• The Journal of the Korea Contents Association
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• v.16 no.10
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• pp.608-616
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• 2016

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.

• KIPS Transactions on Computer and Communication Systems
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• v.9 no.12
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• pp.291-306
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• 2020

Nowadays, Data-Network-AI (DNA)-based intelligent services and applications have become a reality to provide a new dimension of services that improve the quality of life and productivity of businesses. Artificial intelligence (AI) can enhance the value of IoT data (data collected by IoT devices). The internet of things (IoT) promotes the learning and intelligence capability of AI. To extract insights from massive volume IoT data in real-time using deep learning, processing capability needs to happen in the IoT end devices where data is generated. However, deep learning requires a significant number of computational resources that may not be available at the IoT end devices. Such problems have been addressed by transporting bulks of data from the IoT end devices to the cloud datacenters for processing. But transferring IoT big data to the cloud incurs prohibitively high transmission delay and privacy issues which are a major concern. Edge computing, where distributed computing nodes are placed close to the IoT end devices, is a viable solution to meet the high computation and low-latency requirements and to preserve the privacy of users. This paper provides a comprehensive review of the current state of leveraging deep learning within edge computing to unleash the potential of IoT big data generated from IoT end devices. We believe that the revision will have a contribution to the development of DNA-based intelligent services and applications. It describes the different distributed training and inference architectures of deep learning models across multiple nodes of the edge computing platform. It also provides the different privacy-preserving approaches of deep learning on the edge computing environment and the various application domains where deep learning on the network edge can be useful. Finally, it discusses open issues and challenges leveraging deep learning within edge computing.

• Development and Reproduction
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• v.6 no.1
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• pp.7-16
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• 2002

In order to obtain the specific genes of snailfish a subtracted cDNA library was constructed, and analysed by sequencing and GenBank search. Among them C90-171 clone was turned out to be genes showing low homology and nonredundant genes. This novel clone was named Gomsin(C90-171). Gomsin was shown to be intensely expressed in the epithelial cells, some mesenchymal cells, and sheaths of muscle bundles in the result of immunohistochemistry. In the cross reaction assay of Gomsin antibody against various human tissues, the Gomsin was strongly expressed in the ductal and acinar cells of salivary glands, which was similar to the expression patterns of proline-rich proteins(PRPs) of human. The antibody raised against the Gomsin was clearly cross-reacted with human salivary PRPs and also recombinant proteins of human PRPs in the Western blot and immunoprecipitation analysis. Contrast to the salivary PRPs, the Gomsin was not easily degraded in the mixed saliva, but rapidly attacked on the cultured keratocytes in vitro. The simulated protein structure of Gomsin was similar to the whorled pattern of PRPs, even though the amino acid sequence of Gomsin was quite different from those of PRPs. These data suggest that the Gomsin is a characteristic matrix protein in the skin and body of snailfish, which is also utilized for the tissue protection in the similar way to the PRPs of human muco-secretory organs.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.89-101
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• 2014

나노 규모의 좁은 공간에서는 분자들과 벽면과의 상호작용이 커서 분자들의 거동에 큰 영향을 준다. 이와 관련하여 최근에 나노슬릿 (nano-slit)이나 나노채널(nano-channel)과 같은 제한된 공간(confined geometry)에서 DNA의 구조적, 동역학적 거동에 관한 연구가 활발히 진행 중이다. 이러한 연구에서 모티브를 얻어 많은 입자들(spheres)로 이루어진 나노슬릿(nano-slit)사이에 Leonard-Jones potential을 따르는 용매분자들과 고분자가 들어있는 시스템을 구성하여 고분자의 동역학에 관해 연구하고자 하였다. 이때 슬릿(slit)은 약간의 탄성 포텐셜을 가지는 경우와 완전히 고정되어서 움직이지 않는 경우로 나누어 실행하였다. 더불어 고분자의크기, 용매의 종류, slit 사이의 간격 등의 변화가 고분자의 동역학에 어떤 영향을 주는지 살펴보았다. 이를 통해 환경적 조건에 따른 나노슬릿(nano-slit)에서 고분자의 움직임의 양상을 이해할 수 있었다.

• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2007.04a
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• pp.324-328
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• 2007

유비궈터스 헬스케어는 단일화된 서비스가 아니라 다양한 기술들이 복합적으로 결합되어 운용되는 서비스이다. 따라서 서비스의 형태가 고정적이지 않고 매우 다양하게 나타난다. 하지만 실제로 차이가 발생하는 부분은 서비스의 구현에 관한 세부적 내용에서 나타나고, 서비스 운용을 위한 기본 구성요소에 있어서는 큰 차이가 없이 유사한 형태를 가진다. 그 결과 유비쿼터스 헬스케어 서비스 개발 과정에서는 실제 서비스의 구현 외의 통신과 데이터베이스의 이용, 메시지 전달과 같은 중복되는 항목에 대한 고려가 매번 이루어져야 한다. 이것은 개발 과정에 있어 불필요한 비용의 증가를 불러온다. 본 논문에서는 이와 같은 불필요한 비용을 감소시키며 서비스의 개발과 운용이 가능한 유비쿼터스 헬스케어 서비스의 제공을 위한 아키텍처와 서비스 개발을 위한 프레임워크를 제안한다. 제안하는 서비스 제공 아키덱처는 크게 이용자 단말, 유비궈터스 헬스케어 서비스 센터, 외부 기관으로 구성된다. 서비스 개발 프레임워크는 서버와 클라이언트 프레임워크로 구분된다. 서비스 개발 프레임워크는 서비스를 제공하는 서버에서 필요한 유비쿼터스 헬스케어 서비스의 공통 구성요소를 가진다. 서비스의 개발을 위해 우선 프로세스에 대한 정의를 수행하고, 정의된 내용에 따라 필요한 코드 템플릿을 결합하여 서비스의 초기 형태를 만들어낸다. 여기에 각 서비스가 필요로 하는 세부 사항을 작성하는 것으로 서비스의 개발을 수행하게 된다. 제안된 서비스 제공 아키텍처와 서비스 개발 프레임워크를 실제 적용해보기 위해 전림선비대증 환자 진료를 위한 시스템을 설계하고 구현하였다.JSHOP2 계획수립기내에 구현하였다. 계획 실행 방법으로는 주어진 강건한 계획에 대하여 행위들이 직접 실행하수 있도록 한다.며 용량에 의존하는 양상을 보였다. $H_2O_2$에 의해 유발(誘發)된 DNA의 손상은 catalase와 deferoxamine에 의해 억제되었지만 DPPD는 억제시키지 못했다. 배기음(排氣飮)은 $H_2O_2$에 의해 유발(誘發)된 ATP의 소실을 회복시켰다. 이러한 실험결과 $H_2O_2$에 의해 유발(誘發)된 세포(細胞)의 손상(損傷)은 지질(脂質)의 과산화(過酸化)와는 다른 독립적인 기전에 의해 일어남을 나타낸다. 결론 : 이러한 결과들로 볼 때 Caco-2 세포(細胞)에서 배기음(排氣飮)이 항산화작용(亢酸化作用)보다는 다른 기전을 통하여 Caco-2 세포안에서 산화제(酸化劑)에 의해 유발(誘發)된 세포(細胞)의 사망(死亡)와 DNA의 손상(損傷)을 방지할 수 있다는 것을 가리킨다. 따라서 본 연구(硏究)는 배기음(排氣飮)이 반응성산소기(反應性酸素基)에 의해 매개된 인체(人體) 위장관질환(胃腸管疾患)의 치료(治療)에 사용할 수 있을 가능성(可能性)이 있음을 제시하고 있다.에 이를 이용하여 유가배양시 기질을 공급하는 공정변수로 사용하였다 [8]. 생물학적인 폐수처리장치인 활성 슬러지법에서 미생물의 활성을 측정하는 방법은 아직 그다지 개발되어있지 않다. 본 연구에서는 슬러지의 주 구성원이 미생물인 점에 착안하여 침전시 슬러지층과 상등액의 온도차를 측정하여 대사열량의 발생량을 측정하고 슬러지의 활성을 측정할 수 있는 방법을

• Journal of Life Science
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• v.30 no.1
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• pp.106-112
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• 2020

Aminoacyl tRNA synthetase complex interacting multifunctional protein 2 (AIMP2) is a scaffolding protein required for the assembly of multi-tRNA synthetase, and it can exert pro-apoptotic activity in response to DNA damage. In the presence of DNA damage, AIMP2 binds to mouse double minute 2 homolog (MDM2) to protect p53 from MDM2 attack. TGF-β signaling results in the nuclear translocation of AIMP2, whereby AIMP2 interacts with FUSE-binding protein, and, thus, suppresses c-myc. TNF receptor-associated factor 2 (TRAF2) is an important mediator between TNF-receptors 1 and 2 which are involved in the signaling of c-Jun N-terminal kinase (JNK), nuclear factor κB (NF-κB), and p38 mitogen-activated protein kinases (MAPKs). TRAF2 is required for the activations of JNK and NF-κB via TNF-α and the mediation of anti-apoptosis signaling. AIMP2 can also enhance pro-apoptosis in the TNF-α signaling. During this signaling, AIMP2 assists the association of E3 ubiquitin ligase, the cellular inhibitor of apoptosis protein 1 (c-IAP1) which is well known and responsible for the degradation of TRAF2. The formation of a complex among AIMP2, TRAF2, and c-IAP1 results in proteasome-mediated TRAF2 degradation. AIMP2 can induce apoptosis via downregulation of TRAF2 to interact directly in TNF-α signaling. This review provides new insight into the molecular mechanism responsible for AIMP2 and TRAF2 complex formation and treatments for TNFα-associated diseases.

