Big Data Repositories Research Articles

Alveolar Osteitis Following Tooth Extraction: Systematic Review and Google Trends Analysis Instigated by the First Upper Premolar Case Reported from Iraq

Introduction： Alveolar osteitis is a painful condition that may occur following permanent teeth extraction due to the failure of formation of a blood clot or its dislodgement before the complete healing of the wound. We aim to provide a systematic review and trends analytic on the epidemiology and the digital epidemiology as well as the management of alveolar osteitis and to seek any available data in connection with alveolar osteitis following upper premolar tooth extraction. Methods： This study represents a combinatory of literature review, analytics of Google Trends, and the first documented case from Iraq of alveolar osteitis following extraction of the maxillary first premolar. Three literature databases were explored, using Boolean operators, including NCBI-PubMed, Elsevier, and the Cochrane Library. Google Trends database was examined to assess the digital epidemiology. Results：The total number of hits was 54417. There was an overall deficit of literature concerning the condition in connection with the extraction of maxillary premolars. The digital epidemiology was limited to twenty-two countries including three countries from the Middle East accounting for 13.63% of the total geographic mapping while Iraq was absent. Conclusion：Our exceptional case report instigated a systematic analytic of a trends database and the literature. The analysis confirmed the inadequacy of studies from the Middle East. Future studies should deploy the use of machine learning algorithms for a rigour statistical inference based on data from online and offline big data repositories of public health records.
  

Emergency Message Dissemination Schemes Based on Congestion Avoidance in VANET and Vehicular FoG Computing

With the rapid growth in connected vehicles, FoG-assisted vehicular ad hoc network (VANET) is an emerging and novel field of research. For information sharing, a number of messages are exchanged in various applications, including traffic monitoring and area-specific live weather and social aspects monitoring. It is quite challenging where vehicles’ speed, direction, and density of neighbors on the move are not consistent. In this scenario, congestion avoidance is also quite challenging to avoid communication loss during busy hours or in emergency cases. This paper presents emergency message dissemination schemes that are based on congestion avoidance scenario in VANET and vehicular FoG computing. In the similar vein, FoG-assisted VANET architecture is explored that can efficiently manage the message congestion scenarios. We present a taxonomy of schemes that address message congestion avoidance. Next, we have included a discussion about comparison of congestion avoidance schemes to highlight the strengths and weaknesses. We have also identified that FoG servers help to reduce the accessibility delays and congestion as compared to directly approaching cloud for all requests in linkage with big data repositories. For the dependable applicability of FoG in VANET, we have identified a number of open research challenges.

Semantic lifting and reasoning on the personalised activity big data repository for healthcare research

Semantic lifting and reasoning on the personalised activity big data repository for healthcare research

Exploiting Genomic Relations in Big Data Repositories by Graph-Based Search Methods

We are living at a time that allows the generation of mass data in almost any field of science. For instance, in pharmacogenomics, there exist a number of big data repositories, e.g., the Library of Integrated Network-based Cellular Signatures (LINCS) that provide millions of measurements on the genomics level. However, to translate these data into meaningful information, the data need to be analyzable. The first step for such an analysis is the deliberate selection of subsets of raw data for studying dedicated research questions. Unfortunately, this is a non-trivial problem when millions of individual data files are available with an intricate connection structure induced by experimental dependencies. In this paper, we argue for the need to introduce such search capabilities for big genomics data repositories with a specific discussion about LINCS. Specifically, we suggest the introduction of smart interfaces allowing the exploitation of the connections among individual raw data files, giving raise to a network structure, by graph-based searches.

A Spatio-Temporal Entropy-based Framework for the Detection of Trajectories Similarity

The rapid proliferation of sensors and big data repositories offer many new opportunities for data science. Among many application domains, the analysis of large trajectory datasets generated from people’s movements at the city scale is one of the most promising research avenues still to explore. Extracting trajectory patterns and outliers in urban environments is a direction still requiring exploration for many management and planning tasks. The research developed in this paper introduces a spatio-temporal framework, so-called STE-SD (Spatio-Temporal Entropy for Similarity Detection), based on the initial concept of entropy as introduced by Shannon in his seminal theory of information and as recently extended to the spatial and temporal dimensions. Our approach considers several complementary trajectory descriptors whose distribution in space and time are quantitatively evaluated. The trajectory primitives considered include curvatures, stop-points, self-intersections and velocities. These primitives are identified and then qualified using the notion of entropy as applied to the spatial and temporal dimensions. The whole approach is experimented and applied to urban trajectories derived from the Geolife dataset, a reference data benchmark available in the city of Beijing.

