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Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889452972 Year: Pages: 296 DOI: 10.3389/978-2-88945-297-2 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Botany
Added to DOAB on : 2018-02-27 16:16:44
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An increasing population faces the growing demand for agricultural products and accurate global climate models that account for individual plant morphologies to predict favorable human habitat. Both demands are rooted in an improved understanding of the mechanistic origins of plant development. Such understanding requires geometric and topological descriptors to characterize the phenotype of plants and its link to genotypes. However, the current plant phenotyping framework relies on simple length and diameter measurements, which fail to capture the exquisite architecture of plants. The Research Topic “Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences” is the result of a workshop held at National Institute for Mathematical and Biological Synthesis (NIMBioS) in Knoxville, Tennessee. From 2.-4. September 2015 over 40 scientists from mathematics, computer science, engineering, physics and biology came together to set new frontiers in combining plant phenotyping with recent results from shape theory at the interface of geometry and topology. In doing so, the Research Topic synthesizes the views from multiple disciplines to reveal the potential of new mathematical concepts to analyze and quantify the relationship between morphological plant features. As such, the Research Topic bundles examples of new mathematical techniques including persistent homology, graph-theory, and shape statistics to tackle questions in crop breeding, developmental biology, and vegetation modeling. The challenge to model plant morphology under field conditions is a central theme of the included papers to address the problems of climate change and food security, that require the integration of plant biology and mathematics from geometry and topology research applied to imaging and simulation techniques. The introductory white paper written by the workshop participants identifies future directions in research, education and policy making to integrate biological and mathematical approaches and to strengthen research at the interface of both disciplines.

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.

Biomarkers in Drug Hypersensitivity

Authors: --- --- --- --- et al.
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889452262 Year: Pages: 104 DOI: 10.3389/978-2-88945-226-2 Language: English
Publisher: Frontiers Media SA
Subject: Therapeutics --- Science (General)
Added to DOAB on : 2017-10-13 14:57:01
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Biomarkers, especially those based on pharmacogenomics testing, have proved to be extremely useful for type A adverse drug reactions. Clinical practice guidelines based on biomarker testing are presently being developed and updated for type A adverse drug reactions. In contrast, little attention has been paid to the potential use of biomarkers in type B adverse reactions, characterized by the occurrence of reactions not directly related to the pharmacological properties of the drug. Drug-induced hypersensitivity belongs to those type B reactions. Drug-induced hypersensitivity reactions involve complex mechanisms that include, among others, the metabolic activation and haptenization of drug metabolites. Hence, factors that influence the pharmacokinetics of drug and metabolites may contribute to the development of some drug-induced hypersensitivity reactions. This implies that processes such as ADME (absorption, distribution, metabolism and excretion) that are typically involved in type A adverse drug reactions, may have a role in hypersensitivity reactions too. In addition to metabolic activation, several signal transduction pathways participate and modulate the development and the clinical presentation of drug hypersensitivity. The diverse mechanisms underlying such drug-hypersensitivity reactions lead to four major groups of reactions according to the Gell and Coombs classification: immediate, cytotoxic, immune complex and delayed. The enormous complexity of drug-hypersensitivity reactions is a consequence of the variety of mechanisms involved, which may be related, among others, to drug metabolism, generation of antigenic signals, stimulation and maturation of dendritic cells, presentation of haptens and mechanisms of cytotoxicity. In addition, a plethora of possible clinical presentations exists, including urticaria, angioedema, anaphylaxis, cytopenias, nephritis, serum sickness, vasculitis, contact dermatitis, drug rash, eosinophilia and systemic symptoms, Stevens–Johnson syndrome, toxic epidermal necrolysis and acute generalized exanthematous pustulosis. The rapid progress in the field in recent years indicates that the combination of several disciplines is essential to understand the mechanisms involved in this particular, and not completely understood, type of adverse drug reactions. The objective of this Research Topic is to present insights obtained from both basic and clinical scientists, which may include studies related to the identification, validation, refinement and clinical implementation of biomarkers for drug-induced hypersensitivity. The Topic aims to include recent findings related, but not limited to, potential phenomic, genomic, proteomic, metabolomic and signal transduction biomarkers. These biomarkers could eventually be used in clinical practice and/or these might contribute, as a proof of concept, to our understanding of the complex events leading to drug hypersensitivity reactions. In addition the Topic will cover recent developments and methodological advances in the diagnosis, prevention and therapeutic management of drug-induced hypersensitivity.

