Bioinformatics and Biomedical Engineering New Advances

Proceedings of the 9th International Conference on

Bioinformatics and Biomedical Engineering (iCBBE 2015),
Shanghai, China, 18 20 September 2015 1st Edition

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 Computational evolutionary biology
The application of COI and ITS genes in the molecular phylogeny
of water beetles 101
C. Guo, D.J. Bian & L.Z. Ji
Genome-wide identification and phylogenetic analysis of the Ethylene-Insensitive3
(EIN3) and EIN3-Like (EILs) gene family in melons 105
Y. Ma, Y. Tu, X.L. Chen & X.G. Liu

Biomechanics
In vitro and in vivo biomechanical research on cervical arthroplasty and fusion 113
Z.H. Liao & W.Q. Liu
Mechanical conditions affect intervertebral disc degeneration concerning
its water retention 121
W. Weina, W.Q. Liu & Z.H. Liao
Viscoelasticity of the intervertebral segments after fusion under continuous
compression 127
B.Q. Pei, Z.Y. Liu, H. Li & Y.Y. Pei

Biosignal/image processing and analysis

Recognition of sequential upper limb movements based on surface
Electromyography (sEMG) signals 135
B.Y. Zhang, Z.T. Zhou, E.W. Yin, J. Jiang & D.W. Hu
Contrastive study on the enhancement of pitch adjustable Electrolarynx speech
based on spectral subtraction technology 143
Y. Li, L. Wang, Y.J. Feng & H.J. Niu
Comparison between neural network or neural network with genetic algorithm
and analysis of EEG signal 151
Y.A. Rahim & M.M. BkrSudan
Feature optimization for pathological voice based on BP neural network 157
Y. Zeng, W.P. Hu & D.D. Liang
A graph-based method for blood vessel segmentation of retinal images 163
J.D. Zhang, W.H. Jiang, C.X. Zhang & Y.J. Cui
A fusion approach for dynamic skin detection 171
L. Chen & Y.H. Liu
Local gradient thresholds computation in 3D images based
on a vision model 179
J.Y. Li, P. Wang & L.S. Wang
Abnormality detection of specific brain structure in MR images based
on multi-atlas and texture descriptor 187
B.Z. Chen, Y. Wang & L.S. Wang
Retinal images change detection based on fusing multi-features differences 193
S. Yin, B.Z. Chen & L.S. Wang
Effective method for extracting the characteristic value of photoplethysmography
signals 199
Y.Z. Shang, S.S. Yong, D.X. Guo, R. Peng & X.A. Wang

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 Biomedical materials and products
TEOS hydrolysis method synthesize nano silica and its biological
toxicity research 207
L.J. Hu, R. Li, B. Liu, X. Han, X. Zheng & B.B. Tong
Solvothermal method preparation of nano Y2O2S:Eu3+ and research
of luminescence property and cytotoxicity 213
C. Zhou, W.J. Yan, J. Jin, X.X. Li, Y. Li & P. Xie
Enzyme assisted extraction of polysaccharides from Flammulina velutipes
and its radicals scavenging activity 219
G.T. Chen, Y.R. Dong, G.H. Qi, Z.P. Yang, H.X. Wang & S.L. Wang
Preparation of CdTe quantum dots in aqueous phase 227
Y. Hao
Optimization of the preparation of nalmefene hydrochloride injection 233
M.H. Duan, Q. Hao, Y.X. Sun, Z. Zhang, Z. Wang, Y. Yang, L.N. Wang,
Y.H. Jiang, C.L. Zhou & J. Pei
Development and validation of a method for detecting contaminants
in nalmefene hydrochloride injections 239
M.H. Duan, Q. Hao, Y.X. Sun, Z. Zhang, Z. Wang, Y. Yang, Y.H. Jiang,
L.N. Wang, C.L. Zhou & J. Pei
A new technology for the preparation of Deproteinized Extract of Calf Blood 245
H.Y. Li, L.N. Chen, G.X. Yuan, G.Y. Xu, Y. Sheng, P.G. Du, L.P. An & T.C. Li
Preparation of mouse amelotin antibody by synthetic peptides 251
J.J. Zhang & Y. Sun
Optimization of protein depletion technology for polysaccharides from Angelica
and Astragalus by orthogonal test design 257
X.Y. Pu, X.L. Ma, L. Liu, J. Ren, X.Y. Li & H.B. Li

