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<li><a href="./">Practical guide on dissolved organic matter (DOM) optic</a></li>
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<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Introduction and motivations</a></li>
<li class="chapter" data-level="2" data-path="measurements.html"><a href="measurements.html"><i class="fa fa-check"></i><b>2</b> Measurements</a><ul>
<li class="chapter" data-level="2.1" data-path="dom-measurements.html"><a href="dom-measurements.html"><i class="fa fa-check"></i><b>2.1</b> DOM measurements</a></li>
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<li class="chapter" data-level="3.1" data-path="what-is-cdom.html"><a href="what-is-cdom.html"><i class="fa fa-check"></i><b>3.1</b> What is CDOM?</a></li>
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<li class="chapter" data-level="3.3" data-path="absorption-vs-absorbance.html"><a href="absorption-vs-absorbance.html"><i class="fa fa-check"></i><b>3.3</b> Absorption vs absorbance</a></li>
<li class="chapter" data-level="3.4" data-path="mathematical-formulation-of-absorption-spectra.html"><a href="mathematical-formulation-of-absorption-spectra.html"><i class="fa fa-check"></i><b>3.4</b> Mathematical formulation of absorption spectra</a></li>
<li class="chapter" data-level="3.5" data-path="sl.html"><a href="sl.html"><i class="fa fa-check"></i><b>3.5</b> Modeling CDOM absorption spectra in R</a><ul>
<li class="chapter" data-level="3.5.1" data-path="sl.html"><a href="sl.html#potential-drawbacks"><i class="fa fa-check"></i><b>3.5.1</b> Potential drawbacks</a></li>
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<li class="chapter" data-level="3.6" data-path="metrics.html"><a href="metrics.html"><i class="fa fa-check"></i><b>3.6</b> Metrics</a><ul>
<li class="chapter" data-level="3.6.1" data-path="metrics.html"><a href="metrics.html#slope-ratio"><i class="fa fa-check"></i><b>3.6.1</b> Slope ratio</a></li>
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<li class="chapter" data-level="4" data-path="fluorescence.html"><a href="fluorescence.html"><i class="fa fa-check"></i><b>4</b> Fluorescence</a><ul>
<li class="chapter" data-level="4.1" data-path="what-is-a-eem.html"><a href="what-is-a-eem.html"><i class="fa fa-check"></i><b>4.1</b> What is a EEM</a></li>
<li class="chapter" data-level="4.2" data-path="parafac.html"><a href="parafac.html"><i class="fa fa-check"></i><b>4.2</b> PARAFAC</a></li>
<li class="chapter" data-level="4.3" data-path="fluorescence-of-dom-theoretical-and-mathematical-background.html"><a href="fluorescence-of-dom-theoretical-and-mathematical-background.html"><i class="fa fa-check"></i><b>4.3</b> Fluorescence of DOM: theoretical and mathematical background</a><ul>
<li class="chapter" data-level="4.3.1" data-path="fluorescence-of-dom-theoretical-and-mathematical-background.html"><a href="fluorescence-of-dom-theoretical-and-mathematical-background.html#scattering-correction"><i class="fa fa-check"></i><b>4.3.1</b> Scattering correction</a></li>
<li class="chapter" data-level="4.3.2" data-path="fluorescence-of-dom-theoretical-and-mathematical-background.html"><a href="fluorescence-of-dom-theoretical-and-mathematical-background.html#inner-filter-effect-correction"><i class="fa fa-check"></i><b>4.3.2</b> Inner-filter effect correction</a></li>
