Open Bioinformatics Journal最新文献

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The Development of the Vital Signs Tele-monitoring System for the Elderly by Using ‘UML’ Language and the Interoperability Standard ‘Continua’ 用“UML”语言和互操作性标准“Continua”开发老年人生命体征远程监测系统

Q3 Computer Science

Open Bioinformatics Journal

Pub Date : 2020-10-26 DOI: 10.2174/1875036202013010092

S. Mansouri

Aims: We aim to develope a system allowing the telemonitoring of the elderly health status. Medical telemonitoring can make life easy and safe for elderly. The goal of this project is the development of a medical telemonitoring application. Background: Medical telemonitoring can make life easy and safe for elderly. Objective: The goal of this project is the development of a medical telemonitoring application. Methods: In this paper we exposed the different steps of the developing of a medical telemonitoring system designed for the elderly. We studied the medical needs and the system specifications. We used the UML language. Then we detailed the designed system with a total respect to the standard for the interoperability of connected medical equipment, Continua. We presented printed screens of the realized interfaces. Results: We realized an application based on web development, more specifically development of a management application for medical telemonitoring. Conclusion: In terms of perspectives, we aim to integrate security protocols in the developed system, integrate the data sent from the sensors into an E, H & R (HER) and send the patient file to a H, I & S (HIS).

目的：我们旨在开发一个远程监测老年人健康状况的系统。医疗远程监控可以让老年人的生活变得轻松和安全。该项目的目标是开发医疗远程监控应用程序。背景：医疗远程监护可以使老年人的生活更轻松、更安全。目的：本项目的目标是开发医疗远程监测应用程序。方法：本文介绍了为老年人设计的医疗远程监护系统开发的不同步骤。我们研究了医疗需求和系统规范。我们使用了UML语言。然后，我们详细介绍了所设计的系统，并完全参考了联网医疗设备互操作性标准Continua。我们展示了已实现接口的打印屏幕。结果：我们实现了一个基于web开发的应用程序，更具体地说，开发了一个用于医疗远程监测的管理应用程序。结论：从各个角度来看，我们的目标是在开发的系统中集成安全协议，将传感器发送的数据集成到E，H&R（HER）中，并将患者文件发送到H，I&S（HIS）中。

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引用次数: 2

iMPT-FRAKEL: A Simple Multi-label Web-server that Only Uses Fingerprints to Identify which Metabolic Pathway Types Compounds can Participate In iMPT-FRAKEL:一个简单的多标签网络服务器，仅使用指纹来识别化合物可以参与的代谢途径类型

Q3 Computer Science

Open Bioinformatics Journal

Pub Date : 2020-08-18 DOI: 10.2174/1875036202013010083

Yan-juan Jia, Lei Chen, Jian-Peng Zhou, Min Liu

Metabolic pathway is one of the most basic biological pathways in living organisms. It consists of a series of chemical reactions and provides the necessary molecules and energies for organisms. To date, lots of metabolic pathways have been detected. However, there still exist hidden participants (compounds and enzymes) for some metabolic pathways due to the complexity and diversity of metabolic pathways. It is necessary to develop quick, reliable, and non-animal-involved prediction model to recognize metabolic pathways for any compound. In this study, a multi-label classifier, namely iMPT-FRAKEL, was developed for identifying which metabolic pathway types that compounds can participate in. Compounds and 12 metabolic pathway types were retrieved from KEGG. Each compound was represented by its fingerprints, which was the most widely used form for representing compounds and can be extracted from its SMILES format. A popular multi-label classification scheme, Random k-Labelsets (RAKEL) algorithm, was adopted to build the classifier. Classic machine learning algorithm, Support Vector Machine (SVM) with RBF kernel, was selected as the basic classification algorithm. Ten-fold cross-validation was used to evaluate the performance of the iMPT-FRAKEL. In addition, a web-server version of such classifier was set up, which can be assessed at http://cie.shmtu.edu.cn/impt/index. iMPT-FRAKEL yielded the accuracy of 0.804, exact match of 0.745 and hamming loss of 0.039. Comparison results indicated that such classifier was superior to other models, including models with Binary Relevance (BR) or other classification algorithms. The proposed classifier employed limited prior knowledge of compounds but gives satisfying performance for recognizing metabolic pathways of compounds.

