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2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops最新文献

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A novel acupuncture for killing lumbago: Immediate effects of balancing acupuncture for acute lumbar disc herniation 一种治疗腰痛的新针灸:平衡针灸治疗急性腰椎间盘突出症的即时效果
Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470356
Xiaohong Xu, Shudong Chen, Xiaoling Xu
[Purpose] This study aimed to evaluate the immediate effects of Balancing acupuncture as adjuvant therapy for patients with acute lumbar disc herniation (ALDH). [Method] We recruited 47 patients with ALDH in Orthopedic therapy center of Guangdong Provincial Hospital of Chinese Medicine in China. McGill pain questionnaire (MPQ) and clinical effects of Balancing acupuncture were measured. [Results] We found that no case showed clinical cure, 42 cases showed improvement, while 5 cases showed ineffectiveness, indicating an improvement rate of 89.4%. Immediate MPQ total score after Balancing acupuncture was lower than before treatment, which showed a statistical significance between them (P=0.0000<;0.05). Differences in PRI, VAS, and PPI reached statistical significance (P<;0.05). A statistically significant difference was found in Pain perception score before and after treatment (P=0.0125<;0.05), while pain emotion score failed to reach statistical significance (P=0.6983>0.05). [Conclusions] The results suggested that Balancing acupuncture may lead to immediate benefits for patients with ALDH.
【目的】本研究旨在评价平衡针刺辅助治疗急性腰椎间盘突出症(ALDH)的即时效果。[方法]选取广东省中医院骨科治疗中心的ALDH患者47例。测量McGill疼痛问卷(MPQ)和平衡针刺的临床效果。【结果】临床无治愈病例,好转42例,无效5例,改善率89.4%。平衡针刺后即刻MPQ总分低于治疗前,差异有统计学意义(P=0.00000.05)。[结论]结果提示,平衡针刺可使ALDH患者立即获益。
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引用次数: 0
Joint clustering and alignment for nucleosome occupancy analysis 核小体占用分析的联合聚类和排列
Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470269
Teng L. Liu, Yu Zhang, J. Dennis
Several studies show that nucleosome occupancy patterns around transcription starting sites provide evolutionary and regulatory information about genes. However, as transcription starting sites may not accurately reflect physical nucleosome occupancy patterns, clustering of nucleosome occupancy patterns centered at transcription starting sites may give rise to inaccurate and blurred cluster centers, leading to potentially inaccurate conclusions. In this paper, we propose a joint clustering and alignment method and apply it to clustering of nucleosome occupancy patterns around transcription starting sites. The experimental results using the human genome-wide data show that alignment affects the significant majority of genes and leads to more pronounced local nucleosome occupancy patterns.
一些研究表明,转录起始位点周围的核小体占用模式提供了基因的进化和调控信息。然而,由于转录起始位点可能不能准确反映核小体的物理占用模式,以转录起始位点为中心的核小体占用模式聚类可能会产生不准确和模糊的聚类中心,从而导致可能不准确的结论。在本文中,我们提出了一种联合聚类和比对方法,并将其应用于转录起始位点周围核小体占用模式的聚类。使用人类全基因组数据的实验结果表明,比对影响了绝大多数基因,并导致更明显的局部核小体占用模式。
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引用次数: 0
A basin hopping algorithm for protein-protein docking 一种蛋白质-蛋白质对接的跳盆算法
Pub Date : 2012-10-04 DOI: 10.1109/BIBM.2012.6392725
I. Hashmi, Amarda Shehu
We present a novel probabilistic search algorithm to efficiently search the structure space of protein dimers. The algorithm is based on the basin hopping framework that repeatedly follows up structural perturbation with energy minimization to obtain a coarse-grained view of the dimeric energy surface in terms of its local minima. A Metropolis criterion biases the search towards lower-energy minima over time. Extensive analysis highlights efficient and effective implementations for the perturbation and minimization components. Testing on a broad list of dimers shows the algorithm recovers the native dimeric configuration with great accuracy and produces many minima near the native configuration. The algorithm can be employed to efficiently produce relevant decoys that can be further refined at greater detail to predict the native configuration.
