MS-HRM protocol: a simple and low-cost approach for technical validation of next-generation methylation sequencing data.

DNA methylation is a fundamental epigenetic process and have a critical role in many biological processes. The study of DNA methylation at a large scale of genomic levels is widely conducted by several techniques that are next-generation sequencing (NGS)-based methods. Methylome data revealed by DNA methylation next-generation sequencing (mNGS), should be always verified by another technique which they usually have a high cost. In this study, we offered a low-cost approach to corroborate the mNGS data. In this regard, mNGS was performed on 6 colorectal cancer (case group) and 6 healthy individual colon tissue (control group) samples. An R-script detected differentially methylated regions (DMRs), was further validated by high resolution melting (MS-HRM) analysis. After analyzing the data, the algorithm found 194 DMRs. Two locations with the highest level of methylation difference were verified by MS-HRM, which their results were in accordance with the mNGS. Therefore, in the present study, we suggested MS-HRM as a simple, accurate and low-cost method, useful for confirming methylation sequencing results.

Effect of nano clay, nano-graphene oxide and carbon nanotubes on the mechanical and tribological properties of crosslinked epoxy nanocomposite.

The objective of this study is to investigate the effects of different nanoparticles as reinforcement in a polymeric matrix on the mechanical and tribological properties of the composite. The different particles including nanoclay (NC), nano-graphene oxide (NGO), and carbon nanotubes (CNT) with various weight percentages were incorporated into the epoxy matrix. Young's modulus, ultimate tensile strength, strain at the fracture point, and the fracture toughness of nanocomposite samples were investigated. Besides, the tribological performance of these fabricated nanocomposites was evaluated and discussed. The results show that a significant change in the mechanical properties of the nanocomposites compared to the epoxy matrix. Also, the results reveal that the combination of NC with NGO improves the mechanical properties of graphene nanocomposites. It is found that adding NC to the NG/epoxy composite, may increase the fracture toughness up to 2 times as well as improve the ultimate tensile strength and strain at the fracture point. However, there was no significant change in Young's modulus.

Comparison of Dexmedetomidine, Lidocaine, and Fentanyl in Attenuation Hemodynamic Response of Laryngoscopy and Intubation in Patients Undergoing Cardiac Surgery.

MATERIALS AND METHODS: This clinical trial was conducted on 90 patients, aged 30-70 years, who had heart surgery. The participants were categorized into three groups. Group D received 1 µg/kg intravenous dexmedetomidine in 10 minutes, group L received 1.5 mg/kg lidocaine (1%) 90 seconds before intubation, and group F received 2 µg/kg fentanyl. The vital signs (HR, SBP, DBP, and MAP) were measured before intubation and 1st, 3rd, 5th, and 10th minutes after intubation. Data were analyzed with SPSS 19 software (chi-square, one-way ANOVA, or Kruskal-Wallis). RESULTS: The age (P=0.389) and gender distributions of patients were similar in all three groups. Dexmedetomidine significantly attenuated HR in the 3rd (P=0.001), 5th (P=0.001), and 10th (P=0.003) minutes after intervention. It also reduced the systolic blood pressure in the 5th (P=0.024) and 10th (P=0.006) minutes. This reduction was significantly higher in the dexmedetomidine group than that in the two other groups. In addition, dexmedetomidine caused a greater reduction in MAP in the 1st (P=0.048), 5th (P=0.0001), and 10th (P=0.0001) minutes. Discussion. All three medications were effective in controlling HR; however, dexmedetomidine caused bradycardia in the 3rd, 5th, and 10th minutes. Lidocaine resulted in an increase in MAP in the 1st minute after intubation; whereas, dexmedetomidine reduced MAP at the 5th and 10th minutes after intubation. Changes in blood pressure and mean arterial pressure in the fentanyl group was lower than the two other groups. CONCLUSION: As a result, dexmedetomidine was not suitable for hemodynamic control and led to hypotension and bradycardia; on the other hand, fentanyl was more effective than two other medications in patients undergoing cardiac surgery. This trial is registered with IRCT2017013132320N1.

DMRFusion: A differentially methylated region detection tool based on the ranked fusion method.

DNA methylation is an important epigenetic modification involved in many biological processes and diseases. Computational analysis of differentially methylated regions (DMRs) could explore the underlying reasons of methylation. DMRFusion is presented as a useful tool for comprehensive DNA methylation analysis of DMRs on methylation sequencing data. This tool is designed base on the integration of several ranking methods; Information gain, Between versus within Class scatter ratio, Fisher ratio, Z-score and Welch's t-test. In this study, DMRFusion on reduced representation bisulfite sequencing (RRBS) data in chronic lymphocytic leukemia cancer displayed 30 nominated regions and CpG sites with a maximum methylation difference detected in the hypermethylation DMRs. We realized that DMRFusion is able to process methylation sequencing data in an efficient and accurate manner and to provide annotation and visualization for DMRs with high fold difference score (p-value and FDR<0.05 and type I error: 0.04).