代谢途径是生物体内最基本的生物途径之一。它由一系列化学反应组成，为生物体提供必要的分子和能量。迄今为止，已经发现了许多代谢途径。然而，由于代谢途径的复杂性和多样性，一些代谢途径仍然存在隐藏的参与者(化合物和酶)。开发快速、可靠、不涉及动物的预测模型来识别任何化合物的代谢途径是很有必要的。在本研究中，我们开发了一个多标签分类器，即iMPT-FRAKEL，用于识别化合物可以参与哪些代谢途径类型。从KEGG中检索到化合物和12种代谢途径类型。每种化合物都用指纹图谱表示，指纹图谱是最广泛使用的表示化合物的形式，可以从其SMILES格式中提取。采用了一种流行的多标签分类方案Random k-Labelsets (RAKEL)算法来构建分类器。选择经典的机器学习算法——RBF核支持向量机(SVM)作为基本分类算法。采用10倍交叉验证来评价iMPT-FRAKEL的性能。此外，还建立了该分类器的web服务器版本，可以在http://cie.shmtu.edu.cn/impt/index上进行评估。iMPT-FRAKEL的准确度为0.804，精确匹配度为0.745，汉明损失为0.039。对比结果表明，该分类器优于其他模型，包括具有二元相关性(Binary Relevance, BR)的模型或其他分类算法。该分类器利用了有限的化合物先验知识，但在识别化合物代谢途径方面取得了令人满意的效果。

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引用次数: 4

Bacterial DNA Diversity among Clear and Cloudy Sakes, and Sake-kasu 清浊清酒和清酒的细菌DNA多样性

Q3 Computer Science

Open Bioinformatics Journal

Pub Date : 2020-08-13 DOI: 10.2174/1875036202013010074

Momoka Terasaki, H. Nishida

Bacterial DNA frequently detected in sake samples was from environmental bacterial contamination that occurs early in the sake production process. Contaminating bacteria are usually killed by the ethanol produced as the sake yeast grows; after which, if bacteria lyse, the bacterial DNA is released into the sake solution. However, if the bacterial cells do not lyse, they will precipitate toward the sediment. Thus, there is bacterial DNA diversity in clear and cloudy sake, but less diversity in sake-kasu.

在清酒样品中经常检测到的细菌DNA来自清酒生产过程早期发生的环境细菌污染。受污染的细菌通常被清酒酵母生长时产生的乙醇杀死；之后，如果细菌裂解，则细菌DNA被释放到清酒溶液中。然而，如果细菌细胞不裂解，它们就会向沉积物沉淀。因此，清酒和混浊清酒中存在细菌DNA多样性，而清酒中的细菌DNA则较少。

引用次数: 10

Ancestral Area Reconstruction of SARS-CoV-2 Indicates Multiple Sources of Entry into Australia 严重急性呼吸系统综合征冠状病毒2型祖先区重建表明进入澳大利亚的多种来源

