gebhart/patrepeval huggingface dataset:
Negative and positive regulation by a short segment in the 5'-flanking region of the human cytomegalovirus major immediate-early gene. (1987)

To analyze the significance of inducible DNase I-hypersensitive sites occurring in the 5'-flanking sequence of the major immediate-early gene of human cytomegalovirus (HCMV), various deleted portions of the HCMV immediate-early promoter regulatory region were attached to the chloramphenicol acetyltransferase (CAT) gene and assayed for activity in transiently transfected undifferentiated and differentiated human teratocarcinoma cells, Tera-2. Assays of progressive deletions in the promoter regulatory region indicated that removal of a 395-base-pair portion of this element (nucleotides -750 to -1145) containing two inducible DNase I sites which correlate with gene expression resulted in a 7.5-fold increase in CAT activity in undifferentiated cells. However, in permissive differentiated Tera-2, human foreskin fibroblast, and HeLa cells, removal of this regulatory region resulted in decreased activity. In addition, attachment of this HCMV upstream element to a homologous or heterologous promoter increased activity three- to fivefold in permissive cells. Therefore, a cis regulatory element exists 5' to the enhancer of the major immediate-early gene of HCMV. This element negative modulates expression in nonpermissive cells but positively influences expression in permissive cells.
Enzymatic inverse PCR: a restriction site independent, single-fragment method for high-efficiency, site-directed mutagenesis. (1992)

A new method is described for rapid site-directed mutagenesis of plasmid DNA. The new method, termed enzymatic inverse polymerase chain reaction (EIPCR), uses inverse PCR to amplify the entire plasmid. The key step to EIPCR is the incorporation of identical class 2s restriction sites in both primers. Class 2s restriction enzymes have a recognition site that is located 5' of the cut site (e.g., BsaI: GGTCTCN'NNNN,). Thus, after completing PCR, the ends of the full-length linearized plasmid are digested with the class 2s enzyme incorporated into the primers. The enzyme cuts off its entire recognition site and leaves the plasmid with compatible overhangs on both ends. Thus, in the ligation the only part that becomes part of the plasmid is the NNNN overhang, which can be made to be the native sequence. We have used the method for many plasmids and several class 2s enzymes. As an example, we report here the use of EIPCR for an insertion into pUC19 containing an inactive lacZ alpha-peptide, causing a frameshift that restores lacZ alpha-activity. Of 300 colonies evaluated, greater than 95% had the expected blue phenotype. The BsaI overhangs were correctly combined in all of the 35 blue colonies analyzed by restriction digestion and in all four clones that were sequenced. EIPCR is compared with four related PCR-based mutagenesis techniques. The major advantage of EIPCR over the other methods is the combination of greater than 95% correctly mutated clones with the need for only two PCR primers.
Chemical Routes for the Transformation of Biomass into Chemicals (2007)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemical Routes for the Transformation of Biomass into ChemicalsAvelino Corma, Sara Iborra, and Alexandra VeltyView Author Information Instituto de Tecnología Química, UPV-CSIC, Universidad Politécnica de Valencia, Avenida de los Naranjos, s/n, Valencia, Spain Cite this: Chem. Rev. 2007, 107, 6, 2411–2502Publication Date (Web):May 30, 2007Publication History Received31 January 2007Published online30 May 2007Published inissue 1 June 2007https://pubs.acs.org/doi/10.1021/cr050989dhttps://doi.org/10.1021/cr050989dresearch-articleACS PublicationsCopyright © 2007 American Chemical SocietyRequest reuse permissionsArticle Views55308Altmetric-Citations5138LEARN 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 SUBJECTS:Alcohols,Carbohydrates,Catalysts,Lipids,Selectivity Get e-Alerts
Interferon Gamma Enhances Clonal Expansion and Survival of CD4 + T Cells (2008)

