A meshless, high-order integral equation method for smooth surfaces, with application to biomolecular electrostatics

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2006.Includes bibliographical references (p. 87-97).In this thesis, we develop methods for efficient simulation of biomolecular electrostatics based on Poisson-Boltzmann equation. Current techniques using finite-difference solution of differential formulation have many drawbacks. We present an integral formulation that resolves these difficulties and enables an efficient implementation using a recently developed fast solver. The new approach can solve practical engineering problems with good accuracy, but only with an aid of a high quality mesh generator, and sometimes require a large number of panels to discretize a surface. To this end, a novel approach to discretize singular integral equations is proposed. Unlike the traditional boundary element method using panel discretization, the new method is meshless and capable of achieving spectral convergence: numerical errors decrease exponentially fast with increasing size of basis set. We will describe a number of techniques in our approach, including the use of global, high order basis, quadrature-based panel integration, and innovative surface representation. The biomolecular problem is particularly suited for this method because molecular surfaces are typically smooth and can be represented globally using spherical harmonics.(cont.) The use of flat panels in the traditional approach would incur significant geometrical distortion, in addition to much slower convergence rate. Computational results demonstrate that for a practical problem at engineering accuracy (a tolerance of 10¡3) this new approach requires one to two orders of magnitude fewer unknowns than a flat panel method. For a more stringent tolerance of 10¡6, a comparison to an analytically solvable problem reveals that an improvement more than three orders of magnitude has been achieved.by Shih-Hsien Kuo.Ph.D

EVALUATION OF ELBOW AND FOREARM MOTION BETWEEN SIDEARM AND OVERHAND PITCHING

This study is to analyze the differences in kinematics, electromyography (EMG) and ultrasonography between two types of pitchers. We intend to observe and simulate the muscles around glenohumeral and elbow joints in different pitching motions and hope to discover the connections and differences in between. 12 pitchers from the top level were recruited. Larger elbow flexion was found in sidearm pitchers during the acceleration phase. Decrease of the distance of nerve to medial epicondyle was also found as the elbow moved to a more flexed position. More anterior translation of the ulnar nerve might occur during acceleration phase. Slightly lower flexor carpi radialis (FCR) activity was displayed in sidearm pitchers, showing that FCR might play a less crucial role in protecting medial elbow by providing less varus torque

Hesperetin, a Selective Phosphodiesterase 4 Inhibitor, Effectively Suppresses Ovalbumin-Induced Airway Hyperresponsiveness without Influencing Xylazine/Ketamine-Induced Anesthesia

Hesperetin, a selective phosphodiesterase (PDE)4 inhibitor, is present in the traditional Chinese medicine, “Chen Pi.” Therefore, we were interested in investigating its effects on ovalbumin- (OVA-) induced airway hyperresponsiveness, and clarifying its rationale for ameliorating asthma and chronic obstructive pulmonary disease (COPD). Hesperetin was revealed to have a therapeutic (PDE4H/PDE4L) ratio of >11. Hesperetin (10 ~ 30 μmol/kg, intraperitoneally (i.p.)) dose-dependently and significantly attenuated the airway hyperresponsiveness induced by methacholine. It also significantly suppressed the increases in total inflammatory cells, macrophages, lymphocytes, neutrophils, and eosinophils, and levels of cytokines, including interleukin (IL)-2, IL-4, IL-5, interferon-γ, and tumor necrosis factor-α in bronchoalveolar lavage fluid (BALF). It dose-dependently and significantly suppressed total and OVA-specific immunoglobulin E levels in the BALF and serum. However, hesperetin did not influence xylazine/ketamine-induced anesthesia, suggesting that hesperetin has few or no emetic effects. In conclusion, the rationales for ameliorating allergic asthma and COPD by hesperetin are anti-inflammation, immunoregulation, and bronchodilation

