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: Sensors, Vol. 18, Pages 2406: Adaptive Robust Unscented Kalman Filter via Fading Factor and Maximum Correntropy Criterion Sensors doi: 10.3390/s18082406 Authors: Zhihong Deng Lijian Yin Baoyu Huo Yuanqing Xia In most practical applications, the tracking process needs to update the data constantly. However, outliers may occur frequently in the process of sensors’ data collection and sending, which affects the performance of the system state estimate. In order to suppress the impact of observation outliers in the process of target tracking, a novel filtering algorithm, namely a robust adaptive unscented Kalman filter, is proposed. The cost function of the proposed filtering algorithm is derived based on fading factor and maximum correntropy criterion. In this paper, the derivations of cost function and fading factor are given in detail, which enables the proposed algorithm to be robust. Finally, the simulation results show that the presented algorithm has good performance, and it improves the robustness of a general unscented Kalman filter and solves the problem of outliers in system.

Description: Forests, Vol. 9, Pages 448: Shifts in Growing Season of Tropical Deciduous Forests as Driven by El Niño and La Niña during 2001–2016 Forests doi: 10.3390/f9080448 Authors: Phan Kieu Diem Uday Pimple Asamaporn Sitthi Pariwate Varnakovida Katsunori Tanaka Sukan Pungkul Kumron Leadprathom Monique Y. LeClerc Amnat Chidthaisong This study investigated the spatiotemporal dynamics of tropical deciduous forest including dry dipterocarp forest (DDF) and mixed deciduous forest (MDF) and its phenological changes in responses to El Niño and La Niña during 2001–2016. Based on time series of Normalized Difference Vegetation Index (NDVI) extracted from Moderate Resolution Imaging Spectroradiometer (MODIS), the start of growing season (SOS), the end of growing season (EOS), and length of growing season (LOS) were derived. In absence of climatic fluctuation, the SOS of DDF commonly started on 106 ± 7 DOY, delayed to 132 DOY in El Niño year (2010) and advanced to 87 DOY in La Niña year (2011). Thus, there was a delay of about 19 to 33 days in El Niño and an earlier onset of about 13 to 27 days in La Niña year. The SOS of MDF started almost same time as of DDF on the 107 ± 7 DOY during the neutral years and delayed to 127 DOY during El Niño, advanced to 92 DOY in La Niña year. The SOS of MDF was delayed by about 12 to 28 days in El Niño and was earlier about 8 to 22 days in La Niña. Corresponding to these shifts in SOS and LOS of both DDF and MDF were also induced by the El Niño–Southern Oscillation (ENSO).

Description: Forests, Vol. 9, Pages 446: Plant Hydraulic Trait Covariation: A Global Meta-Analysis to Reduce Degrees of Freedom in Trait-Based Hydrologic Models Forests doi: 10.3390/f9080446 Authors: A. Rio Mursinna Erica McCormick Katie Van Horn Lisa Sartin Ashley M. Matheny Current vegetation modeling strategies use broad categorizations of plants to estimate transpiration and biomass functions. A significant source of model error stems from vegetation categorizations that are mostly taxonomical with no basis in plant hydraulic strategy and response to changing environmental conditions. Here, we compile hydraulic traits from 355 species around the world to determine trait covariations in order to represent hydraulic strategies. Simple and stepwise regression analyses demonstrate the interconnectedness of multiple vegetative hydraulic traits, specifically, traits defining hydraulic conductivity and vulnerability to embolism with wood density and isohydricity. Drought sensitivity is strongly (Adjusted R2 = 0.52, p < 0.02) predicted by a stepwise linear model combining rooting depth, wood density, and isohydricity. Drought tolerance increased with increasing wood density and anisohydric response, but with decreasing rooting depth. The unexpected response to rooting depth may be due to other tradeoffs within the hydraulic system. Rooting depth was able to be predicted from sapwood specific conductivity and the water potential at 50% loss of conductivity. Interestingly, the influences of biome or growth form do not increase the accuracy of the drought tolerance model and were able to be omitted. Multiple regression analysis revealed 3D trait spaces and tradeoff axes along which species’ hydraulic strategies can be analyzed. These numerical trait spaces can reduce the necessary input to and parameterization of plant hydraulics modules, while increasing the physical representativeness of such simulations.

