search

curationexperts / laevigata

A Hyrax-based ETD repository including deposit workflow
Other
5 stars 4 forks source link

Errors caused by very long abstracts and TOCs #948

Closed bess closed 6 years ago

bess commented 6 years ago

We thought we had solved this problem by stripping formtting out of abstrct and toc fields, but here it is again.

Also, we have removed the "suggest" field from solr, but somehow it is still tripping on this one.

[laevigata - prod/production] RSolr::Error::Http: RSolr::Error::Http - 400 Bad RequestError: 'Exception writing document id xs55mc071 to the index; possible analysis error: Document contains at least one immense term in field="suggest" (whose UTF8 encoding is longer than the max length 32766), all of which were skipped. Please correct the analyzer to not produce such terms. The prefix of the first immense term is: \'[60, 112, 62, 32, 32, 60, 47, 112, 62, 10, 60, 112, 32, 115, 116, 121, 108, 101, 61, 3...

Backtrace

line 12 of [PROJECT_ROOT]/app/actors/hyrax/default_admin_set_actor.rb: create
line 9 of [PROJECT_ROOT]/app/actors/hyrax/actors/interpret_visibility_actor.rb: create
line 6 of [PROJECT_ROOT]/app/actors/hyrax/create_with_remote_files_actor.rb: create

View full backtrace and more info at honeybadger.io

no-reply commented 6 years ago

Here's an example of a failing TOC:


