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  • 1
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    Ray Tracing RF Field Prediction: An Unforgiving Validation (2015)
    Hindawi
    Details
    Publication Date: 2015-08-13
    Description: The prediction of RF coverage in urban environments is now commonly considered a solved problem with tens of models proposed in the literature showing good performance against measurements. Among these, ray tracing is regarded as one of the most accurate ones available. In the present work, however, we show that a great deal of work is still needed to make ray tracing really unleash its potential in practical use. A very extensive validation of a state-of-the-art 3D ray tracing model is carried out through comparison with measurements in one of the most challenging environments: the city of San Francisco. Although the comparison is based on RF cellular coverage at 850 and 1900 MHz, a widely studied territory, very relevant sources of error and inaccuracy are identified in several cases along with possible solutions.
    Print ISSN: 1687-5869
    Electronic ISSN: 1687-5877
    Topics: Electrical Engineering, Measurement and Control Technology
    Published by Hindawi
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  • 2
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    Poly(A)-binding proteins are required for microRNA-mediated silencing and to promote target deadenylation in C. elegans (2016)
    Oxford University Press
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    Publication Date: 2016-07-09
    Description: Cytoplasmic poly(A)-binding proteins (PABPs) link mRNA 3' termini to translation initiation factors, but they also play key roles in mRNA regulation and decay. Reports from mice, zebrafish and Drosophila further involved PABPs in microRNA (miRNA)-mediated silencing, but through seemingly distinct mechanisms. Here, we implicate the two Caenorhabditis elegans PABPs (PAB-1 and PAB-2) in miRNA-mediated silencing, and elucidate their mechanisms of action using concerted genetics, protein interaction analyses, and cell-free assays. We find that C. elegans PABPs are required for miRNA-mediated silencing in embryonic and larval developmental stages, where they act through a multi-faceted mechanism. Depletion of PAB-1 and PAB-2 results in loss of both poly(A)-dependent and -independent translational silencing. PABPs accelerate miRNA-mediated deadenylation, but this contribution can be modulated by 3'UTR sequences. While greater distances with the poly(A) tail exacerbate dependency on PABP for deadenylation, more potent miRNA-binding sites partially suppress this effect. Our results refine the roles of PABPs in miRNA-mediated silencing and support a model wherein they enable miRNA-binding sites by looping the 3'UTR poly(A) tail to the bound miRISC and deadenylase.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Method for widespread microRNA-155 inhibition prolongs survival in ALS-model mice (2013)
    Oxford University Press
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    Publication Date: 2013-09-25
    Description: microRNAs (miRNAs) are dysregulated in a variety of disease states, suggesting that this newly discovered class of gene expression repressors may be viable therapeutic targets. A microarray of miRNA changes in ALS-model superoxide dismutase 1 (SOD1) G93A rodents identified 12 miRNAs as significantly changed. Six miRNAs tested in human ALS tissues were confirmed increased. Specifically, miR-155 was increased 5-fold in mice and 2-fold in human spinal cords. To test miRNA inhibition in the central nervous system (CNS) as a potential novel therapeutic, we developed oligonucleotide-based miRNA inhibitors (anti-miRs) that could inhibit miRNAs throughout the CNS and in the periphery. Anti-miR-155 caused global derepression of targets in peritoneal macrophages and, following intraventricular delivery, demonstrated widespread functional distribution in the brain and spinal cord. After treating SOD1 G93A mice with anti-miR-155, we significantly extended survival by 10 days and disease duration by 15 days (38%) while a scrambled control anti-miR did not significantly improve survival or disease duration. Therefore, antisense oligonucleotides may be used to successfully inhibit miRNAs throughout the brain and spinal cord, and miR-155 is a promising new therapeutic target for human ALS.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 4
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    Theoretic base of Edge Local Mode triggering by vertical displacements (2015)
    American Institute of Physics (AIP)
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    Publication Date: 2015-05-13
    Description: Vertical instability is studied with R-dependent displacement. For Solovev's configuration, the stability boundary of the vertical instability is calculated. The pressure gradient is a destabilizing factor which is contrary to Rebhan's result. Equilibrium parallel current density, j / / , at plasma boundary is a drive of the vertical instability similar to Peeling-ballooning modes; however, the vertical instability cannot be stabilized by the magnetic shear which tends towards infinity near the separatrix. The induced current observed in the Edge Local Mode (ELM) triggering experiment by vertical modulation is derived. The theory provides some theoretic explanation for the mitigation of type-I ELMS on ASDEX Upgrade. The principle could be also used for ITER.
