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  • Oxford University Press  (87)
  • The Federation of American Societies for Experimental Biology (FASEB)  (16)
  • 2015-2019  (103)
  • 1
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    A long noncoding RNA, lincRNA-Tnfaip3, acts as a coregulator of NF-{kappa}B to modulate inflammatory gene transcription in mouse macrophages [Research] (2017)
    The Federation of American Societies for Experimental Biology (FASEB)
    Details
    Publication Date: 2017-03-01
    Description: Long intergenic noncoding RNAs (lincRNAs) are long noncoding transcripts (〉200 nt) from the intergenic regions of annotated protein-coding genes. We report here that the lincRNA gene lincRNA-Tnfaip3 , located at mouse chromosome 10 proximal to the tumor necrosis factor α-induced protein 3 ( Tnfaip3 ) gene, is an early-primary response gene controlled by nuclear factor-B (NF-B) signaling in murine macrophages. Functionally, lincRNA- Tnfaip3 appears to mediate both the activation and repression of distinct classes of inflammatory genes in macrophages. Specifically, induction of lincRNA-Tnfaip3 is required for the transactivation of NF-B-regulated inflammatory genes in response to bacterial LPSs stimulation. LincRNA-Tnfaip3 physically interacts with the high-mobility group box 1 (Hmgb1), assembling a NF-B/Hmgb1/lincRNA-Tnfaip3 complex in macrophages after LPS stimulation. This resultant NF-B/Hmgb1/lincRNA-Tnfaip3 complex can modulate Hmgb1-associated histone modifications and, ultimately, transactivation of inflammatory genes in mouse macrophages in response to microbial challenge. Therefore, our data indicate a new regulatory role of NF-B-induced lincRNA-Tnfaip3 to act as a coactivator of NF-B for the transcription of inflammatory genes in innate immune cells through modulation of epigenetic chromatin remodeling.—Ma, S., Ming, Z., Gong, A.-Y., Wang, Y., Chen, X., Hu, G., Zhou, R., Shibata, A., Swanson, P. C., Chen, X.-M. A long noncoding RNA, LincRNA-Tnfaip3, acts as a coregulator of NF-B to modulate inflammatory gene transcription in mouse macrophages.
    Print ISSN: 0892-6638
    Electronic ISSN: 1530-6860
    Topics: Biology
    Published by The Federation of American Societies for Experimental Biology (FASEB)
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  • 2
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    Specific recognition of guanines in non-duplex regions of nucleic acids with potassium tungstate and hydrogen peroxide (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-10
    Description: Structural features of nucleic acids have become an integral part of current biomedical research. Highly selective and readily performed methods with little toxicity that target guanosines in non-duplex nucleic acids are needed, which led us to search for an effective agent for guanosine sequencing. Treatment of DNA or RNA with potassium tungstate and hydrogen peroxide produced damaged guanosines in DNA or RNA sequences. The damaged guanosines in non-duplex DNA could be cleaved by hot piperidine. Similarly, damaged guanosines in non-duplex RNA could be cleaved by aniline acetate. We could identify structural features of nucleic acid using this strategy instead of dimethyl sulphate and Ribonuclease T1.
