2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE)最新文献_第3页

Back translated peptide K-mer search and local alignment in large DNA sequence databases using BoND-SD-tree indexing 使用BoND-SD-tree索引在大型DNA序列数据库中进行反向翻译肽K-mer搜索和局部比对

2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2015-11-02 DOI: 10.1109/BIBE.2015.7367638

A. T. Islam, S. Pramanik, Xinge Ji, J. Cole, Qiang Zhu

{"title":"Back translated peptide K-mer search and local alignment in large DNA sequence databases using BoND-SD-tree indexing","authors":"A. T. Islam, S. Pramanik, Xinge Ji, J. Cole, Qiang Zhu","doi":"10.1109/BIBE.2015.7367638","DOIUrl":"https://doi.org/10.1109/BIBE.2015.7367638","url":null,"abstract":"In the past, genome sequence databases had used main memory indexing, such as the suffix tree, for fast sequence searches. With next generation sequencing technologies, the amount of sequence data being generated is huge and main memory indexing is limited by the amount of memory available. K-mer based techniques are being more used for various genome sequence database applications such as local alignment. K-mer can also provide an excellent basis for creating efficient disk based indexing. In this paper, we have proposed a k-mer based database searching and local alignment tool using box queries on BoND-SD-tree indexing. BoND-tree is quite efficient for indexing and searching in Non-Ordered Discrete Data Space (NDDS). We have conducted experiments on searching DNA sequence databases using back translated protein query sequences and have compared with existing methods. We have also implemented local alignment of back translated protein query sequences with large DNA sequence databases using this index based k-mer search. Performances of this local alignment approach has been compared with that of Tblastn of NCBI. The results are quite promising and justify significance of the proposed approach.","PeriodicalId":422807,"journal":{"name":"2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"58 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131317072","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: 6

Appearance-based necrosis detection using textural features and SVM with discriminative thresholding in histopathological whole slide images 基于纹理特征和支持向量机的组织病理学整张切片图像坏死检测

2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2015-11-02 DOI: 10.1109/BIBE.2015.7367702

H. Sharma, N. Zerbe, I. Klempert, Sebastian Lohmann, B. Lindequist, O. Hellwich, P. Hufnagl

{"title":"Appearance-based necrosis detection using textural features and SVM with discriminative thresholding in histopathological whole slide images","authors":"H. Sharma, N. Zerbe, I. Klempert, Sebastian Lohmann, B. Lindequist, O. Hellwich, P. Hufnagl","doi":"10.1109/BIBE.2015.7367702","DOIUrl":"https://doi.org/10.1109/BIBE.2015.7367702","url":null,"abstract":"Automatic detection of necrosis in histological images is an interesting problem of digital pathology that needs to be addressed. Determination of presence and extent of necrosis can provide useful information for disease diagnosis and prognosis, and the detected necrotic regions can also be excluded before analyzing the remaining living tissue. This paper describes a novel appearance-based method to detect tumor necrosis in histopathogical whole slide images. Studies are performed on heterogeneous microscopic images of gastric cancer containing tissue regions with variation in malignancy level and stain intensity. Textural image features are extracted from image patches to efficiently represent necrotic appearance in the tissue and machine learning is performed using support vector machines followed by discriminative thresholding for our complex datasets. The classification results are quantitatively evaluated for different image patch sizes using two cross validation approaches namely three-fold and leave one out cross validation, and the best average cross validation rate of 85.31% is achieved for the most suitable patch size. Therefore, the proposed method is a promising tool to detect necrosis in heterogeneous whole slide images, showing its robustness to varying visual appearances.","PeriodicalId":422807,"journal":{"name":"2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131950434","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: 11

Numerical modeling of the edentulous mandible with different mucosa thickness and resiliency using multiblock method 不同黏膜厚度和弹性的无牙下颌骨多块法数值模拟

2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2015-11-02 DOI: 10.1109/BIBE.2015.7367710

