bluuebunny/crossref_metadata_2025 huggingface dataset:
A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks
Authors: Lan Alexander , Ziv-Ukelson Michal , Yeger-Lotem Esti
Published: June 2013

Motivation: A major challenge in systems biology is to reveal the cellular pathways that give rise to specific phenotypes and behaviours. Current techniques often rely on a network representation of molecular interactions, where each node represents a protein or a gene and each interaction is assigned a single static score. However, the use of single interaction scores fails to capture the tendency of proteins to favour different partners under distinct cellular conditions.

Results: Here, we propose a novel context-sensitive network model, in which genes and protein nodes are assigned multiple contexts based on their gene ontology annotations, and their interactions are associated with multiple context-sensitive scores. Using this model, we developed a new approach and a corresponding tool, ContextNet, based on a dynamic programming algorithm for identifying signalling paths linking proteins to their downstream target genes. ContextNet finds high-ranking context-sensitive paths in the interactome, thereby revealing the intermediate proteins in the path and their path-specific contexts. We validated the model using 18 348 manually curated cellular paths derived from the SPIKE database. We next applied our framework to elucidate the responses of human primary lung cells to influenza infection. Top-ranking paths were much more likely to contain infection-related proteins, and this likelihood was highly correlated with path score. Moreover, the contexts assigned by the algorithm pointed to putative, as well as previously known responses to viral infection. Thus, context sensitivity is an important extension to current network biology models and can be efficiently used to elucidate cellular response mechanisms.

Availability: ContextNet is publicly available at http://netbio.bgu.ac.il/ContextNet.

Contact:  estiyl@bgu.ac.il or michaluz@cs.bgu.ac.il

Supplementary information:  Supplementary data are available at Bioinformatics online.
Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model
Authors: Bonzanni Nicola , Garg Abhishek , Feenstra K. Anton , Schütte Judith , Kinston Sarah , Miranda-Saavedra Diego , Heringa Jaap , Xenarios Ioannis , Göttgens Berthold
Published: June 2013

Motivation: Combinatorial interactions of transcription factors with cis-regulatory elements control the dynamic progression through successive cellular states and thus underpin all metazoan development. The construction of network models of cis-regulatory elements, therefore, has the potential to generate fundamental insights into cellular fate and differentiation. Haematopoiesis has long served as a model system to study mammalian differentiation, yet modelling based on experimentally informed cis-regulatory interactions has so far been restricted to pairs of interacting factors. Here, we have generated a Boolean network model based on detailed cis-regulatory functional data connecting 11 haematopoietic stem/progenitor cell (HSPC) regulator genes.

Results: Despite its apparent simplicity, the model exhibits surprisingly complex behaviour that we charted using strongly connected components and shortest-path analysis in its Boolean state space. This analysis of our model predicts that HSPCs display heterogeneous expression patterns and possess many intermediate states that can act as ‘stepping stones’ for the HSPC to achieve a final differentiated state. Importantly, an external perturbation or ‘trigger’ is required to exit the stem cell state, with distinct triggers characterizing maturation into the various different lineages. By focusing on intermediate states occurring during erythrocyte differentiation, from our model we predicted a novel negative regulation of Fli1 by Gata1, which we confirmed experimentally thus validating our model. In conclusion, we demonstrate that an advanced mammalian regulatory network model based on experimentally validated cis-regulatory interactions has allowed us to make novel, experimentally testable hypotheses about transcriptional mechanisms that control differentiation of mammalian stem cells.

Contact:  j.heringa@vu.nl or ioannis.xenarios@isb-sib.ch or bg200@cam.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets
Authors: Kotera Masaaki , Tabei Yasuo , Yamanishi Yoshihiro , Tokimatsu Toshiaki , Goto Susumu
Published: June 2013

Motivation: The metabolic pathway is an important biochemical reaction network involving enzymatic reactions among chemical compounds. However, it is assumed that a large number of metabolic pathways remain unknown, and many reactions are still missing even in known pathways. Therefore, the most important challenge in metabolomics is the automated de novo reconstruction of metabolic pathways, which includes the elucidation of previously unknown reactions to bridge the metabolic gaps.

Results: In this article, we develop a novel method to reconstruct metabolic pathways from a large compound set in the reaction-filling framework. We define feature vectors representing the chemical transformation patterns of compound–compound pairs in enzymatic reactions using chemical fingerprints. We apply a sparsity-induced classifier to learn what we refer to as ‘enzymatic-reaction likeness’, i.e. whether compound pairs are possibly converted to each other by enzymatic reactions. The originality of our method lies in the search for potential reactions among many compounds at a time, in the extraction of reaction-related chemical transformation patterns and in the large-scale applicability owing to the computational efficiency. In the results, we demonstrate the usefulness of our proposed method on the de novo reconstruction of 134 metabolic pathways in Kyoto Encyclopedia of Genes and Genomes (KEGG). Our comprehensively predicted reaction networks of 15 698 compounds enable us to suggest many potential pathways and to increase research productivity in metabolomics.

