• Journal of Information Processing Systems
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• v.18 no.1
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• pp.159-172
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• 2022

The role of the interconnect network, which connects computing nodes to each other, is important in high-performance computing (HPC) systems. In recent years, the peripheral component interconnect express (PCIe) has become a promising interface as an interconnection network for high-performance and cost-effective HPC systems having the features of non-transparent bridge (NTB) technologies. OpenSHMEM is a programming model for distributed shared memory that supports a partitioned global address space (PGAS). Currently, little work has been done to develop the OpenSHMEM library for PCIe-interconnected HPC systems. This paper introduces a prototype implementation of the OpenSHMEM library through a switchless interconnect network using PCIe NTB to provide a PGAS programming model. In particular, multi-interrupt, multi-thread-based data transfer over the OpenSHMEM shared memory model is applied at the implementation level to reduce the latency and increase the throughput of the switchless ring network system. The implemented OpenSHMEM programming model over the PCIe NTB switchless interconnection network provides a feasible, cost-effective HPC system with a PGAS programming model.

• Korean Journal of Microbiology
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• v.54 no.3
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• pp.188-199
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• 2018

Genomic epidemiology exploits various basic microbial research areas. High-throughput sequencing technologies dramatically have been expanding the number of microbial genome sequences available. Abundant genomic data provide an opportunity to perform strain typing more effectively, helping identify microbial species and strains at a higher resolution than ever before. Genomic epidemiology needs to find antimicrobial resistance genes in addition to standard genome annotations. Strain typing and antimicrobial resistance gene finding are static aspects of genomic epidemiology. Finding which hosts infected which other hosts requires the inference of transient transmission routes among infected hosts. The strain typing, antimicrobial resistance gene finding, and transmission tree inference would allow for better surveillance of microbial infectious diseases, which is one of the ultimate goals of genomic epidemiology. Among several high-throughput sequencing technologies, genomic epidemiology will benefit from the more portability and shorter sequencing time of the Oxford Nanopore Technologies's MinION, the third-generation sequencing technology. Here, this study reviewed computational methods for quantifying antimicrobial resistance genes and inferring disease transmission trees. In addition, the MinION's applications to genomic epidemiology were discussed.

• BMB Reports
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• v.49 no.12
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• pp.653-654
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• 2016

The human reference genome, maintained by the Genome Reference Consortium, is conceivably the most complete genome assembly ever, since its first construction. It has continually been improved by incorporating corrections made to the previous assemblies, thanks to various technological advances. Many currently-ongoing population sequencing projects have been based on this reference genome, heightening hopes of the development of useful medical applications of genomic information, thanks to the recent maturation of high-throughput sequencing technologies. However, just one reference genome does not fit all the populations across the globe, because of the large diversity in genomic structures and technical limitations inherent to short read sequencing methods. The recent success in de novo construction of the highly contiguous Asian diploid genome AK1, by combining single molecule technologies with routine sequencing data without resorting to traditional clone-by-clone sequencing and physical mapping, reveals the nature of genomic structure variation by detecting thousands of novel structural variations and by finally filling in some of the prior gaps which had persistently remained in the current human reference genome. Now it is expected that the AK1 genome, soon to be paired with more upcoming de novo assembled genomes, will provide a chance to explore what it is really like to use ancestry-specific reference genomes instead of hg19/hg38 for population genomics. This is a major step towards the furthering of genetically-based precision medicine.

• Journal of Plant Biotechnology
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• v.5 no.4
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• pp.193-195
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• 2003

A major goal of agricultural biotechnology is the discovery of genes or genetic loci which are associated with characteristics beneficial to crop production. This knowledge of genetic loci may then be applied to improve crop breeding. Agriculturally important genes may also benefit crop production through transgenic technologies. Recent years have seen an application of high throughput technologies to agricultural biotechnology leading to the production of large amounts of genomic data. The challenge today is the effective structuring of this data to permit researchers to search, filter and importantly, make robust associations within a wide variety of datasets. At the Plant Biotechnology Centre, Primary Industries Research Victoria in Melbourne, Australia, we have developed a series of tools and computational pipelines to assist in the processing and structuring of genomic data to aid its application to agricultural biotechnology resear-ch. These tools include a sequence database, ASTRA, for the processing and annotation of expressed sequence tag data. Tools have also been developed for the discovery of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) molecular markers from large sequence datasets. Application of these tools to Brassica research has assisted in the production of genetic and comparative physical maps as well as candidate gene discovery for a range of agronomically important traits.

• Journal of Pharmacopuncture
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• v.18 no.3
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• pp.11-18
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• 2015

Objectives: Systems biology is a novel subject in the field of life science that aims at a systems' level understanding of biological systems. Because of the significant progress in high-throughput technologies and molecular biology, systems biology occupies an important place in research during the post-genome era. Methods: The characteristics of systems biology and its applicability to traditional medicine research have been discussed from three points of view: data and databases, network analysis and inference, and modeling and systems prediction. Results: The existing databases are mostly associated with medicinal herbs and their activities, but new databases reflecting clinical situations and platforms to extract, visualize and analyze data easily need to be constructed. Network pharmacology is a key element of systems biology, so addressing the multi-component, multi-target aspect of pharmacology is important. Studies of network pharmacology highlight the drug target network and network target. Mathematical modeling and simulation are just in their infancy, but mathematical modeling of dynamic biological processes is a central aspect of systems biology. Computational simulations allow structured systems and their functional properties to be understood and the effects of herbal medicines in clinical situations to be predicted. Conclusion: Systems biology based on a holistic approach is a pivotal research methodology for understanding the mechanisms of traditional medicine. If systems biology is to be incorporated into traditional medicine, computational technologies and holistic insights need to be integrated.

