2016 IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE)最新文献_第3页

Fluorescence Microscopy Image Processing and Visualization for Analyzing Cell Kinematics, Proliferation and Attachment in Mouse Embryonic Stem Cell Culture 荧光显微镜图像处理和可视化分析小鼠胚胎干细胞培养细胞运动学、增殖和附着

2016 IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2016-10-01 DOI: 10.1109/BIBE.2016.44

Yuan-Hsiang Chang, H. Yokota, K. Abe, Chih-Cheng Li, Ming-Dar Tsai

{"title":"Fluorescence Microscopy Image Processing and Visualization for Analyzing Cell Kinematics, Proliferation and Attachment in Mouse Embryonic Stem Cell Culture","authors":"Yuan-Hsiang Chang, H. Yokota, K. Abe, Chih-Cheng Li, Ming-Dar Tsai","doi":"10.1109/BIBE.2016.44","DOIUrl":"https://doi.org/10.1109/BIBE.2016.44","url":null,"abstract":"We present an automatic image processing and visualization method to quantitatively analyze kinematics, proliferation and attachment of mouse embryonic stem (mES) cells using time-series confocal time-lapse fluorescence microscopy images. An automatic method is presented to determine the 3D boundary of each cell nucleus in each cell colony. The cells and colonies are then tracked among the time-series images to determine the kinematics, proliferation and attachment of the cells and colonies. The cells and colonies are visualized through a 3D interface, and the kinematics, proliferation and attachment are illustrated in tree structures. The information of cell kinematics, proliferation and attachment indicates how the culturing conditions and cell positions affect the kinematics, proliferation and attachment. The implementation results show that the automatic method can successfully analyze the cell kinematics, proliferation and attachment, thereby yield a potential tool for helping mES cell culture.","PeriodicalId":377504,"journal":{"name":"2016 IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129074631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

ENSPART: An Ensemble Framework Based on Data Partitioning for DNA Motif Analysis 基于数据划分的DNA基序分析集成框架

2016 IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2016-10-01 DOI: 10.1109/BIBE.2016.68

Nung Kion Lee, Allen Chieng Hoon Choong, Norshafrina Omar

{"title":"ENSPART: An Ensemble Framework Based on Data Partitioning for DNA Motif Analysis","authors":"Nung Kion Lee, Allen Chieng Hoon Choong, Norshafrina Omar","doi":"10.1109/BIBE.2016.68","DOIUrl":"https://doi.org/10.1109/BIBE.2016.68","url":null,"abstract":"This paper proposes an ensemble approach based on data partitioning for large-scale DNA motif analysis. Motif prediction using genome-scale dataset is challenging due to high time and space complexity. Existing ensemble approaches, while demonstrated improve performances, are only applicable to small datasets. Our approach called ENSPART first partitions the input dataset into non-overlapping subsets which serve as input to multiple distinct motif prediction tools. It is assumed that the core motifs of a transcription factor protein exists in all data subsets. We employed seven motif prediction tools to obtain initial candidate motifs and they are merged according to their sequence content similarity. An alignment-free method is used to establish motif similarity. A novel motifs merging method is proposed to merge similar motifs obtained by tools in different data partitions. Ten genome-wide ChIP datasets are collected for evaluation. We compare our approach with MEME-ChIP and obtained improved results for nine out of ten of the datasets in terms of Area Under Curve (AUC). Most datasets obtained improved AUC value between 5 to 10%. Our approach shows the promising of data partitioning based ensemble approach for large-scale motif prediction.","PeriodicalId":377504,"journal":{"name":"2016 IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132043899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Influence of Induced Altitude Acclimatization on Development of Acute Mountain Sickness Associated with a Subsequent Rapid Ascent to High Altitude 诱导高原适应对急性高原病发展的影响，并伴有随后的快速上升

