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2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)最新文献

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A randomized, controlled study of efficacy and safety on mild to moderate insomnia intervened by Chinese medicine in the integrated program 中医药干预综合治疗轻、中度失眠症疗效及安全性的随机对照研究
Yan Li, Biyun Xu, Shuhui Chen, Peng Liu, A. Ou, Yan Xu, Z. Wen, Biyang Ou, Ruiyu Xu, Zhaozhang Wei, Liang Zeng
To evaluate the effectiveness and safety in mild to moderate insomnia intervened by Chinese Medicine in the integrated program. Methods: Patients(18 to 56 years old) from the Five National Center, who were with mild to moderate insomnia, were randomly divided into two groups according to the central, experimental group: sleep hygiene instruction + balance acupuncture+ Chinese herbal drug; control group: sleep hygiene instruction + minor acupuncture + placebo capsules. PSQI, ISI and PSG were assessed separately after different stages of treatment and follow-up evaluation. Results: (1) Subjective and objective sleep quality: PSQI scores in the 29th days and ISI scores in the 15th days or 29th days of treatment of the experimental group were lower than the control group. PSG parameters of the experimental group were not significantly different before and after treatment. Conclusion: For patients with mild to moderate insomnia, sleep hygiene education, combined with Balance Acupuncture and Bupleurum chinense and fossil fragment and shellfish decoction can improve the subjective sleep.
评价中药干预综合方案治疗轻中度失眠症的有效性和安全性。方法:将国家五中心18 ~ 56岁轻中度失眠症患者按中心随机分为两组,实验组:睡眠卫生指导+平衡针灸+中药;对照组:睡眠卫生指导+小针灸+安慰剂胶囊。在不同治疗阶段及随访评价后分别评估PSQI、ISI、PSG。结果:(1)主客观睡眠质量:实验组治疗第29天PSQI评分及治疗第15天、第29天ISI评分均低于对照组。实验组治疗前后PSG参数差异无统计学意义。结论:对于轻中度失眠症患者,进行睡眠卫生教育,配合平衡针、柴胡、化石碎片贝类汤可改善主观睡眠。
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引用次数: 1
Detection of lobular carcinoma in situ(LCIS) by image analysis 小叶原位癌(LCIS)的影像学检测
Sujin Kim, Desok Kim, H. Choi, H. Joo
In this study, we aimed to develop a quantitative image analysis method that may enhance the detection of the lobular carcinoma in-situ (LCIS) in breast cancer specimens. Glandular areas were segmented by using mathematical morphology from 5X histologic images of breast cancer cases (n=213). Computational features such as shape, intensity, and texture were extracted from glandular areas. Segmented glandular areas of LCIS were significantly larger, thicker, lower and less variant in intensity, compared to normal areas (Mann-Whitney test, p<0.01). Our models based on data mining algorithms detected LCIS frames at the accuracy rate close to 99%. Our proposed methods may be well incorporated into a further development of computer aided detection (CAD) software for the screening of whole slide images to locate the LCIS areas.
在本研究中,我们旨在建立一种定量图像分析方法,以提高乳腺癌标本中小叶原位癌(LCIS)的检测。利用数学形态学对5X例乳腺癌病例(n=213)的组织学图像进行腺区分割。从腺体区域提取形状、强度和纹理等计算特征。LCIS的分节腺区与正常区相比,明显更大、更厚、更低、强度变化更少(Mann-Whitney检验,p<0.01)。我们基于数据挖掘算法的模型检测LCIS帧的准确率接近99%。我们提出的方法可以很好地结合到计算机辅助检测(CAD)软件的进一步发展中,用于筛选整个幻灯片图像以定位LCIS区域。
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引用次数: 1
Analysis of relevant physicochemical properties in obligate and non-obligate protein-protein interactions 专性和非专性蛋白质相互作用的相关理化性质分析
M. Maleki, Md. Mominul Aziz, L. Rueda
Identification and analysis of types of protein-protein interactions (PPI) is an important problem in molecular biology because of its key role in many biological processes in living cells. In this paper, we focus on obligate and non-obligate complexes, their prediction and analysis. We propose a feature selection scheme called MRMRpro which is based on Minimum Redundancy Maximum Relevance (MRMR) to focus on the most discriminative and relevant properties to distinguish between these two types of complexes. Our prediction approach uses desolvation energies of pairs of atoms or amino acids present in the interfaces of such complexes. Our results on two well-known datasets confirm that MRMRpro leads to significant improvements on performance by finding more relevant features for prediction. Furthermore, the prediction performance of our biologically guided feature selection methods demonstrate that hydrophobic amino acids are more discriminating than hydrophilic and amphipathic amino acids to distinguish between obligate and non-obligate complexes.
