An ensemble correlation-based gene selection algorithm for cancer classification with gene expression data.

Piao, Yongjun,Piao, Minghao,Park, Kiejung,Ryu, Keun Ho Oxford University Press 2012 Bioinformatics Vol.28 No.24

<P>Gene selection for cancer classification is one of the most important topics in the biomedical field. However, microarray data pose a severe challenge for computational techniques. We need dimension reduction techniques that identify a small set of genes to achieve better learning performance. From the perspective of machine learning, the selection of genes can be considered to be a feature selection problem that aims to find a small subset of features that has the most discriminative information for the target.</P>

의사결정 트리 앙상블을 구축하기 위한 상관성 기반 기법을 이용한 속성 중복성 제거

박영준 ( Yongjun Piao ),박명호 ( Minghao Piao ),손호선 ( Ho Sun Shon ),류근호 ( Keun Ho Ryu ) 한국정보처리학회 2011 한국정보처리학회 학술대회논문집 Vol.18 No.2

대량의 분류 규칙 탐사 과정은 앙상블기법을 사용하여 다양한 연구들이 이루어지고 있다. 본 논문에서는 의사결정 트리의 분열 문제와 singleton 포함 한계를 해결하기 위하여 Cascading-and-Sharing 앙상블 기법을 적용하여 점진적 다중 의사결정 트리를 구축하였다. 또한 분류의 정확도를 향상시키고, 트리의 복잡도와 모델 과잉접합을 피하기 위하여 다중 트리 구축과정에서 선형 상관분석기법을 기반으로 훈련 데이터 속성들의 중복성을 제거하였다. 실험 결과, 속성들의 중복성을 제거하여 구축한 트리들은 원래 기법보다 더 좋은 결과를 보여주었다.

Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data

Li, Peipei,Piao, Yongjun,Shon, Ho Sun,Ryu, Keun Ho BioMed Central 2015 BMC bioinformatics Vol.16 No.-

<P><B>Background</B></P><P>Recently, rapid improvements in technology and decrease in sequencing costs have made RNA-Seq a widely used technique to quantify gene expression levels. Various normalization approaches have been proposed, owing to the importance of normalization in the analysis of RNA-Seq data. A comparison of recently proposed normalization methods is required to generate suitable guidelines for the selection of the most appropriate approach for future experiments.</P><P><B>Results</B></P><P>In this paper, we compared eight non-abundance (RC, UQ, Med, TMM, DESeq, Q, RPKM, and ERPKM) and two abundance estimation normalization methods (RSEM and Sailfish). The experiments were based on real Illumina high-throughput RNA-Seq of 35- and 76-nucleotide sequences produced in the MAQC project and simulation reads. Reads were mapped with human genome obtained from UCSC Genome Browser Database. For precise evaluation, we investigated Spearman correlation between the normalization results from RNA-Seq and MAQC qRT-PCR values for 996 genes. Based on this work, we showed that out of the eight non-abundance estimation normalization methods, RC, UQ, Med, TMM, DESeq, and Q gave similar normalization results for all data sets. For RNA-Seq of a 35-nucleotide sequence, RPKM showed the highest correlation results, but for RNA-Seq of a 76-nucleotide sequence, least correlation was observed than the other methods. ERPKM did not improve results than RPKM. Between two abundance estimation normalization methods, for RNA-Seq of a 35-nucleotide sequence, higher correlation was obtained with Sailfish than that with RSEM, which was better than without using abundance estimation methods. However, for RNA-Seq of a 76-nucleotide sequence, the results achieved by RSEM were similar to without applying abundance estimation methods, and were much better than with Sailfish. Furthermore, we found that adding a poly-A tail increased alignment numbers, but did not improve normalization results.</P><P><B>Conclusion</B></P><P>Spearman correlation analysis revealed that RC, UQ, Med, TMM, DESeq, and Q did not noticeably improve gene expression normalization, regardless of read length. Other normalization methods were more efficient when alignment accuracy was low; Sailfish with RPKM gave the best normalization results. When alignment accuracy was high, RC was sufficient for gene expression calculation. And we suggest ignoring poly-A tail during differential gene expression analysis.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/s12859-015-0778-7) contains supplementary material, which is available to authorized users.</P>

A New Direction of Cancer Classification: Positive Effect of Low-Ranking MicroRNAs

Feifei Li,Minghao Piao,Yongjun Piao,Meijing Li,류근호 질병관리본부 2014 Osong Public Health and Research Persptectives Vol.5 No.5