提出了一种新的概率搜索算法,以有效地搜索蛋白质二聚体的结构空间。该算法基于盆地跳跃框架,反复跟踪结构扰动与能量最小化,以获得二聚体能量表面的局部最小值的粗粒度视图。随着时间的推移,Metropolis标准倾向于寻找更低能量的最小值。广泛的分析强调了对扰动和最小化组件的高效和有效的实现。在广泛的二聚体列表上的测试表明,该算法以很高的精度恢复了二聚体的原始构型,并在原始构型附近产生了许多最小值。该算法可以有效地产生相关的诱饵,这些诱饵可以在更大的细节上进一步细化以预测本地配置。
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引用次数: 10
Recognizing drosha processing sites by a two-step prediction model with structure and sequence information 基于结构和序列信息的两步预测模型识别drosha加工位点
Pub Date : 2012-10-04 DOI: 10.1109/BIBM.2012.6392714
Xingchi Hu, Yanhong Zhou, Chuang Ma
Drosha is a class of RNase III enzyme plays important roles in the microRNA (miRNA) generation by cleaving primary miRNAs to release hairpin-shaped miRNA precursors. Accurately predicting the Drosha cleavage positions (i.e., processing sites) is helpful for the identification of miRNAs and the understanding of miRNA biogenesis mechanisms. In this study, we presented a Drosha processing site predictor, termed DroshaPSP, with a two-step prediction model by integrating structure and sequence features. Testing results on the Drosophila melanogaster miRNA data showed that DroshaPSP obtained a sensitivity of 0.859, a specificity of 0.999, and a Matthew's Correlation Coefficient of 0.864. We also found that the Shannon entropy is a powerful structure feature for DroshaPSP to distinguish true Drosha processing sites from the nearby pseudo processing sites effectively.
Drosha是一类RNase III酶,通过切割初级miRNA释放发夹状miRNA前体,在microRNA (miRNA)的生成中起重要作用。准确预测Drosha切割位置(即加工位点)有助于miRNA的鉴定和对miRNA生物发生机制的理解。在这项研究中,我们提出了一个Drosha加工位点预测器,称为DroshaPSP,具有两步预测模型,通过整合结构和序列特征。对黑腹果蝇miRNA数据的检测结果显示,DroshaPSP敏感性为0.859,特异性为0.999,马修相关系数为0.864。我们还发现Shannon熵是一个强大的结构特征,可以有效地区分真正的Drosha处理点和附近的伪处理点。
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引用次数: 1
A new greedy heuristic for 3DHP protein struture prediction with side chain 带侧链的3DHP蛋白结构预测贪心启发式算法
Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470229
L. C. Galvao, L. Nunes, H. S. Lopes, P. Moscato
In spite of the fact that many models of protein structure prediction have been proposed and have also been widely studied in the last years, little attention has been given to the discrete models with side chains. Few papers present algorithms that try to predict the 3 dimensional structures of protein from their amino acid sequences represented by a backbone and the side chains (hydrophobic or hydrophilic). In this paper, we propose a new greedy heuristic with a pull-move set for finding these structures to the 3DHP-SC model, i.e. for a three-dimensional model on a cubic lattice, with side chains. To demonstrate the performance of our method, we have used 25 benchmark instances from the literature. For the instances tested, the proposed technique matched the best known results for 12 instances and obtained better results for the other 13. The computational resources that we have used have been relatively limited in comparison with other studies in the literature, and the quality of our results shows the potential of the approach both in terms of quality and total computation time.
尽管近年来人们提出了许多蛋白质结构预测模型并对其进行了广泛的研究,但对带有侧链的离散模型的关注却很少。很少有论文提出算法,试图预测蛋白质的三维结构,从它们的氨基酸序列表示的主链和侧链(疏水或亲水)。在本文中,我们提出了一种新的贪心启发式算法,用于寻找3DHP-SC模型的这些结构,即在立方晶格上的三维模型,具有侧链。为了演示我们方法的性能,我们使用了文献中的25个基准实例。对于测试的实例,所建议的技术与12个实例的最佳结果相匹配,并在另外13个实例中获得更好的结果。与文献中的其他研究相比,我们使用的计算资源相对有限,我们结果的质量显示了该方法在质量和总计算时间方面的潜力。
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引用次数: 3
Prof. Liu Jinwen's experience on treating knee osteoarthritis 刘金文教授治疗膝关节骨关节炎的经验
Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470347
Jian Li, D. Guo, Liu Jinwen, Jian-ke Pan, Lufeng Huang, Jun Liu
Liu Jinwen is Professor of Guangzhou University of Chinese Medicine of Traditional Chinese medicine bone-setting professional doctoral tutor and postdoctoral supervisor, one of the veteran TCM experts of Guangdong Province. Former director of the department of orthopedics of Guangdong Provencal Hospital of TCM. Over the past 50 years, Professor Liu Jensen has been engaged in research on prevention and treatment of bone and joint degenerative diseases of TCM and expert in theory of TCM research. He always emphasized on the prevention and treatment of diseases in clinical practice to follow the overall concept, principle of correspondence between man and universe and treatment based on syndrome differentiation. Knowledge about osteoarthritis of the knee, in his view, is not just a local issue, but overall to reflect local, and stresses therefore that on the treatment measures must be taken to proceed from the overall, good results can be achieved, overall is strengthening healthy Qi, conditioning of yin and Yang to restore homeostasis.