蛋白质-蛋白质相互作用(PPI)类型的鉴定和分析是分子生物学中的一个重要问题,因为它在活细胞的许多生物过程中起着关键作用。本文主要研究了专性复合物和非专性复合物及其预测和分析。我们提出了一种基于最小冗余最大相关性(MRMR)的特征选择方案MRMRpro,以关注最具区别性和相关性的属性来区分这两种类型的复合物。我们的预测方法使用这种配合物界面中存在的对原子或氨基酸的脱溶能。我们在两个知名数据集上的结果证实,MRMRpro通过找到更多相关的预测特征,显著提高了性能。此外,我们的生物引导特征选择方法的预测性能表明,疏水氨基酸比亲水和两亲氨基酸在区分专性和非专性复合物方面更具歧视性。
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引用次数: 13
Wavelet and PCA for Metabolic Network Comparison 小波与PCA在代谢网络比较中的应用
Yong Luo, Yan Zhao, Lei Cheng
This paper is composed based on principal component analysis and wavelet transform method to compare the metabolic networks. We combine 7 centrality topologies of metabolic network to extract a comprehensive center on principal component analysis and construct the original signal based on statistical method. By using the wavelet tool to describe the metabolic network structure, we build the fuzzy function to compare the metabolic network structure between different species. This method above can effectively analyze the structure similarity of different species' metabolic networks, reveal the species-specific of metabolic networks and lay a mathematical foundation for the evolution of metabolic networks. Also it is the first time to use the wavelet analysis method in studying the metabolic networks, and it makes an attempt on a new research direction.
本文基于主成分分析和小波变换方法对代谢网络进行比较。结合代谢网络的7种中心性拓扑,通过主成分分析提取综合中心,并基于统计方法构建原始信号。利用小波工具对代谢网络结构进行描述,建立模糊函数来比较不同物种之间的代谢网络结构。上述方法可以有效地分析不同物种代谢网络的结构相似性,揭示代谢网络的物种特异性,为代谢网络的进化奠定数学基础。首次将小波分析方法应用到代谢网络的研究中,为新的研究方向进行了尝试。
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引用次数: 0
Ontology Graph Based Query Expansion for Biomedical Information Retrieval 基于本体图的生物医学信息检索查询扩展
Liang Dong, P. Srimani, J. Wang
Query expansion based biomedical information retrieval has been studied for over two decades, most of the studies focus only on taking advantage of one vocabulary: MeSH. We propose a completely different approach utilizing an arbitrary number of controlled vocabularies from Metathesaurus. Experiment shows that our ontology based query expansion scheme achieves 8.2% and 17.7% improvement compared with schemes using pseudo relevance feedback query expansion and using no query expansion respectively. The average improvement is 24.8% in comparison to all other existing strategies. Furthermore, we identify that generalized biomedical concepts are the reason for performance degradation.
基于查询扩展的生物医学信息检索已经研究了二十多年,但大多数研究都集中在利用一个词汇:MeSH。我们提出了一种完全不同的方法,利用来自metthesaurus的任意数量的受控词汇。实验表明,基于本体的查询扩展方案与使用伪相关反馈的查询扩展方案和不使用查询扩展方案相比,分别提高了8.2%和17.7%。与所有其他现有策略相比,平均改进率为24.8%。此外,我们发现广义生物医学概念是性能下降的原因。
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引用次数: 20
A comparative study of text classification approaches for personalized retrieval in PubMed PubMed中个性化检索文本分类方法的比较研究
Sachintha Pitigala, Cen Li, S. Seo
Retrieval of the information relevant to one's need from PubMed is becoming increasingly challenging due to its large volume and rapid growth. The traditional information search techniques based on keyword matching are insufficient for large databases such as PubMed. A personalized article retrieval system that is tailored to individual researcher's specific interests and selects only highly relevant articles can be a helpful tool in the field of Bioinformatics. The text classification methods developed in the text mining community have shown good results in differentiating relevant articles from the irrelevant ones. This study compares two text classification methods, Naïve Bayes and Support Vector Machines, in order to study the effectiveness of the two methods on classifying full text articles in the case when only a small set of training data is available. The comparison results show that the Naïve Bayes method is a better choice than Support Vector Machines in building a personalized article retrieval system which can learn (train) from a small set of full text articles.
