computer simulation

Teaching clinical reasoning to nursing students is essential for professionalizing and improving cancer patient care. This study investigates how training duration with Virtual Patients (VPs) impacts clinical reasoning and learners’ evaluation of their experiences.

The present semi‑experimental study was conducted with a pretest–post‑test design and a control group. Through the census sampling method, 74 nursing students from Isfahan University of Medical Sciences, Iran, (in their 4th and 5th semester) who had taken the cancer course were selected (2019‑2022) and, upon obtaining their consent, were enrolled in the study. The study began with a pretest, followed by engagement in five VP scenarios over 6 weeks, which was followed by the post‑test phase. Data were collected via 23‑item tests and the Huwendiek Questionnaire. The collected data were analyzed in SPSS software using correlation tests and t‑tests.

The outcomes revealed a noteworthy disparity between the mean scores recorded in the pre‑test and post‑test stages after training, for both the 4th and 5th semester cohorts (p ≤ 0.001). Moreover, a notable discrepancy surfaced between the duration of training with VPs and the average post‑test score (p ≤ 0.001). The correlation coefficient, for the 4th semester, stood at 0.65, while for the 5th semester, it was 0.213. Notably, the participants exhibited contentment with the learning experience through VPs.

The survey found that 85.60% of participants prefer using VPs for clinical reasoning education. Our study underscores the link between the duration of VP interaction and improved clinical reasoning skills in nursing students.

In cancer-related diseases, early detection and control of disease progression are very important for successful treatment. Breast cancer is a significant problem due to its high mortality rate in the female population worldwide. By the early diagnosis of breast cancer, the 5-year survival rate reaches 93 to 98%. In this study, to identify breast cancer biomarkers, we construct new protein-protein interaction (PPI) and miRNAs-mRNAs networks by analyzing upregulated and downregulated genes in breast cancer patients. In this in silico study, two gene expression profile datasets, with the accession numbers GSE42568 and GSE154255, were downloaded from the GEO database. GEO2R was used to obtain differentially expressed mRNA (DEMs) and miRNAs (DEMIs) based on |logFC|>2 and adjusted P-value <0.05. Gene Ontology and KEGG Pathway Enrichment Analysis were performed by EnrichR. STRING v9. 1 and cytoHubba plugin in Cytoscape (v3.9.1) were used to investigate PPI network construction and identification of hub genes. Finally, key microRNAs (miRNAs) were predicted. After protein-protein interaction analysis, a total of 10 upregulated DEMs (DLGAP5, CCNB1, TTK, NUSAP1, RRM2, BUB1B, CDK1, CENPF, TOP2A, and ASPM) and 10 downregulated DEMs (PPARG, LIPE, CD36, FABP4, SCD, LPL, DGAT2, PNPLA2, ACSL1, and LEP) were screened as hub genes. Based on miRNAs-mRNAs networks, 4 key miRNAs including hsa-miR-182-5p, hsa-miR-96-5p, hsa-miR-335-3p, and hsa-miR-32-5p play a critical role in network regulation. Our study presents PPI and miRNAs-mRNAs networks for identifying molecular biomarkers in breast cancer. The introduced biomarkers open a new approach to diagnostic and therapeutic indicators for clinical applications.

Proton therapy is a cancer treatment method that uses high‑energy proton beams to target and destroy cancer cells. In recent years, the use of proton therapy in cancer treatment has increased due to its advantages over traditional radiation methods, such as higher accuracy and reduced damage to healthy tissues. For accurate planning and delivery of proton therapy, advanced software tools are needed to model and simulate the interaction between the proton beam and the patient’s body. One of these tools is the Monte Carlo simulation software called Geant4, which provides accurate modeling of physical processes during radiation therapy. The purpose of this study is to investigate the effectiveness of the Geant4 toolbox in proton therapy in the conducted research. This review article searched for published articles between 2002 and 2023 in reputable international databases including Scopus, PubMed, Scholar, Google Web of Science, and ScienceDirect. Geant4 simulations are reliable and accurate and can be used to optimize and evaluate the performance of proton therapy systems. Obtaining some data from experiments carried out in the real world is very effective. This makes it easy to know how close the values obtained from simulations are to the behavior of ions in reality.