<li class="chapter" data-level="4.3.3" data-path="fluorescence-of-dom-theoretical-and-mathematical-background.html"><a href="fluorescence-of-dom-theoretical-and-mathematical-background.html#raman-calibration"><i class="fa fa-check"></i><b>4.3.3</b> Raman calibration</a></li>
<li class="chapter" data-level="4.3.4" data-path="fluorescence-of-dom-theoretical-and-mathematical-background.html"><a href="fluorescence-of-dom-theoretical-and-mathematical-background.html#metrics-1"><i class="fa fa-check"></i><b>4.3.4</b> Metrics</a></li>
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<li class="chapter" data-level="4.4" data-path="r-code-and-study-case.html"><a href="r-code-and-study-case.html"><i class="fa fa-check"></i><b>4.4</b> R code and study case</a><ul>
<li class="chapter" data-level="4.4.1" data-path="r-code-and-study-case.html"><a href="r-code-and-study-case.html#data-importation-and-plotting"><i class="fa fa-check"></i><b>4.4.1</b> Data importation and plotting</a></li>
<li class="chapter" data-level="4.4.2" data-path="r-code-and-study-case.html"><a href="r-code-and-study-case.html#blank-subtraction"><i class="fa fa-check"></i><b>4.4.2</b> Blank subtraction</a></li>
<li class="chapter" data-level="4.4.3" data-path="r-code-and-study-case.html"><a href="r-code-and-study-case.html#raman-and-rayleigh-scattering-removal"><i class="fa fa-check"></i><b>4.4.3</b> Raman and Rayleigh scattering removal</a></li>
<li class="chapter" data-level="4.4.4" data-path="r-code-and-study-case.html"><a href="r-code-and-study-case.html#inner-filter-effect-correction-1"><i class="fa fa-check"></i><b>4.4.4</b> Inner-filter effect correction</a></li>
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<li class="chapter" data-level="4.4.6" data-path="r-code-and-study-case.html"><a href="r-code-and-study-case.html#exporting-to-matlab"><i class="fa fa-check"></i><b>4.4.6</b> Exporting to MATLAB</a></li>
<li class="chapter" data-level="4.4.7" data-path="r-code-and-study-case.html"><a href="r-code-and-study-case.html#metric-extraction"><i class="fa fa-check"></i><b>4.4.7</b> Metric extraction</a></li>
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<li class="chapter" data-level="4.5" data-path="using-r-pipeline.html"><a href="using-r-pipeline.html"><i class="fa fa-check"></i><b>4.5</b> Using R pipeline</a></li>
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<li class="chapter" data-level="5" data-path="definitions.html"><a href="definitions.html"><i class="fa fa-check"></i><b>5</b> Definitions</a></li>
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<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">Practical guide on dissolved organic matter (DOM) optic</a>
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<section class="normal" id="section-">
<div id="definitions" class="section level1">
<h1><span class="header-section-number">Chapter 5</span> Definitions</h1>
<table>
<thead>
<tr class="header">
<th align="left">Acronym</th>
<th align="left">Definition</th>
<th align="left">Reference</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="left">DOM</td>
<td align="left">Dissolved organic matter</td>
<td align="left"></td>
</tr>
<tr class="even">
<td align="left">DOC</td>
<td align="left">Dissolved organic carbon</td>
<td align="left"></td>
</tr>
<tr class="odd">
<td align="left">CDOM</td>
<td align="left">Chromophoric dissolved organic matter</td>
<td align="left"></td>
</tr>
<tr class="even">
<td align="left">SUVA<span class="math inline">\(_{254}\)</span></td>
