Adaptation to host cell environment during experimental evolution of Zika virus.

Zika virus (ZIKV) infection can cause important developmental and neurological defects in Humans. Type I/III interferon responses control ZIKV infection and pathological processes, yet the virus has evolved various mechanisms to defeat these host responses. Here, we established a pipeline to delineate at high-resolution the genetic evolution of ZIKV in a controlled host cell environment.

Clinical ethics consultations in psychiatric compared to non-psychiatric medical settings: characteristics and outcomes.

Background: In the recent years clinical ethics consultations (CEC) received an increasing attention not only in patients with medical conditions but also in those with mental disorders. However, the systematic and empirical knowledge is still small. The aim of this observational study was to investigate whether CECs differ between psychiatric and medical hospital inpatients regarding ethical issues, goals, characteristics, processes, and outcomes.

Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo.

Motivation: In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships.

Efficient Detection of Repeating Sites to Accelerate Phylogenetic Likelihood Calculations.

The phylogenetic likelihood function (PLF) is the major computational bottleneck in several applications of evolutionary biology such as phylogenetic inference, species delimitation, model selection, and divergence times estimation. Given the alignment, a tree and the evolutionary model parameters, the likelihood function computes the conditional likelihood vectors for every node of the tree. Vector entries for which all input data are identical result in redundant likelihood operations which, in turn, yield identical conditional values.

Computing the Internode Certainty and Related Measures from Partial Gene Trees.

We present, implement, and evaluate an approach to calculate the internode certainty (IC) and tree certainty (TC) on a given reference tree from a collection of partial gene trees. Previously, the calculation of these values was only possible from a collection of gene trees with exactly the same taxon set as the reference tree. An application to sets of partial gene trees requires mathematical corrections in the IC and TC calculations.