Accelerating Atomic Orbital-based Electronic Structure Calculation via Pole Expansion and Selected Inversion

We describe how to apply the recently developed pole expansion and selected inversion (PEXSI) technique to Kohn-Sham density function theory (DFT) electronic structure calculations that are based on atomic orbital discretization. We give analytic expressions for evaluating the charge density, the total energy, the Helmholtz free energy and the atomic forces (including both the Hellman-Feynman force and the Pulay force) without using the eigenvalues and eigenvectors of the Kohn-Sham Hamiltonian. We also show how to update the chemical potential without using Kohn-Sham eigenvalues. The advantage of using PEXSI is that it has a much lower computational complexity than that associated with the matrix diagonalization procedure. We demonstrate the performance gain by comparing the timing of PEXSI with that of diagonalization on insulating and metallic nanotubes. For these quasi-1D systems, the complexity of PEXSI is linear with respect to the number of atoms. This linear scaling can be observed in our computational experiments when the number of atoms in a nanotube is larger than a few hundreds. Both the wall clock time and the memory requirement of PEXSI is modest. This makes it even possible to perform Kohn-Sham DFT calculations for 10,000-atom nanotubes with a sequential implementation of the selected inversion algorithm. We also perform an accurate geometry optimization calculation on a truncated (8,0) boron-nitride nanotube system containing 1024 atoms. Numerical results indicate that the use of PEXSI does not lead to loss of accuracy required in a practical DFT calculation

X-ray absorption of liquid water by advanced ab initio methods

Oxygen K-edge X-ray absorption spectra of liquid water are computed based on the configurations from advanced ab initio molecular dynamics simulations, as well as an electron excitation theory from the GW method. One one hand, the molecular structures of liquid water are accurately predicted by including both van der Waals interactions and hybrid functional (PBE0). On the other hand, the dynamic screening effects on electron excitation are approximately described by the recently developed enhanced static Coulomb hole and screened exchange approximation by Kang and Hybertsen [Phys. Rev. B 82, 195108 (2010)]. The resulting spectra of liquid water are in better quantitative agreement with the experimental spectra due to the softened hydrogen bonds and the slightly broadened spectra originating from the better screening model.Comment: 10 pages, 5 figures, accepted by Phys. Rev.

Time scales of epidemic spread and risk perception on adaptive networks

Incorporating dynamic contact networks and delayed awareness into a contagion model with memory, we study the spreading patterns of infectious diseases in connected populations. It is found that the spread of an infectious disease is not only related to the past exposures of an individual to the infected but also to the time scales of risk perception reflected in the social network adaptation. The epidemic threshold $p_{c}$ is found to decrease with the rise of the time scale parameter s and the memory length T, they satisfy the equation $p_{c} =\frac{1}{T}+ \frac{\omega T}{a^s(1-e^{-\omega T^2/a^s})}$. Both the lifetime of the epidemic and the topological property of the evolved network are considered. The standard deviation $\sigma_{d}$ of the degree distribution increases with the rise of the absorbing time $t_{c}$, a power-law relation $\sigma_{d}=mt_{c}^\gamma$ is found

Diffuse Optical Measurements of Head and Neck Tumor Hemodynamics for Early Prediction of Chemoradiation Therapy Outcomes

This study used a hybrid near-infrared diffuse optical instrument to monitor tumor hemodynamic responses to chemoradiation therapy for early prediction of treatment outcomes in patients with head and neck cancer. Forty-seven patients were measured once per week to evaluate the hemodynamic status of clinically involved cervical lymph nodes as surrogates for the primary tumor response. Patients were classified into two groups: complete response (CR) (n = 29) and incomplete response (IR) (n = 18). Tumor hemodynamic responses were found to be associated with clinical outcomes (CR/IR), wherein the associations differed depending on human papillomavirus (HPV-16) status. In HPV-16 positive patients, significantly lower levels in tumor oxygenated hemoglobin concentration ([HbO2]) at weeks 1 to 3, total hemoglobin concentration at week 3, and blood oxygen saturation (StO2) at week 3 were found in the IR group. In HPV-16 negative patients, significantly higher levels in tumor blood flow index and reduced scattering coefficient (μ′s) at week 3 were observed in the IR group. These hemodynamic parameters exhibited significantly high accuracy for early prediction of clinical outcomes, within the first three weeks of therapy, with the areas under the receiver operating characteristic curves (AUCs) ranging from 0.83 to 0.96