• ETRI Journal
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• v.37 no.5
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• pp.856-866
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• 2015

A heterogeneous network (HetNet) is a network topology composed by deploying multiple HetNets under the coverage of macro cells (MCs). It can improve network throughput, extend cell coverage, and offload network traffic; for example, the network traffic of a 5G mobile communications network. A HetNet involves a mix of radio technologies and various cell types working together seamlessly. In a HetNet, coordination between MCs and small cells (SCs) has a positive impact on the performance of the networks contained within, and consequently on the overall user experience. Therefore, to improve user-perceived service quality, HetNets require high-efficiency network protocols and enhanced radio technologies. In this paper, we introduce a 5G HetNet comprised of MCs and both fixed and mobile SCs (mSCs). The featured mSCs can be mounted on a car, bus, or train and have different characteristics to fixed SCs (fSCs). In this paper, we address the technical challenges related to mSCs. In addition, we analyze the network performance under two HetNet scenarios-MCs and fSCs, and MCs and mSCs.

• Journal of Ginseng Research
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• v.44 no.1
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• pp.33-43
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• 2020

Ginseng is popularly known to be the king of ancient medicines and is used widely in most of the traditional medicinal compositions due to its various pharmaceutical properties. Numerous studies are being focused on this plant's curative effects to discover their potential health benefits in most human diseases, including cancer- the most life-threatening disease worldwide. Modern pharmacological research has focused mainly on ginsenosides, the major bioactive compounds of ginseng, because of their multiple therapeutic applications. Various issues on ginseng plant development, physiological processes, and agricultural issues have also been studied widely through state-of-the-art, high-throughput sequencing technologies. Since the beginning of the 21st century, the number of publications on ginseng has rapidly increased, with a recent count of more than 6,000 articles and reviews focusing notably on ginseng. Owing to the implementation of various technologies and continuous efforts, the ginseng plant genomes have been decoded effectively in recent years. Therefore, this review focuses mainly on the cellular biomolecular sequences in ginseng plants from the perspective of the central molecular dogma, with an emphasis on genomes, transcriptomes, and proteomes, together with a few other related studies.

• BioChip Journal
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• v.12 no.4
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• pp.257-267
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• 2018

Inertial microfluidics has attracted significant attention in recent years due to its superior benefits of high throughput, precise control, simplicity, and low cost. Many inertial microfluidic applications have been demonstrated for physiological sample processing, clinical diagnostics, and environmental monitoring and cleanup. In this review, we discuss the fundamental mechanisms and principles of inertial migration and Dean flow, which are the basis of inertial microfluidics, and provide basic scaling laws for designing the inertial microfluidic devices. This will allow end-users with diverse backgrounds to more easily take advantage of the inertial microfluidic technologies in a wide range of applications. A variety of recent applications are also classified according to the structure of the microchannel: straight channels and curved channels. Finally, several future perspectives of employing fluid inertia in microfluidic-based cell sorting are discussed. Inertial microfluidics is still expected to be promising in the near future with more novel designs using various shapes of cross section, sheath flows with different viscosities, or technologies that target micron and submicron bioparticles.

• BMB Reports
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• v.52 no.9
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• pp.540-547
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• 2019

Immune repertoire is a collection of enormously diverse adaptive immune cells within an individual. As the repertoire shapes and represents immunological conditions, identification of clones and characterization of diversity are critical for understanding how to protect ourselves against various illness such as infectious diseases and cancers. Over the past several years, fast growing technologies for high throughput sequencing have facilitated rapid advancement of repertoire research, enabling us to observe the diversity of repertoire at an unprecedented level. Here, we focus on B cell receptor (BCR) repertoire and review approaches to B cell isolation and sequencing library construction. These experiments should be carefully designed according to BCR regions to be interrogated, such as heavy chain full length, complementarity determining regions, and isotypes. We also highlight preprocessing steps to remove sequencing and PCR errors with unique molecular index and bioinformatics techniques. Due to the nature of massive sequence variation in BCR, caution is warranted when interpreting repertoire diversity from error-prone sequencing data. Furthermore, we provide a summary of statistical frameworks and bioinformatics tools for clonal evolution and diversity. Finally, we discuss limitations of current BCR-seq technologies and future perspectives on advances in repertoire sequencing.

• The Korean Journal of Food & Health Convergence
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• v.10 no.3
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• pp.19-22
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• 2024

The field of synthetic biology has emerged in response to the ongoing progress in the life sciences. Advances have been made in medicine, farming, eating, making materials, and more. Synthetic biology is the exploration of using living organisms to create new organisms. By manipulating specific genes to express targeted proteins, proteins can be created that are both productive and cost-effective. Solid-phase extraction (SPE) and liquid-liquid extraction (LLE) are employed for protein separation during the production process involving microorganisms. This study centers on Scanning Probe Microscopy (SPM) to showcase its utility in the food industry and food management. SPE is predominantly utilized as a pretreatment method to eliminate impurities from samples. In comparison to LLE, this method presents benefits such as decreased time and labor requirements, streamlined solvent extraction, automation capabilities, and compatibility with various other analytical instruments. Anion exchange chromatography (AEC) utilizes a similar methodology. Pharmaceutical companies utilize these technologies to improve the purity of biopharmaceuticals, thereby guaranteeing their quality. Used in the food and beverage industry to test chemical properties of raw materials and finished products. This exemplifies the potential of these technologies to enhance industrial development and broaden the scope of applications in synthetic biology.