Studies on Parameters Influencing the Performance of Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) in Detecting Prunus Necrotic Ringpot Virus (PNRSV)

In order to have a more detailed understanding of the various factors influencing a reverse transcriptase polymerase chain reaction (RT-PCR), a number of important parameters such as Mg+2, primer, enzyme concentration and others were optimized for the detection of Prunus necrotic ringspot virus (PNRSV). Using a PNRSV isolate with a pair of primers, complementary DNA of viral genome as template, and an appropriate enzyme together with magnesium chloride, the following optimal conditions were identified: primer concentration between 0.2 and 0.0002 pmol µl-1 and 0.06–2 units µl-1 for Taq DNA polymerase enzyme for a 50 µl reaction volume when other parameters were optimum; magnesium chloride concentration less than 2.5 mM; dNTP concentration between 1 and 10 mM. The optimum cDNA amount should be ~360 ng for a 50 µl reaction mixture. When these optimized concentrations and/or values of the main PCR parameters were brought together for a new RT-PCR, a clear and a reliable PNRSV detection having no background was performed from both growth-chamber and field-grown PNRSV-infected plants

EPIdemiology of Surgery-Associated Acute Kidney Injury (EPIS-AKI) : Study protocol for a multicentre, observational trial

More than 300 million surgical procedures are performed each year. Acute kidney injury (AKI) is a common complication after major surgery and is associated with adverse short-term and long-term outcomes. However, there is a large variation in the incidence of reported AKI rates. The establishment of an accurate epidemiology of surgery-associated AKI is important for healthcare policy, quality initiatives, clinical trials, as well as for improving guidelines. The objective of the Epidemiology of Surgery-associated Acute Kidney Injury (EPIS-AKI) trial is to prospectively evaluate the epidemiology of AKI after major surgery using the latest Kidney Disease: Improving Global Outcomes (KDIGO) consensus definition of AKI. EPIS-AKI is an international prospective, observational, multicentre cohort study including 10 000 patients undergoing major surgery who are subsequently admitted to the ICU or a similar high dependency unit. The primary endpoint is the incidence of AKI within 72 hours after surgery according to the KDIGO criteria. Secondary endpoints include use of renal replacement therapy (RRT), mortality during ICU and hospital stay, length of ICU and hospital stay and major adverse kidney events (combined endpoint consisting of persistent renal dysfunction, RRT and mortality) at day 90. Further, we will evaluate preoperative and intraoperative risk factors affecting the incidence of postoperative AKI. In an add-on analysis, we will assess urinary biomarkers for early detection of AKI. EPIS-AKI has been approved by the leading Ethics Committee of the Medical Council North Rhine-Westphalia, of the Westphalian Wilhelms-University Münster and the corresponding Ethics Committee at each participating site. Results will be disseminated widely and published in peer-reviewed journals, presented at conferences and used to design further AKI-related trials. Trial registration number NCT04165369

Solving Chemical Absorption Equilibria using Free Energy and Quantum Chemistry Calculations: Methodology, Limitations, and New Open-Source Software

We developed an open-source chemical reaction equilibrium solver in Python (CASpy, https://github.com/omoultosEthTuDelft/CASpy) to compute the concentration of species in any reactive liquid-phase absorption system. We derived an expression for a mole fraction-based equilibrium constant as a function of excess chemical potential, standard ideal gas chemical potential, temperature, and volume. As a case study, we computed the CO2 absorption isotherm and speciation in a 23 wt % N-methyldiethanolamine (MDEA)/water solution at 313.15 K, and compared the results with available data from the literature. The results show that the computed CO2 isotherms and speciations are in excellent agreement with experimental data, demonstrating the accuracy and the precision of our solver. The binary absorptions of CO2 and H2S in 50 wt % MDEA/water solutions at 323.15 K were computed and compared with available data from the literature. The computed CO2 isotherms showed good agreement with other modeling studies from the literature while the computed H2S isotherms did not agree well with experimental data. The experimental equilibrium constants used as an input were not adjusted for H2S/CO2/MDEA/water systems and need to be adjusted for this system. Using free energy calculations with two different force fields (GAFF and OPLS-AA) and quantum chemistry calculations, we computed the equilibrium constant (K) of the protonated MDEA dissociation reaction. Despite the good agreement of the OPLS-AA force field (ln[K] = −24.91) with the experiments (ln[K] = −23.04), the computed CO2 pressures were significantly underestimated. We systematically investigated the limitations of computing CO2 absorption isotherms using free energy and quantum chemistry calculations and showed that the computed values of μiex are very sensitive to the point charges used in the simulations, which limits the predictive power of this method.</p