Availability: Softwares are available on request. Supplementary material are available at http://web.kuicr.kyoto-u.ac.jp/supp/kot/ismb2013/.

Contact: goto@kuicr.kyoto-u.ac.jp
Multitask learning for host–pathogen protein interactions
Authors: Kshirsagar Meghana , Carbonell Jaime , Klein-Seetharaman Judith
Published: June 2013

Motivation: An important aspect of infectious disease research involves understanding the differences and commonalities in the infection mechanisms underlying various diseases. Systems biology-based approaches study infectious diseases by analyzing the interactions between the host species and the pathogen organisms. This work aims to combine the knowledge from experimental studies of host–pathogen interactions in several diseases to build stronger predictive models. Our approach is based on a formalism from machine learning called ‘multitask learning’, which considers the problem of building models across tasks that are related to each other. A ‘task’ in our scenario is the set of host–pathogen protein interactions involved in one disease. To integrate interactions from several tasks (i.e. diseases), our method exploits the similarity in the infection process across the diseases. In particular, we use the biological hypothesis that similar pathogens target the same critical biological processes in the host, in defining a common structure across the tasks.

Results: Our current work on host–pathogen protein interaction prediction focuses on human as the host, and four bacterial species as pathogens. The multitask learning technique we develop uses a task-based regularization approach. We find that the resulting optimization problem is a difference of convex (DC) functions. To optimize, we implement a Convex–Concave procedure-based algorithm. We compare our integrative approach to baseline methods that build models on a single host–pathogen protein interaction dataset. Our results show that our approach outperforms the baselines on the training data. We further analyze the protein interaction predictions generated by the models, and find some interesting insights.

Availability: The predictions and code are available at: http://www.cs.cmu.edu/∼mkshirsa/ismb2013_paper320.html

Contact:  j.klein-seetharaman@warwick.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server
Authors: Olimpieri Pier Paolo , Chailyan Anna , Tramontano Anna , Marcatili Paolo
Published: June 2013

Motivation: Antibodies or immunoglobulins are proteins of paramount importance in the immune system. They are extremely relevant as diagnostic, biotechnological and therapeutic tools. Their modular structure makes it easy to re-engineer them for specific purposes. Short of undergoing a trial and error process, these experiments, as well as others, need to rely on an understanding of the specific determinants of the antibody binding mode.

Results: In this article, we present a method to identify, on the basis of the antibody sequence alone, which residues of an antibody directly interact with its cognate antigen. The method, based on the random forest automatic learning techniques, reaches a recall and specificity as high as 80% and is implemented as a free and easy-to-use server, named prediction of Antibody Contacts. We believe that it can be of great help in re-design experiments as well as a guide for molecular docking experiments. The results that we obtained also allowed us to dissect which features of the antibody sequence contribute most to the involvement of specific residues in binding to the antigen.

Availability:  http://www.biocomputing.it/proABC.

Contact:  anna.tramontano@uniroma1.it or paolo.marcatili@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
GRN2SBML: automated encoding and annotation of inferred gene regulatory networks complying with SBML
Authors: Vlaic Sebastian , Hoffmann Bianca , Kupfer Peter , Weber Michael , Dräger Andreas
Published: June 2013

Summary: GRN2SBML automatically encodes gene regulatory networks derived from several inference tools in systems biology markup language. Providing a graphical user interface, the networks can be annotated via the simple object access protocol (SOAP)-based application programming interface of BioMart Central Portal and minimum information required in the annotation of models registry. Additionally, we provide an R-package, which processes the output of supported inference algorithms and automatically passes all required parameters to GRN2SBML. Therefore, GRN2SBML closes a gap in the processing pipeline between the inference of gene regulatory networks and their subsequent analysis, visualization and storage.

Availability: GRN2SBML is freely available under the GNU Public License version 3 and can be downloaded from http://www.hki-jena.de/index.php/0/2/490.

Supplementary information: General information on GRN2SBML, examples and tutorials are available at the tool’s web page.

