351
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Dillon MM, Almeida RN, Laflamme B, Martel A, Weir BS, Desveaux D, Guttman DS. Molecular Evolution of Pseudomonas syringae Type III Secreted Effector Proteins. FRONTIERS IN PLANT SCIENCE 2019; 10:418. [PMID: 31024592 PMCID: PMC6460904 DOI: 10.3389/fpls.2019.00418] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/19/2019] [Indexed: 05/02/2023]
Abstract
Diverse Gram-negative pathogens like Pseudomonas syringae employ type III secreted effector (T3SE) proteins as primary virulence factors that combat host immunity and promote disease. T3SEs can also be recognized by plant hosts and activate an effector triggered immune (ETI) response that shifts the interaction back toward plant immunity. Consequently, T3SEs are pivotal in determining the virulence potential of individual P. syringae strains, and ultimately help to restrict P. syringae pathogens to a subset of potential hosts that are unable to recognize their repertoires of T3SEs. While a number of effector families are known to be present in the P. syringae species complex, one of the most persistent challenges has been documenting the complex variation in T3SE contents across a diverse collection of strains. Using the entire pan-genome of 494 P. syringae strains isolated from more than 100 hosts, we conducted a global analysis of all known and putative T3SEs. We identified a total of 14,613 putative T3SEs, 4,636 of which were unique at the amino acid level, and show that T3SE repertoires of different P. syringae strains vary dramatically, even among strains isolated from the same hosts. We also find substantial diversification within many T3SE families, and in many cases find strong signatures of positive selection. Furthermore, we identify multiple gene gain and loss events for several families, demonstrating an important role of horizontal gene transfer (HGT) in the evolution of P. syringae T3SEs. These analyses provide insight into the evolutionary history of P. syringae T3SEs as they co-evolve with the host immune system, and dramatically expand the database of P. syringae T3SEs alleles.
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Affiliation(s)
- Marcus M. Dillon
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Renan N.D. Almeida
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Bradley Laflamme
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Alexandre Martel
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | | | - Darrell Desveaux
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, Canada
| | - David S. Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, Canada
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352
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Sosnin S, Vashurina M, Withnall M, Karpov P, Fedorov M, Tetko IV. A Survey of Multi-task Learning Methods in Chemoinformatics. Mol Inform 2019; 38:e1800108. [PMID: 30499195 PMCID: PMC6587441 DOI: 10.1002/minf.201800108] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/16/2018] [Indexed: 01/09/2023]
Abstract
Despite the increasing volume of available data, the proportion of experimentally measured data remains small compared to the virtual chemical space of possible chemical structures. Therefore, there is a strong interest in simultaneously predicting different ADMET and biological properties of molecules, which are frequently strongly correlated with one another. Such joint data analyses can increase the accuracy of models by exploiting their common representation and identifying common features between individual properties. In this work we review the recent developments in multi-learning approaches as well as cover the freely available tools and packages that can be used to perform such studies.
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Affiliation(s)
- Sergey Sosnin
- Center for Computational and Data-Intensive Science and EngineeringSkolkovo Institute of Science and Technology Skolkovo Innovation CenterMoscow143026Russia
| | - Mariia Vashurina
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH)Institute of Structural BiologyIngolstädter Landstraße 1D-85764NeuherbergGermany
| | - Michael Withnall
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH)Institute of Structural BiologyIngolstädter Landstraße 1D-85764NeuherbergGermany
| | - Pavel Karpov
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH)Institute of Structural BiologyIngolstädter Landstraße 1D-85764NeuherbergGermany
| | - Maxim Fedorov
- Center for Computational and Data-Intensive Science and EngineeringSkolkovo Institute of Science and Technology Skolkovo Innovation CenterMoscow143026Russia
- University of StrathclydeDepartment of Physics John Anderson Building, 107 Rottenrow EastG40NGGlasgowUnited Kingdom
| | - Igor V. Tetko
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH)Institute of Structural BiologyIngolstädter Landstraße 1D-85764NeuherbergGermany
- BIGCHEM GmbHIngolstädter Landstraße 1, b. 60wD-85764NeuherbergGermany
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353
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A Deep Learning Approach to Position Estimation from Channel Impulse Responses. SENSORS 2019; 19:s19051064. [PMID: 30832327 PMCID: PMC6427749 DOI: 10.3390/s19051064] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/22/2019] [Accepted: 02/25/2019] [Indexed: 11/20/2022]
Abstract
Radio-based locating systems allow for a robust and continuous tracking in industrial environments and are a key enabler for the digitalization of processes in many areas such as production, manufacturing, and warehouse management. Time difference of arrival (TDoA) systems estimate the time-of-flight (ToF) of radio burst signals with a set of synchronized antennas from which they trilaterate accurate position estimates of mobile tags. However, in industrial environments where multipath propagation is predominant it is difficult to extract the correct ToF of the signal. This article shows how deep learning (DL) can be used to estimate the position of mobile objects directly from the raw channel impulse responses (CIR) extracted at the receivers. Our experiments show that our DL-based position estimation not only works well under harsh multipath propagation but also outperforms state-of-the-art approaches in line-of-sight situations.
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354
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Safran M, Che D. Efficient Learning-Based Recommendation Algorithms for Top-
N
Tasks and Top-
N
Workers in Large-Scale Crowdsourcing Systems. ACM T INFORM SYST 2019. [DOI: 10.1145/3231934] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The task and worker recommendation problems in crowdsourcing systems have brought up unique characteristics that are not present in traditional recommendation scenarios, i.e., the huge flow of tasks with short lifespans, the importance of workers’ capabilities, and the quality of the completed tasks. These unique features make traditional recommendation approaches no longer satisfactory for task and worker recommendation in crowdsourcing systems. In this article, we propose a two-tier data representation scheme (defining a
worker--category suitability score
and a
worker--task attractiveness score
) to support personalized task and worker recommendations. We also extend two optimization methods, namely least mean square error and Bayesian personalized rank, to better fit the characteristics of task/worker recommendation in crowdsourcing systems. We then integrate the proposed representation scheme and the extended optimization methods along with the two adapted popular learning models, i.e., matrix factorization and kNN, and result in two lines of top-
N
recommendation algorithms for crowdsourcing systems: (1) Top-
N
-Tasks recommendation algorithms for discovering the top-
N
most suitable tasks for a given worker and (2) Top-
N
-Workers recommendation algorithms for identifying the top-
N
best workers for a task requester. An extensive experimental study is conducted that validates the effectiveness and efficiency of a broad spectrum of algorithms, accompanied by our analysis and the insights gained.
