Link Discovery Research Articles

Towards a systems approach for chronic diseases, based on health state modeling.

Rising pressure from chronic diseases means that we need to learn how to deal with challenges at a different level, including the use of systems approaches that better connect across fragments, such as disciplines, stakeholders, institutions, and technologies. By learning from progress in leading areas of health innovation (including oncology and AIDS), as well as complementary indications (Alzheimer's disease), I try to extract the most enabling innovation paradigms, and discuss their extension to additional areas of application within a systems approach. To facilitate such work, a Precision, P4 or Systems Medicine platform is proposed, which is centered on the representation of health states that enable the definition of time in the vision to provide the right intervention for the right patient at the right time and dose. Modeling of such health states should allow iterative optimization, as longitudinal human data accumulate. This platform is designed to facilitate the discovery of links between opportunities related to a) the modernization of diagnosis, including the increased use of omics profiling, b) patient-centric approaches enabled by technology convergence, including digital health and connected devices, c) increasing understanding of the pathobiological, clinical and health economic aspects of disease progression stages, d) design of new interventions, including therapies as well as preventive measures, including sequential intervention approaches. Probabilistic Markov models of health states, e.g. those used for health economic analysis, are discussed as a simple starting point for the platform. A path towards extension into other indications, data types and uses is discussed, with a focus on regenerative medicine and relevant pathobiology.

Modelling, Verification, and Comparative Performance Analysis of the B.A.T.M.A.N. Protocol

This paper considers on a network routing protocol known as Better Approach to Mobile Ad hoc Networks (B.A.T.M.A.N.). The protocol serves two aims: first, to discover all bidirectional links, and second, to identify the best-next-hop for every other node in the network. A key element is that each node will flood the network at regular intervals with so-called originator messages. This paper describes in detail a formalisation of the B.A.T.M.A.N. protocol. This exercise revealed several ambiguities and inconsistencies in the RFC. We developed two models. The first implements, if possible, a literal reading of the RFC, while the second model tries to be closer to the underlying concepts. The alternative model is in some places less restrictive, and rebroadcasts more often when it helps route discovery, and will on the other hand drop more messages that might interfere with the process. We verify for a basic untimed model that both interpretations ensure loop-freedom, bidirectional link discovery, and route-discovery. We use simulation of a timed model to compare the performance and found that both models are comparable when it comes to the time and number of messages needed for discovering routes. However, the alternative model identifies a significantly lower number of suboptimal routes, and thus improves on the literal interpretation of the RFC.

Pandora's Box: mitochondrial defects in ischaemic heart disease and stroke.

Ischaemic heart disease and stroke are vascular events with serious health consequences worldwide. Recent genetic and epigenetic techniques have revealed many genetic determinants of these vascular events and simplified the approaches to research focused on ischaemic heart disease and stroke. The pathogenetic mechanisms of ischaemic heart disease and stroke are complex, with mitochondrial involvement (partially or entirely) recently gaining substantial support. Not only can mitochondrial reactive oxygen species give rise to ischaemic heart disease and stroke by production of oxidised low-density lipoprotein and induction of apoptosis, but the impact on pericytes contributes directly to the pathogenesis. Over the past two decades, publications implicate the causative role of nuclear genes in the development of ischaemic heart disease and stroke, in contrast to the potential role of mitochondrial DNA (mtDNA) in the pathophysiology of the disorders, which is much less understood, although recent studies do demonstrate that the involvement of mitochondria and mtDNA in the development of ischaemic heart disease and stroke is likely to be larger than originally thought, with the novel discovery of links among mitochondria, mtDNA and vascular events. Here we explore the molecular events and mtDNA alterations in relation to the role of mitochondria in ischaemic heart disease and stroke.

