• Journal of Genetic Medicine
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• v.20 no.2
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• pp.46-51
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• 2023

Exonic copy number variation (CNV), involving deletions and duplications at the gene's exon level, presents challenges in detection due to their variable impact on gene function. The study delves into the complexities of identifying large CNVs and investigates less familiar but recurrent exonic CNVs, notably enriched in East Asian populations. Examining specific cases like DRC1, STX16, LAMA2, and CFTR highlights the clinical implications and prevalence of exonic CNVs in diverse populations. The review addresses diagnostic challenges, particularly for single exon alterations, advocating for a strategic, multi-method approach. Diagnostic methods, including multiplex ligation-dependent probe amplification, droplet digital PCR, and CNV screening using next-generation sequencing data, are discussed, with whole genome sequencing emerging as a powerful tool. The study underscores the crucial role of ethnic considerations in understanding specific CNV prevalence and ongoing efforts to unravel subtle variations. The ultimate goal is to advance rare disease diagnosis and treatment through ethnically-specific therapeutic interventions.

• Korean Journal of Radiology
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• v.21 no.7
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• pp.779-792
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• 2020

Recent advances in computer technology have generated a new area of research known as radiomics. Radiomics is defined as the high throughput extraction and analysis of quantitative features from imaging data. Radiomic features provide information on the gray-scale patterns, inter-pixel relationships, as well as shape and spectral properties of radiological images. Moreover, these features can be used to develop computational models that may serve as a tool for personalized diagnosis and treatment guidance. Although radiomics is becoming popular and widely used in oncology, many problems such as overfitting and reproducibility issues remain unresolved. In this review, we will outline the steps of radiomics used for oncology, specifically addressing applications for breast cancer patients and focusing on technical issues.

• Weed & Turfgrass Science
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• v.4 no.2
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• pp.118-123
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• 2015

Metagenomics is a powerful tool to isolate novel biocatalyst and biomolecules directly from the environmental DNA libraries. Since the metagenomics approach bypasses cultivation of microorganisms, un-cultured microorganisms that are majority of exists can be the richest reservoir for natural products discovery. To discover novel herbicidal substances from soil metagenome, we established three easy, simple and effective high throughput screening methods such as cucumber cotyledon leaf disc assay, microalgae assay and seed germination assay. Employing the methods, we isolated two active single clones (9-G1 and 9-G12) expressing herbicidal activity which whitened leaf discs, inhibited growth of microalgae and inhibited root growth of germinated Arabidopsis seeds. Spraying butanol fraction of the isolated active clones' culture broth led to growth retardation or desiccation of Digitalia sanguinalis (L) Scop. in vivo. These results represent that the screening methods established in this study are useful to screen herbicidal substances from metagenome libraries. Further identifying molecular structure of the herbicidal active substances and analyzing gene clusters encoding synthesis systems for the active substances are in progress.

• Mass Spectrometry Letters
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• v.1 no.1
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• pp.13-16
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• 2010

The active components in a plant extract can be represented as mass profiles. We introduce here a new, multi-compound discovery method known as Scaling of Correlations between Activity and Mass Profiles (SCAMP). In this method, a correlation coefficient is used to quantify similarities between the extract activity and mass profiles. The method was evaluated by first measuring the anti-oxidation activity of eleven fractions of an Astragali Radix extract using DPPH assays. Next, 15 T Fouriertransform ion cyclotron resonance (FT-ICR) MS was employed to generate mass profiles of the eleven fractions. A comparison of correlation coefficients indicated two compounds at m/z 285.076 and 286.076 that were strong antioxidants. Principal component analyses of these profiles yielded the same result. FT-ICR MS, which offers a mass resolving power of 500,000, was used to discern isotopic fine structures and indicated that the molecular formula corresponding to the peak at m/z 285.076 was $C_{16}H_{13}O_5$. SCAMP in combination with high-resolution MS can be applied to any type of mixture to study pharmacological activity and is a powerful tool for active compound discovery in plant extract studies.

• Proceedings of the Korean Society of Precision Engineering Conference
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• 2005.06a
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• pp.633-636
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• 2005

Imprint lithography is a promising method for high-resolution and high-throughput lithography using low-cost equipment. As with other nanoimprint methods, ultraviolet-nanoimprint lithography (UV-NIL) resolution appears to be limited only by template resolution, and offers a significant cost of ownership reduction when compared to other next generation lithography (NGL) methods such as EUVL and 157 nm lithography. The purpose of this paper is to suggest optimum values of control parameters of Imprio 100 manufactured by Molecular Imprint, Inc., which is the first commercially available UV-NIL tool, for sound nanoimprint. UV-NIL experiments were performed on Imprio 100 to find dispensing recipe for avoiding air entrapment. Dispensing recipe related to residual layer thickness and uniformity was optimized and 40 nm thick residual layer was achieved.

