bluuebunny/crossref_metadata_2025_split 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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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
RHYME: musicking for all
Authors: Holone Harald , Herstad Jo 
Published: June 2013

PurposeThe 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/approachCo‐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.FindingsParticipatory 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/valueThe 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

PurposeThe 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/approachThe 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.FindingsThe 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/implicationsWhile 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 implicationsThe 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/valueThe 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

PurposeStudies 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/approachGeographic 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.FindingsThe 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/valueThis 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

PurposeThis 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/approachThis 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.FindingsIf 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 implicationsIf 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/valueThis 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

PurposeAutonomous 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/approachFirst, 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.FindingsThe 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/valueThe 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

PurposeThis 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/approachA 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.FindingsThe 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/valueThe 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

PurposeThe 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/approachThe 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.FindingsThe 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/implicationsAssembling the data highlighted how little information is readily available in the public domain regarding the structure of telecommunications companies.Practical implicationsThere 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 implicationsUnderstanding the structure of mobile operators should enable them to be better regulated and appropriately taxed.Originality/valueNo other paper has examined in detail the organisational structure of Vodafone Group.