Multi-class routing protocol using virtualization and SDN-enabled architecture for smart grid

Routing Protocol for Low Power and Lossy Network (RPL) is standardized and known as the primary solution for the last mile communication network in the smart grid. Various applications with different requirements are rapidly developed in the smart grid. The need to provide Quality of Service (QoS) for such a communication network is inevitable. In this paper, we use the benefits of virtualization and software-defined networking to present a virtual version of the RPL protocol which we name OMC-RPL (Optimized Multi-Class RPL). We present an SDN-enabled architecture consisting of a central controller and some SDN nodes. This implementation reduces the complexity and controls interactions to distribute the network states and other related information in the network. The proposed SDN-enabled architecture consists of different components including Network Link Discovery, Topology Manager, and Virtual Routing. OMC-RPL utilizes a holistic objective function including distinctive metrics related to QoS, and supports the data classification which is an essential requirement in this context. The proposed objective function considers different numbers of traffic classes by using weighting parameters. An optimization algorithm determines the best values of these coefficients. OMC-RPL is evaluated in different aspects. Simulation results show that the new idea significantly decreases both the end-to-end delay and packet loss which are the important factors of QoS. The virtualization idea is also investigated, which results in less message exchange.

A survey of current Link Discovery frameworks

Links build the backbone of the Linked Data Cloud. With the steady growth in size of datasets comes an increased need for end users to know which frameworks to use for deriving links between datasets. In this survey, we comparatively evaluate current Link Discovery tools and frameworks. For this purpose, we outline general requirements and derive a generic architecture of Link Discovery frameworks. Based on this generic architecture, we study and compare the features of state-ofthe-art linking frameworks. We also analyze reported performance evaluations for the different frameworks. Finally, we derive insights pertaining to possible future developments in the domain of Link Discovery.

Resistance of Aerosolized Bacterial Viruses to Relative Humidity and Temperature.

The use of aerosolized bacteriophages as surrogates for hazardous viruses might simplify and accelerate the discovery of links between viral components and their persistence in the airborne state under diverse environmental conditions. In this study, four structurally distinct lytic phages, MS2 (single-stranded RNA [ssRNA]), ϕ6 (double-stranded RNA [dsRNA]), ϕX174 (single-stranded DNA [ssDNA]), and PR772 (double-stranded DNA [dsDNA]), were nebulized into a rotating chamber and exposed to various levels of relative humidity (RH) and temperature as well as to germicidal UV radiation. The aerosolized viral particles were allowed to remain airborne for up to 14 h before being sampled for analysis by plaque assays and quantitative PCRs. Phages ϕ6 and MS2 were the most resistant at low levels of relative humidity, while ϕX174 was more resistant at 80% RH. Phage ϕ6 lost its infectivity immediately after exposure to 30°C and 80% RH. The infectivity of all tested phages rapidly declined as a function of the exposure time to UVC radiation, phage MS2 being the most resistant. Taken altogether, our data indicate that these aerosolized phages behave differently under various environmental conditions and highlight the necessity of carefully selecting viral simulants in bioaerosol studies.

Parental Support during Childhood Predicts Life History-Related Personality Variation and Social Status in Young Adults

Adaptationist theories of development posit the existence of facultative mechanisms designed to calibrate individual differences in life history strategy to cues available in childhood. Such theories have led to the discovery of links between parenting-related cues and multiple life history phenotypes in offspring (e.g., reproductive timing), but less is known about the influences of parental behavior on the development of stable personality traits. This article reports a preliminary test of the hypothesis that life history-related personality variation is developmentally calibrated in response to the level of parental support received during childhood. Consistent with this, in a sample of young adults (N = 321), (i) subjects’ reports of their parents’ income positively predicted the level of parental support they recall having received during childhood; (ii) these measures of parental income and parental support in childhood positively predicted subjects’ standing on the general factor of personality (GFP), long-term mating orientation, and prestige-based social status; and (iii) path analyses fit a model of the following form: parental income → parental support in childhood → GFP → prestige-based status. Moreover, these effects held when controlling for perceptions of current social support, which implies that associations of parental support in childhood with outcomes in adulthood did not reflect current perceptions or global self-evaluative biases. These findings, though preliminary, are consonant with recent theories positing that the GFP and prestige-based status reflect individual differences along a fast-slow life history continuum, and suggest that life history-related personality variation may be developmentally calibrated to parental support during childhood.

Metabolomics and diabetes: analytical and computational approaches.

Diabetes is characterized by altered metabolism of key molecules and regulatory pathways. The phenotypic expression of diabetes and associated complications encompasses complex interactions between genetic, environmental, and tissue-specific factors that require an integrated understanding of perturbations in the network of genes, proteins, and metabolites. Metabolomics attempts to systematically identify and quantitate small molecule metabolites from biological systems. The recent rapid development of a variety of analytical platforms based on mass spectrometry and nuclear magnetic resonance have enabled identification of complex metabolic phenotypes. Continued development of bioinformatics and analytical strategies has facilitated the discovery of causal links in understanding the pathophysiology of diabetes and its complications. Here, we summarize the metabolomics workflow, including analytical, statistical, and computational tools, highlight recent applications of metabolomics in diabetes research, and discuss the challenges in the field.

Marine Microbial Secondary Metabolites: Pathways, Evolution and Physiological Roles.

Microbes produce a huge array of secondary metabolites endowed with important ecological functions. These molecules, which can be catalogued as natural products, have long been exploited in medical fields as antibiotics, anticancer and anti-infective agents. Recent years have seen considerable advances in elucidating natural-product biosynthesis and many drugs used today are natural products or natural-product derivatives. The major contribution to recent knowledge came from application of genomics to secondary metabolism and was facilitated by all relevant genes being organised in a contiguous DNA segment known as gene cluster. Clustering of genes regulating biosynthesis in bacteria is virtually universal. Modular gene clusters can be mixed and matched during evolution to generate structural diversity in natural products. Biosynthesis of many natural products requires the participation of complex molecular machines known as polyketide synthases and non-ribosomal peptide synthetases. Discovery of new evolutionary links between the polyketide synthase and fatty acid synthase pathways may help to understand the selective advantages that led to evolution of secondary-metabolite biosynthesis within bacteria. Secondary metabolites confer selective advantages, either as antibiotics or by providing a chemical language that allows communication among species, with other organisms and their environment. Herewith, we discuss these aspects focusing on the most clinically relevant bioactive molecules, the thiotemplated modular systems that include polyketide synthases, non-ribosomal peptide synthetases and fatty acid synthases. We begin by describing the evolutionary and physiological role of marine natural products, their structural/functional features, mechanisms of action and biosynthesis, then turn to genomic and metagenomic approaches, highlighting how the growing body of information on microbial natural products can be used to address fundamental problems in environmental evolution and biotechnology.

The criminal gene: the link between MAOA and aggression (REVIEW)

BackgroundOne emerging aspect of recent advances in neurocriminology is the discovery of possible links between violent criminal behaviour and genetics. Analysis of data from several studies indicates that the strongest link between genetic variation and aggression comes from monoamine oxidase A (MAOA); a gene encoding an enzyme responsible for catabolising amine neurotransmitters such as dopamine, serotonin and noradrenaline. In this work, we present a critical review of the data available from recent investigations regarding the impact of an allelic variation of the MAOA gene on criminal behaviour.METHODSThe main approach used in this work was reviewing and analysing data presented in a variety of research papers accessed through electronic search.RESULTSThe low activity form of the MAOA gene (MAOA-L) has been linked to increased levels of aggression and violence. Data from a 2007 study suggests that MAOA-L individuals are hypersensitive, so are affected more by negative experiences... Language: en

EARLY EVOLUTION AND NEW CLASSIFICATION OF THE ORDER ROBERTINIDA (FORAMINIFERA)

