• Mass Spectrometry Letters
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• 제12권3호
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• pp.60-65
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• 2021

As a part of the Chromosome-centric Human Proteome Project (C-HPP), we have developed a few algorithms for accurate identification of missing proteins, alternative splicing variants, single amino acid variants, and characterization of function unannotated proteins. We have found missing proteins, novel and known ASVs, and SAAVs using LC-MS/MS data from human brain and olfactory epithelial tissue, where we validated their existence using synthetic peptides. According to the neXtProt database, the number of missing proteins in chromosome 11 shows a decreasing pattern. The development of genomic and transcriptomic sequencing techniques make the number of protein variants in chromosome 11 tremendously increase. We developed a web solution named as SAAvpedia for identification and function annotation of SAAVs, and the SAAV information is automatically transformed into the neXtProt web page using REST API service. For the 73 uPE1 in chromosome 11, we have studied the function annotaion of CCDC90B (NX_Q9GZT6), SMAP (NX_O00193), and C11orf52 (NX_Q96A22).

• KSII Transactions on Internet and Information Systems (TIIS)
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• 제13권8호
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• pp.4300-4314
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• 2019

With the development of video-related applications, media content has increased dramatically through applications. There is a substantial amount of near-duplicate videos (NDVs) among Internet videos, thus NDVR is important for eliminating near-duplicates from web video searches. This paper proposes a novel NDVR system that supports large-scale retrieval and contributes to the efficient and accurate retrieval performance. For this, we extracted keyframes from each video at regular intervals and then extracted both commonly used features (LBP and HSV) and new image features from each keyframe. A recent study introduced a new image feature that can provide more robust information than existing features even if there are geometric changes to and complex editing of images. We convert a vector set that consists of the extracted features to binary code through a set of hash functions so that the similarity comparison can be more efficient as similar videos are more likely to map into the same buckets. Lastly, we calculate similarity to search for NDVs; we examine the effectiveness of the NDVR system and compare this against previous NDVR systems using the public video collections CC_WEB_VIDEO. The proposed NDVR system's performance is very promising compared to previous NDVR systems.

• Genomics & Informatics
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• 제16권4호
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• pp.36.1-36.3
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• 2018

Next generation sequencing (NGS), a high-throughput DNA sequencing technology, is widely used for molecular biological studies. In NGS, RNA-sequencing (RNA-Seq), which is a short-read massively parallel sequencing, is a major quantitative transcriptome tool for different transcriptome studies. To utilize the RNA-Seq data, various quantification and analysis methods have been developed to solve specific research goals, including identification of differentially expressed genes and detection of novel transcripts. Because of the accumulation of RNA-Seq data in the public databases, there is a demand for integrative analysis. However, the available RNA-Seq data are stored in different formats such as read count, transcripts per million, and fragments per kilobase million. This hinders the integrative analysis of the RNA-Seq data. To solve this problem, we have developed a web-based application using Shiny, COEX-seq (Convert a Variety of Measurements of Gene Expression in RNA-Seq) that easily converts data in a variety of measurement formats of gene expression used in most bioinformatic tools for RNA-Seq. It provides a workflow that includes loading data set, selecting measurement formats of gene expression, and identifying gene names. COEX-seq is freely available for academic purposes and can be run on Windows, Mac OS, and Linux operating systems. Source code, sample data sets, and supplementary documentation are available as well.

• Physical Therapy Rehabilitation Science
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• 제11권4호
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• pp.464-470
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• 2022

Objective: Axillary web syndrome (AWS) is a condition comprising fibrous band-like cords that appear in the axilla of patients after axillary lymph node dissection (ALND) during breast cancer surgery and result in pain and reduced mobility. The cords appearing with AWS are hardened veins or lymphatic vessels. Manual therapy and stretching are recommended for pain control and mobility improvement. Therefore, this study investigated the effect of cytoskeletal manual therapy (CMT), which is a new soft tissue mobilization technique. Design: A case report Methods: A 41-year-old woman with AWS after breast cancer surgery and ALND visited a physical therapy clinic because of shoulder pain, decreased function, and decreased mobility. The cords were palpable and pain occurred 2 weeks after surgery. CMT was performed three times per week for a total of 6 weeks. Her pain intensity, range of motion (ROM), and shoulder function were measured. Results: Measurements were performed after 2 weeks and 6 weeks of CMT and evaluated using the numeric pain rating scale (NPRS). Her pain intensity largely decreased after 2 weeks (4-point score reduction) and after 6 weeks (5-point score reduction) of CMT. After CMT, her full ROM was restored and her shoulder function was improved (7-point score reduction). Conclusions: CMT is effective for pain control, mobility improvement, and functional improvement of patients with AWS.

