| 1. |
- Duan, Ming-Rui, et al.
(författare)
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DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein
- 2007
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 35:4, s. 54-1145
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Tidskriftsartikel (refereegranskat)abstract
- WRKY proteins, defined by the conserved WRKYGQK sequence, are comprised of a large superfamily of transcription factors identified specifically from the plant kingdom. This superfamily plays important roles in plant disease resistance, abiotic stress, senescence as well as in some developmental processes. In this study, the Arabidopsis WRKY1 was shown to be involved in the salicylic acid signaling pathway and partially dependent on NPR1; a C-terminal domain of WRKY1, AtWRKY1-C, was constructed for structural studies. Previous investigations showed that DNA binding of the WRKY proteins was localized at the WRKY domains and these domains may define novel zinc-binding motifs. The crystal structure of the AtWRKY1-C determined at 1.6 A resolution has revealed that this domain is composed of a globular structure with five beta strands, forming an antiparallel beta-sheet. A novel zinc-binding site is situated at one end of the beta-sheet, between strands beta4 and beta5. Based on this high-resolution crystal structure and site-directed mutagenesis, we have defined and confirmed that the DNA-binding residues of AtWRKY1-C are located at beta2 and beta3 strands. These results provided us with structural information to understand the mechanism of transcriptional control and signal transduction events of the WRKY proteins.
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| 2. |
- Liu, Ming, et al.
(författare)
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ATCA-based Computation Platform for Data Acquisition and Triggering in Particle Physics Experiments
- 2008
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Ingår i: 2008 INTERNATIONAL CONFERENCE ON FIELD PROGRAMMABLE AND LOGIC APPLICATIONS, VOLS 1 AND 2. ; , s. 287-292
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Konferensbidrag (refereegranskat)abstract
- An ATCA-based computation platform for data acquisition and trigger applications in nuclear and particle physics experiments has been developed. Each Compute Node (CN) which appears as a Field Replaceable Unit (FRU) in an ATCA shelf, features 5 Xilinx Virtex-4 FX60 FPGAs and up to 10 GBytes DDR2 memory. Connectivity is provided with 8 optical links and 5 Gigabit Ethernet ports, which are mounted on each board to receive data from detectors and forward results to outer shelves or PC farms with attached mass storage. Fast point-to-point on-board interconnections between FPGAs as well as the full-mesh shelf backplane provide flexibility and high bandwidth to partition algorithms and correlate results among them. The system represents a highly reconfigurable and scalable solution for multiple applications.
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| 3. |
- Liu, Ming, et al.
(författare)
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Trigger algorithm development on FPGA-based Compute Nodes
- 2009
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Ingår i: 2009 16th IEEE-NPSS Real Time Conference. - New York : IEEE. - 9781424457960 ; , s. 478-484
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Konferensbidrag (refereegranskat)abstract
- Based on the ATCA computation architecture and Compute Nodes (CN), investigation and implementation work has been being executed for HADES and PANDA trigger algorithms. We present our designs for HADES track reconstruction processing, Cherenkov ring recognition, Time-Of-Flight processing, electromagnetic shower recognition.. and the PANDA straw tube tracking algorithm. They will appear as co-processors in the uniform system design to undertake the detector-specific computing. The algorithm principles will be explained and hardware designs are described in the paper. The current progress reveals the feasibility to implement these algorithms on FPGAs. Also experimental results demonstrate the performance speedup when compared to alternative software solutions, as well as the potential capability of high-speed parallel/pipelined processing in Data Acquisition and Trigger systems.
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| 4. |
- Wang, Qiang, et al.