2016 IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2016-10-01 DOI: 10.1109/BIBE.2016.41

Xiaomin Luo, Lei Wang, Lei Yang

{"title":"Influence of Induced Altitude Acclimatization on Development of Acute Mountain Sickness Associated with a Subsequent Rapid Ascent to High Altitude","authors":"Xiaomin Luo, Lei Wang, Lei Yang","doi":"10.1109/BIBE.2016.41","DOIUrl":"https://doi.org/10.1109/BIBE.2016.41","url":null,"abstract":"Objective: Ascent to high altitudes requires adaptation to a hypoxic and hypobaric environment. Induced altitude acclimatization may decrease susceptibility to acute mountain sickness (AMS). We aimed to exam the effects of acclimatization at 1520m on susceptibility to AMS during a subsequent rapid ascent to 3658m. Methods: Rate pressure product (RPP), oxygen saturation (SpO2) and vascular tone, quantified by the reflection index (RI) obtained using photoplethysmography (PPG) technique, were studied in fifty-five participants ascending to 3658m from 300 and 1520m defined as Group A and B respectively. AMS occurrence was evaluated by the Lake Louise Score (LLS) system. Results: Seventeen of the fifty-five participants were diagnosed with AMS. The incidence and severity were lower in Group B than Group A. On initial exposure, we observed a significant increase of RPP and a significant decrease of SpO2. Inside each group, either A or B, RI exhibited a quick and dramatic fall followed by an early recovery back to normal in subjects without AMS but a blunted and slow fall followed by a delayed recovery in subjects with AMS. A moderate level of inverse correlation was found between degree of fall (Δ) in SpO2 and RI within 24 hours. Conclusions: The induced altitude acclimatization provided low-altitude residents in certain degree benefit in prevention of AMS during a subsequent rapid ascent to high altitude. The comparison of data between participants with and without an induced altitude acclimatization exhibited physiological significance during acute phase response after a rapid ascend to altitude.","PeriodicalId":377504,"journal":{"name":"2016 IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115730935","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Deep Learning for Risk Analysis of Specific Cardiovascular Diseases Using Environmental Data and Outpatient Records 使用环境数据和门诊记录进行特定心血管疾病风险分析的深度学习

2016 IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2016-10-01 DOI: 10.1109/BIBE.2016.75

H. Hsiao, Sean H. F. Chen, J. Tsai

引用次数: 15

Identifying Obstructive Sleep Apnea by Exploiting Fine-Grained BCG Features Based on Event Phase Segmentation 基于事件相位分割的细粒度BCG特征识别阻塞性睡眠呼吸暂停

2016 IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2016-10-01 DOI: 10.1109/BIBE.2016.45

Fan Liu, Xingshe Zhou, Zhu Wang, Tianben Wang, Hongbo Ni, Jun Yang

{"title":"Identifying Obstructive Sleep Apnea by Exploiting Fine-Grained BCG Features Based on Event Phase Segmentation","authors":"Fan Liu, Xingshe Zhou, Zhu Wang, Tianben Wang, Hongbo Ni, Jun Yang","doi":"10.1109/BIBE.2016.45","DOIUrl":"https://doi.org/10.1109/BIBE.2016.45","url":null,"abstract":"Obstructive sleep apnea (OSA) is regarded as one of the most common sleep-related breathing disorders, which causes various diseases and affects people's daily life severely. Up to now, massive efforts have been devoted to identifying OSA events during sleep based on different signals (e.g., PSG, ECG, nasal airflow and EMG, etc.). However, there still are more or less shortcomings in current studies. In this paper, we propose a novel framework to improve the performance of identifying OSA events. Particularly, the key idea of our framework is to divide each potential event segment (i.e., a data segment that may or may not contain an OSA event) into different phases, from which we further extract fine-grained features to characterize respiratory pattern comprehensively. Concretely, we first automatically locate potential event segments from raw ballistocardiography (BCG) data by identifying arousals. Afterwards, each potential event segment is divided into three phases (i.e., Apnea Phase, Respiratory Effort Phase and Arousal Phase) by an adaptive threshold-based division algorithm. Based on these phases, we further extract and select efficient features that can characterize respiratory pattern from different aspects. Finally, these potential event segments are classified into OSA events or non-OSA events using BP neural network. Experimental results based on a real BCG dataset that contains 3,790 OSA events and 2,556 non-OSA events show that our framework outperforms the baselines and the precision, recall and AUC reach 94.6%, 93.1%, and 0.951, respectively.","PeriodicalId":377504,"journal":{"name":"2016 IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"24 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115051135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 20

Framework for Rapid Development of Embedded Human-in-the-Loop Cyber-Physical Systems 嵌入式人在环网络物理系统快速开发框架

