MOTIVATION Fluorescence Correlation Spectroscopy (FCS) is a popular tool for measuring molecular mobility and how mobility relates to molecular interaction dynamics and bioactivity in living cells. The FCS technique has been significantly advanced by its combination with super-resolution STED microscopy (STED-FCS). Specifically, the use of gated detection has shown great potential for enhancing...

According to the general understanding, the chondrocyte lineage terminates with the elimination of late hypertrophic cells by apoptosis in the growth plate. However, recent cell tracking studies have shown that murine hypertrophic chondrocytes can survive beyond "terminal" differentiation and give rise to a progeny of osteoblasts participating in endochondral bone formation. The question how ch...

The GIS software sector has developed rapidly over the last ten years. Open Source GIS applications are gaining relevant market shares in academia, business, and public administration. In this paper, we illustrate the history and features of a key Open Source GIS, the Geographical Resources Analysis Support System (GRASS). GRASS has been under development for more than 28 years, has strong ties...

Performing massive data mining experiments with multiple datasets and methods is a common task faced by most bioinformatics and computational biology laboratories. WEKA is a machine learning package designed to facilitate this task by providing tools that allow researchers to select from several classification methods and specific test strategies. Despite its popularity, the current WEKA enviro...

Wnt signaling, a major regulator of bone formation and homeostasis, might be involved in the bone loss of osteoporotic patients and the consequent impaired response to fracture. Therefore we analyzed Wnt-related, osteogenic, and adipogenic genes in bone tissue of elderly postmenopausal women undergoing hip replacement for either femoral fracture or osteoarthritis. Bone specimens derived from th...

Periodontal ligament cells (PDLCs), which have potential for multilineage differentiation, are candidates for use in regeneration of periodontal tissue defects; however, our understanding of the mechanisms underlying the lineage commitment of PDLCs remains limited. C4orf7, which is specifically expressed in the periodontal ligament (PDL) tissue, may be crucial in deciding the fate of PDLCs and ...

In this paper we present an Internet browser plug-in for real-time sound synthesis. The plug-in uses the Pure Data (Pd) sound synthesis engine, and allows flexible and transparent sound generation and control embedded into webpages. Pd is a general sound synthesis language that is based on the MAX graphical programming paradigm. It can be used to construct and implement a broad range of sound s...

PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biolog...

R is a language and environment for statistical computing and graphics, and is available as Free Software under the terms of the Free Software Foundation’s GNU General Public License in source code form. The R community also supports the contribution of packages adding functionality to the software, providing quality assurance services and on-line archives. The archives also contain executable ...

UNLABELLED The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard ...