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CORE:Common Region Extension Based Multiple Protein Structure Alignment for Producing Multiple Solution

Journal of Computer Science & Technology 2013年第4期28卷 647-656页

作者： Woo-Cheol Kim Sanghyun park jung-Im Won College of Information Sciences and Technology The Pennsylvania State University University Park Department of Computer Science Yonsei University Research Center of Information and Electronic Engineering Hallym University Chuncheon

Over the past several decades, biologists have conducted numerous studies examining both general and specific functions of proteins. Generally, if similarities in either the structure or sequence of amino acids exist for two proteins, then a common biological function is expected. Protein function is determined primarily based on the structure rather than the sequence of amino acids. The algorithm for protein structure alignment is an essential tool for the research. The quality of the algorithm depends on the quality of the similarity measure that is used, and the similarity measure is an objective function used to determine the best alignment because of their individual strength and weakness However, none of existing similarity measures became golden standard They require excessive filtering to find a single alignment. In this paper, we introduce a new strategy that finds not a single alignment, but multiple alignments with different lengths. This method has obvious benefits of high quality alignment. However, this novel method leads to a new problem that the running time for this method is considerably longer than that for methods that find only a single alignment. To address this problem~ we propose algorithms that can locate a common region （CORE） of multiple alignment candidates, and can then extend the CORE into multiple alignments. Because the CORE can be defined from a final alignment, we introduce CORE＊ that is similar to CORE and propose an algorithm to identify the CORE＊. By adopting CORE＊ and dynamic programming, our proposed method produces multiple alignments of various lengths with higher accuracy than previous methods. In the experiments, the alignments identified by our algorithm are longer than those obtained by TM-align by 17% and 15.48%, on average, when the comparison is conducted at the level of super-family and fold, respectively.

关键词： structure alignment similarity search protein structure

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Early experience of the compression anastomosis ring (CAR^(TM) 27) in left-sided colon resection

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World Journal of Gastroenterology 2011年第43期17卷 4787-4792页

作者： jung-Yeon Lee Jin-Hee Woo Hong-Jo Choi Ki-Jae park Young-hoon Roh Ki-Han Kim Hak-Yoon Lee Department of Surgery Dong-A University Medical Center

AIM:To evaluate clinical validity of the compression anastomosis ring(CARTM27) anastomosis in left-sided colonic resection. METHODS:A non-randomized prospective data collection was performed for patients undergoing an elective left-sided colon resection,followed by an anastomosis using the CARTM27 between November 2009 and January *** criteria of the use of the CARTM27 were anastomoses between the colon and at or above the intraperitoneal *** primary short-term clinical endpoint,rate of anastomotic leakage,and other clinical outcomes,including intraand postoperative complications,length of operation time and hospital stay,and the ring elimination time were evaluated. RESULTS:A total of 79 patients(male,43;median age,64 years) underwent an elective left-sided colon resection,followed by an anastomosis using *** was performed laparoscopically in 70 patients,in whom two patients converted to open procedure(2.9%) .There was no surgical *** an intraoperative complication,total disruption of the anastomosis occurred by premature enforced tension on the proximal segment of the anastomosis in one *** ring was removed and another new CARTM27 anastomosis was *** patient with sigmoid colon cancer showed postoperative anastomotic leakage after 6 d postoperatively and temporary diverting ileostomy was *** date of expulsion of the ring could not be recorded because most patients were not aware that the ring had been *** patients manifested clinical symptoms of anastomotic stricture. CONCLUSION:Short-term evaluation of the CARTM27 anastomosis in elective left colectomy suggested it to be a safe and efficacious alternative to the standard hand-sewn or stapling technique.