M. Blagojevic, J. Eric, M. Zivkovic, Ljiljana D. Tihacek Sojic

{"title":"Numerical modeling of the edentulous mandible with different mucosa thickness and resiliency using multiblock method","authors":"M. Blagojevic, J. Eric, M. Zivkovic, Ljiljana D. Tihacek Sojic","doi":"10.1109/BIBE.2015.7367710","DOIUrl":"https://doi.org/10.1109/BIBE.2015.7367710","url":null,"abstract":"In spite of numerous studies on biomechanics of the mucous membrane supported dentures, satisfactory determination of the mucous membrane loads is still lacking. The aim of this study was to evaluate the effect of different mucosa thickness and resiliency on stress distribution of complete denture using a three-dimensional finite element analysis. A edentulous mandible with complete denture was converted into a numerical model based on 3D measurements performed by an advanced topometric sensor digitizer (ATOS). This model was transformed into the desired coordinate system and resilient layers were modeled. In each group, mucosa assumed three characteristics of thickness (1, 3 and 5 mm) corresponding to the resiliencies hard, resilient and soft respectively. Evaluation was performed on NASTRAN software with 300N vertical load applied on central incisor teeth. The analyses were based on the maximum and minimum principal stress and displacement values in the supporting tissues. In this study, it was observed that stress decreased at the supporting tissues as mucosa thickness and resiliency increased. The total displacement values increased as the thickness and resiliency of mucosa increased for all structures. Based on the numerical results, the maximum stress values were concentrated in cortical bone.","PeriodicalId":422807,"journal":{"name":"2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"55 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121079438","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: 0

A Kalman-based encoder for electrical stimulation modulation in a thalamic network model 一种基于卡尔曼的丘脑网络模型电刺激调制编码器

2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2015-11-02 DOI: 10.1109/BIBE.2015.7367642

A. Jawwad, Hossam H. Abolfotuh, Bassem A. Abdullah, Hani M. K. Mahdi, S. Eldawlatly

{"title":"A Kalman-based encoder for electrical stimulation modulation in a thalamic network model","authors":"A. Jawwad, Hossam H. Abolfotuh, Bassem A. Abdullah, Hani M. K. Mahdi, S. Eldawlatly","doi":"10.1109/BIBE.2015.7367642","DOIUrl":"https://doi.org/10.1109/BIBE.2015.7367642","url":null,"abstract":"Restoring vision is no longer impossible as a result of recent advances in neural interfaces. Successful demonstrations of retinal implants motivate the development of more effective visual prostheses. The thalamic Lateral Geniculate Nucleus (LGN) is one potential deep-brain interfacing site for visual prostheses. A main challenge in developing thalamic as well as other visual prostheses is optimizing the parameters of electrical stimulation. This paper introduces a Kalman-based optimal encoder whose function is to determine the optimal electrical stimulation parameters required to induce a certain visual sensation. The performance of the proposed approach is demonstrated using a probabilistic model of LGN neurons. Results demonstrate a significant similarity between neuronal responses obtained using electrical stimulation and the responses obtained using the corresponding visual stimuli with a mean correlation of 0.62 (P <; 0.01, n = 54). These results indicate the efficacy of the proposed optimal encoder in driving LGN neurons to induce visual sensations.","PeriodicalId":422807,"journal":{"name":"2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"38 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116688749","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: 3

Metal-enhanced radiotherapy: Gold nanoparticles and beyond 金属增强放射治疗:金纳米粒子及其他

2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2015-11-02 DOI: 10.1109/BIBE.2015.7367636

B. Jeremic, N. Filipovic, Francese Casas, N. Cihoric, T. Djukić

引用次数: 1

A hierarchical neural network for predicting protein functions 预测蛋白质功能的层次神经网络

2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2015-11-02 DOI: 10.1109/BIBE.2015.7367651

