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Apache Spark을 이용한 병렬 DNA 시퀀스 지역 정렬 기법 구현
김보성(Bosung Kim),김진수(Jinsu Kim),최도진(Dojin Choi),김상수(Sangsoo Kim),송석일(Seokil Song) 한국콘텐츠학회 2016 한국콘텐츠학회논문지 Vol.16 No.10
Smith-Waterman(SW) 알고리즘은 DNA 시퀀스 분석에서 중요한 연산 중 하나인 지역 정렬을 처리하는 알고리즘이다. SW 알고리즘은 동적 프로그래밍 방법으로 최적의 결과를 도출할 수 있지만 수행시간이 매우 길다는 문제가 있다. 이를 해결하기 위해서 다수의 노드를 이용한 병렬 분산 처리 기반의 SW 알고리즘이 제안되었다. Apache Spark을 기반으로 하는 병렬 분산 DNA 처리 프레임워크인 ADAM에서도 SW알고리즘을 병렬로 처리하고 있다. 하지만, ADAM의 SW 알고리즘은 Smith-Waterman 이 동적프로그래밍 기법이라는 특성을 고려하지 않고 있어 최대의 성능을 얻지 못하고 있다. 이 논문에서는 ADAM의 병렬 SW 알고리즘을 개선한다. 제안하는 병렬 SW 기법은 두 단계에 걸쳐 실행된다. 첫 번째 단계에서는 지역정렬 대상인 DNA 시퀀스를 다수의 파티션(partition)으로 분할하고 분할된 각 파티션에 대해서 SW 알고리즘을 병렬로 수행한다. 두 번째 단계에서는 파티션 각각에 대해서 독립적으로 SW를 적용함으로써 발생하는 오류를 보완하는 과정을 역시 병렬로 수행한다. 제안하는 병렬 SW 알고리즘은 ADAM을 기반으로 구현하고 기존 ADAM의 SW와 비교를 통해서 성능을 입증한다. 성능 평가 결과 제안하는 병렬 SW 알고리즘이 기존의 SW에 비해서 2배 이상의 좋은 성능을 내는 것을 확인하였다. The Smith-Watrman (SW) algorithm is a local alignment algorithm which is one of important operations in DNA sequence analysis. The SW algorithm finds the optimal local alignment with respect to the scoring system being used, but it has a problem to demand long execution time. To solve the problem of SW, some methods to perform SW in distributed and parallel manner have been proposed. The ADAM which is a distributed and parallel processing framework for DNA sequence has parallel SW. However, the parallel SW of the ADAM does not consider that the SW is a dynamic programming method, so the parallel SW of the ADAM has the limit of its performance. In this paper, we propose a method to enhance the parallel SW of ADAM. The proposed parallel SW (PSW) is performed in two phases. In the first phase, the PSW splits a DNA sequence into the number of partitions and assigns them to multiple nodes. Then, the original Smith-Waterman algorithm is performed in parallel at each node. In the second phase, the PSW estimates the portion of data sequence that should be recalculated, and the recalculation is performed on the portions in parallel at each node. In the experiment, we compare the proposed PSW to the parallel SW of the ADAM to show the superiority of the PSW.
종합병원 입원 환자의 간호대학생 실습허용에 대한 견해 및 인식
김영진 ( Kim Youngjin ),김지선 ( Kim Jeesun ),김혜림 ( Kim Hyerim ),박수비 ( Park Subi ),소샛별 ( So Saetbyul ),정보성 ( Jung Bosung ),조은애 ( Choh Eunae ),이선영 ( Lee Seonyoung ),김정은 ( Kim Jeongeun ) 서울대학교 간호과학연구소 2017 간호학의 지평 Vol.14 No.1
Purpose: The aim of this study was to explore the patients` perspectives on nursing students` clinical practices in the wards, and to investigate their willingness for allowing students to practice on them. Methods: This was a descriptive study. 116 inpatients were recruited from the S University Hospital. A 60-item questionnaire was applied to collect the data. The participants were 19 years and older with sound judgement, and were not in special or intensive care units. Data analysis was done in SPSS/WIN 22.0 using descriptive statistics, Fishers exact test, and the ANOVA test. the participant answered to questionnaire from April 29th 2016 to May 10th. Results: 40 participants (34.5%) stated they would allow students` practice, while 72 (61.2%) said they would allow only under staff supervision. 5 participants (4.3%) stated they would not allow whatsoever. The 3 most allowed were emotional support, oral care, and vital signs measurement while the 3 least allowed were gastric feeding, intravenous catheterization, and urinary catheterization. Conclusion: Patients were more inclined to allow students to practice on them when a member of the medical team was present. A fair number of participants said they would be more inclined to allow students` practice if they felt the student was competent; hence, reinforcing simulation sessions is vital in enhancing students` competency and ultimately practice allowance.
Son, Gahyun,Kwon, Jieun,Cho, Hyejin,Kim, Sangwun,Yoon, Bosung,Nam, Eunji,Kim, Jaehoon,Kim, Youngtae,Kim, Jaewook,Cho, Namhoon,Kim, Sunghoon KOREAN ACADEMY OF MEDICAL SCIENCE 2007 JOURNAL OF KOREAN MEDICAL SCIENCE Vol.22 No.5
<P>Placenta increta is an uncommon and life-threatening complication of pregnancy characterized by complete or partial absence of the decidua basalis. Placenta increta usually presents with vaginal bleeding during difficult placental removal in the third-trimester. Although placenta increta may complicate first and early second-trimester pregnancy loss, the diagnosis can be very difficult during early pregnancy and thus the lesion is difficult to identify. We encountered with a woman who was diagnosed with placenta increta after receiving emergency hysterectomy due to intraperitoneal bleeding 2 months after an uncomplicated dilatation and curettage in the first trimester. Therefore, we report this case with a brief review of the literature.</P>
ENC-MAC: Energy-efficient Non-overlapping Channel MAC for Cognitive Radio enabled Sensor Networks
( Bosung Kim ),( Kwangsoo Kim ),( Byeong-hee Roh ) 한국인터넷정보학회 2015 KSII Transactions on Internet and Information Syst Vol.9 No.11
The concept of Internet of Things (IoT) has shed new light on WSN technologies. MAC protocol issues improving the network performance are important in WSNs because of the increase in demand for various applications to secure spectrum resources. Cognitive radio (CR) technology is regarded as a solution to the problems in this future wireless network. In recent years, energy efficiency has become an issue in CR networks. However, few relevant studies have been conducted. In this paper, an energy-efficient non-overlapping channel MAC (ENC-MAC) for CR-enabled sensor networks (CRSNs) is proposed. Applying the dedicated control channel approach, ENC-MAC allows the SUs to utilize channels in a non-overlapping manner, and thus spectrum efficiency is improved. Moreover, the cooperative spectrum sensing that allows an SU to use only two minislots in the sensing phase is addressed to en-hance energy efficiency. In addition, an analytical model for evaluating the performance, such as saturation throughput, average packet delay, and network lifetime, is developed. It is shown in our results that ENC-MAC remarkably outperforms existing MAC protocols.