Interferon-gamma (IFN-gamma) serves numerous functions in the regulation of the immune response. During the early phase of the immune response IFN-gamma is produced by natural killer and natural killer T cells. Although the effects of this cytokine on antigen presenting cells and other cell types are known, its direct role on CD4(+) T cells remains unclear. We demonstrate that CD4(+) T cells exposed to IFN-gamma proliferate more vigorously than the controls in response to signals through the antigen receptor. The increased proliferation of IFN-gamma-treated CD4(+) T cells is not due to enhanced signaling through the antigen receptor, but is accounted for by their increased survival. Our data suggest that enhanced survival of IFN-gamma-treated CD4(+)T cells is independent of signal transducer and activator of transcription 1 (STAT 1), a transcription factor that controls the expression of a variety of IFN-gamma-targeted genes. In addition, we demonstrate that independent of STAT 1, IFN-gamma treatment increases the expression of double-stranded RNA-dependent protein kinase, a kinase involved in regulating protein synthesis. Taken together, our findings suggest a direct role of IFN-gamma on unstimulated CD4(+) T cells that is likely to enhance the advent of adaptive immunity by augmenting their survival during the initiation of the immune response.
Acoustic signatures of crossflow behind casing in commingled reservoirs: A case study from Teapot Dome (2008)

Abstract Cracks and channels in cement often create unwanted conduits behind casing that lead to crossflow between different producing zones. Crossflow results in lost production or aquifer contamination because fluid flows from a higher-pressure to a lower-pressure zone instead of traveling up the well. We present measurements of acoustic signatures of crossflow behind the pipe in time and frequency domains. Despite being called “noise,” they are shown to be propagating tube waves with impulsive signatures. When multiple crossflow locations are present along the well, these signatures are unique for each location and are highly repeatable. We observe time-lapse change in such signatures during air injection and release and suggest that these changes can be used for real-time acoustic characterization of depletion in stacked commingled reservoirs. We anticipate that such signals are typical for commingled production of multilayered reservoirs. Acoustic signatures can be used to characterize crossflow and depletion. In addition, crossflow signals represent a strong noise affecting downhole seismic surveillance with active sources.
Mechanism of activation of an N-ras oncogene of SW-1271 human lung carcinoma cells. (1984)

An N-ras-related transforming gene was detected in the human lung carcinoma cell line SW-1271 and molecularly cloned. The lesion responsible for its acquisition of transforming activity was localized to a single nucleotide transition from A to G in codon 61 of the predicted protein. This lesion in the second exon results in the substitution of arginine for glutamine at this position. These findings, together with previous studies, indicate that the activation of ras oncogenes in human tumors is most commonly due to point mutations at one of two major "hot spots" in the ras coding sequence.
Column Liquid Chromatography (2012)

Saturated compounds, including paraffinic and naphthenic hydrocarbons.2. Aromatic compounds, (containing at least one benzene ring).Their molecules containing one benzene ring are classified as mono-aromatics, those with two aromatic rings as di-aromatics, etc. 3. Resins, including polar substances containing elements other than C and H in the molecule (nitrogen, sulphur and oxygen in particular) 4. Asphaltenes, including polar substances and asphaltenes only soluble in one or two polar solvents such as quinoline , which have large molecular weight and high aromatic ring number.Now analysis methods existed have some deficiencies.Such as GC method can not be used to analyze compounds having high boiling point.The application of high performance liquid chromatography (HPLC) to hydrocarbon group-type analysis is characteristic with its high efficiency, high speed, and high sensitivity.But HPLC is only suitable for analysis of substances soluble in n-pentane [1].TLC-FID [2-3] method can be also used to analysis the THF-soluble party in asphalt-samples and show great advantages.But, the components were combusted during TLC-FID analysis www.intechopen.comChromatography and Its Applications 2 process and this lack made it not suitable for other analysis with preparation fraction.It should be pointed that the conventional method such as ASTM method use amount of solvent is large and some solvents has high toxicity [4,5].Moreover, there are too troublesome for some operation in traditional method.Hence, the separation of products containing heavy components remains a difficult task up to now.Refereeing the literatures [4-10], the authors of this paper establish an optimum CLC method to analyze group-type of heavy oils through a series of studies.This paper detail introduces this method and its many applications which include preparation of high-level road asphalt, the characterization of molecular weight distributions (MWDs) and analysis of heterocyclic aromatic components of heavy oils.
Mechanism of Action of Antitumor Drug Etoposide: A Review (1988)

