Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints

The factors that determine the origin and fate of cross-species transmission events remain unclear for the majority of human pathogens, despite being central for the development of predictive models and assessing the efficacy of prevention strategies. Here, we describe a flexible Bayesian statistical framework to reconstruct virus transmission between different host species based on viral gene sequences, while simultaneously testing and estimating the contribution of several potential predictors of cross-species transmission. Specifically, we use a generalized linear model extension of phylogenetic diffusion to perform Bayesian model averaging over candidate predictors. By further extending this model with branch partitioning, we allow for distinct host transition processes on external and internal branches, thus discriminating between recent cross-species transmissions, many of which are likely to result in dead-end infections, and host shifts that reflect successful onwards transmission in the new host species. Our approach corroborates genetic distance between hosts as a key determinant of both host shifts and cross-species transmissions of rabies virus in North American bats. Furthermore, our results indicate that geographical range overlap is a modest predictor for cross-species transmission, but not for host shifts. Although our evolutionary framework focused on the multi-host reservoir dynamics of bat rabies virus, it is applicable to other pathogens and to other discrete state transition processes

How to validate a diagnosis recorded in electronic health records

Systematic measurement errors in electronic health record databases can lead to large inferential errors. Validation techniques can help determine the degree of these errors and therefore aid in the interpretation of findings. http://ow.ly/iHQ630np4xU

Single-walled carbon nanotubes as excitonic optical wires

Although metallic nanostructures are useful for nanoscale optics, all of their key optical properties are determined by their geometry. This makes it difficult to adjust these properties independently, and can restrict applications. Here we use the absolute intensity of Rayleigh scattering to show that single-walled carbon nanotubes can form ideal optical wires. The spatial distribution of the radiation scattered by the nanotubes is determined by their shape, but the intensity and spectrum of the scattered radiation are determined by exciton dynamics, quantum-dot-like optical resonances and other intrinsic properties. Moreover, the nanotubes display a uniform peak optical conductivity of ~8 e^2/h, which we derive using an exciton model, suggesting universal behaviour similar to that observed in nanotube conductance. We further demonstrate a radiative coupling between two distant nanotubes, with potential applications in metamaterials and optical antennas

On-Chip Rayleigh Imaging and Spectroscopy of Carbon Nanotubes

We report a novel on-chip Rayleigh imaging technique using wide-field laser illumination to measure optical scattering from individual single-walled carbon nanotubes (SWNTs) on a solid substrate with high spatial and spectral resolution. This method in conjunction with calibrated AFM measurements accurately measures the resonance energies and diameters for a large number of SWNTs in parallel. We apply this technique for fast mapping of key SWNT parameters, including the electronic-types and chiral indices for individual SWNTs, position and frequency of chirality-changing events, and intertube interactions in both bundled and distant SWNTs

“Birthday-Banding” as a Strategy to Moderate the Relative Age Effect: A Case Study Into the England Squash Talent Pathway

The relative age effect (RAE) is almost pervasive throughout youth sports, whereby relatively older athletes are consistently overrepresented compared to their relatively younger peers. Although researchers regularly cite the need for sports programs to incorporate strategies to moderate the RAE, organizational structures often continue to adopt a one-dimensional (bi)annual-age group approach. In an effort to combat this issue, England Squash implemented a “birthday-banding” strategy in its talent pathway, whereby young athletes move up to their next age group on their birthday, with the aim to remove particular selection time points and fixed chronological bandings. Thus, the purpose of this study was to examine the potential effects of the birthday-banding strategy on birth quarter (BQ) distributions throughout the England Squash talent pathway. Three mixed-gender groups were populated and analyzed: (a) ASPIRE athletes (n = 250), (b) Development and Potential athletes (n = 52), and (c) Senior team and Academy athletes (n = 26). Chi-square analysis and odds ratios were used to test BQ distributions against national norms and between quartiles, respectively. Results reveal no significant difference between BQ distributions within all three groups (P > 0.05). In contrast to most studies examining the RAE within athlete development settings, there appears to be no RAE throughout the England Squash talent pathway. These findings suggest that the birthday-banding strategy may be a useful tool to moderate RAE in youth sports

Genetic Crossovers Are Predicted Accurately by the Computed Human Recombination Map

Hotspots of meiotic recombination can change rapidly over time. This instability and the reported high level of inter-individual variation in meiotic recombination puts in question the accuracy of the calculated hotspot map, which is based on the summation of past genetic crossovers. To estimate the accuracy of the computed recombination rate map, we have mapped genetic crossovers to a median resolution of 70 Kb in 10 CEPH pedigrees. We then compared the positions of crossovers with the hotspots computed from HapMap data and performed extensive computer simulations to compare the observed distributions of crossovers with the distributions expected from the calculated recombination rate maps. Here we show that a population-averaged hotspot map computed from linkage disequilibrium data predicts well present-day genetic crossovers. We find that computed hotspot maps accurately estimate both the strength and the position of meiotic hotspots. An in-depth examination of not-predicted crossovers shows that they are preferentially located in regions where hotspots are found in other populations. In summary, we find that by combining several computed population-specific maps we can capture the variation in individual hotspots to generate a hotspot map that can predict almost all present-day genetic crossovers