Q3 Computer Science

Open Bioinformatics Journal

Pub Date : 2020-06-28 DOI: 10.2174/1875036202114010013

N. Phan, H. Faddy, R. Flower, K. Spann, Eileen V. Roulis

The ongoing COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). International travels to Australia during the early stages of the pandemic prior to border closure provided avenues for this virus to spread into Australia. Studies of SARS-CoV-2 biogeographical distribution can contribute to the understanding of the viral original sources to Australia. This study aimed to investigate the clonality and ancestral sources of Australian SARS-CoV-2 isolates using phylogenetic methods. We retrieved 1,346 complete genomes from Australia along with 153 genomes from other countries from the GISAID and NCBI nucleotide databases as of the 14th May 2020. A representative dataset of 270 Australian and international sequences were resulted from performance of nucleotide redundancy reduction by CD-HIT. We then constructed a median-joining network by Network 10.1.0.0, and phylogenies by IQ-Tree, BEAST and FastTree. The Bayesian statistical dispersal-vicariance analysis (S-DIVA) and Bayesian interference for discrete areas (BayArea) built in RASP were used to reconstruct ancestral ranges over the phylogenetic trees. Two major clusters, from Europe and from Asia, were observed on the network of 183 haplotypes with distinct nucleotide variations. Analysis of ancestral area reconstruction over the phylogenies indicated most Australian SARS-CoV-2 sequences were disseminated from Europe and East Asia-Southeast Asia. The finding is genetic evidence for the geographic origins of the Australian SARS-CoV-2 sequences. Most Australian sequences were genetically similar to those from Europe and East Asia-Southeast Asia, which were also suggested as two main sources of introduction of SARS-CoV-2 to Australia.

持续的新冠肺炎大流行是由严重急性呼吸综合征冠状病毒2（SARS-CoV-2）引起的。在边境关闭前的疫情早期，前往澳大利亚的国际旅行为这种病毒传播到澳大利亚提供了途径。对严重急性呼吸系统综合征冠状病毒2型的生物地理分布的研究有助于了解澳大利亚的病毒原始来源。本研究旨在使用系统发育方法调查澳大利亚严重急性呼吸系统综合征冠状病毒2型分离株的克隆性和祖先来源。截至2020年5月14日，我们从GISAID和NCBI核苷酸数据库中检索了1346个来自澳大利亚的完整基因组，以及153个来自其他国家的基因组。270个澳大利亚和国际序列的代表性数据集是由CD-HIT的核苷酸冗余减少性能产生的。然后，我们通过网络10.1.0.0构建了一个中值连接网络，并通过IQ树、BEAST和FastTree构建了系统发育。使用建立在RASP中的贝叶斯统计扩散替代分析（S-DIVA）和离散区域贝叶斯干扰（BayArea）来重建系统发育树上的祖先范围。在183个具有不同核苷酸变异的单倍型网络上观察到来自欧洲和亚洲的两个主要集群。对祖先区域重建的系统发育分析表明，大多数澳大利亚严重急性呼吸系统综合征冠状病毒2型序列分布于欧洲和东亚东南亚。这一发现是澳大利亚严重急性呼吸系统综合征冠状病毒2型序列地理起源的遗传学证据。大多数澳大利亚序列在基因上与欧洲和东亚-东南亚的序列相似，这也被认为是将严重急性呼吸系统综合征冠状病毒2型引入澳大利亚的两个主要来源。

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引用次数: 0

Fuzzy String Matching Procedure 模糊字符串匹配过程

Q3 Computer Science

Open Bioinformatics Journal

Pub Date : 2020-05-23 DOI: 10.2174/1875036202013010050

Zekâi Şen

There are different methodologies for DNA comparison based on two string algorithms, which are dependent on crisp logical principles, where there is no room for verbal (linguistic) uncertainty. These are successfully applicable procedures in DNA bioinformatics researches even by taking into consideration probabilistic random variability components based on the probability distribution functions of various types.

基于两种字符串算法的DNA比较有不同的方法，这取决于清晰的逻辑原则，在这些原则中没有言语（语言）不确定性的空间。即使考虑了基于各种类型的概率分布函数的概率随机变异成分，这些程序也能成功地应用于DNA生物信息学研究。

引用次数: 1

Meta-Analysis of Expression of the Stress Tolerance Associated Genes and Uncover their Cis-Regulatory Elements in Rice (Oryza sativa L.) 水稻(Oryza sativa L.)耐胁迫相关基因表达的meta分析及其顺式调控元件的揭示

Q3 Computer Science

Open Bioinformatics Journal

Pub Date : 2020-04-23 DOI: 10.2174/1875036202013010039

Nikwan Shariatipour, B. Heidari

Rice contributes to the staple food of more than half of the world’s population. However, its productivity is influenced by various biotic and abiotic stresses. Genetic engineering and plant breeding tools help to overcome the adverse effects of environmental stresses. The advanced bioinformatics tools provide information for a better understanding of the mechanisms underlying stress tolerance, gene expression profiles and functions of the important genes and cis-regulatory elements involved in better performance under abiotic stresses.

