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Genomic evidence of lung carcinogenesis associated with coal smoke in Xuanwei area, China

National Science Review 2021年第12期8卷 15-19页

作者： Honglei Zhang Chao Liu Li Li Xu Feng Qing Wang Jihua Li Shaobin Xu Shuting Wang Qianlu Yang Zhenghai Shen Jinhua Su Xiaosan Su Ruifen Sun Xuhong Zhou Junliang Wang Yongchun Zhou Baowei Jiao Wanbao Ding Xianbao Cao Yue Wang Yunchao Huang Lianhua Ye Center for Scientific Research Yunnan University of Chinese Medicine Department of Nuclear Medicine Third Affiliated Hospital of Kunming Medical UniversityYunnan Cancer Hospital Biotherapy Center Third Affiliated Hospital of Kunming Medical University Yunnan Cancer Hospital Department of Oncology Qujing First People's Hospital Qujing Center for Disease Control and Prevention supercomputing platform of kunming institute of zoology Kunming Biological Diversity Center of Instruments Kunming Institute of Zoology Chinese Academy of Sciences Department of Thoracic Surgery Ⅱ Third Affiliated Hospital of Kunming Medical University Yunnan Cancer Hospital Department of Thoracic Surgery Ⅰ Third Affiliated Hospital of Kunming Medical University Yunnan Cancer Hospital Department of Thoracic Surgery Xuanwei People's Hospital State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases Kunming Institute of Zoology Chinese Academy of Sciences Department of Oncology Yan'an Affiliated Hospital of Kunming Medical University Department of Otolaryngology First People's Hospital of Yunnan Province the Affiliated Hospital of Kunming University of Science and Technology The Affiliated Hospital of Guizhou Medical University

Xuanwei area, in southwestern China,harbors the highest female lung cancer rate in the country(Supplementary Table 1) [1]. Epidemiological studies have shown that lung cancer incidence in Xuanwei area is associated with the use of different types of local coal for household cooking and heating [2]. The genomic landscape of Xuanwei female adenocarcinoma(XWFA), the most distinctive feature of lung cancer in Xuanwei, has yet to be elucidated systematically. Here,we provide the fundamental resource of genomic datasets for further exploration of XWFA molecular mechanisms and development of targetable therapy.

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A hardware-based algorithm for virtual machine provisioning in a private cloud

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Journal of Central South University 2014年第11期21卷 4291-4295页

作者： Amol JAIKAR Gyeong-Ryoon KIM Dada HUANG Seo-Young NOH Grid and supercomputing Department University of Science and TechnologyDaejeon National institute of supercomputing and Networking Korea Institute of Science and Technology Information

Cloud computing is becoming a key factor in the market day by day. Therefore, many companies are investing or going to invest in this sector for development of large data centers. These data centers not only consume more energy but also produce greenhouse gases. Because of large amount of power consumption, data center providers go for different types of power generator to increase the profit margin which indirectly affects the environment. Several studies are carried out to reduce the power consumption of a data center. One of the techniques to reduce power consumption is virtualization. After several studies, it is stated that hardware plays a very important role. As the load increases, the power consumption of the CPU is also increased. Therefore, by extending the study of virtualization to reduce the power consumption, a hardware-based algorithm for virtual machine provisioning in a private cloud can significantly improve the performance by considering hardware as one of the important factors.

关键词： virtualization virtual machine algorithm power consumption data center

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Performance evaluations on inner vs. outer decomposition first parallel join algorithms for two nested loop joins

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Journal of Central South University 2014年第10期21卷 3873-3882页

作者： Seo-Young NOH Heejun YOON Il-Yeon YEO Yoon-su JEONG Hyungwoo PARK National institute of supercomputing and Networking Korea Institute of Science and Technology Information Department of Information Communication Engineering Mokwon University

Two popular traditional join algorithms and their parallel versions are introduced. When designing join algorithms in serial computing environment, decomposing inner relation is considered as the right direction to save disk I/Os. However, two different decomposition algorithms are compared, such as inner vs. outer decomposition first algorithms for tuple-based and block-based nested loop joins, showing that the proposed approach is 20% better than general approach. Also lemmas are proved, when we have to use the outer decomposition first parallel join algorithms.

关键词： parallel join performance inner decomposition outer decomposition

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Comparisons of three data storage models in parametric temporal databases

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Journal of Central South University 2013年第7期20卷 1919-1927页

作者： Seo-Young NOH Shashi K. GADIA Haengjin JANG supercomputing Center Korea Institute of Science and Technology Information Department of Computer Science Iowa State University

The parametric temporal data model captures a real world entity in a single tuple, which reduces query language complexity. Such a data model, however, is difficult to be implemented on top of conventional databases because of its unfixed attribute sizes. XML is a matured technology and can be an elegant solution for such challenge. Representing data in XML trigger a question about storage efficiency. The goal of this work is to provide a straightforward answer to such a question. To this end, we compare three different storage models for the parametric temporal data model and show that XML is not worse than any other approaches. Furthermore, XML outperforms the other storages under certain conditions. Therefore, our simulation results provide a positive indication that the myth about XML is not true in the parametric temporal data model.