Molecular basis of vascular damage caused by cigarette smoke exposure and a new approach to the treatment: Alpha-linolenic acid

PubMedID: 29579706Exposure to cigarette smoke (CS) causes vessel damage and mechanism of this damage has not yet been clearly identified. Therefore, in this study we aimed to investigate whether vessel damage due to the CS exposure will be prevented by the alpha-linolenic acid (ALA) or not which has anti-inflammatory effect in mice. For this reason, mice were grouped as controls (with and without CS) and ALA (with and without CS). The CS application continued 5 days a week for two months. At the end of two months, the mice were killed by cervical dislocation and their blood and thoracic aortas were isolated. ALA Treatment increased acetylcholine relaxations. CS decreased acetylcholine relaxation. CS with ALA treatment increased acetylcholine relaxations versus just CS treatment. CS caused rising in cyclooxigenase-2 and phospholipase A2 levels. This rise is inhibited with ALA treatment. CS decreased eNOS levels. But this result was not statistically significant. Furthermore, according to electron microscopic study CS damaged both smooth muscle and endothelium. While ALA treatment prevented smooth muscle damage it didn't prevent endothelial damage. Using cigarette and CS exposure is a risk factor for cardiovascular disease. Our study showed that this disease. © 2018 Elsevier Masson SASTF2010D3Authors are grateful to Cukurova University for funding this study ( TF2010D3 )

Solubility of CO₂in Aqueous Formic Acid Solutions and the Effect of NaCl Addition: A Molecular Simulation Study

There is a growing interest in the development of routes to produce formic acid from CO2, such as the electrochemical reduction of CO2 to formic acid. The solubility of CO2 in the electrolyte influences the production rate of formic acid. Here, the dependence of the CO2 solubility in aqueous HCOOH solutions with electrolytes on the composition and the NaCl concentration was studied by Continuous Fractional Component Monte Carlo simulations at 298.15 K and 1 bar. The chemical potentials of CO2, H2O, and HCOOH were obtained directly from single simulations, enabling the calculation of Henry coefficients and subsequently considering salting in or salting out effects. As the force fields for HCOOH and H2O may not be compatible due to the presence of strong hydrogen bonds, the Gibbs-Duhem integration test was used to test this compatibility. The combination of the OPLS/AA force field with a new set of parameters, in combination with the SPC/E force field for water, was selected. It was found that the solubility of CO2 decreases with increasing NaCl concentration in the solution and increases with the increase of HCOOH concentration. This continues up to a certain concentration of HCOOH in the solution, after which the CO2 solubility is high and the NaCl concentration has no significant effect. Engineering Thermodynamic

Accurate Free Energies of Aqueous Electrolyte Solutions from Molecular Simulations with Non-polarizable Force Fields

