The Rapid Drug Susceptibility Testing of Mycobacterium tuberculosis by GenoType<SUB>®</SUB> MTBDRplus in Contaminated Specimen

Reun Heo,Yoon-Sik Kim 대한의생명과학회 2013 Biomedical Science Letters Vol.19 No.4

There are several methods currently being used to diagnose tuberculosis in patients, such as smear, PCR, tuberculosis culture and X-ray. For a proper medical treatment, antimicrobial susceptibility test and rapid drug susceptibility testing have been operated. Tuberculosis bacilli usually need 3~8 weeks of culture period because of delay in RNA synthesis and require 15~22 hours for generation. After a germ raises in culture, we initiated antimicrobial susceptibility test for a proper treatment. It has some difficulties to give a proper prescription for a tuberculosis patient because antimicrobial susceptibility test requires 4 weeks. To supplement this, we are practicing drug susceptibility testing which allow us to know the sensibility of RMP and INH after 2 or 3 days. But this is only possible when more than 2 positive germ. Therefore, we should practice rapid drug susceptibility testing with culture test. But if media is contaminated by other germs except Mycobacterium tuberculosis, it"s hard to interpret result about culture test and to practice antimicrobial susceptibility test and rapid drug susceptibility testing. Because we have to practice again smear, culture test after extracting specimen from the patient, time is consumed and proper patient treatment is postponed. To address these problems and quick patient treatment, rapid drug susceptibility testing is practiced by using GenoType® MTDRplus method. As a result of this method we detected sensibility 10 and 7 cases and resistance 0 and 3 cases using RIM and INH respectively with other 1 case toward medicals out of the total 11 test. In conclusion rapid drug susceptibility testing can be used from the contaminated specimen after elimination of contaminated source from culture and proved that it can be practiced for rapid examination of a tuberculosis patient.

Query Expansion Using Augmented Terms in an Extended Boolean Model

Nguyen, Tuan-Quang,Heo, Jun-Seok,Lee, Jung-Hoon,Kim, Yi-Reun,Whang, Kyu-Young Korean Institute of Information Scientists and Eng 2008 Journal of Computing Science and Engineering Vol.2 No.1

We propose a new query expansion method in the extended Boolean model that improves precision without degrading recall. For improving precision, our method promotes the ranks of documents having more query terms since users typically prefer such documents. The proposed method consists of the following three steps: (1) expanding the query by adding new terms related to each term of the query, (2) further expanding the query by adding augmented terms, which are conjunctions of the terms, (3) assigning a weight on each term so that augmented terms have higher weights than the other terms. We conduct extensive experiments to show the effectiveness of the proposed method. The experimental results show that the proposed method improves precision by up to 102% for the TREC-6 data compared with the existing query expansion method using a thesaurus proposed by Kwon et al.

Query Expansion Using Augmented Terms in an Extended Boolean Model

Tuan-Quang Nguyen,Jun-Seok Heo,Jun-Hoon Lee,Yi-Reun Kim,Kyu-Young Whang 한국정보과학회 2008 Journal of Computing Science and Engineering Vol.2 No.1

We propose a new query expansion method in the extended Boolean model that improves precision without degrading recall. For improving precision, our method promotes the ranks of documents having more query terms since users typically prefer such documents. The proposed method consists of the following three steps: (1) expanding the query by adding new terms related to each term of the query, (2) further expanding the query by adding augmented terms, which are conjunctions of the terms, (3) assigning a weight on each term so that augmented terms have higher weights than the other terms. We conduct extensive experiments to show the effectiveness of the proposed method. The experimental results show that the proposed method improves precision by up to 102% for the TREC-6 data compared with the existing query expansion method using a thesaurus proposed by Kwon et al. [Kwon et al. 1994].

Krüppel-like factor 4 mediates lysophosphatidic acid-stimulated migration and proliferation of PC3M prostate cancer cells

Shin, Sang Hun,Kwon, Yang Woo,Heo, Soon Chul,Jeong, Geun Ok,Kim, Ba Reun,Seo, Eun Jin,Kim, Jae Ho Nature Publishing Group 2014 Experimental and molecular medicine Vol.46 No.7

