Displaying publications 81 - 100 of 605 in total

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  1. Application of the linear interaction energy method (LIE) to estimate the binding free energy values of Escherichia coli wild-type and mutant arginine repressor C-terminal domain (ArgRc)-l-arginine and ArgRc-l-citrulline protein-ligand complexes
    Asi AM, Rahman NA, Merican AF
    J Mol Graph Model, 2004 Mar;22(4):249-62.
    PMID: 15177077
    Protein-ligand binding free energy values of wild-type and mutant C-terminal domain of Escherichia coli arginine repressor (ArgRc) protein systems bound to L-arginine or L-citrulline molecules were calculated using the linear interaction energy (LIE) method by molecular dynamics (MD) simulation. The binding behaviour predicted by the dissociation constant (K(d)) calculations from the binding free energy values showed preferences for binding of L-arginine to the wild-type ArgRc but not to the mutant ArgRc(D128N). On the other hand, L-citrulline do not favour binding to wild-type ArgRc but prefer binding to mutant ArgRc(D128N). The dissociation constant for the wild-type ArgRc-L-arginine complex obtained in this study is in agreement with reported experimental results. Our results also support the experimental data for the binding of L-citrulline to the mutant ArgRc(D128N). These showed that LIE method for protein-ligand binding free energy calculation could be applied to the wild-type and the mutant E. coli ArgRc-L-arginine and ArgRc-L-citrulline protein-ligand complexes and possibly to other transcriptional repressor-co-repressor systems as well.
    Matched MeSH terms: Computer Simulation*
  2. Investigation of two-way fluid-structure interaction of blood flow in a patient-specific left coronary artery
    Athani A, Ghazali NNN, Badruddin IA, Kamangar S, Anqi AE, Algahtani A
    Biomed Mater Eng, 2022;33(1):13-30.
    PMID: 34366314 DOI: 10.3233/BME-201171
    BACKGROUND: The blood flow in the human artery has been a subject of sincere interest due to its prime importance linked with human health. The hemodynamic study has revealed an essential aspect of blood flow that eventually proved to be paramount to make a correct decision to treat patients suffering from cardiac disease.

    OBJECTIVE: The current study aims to elucidate the two-way fluid-structure interaction (FSI) analysis of the blood flow and the effect of stenosis on hemodynamic parameters.

    METHODS: A patient-specific 3D model of the left coronary artery was constructed based on computed tomography (CT) images. The blood is assumed to be incompressible, homogenous, and behaves as Non-Newtonian, while the artery is considered as a nonlinear elastic, anisotropic, and incompressible material. Pulsatile flow conditions were applied at the boundary. Two-way coupled FSI modeling approach was used between fluid and solid domain. The hemodynamic parameters such as the pressure, velocity streamline, and wall shear stress were analyzed in the fluid domain and the solid domain deformation.

    RESULTS: The simulated results reveal that pressure drop exists in the vicinity of stenosis and a recirculation region after the stenosis. It was noted that stenosis leads to high wall stress. The results also demonstrate an overestimation of wall shear stress and velocity in the rigid wall CFD model compared to the FSI model.

    Matched MeSH terms: Computer Simulation
  3. Visualization of multiphase pulsatile blood over single phase blood flow in a patient specific stenosed left coronary artery using image processing technique
    Athani A, Ghazali NNN, Anjum Badruddin I, Kamangar S, Salman Ahmed NJ, Honnutagi A
    Biomed Mater Eng, 2023;34(1):13-35.
    PMID: 36278331 DOI: 10.3233/BME-211333
    BACKGROUND: Coronary arteries disease has been reported as one of the principal roots of deaths worldwide.

    OBJECTIVE: The aim of this study is to analyze the multiphase pulsatile blood flow in the left coronary artery tree with stenosis.

    METHODS: The 3D left coronary artery model was reconstructed using 2D computerized tomography (CT) scan images. The Red Blood Cell (RBC) and varying hemodynamic parameters for single and multiphase blood flow conditions were analyzed.

    RESULTS: Results asserted that the multiphase blood flow modeling has a maximum velocity of 1.017 m/s and1.339 m/s at the stenosed region during the systolic and diastolic phases respectively. The increase in Wall Shear Stress (WSS) observed at the stenosed region during the diastole phase as compared during the systolic phase. It was also observed that the highest Oscillatory Shear Index (OSI) regions are found in the downstream area of stenosis and across the bifurcations. The increase in RBCs velocity from 0.45 m/s to 0.6 m/s across the stenosis was also noticed.