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Affiliation(s)
- Mejdl Safran
- King Saud University and Southern Illinois University Carbondale, Kingdom of Saudi Arabia
| | - Dunren Che
- Southern Illinois University Carbondale, IL, USA
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355
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Carnein M, Trautmann H. Optimizing Data Stream Representation: An Extensive Survey on Stream Clustering Algorithms. BUSINESS & INFORMATION SYSTEMS ENGINEERING 2019. [DOI: 10.1007/s12599-019-00576-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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356
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Abstract
The present review retraces the steps of the industrial and agriculture revolution that have taken place up to the present day, giving ideas and considerations for the future. This paper analyses the specific challenges facing agriculture along the farming supply chain to permit the operative implementation of Industry 4.0 guidelines. The subsequent scientific value is an investigation of how Industry 4.0 approaches can be improved and be pertinent to the agricultural sector. However, industry is progressing at a much faster rate than agriculture. In fact, already today experts talk about Industry 5.0. On the other hand, the 4.0 revolution in agriculture is still limited to a few innovative firms. For this reason, this work deals with how technological development affects different sectors (industry and agriculture) in different ways. In this innovative background, despite the advantages of industry or agriculture 4.0 for large enterprises, small- and medium-sized enterprises (SMEs) often face complications in such innovative processes due to the continuous development in innovations and technologies. Policy makers should propose strategies, calls for proposals with aim of supporting SMEs to invest on these technologies and making them more competitive in the marketplace.
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357
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Gautam B, Basava A. Performance prediction of data streams on high-performance architecture. HUMAN-CENTRIC COMPUTING AND INFORMATION SCIENCES 2019. [DOI: 10.1186/s13673-018-0163-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
Worldwide sensor streams are expanding continuously with unbounded velocity in volume, and for this acceleration, there is an adaptation of large stream data processing system from the homogeneous to rack-scale architecture which makes serious concern in the domain of workload optimization, scheduling, and resource management algorithms. Our proposed framework is based on providing architecture independent performance prediction model to enable resource adaptive distributed stream data processing platform. It is comprised of seven pre-defined domain for dynamic data stream metrics including a self-driven model which tries to fit these metrics using ridge regularization regression algorithm. Another significant contribution lies in fully-automated performance prediction model inherited from the state-of-the-art distributed data management system for distributed stream processing systems using Gaussian processes regression that cluster metrics with the help of dimensionality reduction algorithm. We implemented its base on Apache Heron and evaluated with proposed Benchmark Suite comprising of five domain-specific topologies. To assess the proposed methodologies, we forcefully ingest tuple skewness among the benchmarking topologies to set up the ground truth for predictions and found that accuracy of predicting the performance of data streams increased up to 80.62% from 66.36% along with the reduction of error from 37.14 to 16.06%.
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358
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Gurke R, Etyemez S, Prvulovic D, Thomas D, Fleck SC, Reif A, Geisslinger G, Lötsch J. A Data Science-Based Analysis Points at Distinct Patterns of Lipid Mediator Plasma Concentrations in Patients With Dementia. Front Psychiatry 2019; 10:41. [PMID: 30804821 PMCID: PMC6378270 DOI: 10.3389/fpsyt.2019.00041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/22/2019] [Indexed: 12/19/2022] Open
Abstract
Based on accumulating evidence of a role of lipid signaling in many physiological and pathophysiological processes including psychiatric diseases, the present data driven analysis was designed to gather information needed to develop a prospective biomarker, using a targeted lipidomics approach covering different lipid mediators. Using unsupervised methods of data structure detection, implemented as hierarchal clustering, emergent self-organizing maps of neuronal networks, and principal component analysis, a cluster structure was found in the input data space comprising plasma concentrations of d = 35 different lipid-markers of various classes acquired in n = 94 subjects with the clinical diagnoses depression, bipolar disorder, ADHD, dementia, or in healthy controls. The structure separated patients with dementia from the other clinical groups, indicating that dementia is associated with a distinct lipid mediator plasma concentrations pattern possibly providing a basis for a future biomarker. This hypothesis was subsequently assessed using supervised machine-learning methods, implemented as random forests or principal component analysis followed by computed ABC analysis used for feature selection, and as random forests, k-nearest neighbors, support vector machines, multilayer perceptron, and naïve Bayesian classifiers to estimate whether the selected lipid mediators provide sufficient information that the diagnosis of dementia can be established at a higher accuracy than by guessing. This succeeded using a set of d = 7 markers comprising GluCerC16:0, Cer24:0, Cer20:0, Cer16:0, Cer24:1, C16 sphinganine, and LacCerC16:0, at an accuracy of 77%. By contrast, using random lipid markers reduced the diagnostic accuracy to values of 65% or less, whereas training the algorithms with randomly permuted data was followed by complete failure to diagnose dementia, emphasizing that the selected lipid mediators were display a particular pattern in this disease possibly qualifying as biomarkers.
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Affiliation(s)
- Robert Gurke
- Institute of Clinical Pharmacology, University Hospital of Frankfurt, Goethe-University, Frankfurt, Germany
| | - Semra Etyemez
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital of Frankfurt, Goethe-University, Frankfurt, Germany
| | - David Prvulovic
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital of Frankfurt, Goethe-University, Frankfurt, Germany
| | - Dominique Thomas
- Institute of Clinical Pharmacology, University Hospital of Frankfurt, Goethe-University, Frankfurt, Germany
| | - Stefanie C Fleck
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology TMP, Frankfurt, Germany
| | - Andreas Reif
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital of Frankfurt, Goethe-University, Frankfurt, Germany
| | - Gerd Geisslinger
- Institute of Clinical Pharmacology, University Hospital of Frankfurt, Goethe-University, Frankfurt, Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology TMP, Frankfurt, Germany
| | - Jörn Lötsch
- Institute of Clinical Pharmacology, University Hospital of Frankfurt, Goethe-University, Frankfurt, Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology TMP, Frankfurt, Germany
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359
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Chakravarthy S, Santra A, Komar KS. Why Multilayer Networks Instead of Simple Graphs? Modeling Effectiveness and Analysis Flexibility and Efficiency! BIG DATA ANALYTICS 2019. [DOI: 10.1007/978-3-030-37188-3_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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360
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Kaur P, Gulati S. Dependency Graph Based Detection of Semantically Equivalent Questions in Online Forums. INTERNATIONAL JOURNAL OF INFORMATION RETRIEVAL RESEARCH 2019. [DOI: 10.4018/ijirr.2019010104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In the present, people increasingly rely on online user forums for clearing their doubts and seeking answers to varied questions. On many online forums, users encounter a similar question asked in different formats. This results in confusion for the user and he may not be able to find appropriate answer to his question even though the appropriate answer exists on some other page, i.e., on the page resultant of a differently formed question. Currently, online forums like Quora only give suggestions to the user about the questions he could ask but do not show all the semantically equivalent questions. This article eases the work of the users searching for answers on online user forums. The proposed technique will allow the users to look at all the existing semantically equivalent questions. A dependency graph-based matching algorithm is applied to accomplish this objective.