刘金文,广州中医药大学教授,中医正骨专业博士生导师、博士后导师,广东省资深中医专家之一。广东省普罗旺斯省中医院骨科原主任。50多年来,刘延森教授一直从事中医防治骨关节退行性疾病的研究,是中医研究理论的专家。在临床实践中,他始终强调疾病的预防和治疗,遵循总体观念、天人对应原则和辨证论治。关于膝关节骨性关节炎的知识,在他看来,不只是局部问题,而是整体要反映局部,因此强调在治疗措施上一定要从整体出发,才能取得良好的效果,整体上就是加强正气,调理阴阳,恢复体内平衡。
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引用次数: 1
ENISI Visual, an agent-based simulator for modeling gut immunity ENISI Visual,一个基于代理的模拟肠道免疫的模拟器
Pub Date : 2012-10-04 DOI: 10.1109/BIBM.2012.6392624
Yongguo Mei, R. Hontecillas, Xiaoying Zhang, K. Bisset, S. Eubank, S. Hoops, M. Marathe, J. Bassaganya-Riera
This paper presents ENISI Visual, an agent-based simulator for modeling gut immunity to enteric pathogens. Gastrointestinal systems are important for in-taking food and other nutritions and gut immunity is an important part of human immune system. ENISI Visual provides quality visualizations and users can control initial cell concentrations and the simulation speed, take snapshots, and record videos. The cells are represented with different icons and the icons change colors as their states change. Users can observe real-time immune responses, including cell recruitment, cytokine and chemokine secretion and dissipation, random or chemotactic movement, cell-cell interactions, and state changes. The case study clearly shows that users can use ENISI Visual to develop models and run novel and insightful in silico experiments.
本文介绍了ENISI Visual,一个基于agent的模拟肠道对肠道病原体免疫的模拟器。胃肠道系统是人体吸收食物和其他营养的重要系统,肠道免疫是人体免疫系统的重要组成部分。ENISI Visual提供高质量的可视化,用户可以控制初始细胞浓度和模拟速度,拍摄快照和录制视频。单元格用不同的图标表示,图标会随着状态的变化而改变颜色。用户可以实时观察免疫反应,包括细胞募集、细胞因子和趋化因子的分泌和消散、随机或趋化运动、细胞间相互作用和状态变化。案例研究清楚地表明,用户可以使用ENISI Visual来开发模型并运行新颖而富有洞察力的计算机实验。
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引用次数: 18
Chemogenomic approach to comprehensive predictions of ligand-target interactions: A comparative study 综合预测配体-靶标相互作用的化学基因组学方法:一项比较研究
Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470295
J. B. Brown, S. Niijima, A. Shiraishi, M. Nakatsui, Y. Okuno
Chemogenomics has emerged as an interdisciplinary field that aims to ultimately identify all possible ligands of all target families in a systematic manner. An ever-increasing need to explore the vast space of both ligands and targets has recently triggered the development of novel computational techniques for chemogenomics, which have the potential to play a crucial role in drug discovery. Among others, a kernel-based machine learning approach has attracted increasing attention. Here, we explore the applicability of several ligand-target kernels by extensively evaluating the prediction performance of ligand-target interactions on five target families, and reveal how different combinations of ligand kernels and protein kernels affect the performance and also how the performance varies between the target families.
