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Reliable data sharing and long-term data archiving and reuse are becoming very important in global cooperative research. Concomitantly, many types of global databased research have been conducted on the Long-Term Ecological Research (LTER) network, with the objective of getting it to respond effectively to future changes in ecology, environment, and climate, by monitoring long-term ecological and environmental data. Korean National Long-Term Ecological Research (KNLTER), however, lacks a systemdoi:10.14257/ijdta.2016.9.9.22 fatcat:g2csfu2r6zdbphlomhc4zjr5oi
more »... for performing data collection, management, curation, and publication, and therefore global cooperative research through global data sharing is difficult in Korea. In this paper, we analyze one of the best practices link models, the TERN network, and the global data-sharing trend in the LTER area. Further, we propose a link model and necessary technologies for KNLTER and suggest a possible future direction for KNLTER. Therefore, two licenses can be used as a mapping format for global linking. Furthermore, DOI needs to be assigned to the datasets for data distribution. Although the data minting service by EZID can be used to receive IDs when the datasets are submitted, the DOI needs to be issued by a separate link to manage DOIs in the data center. Other necessary features include systematic data curation. In order for a data center to register as a member node of DataONE, the published data have to be accessible via long-term storage, each dataset has to be assigned an identifier, and resource maps and reliable data for data packages have to be provided. DOI A DOI is a unique identifier that can be issued to all objects, including internet documents and other digital content. It provides metadata such as authors and dates, and information on the location of the object so that users can have permanent access to the object. The International DOI Foundation (IDF) manages the policies and registrations in
Most Gram-negative bacteria respond to excessive levels of H 2 O 2 using the peroxide-sensing transcriptional regulator OxyR, which can induce the expression of antioxidant genes to restore normality. Vibrio vulnificus has two distinct OxyRs (OxyR1 and OxyR2), which are sensitive to different levels of H 2 O 2 and induce expression of two different peroxidases, Prx1 and Prx2. Although OxyR1 has both high sequence similarity and H 2 O 2 sensitivity comparable with that of other OxyR proteins,doi:10.1074/jbc.m116.743765 pmid:28264933 pmcid:PMC5409488 fatcat:uwi4a2hx6jhojhul73jykeigcu
more »... R2 exhibits limited sequence similarity and is more sensitive to H 2 O 2 . To investigate the basis for this difference, we determined crystal structures and carried out biochemical analyses of OxyR2. The determined structure of OxyR2 revealed a flipped conformation of the peptide bond before Glu-204, a position occupied by glycine in other OxyR proteins. Activity assays showed that the sensitivity to H 2 O 2 was reduced to the level of other OxyR proteins by the E204G mutation. We solved the structure of the OxyR2-E204G mutant with the same packing environment. The structure of the mutant revealed a dual conformation of the peptide bond before Gly-204, indicating the structural flexibility of the region. This structural duality extended to the backbone atoms of Gly-204 and the imidazole ring of His-205, which interact with H 2 O 2 and invariant water molecules near the peroxidatic cysteine, respectively. Structural comparison suggests that Glu-204 in OxyR2 provides rigidity to the region that is important in H 2 O 2 sensing, compared with the E204G structure or other OxyR proteins.
Journal of the Microelectronics and Packaging Society
슈퍼컴퓨터에 사용되는 저전력 프로세서 패키지의 신뢰성 평가
슈퍼컴퓨터에 사용되는 저전력 프로세서 패키지의 신뢰성 평가
While datacenter operation cost increases with electricity price rise, many researchers study low-power processor based supercomputers to reduce power consumption of datacenters. Reliability of low-power processors for supercomputers can be of concern since the reliability of many low-power processors are assessed based on mobile use conditions. This paper assessed the reliability of low-power processor packages based on supercomputer use conditions. Temperature cycling was determined as adoi:10.6117/kmeps.2016.23.2.037 fatcat:whplfld4dfdjhdii6cs3kysd6q
more »... cal failure cause of low-power processor packages through literature surveys and failure mode, effect and criticality analysis. The package temperature was measured at multiple processor load conditions to examine the relationship between processor load and package temperature. A physics-of-failure reliability model associated with temperature cycling predicted the expected lifetime of low-power processors to be less than 3 years. Recommendations to improve the lifetime of low-power processors were presented based on the experimental results.
By 2026, Korea is expected to surpass the UN's definition of an aged society and reach the level of a superaged society. With an aging population come increased disorders involving the spine. To prevent unnecessary spinal surgery and support scientific diagnosis of spinal disease and systematic prediction of treatment outcomes, we have been developinge-Spine, which is a computer simulation model of the human spine. In this paper, we present the Korean spine database and automatic surface meshdoi:10.1155/2014/471756 fatcat:nt6ne7wjmvhh7p2kovy2q34x7i
more »... tersection algorithm to constructe-Spine. To date, the Korean spine database has collected spine data from 77 cadavers and 298 patients. The spine data consists of 2D images from CT, MRI, or X-ray, 3D shapes, geometry data, and property data. The volume and quality of the Korean spine database are now the world's highest ones. In addition, our triangular surface mesh intersection algorithm automatically remeshes the spine-implant intersection model to make it valid for finite element analysis (FEA). This makes it possible to run the FEA using the spine-implant mesh model without any manual effort. Our database and surface mesh intersection algorithm will offer great value and utility in the diagnosis, treatment, and rehabilitation of patients suffering from spinal diseases.
We analyze the relationship between energy consumption and topology in wireless microsensor networks. Energy consumption is the total energy required for a message to be delivered to a destination microsensor from a source microsensor. We first consider the factors in energy consumption -radio propagation models, the topology of microsensors, the probability of connectivity between microsensors and etc. The radio propagation model tells us how much energy the environment of message propagationdoi:10.1145/1089803.1089963 dblp:conf/pe-wasun/NamgoongLN05 fatcat:3d3cv2oq45dgdjpftyxreqojga
more »... equires, and the topology is the logical configuration among microsensors. We analyze the energy consumption from two different aspects: the propagation model and the topology. A propagation model may consume more energy than that of another model at the same topology, or, different topologies may require different amounts of energy in the same propagation model. The result of analysis shows that the consumed energy is in proportion to the number of neighbors, i.e. when the topology has fewer neighboring microsensors, it consumes less energy even though it must experience more hops to the destination. We also prove that the same result can be applied to any of the radio propagation models -such as free space propagation, urban area, obstructed in building, and etc. From the two analyses in the propagation model and topology, we can conclude that when a message goes to the destination of multihop, the topology with fewer neighboring microsensors consumes less energy than that of more neighbors. We also perform a simple analysis on the connectivity among microsensors as one of the energy consumption factors. Microsensors are prone to be disconnected by microsensor failures, temporary broken links, going into sleep mode, and etc. The disconnection requires an alternative path to the destination and (or) retransmission of the same message to the next microssensor, which consumes additional energy.
We discuss a new high performance computing service (HPCS) platform that has been developed to provide domain-neutral computing service under the governmental support from "EDucation-research Integration through Simulation On the Net" (EDISON) project. With a first focus on technical features, we not only present in-depth explanations of the implementation details, but also describe the strengths of the EDISON platform against the successful nanoHUB.org gateway. To validate the performance anddoi:10.1587/transinf.e97.d.1953 fatcat:3orxzpxzkba35e4wojwj5onu7m
more »... tility of the platform, we provide benchmarking results for the resource virtualization framework, and prove the stability and promptness of the EDISON platform in processing simulation requests by analyzing several statistical datasets obtained from a three-month trial service in the initiative area of computational nanoelectronics. We firmly believe that this work provides a good opportunity for understanding the science gateway project ongoing for the first time in Republic of Korea, and that the technical details presented here can be served as an useful guideline for any potential designs of HPCS platforms.
