Exploring Molecular Simulations of a Plausible Prebiotic Reduced Phospholipid Using Hyperchem Software

How the first cells emerged from the primordial milieu is one of the great questions in science. Biomolecular emergence scenarios abound in the literature, but the lack of bioaccessible phosphate and molecular oxygen on the primordial Earth has posed formidable challenges for deducing emergence pathways. One idea gaining wide acceptance invokes delivery of the phosphide mineral schreibersite ((Fe,Ni)3P) to Earth via meteorite impacts ca. 4.2 billion years ago, whereupon they were corroded to reduced phosphorous oxyacids and phosphonates in primordial aquatic environments. We previously proposed that these reduced phosphorus forms could readily combine with putative geochemical species in shallow mineral-rich alkaline hydrothermal systems to form reduced phospholipid analogs of contemporary phosphate-based phospholipids (Fitch, N.W., K.L. Even, L.J. Leinen and M.O. Gaylor. 2016. Plausible prebiotic assembly of a primitive reduced phospholipid from meteoritic phosphorus on the primordial earth. Proceedings of the South Dakota Academy of. Science 95:176.). Lacking resources to empirically validate this idea, we explored “water box” simulations of the proposed phospholipid structure using the HyperChem software package. Simulation results showed the hydrophobic tails migrating away from water molecules, while hydrophilic heads migrated towards them, resulting in quasistacking behaviors consistent with those of known amphiphiles in water. Inspired by these results, we are now investigating more complex primordial simulation scenarios

Probabilistic logic modeling of network reliability for hybrid network architectures

Sandia National Laboratories has found that the reliability and failure modes of current-generation network technologies can be effectively modeled using fault tree-based probabilistic logic modeling (PLM) techniques. We have developed fault tree models that include various hierarchical networking technologies and classes of components interconnected in a wide variety of typical and atypical configurations. In this paper we discuss the types of results that can be obtained from PLMs and why these results are of great practical value to network designers and analysts. After providing some mathematical background, we describe the `plug-and-play` fault tree analysis methodology that we have developed for modeling connectivity and the provision of network services in several current- generation network architectures. Finally, we demonstrate the flexibility of the method by modeling the reliability of a hybrid example network that contains several interconnected ethernet, FDDI, and token ring segments. 11 refs., 3 figs., 1 tab

Information integrity and privacy for computerized medical patient records

Sandia National Laboratories and Oceania, Inc. entered into a Cooperative Research and Development Agreement (CRADA) in November 1993 to provide ``Information Integrity and Privacy for Computerized Medical Patient Records`` (CRADA No. SC93/01183). The main objective of the project was to develop information protection methods that are appropriate for databases of patient records in health information systems. This document describes the findings and alternative solutions that resulted from this CRADA

Information integrity and privacy for computerized medical patient records

Sandia National Laboratories and Oceania, Inc. entered into a Cooperative Research and Development Agreement (CRADA) in November 1993 to provide ``Information Integrity and Privacy for Computerized Medical Patient Records`` (CRADA No. SC93/01183). The main objective of the project was to develop information protection methods that are appropriate for databases of patient records in health information systems. This document describes the findings and alternative solutions that resulted from this CRADA

Dispelling urban myths about default uncertainty factors in chemical risk assessment - Sufficient protection against mixture effects?

© 2013 Martin et al.; licensee BioMed Central LtdThis article has been made available through the Brunel Open Access Publishing Fund.Assessing the detrimental health effects of chemicals requires the extrapolation of experimental data in animals to human populations. This is achieved by applying a default uncertainty factor of 100 to doses not found to be associated with observable effects in laboratory animals. It is commonly assumed that the toxicokinetic and toxicodynamic sub-components of this default uncertainty factor represent worst-case scenarios and that the multiplication of those components yields conservative estimates of safe levels for humans. It is sometimes claimed that this conservatism also offers adequate protection from mixture effects. By analysing the evolution of uncertainty factors from a historical perspective, we expose that the default factor and its sub-components are intended to represent adequate rather than worst-case scenarios. The intention of using assessment factors for mixture effects was abandoned thirty years ago. It is also often ignored that the conservatism (or otherwise) of uncertainty factors can only be considered in relation to a defined level of protection. A protection equivalent to an effect magnitude of 0.001-0.0001% over background incidence is generally considered acceptable. However, it is impossible to say whether this level of protection is in fact realised with the tolerable doses that are derived by employing uncertainty factors. Accordingly, it is difficult to assess whether uncertainty factors overestimate or underestimate the sensitivity differences in human populations. It is also often not appreciated that the outcome of probabilistic approaches to the multiplication of sub-factors is dependent on the choice of probability distributions. Therefore, the idea that default uncertainty factors are overly conservative worst-case scenarios which can account both for the lack of statistical power in animal experiments and protect against potential mixture effects is ill-founded. We contend that precautionary regulation should provide an incentive to generate better data and recommend adopting a pragmatic, but scientifically better founded approach to mixture risk assessment. © 2013 Martin et al.; licensee BioMed Central Ltd.Oak Foundatio

