification techniques for syntax-directed editor generation. NSL allows the editor implementor to define language-specific naming and scoping features in terms of a set of high-level abstractions. This facilitates editor generation by requiring considerably less work than either hand coding or specification using techniques more general than NSL. A modified editor-generator kernel architecture is described that efficiently implements the abstractions of NSL. This architecture supports NSL by a naming layer, which supplements the tree structure with graph edges, providing additional paths for semantic information propagation. The principal source of efficiency in this architecture is the direct propagation of incremental semantic evaluation from name declarations to name references. Also described are means by which NSL could be supported using previously proposed techniques for enhancing the performance of the attribute grammar paradigm. >
New attachment formation on teeth with a reduced but healthy periodontal ligament (1985)

The present investigation was undertaken to examine whether a new connective tissue attachment will form on previously periodontitis-involved roots when reduced but healthy periodontal ligament tissue persists following periodontal treatment and the epithelium is prevented from migrating into the wound. In each of 4 monkeys, periodontal tissue breakdown was induced around one maxillary and one mandibular second premolar or first molar by placing orthodontic elastics around the teeth. The elastics were kept in situ until about 50% of the supporting tissues had been lost. 3 months following removal of the elastics, the crowns of the teeth were resected. The pocket epithelium and subjacent granulation tissue were excised and the cementum of the periodontitis-involved part of the roots was removed using a diamond bur. The roots were covered with a mucosal flap. The animals were sacrificed after 3 months of healing. The jaws were removed and histological sections of the experimental roots including their surrounding periodontal tissues were produced. The microscopic analysis disclosed that in all roots, new cementum with inserting collagen fibers had formed in the apical portion of the previously exposed root surfaces. It was always in continuity with the original cementum layer apical to the instrumental part of the root and was thickest in its apical portion, becoming gradually thinner in the coronal direction. In the roots, which for the entire length of the study remained covered by the oral mucosa, the extension in the coronal direction of this newly formed fibrous attachment amounted to an average of 1.0 mm with a range from 0.1 mm to 2.6 mm. These findings were interpreted to mean that new attachment is formed by coronal migration of cells originating from the periodontal ligament.
Synthesis and characterization of new psoralen derivatives with superior photoreactivity with DNA and RNA (1977)

The synthesis of five new psoralen derivatives is described. Three of these, 4'-hydroxymethyl-4,5',8-trimethylpsoralen, 4'-methoxymethyl-4,5',8-trimethylpsoralen, and 4'-aminomethyl-4,5',8-trimethylpsoralen hydrochloride, and characterized with respect to their photoreactivity with DNA and RNA. They are found to be greatly superior to 4,5',8-trimethylpsoralen and 8-methoxypsoralen, the two commonly used psoralens, in their abilities to saturate the photoreactive sites on DNA and RNA without repeated addition of reagent. A simplified mechanism for the photoreaction of psoralens with nucleic acids is presented and provides a basis for understanding the superior properties of these compounds. The compounds have superior reactivity not only with isolated DNA and RNA but also in viruses and in cells. Psoralens are shown for the first time to cross-link RNA double helices.
Geostatistical inversion - a sequential method of stochastic reservoir modelling constrained by seismic data (1994)

In the petroleum industry, the first applications of geostatistical methods appeared with the use of the kriging technique for mapping horizon depths, seismic velocities, layer thicknesses or petrophysical properties such as porosity or permeability (Haas and Viallix 1976). The maps obtained were then used as input to the calculation of volumes of hydrocarbons in place, or to reservoir simulation programmes (Haas and Jousselin 1976).
ACC/AHA/NHLBI CLINICAL ADVISORY ON STATINS ACC/AHA/NHLBI Clinical Advisory on the Use and Safety of Statins (2002)

Preamble................................................................................................567 Introduction..........................................................................................567 Incidence of Adverse Events............................................................568
Hydrogenation of GaN, AlN, and InN (1994)

Hydrogen incorporation depths of ≥1 μm are measured for 2H plasma exposure of GaN and AlN at 250–400 °C for 30 min. The concentration of 2H incorporated is in the range 5–10×1017 cm−3 for GaN and 5–30×1018 cm−3 for AlN under these conditions. No redistribution of the hydrogen is observed for annealing temperatures up to 800 °C, but at 900 °C there is substantial loss of hydrogen from the samples. Similar results are obtained for 2H implantation into GaN, AlN, and InN, with no significant redistribution observed up to 500–600 °C in either AlN or InN, and motion only at 900 °C in GaN. The thermal stability of hydrogen in III-V nitrides explains previous results for Mg-doped GaN grown using NH3, where post-growth annealing at high temperatures was required to achieve appreciable doping efficiencies.
Developmental biology of hematopoiesis (1995)

Abstract The cellular and environmental regulation of hematopoiesis has been generally conserved throughout vertebrate evolution, although subtle species differences exist. The factors that regulate hematopoietic stem cell homeostasis may closely resemble the inducers of embryonic patterning, rather than the factors that stimulate hematopoietic cell proliferation and differentiation. Comparative study of embryonic hematopoiesis in lower vertebrates can generate testable hypotheses that similar mechanisms occur during hematopoiesis in higher species.
Synthesis and characterization of trans-, 13-cis-, and 11-cis, 13-cis-12-(hydroxymethyl)retinol (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and characterization of trans-, 13-cis-, and 11-cis, 13-cis-12-(hydroxymethyl)retinolAnita H. Lewin, Douglas H. Rector, Steven R. Parker, Mansukh C. Wani, and F. Ivy CarrollCite this: J. Org. Chem. 1984, 49, 4, 649–652Publication Date (Print):February 1, 1984Publication History Published online1 May 2002Published inissue 1 February 1984https://pubs.acs.org/doi/10.1021/jo00178a014https://doi.org/10.1021/jo00178a014research-articleACS PublicationsRequest reuse permissionsArticle Views74Altmetric-Citations1LEARN 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