    Keywords: Nucleic acid structure, Phsyical and Biochemical Characterisation of DNA
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Simultaneous seismic data interpolation and denoising with a new adaptive method based on dreamlet transform (2015)
    Oxford University Press
    Details
    Publication Date: 2015-03-29
    Description: Interpolation and random noise removal is a pre-requisite for multichannel techniques because the irregularity and random noise in observed data can affect their performances. Projection Onto Convex Sets (POCS) method can better handle seismic data interpolation if the data's signal-to-noise ratio (SNR) is high, while it has difficulty in noisy situations because it inserts the noisy observed seismic data in each iteration. Weighted POCS method can weaken the noise effects, while the performance is affected by the choice of weight factors and is still unsatisfactory. Thus, a new weighted POCS method is derived through the Iterative Hard Threshold (IHT) view, and in order to eliminate random noise, a new adaptive method is proposed to achieve simultaneous seismic data interpolation and denoising based on dreamlet transform. Performances of the POCS method, the weighted POCS method and the proposed method are compared in simultaneous seismic data interpolation and denoising which demonstrate the validity of the proposed method. The recovered SNRs confirm that the proposed adaptive method is the most effective among the three methods. Numerical examples on synthetic and real data demonstrate the validity of the proposed adaptive method.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 4
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    Anti-IL-6 neutralizing antibody modulates blood-brain barrier function in the ovine fetus [Research Communication] (2015)
    The Federation of American Societies for Experimental Biology (FASEB)
    Details
    Publication Date: 2015-05-01
    Description: Impaired blood-brain barrier function represents an important component of hypoxic-ischemic brain injury in the perinatal period. Proinflammatory cytokines could contribute to ischemia-related blood-brain barrier dysfunction. IL-6 increases vascular endothelial cell monolayer permeability in vitro . However, contributions of IL-6 to blood-brain barrier abnormalities have not been examined in the immature brain in vivo . We generated pharmacologic quantities of ovine-specific neutralizing anti-IL-6 mAbs and systemically infused mAbs into fetal sheep at 126 days of gestation after exposure to brain ischemia. Anti–IL-6 mAbs were measured by ELISA in fetal plasma, cerebral cortex, and cerebrospinal fluid, blood-brain barrier permeability was quantified using the blood-to-brain transfer constant in brain regions, and IL-6, tight junction proteins, and plasmalemma vesicle protein (PLVAP) were detected by Western immunoblot. Anti–IL-6 mAb infusions resulted in increases in mAb ( P 〈 0.05) in plasma, brain parenchyma, and cerebrospinal fluid and decreases in brain IL-6 protein. Twenty-four hours after ischemia, anti–IL-6 mAb infusions attenuated ischemia-related increases in blood-brain barrier permeability and modulated tight junction and PLVAP protein expression in fetal brain. We conclude that inhibiting the effects of IL-6 protein with systemic infusions of neutralizing antibodies attenuates ischemia-related increases in blood-brain barrier permeability by inhibiting IL-6 and modulates tight junction proteins after ischemia.—Zhang, J., Sadowska, G. B., Chen, X., Park, S. Y., Kim, J.-E., Bodge, C. A., Cummings, E., Lim, Y.-P., Makeyev, O., Besio, W. G., Gaitanis, J., Banks, W. A., Stonestreet, B. S. Anti–IL-6 neutralizing antibody modulates blood-brain barrier function in the ovine fetus.
    Print ISSN: 0892-6638
    Electronic ISSN: 1530-6860
    Topics: Biology
    Published by The Federation of American Societies for Experimental Biology (FASEB)
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  • 5
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    Elastic wave finite-difference simulation using discontinuous curvilinear grid with non-uniform time step: two-dimensional case (2015)
    Oxford University Press
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    Publication Date: 2015-04-24
