UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network models

UMass Morph Server (UMMS) has been developed for the broad impact on the study of molecular dynamics (MD). The elastic network model (ENM) of a given macromolecule has been proven as a useful tool for analyzing thermal behaviors locally and predicting folding pathways globally. UMMS utilizes coarse-grained ENMs at various levels. These simplifications remarkably save computation time compared with all-atom MD simulations so that one can bring down massive computational problems from a supercomputer to a PC. To improve computational efficiency and physical reality of ENMs, the symmetry-constrained, rigid-cluster, hybrid and chemical-bond ENMs have been developed and implemented at UMMS. One can request both harmonic normal mode analysis of a single macromolecule and anharmonic pathway generation between two conformations of a same molecule using elastic network interpolation at

Multivariate p-dic L-function

We construct multivariate p-adic L-function in the p-adic number fild by using Washington method.Comment: 9 page

Müllerian inhibiting substance/anti-Müllerian hormone: A novel treatment for gynecologic tumors

Müllerian inhibiting substance (MIS), also called anti-Müllerian hormone (AMH), is a member of the transforming growth factor-β super-family of growth and differentiation response modifiers. It is produced in immature Sertoli cells in male embryos and binds to MIS/AMH receptors in primordial Müllerian ducts to cause regression of female reproductive structures that are the precursors to the fallopian tubes, the surface epithelium of the ovaries, the uterus, the cervix, and the upper third of the vagina. Because most gynecologic tumors originate from Müllerian duct-derived tissues, and since MIS/AMH causes regression of the Müllerian duct in male embryos, it is expected to inhibit the growth of gynecologic tumors. Purified recombinant human MIS/AMH causes growth inhibition of epithelial ovarian cancer cells and cell lines in vitro and in vitro via MIS receptor-mediated mechanism. Furthermore, several lines of evidence suggest that MIS/AMH inhibits proliferation in tissues and cell lines of other MIS/AMH receptor-expressing gynecologic tumors such as cervical, endometrial, breast, and in endometriosis as well. These findings indicate that bioactive MIS/AMH recombinant protein should be tested in patients against tumors expressing the MIS/AMH receptor complex, perhaps beginning with ovarian cancer because it has the worst prognosis. The molecular tools to identify MIS/AMH receptor expressing ovarian and other cancers are in place, thus, it is possible to select patients for treatment. An MIS/AMH ELISA exists to follow administered doses of MIS/AMH, as well. Clinical trials await the production of sufficient supplies of qualified recombinant human MIS/AMH for this purpose

Free Vibration of Layered Circular Cylindrical Shells of Variable Thickness Using Spline Function Approximation

Free vibration of layered circular cylindrical shells of variable thickness is studied using spline function approximation by applying a point collocation method. The shell is made up of uniform layers of isotropic or specially orthotropic materials. The equations of motions in longitudinal, circumferential and transverse displacement components, are derived using extension of Love's first approximation theory. The coupled differential equations are solved using Bickley-type splines of suitable order, which are cubic and quintic, by applying the point collocation method. This results in the generalized eigenvalue problem by combining the suitable boundary conditions. The effect of frequency parameters and the corresponding mode shapes of vibration are studied with different thickness variation coefficients, and other parameters. The thickness variations are assumed to be linear, exponential, and sinusoidal along the axial direction. The results are given graphically and comparisons are made with those results obtained using finite element method

NonO Is a Novel Co-factor of PRDM1 and Regulates Inflammatory Response in Monocyte Derived-Dendritic Cells

© Copyright © 2020 Lee, Jang, Tian and Kim. Proper expression of the transcription factor, Positive regulatory domain 1 (PRDM1), is required for maintaining homeostasis of human monocyte derived-dendritic cells (MO-DCs). The molecular mechanisms and gene targets of PRDM1 in B and T lymphocytes have been identified. However, the function of PRDM1 in dendritic cells (DCs) remains unclear. We investigate co-regulators of PRDM1 in MO-DCs identified by mass spectrometry (MS) and co-immunoprecipitation (Co-IP). Notably, non-POU domain-containing octamer-binding protein (NonO) was found to be a PRDM1 binding protein in the nucleus of MO-DCs. NonO is recruited to the PRDM1 binding site in the promoter region of IL-6. Knockdown of NonO expression by siRNA lessened suppression of IL-6 promoter activity by PRMD1 following LPS stimulation. While NonO binding to PRDM1 was observed in human myeloma cell lines, an effect of NonO on IL-6 expression was not observed. Thus, loss of NonO interrupted the inhibitory effect of PRDM1 on IL-6 expression in MO-DCs, but not plasma cells. Moreover, MO-DCs with low expression of PRDM1 or NonO induce an increased number of IL-21-producing TFH-like cells in vitro. These data suggest that low level of PRDM1 and NonO lead to enhanced activation of MO-DCs and the regulation of MO-DC function by PRDM1 is mediated through cell lineage-specific mechanisms

Production and optical properties of liquid scintillator for the JSNS2^{2} experiment

The JSNS$^{2}$ (J-PARC Sterile Neutrino Search at J-PARC Spallation Neutron Source) experiment will search for neutrino oscillations over a 24 m short baseline at J-PARC. The JSNS$^{2}$ inner detector will be filled with 17 tons of gadolinium-loaded liquid scintillator (LS) with an additional 31 tons of unloaded LS in the intermediate $\gamma$-catcher and outer veto volumes. JSNS$^{2}$ has chosen Linear Alkyl Benzene (LAB) as an organic solvent because of its chemical properties. The unloaded LS was produced at a refurbished facility, originally used for scintillator production by the RENO experiment. JSNS$^{2}$ plans to use ISO tanks for the storage and transportation of the LS. In this paper, we describe the LS production, and present measurements of its optical properties and long term stability. Our measurements show that storing the LS in ISO tanks does not result in degradation of its optical properties.Comment: 7 pages, 4 figures

Culture of Sea Cucumbers in Korea: A guide to Korean methods and the local sea cucumber in the Northeast U.S.

A paper exploring the potential to grow Korean sea cucumbers in the Northeast of the United States. This paper examines the life history and biology of the Korean cucumber (Cucumaria Frondosa), Korean hatchery culture techniques, Korean sea cucumber culture process, and the viability of culturing the Korean sea cucumber in the Northeast