• Bioinformatics and Biosystems
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• v.2 no.2
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• pp.46-51
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• 2007

In the proteomics research using mass spectrometry, the protein database search gives the protein information from the peptide sequences that show the best match with the tandem mass spectra. The protein sequence database has been a powerful knowledgebase for this protein identification. However, as we accumulate the protein sequence information in the database, the database size gets to be huge. Now it becomes hard to consider all the protein sequences in the database search because it consumes much computing time. For the high-throughput analysis of the proteome, usually we have used the non-redundant refined database such as IPI human database of European Bioinformatics Institute. While the non-redundant database can supply the search result in high speed, it misses the variation of the protein sequences. In this study, we have concerned the proteomics data in the point of protein similarities and used the network analysis tool to build a new analysis method. This method will be able to save the computing time for the database search and keep the sequence variation to catch the modified peptides.

• Journal of Sensor Science and Technology
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• v.19 no.6
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• pp.403-420
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• 2010

Nano and micro structure-based biosensors are promising tool for label-free detection of biomolecular interactions with great accuracy. This review gives a brief survey on nano and micro platforms to sense a variety of analytes such as DNA, proteins and viruses. Among incredible nano and micro structure for bio-analytical applications, the scope of this paper will be limited to micro and nano resonators and nanowire field-effect transistors. Nanomechanical motion of the resonators transducers biological information to readable signals. They are commonly combined with an optical, capacitive or piezo-resistive detection systems. Binding of target molecule to the modified surface of nanowire modulates the current of the nanowire through electrical field-effect. Both detection methods have advantages of label-free, real-time and high sensitive detection. These structures can be extended to fabricate array-type sensors for multiplexed detection and high-throughput analysis. The biosensors based on these structures will be applied to lab-on-a-chip platforms and point-of-care diagnostics. Basic concepts including detection mechanisms and trends in their fields will be covered in this review.

• Bioinformatics and Biosystems
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• v.1 no.1
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• pp.28-37
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• 2006

Recent studies in molecular biology and proteomics have identified a significant number of novel diagnostic, prognostic, and therapeutic disease markers. However, validation of these markers in clinical specimens with traditional histopathological techniques involves low throughput and is time consuming and labor intensive. Tissue microarrays (TMAs) offer a means of combining tens to hundreds of specimens of tissue onto a single slide for simultaneous analysis. This capability is particularly pertinent in the field of cancer for target verification of data obtained from cDNA micro arrays and protein expression profiling of tissues, as well as in epidemiology-based investigations using histochemical/immunohistochemical staining or in situ hybridization. In combination with automated image analysis, TMA technology can be used in the global cellular network analysis of tissues. In particular, this potential has generated much excitement in cardiovascular disease research. The following review discusses recent advances in the construction and application of TMAs and the opportunity for developing novel, highly sensitive diagnostic tools for the early detection of cardiovascular disease.

• The KIPS Transactions:PartA
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• v.11A no.2
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• pp.165-174
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• 2004

Because a quantity wireless internet contents is much less than wired internet contents, it exist high necessities that wired internet contents should be converted into wireless internet contents. The conversion server implemented in this paper, automatically recognizes the type of user agents when they request, retrieves source documents on the web site specified by an URL, generates metaXML documents as an intermediate form, and converts them wireless markup documents appropriate for user agents. The conversion server interoperates with the image converter for image conversion and the clipper which is an authoring tool for clipping existing wired internet documents. We performed experiments about capability of the conversion server transcoding static/dynamic web pages specified by an URL. According to performance results on dynamic web pages, the conversion server showed better throughput when a thread pool in the terror maintains 5 threads compared with 1 and 10 threads.

• The Plant Pathology Journal
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• v.33 no.1
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• pp.80-86
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• 2017

One of the major problems in strawberry production is difficulty in diagnosis of anthracnose caused by Colletotrichum acutatum or Glomerella cingulata in latent infection stage. We here developed a diagnostic tool for the latent infection consisting of initial culturing of fungi, DNA extraction, synthesis of PCR-amplified probes and microtube hybridization (MTH) using a macroarray. The initial culturing step is convenient to lure the fungi out of the plant tissues, and to extract PCR-inhibitor-free DNA directly from fungal hyphae. For specific detection of the fungi, PCR primers were designed to amplify the fungal MAT1-2 gene. The subsequent MTH step using the PCR products as probes can replace the laborious electrophoresis step providing us sequence information and high-throughput screening. Using this method, we have conducted a survey for a few thousands nursery plants every year for three consecutive years, and finally succeeded in eliminating latent infection in the third year of challenge.