Mapping pollution dynamics: utilizing GNOME to model oil spill trajectories in tanker terminals.

The aim of this study is to uncover the multifaceted environmental threats posed by Oil Spill Water Pollution (OSWP) originating from tanker terminals situated in the Qeshm and Hormozgan regions of Iran. In this region, water pollution arises from diverse sources, mostly from ruptured pipelines, corroded valves, unforeseen accidents, and aging facilities. The Qeshm Canal and Qeshm Tanker Terminal emerged as pivotal sites for investigation within this study. The focus is directed towards pinpointing vulnerable areas at risk of water contamination and delving into the intricate pathways and impacts associated with oil spills. Utilizing the sophisticated modeling capabilities of the National Oceanic and Atmospheric Administration's (NOAA) GNOME model, the research explores various scenarios extrapolated from seasonal atmospheric and oceanic data through 2022. The findings show the OSWP hazard zones located northeast of Qeshm. Notably, the wind and currents greatly affect how OSWPs are destined and dispersed. This underscores the intricate interplay between environmental factors and spill dynamics. In essence, this study not only sheds light on the imminent environmental threats posed by OSWP but also underscores the critical need for proactive measures and comprehensive strategies to mitigate the adverse impacts on marine ecosystems and coastal communities.

Association between adherence to the Mediterranean diet with cardiometabolic risk factors: a cross-sectional study on PERSIAN cohort study in Fasa.

The relationship between Mediterranean diet and obesity-related markers is a matter of debate. We investigated the association between adherence to the Mediterranean diet and anthropometric indices, body composition, and cardiometabolic risk factors in Iranian population. The cross-sectional study was performed on data of 3386 participants from Fasa PERSIAN cohort study. The Mediterranean diet score (MDS) was calculated based on consumption of 11 food groups (unrefined cereals, potatoes, fruits, vegetables, legumes, fish, red meat, poultry, dairy, olive oil, and alcoholic beverages). The association between MDS and cardiometabolic risk factors was examined by linear regression analysis. MDS was inversely associated with waist circumference (ß = - 1.11; P = 0.033), waist-to-hip ratio (ß = - 0.007; P = 0.011), waist-to-height ratio (ß = - 0.009; P = 0.015), fasting glucose (ß = - 3.59; P = 0.001), and HDL-cholesterol (ß = - 0.96; P = 0.031) in unadjusted model. After adjusting for energy intake, the associations of MDS with markers of abdominal obesity and HDL-cholesterol disappeared. In fully adjusted model, MDS showed inverse relationships with waist-to-hip ratio (ß = - 0.005; P = 0.037) and fasting glucose (ß = - 2.71; P = 0.013). In conclusion, MDS showed an inverse relationship with fasting glucose and waist-to-hip ratio. Since energy intake increased along with increasing MDS, adherence to the Mediterranean diet may associate with lower abdominal obesity and better glycemic control if an energy-controlled Mediterranean diet is used.

Determination of efficacy of repeated CXL and probable risk factors in patients with progressive keratoconus.

PURPOSE: To evaluate the efficacy of Repeated CXL (Re-CXL) and determine probable risk factors that lead to Re-CXL in patients with progressive keratoconus. METHOD: In this retrospective study, the medical records of patients who had been re-operated in our center between 2014 to 2020 due to progressive keratoconus were evaluated; seven eyes of seven patients had undergone Re-CXL procedure. Pre- and post-treatment variables were recorded and analyzed using IBM SPSS Statistics software. RESULTS: The mean interval between the 1st and 2nd CXL was 49.71 months (range 12-72 months). Out of 7 patients for whom Re-CXL was considered necessary, eye rubbing was detected in 6 patients. Six patients were very young with a mean age of 13 years at primary CXL and 16.83 years at Re-CXL. Visual acuity and astigmatism did not change significantly after the Re-CXL procedure (p-values = 0.18, 0.91, respectively). When measurements of these indices prior to Re-CXL and post Re-CXL were compared, K1 (p-value = 0.01), K2 (p-value = 0.01), Kmean (p-value = 0.01), and Kmax (p-value = 0.008) changed significantly. As to pachymetry (p-value = 0.46), it did not change significantly. Kmax value regressed in all eyes after Re-CXL. CONCLUSION: Re-CXL procedure was effective in halting the progression of disease. As to the risk factors, eye rubbed-related mechanism like eye rubbing and VKC, lower age, and pre-operative Kmax value > 58 D are the risk factors of Re-CXL procedure.

Sea-level projections using a NARX-NN model of tide gauge data for the coastal city of Kuala Terengganu in Malaysia.