KIISE Transactions on Computing Practices
Boyer-Moore 알고리즘을 위한 GPU상에서의 병렬 최적화
Boyer-Moore 알고리즘을 위한 GPU상에서의 병렬 최적화
키워드: Boyer-Moore 알고리즘, 병렬화, 성능 최적화, 알고리즘 cascading, 멀티스레딩 Dukyun Nam) (Jik-Soo Kim) (Soonwook Hwang) 서는 Boyer-Moore 알고리즘 실행시 검색 대상 문자열 이 길어질수록 GPU 상에서 이들을 병렬처리하기 위한 매핑 오버헤드가 증가하는 문제 및 병렬 실행에 참여하 ...doi:10.5626/ktcp.2015.21.2.138 fatcat:juy7lg352bfa3jspflfnru7hqy
Journal of KIISE
MPI 노드 내 통신 성능 향상을 위한 매니코어 프로세서의 온-패키지 메모리 활용
MPI 노드 내 통신 성능 향상을 위한 매니코어 프로세서의 온-패키지 메모리 활용
요 약 고성능 컴퓨팅 환경을 위해서 최근 등장한 차세대 매니코어 프로세서는 전통적인 구조의 메모 리와 함께 고대역 온-패키지 메모리를 장착하고 있다. Intel Xeon Phi Knights Landing(KNL) 프로세서 의 온-패키지 메모리인 Multi-Channel DRAM(MCDRAM)은 기존의 DDR4 메모리보다 이론적으로 네 배 높은 대역폭을 제공한다. 본 논문에서는 MCDRAM을 이용하여 MPI 노드 내 통신 성능을 향상시키기 위한 방안을 제안한다. 실험 결과, 제안된 기법을 사용할 경우 DDR4를 사용하는 경우와 비교해서 MPI 노드 내 통신 성능을 최대 272% 향상시킬 수 있음을 보인다. 또한 MCDRAM 활용 방법에 따른 성능 영 향뿐만 아니라 프로세스의 코어 친화도에 따른 성능 영향을 보인다. 키워드: Knights Landing, 온-패키지 메모리, MPI, 노드 내 통신, 고성능 컴퓨팅 Abstract The emerging next-generationdoi:10.5626/jok.2017.44.2.124 fatcat:72vkuli34beubnxah27jn3p37e
more »... nycore processors for high-performance computing are equipped with a high-bandwidth on-package memory along with the traditional host memory. The Multi-Channel DRAM (MCDRAM), for example, is the on-package memory of the Intel Xeon Phi Knights Landing (KNL) processor, and theoretically provides a four-times-higher bandwidth than the conventional DDR4 memory. In this paper, we suggest a mechanism to exploit MCDRAM for improving the performance of MPI intra-node communication. The experiment results show that the MPI intra-node communication performance can be improved by up to 272 % compared with the case where the DDR4 is utilized. Moreover, we analyze not only the performance impact of different MCDRAM-utilization mechanisms, but also that of core affinity for processes.
