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  • 1
    Publication Date: 2016-01-07
    Description: We have monitored the BL Lacertae object S5 0716+714 simultaneously in the B , R and I bands on three nights in 2014 November. The average time resolution is quite high (73, 34 and 58 s for the filters B , R and I ), which can help us trace the profile of the variation and search for the short inter-band time delay. Intra-day variability was about 0.1 mag on the first two nights and more than 0.3 mag on the third. A bluer-when-brighter colour behaviour was found. A clear loop path can be seen on the colour–magnitude diagram of the third night, revealing possible time delays between variations at high and low energies. It is the first time that the intra-day spectral hysteresis loop has been found so obviously in the optical band. We used the interpolated cross-correlation function method to further confirm the time delay and calculated the values of lag between light curves at different wavelengths on each night. On the third night, variations in the R and B bands are approximately 1.5 min lagging behind the I band. Such optical time delay is probably due to the interplay of different processes of electrons in the jet of the blazar.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 2
    Publication Date: 2016-07-06
    Description: Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. However, we know little of mutational spectrum in the Chinese population. Thus, here we report the identification of somatic mutations for Chinese PTC using 402 tumor-normal pairs (Discovery: 91 pairs via exome sequencing; validation: 311 pairs via Sanger sequencing). We observed three distinct mutational signatures, evidently different from the two mutational signatures among Caucasian PTCs. Ten significantly mutated genes were identified, most previously uncharacterized. Notably, we found that long non-coding RNA (lncRNA) GAS8-AS1 is the secondary most frequently altered gene and acts as a novel tumor suppressor in PTC. As a mutation hotspot, the c.713A〉G/714T〉C dinucleotide substitution was found among 89.1% patients with GAS8-AS1 mutations and associated with advanced PTC disease ( P = 0.009). Interestingly, the wild-type lncRNA GAS8-AS1 (A 713 T 714 ) showed consistently higher capability to inhibit cancer cell growth compared to the mutated lncRNA (G 713 C 714 ). Further studies also elucidated the oncogene nature of the G protein-coupled receptor LPAR4 and its c.872T〉G (p.Ile291Ser) mutation in PTC malignant transformation. The BRAF c.1799T〉A (p.Val600Glu) substitution was present in 59.0% Chinese PTCs, more frequently observed in patients with lymph node metastasis ( P = 1.6 x 10 –4 ). Together our study defines a exome mutational spectrum of PTC in the Chinese population and highlights lncRNA GAS8-AS1 and LPAR4 as potential diagnostics and therapeutic targets.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 3
    Publication Date: 2012-10-10
    Description: A major challenge in metabolic engineering and synthetic biology is to balance the flux of an engineered heterologous metabolic pathway to achieve high yield and productivity in a target organism. Here, we report a simple, efficient and programmable approach named ‘customized optimization of metabolic pathways by combinatorial transcriptional engineering (COMPACTER)’ for rapid tuning of gene expression in a heterologous pathway under distinct metabolic backgrounds. Specifically, a library of mutant pathways is created by de novo assembly of promoter mutants of varying strengths for each pathway gene in a target organism followed by high-throughput screening/selection. To demonstrate this approach, a single round of COMPACTER was used to generate both a xylose utilizing pathway with near-highest efficiency and a cellobiose utilizing pathway with highest efficiency that were ever reported in literature for both laboratory and industrial yeast strains. Interestingly, these engineered xylose and cellobiose utilizing pathways were all host-specific. Therefore, COMPACTER represents a powerful approach to tailor-make metabolic pathways for different strain backgrounds, which is difficult if not impossible to achieve by existing pathway engineering methods.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 4
    Publication Date: 2013-07-17
    Description: Motivation: Tissue samples of tumor cells mixed with stromal cells cause underdetection of gene expression signatures associated with cancer prognosis or response to treatment. In silico dissection of mixed cell samples is essential for analyzing expression data generated in cancer studies. Currently, a systematic approach is lacking to address three challenges in computational deconvolution: (i) violation of linear addition of expression levels from multiple tissues when log-transformed microarray data are used; (ii) estimation of both tumor proportion and tumor-specific expression, when neither is known a priori; and (iii) estimation of expression profiles for individual patients. Results: We have developed a statistical method for deconvolving mixed cancer transcriptomes, DeMix, which addresses the aforementioned issues in array-based expression data. We demonstrate the performance of our model in synthetic and real, publicly available, datasets. DeMix can be applied to ongoing biomarker-based clinical studies and to the vast expression datasets previously generated from mixed tumor and stromal cell samples. Availability: All codes are written in C and integrated into an R function, which is available at http://odin.mdacc.tmc.edu/~wwang7/DeMix.html . Contact: wwang7@mdanderson.org Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 5
