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  • 1
    Publication Date: 2014-01-04
    Description: BACKGROUND Autophagy has recently been found to play important roles in tumorigenesis and leucine-rich pentatricopeptide repeat motif-containing protein (LRPPRC) has been identified as an inhibitor that suppresses autophagy and mitophagy and maintains mitochondrial activity. The authors hypothesized that LRPPRC levels can be used as a biomarker for the diagnosis and prognosis of prostate cancer. METHODS Immunochemistry analysis was performed to evaluate the levels of LRPPRC in 112 samples collected from patients with prostate adenocarcinoma (PCa) and 38 samples from patients with benign prostatic hyperplasia (BPH) who were enrolled in hospitals in Guangzhou City, China and were followed for 10 years. RESULTS Significantly higher levels of LRPPRC were found in PCa samples compared with BPH samples. Greater than 75% of patients with PCa demonstrated high levels of LRPPRC whereas only 10% of patients with BPH were found to have similar levels of LRPPRC. The levels of LRPPRC were found to be positively correlated with tumor grade, metastasis, and serum prostate-specific antigen level, but were negatively correlated with hormone therapy sensitivity after 2 years of surgery and overall survival. The association between high levels of LRPPRC and late-stage PCa or hormone therapy insensitivity was confirmed in tissue samples collected from prostate-specific phosphatase and tensin homolog ( PTEN ) -/- mice or hormone-dependent and hormone-independent PCa cell lines. CONCLUSIONS LRPPRC levels may be used as an independent biomarker for patients with PCa at a late stage with poor prognosis. Cancer 2013;. © 2013 American Cancer Society .
    Print ISSN: 0008-543X
    Electronic ISSN: 1097-0142
    Topics: Biology , Medicine
    Published by Wiley-Blackwell on behalf of The American Cancer Society.
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  • 2
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2016. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 121 (2016): 4392–4415, doi:10.1002/2016JC011634.
    Description: A high-resolution (up to 2 km), unstructured-grid, fully coupled Arctic sea ice-ocean Finite-Volume Community Ocean Model (AO-FVCOM) was employed to simulate the flow and transport through the Canadian Arctic Archipelago (CAA) over the period 1978–2013. The model-simulated CAA outflow flux was in reasonable agreement with the flux estimated based on measurements across Davis Strait, Nares Strait, Lancaster Sound, and Jones Sounds. The model was capable of reproducing the observed interannual variability in Davis Strait and Lancaster Sound. The simulated CAA outflow transport was highly correlated with the along-strait and cross-strait sea surface height (SSH) difference. Compared with the wind forcing, the sea level pressure (SLP) played a dominant role in establishing the SSH difference and the correlation of the CAA outflow with the cross-strait SSH difference can be explained by a simple geostrophic balance. The change in the simulated CAA outflow transport through Davis Strait showed a negative correlation with the net flux through Fram Strait. This correlation was related to the variation of the spatial distribution and intensity of the slope current over the Beaufort Sea and Greenland shelves. The different basin-scale surface forcings can increase the model uncertainty in the CAA outflow flux up to 15%. The daily adjustment of the model elevation to the satellite-derived SSH in the North Atlantic region outside Fram Strait could produce a larger North Atlantic inflow through west Svalbard and weaken the outflow from the Arctic Ocean through east Greenland.
    Description: NSF Grant Numbers: OCE-1203393, PLR-1203643; National Natural Science Foundation of China Grant Number: 41276197; Shanghai Pujiang Program Grant Number: 12PJ1404100; Shanghai Shuguang Program
    Description: 2016-12-25
    Keywords: Water transport ; Canadian Arctic Archipelago ; Atmospheric forcing ; Sea surface height
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 3
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 113 (2008): C07052, doi:10.1029/2007JC004328.
    Description: The tidal flooding/drying process in the Satilla River Estuary was examined using an unstructured-grid finite-volume coastal ocean model (FVCOM). Driven by tidal forcing at the open boundary and river discharge at the upstream end, FVCOM produced realistic tidal flushing in this estuarine tidal-creek intertidal salt-marsh complex, amplitudes and phases of the tidal wave, and salinity observed at mooring sites and along hydrographic transects. The model-predicted residual flow field is characterized by multiscale eddies in the main channel, which are verified by ship-towed ADCP measurements. To examine the impact of complex coastal geometry on water exchange in an estuarine tidal-creek salt-marsh system, FVCOM was compared with our previous structured-grid finite difference Satilla River Estuary model (ECOM-si). The results suggest that by failing to resolve the complex coastal geometry of tidal creeks, barriers and islands, a model can generate unrealistic flow and water exchange and thus predict the wrong dynamics for this estuary. A mass-conservative unstructured-grid model is required to accurately and efficiently simulate tidal flow and flushing in a complex geometrically controlled estuarine dynamical system.
    Description: This research was supported by the Georgia Sea grant (NA26RG0373 and NA66RG0282), the NOAA grant (NA16OP2323), and the NSF grants (OCE0234545, OCE0606928, OCE0712903, OCE0732084, and OCE0726851) for C. Chen, by the Georgia Sea grant (RR746-007/7512067, R/HAB-12-PD, R/HAB-18-PD, RR746-011/7876867), Georgia DNR (RR 100-279-9262764), and NSF grant (OCE-0554674) for C. Li.
    Keywords: Estuary ; Tidal creek ; Salt marsh
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 4
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2013. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 118 (2013): 1624, doi:10.1002/jgrc.20114.
    Description: 2013-09-30
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 5
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Biogeosciences 10 (2013): 5439-5449, doi:10.5194/bg-10-5439-2013.
    Description: The 11 March 2011 tsunami triggered by the M9 and M7.9 earthquakes off the Tōhoku coast destroyed facilities at the Fukushima Dai-ichi Nuclear Power Plant (FNPP) leading to a significant long-term flow of the radionuclide 137Cs into coastal waters. A high-resolution, global-coastal nested ocean model was first constructed to simulate the 11 March tsunami and coastal inundation. Based on the model's success in reproducing the observed tsunami and coastal inundation, model experiments were then conducted with differing grid resolution to assess the initial spread of 137Cs over the eastern shelf of Japan. The 137Cs was tracked as a conservative tracer (without radioactive decay) in the three-dimensional model flow field over the period of 26 March–31 August 2011. The results clearly show that for the same 137Cs discharge, the model-predicted spreading of 137Cs was sensitive not only to model resolution but also the FNPP seawall structure. A coarse-resolution (∼2 km) model simulation led to an overestimation of lateral diffusion and thus faster dispersion of 137Cs from the coast to the deep ocean, while advective processes played a more significant role when the model resolution at and around the FNPP was refined to ∼5 m. By resolving the pathways from the leaking source to the southern and northern discharge canals, the high-resolution model better predicted the 137Cs spreading in the inner shelf where in situ measurements were made at 30 km off the coast. The overestimation of 137Cs concentration near the coast is thought to be due to the omission of sedimentation and biogeochemical processes as well as uncertainties in the amount of 137Cs leaking from the source in the model. As a result, a biogeochemical module should be included in the model for more realistic simulations of the fate and spreading of 137Cs in the ocean.
    Description: This project was supported by the US National Science Foundation RAPID grants No. 1141697 and No. 1141785 and the Japan Science and Technology Agency J-RAPID program. The development of Global-FVCOM was supported by NSF grants ARC0712903, ARC0732084, and ARC0804029. Z. Lai’s contribution was supported by the Natural Science Foundation of China project 41206005, China MOST project 2012CB956004, and Sun Yat-Sen University 985 grant 42000-3281301. C. Chen serves as chief scientist for the International Center for Marine Studies, Shanghai Ocean University, and his contribution was supported by the Program of Science and Technology Commission of Shanghai Municipality (09320503700).
