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  • 1
    Online Resource
    Online Resource
    Hauppauge :Nova Science Publishers, Incorporated,
    Keywords: Biological systems. ; Systems biology. ; Electronic books.
    Type of Medium: Online Resource
    Pages: 1 online resource (319 pages)
    Edition: 1st ed.
    ISBN: 9781629487373
    DDC: 571.7
    Language: English
    Note: Intro -- RECENT ADVANCES IN SYSTEMS BIOLOGY RESEARCH -- Library of Congress Cataloging-in-Publication Data -- Contents -- Preface -- Introduction -- Chapter 1: The Conceptual Foundations ofSystems Biology: An Introduction -- Abstract -- Introduction: What We Do Meanby Systems Biology? -- The Newtonian Paradigm and the Emergenceon Non-Linear Dynamics -- Conclusion -- References -- Chapter 2: The Mesoscopic Level and ItsEpistemological Relevancein Systems Biology -- Abstract -- 1. Introduction -- 2. The Stones and the Bridge -- 3. The Mesoscopic Level -- 4. Old Problems and New Conceptsof Systems Biology -- 5. A Systemic Approach: Essentiality-By-Location -- 6. Beyond the Dichotomies: From Model Choice tothe Framing of the Problem -- References -- Chapter 3: Mathematical Framework for AnalyzingGenome-Wide Association Study Datawith Rational Classes -- Abstract -- Introduction -- Analysis -- Discussion -- Acknowledgments -- References -- Chapter 4: A Review and Perspectiveon Thermodynamics Applied toMolecular Systems and Cancer Biology -- Abstract -- Introduction and Motivation -- Molecular Networks: Thermodynamicsand Kinetics -- Acknowledgments -- References -- Chapter 5: Analysis of Protein-Protein InteractionNetworks for Identificationof Functional Modules -- Abstract -- 1. Protein-Protein Interaction Databases -- 2. Ab initio Methods for Identification of Modulesin PPI Networks -- 3. Model-Based Approaches for Identificationof Modules in PPI Networks -- Summary -- References -- Chapter 6: Mass Spectrometry in Systems Biology -- Abstract -- Introduction -- Protein Identification by Mass Spectrometry -- Quantitative Mass Spectrometry -- Study of Protein Post-Translational Modifications(PTMs) -- Phosphoproteomics -- Study of Protein-Protein Interactions (PPIs) -- Acknowledgments -- References. , Chapter 7: Theory of Reliability in SystemsBiology: Aging versus Reliability -- Abstract -- Introduction -- 1. Basic Terms and Ideas -- 2. Reliability of Enzymes -- 3. Reliability and Mortality of Organismas the Whole -- 4. Reliability and Mortality ofHeterogeneous Populations -- 5. Reliability Testing in Biology -- Conclusion -- Acknowledgment -- References -- Chapter 8: Computational Appraoches in Synthetic and Systems Biology -- Abstract -- 1. Introduction -- 2. Computational Modelling Approaches -- 3. Parameter Estimation Techniques -- 4. Advanced Model Analysis -- 5. Computational Design of Biological Systems -- 6. Conclusion -- References -- Chapter 9: Modelling Transcriptional Regulation with Gaussian Processes -- Abstract -- 1. Introduction -- 2. Methodology -- 3. Evaluation on Simulated Data -- 4. Simulation Results -- 6. Conclusion -- Appendices -- References -- Chapter 10: Cancer Systems Biology -- Abstract -- 1. Introduction -- 2. Conclusion -- References -- Chapter 11: Systems Biology Approach for Human Complexity and Personalized Cardiology -- Abstract -- 1. Introduction -- 2. Human Complexity -- 3. Personalized Cardiology -- Conclusion -- References -- Chapter 12: Football, Airplanes, Diabetes and Systems Biology -- Abstract -- I. Introduction: Football, Planes, Automobiles,and Systems Biology -- II. The Reductionist Approach has DominatedBiological Science for the Past Half Century -- III. The Limits of the Reductionist Approach:Can a "Complete" Knowledge of a Single CellExplain All of Human Physiology? -- IV. Gestalt Physiology, the Whole Is Not a Sumof its Parts -- V. Is Evolution a Smart Designer? Why Should WeHave Endocrine Glands or Organs? -- VI. Geometry and a Physiological Mechanism ThatSupports the Reason for Organs. , VII. Is There Any Hope to Understanding SystemsWithout Complete Details of Individual Parts?Lessons from Physics -- VIII. Newton's Law and Diabetes: F=ma -- IX. Rocket Science and Clinical Diabetes:The Conservation of Uncertainty -- X. Diabetes, DCCT, ACCORD Trial and SuddenDeath: The Failure of Intuition -- Summary -- References -- Chapter 13: Cardiac Systems Biology -- Abstract -- 1. Genomics -- 2. Transcriptomics -- 3. Proteomics -- 4. Metabolomics -- 5. Structural Systems Biology -- 6. Modeling -- 7. Data Integration -- References -- Chapter 14: Systems Biology Approach toTransplant Immune Tolerance -- Abstract -- Abbreviation -- Introduction -- System Biology and Study of Immune System -- Current Status of Transplantation in United States -- Side Effects of Immunosuppression -- Costs -- Non-Adherance -- References -- EDITORS CONTACT INFORMATION -- Index.
