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Recent advances and the future generation of neuroinformatics infrastructure

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889196777 Year: Pages: 388 DOI: 10.3389/978-2-88919-677-7 Language: English
Publisher: Frontiers Media SA
Subject: Neurology --- Science (General)
Added to DOAB on : 2016-04-07 11:22:02
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The huge volume of multi-modal neuroimaging data across different neuroscience communities has posed a daunting challenge to traditional methods of data sharing, data archiving, data processing and data analysis. Neuroinformatics plays a crucial role in creating advanced methodologies and tools for the handling of varied and heterogeneous datasets in order to better understand the structure and function of the brain. These tools and methodologies not only enhance data collection, analysis, integration, interpretation, modeling, and dissemination of data, but also promote data sharing and collaboration. This Neuroinformatics Research Topic aims to summarize the state-of-art of the current achievements and explores the directions for the future generation of neuroinformatics infrastructure. The publications present solutions for data archiving, data processing and workflow, data mining, and system integration methodologies. Some of the systems presented are large in scale, geographically distributed, and already have a well-established user community. Some discuss opportunities and methodologies that facilitate large-scale parallel data processing tasks under a heterogeneous computational environment. We wish to stimulate on-going discussions at the level of the neuroinformatics infrastructure including the common challenges, new technologies of maximum benefit, key features of next generation infrastructure, etc. We have asked leading research groups from different research areas of neuroscience/neuroimaging to provide their thoughts on the development of a state of the art and highly-efficient neuroinformatics infrastructure. Such discussions will inspire and help guide the development of a state of the art, highly-efficient neuroinformatics infrastructure.

MAPPING MAnagement and Processing of images for Population ImagiNG

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889452606 Year: Pages: 139 DOI: 10.3389/978-2-88945-260-6 Language: English
Publisher: Frontiers Media SA
Subject: General and Civil Engineering --- Computer Science
Added to DOAB on : 2018-02-27 16:16:44
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Several recent papers underline methodological points that limit the validity of published results in imaging studies in the life sciences and especially the neurosciences (Carp, 2012; Ingre, 2012; Button et al., 2013; Ioannidis, 2014). At least three main points are identified that lead to biased conclusions in research findings: endemic low statistical power and, selective outcome and selective analysis reporting. Because of this, and in view of the lack of replication studies, false discoveries or solutions persist. To overcome the poor reliability of research findings, several actions should be promoted including conducting large cohort studies, data sharing and data reanalysis. The construction of large-scale online databases should be facilitated, as they may contribute to the definition of a “collective mind” (Fox et al., 2014) facilitating open collaborative work or “crowd science” (Franzoni and Sauermann, 2014). Although technology alone cannot change scientists’ practices (Wicherts et al., 2011; Wallis et al., 2013, Poldrack and Gorgolewski 2014; Roche et al. 2014), technical solutions should be identified which support a more “open science” approach. Also, the analysis of the data plays an important role. For the analysis of large datasets, image processing pipelines should be constructed based on the best algorithms available and their performance should be objectively compared to diffuse the more relevant solutions. Also, provenance of processed data should be ensured (MacKenzie-Graham et al., 2008). In population imaging this would mean providing effective tools for data sharing and analysis without increasing the burden on researchers. This subject is the main objective of this research topic (RT), cross-listed between the specialty section “Computer Image Analysis” of Frontiers in ICT and Frontiers in Neuroinformatics. Firstly, it gathers works on innovative solutions for the management of large imaging datasets possibly distributed in various centers. The paper of Danso et al. describes their experience with the integration of neuroimaging data coming from several stroke imaging research projects. They detail how the initial NeuroGrid core metadata schema was gradually extended for capturing all information required for future metaanalysis while ensuring semantic interoperability for future integration with other biomedical ontologies. With a similar preoccupation of interoperability, Shanoir relies on the OntoNeuroLog ontology (Temal et al., 2008; Gibaud et al., 2011; Batrancourt et al., 2015), a semantic model that formally described entities and relations in medical imaging, neuropsychological and behavioral assessment domains. The mechanism of “Study Card” allows to seamlessly populate metadata aligned with the ontology, avoiding fastidious manual entrance and the automatic control of the conformity of imported data with a predefined study protocol. The ambitious objective with the BIOMIST platform is to provide an environment managing the entire cycle of neuroimaging data from acquisition to analysis ensuring full provenance information of any derived data. Interestingly, it is conceived based on the product lifecycle management approach used in industry for managing products (here neuroimaging data) from inception to manufacturing. Shanoir and BIOMIST share in part the same OntoNeuroLog ontology facilitating their interoperability. ArchiMed is a data management system locally integrated for 5 years in a clinical environment. Not restricted to Neuroimaging, ArchiMed deals with multi-modal and multi-organs imaging data with specific considerations for data long-term conservation and confidentiality in accordance with the French legislation. Shanoir and ArchiMed are integrated into FLI-IAM1, the national French IT infrastructure for in vivo imaging.

