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Removal of mobile genetic elements from the genome of Clostridioides difficile and the implications for the organism’s biology
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Clostridioides difficile is an emerging pathogen of One Health significance. Its highly variable genome contains mobile genetic elements (MGEs) such as transposons and prophages that influence its biology. Systematic deletion of each genetic element is required to determine their precise role in C. difficile biology and contribution to the wider mobilome. Here, Tn5397 (21 kb) and ϕ027 (56 kb) were deleted from C. difficile 630 and R20291, respectively, using allele replacement facilitated by CRISPR-Cas9. The 630 Tn5397 deletant transferred PaLoc at the same frequency (1 × 10−7) as 630 harboring Tn5397, indicating that Tn5397 alone did not mediate conjugative transfer of PaLoc. The R20291 ϕ027 deletant was sensitive to ϕ027 infection, and contained two unexpected features, a 2.7 kb remnant of the mutagenesis plasmid, and a putative catalase gene adjacent to the deleted prophage was also deleted. Growth kinetics of R20291 ϕ027 deletant was similar to wild type (WT) in rich medium but marginally reduced compared with WT in minimal medium. This work indicates the commonly used pMTL8000 plasmid series works well for CRISPR-Cas9-mediated gene deletion, resulting in the largest deleted locus (56.8 kb) described in C. difficile. Removal of MGEs was achieved by targeting conjugative/integrative regions to promote excision and permanent loss. The deletants created will be useful strains for investigating Tn5397 or ϕ027 prophage contribution to host virulence, fitness, and physiology, and a platform for other mutagenesis studies aimed at functional gene analysis without native transposon or phage interference in C. difficile 630 and R20291.

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Publication Date
Fri Aug 15 2025
Journal Name
Baghdad Science Journal
Hydrothermal synthesis of high surface area mesoporous silica as an efficient adsorbent for removal of crystal violet dye from aqueous solution
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Publication Date
Sun Jan 14 2018
Journal Name
Journal Of Engineering
Determination Optimum Inventory Level for Material Using Genetic Algorithm
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The integration of decision-making will lead to the robust of its decisions, and then determination optimum inventory level to the required materials to produce and reduce the total cost by the cooperation of purchasing department with inventory department and also with other company,s departments. Two models are suggested to determine Optimum Inventory Level (OIL), the first model (OIL-model 1) assumed that the inventory level for materials quantities equal to the required materials, while the second model (OIL-model 2) assumed that the inventory level for materials quantities more than the required materials for the next period.             &nb

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Publication Date
Mon Jan 02 2017
Journal Name
European Journal Of Scientific Research
Fast approach for arabic text encryption using genetic algorithm
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As s widely use of exchanging private information in various communication applications, the issue to secure it became top urgent. In this research, a new approach to encrypt text message based on genetic algorithm operators has been proposed. The proposed approach follows a new algorithm of generating 8 bit chromosome to encrypt plain text after selecting randomly crossover point. The resulted child code is flipped by one bit using mutation operation. Two simulations are conducted to evaluate the performance of the proposed approach including execution time of encryption/decryption and throughput computations. Simulations results prove the robustness of the proposed approach to produce better performance for all evaluation metrics with res

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Publication Date
Fri Jan 01 2016
Journal Name
International Journal Of Advanced Computer Science And Applications
Automatic Approach for Word Sense Disambiguation Using Genetic Algorithms
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Abstract: Word sense disambiguation (WSD) is a significant field in computational linguistics as it is indispensable for many language understanding applications. Automatic processing of documents is made difficult because of the fact that many of the terms it contain ambiguous. Word Sense Disambiguation (WSD) systems try to solve these ambiguities and find the correct meaning. Genetic algorithms can be active to resolve this problem since they have been effectively applied for many optimization problems. In this paper, genetic algorithms proposed to solve the word sense disambiguation problem that can automatically select the intended meaning of a word in context without any additional resource. The proposed algorithm is evaluated on a col