Optical Approaches to Capture Plant Dynamics in Time, Space, and Across Scales

Authors: --- --- ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889455430 Year: Pages: 173 DOI: 10.3389/978-2-88945-543-0 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Botany
Added to DOAB on : 2019-01-23 14:53:42
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Quantifying temporal changes in plant geometry as a result of genetic, developmental, or environmental causes is essential to improve our understanding of the structure and function relationships in plants. Over the last decades, optical imaging and remote sensing developed fundamental working tools to monitor and quantify our environment and plants in particular. Increased efficiency of methods lowered the barrier to compare, integrate, and interpret the optically obtained plant data across larger spatial scales and across scales of biological organization. In particular, acquisition speed at high resolutions reached levels that allow capturing the temporal dynamics in plants in three dimensions along with multi-spectral information beyond human visual senses. These advanced imaging capabilities have proven to be essential to detect and focus on analyzing temporal dynamics of plant geometries.The focus of this Research Topic is on optical techniques developed to study geometrical changes at the plant level detected within the wavelength spectrum between near-UV to near infrared. Such techniques typically involve photogrammetric, LiDAR, or imaging spectroscopy approaches but are not exclusively restricted to these. Instruments operating within this range of wavelengths allow capturing a wide range of temporal scales ranging from sub-second to seasonal changes that result from plant development, environmental effects like wind and heat, or genetically controlled adaption to environmental conditions. The Research Topic covered a plethora of methodological approaches as suggestions for best practices in the light of a particular research question and to a wider view to different research disciplines and how they utilize their state-of-the-art techniques in demonstrating potential use cases across different scales.

Energy metabolism

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889193080 Year: Pages: 132 DOI: 10.3389/978-2-88919-308-0 Language: English
Publisher: Frontiers Media SA
Subject: Physiology --- Science (General)
Added to DOAB on : 2016-02-05 17:24:33
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Energy metabolism is central to life and altered energy expenditure (EE) is often cited as a central mechanism responsible for development of the obese phenotype. Resting EE, EE of physical activity, cold induced thermogenesis and thermic effect of feeding add to produce total EE but can also affect each other. It is thus very important that each component be well measured. Measuring energy expenditure by indirect calorimetry is extremely simple in theory but the practice if far more difficult. Taking into account temperature in small sized animals, measuring accurately the effect of activity on EE, correcting EE for body size body composition, age sex etc… add difficulties in producing reliable data. The goal of this Research Topic was to call for the practical experience of main investigators trained to practice calorimetry in order to get their feedback and the way they deal with the various and specific problems of humans and animal calorimetry. The goal is to share the questions/solutions experienced by the contributors to inititate a “guide of the good practices” that can be periodically updated and used by all those who are and will be interested in measuring energy metabolism from the 20g mouse to the human and large farm animals.

Branching and Rooting Out with a CT Scanner: The Why, the How, and the Outcomes, Present and Possibly Future