Keywords

Database --- Infrastructure --- Data --- Workflow --- Neuroimaging --- Image Analysis --- Brain --- MRI

Peripheral Nervous System-Machine Interfaces

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889453924 Year: Pages: 141 DOI: 10.3389/978-2-88945-392-4 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Neurology
Added to DOAB on : 2018-11-16 17:17:57
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For 5 years, the Peripheral Nervous System-Machine Interfaces workgroup has dedicated itself to the recruitment of researchers, clinicians, and general public in a unified effort to advance the frontier of restoration of quality of life to those with limb deficiency. Our group's mission is to bring together experts from various domains to identify promising new technologies and new opportunities for inquiry and discovery in prosthetics research. This e-Book collects 10 cutting edge research articles written by members of the workgroup, covering three domains prioritized by the workgroup: novel prosthetic technology, approaches for reducing device rejection, and prosthetic control. In our summary editorial, we four principals of the workgroup reflect on our first 5 years, and project our vision for the future, as the Society for Prosthetics.

Peripheral Nervous System-Machine Interfaces, 2nd Edition

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889454907 Year: Pages: 143 DOI: 10.3389/978-2-88945-490-7 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Neurology
Added to DOAB on : 2019-01-23 14:53:42
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For 5 years, the Peripheral Nervous System-Machine Interfaces workgroup has dedicated itself to the recruitment of researchers, clinicians, and general public in a unified effort to advance the frontier of restoration of quality of life to those with limb deficiency. Our group's mission is to bring together experts from various domains to identify promising new technologies and new opportunities for inquiry and discovery in prosthetics research. This e-Book collects 10 cutting edge research articles written by members of the workgroup, covering three domains prioritized by the workgroup: novel prosthetic technology, approaches for reducing device rejection, and prosthetic control. In our summary editorial, we four principals of the workgroup reflect on our first 5 years, and project our vision for the future, as the Society for Prosthetics.

Data and Text Processing for Health and Life Sciences

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Book Series: Advances in Experimental Medicine and Biology ISBN: 9783030138455 Year: Pages: 98 DOI: 10.1007/978-3-030-13845-5 Language: English
Publisher: Springer
Subject: Computer Science --- Medicine (General)
Added to DOAB on : 2020-02-05 11:21:03
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This open access book is a step-by-step introduction on how shell scripting can help solve many of the data processing tasks that Health and Life specialists face everyday with minimal software dependencies. The examples presented in the book show how simple command line tools can be used and combined to retrieve data and text from web resources, to filter and mine literature, and to explore the semantics encoded in biomedical ontologies. To store data this book relies on open standard text file formats, such as TSV, CSV, XML, and OWL, that can be open by any text editor or spreadsheet application. The first two chapters, Introduction and Resources, provide a brief introduction to the shell scripting and describe popular data resources in Health and Life Sciences. The third chapter, Data Retrieval, starts by introducing a common data processing task that involves multiple data resources. Then, this chapter explains how to automate each step of that task by introducing the required commands line tools one by one. The fourth chapter, Text Processing, shows how to filter and analyze text by using simple string matching techniques and regular expressions. The last chapter, Semantic Processing, shows how XPath queries and shell scripting is able to process complex data, such as the graphs used to specify ontologies. Besides being almost immutable for more than four decades and being available in most of our personal computers, shell scripting is relatively easy to learn by Health and Life specialists as a sequence of independent commands. Comprehending them is like conducting a new laboratory protocol by testing and understanding its procedural steps and variables, and combining their intermediate results. Thus, this book is particularly relevant to Health and Life specialists or students that want to easily learn how to process data and text, and which in return may facilitate and inspire them to acquire deeper bioinformatics skills in the future.