由于PubMed的庞大容量和快速增长,从PubMed中检索与个人需求相关的信息变得越来越具有挑战性。传统的基于关键词匹配的信息搜索技术对于PubMed这样的大型数据库来说是不够的。一个个性化的文章检索系统,是量身定制的个人研究人员的具体兴趣,只选择高度相关的文章,可以是一个有用的工具,在生物信息学领域。文本挖掘社区开发的文本分类方法在区分相关文章和不相关文章方面取得了良好的效果。本研究比较了Naïve贝叶斯和支持向量机两种文本分类方法,以研究两种方法在训练数据较少的情况下对全文文章进行分类的有效性。对比结果表明,Naïve贝叶斯方法比支持向量机更适合于构建一个能够从少量全文文章中学习(训练)的个性化文章检索系统。
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引用次数: 4
Learning Condition-Dependent Dynamical PPI Networks from Conflict-Sensitive Phosphorylation Dynamics 从冲突敏感磷酸化动力学中学习条件依赖的动态PPI网络
Qiong Cheng, M. Ogihara, Vineet K Gupta
An important issue in protein-protein interaction network studies is the identification of interaction dynamics. Two factors contribute to the dynamics. One, not all proteins may be expressed in a given cell, and two, competition may exist among multiple proteins for a particular protein domain. Taking into account these two factors, we propose a novel approach to predict protein-protein interaction network dynamics by learning from conflict-sensitive phosphorylation dynamics. We built a training model from conflict-sensitive phosphorylation dynamics. In this model, each node is not an individual protein but a protein-protein pair and is labeled with terms representing conditions in which the interaction should be observed. We mapped the protein pairs in a vector space, built hyper-edges over the interaction nodes, and developed rank-like SVM with Laplacian regularizers for PPI network dynamics prediction. We also employed the standard F1 measure for evaluating the effectiveness of classification results.
蛋白质-蛋白质相互作用网络研究中的一个重要问题是相互作用动力学的识别。有两个因素促成了这种动态。首先,不是所有的蛋白质都可以在一个给定的细胞中表达,其次,多个蛋白质之间可能存在竞争,以争夺一个特定的蛋白质结构域。考虑到这两个因素,我们提出了一种通过学习冲突敏感磷酸化动力学来预测蛋白质-蛋白质相互作用网络动力学的新方法。我们根据冲突敏感性磷酸化动力学建立了一个训练模型。在这个模型中,每个节点不是一个单独的蛋白质,而是一个蛋白质-蛋白质对,并用表示相互作用应该被观察到的条件的术语来标记。我们将蛋白质对映射到向量空间中,在交互节点上构建超边缘,并使用拉普拉斯正则化器开发了类秩支持向量机,用于PPI网络动态预测。我们还采用标准的F1测度来评价分类结果的有效性。
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引用次数: 0
Using semantic similarity to detect features in yeast protein complexes 利用语义相似度检测酵母蛋白复合物的特征
P. Guzzi, Marianna Milano, P. Veltri, M. Cannataro
Biological data stored in databases can be associated with information (knowledge) such as experiments, properties and functions, response to drugs etc. Such a knowledge is often stored in biological ontologies. Gene Ontology is one of the main resource of biological knowledge providing both a categorization of terms and a source of annotation for genes and proteins. This enables the use of ontology-based methodologies for the analysis of proteins and their functions. One methodology is based on semantic based similarity measures. Recently there is a growing interest in the use of semantic based methodologies to the analysis of protein interaction data such as the prediction of protein complexes based on semantic similarity measures. Despite this interest, there is the need for an assessment of semantic measures as well as a deep study on the impact of the chosen measure in the obtained results. This paper treats the problem of using semantic similarity measure to analyse protein complexes and to improve protein complexes prediction frameworks. Tests have been performed in yeast protein complexes. Results indicate that there exists a bias among measures as well as an higher value of semantic similarity within proteins that participate in the same complex, proving both a possible use of semantic similarity protein complexes prediction and a suggestion in the measure.
