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

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Structural properties of the outer membrane of Gram-negative bacteria 革兰氏阴性菌外膜的结构特性
T. Galochkina, D. Zlenko, I. Kovalenko, A. Nesterenko
The cell wall of Gram-negative bacteria plays a crucial role in the bacteria resistance to certain antimicrobials and its adaptation to the host environment. The first line of cell defense is its outer membrane composed of glycerophos-pholipids in the inner monolayer, lipopolysaccharides (LPS) in the outer monolayer and integral proteins. To understand the details of the outer membrane structure we build a molecular model of the Ra-LPS/LPS bilayer containing 8 β-barrels of the OmpA protein. We pay particular attention to the structural evolution of the outermost part of the LPS molecules (O-antigen) and analyze its conformational behavior using different computational criteria.
革兰氏阴性菌的细胞壁在细菌对某些抗菌素的耐药性及其对宿主环境的适应中起着至关重要的作用。细胞的第一道防线是它的外膜,由内单层的甘油磷脂,外单层的脂多糖(LPS)和整体蛋白质组成。为了了解外膜结构的细节,我们建立了含有8个β-桶OmpA蛋白的Ra-LPS/LPS双分子层的分子模型。我们特别关注LPS分子(o -抗原)最外层的结构演变,并使用不同的计算标准分析其构象行为。
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引用次数: 0
Numerical simulation of behavior of red blood cells and cancer cells in complex geometrical domains 红细胞和癌细胞在复杂几何域中行为的数值模拟
T. Djukić, N. Filipovic
Investigation of the motion of deformable particles immersed in fluid is clinically very relevant because it can help to improve treatment planning, diagnostics of disease, design of efficient terapeutical procedures, analysis of drug transport, etc. Experimental investigation of these phenomena is difficult and expensive and, therefore, numerical simulations can contribute to the acquisition of a lot of new and useful information. In this paper, a numerical model that simulates solid-fluid interaction is presented and used to simulate the motion of red blood cells and spherical particles through a fluid domain. A comparison with experimental results and other results presented in literature is performed. The good accuracy of the model demonstrates that this method has a great potential for simulating phenomena happening within complex geometric domains, such as microfluidic chips for cancer cell separation.
研究流体中可变形颗粒的运动,有助于改进治疗计划、疾病诊断、设计有效的治疗程序、分析药物转运等,具有重要的临床意义。这些现象的实验研究是困难和昂贵的,因此,数值模拟可以有助于获得许多新的和有用的信息。本文提出了一个模拟固-流相互作用的数值模型,并用于模拟红细胞和球形颗粒在流体域中的运动。并与实验结果和文献中的其他结果进行了比较。该模型具有良好的精度,表明该方法在模拟复杂几何域内发生的现象方面具有很大的潜力,例如用于癌细胞分离的微流控芯片。
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引用次数: 2
Optic disc localization using local vessel based features and support vector machine 基于局部血管特征和支持向量机的视盘定位
A. A. Salam, M. Akram, Sarmad Abbas Khitran, S. Anwar
Optic disc is one of the fundamental regions located in the internal retina that helps ophthalmologists in analysis and early diagnosis of many retinal diseases such as optic atrophy, optic neuritis, papilledema, ischemic optic neuropathy, glaucoma and diabetic retinopathy. An accurate and early diagnosis requires an accurate optic disc examination. Presence of different retinal abnormalities and non-uniform illumination make optic disc localization a challenging task. There is a need to detect and localize optic disc from fundus images with high accuracy to make the diagnosis using Computer Aided Systems developed for ophthalmic disease diagnosis more reliable. Proposed algorithm provides a novel optic disc localization and segmentation technique that detects multiple candidate optic disc regions from fundus image using enhancement and segmentation. The proposed system then extracts a hybrid feature set for each candidate region consisting of vessel based and intensity based features which are finally fed to SVM classifier. Final decision of Optic disc region is done after computing Manhattan distance from the mean of training data feature matrix. The evaluation of proposed system has been done on publicly available datasets and one local dataset and results shows the validity of proposed system.
视盘是位于视网膜内部的基础区域之一,有助于眼科医生分析和早期诊断许多视网膜疾病,如视神经萎缩、视神经炎、视乳头水肿、缺血性视神经病变、青光眼和糖尿病视网膜病变。准确的早期诊断需要精确的视盘检查。不同的视网膜异常和不均匀的光照使得视盘定位成为一项具有挑战性的任务。需要从眼底图像中高精度地检测和定位视盘,以使用于眼科疾病诊断的计算机辅助系统的诊断更加可靠。该算法提供了一种新的视盘定位和分割技术,通过增强和分割从眼底图像中检测出多个候选视盘区域。然后,该系统为每个候选区域提取由基于血管和基于强度的特征组成的混合特征集,最终将这些特征集馈送给SVM分类器。视盘区域的最终确定由训练数据特征矩阵的均值计算曼哈顿距离完成。在公开数据集和一个本地数据集上对系统进行了评估,结果表明了系统的有效性。
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引用次数: 14
Some examples on the performance of density functional theory in the description of bioinorganic systems and processes 关于密度泛函理论在描述生物无机系统和过程中的性能的一些例子
T. Marino, N. Russo, E. Sicilia, M. Toscano
Density functional computations on a series of complex systems and processes are presented and discussed. In particular the following subject have been investigated: i) catalytic mechanism of carbonic anhydrase; ii) structural properties of silver mediated DNA dimers; iii) structural and spectroscopic features of Zn-phthalocyanine derivatives; iv) carnosine-carboplatin, carnosine-oxaliplatin complexes fragmentation pathways. Reported data indicate that good results can be obtained selecting the appropriate computational strategies, exchange-correlation functionals and basis sets.
