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New Trends on Genome and Transcriptome Characterizations

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889456109 Year: Pages: 157 DOI: 10.3389/978-2-88945-610-9 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Genetics
Added to DOAB on : 2019-01-23 14:53:43
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This Research Topic is devoted to bioinformaticians, geneticists and researchers who study or apply methods and algorithms for genomes and transcriptome analyses, aimed at understanding pathology discriminations and classifications. Papers are encouraged that use unconventional approaches and/or where mathematical and computational concepts are applied to biological and medical contexts in original ways. The contributions presented in the Topic should be of interest also to a wide class of scientists and students involved in the several fields where genomic and transcriptomic approaches are becoming essential for future investigations.

Neuroimaging and Neuropsychology of Meditation States

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889451784 Year: Pages: 145 DOI: 10.3389/978-2-88945-178-4 Language: English
Publisher: Frontiers Media SA
Subject: Psychology --- Science (General)
Added to DOAB on : 2017-08-28 14:01:09
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Neurophysiological and psychological modifications induced by meditation practice have been consistently addressed by neuroscience. Training meditation practice induced plasticity (Barinaga, 2003; Knight, 2004), and as a consequence several benefit for mental and physical health (Davidson & McEwen, 2012), and cognitive performance. One goal of meditation is to achieve the light of consciousness observing with equanimity (the right distance) clouds of the mind wandering. This Frontiers Research Topic brings together studies from groups of authors whose research focus on neuropsychological systems involved in meditation demonstrating how meditation activates and can modify brain areas, cognitive mechanisms and well-being.

Methodological Quality of Interventions in Psychology

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889452491 Year: Pages: 120 DOI: 10.3389/978-2-88945-249-1 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Psychology
Added to DOAB on : 2018-02-27 16:16:44
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Evaluations of intervention programs seek to present high-quality design, measures and data to assess their merit and worth. While evaluations differ in their purpose, theoretical framework and methodology, their collective aim is to obtain relevant and meaningful information to inform practice, research, and policy. As such, evaluation findings serve to build a body of knowledge on effective approaches to promote designated psychological outcomes, critical to an individual's overall health and well-being. However, as examined in this e-book, methodological weaknesses directly limit the potential of evaluations of intervention programs. As discussed by Chacón-Moscoso and Sanduvete-Chaves, methodological weaknesses can be attributed to how to define and measure methodological quality and the contextual dependency of instruments designed to measure this quality.In response, this e-book provides a collection of studies on methodological approaches to promote the quality of psychological interventions. Specifically, 10 original works published in the Research Topic Methodological Quality of Interventions in Psychology are included. The papers are organized into two chapters. Concretely, Chapter 1 includes studies pertaining to methodological approaches to enhance the quality of psychological intervention, being context independent solutions. Furthermore, Chapter 2 presents original work in different areas (health, education, sport and social welfare) where methodological quality has been better assessed. Collectively, the papers in this e-book serve to expand the awareness of practitioners and researchers interested in psychological interventions of the critical role of methodological quality in this work. This research was funded by the projects 1150096 (Chilean National Fund of Scientific and Technological Development, FONDECYT); and PSI2015-71947-REDT (Spain’s Ministry of Economy and Competitiveness).

