Inflammation and immunological disarrays are associated with acute exercise in type 2 diabetes.

Objective: Type 2 diabetes (T2D) is the most common metabolic disorder that is associated with insulin resistance. The aim of the present study is to discover details of the molecular mechanism of exercise on control or progress of diabetic condition in patients via network analysis. Methods: Gene expression profiles of patients with T2D before and after doing exercise are retrieved from Gene Expression Omnibus (GEO) and are pre-evaluated by the GEO2R program. Data are studied based on expression values, regulatory relationships between the differentially expressed genes (DEGs), gene ontology analyses, and protein-protein interaction PPI network analysis. Results: A number of 118 significant DEGs were identified and classified based on fold change (FC) values as most dysregulated genes and dysregulated individuals. Action map analysis revealed that 18 DEGs appeared as the critical genes. Gene ontology analysis showed that 24 DEGs are connected to at least four pathways. JUN, IL6, IL1B, PTGS2, FOS, MYC, ATF3, CXCL8, EGR1, EGR2, NR4A1, PLK3, TTN, and UCP3 were identified as central DEGs. Conclusion: Finally; JUN, IL6, IL1B, PTGS2, FOS, ATF3, CXCL8, EGR1, and EGR2 were introduced as the critical targeted genes by exercise. Since the critical genes after exercise are upregulated and mostly are known as the risk factors of T2D, it can be concluded that unsuitable exercise can develop diabetic conditions in patients. Acute exercise-induced inflammation and immune disturbances seem to be associated with the development of T2D in patients.

Acellular Fish Skin for Deep Dermal Traumatic Wounds Management; Introducing a Novel Dressing.

The optimal therapy for deep wounds is based on the early debridement of necrotic tissue followed by wound coverage to avoid a systemic inflammatory response and optimize scar-free healing. The outcomes are affected by available resources and underlying patient factors, which cause challenges in wound care and suboptimal outcomes. Here we report a patient with deep dermal injury wounds, who was treated with platelet-rich fibrin (PRF) gel, plasma rich in growth factor (PRGF) gel, and acellular fish skin. Patient's outcomes regarding healing and scar quality were collected objectively and subjectively for one year after the injury. Wounds treated with acellular fish skin demonstrated accelerated wound healing, a significantly higher water-storage capacity, and better pain relief. Furthermore, improved functional and cosmetic outcomes, such as elasticity, skin thickness, and pigmentation, were demonstrated. It seems that, the PRGF gel and PRF in combination with acellular fish skin grafts resulted in the faster healing of wounds and better functional and aesthetic outcomes than split-thickness skin grafts treatment.

Assessment of Photosensitizer Concentration Effects on the Efficacy of Photodynamic Therapy.

Introduction: Photodynamic therapy (PDT) is an attractive approach in medicine. Due to its noninvasive nature and low side effects, PDT has been developed quickly. In the present study, the gene expression profiles of the human cell line that was treated via PDT in the sub-lethal concentration (LC50) and super-lethal concentration (LC90) of a photosensitizer (PS) from Gene Expression Omnibus (GEO) were extracted and the common differentially expressed genes (DEGs) were investigated. Methods: The gene expression profiles of the treated cells were compared with a control, and the common DEGs were determined. The common DEGs were assessed via protein-protein interaction (PPI) network analysis, and gene ontology enrichment was evaluated. The related biological terms for the common genes were identified. Results: Ninety-four common DEGs were selected to be analyzed. It appeared that the activation and increment of gene expression were prominent processes. Jun, Dusp1, Atf4, and Atf3 as four critical genes were highlighted. "Chromosomal and microsatellite instability in colorectal cancer" was identified as the main class of biological terms related to the assessed DEGs. Conclusion: The major molecular events which happened in both analyses indicated that PDT, independent from the concentration of PS, induced gross molecular changes such as the upregulation of Jun and Dusp1.

Down-regulation of TP53 is a highlighted molecular event in gastric ulcer.