(författare)
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Hardware/Software Co-design of an ATCA-based Computation Platform for Data Acquisition and Triggering
- 2009
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Ingår i: 16th IEEE NPSS Real Time Conference. - 9781424457960 ; , s. 485-489
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Konferensbidrag (refereegranskat)abstract
- An ATCA-based computation platform for data acquisition and trigger(TDAQ) applications has been developed for multiple future projects such its PANDA. HADES, and BESIII. Each Compute Node (CN) appears as one (if the fourteen Field Replaceable Units (FRU) in an ATCA shelf, which in total features a high performance of 1890 Clips inter-FPGA on-board channels, 1456 Gbps inter-board backplane connections, 728 Gbps full-duplex optical links, 70 Gbps Ethernet. 140 GBytes DDR2 SDRAM. and all computing resources of 70 Xilinx Virtex-4 FX60 FPGAs. Corresponding to (the system architecture, a hardware/software co-design approach is proposed to ease and accelerate the development for different experiments. In the uniform system design. application-specific computation is to be implemented as customized hardware co-processors, while the embedded PowerPC processor takes charge of flexible slow controls and transmission protocol processing.
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| 5. |
- He, Lu-Jun, et al.
(författare)
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Genetic polymorphisms of N-acetyltransferase 2 and colorectal cancer risk.
- 2005
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Ingår i: World Journal of Gastroenterology. - 1007-9327 .- 2219-2840. ; 11:27, s. 4268-4271
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Tidskriftsartikel (refereegranskat)abstract
- AIM: To identify the distribution of N-acetyltrasferase 2(NAT2) polymorphism in Hebei Han Chinese and the effects of the polymorphism on the development of colorectal cancer. METHODS: We performed a hospital-based case-control study of 237 healthy individuals and 83 colorectal cancer patients of Hebei Han Chinese. DNA was extracted from peripheral blood and cancer tissues. The genotypes of the polymorphisms were assessed by PCR-restriction fragment length polymorphism (RFLP). RESULTS: There were four NAT2 alleles of WT, M1, M2, and M3 both in the healthy subjects and in the patients, and 10 genotypes of WT/WT, WT/M1, WT/M2, WT/M3, M1/M1, M1/M2, M1/M3, M2/M2, M2/M3, M3/M3. M2 allele was present in 15.61% of healthy subjects and 29.52% of patients (chi(2) = 15.31, P<0.0001), and M3 allele was present in 30.59% of healthy subjects and 16.87% of patients (chi(2) = 25.33, P<0.0001). There were more WT/M2 (chi(2) = 34.42, P<0.0001, odd ratio = 4.99, 95%CI = 2.27-9.38) and less WT/M3 (chi(2) = 3.80, P = 0.03) in the patients than in the healthy subjects. In 70.3% of the patients, there was a difference in NAT2 genotype between their tumors and blood cells. Patients had more WT/M2 (chi(2) = 5.11, P = 0.02) and less M2/M3 (chi(2) = 4.27, P = 0.039) in their blood cells than in the tumors. Furthermore, 53.8% (7/13) of M2/M3 in tumors were from WT/M2 of blood cells. CONCLUSION: There is a possible relationship between the NAT2 polymorphisms and colorectal cancer in Hebei Han Chinese. The genotype WT/M2 may be a risk factor for colorectal cancer.
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| 6. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
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Ingår i: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
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Forskningsöversikt (refereegranskat)abstract
- Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.
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| 7. |
- Liu, Ming, 1982-
(författare)
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A High-end Reconfigurable Computation Platform for Particle Physics Experiments
- 2008
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Modern nuclear and particle physics experiments run at a very high reaction rate and are able to deliver a data rate of up to hundred GBytes/s. This data rate is far beyond the storage and on-line analysis capability. Fortunately physicists have only interest in a very small proportion among the huge amounts of data. Therefore in order to select the interesting data and reject the background by sophisticated pattern recognition processing, it is essential to realize an efficient data acquisition and trigger system which results in a reduced data rate by several orders of magnitude. Motivated by the requirements from multiple experiment applications, we are developing a high-end reconfigurable computation platform for data acquisition and triggering. The system consists of a scalable number of compute nodes, which are fully interconnected by high-speed communication channels. Each compute node features 5 Xilinx Virtex-4 FX60 FPGAs and up to 10 GBytesDDR2 memory. A hardware/software co-design approach is proposed to develop custom applications on the platform, partitioning performance-critical calculation to the FPGA hardware fabric while leaving flexible and slow controls to the embedded CPU plus the operating system. The system is expected to be high-performance and general-purpose for various applications especially in the physics experiment domain. As a case study, the particle track reconstruction algorithm for HADES has been developed and implemented on the computation platform in the format of processing engines. The Tracking Processing Unit (TPU) recognizes peak bins on the projection plane and reconstructs particle tracks in realtime. Implementation results demonstrate its acceptable resource utilization and the feasibility to implement the module together with the sys-tem design on the FPGA. Experimental results show that the online track reconstruction computation achieves 10.8 - 24.3 times performance acceleration per TPU module when compared to the software solution on a Xeon2.4 GHz commodity server.