• Asia pacific journal of information systems
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• 제17권4호
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• pp.31-59
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• 2007

We frequently use search engines to find relevant information in the Web but still end up with too much information. In order to solve this problem of information overload, ranking algorithms have been applied to various domains. As more information will be available in the future, effectively and efficiently ranking search results will become more critical. In this paper, we propose a ranking algorithm for the Semantic Web resources, specifically RDF resources. Traditionally, the importance of a particular Web page is estimated based on the number of key words found in the page, which is subject to manipulation. In contrast, link analysis methods such as Google's PageRank capitalize on the information which is inherent in the link structure of the Web graph. PageRank considers a certain page highly important if it is referred to by many other pages. The degree of the importance also increases if the importance of the referring pages is high. Kleinberg's algorithm is another link-structure based ranking algorithm for Web pages. Unlike PageRank, Kleinberg's algorithm utilizes two kinds of scores: the authority score and the hub score. If a page has a high authority score, it is an authority on a given topic and many pages refer to it. A page with a high hub score links to many authoritative pages. As mentioned above, the link-structure based ranking method has been playing an essential role in World Wide Web(WWW), and nowadays, many people recognize the effectiveness and efficiency of it. On the other hand, as Resource Description Framework(RDF) data model forms the foundation of the Semantic Web, any information in the Semantic Web can be expressed with RDF graph, making the ranking algorithm for RDF knowledge bases greatly important. The RDF graph consists of nodes and directional links similar to the Web graph. As a result, the link-structure based ranking method seems to be highly applicable to ranking the Semantic Web resources. However, the information space of the Semantic Web is more complex than that of WWW. For instance, WWW can be considered as one huge class, i.e., a collection of Web pages, which has only a recursive property, i.e., a 'refers to' property corresponding to the hyperlinks. However, the Semantic Web encompasses various kinds of classes and properties, and consequently, ranking methods used in WWW should be modified to reflect the complexity of the information space in the Semantic Web. Previous research addressed the ranking problem of query results retrieved from RDF knowledge bases. Mukherjea and Bamba modified Kleinberg's algorithm in order to apply their algorithm to rank the Semantic Web resources. They defined the objectivity score and the subjectivity score of a resource, which correspond to the authority score and the hub score of Kleinberg's, respectively. They concentrated on the diversity of properties and introduced property weights to control the influence of a resource on another resource depending on the characteristic of the property linking the two resources. A node with a high objectivity score becomes the object of many RDF triples, and a node with a high subjectivity score becomes the subject of many RDF triples. They developed several kinds of Semantic Web systems in order to validate their technique and showed some experimental results verifying the applicability of their method to the Semantic Web. Despite their efforts, however, there remained some limitations which they reported in their paper. First, their algorithm is useful only when a Semantic Web system represents most of the knowledge pertaining to a certain domain. In other words, the ratio of links to nodes should be high, or overall resources should be described in detail, to a certain degree for their algorithm to properly work. Second, a Tightly-Knit Community(TKC) effect, the phenomenon that pages which are less important but yet densely connected have higher scores than the ones that are more important but sparsely connected, remains as problematic. Third, a resource may have a high score, not because it is actually important, but simply because it is very common and as a consequence it has many links pointing to it. In this paper, we examine such ranking problems from a novel perspective and propose a new algorithm which can solve the problems under the previous studies. Our proposed method is based on a class-oriented approach. In contrast to the predicate-oriented approach entertained by the previous research, a user, under our approach, determines the weights of a property by comparing its relative significance to the other properties when evaluating the importance of resources in a specific class. This approach stems from the idea that most queries are supposed to find resources belonging to the same class in the Semantic Web, which consists of many heterogeneous classes in RDF Schema. This approach closely reflects the way that people, in the real world, evaluate something, and will turn out to be superior to the predicate-oriented approach for the Semantic Web. Our proposed algorithm can resolve the TKC(Tightly Knit Community) effect, and further can shed lights on other limitations posed by the previous research. In addition, we propose two ways to incorporate data-type properties which have not been employed even in the case when they have some significance on the resource importance. We designed an experiment to show the effectiveness of our proposed algorithm and the validity of ranking results, which was not tried ever in previous research. We also conducted a comprehensive mathematical analysis, which was overlooked in previous research. The mathematical analysis enabled us to simplify the calculation procedure. Finally, we summarize our experimental results and discuss further research issues.

• KSII Transactions on Internet and Information Systems (TIIS)
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• 제10권8호
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• pp.4008-4022
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• 2016

This paper tries to extend the conventional conceptual framework of the Internet of Things (IoT) so as to reify an advanced pervasive IoT-community collaboration concept, which is called the process-aware Internet of Things. The extended conceptual framework is embodied as a referential architecture that can be a standardized reference model supporting the conceptual integration of the Internet of Things and the process awareness. The extended referential architecture covers the full range of the architectural details from abstracting the process-aware behavioral semantics to reifying the IoT-process enactments. These extended framework and architecture ought to be the theoretical basis for implementing a process-aware IoT-community computing system supporting process-aware collaborations of Things in pervasive computing environments. In particular, we do point up that the proposed framework of the process-aware Internet of Things is revised from the Internet of Things framework announced in ITU-T SG13³ Y.2060 [26] by integrating the novel concept of process awareness. We strongly believe that the extended conceptual framework and its referential architecture are able to deliver the novel and meaningful insight as a standardized platform for describing and achieving the goals of IoT-communities and societies.