    CONCLUSION: The computational multiphase blood flow analysis improves the understanding and accuracy of the complex flow conditions of blood elements (RBC and Plasma) and provides the progression of the disease development in the coronary arteries. This study helps to enhance the diagnosis of the blocked (stenosed) arteries more precisely compared to the single-phase blood flow modeling.

    Matched MeSH terms: Computer Simulation
  4. Fulltext Seismic performance of RC beam-column connections with continuous rectangular spiral transverse reinforcements for low ductility classes
    Azimi M, Bin Adnan A, Sam AR, Tahir MM, Faridmehr I, Hodjati R
    ScientificWorldJournal, 2014;2014:802605.
    PMID: 25309957 DOI: 10.1155/2014/802605
    The seismic performance of RC columns could be significantly improved by continuous spiral reinforcement as a result of its adequate ductility and energy dissipation capacity. Due to post-earthquake brittle failure observations in beam-column connections, the seismic behaviour of such connections could greatly be improved by simultaneous application of this method in both beams and columns. In this study, a new proposed detail for beam to column connection introduced as "twisted opposing rectangular spiral" was experimentally and numerically investigated and its seismic performance was compared against normal rectangular spiral and conventional shear reinforcement systems. In this study, three full scale beam to column connections were first designed in conformance with Eurocode (EC2-04) for low ductility class connections and then tested by quasistatic cyclic loading recommended by ACI Building Code (ACI 318-02). Next, the experimental results were validated by numerical methods. Finally, the results revealed that the new proposed connection could improve the ultimate lateral resistance, ductility, and energy dissipation capacity.
    Matched MeSH terms: Computer Simulation
  5. Effects of vibration on occupant driving performance under simulated driving conditions
    Azizan A, Fard M, Azari MF, Jazar R
    Appl Ergon, 2017 Apr;60:348-355.
    PMID: 28166895 DOI: 10.1016/j.apergo.2016.12.020
    Although much research has been devoted to the characterization of the effects of whole-body vibration on seated occupants' comfort, drowsiness induced by vibration has received less attention to date. There are also little validated measurement methods available to quantify whole body vibration-induced drowsiness. Here, the effects of vibration on drowsiness were investigated. Twenty male volunteers were recruited for this experiment. Drowsiness was measured in a driving simulator, before and after 30-min exposure to vibration. Gaussian random vibration, with 1-15 Hz frequency bandwidth was used for excitation. During the driving session, volunteers were required to obey the speed limit of 100 kph and maintain a steady position on the left-hand lane. A deviation in lane position, steering angle variability, and speed deviation were recorded and analysed. Alternatively, volunteers rated their subjective drowsiness by Karolinska Sleepiness Scale (KSS) scores every 5-min. Following 30-min of exposure to vibration, a significant increase of lane deviation, steering angle variability, and KSS scores were observed in all volunteers suggesting the adverse effects of vibration on human alertness level.
    Matched MeSH terms: Computer Simulation
  6. Dihydroquinazolin-4(1H)-one derivatives as novel and potential leads for diabetic management
    Babatunde O, Hameed S, Salar U, Chigurupati S, Wadood A, Rehman AU, et al.
    Mol Divers, 2021 Mar 01.
    PMID: 33650031 DOI: 10.1007/s11030-021-10196-5
    A variety of dihydroquinazolin-4(1H)-one derivatives (1-37) were synthesized via "one-pot" three-component reaction scheme by treating aniline and different aromatic aldehydes with isatoic anhydride in the presence of acetic acid. Chemical structures of compounds were deduced by different spectroscopic techniques including EI-MS, HREI-MS, 1H-, and 13C-NMR. Compounds were subjected to α-amylase and α-glucosidase inhibitory activities. A number of derivatives exhibited significant to moderate inhibition potential against α-amylase (IC50 = 23.33 ± 0.02-88.65 ± 0.23 μM) and α-glucosidase (IC50 = 25.01 ± 0.12-89.99 ± 0.09 μM) enzymes, respectively. Results were compared with the standard acarbose (IC50 = 17.08 ± 0.07 μM for α-amylase and IC50 = 17.67 ± 0.09 μM for α-glucosidase). Structure-activity relationship (SAR) was rationalized by analyzing the substituents effects on inhibitory potential. Kinetic studies were implemented to find the mode of inhibition by compounds which revealed competitive inhibition for α-amylase and non-competitive inhibition for α-glucosidase. However, in silico study identified several important binding interactions of ligands (synthetic analogues) with the active site of both enzymes.
    Matched MeSH terms: Computer Simulation
  7. The Repurposing of Ivermectin for Malaria: A Prospective Pharmacokinetics-Based Virtual Clinical Trials Assessment of Dosing Regimen Options
    Badhan R, Zakaria Z, Olafuyi O
    J Pharm Sci, 2018 08;107(8):2236-2250.
    PMID: 29626533 DOI: 10.1016/j.xphs.2018.03.026
    Ivermectin has demonstrated many successes in the treatment of a range of nematode infections. Considering the increase in malaria resistance, attention has turned toward ivermectin as a candidate for repurposing for malaria. This study developed and validated an ivermectin physiology-based pharmacokinetic model in healthy adults (20-50 years), pediatric (3-5 years/15-25 kg) subjects, and a representative adult malaria population group (Thailand). Dosing optimization demonstrating a twice-daily dose for 3- or 5-day regimens would provide a time above the LC50 of more than 7 days for adult and pediatric subjects. Furthermore, to address the occurrence of CYP450 induction that is often encountered with antiretroviral agents, simulated drug-drug interaction studies with efavirenz highlighted that a 1-mg/kg once-daily dose for 5 days would counteract the increased ivermectin hepatic clearance and enable a time above LC50 of 138.8 h in adults and 141.2 h in pediatric subjects. It was also demonstrated that dosage regimen design would require consideration of the age-weight geographical relationship of the subjects, with a dosage regimen for a representative Thailand population group requiring at least a single daily dose for 5 days to maintain ivermectin plasma concentrations and a time above LC50 similar to that in healthy adults.
    Matched MeSH terms: Computer Simulation
  8. Fulltext Vaccines alone are no silver bullets: a modeling study on the impact of efficient contact tracing on COVID-19 infection and transmission in Malaysia
    Baha Raja D, Abdul Taib NA, Teo AKJ, Jayaraj VJ, Ting CY
    Int Health, 2023 Jan 03;15(1):37-46.
    PMID: 35265998 DOI: 10.1093/inthealth/ihac005
    BACKGROUND: The computer simulation presented in this study aimed to investigate the effect of contact tracing on coronavirus disease 2019 (COVID-19) transmission and infection in the context of rising vaccination rates.