Description: Sensors, Vol. 18, Pages 2420: Strain Transfer Characteristics of Resistance Strain-Type Transducer Using Elastic-Mechanical Shear Lag Theory Sensors doi: 10.3390/s18082420 Authors: Yongqian Li Zhigang Wang Chi Xiao Yinming Zhao Yaxin Zhu Zili Zhou The strain transfer characteristics of resistance strain gauge are theoretically investigated. A resistance strain-type transducer is modeled to be a four-layer and two-glue (FLTG) structure model, which comprises successively the surface of an elastomer sensitive element, a ground adhesive glue, a film substrate layer, an upper adhesive glue, a sensitive grids layer, and a polymer cover. The FLTG model is studied in elastic–mechanical shear lag theory, and the strain transfer progress in a resistance strain-type transducer is described. The strain transitional zone (STZ) is defined and the strain transfer ratio (STR) of the FLTG structure is formulated. The dependences of the STR and STZ on both the dimensional sizes of the adhesive glue and structural parameters are calculated. The results indicate that the width, thickness and shear modulus of the ground adhesive glue have a greater influence on the STZ ratio. To ensure that the resistance strain gauge has excellent strain transfer performance and low hysteresis, it is recommended that the paste thickness should be strictly controlled, and the STZ ratio should be less than 10%. Moreover, the STR strongly depends on the length and width of the sensitive grids.

Description: Sensors, Vol. 18, Pages 2416: Design and Optimization of a Novel Three-Dimensional Force Sensor with Parallel Structure Sensors doi: 10.3390/s18082416 Authors: Guanyu Huang Dan Zhang Sheng Guo Haibo Qu To measure large external forces exerted on a loading platform, a novel three-dimensional force sensor is developed in this paper. The proposed sensor was designed with a parallel mechanism with three degrees of freedom. Kinematic analysis of this sensor was performed. Due to its structural characteristics, the working principle of the sensor was analyzed using a Jacobian matrix. The sensitivity diversity index and measuring capability were both calculated. The analysis showed that the proposed sensor is more suitable for measuring large forces than existing strain sensors. In addition, compared with existing strain sensors, this sensor is more suitable for measuring forces along the x and y axes. By changing the stiffness coefficients of the springs, the proposed sensor has reconfigurability. This sensor can change its measuring capability to meet different requirements. Next, the mode shapes and natural frequencies of the proposed sensor were performed. Finally, based on these performance indices, the design variables were optimized using a Multi-Objective Genetic Algorithm.

Description: Sensors, Vol. 18, Pages 2415: Cheeses Made from Raw and Pasteurized Cow’s Milk Analysed by an Electronic Nose and an Electronic Tongue Sensors doi: 10.3390/s18082415 Authors: Nuno I. P. Valente Alisa Rudnitskaya João A. B. P. Oliveira M. Teresa S. R. Gomes Elvira M. M. Gaspar Cheese prepared from whole milk, raw and pasteurized, were analysed by an electronic nose based on piezoelectric quartz crystals and an electronic tongue based on potentiometric sensors, immediately after their preparation and along ripening (after 7 and 21 days). Whey was also analysed by the potentiometric electronic tongue. Results obtained by the electronic nose and tongue were found to be complementary, with the electronic nose being more sensitive to differences in the milk and the electronic tongue being more sensitive to milk pasteurization. Electronic tongue was able to distinguish cheeses made from raw and pasteurized milk, both analysing the whey or the curd, with correct classification rate of 96% and 84%, respectively. Besides, the electronic nose was more sensitive than the electronic tongue to the ripening process, with large differences between samples after 7 and 21 days, while the electronic tongue was only sensitive to the initial maturation stages, with large difference between freshly prepared cheese and with seven days of maturation.