<p style="text-align: center;  margin: 12.0pt 0in .0001pt 0in;"><span style=" font-family: 'Times New Roman',serif;">Table of Contents</span></p>
<p style="text-align: center;  margin: 12.0pt 0in .0001pt 0in;"><span style=" font-family: 'Times New Roman',serif;"> </span></p>
<p><strong><span style=" font-family: 'Times New Roman',serif;">1<span>          </span>Introduction<span>                                                                                                               </span></span></strong></p>
<p><span style=" font-family: 'Times New Roman',serif;">1.1<span>       </span><span>Enzyme Catalysis and Dynamics<span>                                                                                </span></span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">1.1.1 <span>   </span>Timescale of Enzyme Fluctuations<span>                                                                            </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">1.1.2 <span>   </span>Dielectric Relaxation Studies of Protein Fluctuations<span>                                               </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">1.1.3 <span>   </span>Categories of Protein Fluctuations<span>                                                                             </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">1.1.4 <span>   </span>Temperature Dependence on Protein Fluctuations<span>                                                     </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">1.1.5 <span>   </span>Solvent Contributions to Protein Dynamics<span>                                                               </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">1.2 <span>      </span>Ethanolamine Ammonia-Lyase<span>                                                                                  </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">1.2.1 <span>   </span>B12-Dependent Superfamily <span>                                                                                      </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">1.2.2 <span>   </span>Ethanolamine Catabolism Pathway<span>                                                                </span><span>          </span><span>  </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">1.2.3 <span>   </span>Structure of EAL<span>                                                                                            </span><span>          </span><span>  </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">1.2.4 <span>   </span>Minimal Catalytic Mechanism for EAL<span>                                                        </span><span>          </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">1.2.5 <span>   </span>EAL Active Site<span>                                                                                             </span><span>          </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">1.2.6 <span>   </span>Paramagnetic Species in the EAL Catalytic Cycle<span>                                         </span><span>          </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">1.3 <span>      </span>Electron Paramagnetic Resonance<span>                                                                 </span><span>          </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">1.3.1 <span>   </span>Paramagnetic States of EAL<span>                                                                          </span><span>          </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">1.3.2 <span>   </span>CW-EPR Spectral of the Substrate Radical State<span>                                          </span><span>          </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">1.4 <span>      </span>Outline of Dissertation<span>                                                                                    </span><span>          </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; "> </span></p>
<p><span style=" font-family: 'Times New Roman',serif; "> </span></p>
<p><strong><span style=" font-family: 'Times New Roman',serif;">2 <span>         </span>Two Dynamical Regimes of the Substrate Radical Rearrangement Reaction in B12-Dependent Ethanolamine Ammonia-Lyase Resolve Contributions of Native Protein Configurations and Collective Configurational Fluctuations to Catalysis<span>       </span></span></strong></p>
<p><span style=" font-family: 'Times New Roman',serif; ">2.1<span>       </span>Introduction<span>                                                                                                    </span><span>          </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">2.1.1 <span>   </span>Configurational Protein Fluctuations<span>                                                             </span><span>          </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">2.1.2 <span>   </span>Substrate Radical Step in EAL<span>                                                                       </span><span>          </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">2.1.3 <span>   </span>Protein Fluctuation Classification<span>                                                                   </span><span>          </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">2.2 <span>      </span>Materials and Methods<span>                                                                                   </span><span>          </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">2.2.1 <span>   </span>Enzyme Preparation<span>                                                                                        </span><span>          </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">2.2.2 <span>   </span>Standard EPR Sample Preparation for Low-T Decay Measurements<span>            </span><span>          </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">2.2.3 <span>   </span>Time-Resolved, Full Spectrum EPR Measurements of Substrate Radical <span>   </span><span>          </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">Decay at Low-<em>T<span>          </span><span>                                                                                    </span></em><span>          </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">2.2.4 <span>   </span>Steady-State Kinetics Measurements<span>                                                             </span><span>          </span><span> </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">2.2.5 <span>   </span>Transient Kinetics Analysis: Empirical Fitting of the Observed Substrate </span></p>