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  • 2
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    Earth System Science Data
    In:  EPIC3Earth System Science Data, Earth System Science Data, 11, pp. 1037-1068, ISSN: 1866-3508
    Publication Date: 2019-09-19
    Description: A compiled set of in situ data is useful to evaluate the quality of ocean-colour satellite data records. Here we describe the compilation of global bio-optical in situ data (spanning from 1997 to 2018) used for the validation of the ocean-colour products from the ESA Ocean Colour Climate Change Initiative (OC-CCI). The compilation merges and harmonizes several in situ data sources into a simple format that could be used directly for the evaluation of satellite-derived ocean-colour data.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
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  • 3
    Publication Date: 2016-07-06
    Repository Name: EPIC Alfred Wegener Institut
    Type: PANGAEA Documentation , notRev
    Format: application/zip
    Format: application/zip
    Format: application/zip
    Format: application/zip
    Format: application/zip
    Format: application/zip
    Format: application/zip
    Format: application/zip
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  • 4
    Publication Date: 2022-05-25
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sathyendranath, S., Brewin, R. J. W., Brockmann, C., Brotas, V., Calton, B., Chuprin, A., Cipollini, P., Couto, A. B., Dingle, J., Doerffer, R., Donlon, C., Dowell, M., Farman, A., Grant, M., Groom, S., Horseman, A., Jackson, T., Krasemann, H., Lavender, S., Martinez-Vicente, V., Mazeran, C., Melin, F., Moore, T. S., Muller, D., Regner, P., Roy, S., Steele, C. J., Steinmetz, F., Swinton, J., Taberner, M., Thompson, A., Valente, A., Zuhlke, M., Brando, V. E., Feng, H., Feldman, G., Franz, B. A., Frouin, R., Gould, R. W., Hooker, S. B., Kahru, M., Kratzer, S., Mitchell, B. G., Muller-Karger, F. E., Sosik, H. M., Voss, K. J., Werdell, J., & Platt, T. An ocean-colour time series for use in climate studies: The experience of the ocean-colour climate change initiative (OC-CCI). Sensors, 19(19), (2019): 4285, doi: 10.3390/s19194285.
    Description: Ocean colour is recognised as an Essential Climate Variable (ECV) by the Global Climate Observing System (GCOS); and spectrally-resolved water-leaving radiances (or remote-sensing reflectances) in the visible domain, and chlorophyll-a concentration are identified as required ECV products. Time series of the products at the global scale and at high spatial resolution, derived from ocean-colour data, are key to studying the dynamics of phytoplankton at seasonal and inter-annual scales; their role in marine biogeochemistry; the global carbon cycle; the modulation of how phytoplankton distribute solar-induced heat in the upper layers of the ocean; and the response of the marine ecosystem to climate variability and change. However, generating a long time series of these products from ocean-colour data is not a trivial task: algorithms that are best suited for climate studies have to be selected from a number that are available for atmospheric correction of the satellite signal and for retrieval of chlorophyll-a concentration; since satellites have a finite life span, data from multiple sensors have to be merged to create a single time series, and any uncorrected inter-sensor biases could introduce artefacts in the series, e.g., different sensors monitor radiances at different wavebands such that producing a consistent time series of reflectances is not straightforward. Another requirement is that the products have to be validated against in situ observations. Furthermore, the uncertainties in the products have to be quantified, ideally on a pixel-by-pixel basis, to facilitate applications and interpretations that are consistent with the quality of the data. This paper outlines an approach that was adopted for generating an ocean-colour time series for climate studies, using data from the MERIS (MEdium spectral Resolution Imaging Spectrometer) sensor of the European Space Agency; the SeaWiFS (Sea-viewing Wide-Field-of-view Sensor) and MODIS-Aqua (Moderate-resolution Imaging Spectroradiometer-Aqua) sensors from the National Aeronautics and Space Administration (USA); and VIIRS (Visible and Infrared Imaging Radiometer Suite) from the National Oceanic and Atmospheric Administration (USA). The time series now covers the period from late 1997 to end of 2018. To ensure that the products meet, as well as possible, the requirements of the user community, marine-ecosystem modellers, and remote-sensing scientists were consulted at the outset on their immediate and longer-term requirements as well as on their expectations of ocean-colour data for use in climate research. Taking the user requirements into account, a series of objective criteria were established, against which available algorithms for processing ocean-colour data were evaluated and ranked. The algorithms that performed best with respect to the climate user requirements were selected to process data from the satellite sensors. Remote-sensing reflectance data from MODIS-Aqua, MERIS, and VIIRS were band-shifted to match the wavebands of SeaWiFS. Overlapping data were used to correct for mean biases between sensors at every pixel. The remote-sensing reflectance data derived from the sensors were merged, and the selected in-water algorithm was applied to the merged data to generate maps of chlorophyll concentration, inherent optical properties at SeaWiFS wavelengths, and the diffuse attenuation coefficient at 490 nm. The merged products were validated against in situ observations. The uncertainties established on the basis of comparisons with in situ data were combined with an optical classification of the remote-sensing reflectance data using a fuzzy-logic approach, and were used to generate uncertainties (root mean square difference and bias) for each product at each pixel.