Biomedical devices and systems

Detection of C-Reactive Protein based on a Dynabeads-labeled sandwich
immunoassay by using a GMI biosensor 265
Z. Yang, C. Lei & Y. Zhou
Combining eye gaze detection with vision-based object recognition
for a portable Human-Machine Interface 271
C.X. Yuan, J. Jiang, J.S. Tang, Z.T. Zhou & D.W. Hu
The design of a rehabilitation training system with EMG feedback
for stroke patients 277
C.X. Yu, J.Y. Guo, Z.G. Yu, H.J. Niu, Y.B. Fan, Z. Wang,
W.R. Zhao & H.H. Zhao
Image Guided Surgery system for Optic Nerve Decompression Operation 283
Y.J. Wu, C.W. Xiao, C.L. Fang & L.S. Wang
Denitrification under aerobic condition by a reactor packed with corncobs
as carbon source and bio-carrier 289
L. Shao & Y. Ling
Wireless platform for real-time Electrocardiography (ECG) recording
and analysis 295
M. Al-Qahtani, M. Alwahiby, M. Abdelhamid, E.H. Mirza & X. Yang

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 Design of the Invasive Blood Pressure simulator 301
Q.C. Liu & B. Xiao
Needle guide device development for CT system-based biopsy 307
H.K. Yun, G.R. Park, K.C. Choi, T.S. Shin, M.K. Kim & S.K. Joo
A novel target selection approach by incorporating image segmentation
into P300-based Brain-Computer Interfaces 313
P. Du, Y. Yu, E.W. Yin, J. Jiang, Y.D. Liu & D.W. Hu
Rapid identification of Panax ginseng and Panax quinquefolius using SNP-based
probes 319
R.L. Wang, D.J. Gu, C.R. Hou & Q.J. Liu
Study on the range of motion of laparoscopic instruments with a simulator 325
K. Lu, C. Song & C. Wei

Biomedical imaging
The application of photoacoustic tomography in joint tissues 335
X.C. Zhong, X.Y. Jing, S.Q. Jing, N.Z. Zhang & J. Rong
Frequency response mismatch correction in multichannel time interleaved analog
beamformers for ultrasound medical imaging 341
A. Zjajo & R. van Leuken
HIFU based photoacoutic tomography 349
X.C. Zhong, W.Z. Qi, S.Q. Jing, N.Z. Zhang & J. Rong
Analyzer-Based Phase Contrast X-ray Imaging for mouse tissues 355
H. Li, M. Wang, Z. Wang & S.Q. Luo

Biocybernetics and biological effects

Effects of captopril pretreatment on gp130 expression in rats
with acute cardiomyocyte injury 361
Y. Zhou, S.B. Li, Y. Zhang, X.B. Jing & M. Gu
Effects of sleep restriction and circadian rhythm on human vigilance 367
H.Q. Yu, Y. Tian, C.H. Wang, S.G. Chen & J.H. Guo
The impact of environmental factors on the survival status of Rana 375
M.H. Duan, X.H. Li, A.J. Jiang, Y.Y. Pei, D.D. Guan, Y.X. Sun, H. Qiang,
Y. Yue & Y.P. Li
Balance role of dopamine system on exciting and inhibitory involved in motor
function 381
J.L. Cheng, X.W. Wang & L.J. Hou
Pemetrexed and carboplatin chemotherapy combined with whole brain
radiotherapy for non-small cell lung cancer with brain metastasis 387
H.B. Li, Y.F. Yun, X.F. Zhou, J.D. Luo, H. Zhu, L.Y. Zhou & Q. An
Metabolites analysis of functional lactic acid bacteria strain Lactobacillus
paracasei HD1.7 395
R.P. Du, D. Zhao, X.Y. Wang, Q. Wang & J.P. Ge
4-aminopyridine inhibits cell proliferation and affects anti-tumor activities
of cell cycle-specific drugs in human breast cancer cells 403
Q. Ru, X. Tian, J.S. Liu & C.Y. Li