<p><span style=" font-family: 'Times New Roman',serif;">Radical Decay<span>                                                                                                 </span><span>          </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">2.2.6 <span>   </span>Numerical Simulation and Fitting to the Microscopic Model<span>                        </span><span>          </span><span> </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">2.2.7 <span>   </span>Transient Kinetics Analysis: Numerical Simulation and Fitting to </span></p>
<p><span style=" font-family: 'Times New Roman',serif;">the Microscopic<span> <span>                                                                                             </span><span>           </span></span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">2.2.8 <span>   </span>Temperature-Dependence of First-Order Rate Constants<span>                              </span><span>           </span><span> </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">2.3<span>       </span>Results<span>                                                                                                                       </span> </span></p>
<p><span style=" font-family: 'Times New Roman',serif;">2.3.1 <span>   </span>Time-Resolved, Full-Spectrum EPR Measurements of the Co<sup>2+</sup>-Substrate </span></p>
<p><span style=" font-family: 'Times New Roman',serif;">Radical Pair Decay<span>                                                                                                     </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">2.3.2 <span>   </span>Steady-State Measurements of the Co<sup>2+</sup>-Substrate Radical Pair Decay<span>                     </span> </span></p>
<p><span style=" font-family: 'Times New Roman',serif;">2.3.3 <span>   </span>Temperature-Dependence of the Observed Rate Constants <span>                                      </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">2.3.4 <span>   </span>Homogeneity of the Co<sup>2+</sup>-Substrate Radical Pair Decay Population<span>                         </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">2.4 <span>      </span>Discussion<span>                                                                                                                   </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">2.4.1 <span>   </span>Temperature-Dependent Free Energy Landscape Model <span>                                          </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">2.4.2 <span>   </span>Microscopic Kinetic Mechanism<span>                                                                                </span> </span></p>
<p><span style=" font-family: 'Times New Roman',serif;">2.4.3 <span>   </span>Specific Native Collective Protein Configurational Fluctuations Guide </span></p>
<p><span style=" font-family: 'Times New Roman',serif;">the Substrate Radical Rearrangement Reaction in EAL<span>                                            </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">2.4.4 <span>   </span>Correspondence to EAL Protein Structure <span>                                                                </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">2.5 <span>      </span>Conclusion<span>                                                                                                                  </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif; "> </span></p>
<p><span style=" font-family: 'Times New Roman',serif; "> </span></p>
<p><strong><span style=" font-family: 'Times New Roman',serif;">3 <span>         </span></span></strong><strong><span style=" font-family: 'Times New Roman',serif;  ">Characterization of the Kinetic Isotope Effects on the Radical </span></strong></p>
<p><strong><span style=" font-family: 'Times New Roman',serif;  ">Rearrangement and Second Hydrogen Transfer Step</span></strong><strong><span style=" font-family: 'Times New Roman',serif; "><span>      </span><span>                                    </span></span></strong></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.1 <span>      </span>Introduction<span>                                                                                                                </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.1.2 <span>   </span>Kinetic Isotope Effects (KIE)<span>                                                                                     </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.1.3 <span>   </span>Low Temperature Kinetic Isotope Effects (KIE)<span>                                                       </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.1.4 <span>   </span>Microscopic Model Implications<span>                                                                                </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.2 <span>      </span>Materials and Methods<span>                                                                                               </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.2.1 <span>   </span>Enzyme Preparation<span>                                                                                                    </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.2.2<span>    </span> Time-Resolved, Full Spectrum EPR Measurements of Substrate </span></p>
<p><span style=" font-family: 'Times New Roman',serif;">Radical Decay at Low-T<span>                                                                                             </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.2.3 <span>   </span>Steady-State Kinetics Measurements <span>                                                                        </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.2.4 <span>   </span>Transient Kinetics Analysis<span>                                                                                        </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.2.5<span>    </span> Numerical simulation and fitting to the microscopic model<span>                                     </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;  ">3.2.6 <span>   </span>Controlled Sample Decay to Detect Differences in Microscopic States<span>                    </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;  ">3.2.7<span>    </span> Pulsed EPR<span>                                                                                                                </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.2.8<span>    </span> Incorporation of the HT2 step into the Microscopic Model<span>                                      </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.2.9 <span>   </span>Numerical simulation and fitting to the HT2 Incorporated Microscopic </span></p>
