Evaluation of miR-122 levels in chronic HBV and liver cirrhosis patients

Background: MicroRNA is a type of small RNA of about 22 nucleotide length. Most popular miRNAs are found in the liver and are extensively important in determining the biological and clinical functions. MicroRNA, in host cells, may impact the replication of viruses either positively or negatively. In this study the miR-122 expression was examined and compared in three groups, two sample groups of patients with chronic hepatitis and hepatitis B virus-associated cirrhosis, and a healthy control group.Materials and Methods: In this study, 108 samples of whole blood were taken from each participant. Then the miRNA expression evaluation was conducted through relative real time PCR.Results: The results indicated that miR-122 expression was elevated in patients with chronic hepatitis B and HBV related cirrhosis about 1.8 times (P<0.05) more than control group which is statistically significant.Conclusion: According to the results of this study, measuring the miR-122 expression levels may be used as a biomarker and an indicator of the disease progression of chronic hepatitis B to HBV related cirrhosis to HCC, but needs more investigations and more samples

Efficient Bayesian estimation and combination of GARCH-type models

This chapter proposes an up-to-date review of estimation strategies available for the Bayesian inference of GARCH-type models. The emphasis is put on a novel efficient procedure named AdMitIS. The methodology automatically constructs a mixture of Student-t distributions as an approximation to the posterior density of the model parameters. This density is then used in importance sampling for model estimation, model selection and model combination. The procedure is fully automatic which avoids difficult and time consuming tuning of MCMC strategies. The AdMitIS methodology is illustrated with an empirical application to S&P index log-returns where non-nested GARCH-type models are estimated and combined to predict the distribution of next-day ahead log-returns

Assessment and Molecular Docking of SARS-CoV-2 NSP3 and NSP12 Mutants in Iranian Patients in Golestan Province

Background: Molecular analysis of SARS-CoV-2 genome is important to predict viral pathogenicity. In addition to transmission, replication is a key factor in pathogenicity of the virus. Notably, mutations in non-structural proteins (NSP3 and NSP12) can affect host immune response and viral replication. Therefore, this study was conducted to investigate different mutations of SARS-CoV-2 NSP3, and NSP12 during different waves of COVID-19 infection.Methods: We recruited 57 NGS sequences including 8 NGS sequences from Golestan SARS-CoV-2 RNA samples, obtained as part of clinical testing in different referral centers of Iran. After obtaining sequences from the global initiative on sharing all influenza data (GISAID), and evaluating and processing data, all sequences were aligned to the Wuhan variant genome (NC_045512.2) using MEGA6. The HDOCK server was used for molecular docking.Results: In NSP3, mutations in positions (nts 315, 545, 2666, 3264) were more frequent and among them mutation in positions including nt 545 (aa182) and nt 2666 (aa889) were associated with an increase in codon usage. In the term of NSP12, mutations in positions such as nts 406 (aa137), 965 (aa323), 1233, 1653, 1836, 2733 were more frequent. The molecular docking results showed more affinity in some variants of NSP3 and NSP12 as well.Conclusion: This study has assessed mutation in SARS-CoV-2 Nsp3, and NSP12 which are viral protease, and viral polymerase (RdRp). The mutations reported in this study may help this virus to replicate faster and evade the pharmaceutical agents which target viral polymerase activity and be very effective in viral pathogenesis. In addition, this study highlights the importance of ongoing genomic variation studies to be performed on SARS-CoV-2 variants

Evaluation of Mutations in SARS-CoV-2 N and S Genes on the Proteins Stability, Immunogenicity, and Pathogenicity in Iranian Patients from Golestan Province

Background: Natural selection such as mutations is known as a constant process for viral fitness and selective adaptation. Understanding the effects of each mutation, especially on structural proteins in the viral life cycle, is important in tracking the viruses behavior. Here, we evaluated the effects of mutations in SARS-CoV-2 nucleoprotein (N) and spike (S) genes on the protein stability, immunogenicity, and pathogenicity in Iranian COVID-19 patients from Golestan province. Methods: In this study, 8 SARS-CoV-2 RNA samples were enrolled from referral hospitals in Golestan province. These samples were confirmed using a real-time RT-PCR assay targeting the SARS-CoV-2 nucleoprotein (N) and ORF1ab genes (Pishtazteb, Iran). Next-generation sequencing (NGS) was done on samples and subsequent sequences were retrieved from Global Initiative on Sharing All Influenza Data (GISAID) EpiCoV database. Structural analysis was performed between wild type (Wuhan accession number: NC_045512.2) and mutant N and S proteins to evaluate their stability, immunogenicity, and pathogenicity via bioinformatics servers such as Dynamut, Prodigy, IEDB, and software’s (Mega XI and Pymol II.V.II visualizer). Results: Amino acid codon changes in N and S proteins show that mutations could alter the translation efficiency. Normal Mode Analysis (NMA) by Dynamut server shows that stability and flexibility are changed by the mutations of these proteins. Immunogenicity analysis indicates the potential effects of some mutations such as P681H, Q675R, L699I, and D3L on immune escape. Interaction complex binding energy and affinity are higher in the mutant type compared to the Wuhan wild type, indicating higher pathogenicity. Conclusion: The results indicate that there are some important mutations in N and S genes that affect the virus behavior in the infectivity. Regarding the sample size limitation and various mutations in SARS-CoV-2 variants, other studies using whole-genome sequencing with larger sample sizes will be required. Therefore, continuous monitoring of the SARS-CoV-2 genome seems important