Description: Sensors, Vol. 18, Pages 2412: Validation of the Accuracy and Convergence Time of Real Time Kinematic Results Using a Single Galileo Navigation System Sensors doi: 10.3390/s18082412 Authors: Zbigniew Siejka For the last two decades, the American GPS and Russian GLONASS were the basic systems used in global positioning and navigation. In recent years, there has been significant progress in the development of positioning systems. New regional systems have been created, i.e., the Japanese Quasi-Zenith Satellite System (QZSS) and Indian Regional Navigational Satellite System (IRNSS). A plan to build its own regional navigation system named Korean Positioning System (KPS) was announced South Korea on 5 February 2018. Currently, two new global navigation systems are under development: the European Galileo and the Chinese BeiDou. The full operability of both systems by 2020 is planned. The paper deals with a possibility of determination of the user’s position from individual and independent global navigation satellite system (GNSS). The article is a broader concept aimed at independent determination of precise position from individual GPS, GLONASS, BeiDou and Galileo systems. It presents real time positioning results (Real Time Kinematic-RTK) using signals from Galileo satellites only. During the test, 14 Galileo satellites were used and the number of simultaneously observed Galileo satellites varied from five to seven. Real-time measurements were only possible in certain 24-h observation windows. However, their number was completed within 6 days at the end of 2017 and beginning of 2018, so there was possible to infer about the current availability, continuity, convergence time and accuracy of the RTK measurements. In addition, the systematic errors were demonstrated for the Galileo system.

Description: Sensors, Vol. 18, Pages 2409: The Bluetooth Mesh Standard: An Overview and Experimental Evaluation Sensors doi: 10.3390/s18082409 Authors: Mathias Baert Jen Rossey Adnan Shahid Jeroen Hoebeke Mesh networks enable a many-to-many relation between nodes, which means that each node in the network can communicate with every other node using multi-hop communication and path diversity. As it enables the fast roll-out of sensor and actuator networks, it is an important aspect within the Internet of Things (IoT). Utilizing Bluetooth Low Energy (BLE) as an underlying technology to implement such mesh networks has gained a lot of interest in recent years. The result was a variety of BLE meshing solutions that were not interoperable because of the lack of a common standard. This has changed recently with the advent of the Bluetooth Mesh standard. However, a detailed overview of how this standard operates, performs and how it tackles other issues concerning BLE mesh networking is missing. Therefore, this paper investigates this new technology thoroughly and evaluates its performance by means of three approaches, namely an experimental evaluation, a statistical approach and a graph-based simulation model, which can be used as the basis for future research. Apart from showing that consistent results are achieved by means of all three approaches, we also identify possible drawbacks and open issues that need to be dealt with.

Description: Sensors, Vol. 18, Pages 2436: Bio-Inspired Covert Active Sonar Strategy Sensors doi: 10.3390/s18082436 Authors: Jiajia Jiang Xianquan Wang Fajie Duan Chunyue Li Xiao Fu Tingting Huang Lingran Bu Ling Ma Zhongbo Sun The covertness of the active sonar is a very important issue and the sonar signal waveform design problem was studied to improve covertness of the system. Many marine mammals produce call pulses for communication and echolocation, and existing interception systems normally classify these biological signals as ocean noise and filter them out. Based on this, a bio-inspired covert active sonar strategy was proposed. The true, rather than man-made sperm whale, call pulses were used to serve as sonar waveforms so as to ensure the camouflage ability of sonar waveforms. A range and velocity measurement combination (RVMC) was designed by using two true sperm whale call pulses which had excellent range resolution (RR) and large Doppler tolerance (DT). The range and velocity estimation methods were developed based on the RVMC. In the sonar receiver, the correlation technology was used to confirm the start and end time of sonar signals and their echoes, and then based on the developed range and velocity estimation method, the range and velocity of the underwater target were obtained. Then, the RVMC was embedded into the true sperm whale call-train to improve the camouflage ability of the sonar signal-train. Finally, experiment results were provided to verify the performance of the proposed method.

Description: Sensors, Vol. 18, Pages 2435: Quantitative Contact-Less Estimation of Energy Expenditure from Video and 3D Imagery Sensors doi: 10.3390/s18082435 Authors: Gregor Koporec Goran Vučković Radoje Milić Janez Perš Measurement of energy expenditure is an important tool in sport science and medicine, especially when trying to estimate the extent and intensity of physical activity. However, most approaches still rely on sensors or markers, placed directly on the body. In this paper, we present a novel approach using a fully contact-less, fully automatic method, that relies on computer vision algorithms and widely available and inexpensive imaging sensors. We rely on the estimation of the optical and scene flow to calculate Histograms of Oriented Optical Flow (HOOF) descriptors, which we subsequently augment with the Histograms of Absolute Flow Amplitude (HAFA). Descriptors are fed into regression model, which allows us to estimate energy consumption, and to a lesser extent, the heart rate. Our method has been tested both in lab environment and in realistic conditions of a sport match. Results confirm that these energy expenditures could be derived from purely contact-less observations. The proposed method can be used with different modalities, including near infrared imagery, which extends its future potential.

