86 research outputs found
Sediment dynamics in the lower Mekong River : transition from tidal river to estuary
Author Posting. © American Geophysical Union, 2015. 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 120 (2015): 6363–6383, doi:10.1002/2015JC010754.A better understanding of flow and sediment dynamics in the lowermost portions of large-tropical rivers is essential to constraining estimates of worldwide sediment delivery to the ocean. Flow velocity, salinity, and suspended-sediment concentration were measured for 25 h at three cross sections in the tidal Song Hau distributary of the Mekong River, Vietnam. Two campaigns took place during comparatively high-seasonal and low-seasonal discharge, and estuarine conditions varied dramatically between them. The system transitioned from a tidal river with ephemeral presence of a salt wedge during high flow to a partially mixed estuary during low flow. The changing freshwater input, sediment sources, and estuarine characteristics resulted in seaward sediment export during high flow and landward import during low flow. The Dinh An channel of the Song Hau distributary exported sediment to the coast at a rate of about 1 t s−1 during high flow and imported sediment in a spatially varying manner at approximately 0.3 t s−1 during low flow. Scaling these values results in a yearly Mekong sediment discharge estimate about 65% smaller than a generally accepted estimate of 110 Mt yr−1, although the limited temporal and spatial nature of this study implies a relatively high degree of uncertainty for the new estimate. Fluvial advection of sediment was primarily responsible for the high-flow sediment export. Exchange-flow and tidal processes, including local resuspension, were principally responsible for the low-flow import. The resulting bed-sediment grain size was coarser and more variable during high flow and finer during low, and the residual flow patterns support the maintenance of mid-channel islands.Office of Naval Research Grant Numbers: N00014-12-1-0181 , N00014-13-1-0127 , N00014-13-1-0781, and National Defense Science and Engineering2016-03-2
Petrographic Characteristics and Depositional Environment Evolution of Middle Miocene Sediments in the Thien Ung - Mang Cau Structure of Nam Con Son Basin
This paper introduces the petrographic characteristics and depositional environment of Middle Miocene rocks of the Thien Ung - Mang Cau structure in the central area of Nam Con Son Basin based on the results of analyzing thin sections and structural characteristics of core samples. Middle Miocene sedimentary rocks in the studied area can be divided into three groups: (1) Group of terrigenous rocks comprising greywacke sandstone, arkosic sandstone, lithic-quartz sandstone, greywacke-lithic sandstone, oligomictic siltstone, and bitumenous claystone; (2) Group of carbonate rocks comprising dolomitic limestone and bituminous limestone; (3) Mixed group comprising calcareous sandstone, calcarinate sandstone, arenaceous limestone, calcareous claystone, calcareous silty claystone, dolomitic limestone containing silt, and bitumen. The depositional environment is expressed through petrographic characteristics and structure of the sedimentary rocks in core samples. The greywacke and arkosic sandstones are of medium grain size, poor sorting and roundness, and siliceous cement characterizing the alluvial and estuarine fan environment expressed by massive structure of core samples. The mixed calcareous limestone, arenaceous dolomitic limestone, and calcareous and bituminous clayey siltstone in the core samples are of turbulent flow structure characterizing shallow bay environment with the action of bottom currents. The dolomitic limestones are of relatively homogeneous, of microgranular and fine-granular texture, precipitated in a weakly reducing, semi-closed, and relatively calm bay environment
Implicit and explicit solvent models for the simulation of a single polymer chain in solution: Lattice Boltzmann vs Brownian dynamics
We present a comparative study of two computer simulation methods to obtain
static and dynamic properties of dilute polymer solutions. The first approach
is a recently established hybrid algorithm based upon dissipative coupling
between Molecular Dynamics and lattice Boltzmann (LB), while the second is
standard Brownian Dynamics (BD) with fluctuating hydrodynamic interactions.
