SNPSTR: a database of compound microsatellite-SNP markers

There has been widespread and growing interest in genetic markers suitable for drawing population genetic inferences about past demographic events and to detect the effects of selection. In addition to single nucleotide polymorphisms (SNPs), microsatellites (or short tandem repeats, STRs) have received great attention in the analysis of human population history. In the SNPSTR database () we catalogue a relatively new type of compound genetic marker called SNPSTR which combines a microsatellite marker (STR) with one or more tightly linked SNPs. Here, the SNP(s) and the microsatellite are less than 250 bp apart so each SNPSTR can be considered a small haplotype with no recombination occurring between the two individual markers. Thus, SNPSTRs have the potential to become a very useful tool in the field of population genetics. The SNPSTR database contains all inferable human SNPSTRs as well as those in mouse, rat, dog and chicken, i.e. all model organisms for which extensive SNP datasets are available

Influence of denosumab on bone mineral density in a severe case of pregnancy-associated osteoporosis

Pregnancy and lactation-associated osteoporosis (PLO) with predominantly subsequent vertebral fracture is a rare but severe disease with an estimated incidence of 0.4 in 100,000. In the past, patients with PLO have been predominantly treated with oral and i.v. bisphosphonates to reduce subsequent fracture risk. Hereby, the use of bisphosphonates in premenopausal women is controversial, as bisphosphonates know to persist in bone for many years and can be exposed and circulate in maternal serum and subsequently pass the placenta barrier and may have a detrimental effect on fetal bone health. Here we report the effects of denosumab on the bone mineral density (BMD) and subsequent fracture risk in PLO. In this case presentation, denosumab was administered postpartum with 3000 IE vitamin D and 1000 mg of calcium daily in a patient with PLO and vertebral fracture of L1 and L4. After 18 months of treatment with denosumab, we could demonstrate a clinical significant increase of BMD at the lumbar spine, femoral neck, and total hip of 32.2%, 13.0%, and 11.5% respectively with no further subsequent fractures. As the patient had regular menstrual cycles and considered a further pregnancy, denosumab treatment was terminated and soon a second pregnancy occurred. After the second pregnancy, BMD decreased at the lumbar spine, femur neck, and total hip by -8.8%, -6.9%, and -7.0% respectively compared to the maximum values during treatment with denosumab, but was still significantly higher compared to baseline levels with no further fractures

Inference of Temporally Varying Bayesian Networks

When analysing gene expression time series data an often overlooked but crucial aspect of the model is that the regulatory network structure may change over time. Whilst some approaches have addressed this problem previously in the literature, many are not well suited to the sequential nature of the data. Here we present a method that allows us to infer regulatory network structures that may vary between time points, utilising a set of hidden states that describe the network structure at a given time point. To model the distribution of the hidden states we have applied the Hierarchical Dirichlet Process Hideen Markov Model, a nonparametric extension of the traditional Hidden Markov Model, that does not require us to fix the number of hidden states in advance. We apply our method to exisiting microarray expression data as well as demonstrating is efficacy on simulated test data

Finite-temperature hole dynamics in the t-J model: Exact results for high dimensions

We discuss the dynamics of a single hole in the t-J model at finite temperature, in the limit of large spatial dimensions. The problem is shown to yield a simple and physically transparent solution, that exemplifies the continuous thermal evolution of the underlying string picture from the T=0 string-pinned limit through to the paramagnetic phase.Comment: 6 pages, including 2 figure