关键词： data representation parametric data model XML-based representation

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Computational Studies of Photocatalysis with Metal-Organic Frameworks

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Energy & Environmental Materials 2019年第4期2卷 251-263页

作者： Xin-Ping Wu Indrani Choudhuri Donald G.Truhlar Department of Chemistry Chemical Theory Centerand Minnesota Supercomputing InstituteUniversity of MinnesotaMinneapolis MN 55455-0431USA

Metal–organic frameworks (MOFs) as photocatalysts and photocatalyst supports combine several advantages of homogeneous and heterogeneous catalyses, including stability, post-reaction separation, catalyst reusability,and tunability, and they have been intensively studied for photocatalytic applications. There are several reviews that focus mainly or even entirely on experimental work. The present review is intended to complement those reviews by focusing on computational work that can provide a further understanding of the photocatalytic properties of MOF photocatalysts. We first present a summary of computational methods, including density functional theory, combined quantum mechanical and molecular mechanical methods, and force fields for MOFs. Then, computational investigations on MOF-based photocatalysis are briefly discussed. The discussions focus on the electronic structure, photoexcitation, charge mobility, and photoredox catalysis of MOFs, especially the widely studied Ui O-66-based MOFs.

关键词： computation metal doping metal-organic framework photocatalysis QM/MM

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Design and Implementation of an Extended Collectives Library for Unified Parallel C

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Journal of Computer Science & Technology 2013年第1期28卷 72-89页

作者： Carlos Teijeiro Guillermo L.Taboada Juan Tourio Ramón Doallo Jos C.Mourio Damivn A.Mallón Brian Wibecan Computer Architecture Group University of A Corua Galicia supercomputing Center Jlich supercomputing Centre Institute for Advanced SimulationForschungszentrum Jlich Industry Standard Servers Group Hewlett-Packard Company

Unified Parallel C （UPC） is a parallel extension of ANSI C based on the Partitioned Global Address Space （PGAS） programming model, which provides a shared memory view that simplifies code development while it can take advantage of the scalability of distributed memory architectures. Therefore, UPC allows programmers to write parallel applications on hybrid shared/distributed memory architectures, such as multi-core clusters, in a more productive way, accessing remote memory by means of different high-level language constructs, such as assignments to shared variables or collective primitives. However, the standard UPC collectives library includes a reduced set of eight basic primitives with quite limited functionality. This work presents the design and implementation of extended UPC collective functions that overcome the limitations of the standard collectives library, allowing, for example, the use of a specific source and destination thread or defining the amount of data transferred by each particular thread. This library fulfills the demands made by the UPC developers community and implements portable algorithms, independent of the specific UPC compiler/runtime being used. The use of a representative set of these extended collectives has been evaluated using two applications and four kernels as case studies. The results obtained confirm the suitability of the new library to provide easier programming without trading off performance, thus achieving high productivity in parallel programming to harness the performance of hybrid shared/distributed memory architectures in high performance computing.

关键词： Unified Parallel C collective operation programmability partitioned global address space high performance computing

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A new parallel framework of distributed SWAT calibration

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Journal of Arid Land 2015年第1期7卷 122-131页

作者： Qiang LI Xi CHEN Yi LUO ZhongHua LU YanGang WANG supercomputing Center Chinese Academy of Sciences Xinjiang institute of Ecology and Geography Chinese Academy of Sciences University of Chinese Academy of Sciences

With the development of large-scale hydrologic modeling, computational efficiency is becoming more and more important. Rapid modeling and analysis are needed to deal with emergency environmental disasters. The Soil and Water Assessment Tool （SWAT） is a popular hydrologic model, which is less applied in large-scale watershed simulation because of its sequential characteristics. For improving the computational efficiency of the SWAT model, we present a new parallel processing solution for hydrologic cycle and calibration based on MPI （Message Passing Interface）. We partitioned sub-basins during the processes based on a load balancing method Then the calibration was parallelized using a master-slave scheme, in which different input parameters were allocated to different processes to run the hydrologic cycle and compute the function value. Because of the slow convergence and local optimization of the SCE-UA （Shuffled Complex Evolution-developed by University of Arizona） algorithm in SWAT calibration, a genetic algorithm （GA） is developed to optimize the calibration step. Then by dividing the default communicator into several sub-communicators, all the hydrologic cycles were par- allelized in their own sub-communicators to achieve further acceleration. In this paper the results show speedups for the hydrologic cycle calculations, as well as in the optimized calibration step. In the case study, we tested the parallel hydrologic cycle by four processes, and got a speedup of 3.06. In the calibration section, after applying the GA optimization, with 10 cores, we got a speed increase of 8.0 in our GA parallel framework compared with the GA sequential calibration, which is much better than the original SWAT calibration. After the sub-communicators added, this process was speeded up even further. The study demonstrated that the GA parallel framework with multi-sub-communicators is an effective and efficient solution for the hydrologists in large scale hydrology simulations.