We aim to determine and compare the correlation between conventional and digital impression methods for measuring mesiodistal teeth dimensions.

This cross-sectional analytical study was conducted on a total of 120 dental arch samples with less than 5 mm of tooth crowding, complete teeth on the dental arch, no missing teeth, and no fillings on the mesial or distal sides at Can Tho University of Medicine and Pharmacy. Conventional (extra-fast alginate) and digital impressions using a 3D intraoral scanner (CEREC Primescan) were taken from all participants, and the dimensions of the mesiodistal teeth were measured. Using R software, Pearson’s correlation coefficients were used to analyze the correlation between conventional and digital impression methods.

The pooled correlation for the maxilla was 0.8062 [95% confidence interval (CI): 0.7751–0.8334] (very strong positive correlation); for the mandibular, it was 0.7645 (95% CI: 0.7165–0.8054) (strong positive correlation), and for both jaws was 0.7863 (95% CI: 0.7581–0.8115) (strong positive correlation).

In the Vietnamese population measurement of mesiodistal tooth width using a digital dental scanner can be used instead of conventional plaster models.

Intra-articular screw penetration is a probable complication of coronoid fracture fixation. Thepresent study aimed to determine the best radiography technique for visualizing the proximal radioulnar joint(PRUJ) space. Moreover, it aimed to determine the safe angle and length of the screw to avoid PRUJ penetrationduring coronoid fracture fixation. The Mimics software was used to construct a three-dimensional model of a healthy man’s forearmfrom a computer tomography scan. It was analyzed using the Solidworks software to determine the X-ray anglethat clearly showed the PRUJ space to detect penetration of screws from the coronoid process into the PRUJand determine the maximum screw angle and length that could be used without intra-articular penetration. Toverify these findings, a cadaveric study combined with radiographs was conducted. To visualize PRUJ space, the optimal X-ray angle was 13º lateral to the perpendicular line when theforearm was positioned at full supination. If the coronoid process was segmented into zones 1 (closest to theradioulnar joint) to 4 (farthest from the joint), the screw could only be inserted at a right angle in zone 1. In zones2, 3, and 4, inclination angles less than 15, 35, and 60 would prevent intra-articular penetration, respectively. The X-rays could visualize the PRUJ space with an anteroposterior radiograph at an angle of13º ulnar deviation from the perpendicular plane. During coronoid process fracture fixation, shorter screwswith less lateral inclination were safer when inserting screws in the zones of the coronoid process adjacent tothe PRUJ.

Water quality deterioration is becoming a serious challenge for water utility corporations supplying treated water through the use of a centralized distribution system. After water leaves the treatment plant and enters the distribution system, it is subjected to numerous complex physical, chemical, and biological changes. This study aimed to investigate the major physical factors deteriorating water quality in an aged distribution system.

Deterioration modeling was undertaken using an EPANET computer program. For model calibration processes, data collected from field measurements were used. Descriptive statistics were employed to analyze the data. Water age and residual chlorine were selected parameters to investigate the deterioration level. The identification of major factors posing water quality changes was undertaken by examining distinct physical and operational settings.

The maximum water-age variation obtained between two extreme water-use periods was 21.97%. In the same way, the maximum residual chlorine concentration variation obtained was 11.68%. On the contrary, with tested extreme pipe sizes in the study, the maximum water-age variation obtained was only 0.93%. Whereas, the obtained maximum residual chlorine concentration variation between the two extreme pipe sizes was 21.03%.

Water use variation poses more water quality degradation than pipe geometry. Water age in aged distribution is rarely influenced by conditions of pipe geometry.