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Affiliation(s)
- Parmeet Kaur
- Jaypee Institute of Information Technology, Noida, India
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361
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Cobas C. Applications of the Whittaker smoother in NMR spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:1140-1148. [PMID: 29719068 DOI: 10.1002/mrc.4747] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/09/2018] [Accepted: 04/16/2018] [Indexed: 05/26/2023]
Abstract
The Whittaker smoother, a special case of penalized least square, is a multipurpose algorithm that has proven to be very useful in many scientific fields, including image processing, chromatography, and optical spectroscopy. It shares many similarities with the Savitzky-Golay algorithm, but it is significantly faster and easier to automate. Its use in nuclear magnetic resonance, however, is not widespread although several applications have recently been published. In this review, the mathematical background of the method and its main applications in nuclear magnetic resonance spectroscopy will be discussed.
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Affiliation(s)
- Carlos Cobas
- Mestrelab Research S.L., Santiago de Compostela, A Coruña, 15706, Spain
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362
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NLOS Identification in WLANs Using Deep LSTM with CNN Features. SENSORS 2018; 18:s18114057. [PMID: 30463383 PMCID: PMC6263707 DOI: 10.3390/s18114057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/03/2018] [Accepted: 11/13/2018] [Indexed: 11/17/2022]
Abstract
Identifying channel states as line-of-sight or non-line-of-sight helps to optimize location-based services in wireless communications. The received signal strength identification and channel state information are used to estimate channel conditions for orthogonal frequency division multiplexing systems in indoor wireless local area networks. This paper proposes a joint convolutional neural network and recurrent neural network architecture to classify channel conditions. Convolutional neural networks extract the feature from frequency-domain characteristics of channel state information data and recurrent neural networks extract the feature from time-varying characteristics of received signal strength identification and channel state information between packet transmissions. The performance of the proposed methods is verified under indoor propagation environments. Experimental results show that the proposed method has a 2% improvement in classification performance over the conventional recurrent neural network model.
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363
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Wang QF, Xu M, Hussain A. Large-scale Ensemble Model for Customer Churn Prediction in Search Ads. Cognit Comput 2018. [DOI: 10.1007/s12559-018-9608-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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364
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Lötsch J, Schiffmann S, Schmitz K, Brunkhorst R, Lerch F, Ferreiros N, Wicker S, Tegeder I, Geisslinger G, Ultsch A. Machine-learning based lipid mediator serum concentration patterns allow identification of multiple sclerosis patients with high accuracy. Sci Rep 2018; 8:14884. [PMID: 30291263 PMCID: PMC6173715 DOI: 10.1038/s41598-018-33077-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 09/11/2018] [Indexed: 02/07/2023] Open
Abstract
Based on increasing evidence suggesting that MS pathology involves alterations in bioactive lipid metabolism, the present analysis was aimed at generating a complex serum lipid-biomarker. Using unsupervised machine-learning, implemented as emergent self-organizing maps of neuronal networks, swarm intelligence and Minimum Curvilinear Embedding, a cluster structure was found in the input data space comprising serum concentrations of d = 43 different lipid-markers of various classes. The structure coincided largely with the clinical diagnosis, indicating that the data provide a basis for the creation of a biomarker (classifier). This was subsequently assessed using supervised machine-learning, implemented as random forests and computed ABC analysis-based feature selection. Bayesian statistics-based biomarker creation was used to map the diagnostic classes of either MS patients (n = 102) or healthy subjects (n = 301). Eight lipid-markers passed the feature selection and comprised GluCerC16, LPA20:4, HETE15S, LacCerC24:1, C16Sphinganine, biopterin and the endocannabinoids PEA and OEA. A complex classifier or biomarker was developed that predicted MS at a sensitivity, specificity and accuracy of approximately 95% in training and test data sets, respectively. The present successful application of serum lipid marker concentrations to MS data is encouraging for further efforts to establish an MS biomarker based on serum lipidomics.
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Affiliation(s)
- Jörn Lötsch
- Institute of Clinical Pharmacology, Goethe-University, Theodor - Stern - Kai 7, 60590, Frankfurt am Main, Germany.
- Fraunhofer Institute of Molecular Biology and Applied Ecology - Project Group Translational Medicine and Pharmacology (IME-TMP), Theodor - Stern - Kai 7, 60590, Frankfurt am Main, Germany.
