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OpenMP 디렉티브 프로그램의 최초경합 탐지를 위한 도구
강문혜(Mun-Hye Kang),하옥균(Ok-Kyoon Ha),전용기(Yong-Kee Jun) 한국정보과학회 2010 정보과학회논문지 : 시스템 및 이론 Vol.37 No.1
OpenMP 디렉티브 프로그램의 디버깅을 위해서 비결정적인 수행결과를 초래하는 경합을 탐지하는 것은 중요하다. 특히, 프로그램 수행에서 가장 먼저 발생하는 최초경합은 이후에 발생하는 경합에 영향을 줄 수 있으므로 효과적인 디버깅을 위해서 반드시 탐지되어야 한다. 그러나 기존의 경합탐지 도구들은 최초경합의 탐지를 보장하지 못한다. 본 논문에서는 내포병렬성을 포함한 프로그램을 두 번의 수행으로만 프로그램의 수행 중에 최초경합을 탐지하는 도구를 제시한다. 본 도구의 정당성을 합성프로그램을 이용하여 보이고, 기존 경합탐지 도구와 기능성을 비교한다. Detecting data races is important for debugging programs with OpenMP directives, because races result in unintended non-deterministic executions of the program. It is especially important to detect the first data races to occur for effective debugging, because the removal of such races may make other affected races disappear or appear. The previous tools for race detecting can not guarantee that detected races are the first races to occur. This paper suggests a tool what detects the first races to occur on the program with nested parallelism using the two-pass on-the-fly technique. To show functionality of this tool, we empirically compare with the previous tools using a set of the synthetic programs with OpenMP directives.
내포병렬성을 가진 공유메모리 프로그램에서 최초경합의 수행후 탐지도구
강문혜(Mun-Hye Kang),심갑식(Gab-Sig Sim) 한국컴퓨터정보학회 2014 韓國컴퓨터情報學會論文誌 Vol.19 No.4
본 논문에서는 고성능 컴퓨팅 시스템의 성능 향상을 위한 효율적인 동적 작업부하 균등화 정책을 제안한다. 이 정책은 시스템 자원인 CPU와 메모리를 효율적으로 사용하여 고성능 컴퓨팅 시스템의 처리량을 최대화하고, 각 작업의 수행시간을 최소화한다. 또한 이 정책은 수행중인 작업의 메모리 요구량과 각 노드의 부하상태를 파악하여 작업을 동적으로 할당한다. 이때 작업을 할당 받은 노드가 과부하 상태가 되면 다른 노드로 작업을 이주시켜 각 노드의 작업부하를 균등하게 유지함으로써 작업의 대기시간을 줄이고, 각 작업의 수행시간을 단축한다. 본 논문에서는 시뮬레이션을 통하여 제안하는 동적 작업부하 균등화 정책이 기존의 메모리 기반의 작업부하 균등화 정책에 비해 고성능 컴퓨팅 시스템의 성능 향상 면에서 우수함을 보인다. Detecting data races is important for debugging shared-memory programs with nested parallelism, because races result in unintended non-deterministic executions of the program. It is especially important to detect the first occurred data races for effective debugging, because the removal of such races may make other affected races disappear or appear. Previous dynamic detection tools for first race detecting can not guarantee that detected races are unaffected races. Also, the tools does not consider the nesting levels or need support of other techniques. This paper suggests a post-mortem tool which collects candidate accesses during program execution and then detects the first races to occur on the program after execution. This technique is efficient, because it guarantees that first races reported by analyzing a nesting level are the races that occur first at the level, and does not require more analyses to the higher nesting levels than the current level.
