ALBERT

Description: Motivation The traditional view of cancer evolution states that a cancer genome accumulates a sequential ordering of mutations over a long period of time. However, in recent years it has been suggested that a cancer genome may instead undergo a one-time catastrophic event, such as chromothripsis , where a large number of mutations instead occur simultaneously . A number of potential signatures of chromothripsis have been proposed. In this work, we provide a rigorous formulation and analysis of the ‘ability to walk the derivative chromosome’ signature originally proposed by Korbel and Campbell. In particular, we show that this signature, as originally envisioned, may not always be present in a chromothripsis genome and we provide a precise quantification of under what circumstances it would be present. We also propose a variation on this signature, the H/T alternating fraction , which allows us to overcome some of the limitations of the original signature. Results We apply our measure to both simulated data and a previously analyzed real cancer dataset and find that the H/T alternating fraction may provide useful signal for distinguishing genomes having acquired mutations simultaneously from those acquired in a sequential fashion. Availability and implementation An implementation of the H/T alternating fraction is available at https://bitbucket.org/oesperlab/ht-altfrac . Contact loesper@carleton.edu Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation The identification of microRNA (miRNA) target sites is important. In the past decade, dozens of computational methods have been developed to predict miRNA target sites. Despite their existence, rarely does a method consider the well-known competition and cooperation among miRNAs when attempts to discover target sites. To fill this gap, we developed a new approach called CCmiR, which takes the cooperation and competition of multiple miRNAs into account in a statistical model to predict their target sites. Results Tested on four different datasets, CCmiR predicted miRNA target sites with a high recall and a reasonable precision, and identified known and new cooperative and competitive miRNAs supported by literature. Compared with three state-of-the-art computational methods, CCmiR had a higher recall and a higher precision. Availability and implementation CCmiR is freely available at http://hulab.ucf.edu/research/projects/miRNA/CCmiR . Contact xiaoman@mail.ucf.edu or haihu@cs.ucf.edu Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation Eukaryotic chromosomes adapt a complex and highly dynamic three-dimensional (3D) structure, which profoundly affects different cellular functions and outcomes including changes in epigenetic landscape and in gene expression. Making the scenario even more complex, cancer cells harbor chromosomal abnormalities [e.g. copy number variations (CNVs) and translocations] altering their genomes both at the sequence level and at the level of 3D organization. High-throughput chromosome conformation capture techniques (e.g. Hi-C), which are originally developed for decoding the 3D structure of the chromatin, provide a great opportunity to simultaneously identify the locations of genomic rearrangements and to investigate the 3D genome organization in cancer cells. Even though Hi-C data has been used for validating known rearrangements, computational methods that can distinguish rearrangement signals from the inherent biases of Hi-C data and from the actual 3D conformation of chromatin, and can precisely detect rearrangement locations de novo have been missing. Results In this work, we characterize how intra and inter-chromosomal Hi-C contacts are distributed for normal and rearranged chromosomes to devise a new set of algorithms (i) to identify genomic segments that correspond to CNV regions such as amplifications and deletions ( HiCnv ), (ii) to call inter-chromosomal translocations and their boundaries ( HiCtrans ) from Hi-C experiments and (iii) to simulate Hi-C data from genomes with desired rearrangements and abnormalities ( AveSim ) in order to select optimal parameters for and to benchmark the accuracy of our methods. Our results on 10 different cancer cell lines with Hi-C data show that we identify a total number of 105 amplifications and 45 deletions together with 90 translocations, whereas we identify virtually no such events for two karyotypically normal cell lines. Our CNV predictions correlate very well with whole genome sequencing data among chromosomes with CNV events for a breast cancer cell line ( r  = 0.89) and capture most of the CNVs we simulate using Avesim. For HiCtrans predictions, we report evidence from the literature for 30 out of 90 translocations for eight of our cancer cell lines. Furthermore, we show that our tools identify and correctly classify relatively understudied rearrangements such as double minutes and homogeneously staining regions. Considering the inherent limitations of existing techniques for karyotyping (i.e. missing balanced rearrangements and those near repetitive regions), the accurate identification of CNVs and translocations in a cost-effective and high-throughput setting is still a challenge. Our results show that the set of tools we develop effectively utilize moderately sequenced Hi-C libraries (100–300 million reads) to identify known and de novo chromosomal rearrangements/abnormalities in well-established cancer cell lines. With the decrease in required number of cells and the increase in attainable resolution, we believe that our framework will pave the way towards comprehensive mapping of genomic rearrangements in primary cells from cancer patients using Hi-C. Availability and implementation CNV calling: https://github.com/ay-lab/HiCnv , Translocation calling: https://github.com/ay-lab/HiCtrans and Hi-C simulation: https://github.com/ay-lab/AveSim . Contact ferhatay@lji.org Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Summary Cancer hallmarks, a concept that seeks to explain the complexity of cancer initiation and development, provide a new perspective of studying cancer signaling which could lead to a greater understanding of this complex disease. However, to the best of our knowledge, there is currently a lack of tools that support such hallmark-based study of the cancer signaling network, thereby impeding the gain of knowledge in this area. We present TROVE, an user-friendly software that facilitates hallmark annotation, visualization and analysis in cancer signaling networks. In particular, TROVE facilitates hallmark analysis specific to particular cancer types. Availability and implementation Available under the Eclipse Public License from: https://sites.google.com/site/cosbyntu/softwares/trove and https://github.com/trove2017/Trove . Contact hechua@ntu.edu.sg or assourav@ntu.edu.sg

Description: Summary High-throughput screening of the host transcriptional response to various viral infections provides a wealth of data, but utilization of microarray and next generation sequencing (NGS) data for analysis can be difficult. The Ho st T ranscriptional R esponse D ata B ase (HoTResDB), allows visitors to access already processed microarray and NGS data from non-human primate models of viral hemorrhagic fever to better understand the host transcriptional response. Availability HoTResDB is freely available at http://hotresdb.bu.edu Contact jhconnor@bu.edu

Description: Motivation Structural variation, including large deletions, duplications, inversions, translocations and other rearrangements, is common in human and cancer genomes. A number of methods have been developed to identify structural variants from Illumina short-read sequencing data. However, reliable identification of structural variants remains challenging because many variants have breakpoints in repetitive regions of the genome and thus are difficult to identify with short reads. The recently developed linked-read sequencing technology from 10X Genomics combines a novel barcoding strategy with Illumina sequencing. This technology labels all reads that originate from a small number (∼5 to 10) DNA molecules ∼50 Kbp in length with the same molecular barcode. These barcoded reads contain long-range sequence information that is advantageous for identification of structural variants. Results We present Novel Adjacency Identification with Barcoded Reads (NAIBR), an algorithm to identify structural variants in linked-read sequencing data. NAIBR predicts novel adjacencies in an individual genome resulting from structural variants using a probabilistic model that combines multiple signals in barcoded reads. We show that NAIBR outperforms several existing methods for structural variant identification—including two recent methods that also analyze linked-reads—on simulated sequencing data and 10X whole-genome sequencing data from the NA12878 human genome and the HCC1954 breast cancer cell line. Several of the novel somatic structural variants identified in HCC1954 overlap known cancer genes. Availability and implementation Software is available at compbio.cs.brown.edu/software . Contact braphael@princeton.edu Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation Cancers arise as the result of somatically acquired changes in the DNA of cancer cells. However, in addition to the mutations that confer a growth advantage, cancer genomes accumulate a large number of somatic mutations resulting from normal DNA damage and repair processes as well as carcinogenic exposures or cancer related aberrations of DNA maintenance machinery. These mutagenic processes often produce characteristic mutational patterns called mutational signatures. The decomposition of a cancer genome’s mutation catalog into mutations consistent with such signatures can provide valuable information about cancer etiology. However, the results from different decomposition methods are not always consistent. Hence, one needs to be able to not only decompose a patient’s mutational profile into signatures but also establish the accuracy of such decomposition. Results We proposed two complementary ways of measuring confidence and stability of decomposition results and applied them to analyze mutational signatures in breast cancer genomes. We identified both very stable and highly unstable signatures, as well as signatures that previously have not been associated with breast cancer. We also provided additional support for the novel signatures. Our results emphasize the importance of assessing the confidence and stability of inferred signature contributions. Availability and implementation All tools developed in this paper have been implemented in an R package, called SignatureEstimation, which is available from https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi\#signatureestimation . Contact wojtowda@ncbi.nlm.nih.gov or przytyck@ncbi.nlm.nih.gov Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation Brain imaging genetics, which studies the linkage between genetic variations and structural or functional measures of the human brain, has become increasingly important in recent years. Discovering the bi-multivariate relationship between genetic markers such as single-nucleotide polymorphisms (SNPs) and neuroimaging quantitative traits (QTs) is one major task in imaging genetics. Sparse Canonical Correlation Analysis (SCCA) has been a popular technique in this area for its powerful capability in identifying bi-multivariate relationships coupled with feature selection. The existing SCCA methods impose either the ℓ 1 -norm or its variants to induce sparsity. The ℓ 0 -norm penalty is a perfect sparsity-inducing tool which, however, is an NP-hard problem. Results In this paper, we propose the truncated ℓ 1 -norm penalized SCCA to improve the performance and effectiveness of the ℓ 1 -norm based SCCA methods. Besides, we propose an efficient optimization algorithms to solve this novel SCCA problem. The proposed method is an adaptive shrinkage method via tuning τ . It can avoid the time intensive parameter tuning if given a reasonable small τ . Furthermore, we extend it to the truncated group-lasso (TGL), and propose TGL-SCCA model to improve the group-lasso-based SCCA methods. The experimental results, compared with four benchmark methods, show that our SCCA methods identify better or similar correlation coefficients, and better canonical loading profiles than the competing methods. This demonstrates the effectiveness and efficiency of our methods in discovering interesting imaging genetic associations. Availability and implementation The Matlab code and sample data are freely available at http://www.iu.edu/∼shenlab/tools/tlpscca/ . Contact dulei@nwpu.edu.cn or shenli@iu.edu Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation Modelling with multiple servers that use different algorithms for docking results in more reliable predictions of interaction sites. However, the scoring and comparison of all models by an expert is time-consuming and is not feasible for large volumes of data generated by such modelling. Results Quality ASsessment of DOcking Models (QASDOM) Server is a simple and efficient tool for real-time simultaneous analysis, scoring and ranking of data sets of receptor–ligand complexes built by a range of docking techniques. This meta-server is designed to analyse large data sets of docking models and rank them by scoring criteria developed in this study. It produces two types of output showing the likelihood of specific residues and clusters of residues to be involved in receptor–ligand interactions and the ranking of models. The server also allows visualizing residues that form interaction sites in the receptor and ligand sequence and displays 3D model structures of the receptor–ligand complexes. Availability http://qasdom.eimb.ru . Contact alexei.adzhubei@eimb.ru. Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation Protein–protein interactions are vital for protein function with the average protein having between three and ten interacting partners. Knowledge of precise protein–protein interfaces comes from crystal structures deposited in the Protein Data Bank (PDB), but only 50% of structures in the PDB are complexes. There is therefore a need to predict protein–protein interfaces in silico and various methods for this purpose. Here we explore the use of a predictor based on structural features and which exploits random forest machine learning, comparing its performance with a number of popular established methods. Results On an independent test set of obligate and transient complexes, our IntPred predictor performs well (MCC = 0.370, ACC = 0.811, SPEC = 0.916, SENS = 0.411) and compares favourably with other methods. Overall, IntPred ranks second of six methods tested with SPPIDER having slightly better overall performance (MCC = 0.410, ACC = 0.759, SPEC = 0.783, SENS = 0.676), but considerably worse specificity than IntPred. As with SPPIDER, using an independent test set of obligate complexes enhanced performance (MCC = 0.381) while performance is somewhat reduced on a dataset of transient complexes (MCC = 0.303). The trade-off between sensitivity and specificity compared with SPPIDER suggests that the choice of the appropriate tool is application-dependent. Availability and implementation IntPred is implemented in Perl and may be downloaded for local use or run via a web server at www.bioinf.org.uk/intpred/ . Contact andrew@bioinf.org.uk or andrew.martin@ucl.ac.uk Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation Protein function is directly related to amino acid residue composition and the dynamics of these residues. Centrality analyses based on residue interaction networks permit to identify key residues in a protein that are important for its fold or function. Such central residues and their environment constitute suitable targets for mutagenesis experiments. Predicted flexibility and changes in flexibility upon mutation provide valuable additional information for the design of such experiments. Results We combined centrality analyses with DynaMine flexibility predictions in a Cytoscape app called RINspector. The app performs centrality analyses and directly visualizes the results on a graph of predicted residue flexibility. In addition, the effect of mutations on local flexibility can be calculated. Availability and implementation The app is publicly available in the Cytoscape app store. Contact guillaume.brysbaert@univ-lille1.fr Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Summary Fully exploiting the wealth of data in current bacterial population genomics datasets requires synthesizing and integrating different types of analysis across millions of base pairs in hundreds or thousands of isolates. Current approaches often use static representations of phylogenetic, epidemiological, statistical and evolutionary analysis results that are difficult to relate to one another. Phandango is an interactive application running in a web browser allowing fast exploration of large-scale population genomics datasets combining the output from multiple genomic analysis methods in an intuitive and interactive manner. Availability and implementation Phandango is a web application freely available for use at www.phandango.net and includes a diverse collection of datasets as examples. Source code together with a detailed wiki page is available on GitHub at https://github.com/jameshadfield/phandango . Contact jh22@sanger.ac.uk or sh16@sanger.ac.uk

