Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses.

BackgroundFungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments. While most fungal diversity remains unknown, the development of PCR primers for the internal transcribed spacer (ITS) combined with next-generation sequencing has substantially improved our ability to profile fungal microbial diversity. Although the high sequence variability in the ITS region facilitates more accurate species identification, it also makes multiple sequence alignment and phylogenetic analysis unreliable across evolutionarily distant fungi because the sequences are hard to align accurately. To address this issue, we created ghost-tree, a bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach starts with a "foundation" phylogeny based on one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families). Then, "extension" phylogenies are built for more closely related organisms (e.g., fungal species or strains) using a second more rapidly evolving genetic marker. These smaller phylogenies are then grafted onto the foundation tree by mapping taxonomic names such that each corresponding foundation-tree tip would branch into its new "extension tree" child.ResultsWe applied ghost-tree to graft fungal extension phylogenies derived from ITS sequences onto a foundation phylogeny derived from fungal 18S sequences. Our analysis of simulated and real fungal ITS data sets found that phylogenetic distances between fungal communities computed using ghost-tree phylogenies explained significantly more variance than non-phylogenetic distances. The phylogenetic metrics also improved our ability to distinguish small differences (effect sizes) between microbial communities, though results were similar to non-phylogenetic methods for larger effect sizes.ConclusionsThe Silva/UNITE-based ghost tree presented here can be easily integrated into existing fungal analysis pipelines to enhance the resolution of fungal community differences and improve understanding of these communities in built environments. The ghost-tree software package can also be used to develop phylogenetic trees for other marker gene sets that afford different taxonomic resolution, or for bridging genome trees with amplicon trees.Availabilityghost-tree is pip-installable. All source code, documentation, and test code are available under the BSD license at https://github.com/JTFouquier/ghost-tree

Dynamic communities in multichannel data: An application to the foreign exchange market during the 2007--2008 credit crisis

We study the cluster dynamics of multichannel (multivariate) time series by representing their correlations as time-dependent networks and investigating the evolution of network communities. We employ a node-centric approach that allows us to track the effects of the community evolution on the functional roles of individual nodes without having to track entire communities. As an example, we consider a foreign exchange market network in which each node represents an exchange rate and each edge represents a time-dependent correlation between the rates. We study the period 2005-2008, which includes the recent credit and liquidity crisis. Using dynamical community detection, we find that exchange rates that are strongly attached to their community are persistently grouped with the same set of rates, whereas exchange rates that are important for the transfer of information tend to be positioned on the edges of communities. Our analysis successfully uncovers major trading changes that occurred in the market during the credit crisis.Comment: 8 pages, 6 figures, accepted for publication in Chao

Gas Clumping in the Outskirts of Galaxy Clusters, an Assessment of the Sensitivity of STAR-X

In the outskirts of galaxy clusters, entropy profiles measured from X-ray observations of the hot intracluster medium (ICM) drops off unexpectedly. One possible explanation for this effect is gas clumping, where pockets of cooler and denser structures within the ICM are present. Current observatories are unable to directly detect these hypothetical gas clumps. One of the science drivers of the proposed STAR-X observatory is to resolve these or similar structures. Its high spatial resolution, large effective area, and low instrumental background make STAR-X ideal for directly detecting and characterizing clumps and diffuse emission in cluster outskirts. The aim of this work is to simulate observations of clumping in clusters to determine how well STAR-X will be able to detect clumps, as well as what clumping properties reproduce observed entropy profiles. This is achieved by using yt, pyXSIM, SOXS, and other tools to inject ideally modeled clumps into three-dimensional models derived from actual clusters using their observed profiles from other X-ray missions. Radial temperature and surface brightness profiles are then extracted from mock observations using concentric annuli. We find that in simulated observations for STAR-X, a parameter space of clump properties exists where gas clumps can be successfully identified using wavdetect and masked, and are able to recover the true cluster profiles. This demonstrates that STAR-X could be capable of detecting substructure in the outskirts of nearby clusters and that the properties of both the outskirts and the clumps will be revealed.Comment: This is a pre-copyedited, author-produced PDF of an article accepted for publication in RAS Techniques and Instruments (RASTI) following peer review. The version of record is available online at: https://academic.oup.com/rasti/article/doi/10.1093/rasti/rzad042/725882

The demise of the randomised controlled trial: bibliometric study of the German-language health care literature, 1948 to 2004

BACKGROUND: In order to reduce systematic errors (such as language bias) and increase the precision of the summary treatment effect estimate, a comprehensive identification of randomised controlled trials (RCT), irrespective of publication language, is crucial in systematic reviews and meta-analyses. We identified trials in the German general health care literature. METHODS: Eight German language general health care journals were searched for randomised controlled trials and analysed with respect to the number of published RCTs each year and the size of trials. RESULTS: A total of 1618 trials were identified with a median total number of 43 patients per trial. Between 1970 and 2004 a small but constant rise in sample size from a median number of 30 to 60 patients per trial can be observed. The number of published trials was very low between 1948 and 1970, but increased between 1970 and 1986 to a maximum of 11.2 RCTs per journal and year. In the following time period a striking decline of the number of RCTs was observed. Between 1999 and 2001 only 0.8 RCTs per journal and year were published, in the next three years, the number of published trials increased to 1.7 RCTs per journal and year. CONCLUSION: German language general health care journals no longer have a role in the dissemination of trial results. The slight rise in the number of published RCTs in the last three years can be explained by a change of publication language from German to English of three of the analysed journals

Angular momenta creation in relativistic electron-positron plasma

Creation of angular momentum in a relativistic electron-positron plasma is explored. It is shown that a chain of angular momentum carrying vortices is a robust asymptotic state sustained by the generalized nonlinear Schrodinger equation characteristic to the system. The results may suggest a possible electromagnetic origin of angular momenta when it is applied to the MeV epoch of the early Universe.Comment: 20 pages, 6 figure