Research Article| January 01, 2015 EARLY EVOLUTION AND NEW CLASSIFICATION OF THE ORDER ROBERTINIDA (FORAMINIFERA) Sylvain Rigaud; Sylvain Rigaud 3 1Earth Sciences Department, 13 rue des Maraîchers, 1205 Genève, Switzerland 3Correspondence author. E-mail: Sylvain.Rigaud@unige.ch Search for other works by this author on: GSW Google Scholar Rossana Martini; Rossana Martini 1Earth Sciences Department, 13 rue des Maraîchers, 1205 Genève, Switzerland Search for other works by this author on: GSW Google Scholar Daniel Vachard Daniel Vachard 2Université Lille 1, UMR 8217 CNRS Géosystèmes, SN5, 59655 Villeneuve d’Ascq Cédex, France Search for other works by this author on: GSW Google Scholar Author and Article Information Sylvain Rigaud 3 1Earth Sciences Department, 13 rue des Maraîchers, 1205 Genève, Switzerland Rossana Martini 1Earth Sciences Department, 13 rue des Maraîchers, 1205 Genève, Switzerland Daniel Vachard 2Université Lille 1, UMR 8217 CNRS Géosystèmes, SN5, 59655 Villeneuve d’Ascq Cédex, France 3Correspondence author. E-mail: Sylvain.Rigaud@unige.ch Publisher: Cushman Foundation for Foraminiferal Research Received: 06 Jun 2013 Accepted: 31 Jul 2014 First Online: 13 Jul 2017 Online ISSN: 1943-264X Print ISSN: 0096-1191 © 2015 Cushman Foundation for Foraminiferal Research Journal of Foraminiferal Research (2015) 45 (1): 3–28. https://doi.org/10.2113/gsjfr.45.1.3 Article history Received: 06 Jun 2013 Accepted: 31 Jul 2014 First Online: 13 Jul 2017 Cite View This Citation Add to Citation Manager Share Icon Share Facebook Twitter LinkedIn MailTo Tools Icon Tools Get Permissions Search Site Citation Sylvain Rigaud, Rossana Martini, Daniel Vachard; EARLY EVOLUTION AND NEW CLASSIFICATION OF THE ORDER ROBERTINIDA (FORAMINIFERA). Journal of Foraminiferal Research 2015;; 45 (1): 3–28. doi: https://doi.org/10.2113/gsjfr.45.1.3 Download citation file: Ris (Zotero) Refmanager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentBy SocietyJournal of Foraminiferal Research Search Advanced Search Abstract The discovery of Triassic missing links in the Panthalassan domain (Wallowa terrane, U.S.A.) substantiates a direct lineage between internally simple Triassic multichambered aragonitic foraminifers and internally partitioned Jurassic Robertinida. A new hierarchical subdivision is accordingly proposed for the order Robertinida, which is emended to encompass all known post-Paleozoic aragonitic multichambered foraminifers. At the highest taxonomic level, the suborder Robertinina is distinguished from the suborder Duostominina emended to encompass forms without internal structures attached to the aperture, including the planktonic family Favusellidae and the controversial form Pragsoconulus. Two new families (Robertonellidae, Trochosiphoniidae), four new subfamilies (Cassianopapillariinae, Praereinholdellinae, Pragsoconulinae, and Trochosiphoniinae), four new genera (Falsorheinoldella, Praerheinoldella, Robertonella, and Trochosiphonia), and seven new species (Falsorheinoldella ohmi, F. oregonica, Praerheinoldella galei, Robertonella rettorii, R. wallowensis, Trochosiphonia stanleyi, and T. josephi) are introduced. Phylogenetic links between Triassic robertinids, which experienced a rapid diversification during the Triassic, are clarified and their hypothetical long-term relationships with other foraminiferal groups are discussed. You do not have access to this content, please speak to your institutional administrator if you feel you should have access.

NewsMiner: Multifaceted news analysis for event search

Online news has become increasingly prevalent due to its convenience for information acquisition, and meanwhile the rapid development of social applications enables news generate and spread through various ways at an unprecedented rate. How to organize and integrate news from multiple sources, and how to analyze and present news to users are two challenging problems. In this article, we represent news as a link-centric heterogeneous network and formalize news analysis and mining task as link discovery problem. More specifically, we propose a co-mention and context based knowledge linking method and a topic-level social content alignment method to establish the links between news and external sources (i.e. knowledge base and social content), and introduce a unified probabilistic model for topic extraction and inner relationship discovery within events. We further present a multifaceted ranking strategy to rank the linked events, topics and entities simultaneously. Extensive experiments demonstrate the advantage of the proposed approaches over baseline methods and the online system we developed (i.e. NewsMiner) has been running for more than three years.

