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Mitochondrial matrix
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<h2 id="composition">Composition</h2> <h3>Metabolites</h3> <p>The matrix is host to a wide variety of <a href="/facts/Metabolite/nAyywVtA">metabolites</a> involved in processes within the matrix. The <a href="/facts/Citric_acid_cycle/EGJL9NXP">citric acid cycle</a> involves <a href="/facts/Acyl-CoA/uWNxxzSj">acyl-CoA</a>, <a href="/facts/Pyruvate/qJTgl4J9">pyruvate</a>, <a href="/facts/Acetyl-CoA/XyxFfC84">acetyl-CoA</a>, <a href="/facts/Citrate/EgKGQBdl">citrate</a>, <a href="/facts/Isocitrate/l9TFBVbl">isocitrate</a>, <a href="/facts/%CE%91-ketoglutarate/t5gJPVzB">α-ketoglutarate</a>, <a href="/facts/Succinyl-CoA/R8gukjJp">succinyl-CoA</a>, <a href="/facts/Fumarate/VDecBfLQ">fumarate</a>, <a href="/facts/Succinate/v3KJqrQC">succinate</a>, <a href="/facts/Malate/mSbExe77">L-malate</a>, and <a href="/facts/Oxaloacetate/ojLoQw81">oxaloacetate</a>.<a class="footnote-ref" id="fnref:6" href="#fn:6"><sup>6</sup></a> The <a href="/facts/Urea_cycle/rWjAo7DY">urea cycle</a> makes use of <a href="/facts/Ornithine/BtnkQfmk">L-ornithine</a>, <a href="/facts/Carbamoyl_phosphate_synthetase_I/VsVsvp2s">carbamoyl phosphate</a>, and <a href="/facts/L-citrulline/1X1LFYFG">L-citrulline</a>.<a class="footnote-ref" id="fnref:7" href="#fn:7"><sup>7</sup></a> The electron transport chain oxidizes coenzymes <a href="/facts/NADH/BHdLW925">NADH</a> and <a href="/facts/FADH2/uzADx3ES">FADH2</a>. Protein synthesis makes use of mitochondrial <a href="/facts/DNA/nB89Iauz">DNA</a>, <a href="/facts/RNA/HxPeNfNj">RNA</a>, and <a href="/facts/Transfer_RNA/pR9T5XSl">tRNA</a>.<a class="footnote-ref" id="fnref:8" href="#fn:8"><sup>8</sup></a> Regulation of processes makes use of ions (<a href="/facts/Ca2%2B/wgUxKej5">Ca2+</a>/<a href="/facts/Potassium/FWPwS7Rj">K+</a>/<a href="/facts/Magnesium/XyIhd2FG">Mg+</a>).<a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a> Additional metabolites present in the matrix are <a href="/facts/CO2/xGzpppEp">CO2</a>, <a href="/facts/H2O/0lkXnJPK">H2O</a>, <a href="/facts/Oxygen/acyn6o8r">O2</a>, <a href="/facts/Adenosine_triphosphate/nB9bwgcU">ATP</a>, <a href="/facts/Adenosine_diphosphate/JEDnsCjn">ADP</a>, and <a href="/facts/Inorganic_phosphate/FDGVCxUG">Pi</a>.<a class="footnote-ref" id="fnref:10" href="#fn:10"><sup>10</sup></a> </p> <h3>Enzymes</h3> <p>Enzymes from processes that take place in the matrix. The citric acid cycle is facilitated by <a href="/facts/Pyruvate_dehydrogenase/VpJt0RLA">pyruvate dehydrogenase</a>, <a href="/facts/Citrate_synthase/Nnbctuuk">citrate synthase</a>, <a href="/facts/Aconitase/c8R6Qke8">aconitase</a>, <a href="/facts/Isocitrate_dehydrogenase/NhmcNFmh">isocitrate dehydrogenase</a>, <a href="/facts/%CE%91-ketoglutarate_dehydrogenase/svPc1Xl5">α-ketoglutarate dehydrogenase</a>, <a href="/facts/Succinyl_coenzyme_A_synthetase/8hfbJDVF">succinyl-CoA synthetase</a>, <a href="/facts/Fumarase/cGVBA8q5">fumarase</a>, and <a href="/facts/Malate_dehydrogenase/ku0kofwa">malate dehydrogenase</a>.<a class="footnote-ref" id="fnref:11" href="#fn:11"><sup>11</sup></a> The urea cycle is facilitated by <a href="/facts/Carbamoyl_phosphate_synthetase_I/VsVsvp2s">carbamoyl phosphate synthetase I</a> and <a href="/facts/Ornithine_transcarbamylase/5J2rDCej">ornithine transcarbamylase</a>.