Description: Sensors, Vol. 18, Pages 2434: Smart Portable Devices Suitable for Cultural Heritage: A Review Sensors doi: 10.3390/s18082434 Authors: Federica Valentini Andrea Calcaterra Simonetta Antonaroli Maurizio Talamo This article reviews recent portable sensor technologies to apply in the Cultural Heritage (CH) fields. The review has been prepared in the form of a retrospective description of the sensor’s history and technological evolution, having: new nanomaterials for transducers, miniaturized, portable and integrated sensors, the wireless transmission of the analytical signals, ICT_Information Communication Technology and IoT_Internet of Things to apply to the cultural heritage field. In addition, a new trend of movable tattoo sensors devices is discussed, referred to in situ analysis, which is especially important when scientists are in the presence of un-movable and un-tangible Cultural Heritage and Art Work objects. The new proposed portable contact sensors (directly applied to art work objects and surfaces) are non-invasive and non-destructive to the different materials and surfaces of which cultural heritage is composed.

Description: Sensors, Vol. 18, Pages 2433: Multi-Camera Imaging System for UAV Photogrammetry Sensors doi: 10.3390/s18082433 Authors: Damian Wierzbicki In the last few years, it has been possible to observe a considerable increase in the use of unmanned aerial vehicles (UAV) equipped with compact digital cameras for environment mapping. The next stage in the development of photogrammetry from low altitudes was the development of the imagery data from UAV oblique images. Imagery data was obtained from side-facing directions. As in professional photogrammetric systems, it is possible to record footprints of tree crowns and other forms of the natural environment. The use of a multi-camera system will significantly reduce one of the main UAV photogrammetry limitations (especially in the case of multirotor UAV) which is a reduction of the ground coverage area, while increasing the number of images, increasing the number of flight lines, and reducing the surface imaged during one flight. The approach proposed in this paper is based on using several head cameras to enhance the imaging geometry during one flight of UAV for mapping. As part of the research work, a multi-camera system consisting of several cameras was designed to increase the total Field of View (FOV). Thanks to this, it will be possible to increase the ground coverage area and to acquire image data effectively. The acquired images will be mosaicked in order to limit the total number of images for the mapped area. As part of the research, a set of cameras was calibrated to determine the interior orientation parameters (IOPs). Next, the method of image alignment using the feature image matching algorithms was presented. In the proposed approach, the images are combined in such a way that the final image has a joint centre of projections of component images. The experimental results showed that the proposed solution was reliable and accurate for the mapping purpose. The paper also presents the effectiveness of existing transformation models for images with a large coverage subjected to initial geometric correction due to the influence of distortion.

Description: Sensors, Vol. 18, Pages 2432: A Terahertz CMOS V-Shaped Patch Antenna with Defected Ground Structure Sensors doi: 10.3390/s18082432 Authors: Hyeongjin Kim Wonseok Choe Jinho Jeong In this paper, a V-shaped patch antenna with defected ground structure is proposed at terahertz to overcome the limited performance of a standard complementary metal-oxide semiconductor (CMOS) patch antenna consisting of several metal layers and very thin interdielectric layers. The proposed V-shaped patch with slots allows the increased radiation resistance and broadband performance. In addition, the patch resonating at different frequency from the V-shaped patch is stacked on the top to broaden the impedance-matching bandwidth. More importantly, the slots are formed in the ground plane, which is called the defected ground structure, to further increase the radiation resistance and thus improve the bandwidth and efficiency. It is verified from electromagnetic simulations that the leakage waves from the defected ground can enhance the antenna directivity and gain by coherently interfering with the topside radiation. The proposed on-chip antenna is fabricated using a standard 65 nm CMOS process. The on-wafer measurement shows very wide bandwidth in input reflection coefficient (<−10 dB), greater than 28.7% from 240 to >320 GHz. The measured peak gain was as high as 5.48 dBi at 295 GHz. To the best of the authors’ knowledge, these results belong to the best performance among the terahertz CMOS on-chip antennas without using additional components or processes such as dielectric resonators, lens, or substrate thinning.

