• Molecules and Cells
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• v.37 no.5
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• pp.372-382
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• 2014

In this study, the chloroplast (cp) genome sequences from three early diverged leptosporangiate ferns were completed and analyzed in order to understand the evolution of the genome of the fern lineages. The complete cp genome sequence of Osmunda cinnamomea (Osmundales) was 142,812 base pairs (bp). The cp genome structure was similar to that of eusporangiate ferns. The gene/intron losses that frequently occurred in the cp genome of leptosporangiate ferns were not found in the cp genome of O. cinnamomea. In addition, putative RNA editing sites in the cp genome were rare in O. cinnamomea, even though the sites were frequently predicted to be present in leptosporangiate ferns. The complete cp genome sequence of Diplopterygium glaucum (Gleicheniales) was 151,007 bp and has a 9.7 kb inversion between the trnL-CAA and trnV-GCA genes when compared to O. cinnamomea. Several repeated sequences were detected around the inversion break points. The complete cp genome sequence of Lygodium japonicum (Schizaeales) was 157,142 bp and a deletion of the rpoC1 intron was detected. This intron loss was shared by all of the studied species of the genus Lygodium. The GC contents and the effective numbers of codons (ENCs) in ferns varied significantly when compared to seed plants. The ENC values of the early diverged leptosporangiate ferns showed intermediate levels between eusporangiate and core leptosporangiate ferns. However, our phylogenetic tree based on all of the cp gene sequences clearly indicated that the cp genome similarity between O. cinnamomea (Osmundales) and eusporangiate ferns are symplesiomorphies, rather than synapomorphies. Therefore, our data is in agreement with the view that Osmundales is a distinct early diverged lineage in the leptosporangiate ferns.

• Korean Journal of Veterinary Service
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• v.32 no.1
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• pp.11-18
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• 2009

Porcine epidemic diarrhea virus (PEDV), an enveloped single stranded RNA virus in the family Coronaviridae, causes acute viral enteric disease in piglets. Recently outbreaks of porcine epidemic diarrhea (PED) have been rare in Europe but frequent in Asia. In Korea, the increase of PED prevalence is showing specially in postweaning pigs. The purpose of this study was to investigate nucleotide sequence of nucleocapsid protein gene of PEDV field isolates from postweaning pigs in Korea and get more information about the viruses. A total of 15 postweaing pigs clinically suspected of PEDV infection by severe watery diarrhea and dehydration were used in this study. Viral RNA was extracted from small intestines and stools of the pigs. The N gene was amplified by nested RT-PCR, purificated, sequenced, analyzed and then compared with published sequences of other PEDV strains. Three PEDVs were isolated from the suspected postweaning pigs. The N gene of three PEDV field isolates consisted of 483 nucleotides. These PEDV field isolates showed nucleotide sequence homology range from 99.6% to 95% with Chinese strains, from 99.8% to 95.2% with Korean strains, from 97.3% to 95.7% with Japanese strains and from 96.5% to 95.7% with Belgium and British strains. The encoded pritein shared range from 98.8% to 95.6% with Chinese strains, from 99.4% to 95% with Korean strains, from 97.5% to 96.3% with Japanese strains, from 95.6% to 95% with Belgium and British strains. By phylogenetic tree analysis based on nucleotide sequence, three PEDV field isolates were clustered into two groups which were Chinese isolate groups and other Korean isolate groups. These results indicated that some of PEDV field isolates prevailing in Korean postweaning pigs may be associated with those of Chinese strains and other Korean strains.

• Journal of the Korea Institute of Information Security & Cryptology
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• v.13 no.5
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• pp.3-15
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• 2003

The secure group communication enables the members, which belong to the same group, to communicate each other in a secure and secret manner. To do so, it is the most important that a group key is securely distributed among them and also group membership is efficiently managed. In detail, the generation, the distribution and the refreshment of a group key would be highly regarded in terms of low communication and computation complexity. In this paper, we show you a new protocol to generate a group key which will be safely shared within a group, utilizing the 2-party Diffie-Hellman key exchange protocol and the complete binary tree. Our protocol has less complexity of computation per group member by substituting many parts of exponentiation computations for multiplications. Consequently, each group member needs constant computations of exponentiation and multiplication regardless of the group size in the protocol and then it has less complexity of the computation than that of any other protocols.