    Description: This work was funded by the Ocean Colour Climate Change initiative of the European Space Agency (Grant Number 4000101437/10/I-LG). We acknowledge additional funding support by NERC through the National Centre for Earth Observation (Grant Number PR140015). Additional funding from a Simons Foundation Grant (549947, SS) is also gratefully acknowledged. V.B. also acknowledges funding from the European Union’s Horizon 2020 Research and Innovation Programme grant agreement N_ 810139: Project Portugal Twinning for Innovation and Excellence in Marine Science and Earth Observation – PORTWIMS.
    Keywords: ocean colour ; water-leaving radiance ; remote-sensing reflectance ; phytoplankton ; chlorophyll-a ; inherent optical properties ; Climate Change Initiative ; optical water classes ; Essential Climate Variable ; uncertainty characterisation
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 5
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Earth System Science Data 8 (2016): 235-252, doi:10.5194/essd-8-235-2016.
    Description: A compiled set of in situ data is important to evaluate the quality of ocean-colour satellite-data records. Here we describe the data compiled for the validation of the ocean-colour products from the ESA Ocean Colour Climate Change Initiative (OC-CCI). The data were acquired from several sources (MOBY, BOUSSOLE, AERONET-OC, SeaBASS, NOMAD, MERMAID, AMT, ICES, HOT, GeP&CO), span between 1997 and 2012, and have a global distribution. Observations of the following variables were compiled: spectral remote-sensing reflectances, concentrations of chlorophyll a, spectral inherent optical properties and spectral diffuse attenuation coefficients. The data were from multi-project archives acquired via the open internet services or from individual projects, acquired directly from data providers. Methodologies were implemented for homogenisation, quality control and merging of all data. No changes were made to the original data, other than averaging of observations that were close in time and space, elimination of some points after quality control and conversion to a standard format. The final result is a merged table designed for validation of satellite-derived ocean-colour products and available in text format. Metadata of each in situ measurement (original source, cruise or experiment, principal investigator) were preserved throughout the work and made available in the final table. Using all the data in a validation exercise increases the number of matchups and enhances the representativeness of different marine regimes. By making available the metadata, it is also possible to analyse each set of data separately. The compiled data are available at doi:10.1594/PANGAEA.854832 (Valente et al., 2015).
    Description: We thank NASA for project funding for data collection.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 6
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Earth System Science Data 11(3), (2019): 1037-1068, doi: 10.5194/essd-11-1037-2019.
    Description: A global compilation of in situ data is useful to evaluate the quality of ocean-colour satellite data records. Here we describe the data compiled for the validation of the ocean-colour products from the ESA Ocean Colour Climate Change Initiative (OC-CCI). The data were acquired from several sources (including, inter alia, MOBY, BOUSSOLE, AERONET-OC, SeaBASS, NOMAD, MERMAID, AMT, ICES, HOT and GeP&CO) and span the period from 1997 to 2018. Observations of the following variables were compiled: spectral remote-sensing reflectances, concentrations of chlorophyll a, spectral inherent optical properties, spectral diffuse attenuation coefficients and total suspended matter. The data were from multi-project archives acquired via open internet services or from individual projects, acquired directly from data providers. Methodologies were implemented for homogenization, quality control and merging of all data. No changes were made to the original data, other than averaging of observations that were close in time and space, elimination of some points after quality control and conversion to a standard format. The final result is a merged table designed for validation of satellite-derived ocean-colour products and available in text format. Metadata of each in situ measurement (original source, cruise or experiment, principal investigator) was propagated throughout the work and made available in the final table. By making the metadata available, provenance is better documented, and it is also possible to analyse each set of data separately. This paper also describes the changes that were made to the compilation in relation to the previous version (Valente et al., 2016). The compiled data are available at https://doi.org/10.1594/PANGAEA.898188 (Valente et al., 2019).