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 Biostatistics and biometry
Epidemiological characteristics of outpatients in a Grade 3, Class A general hospital 411
Y.M. Li, Y.J. Tan, F. Wu, C. Zheng, N.Y. Sun & K.Y. Wang
Methane estimation of food waste in Chinese household and environmental
benefits from an energy perspective 417
S. Ding, G.B. Song & S.S. Zhang
A method of Chemiluminescence Enzyme Immunoassay for Zearalenone 423
K.H. Li, L.X. Zhu, W. Meng & R.R. Liu
Estimation of blood glucose noninvasively using near infrared spectroscopy 429
R. Peng, D.X. Guo, Y.Z. Shang, S.S. Yong & X.A. Wang
Restrictive factors of the measurement accuracy to estimate Blood
Pressure with Pulse wave Transit Time 435
X.M. Chen, Y.B. Li, Y. Zhang & N. Deng

Rehabilitation engineering
The research on motion recognition based on EMG of residual thigh 445
T.Y. Zhang

Author index 451

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 Bioinformatics and Biomedical Engineering – Chou & Zhou (Eds)
© 2016 Taylor & Francis Group, London, ISBN 978-1-138-02784-8

Preface

It is our great pleasure to present the proceedings of The 9th International Conference on
Bioinformatics and Biomedical Engineering (iCBBE 2015), held September 18–20, 2015 in
Shanghai, China. We would like to take this opportunity to express our sincere gratitude and
appreciation to all the authors and participants for their support of this conference.
The research on Bioinformatics and Biomedical Engineering has enormous impacts on
science, education, culture and society as well. Actually, the discipline of Bioinformatics and
Biomedical Engineering has become a new focus of life science, mathematical science, com-
puter science and electronic information science. More and more scientists all around the
world are dedicating themselves to this interdisciplinary area, accumulating a lot of interest-
ing results.
We are proud to see that the previous iCBBE conferences were successful in providing an
ideal platform for them to exchange their exciting findings, to stimulate the further develop-
ment of Bioinformatics and Biomedical Engineering, and to enhance its impacts to various
areas of both science and medicine (see, e.g., Medicinal Chemistry, 2015, 11, 218–234). We
believe that the 2015 iCBBE will do even better in this regard.
On behalf of the organizing committee, we would like to take this opportunity to express
our gratitude to the conference’s sponsors: Wuhan University and The Gordon Life Science
Institute.
Our appreciation and gratitude are also extended to all the papers’ reviewers and the Con-
ference Organization Committee members. It is impossible to hold such a grand conference
without their help and support.
The papers collected in the “2015 iCBBE Proceedings” provide the detailed results of some
oral presentations that will be of use to the readership.

Editors
Prof. James J. Chou
Harvard Medical School, USA

Prof. Huaibei Zhou

Wuhan University, China
2015

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 Bioinformatics and Biomedical Engineering – Chou & Zhou (Eds)
© 2016 Taylor & Francis Group, London, ISBN 978-1-138-02784-8

Organization

This volume contains the Proceedings of the 9th International Conference on Bioinformat-
ics and Biomedical Engineering (iCBBE 2015)—held September 18–20, 2015 in Shanghai,
China. iCBBE2015 has been organised by Wuhan University and The Gordon Life Science
Institute.

