Publications by authors named "Yongfeng Gu"

6 Publications

  • Page 1 of 1

Polydatin Alleviates Septic Myocardial Injury by Promoting SIRT6-Mediated Autophagy.

Inflammation 2020 Jun;43(3):785-795

Department of Emergency Medicine, Shanghai Gongli Hospital, 219 Miao-Pu Road, Shanghai, 200135, China.

Sepsis is a life-threatening condition. Polydatin (PD), a small natural compound from Polygonum cuspidatum, possesses antioxidant and anti-inflammatory properties. However, the protective mechanism of PD on sepsis-induced acute myocardial damage is still unclear. The aim of this study was to investigate the effect and mechanism of action of PD on lipopolysaccharide (LPS)-induced H9c2 cells and in a rat model of sepsis, and explored the role of PD-upregulated sirtuin (SIRT)6. LPS-induced H9c2 cells were used to simulate sepsis. Cecal ligation and puncture (CLP)-induced sepsis in rats were used to verify the protective effect of PD. ELISA, western blotting, immunofluorescence, immunohistochemistry, and flow cytometry were used to study the protective mechanism of PD against septic myocardial injury. PD pretreatment suppressed LPS-induced H9c2 cell apoptosis by promotion of SIRT6-mediated autophagy. Downregulation of SIRT6 or inhibition of autophagy reversed the protective effect of PD on LPS-induced apoptosis. PD pretreatment also suppressed LPS-induced inflammatory factor expression. CLP-induced sepsis in rats showed that PD pretreatment decreased CLP-induced myocardial apoptosis and serum tumor necrosis factor-α, interleukin (IL)-1β, and IL-6 expression. 3-Methyladenine (autophagy inhibitor) pretreatment prevented the protective effect of PD on septic cardiomyopathy. SIRT6 expression was increased with PD treatment, which confirmed that PD attenuates septic cardiomyopathy by promotion of SIRT6-mediated autophagy. All these results indicate that PD has potential therapeutic effects that alleviate septic myocardial injury by promotion of SIRT6-mediated autophagy.
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http://dx.doi.org/10.1007/s10753-019-01153-4DOI Listing
June 2020

Synoptic weather types and long-range transport patterns for ozone precursors during high-ozone events in southern Sweden.

Ambio 2009 Dec;38(8):459-64

University of Gothenburg, Department of Earth Sciences, Sweden.

We studied long-range transport patterns and related weather types in relation to high-ozone events in southern Sweden. The aim was to deepen the understanding of the relationship between Lamb-Jenkinson weather types and surface ozone concentration variation, thus widening the application of the weather type analysis of air quality at 4 sites in this region. The long-range transport patterns associated with high-ozone events were classified into trajectories from Western Europe, Eastern Europe, and in the vicinity of southern Sweden (VIC). The VIC type, characterized by short and whirling curves, represented more than 40% of the high-ozone events at the studied rural sites. More than half of the high-ozone events occurred under high-pressure conditions, belonging to weather type A (anticyclones). The high correlation coefficient between annual counts of weather type A and those of long-range transport pattern VIC confirmed the strong link between stagnant weather conditions and high-ozone events, especially during the summer. Furthermore, a strong linear anticorrelation was detected between high-ozone events and annual counts of weather type C (cyclones) during the summer. This relationship implies that the frequency of weather type C is a useful indicator for low risk of summertime high-ozone events in southern Sweden. Moreover, the relationship between the weather type and high ozone risk may be useful in examining the potential effect of climate change on the regional air quality.
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http://dx.doi.org/10.1579/0044-7447-38.8.459DOI Listing
December 2009

Explicit Design of FPGA-Based Coprocessors for Short-Range Force Computations in Molecular Dynamics Simulations.

Parallel Comput 2008 May;34(4-5):261-277

Computer Architecture and Automated Design Lab, Department of Electrical and Computer Engineering, Boston University; Boston, MA 02215.

FPGA-based acceleration of molecular dynamics simulations (MD) has been the subject of several recent studies. The short-range force computation, which dominates the execution time, is the primary focus. Here we combine: a high level of FPGA-specific design including cell lists, systematically determined interpolation and precision, handling of exclusion, and support for MD simulations of up to 256K particles. The target system consists of a standard PC with a 2004-era COTS FPGA board. There are several innovations: new microarchitectures for several major components, including the cell list processor and the off-chip memory controller; and a novel arithmetic mode. Extensive experimentation was required to optimize precision, interpolation order, interpolation mode, table sizes, and simulation quality. We obtain a substantial speed-up over a highly tuned production MD code.
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http://dx.doi.org/10.1016/j.parco.2008.01.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2440579PMC
May 2008

Single Pass Streaming BLAST on FPGAs.

Parallel Comput 2007 Nov;33(10-11):741-756

Department of Electrical and Computer Engineering, Boston University; Boston, MA 02215, Web: http://www.bu.edu/caadlab .

Approximate string matching is fundamental to bioinformatics and has been the subject of numerous FPGA acceleration studies. We address issues with respect to FPGA implementations of both BLAST- and dynamic-programming- (DP) based methods. Our primary contribution is a new algorithm for emulating the seeding and extension phases of BLAST. This operates in a single pass through a database at streaming rate, and with no preprocessing other than loading the query string. Moreover, it emulates parameters turned to maximum possible sensitivity with no slowdown. While current DP-based methods also operate at streaming rate, generating results can be cumbersome. We address this with a new structure for data extraction. We present results from several implementations showing order of magnitude acceleration over serial reference code. A simple extension assures compatibility with NCBI BLAST.
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http://dx.doi.org/10.1016/j.parco.2007.09.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2598392PMC
November 2007

Computing Models for FPGA-Based Accelerators.

Comput Sci Eng 2008 Oct;10(6):35-45

Boston University.

Field-programmable gate arrays are widely considered as accelerators for compute-intensive applications. A critical phase of FPGA application development is finding and mapping to the appropriate computing model. FPGA computing enables models with highly flexible fine-grained parallelism and associative operations such as broadcast and collective response. Several case studies demonstrate the effectiveness of using these computing models in developing FPGA applications for molecular modeling.
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http://dx.doi.org/10.1109/MCSE.2008.143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3096930PMC
October 2008

Achieving High Performance with FPGA-Based Computing.

Computer (Long Beach Calif) 2007 Mar;40(3):50-57

Boston University.

Numerous application areas, including bioinformatics and computational biology, demand increasing amounts of processing capability. In many cases, the computation cores and data types are suited to field-programmable gate arrays. The challenge is identifying the design techniques that can extract high performance potential from the FPGA fabric.
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http://dx.doi.org/10.1109/MC.2007.79DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098506PMC
March 2007
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