<p><span style=" font-family: 'Times New Roman',serif;">Model <span>                                                                                                                         </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.2.10  Construction of Simulated Decays<span>                                                                             </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.3<span>       </span> Results<span>                                                                                                                       </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.3.1<span>    </span> Full-Spectrum EPR Measurements of the Co(II)-Substrate Radical Pair<span>                 </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.3.2 <span>   </span>Characterization of the Substrate Radical Rearrangement Step<span>                                </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;  ">3.3.3<span>    </span> ESEEM and Controlled Decays<span>                                                                                </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.4 <span>      </span>Discussion<span>                                                                                                                   </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;  ">3.4.1 <span>   </span>Temperature-Dependent Free Energy Landscape and Microscopic Model<span>               </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.4.2 <span>   </span>Applying the Minimal 3-State/2-Step Microscopic Model <span>                                       </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">(Unincorporated HT2) <span>                                                                                               </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.4.3<span>    </span> Fitting Inconsistencies in HT2 step Incorporated Microscopic Model<span>                     </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.4.4<span>    </span> Determining the <em>k</em>PS : <em>k</em>HT Ratio for <sup>2</sup>H4-Substrate Radical Decays<span>                           </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.4.5 <span>   </span>Four Temperature Regimes for </span><em><span style=" font-family: 'Times New Roman',serif;  ">k</span></em><span style=" font-family: 'Times New Roman',serif;  ">HT</span><span style=" font-family: 'Times New Roman',serif;  "> and <em>k</em>PS<span>                                                                                     </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.4.6 <span>   </span>Arrhenius Dependencies of<span>  </span></span><em><span style=" font-family: 'Times New Roman',serif;  ">k</span></em><span style=" font-family: 'Times New Roman',serif;  ">HT</span><span style=" font-family: 'Times New Roman',serif;  "> and <em>k</em>PS<span>                                                                                           </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.4.7<span>    </span> Temperature Transition of </span><em><span style=" font-family: 'Times New Roman',serif;  ">k</span></em><span style=" font-family: 'Times New Roman',serif;  ">HT</span><span style=" font-family: 'Times New Roman',serif;  "> at 227 K<span>                                                                    </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.4.8<span>    </span> (Lack of) Structural Difference in S1</span><sup><span style=" font-family: Symbol;     "><span>·</span></span></sup><span style=" font-family: 'Times New Roman',serif;"> and S2</span><sup><span style=" font-family: Symbol;     "><span>·</span></span></sup><span style=" font-family: 'Times New Roman',serif;"> States<span>                                                            </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">3.4.9<span>    </span> Possible I.E. on <em>k</em>P,N and <em>k</em>P <span>                                                                                       </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;  ">3.5<span>       </span> Conclusions<span>                                                                                                                </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;  "> </span></p>
<p><strong><span style=" font-family: 'Times New Roman',serif;  ">4</span></strong><span style=" font-family: 'Times New Roman',serif;  "><span>          </span><strong>Protein and Coupled Solvent Dynamic Contributions to the Radical Rearrangement</strong></span></p>
<p><strong><span style=" font-family: 'Times New Roman',serif;  ">Step in a B12-Dependent Enzyme Addressed by Sucrose Effects on Reaction Kinetics</span></strong></p>
<p><strong><span style=" font-family: 'Times New Roman',serif;  ">at 217 K<span>                                                                                                                      </span></span></strong></p>
<p><span style=" font-family: 'Times New Roman',serif;  ">4.1<span>       </span>Introduction<span>                                                                                                    </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">4.1.1 <span>   </span>The Role of Solvent in Protein Dynamics<span>                                                                  </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;  ">4.2<span>       </span> Materials and Methods<span>                                                                                              </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">4.2.1 <span>   </span>Sucrose Sample Preparation<span>                                                                                       </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">4.2.2<span>    </span> Enzyme Purification and Sample Preparation<span>                                                           </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">4.2.3<span>    </span> Full Spectrum EPR Measurements the Substrate Radical Decay at 120 K<span>              </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">4.2.4<span>    </span> Time-Resolved, Full Spectrum EPR Measurements of Substrate <span>                            </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">Radical Decay at Low-T<span>                                                                                             </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">4.2.5<span>    </span> Transient Kinetics Analysis<span>                                                                                       </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;  ">4.3 <span>      </span>Results<span>                                                                                                                        </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">4.3.1 <span>   </span>Full-Spectrum EPR Measurements of Co(II)-Substrate Radical Pair </span></p>