Contact:  Sebastian.Vlaic@hki-jena.de or andraeger@eng.ucsd.edu
RETRACTED: Extracellular HSP27 mediates angiogenesis through Toll‐like receptor 3
Authors: Thuringer Dominique , Jego Gaetan , Wettstein Guillaume , Terrier Olivier , Cronier Laurent , Yousfi Nadhir , Hébrard Sophie , Bouchot André , Hazoumé Adonis , Joly Anne‐Laure , Gleave Martin , Rosa‐Calatrava Manuel , Solary Eric , Garrido Carmen
Published: June 2013

The heat‐shock protein 27 (HSP27) is up‐regulated in tumor cells and released in their microenvironment. Here, we show that extracellular HSP27 has a proangiogenic effect evidenced on chick chorioallantoic membrane. To explore this effect, we test the recombinant human protein (rhHSP27) at physiopathological doses (0.1–10 μg/ml) onto human microvascular endothelial cells (HMECs) grown as monolayers or spheroids. When added onto HMECs, rhHSP27 dose‐dependently accelerates cell migration (with a peak at 5 (μg/ml) and favors spheroid sprouting within 12‐24 h. rhHSP27 increases VEGF gene transcription and promotes secretion of VEGF‐activating VEGF receptor type 2. Increased VEGF transcription is related to NF‐κB activation in 30 min. All of these effects are initiated by rhHSP27 interaction with Toll‐like receptor 3 (TLR3). Such an interaction can be detected by immunoprecipitation but does not seem to be direct, as we failed to detect an interaction between rhHSP27 and monomeric TLR3 by SPR analysis. rhHSP27 is rapidly internalized with a pool of TLR3 to the endosomal compartment (within 15–30 min), which is required for NF‐κB activation in a cytosolic Ca2+ ‐dependent manner. The HSP27/TLR3 interaction induces NF‐κB activation, leading to VEGF‐mediated cell migration and angiogenesis. Such a pathway provides alternative targets for antiangiogenic cancer therapy.—Thuringer, D., Jego, G., Wettstein, G., Terrier, O., Cronier, L., Yousfi, N., Hébrard, S., Bouchot, A., Hazoumé, A., Joly, A‐L., Gleave, M., Rosa‐Calatrava, M., Solary, E., and Garrido, C., Extracellular HSP27 mediates angiogenesis through Toll‐like receptor 3. FASEB J. 27, 4169–4183 (2013). www.fasebj.org
Population dynamics and in vitro antibody pressure of porcine parvovirus indicate a decrease in variability
Authors: Streck André Felipe , Homeier Timo , Foerster Tessa , Truyen Uwe
Published: June 2013

To estimate the impact of porcine parvovirus (PPV) vaccines on the emergence of new phenotypes, the population dynamic history of the virus was calculated using the Bayesian Markov chain Monte Carlo method with a Bayesian skyline coalescent model. Additionally, anin vitromodel was performed with consecutive passages of the ‘Challenge’ strain (a virulent field strain) and NADL2 strain (a vaccine strain) in a PK-15 cell line supplemented with polyclonal antibodies raised against the vaccine strain. A decrease in genetic diversity was observed in the presence of antibodiesin vitroor after vaccination (as estimated by thein silicomodel). We hypothesized that the antibodies induced a selective pressure that may reduce the incidence of neutral selection, which should play a major role in the emergence of new mutations. In this scenario, vaccine failures and non-vaccinated populations (e.g. wild boars) may have an important impact in the emergence of new phenotypes.
Reverse transcriptase backbone can alter the polymerization and RNase activities of non-nucleoside reverse transcriptase mutants K101E+G190S
Authors: Wang Jiong , Li Dongge , Bambara Robert A. , Dykes Carrie
Published: June 2013

Previous work by our group showed that human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) containing non-nucleoside RT inhibitor (NNRTI) drug resistance mutations has defects in RNase H activity as well as reduced amounts of RT protein in virions. These deficits correlate with replication fitness in the absence of NNRTIs. Viruses with the mutant combination K101E+G190S replicated better in the presence of NNRTIs than in the absence of drug. Stimulation of virus growth by NNRTIs occurred during the early steps of the virus life cycle and was modulated by the RT backbone sequence in which the resistance mutations arose. We wanted to determine what effects RT backbone sequence would have on RT content and polymerization and RNase H activities in the absence of NNRTIs. We compared a NL4-3 RT with K101E+G190S to a patient-isolate RT sequence D10 with K101E+G190S. We show here that, unlike the NL4-3 backbone, the D10 backbone sequence decreased the RNA-dependent DNA polymerization activity of purified recombinant RT compared to WT. In contrast, RTs with the D10 backbone had increased RNase H activity compared to WT and K101E+G190S in the NL4-3 backbone. D10 virions also had increased amounts of RT compared to K101E+G190S in the NL4-3 backbone. We conclude that the backbone sequence of RT can alter the activities of the NNRTI drug-resistant mutant K101E+G190S, and that identification of the amino acids responsible will aid in understanding the mechanism by which NNRTI drug-resistant mutants alter fitness and NNRTIs stimulate HIV-1 virus replication.
Genome-wide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regions
Authors: Prickett Adam R. , Barkas Nikolaos , McCole Ruth B. , Hughes Siobhan , Amante Samuele M. , Schulz Reiner , Oakey Rebecca J.
Published: June 2013