• KSII Transactions on Internet and Information Systems (TIIS)
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• v.15 no.11
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• pp.3950-3969
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• 2021

Radio Frequency (RF)-based indoor localization technologies play significant roles in various Internet of Things (IoT) services (e.g., location-based service). Most such technologies require that all the devices comply with a specified technology (e.g., WiFi, ZigBee, and Bluetooth). However, this requirement limits its application scenarios in today's IoT context where multiple devices complied with different standards coexist in a shared environment. To bridge the gap, in this paper, we propose a cross-technology localization approach, which is able to localize target nodes using a different type of devices. Specifically, the proposed framework reuses the existing WiFi infrastructure without introducing additional cost to localize Non-WiFi device (i.e., ZigBee). The key idea is to leverage the interference between devices that share the same operating frequency (e.g., 2.4GHz). Such interference exhibits unique patterns that depend on the target device's location, thus it can be leveraged for cross-technology localization. The proposed framework uses Principal Components Analysis (PCA) to extract salient features of the received WiFi signals, and leverages Dynamic Time Warping (DTW), Gradient Boosting Regression Tree (GBRT) to improve the robustness of our system. We conduct experiments in real scenario and investigate the impact of different factors. Experimental results show that the average localization accuracy of our prototype can reach 1.54m, which demonstrates a promising direction of building cross-technology technologies to fulfill the needs of modern IoT context.

• Research in Plant Disease
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• v.28 no.2
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• pp.98-107
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• 2022

The incidence of Tomato brown rugose fruit virus (ToBRFV) and biological and molecular characterization of the Palestinian isolates of ToBRFV are described in this study. Symptomatic leaf samples obtained from Solanum lycopersicum L. (tomatoes) and Nicotiana tabacum L. (cultivated tobacco) plants were tested for tobamoviruses infection by reverse transcription polymerase chain reaction. Tomato leaf samples collected from Tulkarm and Qalqilia are infected with ToBRFV-PAL with an infection rate of 76% and 72.5%, respectively. Leaf samples collected from Jenin and Nablus were found to be mixed infected with ToBRFV-PAL and Tobacco mosaic virus (TMV) (100%). Sequence analysis of the ToBRFV-PAL genome showed that the net average nucleotide divergence between ToBRFV/F48-PAL strain and the Israeli and Turkish strains was 0.0026398±0.0006638 (±standard error of mean), while it was 0.0033066±0.0007433 between ToBRFV/F42-PAL and these two isolates. In the phylogenetic tree constructed with the complete genomic sequence, all the ToBRFV isolates were clustered together and formed a sister branch with the TMV. The sequenced Palestinian isolates of ToBRFV-PAL shared the highest nucleotide identity with the Israeli ToBRFV isolate suggesting that the virus was introduced to Palestine from Israel. The findings of this study enhance our understanding of the biological and molecular characteristics of ToBRFV which would help in the management of the disease.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.114.1-114
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• 2003

A new isolate of rod-shaped virus was identified from grafted cactus, Gymnocalycium mihanovichii grafted onto Hylocereus trigonus, in Korea. The virus proved to be a new Tobamovirus and called previously as Tobamovirus-Ca for which we suggest the name Cactus mild mottle virus(CMMoV), because it produced systemic mild mosaic symptoms on its original host. CMMoV is distantly related to known species of the genus Tobamovirus on the basis of host range, serological and sequence analyses. Western blot analysis showed that CMMoV is serologically unrelated to Summons' Opuntia virus which is the only known species of the genus found in cactus plants. The 3'-terminal 2,910 nucleotides have been sequenced for the virus. The coat protein (CP) and movement protein (MP) genes encode 161 and 306 amino acids residues, respectively. The nucleotide and amino acid sequences of the CP were 39.6 ％ to 49.2 ％ and 26.4 ％ to 40.3 ％ identical to other tobamoviruses, respectively. The MP and 3' noncoding region shared 16.3 ％ to 23.3 ％ and 44.6 ％ to 63.4 ％ identities, respectively, with the members of the genus. Phylogenetic tree analysis of the CP gene revealed that CMMoV clusters with members of subgroup I of Tobamovirus. CMMoV particles contained genomic RNA along with two subgenomic RNAs, and this characteristics is common in the members of the subgroup II. This is the first information of sequence and comparative analysis of a Tobamovirus that infects cactus.