COVID-19 is caused by SARS-CoV-2 which has structural and non-structural proteins (NSP) essential for infection and viral replication. There is a possible binding of SARS-CoV-2 to the beta-1 chain of hemoglobin in red blood cells and thus, decreasing the oxygen transport capacity. Since hydroxychloroquine (HCQ) can accumulate in red cells, there is a chance of interaction of this drug with the virus. To analyze possible interactions between SARS-CoV-2 NSP and hemoglobin with the HCQ using molecular docking and implications for the infected host. This research consisted of a study using bioinformatics tools. The files of the protein structures and HCQ were prepared using the AutoDock Tools software. These files were used to perform molecular docking simulations by AutoDock Vina. The binding affinity report of the generated conformers was analyzed using PyMol software, as well as the chemical bonds formed. The results showed that HCQ is capable of interacting with both SARS-CoV-2 NSP and human hemoglobin. The HCQ/NSP3 conformer, HCQ/NSP5, HCQ/NSP7-NSP8-NSP12, HCQ/NSP9, HCQ/NSP10-NSP16 showed binding affinity. In addition, the interaction between HCQ and hemoglobin resulted in polar bonds. Interaction between SARS-CoV-2 NSP and HCQ indicates that this drug possibly acts by preventing the continuity of infection.

Ongoing novel coronavirus (COVID-19) with high mortality is an infectious disease in the world which epidemic in 2019 with human-human transmission. According to the literature, S-protein is one of the main proteins of COVID-19 that bind to the human cell receptor angiotensin-converting enzyme 2 (ACE2). In this study, it was attempted to identify the main effective drugs approved that may be repurposed to the binding site of ACE2. High throughput virtual screening based on the docking study was performed to know which one of the small-molecules had a potential interaction with ACE2 structure. Forasmuch as investigating and identifying the best ACE2 inhibitors among more than 3,500 small-molecules is time-consuming, supercomputer was utilized to apply dockingbased virtual screening. Outputs of the proposed computational model revealed that vincristine, vinbelastin and bisoctrizole can significantly bind to ACE2 and may interface with its normal activity

Vaccination against COVID-19 is as a key solution to interrupt its spread. This study aimed to describe the vaccination coverage required to stop the spread of COVID-19 in Sri Lanka using a mathematical modeling strategy.

This longitudinal study used age-stratified and unstratified Susceptible-Infectious-Recovered (SIR) models. Data on the population's age distribution were acquired from the census report of the Census and Statistics Center of Sri Lanka, consisting of groups: below 30, between 30-59, and over 60. Models with differential equations forecasted the spread of COVID-19 with vaccination based on parameter estimates and numerical simulation, assuming fixed population, infection, and recovery rates.

Simulations investigated how the susceptible, infected, and recovered populations varied according to the different vaccination coverages. According to the results, 75% vaccination coverage was required in the entire population of Sri Lanka to interrupt the transmission of COVID-19 completely. The age-stratified SIR model showed that over 90% of vaccination coverage in each age group (below 30, between 30-59, and over 60) was required to interrupt the transmission of COVID-19 in the country altogether.

The number of COVID-19 infections in each age group of Sri Lanka reduces with the increase in vaccination coverage. As 75% vaccination coverage is required in Sri Lanka to interrupt the transmission of the disease, precise vaccination coverage measurement is essential to assess the successfulness of a vaccine campaign and control COVID-19.

The truncation level of human airways is an influential factor in the analysis of respiratory flow in numerical simulations. Due to computational limitations and limited resolution of diagnostic medical imaging equipment, a truncated geometry of airways is always investigated.  This study aimed to employ image-based geometries with zero generation and 5th-generation truncation levels and assess bronchial airways truncation’s effect on tracheal airflow characteristics. In this numerical study, computational fluid dynamics was employed to solve the respiratory flow in a realistic human airway model using the large eddy simulation technique coupling with the wall-adapting local eddy-viscosity (WALE) sub-grid scale model. The accuracy of numerical simulations was ensured by examining the large eddy simulation index of quality and Kolmogorov’s K-5/3 law.  The turbulent kinetic energy along the trachea has increased abnormally in the geometry with the zero-generation truncation level, and more severe fluctuations occurred in the velocity field of this geometry, which increased the tendency of each point to rotate. Compared to the extended model, the airflow’s more chaotic behavior prevented larger-scale vortices from forming in the geometry with the zero-generation truncation level. Larger-scale vortices in the extended model caused the primary flow passing next to the vortices to accelerate more intensely, increasing the wall shear stress peaks in this geometry.   Eliminating the bronchial airways caused changes in tracheal airflow characteristics.