    METHODS: This study proposed a deterministic, compartmental model with contact tracing and vaccination components. We defined contact tracing effectiveness as the proportion of contacts of a positive case that was successfully traced and the vaccination rate as the proportion of daily doses administered per population in Malaysia. Sensitivity analyses on the untraced and infectious populations were conducted.

    RESULTS: At a vaccination rate of 1.4%, contact tracing with an effectiveness of 70% could delay the peak of untraced asymptomatic cases by 17 d and reduce it by 70% compared with 30% contact tracing effectiveness. A similar trend was observed for symptomatic cases when a similar experiment setting was used. We also performed sensitivity analyses by using different combinations of contact tracing effectiveness and vaccination rates. In all scenarios, the effect of contact tracing on COVID-19 incidence persisted for both asymptomatic and symptomatic cases.

    CONCLUSIONS: While vaccines are progressively rolled out, efficient contact tracing must be rapidly implemented concurrently to reach, find, test, isolate and support the affected populations to bring COVID-19 under control.

    Matched MeSH terms: Computer Simulation
  9. Fulltext Primary stability recognition of the newly designed cementless femoral stem using digital signal processing
    Baharuddin MY, Salleh ShH, Hamedi M, Zulkifly AH, Lee MH, Mohd Noor A, et al.
    Biomed Res Int, 2014;2014:478248.
    PMID: 24800230 DOI: 10.1155/2014/478248
    Stress shielding and micromotion are two major issues which determine the success of newly designed cementless femoral stems. The correlation of experimental validation with finite element analysis (FEA) is commonly used to evaluate the stress distribution and fixation stability of the stem within the femoral canal. This paper focused on the applications of feature extraction and pattern recognition using support vector machine (SVM) to determine the primary stability of the implant. We measured strain with triaxial rosette at the metaphyseal region and micromotion with linear variable direct transducer proximally and distally using composite femora. The root mean squares technique is used to feed the classifier which provides maximum likelihood estimation of amplitude, and radial basis function is used as the kernel parameter which mapped the datasets into separable hyperplanes. The results showed 100% pattern recognition accuracy using SVM for both strain and micromotion. This indicates that DSP could be applied in determining the femoral stem primary stability with high pattern recognition accuracy in biomechanical testing.
    Matched MeSH terms: Computer Simulation
  10. Fulltext Design process of cementless femoral stem using a nonlinear three dimensional finite element analysis
    Baharuddin MY, Salleh ShH, Zulkifly AH, Lee MH, Noor AM, A Harris AR, et al.
    BMC Musculoskelet Disord, 2014;15:30.
    PMID: 24484753 DOI: 10.1186/1471-2474-15-30
    Minimal available information concerning hip morphology is the motivation for several researchers to study the difference between Asian and Western populations. Current use of a universal hip stem of variable size is not the best option for all femur types. This present study proposed a new design process of the cementless femoral stem using a three dimensional model which provided more information and accurate analysis compared to conventional methods.
    Matched MeSH terms: Computer Simulation
  11. Biomechanical analysis of rheumatoid arthritis of the wrist joint
    Bajuri MN, Kadir MR, Amin IM, Ochsner A
    Proc Inst Mech Eng H, 2012 Jul;226(7):510-20.
    PMID: 22913098 DOI: 10.1177/0954411912445846
    The wrist is the most complex joint for virtual three-dimensional simulations, and the complexity is even more pronounced when dealing with skeletal disorders of the joint such, as rheumatoid arthritis (RA). In order to analyse the biomechanical difference between healthy and diseased joints, three-dimensional models of these two wrist conditions were developed from computed tomography images. These images consist of eight carpal bones, five metacarpal bones, the distal radius and ulna. The cartilages were developed based on the shape of the available articulations and ligaments were simulated via mechanical links. The RA model was developed accurately by simulating all ten common criteria of the disease related to the wrist. Results from the finite element (FE) analyses showed that the RA model produced three times higher contact pressure at the articulations compared to the healthy model. Normal physiological load transfer also changed from predominantly through the radial side to an increased load transfer approximately 5% towards the ulnar. Based on an extensive literature search, this is the first ever reported work that simulates the pathological conditions of the rheumatoid arthritis of the wrist joint.
    Matched MeSH terms: Computer Simulation
  12. A hyperelastic fibre-reinforced continuum model of healing tendons with distributed collagen fibre orientations
    Bajuri MN, Isaksson H, Eliasson P, Thompson MS
    Biomech Model Mechanobiol, 2016 12;15(6):1457-1466.
    PMID: 26951049