Aim: The current study explored the crucial dysregulate proteins and biochemical pathways in gastric ulcer as its main aim. Background: Gastric ulcer as an acid-related gastrointestinal disease is known as one of the most public gastrointestinal disorders. Methods: A total of 100 proteins from STRING database were analyzed by Cytoscape and its applications to find the central proteins and the related biochemical pathways. Action map analysis was applied to explore regulatory relationships between the critical proteins. Results: Network analysis and gene ontology revealed that IL6, ALB, TNF, INS, IL1B, IL10, TP53, CXCL8, and PTGS2 are the highlighted proteins related to gastric ulcer. Six clusters of biochemical pathways, namely "response to external stimulus," "multicellular organismal process," "regulation of biological quality," "cellular response to stimulus," "cellular response to chemical stimulus," and "transport" were identified as the dysregulated pathway in patients. Conclusion: Down-regulation of TP53 by IL2, PTGS2, and TNF seems to be a main process occurring in gastric ulcer patients.

Introducing critical common dysregulated proteins in esophageal, gastric, and intestinal cancers.

Aim: The current study aimed to determine the common dysregulated proteins between esophageal, gastric, and intestinal cancers. Background: Though there are several documents about the role of AKT1 in promoting of esophageal, gastric, and intestinal cancers, there is not enough evidence about the dominant role of AKT1 relative to the other oncogene genes in the promotion of the three studied cancer types. Methods: One hundred proteins related to each of esophageal, gastric, or intestinal cancer were retrieved from the STRING database and interacted by Cytoscape software v 3.2.7. 2 to create the correlated interactomes. The network was analyzed by the "NetworkAnalyzer" application of Cytoscape to find the centrality parameters of the nodes. Results of network analysis and action map assessment were used to determine the common critical proteins between the three studied cancers. Results: One hundred proteins were extracted for each of the studied cancers. Among 42 common dysregulated proteins, 36 individuals were selected through network analysis and were screened through action map assessment. Eighteen proteins were introduced as the important common proteins. Finally, AKT1 was a candidate for the crucial dysregulated proteins common in the three analyzed diseases. Conclusion: The findings indicate that AKT1, relative to the other oncogene genes, is a suitable candidate to be evaluated in patients as a prediagnostic tool to reduce endoscopy and colonoscopy rates.

Assessment of cancer prevention effect of exercise.

There are many documents about benefits of exercise on human health. However, evidences indicate to positive effect of exercise on disease prevention, understanding of many aspects of this mechanism need more investigations. Determination of critical genes which effect human health.GSE156249 including 12 gene expression profiles of healthy individual biopsy from vastus lateralis muscle before and after 12-week combined exercise training intervention were extracted from gene expression omnibus (GEO) database. The significant DEGs were included in interactome unit by Cytoscape software and STRING database. The network was analyzed to find the central nodes subnetwork clusters. The nodes of prominent cluster were assessed via gene ontology by using ClueGO. Number of 8 significant DEGs and 100 first neighbors analyzed via network analysis. The network includes 2 clusters and COL3A1, BGN, and LOX were determined as central DEGs. The critical DEGs were involved in cancer prevention process.

Effects of 2.45 GHz Non-Ionizing Radiation on Anxiety-Like Behavior, Gene Expression, and Corticosterone Level in Male Rats.

Introduction: The effects of short-term and long-term exposures to 2.45 GHz radiofrequency electromagnetic radiation (RF-EMR) on anxiety-like behavior, corticosterone level, and gene expression were investigated. The goal of this study was to explore the effect of electromagnetic fields of 2.45 GHz on clinical signs such as body weight and anxiety-like behavior, including the elevated plus maze test and open-field test, and also on messenger RNA (mRNA) expression of Bax (Bcl2-associated x) and Bcl-2 (B-cell lymphoma 2) genes on the cognitive memory functions in an animal model of rats. Methods: The animals were classified into eight groups, sham groups and exposed groups for short-term and long-term exposures to the same dose of RF-EMR for one hour daily. The Wi-Fi equipment in the sham control group was not turned on during the experiment. Both genes were further confirmed by reverse transcriptase-polymerase chain reaction (RT-PCR). The semi-quantitative PCR method of electromagnetic fields in the 2.45 GHz range impacted the expression of Bax and Bcl-2 genes in the rat's memory. Results: The present study exhibited that short-term radiation could decrease the percentage of entry into the open arm and the percentage of time spent, while there were no substantial impacts on the long-term radiation effect. Our data support the hypothesis that short-term exposure worked as a systemic stressor, raising plasma corticosterone and changing glucocorticoid receptor expression in the hippocampus. Conclusion: Additional research on this specific frequency and amount of radiation is required to discover strategies for protecting the nervous system from the detrimental effects of RF-EMR radiation.