| | - Susanne Schiffmann
- Fraunhofer Institute of Molecular Biology and Applied Ecology - Project Group Translational Medicine and Pharmacology (IME-TMP), Theodor - Stern - Kai 7, 60590, Frankfurt am Main, Germany
| | - Katja Schmitz
- Institute of Clinical Pharmacology, Goethe-University, Theodor - Stern - Kai 7, 60590, Frankfurt am Main, Germany
| | - Robert Brunkhorst
- Department of Neurology, Goethe-University Hospital, Theodor - Stern - Kai 7, 60590, Frankfurt am Main, Germany
| | - Florian Lerch
- DataBionics Research Group, University of Marburg, Hans - Meerwein - Straße 22, 35032, Marburg, Germany
| | - Nerea Ferreiros
- Institute of Clinical Pharmacology, Goethe-University, Theodor - Stern - Kai 7, 60590, Frankfurt am Main, Germany
| | - Sabine Wicker
- Occupational Health Service, University Hospital Frankfurt, Theodor - Stern - Kai 7, 60590, Frankfurt am Main, Germany
| | - Irmgard Tegeder
- Institute of Clinical Pharmacology, Goethe-University, Theodor - Stern - Kai 7, 60590, Frankfurt am Main, Germany
| | - Gerd Geisslinger
- Institute of Clinical Pharmacology, Goethe-University, Theodor - Stern - Kai 7, 60590, Frankfurt am Main, Germany
- Fraunhofer Institute of Molecular Biology and Applied Ecology - Project Group Translational Medicine and Pharmacology (IME-TMP), Theodor - Stern - Kai 7, 60590, Frankfurt am Main, Germany
| | - Alfred Ultsch
- DataBionics Research Group, University of Marburg, Hans - Meerwein - Straße 22, 35032, Marburg, Germany
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365
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Oussous A, Benjelloun FZ, Ait Lahcen A, Belfkih S. Big Data technologies: A survey. JOURNAL OF KING SAUD UNIVERSITY-COMPUTER AND INFORMATION SCIENCES 2018. [DOI: 10.1016/j.jksuci.2017.06.001] [Citation(s) in RCA: 290] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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366
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Accuracy of Markerless 3D Motion Capture Evaluation to Differentiate between On/Off Status in Parkinson's Disease after Deep Brain Stimulation. PARKINSONS DISEASE 2018; 2018:5830364. [PMID: 30363689 PMCID: PMC6180930 DOI: 10.1155/2018/5830364] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 05/14/2018] [Accepted: 06/28/2018] [Indexed: 12/02/2022]
Abstract
Background Body motion evaluation (BME) by markerless systems is increasingly being considered as an alternative to traditional marker-based technology because they are faster, simpler, and less expensive. They are increasingly used in clinical settings in patients with movement disorders; however, the wide variety of systems available makes results conflicting. Research Question The objective of this study was to determine whether a markerless 3D motion capture system is a useful instrument to objectively differentiate between PD patients with DBS in On and Off states and controls and its correlation with the evaluation by means of MDS-UPDRS. Methods Six PD patients who underwent deep brain stimulation (DBS) bilaterally in the subthalamic nucleus were evaluated using BME and the Unified Parkinson's Disease Rating Scale (UPDRS-III) with DBS turned On and Off. BME of 16 different movements in six controls paired by age and sex was compared with that in PD patients with DBS in On and Off states. Results A better performance in the BME was correlated with a lower UPDRS-III score. There was no statistically significant difference between patients in Off and On states of DBS regarding BME. However, some items such as left shoulder flexion (p=0.038), right shoulder rotation (p=0.011), and left trunk rotation (p=0.023) were different between Off patients and healthy controls. Significance Kinematic data obtained with this markerless system could contribute to discriminate between PD patients and healthy controls. This emerging technology may help to clinically evaluate PD patients more objectively.
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367
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De-Arteaga M, Herlands W, Neill DB, Dubrawski A. Machine Learning for the Developing World. ACM TRANSACTIONS ON MANAGEMENT INFORMATION SYSTEMS 2018. [DOI: 10.1145/3210548] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Researchers from across the social and computer sciences are increasingly using machine learning to study and address global development challenges. This article examines the burgeoning field of machine learning for the developing world (ML4D). First, we present a review of prominent literature. Next, we suggest best practices drawn from the literature for ensuring that ML4D projects are relevant to the advancement of development objectives. Finally, we discuss how developing world challenges can motivate the design of novel machine learning methodologies. This article provides insights into systematic differences between ML4D and more traditional machine learning applications. It also discusses how technical complications of ML4D can be treated as novel research questions, how ML4D can motivate new research directions, and where machine learning can be most useful.
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Affiliation(s)
- Maria De-Arteaga
- Machine Learning Department, Heinz College, Auton Lab, Carnegie Mellon University, Pittsburgh, PA
| | - William Herlands
- Machine Learning Department, Heinz College, Event and Pattern Detection Laboratory, Carnegie Mellon University, Pittsburgh, PA
| | - Daniel B. Neill
- Machine Learning Department, Heinz College, Event and Pattern Detection Laboratory, Carnegie Mellon University, Pittsburgh, PA
| | - Artur Dubrawski
- Auton Lab, Robotics Institute, Carnegie Mellon University, Pittsburgh, PA
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368
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Wattanakitrungroj N, Maneeroj S, Lursinsap C. BEstream: Batch Capturing with Elliptic Function for One-Pass Data Stream Clustering. DATA KNOWL ENG 2018. [DOI: 10.1016/j.datak.2018.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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369
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Wang Y, Li Y, Qiao C, Liu X, Hao M, Shugart YY, Xiong M, Jin L. Nuclear Norm Clustering: a promising alternative method for clustering tasks. Sci Rep 2018; 8:10873. [PMID: 30022093 PMCID: PMC6052164 DOI: 10.1038/s41598-018-29246-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/02/2018] [Indexed: 11/09/2022] Open
Abstract
Clustering techniques are widely used in many applications. The goal of clustering is to identify patterns or groups of similar objects within a dataset of interest. However, many cluster methods are neither robust nor sensitive to noises and outliers in real data. In this paper, we present Nuclear Norm Clustering (NNC, available at https://sourceforge.net/projects/nnc/), an algorithm that can be used in various fields as a promising alternative to the k-means clustering method. The NNC algorithm requires users to provide a data matrix M and a desired number of cluster K. We employed simulated annealing techniques to choose an optimal label vector that minimizes nuclear norm of the pooled within cluster residual matrix. To evaluate the performance of the NNC algorithm, we compared the performance of both 15 public datasets and 2 genome-wide association studies (GWAS) on psoriasis, comparing our method with other classic methods. The results indicate that NNC method has a competitive performance in terms of F-score on 15 benchmarked public datasets and 2 psoriasis GWAS datasets. So NNC is a promising alternative method for clustering tasks.
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Affiliation(s)
- Yi Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Yi Li
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.,Six Industrial Research Institute, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Chunhong Qiao
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Xiaoyu Liu
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Meng Hao
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Yin Yao Shugart
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China. .,Unit on Statistical Genomics, Division of Intramural Division Programs, National, Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA. .,Six Industrial Research Institute, Fudan University, Shanghai, China.
| | - Momiao Xiong
- Human Genetics Center, School of Public Health, University of Texas Houston Health Sciences Center, Houston, Texas, USA.
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China. .,Six Industrial Research Institute, Fudan University, Shanghai, China. .,Human Phenome Institute, Fudan University, Shanghai, China.