<a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a> β-Oxidation uses <a href="/facts/Pyruvate_carboxylase/qH0T0moJ">pyruvate carboxylase</a>, <a href="/facts/Acyl_CoA_dehydrogenase/AyfWuqrH">acyl-CoA dehydrogenase</a>, and <a href="/facts/%CE%92-ketothiolase/rJ5b6E1P">β-ketothiolase</a>.<a class="footnote-ref" id="fnref:13" href="#fn:13"><sup>13</sup></a> Amino acid production is facilitated by <a href="/facts/Transaminase/5xt6gNd3">transaminases</a>.<a class="footnote-ref" id="fnref:14" href="#fn:14"><sup>14</sup></a> Amino acid metabolism is mediated by <a href="/facts/Protease/G1ASdVat">proteases</a>, such as <a href="/facts/PITRM1/gbjlF2tA">presequence protease</a>.<a class="footnote-ref" id="fnref:15" href="#fn:15"><sup>15</sup></a> </p> <h3>Inner membrane components</h3> <p>The inner membrane is a <a href="/facts/Phospholipid_bilayer/CQKQ9l3g">phospholipid bilayer</a> that contains the complexes of oxidative phosphorylation. which contains the <a href="/facts/Electron_transport_chain/QjcIkgeR">electron transport chain</a> that is found on the <a href="/facts/Crista/2PUrXT28">cristae</a> of the inner membrane and consists of four protein complexes and <a href="/facts/ATP_synthase/5NBMxsVX">ATP synthase</a>. These complexes are <a href="/facts/Complex_I/Vn8Lf26t">complex I</a> (NADH:coenzyme Q oxidoreductase), <a href="/facts/Complex_II/AswKYLm3">complex II</a> (succinate:coenzyme Q oxidoreductase), <a href="/facts/Complex_III/ks7D8CzI">complex III</a> (coenzyme Q: cytochrome c oxidoreductase), and <a href="/facts/Complex_IV/U67QVCv8">complex IV</a> (cytochrome c oxidase).<a class="footnote-ref" id="fnref:16" href="#fn:16"><sup>16</sup></a> </p> <h3>Inner membrane control over matrix composition</h3> <p>The electron transport chain is responsible for establishing a pH and <a href="/facts/Electrochemical_gradient/IEfjjoIL">electrochemical gradient</a> that facilitates the production of ATP through the pumping of protons. The gradient also provides control of the concentration of ions such as <a href="/facts/Ca2/wgUxKej5">Ca2+</a> driven by the mitochondrial membrane potential.<a class="footnote-ref" id="fnref:17" href="#fn:17"><sup>17</sup></a> The membrane only allows nonpolar molecules such as <a href="/facts/Carbon_dioxide/xGzpppEp">CO2</a> and <a href="/facts/Oxygen/acyn6o8r">O2</a> and small non charged polar molecules such as <a href="/facts/H2O/0lkXnJPK">H2O</a> to enter the matrix. Molecules enter and exit the mitochondrial matrix through <a href="/facts/Transport_protein/kVVhlTAK">transport proteins</a> and <a href="/facts/Ion_transporter/x41gIvhr">ion transporters</a>. Molecules are then able to leave the mitochondria through <a href="/facts/Porin_(protein)/XeNDIN4x">porin</a>.<a class="footnote-ref" id="fnref:18" href="#fn:18"><sup>18</sup></a> These attributed characteristics allow for control over concentrations of <a href="/facts/Ion/3bePpDna">ions</a> and <a href="/facts/Metabolite/nAyywVtA">metabolites</a> necessary for regulation and determines the rate of ATP production.