Metabolism studies of the antitumor drug etoposide show the formation of metabolites in the lactone ring, which are probably not important for the drug's mechanism of action, and oxidative transformations in the dimethoxyphenol ring (E ring), which lead to products that can cause DNA damage and may play a role in the drug's mechanism of action. The cytotoxicity of etoposide is caused by the induction of DNA damage. The occurrence of the DNA lesions can be explained by the capacity of the drug to interfere with the scission-reunion reaction of mammalian topoisomerase II by stabilizing a cleavable complex.
Inducible T cell antigen 4-1BB. Analysis of expression and function (1993)

4-1BB is an inducible receptor-like protein expressed in both cytolytic and Th cells. Optimal induction of 4-1BB mRNA in T cells required both PMA and ionomycin stimulation, indicating that protein kinase C activation and increases in intracellular Ca2+ were required for its expression. 4-1BB was categorized as an early activation gene since the protein synthesis inhibitor, cycloheximide, blocked the induction of 4-1BB mRNA. A rat mAb, 53A2, was generated against recombinant soluble 4-1BB and was used to characterize this molecule. 4-1BB is a 30-kDa glycoprotein and appears to exist as both a monomer and a 55-kDa dimer on the cell surface of a T cell clone. The 4-1BB protein may be post-translationally modified since its predicted backbone is 25 kDa. FACS analysis indicated that 4-1BB was inducible and expressed on the cell surface of activated splenic T cells and thymocytes. Cross-linking of 4-1BB on anti-CD3-stimulated T cells with 53A2 resulted in a dramatic enhancement of T cell proliferation. This suggests that 4-1BB may function as an accessory signaling molecule during T cell activation.
Acidification of endocytic compartments and the intracellular pathways of ligands and receptors (1984)

Several hormones, serum proteins, toxins, and viruses are brought into the cell by receptor-mediated endocytosis. Initially, many of these molecules and particles are internalized into a common endocytic compartment via the clathrin-coated pit pathway. Subsequently, the ligands and receptors are routed to several destinations, including lysosomes, the cytosol, or the plasma membrane. We have examined the mechanism by which sorting of internalized molecules occurs. A key step in the process is the rapid acidification of endocytic vesicles to a pH of 5.0-5.5 This acidification allows dissociation of several ligands from their receptors, the release of iron from transferrin, and the penetration of diphtheria toxin and some viral nucleocapsids into the cytoplasm. Transferrin, a ligand that cycles through the cell with its receptor, has been used as a marker for the recycling receptor pathway. We have found that in Chinese hamster ovary (CHO) cells transferrin is rapidly segregated from other ligands and is routed to a complex of small vesicles and/or tubules near the Golgi apparatus. The pH of the transferrin-containing compartment is approximately 6.4, indicating that it is not in continuity with the more acidic endocytic vesicles which contain ligands destined to be degraded in lysosomes.
Psoriasis patients have T-cells with reduced responsiveness to common mycobacterial antigens (1998)

Heparinised blood samples were obtained from 20 patients with chronic plaque psoriasis and from 13 age-matched healthy controls. After preliminary titration, mononuclear cells separated over Ficoll-Tryoson were cultured for 5 days with 10 microg ml(-1) of 15 mycobacterial preparations, or with pokeweed mitogen and concanavalin A. Stimulation indices were determined for each reagent and means were determined for patients and controls. Results for patients showed a striking reduction of responsiveness to mycobacteria, apparently due to loss of responses to group i, common mycobacterial antigens, and no differences in responses to mitogens. These observations relate psoriasis to certain other diseases, notably mycobacterial infections, rheumatoid arthritis, Chagas' disease and human immunodeficiency virus infection. The observations may be relevant to the aetiology of psoriasis, and to potential immunotherapy for the disease.
Theoretical Studies of Molecular Electronic Transition Lasers (1979)

Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for an ML revolution and have already been profoundly affected by the application of existing ML ...Read More
Role of Nasal Interleukin-8 in Neutrophil Recruitment and Activation in Children With Virus-Induced Asthma (1997)

Neutrophil infiltration is a major feature in the pathogenesis of the common cold, and respiratory viral infection is the major cause of asthma exacerbations. The factors regulating the neutrophil influx are unknown. Interleukin-8 (IL-8) is a potent neutrophil chemoattractant, which has been implicated in several inflammatory diseases. In this study, we investigated the presence of IL-8 chemokine in the nasal aspirates of asthmatic children (n = 12) in whom asthma was precipitated by proven viral infection. There were increased IL-8 levels in nasal aspirates from children during the virus-induced asthma exacerbations compared with samples from the same children when they had been asymptomatic for 2 wk (medians 863 and < 20 pg/ml, respectively, p < 0.01). Biological relevance was shown in that IL-8 levels correlate with increased nasal aspirate neutrophil myeloperoxidase levels and there was also a correlation between myeloperoxidase levels and upper respiratory symptom severity. Furthermore, we purified IL-8 from these samples, and demonstrated biological neutrophil chemotactic activity. These are the first in vivo data to suggest an important role for IL-8 in neutrophil influx in proven upper respiratory viral infection associated with asthma exacerbations. We suggest that IL-8 might provide a target for therapeutic intervention in virus-induced respiratory diseases.
Momelotinib inhibits ACVR1/ALK2, decreases hepcidin production, and ameliorates anemia of chronic disease in rodents (2017)

Patients with myelofibrosis (MF) often develop anemia and frequently become dependent on red blood cell transfusions. Results from a phase 2 study for the treatment of MF with the Janus kinase 1/2 (JAK1/2) inhibitor momelotinib (MMB) demonstrated that MMB treatment ameliorated anemia, which was unexpected for a JAK1/2 inhibitor, because erythropoietin-mediated JAK2 signaling is essential for erythropoiesis. Using a rat model of anemia of chronic disease, we demonstrated that MMB treatment can normalize hemoglobin and red blood cell numbers. We found that this positive effect is driven by direct inhibition of the bone morphogenic protein receptor kinase activin A receptor, type I (ACVR1), and the subsequent reduction of hepatocyte hepcidin production. Of note, ruxolitinib, a JAK1/2 inhibitor approved for the treatment of MF, had no inhibitory activity on this pathway. Further, we demonstrated the effect of MMB is not mediated by direct inhibition of JAK2-mediated ferroportin (FPN1) degradation, because neither MMB treatment nor myeloid-specific deletion of JAK2 affected FPN1 expression. Our data support the hypothesis that the improvement of inflammatory anemia by MMB results from inhibition of ACVR1-mediated hepcidin expression in the liver, which leads to increased mobilization of sequestered iron from cellular stores and subsequent stimulation of erythropoiesis.
Development of an inducible pol III transcription system essentially requiring a mutated form of the TATA-binding protein (2001)

We attempted to devise a transcription system in which a particular DNA sequence of interest could be inducibly expressed under the control of a modified polymerase III (pol III) promoter. Its activation requires a mutated transcription factor not contained endogenously in human cells. We constructed such a promoter by fusing elements of the beta-lactamase gene of Escherichia coli, containing a modified TATA-box and a pol III terminator, to the initiation region of the human U6 gene. This construct functionally resembles a 5'-regulated pol III gene and its transcribed segment can be exchanged for an arbitrary sequence. Its transcription in vitro by pol III requires the same factors as the U6 gene with the major exception that the modified TATA-box of this construct only interacts with a TATA-binding protein (TBP) mutant (TBP-DR2) but not with TBP wild-type (TBPwt). Its transcription therefore requires TBP-DR2 exclusively instead of TBPWT: In order to render the system inducible, we fused the gene coding for TBP-DR2 to a tetracycline control element and stably transfected this new construct into HeLa cells. Induction of such a stable and viable clone with tetracycline resulted in the expression of functional TBP-DR2. This system may conceptually be used in the future to inducibly express an arbitrary DNA sequence in vivo under the control of the above mentioned promoter.
New immunosuppressive drug PNU156804 blocks IL-2-dependent proliferation and NF-kappa B and AP-1 activation. (1999)