<p><span style=" font-family: 'Times New Roman',serif;">at 120 K<span>                                                                                                                      </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">4.3.2 <span>   </span>Decay of Co(II)-Substrate Radical Amplitude at 217 K for 0-30% </span></p>
<p><span style=" font-family: 'Times New Roman',serif;">Sucrose Concentrations <span>                                                                                             </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;  ">4.4 <span>      </span>Discussion<span>                                                                                                                   </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">4.4.1 <span>   </span>Decreased Amplitude of the Fast Phase<span>                                                                     </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">4.4.2<span>    </span> Rate Distribution of the Slow Phase<span>                                                                          </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;  ">4.4.3 <span>   </span>Sucrose Effect on Local, Incremental Fluctuations<span>                                                    </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;  ">4.5<span>       </span> Conclusions<span>                                                                                                                </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;  "> </span></p>
<p><strong><span style=" font-family: 'Times New Roman',serif;  ">5<span>          </span>Characterization of Contributions of Solvent-Coupled Protein Configurational Dynamics to the Rearrangement Reaction in B12-Dependent Ethanolamine Ammonia-Lyase<span>                            </span><span>                                                                        </span></span></strong></p>
<p><span style=" font-family: 'Times New Roman',serif;  ">5.1<span>       </span>Introduction<span>                                                                                                                </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;  ">5.2<span>       </span>Materials and Methods<span>                                                                                               </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">5.2.1 <span>   </span>Sucrose Sample Preparation<span>                                                                                       </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">5.2.2 <span>   </span>Enzyme Purification and Sample Preparation<span>                                                            </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">5.2.3 <span>   </span>Time-Resolved, Full Spectrum EPR Measurements of Substrate </span></p>
<p><span style=" font-family: 'Times New Roman',serif;">Radical Decay <span>                                                                                                            </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">5.2.4 <span>   </span>Transient Kinetics Analysis<span>                                                                                        </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">5.2.5 <span>   </span>Simulation of Substrate Radical Decay Based on the Distributed </span></p>
<p><span style=" font-family: 'Times New Roman',serif;">Rate Constant Model<span>                                                                                                  </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">5.2.6 <span>   </span>Numerical simulation and fitting to the microscopic model <span>                                     </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;  ">5.3<span>       </span> Results<span>                                                                                                                       </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">5.3.1 <span>   </span>Time-Resolved, Full-Spectrum EPR Measurements of the Co<sup>2+</sup>-</span></p>
<p><span style=" font-family: 'Times New Roman',serif;">Substrate Radical Pair Decay for 1% and 2% (w/v) Sucrose </span></p>
<p><span style=" font-family: 'Times New Roman',serif;">Concentrations<span>                                                                                                            </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">5.3.2 <span>   </span>Temperature-Dependence of the Observed Rate Constants <span>                                      </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;  ">5.4 <span>      </span>Discussion<span>                                                                                                                   </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">5.4.1 <span>   </span>General Features of the Temperature-Dependent Free Energy </span></p>
<p><span style=" font-family: 'Times New Roman',serif;">Landscape Model <span>                                                                                                       </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">5.4.2<span>    </span> Rate Distribution of the Slow Phase<span>                                                                          </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">5.4.3 <span>   </span>Activation Energy Distribution of the Slow Phase<span>                                                     </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">5.4.4.<span>   </span> Reconciliation of the Fast Phase Amplitude Decrease with Increase </span></p>
<p><span style=" font-family: 'Times New Roman',serif;">Sucrose Concentrations<span>                                                                                              </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">5.4.5 <span>   </span>Transition Temperature Region Dependence on Sucrose Concentrations<span>                 </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">5.4.6<span>    </span> Partition of the Observed Slow Phase Distributions for <em>T </em>< 217 <span>                             </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;">5.4.7<span>    </span> Microscopic Kinetic Mechanism <span>                                                                              </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;  ">5.5 <span>      </span>Conclusion<span>                                                                                                                  </span></span></p>
