Analysis of Persian Bioinformatics Research with Topic Modeling.

Purpose: As a scientific field, bioinformatics has drawn remarkable attention from various fields, such as information technology, mathematics, and modern biological sciences, in recent years. The topic models originating from the field of natural language processing have become the focus of attention with the rapid accumulation of biological datasets. Thus, this research is aimed at modeling the topic content of the bioinformatics literature presented by Iranian researchers in the Scopus Citation Database. Methodology. This research was a descriptive-exploratory study, and the studied population included 3899 papers indexed in the Scopus database, which had been indexed in this database until March 9, 2022. The topic modeling was then performed on the abstracts and titles of the papers. A combination of LDA and TF-IDF was utilized for topic modeling. Findings. The data analysis with topic modeling resulted in identifying seven main topics "Molecular Modeling," "Gene Expression," "Biomarker," "Coronavirus," "Immunoinformatics," "Cancer Bioinformatics," and "Systems Biology." Moreover, "Systems Biology" and "Coronavirus" had the largest and smallest clusters, respectively. Conclusion: The present investigation demonstrated an acceptable performance for the LDA algorithm in classifying the topics included in this field. The extracted topic clusters indicated excellent consistency and topic connection with each other.

The potential impact of Covid-19 on CNS and psychiatric sequels.

Due to its high prevalence and fatality, the current Severe Acute Respiratory Syndrome-coronavirus-2 (SARS-CoV-2) virus, which first emerged in China in 2019, quickly spread around the world and immediately became a serious global health concern. Although respiratory issues were initially the most prominent symptom of coronavirus disease 2019 (COVID-19), it became obvious rapidly that COVID-19, like many other coronavirus family members, could affect the central nervous system (CNS). During the pandemic, CNS involvement expressed itself in a variety of forms, including insomnia, anosmia, headaches, encephalopathies, encephalitis, cerebrovascular accidents, cognitive and memory impairment, and increased psychiatric disorders. Almost everyone who has been infected has at least one of these neurological symptoms, demonstrating that the virus has a high ability to impact the CNS. As the coronavirus pandemic passes its second year, the manifestations it can cause in the long run, such as its psychological sequels, have not yet been thoroughly studied. Given the high importance of this issue in today's society and due to the lack of reliable knowledge about the COVID-19 landscape on psychiatric disorders, we intend to investigate coronavirus's possible effect on mental illnesses based on available literature. Because the majority of the psychological effects of the coronavirus can continue for a long period after the pandemic ends, our research can give insight into potential psychiatric sequels associated with COVID-19.

ParsBERT topic modeling of Persian scientific articles about COVID-19.

Purpose: The COVID-19 pandemic has indisputably impacted every aspect of human life, and a host of studies have investigated its different aspects. This paper models the contents of Persian literature on COVID-19. Method: This is a descriptive-exploratory study in which 815 articles were collected from the Magiran database. The articles were published before March 2022. The abstracts and titles were used in the modeling. The modeling was performed by combining the latent Dirichlet allocation (LDA) algorithm with ParsBERT. Findings: Topic modeling indicated ten major topics, including medicine, psychology, humanities, politics, management, biology, economics, culture, engineering, and religion. The articles under the category of medicine had the largest cluster (42.3%), while engineering and religion had the smallest clusters (1.1% each). Conclusion: The found topics in the created clusters have structural relationships. The COVID-19 effect on physical and mental health (medical and psychological topics) is the most crucial factor. These clusters provide evidence that COVID-19 affects all facets of human society at three levels: the individual, family, and society. Aside from the ten critical clusters in the humanities field, the utmost disorder is related to teaching and learning. For the first time, this research has presented a model of scientific communication in the field of COVID-19 based on the data collected from a Persian database - Magiran.

Persistence and occurrence of SARS-CoV-2 in water and wastewater environments: a review of the current literature.

As the world continues to cope with the COVID-19 pandemic, emerging evidence indicates that respiratory transmission may not the only pathway in which the virus can be spread. This review paper aims to summarize current knowledge surrounding possible fecal-oral transmission of SARS-CoV-2. It covers recent evidence of proliferation of SARS-CoV-2 in the gastrointestinal tract, as well as presence and persistence of SARS-CoV-2 in water, and suggested future directions. Research indicates that SARS-CoV-2 can actively replicate in the human gastrointestinal system and can subsequently be shed via feces. Several countries have reported SARS-CoV-2 RNA fractions in wastewater systems, and various factors such as temperature and presence of solids have been shown to affect the survival of the virus in water. The detection of RNA does not guarantee infectivity, as current methods such as RT-qPCR are not yet able to distinguish between infectious and non-infectious particles. More research is needed to determine survival time and potential infectivity, as well as to develop more accurate methods for detection and surveillance.

Acute Macular Neuroretinopathy and COVID-19 Vaccination: Case Report and Review of the Literature Neurorétinopathie maculaire aiguë et vaccination contre la COVID-19 : rapport de cas et revue de la littérature

Objective: To review cases of acute macular neuroretinopathy (AMN) after COVID-19 vaccination and add a similar case to the literature. Methods: A thorough PubMed search was conducted, and data from studies describing AMN after COVID-19 vaccination were extracted, tabulated, pooled, and reviewed. Results: We present a case of AMN in a young woman 5 days after immunization with the BBIBP-CorV (Sinopharm) COVID-19 vaccine. Data from 21 cases were pooled and reviewed. The most frequent vaccines among the cases were recombinant ones (13/21), followed by mRNA-based (6/21) and inactivated vaccines (2/21). Only one patient (5%) was male. 17/21 (81%) were young women, ages 18-33. Most cases (14/21;67%) reported recent/concurrent use of contraceptive medication. In 90% of cases (19/21), symptoms appeared within 8 days of vaccination. A confined wedge-/oval-shaped lesion morphology was more frequent than a diffuse, semilunar one. Resolution of symptoms took 4 to over 15 weeks. Conclusion: Attention should be paid to the history of vaccination and contraceptive use in patients with sudden-onset visual symptoms. Optical coherence tomography is integral to the detection of AMN-related abnormalities.

