Matching-CNN Meets KNN: Quasi-Parametric Human Parsing

Both parametric and non-parametric approaches have demonstrated encouraging performances in the human parsing task, namely segmenting a human image into several semantic regions (e.g., hat, bag, left arm, face). In this work, we aim to develop a new solution with the advantages of both methodologies, namely supervision from annotated data and the flexibility to use newly annotated (possibly uncommon) images, and present a quasi-parametric human parsing model. Under the classic K Nearest Neighbor (KNN)-based nonparametric framework, the parametric Matching Convolutional Neural Network (M-CNN) is proposed to predict the matching confidence and displacements of the best matched region in the testing image for a particular semantic region in one KNN image. Given a testing image, we first retrieve its KNN images from the annotated/manually-parsed human image corpus. Then each semantic region in each KNN image is matched with confidence to the testing image using M-CNN, and the matched regions from all KNN images are further fused, followed by a superpixel smoothing procedure to obtain the ultimate human parsing result. The M-CNN differs from the classic CNN in that the tailored cross image matching filters are introduced to characterize the matching between the testing image and the semantic region of a KNN image. The cross image matching filters are defined at different convolutional layers, each aiming to capture a particular range of displacements. Comprehensive evaluations over a large dataset with 7,700 annotated human images well demonstrate the significant performance gain from the quasi-parametric model over the state-of-the-arts, for the human parsing task.Comment: This manuscript is the accepted version for CVPR 201

Structural basis for activation of trimeric Gi proteins by multiple growth factor receptors via GIV/Girdin.

A long-standing issue in the field of signal transduction is to understand the cross-talk between receptor tyrosine kinases (RTKs) and heterotrimeric G proteins, two major and distinct signaling hubs that control eukaryotic cell behavior. Although stimulation of many RTKs leads to activation of trimeric G proteins, the molecular mechanisms behind this phenomenon remain elusive. We discovered a unifying mechanism that allows GIV/Girdin, a bona fide metastasis-related protein and a guanine-nucleotide exchange factor (GEF) for Gαi, to serve as a direct platform for multiple RTKs to activate Gαi proteins. Using a combination of homology modeling, protein-protein interaction, and kinase assays, we demonstrate that a stretch of ∼110 amino acids within GIV C-terminus displays structural plasticity that allows folding into a SH2-like domain in the presence of phosphotyrosine ligands. Using protein-protein interaction assays, we demonstrated that both SH2 and GEF domains of GIV are required for the formation of a ligand-activated ternary complex between GIV, Gαi, and growth factor receptors and for activation of Gαi after growth factor stimulation. Expression of a SH2-deficient GIV mutant (Arg 1745→Leu) that cannot bind RTKs impaired all previously demonstrated functions of GIV-Akt enhancement, actin remodeling, and cell migration. The mechanistic and structural insights gained here shed light on the long-standing questions surrounding RTK/G protein cross-talk, set a novel paradigm, and characterize a unique pharmacological target for uncoupling GIV-dependent signaling downstream of multiple oncogenic RTKs

Initial spread of 137Cs from the Fukushima Dai-ichi Nuclear Power Plant over the Japan continental shelf : a study using a high-resolution, global-coastal nested ocean model

© 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.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.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)

Seasonal and interannual variability of the Arctic sea ice : a comparison between AO-FVCOM and observations

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): 8320–8350, doi:10.1002/2016JC011841.A high-resolution (up to 2 km), unstructured-grid, fully ice-sea coupled Arctic Ocean Finite-Volume Community Ocean Model (AO-FVCOM) was used to simulate the sea ice in the Arctic over the period 1978–2014. The spatial-varying horizontal model resolution was designed to better resolve both topographic and baroclinic dynamics scales over the Arctic slope and narrow straits. The model-simulated sea ice was in good agreement with available observed sea ice extent, concentration, drift velocity and thickness, not only in seasonal and interannual variability but also in spatial distribution. Compared with six other Arctic Ocean models (ECCO2, GSFC, INMOM, ORCA, NAME, and UW), the AO-FVCOM-simulated ice thickness showed a higher mean correlation coefficient of ∼0.63 and a smaller residual with observations. Model-produced ice drift speed and direction errors varied with wind speed: the speed and direction errors increased and decreased as the wind speed increased, respectively. Efforts were made to examine the influences of parameterizations of air-ice external and ice-water interfacial stresses on the model-produced bias. The ice drift direction was more sensitive to air-ice drag coefficients and turning angles than the ice drift speed. Increasing or decreasing either 10% in water-ice drag coefficient or 10° in water-ice turning angle did not show a significant influence on the ice drift velocity simulation results although the sea ice drift speed was more sensitive to these two parameters than the sea ice drift direction. Using the COARE 4.0-derived parameterization of air-water drag coefficient for wind stress did not significantly influence the ice drift velocity simulation.This work was supported by NSF grants OCE-1203393 for the UMASSD team and PLR-1203643 for R. C. Beardsley.2017-05-2

Impact of current-wave interaction on storm surge simulation : a case study for Hurricane Bob

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.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.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).2013-11-3

Reply to comment on “Current separation and upwelling over the southeast shelf of Vietnam in the South China Sea”

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.20114.2013-09-3

Surface circulation in Block Island Sound and adjacent coastal and shelf regions : a FVCOM-CODAR comparison

© 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.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.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”.2017-03-0