    The healing process of ruptured tendons is problematic due to scar tissue formation and deteriorated material properties, and in some cases, it may take nearly a year to complete. Mechanical loading has been shown to positively influence tendon healing; however, the mechanisms remain unclear. Computational mechanobiology methods employed extensively to model bone healing have achieved high fidelity. This study aimed to investigate whether an established hyperelastic fibre-reinforced continuum model introduced by Gasser, Ogden and Holzapfel (GOH) can be used to capture the mechanical behaviour of the Achilles tendon under loading during discrete timepoints of the healing process and to assess the model's sensitivity to its microstructural parameters. Curve fitting of the GOH model against experimental tensile testing data of rat Achilles tendons at four timepoints during the tendon repair was used and achieved excellent fits ([Formula: see text]). A parametric sensitivity study using a three-level central composite design, which is a fractional factorial design method, showed that the collagen-fibre-related parameters in the GOH model-[Formula: see text] and [Formula: see text]-had almost equal influence on the fitting. This study demonstrates that the GOH hyperelastic fibre-reinforced model is capable of describing the mechanical behaviour of healing tendons and that further experiments should focus on establishing the structural and material parameters of collagen fibres in the healing tissue.
    Matched MeSH terms: Computer Simulation
  13. Generalized variable projective synchronization of time delayed systems
    Banerjee S, Theesar SJ, Kurths J
    Chaos, 2013 Mar;23(1):013118.
    PMID: 23556955 DOI: 10.1063/1.4791589
    We study generalized variable projective synchronization between two unified time delayed systems with constant and modulated time delays. A novel Krasovskii-Lyapunov functional is constructed and a generalized sufficient condition for synchronization is derived analytically using the Lyapunov stability theory and adaptive techniques. The proposed scheme is valid for a system of n-numbers of first order delay differential equations. Finally, a new neural oscillator is considered as a numerical example to show the effectiveness of the proposed scheme.
    Matched MeSH terms: Computer Simulation
  14. Synthesis, in vitro biological activities and in silico study of dihydropyrimidines derivatives
    Barakat A, Islam MS, Al-Majid AM, Ghabbour HA, Fun HK, Javed K, et al.
    Bioorg Med Chem, 2015 Oct 15;23(20):6740-8.
    PMID: 26381063 DOI: 10.1016/j.bmc.2015.09.001
    We describe here the synthesis of dihydropyrimidines derivatives 3a-p, and evaluation of their α-glucosidase enzyme inhibition activities. Compounds 3b (IC50=62.4±1.5 μM), 3c (IC50=25.3±1.26 μM), 3d (IC50=12.4±0.15 μM), 3e (IC50=22.9±0.25 μM), 3g (IC50=23.8±0.17 μM), 3h (IC50=163.3±5.1 μM), 3i (IC50=30.6±0.6 μM), 3m (IC50=26.4±0.34 μM), and 3o (IC50=136.1±6.63 μM) were found to be potent α-glucosidase inhibitors in comparison to the standard drug acarbose (IC50=840±1.73 μM). The compounds were also evaluated for their in vitro cytotoxic activity against PC-3, HeLa, and MCF-3 cancer cell lines, and 3T3 mouse fibroblast cell line. All compounds were found to be non cytotoxic, except compounds 3f and 3m (IC50=17.79±0.66-20.44±0.30 μM), which showed a weak cytotoxic activity against the HeLa, and 3T3 cell lines. In molecular docking simulation study, all the compounds were docked into the active site of the predicted homology model of α-glucosidase enzyme. From the docking result, it was observed that most of the synthesized compounds showed interaction through carbonyl oxygen atom and polar phenyl ring with active site residues of the enzyme.
    Matched MeSH terms: Computer Simulation*
  15. Improvement of production of citric acid from oil palm empty fruit bunches: optimization of media by statistical experimental designs
    Bari MN, Alam MZ, Muyibi SA, Jamal P, Abdullah-Al-Mamun
    Bioresour Technol, 2009 Jun;100(12):3113-20.
    PMID: 19231166 DOI: 10.1016/j.biortech.2009.01.005
    A sequential optimization based on statistical design and one-factor-at-a-time (OFAT) method was employed to optimize the media constituents for the improvement of citric acid production from oil palm empty fruit bunches (EFB) through solid state bioconversion using Aspergillus niger IBO-103MNB. The results obtained from the Plackett-Burman design indicated that the co-substrate (sucrose), stimulator (methanol) and minerals (Zn, Cu, Mn and Mg) were found to be the major factors for further optimization. Based on the OFAT method, the selected medium constituents and inoculum concentration were optimized by the central composite design (CCD) under the response surface methodology (RSM). The statistical analysis showed that the optimum media containing 6.4% (w/w) of sucrose, 9% (v/w) of minerals and 15.5% (v/w) of inoculum gave the maximum production of citric acid (337.94 g/kg of dry EFB). The analysis showed that sucrose (p<0.0011) and mineral solution (p<0.0061) were more significant compared to inoculum concentration (p<0.0127) for the citric acid production.
    Matched MeSH terms: Computer Simulation
  16. Fulltext Fluid Structure Interaction on Paravalvular Leakage of Transcatheter Aortic Valve Implantation Related to Aortic Stenosis: A Patient-Specific Case
    Basri AA, Zuber M, Basri EI, Zakaria MS, Aziz AFA, Tamagawa M, et al.
    Comput Math Methods Med, 2020;2020:9163085.
    PMID: 32454886 DOI: 10.1155/2020/9163085