    Description: A discontinuous grid finite-difference (FD) method with non-uniform time step Runge–Kutta scheme on curvilinear collocated-grid is developed for seismic wave simulation. We introduce two transition zones: a spatial transition zone and a temporal transition zone, to exchange wavefield across the spatial and temporal discontinuous interfaces. A Gaussian filter is applied to suppress artificial numerical noise caused by down-sampling the wavefield from the finer grid to the coarser grid. We adapt the non-uniform time step Runge–Kutta scheme to a discontinuous grid FD method for further increasing the computational efficiency without losing the accuracy of time marching through the whole simulation region. When the topography is included in the modelling, we carry out the discontinuous grid method on a curvilinear collocated-grid to obtain a sufficiently accurate free-surface boundary condition implementation. Numerical tests show that the proposed method can sufficiently accurately simulate the seismic wave propagation on such grids and significantly reduce the computational resources consumption with respect to regular grids.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 6
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    Plasma auto-antibodies to angiotensin II receptors are correlated with blood pressure and inflammatory factors in hypertension patients (2015)
    Oxford University Press
    Details
    Publication Date: 2015-03-24
    Description: Auto-antibodies against to angiotensin II type 1 receptor (AT 1 R-AA) have been discovered in patients with hypertension and they have a close relationship with inflammatory factors. However, auto-antibodies to angiotensin II type 2 receptor (AT 2 R-AA) are seldom investigated in hypertension. Subjects ( n = 138) were enrolled and divided into three groups according to their blood pressure levels by using the Seventh Report of the Joint National Committee on Prevention, Detection, Evaluation, and Treatment of High Blood Pressure (JNC-7) criteria: normotensive (≤120/80 mmHg, n = 31), pre-hypertensive (120–139/80–89 mmHg, n = 39), and hypertensive (≥140/90 mmHg, n = 68) groups. Plasma AT 1 R-AAs and AT 2 R-AAs were detected by enzyme-linked immunosorbent assay. Plasma tumour necrosis factor-α (TNF-α), endothelin-1 (ET-1), and angiotensin II (Ang II) were measured by radioimmunity assay. (i) Plasma AT 1 R-AAs were positively correlated with systolic blood pressure (SBP), diastolic blood pressure (DBP), mean arterial pressure (MAP), TNF-α, ET-1, and Ang II. (ii) AT 2 R-AAs were negatively correlated with SBP, DBP, MAP, TNF-α, ET-1, Ang II, as well as uric acid and serum creatinine. (iii) TNF-α, ET-1, Ang II (all P 〈 0.01, when compared with the normotensive group), blood uric acid, and serum creatinine (both P 〈 0.05, when compared with the normotensive group) increased with BP level. (iv) Multiple linear regression analyses showed that age, AT 1 R-AAs, AT 2 R-AAs, and ET-1 were independent predictors for SBP. AT 1 R-AAs, AT 2 R-AAs, and ET-1 were independent predictors for DBP. AT 1 R-AAs, AT 2 R-AAs, ET-1, and Ang II were independent predictors for MAP. Plasma AT 1 R-AAs and AT 2 R-AAs play an important role in hypertension progression. AT 2 R-AAs are inversely related to renal dysfunction.
    Print ISSN: 1520-765X
    Electronic ISSN: 1554-2815
    Topics: Medicine
    Published by Oxford University Press
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  • 7
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    Simultaneous seismic data interpolation and denoising with a new adaptive method based on dreamlet transform (2015)
    Oxford University Press
    Details
    Publication Date: 2015-03-27
    Description: Interpolation and random noise removal is a pre-requisite for multichannel techniques because the irregularity and random noise in observed data can affect their performances. Projection Onto Convex Sets (POCS) method can better handle seismic data interpolation if the data's signal-to-noise ratio (SNR) is high, while it has difficulty in noisy situations because it inserts the noisy observed seismic data in each iteration. Weighted POCS method can weaken the noise effects, while the performance is affected by the choice of weight factors and is still unsatisfactory. Thus, a new weighted POCS method is derived through the Iterative Hard Threshold (IHT) view, and in order to eliminate random noise, a new adaptive method is proposed to achieve simultaneous seismic data interpolation and denoising based on dreamlet transform. Performances of the POCS method, the weighted POCS method and the proposed method are compared in simultaneous seismic data interpolation and denoising which demonstrate the validity of the proposed method. The recovered SNRs confirm that the proposed adaptive method is the most effective among the three methods. Numerical examples on synthetic and real data demonstrate the validity of the proposed adaptive method.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 8
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    A possible formation channel for blue hook stars in globular clusters (2015)
    Oxford University Press
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    Publication Date: 2015-04-04
