Prediction of drug-target interaction by integrating diverse heterogeneous information source with multiple kernel learning and clustering methods

BackgroundIdentification of potential drug-target interaction pairs is very important for pharmaceutical innovation and drug discovery. Numerous machine learning-based and network-based algorithms have been developed for predicting drug-target interactions. However, large-scale pharmacological, genomic and chemical datum emerged recently provide new opportunity for further heightening the accuracy of drug-target interactions prediction.ResultsIn this work, based on the assumption that similar drugs tend to interact with similar proteins and vice versa, we developed a novel computational method (namely MKLC-BiRW) to predict new drug-target interactions. MKLC-BiRW integrates diverse drug-related and target-related heterogeneous information source by using the multiple kernel learning and clustering methods to generate the drug and target similarity matrices, in which the low similarity elements are set to zero to build the drug and target similarity correction networks. By incorporating these drug and target similarity correction networks with known drug-target interaction bipartite graph, MKLC-BiRW constructs the heterogeneous network on which Bi-random walk algorithm is adopted to infer the potential drug-target interactions.ConclusionsCompared with other existing state-of-the-art methods, MKLC-BiRW achieves the best performance in terms of AUC and AUPR. MKLC-BiRW can effectively predict the potential drug-target interactions.     

Chaos enhanced grey wolf optimization wrapped ELM for diagnosis of paraquat-poisoned patients

Paraquat (PQ) poisoning seriously harms the health of humanity. An effective diagnostic method for paraquat poisoned patients is a crucial concern. Nevertheless, it's difficult to identify the patients with low intake of PQ or delayed treatment. Here, a new efficient diagnostic approach to integrate machine learning and gas chromatography-mass spectrometry (GC–MS), named GEE, is proposed to identify the PQ poisoned patients. First, GC–MS provides the original data that efficiently identified the paraquat-poisoned patients. According to the high dimensionality of the original data, in the second stage, the chaos enhanced grey wolf optimization (EGWO) is adopted to search the optimal feature sets to improve the accuracy of identification. Finally, the extreme learning machine (ELM) is used to identify the PQ poisoned patients. To efficiently evaluate the proposed method, four measures were used in our experiments and comparisons were made with six other methods. The PQ-poisoned patients and robust volunteers can be well identified by GEE and the values of AUC, accuracy, sensitivity and specificity were 95.14%, 93.89%, 94.44% and 95.83%, respectively. Our experimental results demonstrated that GEE had better performance and might serve as a novel candidate diagnosis of PQ-poisoned patients.     

THPep: A machine learning-based approach for predicting tumor homing peptides

In the present era, a major drawback of current anti-cancer drugs is the lack of satisfactory specificity towards tumor cells. Despite the presence of several therapies against cancer, tumor homing peptides are gaining importance as therapeutic agents. In this regard, the huge number of therapeutic peptides generated in recent years, demands the need to develop an effective and interpretable computational model for rapidly, effectively and automatically predicting tumor homing peptides. Therefore, a sequence-based approach referred herein as THPep has been developed to predict and analyze tumor homing peptides by using an interpretable random forest classifier in concomitant with amino acid composition, dipeptide composition and pseudo amino acid composition. An overall accuracy and Matthews correlation coefficient of 90.13% and 0.76, respectively, were achieved from the independent test set on an objective benchmark dataset. Upon comparison, it was found that THPep was superior to the existing method and holds high potential as a useful tool for predicting tumor homing peptides. For the convenience of experimental scientists, a web server for this proposed method is provided publicly at http://codes.bio/thpep/.     