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ABSTRACT Human papillomavirus (HPV) DNA has been identified in esophageal carcinomas. However, the incidence of HPV varies significantly in different geographical locations. In this study, neoplasms from Turkmen Sahra, a region in Golestan province in northeast part of Iran, with a high incidence of squamous cell carcinoma were analyzed for the presence of HPV DNA. Turkmen Sahra is located in the cancer belt in Asia. Eighty-five squamous cell carcinomas were examined for the presence of HPV DNA. PCR was utilized to amplify a 124-bp segment of the HPV L1 gene using the consensus primers. The amplified region was subsequently sequenced to identify the HPV. The results indicated that the rates of HPV detection in squamous cell carcinoma specimen for men and women were 52.8% and 43.7% respectively. The positive cases included HPV-16 (54.7%), HPV-18 (4.8%), HPV-6 (14.3%), HPV-66 (7.1%), HPV-52 (4.8%) and 14.3% of cases were positive for more than one type of HPV. Human papillomavirus type 16 that can be potentially oncogenic was prevalent in 54.8% of the cases of esophageal squamous cell carcinoma. Our results confirm the previously reported HPV involvement in the esophageal squamous cell carcinoma, and support the possible role of HPV as an etiological agent in esophageal carcinogenesis

Opium use and risk of bladder cancer : A multi-centre case-referent study in Iran

Background: Bladder cancer (BC) is the 10th most common type of cancer worldwide and the fourth most common type of cancer in Iran. Opium use is considered as one of the risk factors for BC. We aim to assess the association between various parameters of opium use, which in Iran is mainly ingested or smoked in various forms, and the risk of BC. Method: In this multi-centre case-referent study in Iran, 717 BC cases and 3477 referents were recruited to the study from May 2017 until July 2020. Detailed histories of opium use (duration, amount, frequency) and potential confounders were collected by trained interviewers. Multivariable unconditional logistic regression models were used to measure adjusted odds ratio (OR) and 95% confidence intervals (CI). The ORs were adjusted for age, gender, place of residence and pack-years of cigarette smoking. Results: Regular opium consumption was associated with an increased risk of BC (OR 3.5, 95% CI: 2.8, 4.3) compared with subjects who never used opium. Compared with continuous users, the risk decreased to one-Third for those who stopped opium more than 10 years ago. The adjusted OR for those who used both crude opium (teriak) and opium juice was 7.4 (95% CI: 4.1, 13.3). There was a joint effect of opium and tobacco (OR for users of both opium and tobacco 7.7, 95% CI: 6.0, 9.7). Conclusions: Regular opium use is associated with an approximately 4-fold risk for BC. The OR decreases along with the increasing time since stopping opium use.publishedVersionPeer reviewe

The global burden of cancer attributable to risk factors, 2010-19 : a systematic analysis for the Global Burden of Disease Study 2019