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Publication Date
Sat Jul 31 2021
Journal Name
Iraqi Journal Of Science
A Decision Tree-Aware Genetic Algorithm for Botnet Detection
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     In this paper, the botnet detection problem is defined as a feature selection problem and the genetic algorithm (GA) is used to search for the best significant combination of features from the entire search space of set of features. Furthermore, the Decision Tree (DT) classifier is used as an objective function to direct the ability of the proposed GA to locate the combination of features that can correctly classify the activities into normal traffics and botnet attacks. Two datasets  namely the UNSW-NB15 and the Canadian Institute for Cybersecurity Intrusion Detection System 2017 (CICIDS2017), are used as evaluation datasets. The results reveal that the proposed DT-aware GA can effectively find the relevant features from

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Publication Date
Sun Mar 01 2020
Journal Name
Plant Archives
Thermodynamic and kinetic analysis of Basic green-4 dye Removal from aqueous solutions using adsorption technique
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In this work, a local sunflower husk (SFH) was used as a natural surface for removing Basic Green-4 (BG4) dye, as a watersoluble pollutant. The effect of initial concentration, contact time, the mass of surface of the dye with the SFH as well as the medium temperature was studied. The application of Langmuir, Freundlich isotherms on the collected data of the adsorption process found to harmonize to Freundlich equation more than that of Langmuir. However, the adsorbed mass of BG4 dye showed a direct increase with the increase of SFH mass and equilibrium was achieved within a 60min window. The interaction of BG4 with SFH surface was spontaneous and exothermic. The empirical kinetic outcomes at ambient temperatures were applied to pseudo 1st a

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Publication Date
Fri Jan 01 2021
Journal Name
Desalination And Water Treatment
Removal of toxic dye (Rhodamine B) from aqueous solutions by natural smectite (SMC) and SMC-nanoTiO2
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Publication Date
Fri Mar 31 2017
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Removal of Ni(II), Pb(II), and Cu(II) from Industrial Wastewater by Using NF Membrane
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This article reviews the technical applicability of nanofiltration membrane process for the removal of nickel, lead, and copper ions from industrial wastewater.

Synthetic industrial wastewater samples containing Ni(II), Pb(II), and Cu(II) ions at various concentrations (50, 100, 150 and 200 ppm), under different pressures (1, 2, 3 and 4 bar), temperatures (10, 20, 30 and 40 oC), pH (2, 3, 4, 5 and 5.5), and flow rates (1, 2, 3 and 4 L/hr), were prepared and subjected treated by NF systems in the laboratory. Suitable NF membrane was chosen after testing a number of NF membranes (University of Technology-Baghdad), in terms of production and removal. NF system was capable of removing more than (85%, 78%, and 66% for Ni(II

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Publication Date
Fri Aug 06 2021
Journal Name
Desalination And Water Treatment
Removal of toxic dye (Rhodamine B) from aqueous solutions by natural smectite (SMC) and SMC-nanoTiO2
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Titanium oxide nanoparticles-modified smectite (SMC-nTiO2) as a low-cost adsorbent was investigated for the removal of Rhodamine B (RhB) from aqueous solutions. The adsorbents (SMC and SMC-nTiO2) were characterized by scanning electron microscopy, Fourier transforms infrared spectroscopy, and energy-dispersive X-ray spectroscopy. The effects of various parameters like contact time, adsorbent weight, pH, and temperatures were examined. Three kinetic equations (pseudo-first-order (PFO), pseudo-second-order (PSO), and intra-particle diffusion) were used to evaluate the experimental kinetic of the data and the results showed that the adsorption process is in line with the PSO kinetic model. Adsorption equilibrium isotherms were modeled using La

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Publication Date
Fri May 01 2020
Journal Name
Journal Of Engineering
Removal of Acidic Dye from Aqueous Solution Using Surfactant Modified Bentonite (Organoclay): Batch and Kinetic Study
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Modified bentonite has been used as effective sorbent material for the removal of acidic dye (methyl orange) from aqueous solution in batch system. The natural bentonite has been modified using cationic surfactant (cetyltrimethyl ammonium bromide) in order to obtain an efficient sorbent through converting the properties of bentonite from hydrophilic to organophilic. The characteristics of the natural and modified bentonite were examined through several analyses such as Scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and Surface area. The batch study was provided the maximum dye removal efficiency of 88.75 % with a sorption capacity of 555.56 mg/g at specified conditions (150 min, pH= 2, 250 rpm, and 0.

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