Personalizing Medicine Through Hybrid Imaging and Medical Big Data Analysis

Medical imaging has evolved from a pure visualization tool to representing a primary source of analytic approaches towards in vivo disease characterization. Hybrid imaging is an integral part of this approach, as it provides complementary visual and quantitative information in the form of morphological and functional insights into the living body. As such, non-invasive imaging modalities no longer provide images only, but data, as stated recently by pioneers in the field. Today, such information, together with other, non-imaging medical data creates highly heterogeneous data sets that underpin the concept of medical big data. While the exponential growth of medical big data challenges their processing, they inherently contain information that benefits a patient-centric personalized healthcare. Novel machine learning approaches combined with high-performance distributed cloud computing technologies help explore medical big data. Such exploration and subsequent generation of knowledge require a profound understanding of the technical challenges. These challenges increase in complexity when employing hybrid, aka dual- or even multi-modality image data as input to big data repositories. This paper provides a general insight into medical big data analysis in light of the use of hybrid imaging information. First, hybrid imaging is introduced (see further contributions to this special Research Topic), also in the context of medical big data, then the technological background of machine learning as well as state-of-the-art distributed cloud computing technologies are presented, followed by the discussion of data preservation and data sharing trends. Joint data exploration endeavours in the context of in vivo radiomics and hybrid imaging will be presented. Standardization challenges of imaging protocol, delineation, feature engineering and machine learning evaluation will be detailed. Last, the paper will provide an outlook into the future role of hybrid imaging in view of personalized medicine, whereby a focus will be given to the derivation of prediction models as part of clinical decision support systems, to which machine learning approaches and hybrid imaging can be anchored.

Spatial Blockchain-Based Secure Mass Screening Framework for Children With Dyslexia

In this paper, we present a novel method, process, and system for calculating dyslexic symptoms, generating metric data for an individual user, community, or group in general. We present a mobile multimedia Internet of Things (IoT)-based environment that can capture multimodal smartphone or tab-based user interaction data during dyslexia testing and share it via a mobile edge network, which employs auto-grading algorithms to find dyslexia symptoms. In addition to algorithm-based auto-grading, the captured mobile multimedia payload is stored in a decentralized repository that can be shared with a medical practitioner for replay and further manual analysis purposes. Since the framework is language-independent and based on Blockchain and a decentralized big data repository, dyslexic patterns and a massive amount of captured multimedia IoT test data can be shared for further clinical research, statistical analysis, and quality assurance. Notwithstanding, our proposed Blockchain and off-chain-based decentralized and secure dyslexia data storage, management, and sharing framework will allow security, anonymity, and multimodal visualization of the captured test data for mobile users. This paper presents the detailed design, implementation, and test results, which demonstrate the strong potential for wider adoption of the dyslexia mobile health management globally.

Potential of big data analytics in the French in vitro diagnostics market.

The new paradigm of the big data raises many expectations, particularly in the field of health. Curiously, even though medical biology laboratories generate a great amount of data, the opportunities offered by this new field are poorly documented. For better understanding the clinical context of chronical disease follow-up, for leveraging preventive and/or personalized medicine, the contribution of big data analytics seems very promising. It is within this framework that we have explored to use data of a Breton group of laboratories of medical biology to analyze the possible contributions of their exploitation in the improvement of the clinical practices and to anticipate the evolution of pathologies for the benefit of patients. We report here three practical applications derived from routine laboratory data from a period of 5 years (February 2010-August 2015): follow-up of patients treated with AVK according to the recommendations of the High authority of health (HAS), use of the new troponin markers HS and NT-proBNP in cardiology. While the risks and difficulties of using algorithms in the health domain should not be underestimated - quality, accessibility, and protection of personal data in particular - these first results show that use of tools and technologies of the big data repository could provide decisive support for the concept of "evidence based medicine".

MMRepo - Storing qualitative and quantitative data into one big data repository

MMRepo - Storing qualitative and quantitative data into one big data repository

Research Techniques Made Simple: An Introduction to Use and Analysis of Big Data in Dermatology

Big data is a term used for any collection of datasets whose size and complexity exceeds the capabilities of traditional data processing applications. Big data repositories, including those for molecular, clinical, and epidemiology data, offer unprecedented research opportunities to help guide scientific advancement. Advantages of big data can include ease and low cost of collection, ability to approach prospectively and retrospectively, utility for hypothesis generation in addition to hypothesis testing, and the promise of precision medicine. Limitations include cost and difficulty of storing and processing data; need for advanced techniques for formatting and analysis; and concerns about accuracy, reliability, and security. We discuss sources of big data and tools for its analysis to help inform the treatment and management of dermatologic diseases.