INTERNATIONAL PROGRAMME COMMITTEE

Honorary General Chair

Prof. Kuo-Chen Chou, The Gordon Life Science Institute, USA

General Chair
Prof. James J. Chou, Harvard Medical School, USA

Technical Program Committee

Prof. Shu Q. Liu, Northwestern University, USA
Prof. Fengfeng Zhou, Chinese Academy of Sciences, China
Prof. Ridha Hambli, Orleans University, France
Dr. Fadhl M. Al-Akwaa, University of Science and Technology, Yemen
Dr. Yu Chen, University of Strathclyde, UK
Prof. Musa Hakan Asyali, Antalya International University, Turkey
Prof. Lukasz Kurgan, University of Alberta, Canada
Prof. Huabei Jiang, University of Florida, USA
Prof. Jerzy Tiuryn, University of Warsaw, Poland
Dr. Joseph Chang, Nanyang Technological University, Singapore
Dr. Mengxing Tang, Imperial College London, UK
Dr. Yanmei Tie, Harvard Medical School, USA
Dr. Manuchehr Soleimani, University of Bath, UK
Prof. Jinn-Moon Yang, National Chiao-Tung University, Chinese Taipei
Dr. Humberto González-Díaz, University of the Basque Country, Spain
Dr. Deligianni Despina, University of Patras, Greece
Dr. Shuwei Li, Ambry Genetics, USA
Dr. Suryani Lukman, Khalifa University of Science, Technology and Research, UAE
Prof. Sheng-Xiang Lin, Laval University Medical Center, Canada
Dr. Wei-Zhu Zhong, The Gordon Life Science Institute, USA
Prof. Rajiv Mahendru, BPS Government Medical College for Women, India
Prof. Zodwa Dlamini, University of South Africa, South Africa

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 LOCAL ORGANIZING COMMITTEE

Fang Liu, Wuhan University, China

Liang Li, Wuhan University, China
Ruoshan Kong, Wuhan University, China
Xiaoyan Sheng, Wuhan University, China
Yuanyuan Cheng, Wuhan University, China
Yujing Zhang, Wuhan University, China

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 Bioinformatics and Biomedical Engineering – Chou & Zhou (Eds)
© 2016 Taylor & Francis Group, London, ISBN 978-1-138-02784-8

Acknowledgements

The Organising Committee members wish to express their sincere gratitude for the finan-
cial assistance from the following organisations: Wuhan University, the Gordon Life Science
Institute and the 1000 Think Tank.
The technical assistance of all paper peer reviewers and the publisher CRC Press/Balkema
is gratefully acknowledged. We are also thankful to the International Programme Commit-
tee as well as the members of the Local Organising Committee. Finally, the editors want to
acknowledge all peer reviewers for their great efforts and contributions to us.

Editors
Prof. James J. Chou
Harvard Medical School, USA

Prof. Huaibei Zhou

Wuhan University, China

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 Bioinformatics and Biomedical Engineering – Chou & Zhou (Eds)
© 2016 Taylor & Francis Group, London, ISBN 978-1-138-02784-8

About the editors

Prof. James J. Chou, Harvard Medical School, USA

James J. Chou is a Professor in Biological Chemistry and Molecular Pharmacology at Har-
vard Medical School. He received his BS in Physics from University of Michigan at Ann
Arbor; Ph.D. in Biophysics from Harvard University; and postdoctoral training from NIH.
Since 2002, he joined the faculty at Harvard Medical School. Professor Chou has received
many prestigious awards such as the Pew Scholar Award in Biomedical Sciences, the Smith
Family Award, and the Genzyme Outstanding Achievement in Biomedical Science Award.

Prof. Huaibei Zhou, Wuhan University, China

Prof. Huaibei Zhou received his B.S. in Radio Wave Propagation and Antenna Design in
Wuhan University, China in 1984; Ph.D. in Computational Physics from the University of
Maryland at College Park and Post-Doc in Biotechnology in the National Institute for Stand-
ard and Technology in 1994; and MBA in Engineering Management from George Washington
University in 2001. Prof. Huaibei Zhou discovered the chaotic motion of protein molecules
by simulating the dynamics of protein molecules in water (the simulation is programmed in
C and run in Unix environment), the result has been published as the first paper in this field;
more than 30 scientists around the world have cited this paper in their publications.

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 Biomacromolecular sequence, structure and function

ICBBE15_Book.indb 1 8/25/2015 7:20:20 AM

 Bioinformatics and Biomedical Engineering – Chou & Zhou (Eds)
© 2016 Taylor & Francis Group, London, ISBN 978-1-138-02784-8

Relationship between homo sapiens histamine receptors using

data mining

S.M. Kim, S.R. Kim & T.S. Yoon

Department of Natural Science, Hankuk Academy of Foreign Studies (HAFS), Yongin, South Korea