The impact of global warming presents an increased risk to the world's shorelines. The Intergovernmental Panel on Climate Change (IPCC) reported that the twenty-first century experienced a severe global mean sea-level rise due to human-induced climate change. Therefore, coastal planners require reasonably accurate estimates of the rate of sea-level rise and the potential impacts, including extreme sea-level changes, floods, and shoreline erosion. Also, land loss as a result of disturbance of shoreline is of interest as it damages properties and infrastructure. Using a nonlinear autoregressive network with an exogenous input (NARX) model, this study attempted to simulate (1991 to 2012) and predict (2013-2020) sea-level change along Merang kechil to Kuala Marang in Terengganu state shoreline areas. The simulation results show a rising trend with a maximum rate of 28.73 mm/year and an average of about 8.81 mm/year. In comparison, the prediction results show a rising sea level with a maximum rate of 79.26 mm/year and an average of about 25.34 mm/year. The database generated from this study can be used to inform shoreline defense strategies adapting to sea-level rise, flood, and erosion. Scientists can forecast sea-level increases beyond 2020 using simulated sea-level data up to 2020 and apply it for future research. The data also helps decision-makers choose measures for vulnerable shoreline settlements to adapt to sea-level rise. Notably, the data will provide essential information for policy development and implementation to facilitate operational decision-making processes for coastal cities.

Molecular dynamics analysis predicts ritonavir and naloxegol strongly block the SARS-CoV-2 spike protein-hACE2 binding.

The rapid emergence of COVID-19 pandemics has posed humans particularly vulnerable to the novel SARS-CoV-2 virus. Since de novo drug discovery is both expensive and time-consuming, drug repurposing approaches are believed to be of particular help. The SARS-CoV-2 spike (S) protein is known to attach human angiotensin-converting enzyme-2 (hACE2) through its receptor-binding domain (RBD). We screened 1930 FDA-approved ligands for the selection of optimal ones blocking this interaction. Virtual screening predicted top 25 ligands docking to any of the reported binding sites. After exclusion of those ligands which were unsuitable for systemic use, the remaining 69 RBD-ligand complexes were screened based on the masking capacity of the amino acid residues engaged in RBD-hACE2 interaction, excluding 47 RBD-ligand complexes. A short molecular dynamics (MD) simulation analysis identified 11 globally stable complexes with the lowest RMSD (root-mean-square deviation). Next, a moderately long MD analysis revealed those six RBD-ligand complexes with the lowest RMSD variation, as a measure of global stability. Finally, a long MD analysis revealed two select candidate ligands, including ritonavir and naloxegol, highly stabilizing those key residues engaged in RBD-hACE2 interaction. A similar MD analysis of a few antiviral drugs which are under clinical trials or approved for COVID-19 treatment showed them inferior to both select ligands in terms of stabilizing the RBD globally and locally at binding sites. Because of the crucial role of the S protein in virus virulence, our results highly propose ritonavir and naloxegol as the potentially helpful therapeutics against COVID-19, mandating appropriate clinical trials.Communicated by Ramaswamy H. Sarma.

The association between healthy eating index score with semen parameters in infertile men: A cross-sectional study.

Background: Infertility has been a major problem for young couples in recent years. One way to assay the diet quality is the healthy eating index (HEI), related to infertility. Objective: This study aims to assess the association between the HEI score with semen parameters in Iranian infertile men. Materials and Methods: Two hundred and sixty eligible men (18-55 yr), were referred to the major infertility clinic in the summer of 2018 and entered this cross-sectional study. Based on the 5 th edition of the world health organization laboratory manual, semen parameters including sperm concentration, volume, motility, and morphology were analyzed, and to specify the dietary intake of individuals a 168-item questionnaire was used. Also, to calculate the total HEI score, all 13 components based on HEI-2015 components and scoring standards were summed up. Results: Participants in the highest tertile, had no difference in mean sperm parameters with those in the lowest tertile in the crude model. No significant association was found between sperm parameters and HEI score tertiles in the crude model, even after adjustment for potential confounders, except for concentration (OR: 0.39 and CI: 0.15, 0.99, p = 0.04). Participants in the highest tertile had a lower risk of abnormal concentration and motility in the crude model. The risk of abnormal concentration decreased, and motility increased in the adjusted model. Conclusion: In this cross-sectional study, there was no significant relationship between HEI and sperm indexes, except for sperm concentration. Therefore, more studies need to be done in the future.

Simultaneous monitoring of SARS-CoV-2, bacteria, and fungi in indoor air of hospital: a study on Hajar Hospital in Shahrekord, Iran.

