ThermoPhyl : a software tool for selecting phylogenetically optimized conventional and quantitative-PCR taxon-targeted assays for use with complex samples

The ability to specifically and sensitively target genotypes of interest is critical for the success of many PCR-based analyses of environmental or clinical samples that contain multiple templates.Next-generation sequence data clearly show that such samples can harbour hundreds to thousands of operational taxonomic units; a richness which precludes the manual evaluation of candidate assay specificity and sensitivity using multiple sequence alignments. To solve this problem we have developed and validated a free software tool which automates the identification of PCR assays targeting specific genotypes in complex samples. ThermoPhyl uses user-defined target and non-target sequence databases to assess the phylogenetic sensitivity and specificity of thermodynamically optimised candidate assays derived from primer design software packages. ThermoPhyl takes its name from its central premise of testing Thermodynamically optimal assays for Phylogenetic specificity and sensitivity and can be used for two primer (traditional PCR) or two primers with an internal probe (e.g. TaqMan® qPCR) applications and potentially for oligonucleotide probes.Here we describe the use of ThermoPhyl for traditional PCR and qPCR assays. PCR assays selected using ThermoPhyl were validated using 454 pyrosequencing of a traditional specific PCR assay and with a set of four genotype-specific qPCR assays applied to estuarine sediment samples

Foundations of Language

With so little known about how language is perceived and produced, the field of linguistics could use a fresh perspective on the current state of affairs. Ray Jackendoff’s book draws together current thought from mainstream generative grammar and from more recent thinking on the function of the mind. In integrating these areas, Jackendoff illuminates the interfaces between language and other functions of the mind, and at the same time helps define the scope of contemporary linguistic inquiry

Amplification of Reynolds number dependent processes by wave distortion

A system using a hot-wire transducer as an analog of a liquid droplet of propellant was employed to investigate the ingredients of the acoustic instability of liquid-propellant rocket engines. It was assumed that the combustion process was vaporization-limited and that the combustion chamber was acoustically similar to a closed-closed right-circular cylinder. Before studying the hot-wire closed-loop system (the analog system), a microphone closed-loop system, which used the response of a microphone as the source of a linear feedback exciting signal, was investigated to establish the characteristics of self-sustenance of acoustic fields. Self-sustained acoustic fields were found to occur only at resonant frequencies of the chamber. In the hot-wire closed-loop system, the response of hot-wire anemometer was used as the source of the feedback exciting signal. The self-sustained acoustic fields which developed in the system were always found to be harmonically distorted and to have as their fundamental frquency a resonant frequency for which there also existed a second resonant frequency which was approximately twice the fundamental frequency

Analysis and study of hospital communication via social media from the patient perspective

Currently, the online interaction between citizens and hospitals is poor, as users believe that there are shortcomings that could be improved. This study analyzes patients’ opinions of the online communication strategies of hospitals in Spain. Therefore, a mixed-method is proposed. Firstly, a qualitative analysis through a focus-group was carried out, so around twenty representatives of national, regional and local patients’ associations were brought together. Secondly, the research is supplemented with a content assessment of the Twitter activity of the most influential hospitals in Spain. The results reveal that the general public appreciate hospitals’ communication potential through social media, although they are generally unaware of how it works. The group says that, apart from the lack of interaction, they find it hard to understand certain messages, and some publications give a biased picture. In order to improve communication, patients and relatives are demanding that their perspective be taken into consideration in the messages issued to enhance the quality of life and well-being of society

Sex bias in tuberculosis in the developing world

Tuberculosis (TB), the most deadly global single organism infectious disease, kills nearly twice as many men as women. Understanding the factors that drive this bias in TB mortality is an important aspect of the global effort to reduce the enormous burden of this disease in the developing world. One third of the world’s population is estimated to be infected TB, with Low and Middle Income Countries (LMIC) bearing the greatest disease burden. In LMIC sex bias in TB is influenced by sociocultural, behavioural as well as biological factors, with dynamic interactions between reporting variables, other confounding variables and physiological mechanisms, which each influence one another to produce the male-biased sex ratio observed in TB transmission, prevalence and mortality. While confounding factors are addressed in the existing global drive to tackle TB it is the biological aspects of sex bias in TB that present specific challenges for diagnosis and treatment in men and women as they potentially influence future immunological-based interventions to treat TB

A Bichromatic Incidence Bound and an Application

We prove a new, tight upper bound on the number of incidences between points and hyperplanes in Euclidean d-space. Given n points, of which k are colored red, there are O_d(m^{2/3}k^{2/3}n^{(d-2)/3} + kn^{d-2} + m) incidences between the k red points and m hyperplanes spanned by all n points provided that m = \Omega(n^{d-2}). For the monochromatic case k = n, this was proved by Agarwal and Aronov. We use this incidence bound to prove that a set of n points, no more than n-k of which lie on any plane or two lines, spans \Omega(nk^2) planes. We also provide an infinite family of counterexamples to a conjecture of Purdy's on the number of hyperplanes spanned by a set of points in dimensions higher than 3, and present new conjectures not subject to the counterexample.Comment: 12 page