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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.

Biomass Modification, Characterization and Process Monitoring Analytics to Support Biofuel and Biomaterial Production

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889198672 Year: Pages: 156 DOI: 10.3389/978-2-88919-867-2 Language: English
Publisher: Frontiers Media SA
Subject: Biotechnology --- General and Civil Engineering
Added to DOAB on : 2016-01-19 14:05:46
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The conversion of lignocellulosic biomass into renewable fuels and other commodities has provided an appealing alternative towards supplanting global dependence on fossil fuels. The suitability of multitudes of plants for deconstruction to useful precursor molecules and products is currently being evaluated. These studies have probed a variety of phenotypic traits, including cellulose, non-cellulosic polysaccharide, lignin, and lignin monomer composition, glucose and xylose production following enzymatic hydrolysis, and an assessment of lignin-carbohydrate and lignin-lignin linkages, to name a few. These quintessential traits can provide an assessment of biomass recalcitrance, enabling researchers to devise appropriate deconstruction strategies. Plants with high polysaccharide and lower lignin contents have been shown to breakdown to monomeric sugars more readily. Not all plants contain ideal proportions of the various cell wall constituents, however. The capabilities of biotechnology can alleviate this conundrum by tailoring the chemical composition of plants to be more favorable for conversion to sugars, fuels, etc. Increases in the total biomass yield, cellulose content, or conversion efficiency through, for example, a reduction in lignin content, are pathways being evaluated to genetically improve plants for use in manufacturing biofuels and bio-based chemicals. Although plants have been previously domesticated for food and fiber production, the collection of phenotypic traits prerequisite for biofuel production may necessitate new genetic breeding schemes. Given the plethora of potential plants available for exploration, rapid analytical methods are needed to more efficiently screen through the bulk of samples to hone in on which feedstocks contain the desired chemistry for subsequent conversion to valuable, renewable commodities. The standard methods for analyzing biomass and related intermediates and finished products are laborious, potentially toxic, and/or destructive. They may also necessitate a complex data analysis, significantly increasing the experimental time and add unwanted delays in process monitoring, where delays can incur in significant costs. Advances in thermochemical and spectroscopic techniques have enabled the screening of thousands of plants for different phenotypes, such as cell-wall cellulose, non-cellulosic polysaccharide, and lignin composition, lignin monomer composition, or monomeric sugar release. Some instrumental methods have been coupled with multivariate analysis, providing elegant chemometric predictive models enabling the accelerated identification of potential feedstocks. In addition to the use of high-throughput analytical methods for the characterization of feedstocks based on phenotypic metrics, rapid instrumental techniques have been developed for the real-time monitoring of diverse processes, such as the efficacy of a specific pretreatment strategy, or the formation of end products, such as biofuels and biomaterials. Real-time process monitoring techniques are needed for all stages of the feedstocks-to-biofuels conversion process in order to maximize efficiency and lower costs by monitoring and optimizing performance. These approaches allow researchers to adjust experimental conditions during, rather than at the conclusion, of a process, thereby decreasing overhead expenses. This Frontiers Research Topic explores options for the modification of biomass composition and the conversion of these feedstocks into to biofuels or biomaterials and the related innovations in methods for the analysis of the composition of plant biomass, and advances in assessing up- and downstream processes in real-time. Finally, a review of the computational models available for techno-economic modeling and lifecycle analysis will be presented.

Sensors for Food Safety and Quality

ISBN: 9783038421993 9783038422006 Year: Pages: 334 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Added to DOAB on : 2016-06-07 11:19:06
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Plant Phenotyping and Phenomics for Plant Breeding

Authors: --- --- --- --- et al.
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889455324 Year: Pages: 369 DOI: 10.3389/978-2-88945-532-4 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Botany
Added to DOAB on : 2019-01-23 14:53:42
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As a consequence of the global climate change, both the reduction on yield potential and the available surface area of cultivated species will compromise the production of food needed for a constant growing population. There is consensus about the significant gap between world food consumption projected for the coming decades and the expected crop yield-improvements, which are estimated to be insufficient to meet the demand.The complexity of this scenario will challenge breeders to develop cultivars that are better adapted to adverse environmental conditions, therefore incorporating a new set of morpho-physiological and physico-chemical traits; a large number of these traits have been found to be linked to heat and drought tolerance.Currently, the only reasonable way to satisfy all these demands is through acquisition of high-dimensional phenotypic data (high-throughput phenotyping), allowing researchers with a holistic comprehension of plant responses, or ‘Phenomics’.Phenomics is still under development. This Research Topic aims to be a contribution to the progress of methodologies and analysis to help understand the performance of a genotype in a given environment.

