TTCF4LAMMPS: A toolkit for simulation of the non-equilibrium behaviour of molecular fluids at experimentally accessible shear rates

Program summary: Program title: TTCF4LAMMPS CPC Library link to program files: https://doi.org/10.17632/hh2rkcxbrf.1 Developer's repository link: https://github.com/edwardsmith999/TTCF4LAMMPS Licensing provisions: GNU General Public License 3 Programming language: Python 3 Nature of problem: Measuring the nonequilibrium behaviour of bulk and confined fluids under experimentally accessible strain rates in non-equilibrium molecular dynamics (NEMD) simulations. Solution method: Creating a Python-based code that utilises the transient-time correlation function method and the LAMMPS software to enable the bulk fluid properties (e.g. viscosity) and confined fluid interfacial properties (e.g. shear stress and slip velocity) to be computed at low shear rates with NEMD.Data availability: All data used in this work are freely reproducible using the program provided. The source files are also available at the link https://github.com/edwardsmith999/TTCF4LAMMPS.We present TTCF4LAMMPS, a toolkit for performing non-equilibrium molecular dynamics (NEMD) simulations to study the fluid behaviour at low shear rates using the LAMMPS software. By combining direct NEMD simulations and the transient-time correlation function (TTCF) technique, we study the fluid response to shear rates spanning 15 orders of magnitude. We present two examples for simple monatomic systems: one consisting of a bulk liquid and another with a liquid layer confined between two solid walls. The small bulk system is suitable for testing on personal computers, while the larger confined system requires high-performance computing (HPC) resources. We demonstrate that the TTCF formalism can successfully detect the system response for arbitrarily weak external fields. We provide a brief mathematical explanation for this feature. Although we showcase the method for simple monatomic systems, TTCF can be readily extended to study more complex molecular fluids. Moreover, in addition to shear flows, the method can be extended to investigate elongational or mixed flows as well as thermal or electric fields. The high computational cost needed for the method is offset by the two following benefits: i) the cost is independent of the magnitude of the external field, and ii) the simulations can be made highly efficient on HPC architectures by exploiting the parallel design of the algorithm. We expect the toolkit to be useful for computational researchers striving to study the nonequilibrium behaviour of fluids under experimentally-accessible conditions.We thank the Australian Research Council for a grant obtained through the Discovery Projects Scheme (Grant No. DP200100422) and The Royal Society for support via International Exchanges, Grant No. IES/R3/170/233. J.P.E. was supported by the Royal Academy of Engineering (RAEng) through their Research Fellowships scheme. D.D. was supported through a Shell/RAEng Research Chair in Complex Engineering Interfaces. The authors acknowledge the Swinburne OzSTAR Supercomputing facility and the Imperial College London Research Computing Service (DOI:https://doi.org/10.14469/hpc/2232) for providing computational resources for this work. We thank Debra Bernhardt and Stephen Sanderson (University of Queensland) for useful discussions regarding the implementation of SLLOD in LAMMPS

Evaluation of the zucker diabetic fatty (ZDF) rat as a model for human disease based on urinary peptidomic profiles

Representative animal models for diabetes-associated vascular complications are extremely relevant in assessing potential therapeutic drugs. While several rodent models for type 2 diabetes (T2D) are available, their relevance in recapitulating renal and cardiovascular features of diabetes in man is not entirely clear. Here we evaluate at the molecular level the similarity between Zucker diabetic fatty (ZDF) rats, as a model of T2D-associated vascular complications, and human disease by urinary proteome analysis. Urine analysis of ZDF rats at early and late stages of disease compared to age- matched LEAN rats identified 180 peptides as potentially associated with diabetes complications. Overlaps with human chronic kidney disease (CKD) and cardiovascular disease (CVD) biomarkers were observed, corresponding to proteins marking kidney damage (eg albumin, alpha-1 antitrypsin) or related to disease development (collagen). Concordance in regulation of these peptides in rats versus humans was more pronounced in the CVD compared to the CKD panels. In addition, disease-associated predicted protease activities in ZDF rats showed higher similarities to the predicted activities in human CVD. Based on urinary peptidomic analysis, the ZDF rat model displays similarity to human CVD but might not be the most appropriate model to display human CKD on a molecular level