DNA binding factors are essential for regulating gene expression. CTCF and cohesin are DNA binding factors with central roles in chromatin organization and gene expression. We determined the sites of CTCF and cohesin binding to DNA in mouse brain, genome wide and in an allele-specific manner with high read-depth ChIP-seq. By comparing our results with existing data for mouse liver and embryonic stem (ES) cells, we investigated the tissue specificity of CTCF binding sites. ES cells have fewer unique CTCF binding sites occupied than liver and brain, consistent with a ground-state pattern of CTCF binding that is elaborated during differentiation. CTCF binding sites without the canonical consensus motif were highly tissue specific. In brain, a third of CTCF and cohesin binding sites coincide, consistent with the potential for many interactions between cohesin and CTCF but also many instances of independent action. In the context of genomic imprinting, CTCF and/or cohesin bind to a majority but not all differentially methylated regions, with preferential binding to the unmethylated parental allele. Whether the parental allele-specific methylation was established in the parental germlines or post-fertilization in the embryo is not a determinant in CTCF or cohesin binding. These findings link CTCF and cohesin with the control regions of a subset of imprinted genes, supporting the notion that imprinting control is mechanistically diverse.
Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods
Authors: Stevens Michael , Cheng Jeffrey B. , Li Daofeng , Xie Mingchao , Hong Chibo , Maire Cécile L. , Ligon Keith L. , Hirst Martin , Marra Marco A. , Costello Joseph F. , Wang Ting
Published: June 2013

Recent advancements in sequencing-based DNA methylation profiling methods provide an unprecedented opportunity to map complete DNA methylomes. These include whole-genome bisulfite sequencing (WGBS, MethylC-seq, or BS-seq), reduced-representation bisulfite sequencing (RRBS), and enrichment-based methods such as MeDIP-seq, MBD-seq, and MRE-seq. These methods yield largely comparable results but differ significantly in extent of genomic CpG coverage, resolution, quantitative accuracy, and cost, at least while using current algorithms to interrogate the data. None of these existing methods provides single-CpG resolution, comprehensive genome-wide coverage, and cost feasibility for a typical laboratory. We introduce methylCRF, a novel conditional random fields–based algorithm that integrates methylated DNA immunoprecipitation (MeDIP-seq) and methylation-sensitive restriction enzyme (MRE-seq) sequencing data to predict DNA methylation levels at single-CpG resolution. Our method is a combined computational and experimental strategy to produce DNA methylomes of all 28 million CpGs in the human genome for a fraction (<10%) of the cost of whole-genome bisulfite sequencing methods. methylCRF was benchmarked for accuracy against Infinium arrays, RRBS, WGBS sequencing, and locus-specific bisulfite sequencing performed on the same human embryonic stem cell line. methylCRF transformation of MeDIP-seq/MRE-seq was equivalent to a biological replicate of WGBS in quantification, coverage, and resolution. We used conventional bisulfite conversion, PCR, cloning, and sequencing to validate loci where our predictions do not agree with whole-genome bisulfite data, and in 11 out of 12 cases, methylCRF predictions of methylation level agree better with validated results than does whole-genome bisulfite sequencing. Therefore, methylCRF transformation of MeDIP-seq/MRE-seq data provides an accurate, inexpensive, and widely accessible strategy to create full DNA methylomes.
Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
Authors: Zhang Bo , Zhou Yan , Lin Nan , Lowdon Rebecca F. , Hong Chibo , Nagarajan Raman P. , Cheng Jeffrey B. , Li Daofeng , Stevens Michael , Lee Hyung Joo , Xing Xiaoyun , Zhou Jia , Sundaram Vasavi , Elliott GiNell , Gu Junchen , Shi Taoping , Gascard Philippe , Sigaroudinia Mahvash , Tlsty Thea D. , Kadlecek Theresa , Weiss Arthur , O’Geen Henriette , Farnham Peggy J. , Maire Cécile L. , Ligon Keith L. , Madden Pamela A.F. , Tam Angela , Moore Richard , Hirst Martin , Marra Marco A. , Zhang Baoxue , Costello Joseph F. , Wang Ting
Published: June 2013