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889197910 Year: Pages: 91 DOI: 10.3389/978-2-88919-791-0 Language: English
Publisher: Frontiers Media SA
Subject: Botany --- Science (General)
Added to DOAB on : 2017-02-03 17:04:57
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Until recently, a majority of the applications of X-ray computed tomography (CT) scanning in plant sciences remained descriptive; some included a quantification of the plant materials when the root-soil isolation or branch-leaf separation was satisfactory; and a few involved the modeling of plant biology processes or the assessment of treatment or disease effects on plant biomass and structures during growth. In the last decade, repeated CT scanning of the same plants was reported in an increasing number of studies in which moderate doses of X-rays had been used. Besides the general objectives of Frontiers in Plant Science research topics, “Branching and Rooting Out with a CT Scanner” was proposed to meet specific objectives: (i) providing a non-technical update on knowledge about the application of CT scanning technology to plants, starting with the type of CT scanning data collected (CT images vs. CT numbers) and their processing in the graphical and numerical approaches; (ii) drawing the limits of the CT scanning approach, which because it is based on material density can distinguish materials with contrasting or moderately overlapping densities (e.g., branches vs. leaves, roots vs. non-organic soils) but not the others (e.g., roots vs. organic soils); (iii) explaining with a sufficient level of detail the main procedures used for graphical, quantitative and statistical analyses of plant CT scanning data, including fractal complexity measures and statistics appropriate for repeated plant CT scanning, in experiments where the research hypotheses are about biological processes such as light interception by canopies, root disease development and plant growth under stress conditions; (iv) comparing plant CT scanning with an alternative technology that applies to plants, such as the phenomics platforms which target leaf canopies; and (v) providing current and potential users of plant CT scanning with up-to-date information and exhaustive documentation, including clear perspectives and well-defined goals for the future, for them to be even more efficient or most efficient from start in their research work.

Diagnosis of Neurogenetic Disorders: Contribution of Next Generation Sequencing and Deep Phenotyping

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ISBN: 9783039216109 9783039216116 Year: Pages: 94 DOI: 10.3390/books978-3-03921-611-6 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Medicine (General) --- Neurology
Added to DOAB on : 2019-12-09 11:49:16
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The contribution of genomic variants to the aetiopathogenesis of both paediatric and adult neurological disease is being increasingly recognized. The use of next-generation sequencing has led to the discovery of novel neurodevelopmental disorders, as exemplified by the deciphering developmental disorders (DDD) study, and provided insight into the aetiopathogenesis of common adult neurological diseases. Despite these advances, many challenges remain. Correctly classifying the pathogenicity of genomic variants from amongst the large number of variants identified by next-generation sequencing is recognized as perhaps the major challenge facing the field. Deep phenotyping (e.g., imaging, movement analysis) techniques can aid variant interpretation by correctly classifying individuals as affected or unaffected for segregation studies. The lack of information on the clinical phenotype of novel genetic subtypes of neurological disease creates limitations for genetic counselling. Both deep phenotyping and qualitative studies can capture the clinical and patient’s perspective on a disease and provide valuable information. This Special Issue aims to highlight how next-generation sequencing techniques have revolutionised our understanding of the aetiology of brain disease and describe the contribution of deep phenotyping studies to a variant interpretation and understanding of natural history.

Coffee and Caffeine Consumption for Human Health

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ISBN: 9783039286287 / 9783039286294 Year: Pages: 290 DOI: 10.3390/books978-3-03928-629-4 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology --- Nutrition and Food Sciences
Added to DOAB on : 2020-06-09 16:38:57
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The year 2019 has been prolific in terms of new evidence regarding the effects of coffee and caffeine consumption on diverse aspects of human functioning. This book collects 20 high-quality manuscripts published in Nutrients that include original investigation or systematic review studies of the effects of caffeine intake on human performance and health. The diversity of the articles published in this Special Issue highlights the extent of the effects of coffee and caffeine on human functioning, while underpinning the positive nature of most of these effects. This book will help with understanding why the natural sources of caffeine are so widely present in the nutrition behaviors of modern society.

Keywords

pharmacokinetics --- energy drink --- exercise --- elite athlete --- performance --- football --- RPE --- DOMS --- sport performance --- supplementation --- ergogenic aids --- consumer --- behavior --- perception --- coffee --- health --- consumption motives --- coffee/caffeine --- systematic review and meta-analysis --- prospective studies --- epidemiology --- cancer prevention --- colorectal cancer --- individual responses --- responders --- exercise performance --- ergogenic aids --- caffeine --- coffee --- tea --- energy drinks --- pregnancy --- newborn --- caffeine --- ergogenic aid --- resistance training --- isokinetic testing --- adrenal gland --- caffeine --- corticosterone --- puberty --- rat --- sex-difference --- caffeine --- energy drinks --- fatigue --- mood state --- exercise --- supplement --- resistance exercise --- speed --- repetition --- n/a --- metabolome --- skeletal muscle --- exercise --- muscle contraction --- ergogenic effect --- bench press --- upper limb --- resistance exercise --- ergogenic substances --- time under tension --- 1RM test --- caffeine --- metabolites --- phenotyping --- CYP450 --- NAT --- xanthine oxidase --- actigraphy --- athletic --- coffee --- ergogenic aid --- supplement --- anaerobic --- caffeine --- CMJ --- ergogenic aids --- exercise --- nutrition --- sport supplement --- Wingate --- electromyography --- efficiency --- sport --- exercise --- expectancy --- belief --- perceptions --- placebo effect --- recovery --- strength --- power --- sprint performance --- menstrual cycle --- fatigue --- placebo --- ergogenic --- EEG–EMG coherence --- n/a --- women --- resistance exercise --- exercise training --- velocity --- ergogenic aid --- muscle function --- n/a

