Sophisticated falsification and research cycles: Consequences for differential character weighting in phylogenetic systematics

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72703/1/j.1463-6409.1997.tb00424.x.pd

The Science of Phylogenetic Systematics: Explanation, Prediction, and Test

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73926/1/j.1096-0031.1999.tb00279.x.pd

Clinical and cost effectiveness of a parent mediated intervention to reduce challenging behaviour in pre-schoolers with moderate to severe intellectual disability (EPICC-ID) study protocol: a multicentre, parallel-group randomised controlled trial

Background: Children with intellectual disabilities are likely to present with challenging behaviour. Parent mediated interventions have shown utility in influencing child behaviour, although there is a paucity of UK research into challenging behaviour interventions in this population. NICE guidelines favour Stepping Stones Triple P (SSTP) as a challenging behaviour intervention and this trial aims to evaluate its clinical and cost effectiveness in preschool children with moderate to severe intellectual disabilities. Methods: This trial launched in 2017 at four sites across England, with the aim of recruiting 258 participants (aged 30–59months). The Intervention Group receive nine weeks of SSTP parenting therapy (six group sessions and three individualised face to face or telephone sessions) in addition to Treatment as Usual, whilst the Treatment as Usual only group receive other available services in each location. Both study groups undergo the study measurements at baseline and at four and twelve months. Outcome measures include parent reports and structured observations of behaviour. Service use and health related quality of life data will also be collected to carry out a cost effectiveness and utility evaluation. Discussion: Findings from this study will inform policy regarding interventions for challenging behaviour in young children with moderate to severe intellectual disabilities. Trial registration number: Clinicaltrials.gov, NCT03086876. Registered 22nd March 2017, https://clinicaltrials.gov/ ct2/show/NCT03086876. Keywords: Intellectual disabilities, Challenging behaviour, Randomised control trial, Stepping stones triple P, SSTP, Parenting intervention

PARSIMONY JACKKNIFING OUTPERFORMS NEIGHBOR-JOINING

Because they are designed to produced just one tree, neighbor-joining programs can obscure ambiguities in data. Ambiguities can be uncovered by resampling, but existing neighbor-joining programs may give misleading bootstrap frequencies because they do not suppress zero-length branches and/or are sensitive to the order of terminals in the data. A new procedure, parsimony jackknifing, overcomes these problems while running hundreds of times faster than existing programs for neighbor-joining bootstrapping. For analysis of large matrices, parsimony jackknifing is hundreds of thousands of times faster than extensive branch-swapping, yet is better able to screen out poorly-supported groups.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73544/1/j.1096-0031.1996.tb00196.x.pd

Supermassive Black Hole Binaries: The Search Continues

Gravitationally bound supermassive black hole binaries (SBHBs) are thought to be a natural product of galactic mergers and growth of the large scale structure in the universe. They however remain observationally elusive, thus raising a question about characteristic observational signatures associated with these systems. In this conference proceeding I discuss current theoretical understanding and latest advances and prospects in observational searches for SBHBs.Comment: 17 pages, 4 figures. To appear in the Proceedings of 2014 Sant Cugat Forum on Astrophysics. Astrophysics and Space Science Proceedings, ed. C.Sopuerta (Berlin: Springer-Verlag

Phylogenetic Relationships among Deep-Sea and Chemosynthetic Sea Anemones: Actinoscyphiidae and Actinostolidae (Actiniaria: Mesomyaria)

Sea anemones (Cnidaria, Actiniaria) are present in all marine ecosystems, including chemosynthetic environments. The high level of endemicity of sea anemones in chemosynthetic environments and the taxonomic confusion in many of the groups to which these animals belong makes their systematic relationships obscure. We use five molecular markers to explore the phylogenetic relationships of the superfamily Mesomyaria, which includes most of the species that live in chemosynthetic, deep-sea, and polar sea habitats and to test the monophyly of the recently defined clades Actinostolina and Chemosynthina. We found that sea anemones of chemosynthetic environments derive from at least two different lineages: one lineage including acontiate deep-sea taxa and the other primarily encompassing shallow-water taxa

Improved cosmological constraints from new, old, and combined supernova data sets

We present a new compilation of Type Ia supernovae (SNe Ia), a new data set of low-redshift nearby-Hubble-flow SNe, and new analysis procedures to work with these heterogeneous compilations. This Union compilation of 414 SNe Ia, which reduces to 307 SNe after selection cuts, includes the recent large samples of SNe Ia from the Supernova Legacy Survey and ESSENCE Survey, the older data sets, as well as the recently extended data set of distant supernovae observed with the Hubble Space Telescope (HST). A single, consistent, and blind analysis procedure is used for all the various SN Ia subsamples, and a new procedure is implemented that consistently weights the heterogeneous data sets and rejects outliers. We present the latest results from this Union compilation and discuss the cosmological constraints from this new compilation and its combination with other cosmological measurements (CMB and BAO). The constraint we obtain from supernovae on the dark energy density isΩΛ = 0.713-0.029+0.027(stat) -0.039+0.036(sys), for a flat, ACDM universe. Assuming a constant equation of state parameter, w, the combined constraints from SNe, BAO, and CMB give w = -0.969-0.063+0.059(stat) -0.066+0.063(sys). While our results are consistent with a cosmological constant, we obtain only relatively weak constraints on a w that varies with redshift. In particular, the current SN data do not yet significantly constrain w at z \u3e 1. With the addition of our new nearby Hubble-flow SNe Ia, these resulting cosmological constraints are currently the tightest available. © 2008. The American Astronomical Society. All rights reserved

Jerarca: Efficient Analysis of Complex Networks Using Hierarchical Clustering

Background: How to extract useful information from complex biological networks is a major goal in many fields, especially in genomics and proteomics. We have shown in several works that iterative hierarchical clustering, as implemented in the UVCluster program, is a powerful tool to analyze many of those networks. However, the amount of computation time required to perform UVCluster analyses imposed significant limitations to its use. Methodology/Principal Findings: We describe the suite Jerarca, designed to efficiently convert networks of interacting units into dendrograms by means of iterative hierarchical clustering. Jerarca is divided into three main sections. First, weighted distances among units are computed using up to three different approaches: a more efficient version of UVCluster and two new, related algorithms called RCluster and SCluster. Second, Jerarca builds dendrograms based on those distances, using well-known phylogenetic algorithms, such as UPGMA or Neighbor-Joining. Finally, Jerarca provides optimal partitions of the trees using statistical criteria based on the distribution of intra- and intercluster connections. Outputs compatible with the phylogenetic software MEGA and the Cytoscape package are generated, allowing the results to be easily visualized. Conclusions/Significance: The four main advantages of Jerarca in respect to UVCluster are: 1) Improved speed of a novel UVCluster algorithm; 2) Additional, alternative strategies to perform iterative hierarchical clustering; 3) Automatic evaluatio

TRY plant trait database - enhanced coverage and open access

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives