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  • 1
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    Palaeo-earthquake and palaeo-mudflow events at the Machangyuan Ruins in the Huangshui River valley, northeastern margin of the Tibetan Plateau (2016)
    Sage
    In: Holocene
    Details
    Publication Date: 2016-07-30
    Description: Palaeo-earthquake event recorded by loess rapture fissures (N30°–40°W and N40°–50°E trending) and palaeo-mudflow event recorded by red clay deposits were identified at the Machangyuan Ruins in the Huangshui River valley, at the foot of the northeastern Tibetan Plateau. Comparative analysis of grain-size distributions and geochemical elements of local outcrops indicates that the red mudflows were sourced from the gullies on the valley side where unconsolidated Neogene red clay formation was exposed The palaeo-earthquake was associated with regional tectonic structures including a NNW-trending left-lateral strike-slip fault (Lajishan fault) and a NE-trending local fault (Bazhougou fault). Analysis combining optically stimulated luminescence ages and radiocarbon ages of archaeological record dates the palaeo-earthquake and palaeo-mudflow events to ca. 4.80 ka BP. During that stage, many Neolithic settlements distributed around the Machangyuan Ruins. Enhanced human activities of the Majiayao Culture disturbed the landscape of the Minhe Basin causing widespread soil erosion. Contemporaneous storm rain and earthquake mobilized the loosened sediments in the upper stream gullies forming mudflows. The hollow ground around the Machangyuan Ruins was covered by mudflow and the earthquake fissures were filled in by the mudflow at the same time. This study provides important insights into early human impact during climatic and tectonic events in the environmentally vulnerable zones over the world.
    Print ISSN: 0959-6836
    Electronic ISSN: 1477-0911
    Topics: Geography , Geosciences
    Published by Sage
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  • 2
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    DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels (2015)
    Oxford University Press
    Details
    Publication Date: 2015-05-12
    Description: Motivation : Frameshifting (FS) indels and nonsense (NS) variants disrupt the protein-coding sequence downstream of the mutation site by changing the reading frame or introducing a premature termination codon, respectively. Despite such drastic changes to the protein sequence, FS indels and NS variants have been discovered in healthy individuals. How to discriminate disease-causing from neutral FS indels and NS variants is an understudied problem. Results: We have built a machine learning method called DDIG-in (FS) based on real human genetic variations from the Human Gene Mutation Database (inherited disease-causing) and the 1000 Genomes Project (GP) (putatively neutral). The method incorporates both sequence and predicted structural features and yields a robust performance by 10-fold cross-validation and independent tests on both FS indels and NS variants. We showed that human-derived NS variants and FS indels derived from animal orthologs can be effectively employed for independent testing of our method trained on human-derived FS indels. DDIG-in (FS) achieves a Matthews correlation coefficient (MCC) of 0.59, a sensitivity of 86%, and a specificity of 72% for FS indels. Application of DDIG-in (FS) to NS variants yields essentially the same performance (MCC of 0.43) as a method that was specifically trained for NS variants. DDIG-in (FS) was shown to make a significant improvement over existing techniques. Availability and implementation : The DDIG-in web-server for predicting NS variants, FS indels, and non-frameshifting (NFS) indels is available at http://sparks-lab.org/ddig . Contact : yaoqi.zhou@griffith.edu.au 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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  • 3
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    Tuning carrier density at complex oxide interface with metallic overlayer (2016)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2016-06-09
    Description: We have systematically investigated the electronic transport properties of the LaAlO 3 /SrTiO 3 interfaces with several different metal capping layers. The sheet carrier density can be tuned in a wide range by the metallic overlayer without changing the carrier mobility. The sheet carrier density variation is found to be linearly dependent on the size of metal work function. This behavior is explained by the mechanism of the charge transfer between the oxide interface and the metal overlayer across the LaAlO 3 layer. Our results confirm the existence of a built-in electric field in LaAlO 3 film with an estimated value of 67.7 eV/Å. Since the metallic overlayer is essential for devices, the present phenomena must be considered for future applications.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 4
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    MAPK/JNK signaling: A potential autophagy regulation pathway (2015)
    Portland Press
    Details
    Publication Date: 2015-04-23
    Description: Autophagy refers to a lysosomal degradative pathway or a process of self-cannibalization. This pathway maintains nutrients levels for vital cellular functions during periods of starvation and it provides cells with survival advantages under various stress situations. However, the mechanisms responsible for the induction and regulation of autophagy are poorly understood. The c-Jun NH2-terminal kinase (JNK) signal transduction pathway functions to induce defense mechanisms that protect organisms against acute oxidative and xenobiotic insults. This pathway has also been repeatedly linked to the molecular events involved in autophagy regulation. This review will focus on recent advances in understanding of the relationship between MAPK/JNK signaling and autophagic cell death.