2016 IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2016-10-01 DOI: 10.1109/BIBE.2016.24

Shen Feng, F. Quivira, G. Schirner

{"title":"Framework for Rapid Development of Embedded Human-in-the-Loop Cyber-Physical Systems","authors":"Shen Feng, F. Quivira, G. Schirner","doi":"10.1109/BIBE.2016.24","DOIUrl":"https://doi.org/10.1109/BIBE.2016.24","url":null,"abstract":"Human-in-the-Loop Cyber-Physical Systems (HiLCPS) offers assistive technology that augments human interaction with the physical world, such as self-feeding, communication and mobility for functionally locked-in individuals. HiLCPS applications are typically implemented as networked embedded systems interfacing both human and the physical environment. Developing HiLCPS applications is challenging due to interfacing with hardware with different specifications and physical location (local/remote). Also, while algorithm designers prototype applications in MATLAB benefiting from an algorithm design environment, the gap from prototyping MATLAB application to embedded solution traditionally requires significant manual implementation. In this paper, we propose a HiLCPS Framework for the rapid development of embedded HiLCPS applications. The framework groups similar hardware types to classes, unifying their access and with this offering both hardware and location transparent access. The framework furthermore incorporates a domain-specific synthesis tool, called Hsyn. Hsyn empowers algorithm designers to prototype a portable, hardware-agnostic application in MATLAB while offering an automatic path to embedded deployment without requiring embedded knowledge. We demonstrate the benefit of the framework with a brain-controlled wheelchair application prototyped in MATLAB that transparently accesses a variety of EEG acquisition systems with local or remote connections. Then, by using Hsyn, the application is automatically deployed to a BeagleBone Black equipped with a custom-designed electrophysiological acquisition cape. Hsyn shows six orders of magnitude of productivity gain compared to manual embedded deployment. The wheelchair performs stepwise navigated based on human intent inference with 91% accuracy at 0.9 confidence threshold every 4 seconds on average over 9 users.","PeriodicalId":377504,"journal":{"name":"2016 IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"40 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134125505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 17

An Ensemble Based in Silico Prediction of Saccharomyces Cerevisiae Proteins under Mitochondrion Organization 线粒体组织下酿酒酵母蛋白质的集成预测

2016 IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2016-10-01 DOI: 10.1109/BIBE.2016.61

D. Sumanaweera, Amal Perera

引用次数: 0

Computation of Pharmacologic Therapy Effects on Cognitive Abilities of Alzheimer’s Disease Patients 药物治疗对阿尔茨海默病患者认知能力影响的计算

2016 IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2016-10-01 DOI: 10.1109/BIBE.2016.49

Aydin Saribudak, Adarsha A. Subick, M. U. Uyar

{"title":"Computation of Pharmacologic Therapy Effects on Cognitive Abilities of Alzheimer’s Disease Patients","authors":"Aydin Saribudak, Adarsha A. Subick, M. U. Uyar","doi":"10.1109/BIBE.2016.49","DOIUrl":"https://doi.org/10.1109/BIBE.2016.49","url":null,"abstract":"To explore the impact of pharmacologic therapies on cognitive changes of Alzheimer's disease (AD) patients, we develop an artificial intelligence (AI) based personalized relevance parameterization method, called PReP-AD-PH. Expressions of genes, which are effective in AD related protein biomarkers, and mini mental state examination (MMSE) scores of AD patients in mild cognitive impairment (MCI) stage are inputs for PReP-AD-PH. In this study, AD patients in MCI stage are split into two groups, such that the first group has 81 patients given monotherapy with cholinesterase inhibitor (ChEI) donepezil and the second with 70 patients received combinational therapy with donepezil and memantine. PReP-AD-PH computes parameters characterizing the cognitive changes in AD patients with MCI. Using a leave-one-out-cross-validation (LOOCV) based algorithm, we measure an average LOOCV error rate of 6.53% for patients received donepezil monotherapy, and 8.05% for those under combinational therapy. Cumulative distribution of LOOCV error rates of PReP-AD-PH results points out that AI based computation methods can be useful in assisting clinicians with pharmacologic therapy decisions for AD patients with MCI.","PeriodicalId":377504,"journal":{"name":"2016 IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114218329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

piRNAtarget: The Integrated Database for Mining Functionality of piRNA and Its Targets piRNAtarget:用于挖掘piRNA及其目标功能的集成数据库

2016 IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2016-10-01 DOI: 10.1109/BIBE.2016.64

B. Jiang, Wanyi Wu, Ching-Hsuan Chien, J. Tsai, Wen-Ling Chan

引用次数: 3

Psycho-Physiological Response in 3D Multiple Object Tracking 三维多目标跟踪中的心理生理反应

2016 IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2016-10-01 DOI: 10.1109/BIBE.2016.50

Shuichi Satake, H. Hagiwara

引用次数: 0