Description: Summary MetExploreViz is an open source web component that can be easily embedded in any web site. It provides features dedicated to the visualization of metabolic networks and pathways and thus offers a flexible solution to analyse omics data in a biochemical context. Availability and implementation Documentation and link to GIT code repository (GPL 3.0 license) are available at this URL: http://metexplore.toulouse.inra.fr/metexploreViz/doc/ Contact contact-metexplore@inra.fr

Description: Motivation Single cell transcriptional profiling opens up a new avenue in studying the functional role of cell-to-cell variability in physiological processes. The analysis of single cell expression profiles creates new challenges due to the distributive nature of the data and the stochastic dynamics of gene transcription process. The reconstruction of gene regulatory networks (GRNs) using single cell transcriptional profiles is particularly challenging, especially when directed gene-gene relationships are desired. Results We developed SINCERITIES (SINgle CEll Regularized Inference using TIme-stamped Expression profileS) for the inference of GRNs from single cell transcriptional profiles. We focused on time-stamped cross-sectional expression data, commonly generated from transcriptional profiling of single cells collected at multiple time points after cell stimulation. SINCERITIES recovers directed regulatory relationships among genes by employing regularized linear regression (ridge regression), using temporal changes in the distributions of gene expressions. Meanwhile, the modes of the gene regulations (activation and repression) come from partial correlation analyses between pairs of genes. We demonstrated the efficacy of SINCERITIES in inferring GRNs using in silico time-stamped single cell expression data and single cell transcriptional profiles of THP-1 monocytic human leukemia cells. The case studies showed that SINCERITIES could provide accurate GRN predictions, significantly better than other GRN inference algorithms such as TSNI, GENIE3 and JUMP3. Moreover, SINCERITIES has a low computational complexity and is amenable to problems of extremely large dimensionality. Finally, an application of SINCERITIES to single cell expression data of T2EC chicken erythrocytes pointed to BATF as a candidate novel regulator of erythroid development. Availability and implementation MATLAB and R version of SINCERITIES are freely available from the following websites: http://www.cabsel.ethz.ch/tools/sincerities.html and https://github.com/CABSEL/SINCERITIES . The single cell THP-1 and T2EC transcriptional profiles are available from the original publications ( Kouno et al. , 2013 ; Richard et al. , 2016 ). The in silico single cell data are available on SINCERITIES websites. Contact rudi.gunawan@chem.ethz.ch Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Summary Addressing deleterious effects of noncoding mutations is an essential step towards the identification of disease-causal mutations of gene regulatory elements. Several methods for quantifying the deleteriousness of noncoding mutations using artificial intelligence, deep learning and other approaches have been recently proposed. Although the majority of the proposed methods have demonstrated excellent accuracy on different test sets, there is rarely a consensus. In addition, advanced statistical and artificial learning approaches used by these methods make it difficult porting these methods outside of the labs that have developed them. To address these challenges and to transform the methodological advances in predicting deleterious noncoding mutations into a practical resource available for the broader functional genomics and population genetics communities, we developed SNPDelScore, which uses a panel of proposed methods for quantifying deleterious effects of noncoding mutations to precompute and compare the deleteriousness scores of all common SNPs in the human genome in 44 cell lines. The panel of deleteriousness scores of a SNP computed using different methods is supplemented by functional information from the GWAS Catalog, libraries of transcription factor-binding sites, and genic characteristics of mutations. SNPDelScore comes with a genome browser capable of displaying and comparing large sets of SNPs in a genomic locus and rapidly identifying consensus SNPs with the highest deleteriousness scores making those prime candidates for phenotype-causal polymorphisms. Availability and implementation https://www.ncbi.nlm.nih.gov/research/snpdelscore/ Contact ovcharen@nih.gov Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation The selection of a single nucleotide polymorphism (SNP) using bibliographic methods can be a very time-consuming task. Moreover, a SNP selected in this way may not be easily visualized in its genomic context by a standard user hoping to correlate it with other valuable information. Here we propose a web form built on top of Circos that can assist SNP-centered screening, based on their location in the genome and the regulatory modules they can disrupt. Its use may allow researchers to prioritize SNPs in genotyping and disease studies. Results SiNoPsis is bundled as a web portal. It focuses on the different structures involved in the genomic expression of a gene, especially those found in the core promoter upstream region. These structures include transcription factor binding sites (for promoter and enhancer signals), histones and promoter flanking regions. Additionally, the tool provides eQTL and linkage disequilibrium (LD) properties for a given SNP query, yielding further clues about other indirectly associated SNPs. Possible disruptions of the aforementioned structures affecting gene transcription are reported using multiple resource databases. SiNoPsis has a simple user-friendly interface, which allows single queries by gene symbol, genomic coordinates, Ensembl gene identifiers, RefSeq transcript identifiers and SNPs. It is the only portal providing useful SNP selection based on regulatory modules and LD with functional variants in both textual and graphic modes (by properly defining the arguments and parameters needed to run Circos). Availability and implementation SiNoPsis is freely available at https://compgen.bio.ub.edu/SiNoPsis/ Contact danielboloc@gmail.com Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation Inter-residue contacts in proteins have been widely acknowledged to be valuable for protein 3 D structure prediction. Accurate prediction of long-range transmembrane inter-helix residue contacts can significantly improve the quality of simulated membrane protein models. Results In this paper, we present an updated MemBrain predictor, which aims to predict transmembrane protein residue contacts. Our new model benefits from an efficient learning algorithm that can mine latent structural features, which exist in original feature space. The new MemBrain is a two-stage inter-helix contact predictor. The first stage takes sequence-based features as inputs and outputs coarse contact probabilities for each residue pair, which will be further fed into convolutional neural network together with predictions from three direct-coupling analysis approaches in the second stage. Experimental results on the training dataset show that our method achieves an average accuracy of 81.6% for the top L /5 predictions using a strict sequence-based jackknife cross-validation. Evaluated on the test dataset, MemBrain can achieve 79.4% prediction accuracy. Moreover, for the top L /5 predicted long-range loop contacts, the prediction performance can reach an accuracy of 56.4%. These results demonstrate that the new MemBrain is promising for transmembrane protein’s contact map prediction. Availability and implementation http://www.csbio.sjtu.edu.cn/bioinf/MemBrain/ Contact hbshen@sjtu.edu.cn Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation We recently published MS2LDA, a method for the decomposition of sets of molecular fragment data derived from large metabolomics experiments. To make the method more widely available to the community, here we present ms2lda.org, a web application that allows users to upload their data, run MS2LDA analyses and explore the results through interactive visualizations. Results Ms2lda.org takes tandem mass spectrometry data in many standard formats and allows the user to infer the sets of fragment and neutral loss features that co-occur together (Mass2Motifs). As an alternative workflow, the user can also decompose a data set onto predefined Mass2Motifs. This is accomplished through the web interface or programmatically from our web service. Availability and implementation The website can be found at http://ms2lda.org , while the source code is available at https://github.com/sdrogers/ms2ldaviz under the MIT license. Contact simon.rogers@glasgow.ac.uk Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation Linkage and quantitative trait loci (QTL) maps are critical tools for the study of the genetic basis of complex traits. With the advances in sequencing technology over the past decade, linkage map densities have been increasing dramatically, while the visualization tools have not kept pace. LinkageMapView is a free add-on package written in R that produces high resolution, publication-ready visualizations of linkage and QTL maps. While there is software available to generate linkage map graphics, none are freely available, produce publication quality figures, are open source and can run on all platforms. LinkageMapView can be integrated into map building pipelines as it seamlessly incorporates output from R/qtl and also accepts simple text or comma delimited files. There are numerous options within the package to build highly customizable maps, allow for linkage group comparisons, and annotate QTL regions. Availability and implementation https://cran.r-project.org/web/packages/LinkageMapView/ Contact louellet@uncc.edu

Description: Motivation Rapid and low cost sequencing of genomes enabled widespread use of genomic data in research studies and personalized customer applications, where genomic data is shared in public databases. Although the identities of the participants are anonymized in these databases, sensitive information about individuals can still be inferred. One such information is kinship. Results We define two routes kinship privacy can leak and propose a technique to protect kinship privacy against these risks while maximizing the utility of shared data. The method involves systematic identification of minimal portions of genomic data to mask as new participants are added to the database. Choosing the proper positions to hide is cast as an optimization problem in which the number of positions to mask is minimized subject to privacy constraints that ensure the familial relationships are not revealed. We evaluate the proposed technique on real genomic data. Results indicate that concurrent sharing of data pertaining to a parent and an offspring results in high risks of kinship privacy, whereas the sharing data from further relatives together is often safer. We also show arrival order of family members have a high impact on the level of privacy risks and on the utility of sharing data. Availability and implementation https://github.com/tastanlab/Kinship-Privacy Contact erman@cs.bilkent.edu.tr or oznur.tastan@cs.bilkent.edu.tr Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Summary Precision oncology is an approach that accounts for individual differences to guide cancer management. Omics signatures have been shown to predict clinical traits for cancer patients. However, the vast amount of omics information poses an informatics challenge in systematically identifying patterns associated with health outcomes, and no general purpose data mining tool exists for physicians, medical researchers and citizen scientists without significant training in programming and bioinformatics. To bridge this gap, we built the Omics AnalySIs System for PRecision Oncology (OASISPRO), a web-based system to mine the quantitative omics information from The Cancer Genome Atlas (TCGA). This system effectively visualizes patients’ clinical profiles, executes machine-learning algorithms of choice on the omics data and evaluates the prediction performance using held-out test sets. With this tool, we successfully identified genes strongly associated with tumor stage, and accurately predicted patients’ survival outcomes in many cancer types, including adrenocortical carcinoma. By identifying the links between omics and clinical phenotypes, this system will facilitate omics studies on precision cancer medicine and contribute to establishing personalized cancer treatment plans. Availability and implementation This web-based tool is available at http://tinyurl.com/oasispro ; source codes are available at http://tinyurl.com/oasisproSourceCode . Contact khyu@stanford.edu or mpsnyder@stanford.edu Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Summary Analysis of RNA sequencing (RNA-Seq) data have highlighted the fact that most genes undergo alternative splicing (AS) and that these patterns are tightly regulated. Many of these events are complex, resulting in numerous possible isoforms that quickly become difficult to visualize, interpret and experimentally validate. To address these challenges we developed MAJIQ-SPEL, a web-tool that takes as input local splicing variations (LSVs) quantified from RNA-Seq data and provides users with visualization and quantification of gene isoforms associated with those. Importantly, MAJIQ-SPEL is able to handle both classical (binary) and complex, non-binary, splicing variations. Using a matching primer design algorithm it also suggests to users possible primers for experimental validation by RT-PCR and displays those, along with the matching protein domains affected by the LSV, on UCSC Genome Browser for further downstream analysis. Availability and implementation Program and code will be available at http://majiq.biociphers.org/majiq-spel . Contact yosephb@upenn.edu Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation Accurate molecular structure of the protein dimer representing the elementary building block of intermediate filaments (IFs) is essential towards the understanding of the filament assembly, rationalizing their mechanical properties and explaining the effect of disease-related IF mutations. The dimer contains a ∼300-residue long α-helical coiled coil which cannot be assessed by either direct experimental structure determination or modelling using standard approaches. At the same time, coiled coils are well-represented in structural databases. Results Here we present CCFold, a generally applicable threading-based algorithm which produces coiled-coil models from protein sequence only. The algorithm is based on a statistical analysis of experimentally determined structures and can handle any hydrophobic repeat patterns in addition to the most common heptads. We demonstrate that CCFold outperforms general-purpose computational folding in terms of accuracy, while being faster by orders of magnitude. By combining the CCFold algorithm and Rosetta folding we generate representative dimer models for all IF protein classes. Availability and implementation The source code is freely available at https://github.com/biocryst/IF ; a web server to run the program is at http://pharm.kuleuven.be/Biocrystallography/cc . Contact sergei.strelkov@kuleuven.be Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation Cells process information, in part, through transcription factor (TF) networks, which control the rates at which individual genes produce their products. A TF network map is a graph that indicates which TFs bind and directly regulate each gene. Previous work has described network mapping algorithms that rely exclusively on gene expression data and ‘integrative’ algorithms that exploit a wide range of data sources including chromatin immunoprecipitation sequencing (ChIP-seq) of many TFs, genome-wide chromatin marks, and binding specificities for many TFs determined in vitro . However, such resources are available only for a few major model systems and cannot be easily replicated for new organisms or cell types. Results We present NetProphet 2.0, a ‘data light’ algorithm for TF network mapping, and show that it is more accurate at identifying direct targets of TFs than other, similarly data light algorithms. In particular, it improves on the accuracy of NetProphet 1.0, which used only gene expression data, by exploiting three principles. First, combining multiple approaches to network mapping from expression data can improve accuracy relative to the constituent approaches. Second, TFs with similar DNA binding domains bind similar sets of target genes. Third, even a noisy, preliminary network map can be used to infer DNA binding specificities from promoter sequences and these inferred specificities can be used to further improve the accuracy of the network map. Availability and implementation Source code and comprehensive documentation are freely available at https://github.com/yiming-kang/NetProphet_2.0 . Contact brent@wustl.edu Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation To increase detection power, researchers use gene level analysis methods to aggregate weak marker signals. Due to gene expression controlling biological processes, researchers proposed aggregating signals for expression Quantitative Trait Loci (eQTL). Most gene-level eQTL methods make statistical inferences based on (i) summary statistics from genome-wide association studies (GWAS) and (ii) linkage disequilibrium patterns from a relevant reference panel. While most such tools assume homogeneous cohorts, our G ene-level J oint A nalysis of functional SNPs in C osmopolitan C ohorts (JEPEGMIX) method accommodates cosmopolitan cohorts by using heterogeneous panels. However, JEPGMIX relies on brain eQTLs from older gene expression studies and does not adjust for background enrichment in GWAS signals. Results We propose JEPEGMIX2, an extension of JEPEGMIX. When compared to JPEGMIX, it uses (i) cis-eQTL SNPs from the latest expression studies and (ii) brains specific (sub)tissues and tissues other than brain. JEPEGMIX2 also (i) avoids accumulating averagely enriched polygenic information by adjusting for background enrichment and (ii) to avoid an increase in false positive rates for studies with numerous highly enriched (above the background) genes, it outputs gene q -values based on Holm adjustment of P -values. Availability and implementation https://github.com/Chatzinakos/JEPEGMIX2 . Contact chris.chatzinakos@vcuhealth.org Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation Identification of disease-associated miRNAs (disease miRNAs) is critical for understanding disease etiology and pathogenesis. Since miRNAs exert their functions by regulating the expression of their target mRNAs, several methods based on the target genes were proposed to predict disease miRNA candidates. They achieved only limited success as they all suffered from the high false-positive rate of target prediction results. Alternatively, other prediction methods were based on the observation that miRNAs with similar functions tend to be associated with similar diseases and vice versa. The methods exploited the information about miRNAs and diseases, including the functional similarities between miRNAs, the similarities between diseases, and the associations between miRNAs and diseases. However, how to integrate the multiple kinds of information completely and consider the biological characteristic of disease miRNAs is a challenging problem. Results We constructed a bilayer network to represent the complex relationships among miRNAs, among diseases and between miRNAs and diseases. We proposed a non-negative matrix factorization based method to rank, so as to predict, the disease miRNA candidates. The method integrated the miRNA functional similarity, the disease similarity and the miRNA-disease associations seamlessly, which exploited the complex relationships within the bilayer network and the consensus relationship between multiple kinds of information. Considering the correlation between the candidates related to various diseases, it predicted their respective candidates for all the diseases simultaneously. In addition, the sparseness characteristic of disease miRNAs was introduced to generate more reliable prediction model that excludes those noisy candidates. The results on 15 common diseases showed a superior performance of the new method for not only well-characterized diseases but also new ones. A detailed case study on breast neoplasms, colorectal neoplasms, lung neoplasms and 32 other diseases demonstrated the ability of the method for discovering potential disease miRNAs. Availability and implementation The web service for the new method and the list of predicted candidates for all the diseases are available at http://www.bioinfolab.top . Contact xuanping@hlju.edu.cn or zhang@hlju.edu.cn or lijzh@hit.edu.cn Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Summary The Quest for Orthologs (QfO) is an open collaboration framework for experts in comparative phylogenomics and related research areas who have an interest in highly accurate orthology predictions and their applications. We here report highlights and discussion points from the QfO meeting 2015 held in Barcelona. Achievements in recent years have established a basis to support developments for improved orthology prediction and to explore new approaches. Central to the QfO effort is proper benchmarking of methods and services, as well as design of standardized datasets and standardized formats to allow sharing and comparison of results. Simultaneously, analysis pipelines have been improved, evaluated and adapted to handle large datasets. All this would not have occurred without the long-term collaboration of Consortium members. Meeting regularly to review and coordinate complementary activities from a broad spectrum of innovative researchers clearly benefits the community. Highlights of the meeting include addressing sources of and legitimacy of disagreements between orthology calls, the context dependency of orthology definitions, special challenges encountered when analyzing very anciently rooted orthologies, orthology in the light of whole-genome duplications, and the concept of orthologous versus paralogous relationships at different levels, including domain-level orthology. Furthermore, particular needs for different applications (e.g. plant genomics, ancient gene families and others) and the infrastructure for making orthology inferences available (e.g. interfaces with model organism databases) were discussed, with several ongoing efforts that are expected to be reported on during the upcoming 2017 QfO meeting. Contact selewis@lbl.gov or c.dessimoz@ucl.ac.uk