Identification of Targeted Central Genes (IGF1 and HMOX1) by Indirect Cold Physical Plasma in Human Melanocytes.

Introduction: Cold physical plasma is a growing tool in medicine which is applied for the treatment of different cancers. In the present study, the gene profiles of human melanocytes exposed to indirect cold physical plasma versus control individuals are analyzed via protein-protein interaction (PPI) network analysis. Methods: The gene expression profiles were derived from Gene Expression Omnibus (GEO), and the significant differentially expressed genes (DEGs) were decoded via "Expression Atlas". PPI network analysis was applied to find the targeted central genes by indirect cold physical plasma. Results: The main connected component of the constructed network including 74 queried DEGs and 50 added first neighbors was analyzed. Considering degree value, betweenness centrality, closeness centrality, and stress, IGF1 and HMOX1 were introduced as the central nodes. Conclusion: The finding of this study indicates that the down-regulation of IGF1 and the up-regulation of HMOX are the prominent events in response to indirect cold physical plasma treatment at the cellular level. Detection of related biological terms via gene ontology is suggested.

Introducing Protein Homeostasis and Glycogen Synthesis as Two Targets of Blue Light Radiation in Lentinula edodes.

Introduction: There are documents about the biological effects of blue light radiation on different organisms. An understanding of the molecular mechanism of radiation effects on biological samples is an important event which has attracted researchers' attention. Determining the critical dysregulated proteins of Lentinula edodes following blue light radiation is the aim of this study. Methods: 22 differentially expressed proteins of L. edodes in response to 300 lux of blue light were extracted from the related literature. Experimental, text mining and co-expression connections between the queried proteins were assessed via the STRING database. The maps were compared and the critical proteins were identified. Results: Among the 21 queried proteins, six individuals including heat shock HSP70 protein, 20S proteasome subunit, 26S proteasome subunit P45, Aspartate aminotransferase, phosphopyruvate hydratase, and phosphoglucomutase were highlighted as the critical proteins in response to blue light radiation. Conclusion: The finding indicates that protein homeostasis and glycogen synthesis are affected by blue light radiation. Due to the critical roles of proteins as enzymes and structural elements in life maintenance and involvement of glycogen synthesis in energy consumption, blue light radiation can be considered as a life promotional agent in future investigations.

Assessment of Immunological Effects of Low-Level Er: YAG Laser Radiation.

Introduction: Low-level laser radiation has a significant effect on cell proliferation. Various investigations into the effect of Er: YAG laser on the treated cell lines have been published. Determining core targeted proteins is an attractive subject. This research aimed at identifying the critical targeted protein by a low-level Er: YAG laser in primary osteoblast-like cells. Methods: Data were extracted from the literature about proteomic assessment of 3.3 J/cm2 of low-level Er: YAG laser radiation on osteoblast-like cells of rat calvaria. The significant differentially expressed proteins plus 100 first neighbors were analyzed via network analysis and gene ontology enrichment. Results: Nine differentially expressed proteins among the 12 queried proteins were included in the main connected component. Analysis revealed that Cxcl1 was a key targeted protein in response to laser radiation. The presence of Cxcl1 in the significant cellular pathways indicated that cell growth and proliferation were affected. Conclusion: It can be concluded that the immune system is affected by the laser to activate cellular defense against stress.

The impact of HIV on the risk of COVID-19 death among hospitalized patients.