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370
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Kringel D, Lippmann C, Parnham MJ, Kalso E, Ultsch A, Lötsch J. A machine-learned analysis of human gene polymorphisms modulating persisting pain points to major roles of neuroimmune processes. Eur J Pain 2018; 22:1735-1756. [PMID: 29923268 PMCID: PMC6220816 DOI: 10.1002/ejp.1270] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2018] [Indexed: 12/21/2022]
Abstract
Background Human genetic research has implicated functional variants of more than one hundred genes in the modulation of persisting pain. Artificial intelligence and machine‐learning techniques may combine this knowledge with results of genetic research gathered in any context, which permits the identification of the key biological processes involved in chronic sensitization to pain. Methods Based on published evidence, a set of 110 genes carrying variants reported to be associated with modulation of the clinical phenotype of persisting pain in eight different clinical settings was submitted to unsupervised machine‐learning aimed at functional clustering. Subsequently, a mathematically supported subset of genes, comprising those most consistently involved in persisting pain, was analysed by means of computational functional genomics in the Gene Ontology knowledgebase. Results Clustering of genes with evidence for a modulation of persisting pain elucidated a functionally heterogeneous set. The situation cleared when the focus was narrowed to a genetic modulation consistently observed throughout several clinical settings. On this basis, two groups of biological processes, the immune system and nitric oxide signalling, emerged as major players in sensitization to persisting pain, which is biologically highly plausible and in agreement with other lines of pain research. Conclusions The present computational functional genomics‐based approach provided a computational systems‐biology perspective on chronic sensitization to pain. Human genetic control of persisting pain points to the immune system as a source of potential future targets for drugs directed against persisting pain. Contemporary machine‐learned methods provide innovative approaches to knowledge discovery from previous evidence. Significance We show that knowledge discovery in genetic databases and contemporary machine‐learned techniques can identify relevant biological processes involved in Persitent pain.
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Affiliation(s)
- D Kringel
- Institute of Clinical Pharmacology, Goethe - University, Frankfurt am Main, Germany
| | - C Lippmann
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology TMP, Frankfurt
| | - M J Parnham
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology TMP, Frankfurt
| | - E Kalso
- Institute of Clinical Medicine, University of Helsinki, Pain Clinic, Helsinki University Central Hospital, Helsinki, Finland.,Institute of Biomedicine, Pharmacology, University of Helsinki, Helsinki, Finland
| | - A Ultsch
- DataBionics Research Group, University of Marburg, Germany
| | - J Lötsch
- Institute of Clinical Pharmacology, Goethe - University, Frankfurt am Main, Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology TMP, Frankfurt
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371
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A molecular neuromorphic network device consisting of single-walled carbon nanotubes complexed with polyoxometalate. Nat Commun 2018; 9:2693. [PMID: 30002369 PMCID: PMC6043547 DOI: 10.1038/s41467-018-04886-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 05/24/2018] [Indexed: 11/24/2022] Open
Abstract
In contrast to AI hardware, neuromorphic hardware is based on neuroscience, wherein constructing both spiking neurons and their dense and complex networks is essential to obtain intelligent abilities. However, the integration density of present neuromorphic devices is much less than that of human brains. In this report, we present molecular neuromorphic devices, composed of a dynamic and extremely dense network of single-walled carbon nanotubes (SWNTs) complexed with polyoxometalate (POM). We show experimentally that the SWNT/POM network generates spontaneous spikes and noise. We propose electron-cascading models of the network consisting of heterogeneous molecular junctions that yields results in good agreement with the experimental results. Rudimentary learning ability of the network is illustrated by introducing reservoir computing, which utilises spiking dynamics and a certain degree of network complexity. These results indicate the possibility that complex functional networks can be constructed using molecular devices, and contribute to the development of neuromorphic devices. Neuromorphic hardware is based on principles of neuroscience, and has the potential to provide higher-level brain functions. Here, the authors develop a neuromorphic network device, constructed from single-walled carbon nanotubes and polyoxometalate, that mimics nerve impulse generation.
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372
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Kumar A, Kumar TV. Materialized View Selection Using Set Based Particle Swarm Optimization. INTERNATIONAL JOURNAL OF COGNITIVE INFORMATICS AND NATURAL INTELLIGENCE 2018. [DOI: 10.4018/ijcini.2018070102] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A data warehouse is a central repository of historical data designed primarily to support analytical processing. These analytical queries are exploratory, long and complex in nature. Further, the rapid and continuous growth in the size of data warehouse increases the response times of such queries. Query response times need to be reduced in order to speedup decision making. This problem, being an NP-Complete problem, can be appropriately dealt with by using swarm intelligence techniques. One such technique, i.e. the set-based particle swarm optimization (SPSO), has been proposed to address this problem. Accordingly, a SPSO based view selection algorithm (SPSOVSA), which selects the Top-K views from a multidimensional lattice, is proposed. Experimental based comparison of SPSOVSA with the most fundamental view selection algorithm shows that SPSOVSA is able to select comparatively better quality Top-K views for materialization. The materialization of these selected views would improve the performance of analytical queries and lead to efficient decision making.
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Affiliation(s)
- Amit Kumar
- School of Computer and Systems Sciences, Jawaharlal Nehru University, New Delhi, India
| | - T.V. Vijay Kumar
- School of Computer and Systems Sciences, Jawaharlal Nehru University, New Delhi, India
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373
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Muller S, Lancrenon J, Harpes C, Le Traon Y, Gombault S, Bonnin JM. A training-resistant anomaly detection system. Comput Secur 2018. [DOI: 10.1016/j.cose.2018.02.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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374
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Energy-Aware Task Scheduling Using Hybrid Firefly-BAT (FFABAT) in Big Data. CYBERNETICS AND INFORMATION TECHNOLOGIES 2018. [DOI: 10.2478/cait-2018-0031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract
In modern times there is an increasing trend of applications for handling Big data. However, negotiating with the concepts of the Big data is an extremely difficult issue today. The MapReduce framework has been in focus recently for serious consideration. The aim of this study is to get the task-scheduling over Big data using Hadoop. Initially, we prioritize the tasks with the help of k-means clustering algorithm. Then, the MapReduce framework is employed. The available resource is optimally selected using optimization technique in map-phase. The proposed method uses the FireFly Algorithm and BAT algorithms (FFABAT) for choosing the optimal resource with minimum cost value. The bat-inspired algorithm is a meta-heuristic optimization method developed by Xin-She Yang (2010). This bat algorithm is established on the echo-location behaviour of micro-bats with variable pulse rates of emission and loudness. Finally, the tasks are scheduled with the optimal resource in reducer-phase and stored in the cloud. The performance of the algorithm is analysed, based on the total cost, time and memory utilization.
