Molecular Dynamics Simulation of Iron — A Review

published_or_final_versio

Vaccinia-related kinase 1 promotes hepatocellular carcinoma by controlling the levels of cell cycle regulators associated with G1/S transition

We identified the specific role of vaccinia-related kinase 1 (VRK1) in the progression of hepatocellular carcinoma (HCC) and evaluated its therapeutic and prognostic potential. VRK1 levels were significantly higher in HCC cell lines than a normal hepatic cell line, and were higher in HCC than non-tumor tissue. VRK1 knockdown inhibited the proliferation of SK-Hep1, SH-J1 and Hep3B cells; moreover, depletion of VRK1 suppressed HCC tumor growth in vivo. We also showed that VRK1 knockdown increased the number of G1 arrested cells by decreasing cyclin D1 and p-Rb while upregulating p21 and p27, and that VRK1 depletion downregulated phosphorylation of CREB, a transcription factor regulating CCND1. Additionally, we found that luteolin, a VRK1 inhibitor, suppressed HCC growth in vitro and in vivo, and that the aberrant VRK1 expression correlated with poor prognostic features of HCC. High levels of VRK1 were associated with shorter overall and disease-free survival and higher recurrence rates. Taken together, our findings suggest VRK1 may act as a tumor promoter by controlling the level of cell cycle regulators associated with G1/S transition and could potentially serve as a therapeutic target and/or prognostic biomarker for HCC.1110Ysciescopu

Electro-optically tunable microring resonators in lithium niobate

Optical microresonators have recently attracted a growing attention in the photonics community. Their applications range from quantum electro-dynamics to sensors and filtering devices for optical telecommunication systems, where they are likely to become an essential building block. The integration of nonlinear and electro-optical properties in the resonators represents a very stimulating challenge, as it would incorporate new and more advanced functionality. Lithium niobate is an excellent candidate material, being an established choice for electro-optic and nonlinear optical applications. Here we report on the first realization of optical microring resonators in submicrometric thin films of lithium niobate. The high index contrast films are produced by an improved crystal ion slicing and bonding technique using benzocyclobutene. The rings have radius R=100 um and their transmission spectrum has been tuned using the electro-optic effect. These results open new perspectives for the use of lithium niobate in chip-scale integrated optical devices and nonlinear optical microcavities.Comment: 15 pages, 8 figure

Copy number variation analysis based on AluScan sequences

BACKGROUND: AluScan combines inter-Alu PCR using multiple Alu-based primers with opposite orientations and next-generation sequencing to capture a huge number of Alu-proximal genomic sequences for investigation. Its requirement of only sub-microgram quantities of DNA facilitates the examination of large numbers of samples. However, the special features of AluScan data rendered difficult the calling of copy number variation (CNV) directly using the calling algorithms designed for whole genome sequencing (WGS) or exome sequencing. RESULTS: In this study, an AluScanCNV package has been assembled for efficient CNV calling from AluScan sequencing data employing a Geary-Hinkley transformation (GHT) of read-depth ratios between either paired test-control samples, or between test samples and a reference template constructed from reference samples, to call the localized CNVs, followed by use of a GISTIC-like algorithm to identify recurrent CNVs and circular binary segmentation (CBS) to reveal large extended CNVs. To evaluate the utility of CNVs called from AluScan data, the AluScans from 23 non-cancer and 38 cancer genomes were analyzed in this study. The glioma samples analyzed yielded the familiar extended copy-number losses on chromosomes 1p and 9. Also, the recurrent somatic CNVs identified from liver cancer samples were similar to those reported for liver cancer WGS with respect to a striking enrichment of copy-number gains in chromosomes 1q and 8q. When localized or recurrent CNV-features capable of distinguishing between liver and non-liver cancer samples were selected by correlation-based machine learning, a highly accurate separation of the liver and non-liver cancer classes was attained. CONCLUSIONS: The results obtained from non-cancer and cancerous tissues indicated that the AluScanCNV package can be employed to call localized, recurrent and extended CNVs from AluScan sequences. Moreover, both the localized and recurrent CNVs identified by this method could be subjected to machine-learning selection to yield distinguishing CNV-features that were capable of separating between liver cancers and other types of cancers. Since the method is applicable to any human DNA sample with or without the availability of a paired control, it can also be employed to analyze the constitutional CNVs of individuals.published_or_final_versio

