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  • 1
    Publication Date: 2012-05-03
    Description: Close proximity to roadways has been associated with higher exposure to traffic-related air pollutants. However, analyses of the effects of season and meteorological parameters on horizontal gradient patterns of traffic-generated air pollutants still need to be elucidated. Our objectives were to: (1) determine effects of season on horizontal gradient patterns of polycyclic aromatic hydrocarbons (PAHs), total suspended particles (TSP), and PM2.5 near a heavily trafficked highway; and (2) examine the effect of day-of-the-week variations (weekday versus weekend) associated with traffic counts on measured airborne-contaminant levels. PAHs (Σ8PAHs [MW 228–278]; gas + particulate), TSP and PM2.5 were monitored at nominal distances (50, 100, and 150 m) from the New Jersey Turnpike every 6 days for periods of 24 h, between September 2007 and September 2008. Seasonal variations in the horizontal gradient patterns of Σ8PAHs were observed. In the summer, Σ8PAHs declined significantly between 50–100 m from the highway (23% decrease), but not between the furthermost distances (100–150 m). An inverse pattern was observed in the winter: Σ8PAHs declined between 100–150 m (26% decrease), but not between the closest distances. Σ8PAHs and TSP, but not PM2.5, concentrations measured on weekends were 12–37% lower than those on weekdays, respectively, corresponding to lower diesel traffic volume. This study suggests that people living in the close proximity to highways may be exposed to varying levels of Σ8PAHs, TSP, and PM2.5 depending on distance to highway, season, and day-of-the-week variations.
    Electronic ISSN: 2073-4433
    Topics: Geosciences
    Published by MDPI Publishing
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  • 2
    Publication Date: 2014-02-12
    Description: Growing a GaN film on a patterned Al 2 O 3 substrate is one of the methods of reducing threading dislocations (TDs), which can significantly deteriorate the performance of GaN-based LEDs. In this study, the microstructural details of the GaN film grown on a cone-shaped patterned Al 2 O 3 substrate were investigated using high-resolution transmission electron microscopy and weak-beam dark-field techniques. Various defects such as misfit dislocations (MDs), recrystallized GaN (R-GaN) islands and nano-voids were observed on the patterned Al 2 O 3 surfaces, i.e. the flat surface (FS), the inclined surface (IS) and the top surface (TS), respectively. Especially, the crystallographic orientation of R-GaN between the GaN film and the inclined Al 2 O 3 substrate was identified as $[\overline 1 2\overline 1 0]_{{\rm GaN}} \hbox{//}[\overline 1 101]_{{\rm R - GaN} \,{\rm on}\,{\rm IS}} \hbox{//}[\overline 1 100]_{ {{\rm Al}} _{\rm 2} {\rm O}_{\rm 3}} $ , $(\overline 1 012)_{{\rm GaN}} \hbox{//}(1\overline 1 02)_{{\rm R - Ga}\,{\rm Non}\,{\rm IS}} \hbox{//}(\overline {11} 26)_{ {{\rm Al}} _{\rm 2} {\rm O}_{\rm 3}} $ . In addition, a rotation by 9° between $(10\overline 1 1)_{{\rm R - GaN}} $ and $(0002)_{{\rm GaN}} $ and between $(10\overline 1 1)_{{\rm R - GaN}} $ and $(0006)_{ {{\rm Al}} _{\rm 2} {\rm O}_{\rm 3}} $ was found to reduce the lattice mismatch between the GaN film and the Al 2 O 3 substrate. Many TDs in the GaN film were observed on the FS and TS of Al 2 O 3 . However, few TDs were observed on the IS. Most of the TDs generated from the FS of Al 2 O 3 were bent to the inclined facet rather than propagating to the GaN surface, resulting in a reduction in the dislocation density. Most of the TDs generated from the TS of Al 2 O 3 were characterized as edge dislocations.
