A compact SiGe D-band power amplifier for scalable photonic-enabled phased antenna arrays.

To address the rising demand for high-speed wireless data links, communication systems operating at frequencies beyond [Formula: see text] are being targeted. A key enabling technology in the development of these wireless systems is the phased antenna array. Yet, the design and implementation of such steerable antenna arrays at frequencies over [Formula: see text] comes with a multitude of challenges.

Compact and wideband transmit opto-antenna for radio frequency over fiber.

An advanced transmit remote opto-antenna unit is proposed that accomplishes impedance matching between a photodetector and a low-profile antenna in a specified frequency bandwidth, without requiring an area-consuming matching network. This results in a highly compact design, which also avoids the losses and spurious radiation by such an electrically large matching circuit. Instead, the photodetector is almost directly connected to the antenna, which is designed as a conjugate load, such that the extracted and radiated power are optimized.

STATISTICAL APPROACH FOR HUMAN ELECTROMAGNETIC EXPOSURE ASSESSMENT IN FUTURE WIRELESS ATTO-CELL NETWORKS.

In this article, we study human electromagnetic exposure to the radiation of an ultra dense network of nodes integrated in a floor denoted as ATTO-cell floor, or ATTO-floor. ATTO-cells are a prospective 5 G wireless networking technology, in which humans are exposed by several interfering sources. To numerically estimate this exposure we propose a statistical approach based on a set of finite difference time domain simulations.

Evaluation of the impact of Illumina error correction tools on de novo genome assembly.

Background: Recently, many standalone applications have been proposed to correct sequencing errors in Illumina data. The key idea is that downstream analysis tools such as de novo genome assemblers benefit from a reduced error rate in the input data. Surprisingly, a systematic validation of this assumption using state-of-the-art assembly methods is lacking, even for recently published methods.

Secure Service Proxy: A CoAP(s) Intermediary for a Securer and Smarter Web of Things.

As the IoT continues to grow over the coming years, resource-constrained devices and networks will see an increase in traffic as everything is connected in an open Web of Things. The performance- and function-enhancing features are difficult to provide in resource-constrained environments, but will gain importance if the WoT is to be scaled up successfully. For example, scalable open standards-based authentication and authorization will be important to manage access to the limited resources of constrained devices and networks.

Radiofrequency exposure near an attocell as part of an ultra-high density access network.

In the future, wireless radiofrequency (RF) telecommunications networks will provide users with gigabit-per-second data rates. Therefore, these networks are evolving toward hybrid networks, which will include commonly used macro- and microcells in combination with local ultra-high density access networks consisting of so-called attocells. The use of attocells requires a proper compliance assessment of exposure to RF electromagnetic radiation.

A Cytoscape app for motif enumeration with ISMAGS.

Summary: We present a Cytoscape app for the ISMAGS algorithm, which can enumerate all instances of a motif in a graph, making optimal use of the motif’s symmetries to make the search more efficient. The Cytoscape app provides a handy interface for this algorithm, which allows more efficient network analysis.

Availability And Implementation: The Cytoscape app for ISMAGS can be freely downloaded from the Cytoscape App store http://apps.

Bindings and RESTlets: A Novel Set of CoAP-Based Application Enablers to Build IoT Applications.

Sensors and actuators are becoming important components of Internet of Things (IoT) applications. Today, several approaches exist to facilitate communication of sensors and actuators in IoT applications. Most communications go through often proprietary gateways requiring availability of the gateway for each and every interaction between sensors and actuators.

Experimental Evaluation of Unicast and Multicast CoAP Group Communication.

The Internet of Things (IoT) is expanding rapidly to new domains in which embedded devices play a key role and gradually outnumber traditionally-connected devices. These devices are often constrained in their resources and are thus unable to run standard Internet protocols. The Constrained Application Protocol (CoAP) is a new alternative standard protocol that implements the same principals as the Hypertext Transfer Protocol (HTTP), but is tailored towards constrained devices.

Jabba: hybrid error correction for long sequencing reads.

Background: Third generation sequencing platforms produce longer reads with higher error rates than second generation technologies. While the improved read length can provide useful information for downstream analysis, underlying algorithms are challenged by the high error rate. Error correction methods in which accurate short reads are used to correct noisy long reads appear to be attractive to generate high-quality long reads.

Netter: re-ranking gene network inference predictions using structural network properties.

Background: Many algorithms have been developed to infer the topology of gene regulatory networks from gene expression data. These methods typically produce a ranking of links between genes with associated confidence scores, after which a certain threshold is chosen to produce the inferred topology. However, the structural properties of the predicted network do not resemble those typical for a gene regulatory network, as most algorithms only take into account connections found in the data and do not include known graph properties in their inference process.

BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements.

Motivation: The accurate discovery and annotation of regulatory elements remains a challenging problem. The growing number of sequenced genomes creates new opportunities for comparative approaches to motif discovery. Putative binding sites are then considered to be functional if they are conserved in orthologous promoter sequences of multiple related species.