    Print ISSN: 0144-8463
    Electronic ISSN: 1573-4935
    Topics: Biology , Chemistry and Pharmacology
    Published by Portland Press
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  • 5
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    Ferromagnetic Enhancement of CE-Type Spin Ordering in (Pr,Ca)MnO_{3} (2011)
    American Physical Society (APS)
    Details
    Publication Date: 2011-05-05
    Description: Author(s): S. Y. Zhou, Y. Zhu, M. C. Langner, Y.-D. Chuang, P. Yu, W. L. Yang, A. G. Cruz Gonzalez, N. Tahir, M. Rini, Y.-H. Chu, R. Ramesh, D.-H. Lee, Y. Tomioka, Y. Tokura, Z. Hussain, and R. W. Schoenlein We present resonant soft x-ray scattering results from small bandwidth manganites (Pr,Ca)MnO_{3} , which show that the CE-type spin ordering (SO) at the phase boundary is stabilized only below the canted antiferromagnetic transition temperature and enhanced by ferromagnetism in the macroscopically i... [Phys. Rev. Lett. 106, 186404] Published Wed May 04, 2011
    Keywords: Condensed Matter: Electronic Properties, etc.
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
    Published by American Physical Society (APS)
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  • 6
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    The novel long non-coding RNA CRG regulates Drosophila locomotor behavior (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-14
    Description: Long non-coding RNAs (lncRNAs) that have no protein-coding capacity make up a large proportion of the transcriptome of various species. Many lncRNAs are expressed within the animal central nervous system in spatial- and temporal-specific patterns, indicating that lncRNAs play important roles in cellular processes, neural development, and even in cognitive and behavioral processes. However, relatively little is known about their in vivo functions and underlying molecular mechanisms in the nervous system. Here, we report a neural-specific Drosophila lncRNA, CASK regulatory gene ( CRG ), which participates in locomotor activity and climbing ability by positively regulating its neighboring gene CASK (Ca 2+ /calmodulin-dependent protein kinase). CRG deficiency led to reduced locomotor activity and a defective climbing ability—phenotypes that are often seen in CASK mutant. CRG mutant also showed reduced CASK expression level while CASK over-expression could rescue the CRG mutant phenotypes in reciprocal. At the molecular level, CRG was required for the recruitment of RNA polymerase II to the CASK promoter regions, which in turn enhanced CASK expression. Our work has revealed new functional roles of lncRNAs and has provided insights to explore the pathogenesis of neurological diseases associated with movement disorders.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Myostatin induces mitochondrial metabolic alteration and typical apoptosis in cancer cells (2013)
    Springer Nature
    Details
    Publication Date: 2013-02-15
    Description: Myostatin induces mitochondrial metabolic alteration and typical apoptosis in cancer cells Cell Death and Disease 4, e494 (February 2013). doi:10.1038/cddis.2013.31 Authors: Y Liu, H Cheng, Y Zhou, Y Zhu, R Bian, Y Chen, C Li, Q Ma, Q Zheng, Y Zhang, H Jin, X Wang, Q Chen & D Zhu
    Keywords: myostatinapoptosisVDAC1/HKIImitochondrial metabolism
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
    Published by Springer Nature
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  • 8
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    Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic (2016)
    Oxford University Press
    Details
    Publication Date: 2016-02-02
    Description: Motivation : The three dimensional tertiary structure of a protein at near atomic level resolution provides insight alluding to its function and evolution. As protein structure decides its functionality, similarity in structure usually implies similarity in function. As such, structure alignment techniques are often useful in the classifications of protein function. Given the rapidly growing rate of new, experimentally determined structures being made available from repositories such as the Protein Data Bank, fast and accurate computational structure comparison tools are required. This paper presents SPalignNS, a non-sequential protein structure alignment