BACKGROUND: Little is known about the association between Human Immunodeficiency Virus (HIV) infection and risk of death among hospitalized COVID-19 patients. We aimed to investigate this association using a multicenter study. MATERIAL AND METHODS: This multicenter study was conducted using the registry database of Coronavirus Control Operations Headquarter from March 21, 2021 to January 18, 2020 in the province of Tehran, Iran. The interest outcome was COVID-19 death among hospitalized patients living with and without HIV. The Cox regression models with robust standard error were used to estimate the association between HIV infection and risk of COVID-19 death. The subgroup and interaction analysis were also performed in this study. RESULTS: 326052 patients with COVID-19 were included in the study, of whom 127 (0.04%) were living with HIV. COVID-19 patients with HIV were more likely to be female, older, and to have symptoms such as fever, muscular pain, dyspnea and cough. The death proportion due to COVID-19 was 18 (14.17%) and 21595 (6.63%) among HIV and non-HIV patients, respectively. Patients living with HIV had lower mean survival time compared to those without HIV (26.49 vs. 15.31 days, P-value = 0.047). Crude risk of COVID-19 death was higher among HIV patients than in non-HIV group (hazard ratio[HR]: 1.60, 1.08-2.37). Compared to those without HIV, higher risk of COVID-19 death was observed among patients with HIV after adjusting for sex (1.60, 1.08-2.36), comorbidities (1.49, 1.01-2.19), cancer (1.59, 1.08-2.33), and PO2 (1.68, 1.12-2.50). However, the risk of COVID-19 death was similar in patients with and without HIV after adjusting for age (1.46, 0.98-2.16) and ward (1.30, 0.89-1.89). CONCLUSION: We found no strong evidence of association between HIV infection and higher risk of COVID-19 death among hospitalized patients. To determine the true impact of HIV on the risk of COVID-19 death, factors such as age, comorbidities, hospital ward, viral load, CD4 count, and antiretroviral treatment should be considered.

Evaluating of Gene Expression Alteration after Garlic Consumption, Analyzing through Bioinformatics Approach.

Molecular study of garlic as a popular food ingredient could better understand its health benefits such as immunological effects. For this aim, effects of garlic on the spleen and possible side effects including oxidative stress increment, the molecular mechanism is investigated through network analysis of differentially expressed genes in the treatment of garlic. Protein-protein interaction (PPI) network analysis of spleen gene expression profile of Mus musculus (8-week old male C57BL/6J mice) in garlic treatments from a microarray study with the code of GSE10344 was analyzed via GEO2R software. Furthermore, Cytoscape V 3.7.1 was applied to construct and analyze a network of up- and down-regulated genes. The differentially expressed genes (DEGs) were analyzed via the CluePedia plugin of Cytoscape to determine expression patterns. After the identification of central nodes, an action map was created. A total of 77 DEGs were achieved which were including 40 up-regulated and 37 Down-regulated. The centrality analysis of the network indicated that Vcan, Lamb1, and Ltbp1 are hubs and Glra1, Wdr17, Nefl, and Becn1 are bottlenecks. Mutual regulatory connections between hubs and Alb and App (as two non-queried hubs) were determined. The findings indicate that garlic effect on the spleen and its mechanism may be involved mostly with App dysregulation.

Function of circular RNAs in the pathogenesis of colorectal cancer.

Circular RNAs (circRNAs) comprise a group of noncoding RNAs with a circular conformation being constructed by either classic spliceosome-mediated or lariat-kind of splicing. They have tissue and temporal specificity and are involved in different biological functions. A vast body of literature has demonstrated critical roles of circRNAs in the formation or progression of neoplasms. Hsa_circ_0066631, hsa_circ_0082096, ciRS-7, circMAT2B, circ_052666, circMBOAT2, circPACRGL and circ_0128846 are among up-regulated circRNAs in CRC. Instead, expression levels of circTADA2A, circ_022743, circ_004452, circ-FBXW7, circ0106714, circFNDC3B and circ_cse1 have been decreased in CRC samples. Finally, expression levels of circRNA-100876, hsa_circ_0002320, circNOL10, circ_0056618, circ_0060745, circ-0004277, hsa_circRNA_102958, circPPP1R12A, hsa_circ_0007534, circ_0079993 and hsa_circ_0005075 can be used for prediction of clinical outcome of patients CRC.

Gut microbiota, angiotensin-converting enzyme, celiac disease, and risk of COVID-19 infection: a review.

