• Proceedings of the Korean Society of Computer Information Conference
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• 2022.07a
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• pp.61-62
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• 2022

알츠하이머성 치매는 현존하는 치료법이 없어 경도인지장애 단계에서의 예방이 중요하다. 지금까지의 알츠하이머 연구는 대부분이 뇌영상 마커와 뇌척수액 마커에 집중되어 있었으며, 경도 인지 장애 단계에서의 탐색은 더욱 적었다. 이러한 점에서 혈액 유전자 발현을 이용한 경도 인지장애 단계 예측은 인지 능력에 따른 관련 유전자 식별과 접근 가능한 진단 및 치료 바이오 마커 탐색에 기여할 수 있다. 그러나 유전자 발현 데이터의 경우 환자 수에 비해 높은 차원을 가지기 때문에 과적합을 막고 질병 관련 유전자를 식별하기 위해서는 데이터에서의 의미 있는 차원만을 뽑아내는 차원 축소가 선행되야 한다. 본 연구는 유전자 발현데이터에서의 인지장애 분류를 위해 차원 축소기법과 신경망을 적용하여 인지 장애 정도를 예측하였다. 그 결과, Lasso 이용 차원축소와 신경망을 이용하여 97%의 정확도로 정상과 조기 경도 인지장애, 후기 경도 인지장애 환자를 분류 할 수 있었으며, 더 적은 차원에서도 분류가 가능했다. 이는 혈액 유전자 발현을 이용해 경도 인지장애 단계를 예측한 첫 번째 연구이며, 인지능력 저하에 따른 혈액 유전자 발현의 연관성을 확인하고 향후 조기 진단, 치료 표적 탐색에 기여한다.

• Journal of Sericultural and Entomological Science
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• v.36 no.2
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• pp.115-118
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• 1994

Differences of feeding response of 280 silkworm genetic stocks and 71 breeding lines to MP-O artificial diet and the mode of the inheritance were investigated. Feeding response to MP-O diet varied markedly between the silkworm varieties, and the non-normally distributed curve for the response was observed. From the genetic analysis, the high feeding response to MP-O diet was recessive to the low feeding response. Therefore it is considered that the high feeding response of the newly hatched silkwrom larvae to MP-O diet is controlled by a recessive gene.

• Nuclear Engineering and Technology
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• v.48 no.6
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• pp.1315-1320
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• 2016

The present study aims to predict the heat transfer characteristics around a square cylinder with different corner radii using multivariate adaptive regression splines (MARS). Further, the MARS-generated objective function is optimized by particle swarm optimization. The data for the prediction are taken from the recently published article by the present authors [P. Dey, A. Sarkar, A.K. Das, Development of GEP and ANN model to predict the unsteady forced convection over a cylinder, Neural Comput. Appl. (2015) 1-13]. Further, the MARS model is compared with artificial neural network and gene expression programming. It has been found that the MARS model is very efficient in predicting the heat transfer characteristics. It has also been found that MARS is more efficient than artificial neural network and gene expression programming in predicting the forced convection data, and also particle swarm optimization can efficiently optimize the heat transfer rate.

• Microbiology and Biotechnology Letters
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• v.23 no.2
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• pp.138-144
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• 1995

The cDNA, encoding human lysozyme (HLY) which was isolated from a human placenta cDNA library, has been well characterized (Yoshimura et al., 1988). Based on the communication, we have prepared an artificial HLY gene from chemically synthesized 38-oligomer with high codon usage in Saccharomyces cerevisiae. For directing the synthesis and secretion of HLY in S. cerevisiae, an expression vector, pHKl was constructed by inserting the HLY gene, containing a synthetic HLY secretion signal sequence, between the yeast GAP promoter and PH05 terminator. From a lysoplate assay, we have confirmed an yeast transformant harboring a pHK1 which makes a clearing zone on the overlayed Micrococcus luteus. This result means a chemically synthesized HLY gene which was normally expressed and secreted in yeast.