The bacterial transcriptional regulator OxyR is known to function as a two-state redox switch. OxyR senses cellular levels of H 2 O 2 via a "sensing cysteine" that switches from the reduced to a disulfide state upon H 2 O 2 exposure, inducing the expression of antioxidant genes. The reduced and disulfide states of OxyR, respectively, bind to extended and compact regions of DNA, where the reduced state blocks and the oxidized state allows transcription and further induces target gene expressiondoi:10.1074/jbc.m115.710343 pmid:27268058 pmcid:PMC4965554 fatcat:rbqndqc46nhatlt3ffkjmnzdou
more »... y interacting with RNA polymerase. Vibrio vulnificus OxyR2 senses H 2 O 2 with high sensitivity and induces the gene encoding the antioxidant Prx2. In this study, we used mass spectrometry to identify a third redox state of OxyR2, in which the sensing cysteine was overoxidized to S-sulfonated cysteine (Cys-SO 3 H) by high H 2 O 2 in vitro and in vivo, where the modification deterred the transcription of prx2. The DNA binding preferences of OxyR2 5CA -C206D, which mimics overoxidized OxyR2, suggested that overoxidized OxyR2 binds to the extended DNA site, masking the ؊35 region of the prx2 promoter. These combined results demonstrate that OxyR2 functions as a three-state redox switch to tightly regulate the expression of prx2, preventing futile production of Prx2 in cells exposed to high levels of H 2 O 2 sufficient to inactivate Prx2. We further provide evidence that another OxyR homolog, OxyR1, displays similar three-state behavior, inviting further exploration of this phenomenon as a potentially general regulatory mechanism. Downloaded from FIGURE 3. Expression levels of prx2 in response to various levels of H 2 O 2 and a working model for OxyR2 as a three-state redox switch. A, wild-type V. vulnificus was grown anaerobically to an A 600 of 0.3 and exposed to various concentrations of H 2 O 2 as indicated for 3 min. Total RNAs were isolated, and the relative levels of prx2 (black bars) and oxyR2 (gray bars) transcripts were determined by quantitative real-time PCR analyses. The level of each transcript from wild type unexposed to H 2 O 2 is presented as 1. *, statistically significant difference (p Ͻ 0.05) between groups. B, transcriptional activity of OxyR2-C206D. Cultures were grown aerobically to an A 600 of 0.5, total RNAs were isolated, and the relative levels of prx2 transcript were determined by quantitative real-time PCR analyses. The level of transcript from negative control (NC) is presented as 1. Negative control was OH0703 (pJH0311). OxyR2, OH0703 (pDY1025); OxyR2-C206D, OH0703 (pBANG1416). All data in A and B represent mean Ϯ S.D. (error bars). C, OxyR2 shifts to three different redox states, revealing different transcriptional activities in response to various levels of H 2 O 2 in cells (solid line) as indicated. Concurrently, the prx2 expression (dotted line) varies, depending on the redox states of OxyR2. C 206 -SO 2/3 H, overoxidized Cys 206 with Cys 206 -SO 2 H and/or Cys 206 -SO 3 H.
The Journal of the Korean Institute of Information and Communication Engineering
웹 기반 시뮬레이션 이력출처 데이터 공유 서비스 설계
웹 기반 시뮬레이션 이력출처 데이터 공유 서비스 설계
Web based simulation service is actively utilized to computably analyze various kinds of phenomena in real world according to progress of computing technology and spread of Network. However it is hard to share data and information among users on the services, because most of web based simulation services do not share and open simulation processing information and results. In this paper, we design a simulation provenance data sharing service on EDISON_CFD (EDucation-research Integrationdoi:10.6109/jkiice.2014.18.5.1128 fatcat:2wldyicjenh3xkk3f7pfd7cjky
more »... n On the Net for Computational Fluid Dynamics) to share the calculated simulation performance information. To store and share the simulation processing information, we define the simulation processing step as "Problem → Plan, Design → Mesh → Simulation performance → Result → Report." Users can understand a problem solving method through a computer simulation by searching the simulation performance information with Search/Share API of the store. Besides, this opened simulation information can reduce the waste of calculation resource to process same simulation jobs. 키워드 : EDISON, 웹 기반 시뮬레이션 서비스, 이력출처, 데이터 공개, 워크플로우
A new capability of our well-known NEMO 3-D simulator (Ref. Klimeck et al., 2007 ) is introduced by carefully investigating the utility of III-V semiconductor quantum dots as infrared photodetectors at a wavelength of 1.2-1.5 µm. We not only present a detailed description of the simulation methodology coupled to the atomistic sp 3 d 5 s * tight-binding band model, but also validate the suggested methodology with a focus on a proof of principle on small GaAs quantum dots (QDs). Then, we movedoi:10.1016/j.mcm.2012.11.024 fatcat:z7l47qkybfaptgkfnoxahzth2i
more »... the simulation scope to optical properties of realistically sized dome-shaped InAs/GaAs QDs that are grown by selfassembly and typically contain a few million atoms. Performing numerical experiments with a variation in QD size, we not only show that the strength of ground state interband light transitions can be optimized via QD size-engineering, but also find that the hole ground state wavefunction serves as a control factor of transition strengths. Finally, we briefly introduce the web-based cyber infrastructure that is developed as a governmentfunded project to support online education and research via TCAD simulations. This work not only serves as a useful guideline to experimentalists for potential device designs and other modelers for the self-development of optical TCAD, but also provides a good chance to learn about the science gateway project ongoing in the Republic of Korea.