Biological Ontologies and Semantic Biology

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889192779 Year: Pages: 106 DOI: 10.3389/978-2-88919-277-9 Language: English
Publisher: Frontiers Media SA
Subject: Botany --- Biotechnology --- General and Civil Engineering --- Genetics --- Science (General)
Added to DOAB on : 2015-12-03 13:02:24
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As the amount of biological information and its diversity accumulates massively there is a critical need to facilitate the integration of this data to allow new and unexpected conclusions to be drawn from it. The Semantic Web is a new wave of web- based technologies that allows the linking of data between diverse data sets via standardised data formats (“big data”). Semantic Biology is the application of semantic web technology in the biological domain (including medical and health informatics). The Special Topic encompasses papers in this very broad area, including not only ontologies (development and applications), but also text mining, data integration and data analysis making use of the technologies of the Semantic Web. Ontologies are a critical requirement for such integration as they allow conclusions drawn about biological experiments, or descriptions of biological entities, to be understandable and integratable despite being contained in different databases and analysed by different software systems. Ontologies are the standard structures used in biology, and more broadly in computer science, to hold standardized terminologies for particular domains of knowledge. Ontologies consist of sets of standard terms, which are defined and may have synonyms for ease of searching and to accommodate different usages by different communities. These terms are linked by standard relationships, such as “is_a” (an eye “is_a” sense organ) or “part_of” (an eye is “part_of” a head). By linking terms in this way, more detailed, or granular, terms can be linked to broader terms, allowing computation to be carried out that takes these relationships into account.

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.

Beyond the simple contrastive analysis: Appropriate experimental approaches for unraveling the neural basis of conscious experience

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889195473 Year: Pages: 129 DOI: 10.3389/978-2-88919-547-3 Language: English
Publisher: Frontiers Media SA
Subject: Psychology --- Science (General)
Added to DOAB on : 2016-01-19 14:05:46
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Contrasting conditions with and without conscious experience has served consciousness research well. However, research based on this simple contrast has led to controversies about the neural basis of conscious experience. One key reason for these ongoing debates seems to be that the simple contrast between conditions with and without consciousness is not specific for unraveling the neural basis of conscious experience, but rather also leads to other processes that precede or follow it. Acknowledging this methodological problem implies that some of the previous research findings about the neural underpinnings of conscious experience are actually reflecting the prerequisites and consequences rather than the direct correlates of conscious perception. Thus, it is required to re-evaluate the previous results to find out which of them are telling us anything about the neural basis of consciousness. But first and foremost, to overcome this methodological problem we need new experimental paradigms that go beyond the simple contrastive analysis or find the ways how some older but well forgotten paradigms may foster a new look at this emerging problem. Accordingly, this research topic is looking for empirical and theoretical contributions that: 1) envision new and suitable experimental approaches to study consciousness that are free from the limitations of the simple contrastive analysis; 2) provide empirical data that help to separate the neural correlates of conscious experience from the prerequisites and consequences of it; 3) help to re-assess previous research findings about the neural correlates of conscious perception in the light of the methodological problems with the traditional contrastive analysis. We hope that the theoretical insights and experimental approaches collected within this Research Topic help us to gain a more refined understanding of the neural basis of conscious experience.

Probing auditory scene analysis

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889193714 Year: Pages: 151 DOI: 10.3389/978-2-88919-371-4 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Neurology --- Psychology
Added to DOAB on : 2015-11-19 16:29:12
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In natural environments, the auditory system is typically confronted with a mixture of sounds originating from different sound sources. As sounds spread over time, the auditory system has to continuously decompose competing sounds into distinct meaningful auditory objects or “auditory streams” referring to certain sound sources. This decomposition work, which was termed by Albert Bregman as “Auditory scene analysis” (ASA), involves two kinds of grouping to be done. Grouping based on simultaneous cues, such as harmonicity and on sequential cues, such as similarity in acoustic features over time. Understanding how the brain solves these tasks is a fundamental challenge facing auditory scientist. In recent years, the topic of ASA was broadly investigated in different fields of auditory research, including a wide range of methods, studies in different species, and modeling. Despite the advance in understanding ASA, it still proves to be a major challenge for auditory research. This includes verifying whether experimental findings are transferable to more realistic auditory scenes. A central approach in understanding ASA is the use of certain stimulus parameters that produce an ambiguous percept. The advantage of such an approach is that different perceptual organizations can be studied without varying physical stimulus parameters. Additionally, the perception of ambiguous stimuli can be volitionally controlled by intention or task. By using this one can mirror real hearing situations where listeners intent to identify and to localize auditory sources. Recently it was also found that in classical auditory streaming sequences perceptual ambiguity was not restricted to but was observed over a broad range of stimulus parameters. The proposed Research Topic pursues to bring together scientist in the different fields of auditory research whose work addresses the issue of perceptual ambiguity. Researchers were welcome to contribute experimental reports, computational modeling, and reviews that consider auditory ambiguity in its modality specific characteristics as well as in comparison to visual ambiguous figures. The overall goal of contributions was to consider the experimental findings from the perspective of real auditory scenes. In a broader sense, the Research Topic was open for contributions which are related to the issue of active listening in complex scenes.

Cancer Immunotherapy & Immuno-monitoring: Mechanism, Treatment, Diagnosis, and Emerging Tools

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889193806 Year: Pages: 97 DOI: 10.3389/978-2-88919-380-6 Language: English
Publisher: Frontiers Media SA
Subject: Oncology --- Medicine (General)
Added to DOAB on : 2015-12-03 13:02:24
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In the past decade, significant progresses have taken place in the field of cancer immunotherapy. Tumor-targeting immunotherapies are being developed for most human cancers, including melanoma, prostate cancer, glioblastoma, sarcoma, lung carcinoma and hepatocellular carcinoma. The FDA has approved multiple molecular immunotherapeutics, such as Ipilimumab; cellular immunotherapies (e.g. adoptive cell transfer) are being tested in phase II/III clinical trials. Immunotherapetics has evolved into a sophisticated field: Multimodal therapeutic regimens are administrated to induce focused responses, curtail side- effects and improve therapeutic efficacy. The lack of effective clinical assessment tools remains a major challenge. Because of the intricacy of antitumor response, it is essential to scrutinize individual tumor-targeting immune cells and their functions at the finest details - molecules. In this regard, flow cytometry analysis modernized hematology and allows characterization of surface molecular signature on individual cells. More recently, microchip technologies and new variations of cytometry have enormously expanded the spectrum, throughout and multiplexity of single cell analysis. Nowadays, tens of millions of readouts can be generated through the course of a cancer immunotherapy to monitor the abundance, phenotype and a myriad of effector functions of single immune cells. At the same time, big data analytics and data mining methodologies have been adapted to achieve sensible diagnostic interpretations. Such a marriage of technology and analytics opens the door for informative point-of-care assessment of therapeutic efficacy and ensures timely therapeutic decisions. The new generation of personalized clinical diagnostics will revolutionize healthcare in the years to come.

Identifying the Epileptic Network

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889192960 Year: Pages: 126 DOI: 10.3389/978-2-88919-296-0 Language: English
Publisher: Frontiers Media SA
Subject: Neurology --- Medicine (General)
Added to DOAB on : 2015-12-10 11:59:07
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An important area of current research in epilepsy focuses on identifying the specific regions within the brain that are affected in individuals with recurring seizures. The epileptogenic process may result not only in pathology in focal cortical regions, but abnormalities in subcortical structures, such as thalamus and basal ganglia, and in intercortical and intracortical connecting white matter pathways. Novel methods of treating refractory epilepsy are urgently needed. The goal of identifying for each affected individual the specific brain regions that are involved offers the promise that novel methods of treatment will one day be developed that specifically target those abnormal regions. Researchers from disparate fields are required to develop and advance this area of research, and this current topic proposes to place a spotlight on the “state of the art” of methods to identify the abnormal networks. Recent work covering a wide variety of disciplines and technologies, including dense array electroencephalography (dEEG), novel methods of analyses of both the interictal dEEG and intracranial EEG (icEEG), magnetoencephalography (MEG), high-resolution magnetic resonance imaging (MRI), functional MRI (fMRI), simultaneous fMRI-EEG, fMRI connectivity measures, simultaneous dEEG-icEEG, and techniques to coregister patient-specific MRI (including white matter pathways) and dEEG, are all examples of areas of research that have contributed to a greater understanding of potential epileptogenic regions. We asked for individuals with expertise in an area of research that expands an understanding of identifying epileptic networks to contribute to this research topic.

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