Objectives: Many studies based on microRNA (miRNA) expression profiles showed a new aspect of cancer classification. Because one characteristic of miRNA expression data is the high dimensionality, feature selection methods have been used to facilitate dimensionality reduction. The feature selection methods have one shortcoming thus far: they just consider the problem of where feature to class is 1:1 or n:1. However, because one miRNA may influence more than one type of cancer, human miRNA is considered to be ranked low in traditional feature selection methods and are removed most of the time. In view of the limitation of the miRNA number, low-ranking miRNAs are also important to cancer classification. Methods: We considered both high- and low-ranking features to cover all problems (1:1, n:1, 1:n, and m:n) in cancer classification. First, we used the correlation-based feature selection method to select the high-ranking miRNAs, and chose the support vector machine, Bayes network, decision tree, k-nearestneighbor, and logistic classifier to construct cancer classification. Then, we chose Chi-square test, information gain, gain ratio, and Pearson’s correlation feature selection methods to build the m:n feature subset, and used the selected miRNAs to determine cancer classification. Results: The low-ranking miRNA expression profiles achieved higher classification accuracy compared with just using high-ranking miRNAs in traditional feature selection methods. Conclusion: Our results demonstrate that the m:n feature subset made a positive impression of low-ranking miRNAs in cancer classification.

양와위 자세에서 싸이클 운동 시 각도변화에 따른 운동효과 분석

유미(Mi Yu),박용군(Yongjun Piao),김성진(Sungjin Kim),정구영(Guyoung Jeong),권대규(Taekyu Kwon) 한국HCI학회 2012 한국HCI학회 학술대회 Vol.2012 No.1

본 연구에서는 싸이클 운동을 할 수 있는 보조 운동 모듈, 상∙하 기울기가 가능한 경사침대와 상부의 모니터를 통해 하지운동 훈련 프로그램을 시각적으로 피드백 받을 수 있는 디스플레이장치로 구성된 조기재활치료 시스템을 개발하였다. 시스템의 효용성을 입증하고자 앙와위 자세(spine position)에서 하지 운동 시 하지 근육의 특성을 분석하기 위해 0º 부터 30º와 60º의 침대 경사 조건에서 오른쪽 다리의 대퇴직근(Rectus Femoris, RF), 대퇴이두근(Biceps Femoris, BF), 전경골근(tibialis anterior, TA), 비복근(gastrocnemius, Ga)의 근전도와 심전도 신호를 수집분석하였다. 대퇴이두근의 경우, 경사침대 각도가 증가할수록 근육 사용이 증가하는 경향을 보였으며, 대퇴직근과 전경골근의 경우 감소하는 경향을 보이고, 비복근의 경우 각도와의 상관관계가 없는 것으로 분석되었다. 이번 연구 결과는 노인, 뇌졸중과 같은 편마비 환자의 하지근력 향상을 위한 운동에 적용될 수 있음을 의미하며, 향후 다양한 재활훈련의 프로그램 종류, 강도 및 각 질환별 최적 콘텐츠 개발에 대한 정량적인 데이터 수집 및 분석연구가 필요하다. We investigated an early rehabilitation training system that increase the intensity of patient rehabilitation training to shorten the time it takes for patients to progress to a secondary rehabilitation training stage by allowing patients incapable of self-ambulation. It consisted of tilting bed, cycle ergometer for lower-limb exercise and training program. We performed experimental study on the muscular activities of Rectus Femoris(RF), Biceps Femoris(BF), tibialis anterior(TA), gastrocnemius(GA) in the right lower-limb and ECG(electrocardiogram) during cycling at tilt angle of 0, 30 and 60º. The muscle activities were the opposite effect by muscle location. The results indicate that the early rehabilitation training system could be applied to improve the lower extremity muscular strength for elderly and patients, especially, stroke.

Positive Effect of Baby-Friendly Hospital Initiatives on Improving Mothers' Intention for Successful Breastfeeding in Korea

Park, Hyun Woo,Ryu, Keun Ho,Piao, Yongjun,Li, Peipei,Hong, Jae Shik,Kim, Hee Bum,Chung, Hwanwook,Hoh, Jeong-Kyu,Kim, Yong Joo KOREAN ACADEMY OF MEDICAL SCIENCE 2018 JOURNAL OF KOREAN MEDICAL SCIENCE Vol.33 No.43

<P><B>Background</B></P><P>In Korea, the breastfeeding (BF) rate of infants aged 6 months or more is drastically decreasing, and this phenomenon is particularly worrisome for the future health of the population. The present study aimed to identify an antenatal strategy for initiation and continuation of human BF, and to identify how Baby-Friendly Hospitals (BFHs) may positively influence the intention to breastfeed.</P><P><B>Methods</B></P><P>A total of 414 pregnant Korean antenatal women were surveyed using questionnaires to determine current knowledge of the benefits of human breast milk, whether they planned to breastfeed after delivery, to continue BF after reinstatement in the workforce, are willing to abide by rooming-in care for infants, and plan to give birth at BFHs.</P><P><B>Results</B></P><P>We found that planning room-in care, greater awareness of BF benefits for infant and mother, participation in antenatal education programs, and provision of BF facilities in the workplace were positively associated with plans for exclusive breastfeeding (EBF) and longer BF duration. The mothers who planned to give birth at BFHs also desired to breastfeed immediately after birth, implement in-room care, continue BF at their workplace, participate in antenatal BF educational programs, and were more aware of the benefits of BF.</P><P><B>Conclusion</B></P><P>If the beneficial effects of BFHs were well known to individuals, these would enhance the success rate of BF in Korea. Antenatal education and consequent acquisition of better knowledge of the benefits of BF are important for increasing the rate of BF practices.</P>