Terra Populus' Architecture for Integrated Big Geospatial Services.

Big geospatial data is an emerging sub-area of geographic information science, big data, and cyberinfrastructure. Big geospatial data poses two unique challenges to these and other cognate disciplines. First, raster and vector data structures and analyses have developed on largely separate paths for the last twenty years and this creates an impediment to researchers utilizing big data platforms that do not promote the integration for these classes. Second, big spatial data repositories have yet to be integrated with big data computation platforms in ways that allow researchers to spatio-temporally analyze big geospatial datasets. IPUMS-Terra, a National Science Foundation cyberInfrastructure project, begins to address these challenges. IPUMS-Terra is a spatial data infrastructure project that provides a unified framework for accessing, analyzing, and transforming big heterogeneous spatio-temporal data, and is part of the IPUMS (Integrated Public Use Microdata Series) data infrastructure. It supports big geospatial data analysis and provides integrated big geospatial services to its users. As IPUMS-Terra's data volume grows, we seek to integrate geospatial platforms that will scale geospatial analyses and address current bottlenecks within our system. However, our work shows that there are still unresolved challenges for big geospatial analysis. The most pertinent is that there is a lack of a unified framework for conducting scalable integrated vector and raster data analysis. We conducted a comparative analysis between PostgreSQL with PostGIS and SciDB and concluded that SciDB is the superior platform for scalable raster zonal analyses.

Drug repurposing from the perspective of pharmaceutical companies

This article is part of a themed section on Inventing New Therapies Without Reinventing the Wheel: The Power of Drug Repurposing. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.2/issuetoc.

Toward leveraging big value from data: chronic lymphocytic leukemia cell classification

The goal of Big Data analysis is delineating hidden patterns from data and leverage them into strategies and plans to support informed decision making in a diversity of situations. Big Data are characterized by large volume, high velocity, wide variety, and high value, which may represent difficulties in storage and processing. Research on Big Data repositories has contributed promising results that primarily address how to efficiently mine a variety of large volume of structured and unstructured data. However, innovative insights can emerge while leveraging the value characteristic of Big Data. In other words, any given data can be big if analytics can draw a big value from it. In this paper, we demonstrate the potential of five machine learning algorithms to leverage the value of medium size microscopic blood smear images to classify patients with chronic lymphocytic leukemia (CLL). The maximum majority voting method is used to fuse the predications made by the five classifier models. To validate this work, 11 CLL patients are refereed by flow cytometry equipment and the results are compared to the proposed classifier model. The proposed method proceeds through a sequence of steps while working with the lymphocyte images: it segments the lymphocyte images, extracts/selects features, classifies the selected features using five classifiers, and calculates the majority class for the test image. The proposed composite classifier model has an accuracy of 87.0%, true-positive rate of 84.95%, and 10.96% false-positive rate and can correctly identify 9 out of 11 patients as positive for CLL.

Expanding Access to Large-Scale Genomic Data While Promoting Privacy: A Game Theoretic Approach

Emerging scientific endeavors are creating big data repositories of data from millions of individuals. Sharing data in a privacy-respecting manner could lead to important discoveries, but high-profile demonstrations show that links between de-identified genomic data and named persons can sometimes be reestablished. Such re-identification attacks have focused on worst-case scenarios and spurred the adoption of data-sharing practices that unnecessarily impede research. To mitigate concerns, organizations have traditionally relied upon legal deterrents, like data use agreements, and are considering suppressing or adding noise to genomic variants. In this report, we use a game theoretic lens to develop more effective, quantifiable protections for genomic data sharing. This is a fundamentally different approach because it accounts for adversarial behavior and capabilities and tailors protections to anticipated recipients with reasonable resources, not adversaries with unlimited means. We demonstrate this approach via a new public resource with genomic summary data from over 8,000 individuals-the Sequence and Phenotype Integration Exchange (SPHINX)-and show that risks can be balanced against utility more effectively than with traditional approaches. We further show the generalizability of this framework by applying it to other genomic data collection and sharing endeavors. Recognizing that such models are dependent on a variety of parameters, we perform extensive sensitivity analyses to show that our findings are robust to their fluctuations.