Description: Motivation In recent years, the massively parallel cDNA sequencing (RNA-Seq) technologies have become a powerful tool to provide high resolution measurement of expression and high sensitivity in detecting low abundance transcripts. However, RNA-seq data requires a huge amount of computational efforts. The very fundamental and critical step is to align each sequence fragment against the reference genome. Various de novo spliced RNA aligners have been developed in recent years. Though these aligners can handle spliced alignment and detect splice junctions, some challenges still remain to be solved. With the advances in sequencing technologies and the ongoing collection of sequencing data in the ENCODE project, more efficient alignment algorithms are highly demanded. Most read mappers follow the conventional seed-and-extend strategy to deal with inexact matches for sequence alignment. However, the extension is much more time consuming than the seeding step. Results We proposed a novel RNA-seq de novo mapping algorithm, call DART, which adopts a partitioning strategy to avoid the extension step. The experiment results on synthetic datasets and real NGS datasets showed that DART is a highly efficient aligner that yields the highest or comparable sensitivity and accuracy compared to most state-of-the-art aligners, and more importantly, it spends the least amount of time among the selected aligners. Availability and implementation https://github.com/hsinnan75/DART Contact hsu@iis.sinica.edu.tw Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Provides an overview of the technical articles and features presented in this issue.

Description: Presents the front cover for this issue of the publication.

Description: Six senior computer science educators answer questions about the current state of computer science education, software engineering, and licensing software engineers.

Description: Provides a listing of current staff, committee members and society officers.

Description: The Internet of Things is a new department with the mission of presenting fresh ideas and applications from a practitioner point of view. The authors are interested in showcasing articles about real, implemented Internet of Things (IoT) systems.

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Description: The Industrial Internet of Things is growing fast. But the rapid growth of IIoT devices raises a number of security concerns, because the IIoT device is weak in defending against malware, and the method of managing a large number of IIoT devices is awkward and inconvenient. This article proposes a multi-level DDoS mitigation framework (MLDMF) to defend against DDoS attacks for IIoT, which includes the edge computing level, fog computing level, and cloud computing level. Software defined networking is used to manage a large number of IIoT devices and to mitigate DDoS attacks in IIoT. Experimental results show the effectiveness of the proposed framework.

Description: Commemorating the 20th anniversary of IT Professional, the advisory board chair and four past editors in chief reflect on the first two decades of the magazine.

Description: In a case study where a Dutch small-to-medium enterprise (SME) implemented test-driven development and continuous integration, researchers observed that the SME discovered a higher number of defects compared to a baseline case study, and that there was an increase in the focus on quality and test applications.

Description: By providing access to data from numerous systems in one database and supporting the systems that can produce an appropriate customer experience, a customer data platform overcomes the limitations imposed by fragmented point solutions and presents a holistic approach to customer interactions.

Description: An introduction to the new Life in the C-Suite column, which will help C-level executives understand the vast digital world in which they live, and how they should leverage digital technology into their business processes and business models.

Description: Student Forum is a new column that intends to connect IT students with industry, government, and academia.

Description: The new IT Economics department seeks to advance the understanding of various microeconomic and macroeconomic issues that IT managers need to examine in their decisions to adopt and implement information and communications technology-related systems, services, processes, and practices.

Description: Provides a listing of current committee members and society officers.

Description: Prospective authors are requested to submit new, unpublished manuscripts for inclusion in the upcoming event described in this call for papers.

Description: The efficient integration of optical switching in data center networks is being studied as a means to cope with surging traffic demands. Optically switched, flatter network architectures more efficiently handle the east-west traffic profiles of modern data centers. Limitations in the port count and reconfiguration speed of optical switches require novel network designs offering network scalability and dynamicity. Interaction of the optically switched data plane with a software-defined control and orchestration framework, meeting current common practices in data centers, necessitates the design of custom network control algorithms and software modules as well as the integration of novel functionalities. The approach of the European project NEPHELE is presented, offering an endto- end solution that addresses the optical data plane, the control plane, and its interaction with the application layer.

Description: The comprehensive evolution of information communication technologies on mobile sensing objects has led to the provision of versatile ubiquitous network services embedded with specific- purpose modern sensors and intelligent wearable devices. The universal Internet connectivity of such smart objects has brought about a new era of ubiquitous application development for the Internet of Things. Meanwhile, security has become critically important. In the past decade, academia and industry have dedicated great efforts to the design of continuous authentication for multi-modal networks. Multiform authentication bio-tokens have been introduced for continuous entity identification and verification. With the rapid growth and universality of wearable devices, in this article we target continuous authentication for the IoT-based environment with users possessing wearable healthcare (and wellness) related smart objects. To present the state of the art, we provide a comprehensive review of continuous authentication in recent years. Critical characteristics of new biometrics are then introduced. Second, we present a wearable plantar bio-feature extractor constructed via commercial pressure sensors and the Raspberry PI platform. The prototype is adopted to retrieve user plantar bio-data as the raw (and training) data in the proposed authentication system. Third, we apply machinelearning- based techniques to derive a user's plantar bio-features as authentication tokens in the system to support continual (and real-time) entity verification in the background without the user's notice.

Description: In IoT-based healthcare, medical devices are more vulnerable to numerous security threats and attacks than other network devices. Current solutions are able to provide protection to patients' data during data transmission to some extent, but cannot prevent some sophisticated threats and attacks such as collusion attacks and data leakage. In this article, we first investigate the challenges with privacy protected data collection. Then we propose a practical framework called PrivacyProtector, patient privacy protected data collection, with the objective of preventing these types of attacks. PrivacyProtector includes the ideas of secret sharing and share repairing (in case of data loss or compromise) for patients' data privacy. Since it is the first time, we apply the Slepian- Wolf-coding-based secret sharing (SW-SSS) in PrivacyProtector. In the framework, we use a distributed database consisting of multiple cloud servers, which ensures that the privacy of patients' personal data can remain protected as long as one of the servers remains uncompromised. We also present a patient access control scheme in which multiple cloud servers collaborate in shared construction to offer patients' data to healthcare providers without revealing the content of the data. The privacy performance analysis has shown that the PrivacyProtector framework is secure and privacy-protected against various attacks.

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Description: Widespread use of white light-emitting diodes and ubiquitous smart devices offer the opportunity to establish VLC, which has become a hot research topic based on the growing number of publications over the last decade. Camera-based VLC, namely OCC, provides many unique features when compared to a single-photodiode-based system, such as the ability to separate incident light in the spatial and color domains. OCC technology represents a promising approach to utilize the benefits of VLC in beyond-5G scenarios and is one of the key technologies of the Internet of Things. Establishing a long communication channel in OCC, as well as non-flickering illumination by using low-frame-rate camera detectors, requires special modulation schemes. This article provides an overview of the principles of three categories of modulation schemes for OCC systems using a low-frame-rate camera detector. In addition, a series of undersampled modulation schemes are proposed and discussed to achieve flicker-free OCC with higher spectral efficiency. In addition, framing structures are designed to solve problems occurring in OCC systems using particular modulation schemes. To evaluate the performance of these modulation schemes, measured bit error rate values are shown. Finally, challenges in the implementation of OCC systems are also outlined.

Description: This tutorial article presents an outline of image sensor communication (ISC) technologies realized by light sources and cameras. It discusses the revision of the IEEE 802.15.7-2011 standard, namely, the IEEE 802.15.7m Optical Wireless Communications Task Group, which has significantly influenced the development of the ISC technology. It also reviews the ISC technical proposals of the task group and compares them with related works. The essential technical considerations of the ISC specifications are presented, and the future directions of research and development are discussed.

Description: The limited modulation bandwidth of commercial light-emitting diodes (LEDs) is one of the critical bottlenecks for visible light communications. Possible approaches to increase the bandwidth include the use of micron sized LEDs, which can withstand higher current densities, as well as the use of LED structures that are grown on different crystal planes to the conventional polar c-plane. We compare c-plane InGaN/GaN LEDs with semipolar ( $11overline {2}2$ ) LEDs containing a 4- and 8-nm single quantum well. The modulation bandwidth of semipolar LEDs with active areas varying from $200times 200$ to $30times 30,,mu text{m}^{2}$ is shown to be governed by both current density and size. A small signal bandwidth of over 800 MHz for a relatively low applied current density of 385 A/cm 2 is reported for $30times 30 ,,mu text{m}^{2}$ LEDs with 8-nm thick quantum well. An optical link using an easy non-return-to-zero ON–OFF keying modulation scheme with a data rate of 1.5 Gb/s is demonstrated.

Description: A compact optical fiber sensor based on a Fabry–Perot interferometer (FPI) with an integrated fiber Bragg grating is proposed to measure pressure and temperature simultaneously. The light reflectors of the proposed FPI comprise a graphene film and a fiber end face. The sensitivities of the FPI sensor for measuring pressure and temperature are 501.4 nm/kPa and 306.2 nm/°C, respectively. Conflicting signals of pressure and temperature can cause cross-impact errors at 610 Pa/°C. The introduction of a fiber Bragg grating can effectively prevent the cross-impact of the FPI sensor. The pressure sensitivity obtained is 7.96 to 12 times higher than the previous study. The proposed fiber sensor can simultaneously measure pressure and temperature using a sensitivity matrix.