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375
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Applying Deep Neural Network (DNN) for Robust Indoor Localization in Multi-Building Environment. APPLIED SCIENCES-BASEL 2018. [DOI: 10.3390/app8071062] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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376
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García-Gil D, Ramírez-Gallego S, García S, Herrera F. Principal Components Analysis Random Discretization Ensemble for Big Data. Knowl Based Syst 2018. [DOI: 10.1016/j.knosys.2018.03.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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377
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378
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Kim KS, Lee S, Huang K. A scalable deep neural network architecture for multi-building and multi-floor indoor localization based on Wi-Fi fingerprinting. BIG DATA ANALYTICS 2018. [DOI: 10.1186/s41044-018-0031-2] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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379
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Sukrat S, Papasratorn B. An architectural framework for developing a recommendation system to enhance vendors’ capability in C2C social commerce. SOCIAL NETWORK ANALYSIS AND MINING 2018. [DOI: 10.1007/s13278-018-0500-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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380
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Shi F, Li Q, Zhu T, Ning H. A Survey of Data Semantization in Internet of Things. SENSORS (BASEL, SWITZERLAND) 2018; 18:E313. [PMID: 29361772 PMCID: PMC5795333 DOI: 10.3390/s18010313] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/16/2018] [Accepted: 01/18/2018] [Indexed: 11/17/2022]
Abstract
With the development of Internet of Things (IoT), more and more sensors, actuators and mobile devices have been deployed into our daily lives. The result is that tremendous data are produced and it is urgent to dig out hidden information behind these volumous data. However, IoT data generated by multi-modal sensors or devices show great differences in formats, domains and types, which poses challenges for machines to process and understand. Therefore, adding semantics to Internet of Things becomes an overwhelming tendency. This paper provides a systematic review of data semantization in IoT, including its backgrounds, processing flows, prevalent techniques, applications, existing challenges and open issues. It surveys development status of adding semantics to IoT data, mainly referring to sensor data and points out current issues and challenges that are worth further study.
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Affiliation(s)
- Feifei Shi
- School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China.
- Beijing Engineering Research Center for Cyberspace Data Analysis and Applications, Beijing 100083, China.
| | - Qingjuan Li
- School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China.
- Beijing Engineering Research Center for Cyberspace Data Analysis and Applications, Beijing 100083, China.
| | - Tao Zhu
- Software School,University of South China, Hengyang 421001, China.
| | - Huansheng Ning
- School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China.
- Beijing Engineering Research Center for Cyberspace Data Analysis and Applications, Beijing 100083, China.
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381
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He M, Wang Z, Leach M, Jiang Z, Lim EG. Bio-inspired optimization algorithms applied to rectenna design. BIG DATA ANALYTICS 2018. [DOI: 10.1186/s41044-017-0026-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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382
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383
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MPP SQL Query Optimization with RTCG. BIG DATA ANALYTICS 2018. [DOI: 10.1007/978-3-030-04780-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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384
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How 5G Wireless (and Concomitant Technologies) Will Revolutionize Healthcare? FUTURE INTERNET 2017. [DOI: 10.3390/fi9040093] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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385
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Multi-objective particle swarm optimization algorithm using adaptive archive grid for numerical association rule mining. Neural Comput Appl 2017. [DOI: 10.1007/s00521-017-3278-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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386
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Lohani B, Ghosh S. Airborne LiDAR Technology: A Review of Data Collection and Processing Systems. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES INDIA SECTION A-PHYSICAL SCIENCES 2017. [DOI: 10.1007/s40010-017-0435-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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387
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Mosier EM, Fry AC, Lane MT. Kinetic Contributions of The Upper Limbs During Counter-Movement Verical Jumps With and Without Arm Swing. J Strength Cond Res 2017; 33:2066-2073. [PMID: 29084090 DOI: 10.1519/jsc.0000000000002275] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Mosier, EM, Fry, AC, and Lane, MT. Kinetic contributions of the upper limbs during countermovement. J Strength Cond Res 33(8): 2066-2073, 2019-This study examined the kinetic contributions of the upper extremities during countermovement vertical jumps (CMVJs) while using arm swing (AS) or no arm swing (NAS) conditions. Fourteen healthy men ((Equation is included in full-text article.)± SD; age = 24.1 ± 3.9 years) volunteered for this investigation. Subjects performed in random order a total of 6 jumps consisting of 3 AS and 3 NAS CMVJs. A motion capture system was used to analyze the kinetic data. Paired samples t-tests were used to examine the subjects' mean differences in the AS and NAS CMVJ trials (p<0.05). Results for all subjects were determined for each jump subjects were determined for each jump performed, with statistical analyses performed on mean values for all 3 jumps per subject. The AS significantly increased the vertical jump height (VJH) by an average of 0.07 ± 0.03 m (3.0 ± 1.3 inches). Dual-energy X-ray absorptiometry scans determined that the upper limbs were 12.0% of the total body mass. Movement of the upper limbs during the AS CMVJ produced 32.2 ± 7.0% of the total mean ground reaction force (GRF), and 11.3 ± 2.2% during the NAS CMVJ. The enhancement of performance when jumping using an AS resulted in a 13.6% increase in VJH. The contribution of the upper limbs during the AS CMVJ averaged 31.5% of the peak GRF, which occurred immediately before takeoff. The upper extremities can greatly influence vertical jump performances and the accompanying kinetics. When analyzing jump GRFs, one must be aware of how much the upper limbs contribute to these forces. In addition, proper AS mechanics must be emphasized when instructing correct jump technique.
