Acoustic Wave Backscattering In A Random Inhomogeneous Ocean Sediment

The backscattering of sound by inhomogeneities of the ocean sediment may provide a remarkable effect on underwater acoustic wave propagation. It may also be used as a means of remotely estimating complicated sediment properties. In this paper, a theoretical model of acoustic waves backscattered from an inhomogeneous sediment is formulated based on the Born approximation. The model not only contains the formal homogeneous bottom case but is also extended to the more realistic stratified bottom case. A complex wavenumber, in which an attenuation coefficient is introduced, reveals significant changes of the penetration depth within the sediment. The model predicts that for the stratified bottom, the backscattering strength is rapidly oscillating and decreases sharply at small grazing angles owing to the refraction of the waves caused by the sound velocity gradient. In order to reduce the number of independent variables, Biot's theory is applied to relate three-dimensional density fluctuations to sound speed fluctuations through porosity. A transverse-isotropic model is also developed to access the three-dimensional sound speed fluctuation spectrum. Geoacoustic surface and cross-hole tomographic data acquired from different sites characterizing sandy and silty bottoms are used to obtain three-dimensional sediment volume inhomogeneities. Backscattering strengths are evaluated for those bottom cases. The results agree with intuition and other published data

Modeling and inversion techniques for three-dimensional geoelectrical surveys

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences, 1998.Includes bibliographical references (leaves 196-210).by Weiqun Shi.Ph.D

Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails

<p>Abstract</p> <p>Background</p> <p>Brd2 is a transcriptional regulator and belongs to BET family, a less characterized novel class of bromodomain-containing proteins. Brd2 contains two tandem bromodomains (BD1 and BD2, 46% sequence identity) in the N-terminus and a conserved motif named ET (extra C-terminal) domain at the C-terminus that is also present in some other bromodomain proteins. The two bromodomains have been shown to bind the acetylated histone H4 and to be responsible for mitotic retention on chromosomes, which is probably a distinctive feature of BET family proteins. Although the crystal structure of Brd2 BD1 is reported, no structure features have been characterized for Brd2 BD2 and its interaction with acetylated histones.</p> <p>Results</p> <p>Here we report the solution structure of human Brd2 BD2 determined by NMR. Although the overall fold resembles the bromodomains from other proteins, significant differences can be found in loop regions, especially in the ZA loop in which a two amino acids insertion is involved in an uncommon <it>π</it>-helix, termed <it>π</it>D. The helix <it>π</it>D forms a portion of the acetyl-lysine binding site, which could be a structural characteristic of Brd2 BD2 and other BET bromodomains. Unlike Brd2 BD1, BD2 is monomeric in solution. With NMR perturbation studies, we have mapped the H4-AcK12 peptide binding interface on Brd2 BD2 and shown that the binding was with low affinity (2.9 mM) and in fast exchange. Using NMR and mutational analysis, we identified several residues important for the Brd2 BD2-H4-AcK12 peptide interaction and probed the potential mechanism for the specific recognition of acetylated histone codes by Brd2 BD2.</p> <p>Conclusion</p> <p>Brd2 BD2 is monomeric in solution and dynamically interacts with H4-AcK12. The additional secondary elements in the long ZA loop may be a common characteristic of BET bromodomains. Surrounding the ligand-binding cavity, five aspartate residues form a negatively charged collar that serves as a secondary binding site for H4-AcK12. We suggest that Brd2 BD1 and BD2 may possess distinctive roles and cooperate to regulate Brd2 functions. The structure basis of Brd2 BD2 will help to further characterize the functions of Brd2 and its BET members.</p

The Investigation of Virginiamycin-Added Fungal Fermentation on the Size and Immunoreactivity of Heat-Sensitive Soy Protein

Citation: Chen, L. Y., Vadlani, P. V., Madl, R. L., Wang, W. Q., Shi, Y. C., & Gibbons, W. R. (2015). The Investigation of Virginiamycin-Added Fungal Fermentation on the Size and Immunoreactivity of Heat-Sensitive Soy Protein. International Journal of Polymer Science, 7. doi:10.1155/2015/682596The usage of soy protein for young monogastric animals is restricted due to potential allergens and high molecular weight. The investigation of fungi fermentation effect on soy protein has been interrupted by substrate sterilization. Virginiamycin at 0.05% was added together with Aspergillus oryzae for solid state fermentation (SSF) in unsterilized soymeal (SM). When compared to A. oryzae SSF alone, virginiamycin did not cause the interference of fungal fermentation but elucidated the protein degradation. SDS-PAGE results showed that both alpha and alpha' subunits of beta-conglycinin were degraded significantly. In addition, western blot results showed that the immunoreactive signals of soy protein were considerably reduced in virginiamycin-added fermentation with unsterilized SM. Furthermore, fungal fermentation increased total protein and essential amino acid contents, suggesting the value enhancement of SM products. Taken together, this study demonstrated for the first time that virginiamycin could help investigate fermentation effect on heat-sensitive soy protein. Fermented SM has several potential applications in feed industry

3-D Spectral Induced Polarization (IP) Imaging: Non-Invasive Characterization Of Contaminant Plumes

The overall objective of this project is to develop the scientific basis for characterizing contaminant plumes in the earth's subsurface using field measurements of induced polarization (IP) effects. Three specific objectives towards this end are 1. 2. 3. Understanding IP at the laboratory level through measurements of complex resistivity as a function of frequency in rock and soil samples with varying pore geometries, pore fluid conductivities and saturations, and contaminant chemistries and concentrations. Developing effective data acquisition techniques for measuring the critical IP responses (time domain or frequency domain) in the field. Developing modeling and inversion algorithms that permit the interpretation of field IP data in terms of subsurface geology and contaminant plume properties

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival

Foreword to the special virtual issue on Actinide physics and chemistry with synchrotron radiation

Foreword to the virtual special issue of Journal of Synchrotron Radiation on Actinide Physics and Chemistry with Synchrotron Radiation