Celiac disease (CD) is an autoimmune disorder of the gastrointestinal tract in a genetically susceptible person. Gluten is the most crucial trigger factor for CD, and environmental factors such as microbiota and opportunistic infection risk its pathogenesis. Coronavirus disease 19 (COVID-19) spread rapidly and became a problem for healthcare systems worldwide. Little is known about the risk of severe COVID-19 and the role of dysbiosis among patients with CD. There is also a lack of knowledge about the effects of CD gut microbiota on COVID-19 infection. Therefore, the current review discusses the relationship between CD and risk factors such as microbiota for susceptibility to COVID-19.

Association of IL-22 and IL-22RA1 gene variants in Iranian patients with colorectal cancer.

AIM: In the current study, it was hypothesized that single nucleotide polymorphisms (SNPs) in the regulatory region of the IL-22 signaling pathway genes, including IL-22 and IL-22RA1 variants, may be associated with CRC susceptibility. BACKGROUND: The important role of pro-inflammatory cytokines during tumorigenesis is well-established. In recent years, IL-22 has been linked with colorectal cancer (CRC) through a number of mechanistic and observational studies. METHODS: The association of four polymorphisms in the IL-22 (rs1179251 and rs1179246) and IL-22RA1 (rs4648936 and rs10794665) genes with CRC risk were studied using a case-control design with 304 cases and 345 controls from the Iranian population. All 649 subjects were evaluated by PCR-RFLP method. RESULTS: No significant difference was found in genotype and allele frequencies between the cases and controls for either IL-22 and IL-22RA1 gene variants or CRC risk before or after adjusting for confounders. CONCLUSION: The current findings do not present any significant evidence for associations between variants in IL-22 signaling pathway genes and CRC. Complementary studies with greater sample sizes may be necessary to fully elucidate the nature of these associations.

Intravaginal Pulsed Contractile Radiofrequency for Stress Urinary Incontinence Treatment; A Safety Study.

Introduction: Radiofrequency (RF)-based stress urinary incontinence (SUI) treatment, which has quickly attracted attention, is administered in an office setting. This pilot-safety study assessed the efficacy of transvaginal RF treatment in the quality of life (QOL) and frequency of incontinence episodes in women with SUI. Methods: Twenty-eight women suffering from SUI were treated with an intravaginal quadric applicator while a grounding pad was attached in front of their pubes. The first phase is thermic, which will heat up the vaginal wall up to 40°C for 10 minutes. The second step is contraction to stimulate an aerobic exercise of pelvic floor muscles for 20 minutes (pulsed contractile RF at 20-40 watts and 1000-300 kHz with a modulation of 1 to 300 Hz for muscle exercise). It was scheduled for one session per week for 3 sessions. Patients had follow-up visits before and 1, 6 and 12 months following the treatment for one-day voiding diary, Persian version of urinary incontinence QOL questionnaire (I-QOL), Q-tip test, 24 hours-pad test and daily incontinence episodes' number. Results: The patients' mean age, duration of incontinence and median vesical leak point pressure were 41.6±9.6 years, 5.48±6.84 years and 140 cm H2 O respectively. Significant changes were observed in the mean I-QOL total score and the pad test. Also, a notable reduction was observed in the number of daily leakage episodes and the Q-tip test at any follow-up visit (P=0.001). Conclusion: Preliminary results suggest that transvaginal RF is a convenient method of SUI treatment. Significant changes were observed in the mean I-QOL total score and the pad test. Also, a notable reduction was observed in the number of daily leakage episodes.

Effect of UV Laser Radiation on "Positive Regulation of Telomere Maintenance" in Saccharomyces cerevisiae.

Introduction: Excessive exposure to ultraviolet (UV) radiation may cause a variety of skin cancers and damage to the eye lens. The assessment of different aspects of UV damage has attracted researchers' interest. UV radiation to simple biological models such as Saccharomyces cerevisiae of yeast family could help to find out different molecular changes resulting from radiation. The assessment and network analysis of gene expression data about yeast cells radiated by the UV laser was the aim of this study. Methods: The gene expression profiles of S. cerevisiae samples in the presence of the UV laser at 30 seconds radiation and 15 minutes' post-radiation time are compared with the control profiles. The significant expressed genes interacted and the central nodes and related biological terms were identified. Results: The main connected component of the network including 427 nodes was analyzed and 11 central differentially expressed genes (DEGs) were determined. RPN11, UBI4, HSP82, and HSC82 as critical DEGs and "positive regulation of telomere maintenance" as a related biological term were introduced. Conclusion: The finding has provided a new perspective on laser application in the rejuvenation process. It seems that the laser can be used as a suitable agent against the aging process which is a limiting factor in human life.

