Localized surface optical phonon mode in the InGaN/GaN multiple-quantum- wells nanopillars: Raman spectrum and imaging

An interesting phonon mode at around 685-705 cm -1 was clearly observed in the Raman spectra of InGaN/GaN multiple-quantum-wells nanopillars with different diameters at room temperature. The Raman peak position of this mode is found to show a distinct dependence on the nanopillar size, which is in well agreement with theoretical calculation of the surface optical (SO) phonon modes of nanopillars. Moreover, this kind of SO phonon was evidenced to be located on the pillar surface by using scanning confocal micro-Raman microscopy. © 2011 American Institute of Physics.published_or_final_versio

Dynamics of one-dimensional tight-binding models with arbitrary time-dependent external homogeneous fields

The exact propagators of two one-dimensional systems with time-dependent external fields are presented by following the path-integral method. It is shown that the Bloch acceleration theorem can be generalized to the impulse-momentum theorem in quantum version. We demonstrate that an evolved Gaussian wave packet always keeps its shape in an arbitrary time-dependent homogeneous driven field. Moreover, that stopping and accelerating of a wave packet can be achieved by the pulsed field in a diabatic way.Comment: 8 pages, 6 figure

Different mechanisms of cis-9,trans-11- and trans-10,cis-12- conjugated linoleic acid affecting lipid metabolism in 3T3-L1 cells

Conjugated linoleic acid (CLA) has been shown to reduce body fat mass in various experimental animals. It is valuable to identify its influence on enzymes involved in energy expenditure, apoptosis, fatty acid oxidation and lipolysis. We investigated isomer-specific effects of high dose, long treatment of CLA (75.4 Μmol/L, 8 days) on protein and gene expression of these enzymes in cultured 3T3-L1 cells. Proteomics identified significant up- or down-regulation of 52 proteins by either CLA isomer. Protein and gene expression of uncoupling protein (UCP) 1, UCP3, perilipin and peroxisome proliferator-activated receptor (PPAR) α increased whereas UCP2 reduced for both CLA isomers. And eight-day treatment of trans-10,. cis-12 CLA, but not cis-9,. trans-11 CLA, significantly up-regulated protein and mRNA levels of PKA (P<05), CPT-1 and TNF-α (P<01). Compared to protein expression, both isomers did not significantly influence the mRNA expression of HSL, ATGL, ACO and leptin. In conclusion, high-dose, long treatment of cis-9,. trans-11 CLA did not promote apoptosis, fatty acid oxidation and lipolysis in adipocytes, but may induce an increase in energy expenditure. trans-10,. cis-12 CLA exhibited greater influence on lipid metabolism, stimulated adipocyte energy expenditure, apoptosis and fatty acid oxidation, but its effect on lipolysis was not obvious. © 2010 Elsevier Inc.postprin

The Directed Dominating Set Problem: Generalized Leaf Removal and Belief Propagation

A minimum dominating set for a digraph (directed graph) is a smallest set of vertices such that each vertex either belongs to this set or has at least one parent vertex in this set. We solve this hard combinatorial optimization problem approximately by a local algorithm of generalized leaf removal and by a message-passing algorithm of belief propagation. These algorithms can construct near-optimal dominating sets or even exact minimum dominating sets for random digraphs and also for real-world digraph instances. We further develop a core percolation theory and a replica-symmetric spin glass theory for this problem. Our algorithmic and theoretical results may facilitate applications of dominating sets to various network problems involving directed interactions.Comment: 11 pages, 3 figures in EPS forma

Ordination as a tool to characterize soil particle size distribution, applied to an elevation gradient at the north slope of the Middle Kunlun Mountains