Fate of toxic metals during estuarine mixing of fresh water with saline water.

Metals are among the most common environmental pollutants, and their presence in high concentration in waters and biota have devastating effects on flora, fauna, and human health. Flocculation process of metals during estuarine mixing can reduce the environmental hazards of metals and also can provide micronutrients to the aquatic system. The present investigation provides a thorough study of eliminating colloidal elements of copper, manganese, nickel, lead, and zinc during estuarine mixing of Shalmanrood River water with Caspian Sea water in Iran. The processes of flocculation were carried out in six different salinity regimes (0.45-2.4 ppt). The obtained result is indicative of non-conservative behavior of the studied metals. Higher flocculation resulted in a lower salinity regime. The obtained results indicated that most of the metals were eliminated during the initial mixing of fresh water with sea water at 0.45-0.9 ppt salinity interval. The trend of flocculation rates of elements is as follows: Zn (59.3%) > Pb (47.6%) > Mn (37.5%) > Cu (29.2%) > Ni (27%).The annual average load of copper (Cu), manganese (Mn), nickel (Ni), lead (Pb), and zinc (Zn) from Shalmanrood River to Caspian Sea decreases as a result of flocculation process from 9.9, 7.7, 8.9, 5.1, and 23.2 tons per year to 7, 4.8, 6.5, 2.7, and 9.4 tons per year, respectively. According to the cluster analysis, parameters such as temperature, pH, and Eh do not have any impact on flocculation of elements expect for Pb. The only parameter that influences the flocculation of Mn is the salinity. Metal speciation studies that are carried out by Eh-pH software show that the studied metals are present as oxides (Zn, Cu, and Ni) and hydroxides (Mn and Pb).

Factors influencing therapeutic response to pegylated interferon plus ribavirin in the different genotypes of chronic hepatitis C.

BACKGROUND: Different factors like age, sex, route of infection, initial viral load, levels of liver function tests and genotypes may affect response to treatment in patients with chronic hepatitis C. The purpose of this study was to determine the role of these factors in the treatment of these patients. METHODS: From 2004 to 2012, different genotypes of chronic HCV (Hepatitis C virus) patients in Babol, North of Iran who were treated with pegylated interferon plus ribavirin with standard doses (48 weeks for genotype 1, and 24 weeks for genotypes 2 and 3) were entered in the study. HCV RNA was measured during and after treatment based on genotype and protocol. The outcome measure was defined as sustained virological response (SVR) (negative HCV RNA after six months of therapy) was achieved. The data were collected and analyzed. RESULTS: The mean age of the patients (61 males, 5 females) was 33.82±9.64 years. Twenty seven (40.9%), 37 (56.1%) and 2 (%3) were genotypes 1, 2 and 3, respectively. Twenty one (77.8%) with genotype 1, and 34 (91.9%) with genotype 3 achieved SVR (P=0.045). Fifty-five of 61 men (90.2%) and 2 out of 5 females (40%) achieved SVR (P=0.01). SVR was seen in 22 (88%) of 25 IV drug patients versus in 35 (85.4%) of the non-addict cases (p>0.05). There were no significant differences regarding age, viral load, and liver aminotransferase levels with treatment. CONCLUSION: The results show that genotypes 2 and 3, and the male sex had better SVR. Further studies with large number of cases are recommended.

Incidental finding of congenital thoracic malformations in adult population.

OBJECTIVE: Evaluation of abnormal adult chest computed tomography (CT) scans. STUDY DESIGN: Retrospective series of 3 cases. SETTING: Two University-based hospitals. INTERVENTION: Three adult patients (age range 56 to 61) underwent chest CT scans. Two were trauma patients and one complained of chest pain with a negative cardiac workup. One CT scan revealed a lung mass that was highly suspicious for malignancy and the other two CT scans were suspicious for diaphragmatic hernia. Two patients underwent elective surgery and the third underwent emergent surgery. RESULTS: The CT scan of patient 1 was suspicious for malignancy; however, the pathology of the lung mass revealed only inflammation consistent with an intralobular bronchopulmonary sequestration. Patient 2 had a congenital Morgagni hernia with omentum and colon in the mediastinum, and patient 3 had a diaphragmatic defect combined with a bifid sternum and defective pericardium, fulfilling three criteria of pentalogy of Cantrell. CONCLUSION: Thoracic congenital malformations may go unnoticed and unsuspected until adulthood. They should be kept in mind when reviewing unusual CT scans of the chest in adults. Their surgical management, however, is similar to their counterparts in infancy.