关键词： Compression anastomosis Colon Anastomotic leakage CARTM27

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Development and characterization of novel polymorphic microsatellite markers for the Korean freshwater snail Semisulcospira coreana and cross-species amplification using next-generation sequencing

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Journal of Oceanology and Limnology 2020年第2期38卷 503-508页

作者： Yeon jung park Mi Nan LEE Eun-Mi KIM jung Youn park Jae Koo NOH Tae-Jin CHOI jung-Ha KANG Biotechnology Research Division National Institute of Fisheries ScienceBusan 46083Republic of Korea Department of Microbiology Pukyoung National UniversityBusan 48513Republic of Korea

Korean freshwater snails of the genus Semisulcospira are widely distributed across East *** has been a very popular nutritional food in Korea,and is an ecologically important water quality indicator because it lives only in clean ***,no microsatellite markers have been generated to study the population genetic diversity of this *** the present study,we developed and characterized 18 novel microsatellite loci from Semisulcospira coreana genomic *** microsatellites were isolated using 454 GS-FLX titanium sequencing and 18 markers were used for genotyping in *** addition,we also tested the cross-species transferability of the microsatellite markers in four additional Semisulcospira *** identified 18 polymorphic loci and the number of alleles per loci,and their polymorphism information content values ranged from 2 to 17 and 0.203 to 0.902,*** observed and expected heterozygosities of the loci ranged from 0.063 to 0.924 and 0.226 to 0.924,*** to the analysis of the cross-species transferability of these markers,four species,***,***,***,and ***,showed a very high transferability(80%–85%).These results show that this set of nuclear markers could be useful for population genetics studies of this species and closely related species.

关键词： Semisulcospira next-generation sequencing(NGS) microsatellite markers cross-species transferability

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Spatial Ecology of Translocated and Resident Amur Ratsnakes(Elaphe schrenckii) in Two Mountain Valleys of South Korea

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Asian Herpetological Research 2011年第4期2卷 223-229页

作者： jung-Hyun LEE Daesik park Department of Biology Kangwon National UniversityChuncheonKangwon 200-701South Korea Department of Environmental Resources Research National Institute of Environmental ResearchSeo-GuIncheon 404-708South Korea Division of Science Education Kangwon National UniversityChuncheonKangwon 200-701South Korea

The translocation of snakes has been viewed as a useful tool to augment declining populations and to mitigate human-wildlife conflicts, even though released snakes often exhibit relatively high mortality. We radio-tracked 13 Amur Ratsnakes （Elaphe schrenckii） in the Woraksan National park in South Korea from July 2008 to May 2009. Two of these snakes were residents, and 11 had been illegally captured in areas remote from the study site and were donated by the park office. During the study period, six of the translocated snakes were lost： two were killed by predators, one died of unknown causes, and the radio signals of three of the snakes were lost. In the field, the ratsnakes laid eggs in early August, moved into hibemacula in late November, and moved away from the hibemacula in mid-April. Compared to the resident snakes, five of the translocated snakes traveled approximately 1.3 times farther per week, and the home ranges of the translocated snakes were three to six times larger than those of the resident snakes. In addition, the translocated snakes were found underground more frequently than the resident snakes. The management recommendations resulting from this study will guide biologists and land use managers in making appropriate decisions regarding release sites and the use of gravid females in the translocation of this endangered ratsnake.

关键词： Amur Ratsnake conservation Elaphe schrenckii radiotelemetry translocation

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gscaLCA in R: Fitting Fuzzy Clustering Analysis Incorporated with Generalized Structured Component Analysis

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Computer Modeling in Engineering & Sciences 2022年第9期132卷 801-822页

作者： Ji hoon Ryoo Seohee park Seongeun Kim Heungsun Hwang Department of Education College of Educational SciencesYonsei UniversitySeoul03722South Korea Psychometrics Department American Board of Internal MedicinePhiladelphia19016USA Department of Educational Research Methodology School of EducationUniversity of North Carolina at GreensboroGreensboro27412USA Department of Psychology McGill UniversityMontrealH3A 0G4Canada