<a class="footnote-ref" id="fnref:19" href="#fn:19"><sup>19</sup></a><a class="footnote-ref" id="fnref:20" href="#fn:20"><sup>20</sup></a> </p> <h2 id="processes">Processes</h2> <h3>Citric acid cycle</h3><p> Following glycolysis, the citric acid cycle is activated by the production of acetyl-CoA. The oxidation of <a href="/facts/Pyruvic_acid/qJTgl4J9">pyruvate</a> by pyruvate dehydrogenase in the matrix produces CO2, acetyl-CoA, and NADH. <a href="/facts/Beta_oxidation/mbwIMN7D">Beta oxidation</a> of fatty acids serves as an alternate <a href="/facts/Catabolism/CFWUdphX">catabolic</a> pathway that produces acetyl-CoA, NADH, and <a href="/facts/Flavin_adenine_dinucleotide/uzADx3ES">FADH2</a>.<a class="footnote-ref" id="fnref:21" href="#fn:21"><sup>21</sup></a> The production of acetyl-CoA begins the citric acid cycle while the <a href="/facts/Cofactor_(biochemistry)/AGo0PCUU">co-enzymes</a> produced are used in the <a href="/facts/Electron_transport_chain/QjcIkgeR">electron transport chain</a>.<a class="footnote-ref" id="fnref:22" href="#fn:22"><sup>22</sup></a></p> <p>All of the <a href="/facts/Enzyme/DSI1Fh7y">enzymes</a> for the citric acid cycle are in the matrix (e.g. <i><a href="/facts/Citrate/EgKGQBdl">citrate synthase</a>, <a href="/facts/Isocitrate_dehydrogenase/NhmcNFmh">isocitrate dehydrogenase</a>, <a href="/facts/Alpha-Ketoglutaric_acid/t5gJPVzB">α-ketoglutarate dehydrogenase</a>, <a href="/facts/Fumarate/VDecBfLQ">fumarase</a>, and <a href="/facts/Malate_dehydrogenase/ku0kofwa">malate dehydrogenase</a></i>) except for <a href="/facts/Succinate_dehydrogenase/AswKYLm3">succinate dehydrogenase</a> which is on the inner membrane and is part of protein <a href="/facts/Complex_II/AswKYLm3">complex II</a> in the <a href="/facts/Electron_transport_chain/QjcIkgeR">electron transport chain</a>. The cycle produces coenzymes NADH and FADH2 through the oxidation of carbons in two cycles. The oxidation of NADH and FADH2 produces GTP from succinyl-CoA synthetase.<a class="footnote-ref" id="fnref:23" href="#fn:23"><sup>23</sup></a> </p> <h3>Oxidative phosphorylation</h3> <p>NADH and <a href="/facts/Flavin_adenine_dinucleotide/uzADx3ES">FADH2</a> are produced in the matrix or transported in through porin and transport proteins in order to undergo oxidation through oxidative phosphorylation.<a class="footnote-ref" id="fnref:24" href="#fn:24"><sup>24</sup></a> NADH and FADH2 undergo oxidation in the electron transport chain by transferring an <a href="/facts/Electron/L0KBo5cW">electrons</a> to regenerate <a href="/facts/NAD%2B/BHdLW925">NAD+</a> and <a href="/facts/Flavin_adenine_dinucleotide/uzADx3ES">FAD</a>. Protons are pulled into the <a href="/facts/Intermembrane_space/lEt0NyqY">intermembrane space</a> by the energy of the electrons going through the electron transport chain. Four electrons are finally accepted by oxygen in the matrix to complete the electron transport chain. The protons return to the mitochondrial matrix through the protein <a href="/facts/ATP_synthase/5NBMxsVX">ATP synthase</a>. The energy is used in order to rotate ATP synthase which facilitates the passage of a proton, producing ATP. A pH difference between the matrix and intermembrane space creates an electrochemical gradient by which ATP synthase can pass a proton into the matrix favorably.<a class="footnote-ref" id="fnref:25" href="#fn:25"><sup>25</sup></a> </p> <h3>Urea cycle</h3> <p>The first two steps of the urea cycle take place within the mitochondrial matrix of liver and kidney cells. In the first step <a href="/facts/Ammonia/MtLtJFtz">ammonia</a> is converted into <a href="/facts/Carbamoyl_phosphate/tTLwfema">carbamoyl phosphate</a> through the investment of two ATP molecules. This step is facilitated by <a href="/facts/Carbamoyl_phosphate_synthetase_I/VsVsvp2s">carbamoyl phosphate synthetase I</a>. The second step facilitated by <a href="/facts/Ornithine_transcarbamylase/5J2rDCej">ornithine transcarbamylase</a> converts <a href="/facts/Carbamoyl_phosphate/tTLwfema">carbamoyl phosphate</a> and <a href="/facts/Ornithine/BtnkQfmk">ornithine</a> into <a href="/facts/Citrulline/1X1LFYFG">citrulline</a>. After these initial steps the urea cycle continues in the inner membrane space until ornithine once again enters the matrix through a transport channel to continue the first to steps within matrix.<a class="footnote-ref" id="fnref:26" href="#fn:26"><sup>26</sup></a> </p> <h3>Transamination</h3> <p><a href="/facts/Alpha-Ketoglutaric_acid/t5gJPVzB">α-Ketoglutarate</a> and <a href="/facts/Oxaloacetate/ojLoQw81">oxaloacetate</a> can be converted into amino acids within the matrix through the process of <a href="/facts/Transamination/Ntj23r8y">transamination</a>. These reactions are facilitated by transaminases in order to produce <a href="/facts/Aspartate/9DFSFPa1">aspartate</a> and <a href="/facts/Asparagine/KYIft5Jd">asparagine</a> from oxaloacetate. Transamination of α-ketoglutarate produces <a href="/facts/Glutamate/7oXbNcvu">glutamate</a>, <a href="/facts/Proline/x1ABSW5A">proline</a>, and <a href="/facts/Arginine/y49Hdf1e">arginine</a>. These amino acids are then used either within the matrix or transported into the cytosol to produce proteins.<a class="footnote-ref" id="fnref:27" href="#fn:27"><sup>27</sup></a><a class="footnote-ref" id="fnref:28" href="#fn:28"><sup>28</sup></a> </p> <h3>Regulation</h3> <p>Regulation within the matrix is primarily controlled by ion concentration, metabolite concentration and energy charge. Availability of ions such as <a href="/facts/Calcium_signaling/2zzv1pm6">Ca2+ control</a> various functions of the citric acid cycle. in the matrix activates <a href="/facts/Pyruvate_dehydrogenase/VpJt0RLA">pyruvate dehydrogenase</a>, <a href="/facts/Isocitrate_dehydrogenase/NhmcNFmh">isocitrate dehydrogenase</a>, and <a href="/facts/%CE%91-ketoglutarate_dehydrogenase/svPc1Xl5">α-ketoglutarate dehydrogenase</a> which increases the reaction rate in the cycle.<a class="footnote-ref" id="fnref:29" href="#fn:29"><sup>29</sup></a> Concentration of intermediates and coenzymes in the matrix also increase or decrease the rate of ATP production due to <a href="/facts/Anaplerotic_reactions/dpCVjnBY">anaplerotic</a> and cataplerotic effects. NADH can act as an <a href="/facts/Enzyme_inhibitor/MkFwGXHJ">inhibitor</a> for <a href="/facts/Alpha-Ketoglutaric_acid/t5gJPVzB">α-ketoglutarate</a>, <a href="/facts/Isocitrate_dehydrogenase/NhmcNFmh">isocitrate dehydrogenase</a>, <a href="/facts/Citrate_synthase/Nnbctuuk">citrate synthase</a>, and <a href="/facts/Pyruvate_dehydrogenase_complex/6Cmv35f6">pyruvate dehydrogenase.</a> The concentration of oxaloacetate in particular is kept low, so any fluctuations in this concentrations serve to drive the citric acid cycle forward.<a class="footnote-ref" id="fnref:30" href="#fn:30"><sup>30</sup></a> The production of ATP also serves as a means of regulation by acting as an inhibitor for isocitrate dehydrogenase, pyruvate dehydrogenase, the electron transport chain protein complexes, and ATP synthase. ADP acts as an <a href="/facts/Enzyme_activator/soAFcLGS">activator</a>.<a class="footnote-ref" id="fnref:31" href="#fn:31"><sup>31</sup></a> </p> <h3>Protein synthesis</h3> <p>The mitochondria contains its own set of DNA used to produce proteins found in the electron transport chain. The mitochondrial DNA only codes for about thirteen proteins that are used in processing mitochondrial transcripts, <a href="/facts/Ribosomal_protein/73JJEmgN">ribosomal proteins</a>, <a href="/facts/Ribosomal_RNA/zy5FxddY">ribosomal RNA</a>, <a href="/facts/Transfer_RNA/pR9T5XSl">transfer RNA</a>, and <a href="/facts/Protein_subunit/HhuET9UP">protein subunits</a> found in the <a href="/facts/Multiprotein_complex/GW11Ee34">protein complexes</a> of the electron transport chain.<a class="footnote-ref" id="fnref:32" href="#fn:32"><sup>32</sup></a><a class="footnote-ref" id="fnref:33" href="#fn:33"><sup>33</sup></a> </p> <h2 id="see-also">See also</h2> <ul><li><a href="/facts/Matrix_(biology)/up2ogMb7">Matrix (biology)</a></li> <li><a href="/facts/Mitochondrial_DNA/goC0ex0X">Mitochondrial DNA</a></li> <li><a href="/facts/Mitochondrion/ErHqrdJ1">Mitochondrion</a></li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>Voet, Donald; Voet, Judith; Pratt, Charlotte (2013). Fundamentals of Biochemistry Life at the Molecular Level. New York City: John Wiley & Sons, Inc. pp. 582–584. ISBN 978-1118129180. <a href="978-1118129180" target="_blank">978-1118129180</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>Stryer, L; Berg, J; Tymoczko, JL (2002). Biochemistry. San Francisco: W.H. Freeman. pp. 509–527, 569–579, 614–616, 638–641, 732–735, 739–748, 770–773. ISBN 978-0-7167-4684-3. <a href="978-0-7167-4684-3" target="_blank">978-0-7167-4684-3</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>Mitchell, Peter; Moyle, Jennifer (1967-01-14). "Chemiosmotic Hypothesis of Oxidative Phosphorylation". Nature. 213 (5072): 137–139. Bibcode:1967Natur.213..137M. doi:10.1038/213137a0. PMID 4291593. S2CID 4149605. <a href="/wiki/Bibcode_(identifier)" target="_blank">/wiki/Bibcode_(identifier)</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>Soboll, S; Scholz, R; Freisl, M; Elbers, R; Heldt, H.W. (1976). Distribution of metabolites between mitochondria and cytosol of perfused liver. New york: Elsevier. pp. 29–40. ISBN 978-0-444-10925-5. <a href="978-0-444-10925-5" target="_blank">978-0-444-10925-5</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>Porcelli, Anna Maria; Ghelli, Anna; Zanna, Claudia; Pinton, Paolo; Rizzuto, Rosario; Rugolo, Michela (2005-01-28). "pH difference across the outer mitochondrial membrane measured with a green fluorescent protein mutant". Biochemical and Biophysical Research Communications. 326 (4): 799–804. doi:10.1016/j.bbrc.2004.11.105. PMID 15607740. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>Stryer, L; Berg, J; Tymoczko, JL (2002). Biochemistry. San Francisco: W.H. Freeman. pp. 509–527, 569–579, 614–616, 638–641, 732–735, 739–748, 770–773. ISBN 978-0-7167-4684-3. <a href="978-0-7167-4684-3" target="_blank">978-0-7167-4684-3</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>Soboll, S; Scholz, R; Freisl, M; Elbers, R; Heldt, H.W. (1976). Distribution of metabolites between mitochondria and cytosol of perfused liver. New york: Elsevier. pp. 29–40. ISBN 978-0-444-10925-5. <a href="978-0-444-10925-5" target="_blank">978-0-444-10925-5</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>Porcelli, Anna Maria; Ghelli, Anna; Zanna, Claudia; Pinton, Paolo; Rizzuto, Rosario; Rugolo, Michela (2005-01-28). "pH difference across the outer mitochondrial membrane measured with a green fluorescent protein mutant". Biochemical and Biophysical Research Communications. 326 (4): 799–804. doi:10.1016/j.bbrc.2004.11.105. PMID 15607740. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>Dimroth, P.; Kaim, G.; Matthey, U. (2000-01-01). "Crucial role of the membrane potential for ATP synthesis by F(1)F(o) ATP synthases". The Journal of Experimental Biology. 203 (Pt 1): 51–59. Bibcode:2000JExpB.203...51D. doi:10.1242/jeb.203.1.51. ISSN 0022-0949. PMID 10600673. <a href="/wiki/Bibcode_(identifier)" target="_blank">/wiki/Bibcode_(identifier)</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> <li id="fn:10"><p>Voet, Donald; Voet, Judith; Pratt, Charlotte (2013). Fundamentals of Biochemistry Life at the Molecular Level. New York City: John Wiley & Sons, Inc. pp. 582–584. ISBN 978-1118129180. <a href="978-1118129180" target="_blank">978-1118129180</a> <a href="#fnref:10" class="footnote-back-ref">↩</a></p></li> <li id="fn:11"><p>Stryer, L; Berg, J; Tymoczko, JL (2002). Biochemistry. San Francisco: W.H. Freeman. pp. 509–527, 569–579, 614–616, 638–641, 732–735, 739–748, 770–773. ISBN 978-0-7167-4684-3. <a href="978-0-7167-4684-3" target="_blank">978-0-7167-4684-3</a> <a href="#fnref:11" class="footnote-back-ref">↩</a></p></li> <li id="fn:12"><p>Soboll, S; Scholz, R; Freisl, M; Elbers, R; Heldt, H.W. (1976). Distribution of metabolites between mitochondria and cytosol of perfused liver. New york: Elsevier. pp. 29–40. ISBN 978-0-444-10925-5. <a href="978-0-444-10925-5" target="_blank">978-0-444-10925-5</a> <a href="#fnref:12" class="footnote-back-ref">↩</a></p></li> <li id="fn:13"><p>Voet, Donald; Voet, Judith; Pratt, Charlotte (2013). Fundamentals of Biochemistry Life at the Molecular Level. New York City: John Wiley & Sons, Inc. pp. 582–584. ISBN 978-1118129180. <a href="978-1118129180" target="_blank">978-1118129180</a> <a href="#fnref:13" class="footnote-back-ref">↩</a></p></li> <li id="fn:14"><p>Karmen, A.; Wroblewski, F.; Ladue, J. S. (1955-01-01). "Transaminase activity in human blood". The Journal of Clinical Investigation. 34 (1): 126–131. doi:10.1172/JCI103055. ISSN 0021-9738. PMC 438594. PMID 13221663. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC438594" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC438594</a> <a href="#fnref:14" class="footnote-back-ref">↩</a></p></li> <li id="fn:15"><p>King, John V.; Liang, Wenguang G.; Scherpelz, Kathryn P.; Schilling, Alexander B.; Meredith, Stephen C.; Tang, Wei-Jen (2014-07-08). "Molecular basis of substrate recognition and degradation by human presequence protease". Structure. 22 (7): 996–1007. doi:10.1016/j.str.2014.05.003. ISSN 1878-4186. PMC 4128088. 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