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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

Phenomics

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889456079 Year: Pages: 222 DOI: 10.3389/978-2-88945-607-9 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Botany
Added to DOAB on : 2019-01-23 14:53:43
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"Phenomics" is an emerging area of research whose aspiration is the systematic measurement of the physical, physiological and biochemical traits (the phenome) belonging to a given individual or collection of individuals. Non-destructive or minimally invasive techniques allow repeated measurements across time to follow phenotypes as a function of developmental time. These longitudinal traits promise new insights into the ways in which crops respond to their environment including how they are managed.To maximize the benefit, these approaches should ideally be scalable so that large populations in multiple environments can be sampled repeatedly at reasonable cost. Thus, the development and validation of non-contact sensing technologies remains an area of intensive activity that ranges from Remote Sensing of crops within the landscape to high resolution at the subcellular level. Integration of this potentially highly dimensional data and linking it with variation at the genetic level is an ongoing challenge that promises to release the potential of both established and under-exploited crops.

Image-Guided Radiotherapy for Effective Radiotherapy Delivery

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889198498 Year: Pages: 111 DOI: 10.3389/978-2-88919-849-8 Language: English
Publisher: Frontiers Media SA
Subject: Oncology --- Medicine (General)
Added to DOAB on : 2016-01-19 14:05:46
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Image-guided radiotherapy (IGRT) is a new radiotherapy technology that combines the rapid dose fall off associated with intensity-modulated radiotherapy (IMRT) and daily tumor imaging allowing for high precision tumor dose delivery and effective sparing of surrounding normal organs. The new radiation technology requires close collaboration between radiologists, nuclear medicine specialists, and radiation oncologists to avoid marginal miss. Modern diagnostic imaging such as positron emission tomography (PET) scans, positron emission tomography with Computed Tomograpgy (PET-CT), and magnetic resonance imaging (MRI) allows the radiation oncologist to target the positive tumor with high accuracy. As the tumor is well visualized during radiation treatment, the margins required to avoid geographic miss can be safely reduced , thus sparing the normal organs from excessive radiation. When the tumor is located close to critical radiosensitive structures such as the spinal cord, IGRT can deliver a high dose of radiation to the tumor and simultaneously decreasing treatment toxicity, thus potentially improving cure rates and patient quality of life. During radiotherapy, tumor shrinkage and changes of normal tissues/volumes can be detected daily with IGRT. The volume changes in the target volumes and organs at risk often lead to increased radiation dose to the normal tissues and if left uncorrected may result in late complications. Adaptive radiotherapy with re-planning during the course of radiotherapy is therefore another advantage of IGRT over the conventional radiotherapy techniques. This new technology of radiotherapy delivery provides the radiation oncologist an effective tool to improve patient quality of life. In the future, radiation dose-escalation to the residual tumor may potentially improve survival rates. Because the treatment complexity, a great deal of work is required from the dosimetry staff and physicists to ensure quality of care. Preliminary clinical results with IGRT are encouraging but more prospective studies should be performed in the future to assess the effectiveness of IGRT in improving patient quality of life and local control. In this Frontiers Research Topic, we encourage submission of original papers and reviews dealing with imaging for radiotherapy planning, the physics and dosimetry associated with IGRT, as well as the clinical outcomes for cancer treatment with IGRT for all tumor sites.