ABSTRACT: In this study, we tried to find rules between mRNA sequences of Homo
sapiens histamine receptors H1, H2, H3 and H4 with data mining algorithms, namely Apriori
and Decision tree. In the Apriori algorithm, we split sequences into 5, 7 and 9 windows. The
results showed a strong relationship between the H1 and H4 receptors, and also between the
H2 and H3 receptors. The receptors were divided into two groups according to their compo-
nents. Additionally, we would leave relevancy between the H2 and H3 receptors for another
study with a different data mining algorithm. In the case of the H1 and H4 receptors, we
found that amino acid “F(phenylalanine)” would be a standard to classify the H1 and H4
receptors. We suggest that H4 could be a mutated form of H1. To support our hypothesis, we
conducted an additional experiment with the Decision Tree algorithm, focusing on the exist-
ence of amino acid “F”. The data showed the difference between the H1 and H4 receptors.
In conclusion, the H4 and H1 receptors are related to each other by mutation.

1 INTRODUCTION

Immune system is the system of the animal body that acts as a protection system against
the pathogen from the outer environment. However, there are several diseases caused by
disruptions in immune system functions, such as allergies. Allergies are a result of exagger-
ated and hypersensitive responses to certain antigens called allergens. Antigens of the IgE
class involves in allergic reaction. IgE antibodies are attached to mast cells in connective
tissues by their base. When antigens enter the body, they attach to antigen-binding sites of
IgE antibodies. This connects other antigens near IgE antibodies, causing these antigens to
band together. Mast cells secrete histamines or other inflammation induction substances
from granules. This process is called degranulation. Histamine expands the blood vessel
and increases the permeability of capillaries, which causes typical allergy symptoms such
as sneezing, runny nose, watery eyes and smooth muscle contractions which may lead to
breathing difficulty. Antihistamines blocks histamines from combining to receptor in order
to diminish allergy symptoms (Jane. 2011). Histamine is a type of amine that is produced
and secreted in the animal immune system. It is used in local immune response in order to
cause inflammation. Histamine, which is secreted from mast cells, would bind to its receptor
(histamine receptor). There are four kinds of histamine receptor known in the human body,
which are named H1, H2, H3 and H4. Previously, it was known that histamine receptor 1
(H1) is highly involved in allergic reaction; however, recent studies have shown that hista-
mine receptor 4 (H4) is also involved. It is supposed that there may be some kind of relation-
ships between these two receptors (Thrumond. 2008) (Fung-Leung. 2004). In this study, we
compare the amino acid strand of four types of histamine receptor H1, H2, H3 and H4 by
using an Apriori algorithm and a Decision Tree algorithm in order to see relatedness and
isoforms between the receptors.

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 2 MATERIALS AND METHODS

2.1 Materials
For the experiment, we collected the mRNA sequence of Homo Sapiens histamine receptors
H1 (HRH1)*, H2 (HRH2)**, H3 (HRH3)*** and H4 (HRH4)**** including its transcript
variants. The mRNA sequences used can be found in the NCBI database.

2.2 Methods
To process the data, we used two kinds of algorithms: Apriori and Decision Tree (Lee. 2014)
(Lim. 2014) (Go. 2014).

2.2.1 Apriori algorithm

Apriori algorithm is usually used in data processing and in the field of bioinformatics to find
rules among the continuative data (Kim. 2014). It shows the volume of common parts exist-
ing in the data. By using the Apriori algorithm, we can clearly compare objects with high
frequency in certain data with those found in other data. In this study, 5, 7, and 9 windows
were used to search for amino acid showing high frequency in each data. Also, broken data,
which are rarely found during data processing, were not used in the experiment. This is the
sample of the result of the 5 window Apriori algorithm experiment (Kwon. 2014).

Best rules found:

1. amino5=L 42
2. amino3=L 40
3. amino4=L 35
4. amino1=L 33
5. amino4=S 31
In the example, it showed amino5=L 42 as the first rule. This means that amino acid
L (Leucine, Leu) is the most frequent amino acid in the 5 window as it showed 42 times
repeatedly. Also, statistical compilations focused on the frequency and number of amino acid
appearance instead of its location. According to these data, we constructed a graph in order
to see the data intuitively.