    This study investigated the impact of paravalvular leakage (PVL) in relation to the different valve openings of the transcatheter aortic valve implantation (TAVI) valve using the fluid structure interaction (FSI) approach. Limited studies were found on the subject of FSI with regards to TAVI-PVL condition, which involves both fluid and structural responses in coupling interaction. Hence, further FSI simulation with the two-way coupling method is implemented to investigate the effects of hemodynamics blood flow along the patient-specific aorta model subjected to the interrelationship between PVL and the different valve openings using the established FSI software ANSYS 16.1. A 3D patient-specific aorta model is constructed using MIMICS software. The TAVI valve identical to Edward SAPIEN XT 26 (Edwards Lifesciences, Irvine, California), at different Geometrical Orifice Areas (GOAs), is implanted into the patient's aortic annulus. The leaflet opening of the TAVI valve is drawn according to severity of GOA opening represented in terms of 100%, 80%, 60%, and 40% opening, respectively. The result proved that the smallest percentage of GOA opening produced the highest possibility of PVL, increased the recirculatory flow proximally to the inner wall of the ascending aorta, and produced lower backflow velocity streamlines through the side area of PVL region. Overall, 40% GOA produced 89.17% increment of maximum velocity magnitude, 19.97% of pressure drop, 65.70% of maximum WSS magnitude, and a decrement of 33.62% total displacement magnitude with respect to the 100% GOA.
    Matched MeSH terms: Computer Simulation
  17. Fulltext Classification-based deep neural network vs mixture density network models for insulin sensitivity prediction problem
    Benyó B, Paláncz B, Szlávecz Á, Szabó B, Kovács K, Chase JG
    Comput Methods Programs Biomed, 2023 Oct;240:107633.
    PMID: 37343375 DOI: 10.1016/j.cmpb.2023.107633
    Model-based glycemic control (GC) protocols are used to treat stress-induced hyperglycaemia in intensive care units (ICUs). The STAR (Stochastic-TARgeted) glycemic control protocol - used in clinical practice in several ICUs in New Zealand, Hungary, Belgium, and Malaysia - is a model-based GC protocol using a patient-specific, model-based insulin sensitivity to describe the patient's actual state. Two neural network based methods are defined in this study to predict the patient's insulin sensitivity parameter: a classification deep neural network and a Mixture Density Network based method. Treatment data from three different patient cohorts are used to train the network models. Accuracy of neural network predictions are compared with the current model- based predictions used to guide care. The prediction accuracy was found to be the same or better than the reference. The authors suggest that these methods may be a promising alternative in model-based clinical treatment for patient state prediction. Still, more research is needed to validate these findings, including in-silico simulations and clinical validation trials.
    Matched MeSH terms: Computer Simulation
  18. Harmonic phase interference for the detection of tag line crossings and beyond in homogeneous strain analysis of cardiac tagged MRI data
    Bilgen M
    Australas Phys Eng Sci Med, 2010 Dec;33(4):357-66.
    PMID: 21110236 DOI: 10.1007/s13246-010-0039-z
    Homogenous strain analysis (HSA) was developed to evaluate regional cardiac function using tagged cine magnetic resonance images of heart. Current cardiac applications of HSA are however limited in accurately detecting tag intersections within the myocardial wall, producing consistent triangulation of tag cells throughout the image series and achieving optimal spatial resolution due to the large size of the triangles. To address these issues, this article introduces a harmonic phase (HARP) interference method. In principle, as in the standard HARP analysis, the method uses harmonic phases associated with the two of the four fundamental peaks in the spectrum of a tagged image. However, the phase associated with each peak is wrapped when estimated digitally. This article shows that special combination of wrapped phases results in an image with unique intensity pattern that can be exploited to automatically detect tag intersections and to produce reliable triangulation with regularly organized partitioning of the mesh for HSA. In addition, the method offers new opportunities and freedom for evaluating myocardial function when the power and angle of the complex filtered spectra are mathematically modified prior to computing the phase. For example, the triangular elements can be shifted spatially by changing the angle and/or their sizes can be reduced by changing the power. Interference patterns obtained under a variety of power and angle conditions were presented and specific features observed in the results were explained. Together, the advanced processing capabilities increase the power of HSA by making the analysis less prone to errors from human interactions. It also allows strain measurements at higher spatial resolution and multi-scale, thereby improving the display methods for better interpretation of the analysis results.
    Matched MeSH terms: Computer Simulation
  19. Fulltext Reproductive number of coronavirus: A systematic review and meta-analysis based on global level evidence
    Billah MA, Miah MM, Khan MN
    PLoS One, 2020;15(11):e0242128.
    PMID: 33175914 DOI: 10.1371/journal.pone.0242128
    BACKGROUND: The coronavirus (SARS-COV-2) is now a global concern because of its higher transmission capacity and associated adverse consequences including death. The reproductive number of coronavirus provides an estimate of the possible extent of the transmission. This study aims to provide a summary reproductive number of coronavirus based on available global level evidence.