大米是世界上一半以上人口的主食。然而，其生产力受到各种生物和非生物胁迫的影响。基因工程和植物育种工具有助于克服环境压力的不利影响。先进的生物信息学工具为更好地理解胁迫耐受性的机制、基因表达谱和重要基因的功能以及在非生物胁迫下获得更好表现的顺式调控元件提供了信息。

引用次数: 8

Machine Learning Algorithms in Cardiology Domain: A Systematic Review 心脏病学领域的机器学习算法:系统综述

Q3 Computer Science

Open Bioinformatics Journal

Pub Date : 2020-04-23 DOI: 10.2174/1875036202013010025

Aleksei Dudchenko, Matthias Ganzinger, G. Kopanitsa

For organizing this review, we adopted the PRISMA statement. We used PubMed as the search engine and identified the search keywords as “Machine Learning”, “Data Mining”, “Cardiology”, and “Cardiovascular” in combinations. Scientific articles and conference papers published between 2013-2017 reporting about implementations of ML algorithms in the domain of cardiology have been included in this review.

为了组织这次审查，我们通过了PRISMA声明。我们使用PubMed作为搜索引擎，将搜索关键词确定为“机器学习”、“数据挖掘”、“心脏病学”和“心血管”组合。2013-2017年间发表的关于ML算法在心脏病学领域实现的科学文章和会议论文已被纳入本综述。

引用次数: 7

Network Biology Approaches to Identify the Drug Lead Molecule for Neurodevelopmental Disorders in Human 识别人类神经发育障碍药物先导分子的网络生物学方法

Q3 Computer Science

Open Bioinformatics Journal

Pub Date : 2020-03-20 DOI: 10.2174/1875036202013010015

A. Verma, S. Chauhan, V. Pankaj, Neha Srivastva, P. Srivastava

Background: Neurodevelopmental disorders (NNDs) are disabilities associated chiefly with the functioning of the neurological system and brain. Children with neurodevelopmental disorders have difficulties with speech, behaviour, learning and other neurological functions. Systems biology is a holistic approach to enciphering the complexity of biological systems and their interactions. It opens the way to a more successful discovery of novel therapeutics.

背景：神经发育障碍是一种主要与神经系统和大脑功能相关的残疾。患有神经发育障碍的儿童在言语、行为、学习和其他神经功能方面存在困难。系统生物学是一种对生物系统及其相互作用的复杂性进行加密的整体方法。它为更成功地发现新的治疗方法开辟了道路。

引用次数: 3

Direct At-Sea Observations of Elephant Seals (Mirounga spp.) to Help Interpret Digital Bio-logging Data 直接在海上观察象海豹(米隆加种)，以帮助解释数字生物记录数据

Q3 Computer Science

Open Bioinformatics Journal

Pub Date : 2020-01-01 DOI: 10.2174/1874196702008010001

J. van den Hoff, S. Thalmann

Two deep-sea video recordings and six surface sightings of elephant seals ingesting prey were collated. Each observation either supported or suggested an alternative to behaviours derived from digital time-depth profiles. The tendency for elephant seals to surface following the capture of large prey suggests precipitous drops in stomach temperature at the sea-surface, which have been recorded and interpreted as drinking events, more likely represent the ingestion of large prey items.

研究人员整理了两段深海录像和六次海象吞食猎物的水面目击记录。每个观测结果都支持或建议了一种替代数字时间-深度剖面的行为。海象在捕获大型猎物后会浮上水面，这表明海洋表面胃温度急剧下降，这被记录下来并解释为饮酒事件，更有可能代表摄入了大型猎物。

引用次数: 0

Machine Learning Neuroprotective Strategy Reveals a Unique Set of Parkinson Therapeutic Nicotine Analogs. 机器学习神经保护策略揭示了一套独特的帕金森治疗尼古丁类似物。

Q3 Computer Science

Open Bioinformatics Journal

Pub Date : 2020-01-01 Epub Date: 2020-03-20

Felipe Rojas-Rodríguez, Carlos Morantes, Andrés Pinzón, George E Barreto, Ricardo Cabezas, Leonardo Mariño-Ramírez, Janneth González

Aims: Present a novel machine learning computational strategy to predict the neuroprotection potential of nicotine analogs acting over the behavior of unpaired signaling pathways in Parkinson's disease.