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 6
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2010. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 115 (2010): C10039, doi:10.1029/2009JC006085.
    Description: Wetland-estuarine-shelf interaction processes in the Plum Island Sound and Merrimack River system in the Massachusetts coast are examined using the high-resolution unstructured grid, finite volume, primitive equations, coastal ocean model. The computational domain covers the estuarine and entire intertidal area with a horizontal resolution of 10–200 m. Driven by five tidal constituents forcing at the open boundary on the inner shelf of the eastern coast of the Gulf of Maine, the model has successfully simulated the 3-D flooding/drying process, temporal variability, and spatial distribution of salinity as well as the water exchange flux through the water passage between the Plum Island Sound and Merrimack River. The model predicts a complex recirculation loop around the Merrimack River, shelf, and Plum Island Sound. During the ebb tide, salt water in the Plum Island Sound is injected into the Merrimack River, while during flood tide, a significant amount of the freshwater in the Merrimack River is forced into Plum Island Sound. This water exchange varies with the magnitude of freshwater discharge and wind conditions, with a maximum contribution of ∼30%–40% variability in salinity over tidal cycles in the mouth of the Merrimack River. Nonlinear tidal rectification results in a complex clockwise residual recirculation loop around the Merrimack River, shelf, and Plum Island Sound. The net water flux from Plum Island Sound to the Merrimack River varies with the interaction between tide, river discharge, and wind forcing. This interaction, in turn, affects the salt transport from this system to the shelf. Since the resulting water transport into the shelf significantly varies with the variability of the wind, models that fail to resolve this complex estuarine and shelf system could either overestimate or underestimate the salt content over the shelf.
    Description: The development of FVCOM is supported by NSF grants (OCE‐0234545, OCE‐0227679, OCE‐0606928, OCE‐ 0712903, OCE‐0726851, OCE‐0814505, ARC0712903, ARC0732084, and ARC0804029), MIT Sea Grant funds (2006‐RC‐103 and 2010‐R/ RC‐116) and NOAA NERACOOS Program for the UMASS team. C. Chen’s contribution is also supported by Shanghai Ocean University International Cooperation Program (No. A‐2302‐10‐0003), the Program of Science and Technology Commission of Shanghai Municipality (No. 09320503700), the Leading Academic Discipline Project of Shanghai Municipal Education Commission (Project numbers: J50702), and Zhi jiang Scholar and 111 project funds of the State Key Laboratory for Estuarine and Coastal Research, East China Normal University (ECNU).
    Keywords: Plum Island Sound ; Merrimack River ; FVCOM ; Circulation
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 7
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2013. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 118 (2013): 2685–2701, doi:10.1002/jgrc.20207.
    Description: Hurricane Bob moved up the U.S. east coast and crossed over southern New England and the Gulf of Maine [with peak marine winds up to 54 m/s (100 mph)] on 19–20 August 1991, causing significant damage along the coast and shelf. A 3-D fully wave-current-coupled finite-volume community ocean model system was developed and applied to simulate and examine the coastal ocean responses to Hurricane Bob. Results from process study-oriented experiments showed that the impact of wave-current interaction on surge elevation varied in space and time, more significant over the shelf than inside the inner bays. While sea level change along the coast was mainly driven by the water flux controlled by barotropic dynamics and the vertically integrated highest water transports were essentially the same for cases with and without water stratification, the hurricane-induced wave-current interaction could generate strong vertical current shear in the stratified areas, leading to a strong offshore transport near the bottom and vertical turbulent mixing over the continental shelf. Stratification could also result in a significant difference of water currents around islands where the water is not vertically well mixed.