Description: Summary Gene expression alterations and potentially underlying gene copy number mutations can be measured routinely in the wet lab, but it is still extremely challenging to quantify impacts of altered genes on clinically relevant characteristics to predict putative driver genes. We developed the R package regNet that utilizes gene expression and copy number data to learn regulatory networks for the quantification of potential impacts of individual gene expression alterations on user-defined target genes via network propagation. We demonstrate the value of regNet by identifying putative major regulators that distinguish pilocytic from diffuse astrocytomas and by predicting putative impacts of glioblastoma-specific gene copy number alterations on cell cycle pathway genes and patient survival. Availability and implementation regNet is available for download at https://github.com/seifemi/regNet under GNU GPL-3 . Contact michael.seifert@tu-dresden.de Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation MicroRNAs (miRNAs) play crucial roles in post-transcriptional regulations and various cellular processes. The identification of disease-related miRNAs provides great insights into the underlying pathogenesis of diseases at a system level. However, most existing computational approaches are biased towards known miRNA-disease associations, which is inappropriate for those new diseases or miRNAs without any known association information. Results In this study, we propose a new method with graph regularized non-negative matrix factorization in heterogeneous omics data, called GRNMF, to discover potential associations between miRNAs and diseases, especially for new diseases and miRNAs or those diseases and miRNAs with sparse known associations. First, we integrate the disease semantic information and miRNA functional information to estimate disease similarity and miRNA similarity, respectively. Considering that there is no available interaction observed for new diseases or miRNAs, a preprocessing step is developed to construct the interaction score profiles that will assist in prediction. Next, a graph regularized non-negative matrix factorization framework is utilized to simultaneously identify potential associations for all diseases. The results indicated that our proposed method can effectively prioritize disease-associated miRNAs with higher accuracy compared with other recent approaches. Moreover, case studies also demonstrated the effectiveness of GRNMF to infer unknown miRNA-disease associations for those novel diseases and miRNAs. Availability and implementation The code of GRNMF is freely available at https://github.com/XIAO-HN/GRNMF/ . Contact luojiawei@hnu.edu.cn Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Throughout the past few decades, the separable discrete cosine transform (DCT), particularly the DCT type II, has been widely used in image and video compression. It is well-known that, under first-order stationary Markov conditions, DCT is an efficient approximation of the optimal Karhunen–Loève transform. However, for natural image and video sources, the adaptivity of a single separable transform with fixed core is rather limited for the highly dynamic image statistics, e.g., textures and arbitrarily directed edges. It is also known that non-separable transforms can achieve better compression efficiency for images with directional texture patterns, yet they are computationally complex, especially when the transform size is large. In order to achieve higher transform coding gains with relatively low-complexity implementations, we propose a joint separable and non-separable transform. The proposed separable primary transform, named enhanced multiple transform (EMT), applies multiple transform cores from a pre-defined subset of sinusoidal transforms, and the transform selection is signaled in a joint block level manner. Moreover, a non-separable secondary transform (NSST) method is proposed to operate in conjunction with EMT. Unlike the existing non-separable transform schemes which require excessive amounts of memory and computation, the proposed NSST efficiently improves coding gain with much lower complexity. Extensive experimental results show that the proposed methods, in a state-of-the-art video codec, such as high efficiency video coding, can provide significant coding gains (average 6.9% and 4.5% bitrate reductions for intra and random-access coding, respectively).

Description: This paper presents a compact planar tunable quadrature coupler with improved phase responses. Wide coupling-tuning ratio is achieved by using two varactors loaded on the center of the transmission lines of the modified coupler. Closed-form equations are derived for design parameters. For verification, a 1-GHz tunable coupler is designed and measured. The measured results agree well with the simulated ones. The measured power-dividing ratio can be tuned in a range from 16.2 to −35 dB (from 42 to 3.2E-4) with better than 20-dB return loss and isolation, while the phase imbalance is smaller than 10°. The coupler size is $0.21lambda text{g},,times ,,0.08lambda text{g}$ and reduced by 73.1% compared with the conventional branch-line coupler. The theoretical analysis shows that the phase imbalance and insertion loss are mostly caused by the loss from varactors. Then, a tunable coupler with improved phase and loss responses is proposed, where the additional phase difference and insertion loss resulting from the varactors are compensated for by introducing a negative resistance from the negative impedance converter. Measured results of a demonstrative 1-GHz coupler show a power-dividing ratio tuning range from 24.4 to −22.2 dB (from 275.4 to 6E-4) while maintaining 20-dB return loss and isolation. The phase imbalance is smaller than 1° and the insertion loss is improved by 1 dB and nearly close to theoretical values across the tuning range.

Description: This paper presents a new kind of highly flexible frequency-agile bandpass filters (FA-BPFs) based on the novel synchronously tuned dual-mode resonator (STDR). The bandwidth (BW), BW variation tendency, passband selectivity (stopband rejection level), and frequency tuning range of the filter can be predefined individually. Benefiting from the unique characteristics of the STDR, the FA-BPF with very simple and highly flexible design/control procedures is achieved. Due to the proposed geometry, two self-adaptive transmission zeros are introduced and move with the passband. The predefined mechanism is investigated in detail, and the simple design and predefined procedures are summarized. Then, three 0.75–1.7 GHz single-band examples with elliptic response are developed to achieve three predefined absolute BWs (ABW). The design techniques and filter superiority are confirmed by the experiments. Moreover, aiming at China 2G/3G/4G cellular wireless/mobile communication system (up to band 40:0.825–2.65 GHz), a novel intrinsically switchable single-/dual-band FA-BPF is presented based on the proposed STDR. An example with a constant ABW 1 dB and a fractional bandwidth 1 dB (FBW 1 dB is designed to validate the theory and analysis. The FA-BPF is able to operate as a highly selective dual-band FA-BPF with 0.76–1.78 GHz/1.61–2.63 GHz tuning ranges, and also can be switched to single-band operation with the continuous tuning range of 0.76–2.63 GHz.

Description: For the first time, the 6-port quadrature and rat-race couplers with balanced–unbalanced-hybrid ports are proposed. The corresponding design methodology is presented, which is capable of designing the proposed couplers with arbitrary power divisions and terminated resistances. In this paper, four types including quadrature and rat-race couplers are fully analyzed, covering all the application configurations of the balanced/unbalanced ports. Besides, the design equations are rigorously derived, with the final design procedures presented. Eventually, prototypes of the four coupler types are fabricated and experimentally measured. The final results sufficiently validate the proposed methodology.

Description: This paper presents the design and characterization of a load modulated balanced amplifier for telecom base station applications adopting a novel mode of operation. The theory of operation is described explaining the main differences compared to Doherty amplifiers, in particular the RF bandwidth advantages and, on the other hand, the intrinsic nonlinear behavior. The specific design strategy that adopts prematching for back-off broadband matching is explained in detail. A prototype, based on 25-W GaN packaged devices, has been fabricated and measured with single tone CW and modulated signal stimulus. For CW conditions, on the 1.7–2.5-GHz band, the peak output power is between 63 and 78 W, with power added efficiency higher than 48%, 43%, and 39% at saturation, 6- and 8-dB output power back-off, respectively. With a modulated signal for Long Term Evolution the amplifier provides an average output power of around 10 W, with efficiency higher than 40%, and can be linearized by adopting a low complexity predistorter. If compared to previously published power amplifiers targeting similar power and bandwidth, the measurement shows very good performance, demonstrating the potential of this novel technique in the field of efficiency enhanced transmitters.

Description: A new type of K-band high-Q frequency-tunable waveguide filters is proposed in this paper. The presented filter structure adopts a new technique for tuning the resonant frequency of each resonator. A dielectric plate is inserted in each resonator and rotating it leads to the frequency tuning. Unlike the conventional frequency tuning methodologies for tunable waveguide cavity filters, the new frequency tuning technique alleviates the electrical grounding issue for tuning devices. In addition, we demonstrate a new design method that allows the filter to have an absolute constant bandwidth in the frequency tuning range without using tunable coupling structures.

Description: This paper reports on a broadband high-power amplifier (HPA) millimeter-wave integrated circuit (MMIC) covering the extended W-band (65–125 GHz). The MMIC is based on the Fraunhofer IAF 50-nm gate-length metamorphic high-electron-mobility transistor (mHEMT) technology. The HPA consists of two parallelized unit amplifiers. Each unit amplifier (UA) utilizes four stacked-HEMT unit power cells (UPCs) and four-way power combiners at the input and output. The UPCs stack four transistors with a gate width of $4times 40~mu text{m}$ per HEMT. The UA achieves an average small-signal gain of 19.4 dB and an average saturated output power of 21.6 dBm at least from 70 to 110 GHz. The HPA yields an average small-signal gain of 16.8 dB and an average saturated output power of 22.5 dBm at least from 68 to 110 GHz. A peak output power of 24.1 dBm is achieved at an operating frequency of 75 GHz.

Description: The general coupling matrix representation of bandpass filter (BPF) circuits is a widely used technique that has simplified the analysis and optimization of complex microwave filters. In this paper, we demonstrate a novel application of the general coupling matrix for modeling wireless power-transfer (WPT) systems based on the BPF model of magnetically coupled resonators. Compared to other methods of WPT analysis, our model simplifies accommodation of complex loads and provides direct expressions for impedance matching (IM) in WPT systems. Using this tool, we achieve optimal IM for two resonator systems with a complex load, thus achieving the greatest possible power-transfer efficiency (PTE). Furthermore, our model reveals additional design constraints for optimizing PTE in coupled resonator systems exhibiting low quality factor and small interresonator coupling. Overall, this paper introduces a new, versatile framework for the analysis and optimization of coupled resonator WPT systems. Experimental results are presented, verifying the optimal IM design process.