• Proceedings of the Korea Information Processing Society Conference
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• 2014.11a
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• pp.849-852
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• 2014

Reverse engineering of gene regulatory network is a challenging task in computational biology. To detect a regulatory relationship among genes from time series data is called reverse engineering. Reverse engineering helps to discover the architecture of the underlying gene regulatory network. Besides, it insights into the disease process, biological process and drug discovery. There are many statistical approaches available for reverse engineering of gene regulatory network. In our paper, we propose pairwise mutual information for the reverse engineering of a gene regulatory network from time series data. Firstly, we create random boolean networks by the well-known $Erd{\ddot{o}}s-R{\acute{e}}nyi$ model. Secondly, we generate artificial time series data from that network. Then, we calculate pairwise mutual information for predicting the network. We implement of our system on java platform. To visualize the random boolean network graphically we use cytoscape plugins 2.8.0.

• Journal of information and communication convergence engineering
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• v.21 no.2
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• pp.159-166
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• 2023

The COI gene is a sequence of approximately 650 bp at the 5' terminal of the mitochondrial Cytochrome c Oxidase subunit I (COI) gene. As an effective DeoxyriboNucleic Acid (DNA) barcode, it is widely used for the taxonomic identification and evolutionary analysis of species. We created a CNN-LSTM hybrid model by combining the gene features partially extracted by the Long Short-Term Memory ( LSTM ) network with the feature maps obtained by the CNN. Compared to K-Means Clustering, Support Vector Machines (SVM), and a single CNN classification model, after training 278 samples in a training set that included 15 genera from two orders, the CNN-LSTM hybrid model achieved 94% accuracy in the test set, which contained 118 samples. We augmented the training set samples and four genera into four orders, and the classification accuracy of the test set reached 100%. This study also proposes calculating the cosine similarity between the training and test sets to initially assess the reliability of the predicted results and discover new species.

• The Plant Pathology Journal
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• v.40 no.1
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• pp.83-97
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• 2024

Fusarium graminearum, the causal agent of Fusarium head blight (FHB) in cereal crops, employs the production of sexual fruiting bodies (perithecia) on plant debris as a strategy for overwintering and dissemination. In an artificial condition (e.g., carrot agar medium), the F. graminearum Z3643 strain was capable of producing perithecia predominantly in the central region of the fungal culture where aerial hyphae naturally collapsed. To unravel the intricate relationship between natural aerial hyphae collapse and sexual development in this fungus, we focused on 699 genes differentially expressed during aerial hyphae collapse, with 26 selected for further analysis. Targeted gene deletion and quantitative real-time PCR analyses elucidated the functions of specific genes during natural aerial hyphae collapse and perithecium formation. Furthermore, comparative gene expression analyses between natural collapse and artificial removal conditions reveal distinct temporal profiles, with the latter inducing a more rapid and pronounced response, particularly in MAT gene expression. Notably, FGSG_09210 and FGSG_09896 play crucial roles in sexual development and aerial hyphae growth, respectively. Taken together, it is plausible that if aerial hyphae collapse occurs on plant debris, it may serve as a physical cue for inducing perithecium formation in crop fields, representing a survival strategy for F. graminearum during winter. Insights into the molecular mechanisms underlying aerial hyphae collapse provides offer potential strategies for disease control against FHB caused by F. graminearum.

• Journal of Forest and Environmental Science
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• v.28 no.1
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• pp.1-7
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• 2012

Tropical forests whether fragmented or undisturbed or be they equatorial or deciduous, remain the storehouse of biodiversity for hundreds of thousands of plant and animal species. This unique characteristic continues to attract a wide range of scientists and international organizations to study and attempt to understand tropical forest ecosystems. Gene flow is mediated by pollen, seed and seedling dispersal, and factors affecting this gene flow include phenology, spatial distribution, population structures, seed predation, sexual and mating systems as well as physical and biological barriers to gene flow. Two methods are used in measuring gene flow: direct method that relies on the actual observation of seed and pollen dispersal, whereas indirect methods involve the use of genetic markers such as allozymes and DNA techniques. Political strife, extreme natural and artificial disasters, the lack of a comprehensive forestry research vision, coupled with difficult socio-economic conditions in Africa have made the environment quite difficult for sustained research activities on the part of those undertaking or wishing to undertake such studies. Gene flow studies in this region are few and far between. This review elaborates on the mechanisms of gene flow mediation in Sub-Saharan Africa.

• Computers and Concrete
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• v.26 no.4
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• pp.327-342
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• 2020

The objective of this study is to manufacture environmentally-friendly synthetic lightweight aggregates that may be used in the structural lightweight concrete production. The cold-bonding pelletization process has been used in the agglomeration of the pozzolanic materials to achieve these synthetic lightweight aggregates. In this context, it was aimed to recycle the waste fly ash by employing it in the manufacturing process as the major cementitious component. According to the well-known facts reported in the literature, it is stated that the main disadvantage of the synthetic lightweight aggregate produced by applying the cold-bonding pelletization technique to the pozzolanic materials is that it has a lower strength in comparison with the natural aggregate. Therefore, in this study, the metakaolin made of high purity kaolin and calcined kaolin obtained from impure kaolin have been employed at particular contents in the synthetic lightweight aggregate manufacturing as a cementitious material to enhance the particle crushing strength. Additionally, to propose a curing condition for practical attempts, different curing conditions were designated and their influences on the characteristics of the synthetic lightweight aggregates were investigated. Three substantial features of the aggregates, specific gravity, water absorption capacity, and particle crushing strength, were measured at the end of 28-day adopted curing conditions. Observed that the incorporation of thermally treated kaolin significantly influenced the crushing strength and water absorption of the aggregates. The statistical evaluation indicated that the investigated properties of the synthetic lightweight aggregate were affected by the thermally treated kaolin content more than the kaoline type and curing regime. Utilizing the thermally treated kaolin in the synthetic aggregate manufacturing lead to a more than 40% increase in the crushing strength of the pellets in all curing regimes. Moreover, two numerical formulations having high estimation capacity have been developed to predict the crushing strength of such types of aggregates by using soft-computing techniques: gene expression programming and artificial neural networks. The R-squared values, indicating the estimation performance of the models, of approximately 0.97 and 0.98 were achieved for the numerical formulations generated by using gene expression programming and artificial neural networks techniques, respectively.

• Journal of Microbiology and Biotechnology
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• v.32 no.7
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• pp.911-917
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• 2022

As valuable antibiotics, microbial natural products have been in use for decades in various fields. Among them are polyene compounds including nystatin, amphotericin, and nystatin-like Pseudonocardia polyenes (NPPs). Polyene macrolides are known to possess various biological effects, such as antifungal and antiviral activities. NPP A1, which is produced by Pseudonocardia autotrophica, contains a unique disaccharide moiety in the tetraene macrolide backbone. NPP B1, with a heptane structure and improved antifungal activity, was then developed via genetic manipulation of the NPP A1 biosynthetic gene cluster (BGC). Here, we generated a Streptomyces artificial chromosomal DNA library to isolate a large-sized NPP B1 BGC. The NPP B1 BGC was successfully isolated from P. autotrophica chromosome through the construction and screening of a bacterial artificial chromosome (BAC) library, even though the isolated 140-kb BAC clone (named pNPPB1s) lacked approximately 8 kb of the right-end portion of the NPP B1 BGC. The additional introduction of the pNPPB1s as well as co-expression of the 32-kb portion including the missing 8 kb led to a 7.3-fold increase in the production level of NPP B1 in P. autotrophica. The qRT-PCR confirmed that the transcription level of NPP B1 BGC was significantly increased in the P. autotrophica strain containing two copies of the NPP B1 BGCs. Interestingly, the NPP B1 exhibited a previously unidentified SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) inhibition activity in vitro. These results suggest that the Streptomyces BAC cloning of a large-sized, natural product BGC is a valuable approach for titer improvement and biological activity screening of natural products in actinomycetes.