Non-polarizable force fields fail to accurately predict free energies of aqueous electrolytes without compromising the predictive ability for densities and transport properties. A new approach is presented in which (1) TIP4P/2005 water and scaled charge force fields are used to describe the interactions in the liquid phase and (2) an additional Effective Charge Surface (ECS) is used to compute free energies at zero additional computational expense. The ECS is obtained using a single temperature-independent charge scaling parameter per species. Thereby, the chemical potential of water and the free energies of hydration of various aqueous salts (e.g., NaCl and LiCl) are accurately described (deviations less than 5% from experiments), in sharp contrast to calculations where the ECS is omitted (deviations larger than 20%). This approach enables accurate predictions of free energies of aqueous electrolyte solutions using non-polarizable force fields, without compromising liquid-phase properties.Engineering ThermodynamicsTeam Poulumi De

Densities, viscosities, and diffusivities of loaded and unloaded aqueous CO₂/H₂S/MDEA mixtures: A molecular dynamics simulation study

Experimentally measuring the diffusivities of CO2 and H2S in aqueous alkanolamine solutions presents an extremely challenging task. To overcome this challenge, we performed Molecular Dynamics (MD) simulations to study the effects of temperature and N-methyldiethanolamine (MDEA) concentration on self-diffusivities of CO2 (DCO2) and H2S (DH2S) in aqueous MDEA solutions. We compute the densities and viscosities of aqueous MDEA solutions for an MDEA concentration range of 10–50 wt% and a temperature range of 288–333 K showing an excellent agreement with experimental data from literature. We compute the self-diffusivity of MDEA (DMDEA) in aqueous MDEA solutions and our findings show that the computed values of DMDEA are in excellent agreement with experimental and simulation results from literature. The self-diffusivities DCO2 and DH2S in aqueous MDEA solutions are computed for a wide range of temperatures and MDEA concentrations and our results show that both DCO2 and DH2S depend significantly on temperature and MDEA concentration. We also show that both CO2 and H2S diffuse slower in aqueous MDEA solutions than in aqueous MEA solutions. By comparing the radial distribution functions of CO2, H2S, water, and MDEA, we show that H2S has stronger interactions with the surrounding molecules than CO2, which makes H2S diffuse slower in aqueous MDEA solutions. We also investigate the densities and viscosities of acid gas loaded aqueous MDEA solutions and self-diffusivities of the reaction products of CO2 and H2S with aqueous MDEA solutions. We show that the self-diffusivities of CO2-loaded solutions significantly decrease with increasing CO2 loading while the self-diffusivities of H2S-loaded solutions do not change with changing H2S loading. Our results will be helpful in the design and optimization of acid gas removal units.Engineering Thermodynamic

Vapor pressures and vapor phase compositions of choline chloride urea and choline chloride ethylene glycol deep eutectic solvents from molecular simulation

Despite the widespread acknowledgment that deep eutectic solvents (DESs) have negligible vapor pressures, very few studies in which the vapor pressures of these solvents are measured or computed are available. Similarly, the vapor phase composition is known for only a few DESs. In this study, for the first time, the vapor pressures and vapor phase compositions of choline chloride urea (ChClU) and choline chloride ethylene glycol (ChClEg) DESs are computed using Monte Carlo simulations. The partial pressures of the DES components were obtained from liquid and vapor phase excess Gibbs energies, computed using thermodynamic integration. The enthalpies of vaporization were computed from the obtained vapor pressures, and the results were in reasonable agreement with the few available experimental data in the literature. It was found that the vapor phases of both DESs were dominated by the most volatile component (hydrogen bond donor, HBD, i.e., urea or ethylene glycol), i.e., 100% HBD in ChClEg and 88%-93% HBD in ChClU. Higher vapor pressures were observed for ChClEg compared to ChClU due to the higher volatility of ethylene glycol compared to urea. The influence of the liquid composition of the DESs on the computed properties was studied by considering different mole fractions (i.e., 0.6, 0.67, and 0.75) of the HBD. Except for the partial pressure of ethylene glycol in ChClEg, all the computed partial pressures and enthalpies of vaporization showed insensitivity toward the liquid composition. The activity coefficient of ethylene glycol in ChClEg was computed at different liquid phase mole fractions, showing negative deviations from Raoult’s law.Engineering Thermodynamic