Noninvasive Assessment of Kidney Injury by Combining Structure and Function Using Artificial Intelligence-Based Manganese-Enhanced Magnetic Resonance Imaging.

Contrast-enhanced magnetic resonance imaging (MRI) is seriously limited in kidney injury detection due to the nephrotoxicity of clinically used gadolinium-based contrast agents. Herein, we propose a noninvasive method for the assessment of kidney injury by combining structure and function information based on manganese (Mn)-enhanced MRI for the first time. As a proof of concept, the Mn-melanin nanoprobe with good biocompatibility and excellent T1 relaxivity is applied in MRI of a unilateral ureteral obstruction mice model. The abundant renal structure and function information is obtained through qualitative and quantitative analysis of MR images, and a brand new comprehensive assessment framework is proposed to precisely identify the degree of kidney injury successfully. Our study demonstrates that Mn-enhanced MRI is a promising approach for the highly sensitive and biosafe assessment of kidney injury in vivo.

GMNN2CD: identification of circRNA-disease associations based on variational inference and graph Markov neural networks.

MOTIVATION: With the analysis of the characteristic and function of circular RNAs (circRNAs), people have realized that they play a critical role in the diseases. Exploring the relationship between circRNAs and diseases is of far-reaching significance for searching the etiopathogenesis and treatment of diseases. Nevertheless, it is inefficient to learn new associations only through biotechnology. RESULTS: Consequently, we present a computational method, GMNN2CD, which employs a graph Markov neural network (GMNN) algorithm to predict unknown circRNA-disease associations. First, used verified associations, we calculate semantic similarity and Gaussian interactive profile kernel similarity (GIPs) of the disease and the GIPs of circRNA and then merge them to form a unified descriptor. After that, GMNN2CD uses a fusion feature variational map autoencoder to learn deep features and uses a label propagation map autoencoder to propagate tags based on known associations. Based on variational inference, GMNN alternate training enhances the ability of GMNN2CD to obtain high-efficiency high-dimensional features from low-dimensional representations. Finally, 5-fold cross-validation of five benchmark datasets shows that GMNN2CD is superior to the state-of-the-art methods. Furthermore, case studies have shown that GMNN2CD can detect potential associations. AVAILABILITY AND IMPLEMENTATION: The source code and data are available at https://github.com/nmt315320/GMNN2CD.git.

Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction.

Promoters are crucial regulatory DNA regions for gene transcriptional activation. Rapid advances in next-generation sequencing technologies have accelerated the accumulation of genome sequences, providing increased training data to inform computational approaches for both prokaryotic and eukaryotic promoter prediction. However, it remains a significant challenge to accurately identify species-specific promoter sequences using computational approaches. To advance computational support for promoter prediction, in this study, we curated 58 comprehensive, up-to-date, benchmark datasets for 7 different species (i.e. Escherichia coli, Bacillus subtilis, Homo sapiens, Mus musculus, Arabidopsis thaliana, Zea mays and Drosophila melanogaster) to assist the research community to assess the relative functionality of alternative approaches and support future research on both prokaryotic and eukaryotic promoters. We revisited 106 predictors published since 2000 for promoter identification (40 for prokaryotic promoter, 61 for eukaryotic promoter, and 5 for both). We systematically evaluated their training datasets, computational methodologies, calculated features, performance and software usability. On the basis of these benchmark datasets, we benchmarked 19 predictors with functioning webservers/local tools and assessed their prediction performance. We found that deep learning and traditional machine learning-based approaches generally outperformed scoring function-based approaches. Taken together, the curated benchmark dataset repository and the benchmarking analysis in this study serve to inform the design and implementation of computational approaches for promoter prediction and facilitate more rigorous comparison of new techniques in the future.

Analysis of gene expression profiles of lung cancer subtypes with machine learning algorithms.

Lung cancer is one of the most common cancer types worldwide and causes more than one million deaths annually. Lung adenocarcinoma (AC) and lung squamous cell cancer (SCC) are two major lung cancer subtypes and have different characteristics in several aspects. Identifying their differentially expressed genes and different gene expression patterns can deepen our understanding of these two subtypes at the transcriptomic level. In this work, we used several machine learning algorithms to investigate the gene expression profiles of lung AC and lung SCC samples retrieved from Gene Expression Omnibus. First, the profiles were analyzed by using a powerful feature selection method, namely, Monte Carlo feature selection. A feature list, ranking all features according to their importance, and some informative features were obtained. Then, the feature list was used in the incremental feature selection method to extract optimal features, which can allow the support vector machine (SVM) to yield the best performance for classifying lung AC and lung SCC samples. Some top genes (CSTA, TP63, SERPINB13, CLCA2, BICD2, PERP, FAT2, BNC1, ATP11B, FAM83B, KRT5, PARD6G, PKP1) were extensively analyzed to prove that they can be differentially expressed genes between lung AC and lung SCC. Meanwhile, a rule learning procedure was applied on informative features to construct the classification rules. These rules provide a clear procedure of classification and show some different gene expression patterns between lung AC and lung SCC.

Computational methods for identifying the critical nodes in biological networks.

A biological network is complex. A group of critical nodes determines the quality and state of such a network. Increasing studies have shown that diseases and biological networks are closely and mutually related and that certain diseases are often caused by errors occurring in certain nodes in biological networks. Thus, studying biological networks and identifying critical nodes can help determine the key targets in treating diseases. The problem is how to find the critical nodes in a network efficiently and with low cost. Existing experimental methods in identifying critical nodes generally require much time, manpower and money. Accordingly, many scientists are attempting to solve this problem by researching efficient and low-cost computing methods. To facilitate calculations, biological networks are often modeled as several common networks. In this review, we classify biological networks according to the network types used by several kinds of common computational methods and introduce the computational methods used by each type of network.

Future Health and Economic Impact of Comprehensive Tobacco Control in DoD: A Microsimulation Approach.

Background: Tobacco use is a major concern to the Military Health System of the Department of Defense (DoD). The 2011 DoD Health Related Behavior Survey reported that 24.5% of active duty personnel are current smokers, which is higher than the national estimate of 20.6% for the civilian population. Overall, it is estimated that tobacco use costs the DoD $1.6 billion a year through related medical care, increased hospitalization, and lost days of work, among others. Methods: This study evaluated future health outcomes of Tricare Prime beneficiaries aged 18-64 yr (N = 3.2 million, including active duty and retired military members and their dependents) and the potential economic impact of initiatives that DoD may take to further its effort to transform the military into a tobacco-free environment. Our analysis simulated the future smoking status, risk of developing 25 smoking-related diseases, and associated medical costs for each individual using a Markov Chain Monte Carlo microsimulation model. Data sources included Tricare administrative data, national data such as Centers for Disease Control and Prevention mortality data and National Cancer Institute's cancer registry data, as well as relative risks of diseases obtained from a literature review. Findings: We found that the prevalence of active smoking among the Tricare Prime population will decrease from about 24% in 2015 to 18% in 2020 under a status quo scenario. However, if a comprehensive tobacco control initiative that includes a 5% price increase, a tighter clean air policy, and an intensified media campaign were to be implemented between 2016 and 2020, the prevalence of smoking could further decrease to 16%. The near 2 percentage points reduction in smoking prevalence represents an additional 81,240 quitters and translates to a total lifetime medical cost savings (in 2016 present value) of $968 million, with 39% ($382 million) attributable to Tricare savings. Discussion: A comprehensive tobacco control policy within the DoD could significantly decrease the prevalence and lifetime medical cost of tobacco use. If the smoking prevalence among Prime beneficiaries could reach the Healthy People 2020 goal of 12%, through additional measures, the lifetime savings could mount to $2.08 billion. To achieve future savings, DoD needs to pay close attention to program design and implementation issues of any additional tobacco control initiatives.