• Journal of Korean Society of Industrial and Systems Engineering
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• v.34 no.2
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• pp.60-67
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• 2011

Since the non-metric Multidimensional scaling (nMDS), a data visualization technique, provides with insights about engineering, economic, and scientific applications, it is widely used for analyzing large non-metric multidimensional data sets. The nMDS requires a fitness function to measure fit of the proximity data by the distances among n objects. Most commonly used fitness functions are nonlinear and have a difficulty to find a good configuration. In this paper, we propose a new fitness function, an absolute value type, and show its advantages.

• Journal of KIISE:Computing Practices and Letters
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• v.16 no.6
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• pp.648-653
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• 2010

The non-metric multidimensional scaling (nMDS) is a method for analyzing the relation among objects by mapping them onto the Euclidean space. The nMDS is useful when it is difficult to use the concept of distance between pairs of objects due to non-metric dissimilarities between objects. The nMDS can be regarded as an optimization problem in which there are many local optima. Since the conventional nMDS algorithm utilizes the steepest descent method, it has a drawback in that the method can hardly find a better solution once it falls into a local optimum. To remedy this problem, in this paper, we applied the simulated annealing to the nMDS and proposed a new optimization algorithm which could search for a global optimum more effectively. We examined the algorithm using benchmarking problems and found that improvement rate of the proposed algorithm against the conventional algorithm ranged from 0.7% to 3.2%. In addition, the statistical hypothesis test also showed that the proposed algorithm outperformed the conventional one.

• Journal of Environmental Science International
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• v.16 no.5
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• pp.549-559
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• 2007

Vegetation surveys were performed at 45 plots along 10 highways cut slopes in South Korea. Total floral inventory, species richness and exotic plant percentage were obtained within each plot. Life history and life form of each species appeared were analyzed. Community types were classified using hierarchical cluster analysis and detrended correspondence analysis and non-metric multidimensional scaling were conducted from vegetation matrix. 292 species of vascular plants were discovered and the number of natives and exotics were 226 and 66, respectively. There were no significant differences of species richness and exotic plant percentage between cut slopes and rest areas. Hierarchical cluster analysis indicated five clear vegetation associations in cut slopes and rest areas. Detrended correspondence analysis indicated that species composition of total and native plants were similar along the highway cut slopes whereas exotic plants were distributed differentially along the highway cut slopes. in non-metric multidimensional scaling, the studied sites were more separated from each other on the basis of their species composition than the results of detrended correspondence analysis with respect to total, native and exotic plants. The both ordination represented that exotic plants have not been made uniform yet on cut slopes and rest areas by highway corridor in spite of diverse chronosequences after highway construction termination (1 to 22 years). This study showed that the distribution of species composition in exotic plants was different and localized on cut slopes and rest areas of highway in this representative peninsula area of North East Asia and the invasion of exotic plants can retard the process of plant species homogenization.

• The Korean Journal of Applied Statistics
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• v.28 no.6
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• pp.1171-1180
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• 2015

Multidimensional scaling (MDS) is a graphical technique of multivariate analysis to display dissimilarities among individuals into low-dimensional space. We often have two kinds of MDS which are metric MDS and non-metric MDS. Metric MDS can be applied to quantitative data; however, we need additional information about variables because it only shows relationships among individuals. Gower (1992) proposed a method that can represent variable information using trajectories of the pseudo-points for quantitative variables on the metric MDS space. We will call his method a 'replacement method'. However, the trajectory can not be represented even though metric MDS can be applied to binary data when we apply his method to binary data. Therefore, we propose a method to represent information of binary variables using pseudo-points called a 'partition method'. The proposed method partitions pseudo-points, accounting both the rate of zeroes and ones. Our metric MDS using the proposed partition method can show the relationship between individuals and variables for binary data.

• ALGAE
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• v.31 no.1
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• pp.1-16
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• 2016

Paralia species have been frequently reported as P. sulcata in Korea, despite the species diversity within the genus. To understand the species diversity of Paralia in Korea, we collected phytoplankton samples at 79 sites from April 2006 to April 2015. Five Paralia species, P. fenestrata, P. guyana, P. marina, P. cf. obscura, and P. sulcata, were observed during this study, and we described their fine structure in terms of quantitative and qualitative morphological characteristics. To provide additional criteria to identify Paralia species more clearly, we morphometrically analysed four quantitative characteristics on valve diameter: pervalvar axis / diameter, internal linking spines / diameter, marginal linking spines / diameter, and fenestrae/diameter using non-metric multidimensional scaling (MDS). MDS analysis distinguished four Paralia species: P. guyana, P. marina, P. cf. obscura, and P. sulcata, with the exception of P. fenestrata. This new approach in using morphometric analysis is useful for the accurate identification of Paralia species.