Clustering analysis identifying unknown heterogenous subgroups of a population(or a sample)has become increasingly popular along with the popularity of machine learning *** there are many software packages running clustering analysis,there is a lack of packages conducting clustering analysis within a structural equation modeling *** package,gscaLCA which is implemented in the R statistical computing environment,was developed for conducting clustering analysis and has been extended to a latent variable *** specifically,by applying both fuzzy clustering(FC)algorithm and generalized structured component analysis(GSCA),the package gscaLCA computes membership prevalence and item response probabilities as posterior probabilities,which is applicable in mixture modeling such as latent class analysis in *** a hybrid model between data clustering in classifications and model-based mixture modeling approach,fuzzy clusterwise GSCA,denoted as gscaLCA,encompasses many advantages from both methods:(1)soft partitioning from FC and(2)efficiency in estimating model parameters with bootstrap method via resolution of global optimization problem from *** main function,gscaLCA,works for both binary and ordered categorical *** addition,gscaLCA can be used for latent class regression as *** of profiles of latent classes based on the posterior probabilities is also available in the package *** paper contributes to providing a methodological tool,gscaLCA that applied researchers such as social scientists and medical researchers can apply clustering analysis in their research.

关键词： Fuzzy clustering generalized structured component analysis gscaLCA latent class analysis

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Aging Analysis Framework of Windows-Based Systems through Differential-Analysis of System Snapshots

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Computers, Materials & Continua 2022年第12期73卷 5091-5102页

作者： Eun-Tae Jang Sung hoon Baek Ki-Woong park SysCore Lab Sejong UniversitySeoul05006Korea Department of Computer System Engineering Jungwon UniversityChungcheongbuk-do28024Korea

When aWindows-based system is used for an exceedingly long time,its performance degrades,and the error occurrence rate tends to *** is generally called system *** investigate the reasons for system aging,various studies have been conducted within the range of the operating system kernel to the user ***,finding an accurate reason for system performance degradation remains challenging research *** this study,system monitoring was conducted by dividing a system into‘before software installation,’‘after software installation,’and‘after software removal.’We confirmed that when a software installed in a system is removed,various system elements,such as storage and memory,are not restored to the level prior to the software ***,we established a hypothesis regarding the performance degradation of a computer system owing to repeated software installation/removal operations,investigated the correlation between system aging and repeated software installation/removal operations,and proposed a system aging analysis framework for analyzing the reason behind system *** the proposed system aging analysis framework,we aim to forcibly age a Windows-based system by repeating the software installation/removal operation by utilizing the system forced aging *** framework identifies the elements affecting system performance through a differential data analysis of the system time-series data extracted by the system performance extraction and system component snapshot ***,the aging analysis framework presented in this study is expected to be effectively utilized as an index for studying system aging.

关键词： System aging virtual machine system analysis

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Use of a Digital Image Correlation Technique for Measuring the Material Properties of Beetle Wing

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Journal of Bionic Engineering 2009年第3期6卷 224-231页

作者： Tailie Jin Nam Seo Goo Sung-Choong Woo hoon Cheol park Biomemitics and Intelligent Microsystem Laboratory Department of Advanced Technology FusionKonkuk University

Beetle wings are very specialized flight organs consisting of the veins and *** it is necessary from a bionic view to investigate the material properties of a beetle wing *** the present study,we have used a Digital Image Correlation (DIC) technique to measure the elastic modulus of a beetle wing *** were prepared by carefully cutting a beetle hind wing into 3.0 mm by 7.0 mm segments (the gage length was 5 mm).We used a scanning electron microscope for a precise measurement of the thickness of the beetle wing *** specimen was attached to a designed fixture to induce a uniform displacement by means of a *** used an ARAMISTM system based on the digital image correlation technique to measure the corresponding displacement of a *** thickness of the beetle wing varied at different points of the *** elastic modulus differed in relation to the membrane arrangement showing a structural anisotropy;the elastic modulus in the chordwise direction is approximately 2.65 GPa,which is three times larger than the elastic modulus in the spanwise direction of 0.84 *** a result,the digital image correlation-based ARAMIS system was suc- cessfully used to measure the elastic modulus of a beetle *** addition to membrane's elastic modulus,we considered the Poisson's ratio of the membrane and measured the elastic modulus of a vein using an Instron universal tensile *** result reveals the Poisson's ratio is nearly zero and the elastic modulus of a vein is about 11 GPa.

