Species Abundance Patterns in Complex Evolutionary Dynamics

An analytic theory of species abundance patterns (SAPs) in biological networks is presented. The theory is based on multispecies replicator dynamics equivalent to the Lotka-Volterra equation, with diverse interspecies interactions. Various SAPs observed in nature are derived from a single parameter. The abundance distribution is formed like a widely observed left-skewed lognormal distribution. As the model has a general form, the result can be applied to similar patterns in other complex biological networks, e.g. gene expression.Comment: 4 pages, 3 figures. Physical Review Letters, in pres

Overcoming the barriers to implementing urban road user charging schemes

Urban road user charging offers the potential to achieve significant improvements in urban transport, but is notoriously difficult to implement. Cities need guidance on the range of factors to be considered in planning and implementing such schemes. This paper summarises the results of a 3 year programme which has collated evidence on the issues of most concern to cities. A state of the art report has provided evidence on 14 themes, ranging from objectives and design to implementation and evaluation. A set of 16 case studies has reviewed experience in design and implementation across Europe. The paper summarises their findings, provides references to more detailed information, presents the resulting policy recommendations to European, national and local government, and outlines the areas in which further research is needed

Benchmarking calculations of excitonic couplings between bacteriochlorophylls

Excitonic couplings between (bacterio)chlorophyll molecules are necessary for simulating energy transport in photosynthetic complexes. Many techniques for calculating the couplings are in use, from the simple (but inaccurate) point-dipole approximation to fully quantum-chemical methods. We compared several approximations to determine their range of applicability, noting that the propagation of experimental uncertainties poses a fundamental limit on the achievable accuracy. In particular, the uncertainty in crystallographic coordinates yields an uncertainty of about 20% in the calculated couplings. Because quantum-chemical corrections are smaller than 20% in most biologically relevant cases, their considerable computational cost is rarely justified. We therefore recommend the electrostatic TrEsp method across the entire range of molecular separations and orientations because its cost is minimal and it generally agrees with quantum-chemical calculations to better than the geometric uncertainty. We also caution against computationally optimizing a crystal structure before calculating couplings, as it can lead to large, uncontrollable errors. Understanding the unavoidable uncertainties can guard against striving for unrealistic precision; at the same time, detailed benchmarks can allow important qualitative questions--which do not depend on the precise values of the simulation parameters--to be addressed with greater confidence about the conclusions

Communication interventions to promote the public's awareness of antibiotics: a systematic review.

BackgroundInappropriate antibiotic use is implicated in antibiotic resistance and resultant morbidity and mortality. Overuse is particularly prevalent for outpatient respiratory infections, and perceived patient expectations likely contribute. Thus, various educational programs have been implemented to educate the public.MethodsWe systematically identified public-directed interventions to promote antibiotic awareness in the United States. PubMed, Google Scholar, Embase, CINAHL, and Scopus were queried for articles published from January 1996 through January 2016. Two investigators independently assessed titles and abstracts of retrieved articles for subsequent full-text review. References of selected articles and three review articles were likewise screened for inclusion. Identified educational interventions were coded for target audience, content, distribution site, communication method, and major outcomes.ResultsOur search yielded 1,106 articles; 34 met inclusion criteria. Due to overlap in interventions studied, 29 distinct educational interventions were identified. Messages were primarily delivered in outpatient clinics (N = 24, 83%) and community sites (N = 12, 41%). The majority included clinician education. Antibiotic prescription rates were assessed for 22 interventions (76%). Patient knowledge, attitudes, and beliefs (KAB) were assessed for 10 interventions (34%). Similar rates of success between antibiotic prescription rates and patient KAB were reported (73 and 70%, respectively). Patient interventions that did not include clinician education were successful to increase KAB but were not shown to decrease antibiotic prescribing. Three interventions targeted reductions in Streptococcus pneumoniae resistance; none were successful.ConclusionsMessaging programs varied in their designs, and many were multifaceted in their approach. These interventions can change patient perspectives regarding antibiotic use, though it is unclear if clinician education is also necessary to reduce antibiotic prescribing. Further investigations are needed to determine the relative influence of interventions focusing on patients and physicians and to determine whether these changes can influence rates of antibiotic resistance long-term

Transcriptional Response to Acute Thermal Exposure in Juvenile Chinook Salmon Determined by RNAseq.

Thermal exposure is a serious and growing challenge facing fish species worldwide. Chinook salmon (Oncorhynchus tshawytscha) living in the southern portion of their native range are particularly likely to encounter warmer water due to a confluence of factors. River alterations have increased the likelihood that juveniles will be exposed to warm water temperatures during their freshwater life stage, which can negatively impact survival, growth, and development and pose a threat to dwindling salmon populations. To better understand how acute thermal exposure affects the biology of salmon, we performed a transcriptional analysis of gill tissue from Chinook salmon juveniles reared at 12° and exposed acutely to water temperatures ranging from ideal to potentially lethal (12° to 25°). Reverse-transcribed RNA libraries were sequenced on the Illumina HiSeq2000 platform and a de novo reference transcriptome was created. Differentially expressed transcripts were annotated using Blast2GO and relevant gene clusters were identified. In addition to a high degree of downregulation of a wide range of genes, we found upregulation of genes involved in protein folding/rescue, protein degradation, cell death, oxidative stress, metabolism, inflammation/immunity, transcription/translation, ion transport, cell cycle/growth, cell signaling, cellular trafficking, and structure/cytoskeleton. These results demonstrate the complex multi-modal cellular response to thermal stress in juvenile salmon

Ab Initio Molecular Dynamics on the Electronic Boltzmann Equilibrium Distribution

We prove that for a combined system of classical and quantum particles, it is possible to write a dynamics for the classical particles that incorporates in a natural way the Boltzmann equilibrium population for the quantum subsystem. In addition, these molecular dynamics do not need to assume that the electrons immediately follow the nuclear motion (in contrast to any adiabatic approach), and do not present problems in the presence of crossing points between different potential energy surfaces (conical intersections or spin-crossings). A practical application of this molecular dynamics to study the effect of temperature in molecular systems presenting (nearly) degenerate states - such as the avoided crossing in the ring-closure process of ozone - is presented.Comment: published in New J. Phy

Organization of Ecosystems in the Vicinity of a Novel Phase Transition

It is shown that an ecosystem in equilibrium is generally organized in a state which is poised in the vicinity of a novel phase transition.Comment: 4 pages, 2 figure

Self-Organized Criticality Driven by Deterministic Rules

We have investigated the essential ingredients allowing a system to show Self Organized Criticality (SOC) in its collective behavior. Using the Bak-Sneppen model of biological evolution as our paradigm, we show that the random microscopic rules of update can be effectively substituted with a chaotic map without changing the universality class. Using periodic maps SOC is preserved, but in a different universality class, as long as the spectrum of frequencies is broad enough.Comment: 4 pages, RevTex (tar.gz), 4 eps-figures include

The Adelaide VHF radar: Capabilities and future plans

The VHF radar at Buckland Park, South Australia commenced operation in January, 1984. The radar is located adjacent to the 2-MHz ionospheric radar. The routine method for measuring horizontal wind velocity is the space antenna technique (SA) while the Doppler technique is used to measure vertical velocities. It is possible to swing the transmitting beam in the east-west plane, allowing Doppler measurements of the EW wind component