Mosaic DNA imports with interspersions of recipient sequence after natural transformation of Helicobacter pylori

Helicobacter pylori colonizes the gastric mucosa of half of the human population, causing gastritis, ulcers, and cancer. H. pylori is naturally competent for transformation by exogenous DNA, and recombination during mixed infections of one stomach with multiple H. pylori strains generates extensive allelic diversity. We developed an in vitro transformation protocol to study genomic imports after natural transformation of H. pylori. The mean length of imported fragments was dependent on the combination of donor and recipient strain and varied between 1294 bp and 3853 bp. In about 10% of recombinant clones, the imported fragments of donor DNA were interrupted by short interspersed sequences of the recipient (ISR) with a mean length of 82 bp. 18 candidate genes were inactivated in order to identify genes involved in the control of import length and generation of ISR. Inactivation of the antimutator glycosylase MutY increased the length of imports, but did not have a significant effect on ISR frequency. Overexpression of mutY strongly increased the frequency of ISR, indicating that MutY, while not indispensable for ISR formation, is part of at least one ISR-generating pathway. The formation of ISR in H. pylori increases allelic diversity, and contributes to the uniquely low linkage disequilibrium characteristic of this pathogen

THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites.

As many malaria-endemic countries move towards elimination of Plasmodium falciparum, the most virulent human malaria parasite, effective tools for monitoring malaria epidemiology are urgent priorities. P. falciparum population genetic approaches offer promising tools for understanding transmission and spread of the disease, but a high prevalence of multi-clone or polygenomic infections can render estimation of even the most basic parameters, such as allele frequencies, challenging. A previous method, COIL, was developed to estimate complexity of infection (COI) from single nucleotide polymorphism (SNP) data, but relies on monogenomic infections to estimate allele frequencies or requires external allele frequency data which may not available. Estimates limited to monogenomic infections may not be representative, however, and when the average COI is high, they can be difficult or impossible to obtain. Therefore, we developed THE REAL McCOIL, Turning HEterozygous SNP data into Robust Estimates of ALelle frequency, via Markov chain Monte Carlo, and Complexity Of Infection using Likelihood, to incorporate polygenomic samples and simultaneously estimate allele frequency and COI. This approach was tested via simulations then applied to SNP data from cross-sectional surveys performed in three Ugandan sites with varying malaria transmission. We show that THE REAL McCOIL consistently outperforms COIL on simulated data, particularly when most infections are polygenomic. Using field data we show that, unlike with COIL, we can distinguish epidemiologically relevant differences in COI between and within these sites. Surprisingly, for example, we estimated high average COI in a peri-urban subregion with lower transmission intensity, suggesting that many of these cases were imported from surrounding regions with higher transmission intensity. THE REAL McCOIL therefore provides a robust tool for understanding the molecular epidemiology of malaria across transmission settings

Damaging real lives through obstinacy: re-emphasising why significance testing is wrong

This paper reminds readers of the absurdity of statistical significance testing, despite its continued widespread use as a supposed method for analysing numeric data. There have been complaints about the poor quality of research employing significance tests for a hundred years, and repeated calls for researchers to stop using and reporting them. There have even been attempted bans. Many thousands of papers have now been written, in all areas of research, explaining why significance tests do not work. There are too many for all to be cited here. This paper summarises the logical problems as described in over 100 of these prior pieces. It then presents a series of demonstrations showing that significance tests do not work in practice. In fact, they are more likely to produce the wrong answer than a right one. The confused use of significance testing has practical and damaging consequences for people's lives. Ending the use of significance tests is a pressing ethical issue for research. Anyone knowing the problems, as described over one hundred years, who continues to teach, use or publish significance tests is acting unethically, and knowingly risking the damage that ensues

Expanding global access to essential medicines: investment priorities for sustainably strengthening medical product regulatory systems.

Access to quality-assured medical products improves health and save lives. However, one third of the world's population lacks timely access to quality-assured medicines while estimates indicate that at least 10% of medicine in low- and middle-income countries (LMICs) are substandard or falsified (SF), costing approximately US$ 31 billion annually. National regulatory authorities are the key government institutions that promote access to quality-assured medicines and combat SF medical products but despite progress, regulatory capacity in LMICs is still insufficient. Continued and increased investment in regulatory system strengthening (RSS) is needed. We have therefore reviewed existing global normative documents and resources and engaged with our networks of global partners and stakeholders to identify three critical challenges being faced by NRAs in LMICs that are limiting access to medical products and impeding detection of and response to SF medicines. The challenges are; implementing value-added regulatory practices that best utilize available resources, a lack of timely access to new, quality medical products, and limited evidence-based data to support post-marketing regulatory actions. To address these challenges, we have identified seven focused strategies; advancing and leveraging convergence and reliance initiatives, institutionalizing sustainability, utilizing risk-based approaches for resource allocation, strengthening registration efficiency and timeliness, strengthening inspection capacity and effectiveness, developing and implementing risk-based post-marketing quality surveillance systems, and strengthening regulatory management of manufacturing variations. These proposed solutions are underpinned by 13 focused recommendations, which we believe, if financed, technically supported and implemented, will lead to stronger health system and as a consequence, positive health outcomes