Modeling DNA Structure, Elasticity and Deformations at the Base-pair Level

We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between neighboring base-pairs. The sugar-phosphate backbones are taken into account by semi-rigid harmonic springs with a non-zero spring length. The competition of these two interactions and the introduction of a simple geometrical constraint leads to a stacked right-handed B-DNA-like conformation. The mapping of the presented model to the Marko-Siggia and the Stack-of-Plates model enables us to optimize the free model parameters so as to reproduce the experimentally known observables such as persistence lengths, mean and mean squared base-pair step parameters. For the optimized model parameters we measured the critical force where the transition from B- to S-DNA occurs to be approximately $140{pN}$. We observe an overstretched S-DNA conformation with highly inclined bases that partially preserves the stacking of successive base-pairs.Comment: 15 pages, 25 figures. submitted to PR

Perceived Noise Analysis for Offset Jets Applied to Commercial Supersonic Aircraft

A systems analysis was performed with experimental jet noise data, engine/aircraft performance codes and aircraft noise prediction codes to assess takeoff noise levels and mission range for conceptual supersonic commercial aircraft. A parametric study was done to identify viable engine cycles that meet NASA's N+2 goals for noise and performance. Model scale data from offset jets were used as input to the aircraft noise prediction code to determine the expected sound levels for the lateral certification point where jet noise dominates over all other noise sources. The noise predictions were used to determine the optimal orientation of the offset nozzles to minimize the noise at the lateral microphone location. An alternative takeoff procedure called "programmed lapse rate" was evaluated for noise reduction benefits. Results show there are two types of engines that provide acceptable mission range performance; one is a conventional mixed-flow turbofan and the other is a three-stream variable-cycle engine. Separate flow offset nozzles reduce the noise directed toward the thicker side of the outer flow stream, but have less benefit as the core nozzle pressure ratio is reduced. At the systems level for a three-engine N+2 aircraft with full throttle takeoff, there is a 1.4 EPNdB margin to Chapter 3 noise regulations predicted for the lateral certification point (assuming jet noise dominates). With a 10% reduction in thrust just after clearing the runway, the margin increases to 5.5 EPNdB. Margins to Chapter 4 and Chapter 14 levels will depend on the cumulative split between the three certification points, but it appears that low specific thrust engines with a 10% reduction in thrust (programmed lapse rate) can come close to meeting Chapter 14 noise levels. Further noise reduction is possible with engine oversizing and derated takeoff, but more detailed mission studies are needed to investigate the range impacts as well as the practical limits for safety and takeoff regulations

Starch safety in resuscitation

The Western Cape Department of Health (WC DoH) has taken a decision to withdraw all intravenous fluids (IVFs) containing hydroxyethyl starch (HES) from hospitals in the Western Cape, with similar action contemplated in the Free State and Gauteng. This was in response to recommendations from: The European Medicines Agency's Pharmacovigilance Risk Assessment Committee (EMA PRAC) that HES IVFs be withdrawn from clinical use. The United Kingdom Medicines and Healthcare Products Regulatory Agency (MHRA) which has issued a recall of all HES IVFs in the UK. The United States Food and Drug Administration which advises that HES IVFs be used with caution in ICU, cardiac surgery and patients with known kidney disease or coagulopathy. Further advice was that HES should be stopped if coagulopathy or renal dysfunction develops, as well as that renal function should be monitored for 90 days after HES administration.http://www.samj.org.zaam2013ay201

Panspermia, Past and Present: Astrophysical and Biophysical Conditions for the Dissemination of Life in Space

Astronomically, there are viable mechanisms for distributing organic material throughout the Milky Way. Biologically, the destructive effects of ultraviolet light and cosmic rays means that the majority of organisms arrive broken and dead on a new world. The likelihood of conventional forms of panspermia must therefore be considered low. However, the information content of dam-aged biological molecules might serve to seed new life (necropanspermia).Comment: Accepted for publication in Space Science Review

Changes in the Frontotemporal Cortex and Cognitive Correlates in First-Episode Psychosis

Background: Loss of cortical volume in frontotemporal regions has been reported in patients with schizophrenia and their relatives. Cortical area and thickness are determined by different genetic processes, and measuring these parameters separately may clarify disturbances in corticogenesis relevant to schizophrenia. Our study also explored clinical and cognitive correlates of these parameters.Methods: Thirty-seven patients with first-episode psychosis (34 schizophrenia, 3 schizoaffective disorder) and 38 healthy control subjects matched for age and sex took part in the study. Imaging was performed on an magnetic resonance imaging 1.5-T scanner. Area and thickness of the frontotemporal cortex were measured using a surface-based morphometry method (Freesurfer). All subjects underwent neuropsychologic testing that included measures of premorbid and current IQ, working and verbal memory, and executive function.Results: Reductions in cortical area, more marked in the temporal cortex, were present in patients. Overall frontotemporal cortical thickness did not differ between groups, although regional thinning of the right superior temporal region was observed in patients. There was a significant association of both premorbid IQ and IQ at disease onset with area, but not thickness, of the frontotemporal cortex, and working memory span was associated with area of the frontal cortex. These associations remained significant when only patients with schizophrenia were considered.Conclusions: Our results suggest an early disruption of corticogenesis in schizophrenia, although the effect of subsequent environmental factors cannot be excluded. In addition, cortical abnormalities are subject to regional variations and differ from those present in neurodegenerative diseases

Definitions and nomenclature of nucleic acid structure components

We report here recommendations for the definitions and nomenclature of nucleic acid structure parameters. These recommendations result from discussions at an EMBO Workshop on DNA Curvature and Bending held at Churchill College, Cambridge, in September 1988