DNA methylation plays key roles in diverse biological processes such as X chromosome inactivation, transposable element repression, genomic imprinting, and tissue-specific gene expression. Sequencing-based DNA methylation profiling provides an unprecedented opportunity to map and compare complete DNA methylomes. This includes one of the most widely applied technologies for measuring DNA methylation: methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq), coupled with a complementary method, methylation-sensitive restriction enzyme sequencing (MRE-seq). A computational approach that integrates data from these two different but complementary assays and predicts methylation differences between samples has been unavailable. Here, we present a novel integrative statistical framework M&M (for integration of MeDIP-seq and MRE-seq) that dynamically scales, normalizes, and combines MeDIP-seq and MRE-seq data to detect differentially methylated regions. Using sample-matched whole-genome bisulfite sequencing (WGBS) as a gold standard, we demonstrate superior accuracy and reproducibility of M&M compared to existing analytical methods for MeDIP-seq data alone. M&M leverages the complementary nature of MeDIP-seq and MRE-seq data to allow rapid comparative analysis between whole methylomes at a fraction of the cost of WGBS. Comprehensive analysis of nineteen human DNA methylomes with M&M reveals distinct DNA methylation patterns among different tissue types, cell types, and individuals, potentially underscoring divergent epigenetic regulation at different scales of phenotypic diversity. We find that differential DNA methylation at enhancer elements, with concurrent changes in histone modifications and transcription factor binding, is common at the cell, tissue, and individual levels, whereas promoter methylation is more prominent in reinforcing fundamental tissue identities.
GAIA: Framework Annotation of Genomic Sequence
Authors: Bailey L. Charles , Fischer Stephen , Schug Jonathan , Crabtree Jonathan , Gibson Mark , Overton G. Christian
Published: June 2013

As increasing amounts of genomic sequence from many organisms become available, and as DNA sequences become a primary reagent in biologic investigations, the role of annotation as a prospective guide for laboratory experiments will expand rapidly. Here we describe a process of high-throughput, reliable annotation, called framework annotation, which is designed to provide a foundation for initial biologic characterization of previously unexamined sequence. To examine this concept in practice, we have constructed Genome Annotation and Information Analysis (GAIA), a prototype software architecture that implements several elements important for framework annotation. The center of GAIA consists of an annotation database and the associated data management subsystem that forms the software bus along which other components communicate. The schema for this database defines three principal concepts: (1) Entries, consisting of sequence and associated historical data; (2) Features, comprising information of biologic interest; and (3) Experiments, describing the evidence that supports Features. The database permits tracking of annotation results over time, as well as assessment of the reliability of particular results. New framework annotation is produced by CARTA, a set of autonomous sensors that perform automatic analyses and assert results into the annotation database. These results are available via a Web-based query interface that uses graphical Java applets as well as text-based HTML pages to display data at different levels of resolution and permit interactive exploration of annotation. We present results for initial application of framework annotation to a set of test sequences, demonstrating its effectiveness in providing a starting point for biologic investigation, and discuss ways in which the current prototype can be improved. The prototype is available for public use and comment at http://www.cbil.upenn.edu/gaia.
BioViews: Java-Based Tools for Genomic Data Visualization
Authors: Helt Gregg A. , Lewis Suzanna , Loraine Ann E. , Rubin Gerald M.
Published: June 2013

Visualization tools for bioinformatics ideally should provide universal access to the most current data in an interactive and intuitive graphical user interface. Since the introduction of Java, a language designed for distributed programming over the Web, the technology now exists to build a genomic data visualization tool that meets these requirements. Using Java we have developed a prototype genome browser applet (BioViews) that incorporates a three-level graphical view of genomic data: a physical map, an annotated sequence map, and a DNA sequence display. Annotated biological features are displayed on the physical and sequence-based maps, and the different views are interconnected. The applet is linked to several databases and can retrieve features and display hyperlinked textual data on selected features. In addition to browsing genomic data, different types of analyses can be performed interactively and the results of these analyses visualized alongside prior annotations. Our genome browser is built on top of extensible, reusable graphic components specifically designed for bioinformatics. Other groups can (and do) reuse this work in various ways. Genome centers can reuse large parts of the genome browser with minor modifications, bioinformatics groups working on sequence analysis can reuse components to build front ends for analysis programs, and biology laboratories can reuse components to publish results as dynamic Web documents.
SeqHelp: A Program to Analyze Molecular Sequences Utilizing Common Computational Resources
Authors: Lee Ming K. , Lynch Eric D. , King Mary-Claire
Published: June 2013

Here we descibe a tool to analyze molecular sequences utilizing the internet and existing computational resources for molecular biology. The computer program SeqHelp organizes information from database searches, gene structure prediction, and other information to generate multiply aligned, hypertext-linked reports to allow for fast analysis of molecular sequences. The efficient and economical strategy in this program can be employed to study molecular sequences for gene cloning, mutation analysis, and identical sequence search projects.
RHYME: musicking for all
Authors: Holone Harald , Herstad Jo
Published: June 2013

Purpose

The purpose of this paper is to bring together the fields of participatory design, design for all, accessible music, tangible interaction and musicking to propose musicking for all, where participants can take part on their own terms, with their own intentions, initiatives and interpretations. The goal is to promote well‐being and health among the participants.

Design/methodology/approach

Co‐creative tangibles to enable musicking for all have been created and evaluated in a research project. The paper uses the experiences so far in this project to propose “musicking for all”, based on the fields mentioned in “Purpose” above.