Relationships among Constitution, Stress, and Discomfort in the First Trimester

The purpose of this study was to explore correlations among constitution, stress, and discomfort symptoms during the first trimester of pregnancy. We adopted a descriptive and correlational research design and collected data from 261 pregnant women during their first trimester in southern Taiwan using structured questionnaires. Results showed that (1) stress was significantly and positively correlated with Yang-Xu, Yin-Xu, and Tan-Shi-Yu-Zhi constitutions, respectively; (2) Yin-Xu and Tan-Shi-Yu-Zhi constitutions had significant correlations with all symptoms of discomfort, while Yang-Xu had significant correlations with all symptoms of discomfort except for “running nose”; (3) Tan-Shi-Yu-Zhi constitution and stress were two indicators for “fatigue”; Tan-Shi-Yu-Zhi was the indicator for “nausea”; Yang-Xu and Yin-Xu were indicators for “frequent urination.” Our findings also indicate that stress level affects constitutional changes and that stress and constitutional change affect the incidence of discomfort. This research can help healthcare professionals observe these discomforts and provide individualized care for pregnant women, to nurture pregnant women into neutral-type constitution, minimize their levels of discomfort, and promote the health of the fetus and the mother

RSC96 Schwann Cell Proliferation and Survival Induced by Dilong through PI3K/Akt Signaling Mediated by IGF-I

Schwann cell proliferation is critical for the regeneration of injured nerves. Dilongs are widely used in Chinese herbal medicine to remove stasis and stimulate wound-healing functions. Exactly how this Chinese herbal medicine promotes tissue survival remains unclear. The aim of the present study was to investigate the molecular mechanisms by which Dilong promote neuron regeneration. Our results show that treatment with extract of Dilong induces the phosphorylation of the insulin-like growth factor-I (IGF-I)-mediated phosphatidylinositol 3-kinase/serine-threonine kinase (PI3K/Akt) pathway, and activates protein expression of cell nuclear antigen (PCNA) in a time-dependent manner. Cell cycle analysis showed that G1 transits into the S phase in 12–16 h, and S transits into the G2 phase 20 h after exposure to earthworm extract. Strong expression of cyclin D1, cyclin E and cyclin A occurs in a time-dependent manner. Small interfering RNA (siRNA)-mediated knockdown of PI3K significantly reduced PI3K protein expression levels, resulting in Bcl2 survival factor reduction and a marked blockage of G1 to S transition in proliferating cells. These results demonstrate that Dilong promotes the proliferation and survival of RSC96 cells via IGF-I signaling. The mechanism is mainly dependent on the PI3K protein

Dichlorido{(E)-2,4,6-trimethyl-N-[phen­yl(2-pyridyl)methyl­idene]aniline-κ2 N,N′}palladium(II)

The title complex, [PdCl2(C21H20N2)], contains a PdII atom in a slightly distorted square-planar coordination environment defined by two N atoms from one 2,4,6-trimethyl-N-[phen­yl(2-pyrid­yl)methyl­idene]aniline ligand and two Cl atoms, forming a five-membered ring (N—Pd—N—C—C)

Morphological and Molecular Defects in Human Three-Dimensional Retinal Organoid Model of X-Linked Juvenile Retinoschisis

X-linked juvenile retinoschisis (XLRS), linked to mutations in the RS1 gene, is a degenerative retinopathy with a retinal splitting phenotype. We generated human induced pluripotent stem cells (hiPSCs) from patients to study XLRS in a 3D retinal organoid in vitro differentiation system. This model recapitulates key features of XLRS including retinal splitting, defective retinoschisin production, outer-segment defects, abnormal paxillin turnover, and impaired ER-Golgi transportation. RS1 mutation also affects the development of photoreceptor sensory cilia and results in altered expression of other retinopathy-associated genes. CRISPR/Cas9 correction of the disease-associated C625T mutation normalizes the splitting phenotype, outer-segment defects, paxillin dynamics, ciliary marker expression, and transcriptome profiles. Likewise, mutating RS1 in control hiPSCs produces the disease-associated phenotypes. Finally, we show that the C625T mutation can be repaired precisely and efficiently using a base-editing approach. Taken together, our data establish 3D organoids as a valid disease model

Transcriptome analysis of Dnmt3l knock-out mice derived multipotent mesenchymal stem/stromal cells during osteogenic differentiation

Multipotent mesenchymal stem/stromal cells (MSCs) exhibit great potential for cell-based therapy. Proper epigenomic signatures in MSCs are important for the maintenance and the subsequent differentiation potential. The DNA methyltransferase 3-like (DNMT3L) that was mainly expressed in the embryonic stem (ES) cells and the developing germ cells plays an important role in shaping the epigenetic landscape. Here, we report the reduced colony forming ability and impaire