The Future of Hyperspectral Imaging

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ISBN: 9783039218226 9783039218233 Year: Pages: 220 DOI: 10.3390/books978-3-03921-823-3 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Chemistry (General)
Added to DOAB on : 2019-12-09 16:39:37
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hyperspectral imaging --- Raman --- fluorescence --- sorting --- quality control --- black polymers --- PZT --- classification --- machine learning --- alternating direction method of multipliers --- Cramer–Rao lower bound --- forward observation model --- linear mixture model --- maximum likelihood --- multiband image fusion --- total variation --- fingerprints --- blood detection --- age determination --- hyperspectral imaging --- lossless compression --- multitemporal hyperspectral images --- information theoretic analysis --- predictive coding --- hyperspectral imaging --- plant phenotyping --- disease detection --- spectral tracking --- time series --- hyperspectral imaging --- principal component analysis --- oxygen saturation --- wound healing --- diabetic foot ulcer --- Raman spectroscopy --- chemical imaging --- compressive detection --- spatial light modulators (SLM) --- digital micromirror device (DMD) --- digital light processor (DLP) --- optimal binary filters --- Chemometrics --- multivariate data analysis --- compressive sensing --- hyperspectral imaging --- multiplexing system --- liquid crystal --- three-dimensional imaging --- integral imaging --- remote sensing --- point target detection --- CS-MUSI --- hyperspectral --- video --- imaging --- coastal dynamics --- moving vehicle imaging --- bi-directional reflectance distribution function (BRDF) --- hemispherical conical reflectance factor (HCRF) --- stereo imaging --- digital elevation model --- Virginia Coast Reserve Long Term Ecological Research (VCR LTER) --- Hyperspectral imaging --- painting samples --- retouching pigments --- watercolours --- multivariate analysis --- potatoes --- sprouting --- primordial leaf count --- hyperspectral imaging --- spectroscopy --- fusion --- wavelength selection --- PLSR --- interval partial least squares --- deep learning --- hyperspectral imaging --- neural networks --- machine learning --- image processing --- hyperspectral imaging --- medical imaging by HSI --- HSI for biology --- remote sensing --- hyperspectral microscopy --- fluorescence hyperspectral imaging --- Raman hyperspectral imaging --- infrared hyperspectral imaging --- statistical methods for HSI --- hyperspectral data mining and compression --- statistical methods for HSI --- hyperspectral data mining and compression

Sensors in Agriculture

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ISBN: 9783038974123 9783038974130 Year: Pages: 346 DOI: 10.3390/books978-3-03897-413-0 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Technology (General) --- General and Civil Engineering
Added to DOAB on : 2019-06-26 08:44:06
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Agriculture requires technical solutions for increasing production while lessening environmental impact by reducing the application of agro-chemicals and increasing the use of environmentally friendly management practices. A benefit of this is the reduction of production costs. Sensor technologies produce tools to achieve the abovementioned goals. The explosive technological advances and developments in recent years have enormously facilitated the attainment of these objectives, removing many barriers for their implementation, including the reservations expressed by farmers. Precision agriculture and ‘smart farming’ are emerging areas where sensor-based technologies play an important role. Farmers, researchers, and technical manufacturers are joining their efforts to find efficient solutions, improvements in production, and reductions in costs. This book brings together recent research and developments concerning novel sensors and their applications in agriculture. Sensors in agriculture are based on the requirements of farmers, according to the farming operations that need to be addressed.