    METHODS: A total of three databases were searched on September 15, 2020: PubMed, Web of Science, and Science Direct. The searches were conducted using a pre-specified search strategy to record studies reported the reproductive number of coronavirus from its inception in December 2019. It includes keywords of coronavirus and its reproductive number, which were combined using the Boolean operators (AND, OR). Based on the included studies, we estimated a summary reproductive number by using the meta-analysis. We used narrative synthesis to explain the results of the studies where the reproductive number was reported, however, were not possible to include in the meta-analysis because of the lack of data (mostly due to confidence interval was not reported).

    RESULTS: Total of 42 studies included in this review whereas 29 of them were included in the meta-analysis. The estimated summary reproductive number was 2.87 (95% CI, 2.39-3.44). We found evidence of very high heterogeneity (99.5%) of the reproductive number reported in the included studies. Our sub-group analysis was found the significant variations of reproductive number across the country for which it was estimated, method and model that were used to estimate the reproductive number, number of case that was considered to estimate the reproductive number, and the type of reproductive number that was estimated. The highest reproductive number was reported for the Diamond Princess Cruise Ship in Japan (14.8). In the country-level, the higher reproductive number was reported for France (R, 6.32, 95% CI, 5.72-6.99) following Germany (R, 6.07, 95% CI, 5.51-6.69) and Spain (R, 3.56, 95% CI, 1.62-7.82). The higher reproductive number was reported if it was estimated by using the Markov Chain Monte Carlo method (MCMC) method and the Epidemic curve model. We also reported significant heterogeneity of the type of reproductive number- a high-value reported if it was the time-dependent reproductive number.