Background: Dopaminergic replacement has been used for Parkinson's Disease (PD) treatment with positive effects on motor symptomatology but low progression and prevention effects. Epidemiological studies have shown that nicotine consumption decreases PD prevalence through neuroprotective mechanisms activation associated with the overstimulation of signaling pathways (SP) such as PI3K/AKT through nicotinic acetylcholine receptors (e.g α7 nAChRs) and over-expression of anti-apoptotic genes such as Bcl-2. Nicotine analogs with similar neuroprotective activity but decreased secondary effects remain as a promissory field.

Objective: The objective of this study is to develop an interdisciplinary computational strategy predicting the neuroprotective activity of a series of 8 novel nicotine analogs over Parkinson's disease.

Methods: We present a computational strategy integrating structural bioinformatics, SP manual reconstruction, and deep learning to predict the potential neuroprotective activity of 8 novel nicotine analogs over the behavior of PI3K/AKT. We performed a protein-ligand analysis between nicotine analogs and α7 nAChRs receptor using geometrical conformers, physicochemical characterization of the analogs and developed manually curated neuroprotective datasets to analyze their potential activity. Additionally, we developed a predictive machine-learning model for neuroprotection in PD through the integration of Markov Chain Monte-Carlo transition matrix for the 2 SP with synthetic training datasets of the physicochemical properties and structural dataset.

Results: Our model was able to predict the potential neuroprotective activity of seven new nicotine analogs based on the binomial Bcl-2 response regulated by the activation of PI3K/AKT.

Conclusion: Hereby, we present a robust novel strategy to assess the neuroprotective potential of biomolecules based on SP architecture. Our theoretical strategy can be further applied to the study of new treatments related to SP deregulation and may ultimately offer new opportunities for therapeutic interventions in neurodegenerative diseases.

目的：提出一种新颖的机器学习计算策略，以预测尼古丁类似物对帕金森病中未配对信号通路行为的神经保护潜力：背景：多巴胺能替代物已被用于帕金森病（PD）的治疗，对运动症状有积极作用，但对病情发展和预防作用较低。流行病学研究表明，尼古丁可通过神经保护机制激活信号通路（SP），如通过尼古丁乙酰胆碱受体（如α7 nAChRs）过度刺激PI3K/AKT和Bcl-2等抗凋亡基因的过度表达，从而降低帕金森病的发病率。具有类似神经保护活性但副作用较小的尼古丁类似物仍是一个前景广阔的领域：本研究旨在开发一种跨学科计算策略，预测 8 种新型尼古丁类似物对帕金森病的神经保护活性：我们提出了一种整合了结构生物信息学、SP人工重构和深度学习的计算策略，以预测8种新型尼古丁类似物对PI3K/AKT行为的潜在神经保护活性。我们利用尼古丁类似物的几何构象和理化特性，在尼古丁类似物和α7 nAChRs受体之间进行了蛋白质配体分析，并开发了人工策划的神经保护数据集，以分析它们的潜在活性。此外，我们还通过整合 2 种 SP 的马尔可夫链蒙特卡洛转换矩阵以及理化性质和结构数据集的合成训练数据集，开发了一种预测 PD 神经保护的机器学习模型：结果：我们的模型能够根据PI3K/AKT激活调控的二项式Bcl-2反应预测7种新型尼古丁类似物的潜在神经保护活性：在此，我们提出了一种基于 SP 结构评估生物大分子神经保护潜力的新策略。我们的理论策略可进一步应用于研究与 SP 失调相关的新疗法，并最终为神经退行性疾病的治疗干预提供新的机会。

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