• 한국콘텐츠학회:학술대회논문집
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• 한국콘텐츠학회 2003년도 춘계종합학술대회논문집
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• pp.102-106
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• 2003

본 논문에서는 웹을 이용한 사이버교육에 있어 가장 중시되고 있는 콘텐츠의 상호작용과 그 저작효율을 향상시키는 새로운 모델과 방안을 제안하였다. 특히, 수학적 기반으로 구조도를 비롯한 다양한 모델과 개념단위가 제시되며, 실험·실습을 위주로 하는 공학교육용 콘텐츠를 저작함에 있어, 자바(JAVA)를 이용한 단위 콘텐츠 애플릿의 라이브러리를 구축하는 기술과 개념단위를 기반으로 분기·접속하는 기술을 적용함으로써 콘텐츠의 융통성과 상호작용을 개선하고 그 저작의 수월성을 제고함으로써 궁극적으로 사이버강좌의 학습효과를 향상시키는 학습자 중심의 새로운 모델을 제시한다. 본 논문에서 제안하는 개념단위 분기 방법은 기존의 페이지별 분기방법과 병행하여 구현함으로써 더욱 융통성 있는 상호작용을 제공하며, 이와 더불어 자바 애플릿에 의한 단위 콘텐츠의 구성으로 공학분야 콘텐츠의 품질을 크게 향상시킬 것으로 기대된다.

• Journal of Information Processing Systems
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• 제10권3호
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• pp.365-383
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• 2014

Service-oriented computing offers efficient solutions for executing complex applications in an acceptable amount of time. These solutions provide important computing and storage resources, but they are too difficult for individual users to handle. In fact, Service-oriented architectures are usually sophisticated in terms of design, specifications, and deployment. On the other hand, workflow management systems provide frameworks that help users to manage cooperative and interdependent processes in a convivial manner. In this paper, we propose a workflow-based approach to fully take advantage of new service-oriented architectures that take the users' skills and the internal complexity of their applications into account. To get to this point, we defined a novel framework named JASMIN, which is responsible for managing service-oriented workflows on distributed systems. JASMIN has two main components: unified modeling language (UML) to specify workflow models and business process execution language (BPEL) to generate and compose Web services. In order to cover both workflow and service concepts, we describe in this paper a refinement of UML activity diagrams and present a set of rules for mapping UML activity diagrams into BPEL specifications.

• KSII Transactions on Internet and Information Systems (TIIS)
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• 제12권8호
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• pp.3725-3748
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• 2018

Text data distribution is often imbalanced. Imbalanced data is one of the challenges in text classification, as it leads to the loss of performance of classifiers. Many studies have been conducted so far in this regard. The proposed solutions are divided into several general categories, include sampling-based and algorithm-based methods. In recent studies, feature selection has also been considered as one of the solutions for the imbalance problem. In this paper, a novel one-sided feature selection known as probabilistic feature selection (PFS) was presented for imbalanced text classification. The PFS is a probabilistic method that is calculated using feature distribution. Compared to the similar methods, the PFS has more parameters. In order to evaluate the performance of the proposed method, the feature selection methods including Gini, MI, FAST and DFS were implemented. To assess the proposed method, the decision tree classifications such as C4.5 and Naive Bayes were used. The results of tests on Reuters-21875 and WebKB figures per F-measure suggested that the proposed feature selection has significantly improved the performance of the classifiers.

• 한국축산식품학회지
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• 제33권4호
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• pp.463-473
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• 2013

Through the development of efficient data collecting technologies like RFID, and inter-enterprise collaboration platforms such as web services, companies which participate in supply chains can acquire visibility over the whole supply chain, and can make decisions to optimize the overall supply chain networks and processes, based on the extracted knowledge from historical data collected by the visibility system. Although not currently active, the MeatWatch system has been developed, and is used in part for this purpose, in the imported beef distribution network in Korea. However, the imported beef distribution network is too complicated to analyze its various aspects using ordinary process analysis approaches. In this paper, we suggest a novel approach, called RFID-based supply chain process mining, to automatically discover and analyze the overall supply chain processes from the distributed RFID event data, without any prior knowledge. The proposed approach was implemented and validated, by using a case study of the imported beef distribution network in Korea. Specifically we demonstrated that the proposed approach can be successfully applied to discover supply chain networks from the distributed event data, to simplify the supply chain networks, and to analyze anomaly of the distribution networks. Such novel process mining functionalities can reinforce the capability of traceability services like MeatWatch in the future.