Journal of KIISE
인텔 차세대 매니코어 프로세서에서의 다중 병렬 프로그램 성능 향상기법 연구
인텔 차세대 매니코어 프로세서에서의 다중 병렬 프로그램 성능 향상기법 연구
Nam) (Geunchul Park) (Jik-Soo Kim) 그림 1 KNL 구조 개요 Fig. 1 KNL Architecture Overview 1. ... Applications using Heterogeneous Memory on the Intel's Next-Generation Many-core Processor) 노 승 우 † 김 서 영 † 남 덕 윤 † † 박 근 철 † † 김 직 수 † † † (Seungwoo Rho) (Seoyoung Kim) (Dukyun ...doi:10.5626/jok.2017.44.9.878 fatcat:6fkqpdh6knbblmqvprcvh2tkea
Nitric oxide (NO) and its derivatives are important effectors of host innate immunity, disrupting cellular function of infecting pathogens. Transcriptome analysis of Vibrio vulnificus, an opportunistic human pathogen, identified a set of genes induced upon exposure to NO. Among them, VvhmpA (V. vulnificus hmpA), encoding a multidomain NO dioxygenase, was the most greatly induced upon exposure to NO and was thus further characterized. Absorption spectra demonstrated that VvHmpA is a heme proteindoi:10.3389/fmicb.2019.02208 pmid:31616401 pmcid:PMC6768983 fatcat:zf3cr2dxsvgpdoc5rn25rxdtam
more »... in which the heme iron can exist in either reduced, NO-bound, or oxidized state. Biochemical studies revealed that VvHmpA is a flavohemoglobin containing equimolar amounts of heme and FAD as cofactors. The K M and k cat values of VvHmpA for NO at 37°C, the temperature encountered by V. vulnificus in the host, were greater than those at 30°C, indicating that VvHmpA detoxifies high levels of NO effectively during infection. Compared with the wild type, the VvhmpA mutant exhibited a lower NO-decomposition activity and impaired growth in the presence of NO in vitro. Also, the cytotoxicity and survival of the VvhmpA mutant infecting the NO-producing murine macrophage cells were lower than those of the wild type. Furthermore, the mouse lethality of the VvhmpA mutant was reduced compared to that of the parental wild type. The combined results revealed that VvHmpA is a potent virulence factor that is induced upon exposure to NO and important for the survival and pathogenesis of V. vulnificus during infection.
Group communication system (GCS) is a useful mechanism for constructing reliable, fault-tolerant distributed application. When GCS is extended in mobile environment, the membership change occurs frequently due to the mobility of mobile nodes and unreliable wireless communication within a cell. In this paper, we propose a scalable group communication scheme to support mobile systems in an Internet environment with wireless cells. Our scheme leverages the layered approach, our previous work, todoi:10.1109/words.2002.1000065 dblp:conf/words/KimLN02 fatcat:3piny4wbkbctbmivr26676ajxu
more »... hance the scalability. Furthermore, to shield group view from the mobility and temporary disconnection of mobile hosts, we extend the hierarchical view management of layered approach. The simulation result shows that our scheme can reduce the overhead of membership management and the number of messages exchanged to complete the view event process.
Object replication is a technique to enhance fault tolerance and high availability. Group communication is a useful mechanism guaranteeing the consistency among replicated objects. We propose a generic group communication framework that allows transparent plug-in of various group communication protocols with no modification of existing CORBA. For this, we extend the Open Communications Interface (OCI) to support interoperability, reusability of existing group communication, and independency ondoi:10.1109/prdc.2001.992709 dblp:conf/prdc/LeeNYY01 fatcat:qn5fdxrzfncsvai5hvjio67pbu