Description: Sensors, Vol. 18, Pages 2430: Relative Pose Based Redundancy Removal: Collaborative RGB-D Data Transmission in Mobile Visual Sensor Networks Sensors doi: 10.3390/s18082430 Authors: Xiaoqin Wang Y. Ahmet Şekercioğlu Tom Drummond Vincent Frémont Enrico Natalizio Isabelle Fantoni In this paper, the Relative Pose based Redundancy Removal (RPRR) scheme is presented, which has been designed for mobile RGB-D sensor networks operating under bandwidth-constrained operational scenarios. The scheme considers a multiview scenario in which pairs of sensors observe the same scene from different viewpoints, and detect the redundant visual and depth information to prevent their transmission leading to a significant improvement in wireless channel usage efficiency and power savings. We envisage applications in which the environment is static, and rapid 3D mapping of an enclosed area of interest is required, such as disaster recovery and support operations after earthquakes or industrial accidents. Experimental results show that wireless channel utilization is improved by 250% and battery consumption is halved when the RPRR scheme is used instead of sending the sensor images independently.

Description: Sensors, Vol. 18, Pages 2439: HemoKinect: A Microsoft Kinect V2 Based Exergaming Software to Supervise Physical Exercise of Patients with Hemophilia Sensors doi: 10.3390/s18082439 Authors: Fernando Mateo Emilio Soria-Olivas Juan Carrasco Santiago Bonanad Felipe Querol Sofía Pérez-Alenda Patients with hemophilia need to strictly follow exercise routines to minimize their risk of suffering bleeding in joints, known as hemarthrosis. This paper introduces and validates a new exergaming software tool called HemoKinect that intends to keep track of exercises using Microsoft Kinect V2’s body tracking capabilities. The software has been developed in C++ and MATLAB. The Kinect SDK V2.0 libraries have been used to obtain 3D joint positions from the Kinect color and depth sensors. Performing angle calculations and center-of-mass (COM) estimations using these joint positions, HemoKinect can evaluate the following exercises: elbow flexion/extension, knee flexion/extension (squat), step climb (ankle exercise) and multi-directional balance based on COM. The software generates reports and progress graphs and is able to directly send the results to the physician via email. Exercises have been validated with 10 controls and eight patients. HemoKinect successfully registered elbow and knee exercises, while displaying real-time joint angle measurements. Additionally, steps were successfully counted in up to 78% of the cases. Regarding balance, differences were found in the scores according to the difficulty level and direction. HemoKinect supposes a significant leap forward in terms of exergaming applicability to rehabilitation of patients with hemophilia, allowing remote supervision.

Description: Sensors, Vol. 18, Pages 2428: Narrowband Characterization of Near-Ground Radio Channel for Wireless Sensors Networks at 5G-IoT Bands Sensors doi: 10.3390/s18082428 Authors: Hicham Klaina Ana Vazquez Alejos Otman Aghzout Francisco Falcone In this contribution, a narrowband radio channel model is proposed for rural scenarios in which the radio link operates under near-ground conditions for application in wireless sensor networks dedicated to smart agriculture. The received power attenuation was measured for both transmitter and receiver antennas placed at two different heights above ground: 0.2 and 0.4 m. Three frequency ranges, proposed for future 5G-IoT use case in agriculture, were chosen: 868 MHz, 2.4 GHz and 5.8 GHz. Three ground coverings were tested in a rural scenario: soil, short and tall grass fields. The path loss was then estimated as dependent of the radio link range and a three-slope log-normal path loss model was tailored. Results are explained in terms of the first Fresnel zone obstruction. Commercial Zigbee sensor nodes operating at 2.4 GHz were used in a second experiment to estimate the link quality from the experimental Radio Signal Strength Indicator (RSSI) received values. Two sensor nodes were placed at the same elevation above ground as in the previous experiment, only for short grass field case. The Quality of Service performance was determined in terms of theoretical bit error rate achieved for different digital modulations—BPSK, 8PSK and 16QAM—concluding remarkable results for an obstructed radio link.

