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anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data
(2008)BMC BioinformaticsBackground Compared to other omics techniques, quantitative metabolomics is still at its infancy. Complex sample preparation and analytical procedures render exact quantification extremely difficult. Furthermore, not only the actual measurement but also the subsequent interpretation of quantitative metabolome data to obtain mechanistic insights is still lacking behind the current expectations. Recently, the method of network-embedded ...Journal Article -
Bunched, the Drosophila homolog of the mammalian tumor suppressor TSC-22, promotes cellular growth
(2008)BMC Developmental BiologyBackground Transforming Growth Factor-β1 stimulated clone-22 (TSC-22) is assumed to act as a negative growth regulator and tumor suppressor. TSC-22 belongs to a family of putative transcription factors encoded by four distinct loci in mammals. Possible redundancy among the members of the TSC-22/Dip/Bun protein family complicates a genetic analysis. In Drosophila, all proteins homologous to the TSC-22/Dip/Bun family members are derived ...Journal Article -
Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences
(2006)BMC BioinformaticsBackground The estimation of the difference between two evolutionary distances within a triplet of homologs is a common operation that is used for example to determine which of two sequences is closer to a third one. The most accurate method is currently maximum likelihood over the entire triplet. However, this approach is relatively time consuming. Results We show that an alternative estimator, based on pairwise estimates and therefore ...Journal Article -
Movement control tests of the low back; evaluation of the difference between patients with back pain and healthy controls
(2008)BMC Musculoskeletal DisordersBackground To determine whether there is a difference between patients with low back pain and healthy controls in a test battery score for movement control of the lumbar spine. Methods This was a case control study, carried out in five outpatient physiotherapy practices in the German-speaking part of Switzerland. Twelve physiotherapists tested the ability of 210 subjects (108 patients with non-specific low back pain and 102 control ...Journal Article -
A Computationally Efficient Method for Polyphonic Pitch Estimation
(2009)EURASIP Journal on Advances in Signal ProcessingThis paper presents a computationally efficient method for polyphonic pitch estimation. The method employs the Fast Resonator Time-Frequency Image (RTFI) as the basic time-frequency analysis tool. The approach is composed of two main stages. First, a preliminary pitch estimation is obtained by means of a simple peak-picking procedure in the pitch energy spectrum. Such spectrum is calculated from the original RTFI energy spectrum according ...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 -
Effectiveness of Active-Online, an Individually Tailored Physical Activity Intervention, in a Real-Life Setting: Randomized Controlled Trial
(2009)Journal of Medical Internet ResearchBackground: Effective interventions are needed to reduce the chronic disease epidemic. The Internet has the potential to provide large populations with individual advice at relatively low cost. Objective: The focus of the study was the Web-based tailored physical activity intervention Active-online. The main research questions were (1) How effective is Active-online, compared to a nontailored website, in increasing self-reported and ...Journal Article -
Systematic assignment of thermodynamic constraints in metabolic network models
(2006)BMC BioinformaticsBackground The availability of genome sequences for many organisms enabled the reconstruction of several genome-scale metabolic network models. Currently, significant efforts are put into the automated reconstruction of such models. For this, several computational tools have been developed that particularly assist in identifying and compiling the organism-specific lists of metabolic reactions. In contrast, the last step of the model ...Journal Article -
A microarray-based system for the simultaneous analysis of single nucleotide polymorphisms in human genes involved in the metabolism of anti-malarial drugs
(2009)Malaria JournalBackground In order to provide a cost-effective tool to analyse pharmacogenetic markers in malaria treatment, DNA microarray technology was compared with sequencing of polymerase chain reaction (PCR) fragments to detect single nucleotide polymorphisms (SNPs) in a larger number of samples. Methods The microarray was developed to affordably generate SNP data of genes encoding the human cytochrome P450 enzyme family (CYP) and ...Journal Article -
Hand-held dynamometry in patients with haematological malignancies: Measurement error in the clinical assessment of knee extension strength
(2009)BMC Musculoskeletal DisordersBackground Hand-held dynamometry is a portable and inexpensive method to quantify muscle strength. To determine if muscle strength has changed, an examiner must know what part of the difference between a patient's pre-treatment and post-treatment measurements is attributable to real change, and what part is due to measurement error. This study aimed to determine the relative and absolute reliability of intra and inter-observer strength ...Journal Article