Pleural aspergillosis complicated by recurrent pneumothorax: a case report

<p>Abstract</p> <p>Introduction</p> <p>Pneumothorax as the first symptom of pleural aspergillosis is rare.</p> <p>Case presentation</p> <p>A 31-year-old asthmatic Chinese man presented with recurrent spontaneous pneumothorax and underwent lobectomy due to persistent air leakage. Aspergillus was detected histopathologically in the visceral pleural cavity. He was treated with itraconazole at 200 mg a day, and nine months later he had no recurrent pneumothorax or aspergillus infection.</p> <p>Conclusion</p> <p>Recurrent pneumothorax may be a rare manifestation of aspergillus infection. Aspergillus species infection should be considered in the differential diagnosis of recurrent pneumothorax patients, particularly those with chronic lung disease.</p

Observational constraints on holographic dark energy with varying gravitational constant

We use observational data from Type Ia Supernovae (SN), Baryon Acoustic Oscillations (BAO), Cosmic Microwave Background (CMB) and observational Hubble data (OHD), and the Markov Chain Monte Carlo (MCMC) method, to constrain the cosmological scenario of holographic dark energy with varying gravitational constant. We consider both flat and non-flat background geometry, and we present the corresponding constraints and contour-plots of the model parameters. We conclude that the scenario is compatible with observations. In 1$\sigma$ we find $\Omega_{\Lambda0}=0.72^{+0.03}_{-0.03}$, $\Omega_{k0}=-0.0013^{+0.0130}_{-0.0040}$, $c=0.80^{+0.19}_{-0.14}$ and $\Delta_G\equiv G'/G=-0.0025^{+0.0080}_{-0.0050}$, while for the present value of the dark energy equation-of-state parameter we obtain $w_0=-1.04^{+0.15}_{-0.20}$.Comment: 12 pages, 2 figures, version published in JCA

S-adenosylmethionine and methylthioadenosine are antiapoptotic in cultured rat hepatocytes but proapoptotic in human hepatoma cells

S-adenosylmethionine (AdoMet) is an essential compound in cellular transmethylation reactions and a precursor of polyamine and glutathione synthesis in the liver. In liver injury, the synthesis of AdoMet is impaired and its availability limited. AdoMet administration attenuates experimental liver damage, improves survival of alcoholic patients with cirrhosis, and prevents experimental hepatocarcinogenesis. Apoptosis contributes to different liver injuries, many of which are protected by AdoMet. The mechanism of AdoMet's hepatoprotective and chemopreventive effects are largely unknown. The effect of AdoMet on okadaic acid (OA)-induced apoptosis was evaluated using primary cultures of rat hepatocytes and human hepatoma cell lines. AdoMet protected rat hepatocytes from OA-induced apoptosis dose dependently. It attenuated mitochondrial cytochrome c release, caspase 3 activation, and poly(ADP-ribose) polymerase cleavage. These effects were independent from AdoMet-dependent glutathione synthesis, and mimicked by 5'-methylthioadenosine (MTA), which is derived from AdoMet. Interestingly, AdoMet and MTA did not protect HuH7 cells from OA-induced apoptosis; conversely both compounds behaved as proapoptotic agents. AdoMet's proapoptotic effect was dose dependent and observed also in HepG2 cells. In conclusion, AdoMet exerts opposing effects on apoptosis in normal versus transformed hepatocytes that could be mediated through its conversion to MTA. These effects may participate in the hepatoprotective and chemopreventive properties of this safe and well-tolerated drug

Impaired liver regeneration in mice lacking methionine adenosyltransferase 1A

Methionine adenosyltransferase (MAT) is an essential enzyme because it catalyzes the formation of S-adenosylmethionine (SAMe), the principal biological methyl donor. Of the two genes that encode MAT, MAT1A is mainly expressed in adult liver and MAT2A is expressed in all extrahepatic tissues. Mice lacking MAT1A have reduced hepatic SAMe content and spontaneously develop hepatocellular carcinoma. The current study examined the influence of chronic hepatic SAMe deficiency on liver regeneration. Despite having higher baseline hepatic staining for proliferating cell nuclear antigen, MAT1A knockout mice had impaired liver regeneration after partial hepatectomy (PH) as determined by bromodeoxyuridine incorporation. This can be explained by an inability to up-regulate cyclin D1 after PH in the knockout mice. Upstream signaling pathways involved in cyclin D1 activation include nuclear factor kappaB (NFkappaB), the c-Jun-N-terminal kinase (JNK), extracellular signal-regulated kinases (ERKs), and signal transducer and activator of transcription-3 (STAT-3). At baseline, JNK and ERK are more activated in the knockouts whereas NFkappaB and STAT-3 are similar to wild-type mice. Following PH, early activation of these pathways occurred, but although they remained increased in wild-type mice, c-jun and ERK phosphorylation fell progressively in the knockouts. Hepatic SAMe levels fell progressively following PH in wild-type mice but remained unchanged in the knockouts. In culture, MAT1A knockout hepatocytes have higher baseline DNA synthesis but failed to respond to the mitogenic effect of hepatocyte growth factor. Taken together, our findings define a critical role for SAMe in ERK signaling and cyclin D1 regulation during regeneration and suggest chronic hepatic SAMe depletion results in loss of responsiveness to mitogenic signals

The transcriptional coactivator TAZ regulates reciprocal differentiation of T(h)17 cells and T(reg) cells

自身免疫性疾病是一类机体对自身抗原发生免疫反应而导致自身多器官、组织受累的慢性炎症性疾病。目前大量研究表明机体内促炎症的TH17细胞和抑制炎症Treg细胞在类群数量和活化状态的失衡是造成自身免疫疾病的主要致病因素。陈兰芬教授和周大旺教授团队的前期研究发现小鼠中Hippo信号通路中激酶Mst1/2缺失导致免疫缺陷，机体易受病原体感染并伴随着严重自身免疫疾病。该研究揭示了Hippo 信号通路转录共激活因子TAZ在决定CD4+初始T细胞分化为促进炎症的TH17效应细胞和抑制免疫反应的Treg调节性细胞过程中发挥着关键作用，拓展了当前对于Hippo信号通路的相关研究内容。 陈兰芬，博士，厦门大学生命科学学院教授。【Abstraact】An imbalance in the lineages of immunosuppressive regulatory T cells (Treg cells) and the inflammatory TH17 subset of helper T cells leads to the development of autoimmune and/or inflammatory disease. Here we found that TAZ, a coactivator of TEAD transcription factors of Hippo signaling, was expressed under T H17 cell–inducing conditions and was required for TH17 differentiation and TH17 cell–mediated inflammatory diseases. TAZ was a critical co-activator of the TH17-defining transcription factor RORγt. In addition, TAZ attenuated Treg cell development by decreasing acetylation of the Treg cell master regulator Foxp3 mediated by the histone acetyltransferase Tip60, which targeted Foxp3 for proteasomal degradation. In contrast, under T regcell–skewing conditions, TEAD1 expression and sequestration of TAZ from the transcription factors RORγt and Foxp3 promoted Treg cell differentiation. Furthermore, deficiency in TAZ or overexpression of TEAD1 induced Treg cell differentiation, whereas expression of a transgene encoding TAZ or activation of TAZ directed TH17 cell differentiation. Our results demonstrate a pivotal role for TAZ in regulating the differentiation of Treg cells and TH17 cells.J. Avruch for comments on the manuscript.Supported by the National Basic Research Program (973) of China (2015CB910502 to L.C.), the National Natural Science Foundation of China (81422018 to L.C.; 31625010 and U1505224 to D.Z.; U1405225 and 81372617 to L.C.; J1310027 to D.Z.; 81472229 to L.H.; and 31600698 to J. Geng), the 111 Projects (B12001 and B06016), China's 1000 Young Talents Program (D.Z., and L.C.), the Fundamental Research Funds for the Central Universities of China-Xiamen University (20720160071 to D.Z. and 20720160054 to L.H.) and Major disease research projects of Xiamen (3502Z20149029 to L.C.)