    Print ISSN: 1070-664X
    Electronic ISSN: 1089-7674
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 5
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    PDE3B knockout protects heart against I/R injury [Physiology] (2015)
    National Academy of Sciences
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    Publication Date: 2015-04-29
    Description: Although inhibition of cyclic nucleotide phosphodiesterase type 3 (PDE3) has been reported to protect rodent heart against ischemia/reperfusion (I/R) injury, neither the specific PDE3 isoform involved nor the underlying mechanisms have been identified. Targeted disruption of PDE3 subfamily B (PDE3B), but not of PDE3 subfamily A (PDE3A), protected mouse heart...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 6
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    Host mitochondria influence gut microbiome diversity: A role for ROS (2019)
    The American Association for the Advancement of Science (AAAS)
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    Publication Date: 2019
    Description: 〈p〉Changes in the gut microbiota and the mitochondrial genome are both linked with the development of disease. To investigate why, we examined the gut microbiota of mice harboring various mutations in genes that alter mitochondrial function. These studies revealed that mitochondrial genetic variations altered the composition of the gut microbiota community. In cross-fostering studies, we found that although the initial microbiota community of newborn mice was that obtained from the nursing mother, the microbiota community progressed toward that characteristic of the microbiome of unfostered pups of the same genotype within 2 months. Analysis of the mitochondrial DNA variants associated with altered gut microbiota suggested that microbiome species diversity correlated with host reactive oxygen species (ROS) production. To determine whether the abundance of ROS could alter the gut microbiota, mice were aged, treated with 〈i〉N〈/i〉-acetylcysteine, or engineered to express the ROS scavenger catalase specifically within the mitochondria. All three conditions altered the microbiota from that initially established. Thus, these data suggest that the mitochondrial genotype modulates both ROS production and the species diversity of the gut microbiome, implying that the connection between the gut microbiome and common disease phenotypes might be due to underlying changes in mitochondrial function.〈/p〉
    Print ISSN: 1945-0877
    Electronic ISSN: 1937-9145
    Topics: Biology , Medicine
    Published by The American Association for the Advancement of Science (AAAS)
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  • 7
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    Magnetization switching using topological surface states (2019)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2019
    Description: 〈p〉Topological surface states (TSSs) in a topological insulator are expected to be able to produce a spin-orbit torque that can switch a neighboring ferromagnet. This effect may be absent if the ferromagnet is conductive because it can completely suppress the TSSs, but it should be present if the ferromagnet is insulating. This study reports TSS-induced switching in a bilayer consisting of a topological insulator Bi〈sub〉2〈/sub〉Se〈sub〉3〈/sub〉 and an insulating ferromagnet BaFe〈sub〉12〈/sub〉O〈sub〉19〈/sub〉. A charge current in Bi〈sub〉2〈/sub〉Se〈sub〉3〈/sub〉 can switch the magnetization in BaFe〈sub〉12〈/sub〉O〈sub〉19〈/sub〉 up and down. When the magnetization is switched by a field, a current in Bi〈sub〉2〈/sub〉Se〈sub〉3〈/sub〉 can reduce the switching field by ~4000 Oe. The switching efficiency at 3 K is 300 times higher than at room temperature; it is ~30 times higher than in Pt/BaFe〈sub〉12〈/sub〉O〈sub〉19〈/sub〉. These strong effects originate from the presence of more pronounced TSSs at low temperatures due to enhanced surface conductivity and reduced bulk conductivity.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 8
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    Predicting tumor purity from methylation microarray data (2015)
    Oxford University Press
    Details
    Publication Date: 2015-10-21
    Description: Motivation: In cancer genomics research, one important problem is that the solid tissue sample obtained from clinical settings is always a mixture of cancer and normal cells. The sample mixture brings complication in data analysis and results in biased findings if not correctly accounted for. Estimating tumor purity is of great interest, and a number of methods have been developed using gene expression, copy number variation or point mutation data. Results: We discover that in cancer samples, the distributions of data from Illumina Infinium 450 k methylation microarray are highly correlated with tumor purities. We develop a simple but effective method to estimate purities from the microarray data. Analyses of the Cancer Genome Atlas lung cancer data demonstrate favorable performance of the proposed method. Availability and implementation: The method is implemented in InfiniumPurify, which is freely available at https://bitbucket.org/zhengxiaoqi/infiniumpurify . Contact: xqzheng@shnu.edu.cn or hao.wu@emory.edu Supplementary information : Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 9
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    ACFIS: a web server for fragment-based drug discovery (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-06
    Description: In order to foster innovation and improve the effectiveness of drug discovery, there is a considerable interest in exploring unknown ‘chemical space’ to identify new bioactive compounds with novel and diverse scaffolds. Hence, fragment-based drug discovery (FBDD) was developed rapidly due to its advanced expansive search for ‘chemical space’, which can lead to a higher hit rate and ligand efficiency (LE). However, computational screening of fragments is always hampered by the promiscuous binding model. In this study, we developed a new web server Auto Core Fragment in silico Screening (ACFIS). It includes three computational modules, PARA_GEN, CORE_GEN and CAND_GEN. ACFIS can generate core fragment structure from the active molecule using fragment deconstruction analysis and perform in silico screening by growing fragments to the junction of core fragment structure. An integrated energy calculation rapidly identifies which fragments fit the binding site of a protein. We constructed a simple interface to enable users to view top-ranking molecules in 2D and the binding mode in 3D for further experimental exploration. This makes the ACFIS a highly valuable tool for drug discovery. The ACFIS web server is free and open to all users at http://chemyang.ccnu.edu.cn/ccb/server/ACFIS/ .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Genome-wide profiling of polyadenylation sites reveals a link between selective polyadenylation and cancer metastasis (2015)
    Oxford University Press
    Details
    Publication Date: 2015-05-20
    Description: Alternative polyadenylation (APA) is an important post-transcriptional modification implicated in many diseases, including cancer. Although extensively characterized, the functional consequence of APA modulation on tumorigenesis remains elusive. Here, we developed a deep sequencing-based approach that specifically profiles 3' termini of polyadenylated RNAs (herein termed 3T-seq) and analyzed APA events in two gastric cancer cell lines and one non-transformed counterpart. Overall, we identified 〉28 000 poly(A) sites, 70% of which are potentially novel. Further, we observed widespread APA-mediated 3' UTR shortening of 513 genes (false discovery rate 〈 0.05) across gastric cancer genome. We characterized one of these genes, NET1 , in detail and found that the shortening of NET1 3' UTR significantly enhances transcriptional activity. Moreover, the NET1 isoform with short 3' UTR promotes cellular migration and invasion in vitro . Collectively, our work provides an effective approach for genome-wide APA site profiling and reveals a link between APA modulation and gastric cancer metastasis.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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