Findings

Participatory design, design for all and tangible interaction forms a promising basis for musicking for all. Challenges/paradoxes emerge when applying participatory design approaches to design work involving disabled children.

Originality/value

The paper contributes with an original view on musicking for disabled children, and proposes musicking for all based on the fields of research mentioned in “Purpose” above. The value in the contribution is a fresh view on co‐creative tangibles for disabled children, and a suggested way forward to improve health and well‐being for this user group.
Crosswatch: a system for providing guidance to visually impaired travelers at traffic intersection
Authors: Coughlan James M. , Shen Huiying
Published: June 2013

Purpose

The purpose of this paper is to describe recent progress on the “Crosswatch” project, a smartphone‐based system developed for providing guidance to blind and visually impaired travelers at traffic intersections. Building on past work on Crosswatch functionality to help the user achieve proper alignment with the crosswalk and read the status of walk lights to know when it is time to cross, the authors outline the directions Crosswatch is now taking to help realize its potential for becoming a practical system: namely, augmenting computer vision with other information sources, including geographic information systems (GIS) and sensor data, and inferring the user's location much more precisely than is possible through GPS alone, to provide a much larger range of information about traffic intersections to the pedestrian.

Design/methodology/approach

The paper summarizes past progress on Crosswatch and describes details about the development of new Crosswatch functionalities. One such functionality, which is required for determination of the user's precise location, is studied in detail, including the design of a suitable user interface to support this functionality and preliminary tests of this interface with visually impaired volunteer subjects.

Findings

The results of the tests of the new Crosswatch functionality demonstrate that the functionality is feasible in that it is usable by visually impaired persons.

Research limitations/implications

While the tests that were conducted of the new Crosswatch functionality are preliminary, the results of the tests have suggested several possible improvements, to be explored in the future.

Practical implications

The results described in this paper suggest that the necessary technologies used by the Crosswatch system are rapidly maturing, implying that the system has an excellent chance of becoming practical in the near future.

Originality/value

The paper addresses an innovative solution to a key problem faced by blind and visually impaired travelers, which has the potential to greatly improve independent travel for these individuals.
Ripple effects of house prices: considering spatial correlations in geography and demography
Authors: Ma Le , Liu Chunlu
Published: June 2013

Purpose

Studies into ripple effects have previously focused on the interconnections between house price movements across cities over space and time. These interconnections were widely investigated in previous research using vector autoregression models. However, the effects generated from spatial information could not be captured by conventional vector autoregression models. This research aimed to incorporate spatial lags into a vector autoregression model to illustrate spatial‐temporal interconnections between house price movements across the Australian capital cities.

Design/methodology/approach

Geographic and demographic correlations were captured by assessing geographic distances and demographic structures between each pair of cities, respectively. Development scales of the housing market were also used to adjust spatial weights. Impulse response functions based on the estimated SpVAR model were further carried out to illustrate the ripple effects.

Findings

The results confirmed spatial correlations exist in housing price dynamics in the Australian capital cities. The spatial correlations are dependent more on the geographic rather than the demographic information.

Originality/value

This research investigated the spatial heterogeneity and autocorrelations of regional house prices within the context of demographic and geographic information. A spatial vector autoregression model was developed based on the demographic and geographic distance. The temporal and spatial effects on house prices in Australian capital cities were then depicted.
Demographic changes and housing demands by scenarios with ASFRs
Authors: Lim Jonghyun , Hyung Lee Joo
Published: June 2013

Purpose

This paper's objective is to provide improvement plans that take into account problems in the housing sector, as well as low fertility and demographic problems caused by aging, by suggesting long‐term policy directions considering all future possible changes in fertility and housing policies.

Design/methodology/approach

This research analyzes age specific fertility rates by socioeconomic index, composition of three scenarios about the total fertility rate, the forecast of the future population by the cohort component method, and the forecast of housing demand according to the Mankiw‐Weil (M‐W) model.

Findings

If the fertility rate increases through improvements in socioeconomic conditions, then we see that housing demand also increases. If the fertility rate level is higher than that of scenario 3, then a housing demand decrease comes later. However, even if the low fertility rate issue is addressed, the problem with the housing market due to the aging is expected to continue for the time being.

Practical implications

If the population decrease cohort is accumulated due to the continuously low fertility, then it will cause an increase in the reduction effect of housing demand. Considering housing spaces, the elderly require a relatively large amount of available space in Korea where the aged population is rapidly increasing. This increase in seniors could counterbalance the reduced demand for housing.

