Genes from cluster <i>daf-21</i>Down_2 are suppressed by Hsp90 RNAi in gonads and embryos.

<p>A) HZ455 nematodes were imaged to visualize the expression and subcellular localization of SEPA-1 protein. Yellow arrows indicate the position of developed embryos, while green arrows indicate the fluorescence prior to passage through the spermathecum. B) RT688 nematodes were imaged to visualize subcellular localization of CAV-1 protein. The CAV-1 protein in the meiotic zone of the gonad arm is indicated in both panels with a green arrow, while yellow arrows indicate the position of developed embryos. C) BC12422 nematodes were imaged to visualize the cells expressing <i>zip-8</i>. The scale bar represents 100 μm. Yellow arrows show the position of a <i>bzip-8</i>::GFP expressing embryo. D) GFP::PUD-1.1 can be observed in intestinal tissues in later larval stages. After Hsp90 RNAi this expression is strongly diminished. The scale bar represents 100 μm.</p

Transcriptional networks affected by RNAi against <i>daf-21</i>.

<p>Networks for upregulated (A) and downregulated (B) genes after Hsp90-depletion. The networks were constructed as described in the Materials and Methods section. The color code uses four shadings of blue and red to indicate the expression differences with darkest blue being log₂(DiffExp) < -1, lightest blue being log₂(DiffExp) < -0.25, darkest red being log₂(DiffExp) > 1 and lightest red being log₂(DiffExp) > 0.25. In between 0.25 and -0.25 the nodes are white as indicated in the legend. Large clusters have been subjected to GO-term enrichment analysis and the results are depicted adjacent to the respective cluster in the network figure.</p

PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface

Protein inference connects the peptide spectrum matches (PSMs) obtained from database search engines back to proteins, which are typically at the heart of most proteomics studies. Different search engines yield different PSMs and thus different protein lists. Analysis of results from one or multiple search engines is often hampered by different data exchange formats and lack of convenient and intuitive user interfaces. We present PIA, a flexible software suite for combining PSMs from different search engine runs and turning these into consistent results. PIA can be integrated into proteomics data analysis workflows in several ways. A user-friendly graphical user interface can be run either locally or (e.g., for larger core facilities) from a central server. For automated data processing, stand-alone tools are available. PIA implements several established protein inference algorithms and can combine results from different search engines seamlessly. On several benchmark data sets, we show that PIA can identify a larger number of proteins at the same protein FDR when compared to that using inference based on a single search engine. PIA supports the majority of established search engines and data in the mzIdentML standard format. It is implemented in Java and freely available at https://github.com/mpc-bioinformatics/pia

Overlapping coalition formation games in wireless communication networks

This brief introduces overlapping coalition formation games (OCF games), a novel mathematical framework from cooperative game theory that can be used to model, design and analyze cooperative scenarios in future wireless communication networks. The concepts of OCF games are explained, and several algorithmic aspects are studied. In addition, several major application scenarios are discussed. These applications are drawn from a variety of fields that include radio resource allocation in dense wireless networks, cooperative spectrum sensing for cognitive radio networks, and resource management for crowd sourcing. For each application, the use of OCF games is discussed in detail in order to show how this framework can be used to solve relevant wireless networking problems. Overlapping Coalition Formation Games in Wireless Communication Networks provides researchers, students and practitioners with a concise overview of existing works in this emerging area, exploring the relevant fundamental theories, key techniques, and significant applications.

Cyber-physical system design with sensor networking technologies

This book describes how wireless sensor networking technologies can help in establishing and maintaining seamless communications between the physical and cyber systems to enable efficient, secure, reliable acquisition, management, and routing of data