Study on the thermoelectric properties of porous Bi-Te films deposited using thermal evaporation on AAO template

Shiying Liu,GUOJIAN LI,Mingdi Lan,Yongjun Piao,Yanan Zhang,QIANG WANG 한국물리학회 2020 Current Applied Physics Vol.20 No.3

The application of thermoelectric films is limited to retain the temperature gradient. In this study, the Bi-Te films are deposited on the AAO template with a pore size of 100 nm using thermal evaporation. The results show that the conductive types of the Bi-Te film are tuned by source temperature. The power factor of the p-type porous film decreases 36% by comparing to that of the p-type nonporous film (1020 μW/mK2 at 250 °C). Meanwhile, the temperature difference in the porous device is maintained and is approximately 5.0 °C. Thus, the maximum output power is achieved in the porous device (about 25 pW), which is 5 times higher than that of the nonporous device. This provides a method to improve the conversion efficiency of thermoelectric film device by maintaining the temperature difference by using porous structure.

Parkinson’s Disease with Fatigue: Clinical Characteristics and Potential Mechanisms Relevant to α-Synuclein Oligomer

Li-Jun Zuo,Shu-Yang Yu,Fang Wang,Yanghui Xia,Ying-Shan Piao,Yang Du,Teng-Hong Lian,Rui-Dan Wang,Qiu-Jin Yu,Ya-Jie Wang,Xiao-Min Wang,Piu Chan,Sheng-Di Chen,Yongjun Wang,Wei Zhang 대한신경과학회 2016 Journal of Clinical Neurology Vol.12 No.2

Background and Purpose The aim of this study was to identify the clinical characteristics and potential mechanisms relevant to pathological proteins in Parkinson’s disease (PD) patients who experience fatigue. Methods PD patients (n=102) were evaluated using a fatigue severity scale and scales for motor and nonmotor symptoms. The levels of three pathological proteins—α-synuclein oligomer, β-amyloid (Aβ)1-42, and tau—were measured in 102 cerebrospinal fluid (CSF) samples from these PD patients. Linear regression analyses were performed between fatigue score and the CSF levels of the above-listed pathological proteins in PD patients. Results The frequency of fatigue in the PD patients was 62.75%. The fatigue group had worse motor symptoms and anxiety, depression, and autonomic dysfunction. The CSF level of α-synuclein oligomer was higher and that of Aβ1-42 was lower in the fatigue group than in the non-fatigue group. In multiple linear regression analyses, fatigue severity was significantly and positively correlated with the α-synuclein oligomer level in the CSF of PD patients, after adjusting for confounders. Conclusions PD patients experience a high frequency of fatigue. PD patients with fatigue have worse motor and part nonmotor symptoms. Fatigue in PD patients is associated with an increased α-synuclein oligomer level in the CSF

75톤급 로켓엔진 짐벌마운트 시험장치 개발

김인성(Insung Kim),이준호(Joonho Lee),손갑식(Gapsik Son),장익수(Iksoo Jang),박용균(Yongjun Piao),이문석(Moonseok Lee),정은환(Eunhwan Jung),박종연(Jongyoun Park) 한국추진공학회 2015 한국추진공학회 학술대회논문집 Vol.2015 No.11

액체로켓 엔진의 짐벌마운트는 엔진 조립체와 발사체 후방동체 사이에서 두 축 회전운동을 통해 발사체의 피치(pitch) 및 요(yaw) 방향 운동을 가능케 하는 중요 엔진 구성품이다. 짐벌마운트는 높은 구조 강도와 강성, 낮은 베어링 마찰토크, 엔진 연소시간 동안의 충분한 수명 등의 요구조건들을 기준으로 개발되고 그 적합성이 시험을 통해 검증되어야 한다. 75톤급 액체로켓 엔진의 짐벌마운트 개발적합성을 확인하기 위해 엔진 연소 및 비행 중 발생할 축뱡향 및 횡방향 하중 등 방향별 하중인가와 발사체의 방향제어를 위한 짐벌링 운동 모사가 가능하도록 시험장치를 개발하였고, 이 시험장치를 이용해 짐벌마운트의 정하중 시험, 강성 시험, 마찰토크 시험, 수명시험 등을 수행할 수 있도록 하였다. A gimbal mount of rocket engine is an engine component to make a pitch and yaw movement of the launch vehicle possible by its two axis gimbaling motion. The gimbal mount requires high structural strength, high stiffness, low bearing friction torque and enough life cycle to guarantee its safe operation during the full duration of combustion. Test facility for the gimbal mount of 75 ton engine which has the function of load application, gimbaling motion and measurement of the strength, stiffness and friction torque is developed to perform gimbal mount tests such as static test, stiffness test, friction torque test, life cycle test.