Using Noise to Characterize Vision

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889197538 Year: Pages: 127 DOI: 10.3389/978-2-88919-753-8 Language: English
Publisher: Frontiers Media SA
Subject: Psychology --- Science (General)
Added to DOAB on : 2016-04-07 11:22:02
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Noise has been widely used to investigate the processing properties of various visual functions (e.g. detection, discrimination, attention, perceptual learning, averaging, crowding, face recognition), in various populations (e.g. older adults, amblyopes, migrainers, dyslexic children), using noise along various dimensions (e.g. pixel noise, orientation jitter, contrast jitter). The reason to use external noise is generally not to characterize visual processing in external noise per se, but rather to reveal how vision works in ordinary conditions when performance is limited by our intrinsic noise rather than externally added noise. For instance, reverse correlation aims at identifying the relevant information to perform a given task in noiseless conditions and measuring contrast thresholds in various noise levels can be used to understand the impact of intrinsic noise that limits sensitivity to noiseless stimuli. Why use noise? Since Fechner named it, psychophysics has always emphasized the systematic investigation of conditions that break vision. External noise raises threshold hugely and selectively. In hearing, Fletcher used noise in his famous critical-band experiments to reveal frequency-selective channels in hearing. Critical bands have been found in vision too. More generally, the big reliable effects of noise give important clues to how the system works. And simple models have been proposed to account for the effects of visual noise. As noise has been more widely used, questions have been raised about the simplifying assumptions that link the processing properties in noiseless conditions to measurements in external noise. For instance, it is usually assumed that the processing strategy (or mechanism) used to perform a task and its processing properties (e.g. filter tuning) are unaffected by the addition of external noise. Some have suggested that the processing properties could change with the addition of external noise (e.g. change in filter tuning or more lateral masking in noise), which would need to be considered before drawing conclusions about the processing properties in noiseless condition. Others have suggested that different processing properties (or mechanisms) could be solicited in low and high noise conditions, complicating the characterization of processing properties in noiseless condition based on processing properties identified in noise conditions. The current Research Topic probes further into what the effects of visual noise tell us about vision in ordinary conditions. Our Editorial gives an overview of the articles in this special issue.

Computational Systems Biology of Pathogen-Host Interactions

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889198214 Year: Pages: 198 DOI: 10.3389/978-2-88919-821-4 Language: English
Publisher: Frontiers Media SA
Subject: Microbiology --- Science (General)
Added to DOAB on : 2016-01-19 14:05:46
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A thorough understanding of pathogenic microorganisms and their interactions with host organisms is crucial to prevent infectious threats due to the fact that Pathogen-Host Interactions (PHIs) have critical roles in initiating and sustaining infections. Therefore, the analysis of infection mechanisms through PHIs is indispensable to identify diagnostic biomarkers and next-generation drug targets and then to develop strategic novel solutions against drug-resistance and for personalized therapy. Traditional approaches are limited in capturing mechanisms of infection since they investigate hosts or pathogens individually. On the other hand, the systems biology approach focuses on the whole PHI system, and is more promising in capturing infection mechanisms. Here, we bring together studies on the below listed sections to present the current picture of the research on Computational Systems Biology of Pathogen-Host Interactions:- Computational Inference of PHI Networks using Omics Data- Computational Prediction of PHIs- Text Mining of PHI Data from the Literature- Mathematical Modeling and Bioinformatic Analysis of PHIs Computational Inference of PHI Networks using Omics Data Gene regulatory, metabolic and protein-protein networks of PHI systems are crucial for a thorough understanding of infection mechanisms. Great advances in molecular biology and biotechnology have allowed the production of related omics data experimentally. Many computational methods are emerging to infer molecular interaction networks of PHI systems from the corresponding omics data. Computational Prediction of PHIs Due to the lack of experimentally-found PHI data, many computational methods have been developed for the prediction of pathogen-host protein-protein interactions. Despite being emerging, currently available experimental PHI data are far from complete for a systems view of infection mechanisms through PHIs. Therefore, computational methods are the main tools to predict new PHIs. To this end, the development of new computational methods is of great interest. Text Mining of PHI Data from Literature Despite the recent development of many PHI-specific databases, most data relevant to PHIs are still buried in the biomedical literature, which demands for the use of text mining techniques to unravel PHIs hidden in the literature. Only some rare efforts have been performed to achieve this aim. Therefore, the development of novel text mining methods specific for PHI data retrieval is of key importance for efficient use of the available literature. Mathematical Modeling and Bioinformatic Analysis of PHIs After the reconstruction of PHI networks experimentally and/or computationally, their mathematical modeling and detailed computational analysis is required using bioinformatics tools to get insights on infection mechanisms. Bioinformatics methods are increasingly applied to analyze the increasing amount of experimentally-found and computationally-predicted PHI data. Acknowledgements: We, editors of this e-book, acknowledge Emrah Nikerel (Yeditepe University, Turkey) and Arzucan Özgür (Bogaaziçi University, Turkey) for their contributions during the initiation of the Research Topic.

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