    Print ISSN: 0022-0744
    Electronic ISSN: 1477-9986
    Topics: Electrical Engineering, Measurement and Control Technology , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2011-09-22
    Description: Close proximity to roadways has been associated with higher exposure to traffic-related air pollutants. However, analyses of the effects of season and meteorological parameters on horizontal gradient patterns of traffic-generated air pollutants still need to be elucidated. Our objectives were to: (1) determine effects of season on horizontal gradient patterns of polycyclic aromatic hydrocarbons (PAHs), total suspended particles (TSP), and PM2.5 near a heavily trafficked highway; and (2) examine the effect of day-of-the-week variations (weekday versus weekend) associated with traffic counts on measured airborne-contaminant levels. PAHs (Σ8PAHs [MW 228–278]; gas + particulate), TSP and PM2.5 were monitored at nominal distances (50, 100, and 150 m) from the New Jersey Turnpike every 6 days for periods of 24 h, between September 2007 and September 2008. Seasonal variations in the horizontal gradient patterns of Σ8PAHs were observed. In the summer, Σ8PAHs declined significantly between 50–100 m from the highway (23% decrease), but not between the furthermost distances (100–150 m). An inverse pattern was observed in the winter: Σ8PAHs declined between 100–150 m (26% decrease), but not between the closest distances. Σ8PAHs and TSP, but not PM2.5, concentrations measured on weekends were 12–37% lower than those on weekdays, respectively, corresponding to lower diesel traffic volume. This study suggests that people living in the close proximity to highways may be exposed to varying levels of Σ8PAHs, TSP, and PM2.5 depending on distance to highway, season, and day-of-the-week variations.
    Electronic ISSN: 2073-4433
    Topics: Geosciences
    Published by MDPI Publishing
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  • 4
    Publication Date: 2014-04-16
    Description: A direct waveform inversion based on perturbation theory is proposed to delineate a subsurface velocity structure from seismic data. This technique can directly compute the difference between the actual subsurface velocity and an initial guess of the velocity, while full waveform inversion updates the velocity model in the directions of reducing the data residual. Unlike full waveform inversion using the steepest descent method, the direct waveform inversion does not require a proper step length to iteratively update the velocity model. We present an algorithm for the waveform inversion method in the frequency domain and numerical examples demonstrating how the inversion method can reconstruct subsurface velocity structures using surface seismic data. The time-domain seismograms synthesized in the inversion procedure match the corresponding shot-gather seismograms of field data.
    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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  • 5
    Publication Date: 2012-08-08
    Description: Motivation: Feedback circuits are crucial network motifs, ubiquitously found in many intra- and inter-cellular regulatory networks, and also act as basic building blocks for inducing synchronized bursting behaviors in neural network dynamics. Therefore, the system-level identification of feedback circuits using time-series measurements is critical to understand the underlying regulatory mechanism of synchronized bursting behaviors. Results: Multi-Step Granger Causality Method (MSGCM) was developed to identify feedback loops embedded in biological networks using time-series experimental measurements. Based on multivariate time-series analysis, MSGCM used a modified Wald test to infer the existence of multi-step Granger causality between a pair of network nodes. A significant bi-directional multi-step Granger causality between two nodes indicated the existence of a feedback loop. This new identification method resolved the drawback of the previous non-causal impulse response component method which was only applicable to networks containing no co-regulatory forward path. MSGCM also significantly improved the ratio of correct identification of feedback loops. In this study, the MSGCM was testified using synthetic pulsed neural network models and also in vitro cultured rat neural networks using multi-electrode array. As a result, we found a large number of feedback loops in the in vitro cultured neural networks with apparent synchronized oscillation, indicating a close relationship between synchronized oscillatory bursting behavior and underlying feedback loops. The MSGCM is an efficient method to investigate feedback loops embedded in in vitro cultured neural networks. The identified feedback loop motifs are considered as an important design principle responsible for the synchronized bursting behavior in neural networks. Contact: ckh@kaist.ac.kr Availability: The software implementing MSGCM is available at Supplementary Information. Supplementary Information: Supplementary material are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 6
    Publication Date: 2013-03-23
    Description: This study reports the physical and functional interplay between Fas-associated factor 1 (FAF1), a death-promoting protein, and parkin, a key susceptibility protein for Parkinson's disease (PD). We found that parkin acts as an E3 ubiquitin ligase to ubiquitinate FAF1 both in vitro and at cellular level, identifying FAF1 as a direct substrate of parkin. The loss of parkin function due to PD-linked mutations was found to disrupt the ubiquitination and degradation of FAF1, resulting in elevated FAF1 expression in SH-SY5Y cells. Moreover, FAF1-mediated cell death was abolished by wild-type parkin, but not by PD-linked parkin mutants, implying that parkin antagonizes the death potential of FAF1. This led us to investigate whether FAF1 participates in the pathogenesis of PD. To address this, we used a gene trap mutagenesis approach to generate mutant mice with diminished levels of FAF1 ( Faf1 gt/gt ). Using the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated mouse model of PD, we found that FAF1 accumulated in the substantia nigra pars compacta (SNc) of MPTP-treated PD mice, and that MPTP-induced dopaminergic cell loss in the SNc was significantly attenuated in Faf1 gt/gt mice versus Faf1 +/+ mice. MPTP-induced reduction of locomotor activity was also lessened in Faf1 gt/gt mice versus Faf1 +/+ mice. Furthermore, we found that FAF1 deficiency blocked PD-linked biochemical events, including caspase activation, ROS generation, JNK activation and cell death. Taken together, these results suggest a new role for FAF1: that of a positive modulator for PD.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 7
    Publication Date: 2012-08-29
    Description: The metalloprotease ADAMTS13 affects platelet adhesion and aggregation through depolymerization of von Willebrand factor (VWF) multimers. Identification of ADAMTS13-binding proteins would reveal the hitherto unrecognized mechanisms underlying microvascular thrombus. To identify ADAMTS13-binding proteins, we performed a yeast two-hybrid screen using the Cys-rich and spacer domains of ADAMTS13, the critical regions for the binding and cleavage of VWF, as a bait region. We identified Lys-plasminogen, an amino-terminal truncated form of plasminogen, as the binding protein to ADAMTS13. Intact Glu-plasminogen did not bind to ADAMTS13. Active-site blocked Lys-plasmin bound to ADAMTS13. Domain truncation of ADAMTS13 and elastase digest of plasminogen indicated that the Cys-rich and spacer domains of ADAMTS13 and the kringle 5 and protease domains of plasminogen served as the main binding sites. Biacore measurements revealed that Lys-plasminogen bound to ADAMTS13 with a K d of 1.9 ± 0.1 x 10 –7 M and Glu-plasminogen exhibited a significantly lower affinity to ADAMTS13. Specific activity measurements revealed that ADAMTS13 and Lys-plasmin were still active even after the binary complex was formed. The binding of ADAMTS13 to Lys-plasminogen may play an important role to localize these two proteases at sites of thrombus formation or vascular injury where the fibrinolytic system is activated.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
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  • 8
    Publication Date: 2014-05-20
    Description: MUS81 shares a high-degree homology with the catalytic XPF subunit of the XPF–ERCC1 endonuclease complex. It is catalytically active only when complexed with the regulatory subunits Mms4 or Eme1 in budding and fission yeasts, respectively, and EME1 or EME2 in humans. Although Mus81 complexes are implicated in the resolution of recombination intermediates in vivo , recombinant yeast Mus81-Mms4 and human MUS81-EME1 isolated from Escherichia coli fail to cleave intact Holliday junctions (HJs) in vitro . In this study, we show that human recombinant MUS81-EME2 isolated from E. coli cleaves HJs relatively efficiently, compared to MUS81-EME1. Furthermore, MUS81-EME2 catalyzed cleavage of nicked and gapped duplex deoxyribonucleic acids (DNAs), generating double-strand breaks. The presence of a 5' phosphate terminus at nicks and gaps rendered DNA significantly less susceptible to the cleavage by MUS81-EME2 than its absence, raising the possibility that this activity could play a role in channeling damaged DNA duplexes that are not readily repaired into the recombinational repair pathways. Significant differences in substrate specificity observed with unmodified forms of MUS81-EME1 and MUS81-EME2 suggest that they play related but non-overlapping roles in DNA transactions.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 9
    Publication Date: 2006-05-16
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 10
    Publication Date: 2010-10-18
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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