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| 8. |
- Liu, Ming, et al.
(författare)
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A Reconfigurable Design Framework for FPGA Adaptive Computing
- 2009
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Ingår i: 2009 INTERNATIONAL CONFERENCE ON RECONFIGURABLE COMPUTING AND FPGAS. - : IEEE. - 9781424452934 ; , s. 439-444
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Konferensbidrag (refereegranskat)abstract
- Partial Reconfiguration (PR) offers the possibility to adaptively change part of the FPGA design without stopping the remaining system. In this paper, we present a comprehensive framework for adaptive computing, in which design key points of hardware processes, system interconnections, Operating Systems (OS), device drivers, scheduler software as well as context switching are respectively concerned in different hardware/software layers. A case study is discussed to demonstrate an example of swapping a Flash memory controller and an SRAM controller in response to diverse memory access needs. Result analysis reveals a more efficient resource utilization of 52.1% I/O pads, 86.5% LUTs and 81.3% Flip-Flops, when compared to the static design with same functionalities. A small reconfiguration overhead of context switching is measured within the range from hundreds of microseconds to milliseconds. Moreover, technical perspectives are analyzed and it is foreseen to obtain great benefits with the proposed design framework in object applications of particle physics experiments.
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| 9. |
- Liu, Ming, et al.
(författare)
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Hardware/Software co-design of a general-purpose computation platform in particle physics
- 2007
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Ingår i: ICFPT 2007. - 9781424414710 ; , s. 177-183
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Konferensbidrag (refereegranskat)abstract
- In this paper we present a hardware/software co-design based computation platform for online data processing in particle physics experiments. Our goal is to ease and accelerate the development and make it universal and scalable for multiple applications, on the premise of guaranteeing high communicating and processing capabilities. The entire computation network consists of quite a few interconnected compute nodes, each of which has multiple FPGAs to implement specific algorithms for data processing. High-speed communication features including RocketIO multi-gigabit transceiver and Gigabit Ethernet are supported by FPGAs to construct internal and external connections. An embedded Linux operating system is fitted on the PowerPC CPU core inside the Xilinx Virtex-4 FX FPGA. Thus programmers can access hardware resources via device drivers and write application programs to manage the system from the high level. Furthermore measurements have been executed using the development board to investigate both communicating and processing performances of the system. Results show that the computation platform is able to communicate at a UDP/IP data rate of around 400 Mbps per Ethernet link, and the event selection engine could process an event rate of 25%.
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| 10. |
- Liu, Ming, et al.
(författare)
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Run-time Partial Reconfiguration Speed Investigation and Architectural Design Space Exploration
- 2009
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Ingår i: FPL 09. - 9781424438914 ; , s. 498-502
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Konferensbidrag (refereegranskat)abstract
- Run-time Partial Reconfiguration (PR) speed is significant in applications especially when fast IP core switching is required. In this paper, we propose to use Direct Memory Access (DMA), Master (MST) burst, and a dedicated Block RAM (BRAM) cache respectively to reduce the reconfiguration time. Based on the Xilinx PR technology and the Internal Configuration Access Port (ICAP) primitive in the FPGA fabric, we discuss multiple design architectures and thoroughly investigate their performance with measurements for different partial bitstream sizes. Compared to the reference OPB_HWICAP and XPS_HWICAP designs, experimental results show that DMA_HWICAP and MST_HWICAP reduce the reconfiguration time by one order of magnitude, with little resource consumption overhead. The BRAM_HWICAP design can even approach the reconfiguration speed limit of the ICAP primitive at the cost of large Block RAM utilization.
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