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Interactive visual analysis of biological high-throughput data in the context of the underlying networks is an essential task in modern biomedicine with applications ranging from metabolic engineering to personalized medicine. The complexity and heterogeneity of data sets require flexible software architectures for data analysis. Concise and easily readable graphical representation of data and interactive navigation of large data sets are essential in this context. We present BiNA--the Biological Network Analyzer--a flexible open-source software for analyzing and visualizing biological networks. Highly configurable visualization styles for regulatory and metabolic network data offer sophisticated drawings and intuitive navigation and exploration techniques using hierarchical graph concepts. The generic projection and analysis framework provides powerful functionalities for visual analyses of high-throughput omics data in the context of networks, in particular for the differential analysis and the analysis of time series data. A direct interface to an underlying data warehouse provides fast access to a wide range of semantically integrated biological network databases. A plugin system allows simple customization and integration of new analysis algorithms or visual representations. BiNA is available under the 3-clause BSD license at http://bina.unipax.info/.

The RGASP consortium compared 25 RNA-seq analysis programs in their ability to identify exons, reconstruct transcripts and quantify expression levels. Assembly of isoforms and their expression levels in higher eukaryotes remains a challenge. We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete transcript components with high success rates but that assembly of complete isoform structures poses a major challenge even when all constituent elements are identified. Expression-level estimates also varied widely across methods, even when based on similar transcript models. Consequently, the complexity of higher eukaryotic genomes imposes severe limitations on transcript recall and splice product discrimination that are likely to remain limiting factors for the analysis of current-generation RNA-seq data.

The integration of dislocation-free Ge nano-islands was realized via selective molecular beam epitaxy on Si nano-tip patterned substrates. The Si-tip wafers feature a rectangular array of nanometer sized Si tips with (001) facet exposed among a SiO 2 matrix. These wafers were fabricated by complementary metal-oxide-semiconductor (CMOS) compatible nanotechnology. Calculations based on nucleation theory predict that the selective growth occurs close to thermodynamic equilibrium, where condensation of Ge adatoms on SiO 2 is disfavored due to the extremely short re-evaporation time and diffusion length. The growth selectivity is ensured by the desorption-limited growth regime leading to the observed pattern independence, i.e. the absence of loading effect commonly encountered in chemical vapor deposition. The growth condition of high temperature and low deposition rate is responsible for the observed high crystalline quality of the Ge islands which is also associated with negligible Si-Ge intermixing owing to geometric hindrance by the Si nano-tip approach. Single island as well as area-averaged characterization methods demonstrate that Ge islands are dislocation-free and heteroepitaxial strain is fully relaxed. Such well-ordered high quality Ge islands present a step towards the achievement of materials suitable for optical applications.

There is increasing evidence that not only the way of data acquisition but also the design of data visualization (i.e., the format) has impact on the quality of pathology reports. Therefore, we investigated the correlation between the format of pathology reports and the amount as well as the detection time of transmitted data. All reports of oncological breast resection specimens referred to the Institute for Surgical Pathology, University Medical Center Freiburg, between 2003 and 2011 ( n  = 4181) were classified into descriptive reports (DR, n  = 856), structured reports (SR, n  = 2455), or template-based synoptic reports (TBSR, n  = 870). The reports were screened regarding the content of nine organ-specific essential data. The amount of recorded essential data per report was summarized in an essential data score (EDS) and the format types were statistically compared regarding their EDS. Additionally, we measured the time a gynecologist needed to detect all nine essential data within a subset of reports and compared the format types regarding the detection times statistically. A full-score EDS of 9 was seen in 28.4 % of all reports, in 4 % of DRs, in 21.4 % of SRs, and in 72.3 % of TBSRs ( p  < 0.0001). Median EDS of DRs was 7, of SRs 8, and of TBSRs 9 ( p  < 0.0001). Data regarding tumor localization, tumor size, specific grading, angioinvasion, hormone receptor status, and additional findings were mentioned more frequently in TBSRs compared to other format type reports with a statistically highly significant difference ( p  < 0.0001). Mean data detection time decreased significantly from 26 to 20 and 14 s in DRs, SRs, and TBSRs, respectively. Our results clearly show that due to the use of TBSRs reporting of oncological breast resection specimens are improved regarding the content of essential data and the clarity of the data layout resulting in a rapid detection of essential data by clinicians.

Creating a converged multiservice network, seamlessly integrating existing services with new technologies, can be complex and challenging. Implementation of new technologies over the public switched telephone network offers new revenue-generating services, reduces costs and protects investment in existing infrastructure. The converged network has to maintain the characteristics and services of the circuit switched network in terms of reliability, quality of service, interoperability and manageability. In order to bridge the interface between the PSTN and IP networks, carriers are turning to open network signaling gateways. Protocols are optimized for adapting signaling system 7 signaling to the IP network. To enable a smooth transition, all variants of integrated services user part protocols are supported.

Cet article est consacré à l'étude des conditions de travail et de formation des apprentis dans le secteur du petit commerce d'après l'exemple de la ville de Brême. Il montre que le maintien des exigences traditionnelles quant à la formation des futurs commerçants dissimule une exploitation croissante d'une main-d'œuvre à bon marché. C'est la raison pour laquelle de nombreux petits commerçants manifestent une vive opposition à une réforme de l'apprentissage, qui passerait par la prolongation de la scolarité au sein d'une école professionnelle. Il en résulte des conflits avec les associations professionnelles. Ces différends entraînent finalement l'intervention de l'Etat, qui se révèle nécessaire pour établir un allongement de la formation professionnelle qui soit obligatoire. /// Based on a case-study of the city of Bremen, the essay has for purpose the investigation of apprentices' working and training condition in the small trading branch. The results show that behind the traditional claim to train future tradesmen, an increasing exploitation of cheap labour is taking place. For this reason many small tradesmen are opposed to reform measures in this field which would see the creation of a training period for apprentices as an extended school term programme. This situation leads consequently to conflicts of interest with civic authorities whose intervention will eventually be necessary in order to implement a compulsory extended training programme for apprentices integrated as a whole to the existing school system.