Density matrix based time-dependent density functional theory and the solution of its linear response in real time domain

A density matrix based time-dependent density functional theory is extended in the present work. Chebyshev expansion is introduced to propagate the linear response of the reduced single-electron density matrix upon the application of a time-domain δ -type external potential. The Chebyshev expansion method is more efficient and accurate than the previous fourth-order Runge-Kutta method and removes a numerical divergence problem. The discrete Fourier transformation and filter diagonalization of the first-order dipole moment are implemented to determine the excited state energies. It is found that the filter diagonalization leads to highly accurate values for the excited state energies. Finally, the density matrix based time-dependent density functional is generalized to calculate the energies of singlet-triplet excitations. © 2007 American Institute of Physics.published_or_final_versio

Long-term Variability Properties and Periodicity Analysis for Blazars

In this paper, the compiled long-term optical and infrared measurements of some blazars are used to analyze the variation properties and the optical data are used to search for periodicity evidence in the lightcurve by means of the Jurkevich technique and the discrete correlation function (DCF) method. Following periods are found: 4.52-year for 3C 66A; 1.56 and 2.95 years for AO 0235+164; 14.4, 18.6 years for PKS 0735+178; 17.85 and 24.7 years for PKS 0754+100; 5.53 and 11.75 for OJ 287. 4.45, and 6.89 years for PKS 1215; 9 and 14.84 years for PKS 1219+285; 2.0, 13.5 and 22.5 for 3C273; 7.1 year for 3C279; 6.07 for PKS 1308+326; 3.0 and 16.5 years for PKS 1418+546; 2.0 and 9.35 years for PKS 1514-241; 18.18 for PKS 1807+698; 4.16 and 7.0 for 2155-304; 14 and 20 years for BL Lacertae. Some explanations have been discussed.Comment: 10 pages, 2 table, no figure, a proceeding paper for Pacific Rim Conference on Stellar Astrophysics, Aug. 1999, HongKong, Chin

Incremental anisotropic damage theory and its numerical analysis

2004-2005 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

Resection of phaeochromocytoma extending into the right atrium in a patient with multiple endocrine neoplasia type 2A

We report the first case of successful surgical resection of a malignant phaeochromocytoma with tumour extension into vena cava and right atrium in a patient with multiple endocrine neoplasia type 2A. A 21-year-old woman with genetic confirmation of multiple endocrine neoplasia type 2A syndrome was diagnosed with a very rare case of malignant phaeochromocytoma with tumour thrombus extension into vena cava and right atrium causing Budd-Chiari syndrome. It posed a challenge to the surgeons with regard to complete tumour resection and vascular control. Reviewing the limited literature, surgical resection by means of cardiopulmonary bypass with hypothermic circulatory arrest has been reported with success in phaeochromocytoma with advance vascular involvement. Adopting this approach, adrenalectomy with complete thrombus excision by inferior vena cava exploration and right atriotomy were performed successfully by a multidisciplinary team.published_or_final_versio

Identification and characterization of tropomyosin 3 associated with granulin-epithelin precursor in human hepatocellular carcinoma

Background and Aim: Granulin-epithelin precursor (GEP) has previously been reported to control cancer growth, invasion, chemo-resistance, and served as novel therapeutic target for cancer treatment. However, the nature and characteristics of GEP interacting partner remain unclear. The present study aims to identify and characterize the novel predominant interacting partner of GEP using co-immunoprecipitation and mass spectrometry. Methods and Results: Specific anti-GEP monoclonal antibody was used to capture GEP and its interacting partner from the protein extract of the liver cancer cells Hep3B. The precipitated proteins were analyzed by SDS-PAGE, followed by mass spectrometry and the protein identity was demonstrated to be tropomyosin 3 (TPM3). The interaction has been validated in additional cell models using anti-TPM3 antibody and immunoblot to confirm GEP as the interacting partner. GEP and TPM3 expressions were then examined by real-time quantitative RT-PCR in clinical samples, and their transcript levels were significantly correlated. Elevated TPM3 levels were observed in liver cancer compared with the adjacent non-tumorous liver, and patients with elevated TPM3 levels were shown to have poor recurrence-free survival. Protein expression of GEP and TPM3 was observed only in the cytoplasm of liver cancer cells by immunohistochemical staining. Conclusions: TPM3 is an interacting partner of GEP and may play an important role in hepatocarcinogenesis. © 2012 Lam et al.published_or_final_versio

Copy number gain of granulin-epithelin precursor (GEP) at chromosome 17q21 associates with overexpression in human liver cancer

