Machine Learning-Enabled Regional Multi-Hazards Risk Assessment Considering Social Vulnerability

The regional multi-hazards risk assessment poses difficulties due to data access challenges, and the potential interactions between multi-hazards and social vulnerability. For better natural hazards risk perception and preparedness, it is important to study the nature-hazards risk distribution in different areas, specifically a major priority in the areas of high hazards level and social vulnerability. We propose a multi-hazards risk assessment method which considers social vulnerability into the analyzing and utilize machine learning-enabled models to solve this issue. The proposed methodology integrates three aspects as follows: (1) characterization and mapping of multi-hazards (Flooding, Wildfires, and Seismic) using five machine learning methods including Naïve Bayes (NB), K-Nearest Neighbors (KNN), Logistic Regression (LR), Random Forest (RF), and K-Means (KM); (2) evaluation of social vulnerability with a composite index tailored for the case-study area and using machine learning models for classification; (3) risk-based quantification of spatial interaction mechanisms between multi-hazards and social vulnerability. The results indicate that RF model performs best in both hazard-related and social vulnerability datasets. The most cities at multi-hazards risk account for 34.12% of total studied cities (covering 20.80% land). Additionally, high multi-hazards level and socially vulnerable cities account for 15.88% (covering 4.92% land). This study generates a multi-hazards risk map which show a wide variety of spatial patterns and a corresponding understanding of where regional high hazards potential and vulnerable areas are. It emphasizes an urgent need to implement information-based prioritization when natural hazards coming, and effective policy measures for reducing natural-hazards risks in future

Hidden topic–emotion transition model for multi-level social emotion detection

With the fast development of online social platforms, social emotion detection, focusing on predicting readers’ emotions evoked by news articles, has been intensively investigated. Considering emotions as latent variables, various probabilistic graphical models have been proposed for emotion detection. However, the bag-of-words assumption prohibits those models from capturing the inter-relations between sentences in a document. Moreover, existing models can only detect emotions at either the document-level or the sentence-level. In this paper, we propose an effective Bayesian model, called hidden Topic–Emotion Transition model, by assuming that words in the same sentence share the same emotion and topic and modeling the emotions and topics in successive sentences as a Markov chain. By doing so, not only the document-level emotion but also the sentence-level emotion can be detected simultaneously. Experimental results on the two public corpora show that the proposed model outperforms state-of-the-art approaches on both document-level and sentence-level emotion detection

Conservation and implications of eukaryote transcriptional regulatory regions across multiple species

<p>Abstract</p> <p>Background</p> <p>Increasing evidence shows that whole genomes of eukaryotes are almost entirely transcribed into both protein coding genes and an enormous number of non-protein-coding RNAs (ncRNAs). Therefore, revealing the underlying regulatory mechanisms of transcripts becomes imperative. However, for a complete understanding of transcriptional regulatory mechanisms, we need to identify the regions in which they are found. We will call these transcriptional regulation regions, or TRRs, which can be considered functional regions containing a cluster of regulatory elements that cooperatively recruit transcriptional factors for binding and then regulating the expression of transcripts.</p> <p>Results</p> <p>We constructed a hierarchical stochastic language (HSL) model for the identification of core TRRs in yeast based on regulatory cooperation among TRR elements. The HSL model trained based on yeast achieved comparable accuracy in predicting TRRs in other species, e.g., fruit fly, human, and rice, thus demonstrating the conservation of TRRs across species. The HSL model was also used to identify the TRRs of genes, such as p53 or <it>OsALYL1</it>, as well as microRNAs. In addition, the ENCODE regions were examined by HSL, and TRRs were found to pervasively locate in the genomes.</p> <p>Conclusion</p> <p>Our findings indicate that 1) the HSL model can be used to accurately predict core TRRs of transcripts across species and 2) identified core TRRs by HSL are proper candidates for the further scrutiny of specific regulatory elements and mechanisms. Meanwhile, the regulatory activity taking place in the abundant numbers of ncRNAs might account for the ubiquitous presence of TRRs across the genome. In addition, we also found that the TRRs of protein coding genes and ncRNAs are similar in structure, with the latter being more conserved than the former.</p

pirScan: a webserver to predict piRNA targeting sites and to avoid transgene silencing in C. elegans

pirScan is a web-based tool for identifying C. elegans piRNA-targeting sites within a given mRNA or spliced DNA sequence. The purpose of our tool is to allow C. elegans researchers to predict piRNA targeting sites and to avoid the persistent germline silencing of transgenes that has rendered many constructs unusable. pirScan fulfills this purpose by first enumerating the predicted piRNA-targeting sites present in an input sequence. This prediction can be exported in a tabular or graphical format. Subsequently, pirScan suggests silent mutations that can be introduced to the input sequence that would allow the modified transgene to avoid piRNA targeting. The user can customize the piRNA targeting stringency and the silent mutations that he/she wants to introduce into the sequence. The modified sequences can be re-submitted to be certain that any previously present piRNA-targeting sites are now absent and no new piRNA-targeting sites are accidentally generated. This revised sequence can finally be downloaded as a text file and/or visualized in a graphical format. pirScan is freely available for academic use at http://cosbi4.ee.ncku.edu.tw/pirScan/

Development of a Novel miR-3648-Related Gene Signature as a Prognostic Biomarker in Esophageal Adenocarcinoma

Background: Esophageal adenocarcinoma (EA) is a typical immunogenic malignant tumor with a dismal 5-year survival rate lower than 20%. Although miRNA-3648 (miR-3648) is expressed abnormally in EA, its impact on the tumor immune microenvironment remains unknown. In this study, we sought to identify immune-related genes (IRGs) that are targeted by miR-3648 and develop an EA multigene signature. Methods: The gene expression data of 87 EA tumor samples and 67 normal tissue samples from The Cancer Genome Atlas (TCGA) database and the Genotype-Tissue Expression (GTEx) database were downloaded, respectively. Weighted gene co-expression network analysis (WGCNA), the CIBERSORT algorithm, and Cox regression analysis were applied to identify IRGs and to construct a prognostic signature and nomogram. Results: MiR-3648 was expectedly highly expressed in EA tumor tissues (P=2.6e-8), and related to the infiltration of activated natural killer cells (NK cells) and activated CD4 T lymphocytes (CD4 cells). A total of 70 miR-3648-targeted genes related to immune cell infiltration were identified. Among them, 4 genes (C10orf55, DLL4, PANX2, and NKAIN1) were closely related to overall survival (OS), and were thus selected to construct a 4-gene risk score (RS). The RS had a superior capability to predict OS [area under the curve (AUC) =0.740 for 1 year; AUC =0.717 for 3 years; AUC =0.622 for 5 years]. A higher score was indicative of a poorer prognosis than a lower score [hazard ratio (HR) =2.71; 95% confidence interval (CI): 1.45–5.09; P=0.002]. Furthermore, the nomogram formed by combining the RS and the TNM classification of malignant tumors (TNM stage) improved the accuracy of survival prediction [Harrell’s concordance index (C-index) =0.698]. Conclusions: MiR-3648 may play a critical role in EA pathogenesis. The novel 4-gene signature may serve as a prognostic tool to manage patients with EA