Description: In this paper, we present a new architecture for implementation of millimeter-wave (mm-wave) and terahertz (THz) radiator arrays based on standing-wave properties. This structure is a continuous distributed coherent array that avoids lossy and parasitic coupling networks. Moreover, it can be scaled simply by extending the size of the structure and replicating the unit cell. The absence of coupling parasitics in addition to the unique characteristics of standing waves allows us to extend the tuning range without using varactors. The 0.34-THz four-element radiator array is designed and fabricated in a 130-nm SiGe BiCMOS process using microstrip transmission lines as the standing-wave mediums and on-chip patch antennas to radiate the desired fourth harmonic of the oscillation. The circuit was measured with no post processing or silicon lens and has 5.9% frequency tuning range (332.5–352.8 GHz) with less than 6-dB output power variation across the band. It consumes 425-mW power from 1.8-V supply and the radiated power is −10.5 dBm at center frequency with −98.2 dBc/Hz phase noise at 10-MHz offset frequency.

Description: This paper presents an extension of synthetic aperture radar (SAR) techniques to enable simultaneous radar imaging, sensor tag localization, and backscatter-based data uplink from multiple sensor tags in a cluttered environment. A unified system model is presented that leverages coherent processing of backscattered signals gathered over the synthetic aperture for all three of these purposes. The proposed approach, using balanced orthogonal codes for SAR-based localization as well as the backscatter data uplink, is shown to have several favorable properties, including straightforward tag-vs-clutter discrimination, straightforward multiple access among tags, and improved signal-to-noise ratio during localization. A proof-of-principle indoor experiment is presented in the X-band (10–13 GHz) using two custom-designed backscatter tags interrogated by a vector network analyzer functioning as an FMCW radar. The proposed system model is validated by simultaneous imaging of a cluttered scene, tag localization with a maximum range error of 9 mm, and data demodulation from both tags telemetering temperature changes at a rate of 1 bit/s at ranges of 4.4 m and 4.7 m. The resulting point-spread functions of tags demonstrate a range resolution of 4.7 cm and a cross-range resolution of 9.1 cm.

Description: A two-stage, high-power symmetric Doherty power amplifier (PA) at 15 GHz is presented. The PA is implemented in 45 nm CMOS silicon on insulator and achieves more than 23 dB power gain with 25.7 dBm saturated output power and 31% peak power added efficiency (PAE). The 6 dB back-off PAE is 25%, which is a 64% improvement compared to ideal class B PA back-off performance. High output power is obtained by employing four-stack multigate devices at the output stage; driver stages employ two-stack devices. A simple analog predistortion linearizer is proposed that effectively corrects the AM–AM response of the Doherty PA and extends the P1dB from 23 to 25.1 dBm. The PA also exhibits excellent AM–PM response. The amplifier has compact dimensions and occupies only 1 mm 2 chip area, including pads.

Description: In this paper, a novel design theory of two-section two-resistor Wilkinson power divider (WPD) is introduced. By selecting two different physical lengths of two-section transmission lines (TLs), two arbitrary frequency band WPD can be achieved. Compared with the former work, the designable frequency ratio range $u$ can be extremely extended from $1 〈 u 〈 3$ to $1 〈 u 〈 infty$ , general design equations for characteristic impedances, physical lengths, absorption resistors, and frequency ratio ranges are newly derived and proved from even- and odd-mode analysis. Because of no capacitors or inductors, the proposed WPD can be used for high-frequency applications. Spurious band of $S_{21}$ appears between two passbands under the condition of two different physical lengths; therefore, a $Pi$ -type dual-band transformer is newly introduced to replace single TL for spurious band suppression. We proved that $Pi$ -type structure could effectively suppress spurious band of $S_{11}$ , maintain two arbitrary frequency passband of $S_{21}$ , and provide an extra isolation band of $S_{32}$ at center frequency. Finally, three proposed WPD examples with $Pi$ -type structure are selected with diffe- ent frequency ratios, where frequency ratio $u = 4$ in Example A, $u = 6$ in Example B, and $u = 20$ in Example C are designed and fabricated in the experiment. Measured results show good agreement with the theoretical results.

Description: In this paper, a technique to extend the linearity and to improve the efficiency of power amplifiers (PAs) is analyzed. The method avoids complex topologies, often affecting the radio-frequency performance and increasing the power consumption, chip area, and costs. In contrast, this approach can be implemented by a simple, but sophisticated design of the input biasing network. In this case, the input biasing network works in such a way that the dc current consumption adapts inherently to the demanded output power while ensuring high linearity. The large-signal behavior is analyzed, and analytical equations for the optimum parameter of the bias network are derived. For integration reason, the network is extended to a compact solution, which also includes the source resistance. According to these theoretical considerations, a PA is implemented in a 0.25- $ {mu }text{m}$ SiGe BiCMOS process. The analytical solutions are verified by the measured output-referred 1-dB compression point of 23.6 dBm. To estimate the improvement by using optimum values of the elements, simulations reveal an increase of the input-referred compression point by 2 dB and by 7% of power-added efficiency.

Description: In this paper, a receiver architecture is presented which is capable of handling angle-of-arrival (AOA) detection as well as data communication. The architecture of the proposed multifunction receiver is based on the multiport interferometer technique, and it integrates two previously reported six-port-based system functions that were realized as two distinct six-port receivers (SPRs). This unification of two SPRs is mainly achieved through a new configuration of RF/local oscillator (LO) signals at input ports, a new phase processing of the input signals within a structured eight-port passive network and a complementary postprocessing of the signals at the output of detectors. Using two RF input ports and two LO input ports that are switched in two consecutive time slots, the proposed multiport-based receiver (MPR) can estimate the AOA with a simple signal-processing algorithm. The plurality of the RF input ports can cause self-interference for the received communication signals. Therefore, a phasing network within the proposed eight-port wave correlator is devised such that the incoming quadrature modulated RF carriers are demodulated in an orthogonal manner at four output ports. It is found that receiving communication signal from a nonzero AOA makes imbalance between demodulated components. To this end, the proposed MPR can first find the angular position of the other unit and then recover the demodulation components through data fusion and postprocessing. The mathematical model for the developed MPR is derived along with the development of an appropriate calibration technique, and its principal functionality is theoretically analyzed. In addition, a transceiver architecture based on this MPR is implemented, and prototyped for operation around 77 GHz. The techniques for hybrid millimeter-wave system integration are explained in this paper. The proposed concept is proven and concluded with satisfactory measurements for both functions. This unified multifunction M- R can find applications in the future vehicle-to-vehicle radios and joint radar-communication systems.

Description: The transmitter (TX)-induced interference due to power amplifier nonlinearities poses severe desensitization problems to the receiver chain in frequency-division duplexing transceivers. Due to nonlinear signal process involved, a high sampling rate is normally required in the existing digital suppression approaches, which can result in high cost and high power consumption in wideband systems. In this paper, a new digital suppression model is proposed to cancel the TX leakage at baseband with a low sampling rate. The cancellation model is based on the modified decomposed vector rotation model. With the addition of cross-term products, the enhanced model is capable of eliminating the aliasing effect arising from the reduced sampling rate. Theoretical analysis of aliasing elimination is presented, and the algorithm is subsequently verified by both simulation and experiment results, confirming the effectiveness and feasibility of the proposed cancellation technique for TX leakage suppression. Compared with conventional solutions, the new approach uses much less hardware resource and consumes much lower power while achieving comparable performance.

Description: In this paper, we propose an experimental approach for determining the internal electric field for exposure evaluation of wireless power transfer (WPT) systems by using measured magnetic near-field data. Two WPT systems are fabricated and used in the measurements: one without ferrite tiles, and the other with ferrite tiles and a metal plate. The amplitude and phase of the magnetic near field in the vicinity of the WPT systems are then measured by using in-house magnetic-field probes and a near-field measurement system. Numerical dosimetry of human exposure is performed using the measured near field as an incident field in the impedance method to derive the internal electric field strength inside numerical human models. Validation of the proposed approach has been demonstrated by comparing measurement results with those obtained from numerical simulations. Additionally, the coupling factor, which represents the relationship between the incident magnetic field and the induced electric field in the human body, at different distances is derived for realistic exposure scenarios.

Description: In this paper, a new method to design a digitally assisted and spurious-free direct carrier mixerless modulator based on the six-port correlator is proposed. The calibration of the modulator based on modified Cartesian memory polynomial (MCMP) is used to linearize and mitigate hardware impairment of the whole system. The modulation and the up conversion are performed by using the variable loads controlled by the differential in-phase and quadrature-phase baseband voltages together with common-mode voltages. The proposed MCMP is able to compensate for nonlinearity, frequency responses, residual carrier leakage, crosstalk between the in-phase and the quadrature-phase data. The proof-of-concept of digitally assisted mixerless modulator is developed and its performance is assessed at 2.6 GHz with modern communication signals. The error vector magnitudes between the input ideal baseband signals and the up-converted radio frequency signals are all between 2% and 4%. The residual carrier leakage, which remains present after imperfect suppression through hardware means, degrades the overall system performance and it can be suppressed completely by means of the proposed memory polynomial model.

Description: Real-time spectrum sensing refers to searching for possible signals at a specific time and location, which is applicable to cognitive radio for primary signal detection. The simplicity and low sensing time of phaser-based spectrum sensors, implemented in a discrete manner previously, provided the incentive for this paper. In this paper, an integrated CMOS wideband real-time spectrum sensor with a novel on-chip phaser in 57–354-MHz band, as part of VHF/UHF TV broadcast bands, is presented. The proposed approach provides a fast, simple, area-efficient analog solution for real-time spectrum sensing with low noise figure and power consumption. The integrated chip has been fabricated in a standard 0.18- $mu text{m}$ CMOS IBM technology and has achieved a sensing time of as low as 2.5 $mu text{s}$ for 27-MHz frequency resolution.

Description: A novel photonic beam-space beam-former concept is reviewed and an additional theory addressing precise sampling of desired beam locations for linear arrays is presented. A new, power efficient, method of apodizing an input array's beam pattern via a weighted distribution of the master feed laser to each RF-to-optical up-conversion stage behind the array elements is then presented along with results from several apodization experiments. The experimental results are shown to produce effective, low-sidelobe responses, while also reducing the required prime input power to the system until an artificial side-lobe floor is reached. The root cause of the side-lobe floor is discovered to be due to phase and amplitude errors introduced within the photonic components currently used. Finally, key findings and design considerations are presented with respect to the usage of photonic beam-space sampling on large arrays and several suggestions for performance improvement in future system designs are discussed.

