Error correction and diversity analysis of population mixtures determined by NGS

The impetus for this work was the need to analyse nucleotide diversity in a viral mix taken from honeybees. The paper has two findings. First, a method for correction of next generation sequencing error in the distribution of nucleotides at a site is developed. Second, a package of methods for assessment of nucleotide diversity is assembled. The error correction method is statistically based and works at the level of the nucleotide distribution rather than the level of individual nucleotides. The method relies on an error model and a sample of known viral genotypes that is used for model calibration. A compendium of existing and new diversity analysis tools is also presented, allowing hypotheses about diversity and mean diversity to be tested and associated confidence intervals to be calculated. The methods are illustrated using honeybee viral samples. Software in both Excel and Matlab and a guide are available at http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software/,the Warwick University Systems Biology Centre software download site.Publisher PDFPeer reviewe

Views of Coaching Practice Expressed by School-Based Coaches

This study reports on the views of coaching expressed by school-based coaches and coaching experts in response to observing the practice of a novice coach featured in a video. Researchers hypothesized that a coach participant\u27s observations about another coach\u27s practice would be a useful tool for examining participants\u27 beliefs about coaching. Researchers compared responses from school-based coaches to the responses of coaching experts and views expressed in leading coaching literature in order to examine the variation in school-based coaches\u27 views. Analysis of responses from both practicing coaches and coaching experts revealed eight themes that describe components of the videotaped coaching cycle: 1) coaching relationships; 2) the use of praise by the coach; 3) discussions of student learning; 4) how coaches respond to teachers\u27 questions; 5) how coaches prompt reflection; 6) how coaches address teacher knowledge and learning; 7) discussions of mathematics content; and, 8) facilitation of the coaching session. The analysis also revealed that these themes correspond to accepted domains of coaching knowledge reported in the coaching literature

A simulation model for wind energy storage systems. Volume 2: Operation manual

A comprehensive computer program (SIMWEST) developed for the modeling of wind energy/storage systems utilizing any combination of five types of storage (pumped hydro, battery, thermal, flywheel, and pneumatic) is described. Features of the program include: a precompiler which generates computer models (in FORTRAN) of complex wind source/storage/application systems, from user specifications using the respective library components; a program which provides the techno-economic system analysis with the respective I/O the integration of system dynamics, and the iteration for conveyance of variables; and capability to evaluate economic feasibility as well as general performance of wind energy systems. The SIMWEST operation manual is presented and the usage of the SIMWEST program and the design of the library components are described. A number of example simulations intended to familiarize the user with the program's operation is given along with a listing of each SIMWEST library subroutine

Calculating error bars for neutrino mixing parameters

One goal of contemporary particle physics is to determine the mixing angles and mass-squared differences that constitute the phenomenological constants that describe neutrino oscillations. Of great interest are not only the best fit values of these constants but also their errors. Some of the neutrino oscillation data is statistically poor and cannot be treated by normal (Gaussian) statistics. To extract confidence intervals when the statistics are not normal, one should not utilize the value for chisquare versus confidence level taken from normal statistics. Instead, we propose that one should use the normalized likelihood function as a probability distribution; the relationship between the correct chisquare and a given confidence level can be computed by integrating over the likelihood function. This allows for a definition of confidence level independent of the functional form of the !2 function; it is particularly useful for cases in which the minimum of the !2 function is near a boundary. We present two pedagogic examples and find that the proposed method yields confidence intervals that can differ significantly from those obtained by using the value of chisquare from normal statistics. For example, we find that for the first data release of the T2K experiment the probability that chisquare is not zero, as defined by the maximum confidence level at which the value of zero is not allowed, is 92%. Using the value of chisquare at zero and assigning a confidence level from normal statistics, a common practice, gives the over estimation of 99.5%.Comment: 9 pages, 6 figure

Coadjoint Orbits of the Generalised Sl(2) Sl(3) Kdv Hierarchies

In this paper we develop two coadjoint orbit constructions for the phase spaces of the generalised $Sl(2)$ and $Sl(3)$ KdV hierachies. This involves the construction of two group actions in terms of Yang Baxter operators, and an Hamiltonian reduction of the coadjoint orbits. The Poisson brackets are reproduced by the Kirillov construction. From this construction we obtain a `natural' gauge fixing proceedure for the generalised hierarchies.Comment: 37 page

Evidence for the intense exchange of MazG in marine cyanophages by horizontal gene transfer

Background: S-PM2 is a phage capable of infecting strains of unicellular cyanobacteria belonging to the genus Synechococcus. S-PM2, like other myoviruses infecting marine cyanobacteria, encodes a number of bacterial-like genes. Amongst these genes is one encoding a MazG homologue that is hypothesized to be involved in the adaption of the infected host for production of progeny phage. Methodology/Principal Findings: This study focuses on establishing the occurrence of mazG homologues in other cyanophages isolated from different oceanic locations. Degenerate PCR primers were designed using the mazG gene of S-PM2. The mazG gene was found to be widely distributed and highly conserved among Synechococcus myoviruses and podoviruses from diverse oceanic provinces. Conclusions/Significance: This study provides evidence of a globally connected cyanophage gene pool, the cyanophage mazG gene having a small effective population size indicative of rapid lateral gene transfer despite being present in a substantial fraction of cyanophage. The Prochlorococcus and Synechococcus phage mazG genes do not cluster with the host mazG gene, suggesting that their primary hosts are not the source of the mazG gene

Symbiotic Epistemologies for Forward-Error Correction

Cyberneticists agree that autonomous configurations are an interesting new topic in the field of software engineering, and leading analysts concur. Given the current status of highly- available epistemologies, computational biologists famously desire the exploration of sensor networks. In order to accomplish this intent, we prove that I/O automata and agents [14] can synchronize to solve this quandary