Applying these methods to the same physical system (a single polymer chain in a
good solvent in thermal equilibrium) allows us to draw a detailed and
quantitative comparison in terms of both accuracy and efficiency. It is found
that the static conformations of the LB model are distorted when the box length
L is too small compared to the chain size. Furthermore, some dynamic properties
of the LB model are subject to an finite size effect, while the BD
model directly reproduces the asymptotic behavior. Apart from
these finite size effects, it is also found that in order to obtain the correct
dynamic properties for the LB simulations, it is crucial to properly thermalize
all the kinetic modes. Only in this case, the results are in excellent
agreement with each other, as expected. Moreover, Brownian Dynamics is found to
be much more efficient than lattice Boltzmann as long as the degree of
polymerization is not excessively large.Comment: 11 figures, submitted to J. Chem. Phy
LVM-Med: Learning Large-Scale Self-Supervised Vision Models for Medical Imaging via Second-order Graph Matching
Obtaining large pre-trained models that can be fine-tuned to new tasks with
limited annotated samples has remained an open challenge for medical imaging
data. While pre-trained deep networks on ImageNet and vision-language
foundation models trained on web-scale data are prevailing approaches, their
effectiveness on medical tasks is limited due to the significant domain shift
between natural and medical images. To bridge this gap, we introduce LVM-Med,
the first family of deep networks trained on large-scale medical datasets. We
have collected approximately 1.3 million medical images from 55 publicly
available datasets, covering a large number of organs and modalities such as
CT, MRI, X-ray, and Ultrasound. We benchmark several state-of-the-art
self-supervised algorithms on this dataset and propose a novel self-supervised
contrastive learning algorithm using a graph-matching formulation. The proposed
approach makes three contributions: (i) it integrates prior pair-wise image
similarity metrics based on local and global information; (ii) it captures the
structural constraints of feature embeddings through a loss function
constructed via a combinatorial graph-matching objective; and (iii) it can be
trained efficiently end-to-end using modern gradient-estimation techniques for
black-box solvers. We thoroughly evaluate the proposed LVM-Med on 15 downstream
medical tasks ranging from segmentation and classification to object detection,
and both for the in and out-of-distribution settings. LVM-Med empirically
outperforms a number of state-of-the-art supervised, self-supervised, and
foundation models. For challenging tasks such as Brain Tumor Classification or
Diabetic Retinopathy Grading, LVM-Med improves previous vision-language models
trained on 1 billion masks by 6-7% while using only a ResNet-50.Comment: Update Appendi
BIOCHEMICAL AND ELECTROCHEMICAL CHARACTERIZATION OF BIOFILMS FORMED ON EVEROLIMUS-ELUTING CORONARY STENTS
Drug-eluting stents (DES) are mostly used in percutaneous coronary intervention, which is the main treatment for
coronary artery occlusion. This procedure aims to restore the natural lumen, while minimizing the risk of
restenosis. However, stent insertion increases the risk for infections, due to contamination of the device or
insertion hub with normal skin flora. While coronary stent infection is a rare complication, it can be fatal.
Currently, there is little information on biofilm formation on everolimus-eluting stents. Although everolimus is
not designed as an antimicrobial agent, its antimicrobial activity should be investigated. In this study, biofilm
formation on everolimus-eluting and bare metal stents (BMS) is characterized through biochemical and electrochemical
methods. DES and BMS are inoculated with Pseudomonas aeruginosa and Staphylococcus epidermidis,
both independently and in co-culture. Biofilms formed on DES were 49.6 %, 12.9 % and 47.5 % higher than on
BMS for P. aeruginosa, S. epidermidis and their co-culture, respectively. Further, the charge output for DES was
18.9 % and 59.7 % higher than BMS for P. aeruginosa and its co-culture with S. epidermidis, respectively. This
observation is most likely due to higher surface roughness of DES, which favors biofilm formation. This work
shows that bioelectrochemical methods can be used for rapid detection of biofilms on drug-eluting and bare
metal stents, which may find application in quality assessment of stents and in characterization of stents removed
after polymicrobial infections
CBESW: Sequence Alignment on the Playstation 3
<p>Abstract</p> <p>Background</p> <p>The exponential growth of available biological data has caused bioinformatics to be rapidly moving towards a data-intensive, computational science. As a result, the computational power needed by bioinformatics applications is growing exponentially as well. The recent emergence of accelerator technologies has made it possible to achieve an excellent improvement in execution time for many bioinformatics applications, compared to current general-purpose platforms. In this paper, we demonstrate how the PlayStation<sup>® </sup>3, powered by the Cell Broadband Engine, can be used as a computational platform to accelerate the Smith-Waterman algorithm.</p> <p>Results</p> <p>For large datasets, our implementation on the PlayStation<sup>® </sup>3 provides a significant improvement in running time compared to other implementations such as SSEARCH, Striped Smith-Waterman and CUDA. Our implementation achieves a peak performance of up to 3,646 MCUPS.</p> <p>Conclusion</p> <p>The results from our experiments demonstrate that the PlayStation<sup>® </sup>3 console can be used as an efficient low cost computational platform for high performance sequence alignment applications.</p
Mapping for engagement: setting up a community based participatory research project to reach underserved communities at risk for Hepatitis C in Ho Chi Minh City, Vietnam
Background: Approximately 1. 07 million people in Vietnam are infected with hepatitis C virus (HCV). To address this epidemic, the South East Asian Research Collaborative in Hepatitis (SEARCH) launched a 600-patient cohort study and two clinical trials, both investigating shortened treatment strategies for chronic HCV infection with direct-acting antiviral drugs. We conducted ethnographic research with a subset of trial participants and found that the majority were aware of HCV infection and its implications and were motivated to seek treatment. However, people who inject drugs (PWID), and other groups at risk for HCV were under-represented, although injecting drug use is associated with high rates of HCV. Material and Methods: We designed a community-based participatory research (CBPR) study to engage in dialogues surrounding HCV and other community-prioritized health issues with underserved groups at risk for HCV in Ho Chi Minh City. The project consists of three phases: situation analysis, CBPR implementation, and dissemination. In this paper, we describe the results of the first phase (i.e., the situation analysis) in which we conducted desk research and organized stakeholder mapping meetings with representatives from local non-government and community-based organizations where we used participatory research methods to identify and analyze key stakeholders working with underserved populations. Results: Twenty six institutions or groups working with the key underserved populations were identified. Insights about the challenges and dynamics of underserved communities were also gathered. Two working groups made up of representatives from the NGO and CBO level were formed. Discussion: Using the information provided by local key stakeholders to shape the project has helped us to build solid relationships, give the groups a sense of ownership from the early stages, and made the project more context specific. These steps are not only important preliminary steps for participatory studies but also for other research that takes place within the communities
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