81 research outputs found
sj-docx-1-evb-10.1177_11769343241229278 – Supplemental material for A Comprehensive Analysis of 3 Moroccan Genomes Revealed Contributions From Both African and European Ancestries
No full textSupplemental material, sj-docx-1-evb-10.1177_11769343241229278 for A Comprehensive Analysis of 3 Moroccan Genomes Revealed Contributions From Both African and European Ancestries by Nasma Boumajdi, Houda Bendani, Souad Kartti, Tarek Alouane, Lahcen Belyamani and Azeddine Ibrahimi in Evolutionary Bioinformatics</p
sj-docx-1-evb-10.1177_11769343231169374 – Supplemental material for In Silico Analyses of All STAT3 Missense Variants Leading to Explore Divergent AD-HIES Clinical Phenotypes
No full textSupplemental material, sj-docx-1-evb-10.1177_11769343231169374 for In Silico Analyses of All STAT3 Missense Variants Leading to Explore Divergent AD-HIES Clinical Phenotypes by Mariam Mansouri, Ghyzlane El Haddoumi, Houda Bendani, Nasma Boumajdi, Mohammed Hakmi, Hanane Abbou, El Mehdi Bouricha, Boutaina Elgharbaoui, Souad Kartti, Rachid El Jaoudi, Lahcen Belyamani, Ilham Kandoussi, Azeddine Ibrahimi and Naima El Hafidi in Evolutionary Bioinformatics</p
Deep Learning and Support Vector Machine Algorithms Applied for Fault Detection in Electrical Power Transmission Network
No full textIn this paper, an interesting application of machine learning algorithms is presented. The main idea consists of applying both deep-learning and support vector machine supervised machine learning approaches to improve the quality and to guarantee the stability and the reliability of an electric power transmission system. These techniques are used mainly to detect, classify, and consequently locate faults in the electric power transmission network. To test the performance of the proposed techniques, the standard IEEE 14-bus power system is used. The fault free, the one fault and the multiple fault cases are investigated. Faults are applied to the IEEE 14-bus system and simulated using SimPowerSystems toolbox of Matlab. The accuracy score is used to compare the proposed techniques performances. Different results proved that studied machine learning methods made correct predictions. Nevertheless, the deep learning algorithm performances are proved while classifying all types of faults. Simulation results demonstrate that the deep learning technique can achieve an accuracy of 100% compared to the support vector machine which had an accuracy of 87%. © 2023, The Author(s), under exclusive license to Springer Nature Switzerland AG.udemauteur: Azeddine Kaddour
Hypothesis Insight into the mechanism of lipids binding and uptake by CD36 receptor
No full textAbstract: The membrane protein CD36 is a member of the class B scavenger receptor family. It plays a crucial role in some cardiovascular pathologies and metabolic diseases. Studying the mechanism of action of CD36 receptor is limited due to the absence of its tridimensional crystallized structure. The molecular docking method has allowed us to perform various simulation of the CD36 receptor interaction with their ligands involved in the development of some diseases. In this work, we predicted a tridimensional structure model of CD36 extracellular domain. In addition, we have achieved several tests of rigid and flexible docking by acting on residues proposed in previous experimental researches as essential in fixing of LFCAs. Furthermore, we have acted on regions that appear a key binding site of LFCAs. The physicoc hemical evaluation indicated the reliability of the proposed CD36 structure used for different molecular docking tests. Based on the docking outcome, we were able to propose the different steps of the mechanism allowing the interaction of fatty acids on CD36 receptor and their penetration into the cell cytoplasm. The obtained results and taking in consideration CD36 receptor as a therapeutic target will help us to suggest the mechanism by which an antagonist may inhibit this receptor by acting on its extracellular domain. Keywords: CD36-LCFAs interaction, rigid docking, flexible docking. Background: CD36 is a transmembrane glycoprotein which consists of a single peptide chain of 472 amino acids and has a molecular weight of 88 kDa. CD36 belongs to the class B scavenger receptor family, which includes the receptor for selective cholesteryl ester uptake, scavenger receptor class B type I (SR-BI), and lysosomal integral membrane protein 2 (LIMP-
Recommended from our members
Advocating for People with Disabilities
No full textThe Global Partnership for Education estimates that in low and lower-middle income countries, 90% of children with disabilities do not go to school (Right to Education Initiative,2018). This project set to improve the accessibility for people with disabilities in the Faculty of Medicine and Pharmacy of Rabat (FMP-Rabat) in collaboration with our sponsor Dr. Azeddine Ibrahimi. We conducted building assessments using ADA Standards, interviews with professionals, and focus groups to identify and prioritize needs that would improve handicap accessibility. We found that the infrastructure and lack of sensibilization at the school made it difficult for students with disabilities to attend. We recommended improvements in areas such as navigation, space accessibility, and services