A deep learning ensemble for function prediction of hypothetical proteins from pathogenic bacterial species

Protein function prediction is a crucial task in the post-genomics era due to their diverse irreplaceable roles in a biological system. Traditional methods involved cost-intensive and time-consuming molecular biology techniques but they proved to be ineffective after the outburst of sequencing data through the advent of cost-effective and advanced sequencing techniques. To manage the pace of annotation with that of data generation, there is a shift to computational approaches which are based on homology, sequence and structure-based features, protein-protein interaction networks, phylogenetic profiles, and physicochemical properties, etc. A combination of these features has proven to be promising for protein function prediction in terms of improving prediction accuracy. In the present work, we have employed a combination of features based on sequence, physicochemical property, subsequence and annotation features with a total of 9890 features extracted and/or calculated for 171,212 reviewed prokaryotic proteins of 9 bacterial phyla from UniProtKB, to train a supervised deep learning ensemble model with the aim to categorize a bacterial hypothetical/unreviewed protein’s function into 1739 GO terms as functional classes. The proposed system being fully dedicated to bacterial organisms is a novel attempt amongst various existing machine learning based protein function prediction systems based on mixed organisms. Experimental results demonstrate the success of the proposed deep learning ensemble model based on deep neural network method with F1 measure of 0.7912 on the prepared Test dataset 1 of reviewed proteins.     

Re-casting traditional organic experiments into green guided-inquiry based experiments: student perceptions

ABSTRACT

Green Chemistry principles can be used to re-cast traditional Organic chemistry experiments into more guided-inquiry based experiments. Inquiry questions related to green chemistry principles and metrics have been incorporated into our laboratory for the development of more guided-inquiry based experiments. Re-casting traditional experiments provides time for guided-inquiry by allowing students to evaluate reaction conditions and wastefulness of reactions. This includes evaluating solvent choices, heating methods, use of renewal materials, and contemplating reactants and products impacts on human health and environment. Students examine the changes as it pertains to green chemistry, the success of the reaction and the potential impacts on the mechanism. Involving students in these discoveries rooted in a guiding question made the Organic experiments guided-inquiry. Students were surveyed about their exposure to green chemistry and guided-inquiry based labs. Examples of some of the re-casted experiments, excerpts from student reports, and student impressions of the theme are presented.     

国际“物理化学”课程与教学研究评述

通过文献的计量分析和阅读总结,我国物理化学课程与教学研究还局限于经验与思辨。我们梳理了国际权威期刊上研究物理化学教学的文献,将其分为教科书研究、学习研究、教学研究、教师研究和教学媒体研究等5类,并对其中核心成果进行评述。总结出国外物理化学课程与教学研究注重学习证据的收集和分析,注重教育研究方法的运用,并对于未来高等化学教育研究提出建议。     

Distance versus Capillary Flow Dynamics-Based Detection Methods on a Microfluidic Paper-Based Analytical Device (μPAD)

In recent years, there has been high interest in paper-based microfluidic sensors or microfluidic paper-based analytical devices (μPADs) towards low-cost, portable, and easy-to-use sensing for chemical and biological targets. μPAD allows spontaneous liquid flow without any external or internal pumping, as well as an innate filtration capability. Although both optical (colorimetric and fluorescent) and electrochemical detection have been demonstrated on μPADs, several limitations still remain, such as the need for additional equipment, vulnerability to ambient lighting perturbation, and inferior sensitivity. Herein, alternative detection methods on μPADs are reviewed to resolve these issues, including relatively well studied distance-based measurements and the newer capillary flow dynamics-based method. Detection principles, assay performance, strengths, and weaknesses are explained for these methods, along with their potential future applications towards point-of-care medical diagnostics and other field-based applications.     

基于课程标准的教学——以常见阴、阳离子的检验为例

以常见的阴、阳离子的检验为例，研究了如何实施基于标准的教学。校本教材的开发为标准、教材、教学、评价的一致性提供保障；以学生应知的和能做的驱动课堂活动；根据达成标准应有怎样的质量表现，试卷编制先于教学设计。课堂上，“教”“学”双方都明确学习目标，教师提供多种策略来满足学生多样的学习需要，如提供工具，搭建脚手架，并以“微”研究性学习的方式展开教学，给学生提供了充分的进步空间。     

基于结构性思维的生物化学实验教学探索

为了多维度地培养学生的实践创新能力、终身学习能力及信息获取能力等核心素养,以具体实验为例,探讨结构性思维在生物化学实验教学中的综合应用。教学实践表明：结构性思维可使知识更有序、梯度更明确、更易表达,实验操作变得程序化,学生学习倾向主动,是一种多维度地培养学生核心素养的教学模式。