    Description: The formation mechanism for blue hook (BHk) stars in globular clusters (GCs) is still unclear. Following one of the possible scenarios, called the late hot flash scenario, we propose that a tidally enhanced stellar wind in binary evolution might provide the huge mass loss on the red giant branch (RGB) and produce BHk stars. Employing the detailed stellar evolution code mesa (Modules for Experiments in Stellar Astrophysics), we have investigated the contributions of tidally enhanced stellar wind as a possible formation channel for BHk stars in GCs. We evolved the primary stars with different initial orbital periods using the binary module in mesa (version 6208) from the zero-age main-sequence (ZAMS) to the post-horizontal branch (HB) stage, and obtained their evolution parameters, which are compared with the observation. The results are consistent with observations in the colour–magnitude diagram and the log g – T eff plane for NGC 2808, which is an example GC hosting BHk stars. However, the helium abundance in the surface for our models is higher than the one obtained in BHk stars. This discrepancy between our models and observations is possibly due to the fact that gravitational settling and radiative levitation, which are common processes in hot HB stars, are not considered in the models as well as the fact that the flash mixing efficiency might be overestimated in the calculations. Our results suggest that tidally enhanced stellar wind in binary evolution is able to naturally provide the huge mass loss on the RGB needed for the late hot flash scenario, and it is a possible and reasonable formation channel for BHk stars in GCs.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 9
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    Prothymosin {alpha} Variants Isolated From CD8+ T Cells and Cervicovaginal Fluid Suppress HIV-1 Replication Through Type I Interferon Induction (2015)
    Oxford University Press
    Details
    Publication Date: 2015-04-11
    Description: Soluble factors from CD8 + T cells and cervicovaginal mucosa of women are recognized as important in controlling human immunodeficiency virus type 1 (HIV-1) infection and transmission. Previously, we have shown the strong anti-HIV-1 activity of prothymosin α (ProTα) derived from CD8 + T cells. ProTα is a small acidic protein with wide cell distribution, to which several functions have been ascribed, depending on its intracellular or extracellular localization. To date, activities of ProTα have been attributed to a single protein known as isoform 2. Here we report the isolation and identification of 2 new ProTα variants from CD8 + T cells and cervicovaginal lavage with potent anti-HIV-1 activity. The first is a splice variant of the ProTα gene, known as isoform CRA_b, and the second is the product of a ProTα gene, thus far classified as a pseudogene 7. Native or recombinant ProTα variants potently restrict HIV-1 replication in macrophages through the induction of type I interferon. The baseline expression of interferon-responsive genes in primary human cervical tissues positively correlate with high levels of intracellular ProTα, and the knockdown of ProTα variants by small interfering RNA leads to downregulation of interferon target genes. Overall, these findings suggest that ProTα variants are innate immune mediators involved in immune surveillance.
    Print ISSN: 0022-1899
    Electronic ISSN: 1537-6613
    Topics: Medicine
    Published by Oxford University Press on behalf of The Infectious Diseases Society of America (IDSA).
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  • 10
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    Diagnostic studies in sufficient dimension reduction (2015)
    Oxford University Press
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    Publication Date: 2015-08-21
    Description: Sufficient dimension reduction in regression aims to reduce the predictor dimension by replacing the original predictors with some set of linear combinations of them without loss of information. Numerous dimension reduction methods have been developed based on this paradigm. However, little effort has been devoted to diagnostic studies within the context of dimension reduction. In this paper we introduce methods to check goodness-of-fit for a given dimension reduction subspace. The key idea is to extend the so-called distance correlation to measure the conditional dependence relationship between the covariates and the response given a reduction subspace. Our methods require minimal assumptions, which are usually much less restrictive than the conditions needed to justify the original methods. Asymptotic properties of the test statistic are studied. Numerical examples demonstrate the effectiveness of the proposed approach.
    Print ISSN: 0006-3444
    Electronic ISSN: 1464-3510
    Topics: Biology , Mathematics , Medicine
    Published by Oxford University Press
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