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  • 1
    Publication Date: 2017-09-28
    Description: Recent studies have reported that thermospheric effects due to solar wind driving can be observed poleward of auroral latitudes. In these papers, the measured neutral mass density perturbations appear as narrow, localized maxima in the cusp and polar cap. They conclude that Joule heating below the spacecraft is the cause of the mass density increases which are sometimes associated with local field-aligned current structures, but not always. In this paper we investigate neutral mass densities measured by accelerometers on the CHAllenging Minisatellite Payload (CHAMP) and Gravity Recovery and Climate Experiment (GRACE) spacecraft from launch until years 2010 (CHAMP) and 2012 (GRACE), approximately 10 years of observations from each satellite. We extract local maxima in neutral mass densities over the background using a smoothing window with size of one quarter of the orbit. The maxima have been analyzed for each year, and also for the duration of each set of satellite observations. We show where they occur, under what solar wind conditions, and their relation to magnetic activity. The region with the highest frequency of occurrence coincides approximately with the cusp and mantle, with little direct evidence of an auroral zone source. Our conclusions agree with the “hot polar cap” observations which have been reported and studied in the past.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 2
    Publication Date: 2015-11-05
    Description: Overpressure and buoyant effect of underlying sediments are generally used to account for the upward motion or formation of submarine mud volcanoes and mud diapirs. In this study, we process and interpret the gravity anomalies associated with the active mud diapirs off SW Taiwan. Geologically, the mud diapirs are just formed and are still very active, thus we can better understand the initial process of the mud diapirs formation through the gravity analysis. Our results show that the density contrasts of the submarine mud diapirs with respect to the surroundings are generally positive. Because the study area is in a tectonically compressive regime and the gas plume venting from the submarine mud volcanoes is very active, we thus infer that mechanically the mud diapirs off SW Taiwan have been formed mainly due to the tectonic compression on the underlying sediments of high pore-fluid pressure, instead of the buoyancy of the buried sediments. The overpressured sediments and fluid are compressed and pushed upwards to pierce the overlying sediments and form the more compacted mud diapirs. The relatively denser material of the mud diapirs probably constrains the flowing courses of the submarine canyons off SW Taiwan, especially for the upper reaches of the Kaoping and Fangliao submarine canyons.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 3
    Publication Date: 2013-09-21
    Description: Aims Clear-cutting is a common forest management practice, especially in subtropical China. However, the potential ecological consequences of clear-cutting remain unclear. In particular, the effect of clear-cutting on soil processes, such as the carbon cycle, has not been quantified in subtropical forests. Here, we investigated the response of soil respiration (Rs) to clear-cutting during a 12-month period in a subtropical forest in eastern China. Methods We randomly selected four clear-cut (CC) plots and four corresponding undisturbed forest (UF) plots. Measurements of Rs were made at monthly time points and were combined with continuous climatic measurements in both CC and UF. Daily Rs was estimated by interpolating data with an exponential model dependent on soil temperature. Daily Rs was cumulated to annual Rs estimates. Important Findings In the first year after clear-cutting, annual estimates of Rs in CC (508±23g C m –2 yr –1 ) showed no significant difference to UF plots (480±12g C m –2 yr –1 ). During the summer, soil temperatures were usually higher, whereas the soil volumetric water content was lower in CC than in UF plots. The long-term effects of clear-cutting on Rs are not significant, although there might be effects during the first several months after clear-cutting. Compared with previous work, this pattern was more pronounced in our subtropical forest than in the temperate and boreal forests that have been studied by others. With aboveground residuals off-site after clear-cutting, our results indicate that the stimulation of increasing root debris, as well as environmental changes, will not lead to a significant increase in Rs. In addition, long-term Rs will not show a significant decrease from the termination of root respiration, and this observation might be because of the influence of fast-growing vegetation after clear-cutting in situ .