Scanning and filling : ultra-dense SNP genotyping combining genotyping-by-sequencing, SNP array and whole-genome resequencing data

Genotyping-by-sequencing (GBS) represents a highly cost-effective high-throughput genotyping approach. By nature, however, GBS is subject to generating sizeable amounts of missing data and these will need to be imputed for many downstream analyses. The extent to which such missing data can be tolerated in calling SNPs has not been explored widely. In this work, we first explore the use of imputation to fill in missing genotypes in GBS datasets. Importantly, we use whole genome resequencing data to assess the accuracy of the imputed data. Using a panel of 301 soybean accessions, we show that over 62,000 SNPs could be called when tolerating up to 80% missing data, a five-fold increase over the number called when tolerating up to 20% missing data. At all levels of missing data examined (between 20% and 80%), the resulting SNP datasets were of uniformly high accuracy (96– 98%). We then used imputation to combine complementary SNP datasets derived from GBS and a SNP array (SoySNP50K). We thus produced an enhanced dataset of >100,000 SNPs and the genotypes at the previously untyped loci were again imputed with a high level of accuracy (95%). Of the >4,000,000 SNPs identified through resequencing 23 accessions (among the 301 used in the GBS analysis), 1.4 million tag SNPs were used as a reference to impute this large set of SNPs on the entire panel of 301 accessions. These previously untyped loci could be imputed with around 90% accuracy. Finally, we used the 100K SNP dataset (GBS + SoySNP50K) to perform a GWAS on seed oil content within this collection of soybean accessions. Both the number of significant marker-trait associations and the peak significance levels were improved considerably using this enhanced catalog of SNPs relative to a smaller catalog resulting from GBS alone at 20% missing data. Our results demonstrate that imputation can be used to fill in both missing genotypes and untyped loci with very high accuracy and that this leads to more powerful genetic analyses

Effect of laser remelting on microstructure and properties of WC reinforced Fe-based amorphous composite coatings by laser cladding

The WC reinforced Fe-based amorphous composite coatings were prepared by laser cladding with rectangular spot. The effect of laser remelting on the microstructure and properties of composite coatings was investigated. The results showed that laser remelting can reduce the cracks and porosities of the cladding coating and improve its surface quality. Large amounts of crystalline phases were precipitated at the top of the cladding and remelting coatings. However, the microstructure at the top of the remelting coating was finer compared to that at the top of the cladding coating. With increasing distance from the surface of substrate, the amorphous phase appeared within the remelting coating and large amounts of carbides rich in Fe and Mo, Fe23B6, gamma-Fe and Cr-9.1.Si-0.9 Slag phases were also precipitated in the remelting coating. As a result, the corrosion resistance of the remelting coating was higher than that of the cladding coating. The microhardness of the remelting coating was approximately 1.13 times higher than that of the cladding coating. (C) 2018 Elsevier Ltd. All rights reserved

STUDY ON TOTAL LUMINESCENCE SPECTRA - APPLICATION OF THE MONTE-CARLO METHOD TO 3-DIMENSIONAL SYNCHRONOUS FLUORESCENCE SPECTROMETRY

Three-dimensional synchronous fluorescence spectrometry (TDSFS, a combination of synchronous fluorescence spectrometry and three-dimensional fluorescence spectrometry) is a new method which has been developed recently. The method has usually been used as an efficient tool to select the best Delta lambda value for synchronous fluorescence spectra. This paper studies the sensitivity of the method, which was not been done in the past. The total fluorescence intensity has been used instead of the conventional single point intensity, calculated by the Monte-Carlo method, as the experimental parameter to determine fluorescein and tryptophan. The sensitivity of the total fluorescence method is nearly one hundred times better than that of the single point method. The new method has been used to simultaneously determine naphthalene, pyrene and perylene successfully. The mechanism of the method has also been studied

Association of Traffic-Related Air Pollution with Children’s Neurobehavioral Functions in Quanzhou, China

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