The novel SARS-CoV-2 outbreak was declared as pandemic by the World Health Organization (WHO) on March 11, 2020. Understanding the airborne route of SARS-CoV-2 transmission is essential for infection prevention and control. In this study, a total of 107 indoor air samples (45 SARS-CoV-2, 62 bacteria, and fungi) were collected from different wards of the Hajar Hospital in Shahrekord, Iran. Simultaneously, bacterial and fungal samples were also collected from the ambient air of hospital yard. Overall, 6 positive air samples were detected in the infectious 1 and infectious 2 wards, intensive care unit (ICU), computed tomography (CT) scan, respiratory patients' clinic, and personal protective equipment (PPE) room. Also, airborne bacteria and fungi were simultaneously detected in the various wards of the hospital with concentrations ranging from 14 to 106 CFU m-3 and 18 to 141 CFU m-3, respectively. The highest mean concentrations of bacteria and fungi were observed in respiratory patients' clinics and ICU wards, respectively. Significant correlation (p < 0.05) was found between airborne bacterial concentration and the presence of SARS-CoV-2, while no significant correlation was found between fungi concentration and the virus presence. This study provided an additional evidence about the presence of SARS-CoV-2 in the indoor air of a hospital that admitted COVID-19 patients. Moreover, it was revealed that the monitoring of microbial quality of indoor air in such hospitals is very important, especially during the COVID-19 pandemic, for controlling the nosocomial infections.

Performing an In Silico Repurposing of Existing Drugs by Combining Virtual Screening and Molecular Dynamics Simulation.

Drug repurposing has become one of the most widely used methods that can make drug discovery more efficient and less expensive. Additionally, computational methods such as structure-based drug designing can be utilized to make drug discovery more efficient and more accurate. Now imagine what can be achieved by combining drug repurposing and computational methods together in drug discovery, "in silico repurposing." In this chapter, we tried to describe a method that combines structure-based virtual screening and molecular dynamics simulation which can find effective compounds among existing drugs that may affect on a specific molecular target. By using molecular docking as a tool for the screening process and then by calculating ligand binding in an active receptor site using scoring functions and inspecting the proper orientation of pharmacophores in the binding site, the potential compounds will be chosen. After that, in order to test the potential compounds in a realistic environment, molecular dynamics simulation and related analysis have to be carried out for separating the false positives and the true positives from each other and finally identifying true "Hit" compounds. It's good to emphasize that if any of these identified potential compounds turn out to have the efficacy to affect that specific molecular target, it can be taken to the phase 2 clinical trials straightaway.

Repurposing existing drugs for new AMPK activators as a strategy to extend lifespan: a computer-aided drug discovery study.

Dietary restriction is one of the several ways which could putatively extend organisms' lifespan, ranging from Saccharomyces cerevisiae to rodents, by activating the AMP-activated protein kinase (AMPK), an ATP/AMP sensor. Extensive researches have shown that aging reduces sensibility of AMPK and eventually causes energy imbalance in cells. Research in mammals' AMPK depicts that this signaling molecule could control autophagy, improve cellular stress resistance and suppress inflammatory responses. Hence, in this study we performed a drug repurposing of 1908 FDA-approved drugs in order to discover putative safe activators of AMPK and to find new applications for existing drugs. For this purpose, FDA-approved drugs were screened by virtual screening and the ligand-protein interactions were carefully inspected. Moreover, through MM/PBSA analysis, the binding affinity of hit compounds in γ and αß binding sites were investigated. As Cangrelor, Nacitentan, Levoleucovorin and Glisoxepide had lower binding affinities; we predicted that they would probably prove to be more potential activators than C2. However, hit-compounds in αß binding site, exhibited higher unfavorable binding affinity. Hence, present findings can prove to be valuable for discovering new activators for AMPK.

In silico drug repurposing of FDA-approved drugs to predict new inhibitors for drug resistant T315I mutant and wild-type BCR-ABL1: A virtual screening and molecular dynamics study.

The BCR-ABL fusion gene is one of the major causes of 95% of Chronic Myeloid Leukemia (CML). While, BCR-ABL protein is currently being used as a major target to treat CML. Although, current FDA-approved drugs such as; Imatinib and Nilotinib have stupendously improved the patients 5-year's survival rates, the drug resistance has dramatically reduced their effects. So, more accurate and effective alternative treatments are crucially needed. To address this issue, we screened the FDA-approved drugs by virtual screening and binding free energy calculations to identify new inhibitors for the wild-type and T315I gatekeeper mutant ABL1. It was invigorating to identify that chlorohexidine, paromomycin and deferoxamine could inhibit the wild-type ABL1, while chlorohexidine and ritonavir could inhibit the T315I mutant ABL1. The applications of these newly identified drugs are not just an effortless hypothesis in drug discovery. These drugs can be evaluated in phase 2 clinical trials after a simple kinase selectivity assay.