<P>Prostate cancer is the most frequently diagnosed malignancy and the second leading cause of cancer mortality among men in the United States. Accumulating evidence suggests that lysophosphatidic acid (LPA) serves as an autocrine/paracrine mediator to affect initiation, progression and metastasis of prostate cancer. In the current study, we demonstrate that LPA stimulates migration and proliferation of highly metastatic human prostate cancer, PC-3M-luc-C6 cells. LPA-induced migration of PC-3M-luc-C6 cells was abrogated by pretreatment of PC-3M-luc-C6 cells with the LPA receptor 1/3 inhibitor Ki16425 or small interfering RNA (siRNA)-mediated silencing of endogenous LPA receptor 1, implicating a key role of the LPA-LPA receptor 1 signaling axis in migration of PC-3M-luc-C6 cells. In addition, LPA treatment resulted in augmented expression levels of Krüppel-like factor 4 (KLF4), and siRNA or short-hairpin RNA (shRNA)-mediated silencing of KLF4 expression resulted in the abolishment of LPA-stimulated migration and proliferation of PC-3M-luc-C6 cells. shRNA-mediated silencing of KLF4 expression resulted in the inhibition of <I>in vivo</I> growth of PC-3M-luc-C6 cells in a xenograft transplantation animal model. Taken together, these results suggest a key role of LPA-induced KLF4 expression in cell migration and proliferation of prostate cancer cells <I>in vitro</I> and <I>in vivo</I>.</P>

오디세우스 대용량 검색 엔진을 위한 병렬 웹 크롤러의 구현

신은정(Eun-Jeong Shin),김이른(Yi-Reun Kim),허준석(Jun-Seok Heo),황규영(Kyu-Young Whang) 한국정보과학회 2008 정보과학회 컴퓨팅의 실제 논문지 Vol.14 No.6

웹의 크기가 폭발적으로 증가함에 따라 인터넷에서 정보를 얻는 수단으로서 검색 엔진의 중요성이 부각되고 있다. 검색 엔진은 사용자에게 최신의 정보를 검색 결과로서 제공하기 위해 웹 페이지를 주기적으로 수집하고 이를 데이타베이스에 저장한다. 웹 크롤러는 이러한 목적으로 웹 페이지를 수집하는 프로그램이다. 대부분의 검색 엔진은 제한된 시간 내에 많은 수의 웹 페이지를 수집하기 위해 다수의 머신을 사용하는 병렬 웹 크롤러를 이용한다. 그러나, 병렬 웹 크롤러의 아키텍처와 세부 구현 방법이 잘 알려져 있지 않기 때문에 실제로 병렬 웹 크롤러를 구현하는 데에 어려움이 많다. 본 논문에서는 병렬 웹 크롤러(parallel web crawler)의 아키텍처와 세부 구현 방법을 제시한다. 병렬웹 크롤러는 다수의 머신에서 웹 페이지를 병렬적으로 수집하기 위해 조정자(coordinator) 대리자(agent) 구조의 2-티어(tier) 모델을 사용한다. 조정자/대리자 모델은 각 머신에서 웹 페이지를 수집하기 위한 다수의 대리자들과 이 대리자들을 관리하기 위한 하나의 조정자로 구성된다. 병렬 웹 크롤러는 웹 페이지를 수집하기 위한 크롤링(crawling) 모듈, 수집한 웹 페이지를 데이타베이스 로딩 포맷으로 변환하기 위한 컨버팅(converting) 모듈, 수집된 웹 페이지의 중요도를 계산하기 위한 랭킹(ranking) 모듈로 구성된다. 본 논문에서는 병렬 웹 크롤러의 각 모듈들을 설명하고, 세부 구현 방법을 설명한다. 마지막으로, 실험을 통해 병렬 웹 크롤러의 성능을 평가하였다. 실험 결과, 제안된 병렬 웹 크롤러가 수집해야할 웹 페이지 개수와 머신 개수에 따라 확장 가능함을 보였다. As the size of the web is growing explosively, search engines are becoming increasingly important as the primary means to retrieve information from the Internet. A search engine periodically downloads web pages and stores them in the database to provide readers with up-to-date search results. The web crawler is a program that downloads and stores web pages for this purpose. A large-scale search engines uses a parallel web crawler to retrieve the collection of web pages maximizing the download rate. However, the service architecture or experimental analysis of parallel web crawlers has not been fully discussed in the literature. In this paper, we propose an architecture of the parallel web crawler and discuss implementation issues in detail. The proposed parallel web crawler is based on the coordinator/agent model using multiple machines to download web pages in parallel. The coordinator/agent model consists of multiple agent machines to collect web pages and a single coordinator machine to manage them. The parallel web crawler consists of three components: a crawling module for collecting web pages, a converting module for transforming the web pages into a database-friendly format, a ranking module for rating web pages based on their relative importance. We explain each component of the parallel web crawler and implementation methods in detail. Finally, we conduct extensive experiments to analyze the effectiveness of the parallel web crawler. The experimental results clarify the merit of our architecture in that the proposed parallel web crawler is scalable to the number of web pages to crawl and the number of machines used.