Description: Due to internal optical absorption loss, which varies with carrier density in the optical confinement region, the operating characteristics can be two valued in semiconductor quantum well lasers. Particularly, there can be two lasing thresholds and two branches in the light–current characteristic. While the internal differential quantum efficiency for the first (conventional) branch of the light–current characteristic is less than 1 and decreases with increasing pump current, that for the second (unconventional) branch is greater than 1 and nonmonotonous.

Description: In January 2016, a Priorities and Solutions Project was initiated to identify the most pressing issues facing society with input from a broad spectrum of the agricultural and applied economics profession. This consensus-building endeavor was facilitated by the Council on Food, Agriculture and Resource Economics (C-FARE), working in partnership with the Agricultural and Applied Economics Association (AAEA). The Economic Research Service (ERS) of the USDA provided expertise and logistical support.1 1 The Priorities and Solutions Project is intended to provide the profession with the opportunity to shape its own future by identifying and communicating research opportunities to our profession, our stakeholders, policymakers, and the public. Agricultural and applied economists can work to provide solutions to some of society’s most difficult problems or challenges. This special issue is based on the findings of the project.

Description: Research priorities for the U.S. farm economy include increasing the productivity and cost efficiency on current land resources while understanding production agriculture across the globe. Providing unbiased objective analysis to policymakers with regard to commodity programs, insurance markets, agricultural credit, and the production of bioenergy are important issues that directly affect not only the U.S. farm economy but other agricultural regions. The ability to manage risk, the increasing complexity of farm operations, the ability of the U.S. farm sector to be nimble to changes in individual and societal preferences, and the efficient discovery of information through efficient markets offer a wealth of research opportunities.

Description: Climate change is not just a topic for the future—it is already producing real consequences. Economically, the issue has three principal dimensions: impacts, that is, how vulnerable are we; adaptation, that is, what can we do to reduce the impacts by altering operations; and mitigation, that is, what can we do to reduce the drivers causing climate change and thus the long-term extent of climate change? All of these issues have economic dimensions, including appraising damages and the value of effects reducing actions, as well as the formulation of efficient policies. Thus, it is not surprising that this is both an active agricultural economic research area and one with many more research possibilities. We review the impacts, adaptation, and mitigation literature, identifying issues, summarizing main findings, commenting on methods, and pointing out research needs, with a special focus on what agricultural/applied economists have to offer.

Description: Motivation A deleterious amino acid change in a protein can be compensated by a second-site rescue mutation. These compensatory mechanisms can be mimicked by drugs. In particular, the location of rescue mutations can be used to identify protein regions that can be targeted by small molecules to reactivate a damaged mutant. Results We present the first general computational method to detect rescue sites. By mimicking the effect of mutations through the application of forces, the double force scanning (DFS) method identifies the second-site residues that make the protein structure most resilient to the effect of pathogenic mutations. We tested DFS predictions against two datasets containing experimentally validated and putative evolutionary-related rescue sites. A remarkably good agreement was found between predictions and experimental data. Indeed, almost half of the rescue sites in p53 was correctly predicted by DFS, with 65% of remaining sites in contact with DFS predictions. Similar results were found for other proteins in the evolutionary dataset. Availability and implementation The DFS code is available under GPL at https://fornililab.github.io/dfs/ Contact m.tiberti@qmul.ac.uk or a.fornili@qmul.ac.uk Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Encouraged by the recent progress in pedestrian detection, we investigate the gap between current state-of-the-art methods and the “perfect single frame detector”. We enable our analysis by creating a human baseline for pedestrian detection (over the Caltech pedestrian dataset). After manually clustering the frequent errors of a top detector, we characterise both localisation and background-versus-foreground errors. To address localisation errors we study the impact of training annotation noise on the detector performance, and show that we can improve results even with a small portion of sanitised training data. To address background/foreground discrimination, we study convnets for pedestrian detection, and discuss which factors affect their performance. Other than our in-depth analysis, we report top performance on the Caltech pedestrian dataset, and provide a new sanitised set of training and test annotations.

Description: This paper addresses the problem of robust and efficient relative rotation averaging in the context of large-scale Structure from Motion. Relative rotation averaging finds global or absolute rotations for a set of cameras from a set of observed relative rotations between pairs of cameras. We propose a generalized framework of relative rotation averaging that can use different robust loss functions and jointly optimizes for all the unknown camera rotations. Our method uses a quasi-Newton optimization which results in an efficient iteratively reweighted least squares (IRLS) formulation that works in the Lie algebra of the 3D rotation group. We demonstrate the performance of our approach on a number of large-scale data sets. We show that our method outperforms existing methods in the literature both in terms of speed and accuracy.

Description: Two passive plasmonic demultiplexers with multimode interferometer (MMI) based rectangular and bow-tie designs are demonstrated for 1.31- and 1.55-μm-band wavelength division multiplexing system operation in plasmonic circuits. These demultiplexers are designed using the finite-difference time-domain (FDTD) method and fabricated using complementary metal–oxide–semiconductor compatible processes. SiO 2 films deposited on metal films are etched to form mesa structures by focused ion beam milling, and single-mode waveguides, MMIs, and bow-tie structures are then formed on the metal films. In the plasmonic circuits, 1.31- or 1.55-μm-wavelength surface plasmon polariton (SPP) signals can be distributed to each of the different demultiplexer outputs without any change in signal propagation speed. The SPP intensity distributions that are measured using a scanning near-field optical microscope agree well with the distributions that were calculated using the FDTD method. The insertion loss and crosstalk are then calculated for each demultiplexer. In the rectangular-type demultiplexer, the calculated values were less than 9.5 dB and –2.4 dB, and in the bow-tie-type demultiplexer, the corresponding values were 8.9 dB and less than –2.3 dB, respectively. These results demonstrate the applicability of the developed plasmonic demultiplexers to plasmonic circuits when monolithically integrated on a silicon substrate.

Description: In this paper, we present a self-referenced broad range optical rotary sensor (ORS) for avionics applications. To achieve the high reliability required for aerospace use, the rotary encoder operates ratiometrically to make it insensitive to source light power variation. This sensor has a higher operating range than rotary variable differential transformers (RVDTs) currently used in fly-by-wire aircraft. The ORS encoder is fabricated on an antireflection coated glass substrate with a reflective aluminum coating. Experimental results prove that the sensor accuracy is 0.8% over the full rotation range from 0° to 356.5°. The proposed ORS has better accuracy and an operating range of at least twice that of RVDTs, which have an accuracy of 1% over a full range of only 80°. We also test the insensitivity of the sensor to source fluctuations, which confirms that the sensor is self-referencing.

Description: The design and photonic generation of power-efficient impulse radio ultra-wideband (IR-UWB) waveforms is a challenging step in the design and development of IR-UWB over fiber (IR-UWBoF) systems with combined optical and wireless transmission. In this paper, the definition of the spectral power efficiency (SPE) and its associated optimization problem are reformulated. Based on this reformulation, a theoretical upper bound for the SPE is derived and applied to two of the most common types of photonically generated IR-UWB waveforms. Accurate closed-form analytical expressions for the SPE upper bounds of these two waveform types are obtained and optimized. The analytical framework presented in this paper can be extended and applied to other waveform types. Simulation results show excellent agreement with the analytically obtained expressions. Accordingly, these analytical expressions can be used as reliable guidelines for precise and efficient design of practical IR-UWBoF systems that guarantee optimal design, generation, and distribution of IR-UWB waveforms.

Description: We report two kinds of Q-switched Yb-doped fiber lasers based on a black phosphorus saturable absorber (BP-SA). The BP-SAs are prepared by two different methods, one of which is the mechanical exfoliation method and the other is the liquid-phase exfoliation method. The BP-SAs are inserted into the all-fiber Yb-doped oscillation cavity in different forms. We have experimentally shown that the passively Q-switched pulse trains could be obtained by the two methods. First, we achieve the Q-switched pulse in 1029.63 nm by using a few-layer black phosphorus sheet. The fiber laser was capable of generating pulses with a maximum average output power of 13.12 mW and a repetition rate of 79.46 kHz, corresponding to the maximum single-pulse energy of 165.11 nJ and the shortest single-pulse width of 1.55 μs. In addition, we obtain narrower pulsewidth by dropping the black phosphorus solution onto the tapered fiber. The maximum single pulse energy of 114.72 nJ and the minimum pulsewidth of 1.09 μs were obtained. The repetition rate ranges from 49.13 to 101.3 kHz.

Description: We propose mode couplers and converters based on dual-core hollow-core photonic bandgap fiber (HC-PBGF) structures, which might be potential solutions for integrated all-fiber multiplexers or demultiplexers of a mode-division multiplexed (MDM) transmission system using HC-PBGFs. Coupling properties of ${text{LP}}_{01}$ and ${text{LP}}_{11}$ mode in the mode coupler are investigated and applied to mode separators and polarization separators. Mode transition from ${text{LP}}_{01}$ to ${text{LP}}_{11}$ and ${text{LP}}_{21}$ mode are demonstrated in the mode converter whose smaller core is expected as input end and matched with single-mode fiber. The coupling between fundamental mode and high-order modes is accomplished through the resonant effect, which is fulfilled by modifying the structure parameter of the smaller core. Such mode converters based on dual-core HC-PBGF could be a promising substitute for the free-space coupling device, which is costly and not suitable for integration design in MDM systems and other hollow-core fiber experiments and applications.

Description: Interferometric lithography with curved wavefronts produces chirped gratings. The chirp can be longitudinal, with the periodicity changing along the grating wavevector, or transverse, with the periodicity changing in the perpendicular direction. The chirp is investigated for a range of configurations, and specific optical systems to generate a wide range of grating chirp parameters are analyzed.

Description: We demonstrate a Gb/s real-time visible light communication (VLC) system based on NRZ-OOK by a phosphorescent white light-emitting diode (LED). We propose an equalizer employed by an RC series-parallel connection cascade circuit based on the T-bridge structure. With the proposed circuit, the 3-dB bandwidth of the VLC system can be extended from 1 to 520 MHz. The Bit Error Ratio (BER) of the system was $7.36 times 10^{-4}$ , and the data rate was 1 Gb/s at a distance of 1.5 m. To the best of our knowledge, this is the highest real-time data rate and 3-dB bandwidth achieved based on a white LED.