<td align="left">Specific UV absorbance at 254 nm</td>
<td align="left"><span class="citation">Weishaar et al. (<a href="#ref-Weishaar2003">2003</a>)</span></td>
</tr>
<tr class="odd">
<td align="left">S<span class="math inline">\(_\text{R}\)</span></td>
<td align="left">Slope ratio</td>
<td align="left"><span class="citation">Helms et al. (<a href="#ref-Helms2008">2008</a>)</span></td>
</tr>
<tr class="even">
<td align="left"><span class="math inline">\(a_\text{CDOM}\)</span></td>
<td align="left">Absorption coefficient of CDOM (m<span class="math inline">\(^{-1}\)</span>)</td>
<td align="left"></td>
</tr>
<tr class="odd">
<td align="left"><span class="math inline">\(S_\lambda\)</span></td>
<td align="left">Spectral slope curve</td>
<td align="left"><span class="citation">Loiselle et al. (<a href="#ref-Loiselle2009">2009</a>)</span></td>
</tr>
<tr class="even">
<td align="left">FMAX</td>
<td align="left"></td>
<td align="left"></td>
</tr>
<tr class="odd">
<td align="left">FDOM</td>
<td align="left">Fluorescent dissolved organic matter</td>
<td align="left"></td>
</tr>
<tr class="even">
<td align="left">S</td>
<td align="left">Spectral slope (nm<span class="math inline">\(^{-1}\)</span>)</td>
<td align="left"></td>
</tr>
<tr class="odd">
<td align="left"><span class="math inline">\(\lambda\)</span></td>
<td align="left">Greek symbol referring to wavelength (nm)</td>
<td align="left"></td>
</tr>
<tr class="even">
<td align="left"></td>
<td align="left"></td>
<td align="left"></td>
</tr>
<tr class="odd">
<td align="left"></td>
<td align="left"></td>
<td align="left"></td>
</tr>
</tbody>
</table>
<div id="refs" class="references">
<div>
<p>Bahram, Morteza, Rasmus Bro, Colin Stedmon, and Abbas Afkhami. 2006. “Handling of Rayleigh and Raman scatter for PARAFAC modeling of fluorescence data using interpolation.” <em>Journal of Chemometrics</em> 20 (3-4): 99–105. doi:<a href="https://doi.org/10.1002/cem.978">10.1002/cem.978</a>.</p>
</div>
<div>
<p>Benner, R. 2002. “Chemical composition and reactivity.” In <em>Biogeochemistry of Marine Dissolved Organic Matter</em>, edited by Dennis A Hansell and Craig A Carlson, 59–90. San Diego, CA: Academic Press.</p>
</div>
<div>
<p>Blough, Neil V, and Rossana Del Vecchio. 2002. “Chapter 10 - Chromophoric {DOM} in the Coastal Environment.” In <em>Biogeochemistry of Marine Dissolved Organic Matter</em>, edited by Dennis A HansellCraig A Carlson, 509–46. San Diego: Academic Press. doi:<a href="https://doi.org/http://dx.doi.org/10.1016/B978-012323841-2/50012-9">http://dx.doi.org/10.1016/B978-012323841-2/50012-9</a>.</p>
</div>
<div>
<p>Borchers, Hans Werner. 2015. “pracma: Practical Numerical Math Functions.” <a href="https://cran.r-project.org/package=pracma" class="uri">https://cran.r-project.org/package=pracma</a>.</p>
</div>
<div>
<p>Bricaud, Annick, André Morel, and Louis Prieur. 1981. “Absorption by dissolved organic matter of the sea (yellow substance) in the UV and visible domains.” <em>Limnology and Oceanography</em> 26 (1): 43–53. doi:<a href="https://doi.org/10.4319/lo.1981.26.1.0043">10.4319/lo.1981.26.1.0043</a>.</p>
</div>
<div>
<p>Bro, Rasmus. 1997. “PARAFAC. Tutorial and applications.” <em>Chemometrics and Intelligent Laboratory Systems</em> 38 (2): 149–71. doi:<a href="https://doi.org/10.1016/S0169-7439(97)00032-4">10.1016/S0169-7439(97)00032-4</a>.</p>
</div>
<div>