Description: Sensors, Vol. 18, Pages 2429: A PUF- and Biometric-Based Lightweight Hardware Solution to Increase Security at Sensor Nodes Sensors doi: 10.3390/s18082429 Authors: Rosario Arjona Miguel Ángel Prada-Delgado Javier Arcenegui Iluminada Baturone Security is essential in sensor nodes which acquire and transmit sensitive data. However, the constraints of processing, memory and power consumption are very high in these nodes. Cryptographic algorithms based on symmetric key are very suitable for them. The drawback is that secure storage of secret keys is required. In this work, a low-cost solution is presented to obfuscate secret keys with Physically Unclonable Functions (PUFs), which exploit the hardware identity of the node. In addition, a lightweight fingerprint recognition solution is proposed, which can be implemented in low-cost sensor nodes. Since biometric data of individuals are sensitive, they are also obfuscated with PUFs. Both solutions allow authenticating the origin of the sensed data with a proposed dual-factor authentication protocol. One factor is the unique physical identity of the trusted sensor node that measures them. The other factor is the physical presence of the legitimate individual in charge of authorizing their transmission. Experimental results are included to prove how the proposed PUF-based solution can be implemented with the SRAMs of commercial Bluetooth Low Energy (BLE) chips which belong to the communication module of the sensor node. Implementation results show how the proposed fingerprint recognition based on the novel texture-based feature named QFingerMap16 (QFM) can be implemented fully inside a low-cost sensor node. Robustness, security and privacy issues at the proposed sensor nodes are discussed and analyzed with experimental results from PUFs and fingerprints taken from public and standard databases.

Description: Algorithms, Vol. 11, Pages 112: A Novel Parallel Auto-Encoder Framework for Multi-Scale Data in Civil Structural Health Monitoring Algorithms doi: 10.3390/a11080112 Authors: Ruhua Wang Ling Li Jun Li In this paper, damage detection/identification for a seven-storey steel structure is investigated via using the vibration signals and deep learning techniques. Vibration characteristics, such as natural frequencies and mode shapes are captured and utilized as input for a deep learning network while the output vector represents the structural damage associated with locations. The deep auto-encoder with sparsity constraint is used for effective feature extraction for different types of signals and another deep auto-encoder is used to learn the relationship of different signals for final regression. The existing SAF model in a recent research study for the same problem processed all signals in one serial auto-encoder model. That kind of models have the following difficulties: (1) the natural frequencies and mode shapes are in different magnitude scales and it is not logical to normalize them in the same scale in building the models with training samples; (2) some frequencies and mode shapes may not be related to each other and it is not fair to use them for dimension reduction together. To tackle the above-mentioned problems for the multi-scale dataset in SHM, a novel parallel auto-encoder framework (Para-AF) is proposed in this paper. It processes the frequency signals and mode shapes separately for feature selection via dimension reduction and then combine these features together in relationship learning for regression. Furthermore, we introduce sparsity constraint in model reduction stage for performance improvement. Two experiments are conducted on performance evaluation and our results show the significant advantages of the proposed model in comparison with the existing approaches.

Description: Algorithms, Vol. 11, Pages 113: Improved Parameter Identification Method for Envelope Current Signals Based on Windowed Interpolation FFT and DE Algorithm Algorithms doi: 10.3390/a11080113 Authors: Xiangfeng Su Huaiqing Zhang Lin Chen Ling Qin Lili Yu Envelope current signals are increasingly emerging in power systems, and their parameter identification is particularly necessary for accurate measurement of electrical energy. In order to analyze the envelope current signal, the harmonic parameters, as well as the envelope parameters, need to be calculated. The interpolation fast Fourier transform (FFT) is a widely used approach which can estimate the signal frequency with high precision, but it cannot calculate the envelope parameters of the signal. Therefore, this paper proposes an improved method based on windowed interpolation FFT (WIFFT) and differential evolution (DE). The amplitude and phase parameters obtained through WIFFT and the envelope parameters estimated by the envelope analysis are optimized using the DE algorithm, which makes full use of the performance advantage of DE. The simulation results show that the proposed method can improve the accuracy of the harmonic parameters and the envelope parameter significantly. In addition, it has good anti-noise ability and high precision.