    Description: This research has been supported by the ESA Climate Change Initiative – Ocean Colour project (ref: AO-1/6207/09/I-LG).
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 7
    Publication Date: 2013-02-08
    Description: Chemical Reviews DOI: 10.1021/cr300289z
    Print ISSN: 0009-2665
    Electronic ISSN: 1520-6890
    Topics: Chemistry and Pharmacology
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  • 8
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    PANGAEA
    In:  Supplement to: Valente, André; Sathyendranath, Shubha; Brotas, Vanda; Groom, Steve; Grant, Michael; Taberner, Malcolm; Antoine, David; Arnone, Robert; Balch, William M; Barker, Kathryn; Barlow, Raymond G; Bélanger, Simon; Berthon, Jean-François; Besiktepe, Sukru; Brando, Vittorio E; Canuti, Elisabetta; Chavez, Francisco P; Claustre, Hervé; Crout, Richard; Frouin, Robert; García-Soto, Carlos; Gibb, Stuart W; Gould, Richard; Hooker, Stanford B; Kahru, Mati; Klein, Holger; Kratzer, Susanne; Loisel, Hubert; McKee, David; Mitchell, Brian G; Moisan, Tiffany; Muller-Karger, Frank E; O'Dowd, Leonie; Ondrusek, Michael; Poulton, Alex J; Repecaud, Michel; Smyth, Timothy J; Sosik, Heidi; Twardowski, Michael S; Voss, Kenneth; Werdell, P Jeremy; Wernand, Marcel Robert; Zibordi, Giuseppe (2016): A compilation of global bio-optical in situ data for ocean-colour satellite applications. Earth System Science Data, 8(1), 235-252, https://doi.org/10.5194/essd-8-235-2016
    Publication Date: 2023-05-12
    Description: A compiled set of in situ data is important to evaluate the quality of ocean-colour satellite-data records. Here we describe the data compiled for the validation of the ocean-colour products from the ESA Ocean Colour Climate Change Initiative (OC-CCI). The data were acquired from several sources (MOBY, BOUSSOLE, AERONET-OC, SeaBASS, NOMAD, MERMAID, AMT, ICES, HOT, GeP&CO), span between 1997 and 2012, and have a global distribution. Observations of the following variables were compiled: spectral remote-sensing reflectances, concentrations of chlorophyll a, spectral inherent optical properties and spectral diffuse attenuation coefficients. The data were from multi-project archives acquired via the open internet services or from individual projects, acquired directly from data providers. Methodologies were implemented for homogenisation, quality control and merging of all data. No changes were made to the original data, other than averaging of observations that were close in time and space, elimination of some points after quality control and conversion to a standard format. The final result is a merged table designed for validation of satellite-derived ocean-colour products and available in text format. Metadata of each in situ measurement (original source, cruise or experiment, principal investigator) were preserved throughout the work and made available in the final table. Using all the data in a validation exercise increases the number of matchups and enhances the representativeness of different marine regimes. By making available the metadata, it is also possible to analyse each set of data separately.
    Type: Dataset
    Format: application/zip, 3 datasets
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  • 9
    Publication Date: 2023-02-25
    Keywords: Absorption coefficient, colored dissolved organic matter at given wavelength; Algal pigment absorption coefficient at given wavelength; Backscattering coefficient of particles at given wavelength; Comment; DATE/TIME; DEPTH, water; Identification; Irradiance coefficient, diffuse downwelling at given wavelength; LATITUDE; LONGITUDE; Quality flag, time; Suspended matter, total; Wavelength
    Type: Dataset
    Format: text/tab-separated-values, 439720 data points
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  • 10
    Publication Date: 2023-02-25
    Keywords: Absorption coefficient, colored dissolved organic matter at given wavelength; Algal pigment absorption coefficient at given wavelength; Backscattering coefficient of particles at given wavelength; Comment; DATE/TIME; DEPTH, water; Identification; Irradiance coefficient, diffuse downwelling at given wavelength; LATITUDE; LONGITUDE; Quality flag, time; Suspended matter, total; Wavelength
    Type: Dataset
    Format: text/tab-separated-values, 497100 data points
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