    CONCLUSION: The estimated summary reproductive number indicates an exponential increase of coronavirus infection in the coming days. Comprehensive policies and programs are important to reduce new infections as well as the associated adverse consequences including death.

    Matched MeSH terms: Computer Simulation
  20. Fulltext A hybrid multi objective cellular spotted hyena optimizer for wellbore trajectory optimization
    Biswas K, Nazir A, Rahman MT, Khandaker MU, Idris AM, Islam J, et al.
    PLoS One, 2022;17(1):e0261427.
    PMID: 35085239 DOI: 10.1371/journal.pone.0261427
    Cost and safety are critical factors in the oil and gas industry for optimizing wellbore trajectory, which is a constrained and nonlinear optimization problem. In this work, the wellbore trajectory is optimized using the true measured depth, well profile energy, and torque. Numerous metaheuristic algorithms were employed to optimize these objectives by tuning 17 constrained variables, with notable drawbacks including decreased exploitation/exploration capability, local optima trapping, non-uniform distribution of non-dominated solutions, and inability to track isolated minima. The purpose of this work is to propose a modified multi-objective cellular spotted hyena algorithm (MOCSHOPSO) for optimizing true measured depth, well profile energy, and torque. To overcome the aforementioned difficulties, the modification incorporates cellular automata (CA) and particle swarm optimization (PSO). By adding CA, the SHO's exploration phase is enhanced, and the SHO's hunting mechanisms are modified with PSO's velocity update property. Several geophysical and operational constraints have been utilized during trajectory optimization and data has been collected from the Gulf of Suez oil field. The proposed algorithm was compared with the standard methods (MOCPSO, MOSHO, MOCGWO) and observed significant improvements in terms of better distribution of non-dominated solutions, better-searching capability, a minimum number of isolated minima, and better Pareto optimal front. These significant improvements were validated by analysing the algorithms in terms of some statistical analysis, such as IGD, MS, SP, and ER. The proposed algorithm has obtained the lowest values in IGD, SP and ER, on the other side highest values in MS. Finally, an adaptive neighbourhood mechanism has been proposed which showed better performance than the fixed neighbourhood topology such as L5, L9, C9, C13, C21, and C25. Hopefully, this newly proposed modified algorithm will pave the way for better wellbore trajectory optimization.
    Matched MeSH terms: Computer Simulation
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