Background Understanding the magnitude of cancer burden attributable to potentially modifiable risk factors is crucial for development of effective prevention and mitigation strategies. We analysed results from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019 to inform cancer control planning efforts globally. Methods The GBD 2019 comparative risk assessment framework was used to estimate cancer burden attributable to behavioural, environmental and occupational, and metabolic risk factors. A total of 82 risk-outcome pairs were included on the basis of the World Cancer Research Fund criteria. Estimated cancer deaths and disability-adjusted life-years (DALYs) in 2019 and change in these measures between 2010 and 2019 are presented. Findings Globally, in 2019, the risk factors included in this analysis accounted for 4.45 million (95% uncertainty interval 4.01-4.94) deaths and 105 million (95.0-116) DALYs for both sexes combined, representing 44.4% (41.3-48.4) of all cancer deaths and 42.0% (39.1-45.6) of all DALYs. There were 2.88 million (2.60-3.18) risk-attributable cancer deaths in males (50.6% [47.8-54.1] of all male cancer deaths) and 1.58 million (1.36-1.84) risk-attributable cancer deaths in females (36.3% [32.5-41.3] of all female cancer deaths). The leading risk factors at the most detailed level globally for risk-attributable cancer deaths and DALYs in 2019 for both sexes combined were smoking, followed by alcohol use and high BMI. Risk-attributable cancer burden varied by world region and Socio-demographic Index (SDI), with smoking, unsafe sex, and alcohol use being the three leading risk factors for risk-attributable cancer DALYs in low SDI locations in 2019, whereas DALYs in high SDI locations mirrored the top three global risk factor rankings. From 2010 to 2019, global risk-attributable cancer deaths increased by 20.4% (12.6-28.4) and DALYs by 16.8% (8.8-25.0), with the greatest percentage increase in metabolic risks (34.7% [27.9-42.8] and 33.3% [25.8-42.0]). Interpretation The leading risk factors contributing to global cancer burden in 2019 were behavioural, whereas metabolic risk factors saw the largest increases between 2010 and 2019. Reducing exposure to these modifiable risk factors would decrease cancer mortality and DALY rates worldwide, and policies should be tailored appropriately to local cancer risk factor burden. Copyright (C) 2022 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license.Peer reviewe

Plasma Lipid Peroxidation Zinc and Erythrocyte Cu-Zn Superoxide Dismutase Enzyme Activity in Patients with Type 2 Diabetes Mellitus in Gorgan City (South East of the Caspian Sea)

Le dernier morceau de l’opus de Michel Vovelle est, à double titre, un retour aux sources. Retour vers des sources régionales d’une part. Les folies aixoises nous ramènent en effet sur le terrain originel d’un historien qui fut, à l’aune de l’observatoire provençal, l’un des meilleurs décrypteurs des attitudes des hommes devant la mort avant de conduire dans cette province une entreprise d’anthropologie sociale qui reste un modèle inégalé.  Quant au choix de traiter la crise ayant affecté la ..

Polymorphisms in CCR5Δ32 and Risk of HIV-1 Infection in the Southeast of Caspian Sea, Iran

Prevalence of CCR5Δ32 among blood samples of more than 400 healthy and HIV-1-infected people was investigated in Iran. Polymerase chain reaction (PCR) following DNA extraction was used. Desired frequency was analyzed by Hardy–Weinberg equilibrium (HWE) analysis and SPSS 16.0 software to harvest the results. The prevalence of CCRΔ32 heterozygote genotype was 3% in healthy people and 0.7% in HIV-1–infected individuals. There was no homozygote CCR5Δ32 in both groups, and the allele Δ32 was only observed in 1.5% and 0.36% of healthy and HIV-1–infected participants, respectively. Therefore according to this study, the frequency of the allele CCR5Δ32 indicates no significant difference between either groups (p=0.18) and it sounds that the mentioned mutation in heterozygote people would not affect their susceptibility against HIV infection. Genotyping trial in Iranians with HIV infection is supposed to be helpful as a matter of prognostic purposes

Study of Hepatitis B Virus Genotypes and Mutation in 1762 & 1764 Nucleotides of X Gene in Chronic HBV Patients from Golestan Province-Iran

Abstract Introduction: More than 350 million people are chronic carriers of HBV and many of them develop progressive diseases, including cirrhosis and hepatocellular carcinoma. Many of those infected develop persistent disease and a proportion goes on to develop liver failure and cancer. Researchers showed that double mutations of the x gene at position 1762 and 1764, have been found in chronic hepatitis B. These mutations were proposed to be associated with fulminant hepatitis B increasing risk of hepatocellular carcinoma. This project aimed to investigate mutation in the x gene region of HBV infected patients in Golestan province, Iran. Method: 100 patients were entered in this study. Hepatitis B viral DNA was extracted from plasma and PCR was performed using specific primers. Direct sequencing and alignment of x gene were applied using reference sequence from Gene Bank database (Okamoto, 1988; Accession number AB033559). Results: Among the chronic HBV patients 51% were male. The results showed that 49% of patients had A1762T, G1764A mutations changing AGG to stop codon TGA. 27% and 24% of cases were showed mutation only in A1762T and G1764A positions respectively. Conclusion: This study was shown presence of X gene mutation in HBV infected people in Golestan province, Iran. The rate of mutation in two positions 1762 and 1764 of HBV genotype D X gene was higher than the average rate of the world (34%)