    Description: This work was supported by the MIT Sea Grant College Program through grant 2012-R/RC-127 and the NOAA NERACOOS Program funds for NECOFS. The development of the FVCOM system has been supported by the NSF Ocean Sciences Division through grants OCE-0234545, OCE-0227679, OCE-0606928, and OCE- 0712903 and the NSF Office of Polar Programs-Arctic Sciences Division through grants ARC0712903, ARC0732084, ARC0804029, and ARC1203393. C.C.’s contribution was also supported by Shanghai Ocean University International Cooperation Program (A-2302-11-0003), the Program of Science and Technology Commission of Shanghai Municipality (09320503700), and the Leading Academic Discipline Project of Shanghai Municipal Education Commission (J50702).
    Description: 2013-11-30
    Keywords: Hydrodynamic modeling ; Surface waves and tides ; Tsunamis ; Storm surges
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 8
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2013. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 118 (2013): 5054–5073, doi:10.1002/jgrc.20397.
    Description: The Integrated Ocean Observing System Super-regional Coastal Modeling Testbed had one objective to evaluate the capabilities of three unstructured-grid fully current-wave coupled ocean models (ADCIRC/SWAN, FVCOM/SWAVE, SELFE/WWM) to simulate extratropical storm-induced inundation in the US northeast coastal region. Scituate Harbor (MA) was chosen as the extratropical storm testbed site, and model simulations were made for the 24–27 May 2005 and 17–20 April 2007 (“Patriot's Day Storm”) nor'easters. For the same unstructured mesh, meteorological forcing, and initial/boundary conditions, intermodel comparisons were made for tidal elevation, surface waves, sea surface elevation, coastal inundation, currents, and volume transport. All three models showed similar accuracy in tidal simulation and consistency in dynamic responses to storm winds in experiments conducted without and with wave-current interaction. The three models also showed that wave-current interaction could (1) change the current direction from the along-shelf direction to the onshore direction over the northern shelf, enlarging the onshore water transport and (2) intensify an anticyclonic eddy in the harbor entrance and a cyclonic eddy in the harbor interior, which could increase the water transport toward the northern peninsula and the southern end and thus enhance flooding in those areas. The testbed intermodel comparisons suggest that major differences in the performance of the three models were caused primarily by (1) the inclusion of wave-current interaction, due to the different discrete algorithms used to solve the three wave models and compute water-current interaction, (2) the criterions used for the wet-dry point treatment of the flooding/drying process simulation, and (3) bottom friction parameterizations.
    Description: This project was supported by NOAA via the U.S.IOOS Office (award: NA10NOS0120063 and NA11NOS0120141) and was managed by the Southeastern Universities Research Association. The Scituate FVCOM setup was supported by the NOAA-funded IOOS NERACOOS program for NECOFS and the MIT Sea Grant College Program through grant 2012-R/RC-127.
    Description: 2014-04-07
    Keywords: Intermodel comparisons ; Inundation prediction
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 9
    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This is the author's version of the work and is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Progress in Oceanography 143 (2016): 26-45, doi:10.1016/j.pocean.2016.02.005.
    Description: CODAR-derived surface currents in Block Island Sound over the period of June 2000 through September 2008 were compared to currents computed using the Northeast Coastal Ocean Forecast System (NECOFS). The measurement uncertainty of CODAR-derived currents, estimated using statistics of a screened nine-year time series of hourly-averaged flow field, ranged from 3-7 cm/s in speed and 4°-14° in direction. The CODAR-derived and model-computed kinetic energy spectrum densities were in good agreement at subtidal frequencies, but the NECOFS-derived currents were larger by about 28% at semi-diurnal and diurnal tidal frequencies. The short-term (hourly to daily) current variability was dominated by the semidiurnal tides (predominantly the M2 tide), which on average accounted for ~87% of the total kinetic energy. The diurnal tidal and subtidal variability accounted for ~4% and ~9% of the total kinetic energy, respectively. The monthly-averaged difference between the CODAR-derived and model-computed velocities over the study area was 6 cm/s or less in speed and 28° or less in direction over the study period. An EOF analysis for the low-frequency vertically-averaged model current field showed that the water transport in the Block Island Sound region was dominated by modes 1 and 2, which accounted for 89% and 7% of the total variance, respectively. Mode 1 represented a relatively stationary spatial and temporal flow pattern with a magnitude that varied with season. Mode 2 was characterized mainly by a secondary cross-shelf flow and a relatively strong along-shelf flow. Process-oriented model experiments indicated that the relatively stationary flow pattern found in mode 1 was a result of tidal rectification and its magnitude changed with seasonal stratification. Correlation analysis between the flow and wind stress suggested that the cross-shelf water transport and its temporal variability in mode 2 were highly correlated to the surface wind forcing. The mode 2 derived onshore and offshore water transport, and was consistent with wind-driven Ekman theory. The along-shelf water transport over the outer shelf, where a large portion of the water flowed from upstream Nantucket Shoals, was not highly correlated to the surface wind stress.