*“Homo sapiens histamine receptor H1 (HRH1), transcript variant 1, mRNA”, NCBI Reference
Sequence: NM_001098213.1 (4,578 bp linear mRNA).
“Homo sapiens histamine receptor H1 (HRH1), transcript variant 2, mRNA”, NCBI Reference
Sequence: NM_001098212.1 (4,298 bp linear mRNA).
“Homo sapiens histamine receptor H1 (HRH1), transcript variant 3, mRNA”, NCBI Reference
Sequence: NM_001098211.1 (4,348 bp linear mRNA).
“Homo sapiens histamine receptor H1 (HRH1), transcript variant 4, mRNA”, NCBI Reference
Sequence: NM_000861.3 (4,427 bp linear mRNA).
**“Homo sapiens histamine receptor H2 (HRH2), transcript variant 1, mRNA”, NCBI Reference
Sequence: NM_001131055.1 (2,624 bp linear mRNA).
“Homo sapiens histamine receptor H2 (HRH2), transcript variant 2, mRNA”, NCBI Reference
Sequence: NM_022304.2 (3,095 bp linear mRNA).
***“Homo sapiens histamine receptor H3 (HRH3), mRNA”, NCBI Reference Sequence: NM_007232.2
(2,680 bp linear mRNA).
****“Homo sapiens histamine receptor H4 (HRH4), transcript variant 1, mRNA”, NCBI Reference
Sequence: NM_021624.3 (3,686 bp linear mRNA).
“Homo sapiens histamine receptor H4 (HRH4), transcript variant 2, mRNA”, NCBI Reference
Sequence: NM_001143828.1 (3,422 bp linear mRNA).
“Homo sapiens histamine receptor H4 (HRH4), transcript variant 3, mRNA”, NCBI Reference
Sequence: NM_001160166.1 (3,522 bp linear mRNA).

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 2.2.2 Decision tree algorithm
While the Apriori algorithm is used to extract the frequency of various amino acids, Deci-
sion Tree is an effective alternative method to show the difference between the data clearly
or definitely (Lim 2014). With the Decision Tree algorithm, isoform data were gathered from
those sequences that were not able to classify with the Apriori algorithm. We determined
that the Decision tree Algorithm is the most appropriate data mining algorithm and well-
ordered lists, which can perform the function of classifying data and finding classes that
represent ability. We compared the histamine receptors H1 and H4, which were expected to
give clear data. We divided into 3 window sizes (5, 7 and 9) and split the data up to 7 classes.
Class 1 to 4 each responds to the Homo sapiens histamine receptor H1 (HRH1) transcript
variant 1 through 4, and class 5 to 7 each responds to the Homo sapiens histamine receptor
H4 (HRH4) transcript variant 1 through 3. In this study, we used a 10-fold cross-validation
method and rule-based classifiers. To retain accuracy, sets of the rules with a frequency over
0.800 in each class were only used to obtain the conclusion.

3 DISCUSSION

3.1 Apriori algorithm

From the result of the Apriori algorithm, we obtained two significant results. The hista-
mine receptors may be divided into two groups by their amino acid, which would put the
H1 and H4 receptors in the same group and the H2 and H3 receptors in the other group.
From Table 1, for each histamine receptor, high frequencies of L (Leucine, Leu) and S
(Serine, Ser) amino acid were found. As these amino acids exist commonly in all receptors,
we defined these two amino acids as a “Basic Group”. In contrast, there were amino acids
that were only found in a certain type of histamine receptors such as A (Alanine, Ala), F
(Phenylalanine, Phe) and G (Glycine, Gly). A and G amino acids were found frequently in
the H2 and H3 receptors; however, F amino acid was only found in the H4 receptor. We
defined these amino acids as an “Additional Group”. We define that “Basic Group” amino
acids would carry out a common function of histamine receptor, while “Additional Group”
amino acids assigns a distinct function to the receptor. According to this definition, we sug-
gest that the H2 and H3 receptors take a similar position in the immune system such as local
inflammation, which differs from the H1 and H4 receptors that takes position in allergy
reaction. As the H1 receptor only has peaks of “Basic Group” amino acids, we would name
the receptor as a type 0 receptor. Also, the H4 receptor is named as type 0` receptor since it
has only one additional amino acid (F) compared with H1 that does not overlap with any
other receptors. As this receptor differs only in F amino acid, we believe this single amino

Figure 1. Graph of HRH1_5,7,9 window.

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