提出并讨论了一系列复杂系统和过程的密度泛函计算。重点研究了碳酸酐酶的催化机理;ii)银介导的DNA二聚体的结构性质;iii)酞菁锌衍生物的结构和光谱特征;Iv)肌肽-卡铂,肌肽-奥沙利铂复合物破碎途径。报告的数据表明,选择适当的计算策略、交换相关函数和基集可以获得良好的结果。
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引用次数: 0
Semi-automatic scoring tool for comet assay 用于彗星分析的半自动评分工具
E. Kiziltan, E. Yurtçu
Comet assay or single-cell gel electrophoresis is a widely used method for DNA damage assessment. The results of the method can be scored under microscopic examination either with the naked eye or automated systems. In this study, we present a semi-automatic comet assay analysis tool that was developed in our laboratory. The results obtained with our tool were compared with that of fully automatic shareware software. The preliminary results suggest that the presented semi-automatic software is an accurate and reliable tool for evaluation of comet assay.
彗星试验或单细胞凝胶电泳是一种广泛使用的DNA损伤评估方法。该方法的结果可以在显微镜下进行评分,无论是用肉眼还是自动系统。在这项研究中,我们提出了在我们实验室开发的半自动彗星测定分析工具。用该工具得到的结果与全自动共享软件的结果进行了比较。初步结果表明,该软件是一种准确、可靠的彗星分析评价工具。
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引用次数: 7
SIMBio: Searching and inferring colorful motifs in biological networks SIMBio:在生物网络中搜索和推断彩色基序
Diego P. Rubert, Elói Araújo, M. A. Stefanes
The study of motifs plays a central role in recognition of relations among components in biological networks such that gene regulation, protein interaction, and metabolic networks. Since these relations are not well-known, motifs inference appears as a way for understanding the principles involved in the relationship between cellular components. On the other hand, motifs search is a basic step for constructing models which represent biological behavior and explain functional and/or structural effects in biological networks. In this work we address the problem of infer all relevant motifs in a biological network. We also provide a solution for searching colorful motifs which can be topological-free or have an acyclic topology. We developed a tool for searching and inferring motifs, named SIMBio, and we implemented sequential and parallel versions. When comparing performance, our experiments have showed that SIMBio is faster than MOTUS for inferring motifs, even in the sequential version. We also compared it to Torque, and SIMBio has found more occurrences of motifs under the same experiments.
基序的研究在识别基因调控、蛋白质相互作用和代谢网络等生物网络中组分之间的关系方面起着核心作用。由于这些关系不为人所知,基序推理似乎是理解细胞成分之间关系所涉及的原则的一种方式。另一方面,基序搜索是构建代表生物行为和解释生物网络中功能和/或结构效应的模型的基本步骤。在这项工作中,我们解决了在生物网络中推断所有相关基序的问题。我们还提供了一种搜索无拓扑或无环拓扑的彩色图案的解决方案。我们开发了一个用于搜索和推断motif的工具,名为SIMBio,并实现了顺序和并行版本。当比较性能时,我们的实验表明SIMBio在推断基序方面比MOTUS更快,即使在顺序版本中也是如此。我们还将其与Torque进行了比较,SIMBio在相同的实验中发现了更多的motif。
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引用次数: 3
Electro-mechanical cochlea model 机电耳蜗模型
Milica G. Nikolić, V. Isailović, Paul D. Teal, Milos D. Radovic, N. Filipovic
Cochlea is a part of the inner ear and it has complex anatomy and function. The proper functioning of the cochlea includes the generation of a traveling wave along the basilar membrane, which leads to depolarization of hair cells in the Organ of Corti and subsequent auditory nerve excitation (mechanoelectrical transduction). To represent the behavior of the organ of Corti, electro-mechanical cochlea model needs to be developed. This paper presents a simplified electro-mechanical state space model of the cochlea.