Synesthesia on Our Mind

Synesthesia in perception and metaphor in language both provide ways to categorize and comprehend the world. Both operate through mechanisms that capitalize on the creation or discovery of links across disparate domains – notably, sensory experiences in different modalities, with cross-modal correspondences serving as perceptual links in synesthesia and as conceptual links in metaphor. The perceptual links in synesthesia are typically fixed and rigid. The conceptual links in metaphor, however, enable meanings to expand, creatively, through the active construction of novel, emergent relations: Metaphors transform meanings, thereby transcending the fixed correspondences of synesthesia. Recent evidence associates the presence of synesthesia with an augmented capacity for creative cognition. Other evidence associates synesthesia with neural hyperconnectivity – augmented connectivity between regions of the cerebral cortex that process the synesthetically linked domains. We suggest that mechanisms underlying synesthesia may also play a role in processes that foster creative transformations of meanings in metaphor.

A three-way parallel ICA approach to analyze links among genetics, brain structure and brain function

Multi-modal data analysis techniques, such as the Parallel Independent Component Analysis (pICA), are essential in neuroscience, medical imaging and genetic studies. The pICA algorithm allows the simultaneous decomposition of up to two data modalities achieving better performance than separate ICA decompositions and enabling the discovery of links between modalities. However, advances in data acquisition techniques facilitate the collection of more than two data modalities from each subject. Examples of commonly measured modalities include genetic information, structural magnetic resonance imaging (MRI) and functional MRI. In order to take full advantage of the available data, this work extends the pICA approach to incorporate three modalities in one comprehensive analysis. Simulations demonstrate the three-way pICA performance in identifying pairwise links between modalities and estimating independent components which more closely resemble the true sources than components found by pICA or separate ICA analyses. In addition, the three-way pICA algorithm is applied to real experimental data obtained from a study that investigate genetic effects on alcohol dependence. Considered data modalities include functional MRI (contrast images during alcohol exposure paradigm), gray matter concentration images from structural MRI and genetic single nucleotide polymorphism (SNP). The three-way pICA approach identified links between a SNP component (pointing to brain function and mental disorder associated genes, including BDNF, GRIN2B and NRG1), a functional component related to increased activation in the precuneus area, and a gray matter component comprising part of the default mode network and the caudate. Although such findings need further verification, the simulation and in-vivo results validate the three-way pICA algorithm presented here as a useful tool in biomedical data fusion applications.

Unilateral Wakeup for Mobile Ad Hoc Networks with Group Mobility

Asynchronous wakeup schemes have been proposed for ad hoc networks to increase the energy efficiency of wireless communication. The basic idea is to allow a node to sleep when it is idle, and wakeup periodically to check if there are pending transmissions. In this paper, we examine the applicability of asynchronous wakeup schemes to the Mobile Ad Hoc NETworks (MANETs). We discover that, although it is desirable to have nodes with lower mobility to sleep more in reaction to the less-changing link states, in practice this is prohibited due to an unwanted tradeoff between the energy saving and in-time link discovery. All nodes in a network must stay awake frequently based on their highest possible moving speed to avoid network partition. To address this problem, we propose a new wakeup scheme, named Unilateral- (Uni-) scheme, for MANETs that allows nodes with slower moving speed to sleep more without losing the network connectivity. The Uni-scheme supports both the entity mobility and group mobility of nodes, thus has broad applicability. Theoretical analysis and simulation are conducted and show that the Uni-scheme can render significant energy saving as compared with the previous arts.

An evaluation framework for cross-lingual link discovery

Cross-Lingual Link Discovery (CLLD) is a new problem in Information Retrieval. The aim is to automatically identify meaningful and relevant hypertext links between documents in different languages. This is particularly helpful in knowledge discovery if a multi-lingual knowledge base is sparse in one language or another, or the topical coverage in each language is different; such is the case with Wikipedia. Techniques for identifying new and topically relevant cross-lingual links are a current topic of interest at NTCIR where the CrossLink task has been running since the 2011 NTCIR-9. This paper presents the evaluation framework for benchmarking algorithms for cross-lingual link discovery evaluated in the context of NTCIR-9.This framework includes topics, document collections, assessments, metrics, and a toolkit for pooling, assessment, and evaluation. The assessments are further divided into two separate sets: manual assessments performed by human assessors; and automatic assessments based on links extracted from Wikipedia itself. Using this framework we show that manual assessment is more robust than automatic assessment in the context of cross-lingual link discovery.