    Publication Date: 2012-06-28
    Description: T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy. The understanding of its gene expression regulation and molecular mechanisms still remains elusive. Started from experimentally verified T-ALL-related miRNAs and genes, we obtained 120 feed-forward loops (FFLs) among T-ALL-related genes, miRNAs and TFs through combining target prediction. Afterwards, a T-ALL miRNA and TF co-regulatory network was constructed, and its significance was tested by statistical methods. Four miRNAs in the miR-17–92 cluster and four important genes (CYLD, HOXA9, BCL2L11 and RUNX1) were found as hubs in the network. Particularly, we found that miR-19 was highly expressed in T-ALL patients and cell lines. Ectopic expression of miR-19 represses CYLD expression, while miR-19 inhibitor treatment induces CYLD protein expression and decreases NF-B expression in the downstream signaling pathway. Thus, miR-19, CYLD and NF-B form a regulatory FFL, which provides new clues for sustained activation of NF-B in T-ALL. Taken together, we provided the first miRNA-TF co-regulatory network in T-ALL and proposed a model to demonstrate the roles of miR-19 and CYLD in the T-cell leukemogenesis. This study may provide potential therapeutic targets for T-ALL and shed light on combining bioinformatics with experiments in the research of complex diseases.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 6
    Publication Date: 2013-06-18
    Description: The recent spectacular progress in the experimental and theoretical understanding of graphene, the basic constituent of graphite, is applied here to compute, from first principles, the ultraviolet extinction of nanoparticles made of stacks of graphene layers. The theory also covers cases where graphene is affected by structural, chemical or orientation disorder, each disorder type being quantitatively defined by a single parameter. The extinction bumps carried by such model materials are found to have positions and widths falling in the same range as the known astronomical 2175 Å features: as the disorder parameter increases, the bump width increases from 0.85 to 2.5 μm –1 , while its peak position shifts from 4.65 to 4.75 μm –1 . Moderate degrees of disorder are enough to cover the range of widths of the vast majority of observed bumps (0.75 to 1.3 μm –1 ). Higher degrees account for outliers, also observed in the sky. The introduction of structural or chemical disorder amounts to changing the initial $\text{sp}^{2}$ bondings into $\text{sp}^{3}$ or $\text{sp}^{1}$ , so the optical properties of the model material become similar to those of the more or less amorphous carbon-rich materials studied in the laboratory: a-C, a-C:H, HAC, ACH, coals, etc. The present treatment thus bridges gaps between physically different model materials.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 7
    Publication Date: 2013-10-30
    Description: Named entity recognition seeks to locate atomic elements in texts and classify them into predefined categories. It is essentially useful for many applications, including microblog analysis and query suggestion. In recent years, with the explosion of Web 2.0, people have found it a promising way to extract large-scale, high-quality entities from structured web content. However, existing studies seldom provide an integrated system for simultaneously extracting and categorizing both the head and tail entities, and the identification of ambiguous entities is still a challenging task. In light of these, we propose a system named quasi-Automatic Named Entity Extraction and Categorization (ANEEC) for massive named-entity management. Specifically, ANEEC first identifies representative websites by using a small seed-set of entities and the query logs of a search engine, and then extracts high-quality entities from the parallel structures in the webpages. ANEEC then employs the extracted entities and their corresponding atom-level groups to establish an entity taxonomy as well as a hierarchical classifier ensemble. Two problems, i.e. definition abnormality and granularity unfitness, have also been addressed to further improve the quality of the taxonomy. An application case using 932 seed entities and the query logs of the search engine Bing demonstrates that ANEEC can effectively identify over 870 000 named entities in 32 bottom-level categories, and the resulting taxonomy has an excellent classification performance with F 1 =85.17%, provided that the entity features are properly preprocessed and weighted. In particular, ANEEC shows the potential for tail entity recognition and ambiguous entity detection.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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  • 8
  • 9
    Publication Date: 2016-07-01
    Print ISSN: 1757-8981
    Electronic ISSN: 1757-899X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Institute of Physics
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  • 10
    Publication Date: 2016-06-26
    Description: We present proper motions for 15 pulsars which are observed regularly by the Nanshan 25-m radio telescope. Two methods, the frequentist method and the Bayesian method, are used and the results are compared. We demonstrate that the two methods can be applied to young pulsar data sets that exhibit large amounts of timing noise with steep spectral exponents and give consistent results. The measured positions also agree with very long baseline interferometric positions. Proper motions for four pulsars are obtained for the first time, and improved values are obtained for five pulsars.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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