오디세우스/Parallel-OOSQL : 오디세우스 정보검색용 밀결합 DBMS를 사용한 병렬 정보 검색 엔진

류재준(Jae-Joon Ryu),황규영(Kyu-Young Whang),이재길(Jae-Gil Lee),권혁윤(Hyuk-Yoon Kwon),김이른(Yi-Reun Kim),허준석(Jun-Suk Heo),이기훈(Ki-Hoon Lee) 한국정보과학회 2008 정보과학회 컴퓨팅의 실제 논문지 Vol.14 No.4

최근 들어 인터넷의 성장으로 인하여 문서의 양이 기하급수적으로 증가함에 따라, 대용량의 문서를 빠르게 검색 할 수 있는 병렬 정보 검색 엔진에 대한 중요성이 더욱 대두되고 있다. 병렬 정보 검색엔진을 구현하기 위하여서는 역 색인을 분할하고, 분할된 역 색인을 통하여 병렬적으로 검색하는 것이 필요하다. 역 색인을 분할하는 기존 방법으로는 1) 문서 식별자 분할 방법과 2) 키워드 식별자 분할 방법이 있다. 그러나 각 분할 방법은 다음과 같은 단점들을 가지고 있다. 문서 식별자 분할 방법은 문서의 추가가 용이하고 처리량(throughput)이 높은 반면에 top-k 질의 처리 성능이 좋지 않다. 그리고 키워드 식별자 분할 방법은 top-k 질의 처리 성능이 좋은 반면에 문서의 추가가 어렵고 처리량이 낮다. 본 논문에서는 이러한 단점들을 해결하기 위하여 혼합 분할 방법을 제안하고 이를 정보 검색 기능과 밀결합된 DBMS인 오디세우스에 실현한 병렬 정보 검색 엔진을 설계하고 구현한다. 먼저, 제안된 병렬 정보 검색 엔진인 오디세우스/Parallel-OOSQL의 아키텍쳐를 설명한다. 그리고 체계적인 실험을 통하여 제안된 시스템의 유용성을 보인다. 실험 결과, 문서 식별자 분할 방법은 질의 처리 시간이 역 색인 분할의 블록의 개수에 근사적으로 역 비례함을 보였으며, 키워드 식별자 분할 방법은 top-k 질의 처리에 좋은 성능을 보였다. 본 논문에서 제안된 병렬 정보 검색 엔진은 세 가지 분할 방법을 모두 제공하기 때문에 응용 환경에 따라 분할방법을 커스터마이즈함으로써 항상 좋은 성능을 낼 수 있다. 오디세우스/Parallel-OOSQL 병렬 정보 검색엔진은 각 슬레이브 노드 당 1억 건의 웹 문서를, 시스템 전체로는 수십억 건의 웹 문서를 인덱스하여 저장하고 질의를 처리할 수 있다. As the amount of electronic documents increases rapidly with the growth of the Internet, a parallel search engine capable of handling a large number of documents are becoming ever important. To implement a parallel search engine, we need to partition the inverted index and search through the partitioned index in parallel. There are two methods of partitioning theinverted index: 1) document identifier based partitioning and 2) keyword-identifier based partitioning. However, each method alone has the following drawbacks. The former is convenient in inserting documents and has high throughput, but has poor performance for top-k query processing. The latter has good performance for top-k query processing, but is inconvenient in inserting documents and has low throughput. In this paper, we propose a hybrid partitioning method to compensate for the drawback of each method. We design and implement a parallel search engine that supports the hybrid partitioning method using the Odysseus DBMS tightly coupled with information retrieval capability. We first introduce the architecture of the parallel search engine-Odysseus/Parallel-OOSQL. We then show the effectiveness of the proposed system through systematic experiments. The experimental results show that the query processing time of the document-identifier based partitioning method is approximately inversely proportional to the number of blocks in the partition of the inverted index. The results also show that the keyword-identifier based partitioning method has good performance in top-k query processing. The proposed parallel search engine can be optimized for performance by customizing the methods of partitioning the inverted index according to the application environment. The Odysseus/Parallel-OOSQL parallel search engine is capable of indexing, storing, and querying 100 million web documents per node or tens of billions of web documents for the entire system.