关键词： parallel computing hydrologic model SWAT parameter optimization calibration

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Wave-Tide-Surge Coupled Simulation for Typhoon Maemi

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China Ocean Engineering 2013年第2期27卷 141-158页

作者： Byung Ho Choi Byung Il Min Kyeong Ok Kim Jin Hee Yuk Department of Civil and Environmental Engineering Sungkyunkwan University Marine Environments & Conservation Research Division Korea Institute of Ocean Science & Technology supercomputing Center Korea Institute of Science and Technology Information

The main task of this study focuses on studying the effect of wave-current interaction on currents, storm surge and wind wave as well as effects of current induced wave refraction and current on waves by using numerical models which consider the bottom boundary layer and sea surface roughness parameter for shallow and smooth bed area around Korean Peninsula. The coupled system （unstructured-mesh SWAN wave and ADCIRC） run on the same unstructured mesh. This identical and homogeneous mesh allows the physics of wave-circulation interactions to be correctly resolved in both models. The unstructured mesh can be applied to a large domain allowing all energy from deep to shallow waters to be seamlessly followed. There is no nesting or overlapping of structured wave meshes, and no interpolation is required. In response to typhoon Maemi （2003）, all model components were validated independently, and shown to provide a faithful representation of the system＇s response to this storm. The waves and storm surge were allowed to develop on the continental shelf and interact with the complex nearshore environment. The resulting modeling system can be used extensively for prediction of the typhoon surge. The result show that it is important to incorporate the wave-current interaction effect into coastal area in the wave-tide-surge coupled model. At the same time, it should consider effects of depth-induced wave breaking, wind field, currents and sea surface elevation in prediction of waves. Specially, we found that：（1） wave radiation stress enhanced the current and surge elevation otherwise wave enhanced nonlinear bottom boundary layer decreased that, （2） wind wave was significantly controlled by sea surface roughness thus we cautiously took the experimental expression. The resulting modeling system can be used for hindcasting （prediction） the wave-tide-surge coupled environments at complex coastline, shallow water and fine sediment area like areas around Korean Peninsula.

关键词： typhoon Maemi finite element model tide-surge-wave coupling

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AINV AND BILUM PRECONDITIONING TECHNIQUES

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Applied Mathematics and Mechanics(English Edition) 2004年第9期25卷 1012-1021页

作者：谷同祥迟学斌刘兴平 Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics supercomputing Center of Computer Network Information Center Chinese Academy of Science

It was proposed that a robust and efficient parallelizable preconditioner for solving general sparse linear systems of equations, in which the use of sparse approximate inverse (AINV) techniques in a multi-level block ILU (BILUM) preconditioner were investigated. The resulting preconditioner retains robustness of BILUM preconditioner and has two advantages over the standard BILUM preconditioner: the ability to control sparsity and increased parallelism. Numerical experiments are used to show the effectiveness and efficiency of the new preconditioner.

关键词： sparse matrix preconditioning technique BILUM AINV Krylov subspace method

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Distinct Modes of Winter Arctic Sea Ice Motion and Their Associations with Surface Wind Variability

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Advances in Atmospheric Sciences 2010年第2期27卷 211-229页

作者：武炳义 Mark A. JOHNSON Chinese Academy of Meteorological Sciences Arctic Region supercomputing Center University of Alaska Fairbanks institute of Marine Science University of Alaska Fairbanks

Using monthly mean sea ice velocity data obtained from the International Arctic Buoy Programme （IABP） for the period of 1979–1998 and the monthly mean NCEP/NCAR re-analysis dataset （1960–2002）, we investigated the spatiotemporal evolution of the leading sea ice motion mode （based on a complex correlation matrix constructed of normalized sea ice motion velocity） and their association with sea level pressure （SLP） and the predominant modes of surface wind field variability. The results indicate that the leading winter sea ice motion mode’s spatial evolution is characterized by two alternating and distinct sea ice modes, or their linear combination. One mode （M1） shows a nearly closed cyclonic or anti-cyclonic circulation anomaly in the Arctic Basin and its marginal seas, resembling to a large extent the response of sea ice motion to the Arctic Oscillation （AO）, as many previous studies have revealed. The other mode （M2） displays a coherent cyclonic or anti-cyclonic circulation anomaly with its center close to the Laptev Sea, which has not been identified in previous observational studies. In fact, M1 and M2 respectively reflect the responses of sea ice motion to two predominant modes of winter surface wind variability north of 70 ？ N, which well correspond, with slight differences, to the first two modes of EOF analysis of winter monthly mean SLP north of 70 ？ N. These slight differences in SLP anomalies lead to a difference of M2 from the response of sea ice motion to the dipole anomaly. Although the AO significantly influences sea ice motion, it is not crucial for the existence of M1. The new sea ice motion mode （M2） has the largest variance and clearly differs from the response of winter monthly mean sea ice motion to the dipole anomaly in SLP fields, and corresponding SLP anomalies also show differences compared to the dipole anomaly. This study indicates that in the Arctic Basin and its marginal seas, slight differences in SLP anomaly patterns can force distinctl

关键词： distinct mode Arctic sea ice motion Arctic surface wind forcing

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