Soil particle-size distribution (PSD) is one of the most fundamental physical attributes of soil due to its strong influence on other soil properties related to water movement, productivity, and soil erosion. Characterizing variation of PSD in soils is an important issue in environmental research. Using ordination methods to characterize particle size distributions (PSDs) on a small-scale is very limited. In this paper, we selected the Cele River Basin on the north slope of the Middle Kunlun Mountains as a study area and investigated vegetation and soil conditions from 1960 to 4070 m a.s.l. Soil particle-size distributions obtained by laser diffractometry were used as a source data matrix. The Canonical Correspondence Analysis (CCA) ordination was applied to analyse the variation characteristics of PSDs and the relationships between PSDs and environmental factors. Moreover, single fractal dimensions were calculated to support the interpretation of the ordination results. Our results indicate that a differentiation of 16 particle fractions can sufficiently characterize the PSDs in CCA biplots. Elevation has the greatest effect on PSDs: the soil fine fractions increase gradually with increasing elevation. In addition, soil pH, water and total salt content are significantly correlated with PSDs. CCA ordination biplots show that soil and vegetation patterns correspond with one another, indicating a tight link between soil PSDs and plant communities on a small scale in arid regions. The results of fractal dimensions analysis were rather similar to CCA ordination results, but they yielded less detailed information about PSDs. Our study shows that ordination methods can be beneficially used in research into PSDs and, combined with fractal measures, can provide comprehensive information about PSDs. Crown Copyright (C) 2010 Published by Elsevier B.V. All rights reserved

Phosphorylation of the androgen receptor is associated with reduced survival in hormonerefractory prostate cancer patients

Cell line studies demonstrate that the PI3K/Akt pathway is upregulated in hormone-refractory prostate cancer (HRPC) and can result in phosphorylation of the androgen receptor (AR). The current study therefore aims to establish if this has relevance to the development of clinical HRPC. Immunohistochemistry was employed to investigate the expression and phosphorylation status of Akt and AR in matched hormone-sensitive and -refractory prostate cancer tumours from 68 patients. In the hormone-refractory tissue, only phosphorylated AR (pAR) was associated with shorter time to death from relapse (&lt;i&gt;P&lt;/i&gt;=0.003). However, when an increase in expression in the transition from hormone-sensitive to -refractory prostate cancer was investigated, an increase in expression of PI3K was associated with decreased time to biochemical relapse (&lt;i&gt;P&lt;/i&gt;=0.014), and an increase in expression of pAkt&lt;sup&gt;473&lt;/sup&gt; and pAR&lt;sup&gt;210&lt;/sup&gt; were associated with decreased disease-specific survival (&lt;i&gt;P&lt;/i&gt;=0.0019 and 0.0015, respectively). Protein expression of pAkt&lt;sup&gt;473&lt;/sup&gt; and pAR&lt;sup&gt;210&lt;/sup&gt; also strongly correlated (&lt;i&gt;P&lt;/i&gt;&#60;0.001, c.c.=0.711) in the hormone-refractory prostate tumours. These results provide evidence using clinical specimens, that upregulation of the PI3K/Akt pathway is associated with phosphorylation of the AR during development of HRPC, suggesting that this pathway could be a potential therapeutic target

Proteomic analysis of Artemisia annua – towards elucidating the biosynthetic pathways of the antimalarial pro-drug artemisinin

Background: MS-based proteomics was applied to the analysis of the medicinal plant Artemisia annua, exploiting a recently published contig sequence database (Graham et al. (2010) Science 327, 328–331) and other genomic and proteomic sequence databases for comparison. A. annua is the predominant natural source of artemisinin, the precursor for artemisinin-based combination therapies (ACTs), which are the WHO-recommended treatment for P. falciparum malaria. Results: The comparison of various databases containing A. annua sequences (NCBInr/viridiplantae, UniProt/ viridiplantae, UniProt/A. annua, an A. annua trichome Trinity contig database, the above contig database and another A. annua EST database) revealed significant differences in respect of their suitability for proteomic analysis, showing that an organism-specific database that has undergone extensive curation, leading to longer contig sequences, can greatly increase the number of true positive protein identifications, while reducing the number of false positives. Compared to previously published data an order-of-magnitude more proteins have been identified from trichome-enriched A. annua samples, including proteins which are known to be involved in the biosynthesis of artemisinin, as well as other highly abundant proteins, which suggest additional enzymatic processes occurring within the trichomes that are important for the biosynthesis of artemisinin. Conclusions: The newly gained information allows for the possibility of an enzymatic pathway, utilizing peroxidases, for the less well understood final stages of artemisinin’s biosynthesis, as an alternative to the known non-enzymatic in vitro conversion of dihydroartemisinic acid to artemisinin. Data are available via ProteomeXchange with identifier PXD000703

