The gut microbiota plays an important role in human health and disease by acting as a metabolic organ. Metagenomic sequencing has shown how dysbiosis in the gut microbiota is associated with human metabolic diseases such as obesity and diabetes. Modeling may assist to gain insight into the metabolic implication of an altered microbiota. Fast and accurate reconstruction of metabolic models for members of the gut microbiota, as well as methods to simulate a community of microorganisms, are therefore needed. The Integrated Microbial Genomes (IMG) database contains functional annotation for nearly 4,650 bacterial genomes. This tremendous new genomic information adds new opportunities for systems biology to reconstruct accurate genome scale metabolic models (GEMs).

Social networks have become one of our daily life activities not only in socializing but in e-commerce, e-learning, and politics. However, they have more effect on the youth generation all over the world, specifically in the Middle East. Arabic slang language is widely used on social networks more than classical Arabic since most of the users of social networks are young-mid age. However, Arabic slang language suffers from the new expressive (opinion) words and idioms as well as the unstructured format. Mining Arabic slang language requires efficient techniques to extract youth opinions on various issues, such as news websites. In this paper, we constructed a Slang Sentimental Words and Idioms Lexicon (SSWIL) of opinion words is built. In addition, we propose a Gaussian kernel SVM classifier for Arabic slang language to classify Arabic news comments on Facebook. To test the performance of the proposed classifier, several Facebook news comments are used, where 86.86% accuracy rate is obtained with precision 88.63 and recall 78.

Hepatitis C virus (HCV) infection is a worldwide healthcare problem; however, traditional treatment methods have failed to cure all patients, and HCV has developed resistance to new drugs. Systems biology-based analyses could play an important role in the holistic analysis of the impact of HCV on hepatocellular metabolism. Here, we integrated HCV assembly reactions with a genome-scale hepatocyte metabolic model to identify metabolic targets for HCV assembly and metabolic alterations that occur between different HCV progression states (cirrhosis, dysplastic nodule, and early and advanced hepatocellular carcinoma (HCC)) and healthy liver tissue. We found that diacylglycerolipids were essential for HCV assembly. In addition, the metabolism of keratan sulfate and chondroitin sulfate was significantly changed in the cirrhosis stage, whereas the metabolism of acyl-carnitine was significantly changed in the dysplastic nodule and early HCC stages. Our results explained the role of the upregulated expression of BCAT1, PLOD3 and six other methyltransferase genes involved in carnitine biosynthesis and S-adenosylmethionine metabolism in the early and advanced HCC stages. Moreover, GNPAT and BCAP31 expression was upregulated in the early and advanced HCC stages and could lead to increased acyl-CoA consumption. By integrating our results with copy number variation analyses, we observed that GNPAT, PPOX and five of the methyltransferase genes (ASH1L, METTL13, SMYD2, TARBP1 and SMYD3), which are all located on chromosome 1q, had increased copy numbers in the cancer samples relative to the normal samples. Finally, we confirmed our predictions with the results of metabolomics studies and proposed that inhibiting the identified targets has the potential to provide an effective treatment strategy for HCV-associated liver disorders.

Spatiotemporal data represent the real-world objects that move in geographic space over time. The enormous numbers of mobile sensors and location tracking devices continuously produce massive amounts of such data. This leads to the need for scalable spatiotemporal data management systems. Such systems shall be capable of representing spatiotemporal data in persistent storage and in memory. They shall also provide a range of query processing operators that may scale out in a cloud setting. Currently, very few researches have been conducted to meet this requirement. This paper proposes a Hadoop extension with a spatiotemporal algebra. The algebra consists of moving object types added as Hadoop native types, and operators on top of them. The Hadoop file system has been extended to support parameter passing for files that contain spatiotemporal data, and for operators that can be unary or binary. Both the types and operators are accessible for the MapReduce jobs. Such an extension allows users to write Hadoop programs that can perform spatiotemporal analysis. Certain queries may call more than one operator for different jobs and keep these operators running in parallel. This paper describes the design and implementation of this algebra, and evaluates it using a benchmark that is specific to moving object databases.;

Multi-Objective Problems (MOPs) are common real-life problems that can be found in different fields, such as bioinformatics and scheduling. Pareto Optimization (PO) is a popular method for solving MOPs, which optimizes all objectives simultaneously. It provides an effective way to evaluate the quality of multi-objective solutions. Swarm Intelligence (SI) methods are population-based methods that generate multiple solutions to the problem, providing SI methods suitable for MOP solutions. SI methods have certain drawbacks when applied to MOPs, such as swarm leader selection and obtaining evenly distributed solutions over solution space. Whale Optimization Algorithm (WOA) is a recent SI method. In this paper, we propose combining WOA with Tabu Search (TS) for MOPs (MOWOATS). MOWOATS uses TS to store non-dominated solutions in elite lists to guide swarm members, which overcomes the swarm leader selection problem. MOWOATS employs crossover in both intensification and diversification phases to improve diversity of the population. MOWOATS proposes a new diversification step to eliminate the need for local search methods. MOWOATS has been tested over different benchmark multi-objective test functions, such as CEC2009, ZDT, and DTLZ. Results present the efficiency of MOWOATS in finding solutions near Pareto front and evenly distributed over solution space.

The increase of the amount of DNA sequences requires efficient computational algorithms for performing sequence comparison and analysis. Standard compression algorithms are not able to compress DNA sequences because they do not consider special characteristics of DNA sequences (i.e., DNA sequences contain several approximate repeats and complimentary palindromes). Recently, new algorithms have been proposed to compress DNA sequences, often using detection of long approximate repeats. The current work proposes a Lossless Compression Algorithm (LCA), providing a new encoding method. LCA achieves a better compression ratio than that of existing DNA-oriented compression algorithms, when compared to GenCompress, DNACompress, and DNAPack.