耳蜗是内耳的一部分,具有复杂的解剖结构和功能。耳蜗的正常功能包括沿基底膜产生行波,这导致Corti器官毛细胞去极化和随后的听神经兴奋(机电转导)。为了表征耳蜗器官的行为,需要建立机电耳蜗模型。提出了一种简化的耳蜗机电状态空间模型。
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引用次数: 0
Automated SOSORT-recommended angles measurement in patients with adolescent idiopathic scoliosis 自动sosort推荐的角度测量在青少年特发性脊柱侧凸患者
S. Ćuković, Vanja Luković, Karupppasamy Subburaj, W. Birkfellner, D. Milosevic, B. Ristic, G. Devedžić
In this article we describe a 3D methodology to characterize dorsal surface for the diagnosis of idiopathic scoliosis and its implementation. This characterization is based on the set of external and internal parameters recommended by SOSORT consortium. Parameterized 3D model of the spine and 3D optical scans of dorsal surfaces are used to generate patient-specific surface model for the analysis. The methodology is implemented using Visual Basic Application (VBA) macros in a CAD environment to study relationship between dorsal and internal parameters of spinal deformities and 3D visualization.
在这篇文章中,我们描述了一个三维的方法来表征背表面特发性脊柱侧凸的诊断及其实施。这种特征是基于SOSORT联盟推荐的一组外部和内部参数。使用参数化的脊柱三维模型和背部表面的三维光学扫描来生成患者特定的表面模型进行分析。该方法在CAD环境下使用Visual Basic Application (VBA)宏实现,研究脊柱畸形的背侧和内部参数之间的关系,并进行三维可视化。
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引用次数: 0
False alarm suppression in early prediction of cardiac arrhythmia 虚警抑制在心律失常早期预测中的应用
S. Roychoudhury, Mohamed F. Ghalwash, Z. Obradovic
High false alarm rates in intensive care units (ICUs) cause desensitization among care providers, thus risking patients' lives. Providing early detection of true and false cardiac arrhythmia alarms can alert hospital personnel and avoid alarm fatigue, so that they can act only on true life-threatening alarms, hence improving efficiency in ICUs. However, suppressing false alarms cannot be an excuse to suppress true alarm detection rates. In this study, we investigate a cost-sensitive approach for false alarm suppression while keeping near perfect true alarm detection rates. Our experiments on two life threatening cardiac arrhythmia datasets from Physionet's MIMIC II repository provide evidence that the proposed method is capable of identifying patterns that can distinguish false and true alarms using on average 60% of the available time series' length. Using temporal uncertainty estimates of time series predictions, we were able to estimate the confidence in our early classification predictions, therefore providing a cost-sensitive prediction model for ECG signal classification. The results from the proposed method are interpretable, providing medical personnel a visual verification of the predicted results. In conducted experiments, moderate false alarm suppression rates were achieved (34.29% for Asystole and 20.32% for Ventricular Tachycardia) while keeping near 100% true alarm detection, outperforming the state-of-the-art methods, which compromise true alarm detection rate for higher false alarm suppression rate, on these challenging applications.
重症监护病房(icu)的高虚警率导致护理人员脱敏,从而危及患者的生命。早期发现真假心律失常报警,可以提醒医院人员,避免报警疲劳,使他们只对真正危及生命的报警采取行动,从而提高icu的效率。但是,抑制虚警不能成为抑制真警检测率的借口。在这项研究中,我们研究了一种成本敏感的方法来抑制假警报,同时保持接近完美的真警报检测率。我们对来自Physionet的MIMIC II存储库的两个危及生命的心律失常数据集进行的实验证明,所提出的方法能够识别出能够区分假警报和真警报的模式,平均使用60%的可用时间序列长度。利用时间序列预测的时间不确定性估计,我们能够估计早期分类预测的置信度,因此为心电信号分类提供了一个成本敏感的预测模型。所提出方法的结果是可解释的,为医务人员提供了对预测结果的直观验证。在进行的实验中,在保持接近100%的真警检测的同时,实现了中等的假警抑制率(心跳停止34.29%和室性心动过速20.32%),在这些具有挑战性的应用中,优于最先进的方法,这些方法会牺牲真警检测率以获得更高的假警抑制率。
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引用次数: 6
An efficient mesh deformation method for mass-spring muscle models 一种有效的质量-弹簧肌肉模型网格变形方法
Tomás Janák, J. Kohout
This paper will consider a framework for simulation of musculoskeletal system via mass-spring system as the target application. The framework uses a mass-spring systems to simulate the muscle fibres of each muscle and an additional triangle model to visually represent the surface of the muscles. This requires establishing some relationship between the two models so that when some nodes of the mass-spring model move, i.e. the object deforms, this deformation is correctly carried over to the visualization. Mean Value Coordinates are often used for this purpose. In this paper, we will present a simpler method that produces deformation that is visually similar to that by the Mean Value Coordinates while consuming less memory and time.
本文将考虑一个基于质量-弹簧系统的肌肉骨骼系统仿真框架作为目标应用。该框架使用一个质量弹簧系统来模拟每块肌肉的肌纤维,并使用一个额外的三角形模型来直观地表示肌肉的表面。这需要在两个模型之间建立某种关系,以便当质量-弹簧模型的某些节点移动时,即物体变形,这种变形被正确地传递到可视化中。平均值坐标通常用于此目的。在本文中,我们将提出一种更简单的方法,该方法产生的变形在视觉上与均值坐标相似,同时消耗更少的内存和时间。
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引用次数: 0
期刊
2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE)
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