Keywords

wireless sensor network (WSN) --- Wi-SUN --- vine --- mandarin orange --- thermal image --- fluorescent measurement --- X-ray fluorescence spectroscopy --- visible and near-infrared reflectance spectroscopy --- heavy metal contamination --- spectral pre-processing --- feature selection --- machine-learning --- LiDAR --- light-beam --- plant localization --- Kinect --- leaf area index --- radiative transfer model --- neural networks --- GF-1 satellite --- wide field view --- big data --- geo-information --- plant phenotyping --- grapevine breeding --- Vitis vinifera --- ambient intelligence --- wireless sensor --- fuzzy logic --- smart irrigation --- virtual organizations of agents --- CIE-Lab --- precision plant protection --- optical sensor --- weed control --- classification --- NIR hyperspectral imaging --- chemometrics analysis --- weeds --- UAS --- RPAS --- one-class --- machine learning --- remote sensing --- geoinformatics --- plant disease --- pest --- deep convolutional neural networks --- real-time processing --- detection --- hyperspectral imaging --- soil type classification --- total nitrogen --- texture features --- data fusion --- Fusarium --- near-infrared --- spectroscopy --- hulled barely --- partial least squares-discriminant analysis --- remote sensing --- precision agriculture --- crop monitoring --- data fusion --- speckle --- diffusion --- scattering --- biological sensing --- apparent soil electrical conductivity --- ECa-directed soil sampling --- electromagnetic induction --- proximal sensor --- response surface sampling --- salt tolerance --- boron tolerance --- soil mapping --- soil salinity --- spatial variability --- irrigation --- energy balance --- water management --- semi-arid regions --- on-line vis-NIR measurement --- total nitrogen --- total carbon --- spiking --- gradient boosted machines --- artificial neural networks --- random forests --- rice --- striped stem-borer --- hyperspectral imaging --- texture feature --- data fusion --- greenhouse --- wireless sensor network --- data fusion --- dynamic weight --- dataset --- agriculture --- obstacle detection --- computer vision --- cameras --- stereo imaging --- thermal imaging --- LiDAR --- radar --- object tracking --- crop area --- remote sensing image classification --- area frame sampling --- stratification --- regression estimator --- agriculture --- meat spoilage --- vegetable oil --- quality assessment --- electronic nose --- electrochemical sensors --- spectral analysis --- feature selection --- genetic algorithms --- classification --- vegetation indices --- vineyard --- diseases --- spatial data --- sensor --- data fusion --- change of support --- geostatistics --- precision agriculture --- management zones --- event detection --- back propagation model --- multivariate water quality parameters --- time-series data --- spatial-temporal model --- connected dominating set --- water supply network --- SS-OCT --- Capsicum annuum --- germination --- salt concentration --- deep learning --- clover-grass --- precision agriculture --- dry matter composition --- proximity sensing --- 3D reconstruction --- RGB-D sensor --- crop inspection platform --- water depth sensors --- soil moisture sensors --- temperature sensors --- rice field monitoring --- irrigation --- silage --- packing density --- moisture content --- compound sensor --- simultaneous measurement --- birth sensor --- bovine embedded hardware --- ambient intelligence --- virtual organizations of agents --- Fusarium --- near infrared --- discrimination --- hulled barely --- naked barley --- wheat --- dielectric probe --- apple shelf-life --- dielectric dispersion --- electronic nose --- pest scouting --- pest management --- gas sensor --- noninvasive detection --- nitrogen --- near infrared sensors --- drying temperature --- SPA-MLR --- PLS --- CARS --- hyperspectral camera --- handheld --- sensor evaluation --- case studies --- soil --- moisture --- sensor --- landslide --- rice leaves --- chromium content --- laser-induced breakdown spectroscopy --- laser wavelength --- preprocessing methods --- agricultural land --- field crops --- land cover --- photograph-grid method --- remote sensing --- data validation and calibration --- mobile app --- wireless sensor networks (WSN) --- energy efficiency --- distributed systems --- processing of sensed data --- WSN distribution algorithms --- recognition patterns --- agriculture

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