ALBERT

Description: The frequency content of strong ground motions from subduction slab earthquakes differs significantly from that of ground motions produced by other categories (tectonic locations: shallow crustal, upper mantle, and subduction interface) of earthquakes in subduction zones. In the last two decades, a large number of records from subduction slab events have been obtained in Japan. We present a ground-motion prediction equation (GMPE) for this category of earthquakes. We used a large dataset from reliably identified slab events up to the end of 2012. The GMPEs were based on a set of simple geometric attenuation functions, site classes were used as site terms, and nonlinear site amplification ratios were adopted. A bilinear magnitude-scaling function was adopted for large earthquakes with moment magnitude M w ≥7.1, with the scaling rates for large events being much smaller than for the smaller events. A magnitude-squared term was used for events with M w 〈7.1 as well as the bilinear magnitude-scaling function. We also modeled the effect of volcanic zones using an anelastic attenuation coefficient applied to a horizontal portion of the seismic-wave travel distance within possible volcanic zones. We found that excluding the records from sites with inferred site classes improved the model goodness of fit. The within-event residuals were approximately separated into within-site and between-site residuals, and the corresponding standard deviations were calculated using a random effects model. The separation of within-event residuals into within-site and between-site components allows for the possibility of adopting different standard deviations for different site classes in a probabilistic seismic-hazard analysis if desired. Online Material: Figures showing the distribution of between-event residuals with respect to magnitude and fault-top depth and the distribution of within-event residuals with respect to magnitude and source distance.

Description: We report an investigation of a GeSn-based p-i-n photodetector grown on a Ge wafer that collects light signal from the back of the wafer. Temperature dependent absorption measurements performed over a wide temperature range (300 K down to 25 K) show that (a) absorption starts at the indirect bandgap of the active GeSn layer and continues up to the direct bandgap of the Ge wafer, and (b) the peak responsivity increases rapidly at first with decreasing temperature, then increases more slowly, followed by a decrease at the lower temperatures. The maximum responsivity happens at 125 K, which can easily be achieved with the use of liquid nitrogen. The temperature dependence of the photocurrent is analyzed by taking into consideration of the temperature dependence of the electron and hole mobility in the active layer, and the analysis result is in reasonable agreement with the data in the temperature regime where the rapid increase occurs. This investigation demonstrates the feasibility of a GeSn-based photodiode that can be operated with back-side illumination for applications in image sensing systems.

Description: Owing to the importance of the post-translational modifications (PTMs) of proteins in regulating biological processes, the dbPTM ( http://dbPTM.mbc.nctu.edu.tw/ ) was developed as a comprehensive database of experimentally verified PTMs from several databases with annotations of potential PTMs for all UniProtKB protein entries. For this 10th anniversary of dbPTM, the updated resource provides not only a comprehensive dataset of experimentally verified PTMs, supported by the literature, but also an integrative interface for accessing all available databases and tools that are associated with PTM analysis. As well as collecting experimental PTM data from 14 public databases, this update manually curates over 12 000 modified peptides, including the emerging S -nitrosylation, S -glutathionylation and succinylation, from approximately 500 research articles, which were retrieved by text mining. As the number of available PTM prediction methods increases, this work compiles a non-homologous benchmark dataset to evaluate the predictive power of online PTM prediction tools. An increasing interest in the structural investigation of PTM substrate sites motivated the mapping of all experimental PTM peptides to protein entries of Protein Data Bank (PDB) based on database identifier and sequence identity, which enables users to examine spatially neighboring amino acids, solvent-accessible surface area and side-chain orientations for PTM substrate sites on tertiary structures. Since drug binding in PDB is annotated, this update identified over 1100 PTM sites that are associated with drug binding. The update also integrates metabolic pathways and protein–protein interactions to support the PTM network analysis for a group of proteins. Finally, the web interface is redesigned and enhanced to facilitate access to this resource.

Description: Protein Numb, first identified as a cell-fate determinant in Drosophila, has been shown to promote the development of neurites in mammals and to be cotransported with endocytic receptors in clathrin-coated vesicles in vitro. Nevertheless, its function in mature neurons has not yet been elucidated. Here we show that cerebellar Purkinje...

Description: Many $${\mathrm{CO}}_{2}$$ -rich (up to 97% by volume) natural gas pools have been found in the continental margin basins of the northern South China Sea. By combining the geochemical data from 53 samples with their geologic backgrounds, this study investigated the origins and accumulation mechanism of $${\mathrm{CO}}_{2}$$ , and discussed the role of $${\mathrm{CO}}_{2}$$ in driving oil as it charged the reservoirs. The results reveal that the $${\mathrm{CO}}_{2}$$ gases in the Yinggehai basin originate mainly from the thermal decomposition of both Miocene calcareous shales and Paleozoic carbonates, and that $${\mathrm{CO}}_{2}$$ from mantle degassing is only a minor contributor. The $${\mathrm{CO}}_{2}$$ accumulations in the Yinggehai basin are mainly controlled by diapiric faults and episodic thermal fluid movements. The $${\mathrm{CO}}_{2}$$ gases in the eastern Qiongdongnan and western Pearl River Mouth basins are mainly related to magmatic or mantle degassing, and the volatiles from magmatic degassing during the igneous intrusion stage are the most likely major source of $${\mathrm{CO}}_{2}$$ in these reservoirs, with basement faults providing pathways for upward migration of $${\mathrm{CO}}_{2}$$ -rich mantle fluids. Natural displacements of oil by $${\mathrm{CO}}_{2}$$ appear to be common in the eastern Qiongdongnan and western Pearl River Mouth basins. The $${\mathrm{CO}}_{2}$$ -flooded oil or gas reservoirs have two common features that the present $${\mathrm{CO}}_{2}$$ gas pools or oil-bearing structures have residual oils representing prior charge, and are close to the basement faults that provide pathways along which the mantle-derived $${\mathrm{CO}}_{2}$$ -rich gas was migrated. The oils from prior hydrocarbon reservoirs have been naturally driven out by $${\mathrm{CO}}_{2}$$ to form secondary oil reservoirs in the eastern Qiongdongnan and western Pearl River Mouth basins. Therefore, a full understanding of the origin and distribution of $${\mathrm{CO}}_{2}$$ cannot just be used to trace hydrocarbon migration pathways, but also provide useful information for risk assessment prior to drilling.

