An Efficient Analytic Approach for Calculation of Multi-Dimensional Franck-Condon Factors and Associated Photoelectron Spectra.

The implementation, optimization, and performance of a generalized analytic treatment of multidimensional Franck-Condon Factors (FCF) within the harmonic oscillator approximation and associated photoelectron spectra (PES) for N-dimensional systems, including consideration of Eckart conditions in the displacement minimization and Cartesian coordinate handedness for evaluation of the Duschinsky Effect, is carried out in this work. A new efficient strategy for algorithmic efficiency for high dimensional systems is introduced, and demonstrated for 3-, 15-, and 30-dimensional systems. Determination of the photoelectron spectra for H2O+ (B̃2B2), vinyl alcohol, and C6H6+ (X̃2E1g) validates the capabilities with a high degree of accuracy with respect to experiment.

TRAL: tandem repeat annotation library.

MOTIVATION: Currently, more than 40 sequence tandem repeat detectors are published, providing heterogeneous, partly complementary, partly conflicting results. RESULTS: We present TRAL, a tandem repeat annotation library that allows running and parsing of various detection outputs, clustering of redundant or overlapping annotations, several statistical frameworks for filtering false positive annotations, and importantly a tandem repeat annotation and refinement module based on circular profile hidden Markov models (cpHMMs). Using TRAL, we evaluated the performance of a multi-step tandem repeat annotation workflow on 547 085 sequences in UniProtKB/Swiss-Prot. The researcher can use these results to predict run-times for specific datasets, and to choose annotation complexity accordingly. AVAILABILITY AND IMPLEMENTATION: TRAL is an open-source Python 3 library and is available, together with documentation and tutorials via http://www.vital-it.ch/software/tral. CONTACT: elke.schaper@isb-sib.ch.

Cerebellar vermis abnormalities and cognitive functions in individuals with Williams syndrome.

In Williams syndrome (WS) cerebellar measures were only indirectly related to behavioral outcomes. T1-weighted magnetic resonance images and neuropsychological data were acquired to investigate whether cerebellar vermis differences were present in 12 WS individuals compared with 13 chronological age-matched controls and whether WS cerebellar vermis measures were related to cognitive scores. In WS participants, we observed a significant increase in the volume of the posterior superior cerebellar vermis (lobules VI-VII) and an atypical ratio between width and height of the cerebellar vermis. Furthermore, we found an inverse correlation between cerebellar posterior vermis volume and scores on implicit learning, phonological fluency and the verbal short-term memory tasks. The present study supported a role for the posterior cerebellar vermis in higher cognitive processes and indicated that the cerebellar vermis abnormalities (enlargement) in WS individuals have an effect in worsening the cognitive performance in specific domains.

gcodeml: a Grid-enabled tool for detecting positive selection in biological evolution.

One of the important questions in biological evolution is to know if certain changes along protein coding genes have contributed to the adaptation of species. This problem is known to be biologically complex and computationally very expensive. It, therefore, requires efficient Grid or cluster solutions to overcome the computational challenge. We have developed a Grid-enabled tool (gcodeml) that relies on the PAML (codeml) package to help analyse large phylogenetic datasets on both Grids and computational clusters. Although we report on results for gcodeml, our approach is applicable and customisable to related problems in biology or other scientific domains.