    Description: This work was supported by the NSF grants OCE-1332207 and OCE-1332666, MIT Sea Grant College Program through grant 2012-R/RC-127, and the NOAA NERACOOS program funds for NECOFS. Operational funding for the CODAR systems used in this study was provided by the Mid-Atlantic Regional Association Coastal Ocean Observing System. The development of the Global-FVCOM system has been supported by NSF grants OCE-1203393. C. Chen’s contribution was also supported by the International Center for Marine Studies at Shanghai Ocean University through the “Shanghai Universities First-class Disciplines Project”.
    Description: 2017-03-04
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 10
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2009. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 114 (2009): C02006, doi:10.1029/2008JC004831.
    Description: The Changjiang River (CR) is divided into a southern branch (SB) and a northern branche (NB) by Chongming Island as the river enters the East China Sea. Observations reveal that during the dry season the saltwater in the inner shelf of the East China Sea flows into the CR through the NB and forms an isolated mass of saltwater in the upstream area of the SB. The physical mechanism causing this saltwater intrusion has been studied using the high-resolution unstructured-grid Finite-Volume Coastal Ocean Model (FVCOM). The results suggest that the intrusion is caused by a complex nonlinear interaction process in relation to the freshwater flux upstream, tidal currents, mixing, wind, and the salt distribution in the inner shelf of the East China Sea. The tidal rectification, resulting from the interaction of the convergence or divergence of tidal momentum flux and bottom friction over abrupt topography, produces a net upstreamward volume flux from NB to SB. With river discharge the net water transport in the NB is driven through a momentum balance of surface elevation gradient forcing, horizontal advection, and vertical diffusion. In the dry season, reducing the surface elevation gradient forcing makes tidal rectification a key process favorable for the saltwater intrusion. A northerly wind tends to enhance the saltwater intrusion by reducing the seaward surface elevation gradient forcing rather than either the baroclinic pressure gradient forcing or the wind-driven Ekman transport. A convergence experiment suggests that high grid resolution (∼100 m or less) is required to correctly resolve the net water transport through the NB, particularly in the narrow channel on the northern coast of Chongming Island.
    Description: The development of FVCOM is supported by the Massachusetts Fisheries Institute through NOAA grants DOC/ NOAA/NA04NMF4720332 and DOC/NOAA/NA05NMF4721131; NSF grants OCE-0234545, OCE-0227679, OCE-0606928, OCE-0712903, OCE-0732084, OCE-0726851, ARC0712903; ARC0732084, and ARC0804029; NOAA grant NA160P2323; and an ONR subcontract grant from the Woods Hole Oceanographic Institution. The development of the nested modeling approach is supported by MIT and URI Sea Grant projects NA060AR41700019 and R/P-061. C. Chen serves as Zi Jiang Scholar at the State Key Laboratory for Estuarine and Coastal Research, East China Normal University (ECNU), and is an adjunct professor at Shanghai Ocean University (SHOU). His contribution is also supported by both ECNU and SHOU. P. Ding is supported by the Chinese National Key Basic Research Project grant 2002CB412403.
    Keywords: Estuary dynamics ; Saltwater intrusion ; Tidal rectification
    Repository Name: Woods Hole Open Access Server
    Type: Article
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