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Standardized voluntary force measurement in a lower extremity rehabilitation robot
(2008)Journal of NeuroEngineering and RehablilitationBackground Isometric force measurements in the lower extremity are widely used in rehabilitation of subjects with neurological movement disorders (NMD) because walking ability has been shown to be related to muscle strength. Therefore muscle strength measurements can be used to monitor and control the effects of training programs. A new method to assess isometric muscle force was implemented in the driven gait orthosis (DGO) Lokomat. To ...Journal Article -
The Red Queen and the persistence of linkage-disequilibrium oscillations in finite and infinite populations
(2007)BMC Evolutionary BiologyBackground The Red Queen Hypothesis (RQH) suggests that the coevolutionary dynamics of host-parasite systems can generate selection for increased host recombination. Since host-parasite interactions often have a strong genetic basis, recombination between different hosts can increase the fraction of novel and potentially resistant offspring genotypes. A prerequisite for this mechanism is that host-parasite interactions generate persistent ...Journal Article -
Cophylogeny of the anther smut fungi and their caryophyllaceous hosts: Prevalence of host shifts and importance of delimiting parasite species for inferring cospeciation
(2008)BMC Evolutionary BiologyBackground Using phylogenetic approaches, the expectation that parallel cladogenesis should occur between parasites and hosts has been validated in some studies, but most others provided evidence for frequent host shifts. Here we examine the evolutionary history of the association between Microbotryum fungi that cause anther smut disease and their Caryophyllaceous hosts. We investigated the congruence between host and parasite phylogenies, ...Journal Article -
Recombination in Glomus intraradices, a supposed ancient asexual arbuscular mycorrhizal fungus
(2009)BMC Evolutionary BiologyBackground Arbuscular mycorrhizal fungi (AMF) are important symbionts of most plant species, promoting plant diversity and productivity. This symbiosis is thought to have contributed to the early colonisation of land by plants. Morphological stasis over 400 million years and the lack of an observed sexual stage in any member of the phylum Glomeromycota led to the controversial suggestion of AMF being ancients asexuals. Evidence for ...Journal Article -
Imp-L2, a putative homolog of vertebrate IGF-binding protein 7, counteracts insulin signaling in Drosophila and is essential for starvation resistance
(2008)Journal of BiologyBackground. Insulin and insulin-like growth factors (IGFs) signal through a highly conserved pathway and control growth and metabolism in both vertebrates and invertebrates. In mammals, insulin-like growth factor binding proteins (IGFBPs) bind IGFs with high affinity and modulate their mitogenic, anti-apoptotic and metabolic actions, but no functional homologs have been identified in invertebrates so far. Results. Here, we show that the ...Journal Article -
Measurement of left ventricular dimensions with contrast-enhanced three-dimensional cine imaging facilitated by k-t SENSE
(2008)Journal of Cardiovascular Magnetic ResonanceAim: To compare three-dimensional (3D) k-t sensitivity encoded (k-t SENSE) cine cardiovascular magnetic resonance (CMR), before and after contrast administration, against standard 2D imaging for the assessment of left ventricular volumes and mass. Method: Twenty-six subjects (14 volunteers, 12 patients) underwent multiple breathhold 2D balanced turbo-field echo cine CMR in addition to k-t SENSE accelerated 3D imaging (acceleration factor ...Journal Article -
Gene conversion in the rice genome
(2008)BMC GenomicsBackground Gene conversion causes a non-reciprocal transfer of genetic information between similar sequences. Gene conversion can both homogenize genes and recruit point mutations thereby shaping the evolution of multigene families. In the rice genome, the large number of duplicated genes increases opportunities for gene conversion. Results To characterize gene conversion in rice, we have defined 626 multigene families in which 377 ...Journal Article -
SWPS3 - fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2
(2008)BMC Research NotesBackground. We present swps3, a vectorized implementation of the Smith-Waterman local alignment algorithm optimized for both the Cell/BE and ×86 architectures. The paper describes swps3 and compares its performances with several other implementations. Findings. Our benchmarking results show that swps3 is currently the fastest implementation of a vectorized Smith-Waterman on the Cell/BE, outperforming the only other known implementation ...Journal Article -
Annotating novel genes by integrating synthetic lethals and genomic information
(2008)BMC Systems BiologyBackground Large scale screening for synthetic lethality serves as a common tool in yeast genetics to systematically search for genes that play a role in specific biological processes. Often the amounts of data resulting from a single large scale screen far exceed the capacities of experimental characterization of every identified target. Thus, there is need for computational tools that select promising candidate genes in order to reduce ...Journal Article -
Chicken genome analysis reveals novel genes encoding biotin-binding proteins related to avidin family
(2005)BMC GenomicsBackground A chicken egg contains several biotin-binding proteins (BBPs), whose complete DNA and amino acid sequences are not known. In order to identify and characterise these genes and proteins we studied chicken cDNAs and genes available in the NCBI database and chicken genome database using the reported N-terminal amino acid sequences of chicken egg-yolk BBPs as search strings. Results Two separate hits showing significant homology ...Journal Article