<p>Coble, P.G., R.G.M. Spencer, A. Baker, and D.M. Reynolds. 2014. <em>Aquatic Organic Matter Fluorescence</em>. Edited by Paula Coble, Jaimie Lead, Andy Baker, Darren M. Reynolds, and Robert G.M. Spencer. 1st ed. Cambridge: Cambridge University Press. <a href="http://ebooks.cambridge.org/ref/id/CBO9781139045452A011 http://amazon.com/o/ASIN/0521764610/" class="uri">http://ebooks.cambridge.org/ref/id/CBO9781139045452A011 http://amazon.com/o/ASIN/0521764610/</a>.</p>
</div>
<div>
<p>Coble, Paula G. 1996. “Characterization of marine and terrestrial DOM in seawater using excitation-emission matrix spectroscopy.” <em>Marine Chemistry</em> 51 (4): 325–46. doi:<a href="https://doi.org/10.1016/0304-4203(95)00062-3">10.1016/0304-4203(95)00062-3</a>.</p>
</div>
<div>
<p>Coble, Paula G, Sarah A Green, Neil V Blough, and Robert B Gagosian. 1990. “Characterization of dissolved organic matter in the Black Sea by fluorescence spectroscopy.” <em>Nature</em> 348 (6300). Coble, Pg Univ Washington,Sch Oceanog,Seattle,Wa 98195, USA Univ Washington,Sch Oceanog,Seattle,Wa 98195, USA Woods Hole Oceanog Inst,Woods Hole,Ma 02543: 432–35. doi:<a href="https://doi.org/10.1038/348432a0">10.1038/348432a0</a>.</p>
</div>
<div>
<p>Coble, Paula G., Christopher a. Schultz, and Kenneth Mopper. 1993. “Fluorescence contouring analysis of DOC intercalibration experiment samples: a comparison of techniques.” <em>Marine Chemistry</em> 41 (1-3): 173–78. doi:<a href="https://doi.org/10.1016/0304-4203(93)90116-6">10.1016/0304-4203(93)90116-6</a>.</p>
</div>
<div>
<p>Cole, J J, Y T Prairie, N F Caraco, W H McDowell, L J Tranvik, R G Striegl, C M Duarte, et al. 2007. “Plumbing the Global Carbon Cycle: Integrating Inland Waters into the Terrestrial Carbon Budget.” <em>Ecosystems</em> 10 (1): 172–85. doi:<a href="https://doi.org/10.1007/s10021-006-9013-8">10.1007/s10021-006-9013-8</a>.</p>
</div>
<div>
<p>Fellman, J B, D V D’Amore, E Hood, and R D Boone. 2008. “Fluorescence characteristics and biodegradability of dissolved organic matter in forest and wetland soils from coastal temperate watersheds in southeast Alaska.” <em>Biogeochemistry</em> 88 (2): 169–84.</p>
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<div>
<p>Fellman, Jason B, Eran Hood, and Robert G M Spencer. 2010. “Fluorescence spectroscopy opens new windows into dissolved organic matter dynamics in freshwater ecosystems: A review.” <em>Limnology and Oceanography</em> 55 (6): 2452–62. doi:<a href="https://doi.org/10.4319/lo.2010.55.6.2452">10.4319/lo.2010.55.6.2452</a>.</p>
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<div>
<p>Findlay, Stuart., and Robert L. Sinsabaugh. 2003. <em>Aquatic ecosystems : interactivity of dissolved organic matter</em>. Academic Press.</p>
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<div>
<p>Foreman, C.M., and J.S. Covert. 2003. “Linkages between Dissolved Organic Matter Composition and Bacterial Community Structure.” In <em>Aquatic Ecosystems : Interactivity of Dissolved Organic Matter</em>, 343–62. Elsevier. doi:<a href="https://doi.org/10.1016/B978-012256371-3/50015-9">10.1016/B978-012256371-3/50015-9</a>.</p>
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<div>
<p>Hansell, Dennis A., and Craig A. Carlson. 2014. <em>Biogeochemistry of Marine Dissolved Organic Matter</em>. Edited by Dennis A Hansell and Craig A Carlson. 2nd ed. Academic Press.</p>
</div>
<div>
<p>Harshman, Richard a. 1970. “Foundations of the PARAFAC procedure: Models and conditions for an ‘explanatory’ multimodal factor analysis.” <em>UCLA Working Papers in Phonetics</em> 16 (10): 1–84.</p>
</div>
<div>
<p>Helms, John R., Aron Stubbins, E. Michael Perdue, Nelson W. Green, Hongmei Chen, and Kenneth Mopper. 2013. “Photochemical bleaching of oceanic dissolved organic matter and its effect on absorption spectral slope and fluorescence.” <em>Marine Chemistry</em> 155. Elsevier B.V.: 81–91. doi:<a href="https://doi.org/10.1016/j.marchem.2013.05.015">10.1016/j.marchem.2013.05.015</a>.</p>
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<p>Helms, John R., Aron Stubbins, Jason D. Ritchie, Elizabeth C. Minor, David J. Kieber, and Kenneth Mopper. 2008. “Absorption spectral slopes and slope ratios as indicators of molecular weight, source, and photobleaching of chromophoric dissolved organic matter.” <em>Limnology and Oceanography</em> 53 (3): 955–69. doi:<a href="https://doi.org/10.4319/lo.2008.53.3.0955">10.4319/lo.2008.53.3.0955</a>.</p>
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<p>Kritzberg, Emma S, Jonathan J Cole, Michael M Pace, and Wilhelm Granéli. 2006. “Bacterial Growth on Allochthonous Carbon in Humic and Nutrient-enriched Lakes: Results from Whole-Lake 13C Addition Experiments.” <em>Ecosystems</em> 9 (3): 489–99. doi:<a href="https://doi.org/10.1007/s10021-005-0115-5">10.1007/s10021-005-0115-5</a>.</p>
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<div>
<p>Lawaetz, A J, and C A Stedmon. 2009. “Fluorescence Intensity Calibration Using the Raman Scatter Peak of Water.” <em>Applied Spectroscopy</em> 63 (8): 936–40. doi:<a href="https://doi.org/10.1366/000370209788964548">10.1366/000370209788964548</a>.</p>
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<div>
<p>Loiselle, Steven A., Luca Bracchini, Arduino M. Dattilo, Maso Ricci, Antonio Tognazzi, Andres Cézar, and Claudio Rossi. 2009. “The optical characterization of chromophoric dissolved organic matter using wavelength distribution of absorption spectral slopes.” <em>Limnology and Oceanography</em> 54 (2): 590–97. doi:<a href="https://doi.org/10.4319/lo.2009.54.2.0590">10.4319/lo.2009.54.2.0590</a>.</p>
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<p>Massicotte, Philippe, and Stiig Markager. 2016. “Using a Gaussian decomposition approach to model absorption spectra of chromophoric dissolved organic matter.” <em>Marine Chemistry</em> 180 (March): 24–32. doi:<a href="https://doi.org/10.1016/j.marchem.2016.01.008">10.1016/j.marchem.2016.01.008</a>.</p>
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<p>Murphy, Kathleen R., Colin a. Stedmon, Daniel Graeber, and Rasmus Bro. 2013. “Fluorescence spectroscopy and multi-way techniques. PARAFAC.” <em>Analytical Methods</em> 5 (23): 6557. doi:<a href="https://doi.org/10.1039/c3ay41160e">10.1039/c3ay41160e</a>.</p>
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<p>Stedmon, C A, and S Markager. 2001. “The optics of chromophoric dissolved organic matter (CDOM) in the Greenland Sea: An algorithm for differentiation between marine and terrestrially derived organic matter.” <em>Limnology and Oceanography</em> 46 (8): 2087–93. doi:<a href="https://doi.org/10.4319/lo.2001.46.8.2087">10.4319/lo.2001.46.8.2087</a>.</p>
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<p>Stedmon, Colin A, and Rasmus Bro. 2008. “Characterizing dissolved organic matter fluorescence with parallel factor analysis: a tutorial.” <em>Limnology and Oceanography: Methods</em> 6 (11): 572–79. doi:<a href="https://doi.org/10.4319/lom.2008.6.572">10.4319/lom.2008.6.572</a>.</p>
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<p>Stedmon, Colin A., and Norman B. Nelson. 2015. “The Optical Properties of DOM in the Ocean.” In <em>Biogeochemistry of Marine Dissolved Organic Matter</em>, edited by Dennis A. Hansell and Craig A. Carlson, Academic P, 481–508. Burlington: Elsevier. doi:<a href="https://doi.org/10.1016/B978-0-12-405940-5.00010-8">10.1016/B978-0-12-405940-5.00010-8</a>.</p>
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<div>
<p>Stedmon, Colin A., Stiig Markager, and Rasmus Bro. 2003. “Tracing dissolved organic matter in aquatic environments using a new approach to fluorescence spectroscopy.” <em>Marine Chemistry</em> 82 (3-4): 239–54. doi:<a href="https://doi.org/10.1016/S0304-4203(03)00072-0">10.1016/S0304-4203(03)00072-0</a>.</p>
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<div>
<p>Twardowski, Michael S., Emmanuel Boss, James M. Sullivan, and Percy L. Donaghay. 2004. “Modeling the spectral shape of absorption by chromophoric dissolved organic matter.” <em>Marine Chemistry</em> 89 (1-4): 69–88. doi:<a href="https://doi.org/10.1016/j.marchem.2004.02.008">10.1016/j.marchem.2004.02.008</a>.</p>
</div>
<div>
<p>Weishaar, James L, George R Aiken, Brian A Bergamaschi, Miranda S Fram, Roger Fujii, and Kenneth Mopper. 2003. “Evaluation of Specific Ultraviolet Absorbance as an Indicator of the Chemical Composition and Reactivity of Dissolved Organic Carbon.” <em>Environmental Science & Technology</em> 37 (20): 4702–8. doi:<a href="https://doi.org/10.1021/es030360x">10.1021/es030360x</a>.</p>
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<div>
<p>Zepp, Richard G, Wade M Sheldon, and Mary Ann Moran. 2004. “Dissolved organic fluorophores in southeastern US coastal waters: correction method for eliminating Rayleigh and Raman scattering peaks in excitation–emission matrices.” <em>Marine Chemistry</em> 89 (1-4): 15–36. doi:<a href="https://doi.org/10.1016/j.marchem.2004.02.006">10.1016/j.marchem.2004.02.006</a>.</p>
</div>
</div>
</div>
<h3>References</h3>
<div id="refs" class="references">
<div id="ref-Weishaar2003">
<p>Weishaar, James L, George R Aiken, Brian A Bergamaschi, Miranda S Fram, Roger Fujii, and Kenneth Mopper. 2003. “Evaluation of Specific Ultraviolet Absorbance as an Indicator of the Chemical Composition and Reactivity of Dissolved Organic Carbon.” <em>Environmental Science & Technology</em> 37 (20): 4702–8. doi:<a href="https://doi.org/10.1021/es030360x">10.1021/es030360x</a>.</p>
</div>
<div id="ref-Helms2008">
<p>Helms, John R., Aron Stubbins, Jason D. Ritchie, Elizabeth C. Minor, David J. Kieber, and Kenneth Mopper. 2008. “Absorption spectral slopes and slope ratios as indicators of molecular weight, source, and photobleaching of chromophoric dissolved organic matter.” <em>Limnology and Oceanography</em> 53 (3): 955–69. doi:<a href="https://doi.org/10.4319/lo.2008.53.3.0955">10.4319/lo.2008.53.3.0955</a>.</p>
</div>
<div id="ref-Loiselle2009">
<p>Loiselle, Steven A., Luca Bracchini, Arduino M. Dattilo, Maso Ricci, Antonio Tognazzi, Andres Cézar, and Claudio Rossi. 2009. “The optical characterization of chromophoric dissolved organic matter using wavelength distribution of absorption spectral slopes.” <em>Limnology and Oceanography</em> 54 (2): 590–97. doi:<a href="https://doi.org/10.4319/lo.2009.54.2.0590">10.4319/lo.2009.54.2.0590</a>.</p>
</div>
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