Performance of Ultra-Deep Pyrosequencing in Analysis of HIV-1 pol Gene Variation

INTRODUCTION: Ultra-deep pyrosequencing (UDPS) has been used to detect minority variants within HIV-1 populations. Some aspects of the quality and reproducibility of UDPS have been previously evaluated, but comprehensive studies are still needed. PRINCIPAL FINDING: In this study the UDPS technology (FLX platform) was evaluated by analyzing a 120 base pair fragment of the HIV-1 pol gene from plasma samples from two patients and artificial mixtures of molecular clones. UDPS was performed using an optimized experimental protocol and an in-house data cleaning strategy. Nine samples and mixtures were analyzed and the average number of reads per sample was 19,404 (range 8,858-26,846). The two patient plasma samples were analyzed twice and quantification of viral variants was found to be highly repeatable for variants representing >0.27% of the virus population, whereas some variants representing 0.11-0.27% were detected in only one of the two UDPS runs. Bland-Altman analysis showed that a repeated measurement would have a 95% likelihood to lie approximately within ±0.5 log(10) of the initial estimate. A similar level of agreement was observed for variant frequency estimates in forward vs. reverse sequencing direction, but here the agreement was higher for common variants than for rare variants. UDPS following PCR amplification with alternative primers indicated that some variants may be incorrectly quantified due to primer-related selective amplification. Finally, the in vitro recombination rate during PCR was evaluated using artificial mixtures of clones and was found to be low. The most abundant in vitro recombinant represented 0.25% of all UDPS reads. CONCLUSION: This study demonstrates that this UDPS protocol results in low experimental noise and high repeatability, which is relevant for future research and clinical use of the UDPS technology. The low rate of in vitro recombination suggests that this UDPS system can be used to study genetic variants and mutational linkage

Parks and Tourism

To protect biodiversity, parks agencies need political and financial support. Recreational visitors can bring both, but commercial tourism carries risks

Structural and Functional Analysis of Laninamivir and its Octanoate Prodrug Reveals Group Specific Mechanisms for Influenza NA Inhibition

The 2009 H1N1 influenza pandemic (pH1N1) led to record sales of neuraminidase (NA) inhibitors, which has contributed significantly to the recent increase in oseltamivir-resistant viruses. Therefore, development and careful evaluation of novel NA inhibitors is of great interest. Recently, a highly potent NA inhibitor, laninamivir, has been approved for use in Japan. Laninamivir is effective using a single inhaled dose via its octanoate prodrug (CS-8958) and has been demonstrated to be effective against oseltamivir-resistant NA in vitro. However, effectiveness of laninamivir octanoate prodrug against oseltamivir-resistant influenza infection in adults has not been demonstrated. NA is classified into 2 groups based upon phylogenetic analysis and it is becoming clear that each group has some distinct structural features. Recently, we found that pH1N1 N1 NA (p09N1) is an atypical group 1 NA with some group 2-like features in its active site (lack of a 150-cavity). Furthermore, it has been reported that certain oseltamivir-resistant substitutions in the NA active site are group 1 specific. In order to comprehensively evaluate the effectiveness of laninamivir, we utilized recombinant N5 (typical group 1), p09N1 (atypical group 1) and N2 from the 1957 pandemic H2N2 (p57N2) (typical group 2) to carry out in vitro inhibition assays. We found that laninamivir and its octanoate prodrug display group specific preferences to different influenza NAs and provide the structural basis of their specific action based upon their novel complex crystal structures. Our results indicate that laninamivir and zanamivir are more effective against group 1 NA with a 150-cavity than group 2 NA with no 150-cavity. Furthermore, we have found that the laninamivir octanoate prodrug has a unique binding mode in p09N1 that is different from that of group 2 p57N2, but with some similarities to NA-oseltamivir binding, which provides additional insight into group specific differences of oseltamivir binding and resistance

Complete Genome Sequence of Avian Paramyxovirus (APMV) Serotype 5 Completes the Analysis of Nine APMV Serotypes and Reveals the Longest APMV Genome

Avian paramyxoviruses (APMV) consist of nine known serotypes. The genomes of representatives of all APMV serotypes except APMV type 5 have recently been fully sequenced. Here, we report the complete genome sequence of the APMV-5 prototype strain budgerigar/Kunitachi/74.APMV-5 Kunitachi virus is unusual in that it lacks a virion hemagglutinin and does not grow in the allantoic cavity of embryonated chicken eggs. However, the virus grew in the amniotic cavity of embryonated chicken eggs and in twelve different established cell lines and two primary cell cultures. The genome is 17,262 nucleotides (nt) long, which is the longest among members of genus Avulavirus, and encodes six non-overlapping genes in the order of 3'N-P/V/W-M-F-HN-L-5' with intergenic regions of 4-57 nt. The genome length follows the 'rule of six' and contains a 55-nt leader sequence at the 3'end and a 552 nt trailer sequence at the 5' end. The phosphoprotein (P) gene contains a conserved RNA editing site and is predicted to encode P, V, and W proteins. The cleavage site of the F protein (G-K-R-K-K-R downward arrowF) conforms to the cleavage site motif of the ubiquitous cellular protease furin. Consistent with this, exogenous protease was not required for virus replication in vitro. However, the intracerebral pathogenicity index of APMV-5 strain Kunitachi in one-day-old chicks was found to be zero, indicating that the virus is avirulent for chickens despite the presence of a polybasic F cleavage site.Phylogenetic analysis of the sequences of the APVM-5 genome and proteins versus those of the other APMV serotypes showed that APMV-5 is more closely related to APMV-6 than to the other APMVs. Furthermore, these comparisons provided evidence of extensive genome-wide divergence that supports the classification of the APMVs into nine separate serotypes. The structure of the F cleavage site does not appear to be a reliable indicator of virulence among APMV serotypes 2-9. The availability of sequence information for all known APMV serotypes will facilitate studies in epidemiology and vaccinology