The effect of wetting on the relative permeability behavior and oil recovery
No full textOil is one of the major contributors to energy consumption. Oil reserves are expressed as the total amount of economically and technically producible oil. Total oil consumption is increasing (per capita it remains more or less the same) but it has no unambiguous influence on the remaining reserves due to new discoveries. However, increasingly sophisticated recovery methods are used to produce oil i.e. enhanced oil recovery methods. A recently proposed enhanced oil recovery method is by injection of low-salinity water in completely oil-wet reservoirs, which leads to more water-wet behavior and “consequently” to improved oil recovery.This report will focus on the effect of wettability on the recovery efficiency. Based on the papers by Lomeland, Ebeltoft and Thomas we derive so-called LET relative permeability curves that only depend on irreducible water saturation. This is possible by using the irreducible water saturation dependence of the residual oil saturation, end point relative water permeability and the sketched behavior (Lomeland, Ebeltoft and Thomas) of the other six parameters. Admittedly this is a gross simplification, but it grasps the essence of the relative permeability behavior and makes it possible to study the recovery in terms of two parameters viz. the irreducible water saturation and viscosity ratio as opposed to eight relative permeability parameters and the viscosity ratio. High irreducible water saturation is both indicative of pore size heterogeneity and water-wet behavior. We use the theory of Buckley-Leverett to construct recovery curves for 1D and 2D displacement and various mobility (M = displacing fluid mobility / displaced fluid mobility) ratios. We solve the 1-D equations both analytically (using fractional flow theory) and numerically. For the numerical simulations in 1D and 2D we use COMSOL 5.2©. The simulations show that water-wet behavior is conducive to stable displacement, however, low recovery at breakthrough, whereas intermediate oil-wet behavior is more unstable but conducive to high ultimate recoveries. Completely oil-wet behavior leads to less stable displacement and low ultimate recoveries.Applied Earth Science
Drag Reduction in Turbulent Flows by Polymers and Surfactants: An Experimental Study Into the Mechanisms of Drag Reduction by Additives
No full textIn 1949, Toms (Toms B.A., (1949, 1977)) observed that small amounts of a drag reducing agent (DRA) could cause a considerable drag reduction in turbulent pipe flow. In application of polymer enhanced oil recovery, degradation of polymers in the supply lead could cause clogging. It was, however observed that surfactants at sufficiently high concentration also showed drag reduction without the problem clogging. A DRA reduces the energy loss by friction and unstable flow, thus improving injection throughput with the same pressure pump and thereby reducing the exergetic pumping costs. This study investigates experimentally the drag reducing capacity of surfactants and compares it to the drag reducing capacity of polymers.For the experiment, a set-up consisting of a pump, a coiled test tube with a length of 1.48 m and an inner diameter of 0.5 mm and pressure gauges is built. The diameter of the coil is 12.5 cm. We use a pump capable of injection up to 200 ml/min. The pressure drop is measured between the entrance and end of the tube. The injection rate is varied between 1 and 200 ml/min, roughly corresponding to Reynolds numbers between 50 and 10,000. The additives are dissolved in brine with a 33,000 ppm salt concentration. The viscosity of the solution is dependent on the concentration of the DRA. The ratio of the measured pressure drop with only brine and the pressure drop with the DRA solution was used to calculate the drag reduction (DR) factor, as from a technical point of view we are only interested whether adding DRA reduces the drag with respect to the original brine solution. From an academic point of view, we remark that for low concentrations the viscosity enhancement due to the presence of the DRA is negligible. As polymers we use xanthan (a biopolymer), and a synthetic emulsion polymer based on polyacrylamide. Maximum DR factors are 23% for xanthan at 90ppm and 32% at 90ppm for the synthetic emulsion polymer. DR only occurs at turbulent conditions.Three types of surfactants, each from a different branch of surfactants are used in this study. The surfactants used are AOS {훼-Olefin Sulfonate}, CTAB {hexadeCylTrimethylAmmonium Bromide} and APG {Alkyl PolyGlucoside} which are a