J. C. Nievola, E. Paraiso, A. Freitas

{"title":"A hierarchical neural network for predicting protein functions","authors":"J. C. Nievola, E. Paraiso, A. Freitas","doi":"10.1109/BIBE.2015.7367651","DOIUrl":"https://doi.org/10.1109/BIBE.2015.7367651","url":null,"abstract":"This paper introduces the use of a modified feedforward neural network to cope with the problem of predicting protein functions. Since this kind of classification task is inherently hierarchical, this work proposes the use of two different architectures for the modified feedforward neural network, both mimicking the hierarchical nature of the classes (protein functions) to be predicted. The first approach consists of four feed-forward neural networks in cascade, each one taking as input the classification obtained by the previous network, which means, the input to a network is the classes that could be assigned to the protein at the immediately higher (parent) level in the class hierarchy. The second approach is an extension of the first one, which also adds as input to each sub-network the attributes of the protein being classified. In both situations, it was used two kinds of feed-forward architectures: an Adaline network, which is composed of a single layer of adjustable weights, and a MLP (\"Multi-Layer Perceptron\"), composed by two layers of adjustable weights. Both approaches were compared with a baseline consisting of a single MLP that maps the input attributes to the classes of the lowest level in the hierarchy. The MLP was built with the input layer, plus one hidden layer and one output layer. The three approaches were compared on eight datasets, the first four involving the prediction of GPCR (G-Protein Coupled Receptor) functions and the second four datasets involving the prediction of enzymes functions. The results show that a big-bang hierarchical neural network, based on the MLP paradigm, using a top-down evaluation for new instances has better behavior in hierarchical problems, when compared to its flat version.","PeriodicalId":422807,"journal":{"name":"2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"40 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123355720","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

Using force plate, computer simulation and image alignment in jumping analysis 采用测力板、计算机模拟和图像对准等方法进行跳变分析

2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2015-11-02 DOI: 10.1109/BIBE.2015.7367672

N. Mijailovic, R. Radakovic, A. Peulić, I. Milankovic, N. Filipovic

引用次数: 3

The reliability of motion analysis of elite soccer players during match measured by the Tracking Motion software system 用运动跟踪软件系统测量了优秀足球运动员在比赛中运动分析的可靠性

2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2015-11-02 DOI: 10.1109/BIBE.2015.7367676

R. Radakovic, M. Dopsaj, Radun Vulović, B. Leontijević, N. Mijailovic, N. Filipovic

引用次数: 3

Customized anatomically adjusted plate for fixation of mandible internal fractures 定制解剖调整钢板固定下颌骨内骨折

2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2015-11-02 DOI: 10.1109/BIBE.2015.7367668

M. Manic, Z. Stamenkovic, N. Vitković, M. Stojković, M. Trajanovic, J. Mitic, Sladjana Petrovic

{"title":"Customized anatomically adjusted plate for fixation of mandible internal fractures","authors":"M. Manic, Z. Stamenkovic, N. Vitković, M. Stojković, M. Trajanovic, J. Mitic, Sladjana Petrovic","doi":"10.1109/BIBE.2015.7367668","DOIUrl":"https://doi.org/10.1109/BIBE.2015.7367668","url":null,"abstract":"Mandible internal fractures are a common injury because of the mandible's lack of structural support. For the treatment of such injuries various fixation elements are used. In order to improve quality of the orthodontists interventions anatomically correct and geometrically accurate customized implants are necessary. In this paper an example of accurate geometrical model of the customized plate implant for the fixation of mandible fracture is presented. For the creation of such model new method has been developed. This method is based on reverse engineering techniques applied on the CT scan of the specific patient mandible. With the application of this method it is possible to create geometrical model of the customized plate implant which geometry and topology conforms to the shape of the mandible of the specific patient. The side of the implant, which is in contact with a periosteum outer layer of the mandible, is fully aligned with the shape of the mandible outer surface near the fracture. The obtained model(s) can be used for production of plate implants, and/or for simulation of orthodontist interventions.","PeriodicalId":422807,"journal":{"name":"2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129830409","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

Biofeedback in sport: Challenges in real-time motion tracking and processing 运动中的生物反馈:实时运动跟踪和处理的挑战

2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2015-11-02 DOI: 10.1109/BIBE.2015.7367681

A. Kos, A. Umek, S. Tomažič

引用次数: 4