Shigella spp. is the cause of dysentery and is widespread worldwide. On the other hand, antibiotic resistance is increasing in this bacterium. Bioinformatics is a new approach to vaccine and drug design involving the selection of appropriate antigens. This study aimed to design a chimeric protein consisting of IpaD, StxB, and TolC proteins from Shigella through a bioinformatics approach as an immunogen candidate.

The sequences of ipaD, stxB, and tolC genes were obtained. Additionally, the immunogenic regions of the associated protein, physicochemical characteristics, protein structures, B and T cells epitopes, and molecular docking were determined using in silico servers. Besides, the chimeric gene was synthesized following sequence optimization by utilizing the codon usage of Escherichia coli (E. coli). The expression of the recombinant protein was confirmed via SDS-PAGE and Western blot technique.

The residues 41-160 of IpaD, 21-89 of StxB, and 40-335 of TolC were selected. According to half-life, instability, and buried indices, IpaD-StxB-TolC was selected as the best arrangement. The Ramachandran plot showed that 97.077% of the amino acids were in the favored area. Linear and conformational epitopes were also present throughout the chimeric protein sequence. Moreover, the C-ImmSim server indicated that IgG and IgM titers could reach desirable values by the third injection .Furthermore, the stability of the mRNA-optimized gene was enhanced, increasing the Codon Adaptive Index (CAI) to 0.9. Finally, the chimeric gene was transferred to E. coli BL21, and the expression of the 60.6 kDa recombinant protein was confirmed.

The results indicated that the recombinant protein could act as a proper immunogen candidate against Shigella spp.

This study aimed to develop the algorithm for choosing both effective and safe mode of dual-wavelengths copper vapor laser (CVL) photodestruction of dilated dermal vessels in PWS for different skin phototypes. This study is expected to assess the safe parameters for CVL treatment.

We used the multilayered skin model with different melanin content for simulation. The calculation of the vascular component’s selective heating with CVL radiation at the green and yellow wavelengths for different skin phototypes was performed with Matlab mathematical programming system and its application Femlab for solving partial differential equations using the Finite element method.

We determined the location depth and size of blood vessels that could be selectively heated to the coagulation temperature for different skin phototypes.

CVL can selectively heat 15-300 mcm vessel diameters that correspond to the PWS vessel diameter range. CVL fluence values need to be reduced almost twice for the IV skin phototype than the II skin phototype. The maximum depth of the vessels’ location also decreased for dark skin phototypes.

The ability of ambulance centers to respond to emergency calls is an important factor in the recovery of patients' health. This study aimed to provide a model for the establishment of emergency relief in the road network in 2020 in East Azerbaijan province.

This applied-descriptive and experimental research with an explanatory modelling approach used the comments of 70 experts to run a model, which was based on the use of a metaheuristic (genetic) algorithm ,Simulation for the number of ambulances and the composition of the monitoring list simultaneously , objective and subjective data combined ,the agent and environmental variables, were determined and modelled through a meta-hybrid approach during the agent-based simulation and the metaheuristic algorithm.

To travel the initial structure for 40 dangerous points and five stations, the initial time was equal to 7860 Minutes, which reached a number between 2700 and 4000 Minutes after genetic optimization, production of a new list, and the mutation of ambulances from one station to another.

This type of optimization can be used to accelerate activities and reduce costs. Due to the dissimilar traffic of the areas, the ambulance does not arrive at dangerous points at equal times. The travel time of all dangerous points can be reduced by changing the location of points, moving forward or backwards depending on the conditions, customizing the features of ambulances and dangerous points, and combining the list of areas to find the best location for emergencies according to the interaction between agents, environmental constraints, and different behavioral features.

Introduction:

Congenital melanocytic nevus (CMN) is a severechallenge for dermatology. This pigmented skin lesion is undesirable for patients because of its localization in open areas of the body. Various visible and near-infrared laser systems and intense pulsed light (IPL) sources have been applied for CMN treatment. However, post-traumatic hyperpigmentation, structural changes, atrophy, and scarring due to non-specific thermal damage have been observed. Many patients have shown recurrence after treatment. Therefore, it highlights the need for testing new laser modalities for the management of CMN.

