42 research outputs found
Evolutionary distances in the twilight zone -- a rational kernel approach
Phylogenetic tree reconstruction is traditionally based on multiple sequence
alignments (MSAs) and heavily depends on the validity of this information
bottleneck. With increasing sequence divergence, the quality of MSAs decays
quickly. Alignment-free methods, on the other hand, are based on abstract
string comparisons and avoid potential alignment problems. However, in general
they are not biologically motivated and ignore our knowledge about the
evolution of sequences. Thus, it is still a major open question how to define
an evolutionary distance metric between divergent sequences that makes use of
indel information and known substitution models without the need for a multiple
alignment. Here we propose a new evolutionary distance metric to close this
gap. It uses finite-state transducers to create a biologically motivated
similarity score which models substitutions and indels, and does not depend on
a multiple sequence alignment. The sequence similarity score is defined in
analogy to pairwise alignments and additionally has the positive semi-definite
property. We describe its derivation and show in simulation studies and
real-world examples that it is more accurate in reconstructing phylogenies than
competing methods. The result is a new and accurate way of determining
evolutionary distances in and beyond the twilight zone of sequence alignments
that is suitable for large datasets.Comment: to appear in PLoS ON
The effects of Cognitive Bias Modification training and oxytocin administration on trust in maternal support: study protocol for a randomized controlled trial
Crystal Structure Determination of Glycerol-Containing Lipids from Electron Diffraction Data. Use of Analog Compounds Based upon Configurational Isomers of Cyclopentane-1, 2, 3-TRIOL
The Rules of Ferrous Metallurgy : Genesis and Structure of a Field of Engineering Science, 1870–1914
The ways in which the sciences have been delineated and categorized throughout history provide insights into the formation, stabilization, and establishment of scientific systems of knowledge. The Dresdener school’s approach for explaining and categorizing the genesis of the engineering disciplines is still valid, but needs to be complemented by further-reaching methodological and theoretical reflections. Pierre Bourdieu’s theory of social practice is applied to the question of how individual agents succeed in influencing decisively a discipline’s changing object orientation, institutionalisation and self-reproduction. Through the accumulation of social, cultural and economic capital, they succeed in realising their own organisational ideas and scientific programs. Key concepts for the analysis include the struggle for power and resources, monopolies of interpretation, and the degree of autonomy. A case study from the Aachener Technische Hochschule shows that the consolidation of ferrous metallurgy can be conceived as a symbolical struggle between Fritz Wüst, professor for ferrous metallurgy, and the German Iron and Steel Institute, leading to a construction of a system of differences in which scientists accepted being scientists rather than entrepreneurs, and entrepreneurs accepted becoming
entrepreneurs and renounced science