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  • 1
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ocean Modelling 121 (2018): 49-75, doi:10.1016/j.ocemod.2017.11.008.
    Description: Lagrangian analysis is a powerful way to analyse the output of ocean circulation models and other ocean velocity data such as from altimetry. In the Lagrangian approach, large sets of virtual particles are integrated within the three-dimensional, time-evolving velocity fields. Over several decades, a variety of tools and methods for this purpose have emerged. Here, we review the state of the art in the field of Lagrangian analysis of ocean velocity data, starting from a fundamental kinematic framework and with a focus on large-scale open ocean applications. Beyond the use of explicit velocity fields, we consider the influence of unresolved physics and dynamics on particle trajectories. We comprehensively list and discuss the tools currently available for tracking virtual particles. We then showcase some of the innovative applications of trajectory data, and conclude with some open questions and an outlook. The overall goal of this review paper is to reconcile some of the different techniques and methods in Lagrangian ocean analysis, while recognising the rich diversity of codes that have and continue to emerge, and the challenges of the coming age of petascale computing.
    Description: EvS has received funding from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation programme (grant agreement No 715386). This research for PJW was supported as part of the Energy Exascale Earth System Model (E3SM) project, funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research. Funding for HFD was provided by Grant No. DE-SC0012457 from the US Department of Energy. PB acknowledges support for this work from NERC grant NE/R011567/1. SFG is supported by NERC National Capability funding through the Extended Ellett Line Programme.
    Keywords: Ocean circulation ; Lagrangian analysis ; Connectivity ; Particle tracking ; Future modelling
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of agricultural and food chemistry 26 (1978), S. 1253-1255 
    ISSN: 1520-5118
    Source: ACS Legacy Archives
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
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  • 3
    Publication Date: 2021-02-08
    Description: Highlights: • Lagrangian ocean analysis is a powerful way to analyse the output of ocean circulation models • We present a review of the Kinematic framework, available tools, and applications of Lagrangian ocean analysis • While there are unresolved questions, the framework is robust enough to be used widely in ocean modelling Abstract: Lagrangian analysis is a powerful way to analyse the output of ocean circulation models and other ocean velocity data such as from altimetry. In the Lagrangian approach, large sets of virtual particles are integrated within the three-dimensional, time-evolving velocity fields. Over several decades, a variety of tools and methods for this purpose have emerged. Here, we review the state of the art in the field of Lagrangian analysis of ocean velocity data, starting from a fundamental kinematic framework and with a focus on large-scale open ocean applications. Beyond the use of explicit velocity fields, we consider the influence of unresolved physics and dynamics on particle trajectories. We comprehensively list and discuss the tools currently available for tracking virtual particles. We then showcase some of the innovative applications of trajectory data, and conclude with some open questions and an outlook. The overall goal of this review paper is to reconcile some of the different techniques and methods in Lagrangian ocean analysis, while recognising the rich diversity of codes that have and continue to emerge, and the challenges of the coming age of petascale computing.
    Type: Article , PeerReviewed
    Format: text
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  • 4
    Publication Date: 2015-03-10
    Description: Oral squamous cell carcinoma (OSCC) is a common human malignant tumor with high mortality. So far, the molecular pathogenesis of OSCC remains largely unclear. Heterogeneous nuclear ribonucleoprotein (HnRNP) A1 is an important multi-function splicing factor and closely related to tumorigenesis. HnRNP A1 is overexpressed in various tumors, and promotes aerobic glycolysis and elongation of telomere, but the function of hnRNP A1 in cell cycle and proliferation remains unclear. We found that hnRNP A1 was overexpressed in OSCC tissues, and was required for the growth of OSCC cells. Moreover, hnRNP A1 was highly expressed in the G2/M cell cycle phase. Knockdown of hnRNP A1 induced G2/M arrest. DNA microarray assay result showed that hnRNP A1 regulated the expression of a number of target genes associated with G2/M phase. Moreover, hnRNP A1 controlled the alternative splicing of CDK2 exon 5. These findings suggested that hnRNP A1 plays key roles in the regulation of cell cycle progression and pathogenesis of OSCC. This article is protected by copyright. All rights reserved
    Electronic ISSN: 1097-4652
    Topics: Biology , Medicine
    Published by Wiley-Blackwell
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  • 5
    Publication Date: 2015-03-10
    Description: Glucuronidation is a major metabolism process of detoxification for carcinogens, 4-(methylnitrosamino)-1-(3-pyridy)-1-butanone (NNK) and 1,2-dimethylhydrazine (DMH), of reactive oxygen species (ROS). However, intestinal E. coli   -glucuronidase (eG) has been considered pivotal to colorectal carcinogenesis. Specific inhibition of eG may prevent reactivating the glucuronide-carcinogen and protect the intestine from ROS-mediated carcinogenesis. In order to develop specific eG inhibitors, we found that 59 candidate compounds obtained from the initial virtual screening had high inhibition specificity against eG but not human G. In particular, we found that compounds 7145 and 4041 with naphthalenylidene-benzenesulfonamide (NYBS) are highly effective and selective to inhibit eG activity. Compound 4041  (μM) shows a higher inhibiting ability than compound 7145  (μM) against eG. Furthermore, the molecular docking analysis indicates that compound 4041 has two hydrophobic contacts to residues L361 and I363 in the bacterial loop, but 7145 has one contact to L361. Only compound 4041 can bind to key residue (E413) at active site of eG via hydrogen-bonding interactions. These novel NYBS-based eG specific inhibitors may provide as novel candidate compounds, which specifically inhibit eG to reduce eG-based carcinogenesis and intestinal injury.
    Electronic ISSN: 1537-744X
    Topics: Natural Sciences in General
    Published by Hindawi
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  • 6
    Publication Date: 2015-05-07
    Description: The ninety day toxicity and toxicokinetics of fluorochloridone (FLC) were accessed in Wistar rats. Animals were gavaged with FLC at doses of 31.25 mg/kg, 125 mg/kg and 500 mg/kg for ninety days, followed by thirty days for recovery. On the 1st, 60th, 75th and 90th days of the dosing phase, plasma of ten animals of all groups treated with FLC was collected for toxicokinetic analysis of FLC by an UPLC-MS/MS method. Numerous changes in body weight, hematology, serum chemistry, and organ weight ratios were observed by the 45th and 90th dosing day. Most changes in groups treated with FLC were absent on the last recovery day. Testis and epididymis lesions were consistently seen in histopathological observations on the 45th, 90th dosing day and the last recovery day. Repeated administration of FLC increased the level of testosterone in serum in male rats on the 90th dosing day. FLC plasma concentrations could be detected in all animal drug-treated groups during the dosing phase, and a dose proportional relationship was seen between FLC dose and AUC or Cmax. This study will support future studies on the mechanism of FLC-induced toxicity.
    Print ISSN: 1661-7827
    Electronic ISSN: 1660-4601
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
    Published by MDPI Publishing
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  • 7
    Publication Date: 2015-12-04
    Description: Background: Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited. Results: In the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted other carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions. Conclusions: Our study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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  • 8
    Publication Date: 2015-06-18
    Description: Manganese-enhanced MRI studies have proven to be useful in monitoring physiological activities associated with calcium ions (Ca 2+ ) due to the paramagnetic property of the manganese ion (Mn 2+ ), which makes it an excellent probe of Ca 2+ . In this study, we developed a method in which a Mn 2+ -enhanced T 1 -map MRI could enable the monitoring of Ca 2+ influx during the early stages of intestinal ischemia–reperfusion (I/R) injury. The Mn 2+ infusion protocol was optimized by obtaining dose-dependent and time-course wash-out curves using a Mn 2+ -enhanced T 1 -map MRI of rabbit abdomens following an intravenous infusion of 50 mmol/l MnCl 2 (5–10 nmol/g body weight (BW)). In the rabbit model of intestinal I/R injury, T 1 values were derived from the T 1 maps in the intestinal wall region and revealed a relationship between the dose of the infused MnCl 2 and the intestinal wall relaxation time. Significant Mn 2+ clearance was also observed over time in control animals after the infusion of Mn 2+ at a dose of 10 nmol/g BW. This technique was also shown to be sensitive enough to monitor variations in calcium ion homeostasis in vivo after small intestinal I/R injury. The T 1 values of the intestinal I/R group were significantly lower ( P  〈 0.05) than that of the control group at 5, 10, and 15 min after Mn 2+ infusion. Our data suggest that MnCl 2 has the potential to be an MRI contrast agent that can be effectively used to monitor changes in intracellular Ca 2+ homeostasis during the early stages of intestinal I/R injury. Copyright © 2015 John Wiley & Sons, Ltd. Manganese (Mn 2+ ) acts as an excellent probe of calcium ion (Ca 2+ ) influx for monitoring Ca 2+ -associated physiological activities in a Mn 2+ -enhanced MRI (MEMRI) study. In this study, we prospectively demonstrated that Mn 2+ -enhanced T 1 -map MRI has the sensitivity to monitor variations in Ca 2+ homeostasis in vivo directly related to Ca 2+ overload in the early stage of intestinal ischemia–reperfusion injury. MEMRI provides additional information in intestinal ischemia–reperfusion injury models used to monitor disease development.
    Print ISSN: 0952-3480
    Electronic ISSN: 1099-1492
    Topics: Medicine
    Published by Wiley-Blackwell
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  • 9
    Publication Date: 2015-12-19
    Description: This paper presents an AC-excited argon discharge generated using a gas-liquid (two-phase) hybrid plasma reactor, which mainly consists of a powered needle electrode enclosed in a conical quartz tube and grounded deionized water electrode. The discharges in the gas-phase, as well as in the two-phase, exhibit two discharge modes, i.e., the low current glow-like diffuse mode and the high current streamer-like constrict mode, with a mode transition, which exhibits a negative resistance of the discharges. The optical emission spectral analysis shows that the stronger diffusion of the water vapor into the discharge region in the two-phase discharges boosts up the generation of OH (A–X) radicals, and consequently, leads to a higher rotational temperature in the water-phase plasma plume than that of the gas-phase discharges. Both the increase of the power input and the decrease of the argon flow rate result in the increase of the rotational temperature in the plasma plume of the water-phase discharge. The stable two-phase discharges with a long plasma plume in the water-phase under a low power input and gas flow rate may show a promising prospect for the degradation of organic pollutants, e.g., printing and dyeing wastewater, in the field of environmental protection.
    Print ISSN: 1070-664X
    Electronic ISSN: 1089-7674
    Topics: Physics
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  • 10
    Publication Date: 2015-08-08
    Description: Article In situ probing electrochemical interfaces is important for the development of improved electrocatalysts. Here, the authors present an on-chip electrical transport spectroscopy approach, which enables in situ monitoring the dynamic electrochemical interface characteristics. Nature Communications doi: 10.1038/ncomms8867 Authors: Mengning Ding, Qiyuan He, Gongming Wang, Hung-Chieh Cheng, Yu Huang, Xiangfeng Duan
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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