Unraveling the mysteries of dog evolution

The increased battery of molecular markers, derived from comparative genomics, is aiding our understanding of the genetics of domestication. The recent BMC Biology article pertaining to the evolution of small size in dogs is an example of how such methods can be used to study the origin and diversification of the domestic dog. We are still challenged, however, to appreciate the genetic mechanisms responsible for the phenotypic diversity seen in 'our best friend'

Inference of hidden structures in complex physical systems by multi-scale clustering

We survey the application of a relatively new branch of statistical physics--"community detection"-- to data mining. In particular, we focus on the diagnosis of materials and automated image segmentation. Community detection describes the quest of partitioning a complex system involving many elements into optimally decoupled subsets or communities of such elements. We review a multiresolution variant which is used to ascertain structures at different spatial and temporal scales. Significant patterns are obtained by examining the correlations between different independent solvers. Similar to other combinatorial optimization problems in the NP complexity class, community detection exhibits several phases. Typically, illuminating orders are revealed by choosing parameters that lead to extremal information theory correlations.Comment: 25 pages, 16 Figures; a review of earlier work

A Pipeline for the ROTSE-IIId Archival Data

We have constructed a new, fast, robust and reliable pipeline to detect variable stars from the ROTSE-IIId archival data. Turkish share of ROTSE-III archive contains approximately one million objects from a large field of view (1.85\dgr) and it considerably covers a large portion of northern sky (\delta>-25\dgr). The unfiltered ROTSE-III magnitude of the objects ranges from 7.7 to 16.9. The main stages of the new pipeline are as follows: Source extraction, astrometry of the objects, light curve generation and inhomogeneous ensemble photometry. A high performance computing (HPC) algorithm has also been implemented into the pipeline where we had a good performance even on a personal computer. Running the algorithms of the pipeline on a cluster decreases analysis time significantly from weeks to hours. The pipeline is especially tested against long period variable stars with periods of a few hundred days (e.g Mira and SR) and variables having periods starting from a few days to a few hundred days were detected.Comment: 8 pages, 5 figures 2 tables; last revision before publishe

Magnetically gated accretion in an accreting ‘non-magnetic’ white dwarf

White dwarfs are often found in binary systems with orbital periods ranging from tens of minutes to hours in which they can accrete gas from their companion stars. In about 15 per cent of these binaries, the magnetic field of the white dwarf is strong enough (at 106 gauss or more) to channel the accreted matter along field lines onto the magnetic poles1,2. The remaining systems are referred to as ‘non-magnetic’, because until now there has been no evidence that they have a magnetic field that is strong enough to affect the accretion dynamics. Here we report an analysis of archival optical observations of the ‘non-magnetic’ accreting white dwarf in the binary system MV Lyrae, whose light curve displays quasi-periodic bursts of about 30 minutes duration roughly every 2 hours. The timescale and amplitude of these bursts indicate the presence of an unstable, magnetically regulated accretion mode, which in turn implies the existence of magnetically gated accretion3,4,5, in which disk material builds up around the magnetospheric boundary (at the co-rotation radius) and then accretes onto the white dwarf, producing bursts powered by the release of gravitational potential energy. We infer a surface magnetic field strength for the white dwarf in MV Lyrae of between 2 × 104 gauss and 1 × 105 gauss, too low to be detectable by other current methods. Our discovery provides a new way of studying the strength and evolution of magnetic fields in accreting white dwarfs and extends the connections between accretion onto white dwarfs, young stellar objects and neutron stars, for which similar magnetically gated accretion cycles have been identified6,7,8,9

Analysis of meniscal degeneration and meniscal gene expression

<p>Abstract</p> <p>Background</p> <p>Menisci play a vital role in load transmission, shock absorption and joint stability. There is increasing evidence suggesting that OA menisci may not merely be bystanders in the disease process of OA. This study sought: 1) to determine the prevalence of meniscal degeneration in OA patients, and 2) to examine gene expression in OA meniscal cells compared to normal meniscal cells.</p> <p>Methods</p> <p>Studies were approved by our human subjects Institutional Review Board. Menisci and articular cartilage were collected during joint replacement surgery for OA patients and lower limb amputation surgery for osteosarcoma patients (normal control specimens), and graded. Meniscal cells were prepared from these meniscal tissues and expanded in monolayer culture. Differential gene expression in OA meniscal cells and normal meniscal cells was examined using Affymetrix microarray and real time RT-PCR.</p> <p>Results</p> <p>The grades of meniscal degeneration correlated with the grades of articular cartilage degeneration (r = 0.672; P < 0.0001). Many of the genes classified in the biological processes of immune response, inflammatory response, biomineral formation and cell proliferation, including major histocompatibility complex, class II, DP alpha 1 (<it>HLA-DPA1</it>), integrin, beta 2 (<it>ITGB2</it>), ectonucleotide pyrophosphatase/phosphodiesterase 1 (<it>ENPP1</it>), ankylosis, progressive homolog (<it>ANKH</it>) and fibroblast growth factor 7 (<it>FGF7</it>), were expressed at significantly higher levels in OA meniscal cells compared to normal meniscal cells. Importantly, many of the genes that have been shown to be differentially expressed in other OA cell types/tissues, including ADAM metallopeptidase with thrombospondin type 1 motif 5 (<it>ADAMTS5</it>) and prostaglandin E synthase (<it>PTGES</it>), were found to be expressed at significantly higher levels in OA meniscal cells. This consistency suggests that many of the genes detected in our study are disease-specific.</p> <p>Conclusion</p> <p>Our findings suggest that OA is a whole joint disease. Meniscal cells may play an active role in the development of OA. Investigation of the gene expression profiles of OA meniscal cells may reveal new therapeutic targets for OA therapy and also may uncover novel disease markers for early diagnosis of OA.</p