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Affiliation(s)
- Eric M Mosier
- Osness Human Performance Laboratories, Department of Health, Sport, and Exercise Sciences, University of Kansas, Lawrence, Kansas
| | - Andrew C Fry
- Osness Human Performance Laboratories, Department of Health, Sport, and Exercise Sciences, University of Kansas, Lawrence, Kansas
| | - Michael T Lane
- Department of Exercise and Sports Science, Eastern Kentucky University, Richmond, Kentucky
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388
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Nichio BTL, Marchaukoski JN, Raittz RT. New Tools in Orthology Analysis: A Brief Review of Promising Perspectives. Front Genet 2017; 8:165. [PMID: 29163633 PMCID: PMC5674930 DOI: 10.3389/fgene.2017.00165] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/16/2017] [Indexed: 11/23/2022] Open
Abstract
Nowadays defying homology relationships among sequences is essential for biological research. Within homology the analysis of orthologs sequences is of great importance for computational biology, annotation of genomes and for phylogenetic inference. Since 2007, with the increase in the number of new sequences being deposited in large biological databases, researchers have begun to analyse computerized methodologies and tools aimed at selecting the most promising ones in the prediction of orthologous groups. Literature in this field of research describes the problems that the majority of available tools show, such as those encountered in accuracy, time required for analysis (especially in light of the increasing volume of data being submitted, which require faster techniques) and the automatization of the process without requiring manual intervention. Conducting our search through BMC, Google Scholar, NCBI PubMed, and Expasy, we examined more than 600 articles pursuing the most recent techniques and tools developed to solve most the problems still existing in orthology detection. We listed the main computational tools created and developed between 2011 and 2017, taking into consideration the differences in the type of orthology analysis, outlining the main features of each tool and pointing to the problems that each one tries to address. We also observed that several tools still use as their main algorithm the BLAST "all-against-all" methodology, which entails some limitations, such as limited number of queries, computational cost, and high processing time to complete the analysis. However, new promising tools are being developed, like OrthoVenn (which uses the Venn diagram to show the relationship of ortholog groups generated by its algorithm); or proteinOrtho (which improves the accuracy of ortholog groups); or ReMark (tackling the integration of the pipeline to turn the entry process automatic); or OrthAgogue (using algorithms developed to minimize processing time); and proteinOrtho (developed for dealing with large amounts of biological data). We made a comparison among the main features of four tool and tested them using four for prokaryotic genomas. We hope that our review can be useful for researchers and will help them in selecting the most appropriate tool for their work in the field of orthology.
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Affiliation(s)
| | | | - Roberto Tadeu Raittz
- Department of Bioinformatics, Professional and Technical Education Sector, Federal University of Paraná, Curitiba, Brazil
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389
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Abbes H, Gargouri F. MongoDB-Based Modular Ontology Building for Big Data Integration. JOURNAL ON DATA SEMANTICS 2017. [DOI: 10.1007/s13740-017-0081-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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390
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391
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Fuller D, Buote R, Stanley K. A glossary for big data in population and public health: discussion and commentary on terminology and research methods. J Epidemiol Community Health 2017; 71:1113-1117. [PMID: 28918390 DOI: 10.1136/jech-2017-209608] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/15/2017] [Accepted: 08/15/2017] [Indexed: 11/03/2022]
Abstract
The volume and velocity of data are growing rapidly and big data analytics are being applied to these data in many fields. Population and public health researchers may be unfamiliar with the terminology and statistical methods used in big data. This creates a barrier to the application of big data analytics. The purpose of this glossary is to define terms used in big data and big data analytics and to contextualise these terms. We define the five Vs of big data and provide definitions and distinctions for data mining, machine learning and deep learning, among other terms. We provide key distinctions between big data and statistical analysis methods applied to big data. We contextualise the glossary by providing examples where big data analysis methods have been applied to population and public health research problems and provide brief guidance on how to learn big data analysis methods.
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Affiliation(s)
- Daniel Fuller
- School of Human Kinetics and Recreation, Memorial University of Newfoundland, Saint John's, Canada
| | - Richard Buote
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St John's, Canada
| | - Kevin Stanley
- Department of Computer Science, College of Arts and Science, University of Saskatchewan, Saskatoon, Canada
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392
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Herrick T, Harner-Jay C, Shaffer C, Zwisler G, Digre P, Batson A. Modeling the potential impact of emerging innovations on achievement of Sustainable Development Goals related to maternal, newborn, and child health. COST EFFECTIVENESS AND RESOURCE ALLOCATION 2017; 15:12. [PMID: 28706466 PMCID: PMC5506623 DOI: 10.1186/s12962-017-0074-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 07/03/2017] [Indexed: 11/17/2022] Open
Abstract
Background Innovations that improve the affordability, accessibility, or effectiveness of health care played a major role in the Millennium Development Goal achievements and will be critical for reaching the ambitious new Sustainable Development Goal (SDG) health targets. Mechanisms to identify and prioritize innovations are essential to inform future investment decisions. Methods Innovation Countdown 2030 crowdsourced health innovations from around the world and engaged recognized experts to systematically assess their lifesaving potential by 2030. A health impact modeling approach was developed and used to quantify the costs and lives saved for select innovations identified as having great promise for improving maternal, newborn, and child health. Results Preventive innovations targeting health conditions with a high mortality burden had the greatest impact in regard to the absolute number of estimated lives saved. The largest projected health impact was for a new tool for small-scale water treatment that automatically chlorinates water to a safe concentration without using electricity or moving parts. An estimated 1.5 million deaths from diarrheal disease among children under five could be prevented by 2030 by scaling up use of this technology. Use of chlorhexidine for umbilical cord care was associated with the second highest number of lives saved. Conclusions The results show why a systematic modeling approach that can compare and contrast investment opportunities is important for prioritizing global health innovations. Rigorous impact estimates are needed to allocate limited resources toward the innovations with great potential to advance the SDGs. Electronic supplementary material The online version of this article (doi:10.1186/s12962-017-0074-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tara Herrick
- PATH, 2201 Westlake Ave. Suite 200, Seattle, WA USA
| | | | - Craig Shaffer
- Applied Strategies, 951 Mariners Island Blvd. Suite 400, San Mateo, CA USA
| | - Greg Zwisler
- PATH, 2201 Westlake Ave. Suite 200, Seattle, WA USA
| | - Peder Digre
- PATH, 2201 Westlake Ave. Suite 200, Seattle, WA USA
| | - Amie Batson
- PATH, 2201 Westlake Ave. Suite 200, Seattle, WA USA
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393
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Arun B, Kumar TV. Materialized View Selection Using Bumble Bee Mating Optimization. INTERNATIONAL JOURNAL OF DECISION SUPPORT SYSTEM TECHNOLOGY 2017. [DOI: 10.4018/ijdsst.2017070101] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Decision support systems (DSS) constitute one of the most crucial components of almost every corporation's information system. Data warehouse provides the DSS with massive volumes of quality corporate data for analysis. On account of the volume of corporate data, its processing time of on-line analytical queries is huge (in hours and days). Materialized views have been used to substantially improve query performance. Nevertheless, selecting appropriate sets of materialized views is an NP-Complete problem. In this paper, a new discrete bumble bee mating inspired view selection algorithm (BBMVSA) that selects Top-K views from a multidimensional lattice has been proposed. Experimental results show that BBMVSA was able to select fairly good quality Top-K views incurring a lower TVEC. Materialization of the selected views would improve the overall data analysis of DSS and would facilitate the decision making process.