Pathway Relevance Ranking for Tumor Samples through Network-Based Data Integration.

The study of cancer, a highly heterogeneous disease with different causes and clinical outcomes, requires a multi-angle approach and the collection of large multi-omics datasets that, ideally, should be analyzed simultaneously. We present a new pathway relevance ranking method that is able to prioritize pathways according to the information contained in any combination of tumor related omics datasets. Key to the method is the conversion of all available data into a single comprehensive network representation containing not only genes but also individual patient samples.

FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data.

The number of markers measured in both flow and mass cytometry keeps increasing steadily. Although this provides a wealth of information, it becomes infeasible to analyze these datasets manually. When using 2D scatter plots, the number of possible plots increases exponentially with the number of markers and therefore, relevant information that is present in the data might be missed.

Flexible unicast-based group communication for CoAP-enabled devices.

Smart embedded objects will become an important part of what is called the Internet of Things. Applications often require concurrent interactions with several of these objects and their resources. Existing solutions have several limitations in terms of reliability, flexibility and manageability of such groups of objects.

NIMEFI: gene regulatory network inference using multiple ensemble feature importance algorithms.

One of the long-standing open challenges in computational systems biology is the topology inference of gene regulatory networks from high-throughput omics data. Recently, two community-wide efforts, DREAM4 and DREAM5, have been established to benchmark network inference techniques using gene expression measurements. In these challenges the overall top performer was the GENIE3 algorithm.

The index-based subgraph matching algorithm (ISMA): fast subgraph enumeration in large networks using optimized search trees.

Subgraph matching algorithms are designed to find all instances of predefined subgraphs in a large graph or network and play an important role in the discovery and analysis of so-called network motifs, subgraph patterns which occur more often than expected by chance. We present the index-based subgraph matching algorithm (ISMA), a novel tree-based algorithm. ISMA realizes a speedup compared to existing algorithms by carefully selecting the order in which the nodes of a query subgraph are investigated.

EPSILON: an eQTL prioritization framework using similarity measures derived from local networks.

Motivation: When genomic data are associated with gene expression data, the resulting expression quantitative trait loci (eQTL) will likely span multiple genes. eQTL prioritization techniques can be used to select the most likely causal gene affecting the expression of a target gene from a list of candidates. As an input, these techniques use physical interaction networks that often contain highly connected genes and unreliable or irrelevant interactions that can interfere with the prioritization process.

Introduction: ECOC 2012 in Amsterdam.

We introduce the Optics Express special issue from the 38th European Conference on Optical Communication and Exhibition (ECOC). A total of 134 expanded papers from ECOC 2012 are included in this special issue.

ONU power saving modes in next generation optical access networks: progress, efficiency and challenges.

The optical network unit (ONU), installed at a customer's premises, accounts for about 60% of power in current fiber-to-the-home (FTTH) networks. We propose a power consumption model for the ONU and evaluate the ONU power consumption in various next generation optical access (NGOA) architectures. Further, we study the impact of the power savings of the ONU in various low power modes such as power shedding, doze and sleep.

i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets.

Comparative genomics is a powerful means to gain insight into the evolutionary processes that shape the genomes of related species. As the number of sequenced genomes increases, the development of software to perform accurate cross-species analyses becomes indispensable. However, many implementations that have the ability to compare multiple genomes exhibit unfavorable computational and memory requirements, limiting the number of genomes that can be analyzed in one run.

CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks.

Summary: Network motifs in integrated molecular networks represent functional relationships between distinct data types. They aggregate to form dense topological structures corresponding to functional modules which cannot be detected by traditional graph clustering algorithms. We developed CyClus3D, a Cytoscape plugin for clustering composite three-node network motifs using a 3D spectral clustering algorithm.

A greedy, graph-based algorithm for the alignment of multiple homologous gene lists.

Motivation: Many comparative genomics studies rely on the correct identification of homologous genomic regions using accurate alignment tools. In such case, the alphabet of the input sequences consists of complete genes, rather than nucleotides or amino acids. As optimal multiple sequence alignment is computationally impractical, a progressive alignment strategy is often employed.

A hybrid tabu search algorithm for automatically assigning patients to beds.

Objective: We describe a patient admission scheduling algorithm that supports the operational decisions in a hospital. It involves efficiently assigning patients to beds in the appropriate departments, taking into account the medical needs of the patients as well as their preferences, while keeping the number of patients in the different departments balanced.

Methods: Due to the combinatorial complexity of the admission scheduling problem, there is a need for an algorithm that intelligently assists the admission scheduler in taking decisions fast.

On the design of a generic and scalable multilayer software architecture for data flow management in the intensive care unit.

Objectives: The current Intensive Care Information Systems (IC-ISs) collect and store monitoring data in on automated way and can replace all paper forms by an electronic equivalent, resulting in a paperless ICU. Future development of IC-ISs will now have to focus on bedside clinical decision support. The current IC-ISs are data-driven systems, with a two-layer software architecture.