Search

The node deployment problem is a non-deterministic polynomial time (NP-hard). This study proposes a new and efficient method to solve this problem without the need for predefined circumstances about the environments independent of terrain. The proposed method is based on a metaheuristic algorithm and mimics the grey wolf optimizer (GWO) algorithm. In this study, we also suggested an enhanced version of the GWO algorithm to work adaptively in such problems and named it Mutant-GWO (MuGWO). Also, the suggested model ensures connectivity by generating topology graphs and potentially supports data transmission mechanisms. Therefore, the proposed method based on MuGWO can enhance resources utilization, such as reducing the number of nodes, by maximizing the coverage rate and maintaining the connectivity. While most studies assume classical rectangle uniform environments, this study also focuses on custom (environment-aware) maps in line with the importance and requirements of the real world. The motivation of supporting custom maps by this study is that environments can consist of custom shapes with prioritized and critical areas. In this way, environment awareness halts the deployment of nodes in undesired regions and averts resource waste. Besides, novel multi-purpose fitness functions of the proposed method satisfy a convenient approach to calculate costs instead of using complicated processes. Accordingly, this method is suitable for large-scale networks thanks to the capability of the distributed architecture and the metaheuristic-based approach. This study justifies the improvements in the suggested model by presenting comparisons with a Deterministic Grid-based approach and the Original GWO. Moreover, this method outperforms the fruit fly optimization algorithm, bat algorithm (BA), Optimized BA, harmony search, and improved dynamic deployment technique based on genetic algorithm methods in declared scenarios in literature, considering the results of simulations. [ABSTRACT FROM AUTHOR]

Lung cancer is the most common cancer in men and women. This cancer is divided into two main types, namely non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC). Around 85 to 90 percent of lung cancers are NSCLC. Repositioning potent candidate drugs in NSCLC treatment is one of the important topics in cancer studies. Drug repositioning (DR) or drug repurposing is a method for identifying new therapeutic uses of existing drugs. The current study applies a computational drug repositioning method to identify candidate drugs to treat NSCLC patients. To this end, at first, the transcriptomics profile of NSCLC and healthy (control) samples was obtained from the GEO database with the accession number GSE21933. Then, the gene co-expression network was reconstructed for NSCLC samples using the WGCNA, and two significant purple and magenta gene modules were extracted. Next, a list of transcription factor genes that regulate purple and magenta modules' genes was extracted from the TRRUST V2.0 online database, and the TF–TG (transcription factors–target genes) network was drawn. Afterward, a list of drugs targeting TF–TG genes was obtained from the DGIdb V4.0 database, and two drug–gene interaction networks, including drug-TG and drug-TF, were drawn. After analyzing gene co-expression TF–TG, and drug–gene interaction networks, 16 drugs were selected as potent candidates for NSCLC treatment. Out of 16 selected drugs, nine drugs, namely Methotrexate, Olanzapine, Haloperidol, Fluorouracil, Nifedipine, Paclitaxel, Verapamil, Dexamethasone, and Docetaxel, were chosen from the drug-TG sub-network. In addition, nine drugs, including Cisplatin, Daunorubicin, Dexamethasone, Methotrexate, Hydrocortisone, Doxorubicin, Azacitidine, Vorinostat, and Doxorubicin Hydrochloride, were selected from the drug-TF sub-network. Methotrexate and Dexamethasone are common in drug-TG and drug-TF sub-networks. In conclusion, this study proposed 16 drugs as potent candidates for NSCLC treatment through analyzing gene co-expression, TF–TG, and drug–gene interaction networks. [ABSTRACT FROM AUTHOR]

Aptamers can be regarded as efficient substitutes for monoclonal antibodies in many diagnostic and therapeutic applications. Due to the tedious and prohibitive nature of SELEX (systematic evolution of ligands by exponential enrichment), the in silico methods have been developed to improve the enrichment processes rate. However, the majority of these methods did not show any effort in designing novel aptamers. Moreover, some target proteins may have not any binding RNA candidates in nature and a reductive mechanism is needed to generate novel aptamer pools among enormous possible combinations of nucleotide acids to be examined in vitro. We have applied a genetic algorithm (GA) with an embedded binding predictor fitness function to in silico design of RNA aptamers. As a case study of this research, all steps were accomplished to generate an aptamer pool against aminopeptidase N (CD13) biomarker. First, the model was developed based on sequential and structural features of known RNA–protein complexes. Then, utilizing RNA sequences involved in complexes with positive prediction results, as the first-generation, novel aptamers were designed and top-ranked sequences were selected. A 76-mer aptamer was identified with the highest fitness value with a 3 to 6 time higher score than parent oligonucleotides. The reliability of obtained sequences was confirmed utilizing docking and molecular dynamic simulation. The proposed method provides an important simplified contribution to the oligonucleotide–aptamer design process. Also, it can be an underlying ground to design novel aptamers against a wide range of biomarkers. [ABSTRACT FROM AUTHOR]