Originality/value

This is a long‐term‐oriented paper about housing demand and the changing trends in Korea, which is undergoing demographic changes due to low fertility and ongoing aging. We need to monitor fertility rates and the structure of population changes to achieve a stable housing market, and we should also recognize that these structural changes by age will have diverse ripple effects on housing demand.
Equidistance target‐following controller for underactuated autonomous underwater vehicles
Authors: Taheri Behzad , Richer Edmond
Published: June 2013

Purpose

Autonomous Underwater Vehicles (AUVs) play a crucial role in marine biology research and oceanic natural resources exploration. Since most AUVs are underactuated they require sophisticated trajectory planning and tracking algorithms. The purpose of this paper is to develop a new method that allows an underactuated AUV to track a moving object while constraining the approach to a direction tangent to the path of the target. Furthermore, the distance at which the AUV follows the target is constrained, reducing the probability of detection and unwanted behavior change of the target.

Design/methodology/approach

First, a kinematic controller that generates a trajectory tangent to the path of the moving target is designed such that the AUV maintains a prescribed distance and approaches the target from behind. Using a Lyapunov based method the stability of the kinematic controller is proven. Second, a dynamic sliding mode controller is employed to drive the vehicle on the trajectory computed in the first step.

Findings

The kinematic and dynamic controllers are shown to be stable and robust against parameter uncertainty in the dynamic model of the vehicle. Results of numerical simulations for equidistant tracking of a target on both smooth and discontinuous derivatives trajectories for a variety of relative initial positions and orientations are shown.

Originality/value

The contribution of this research is development of a new method for path planning and tracking of moving targets for underactuated AUVs in the horizontal plane. The method allows control of both the direction of approach and the distance from a moving object.
Intra‐regional diffusion of spectrum license allocation policies
Authors: Pogrebnyakov Nicolai , Maitland Carleen F.
Published: June 2013

Purpose

This paper aims to develop a greater understanding of international telecommunications policy diffusion through preliminary, qualitative analysis of an expected utility model. The model is tested through analyses of diffusion of spectrum license allocation policies within and between regions.

Design/methodology/approach

A qualitative comparative case method is used. Cases are developed from secondary data from the European Union and South America, and analyzed at the national and regional levels.

Findings

The results suggest: the expected utility model can be used for in‐depth qualitative analyses to compare effects of various diffusion mechanisms; diffusion of spectrum license allocation policies at the regional level was more strongly driven by a policy's likely effectiveness, as compared to potential payoffs for policymakers; and conversely, at the national level diffusion was driven by both payoffs for the policymakers and likely policy effectiveness.

Originality/value

The two academic contributions of the paper are its expansion of a unified policy diffusion model to simultaneously account for regional and national levels of governance, as well as for technological change and its application in the telecommunications domain. Practical contributions include providing a framework for systematic analysis of a telecommunications policy's benefits for the public as well as policymakers.
Unravelling complex organisational structures among mobile operators
Authors: Whalley Jason , Curwen Peter
Published: June 2013

Purpose

The purpose is to map the corporate structure of Vodafone Group. Through this, the paper will demonstrate the complexity of the company and argue for improved data availability to facilitate a better understanding of the mobile industry.

Design/methodology/approach

The paper begins by briefly recounting some relevant literature before detailing the data sources used in the analysis of Vodafone Group. A structure of Vodafone Group, highlighting the use of holding companies, is then presented, after which a series of national case studies are detailed. The case studies are used to shed light on a series of topics that are subsequently discussed.

Findings

The paper highlights the organisational complexity of Vodafone Group. There are many more companies within the Vodafone Group than expected. These companies are held through a series of holding companies, some of which are located in tax havens.

Research limitations/implications

Assembling the data highlighted how little information is readily available in the public domain regarding the structure of telecommunications companies.

Practical implications

There is a need for more data regarding the structure of mobile operators to be available in the public domain, so that a better appraisal of their actions by investors, regulators and governments can be made.

Social implications

Understanding the structure of mobile operators should enable them to be better regulated and appropriately taxed.

Originality/value

No other paper has examined in detail the organisational structure of Vodafone Group.
Generating innovative interconnection business models for the future internet
Authors: Ghezzi Antonio , Georgiades Michael , Reichl Peter , Le‐Sauze Nicolas , Di Cairano‐Gilfedder Carla , Managiaracina Riccardo
Published: June 2013

Purpose

The future development of the internet is not only heavily dependent on its technological evolution, but also on business sustainability for the interconnection ecosystem the web relies on, where various players characterized by fairly different economic structures and interests are coexisting. Therefore, in this paper the authors aim to propose a methodological framework for developing innovative interconnection business models.

Design/methodology/approach

Starting from a comprehensive as‐is analysis including the selection of appropriate service scenarios, market activities are abstracted through an archetypization process. Based on that, a value network for the future marketplace is proposed and makes it possible to design a business model for carriers, before, as last step, both the value network configurations and the to‐be business model are evaluated.

Findings

The framework to assess the future internet ecosystem depicts the interconnections value network, shedding light on its key activities; it proposes the establishment of a new dynamic interconnection marketplace based on an emerging interconnection value network where traditional and original roles coexist; and it evaluates the introduction of sending party pays and bid‐and‐ask solutions for governing the marketplace and its business models.