cationic, anionic and a nonionic surfactant respectively. The surfactants did not show any DR at (for DRA applications) high concentrations up to 20.000ppm. Addition of Sodium Salicylate (NaSaL) to CTAB with a 1:1 ratio led to a maximum DR of 33% at 2500 ppm concentration.Several pressure gauges have been installed along the test tube in order to observe how the pressure drops along the tube, how the DRAs affect these pressure drops and at what location of the test tube the DR factor is the highest. It is found that xanthan has the same DR factor at each location of the test tube, the emulsion polymer has a decreasing DR factor as the distance from the inlet of the test tube increases and the CTAB+NaSaL DRA has an increasing DR factor as the distance from the inlet increases.The DRAs are sheared using a constriction in the flow loop while the degradation is monitored. It is observed that xanthan is less susceptible to degradation in comparison to the emulsion polymer due to its more rigid chemical structure. But xanthan and the emulsion polymer would be inefficient to use in looped flow systems as they are affected by degradation. The CTAB+NaSaL DRA on the other hand shows no degradation meaning that the micellar rod-like structures that give the DR effect are being repaired when the shear force is being removed. However, for surfactants higher concentrations (1000-2500 ppm) are required.Petroleum Engineering and Geo-science
Functional analysis and comparative genomics of Rahnella perminowiae S11P1 and Variovorax sp. S12S4, two plant growth-promoting rhizobacteria isolated from Crocus sativus L. (saffron) rhizosphere
No full textAbstract Background Rahnella perminowiae S11P1 and Variovorax sp. S12S4 are two plant growth-promoting rhizobacteria that were previously isolated from the rhizosphere of Crocus sativus L. (saffron), and have demonstrated interesting PGP activities and promising results when used as inoculants in field trials. To further elucidate the molecular mechanisms underlying their beneficial effects on plant growth, comprehensive genome mining of S11P1 and S12S4 and comparative genomic analysis with closely related strains were conducted. Results Functional annotation of the two strains predicted a large number of genes involved in auxin and siderophore production, nitrogen fixation, sulfur metabolism, organic acid biosynthesis, pyrroloquinoline quinone production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, volatile organic compounds production, and polyamine biosynthesis. In addition, numerous genes implicated in plant-bacteria interactions, such as those involved in chemotaxis and quorum sensing, were predicted. Moreover, the two strains carried genes involved in bacterial fitness under abiotic stress conditions. Comparative genomic analysis revealed an open pan-genomic structure for the two strains. COG annotation showed that higher fractions of core and accessory genes were involved in the metabolism and transport of carbohydrates and amino acids, suggesting the metabolic versatility of the two strains as effective rhizosphere colonizers. Furthermore, this study reports the first comparison of Multilocus sequence analysis (MLSA) and core-based phylogenies of the Rahnella and Variovorax genera. Conclusions The present study unveils the molecular mechanisms underlying plant growth promotion and biocontrol activity of S11P1 and S12S4, and provides a basis for their further biotechnological application in agriculture
Virtual docking screening and QSAR studies to explore AKT and mTOR inhibitors acting on PI3K in cancers
No full textThe phosphoinositide 3-kinase (PI3K) pathway is an important regulator of cell proliferation and metabolism. PI3K activation initiates a signal transduction cascade, of which the major effectors are the kinases AKT and mTOR. Aberrant activation of the PI3K/AKT/mTOR pathway is frequently observed in many human malignancies and the combination of compounds simultaneously targeting different related molecules in the PI3K/AKT/mTOR pathway leads to synergistic activity. To explore the competing common ATP inhibitors PI3K/AKT and PI3K/mTOR we developed a model PI3K-SAR 2D which made it possible to predict the bioactivity of inhibitors of AKT and mTOR towards PI3K; the interaction of the best inhibitors was evaluated by docking analysis and compared to that of dactolisib and pictilisib. A PI3K-SAR model with a correlation coefficient (R2) of 0.81706 and an RMSE of 0.16029 was obtained, which was validated and evaluated by a cross-validation method, LOO. The most predicted AKT and mTOR inhibitors present respectively pIC50 activities between 9.26–9.93 and 9.59–9.87.
After docking and several comparisons, inhibitors with better predictions showed better affinity and interaction with PI3K compared to pictilisib and dactolisib, so we found that 4 inhibitors of AKT and 14 mTOR inhibitors met the criteria of Lipinski and Veber and could be future drugs
- …