Description: Forests, Vol. 9, Pages 459: Pedunculate and Sessile Mixed Oak Forest Regeneration Process in Lithuania Forests doi: 10.3390/f9080459 Authors: Girmantė Jurkšienė Virginijus Baliuckas Pedunculate and sessile oak species are sympatric. These oaks hybridize with one another, and this process influences the development of undergrowth. The purpose of this study was to determine how different oak species influence the forest regeneration process. For this purpose, the forest was divided into eight transects of 300 m and 100 m widths, distinguished into temporary plots of 10 m in diameter covering the whole territory of the forest. The distribution of oak undergrowth was calculated by four oak height groups, determining the composition of the first storey, covering of underbrush and herbaceous plant, and forest site. We determined that the spread of oak differed depending on the first storey tree species and underbrush. Grass cover was the biggest influence on the sessile oak. The impurity of sessile oak in oak stands had a positive impact on the development of undergrowth, since the entire undergrowth develops faster than separate components of the undergrowth.

Description: Forests, Vol. 9, Pages 455: Measuring Eco-Efficiency of State-Owned Forestry Enterprises in Northeast China Forests doi: 10.3390/f9080455 Authors: Youliang Ning Zhen Liu Zekui Ning Han Zhang State-owned forestry enterprises (SOFEs) play an important role in the forestry economy in China. Understanding the eco-efficiency of their production is beneficial for the development of sustainable forestry and for achieving Goal 8 of the United Nations’ Sustainable Development Goals (SDGs): Decent Work and Economic Growth. This paper assesses SOFEs’ overall eco-efficiency by analyzing various undesirable outputs using the Slacks-Based Measure of efficiency in Data Envelopment Analysis (SBM-DEA) model. Using basic data from 87 SOFEs in Northeast China from 2003 to 2016, this paper evaluated the eco-efficiency development level and spatial patterns of that region. The results show that SOFEs’ low eco-efficiency was caused by low pure-technical efficiency. Regional differences in eco-efficiency were very significant and became larger, but a market-oriented reform might help to improve such efficiency. The eco-efficiency of SOFEs was in decline from 2003 to 2016 due to the implementation of the Natural Forest Protection Project (NFPP). However, due to a relative lack of production factor inputs, most SOFEs’ scale returns are now increasing. In the future, efforts should be made to promote market-oriented reforms and take the path of large-scale development.

Description: Sensors, Vol. 18, Pages 2448: Application-Aware Anomaly Detection of Sensor Measurements in Cyber-Physical Systems Sensors doi: 10.3390/s18082448 Authors: Amin Ghafouri Aron Laszka Koutsoukos Detection errors such as false alarms and undetected faults are inevitable in any practical anomaly detection system. These errors can create potentially significant problems in the underlying application. In particular, false alarms can result in performing unnecessary recovery actions while missed detections can result in failing to perform recovery which can lead to severe consequences. In this paper, we present an approach for application-aware anomaly detection (AAAD). Our approach takes an existing anomaly detector and configures it to minimize the impact of detection errors. The configuration of the detectors is chosen so that application performance in the presence of detection errors is as close as possible to the performance that could have been obtained if there were no detection errors. We evaluate our result using a case study of real-time control of traffic signals, and show that the approach outperforms significantly several baseline detectors.

Description: Sensors, Vol. 18, Pages 2444: Utilization of Inexpensive Carbon-Based Substrates as Platforms for Sensing Sensors doi: 10.3390/s18082444 Authors: Minh Tran Ahmad Fallatah Alison Whale Sonal Padalkar Gold (Au) has been widely used as a material for Surface Enhanced Raman Spectroscopy (SERS) due to its plasmonic properties, stability and biocompatibility. Conventionally for SERS application, Au is deposited on a rigid substrate such as glass or silicon. The rigid substrates severely limit analyte collection efficiency as well as portability. Here, flexible substrates like carbon cloth and carbon paper were investigated as potential substrate candidates for SERS application. The flexible substrates were coated with Au nanostructures by electrodeposition. Model analyte, Rhodamine 6G was utilized to demonstrate the capabilities of the flexible SERS substrates. Additionally, the pesticide paraoxon was also detected on the flexible SERS substrates as well as on a real sample like the apple fruit.