    Print ISSN: 1752-993X
    Electronic ISSN: 1752-9921
    Topics: Biology
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  • 4
    Publication Date: 2013-06-06
    Description: Motivation: Fragmented RNA immunoprecipitation combined with RNA sequencing enabled the unbiased study of RNA epigenome at a near single-base resolution; however, unique features of this new type of data call for novel computational techniques. Result: Through examining the connections of RNA epigenome sequencing data with two well-studied data types, ChIP-Seq and RNA-Seq, we unveiled the salient characteristics of this new data type. The computational strategies were discussed accordingly, and a novel data processing pipeline was proposed that combines several existing tools with a newly developed exome-based approach ‘exomePeak’ for detecting, representing and visualizing the post-transcriptional RNA modification sites on the transcriptome. Availability: The MATLAB package ‘exomePeak’ and additional details are available at http://compgenomics.utsa.edu/exomePeak/ . Contact: yufei.huang@utsa.edu or jmeng@mit.edu 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: 2014-11-05
    Description: Influenza viruses typically cause the most severe disease in children and elderly individuals. However, H1N1 viruses disproportionately affected middle-aged adults during the 2013–2014 influenza season. Although H1N1 viruses recently acquired several mutations in the hemagglutinin (HA) glycoprotein, classic serological tests used by surveillance laboratories indicate that these mutations do not...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 6
    Publication Date: 2019
    Description: 〈p〉Genetically encoded voltage indicators (GEVIs) enable monitoring of neuronal activity at high spatial and temporal resolution. However, the utility of existing GEVIs has been limited by the brightness and photostability of fluorescent proteins and rhodopsins. We engineered a GEVI, called Voltron, that uses bright and photostable synthetic dyes instead of protein-based fluorophores, thereby extending the number of neurons imaged simultaneously in vivo by a factor of 10 and enabling imaging for significantly longer durations relative to existing GEVIs. We used Voltron for in vivo voltage imaging in mice, zebrafish, and fruit flies. In the mouse cortex, Voltron allowed single-trial recording of spikes and subthreshold voltage signals from dozens of neurons simultaneously over a 15-minute period of continuous imaging. In larval zebrafish, Voltron enabled the precise correlation of spike timing with behavior.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2019
    Description: 〈p〉Imaging changes in membrane potential using genetically encoded fluorescent voltage indicators (GEVIs) has great potential for monitoring neuronal activity with high spatial and temporal resolution. Brightness and photostability of fluorescent proteins and rhodopsins have limited the utility of existing GEVIs. We engineered a novel GEVI, "Voltron", that utilizes bright and photostable synthetic dyes instead of protein-based fluorophores, extending the combined duration of imaging and number of neurons imaged simultaneously by more than tenfold relative to existing GEVIs. We used Voltron for in vivo voltage imaging in mice, zebrafish, and fruit flies. In mouse cortex, Voltron allowed single-trial recording of spikes and subthreshold voltage signals from dozens of neurons simultaneously, over 15 min of continuous imaging. In larval zebrafish, Voltron enabled the precise correlation of spike timing with behavior.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Natural Sciences in General
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  • 8
    Publication Date: 2018
    Description: 〈p〉With accelerating trends in miniaturization of semiconductor devices, techniques for energy harvesting become increasingly important, especially in wearable technologies and sensors for the internet of things. Although thermoelectric systems have many attractive attributes in this context, maintaining large temperature differences across the device terminals and achieving low–thermal impedance interfaces to the surrounding environment become increasingly difficult to achieve as the characteristic dimensions decrease. Here, we propose and demonstrate an architectural solution to this problem, where thin-film active materials integrate into compliant, open three-dimensional (3D) forms. This approach not only enables efficient thermal impedance matching but also multiplies the heat flow through the harvester, thereby increasing the efficiencies for power conversion. Interconnected arrays of 3D thermoelectric coils built using microscale ribbons of monocrystalline silicon as the active material demonstrate these concepts. Quantitative measurements and simulations establish the basic operating principles and the key design features. The results suggest a scalable strategy for deploying hard thermoelectric thin-film materials in harvesters that can integrate effectively with soft materials systems, including those of the human body.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 9
    Publication Date: 2015-08-26
    Description: Acute hepatopancreatic necrosis disease (AHPND) is a severe, newly emergent penaeid shrimp disease caused by Vibrio parahaemolyticus that has already led to tremendous losses in the cultured shrimp industry. Until now, its disease-causing mechanism has remained unclear. Here we show that an AHPND-causing strain of V. parahaemolyticus contains a 70-kbp...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 10
    Publication Date: 2016-06-16
    Description: Motivation: N 6 -methyl-adenosine (m 6 A) is the most prevalent mRNA methylation but precise prediction of its mRNA location is important for understanding its function. A recent sequencing technology, known as Methylated RNA Immunoprecipitation Sequencing technology (MeRIP-seq), has been developed for transcriptome-wide profiling of m 6 A. We previously developed a peak calling algorithm called exomePeak. However, exomePeak over-simplifies data characteristics and ignores the reads’ variances among replicates or reads dependency across a site region. To further improve the performance, new model is needed to address these important issues of MeRIP-seq data. Results: We propose a novel, graphical model-based peak calling method, MeTPeak, for transcriptome-wide detection of m 6 A sites from MeRIP-seq data. MeTPeak explicitly models read count of an m 6 A site and introduces a hierarchical layer of Beta variables to capture the variances and a Hidden Markov model to characterize the reads dependency across a site. In addition, we developed a constrained Newton’s method and designed a log-barrier function to compute analytically intractable, positively constrained Beta parameters. We applied our algorithm to simulated and real biological datasets and demonstrated significant improvement in detection performance and robustness over exomePeak. Prediction results on publicly available MeRIP-seq datasets are also validated and shown to be able to recapitulate the known patterns of m 6 A, further validating the improved performance of MeTPeak. Availability and implementation: The package ‘MeTPeak’ is implemented in R and C ++, and additional details are available at https://github.com/compgenomics/MeTPeak Contact: yufei.huang@utsa.edu or xdchoi@gmail.com 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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