关键词： digital image correlation technique beetle wing elastic modulus Poisson's ratio vein membrane

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Design,fabrication,and structural safety validation of 3D-printable biporous bone augments

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Bio-Design and Manufacturing 2023年第1期6卷 26-37页

作者： Yeokyung Kang Dasol Lim Doo-hoon Sun Jong-Chul park jungsung Kim Central Research&Development Center Corentec Company Ltd.33-2Banpo-daero 20-gilSeocho-guSeoulRepublic of Korea Cellbiocontrol Laboratory Department of Medical EngineeringYonsei University College of Medicine50-1 Yonsei-roSinchon-dongSeodaemun-guSeoulRepublic of Korea Department of Orthopaedic Surgery Daejeon Sun Hospital10-7 Mok-dongJung-guDaejeonRepublic of Korea

The use of commercial products such as a cup and liner for total hip arthroplasty for patients with severe bone defects has a high probability of *** these patients the cup alone cannot cover the bone defect,and thus,an additional augment or cage is *** this study,we designed three-dimensional(3D)printable bone augments as an alternative to surgeries using reinforcement ***-five sharp-edged bone augments of various sizes were 3D printed.A biporous structure was designed to reduce the weight of the augment and to facilitate bone *** types of frames were used to prevent damage to the augment’s porous structure and maintain its stability during ***,two types of holes were provided for easy augment fixation at various *** tests were performed on a combination of worst-case sizes derived using finite element *** test results confirmed the structural stability of the specimens at a load of 5340 *** the porosity of the specimens was measured to be 63.70%,it cannot be said that the porous nature was uniformly distributed because porosity tests were performed locally and *** summary,3D-printable biporous bone augments capable of bonding from various angles and bidirectionally through angulation and bottom-plane screw holes are *** mechanical results with bone augments indicate good structural safety in ***,further research is necessary to study the clinical applications of the proposed bone augment.

关键词： Bone augment 3D printing Biporous structure Total hip arthroplasty Metal implant

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Optimal Age Replacement Policy with Replacement Occurrence While the Warranty is in Effect

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Journal of Shanghai Jiaotong university(Science) 2015年第3期20卷 374-379页

作者： park Minjae jung Ki Mun park Dong Ho College of Business Administration Hongik University Department of Informational Statistics Kyungsung University Industry Academic Cooperation Foundation Hallym University

This study considers an age replacement policy(ARP) for a repairable product with an increasing failure rate with and without a product warranty. As for the warranty policy to consider in association with such an age replacement policy, we adapt a renewable minimal repair-replacement warrant(MRRW) policy with 2D factors of failure time of the product and its corresponding repair time. The expected cost rate during the life cycle of the product is utilized as a criterion to find the optimal policies for both with and without the product warranty. We determine the optimal replacement age that minimizes the objective function which evaluates the expected cost rate during the product cycle and investigate the impact of several factors on the optimal replacement age. The main objective of this study lies on the generalization of the classical age replacement policy to the situation where a renewable warranty depending on 2D factors is in effect. We present some interesting observations regarding the effect of relevant factors based on numerical analysis.

关键词： age replacement policy(ARP) expected cost rate failure times renewable minimal repairreplacement warranty(MRRW) warranty servicing times

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PotholeEye^(+): Deep-Learning Based Pavement Distress Detection System toward Smart Maintenance

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Computer Modeling in Engineering & Sciences 2021年第6期127卷 965-976页

作者： Juyoung park jung Hee Lee Junseong Bang Korea Expressway Corporation 77Hyeoksin8-roGimcheon-siKorea Electronics and Telecommunications Research Institute(ETRI) 218 Gajeong-roYuseong-guDaejun-siKorea University of Science&Technology(UST) 217 Gajeong-roYuseong-guDaejun-siKorea

We propose a mobile system,called PotholeEye+,for automatically monitoring the surface of a roadway and detecting the pavement distress in real-time through analysis of a ***+pre-processes the images,extracts features,and classifies the distress into a variety of types,while the road manager is *** day for a year,we have tested PotholeEye+on real highway involving real settings,a camera,a mini computer,a GPS receiver,and so ***,PotholeEye+detected the pavement distress with accuracy of 92%,precision of 87%and recall 74%averagely during driving at an average speed of 110 km/h on a real highway.

关键词： Pavement distress detection classification convolutional neural network deep learning video analysis

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