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Affiliation(s)
- Biri Arun
- School of Computer and Systems Sciences, Jawaharlal Nehru University, New Delhi, India
| | - T.V. Vijay Kumar
- School of Computer and Systems Sciences, Jawaharlal Nehru University, New Delhi, India
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394
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Venkatram K, Geetha MA. Review on Big Data & Analytics – Concepts, Philosophy, Process and Applications. CYBERNETICS AND INFORMATION TECHNOLOGIES 2017. [DOI: 10.1515/cait-2017-0013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Big Data analytics has been the main focus in all the industries today. It is not overstating that if an enterprise is not using Big Data analytics, it will be a stray and incompetent in their businesses against their Big Data enabled competitors. Big Data analytics enables business to take proactive measure and create a competitive edge in their industry by highlighting the business insights from the past data and trends. The main aim of this review article is to quickly view the cutting-edge and state of art work being done in Big Data analytics area by different industries. Since there is an overwhelming interest from many of the academicians, researchers and practitioners, this review would quickly refresh and emphasize on how Big Data analytics can be adopted with available technologies, frameworks, methods and models to exploit the value of Big Data analytics.
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Affiliation(s)
- Kari Venkatram
- School of Computing Science and Engineering , VIT University , Vellore 632 014 , Tamil Nadu, India
| | - Mary A. Geetha
- School of Computing Science and Engineering , VIT University , Vellore 632 014 , Tamil Nadu, India
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395
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396
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Jin H, Abu-Raya YS, Haick H. Advanced Materials for Health Monitoring with Skin-Based Wearable Devices. Adv Healthc Mater 2017; 6. [PMID: 28371294 DOI: 10.1002/adhm.201700024] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 02/14/2017] [Indexed: 12/16/2022]
Abstract
Skin-based wearable devices have a great potential that could result in a revolutionary approach to health monitoring and diagnosing disease. With continued innovation and intensive attention to the materials and fabrication technologies, development of these healthcare devices is progressively encouraged. This article gives a concise, although admittedly non-exhaustive, didactic review of some of the main concepts and approaches related to recent advances and developments in the scope of skin-based wearable devices (e.g. temperature, strain, biomarker-analysis werable devices, etc.), with an emphasis on emerging materials and fabrication techniques in the relevant fields. To give a comprehensive statement, part of the review presents and discusses different aspects of these advanced materials, such as the sensitivity, biocompatibility and durability as well as the major approaches proposed for enhancing their chemical and physical properties. A complementary section of the review linking these advanced materials with wearable device technologies is particularly specified. Some of the strong and weak points in development of each wearable material/device are highlighted and criticized. Several ideas regarding further improvement of skin-based wearable devices are also discussed.
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Affiliation(s)
- Han Jin
- Department of Chemical Engineering; Technion - Israel Institute of Technology; Haifa 3200003 Israel
- Faculty of Information Science and Engineering; Ningbo University; Ningbo 315211 P. R. China
| | - Yasmin Shibli Abu-Raya
- Department of Chemical Engineering and The Russell Berrie Nanotechnology Institute; Technion - Israel Institute of Technology; Haifa 3200003 Israel
| | - Hossam Haick
- Department of Chemical Engineering and The Russell Berrie Nanotechnology Institute; Technion - Israel Institute of Technology; Haifa 3200003 Israel
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397
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Kache F, Seuring S. Challenges and opportunities of digital information at the intersection of Big Data Analytics and supply chain management. INTERNATIONAL JOURNAL OF OPERATIONS & PRODUCTION MANAGEMENT 2017. [DOI: 10.1108/ijopm-02-2015-0078] [Citation(s) in RCA: 341] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Purpose
Despite the variety of supply chain management (SCM) research, little attention has been given to the use of Big Data Analytics for increased information exploitation in a supply chain. The purpose of this paper is to contribute to theory development in SCM by investigating the potential impacts of Big Data Analytics on information usage in a corporate and supply chain context. As it is imperative for companies in the supply chain to have access to up-to-date, accurate, and meaningful information, the exploratory research will provide insights into the opportunities and challenges emerging from the adoption of Big Data Analytics in SCM.
Design/methodology/approach
Although Big Data Analytics is gaining increasing attention in management, empirical research on the topic is still scarce. Due to the limited availability of comparable material at the intersection of Big Data Analytics and SCM, the authors apply the Delphi research technique.
Findings
Portraying the emerging transition trend from a digital business environment, the presented Delphi study findings contribute to extant knowledge by identifying 43 opportunities and challenges linked to the emergence of Big Data Analytics from a corporate and supply chain perspective.
Research limitations/implications
These constructs equip the research community with a first collection of aspects, which could provide the basis to tailor further research at the nexus of Big Data Analytics and SCM.
Originality/value
The research adds to the existing knowledge base as no empirical research has been presented so far specifically assessing opportunities and challenges on corporate and supply chain level with a special focus on the implications imposed through Big Data Analytics.
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399
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Fujita T. Hierarchical nanoporous metals as a path toward the ultimate three-dimensional functionality. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2017; 18:724-740. [PMID: 29057026 PMCID: PMC5642827 DOI: 10.1080/14686996.2017.1377047] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 08/23/2017] [Accepted: 09/05/2017] [Indexed: 05/20/2023]
Abstract
Nanoporous metals prepared via dealloying or selective leaching of solid solution alloys and compounds represent an emerging class of materials. They possess a three-dimensional (3D) structure of randomly interpenetrating ligaments/nanopores with sizes between 5 nm and several tens of micrometers, which can be tuned by varying their preparation conditions (such as dealloying time and temperature) or additional thermal coarsening. As compared to other nanostructured materials, nanoporous metals have many advantages, including their bicontinuous structure, tunable pore sizes, bulk form, good electrical conductivity, and high structural stability. Therefore, nanoporous metals represent ideal 3D materials with versatile functionality, which can be utilized in various fields. In this review, we describe the recent applications of nanoporous metals in molecular detection, catalysis, 3D graphene synthesis, hierarchical pore formation, and additive manufacturing (3D printing) together with our own achievements in these areas. Finally, we discuss possible ways of realizing the ultimate 3D functionality beyond the scope of nanoporous metals.
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Affiliation(s)
- Takeshi Fujita
- WPI Advanced Institute for Materials Research, Tohoku University, Sendai, Japan
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A Framework to Improve Reuse in Weather-Based DSS Based on Coupling Weather Conditions. BIG DATA ANALYTICS 2017. [DOI: 10.1007/978-3-319-72413-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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