Relevance of eHealth standards for big data interoperability in radiology and beyond.

The aim of this paper is to report on the implementation of radiology and related information technology standards to feed big data repositories and so to be able to create a solid substrate on which to operate with analysis software. Digital Imaging and Communications in Medicine (DICOM) and Health Level 7 (HL7) are the major standards for radiology and medical information technology. They define formats and protocols to transmit medical images, signals, and patient data inside and outside hospital facilities. These standards can be implemented but big data expectations are stimulating a new approach, simplifying data collection and interoperability, seeking reduction of time to full implementation inside health organizations. Virtual Medical Record, DICOM Structured Reporting and HL7 Fast Healthcare Interoperability Resources (FHIR) are changing the way medical data are shared among organization and they will be the keys to big data interoperability. Until we do not find simple and comprehensive methods to store and disseminate detailed information on the patient's health we will not be able to get optimum results from the analysis of those data.

Applications of Big Data in the Digital India: Opportunities and Challenges

<div><p><em>With the advent of Social Networking Sites (SNS), volumes of data are generated daily. Most of these data are multimedia type and unstructured with exponential growth. This exponential growth of variety, volume and complexity of structured and unstructured data leads to the concept of big data. Managing big data and harnessing its benefits is a real challenge. With increase in access to big data repository for various applications, security and access control is another aspect that needs to be considered while managing big data. We have discussed area of application of big data, opportunities it provides and challenges that we face in the managing such huge amount of data for various applications. Issues related to security against different threat perception of big data are also discussed. </em></p></div>

Real-time stream processing for Big Data

Abstract With the rise of the web 2.0 and the Internet of things, it has become feasible to track all kinds of information over time, in particular fine-grained user activities and sensor data on their environment and even their biometrics. However, while efficiency remains mandatory for any application trying to cope with huge amounts of data, only part of the potential of today's Big Data repositories can be exploited using traditional batch-oriented approaches as the value of data often decays quickly and high latency becomes unacceptable in some applications. In the last couple of years, several distributed data processing systems have emerged that deviate from the batch-oriented approach and tackle data items as they arrive, thus acknowledging the growing importance of timeliness and velocity in Big Data analytics. In this article, we give an overview over the state of the art of stream processors for low-latency Big Data analytics and conduct a qualitative comparison of the most popular contenders, namely Storm and its abstraction layer Trident, Samza and Spark Streaming. We describe their respective underlying rationales, the guarantees they provide and discuss the trade-offs that come with selecting one of them for a particular task.

Acquisition, Analysis, and Sharing of Data in 2015 and Beyond: A Survey of the Landscape: A Conference Report From the American Heart Association Data Summit 2015.

BackgroundA 1.5‐day interactive forum was convened to discuss critical issues in the acquisition, analysis, and sharing of data in the field of cardiovascular and stroke science. The discussion will serve as the foundation for the American Heart Association's (AHA's) near‐term and future strategies in the Big Data area. The concepts evolving from this forum may also inform other fields of medicine and science.Methods and ResultsA total of 47 participants representing stakeholders from 7 domains (patients, basic scientists, clinical investigators, population researchers, clinicians and healthcare system administrators, industry, and regulatory authorities) participated in the conference. Presentation topics included updates on data as viewed from conventional medical and nonmedical sources, building and using Big Data repositories, articulation of the goals of data sharing, and principles of responsible data sharing. Facilitated breakout sessions were conducted to examine what each of the 7 stakeholder domains wants from Big Data under ideal circumstances and the possible roles that the AHA might play in meeting their needs. Important areas that are high priorities for further study regarding Big Data include a description of the methodology of how to acquire and analyze findings, validation of the veracity of discoveries from such research, and integration into investigative and clinical care aspects of future cardiovascular and stroke medicine. Potential roles that the AHA might consider include facilitating a standards discussion (eg, tools, methodology, and appropriate data use), providing education (eg, healthcare providers, patients, investigators), and helping build an interoperable digital ecosystem in cardiovascular and stroke science.ConclusionThere was a consensus across stakeholder domains that Big Data holds great promise for revolutionizing the way cardiovascular and stroke research is conducted and clinical care is delivered; however, there is a clear need for the creation of a vision of how to use it to achieve the desired goals. Potential roles for the AHA center around facilitating a discussion of standards, providing education, and helping establish a cardiovascular digital ecosystem. This ecosystem should be interoperable and needs to interface with the rapidly growing digital object environment of the modern‐day healthcare system.