Real-time Linked Dataspaces

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ISBN: 9783030296650 Year: Pages: 325 DOI: 10.1007/978-3-030-29665-0 Language: English
Publisher: Springer
Subject: Computer Science
Added to DOAB on : 2020-02-05 11:21:05
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This open access book explores the dataspace paradigm as a best-effort approach to data management within data ecosystems. It establishes the theoretical foundations and principles of real-time linked dataspaces as a data platform for intelligent systems. The book introduces a set of specialized best-effort techniques and models to enable loose administrative proximity and semantic integration for managing and processing events and streams. The book is divided into five major parts: Part I “Fundamentals and Concepts” details the motivation behind and core concepts of real-time linked dataspaces, and establishes the need to evolve data management techniques in order to meet the challenges of enabling data ecosystems for intelligent systems within smart environments. Further, it explains the fundamental concepts of dataspaces and the need for specialization in the processing of dynamic real-time data. Part II “Data Support Services” explores the design and evaluation of critical services, including catalog, entity management, query and search, data service discovery, and human-in-the-loop. In turn, Part III “Stream and Event Processing Services” addresses the design and evaluation of the specialized techniques created for real-time support services including complex event processing, event service composition, stream dissemination, stream matching, and approximate semantic matching. Part IV “Intelligent Systems and Applications” explores the use of real-time linked dataspaces within real-world smart environments. In closing, Part V “Future Directions” outlines future research challenges for dataspaces, data ecosystems, and intelligent systems. Readers will gain a detailed understanding of how the dataspace paradigm is now being used to enable data ecosystems for intelligent systems within smart environments. The book covers the fundamental theory, the creation of new techniques needed for support services, and lessons learned from real-world intelligent systems and applications focused on sustainability. Accordingly, it will benefit not only researchers and graduate students in the fields of data management, big data, and IoT, but also professionals who need to create advanced data management platforms for intelligent systems, smart environments, and data ecosystems.

Unlocking the Right to Data Portability

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ISBN: 9783748902706 Year: Volume: 38 Pages: 76 DOI: https://doi.org/10.5771/9783748902706 Language: en
Publisher: Nomos Verlagsgesellschaft mbH & Co. KG
Subject: Law
Added to DOAB on : 2019-10-25 11:57:14
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Linked Open Data - Creating Knowledge Out of Interlinked Data: Results of the LOD2 Project

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Book Series: Lecture Notes in Computer Science ISSN: 03029743 ISBN: 9783319098456 9783319098463 Year: Volume: 8661 Pages: 215 DOI: 10.1007/978-3-319-09846-3 Language: English
Publisher: Springer
Subject: Computer Science --- Pharmacy and materia medica --- Media and communication --- Business and Management --- Biotechnology --- General and Civil Engineering --- Materials --- Electrical and Nuclear Engineering
Added to DOAB on : 2014-10-06 14:35:35
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Linked Open Data (LOD) is a pragmatic approach for realizing the Semantic Web vision of making the Web a global, distributed, semantics-based information system. This book presents an overview on the results of the research project “LOD2 -- Creating Knowledge out of Interlinked Data”. LOD2 is a large-scale integrating project co-funded by the European Commission within the FP7 Information and Communication Technologies Work Program. Commencing in September 2010, this 4-year project comprised leading Linked Open Data research groups, companies, and service providers from across 11 European countries and South Korea. The aim of this project was to advance the state-of-the-art in research and development in four key areas relevant for Linked Data, namely 1. RDF data management; 2. the extraction, creation, and enrichment of structured RDF data; 3. the interlinking and fusion of Linked Data from different sources and 4. the authoring, exploration and visualization of Linked Data.

Drug Repositioning: Current Advances and Future Perspectives

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889456963 Year: Pages: 153 DOI: 10.3389/978-2-88945-696-3 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Therapeutics
Added to DOAB on : 2019-01-23 14:53:43
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Drug repositioning is the process of identifying new indications for existing drugs. At present, the conventional de novo drug discovery process requires an average of about 14 years and US$2.5 billion to approve and launch a drug. Drug repositioning can reduce the time and cost of this process because it takes advantage of drugs already in clinical use for other indications or drugs that have cleared phase I safety trials but have failed to show efficacy in the intended diseases. Historically, drug repositioning has been realized through serendipitous clinical observations or improved understanding of disease mechanisms. However, recent technological advances have enabled a more systematic approach to drug repositioning. This eBook collects 16 articles from 112 authors, providing readers with current advances and future perspectives of drug repositioning.

Tunable Security for Deployable Data Outsourcing

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ISBN: 9783731504115 Year: Pages: XIII, 257 p. DOI: 10.5445/KSP/1000048084 Language: ENGLISH
Publisher: KIT Scientific Publishing
Subject: Computer Science
Added to DOAB on : 2019-07-30 20:02:00

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Security mechanisms like encryption negatively affect other software quality characteristics like efficiency. To cope with such trade-offs, it is preferable to build approaches that allow to tune the trade-offs after the implementation and design phase. This book introduces a methodology that can be used to build such tunable approaches. The book shows how the proposed methodology can be applied in the domains of database outsourcing, identity management, and credential management.

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