Originality/value

The authors' approach addresses carriers, over‐the‐top providers and technology providers as well as end user groups, specifically aiming at fostering the evolution of the future internet by means of developing innovative value configurations and business model options with a substantial impact for a broad set of stakeholders on a global scale. Thus, the canvas of guidelines presented and discussed in this paper covers all stakeholders in the interconnection ecosystem and provides a solid starting point for upcoming implementations.
The extra‐territorial reach of the broker‐dealer registration requirements under the US Securities Exchange Act of 1934: the staff of the Securities and Exchange Commission addresses frequently asked questions regarding Rule 15a‐6 and foreign broker‐dealers
Authors: Eisert Edward , Katz Tony , Carotenuto Giovanni , Ball Melanie F.
Published: June 2013

Purpose

The purpose of this paper is to summarize the significant responses of the staff of the SEC to 16 frequently asked questions (FAQs) which supplement prior guidance on Rule 15a‐6 under the Securities Exchange Act of 1934.

Design/methodology/approach

The paper lists Rule 15a‐6 activities, refers to prior guidance on the rule, and summarizes the following issues, among others, covered in the FAQs: transactions between a foreign broker‐dealer and a person temporarily in the USA, distribution by a foreign broker‐dealer of research reports to major US institutional investors, activities of foreign broker‐dealers taken with unaffiliated registered broker‐dealers, boundaries to the definition of “solicitation” by a foreign broker‐dealer of a US investor, and minimum net capital requirements for a registered broker‐dealer in a chaperoning arrangement with a foreign broker‐dealer.

Findings

This guidance does not break new ground and may be supplemented in the future. An amendment of Rule 15a‐6 is still necessary to address its fundamental limitations.

Originality/value

The paper provides practical explanation by experienced financial services lawyers.
An appraisal of urban renewal in Nigeria
Authors: Ibem Eziyi O. , Uwakonye Obioha , Aduwo Egidario B.
Published: June 2013

Purpose

The purpose of this paper is to appraise the sustainability of the Nigerian Army Shopping Arena urban renewal project in Oshodi‐Lagos, Nigeria.

Design/methodology/approach

Case study research design was adopted for the study and both quantitative and qualitative data collection methods were used. Data were collected from randomly selected 94 business operators in the shopping complex using structured questionnaires, while oral interviews were conducted with two purposively selected members of the project management team. Data were also collected through non‐participant observation and analysed by using both descriptive statistics and content analysis.

Findings

The project was executed using the build‐operate‐transfer (BOT) arrangement, and users were generally satisfied with facilities provided, except for the provision of utilities. Access to public facilities, creation of job opportunities, community involvement and sense of ownership, as well as the provision of facilities for pedestrian and vehicle users were considered as contributing optimally, while adherence to the principle of green design and construction was rated as contributing minimally to the sustainability of the project.

Practical implications

The adoption of BOT can facilitate access to funds for urban renewal projects in the developing countries. Creation of job opportunities, ensuring users' satisfaction, community involvement and compatibility with environment can promote the sustainability of urban renewal projects in the developing countries.

Originality/value

The study extents our understanding of funding mechanisms, users' satisfaction with, and the sustainability of urban renewal projects from the Nigerian perspective.
Representative bureaucracy, public‐private partnerships, and urban development
Authors: Leland Suzanne , Read Dustin C.
Published: June 2013

Purpose

The purpose of this paper is to expand the study of representative bureaucracy by exploring attitudes about the use of public funds to support privately‐owned real estate development projects. Data collected from over 1,400 members of the American Planning Association are used to determine if urban planners' demographic characteristics influence attitudes about public‐private partnerships designed to achieve different policy goals. By examining these linkages, conclusions can be drawn as to whether diversity in the planning profession offers a means of ensuring citizen preferences are taken into account when collaborative arrangements are formed to encourage urban development.

Design/methodology/approach

Ordinal logistic regression models are estimated to determine if the characteristics of urban planners influence perceptions about real estate projects designed to: provide affordable housing; eliminate urban blight; encourage the use of public transportation; prevent urban sprawl; enhance pedestrian mobility; and preserve historic structures.

Findings

Strong support for public‐private partnerships was observed in the sample and demographic characteristics were found to influence attitudes. Minority planners tended to be more supportive of programs designed to provide affordable housing and eliminate blight, while female planners and planners in older age cohorts were more supportive of efforts to rejuvenate urban areas. Political ideology was, however, found to have the most consistent impact on attitudes.

Originality/value

The paper's results suggest diversity in the planning profession offers one means of protecting citizen preferences when public‐private partnerships are formed to encourage urban development. However, the benefits of diversity must be evaluated in conjunction with planners' attitudes about the appropriate role of government in real estate development.