A mathematical model of the mevalonate cholesterol biosynthesis pathway

We formulate, parameterise and analyse a mathematical model of the mevalonate pathway, a key pathway in the synthesis of cholesterol. Of high clinical importance, the pathway incorporates rate limiting enzymatic reactions with multiple negative feedbacks. In this work we investigate the pathway dynamics and demonstrate that rate limiting steps and negative feedbacks within it act in concert to tightly regulate intracellular cholesterol levels. Formulated using the theory of nonlinear ordinary differential equations and parameterised in the context of a hepatocyte, the governing equations are analysed numerically and analytically. Sensitivity and mathematical analysis demonstrate the importance of the two rate limiting enzymes 3-hydroxy-3-methylglutaryl-CoA reductase and squalene synthase in controlling the concentration of substrates within the pathway as well as that of cholesterol. The role of individual feedbacks, both global (between that of cholesterol and sterol regulatory element-binding protein 2; SREBP-2) and local internal (between substrates in the pathway) are investigated. We find that whilst the cholesterol SREBP-2 feedback regulates the overall system dynamics, local feedbacks activate within the pathway to tightly regulate the overall cellular cholesterol concentration. The network stability is analysed by constructing a reduced model of the fall pathway and is shown to exhibit one real, stable steady-state. We close by addressing the biological question as to how farnesyl-PP levels are affected by CYP51 inhibition, and demonstrate that the regulatory mechanisms within the network work in unison to ensure they remain bounded

Practice development plans to improve the primary care management of acute asthma: randomised controlled trial

Background: Our professional development plan aimed to improve the primary care management of acute asthma, which is known to be suboptimal. Methods: We invited 59 general practices in Grampian, Scotland to participate. Consenting practices were randomised to early and delayed intervention groups. Practices undertook audits of their management of all acute attacks (excluding children under 5 years) occurring in the 3 months preceding baseline, 6-months and 12-months study time-points. The educational programme [including feedback of audit results, attendance at a multidisciplinary interactive workshop, and formulation of development plan by practice teams] was delivered to the early group at baseline and to the delayed group at 6 months. Primary outcome measure was recording of peak flow compared to best/predicted at 6 months. Analyses are presented both with, and without adjustment for clustering. Results: 23 consenting practices were randomised: 11 to early intervention. Baseline practice demography was similar. Six early intervention practices withdraw before completing the baseline audit. There was no significant improvement in our primary outcome measure (the proportion with peak flow compared to best/predicted) at either the 6 or 12 month time points after adjustment for baseline and practice effects. However, the between group difference in the adjusted combined assessment score, whilst non-significant at 6 months (Early: 2.48 (SE 0.43) vs. Delayed 2.26 (SE 0.33) p = 0.69) reached significance at 12 m (Early:3.60 (SE 0.35) vs. Delayed 2.30 (SE 0.28) p = 0.02). Conclusion: We demonstrated no significant benefit at the a priori 6-month assessment point, though improvement in the objective assessment of attacks was shown after 12 months. Our practice development programme, incorporating audit, feedback and a workshop, successfully engaged the healthcare team of participating practices, though future randomised trials of educational interventions need to recognise that effecting change in primary care practices takes time. Monitoring of the assessment of acute attacks proved to be a feasible and responsive indicator of quality care

Vitamin d status predicts 30 day mortality in hospitalised cats

Vitamin D insufficiency, defined as low serum concentrations of the major circulating form of vitamin D, 25 hydroxyvitamin D (25(OH)D), has been associated with the development of numerous infectious, inflammatory, and neoplastic disorders in humans. In addition, vitamin D insufficiency has been found to be predictive of mortality for many disorders. However, interpretation of human studies is difficult since vitamin D status is influenced by many factors, including diet, season, latitude, and exposure to UV radiation. In contrast, domesticated cats do not produce vitamin D cutaneously, and most cats are fed a commercial diet containing a relatively standard amount of vitamin D. Consequently, domesticated cats are an attractive model system in which to examine the relationship between serum 25(OH)D and health outcomes. The hypothesis of this study was that vitamin D status would predict short term, all-cause mortality in domesticated cats. Serum concentrations of 25(OH)D, together with a wide range of other clinical, hematological, and biochemical parameters, were measured in 99 consecutively hospitalised cats. Cats which died within 30 days of initial assessment had significantly lower serum 25(OH)D concentrations than cats which survived. In a linear regression model including 12 clinical variables, serum 25(OH)D concentration in the lower tertile was significantly predictive of mortality. The odds ratio of mortality within 30 days was 8.27 (95% confidence interval 2.54-31.52) for cats with a serum 25(OH)D concentration in the lower tertile. In conclusion, this study demonstrates that low serum 25(OH)D concentration status is an independent predictor of short term mortality in cats