Description: We present electroabsorption modulators integrated with distributed feedback lasers (EMLs) fabricated by a simple method, which combines the advantages of the selective area growth and double stack active layer techniques. The obtained EML device has a threshold current as low as 16 mA and optical power of larger than 10 mW at 85 mA laser current. Quite low chirp parameter of the fabricated EMLs is obtained. Negative chirp parameters can be obtained at only about 0.5 V reverse bias voltage. Open eye diagrams are demonstrated from the EML at both 10 and 20 Gb/s modulations with the driving voltage of only 0.65 V while securing high dynamic extinction ratio. The exhibited performance makes our device a very promising candidate as a simple light source in long distance and cost sensitive applications.

Description: In this paper, a broadband wireless optical nanolink with plasmonic optical nanoantennas is theoretically proposed and analyzed. The nanolink is formed by linear dipole-loop nanoantennas for transmitter and receiver. The analysis is performed using the linear method of moments with equivalent surface impedance, where we apply a voltage source in the transmitting antenna and connect a load in the receiving antenna. The power received in the load is investigated as a function of frequency and distance between transmitter and receiver. In addition, a comparison is made between this wireless nanolink with a bifilar optical transmission line. The results show that the proposed nanolink, with dipole-loop nanoantenna, can increase the operating bandwidth in the range of 179.1–202.5 THz, when compared with conventional nanolink based only on dipole antennas. In addition, wireless nanolinks, based on dipole or dipole-loop antennas, are more suitable than wired nanolink for distances above approximately 22 μm.

Description: One of the main challenges in establishing a robust visible light communication (VLC) link is to prevent optical interference produced by other light sources from corrupting the signal. Previous solutions catering for this issue assume that optical interference and the signal operate in nonoverlapping frequency bands. This paper presents an innovative transceiver architecture for establishing a frequency-independent interference-tolerant VLC link. The transmitter exploits the polarization property of light to transmit differential signals over adjacent channels, and the receiver utilizes differential amplification in conjunction with polarization to implement a common noise rejection technique. The implemented system demonstrated a 32.6% more robust VLC link compared to the conventional transceiver under severe optical interference.

Description: We propose a wideband linear polarization converter in transmission mode by bilayer metamaterial. The polarization converter operates from 0.55 to 1.37 THz with polarization conversion ratio maintaining nearly 100%. The distribution of surface current and electrical field was numerically simulated to clarify physical mechanism of polarization conversion. Importantly, we introduced the Stokes method to assess the polarization state of transmitted converter. The Fabry–Pérot-like cavity model was established to reveal the enhancement of polarization conversion ratio. The clear expressions including ideal and approximate model were deduced to provide an excellent explanation of Fabry–Pérot cavity in subwavelength bilayer metamaterials structure.

Description: Non-uniform pulse amplitude modulation (PAM) utilizes unequal distances between its modulation levels. In a multilevel PAM symbol, multiple bits are encoded. Due to the unequal level spacing, some bits can be decoded successfully at a lower received optical power than others. This is well suited for practical passive optical network (PON) deployments wherein the optical powers received by the different optical network units (ONUs) typically vary over a broad range. Thus, more ONUs in the PON can successfully decode non-uniform PAM-4 and PAM-8 than standard PAM-4/8, thereby increasing the aggregated capacity of the network. In systems where signal-dependent noise makes up a significant part of the total received noise level, the non-uniform PAM constellation can be adapted to take this signal-dependent variance into account. In doing so, a lower unequal level spacing can be used, decreasing the received optical power required to successfully decode all the bits in the PAM symbol. The impact of non-uniform PAM on the network throughput is presented by comparison of the experimental results with the actual loss distribution of a commercially deployed PON.

Description: Infrared photodetector based on lead sulfide (PbS) colloidal quantum dot has been shown to be a promising candidate for infrared detectors, due to the low-cost process of fabrication and their extremely high sensitivity. Moreover, these photodetectors have successfully achieved ultrahigh detectivity—exceeding the indium gallium arsenide-based photodetectors—at room temperature. In this paper, PbS colloidal quantum dots have been synthesized through an all-chemical solution process and their X-ray diffraction patterns have been analyzed to verify the quality of the product. Transmission electron micrograph microscopy image confirms the production of 10-nm PbS nanoparticles. The as-synthesized PbS colloidal quantum dots were mixed with MEH-PPV to form a hybrid nanocomposite. PbS/MEH-PPV hybrid nanocomposite was used as an active material to detect infrared photons and convert into electrical current. The photoconductive photodetector was fabricated by drop casting the hybrid nanocomposite on interdigitated electrodes and tested under different conditions. To study the effect of silver nanoparticles on the performance of the device, different concentrations of Ag/PbS composition were used in the structure of the photodetector. The results show that the Ag additive reduces dark current due to band bending and increases photocurrent through plasmonic effect. Thus, a photoconductive photodetector with improved photosensitivity and enhanced performance has been achieved.

Description: We experimentally demonstrate a thermally induced reflective optical limiter using Ge $_2$ Sb $_2$ Te $_5$ (GST) and SiO $_2$ in a multilayer photonic bandgap edge-filter configuration. In the PASS state, greater than 80% transmission was achieved at $lambda sim 1500$  nm over a 300 nm spectral bandwidth and $pm 45^{circ }$ angles of incidence. In the BLOCK state, extinction ratios higher than 30 dB were achieved. By comparison, all previous optical limiters based on nonlinear photonic crystals have severe spectral bandwidth and/or angle of incidence limitations in either the PASS or BLOCK states. A nine-layer implementation of this device was fabricated and tested in this paper. Numerical modeling results show reasonable agreement with measured values. To the best of our knowledge, this is the first demonstration of optical limiting over a broad spectral band using phase change materials with this level of performance. However, it should be noted that although GST can be switched in both directions, the experimental results demonstrated in this paper are limited to PASS-to-BLOCK switching only.

Description: We report an effective strategy to enhance the localized surface plasmon resonances (LSPRs) of metallic nanoparticles by introducing a Fabry–Pérot (FP) cavity for high-quality sensing. The concept is based on the combined excitation of LSPRs in metallic nanoparticles and optical cavity modes supported by the FP cavities, whose strong interactions result in two ultra-narrowband hybridized plasmon modes with a huge electric field enhancement. A high-quality double-band plasmonic nanosensor, with the refractive index sensitivity approaching 600 nm/RIU and a figure of merit exceeding 28 is achieved here, which suggests that the cavity-coupling strategy could offer new perspectives for achieving ultra-compact efficient biosensors.

Description: Families of vortex-like and Gaussian-like localized Airy wave packets, propagating in a self-defocusing Kerr medium, are discovered. Their propagation is described by the cylindrical Korteweg–de Vries (CKdV) equation, reduced from the nonlinear Schrödinger equation by utilizing the reductive perturbation technique. The CKdV equation is solved using the Hirota bilinear method to obtain analytical Airy wave packet families of different order. In particular, we focus on the distribution of optical intensity via numerical simulations of the Airy wave packet solutions, obtained for different initial phases and amplitudes, at given propagation distances. In distinction to the usual ring solitons, the Airy wave packets display a novel internal structure, which reveals novel nonlinear phenomena during the propagation of packets.

Description: Complementary metal-oxide-semiconductor (CMOS) sensor based visible light positioning (VLP) has been widely studied in recent years due to its high robustness and high precision. In most researches about CMOS sensor based VLP, researchers always focus on the high-precision positioning algorithm but ignore that the accuracy of LED-ID detection and recognition plays a more important role in a VLP system. Without the correct recognition of LED-ID, the positioning algorithm would be meaningless no matter how effective it is. In addition, high-precision positioning is not required in most applications since it is enough for people to know just the approximate location. To solve these problems, in this paper, an LED-ID detection and recognition method based on visible light positioning using proximity method is propose. Different from the traditional LED-ID coding and decoding method, we create different features for different LED-ID, and use a machine learning method to identify the LED-ID once the feature extraction and selection of the LED image is achieved with an image processing method. It is the first time the machine learning method is used for LED-ID recognition in VLP. Moreover, we use a proximity-based positioning method to get the approximate location since it is easy to obtain once the LED-ID is recognized. The studies we have demonstrated shows that the proposed method can achieve high LED-ID recognition rate, and provide enough unique LED-ID for variable large-scale indoor VLP system. Furthermore, with the development of camera technology, the number of the unique LED-ID and the maximum recognizable distance would increase. Therefore, this scheme may be considered as one of the useful LED-ID detection and recognition method for visible light positioning in the future.

Description: We demonstrate a method for absolute distance measurement based on an optical frequency comb and an optoelectronic oscillator. The unknown distance is measured using optical sampling by cavity tuning. A 1000-m-long fiber is used as a reference path and actively stabilized by the optoelectronic oscillator without ambiguous range. The optical path length of the long fiber is converted to oscillation frequency of the optoelectronic oscillator and locked to an atomic clock. A 0.357- $mu text{m}$ standard deviation of the long fiber reference path is verified by the experimental results, corresponding to a 10 −10 level relative stability. The proof-of-principle absolute distance measurement is implemented and compared with a commercial interferometer. An agreement better than $4~mu text{m}$ is achieved in 22-mm tuning range with the 1000-m imbalanced interferometer setup.

Description: In this letter, we investigate optimal and relaxed constructive interference regions (CIR) for the symbol-level precoding (SLP) problem in the downlink of a multiuser multiple-input single-output (MISO) channel. We define two types of CIRs, namely, distance preserving CIR (DPCIR) and union bound CIR (UBCIR) for any given constellation shape and size. We then provide a systematic way to describe these regions as convex sets. Using the definitions of DPCIR and UBCIR, we show that the SLP power minimization problem, minimizing either sum or peak (per-antenna) transmit power, can always be formulated as a convex optimization problem. Our results indicate that these regions allow further reduction of the transmit power compared to the current state of the art without increasing the computational complexity at the transmitter or receiver.