Genomics in Aquaculture to Better Understand Species Biology and Accelerate Genetic Progress

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889199570 Year: Pages: 151 DOI: 10.3389/978-2-88919-957-0 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Genetics
Added to DOAB on : 2016-01-19 14:05:46
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From a global perspective aquaculture is an activity related to food production with large potential for growth. Considering a continuously growing population, the efficiency and sustainability of this activity will be crucial to meet the needs of protein for human consumption in the near future. However, for continuous enhancement of the culture of both fish and shellfish there are still challenges to overcome, mostly related to the biology of the cultured species and their interaction with (increasingly changing) environmental factors. Examples of these challenges include early sexual maturation, feed meal replacement, immune response to infectious diseases and parasites, and temperature and salinity tolerance. Moreover, it is estimated that less than 10% of the total aquaculture production in the world is based on populations genetically improved by means of artificial selection. Thus, there is considerable room for implementing breeding schemes aimed at improving productive traits having significant economic impact. By far the most economically relevant trait is growth rate, which can be efficiently improved by conventional genetic selection (i.e. based on breeding values of selection candidates). However, there are other important traits that cannot be measured directly on selection candidates, such as resistance against infectious and parasitic agents and carcass quality traits (e.g. fillet yield and meat color). However, these traits can be more efficiently improved using molecular tools to assist breeding programs by means of marker-assisted selection, using a few markers explaining a high proportion of the trait variation, or genomic selection, using thousands of markers to estimate genomic breeding values. The development and implementation of new technologies applied to molecular biology and genomics, such as next-generation sequencing methods and high-throughput genotyping platforms, are allowing the rapid increase of availability of genomic resources in aquaculture species. These resources will provide powerful tools to the research community and will aid in the determination of the genetic factors involved in several biological aspects of aquaculture species. In this regard, it is important to establish discussion in terms of which strategies will be more efficient to solve the primary challenges that are affecting aquaculture systems around the world. The main objective of this Research Topic is to provide a forum to communicate recent research and implementation strategies in the use of genomics in aquaculture species with emphasis on (1) a better understanding of fish and shellfish biological processes having considerable impact on aquaculture systems; and (2) the efficient incorporation of molecular information into breeding programs to accelerate genetic progress of economically relevant traits.

30 years of the Comet Assay: an overview with some new insights

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889196494 Year: Pages: 174 DOI: 10.3389/978-2-88919-649-4 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Genetics
Added to DOAB on : 2016-08-16 10:34:25
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By means of this ‘Frontiers in Genetics’ research topic, we are celebrating 30 years of the Comet Assay. The first paper on this single-cell gel electrophoresis assay was published in 1984 by O. Ostling and K.J. Johanson (Biochem. Biophys. Res. Commun. Vol.123: 291-298). The comet assay is a versatile and sensitive method for measuring single - and double-strand breaks in DNA. By including lesion-specific enzymes in the assay, its range and sensitivity are greatly increased, but it is important to bear in mind that their specificity is not absolute. The comet assay (with and without inclusion of lesion-specific enzymes) is widely used as a biomarker assay in human population studies - primarily to measure DNA damage, but increasingly also to assess the capacity of cells for DNA repair. Ostling and Johanson (Biochem. Biophys. Res. Commun., 1984) were also the first to report experiments to measure DNA repair, by simply following the decrease of DNA damage over time after challenging cells with ionising radiation. However, this approach is time-consuming and laborious as it requires an extended period of cell culture and is therefore not ideal for biomonitoring studies, which typically require high-throughput processing of many samples. As an alternative approach, the in vitro comet-based repair assay was developed: a cell extract is incubated with a DNA substrate containing specific lesions, and DNA incisions accumulate. The in vitro comet-based repair assay has been modified and improved over the past decade: it was first devised to measure base excision repair of oxidised purines in lymphocytes (Collins et al., Mutagenesis, 2001), but has since been adapted for other lesions and thus other repair pathways, as well as being applied to tissue samples in addition to cell suspensions. Even after 30 years, the comet assay is still in a growth phase, with many new users each year. Many questions are repeatedly raised, which may seem to have self-evident answers, but clearly, it is necessary to reiterate them for the benefit of the new audience, and sometimes being forced to think again about old topics can shed new light. Different applications of the comet assay are discussed in this special issue, including: genotoxicity testing in different organisms, human biomonitoring, DNA repair studies, environmental biomonitoring and clinical studies. Furthermore, we consider and where possible answer questions, including the ones raised by Raymond Tice at the 8th International Comet Assay Workshop in Perugia (Italy 2009): What is the spectrum of DNA damage detected by the various versions of the comet assay?; What are the limitations associated with each application?; What should be done to standardize the assay for biomonitoring studies?; Can the comet assay be used to monitor changes in global methylation status?; What cell types are suitable for detecting genotoxic substances and their effects in vivo and in vitro?; Can the assay be fully automated?; and more. So this ‘Frontiers in Genetics’ research topic is written for the beginner as well as for the experienced users of the comet assay.

Computational and Experimental Approaches in Multi-Target Pharmacology

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889452521 Year: Pages: 122 DOI: 10.3389/978-2-88945-252-1 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Therapeutics
Added to DOAB on : 2018-02-27 16:16:44
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The next frontier in pharmacology is the development of multi-target strategies in which pathological processes are controlled by pharmacologically manipulating them at many different points at once. Designing multi-target strategies will require deep understanding of the complex physiology that underlies pathological processes. It will also require the development of single drugs with multiple targets, or combinations of drugs with compatible pharmacokinetics that work synergistically to maximize desirable effects while minimizing unwanted side effects. This e-Book contains ten original articles, each addressing a different aspect of this challenge. Together they open new perspectives and show the way forward in the development of multi-target therapeutics.

Hydrogels in Tissue Engineering

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ISBN: 9783038971214 9783038971221 Year: Pages: XII, 146 Language: Englisch
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Medicine (General)
Added to DOAB on : 2018-08-24 16:21:01
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Hydrogels are the foundation of regenerative medicine as a supportive matrix for cell immobilization and growth factor delivery. The fate of implanted cells is mediated by cell-matrix interaction at multiple scales and timed-release of growth factors to guide the differentiation and maturation of cells. Recently, there has been great interest in hydrogels with a hierarchical structure that mimics the complex interaction of cells with a microenvironment that can locally release growth factors to specific cells. Related topics in this Special Issue include hydrogels with a hierarchical structure; hybrid, degradable, and load-bearing hydrogels; hydrogels for cell encapsulation, micro-patterning, microfluidic devices, biofabrication, and high-throughput screening; and hydrogels that modulate the body’s immune response.

When Chemistry Meets Biology - Generating Innovative Concepts, Methods and Tools for Scientific Discovery in the Plant Sciences

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889199280 Year: Pages: 146 DOI: 10.3389/978-2-88919-928-0 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Botany
Added to DOAB on : 2016-01-19 14:05:46
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Biologically active small molecules have increasingly been applied in plant biology to dissect and understand biological systems. This is evident from the frequent use of potent and selective inhibitors of enzymes or other biological processes such as transcription, translation, or protein degradation. In contrast to animal systems, which are nurtured from drug research, the systematic development of novel bioactive small molecules as research tools for plant systems is a largely underexplored research area. This is surprising since bioactive small molecules bear great potential for generating new, powerful tools for dissecting diverse biological processes. In particular, when small molecules are integrated into genetic strategies (thereby defining “chemical genetics”), they may help to circumvent inherent problems of classical (forward) genetics. There are now clear examples of important, fundamental discoveries originating from plant chemical genetics that demonstrate the power, but not yet fully exploited potential, of this experimental approach. These include the unraveling of molecular mechanisms and critical steps in hormone signaling, activation of defense reactions and dynamic intracellular processes. The intention of this Research Topic of Frontiers in Plant Physiology is to summarize the current status of research at the interface between chemistry and biology and to identify future research challenges. The research topic covers diverse aspects of plant chemical biology, including the identification of bioactive small molecules through screening processes from chemical libraries and natural sources, which rely on robust and quantitative high-throughput bioassays, the critical evaluation and characterization of the compound’s activity (selectivity) and, ultimately, the identification of its protein target(s) and mode-of-action, which is yet the biggest challenge of all. Such well-characterized, selective chemicals are attractive tools for basic research, allowing the functional dissection of plant signaling processes, or for applied purposes, if designed for protection of crop plants from disease. New methods and data mining tools for assessing the bioactivity profile of compounds, exploring the chemical space for structure–function relationships, and comprehensive chemical fingerprinting (metabolomics) are also important strategies in plant chemical biology. In addition, there is a continuing need for diverse target-specific bioprobes that help profiling enzymatic activities or selectively label protein complexes or cellular compartments. To achieve these goals and to add suitable probes and methods to the experimental toolbox, plant biologists need to closely cooperate with synthetic chemists. The development of such tailored chemicals that beyond application in basic research can modify traits of crop plants or target specific classes of weeds or pests by collaboration of applied and academic research groups may provide a bright future for plant chemical biology. The current Research Topic covers the breadth of the field by presenting original research articles, methods papers, reviews, perspectives and opinions.

Immune System Modeling and Analysis

Authors: --- --- --- --- et al.
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889195015 Year: Pages: 401 DOI: 10.3389/978-2-88919-501-5 Language: English
Publisher: Frontiers Media SA
Subject: Allergy and Immunology --- Medicine (General)
Added to DOAB on : 2015-12-03 13:02:24
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The rapid development of new methods for immunological data collection - from multicolor flow cytometry, through single-cell imaging, to deep sequencing - presents us now, for the first time, with the ability to analyze and compare large amounts of immunological data in health, aging and disease. The exponential growth of these datasets, however, challenges the theoretical immunology community to develop methods for data organization and analysis. Furthermore, the need to test hypotheses regarding immune function, and generate predictions regarding the outcomes of medical interventions, necessitates the development of mathematical and computational models covering processes on multiple scales, from the genetic and molecular to the cellular and system scales. The last few decades have seen the development of methods for presentation and analysis of clonal repertoires (those of T and B lymphocytes) and phenotypic (surface-marker based) repertoires of all lymphocyte types, and for modeling the intricate network of molecular and cellular interactions within the immune systems. This e-Book, which has first appeared as a ‘Frontiers in Immunology’ research topic, provides a comprehensive, online, open access snapshot of the current state of the art on immune system modeling and analysis.

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