Needed Relapse-Prevention Research on Novel Framework (ASPIRE Model) for Substance Use Disorders Treatment.

According to a recent United States (U.S.) national survey on drug use and health, substance use disorders (SUDs) characterized by hazardous use of alcohol, non-prescribed drugs, and illicit drugs are common. In 2013, 22.7 million persons (8.6% of persons aged 12 years or older) needed treatment for an illicit drug or alcohol-use problem (1). Drug use disorders produce a wide variety of medical problems and are important contributors to years of life lost due to disability and preventable death (2). Yet, screening, intervening, and treating SUDs have not been embraced within general medical settings (3). In fact, even though untreated SUDs place individuals at substantially greater risk for a wide range of diseases and are a pervasive public health burden, only approximately one-tenth of Americans aged 12 years or older with SUDs received treatment in 2013 (1). A main obstacle to patient engagement in and initiation of SUDs treatment is lack of motivation to seek out follow-up care. Motivation to do so may be compromised by a lack of a personalized-medicine approach, in which patients are frequently only offered a single or narrow set of care options, which do not align with their individual needs. A gap exists in research in medical settings regarding how to effectively implement shared-decision making between patients and their providers, concerning how to tailor evidence-based care options to personalized needs and preferences of clients (4–6). Converging research over the past 30 years indicates that core features of SUDs comprise of a spectrum of neurobiological components, which in 2014, I distilled into a shared-decision-making and personalized/precision medicine framework for SUD treatment, the ASPIRE model (7). This integrative model stresses the need for translational research on how to most effectively optimize implementation of patient-centered care using this model in general medical settings and specialty SUD-treatment programs, in a manner whereby patients have an active role as partners in deciding with their providers on treatment strategies for evidence-based care tailored to their risk categories and values (7). This precision medicine approach should be customized to genetic, psychological, and physiological profiles and environmental events that patients experience as presenting an obstacle to their overall wellness and recovery (7). Accordingly, treatment and follow-up care plans should be matched with individual disease characteristics, which may enhance motivation of patients to cease hazardous substance use and associated health risk behaviors (7). Thus, the ASPIRE model uses as its foundational principle shared-decision-making between patients and healthcare providers to customize personalized medical care to particular neuroscience-research-grounded profiles, psychiatric comorbidities, readiness to change, risk categories, and problems that individual patients report as most distressing to their daily lives (7). Recent advances in genomic and health information technologies [for instance, meaningful use of electronic health record systems (EHRs), telemedicine, mobile-health technologies, EHRs-linked patient registries, EHRs-linked genomic data and lifestyle information, etc.] and bioinformatics methods for analyzing EHRs-linked biomedical big-data repositories should be leveraged to accelerate rigorous big-data science research on how to effectively implement such a personalized-medicine framework in general medical settings. In circumstances where individual patients are cognitively impaired and have limited insight, such a shared-decision-making approach to SUD treatment may actively involve patients’ caregivers or other family members, if patients consent to their involvement in their medical care (4–7). In such cases, family members may be recruited to help ensure patients follow through and adhere to their treatment plan mutually agreed upon with their medical provider. Systematic rigorous research is needed using a shared-decision-making approach to find more effective ways of reducing the burden of SUD and enhancing quality of lives not only for individual patients but also for their family members affected by an individual’s SUD.

Managing big data experiments on smartphones

The explosive number of smartphones with ever growing sensing and computing capabilities have brought a paradigm shift to many traditional domains of the computing field. Re-programming smartphones and instrumenting them for application testing and data gathering at scale is currently a tedious and time-consuming process that poses significant logistical challenges. Next generation smartphone applications are expected to be much larger-scale and complex, demanding that these undergo evaluation and testing under different real-world datasets, devices and conditions. In this paper, we present an architecture for managing such large-scale data management experiments on real smartphones. We particularly present the building blocks of our architecture that encompassed smartphone sensor data collected by the crowd and organized in our big data repository. The given datasets can then be replayed on our testbed comprising of real and simulated smartphones accessible to developers through a web-based interface. We present the applicability of our architecture through a case study that involves the evaluation of individual components that are part of a complex indoor positioning system for smartphones, coined Anyplace, which we have developed over the years. The given study shows how our architecture allows us to derive novel insights into the performance of our algorithms and applications, by simplifying the management of large-scale data on smartphones.