Two adult II Fitzpatrick phototype patients (a 55-year-old male and a 30-year-old female) with middle-sized facial CMN (on the forehead and lower eyelid) are presented. All patients were treated with dual-wavelength copper vapor laser (CVL) radiation at 511 nm and 578 nm wavelengths with a power ratio of 3:2. The average power was 0.7-0.85 W with an exposure time of 0.3 seconds. The spot size amounted to 1 mm.

Both patients showed complete resolution of CMN after CVL treatments. CMN became crusted within a few days after the laser treatment and peeled off within seven days. No recurrences were observed during the follow-up period up to 24 months.

The middle-sized CMN can be successfully treated with dual-wavelength CVL radiation.

Online Monte Carlo (MC) treatment planning is very crucial to increase the precision of intraoperative radiotherapy (IORT). However, the performance of MC methods depends on the geometries and energies used for the problem under study.

This study aimed to compare the performance of MC N-Particle Transport Code version 4c (MCNP4c) and Electron Gamma Shower, National Research Council/easy particle propagation (EGSnrc/Epp) MC codes using similar geometry of an INTRABEAM® system.

This simulation study was done by increasing the number of particles and compared the performance of MCNP4c and EGSnrc/Epp simulations using an INTRABEAM® system with 1.5 and 5 cm diameter spherical applicators. A comparison of these two codes was done using simulation time, statistical uncertainty, and relative depth-dose values obtained after doing the simulation by each MC code.

The statistical uncertainties for the MCNP4c and EGSnrc/Epp MC codes were below 2% and 0.5%, respectively. 1e9 particles were simulated in 117.89 hours using MCNP4c but a much greater number of particles (5e10 particles) were simulated in a shorter time of 90.26 hours using EGSnrc/Epp MC code. No significant deviations were found in the calculated relative depth-dose values for both in the presence and absence of an air gap between MCNP4c and EGSnrc/Epp MC codes. Nevertheless, the EGSnrc/Epp MC code was found to be speedier and more efficient to achieve accurate statistical precision than MCNP4c.

Therefore, in all comparisons criteria used, EGSnrc/Epp MC code is much better than MCNP4c MC code for simulating an INTRABEAM® system.

The most prevalent cancer in women over the world is breast cancer. Immunotherapy is a promising method to effectively treat cancer patients. Among various immunotherapy methods, tumor antigens stimulate the immune system to eradicate cancer cells. Preferentially expressed antigen in melanoma (PRAME) is mainly overexpressed in breast cancer cells, and has no expression in normal tissues. FliCΔD2D3, as truncated flagellin (FliC), is an effective toll-like receptor 5 (TLR5) agonist with lower inflammatory responses. The objective of the present study was to utilize bioinformatics methods to design a chimeric protein against breast cancer.

The physicochemical properties, solubility, and secondary structures of PRAME+FliCΔD2D3 were predicted using the tools ProtParam, Protein-sol, and GOR IV, respectively. The 3D structure of the chimeric protein was built using I-TASSER and refined with GalaxyRefine, RAMPAGE, and PROCHECK. ANTIGENpro and VaxiJen were used to evaluate protein antigenicity, and allergenicity was checked using AlgPred and Allergen FP. Major histocompatibility complex )MHC( and cytotoxic T-lymphocytes )CTL( binding peptides were predicted using HLApred and CTLpred. Finally, B-cell continuous and discontinuous epitopes were predicted using ABCpred and ElliPro, respectively.

The stability and solubility of PRAME+FliCΔD2D3 were analyzed, and its secondary and tertiary structures were predicted. The results showed that the derived peptides could bind to MHCs and CTLs. The designed chimeric protein possessed both linear and conformational epitopes with a high binding affinity to B-cell epitopes.

PRAME+FliCΔD2D3 is a stable and soluble chimeric protein that can stimulate humoral and cellular immunity. The obtained results can be utilized for the development of an experimental vaccine against breast cancer.