We had previously shown that the drug undecylprodigiosin (UP) blocks human lymphocyte proliferation in vitro. We have now investigated the mechanism of action of a new analogue of UP, PNU156804, which shows a more favorable activity profile than UP in mice. We demonstrate here that the biological effect of PNU156804 in vitro is indistinguishable from UP: PNU156804 blocks human T cell proliferation in mid-late G1, as determined by cell cycle analysis, expression of cyclins, and cyclin-dependent kinases and retinoblastoma phosphorylation. In addition, we show that PNU156804 does not block significantly the induction of either IL-2 or IL-2R alpha- and gamma-chains but inhibits IL-2-dependent T cell proliferation. We have investigated several molecular pathways that are known to be activated by IL-2 in T cells. We show that PNU156804 does not inhibit c-myc and bcl-2 mRNA induction. On the other hand, PNU156804 efficiently inhibits the activation of the NF-kappa B and AP-1 transcription factors. PNU156804 inhibition of NF-kappa B activation is due to the inhibition of the degradation of I kappa B-alpha and I kappa B-beta. PNU156804 action is restricted to some signaling pathways; it does not affect NF-kappa B activation by PMA in T cells but blocks that induced by CD40 cross-linking in B lymphocytes. We conclude that the prodigiosin family of immunosuppressants is a new family of molecules that show a novel target specificity clearly distinct from that of other immunosuppressive drugs such as cyclosporin A, FK506, and rapamycin.
Learning-related coordination of striatal and hippocampal theta rhythms during acquisition of a procedural maze task (2007)

The striatum and hippocampus are conventionally viewed as complementary learning and memory systems, with the hippocampus specialized for fact-based episodic memory and the striatum for procedural learning and memory. Here we directly tested whether these two systems exhibit independent or coordinated activity patterns during procedural learning. We trained rats on a conditional T-maze task requiring navigational and cue-based associative learning. We recorded local field potential (LFP) activity with tetrodes chronically implanted in the caudoputamen and the CA1 field of the dorsal hippocampus during 6-25 days of training. We show that simultaneously recorded striatal and hippocampal theta rhythms are modulated differently as the rats learned to perform the T-maze task but nevertheless become highly coherent during the choice period of the maze runs in rats that successfully learned the task. Moreover, in the rats that acquired the task, the phase of the striatal-hippocampal theta coherence was modified toward a consistent antiphase relationship, and these changes occurred in proportion to the levels of learning achieved. We suggest that rhythmic oscillations, including theta-band activity, could influence not only neural processing in cortico-basal ganglia circuits but also dynamic interactions between basal ganglia-based and hippocampus-based forebrain circuits during the acquisition and performance of learned behaviors. Experience-dependent changes in coordination of oscillatory activity across brain structures thus may parallel the well known plasticity of spike activity that occurs as a function of experience.
Single lithium niobate crystal for mode selection and phase modulation in a tunable extended-cavity laser diode (1994)

A 1540-nm external-cavity laser diode with an intracavity electro-optic wavelength tuner is demonstrated. Coarse- and fine-wavelength tuning is achieved with a single lithium niobate wavelength tuner. One section of the crystal is used as a tunable-wavelength filter to tune the wavelength by mode hopping. The other operates as a phase modulator to change the optical length of the cavity and to tune the wavelength continuously. Coarse tuning by mode hopping is obtained over a range of 5.3 nm with a tuning rate of 580 MHz/V. Continuous tuning is obtained over 82% of the free spectral range of the cavity. The wavelength switching time is 10 ns for the cavity used.