Crystal structure of <i>Helicobacter pylori</i> MinE, a cell division topological specificity factor
Kang, Gil Bu,Song, Hye-Eun,Kim, Mun-Kyoung,Youn, Hyung-Seop,Lee, Jung-Gyu,An, June Yop,Chun, Jang-Soo,Jeon, Hyesung,Eom, Soo Hyun Blackwell Publishing Ltd 2010 Molecular microbiology Vol.76 No.5
<P>In Gram-negative bacteria, proper placement of the FtsZ ring, mediated by nucleoid occlusion and the activities of the dynamic oscillating Min proteins MinC, MinD and MinE, is required for correct positioning of the cell division septum. MinE is a topological specificity factor that counters the activity of MinCD division inhibitor at the mid-cell division site. Its structure consists of an anti-MinCD domain and a topology specificity domain (TSD). Previous NMR analysis of truncated <I>Escherichia coli</I> MinE showed that the TSD domain contains a long α-helix and two anti-parallel β-strands, which mediate formation of a homodimeric α/β structure. Here we report the crystal structure of full-length <I>Helicobacter pylori</I> MinE and redefine its TSD based on that structure. The N-terminal region of the TSD (residues 19–26), previously defined as part of the anti-MinCD domain, forms a β-strand (βA) and participates in TSD folding. In addition, <I>H. pylori</I> MinE forms a dimer through the interaction of anti-parallel βA-strands. Moreover, we observed serial dimer–dimer interactions within the crystal packing, resulting in the formation of a multimeric structure. We therefore redefine the functional domain of MinE and propose that a multimeric filamentous structure is formed through anti-parallel β-strand interactions.</P>
선천성 대사 이상 환아에서 발생한 대사 위기의 복막 투석 치료 효과
강정혜,이동환,문철,김은미 순천향의학연구소 1996 Journal of Soonchunhyang Medical Science Vol.2 No.2
Purpose : We have evaluated the outcomes of peritoneal dialysis in patients with metabolic crises caused by in born error of metabolism. Methods : There are 6 patients(8 episodes, 4 males and 2 females) who had inherited inborn errors of metabolism and were admitted to the department of pediatrics, Shoonchunhyang university hospital in Seoul from December 1991 to December 1994. The technique of dialysis is discribed, in short: A Tenckhoff catheter was inserted surgically in all patients through the lateral abdominal wall. Commerically available dialysate solutions(Peritosol, Korea Green Cross Co.) was applied to 5 patients(7 cases) with hyperammonemia. In a patient with propionic acidemia, we used a special custiom made dialysate that replaces lactate by bicarbonate. Results : 1) The mean age was 5.3 months old. There were 6 patients with 8 episodes. Six cases had Ornithin transcarbamylase deficiency. The remaining cases are Multiple carboxylase deficiency and Propionic acidemia (Table 1) 2) In 7 cases with hyperammonemia, mean levels of pre and post 24hrs peritoneal dialysis serum ammonia were 1000.2±310.9 ㎍/dl and 388.8 ±156.7 ㎍/dl at 24 hours respectively. Time on serum ammonia levels reached below 300 ㎍/dl was 88.7 ±39.6 ㎍/dl hours. 3) Four out of seven cases were a recorvert of mental status. Each episode of serum ammonia mean levels was 388.8 ±156.7 ㎍/dl after 19.7 ±5.8 hours of peritoneal dialysis (Table 3). 4) Peak serum ammonia levels of the survived group reached 1356.5 ㎍/dl, higher than the expired group of 847.5 ㎍/dl and time period of starting peritoneal dialysis after onset of the survived group was 15.5 hours earlier than the expired group of 23 hours(P>0.05)(Table 4). 5) 3 out of 7 cases of hyperammonemia died. The cause if death were 3 brain edema, 1 hyperkalemla and 1 intracranlal hemorrhage. 6) In onecase with Multiple carboxylase deficiency, serum ammonia level was normalized after 12 hours of peritoneal dialysis. The reduction of serum levels of the branched amino acid was also observed. 7) In a case of Propionic acidemia with severe metabolic acidosis, the prior serum bicarbonate level was 8 mmol/L and was increased up to 18 mmol/L by peritoneal dialysis lasting 19 hours. 8) Among 8 cases, complications of peritoneal dialysis were 5 hypoalbuminemia, 4 hyoercalcemia, 4 hyperglycemia and leakage of peritoneal dialysate. Conclusions : In cases of hyperammonemia, survival rate is 57.1%. They are showed excellant efficacy of treatment of peritoneal dialysis for metabolic crises. In a case of propinic acidemia is fastly corrected by peritoneal dialysis. But unfortunally clinical manifestations is not improved. Therefore, further studies is required with treatment of severe metabolic acidic conditions.
The length of CpG islands is associated with the distribution of <i>Alu</i> and L1 retroelements
Kang, Moo-Il,Rhyu, Mun-Gan,Kim, Young-Ho,Jung, Yu-Chae,Hong, Seung-Jin,Cho, Chul-Soo,Kim, Hye-Soo Elsevier 2006 Genomics Vol.87 No.5
<P><B>Abstract</B></P><P><I>Alu</I> and L1 retroelements have been suggested to initiate the spread of CpG methylation. In this study, the spread of CpG methylation was estimated based on the distance between the CpG islands and the nearest retroelements. All human genes (23,116) were examined and the correlations between the length of the CpG islands and the distance and density of the confronting retroelements were examined using nonoverlapping 5-kb windows. There was a linear relationship between the length of the CpG islands and the density of the <I>Alu</I> elements and an inverse relationship between the CpG islands and the L1 elements located more distantly, suggesting a suppressive effect of the <I>Alu's</I> on the spread of L1 methylation. Methylation analysis of the transitional CpG sites between the CpG islands and the nearest retroelements upstream of 16 genes was then carried out using DNA preparations from 11 different human tissues. Methylation-variable transitional CpGs were observed for the selected genes and the different tissues.</P>