化学基因组学已经成为一个跨学科的领域,其目的是最终确定所有目标家族的所有可能的配体以系统的方式。近年来,对探索配体和靶标广阔空间的需求不断增加,这引发了化学基因组学新计算技术的发展,这些技术有可能在药物发现中发挥关键作用。其中,基于核的机器学习方法引起了越来越多的关注。本文通过广泛评估配体-靶标相互作用在5个靶标家族上的预测性能,探讨了几种配体-靶标核的适用性,揭示了配体核和蛋白核的不同组合对预测性能的影响,以及不同靶标家族的预测性能差异。
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引用次数: 5
Phylogenetic analysis of some leguminous trees using CLUSTALW2 bioinformatics tool 利用CLUSTALW2生物信息学工具分析豆科树木的系统发育
Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470264
Sagar Patel, H. Panchal, K. Anjaria
A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally for Protein. MSA has wide range of applications and to cite few of them such as phylogenetic analysis, protein pattern identification, protein domain identification, prediction of protein structure, structural similarity of amino acids and to get evolutionary similarity. ClustalW2 is a general purpose global multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. The output from ClustalW2 shows the best match for the selected sequences and lines up them in such a way that the identities, similarities and differences can be easily understood. Evolutionary relationships can be seen by creating Cladograms or Phylograms. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. In this paper, protein sequences of few legume species from UNIPROT database were taken and focused on MSA for protein sequences for these tree species of family Leguminosae, where ClustalW2 tool have used to generate biological data. The results are discussed with the help of Cladograms and Phylograms for selected tree species.
多序列比对(multiple sequence alignment, MSA)是对三个或更多生物序列的比对,通常用于蛋白质。MSA具有广泛的应用,在系统发育分析、蛋白质模式鉴定、蛋白质结构域鉴定、蛋白质结构预测、氨基酸结构相似性以及获得进化相似性等方面都有广泛的应用。ClustalW2是一个通用的蛋白质全局多序列比对程序。它产生具有生物学意义的不同序列的多序列比对。ClustalW2的输出显示了所选序列的最佳匹配,并以一种易于理解的同一性、相似性和差异性的方式将它们排列起来。进化关系可以通过创建枝状图或系统图来观察。首先,对部分比对的序列赋予单独的权值,降低近重复序列的权值,提高差异最大的序列的权值;其次,在不同的比对阶段,氨基酸取代矩阵根据待比对序列的差异而变化。第三,残基特异性间隙惩罚和亲水区域局部减少的间隙惩罚鼓励潜在环区域产生新的间隙,而不是规则的二级结构。第四,在已经打开缺口的早期队列中的位置,当地会减少缺口处罚,以鼓励在这些位置上打开新的缺口。本文选取UNIPROT数据库中少数豆科植物的蛋白质序列,利用ClustalW2工具对这些豆科植物的蛋白质序列进行MSA分析。通过对所选树种的枝状图和系统图进行了讨论。
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引用次数: 13
The mechanism of acupuncture for obsessive-complusive disorder on TCM heart-gallbladder concept 针刺治疗强迫症的中医心胆观机制探讨
Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470328
Nipeng Lin, Changeai Xie, Xiaohong Xu, W. Fu
Obsessive-compulsive disorder (obsessive - compulsive disorder) is a neurotic mental disorders characterized by the uncontrolled obsessions and compulsive behavior. Patients know that the continued obsessive-compulsive symptoms are pointless and unreasonable, but can not get rid of it. Therefore they feel very nervous and suffering. Acupuncture for obsessive - compulsive disorder guided by TCM Heart and Gall Theory can improve the blood supply in brain, adjust the HPA function, regulate immune function, bidirectionally regulate the release of SP and affect the metabolism of NE. Hence, the efficacy and effectiveness of acupuncture for OCD on TCM Heart-Gall Bladder Concept have been widely recognized.
强迫症(obsessive -compulsive disorder)是一种以无法控制的强迫行为和强迫行为为特征的神经性精神障碍。患者知道持续的强迫症症状是毫无意义和不合理的,但却无法摆脱。因此,他们感到非常紧张和痛苦。中医心胆理论指导下针灸治疗强迫症,可改善脑血供,调节HPA功能,调节免疫功能,双向调节SP的释放,影响NE的代谢。因此,针灸治疗强迫症的疗效和效果在中医心胆概念上得到了广泛的认可。
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引用次数: 0
期刊
2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops
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