• Journal of the Korean Society of Marine Environment & Safety
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• v.24 no.2
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• pp.171-178
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• 2018

The ocean is a harsh environment and Korea Coast Guard officers often face the threat of death or going missing in the line of duty. In order to promptly identify unknown bodies during mishaps, Korea Coast Guard Research Center has established an identification system using the DNA of its officers. This collected DNA can also be entombed in National Cemeteries when the remains are not recovered. The storage, disposal and quality control of the materials are overseen by the Governing Committee according to the Enforcement Rules for the Human Biological Materials Storage Project for the Identification of Officers Killed or Gone Missing in Action. Approximately 700 bodies are found per year along the Korean coast. An alternative method should be put in place for when identification through fingerprints and teeth are not applicable due to severe decomposition or partial recovery. We believe it would greatly contribute to helping identify the unknown bodies if the storage project could expand its data to include marine industry workers, relevant researchers and those involved in marine leisure activities.

• Journal of Life Science
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• v.14 no.4
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• pp.593-607
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• 2004

The nucleotide sequence for a nuclear-encoded small subunit rDNA (SSU rDNA) was determined for 43 species of the class Dinophyceae, including harmful algae Cochlodinium polykrikoides and Gyrodinium aureolum. These sequences and data analyses were performed by parsimony, distances and maximum likelihood methods in PHYLIP (Phylogenetic Inference Package) version 3.573c. The species Noctiluca scintillans, Gonyaulax spinifern and Crypthecodinium cohnii occupied a basal position within the Dino- phyceae in our analyses. The genera Alexandrium and Symbiodinium were monophyletic (supported by a bootstrap value of >70%), whereas the genera Gymnedinium and Gyrodinium formed polyphyletic nodes, for which bootstrap support was strong (>70%) in the neighbor-joining and maximum likelihood methods except for the PHYLIP parsimony analysis (=59%). The sequence divergence between G. aureolum and G. dorsum/ G. galathenum was the largest at 7.4% (45 bp), whereas G. aureolum and G. mikimotoi showed an extremely low value of genetic divergence of 0.9% (5 bp). The genetic divergence between C. polykrikoides and G. aureolum was a low value of 5.2% (31 bp). In the phylogenetic analysis, the placement of G. aureolum and C. polykrikoides was closer to the genus Gymnodinium than to the genus Gyrodinium, which was supported by a moderate bootstrap value.

• Journal of the Korea Society of Computer and Information
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• v.18 no.6
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• pp.1-8
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• 2013

In this paper, we design and implement a firmware for low-cost small PCR devices. To minimize machine code size, the proposed firmware controls real-time tasks simultaneously only with support of the hardware interrupt, but without support of the operating system program. The proposed firmware has the host-local structure in which the firmware receives operation commands from PC and sends operation results to PC through usb communication. We implement a low-cost small PCR device with the proposed firmware loaded on microchip PIC18F4550 chip, and verify that the implemented PCR device significantly reduces cost and volume size of existing commercial PCR devices with a similar performance.

• Journal of Life Science
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• v.24 no.7
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• pp.757-761
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• 2014

Olive flounder (Paralichthys olivaceus) is an important aquaculture fish species in Jeju Island, South Korea. Due to the intensification of flounder fish farming, huge amounts of chemical antibiotics are used against several fish diseases. This has many harmful side effects on fish, as well as human consumers. Hence, an alternative to chemical antibiotic agents is needed for disease control. In this study, three strains of rhizobacteria (BRH433-2, TRH415-2, and THJ609-3) were isolated from the rhizosphere of plants. Assays of their antibacterial activity against fish pathogens, such as S. iniae, S. parauberis, V. anguillarum, and E. tarda, were performed with untreated broth culture (without cell separation), supernatant, and precipitated pellets separated by centrifugation. Among these, the cell suspension prepared from the precipitated pellet showed significant antimicrobial activity when compared with that of the untreated broth culture and centrifugal supernatant. These results indicate that the three isolated rhizobacterial strains exhibit antibacterial activity. Analysis of the 16S rDNA sequences of the BRH-433-2, THJ609-3, and TRH415-2 strains showed the highest similarity to Burkholderia gladioli (99.5%), Pseudomonas baetica (97.7%), and P. koreensis and P. baetica (98.4%), respectively. We suggest that the strains hold promise in disease management of fish.