Background: Granulin-epithelin precursor (GEP), a secretory growth factor, demonstrated overexpression in various human cancers, however, mechanism remain elusive. Primary liver cancer, hepatocellular carcinoma (HCC), ranks the second in cancer-related death globally. GEP controlled growth, invasion, metastasis and chemo-resistance in liver cancer. Noted that GEP gene locates at 17q21 and the region has been frequently reported to be amplified in subset of HCC. The study aims to investigate if copy number gain would associate with GEP overexpression. Methods: Quantitative Microsatellite Analysis (QuMA) was used to quantify the GEP DNA copy number, and fluorescent in situ hybridization (FISH) was performed to consolidate the amplification status. GEP gene copy number, mRNA expression level and clinico-pathological features were analyzed. Results: GEP DNA copy number determined by QuMA corroborated well with the FISH data, and the gene copy number correlated with the expression levels (n = 60, r = 0.331, P = 0.010). Gain of GEP copy number was observed in 20% (12/60) HCC and associated with hepatitis B virus infection status (P = 0.015). In HCC with increased GEP copy number, tight association between GEP DNA and mRNA levels were observed (n = 12, r = 0.664, P = 0.019). Conclusions: Gain of the GEP gene copy number was observed in 20% HCC and the frequency comparable to literatures reported on the chromosome region 17q. Increased gene copy number contributed to GEP overexpression in subset of HCC. © Yung et al; licensee BioMed Central.published_or_final_versio

Lysosomal membrane permeabilization is involved in oxidative stress-induced apoptotic cell death in LAMP2-deficient iPSCs-derived cerebral cortical neurons

postprin

Virulence determinants, drug resistance and mobile genetic elements of Laribacter hongkongensis: a genome-wide analysis

<p>Abstract</p> <p>Background</p> <p><it>Laribacter hongkongensis </it>is associated with community-acquired gastroenteritis and traveler's diarrhea. In this study, we performed an in-depth annotation of the genes in its genome related to the various steps in the infective process, drug resistance and mobile genetic elements.</p> <p>Results</p> <p>For acid and bile resistance, <it>L. hongkongensis </it>possessed a urease gene cassette, two <it>arc </it>gene clusters and bile salt efflux systems. For intestinal colonization, it possessed a putative adhesin of the autotransporter family homologous to those of diffusely adherent <it>Escherichia coli </it>(<it>E. coli</it>) and enterotoxigenic <it>E. coli</it>. To evade from host defense, it possessed superoxide dismutase and catalases. For lipopolysaccharide biosynthesis, it possessed the same set of genes that encode enzymes for synthesizing lipid A, two Kdo units and heptose units as <it>E. coli</it>, but different genes for its symmetrical acylation pattern, and nine genes for polysaccharide side chains biosynthesis. It contained a number of CDSs that encode putative cell surface acting (RTX toxin and hemolysins) and intracellular cytotoxins (patatin-like proteins) and enzymes for invasion (outer membrane phospholipase A). It contained a broad variety of antibiotic resistance-related genes, including genes related to β-lactam (n = 10) and multidrug efflux (n = 54). It also contained eight prophages, 17 other phage-related CDSs and 26 CDSs for transposases.</p> <p>Conclusions</p> <p>The <it>L. hongkongensis </it>genome possessed genes for acid and bile resistance, intestinal mucosa colonization, evasion of host defense and cytotoxicity and invasion. A broad variety of antibiotic resistance or multidrug resistance genes, a high number of prophages, other phage-related CDSs and CDSs for transposases, were also identified.</p

Transport genes and chemotaxis in Laribacter hongkongensis: a genome-wide analysis

<p>Abstract</p> <p>Background</p> <p><it>Laribacter hongkongensis </it>is a Gram-negative, sea gull-shaped rod associated with community-acquired gastroenteritis. The bacterium has been found in diverse freshwater environments including fish, frogs and drinking water reservoirs. Using the complete genome sequence data of <it>L. hongkongensis</it>, we performed a comprehensive analysis of putative transport-related genes and genes related to chemotaxis, motility and quorum sensing, which may help the bacterium adapt to the changing environments and combat harmful substances.</p> <p>Results</p> <p>A genome-wide analysis using Transport Classification Database TCDB, similarity and keyword searches revealed the presence of a large diversity of transporters (n = 457) and genes related to chemotaxis (n = 52) and flagellar biosynthesis (n = 40) in the <it>L. hongkongensis </it>genome. The transporters included those from all seven major transporter categories, which may allow the uptake of essential nutrients or ions, and extrusion of metabolic end products and hazardous substances. <it>L. hongkongensis </it>is unique among closely related members of <it>Neisseriaceae </it>family in possessing higher number of proteins related to transport of ammonium, urea and dicarboxylate, which may reflect the importance of nitrogen and dicarboxylate metabolism in this assacharolytic bacterium. Structural modeling of two C^₄-dicarboxylate transporters showed that they possessed similar structures to the determined structures of other DctP-TRAP transporters, with one having an unusual disulfide bond. Diverse mechanisms for iron transport, including hemin transporters for iron acquisition from host proteins, were also identified. In addition to the chemotaxis and flagella-related genes, the <it>L. hongkongensis </it>genome also contained two copies of <it>qseB/qseC </it>homologues of the AI-3 quorum sensing system.</p> <p>Conclusions</p> <p>The large number of diverse transporters and genes involved in chemotaxis, motility and quorum sensing suggested that the bacterium may utilize a complex system to adapt to different environments. Structural modeling will provide useful insights on the transporters in <it>L. hongkongensis</it>.</p

Identification of Novel Rosavirus Species That Infects Diverse Rodent Species and Causes Multisystemic Dissemination in Mouse Model

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