Exploring the Reversible Effects of UV Laser Radiation on the Gene Expression Profiles of Saccharomyces cerevisiae Via Network Analysis.

Introduction: The reversibility of biological processes is an important challenge in the study of environmental pollutants and also natural and artificial radiation. There are many pieces of evidence about the reversible and irreversible effects of UV radiation on the human body. Assessment of the reversibility of UV laser effects on Saccharomyces cerevisiae was the aim of this study. Methods: Gene expression alteration in S. cerevisiae samples radiated by a 30s UV laser for 15, 30, and 60 minutes post-radiation times were investigated via network analysis to explore time-dependent reversible alteration in the gene expression profiles of the samples. Results: 19 differentially expressed genes (DEGs) were identified as targeted genes for the samples which were harvested 60 minutes after radiation; network analysis revealed no significant alteration in biological processes. Conclusion: It can be concluded that the gross effects of the UV laser on S. cerevisiae samples disappear after 60 minutes of radiation.

Baseline Characteristics and Associated Factors of Mortality in COVID-19 Patients; an Analysis of 16000 Cases in Tehran, Iran.

Introduction. INTRODUCTION: Given the importance of evidence-based decision-making, this study aimed to evaluate epidemiological and clinical characteristics as well as associate factors of mortality among admitted COVID-19 cases. METHODS: This multicenter, cross-sectional study was conducted on confirmed and suspected COVID-19 cases who were hospitalized in 19 public hospitals affiliated to Shahid Beheshti University of Medical Sciences (SBMU), Tehran, Iran, between February 19 and May 12, 2020. Epidemiological and clinical characteristics of the infected cases were compared between the deceased and survivors after discharge. Case fatality rates (CFRs) were calculated across all study variables. Single and multiple logistic regressions were used to explore the risk factors associated with COIVD-19 mortality. RESULTS: Out of the 16035 cases that referred to the hospitals affiliated to SBMU, 16016 patients (99.93% of Confirmed and 99.83% of suspected cases) were hospitalized. 1612 patients died with median hospitalization days of 5 (interquartile range (IQR): 2-9) and 3 (1-7) for confirmed and suspected COVID-19 cases, respectively. The highest death rate was observed among ages>65 (63.4% of confirmed cases, 62.3% of suspected cases) and intensive care unit (ICU)/critical care unit (CCU) patients (62.7% of confirmed cases, 52.2% of suspected cases). Total case fatality rate (CFR) was 10.05% (13.52% and 6.37% among confirmed and suspected cases, respectively). The highest total CFR was observed in patients with age>65 years (25.32%), underlying comorbidities (25.55%), and ICU/CCU patients (41.7%). The highest CFR was reported for patients who had diabetes and cardiovascular diseases (38.46%) as underlying non-communicable diseases (NCDs), and patients with cancer (35.79%). CONCLUSION: This study showed a high CFR among suspected and confirmed COVID-19 cases, and highlighted the main associated risk factors including age, sex, underlying NCDs, and ICU/CCU admission affecting survival of COVID-19 patients.

MicroRNAs in gastric cancer: Biomarkers and therapeutic targets.

MicroRNAs (miRNAs) are a group of non-coding RNAs that have critical roles in regulation of expression of genes. They can inhibit or decrease expression of target genes mostly via interaction with 3' untranslated region of their targets. Their crucial roles in the regulation of expression of tumor suppressor genes and oncogenes have potentiated them as contributors in tumorigenesis. Moreover, their stability in body fluids has enhanced their potential as cancer biomarkers. In the present review article, we describe the role of miRNAs in the pathogenesis of gastric cancer and advances in application of miRNAs as biomarkers and therapeutic targets in this kind of malignancy.