tool using a novel asymmetrical greedy search technique. Results : The performance of SPalignNS was evaluated against existing sequential and non-sequential structure alignment methods by performing trials with commonly used datasets. These benchmark datasets used to gauge alignment accuracy include (i) 9538 pairwise alignments implied by the HOMSTRAD database of homologous proteins; (ii) a subset of 64 difficult alignments from set (i) that have low structure similarity; (iii) 199 pairwise alignments of proteins with similar structure but different topology; and (iv) a subset of 20 pairwise alignments from the RIPC set. SPalignNS is shown to achieve greater alignment accuracy (lower or comparable root-mean squared distance with increased structure overlap coverage) for all datasets, and the highest agreement with reference alignments from the challenging dataset (iv) above, when compared with both sequentially constrained alignments and other non-sequential alignments. Availability and implementation : SPalignNS was implemented in C++. The source code, binary executable, and a web server version is freely available at: http://sparks-lab.org Contact : yaoqi.zhou@griffith.edu.au
    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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    Model Misfit Minimization (2019)
    Seismological Society of America (SSA)
    Details
    Publication Date: 2019
    Description: 〈span〉〈div〉Abstract〈/div〉In geophysical applications, solutions to ill‐posed inverse problems Ax=b are often obtained by analyzing the trade‐off between data residue ‖Ax−b‖2 and model norm ‖x‖2. In this study, we show that the traditional L‐curve analysis does not lead to solutions closest to the true models because the maximum curvature (or the corner of the L‐curve) depends on the relative scaling between data residue and model norm. A Bayes approach based on empirical risk function minimization using training datasets may be designed to find a statistically optimal solution, but its success depends on the true realization of the model. To overcome this limitation, we construct training models using eigenvectors of matrix ATA as well as spectral coefficients calculated from the correlation between observations and eigenvector projected data. This approach accounts for data noise level but does not require it as 〈span〉a priori〈/span〉 knowledge. Using global tomography as an example, we show that the solutions are closest to true models.〈/span〉
    Print ISSN: 0037-1106
    Electronic ISSN: 1943-3573
    Topics: Geosciences , Physics
    Published by Seismological Society of America (SSA)
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  • 10
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    Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome (2013)
    Oxford University Press
    Details
    Publication Date: 2013-12-07
    Description: Defining the target genes of distal regulatory elements (DREs), such as enhancer, repressors and insulators, is a challenging task. The recently developed Hi-C technology is designed to capture chromosome conformation structure by high-throughput sequencing, and can be potentially used to determine the target genes of DREs. However, Hi-C data are noisy, making it difficult to directly use Hi-C data to identify DRE–target gene relationships. In this study, we show that DREs–gene pairs that are confirmed by Hi-C data are strongly phylogenetic correlated, and have thus developed a method that combines Hi-C read counts with phylogenetic correlation to predict long-range DRE–target gene relationships. Analysis of predicted DRE–target gene pairs shows that genes regulated by large number of DREs tend to have essential functions, and genes regulated by the same DREs tend to be functionally related and co-expressed. In addition, we show with a couple of examples that the predicted target genes of DREs can help explain the causal roles of disease-associated single-nucleotide polymorphisms located in the DREs. As such, these predictions will be of importance not only for our understanding of the function of DREs but also for elucidating the causal roles of disease-associated noncoding single-nucleotide polymorphisms.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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