2,101 research outputs found
Quantum fluctuations in high field magnetization of 2D square lattice J1-J2 antiferromagnets
The J1-J2 square lattice Heisenberg model with spin S=1/2 has three phases
with long-range magnetic order and two unconventionally ordered phases
depending on the ratio of exchange constants. It describes a number of recently
found layered vanadium oxide compounds. A simple means of investigating the
ground state is the study of the magnetization curve and high-field
susceptibility. We discuss these quantities by using the spin-wave theory and
the exact diagonalization in the whole J1-J2 plane. We compare both results and
find good overall agreement in the sectors of the phase diagram with magnetic
order. Close to the disordered regions the magnetization curve shows strong
deviations from the classical linear behaviour caused by large quantum
fluctuations and spin-wave approximation breaks down. On the FM side (J1<0)
where one approaches the quantum gapless spin nematic ground state this region
is surprisingly large. We find that inclusion of second order spin-wave
corrections does not lead to fundamental improvement. Quantum corrections to
the tilting angle of the ordered moments are also calculated. They may have
both signs, contrary to the always negative first order quantum corrections to
the magnetization. Finally we investigate the effect of the interlayer coupling
and find that the quasi-2D picture remains valid up to |J_\perp/J1| ~ 0.3.Comment: 13 pages, 6figure
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Inter-comparison of three-dimensional models of volcanic plumes
We performed an inter-comparison study of three-dimensional models of volcanic plumes. A set of common volcanological input parameters and meteorological conditions were provided for two kinds of eruptions, representing a weak and a strong eruption column. From the different models, we compared the maximum plume height, neutral buoyancy level (where plume density equals that of the atmosphere), and level of maximum radial spreading of the umbrella cloud. We also compared the vertical profiles of eruption column properties, integrated across cross-sections of the plume (integral variables). Although the models use different numerical procedures and treatments of subgrid turbulence and particle dynamics, the inter-comparison shows qualitatively consistent results. In the weak plume case (mass eruption rate 1.5 × 106 kg s− 1), the vertical profiles of plume properties (e.g., vertical velocity, temperature) are similar among models, especially in the buoyant plume region. Variability among the simulated maximum heights is ~ 20%, whereas neutral buoyancy level and level of maximum radial spreading vary by ~ 10%. Time-averaging of the three-dimensional (3D) flow fields indicates an effective entrainment coefficient around 0.1 in the buoyant plume region, with much lower values in the jet region, which is consistent with findings of small-scale laboratory experiments. On the other hand, the strong plume case (mass eruption rate 1.5 × 109 kg s− 1) shows greater variability in the vertical plume profiles predicted by the different models. Our analysis suggests that the unstable flow dynamics in the strong plume enhances differences in the formulation and numerical solution of the models. This is especially evident in the overshooting top of the plume, which extends a significant portion (~ 1/8) of the maximum plume height. Nonetheless, overall variability in the spreading level and neutral buoyancy level is ~ 20%, whereas that of maximum height is ~ 10%. This inter-comparison study has highlighted the different capabilities of 3D volcanic plume models, and identified key features of weak and strong plumes, including the roles of jet stability, entrainment efficiency, and particle non-equilibrium, which deserve future investigation in field, laboratory, and numerical studies.YJS was partially supported by the ERI Cooperative Research Program and KAKENHI (25750142). The computations of SK-3D were carried out in part on the Earth Simulator at the JAMSTEC and also on the Primergy RX200S6 at the Research Computer System, Kyushu University. AC was partially supported by a grant of the International Research Promotion Office Earthquake Research Institute, the University of Tokyo. AC, TEO and MC were partially supported by the EU-funded project MEDiterranean Supersite Volcanoes (MEDSUV; grant no. 308665). MC acknowledges CINECA award N. HP10BKFD9F (2013) for high performance computing resources and support. AVE acknowledges NSF Postdoctoral Fellowship EAR1250029, a U.S. Geological Survey Mendenhall fellowship, and grant GID 61233 from NASA Ames Supercomputing Center
Aberrant methylation of N-methyl-D-aspartate receptor type 2B (NMDAR2B) in non-small cell carcinoma
<p>Abstract</p> <p>Background</p> <p>N-methyl-D-aspartate receptors (NMDAR) act as tumor suppressors of digestive malignancies. The expression and genetic methylation patterns of <it>NMDAR2B </it>in non-small cell lung cancer (NSCLC) are unknown.</p> <p>Methods</p> <p>The relationship between gene methylation and expression of <it>NMDAR2B </it>was analyzed in NSCLC cell lines (N = 9) and clinical tissues (N = 216). The cell lines were studied using RT-PCR and 5-aza-2'-deoxycytidine treatment, while the clinical tissues were examined by methylation specific real-time quantitative PCR and immunohistochemistry. Retrospective investigation of patient records was used to determine the clinical significance of <it>NMDAR2B </it>methylation.</p> <p>Results</p> <p><it>NMDAR2B </it>was silenced in five of the nine cell lines; 5-aza-2'-deoxycytidine treatment restored expression, and was inversely correlated with methylation. Aberrant methylation of <it>NMDAR2B</it>, detected in 61% (131/216) of clinical NSCLC tissues, was inversely correlated with the status of protein expression in 20 randomly examined tumors. Aberrant methylation was not associated with clinical factors such as gender, age, histological type, or TNM stage. However, aberrant methylation was an independent prognostic factor in squamous cell carcinoma cases.</p> <p>Conclusions</p> <p>Aberrant methylation of the <it>NMDAR2B </it>gene is a common event in NSCLC. The prognosis was significantly better for cases of squamous cell carcinoma in which <it>NMDAR2B </it>was methylated. It may have different roles in different histological types.</p
Fully automated high-quality NMR structure determination of small 2H-enriched proteins
Determination of high-quality small protein structures by nuclear magnetic resonance (NMR) methods generally requires acquisition and analysis of an extensive set of structural constraints. The process generally demands extensive backbone and sidechain resonance assignments, and weeks or even months of data collection and interpretation. Here we demonstrate rapid and high-quality protein NMR structure generation using CS-Rosetta with a perdeuterated protein sample made at a significantly reduced cost using new bacterial culture condensation methods. Our strategy provides the basis for a high-throughput approach for routine, rapid, high-quality structure determination of small proteins. As an example, we demonstrate the determination of a high-quality 3D structure of a small 8 kDa protein, E. coli cold shock protein A (CspA), using <4 days of data collection and fully automated data analysis methods together with CS-Rosetta. The resulting CspA structure is highly converged and in excellent agreement with the published crystal structure, with a backbone RMSD value of 0.5 Å, an all atom RMSD value of 1.2 Å to the crystal structure for well-defined regions, and RMSD value of 1.1 Å to crystal structure for core, non-solvent exposed sidechain atoms. Cross validation of the structure with 15N- and 13C-edited NOESY data obtained with a perdeuterated 15N, 13C-enriched 13CH3 methyl protonated CspA sample confirms that essentially all of these independently-interpreted NOE-based constraints are already satisfied in each of the 10 CS-Rosetta structures. By these criteria, the CS-Rosetta structure generated by fully automated analysis of data for a perdeuterated sample provides an accurate structure of CspA. This represents a general approach for rapid, automated structure determination of small proteins by NMR
hTERT mediates gastric cancer metastasis partially through the indirect targeting of ITGB1 by microRNA-29a.
Human telomerase reverse transcriptase (hTERT) plays a key role in tumor invasion and metastasis, but the mechanism of its involvement in these processes is not clear. The purpose of this study is to investigate the possible molecular mechanism of hTERT in the promotion of gastric cancer (GC) metastasis. We found that the up-regulation of hTERT in gastric cancer cells could inhibit the expression of miR-29a and enhance the expression of Integrin β1 (ITGB1). In addition, the invasive capacity of gastric cancer cells was also highly increased after hTERT overexpression. Our study also found that the restoration of miR-29a suppressed the expression of ITGB1 and inhibited GC cell metastasis both in vitro and in vivo. Taken together, our results suggested that hTERT may promote GC metastasis through the hTERT-miR-29a-ITGB1 regulatory pathway
Intragenic DNA methylation: implications of this epigenetic mechanism for cancer research
Epigenetics is the study of all mechanisms that regulate gene transcription and genome stability that are maintained throughout the cell division, but do not include the DNA sequence itself. The best-studied epigenetic mechanism to date is DNA methylation, where methyl groups are added to the cytosine base within cytosine–guanine dinucleotides (CpG sites). CpGs are frequently clustered in high density (CpG islands (CGIs)) at the promoter of over half of all genes. Current knowledge of transcriptional regulation by DNA methylation centres on its role at the promoter where unmethylated CGIs are present at most actively transcribed genes, whereas hypermethylation of the promoter results in gene repression. Over the last 5 years, research has gradually incorporated a broader understanding that methylation patterns across the gene (so-called intragenic or gene body methylation) may have a role in transcriptional regulation and efficiency. Numerous genome-wide DNA methylation profiling studies now support this notion, although whether DNA methylation patterns are a cause or consequence of other regulatory mechanisms is not yet clear. This review will examine the evidence for the function of intragenic methylation in gene transcription, and discuss the significance of this in carcinogenesis and for the future use of therapies targeted against DNA methylation
Quantum-chemical investigation of the structure and the antioxidant properties of α-lipoic acid and its metabolites
Quantum-chemical computations were used to investigate the structure–antioxidant parameter relationships of α-lipoic acid and its natural metabolites bisnorlipoic acid and tetranorlipoic acid in their oxidized and reduced forms. The enantiomers of lipoic and dihydrolipoic acid were optimized using the B3LYP/6-311+G(3df,2p), B3LYP/aug-cc-pVDZ and MP2(full)/6-31+G(d,p) levels of theory as isolated molecules and in the presence of water. The geometries of the metabolites and the values of their antioxidant parameters (proton affinity, bond dissociation enthalpy, adiabatic ionization potential, spin density, and the highest occupied molecular orbital energy) were calculated at the B3LYP/6-311+G(3df,2p) level of theory. The results obtained reveal similarities between these structures: a pentatomic, nonaromatic ring is present in the oxidized forms, while an unbranched aliphatic chain (as found in saturated fatty acids) is present in both the oxidized and the reduced forms. Analysis of the spin density and the highest occupied molecular orbital energy revealed that the SH groups exhibited the greatest electron-donating activities. The values obtained for the proton affinity, bond dissociation enthalpy and adiabatic ionization potential indicate that the preferred antioxidant mechanisms for α-lipoic acid and its metabolites are sequential proton loss electron transfer in polar media and hydrogen atom transfer in vacuum
Improved Measurements of Partial Rate Asymmetry in B -> h h Decays
We report improved measurements of the partial rate asymmetry (Acp) in B -> h
h decays with 140fb^-1 of data collected with the Belle detector at the KEKB
e+e- collider. Here h stands for a charged or neutral pion or kaon and in total
five decay modes are included: K-+ pi+-, K0s pi-+, K-+ pi0, pi-+ pi0 and K0s
pi0. The flavor of the last decay mode is determined from the accompanying B
meson. Using a data sample 4.7 times larger than that of our previous
measurement, we find Acp(K-+ pi+-) -0.088+-0.035+-0.013, 2.4 sigma from zero.
Results for other decay modes are also presented.Comment: 9 pages, 1 figur
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