A Generic System for the Expression and Purification of Soluble and Stable Influenza Neuraminidase

The influenza surface glycoprotein neuraminidase (NA) is essential for the efficient spread of the virus. Antiviral drugs such as Tamiflu (oseltamivir) and Relenza (zanamivir) that inhibit NA enzyme activity have been shown to be effective in the treatment of influenza infections. The recent ‘swine flu’ pandemic and world-wide emergence of Tamiflu-resistant seasonal human influenza A(H1N1) H274Y have highlighted the need for the ongoing development of new anti-virals, efficient production of vaccine proteins and novel diagnostic tools. Each of these goals could benefit from the production of large quantities of highly pure and stable NA. This publication describes a generic expression system for NAs in a baculovirus Expression Vector System (BEVS) that is capable of expressing milligram amounts of recombinant NA. To construct NAs with increased stability, the natural influenza NA stalk was replaced by two different artificial tetramerization domains that drive the formation of catalytically active NA homotetramers: GCN4-pLI from yeast or the Tetrabrachion tetramerization domain from Staphylothermus marinus. Both recombinant NAs are secreted as FLAG-tagged proteins to allow for rapid and simple purification. The Tetrabrachion-based NA showed good solubility, increased stability and biochemical properties closer to the original viral NA than the GCN4-pLI based construct. The expressed quantities and high quality of the purified recombinant NA suggest that this expression system is capable of producing recombinant NA for a broad range of applications including high-throughput drug screening, protein crystallisation, or vaccine development

Predictors of packed red cell transfusion after isolated primary coronary artery bypass grafting – The experience of a single cardiac center: A prospective observational study

<p>Abstract</p> <p>Background</p> <p>Preoperative patients' characteristics can predict the need for perioperative blood component transfusion in cardiac surgical operations. The aim of this prospective observational study is to identify perioperative patient characteristics predicting the need for allogeneic packed red blood cell (PRBC) transfusion in isolated primary coronary artery bypass grafting (CABG) operations.</p> <p>Patients and Methods</p> <p>105 patients undergoing isolated, first-time CABG were reviewed for their preoperative variables and followed for intraoperative and postoperative data. Patients were 97 males and 8 females, with mean age 58.28 ± 10.97 years. Regression logistic analysis was used for identifying the strongest perioperative predictors of PRBC transfusion.</p> <p>Results</p> <p>PRBC transfusion was used in 71 patients (67.6%); 35 patients (33.3%) needed > 2 units and 14 (13.3%) of these needed > 4 units. Univariate analysis identified female gender, age > 65 years, body weight ≤ 70 Kg, BSA ≤ 1.75 m², BMI ≤ 25, preoperative hemoglobin ≤ 13 gm/dL, preoperative hematocrit ≤ 40%, serum creatinine > 100 μmol/L, Euro SCORE (standard/logistic) > 2, use of CPB, radial artery use, higher number of distal anastomoses, and postoperative chest tube drainage > 1000 mL as significant predictors. The strongest predictors using multivariate analysis were CPB use, hematocrit, body weight, and serum creatinine.</p> <p>Conclusion</p> <p>The predictors of PRBC transfusion after primary isolated CABG are use of CPB, hematocrit ≤ 40%, weight ≤ 70 Kg, and serum creatinine > 100 μmol/L. This leads to better utilization of blood bank resources and cost-efficient targeted use of expensive blood conservation modalities.</p

Layer-by-layer deposition of open-pore mesoporous TiO 2- Nafion® film electrodes

The formation of variable thickness TiO2 nanoparticle-Nafion® composite films with open pores is demonstrated via a layer-by-layer deposition process. Films of about 6 nm diameter TiO2 nanoparticles grow in the presence of Nafion® by “clustering” of nanoparticles into bigger aggregates, and the resulting hierarchical structure thickens with about 25 nm per deposition cycle. Film growth is characterized by electron microscopy, atomic force microscopy, and quartz crystal microbalance techniques. Simultaneous small-angle X-ray scattering and wide-angle X-ray scattering measurements for films before and after calcination demonstrate the effect of Nafion® binder causing aggregation. Electrochemical methods are employed to characterize the electrical conductivity and diffusivity of charge through the TiO2-Nafion® composite films. Characteristic electrochemical responses are observed for cationic redox systems (diheptylviologen2+/+, Ru(NH3)3+/2+6, and ferrocenylmethyl-trimethylammonium2+/+) immobilized into the TiO2-Nafion® nanocomposite material. Charge conduction is dependent on the type of redox system and is proposed to occur either via direct conduction through the TiO2 backbone (at sufficiently negative potentials) or via redox-center-based diffusion/electron hopping (at more positive potentials)