Machine-learning of atomic-scale properties based on physical principles

We briefly summarize the kernel regression approach, as used recently in materials modelling, to fitting functions, particularly potential energy surfaces, and highlight how the linear algebra framework can be used to both predict and train from linear functionals of the potential energy, such as the total energy and atomic forces. We then give a detailed account of the Smooth Overlap of Atomic Positions (SOAP) representation and kernel, showing how it arises from an abstract representation of smooth atomic densities, and how it is related to several popular density-based representations of atomic structure. We also discuss recent generalisations that allow fine control of correlations between different atomic species, prediction and fitting of tensorial properties, and also how to construct structural kernels---applicable to comparing entire molecules or periodic systems---that go beyond an additive combination of local environments

Wide-Scale Analysis of Human Functional Transcription Factor Binding Reveals a Strong Bias towards the Transcription Start Site

We introduce a novel method to screen the promoters of a set of genes with shared biological function, against a precompiled library of motifs, and find those motifs which are statistically over-represented in the gene set. The gene sets were obtained from the functional Gene Ontology (GO) classification; for each set and motif we optimized the sequence similarity score threshold, independently for every location window (measured with respect to the TSS), taking into account the location dependent nucleotide heterogeneity along the promoters of the target genes. We performed a high throughput analysis, searching the promoters (from 200bp downstream to 1000bp upstream the TSS), of more than 8000 human and 23,000 mouse genes, for 134 functional Gene Ontology classes and for 412 known DNA motifs. When combined with binding site and location conservation between human and mouse, the method identifies with high probability functional binding sites that regulate groups of biologically related genes. We found many location-sensitive functional binding events and showed that they clustered close to the TSS. Our method and findings were put to several experimental tests. By allowing a "flexible" threshold and combining our functional class and location specific search method with conservation between human and mouse, we are able to identify reliably functional TF binding sites. This is an essential step towards constructing regulatory networks and elucidating the design principles that govern transcriptional regulation of expression. The promoter region proximal to the TSS appears to be of central importance for regulation of transcription in human and mouse, just as it is in bacteria and yeast.Comment: 31 pages, including Supplementary Information and figure

An activity-based integrated land-use transport model for urban spatial distribution simulation

This research develops an activity-based integrated land use/transport interaction model based on the concepts – activities (mainly, households and employment activities), activity location and relocation for Chinese regions. It consists of a residential and employment location sub-model, a transport sub-model and an implicit real estate rent adjustment sub-model. The model is developed to model the urban activity distribution evolution, predict urban spatial development trends and examine various planning decision implications. It spatially distributes household and employment activity change of a study area by zone based on the current activity distribution, land use policies and the accessibilities of the zones. The model is subsequently calibrated to predict the distribution of households and employment activities in Beijing metropolitan area in 2025. Model results show that the resident and employment densities are still high in central Beijing in 2025, and most zones’ resident densities are higher than their employment densities. However, there is also significant population density increase along the 6th ring road, indicating the relocation trend of the residents and businesses to the outskirts. This is consistent with the government objectives to decentralize activities within the central urban area. The paper also suggests that the model should be used mainly in examining the possible differences arising from the adoption of different policies though predicting future of a city distribution proves feasible