Description: Sensors, Vol. 18, Pages 2441: A Label-Free Fluorescent Assay for the Rapid and Sensitive Detection of Adenosine Deaminase Activity and Inhibition Sensors doi: 10.3390/s18082441 Authors: Xinxing Tang Kefeng Wu Han Zhao Mingjian Chen Changbei Ma Adenosine deaminase (ADA), able to catalyze the irreversible deamination of adenosine into inosine, can be found in almost all tissues and plays an important role in several diseases. In this work, we developed a label-free fluorescence method for the detection of adenosine deaminase activity and inhibition. In the presence of ADA, ATP has been shown to be hydrolyzed. The ATP aptamer was shown to form a G-quadruplex/thioflavin T (ThT) complex with ThT and exhibited an obvious fluorescence signal. However, the ATP aptamer could bind with ATP and exhibited a low fluorescence signal because of the absence of ADA. This assay showed high sensitivity to ADA with a detection limit of 1 U/L based on an SNR of 3 and got a good linear relationship within the range of 1–100 U/L with R2 = 0.9909. The LOD is lower than ADA cutoff value (4 U/L) in the clinical requirement and more sensitive than most of the reported methods. This technique exhibited high selectivity for ADA against hoGG I, UDG, RNase H and λexo. Moreover, this strategy was successfully applied for assaying the inhibition of ADA using erythro-9-(2-hydroxy-3-nonyl) adenine (EHNA) and, as such, demonstrated great potential for the future use in the diagnosis of ADA-relevant diseases, particularly in advanced drug development.

Description: Sensors, Vol. 18, Pages 2440: A Privacy Preserving Scheme for Nearest Neighbor Query Sensors doi: 10.3390/s18082440 Authors: Yuhang Wang Zhihong Tian Hongli Zhang Shen Su Wei Shi In recent years, location privacy concerns that arise when using the nearest neighbor query services have gained increasing attention, as such services have become pervasive in mobile social networks devices and the IoT environments. State-of-the-art privacy preservation schemes focus on the obfuscation of the location information, which has suffered from various privacy attacks and the tradeoff of the quality of service. By noticing the fact that the user’s location could be replaced by their surrounding wireless sensor infrastructures in proximity, in this paper, we propose a wireless sensor access point-based scheme for the nearest neighbor query, without using the location of the user. Then, a noise-addition-based method that preserves user’s location privacy was proposed. To further strengthen the adaptability of the approach to real-world environments, several performance-enhancing methods are introduced, including an R-tree-based Noise-Data Retrieval Algorithm (RNR), and a nearest neighbor query method based on our research. Both performance and security evaluations are conducted to validate our approach. The results show the effectiveness and the practicality of our work.

Description: Algorithms, Vol. 11, Pages 114: Revisiting Chameleon Sequences in the Protein Data Bank Algorithms doi: 10.3390/a11080114 Authors: Mihaly Mezei The steady growth of the Protein Data Bank (PDB) suggests the periodic repetition of searches for sequences that form different secondary structures in different protein structures; these are called chameleon sequences. This paper presents a fast (nlog(n)) algorithm for such searches and presents the results on all protein structures in the PDB. The longest such sequence found consists of 20 residues.

Description: Algorithms, Vol. 11, Pages 115: Color-Based Image Retrieval Using Proximity Space Theory Algorithms doi: 10.3390/a11080115 Authors: Jing Wang Lidong Wang Xiaodong Liu Yan Ren Ye Yuan The goal of object retrieval is to rank a set of images by their similarity compared with a query image. Nowadays, content-based image retrieval is a hot research topic, and color features play an important role in this procedure. However, it is important to establish a measure of image similarity in advance. The innovation point of this paper lies in the following. Firstly, the idea of the proximity space theory is utilized to retrieve the relevant images between the query image and images of database, and we use the color histogram of an image to obtain the Top-ranked colors, which can be regard as the object set. Secondly, the similarity is calculated based on an improved dominance granule structure similarity method. Thus, we propose a color-based image retrieval method by using proximity space theory. To detect the feasibility of this method, we conducted an experiment on COIL-20 image database and Corel-1000 database. Experimental results demonstrate the effectiveness of the proposed framework and its applications.