• International Journal of Computer Science & Network Security
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• v.23 no.3
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• pp.67-80
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• 2023

Rice is an important food crop for most of the population in Nowadays, psychologists consider social media an important tool to examine mental disorders. Among these disorders, depression is one of the most common yet least cured disease Since abundant of writers having extensive followers express their feelings on social media and depression is significantly increasing, thus, exploring the literary text shared on social media may provide multidimensional features of depressive behaviors: (1) Background: Several studies observed that depressive data contains certain language styles and self-expressing pronouns, but current study provides the evidence that posts appearing with self-expressing pronouns and depressive language styles contain high emotional temperatures. Therefore, the main objective of this study is to examine the literary cyber writers' posts for discovering the symptomatic signs of depression. For this purpose, our research emphases on extracting the data from writers' public social media pages, blogs, and communities; (3) Results: To examine the emotional temperatures and sentences usage between depressive and not depressive groups, we employed the SentiStrength algorithm as a psycholinguistic method, TF-IDF and N-Gram for ranked phrases extraction, and Latent Dirichlet Allocation for topic modelling of the extracted phrases. The results unearth the strong connection between depression and negative emotional temperatures in writer's posts. Moreover, we used Naïve Bayes, Support Vector Machines, Random Forest, and Decision Tree algorithms to validate the classification of depressive and not depressive in terms of sentences, phrases and topics. The results reveal that comparing with others, Support Vectors Machines algorithm validates the classification while attaining highest 79% f-score; (4) Conclusions: Experimental results show that the proposed system outperformed for detection of depression trends in literary cyber writers using sentiment analysis.

• Fisheries and Aquatic Sciences
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• v.26 no.9
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• pp.569-581
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• 2023

The morphology and genetic identification of Rasbora lateristriata and Rasbora argyrotaenia between cultivated and wild populations has never been reported. This study compares morphology and cytochrome c oxidase (COI) genes between farmed and wild stock Rasbora spp. in Java and Sumatra island, Indonesia. We analyzed the truss network measurement (TNM) characters of 80 fish using discriminant function analysis statistical tests. DNA was extracted from muscle tissue of 24 fish specimens, which was then followed by polymerase chain reaction, sequencing, phylogenetic analysis, fixation index analysis, and statistical analysis of haplotype networks. Basic Local Alignment Search Tool analysis validated the following species: R. lateristriata and R. argyrotaenia from farming (Jogjakarta); Rasbora agryotaenia (Purworejo), R. lateristriata (Purworejo and Malang), Rasbora dusonensis (Palembang), and Rasbora einthovenii (Riau) from natural resources. Based on TNM characters, Rasbora spp. were divided into four groups, referring to four distinct characters in the middle of the body. The phylogenetic tree is divided into five clades. The genetic distance between R. argyrotaenia (Jogjakarta) and R. lateristriata (Malang) populations (0.66) was significantly different (p < 0.05). R. lateristriata (Purworejo) has the highest nucleotide diversity (0.43). R. argyrotaenia from Jogjakarta and Purworejo shared the same haplotype. The pattern of gene flow among them results from the two populations' close geographic proximity and environmental effects. R. argyrotaenia had low genetic diversity, therefore, increasing heterozygosity in cultivated populations is necessary to avoid inbreeding. Otherwise, R. lateristriata (Purworejo) had a greater gene variety that could be used to develop breeding. In conclusion, the middle body parts are a distinguishing morphometric character of Rasbora spp., and the COI gene is more heterozygous in the wild population than in farmed fish, therefore, enrichment of genetic variation is required for sustainable Rasbora fish farming.

• Research in Plant Disease
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• v.30 no.2
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• pp.157-164
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• 2024

Jack bean (Canavalia ensiformis) is one of healthy products for fermented or functional food in Korea and is widely distributed and cultivated worldwide. During August 2022, Jack bean plants showing symptoms of yellow flecks, chlorosis, necrotic spots and mosaic were observed in Jangheung-gun, South Korea. By transmission electron microscopy, flexuous filamentous virus particles of approximately 750×13 nm in size were observed in the symptomatic leaf samples. The infection of a Korean isolate of clover yellow vein virus (ClYVV-Ce-JH) was confirmed using double antibody sandwich enzyme-linked sorbent assay, reverse transcription polymerase chain reaction and high-throughput sequencing. The complete genome sequence of ClYVV-Ce-JH consists of 9,549 nucleotides (nt) excluding the poly (A) tail and encodes 3,072 amino acids (aa), with an AUG start and UAG stop codon, containing one open reading frame that is typical of a potyvirus polyprotein. The polyprotein of ClYVV-Ce-JH was divided into ten proteins and each protein's cleavage sites were determined. The coat protein (CP) and polyprotein of ClYVV-Ce-JH were compared at the nt and aa levels with those of the previously reported 14 ClYVV isolates. ClYVV-Ce-JH shared 92.62% to 99.63% and 93.39% to 98.05% at the CP and polyprotein homology. To our knowledge, this is the first report of a Korean isolate of ClYVV from Jack bean plants and the complete genome sequence of a ClYVV Jack bean isolate in the world.

• Journal of Intelligence and Information Systems
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• v.19 no.1
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• pp.19-33
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• 2013

In this research, a proposed Dynamic Virtual Ontology using Tags (DyVOT) supports dynamic search of resources depending on user's requirements using tags from social web driven resources. It is general that the tags are defined by annotations of a series of described words by social users who usually tags social information resources such as web-page, images, u-tube, videos, etc. Therefore, tags are characterized and mirrored by information resources. Therefore, it is possible for tags as meta-data to match into some resources. Consequently, we can extract semantic relationships between tags owing to the dependency of relationships between tags as representatives of resources. However, to do this, there is limitation because there are allophonic synonym and homonym among tags that are usually marked by a series of words. Thus, research related to folksonomies using tags have been applied to classification of words by semantic-based allophonic synonym. In addition, some research are focusing on clustering and/or classification of resources by semantic-based relationships among tags. In spite of, there also is limitation of these research because these are focusing on semantic-based hyper/hypo relationships or clustering among tags without consideration of conceptual associative relationships between classified or clustered groups. It makes difficulty to effective searching resources depending on user requirements. In this research, the proposed DyVOT uses tags and constructs ontologyfor effective search. We assumed that tags are extracted from user requirements, which are used to construct multi sub-ontology as combinations of tags that are composed of a part of the tags or all. In addition, the proposed DyVOT constructs ontology which is based on hierarchical and associative relationships among tags for effective search of a solution. The ontology is composed of static- and dynamic-ontology. The static-ontology defines semantic-based hierarchical hyper/hypo relationships among tags as in (http://semanticcloud.sandra-siegel.de/) with a tree structure. From the static-ontology, the DyVOT extracts multi sub-ontology using multi sub-tag which are constructed by parts of tags. Finally, sub-ontology are constructed by hierarchy paths which contain the sub-tag. To create dynamic-ontology by the proposed DyVOT, it is necessary to define associative relationships among multi sub-ontology that are extracted from hierarchical relationships of static-ontology. The associative relationship is defined by shared resources between tags which are linked by multi sub-ontology. The association is measured by the degree of shared resources that are allocated into the tags of sub-ontology. If the value of association is larger than threshold value, then associative relationship among tags is newly created. The associative relationships are used to merge and construct new hierarchy the multi sub-ontology. To construct dynamic-ontology, it is essential to defined new class which is linked by two more sub-ontology, which is generated by merged tags which are highly associative by proving using shared resources. Thereby, the class is applied to generate new hierarchy with extracted multi sub-ontology to create a dynamic-ontology. The new class is settle down on the ontology. So, the newly created class needs to be belong to the dynamic-ontology. So, the class used to new hyper/hypo hierarchy relationship between the class and tags which are linked to multi sub-ontology. At last, DyVOT is developed by newly defined associative relationships which are extracted from hierarchical relationships among tags. Resources are matched into the DyVOT which narrows down search boundary and shrinks the search paths. Finally, we can create the DyVOT using the newly defined associative relationships. While static data catalog (Dean and Ghemawat, 2004; 2008) statically searches resources depending on user requirements, the proposed DyVOT dynamically searches resources using multi sub-ontology by parallel processing. In this light, the DyVOT supports improvement of correctness and agility of search and decreasing of search effort by reduction of search path.