• Korean Journal of Ecology and Environment
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• v.53 no.1
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• pp.22-30
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• 2020

In this study, we investigated the relationships between benthic macroinvertebrate assemblages and various environmental factors in Iancheon (NIA) and Bukcheon (NBC) streams, Korea. We collected benthic macroinvertebrates and 33 environmental factors in April 2017 at 9 sites (5 sites in NIA and 4 sites in NBC). We identified 93 species(5 phyla, 9 classes, 16 orders, and 53 families) and 69 species(5 phyla, 9 classes, 17 orders, and 47 families) in NIA and NBC streams, respectively. Considering benthic macroinvertebrate index (BMI), NIA (88.2) and NBC (80.2) streams were in "very good" status. Upstream areas showed the highest scores, 95.5 (NIA1) and 94.2 (NBC1), whereas BMI score was the lowest in downstream areas of both streams, especially in NBC4 (51.0 "bad" status). Cluster analysis and non-metric multidimensional scaling analysis represented the differences of benthic macroinvertebrate assemblages according to spatial and anthropogenic gradients. Our findings provide reference data and highlight the need for the continued monitoring to maintain the good status and manage macroinvertebrate diversity in these two streams, in Sangju-si, Korea.

• Korean Journal of Ecology and Environment
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• v.54 no.3
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• pp.221-228
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• 2021

Recently, environmental DNA (eDNA)-based metabarcoding approaches have been proposed to evaluate the status of freshwater ecosystems owing to various advantages, including fast and easy sampling and minimal habitat disruption from sampling. Therefore, as a case study, we applied eDNA metabarcoding techniques to evaluate the effects of an abandoned mine land located near a headwater stream of Nakdonggang River, South Korea, by examining benthic macroinvertebrate diversity and compared the results with those obtained using the traditional Surber-net sampling method. The number of genera was higher in Surber-net sampling (29) than in the eDNA analysis (20). The genus richness tended to decrease from headwater to downstream in eDNA analysis, whereas richness tended to decrease at sites with acid-sulfated sediment areas using Surber-net sampling. Through cluster analysis and non-metric multidimensional scaling, the sampling sites were differentiated into two parts: acid-sulfated and other sites using Surber-net sampling, whereas they were grouped into the two lowest downstream and other sites using eDNA sampling. To evaluate freshwater ecosystems using eDNA analysis in practical applications, it is necessary to constantly upgrade the methodologies and compare the data with field survey methods.

• Korean Journal of Ichthyology
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• v.28 no.2
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• pp.79-86
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• 2016

Stomach contents of Amblychaeturichthys hexanema and A. sciistius (Perciformes: Gobiidae) from southeastern waters off Korea were analyzed to determine dietary habits and the presence of any inter- and intra-specific partitioning of food resources. These two species were bottom-feeding carnivores that consumed mainly benthic crustaceans, and other demersal invertebrates and planktonic organisms were also important in their diets. Non-metric multidimensional scaling (nMDS) ordination and multivariate analyses based on gravimetric contributions of the different prey taxa to stomach contents revealed significant inter-specific dietary differences; i.e. partitioning of food resources between the two species. Size-related changes, however, were not significant for their diets. Differences in the types and range of prey ingested by the two species could often be related to differences in the feeding behaviors. Our results of stomach contents analyses provide clear evidence of niche segregation between co-occurring A. hexanema and A. sciistius in southeastern Korean waters, which would reduce the likelihood of inter-specific competition for food resources.

• Journal of Wetlands Research
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• v.23 no.3
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• pp.201-212
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• 2021

In wetland protection areas, a phytosociological research was conducted on willow forests, which plays an important ecological and environmental role and is the main material for ecological restoration. A total of 61 relevés were collected according to the Z-M(Zürich-Montpellier) school's method and the characteristics of plant communities and the composition of the species were identified. A total of 9 plant communities including 237 taxa were differentiated. Willow species showing the high r-NCD(relative net contribution degree) value in study areas were Salix koriyanagi, Salix chaenomeloides, Salix triandra subsp. nipponica, Salix gracilistyla and Salix pierotii. Poaceae was the most diverse in species, followed by Asteraceae, Apiaceae, Polygonaceae and Fabaceae. Life form type of willow forests in wetland protection areas was determined to be Th(therophytes)-R₅(non-clonal form)-D₄(clitochores)-e(erect form) type. The naturalized plants and invasive alien species were identified as 24 taxa and 4 taxa, respectively. Naturalized and disturbance indices were 10.1% and 41.4%, respectively. The results of the site-species ordination by Non-Metric Multidimensional Scaling(NMDS), wetland types and altitude gradient were the main ecological factors determining the spatial distribution of plant communities. Diversity index and evenness index were high in mountainous palustrine wetlands with relatively high altitude, and the disturbance index, naturalized index and appearance rate of annual plant were high in riverine and lacustrine wetlands with low altitude.

• Korean Journal of Ichthyology
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• v.30 no.1
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• pp.36-45
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• 2018

The temporal and depth-related variations in the species composition and abundance of demersal fish assemblage were studied in the coastal waters off Hupo, East Sea. Fish samples were collected seasonally between 2011 and 2017 at two stations of study area using trammel net and bottom gill net. In total, 46 fish species belonging to 17 families were collected during study period, with 36 and 22 species occurring in depths of ~80 m (site A) and ~140 m (site B), respectively. Glyptocephalus stelleri, Cleisthenes pinetorum and Gymnocanthus herzensteini were abundant at shallower site, and Dasycottus setiger at deeper site. The number of species, abundance, biomass and diversity fluctuated with water depth, but not temporally (both seasonally and annually). Analysis of similarity (ANOSIM) revealed that the fish assemblage structures were significantly different with water depth, but not by year or season. Non-metric multidimensional scaling (MDS) ordination plot emphasized visually in spatial difference of fish assemblages, and it was due to differential contributions of dominant species in relation to water depth and temperature.