On the Discovery of Critical Links and Nodes for Assessing Network Vulnerability

The assessment of network vulnerability is of great importance in the presence of unexpected disruptive events or adversarial attacks targeting on critical network links and nodes. In this paper, we study Critical Link Disruptor (CLD) and Critical Node Disruptor (CND) optimization problems to identify critical links and nodes in a network whose removals maximally destroy the network's functions. We provide a comprehensive complexity analysis of CLD and CND on general graphs and show that they still remain NP-complete even on unit disk graphs and power-law graphs. Furthermore, the CND problem is shown NP-hard to be approximated within Ω([( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</i> - <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</i> )/( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</i> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ε</sup> )] ) on general graphs with <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</i> vertices and <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</i> critical nodes. Despite the intractability of these problems, we propose HILPR, a novel LP-based rounding algorithm, for efficiently solving CLD and CND problems in a timely manner. The effectiveness of our solutions is validated on various synthetic and real-world networks.

Complement: new therapies and emergence of the complotype

AbstractComplement, an ancient and rather neglected part of the innate immune system, is undergoing a renaissance. Informed by basic discoveries on structure and function of complement proteins and fuelled by discovery of genetic links to diverse diseases, complement is rapidly emerging from the shadows. The recognition that aberrant complement activation is a drive to pathology in many degenerative and inflammatory disorders has driven the development of new drugs targeting the complement system that are proving effective in haemolytic, renal, rheumatological and neurological diseases. In this brief overview, I will attempt to give a flavour of the key current developments that are transforming the field and provide signposts to guide the interested reader to more detailed and scholarly reviews.

Compensating for literature annotation bias when predicting novel drug-disease relationships through Medical Subject Heading Over-representation Profile (MeSHOP) similarity

BackgroundUsing annotations to the articles in MEDLINE®/PubMed®, over six thousand chemical compounds with pharmacological actions have been tracked since 1996. Medical Subject Heading Over-representation Profiles (MeSHOPs) quantitatively leverage the literature associated with biological entities such as diseases or drugs, providing the opportunity to reposition known compounds towards novel disease applications.MethodsA MeSHOP is constructed by counting the number of times each medical subject term is assigned to an entity-related research publication in the MEDLINE database and calculating the significance of the count by comparing against the count of the term in a background set of publications. Based on the expectation that drugs suitable for treatment of a disease (or disease symptom) will have similar annotation properties to the disease, we successfully predict drug-disease associations by comparing MeSHOPs of diseases and drugs.ResultsThe MeSHOP comparison approach delivers an 11% improvement over bibliometric baselines. However, novel drug-disease associations are observed to be biased towards drugs and diseases with more publications. To account for the annotation biases, a correction procedure is introduced and evaluated.ConclusionsBy explicitly accounting for the annotation bias, unexpectedly similar drug-disease pairs are highlighted as candidates for drug repositioning research. MeSHOPs are shown to provide a literature-supported perspective for discovery of new links between drugs and diseases based on pre-existing knowledge.

L'Italia paese cattolico considerazioni a margine di una lettura dei dati

It has been a long time since the religious dimension was an object of interest transcending the boundaries of religious studies. Such an interest deals with the discovery of links between the political and the religious dimensions. This phenomenon poses a double problem. On one hand, the data analysis risks to limit the research to the description of political influences. On the other hand, the little attention paid to the religious dimension does not allow the possibility to evaluate and consider how this specific dimension could influence the specific forms of political participation. Overall, the main limit of this analysis is to consider the political plan as an independent variable of this interpretative framework. Roberto Cartocci's recent book (Geografia dell'Italia cattolica) represents the latest example of this approach. This article focuses on the reductions political science runs the risk to cause, when it does not consider the specific features of the religious sphere. The latter plays the role of an independent variable in the relationship with the political game. A redefinition of the role of religion in post-modern society is coming. The religious dimension, that is at the centre of a process of reassessment, has already a lot to say.