Evaluation of Nutritional Status of Intensive Care Unit COVID-19 Patients Based on the Nutritional Risk Screening 2002 Score.

Background: Patients with COVID-19 are susceptible to malnutrition, which is particularly concerning among critically ill patients. We evaluated the Nutritional Risk Screening 2002 (NRS-2002) score in such patients and determined its relationship with the hospitalization outcome. Methods: This cross-sectional study involved COVID-19 patients admitted to the intensive care units (ICUs) of Shahid Faghihi Hospital, Shiraz, Iran, between February and March 2021. We assessed the nutritional status using NRS-2002 and determined disease severity with the APACHE II index. Demographic information, weight, height, clinical signs, previous illness, medications, biochemical test results, and history of anorexia and weight loss were recorded. Data were analyzed using SPSS version 18. Results: The mean age of 100 patients was 55.36 ± 18.86 years. According to NRS-2002, 30%, 29%, and 41% of patients were at low risk, moderate risk, and high risk of malnutrition, respectively. Age and BUN increased significantly with NRS-2002, while albumin and hematocrit followed the opposite trend (P < 0.001). Patients who died had lower albumin and hematocrit levels but higher age, NRS-2002 scores, and BUN/creatinine levels than those who recovered. Multivariable logistic regression revealed that for every unit increase in the NRS-2002 score, the odds of mortality increased by 354% (OR: 4.54, CI: 1.48, 13.95, P=0.008). Conclusion: NRS-2002 is a valuable prognostic tool for critically ill COVID-19 patients, with each unit's rise in the score being associated with a 354% rise in the odds of mortality. Increased malnutrition risk was linked with higher age and BUN and lower albumin and hematocrit levels.

A critical review on the existing wastewater treatment methods in the COVID-19 era: What is the potential of advanced oxidation processes in combatting viral especially SARS-CoV-2?

The COVID-19 epidemic has put the risk of virus contamination in water bodies on the horizon of health authorities. Hence, finding effective ways to remove the virus, especially SARS-CoV-2, from wastewater treatment plants (WWTPs) has emerged as a hot issue in the last few years. Herein, this study first deals with the fate of SARS-CoV-2 genetic material in WWTPs, then critically reviews and compares different wastewater treatment methods for combatting COVID-19 as well as to increase the water quality. This critical review sheds light the efficiency of advanced oxidation processes (AOPs) to inactivate virus, specially SARS-CoV-2 RNA. Although several physicochemical treatment processes (e.g. activated sludge) are commonly used to eliminate pathogens, AOPs are the most versatile and effective virus inactivation methods. For instance, TiO2 is the most known and widely studied photo-catalyst innocuously utilized to degrade pollutants as well as to photo-induce bacterial and virus disinfection due to its high chemical resistance and efficient photo-activity. When ozone is dissolved in water and wastewater, it generates a wide spectrum of the reactive oxygen species (ROS), which are responsible to degrade materials in virus membranes resulting in destroying the cell wall. Furthermore, electrochemical advanced oxidation processes act through direct oxidation when pathogens react at the anode surface or by indirect oxidation through oxidizing species produced in the bulk solution. Consequently, they represent a feasible choice for the inactivation of a wide range of pathogens. Nonetheless, there are some challenges with AOPs which should be addressed for application at industrial-scale.

Propolis efficacy on SARS-COV viruses: a review on antimicrobial activities and molecular simulations.

This current study review provides a brief review of a natural bee product known as propolis and its relevance toward combating SARS-CoV viruses. Propolis has been utilized in medicinal products for centuries due to its excellent biological properties. These include anti-oxidant, immunomodulatory, anti-inflammatory, anti-viral, anti-fungal, and bactericidal activities. Furthermore, studies on molecular simulations show that flavonoids in propolis may reduce viral replication. While further research is needed to validate this theory, it has been observed that COVID-19 patients receiving propolis show earlier viral clearance, enhanced symptom recovery, quicker discharge from hospitals, and a reduced mortality rate relative to other patients. As a result, it appears that propolis could probably be useful in the treatment of SARS-CoV-2-infected patients. Therefore, this review sought to explore the natural properties of propolis and further evaluated past studies that investigated propolis as an alternative product for the treatment of COVID-19 symptoms. In addition, the review also highlights the possible mode of propolis action as well as molecular simulations of propolis compounds that may interact with the SARS-CoV-2 virus. The activity of propolis compounds in decreasing the impact of COVID-19-related comorbidities, the possible roles of such compounds as COVID-19 vaccine adjuvants, and the use of nutraceuticals in COVID-19 treatment, instead of pharmaceuticals, has also been discussed.

COVID-19 transmission, vulnerability, persistence and nanotherapy: a review.

End 2019, the zoonotic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), named COVID-19 for coronavirus disease 2019, is the third adaptation of a contagious virus following the severe acute respiratory syndrome coronavirus in 2002, SARS-CoV, and the Middle East respiratory syndrome virus in 2012, MERS-CoV. COVID-19 is highly infectious and virulent compared to previous outbreaks. We review sources, contagious routes, preventive measures, pandemic, outbreak, epidemiology of SARS-CoV, MERS-CoV and SARS-CoV-2 from 2002 to 2020 using a Medline search. We discuss the chronology of the three coronaviruses, the vulnerability of healthcare workers, coronaviruses on surface and in wastewater, diagnostics and cures, and measures to prevent spreading.