Description: Author(s): X. L. Xu, J. F. Hua, F. Li, C. J. Zhang, L. X. Yan, Y. C. Du, W. H. Huang, H. B. Chen, C. X. Tang, W. Lu, P. Yu, W. An, C. Joshi, and W. B. Mori The evolution of beam phase space in ionization injection into plasma wakefields is studied using theory and particle-in-cell simulations. The injection process involves both longitudinal and transverse phase mixing, leading initially to a rapid emittance growth followed by oscillation, decay, and a... [Phys. Rev. Lett. 112, 035003] Published Thu Jan 23, 2014

Description: The newly developed transcription activator-like effector protein (TALE) and clustered regularly interspaced short palindromic repeats/Cas9 transcription factors (TF) offered a powerful and precise approach for modulating gene expression. In this article, we systematically investigated the potential of these new tools in activating the stringently silenced pluripotency gene Oct4 ( Pou5f1 ) in mouse and human somatic cells. First, with a number of TALEs and sgRNAs targeting various regions in the mouse and human Oct4 promoters, we found that the most efficient TALE-VP64s bound around –120 to –80 bp, while highly effective sgRNAs targeted from –147 to –89-bp upstream of the transcription start sites to induce high activity of luciferase reporters. In addition, we observed significant transcriptional synergy when multiple TFs were applied simultaneously. Although individual TFs exhibited marginal activity to up-regulate endogenous gene expression, optimized combinations of TALE-VP64s could enhance endogenous Oct4 transcription up to 30-fold in mouse NIH3T3 cells and 20-fold in human HEK293T cells. More importantly, the enhancement of OCT4 transcription ultimately generated OCT4 proteins. Furthermore, examination of different epigenetic modifiers showed that histone acetyltransferase p300 could enhance both TALE-VP64 and sgRNA/dCas9-VP64 induced transcription of endogenous OCT4 . Taken together, our study suggested that engineered TALE-TF and dCas9-TF are useful tools for modulating gene expression in mammalian cells.

Description: Author(s): F. Li, J. F. Hua, X. L. Xu, C. J. Zhang, L. X. Yan, Y. C. Du, W. H. Huang, H. B. Chen, C. X. Tang, W. Lu, C. Joshi, W. B. Mori, and Y. Q. Gu The production of ultrabright electron bunches using ionization injection triggered by two transversely colliding laser pulses inside a beam-driven plasma wake is examined via three-dimensional particle-in-cell simulations. The relatively low intensity lasers are polarized along the wake axis and ov... [Phys. Rev. Lett. 111, 015003] Published Tue Jul 02, 2013

Description: Motivation: Staining the mRNA of a gene via in situ hybridization (ISH) during the development of a Drosophila melanogaster embryo delivers the detailed spatio-temporal patterns of the gene expression. Many related biological problems such as the detection of co-expressed genes, co-regulated genes and transcription factor binding motifs rely heavily on the analysis of these image patterns. To provide the text-based pattern searching for facilitating related biological studies, the images in the Berkeley Drosophila Genome Project (BDGP) study are annotated with developmental stage term and anatomical ontology terms manually by domain experts. Due to the rapid increase in the number of such images and the inevitable bias annotations by human curators, it is necessary to develop an automatic method to recognize the developmental stage and annotate anatomical terms. Results: In this article, we propose a novel computational model for jointly stage classification and anatomical terms annotation of Drosophila gene expression patterns. We propose a novel Tri - Relational Graph (TG) model that comprises the data graph, anatomical term graph, developmental stage term graph, and connect them by two additional graphs induced from stage or annotation label assignments. Upon the TG model, we introduce a Preferential Random Walk (PRW) method to jointly recognize developmental stage and annotate anatomical terms by utilizing the interrelations between two tasks. The experimental results on two refined BDGP datasets demonstrate that our joint learning method can achieve superior prediction results on both tasks than the state-of-the-art methods. Availability: http://ranger.uta.edu/%7eheng/Drosophila/ Contact: heng@uta.edu

Description: Author(s): H. Huang, H. Jang, M. Fujita, T. Nishizaki, Y. Lin, J. Wang, J. Ying, J. S. Smith, C. Kenney-Benson, G. Shen, W. L. Mao, C.-C. Kao, Y.-J. Liu, and J.-S. Lee Compelling efforts to improve the critical temperature ( T c ) of superconductors have been made through high-pressure application. Understanding the underlying mechanism behind such improvements is critically important; however, much remains unclear. Here we studied ortho-III YBa 2 Cu 3 O 6.73 (YBCO) using... [Phys. Rev. B 97, 174508] Published Wed May 09, 2018