存储在数据库中的生物数据可以与实验、特性和功能、对药物的反应等信息(知识)相关联。这样的知识通常存储在生物本体中。基因本体论是生物学知识的主要来源之一,为基因和蛋白质提供术语分类和注释来源。这使得使用基于本体的方法来分析蛋白质及其功能成为可能。一种方法是基于基于语义的相似度度量。最近,人们对使用基于语义的方法来分析蛋白质相互作用数据越来越感兴趣,例如基于语义相似度量的蛋白质复合物的预测。尽管有这种兴趣,仍然需要对语义度量进行评估,以及对所选度量在获得结果中的影响进行深入研究。本文研究了利用语义相似度来分析蛋白质复合体的问题,并改进了蛋白质复合体的预测框架。已经在酵母蛋白复合物中进行了试验。结果表明,测量之间存在偏差,并且参与同一复合体的蛋白质之间的语义相似值较高,这证明了语义相似蛋白复合体预测的可能用途和测量中的建议。
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引用次数: 0
Reduction of periodic motion artifacts from impedance plethysmography 减少阻抗脉搏波的周期性运动伪影
Sardar Ansari, Ashwin Belle, Kevin Ward, R. Hobson, K. Najarian
Motion artifact reduction is a fundamental part in portable monitoring of physiological signals. Here, the performance of three different motion artifact reduction methods, independent component analysis, least mean square filters and normalized least mean square filters are compared when applied to the impedance plethysmography signal. The results show that the performance of each method depends on the type of motion artifact it is being applied to, and that none of the methods universally performs better than the other ones. As a result, authors suggest that the motion artifact reduction algorithm should be designed based on the nature of the motion artifact.
运动伪影还原是生理信号便携式监测的基础。本文比较了独立分量分析、最小均方滤波器和归一化最小均方滤波器三种不同的运动伪影抑制方法对阻抗容积脉搏波信号的处理效果。结果表明,每种方法的性能取决于它所应用的运动伪影的类型,并且没有一种方法的性能普遍优于其他方法。因此,作者建议根据运动伪影的性质设计运动伪影减少算法。
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引用次数: 3
The Traditional Chinese Medicine syndromes of psoriasis in Chinese patients: Contribution of demographic and clinical variables 中国银屑病患者的中医证候:人口统计学和临床变量的贡献
Zehui He, Chuanjian Lu, A. Ou
This article was to examine the specific contribution of demographic, medical and psychological variables to the Traditional Chinese Medicine (TCM) Syndromes of psoriasis. A cross-sectional survey of psoriasis patients was conducted at 7 hospitals of TCM of different regions. In all, 671 psoriasis patients underwent a clinical assessment including differentiation of TCM syndromes and psoriasis severity (assessed by Psoriasis Area and Severity Index, PASI). Patients also completed questions on demographic data and a quality of life scale (Dermatology Life Quality Index, DLQI). The three main TCM syndromes were included: 354 patients with Wind-heat (52.8%), 161 with Blood-stasis (24.0%), and 156 with Blood-dryness (23.2%). They distributed differently in subgroups of patients with different gender, age, chronic disease, duration of psoriasis, PASI, and DLQI score. The TCM syndromes were close related to demographic and clinical conditions of patients. TCM clinical treatment should consider both characteristics of syndrome and demographic variables of psoriasis.
本文旨在探讨人口统计学、医学和心理变量对银屑病中医证候的具体贡献。对不同地区7家中医院的银屑病患者进行了横断面调查。对671例银屑病患者进行临床评估,包括中医证候辨证和银屑病严重程度(用银屑病面积和严重程度指数PASI评估)。患者还完成了人口统计数据和生活质量量表(皮肤病生活质量指数,DLQI)的问题。3个主要中医证型包括:风热型354例(52.8%),血瘀型161例(24.0%),血燥型156例(23.2%)。在不同性别、年龄、慢性疾病、银屑病病程、PASI和DLQI评分的患者亚组中分布不同。中医证候与患者的人口学特征和临床条件密切相关。中医临床治疗应兼顾银屑病的证候特点和人口学变量。
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引用次数: 0
期刊
2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
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