<p><span style=" font-family: 'Times New Roman',serif;  "> </span></p>
<p><strong><span style=" font-family: 'Times New Roman',serif;  ">6 <span>         </span>Conclusions<span>                                                                                                                </span></span></strong></p>
<p style="  margin: 12.0pt 0in 8.0pt .5in;"><span style=" font-family: 'Times New Roman',serif;  ">6.1<span>       </span>Chapter Two: </span><span style=" font-family: 'Times New Roman',serif; ">Two Dynamical Regimes of the Substrate Radical Rearrangement Reaction in B12-Dependent Ethanolamine Ammonia-Lyase Resolve Contributions of Native Protein Configurations and Collective Configurational Fluctuations to Catalysis<span>                  </span></span></p>
<p style="  margin: 12.0pt 0in 8.0pt .5in;"><span style=" font-family: 'Times New Roman',serif;  ">6.2<span>       </span>Chapter Three: Characterization of the Kinetic Isotope Effects on the Radical Rearrangement and Second Hydrogen Transfer Step<span>                                                         </span></span></p>
<p style="  margin: 12.0pt 0in 8.0pt .5in;"><span style=" font-family: 'Times New Roman',serif;  ">6.3<span>       </span>Chapter Four: Protein and Coupled Solvent Dynamic Contributions to the Radical Rearrangement Step in a B12-Dependent Enzyme Addressed by Sucrose Effects on Reaction Kinetics at 217 K<span>     </span><span>                        </span></span></p>
<p style="  margin: 12.0pt 0in .0001pt .5in;"><span style=" font-family: 'Times New Roman',serif;  ">6.4<span>       </span>Chapter Five: Characterization of Contributions of Solvent-Coupled Protein Configurational Dynamics to the Rearrangement Reaction in B12-Dependent Ethanolamine Ammonia-Lyase<span>        </span><span>                                                                        </span></span></p>
<p style="  margin: 12.0pt 0in .0001pt .5in;"><span><span style=" font-family: 'Times New Roman',serif;  "> </span></span></p>
<p><strong><span style=" font-family: 'Times New Roman',serif;  ">References<span>                                                                                                                             </span></span></strong></p>
<p><strong><span style=" font-family: 'Times New Roman',serif;  ">Appendix<span>                                                                                                                               </span></span></strong></p>
<p><strong><span style=" font-family: 'Times New Roman',serif;  "> </span></strong></p>
<p style="text-align: center; "><strong><span style=" font-family: 'Times New Roman',serif;  ">List of Tables and Figures</span></strong></p>
<p style="text-align: center; "><strong><span style=" font-family: 'Times New Roman',serif;  ">Chapter 1</span></strong></p>
<p><strong><span style=" font-family: 'Times New Roman',serif;  ">Figures</span></strong></p>
<p><span style=" font-family: 'Times New Roman',serif; ">Figure 1.1</span><span style=" font-family: 'Times New Roman',serif;">. <span>      </span>Qualitative energy</span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">Figure 1.2</span><span style=" font-family: 'Times New Roman',serif;">.<span>       </span> Hierarchies of protein fluctuations</span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">Figure 1.3</span><span style=" font-family: 'Times New Roman',serif;">. <span>      </span>Representation of the EAL hexamer</span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">Figure 1.4. <span>      </span></span><span style=" font-family: 'Times New Roman',serif;">Minimal mechanism for the catalytic cycle of EAL</span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">Figure 1.5</span><span style=" font-family: 'Times New Roman',serif;">. <span>      </span>Pymol representation of the EAL active site.</span></p>
<p><span style=" font-family: 'Times New Roman',serif; ">Figure 1</span><span style=" font-family: 'Times New Roman',serif;">.6. <span>      </span>Energy level diagram for a free electron showing resonance absorption</span></p>
<p style=" text-align: center; "><strong><span style=" font-family: 'Times New Roman',serif;">Chapter 2</span></strong></p>
<p><strong><span style=" font-family: 'Times New Roman',serif;">Tables</span></strong></p>
<p><span style="font-family: 'Times New Roman',serif;">Table 2.1<span>          </span> Observed first-order rate constant and normalized amplitude parameters</span></p>
<p style="  margin: 12.0pt 0in 8.0pt 1.0in;"><span style="font-family: 'Times New Roman',serif;">Table 2.2 <span>         </span>First-order microscopic rate constant and amplitude parameters for the Co2+ - substrate radical pair decay kinetics</span></p>
<p style="  margin: 12.0pt 0in 8.0pt 1.0in;"><span style="font-family: 'Times New Roman',serif;"> </span></p>
<p><span style="font-family: 'Times New Roman',serif;">Table 2.3 <span>         </span>Arrhenius reaction rate parameters for the microscopic rate constants of the Co2+-substrate radical pair decay</span></p>
<p><span style="font-family: 'Times New Roman',serif;"> </span></p>
<p><span style="font-family: 'Times New Roman',serif;">Table 2.4 <span>         </span>Activation enthalpy and entropy values obtained from Eyring analysis of the microscopic rate constants</span></p>
<p><strong><span style=" font-family: 'Times New Roman',serif;">Figures</span></strong></p>
<p style="  margin: 12.0pt 0in 8.0pt 1.0in;"><span style="font-family: 'Times New Roman',serif;">Figure 2.1 <span>        </span>Structure of the aminoethanol substrate radical and EAL protein in the active site region and substrate radical decay reaction sequence</span></p>
<p style="  margin: 12.0pt 0in 8.0pt 1.0in;"><span style="font-family: 'Times New Roman',serif;"> </span></p>
<p style="  margin: 12.0pt 0in 8.0pt 1.0in;"><span style="font-family: 'Times New Roman',serif;">Figure 2.2 <span>        </span>Electron paramagnetic resonance spectrum of the aminoethanol-generated Co(II)-substrate radical pair EPR spectrum in EAL</span></p>
<p><span style="font-family: 'Times New Roman',serif;">Figure 2.3 <span>        </span>EPR spectrum</span></p>
<p><span style="font-family: 'Times New Roman',serif;">Figure 2.4<span>         </span>Time-dependence of the EPR amplitude of the substrate radical decays</span></p>
<p><span style="font-family: 'Times New Roman',serif;">Figure 2.5<span>         </span> Arrhenius plot of observed first-order rate constants</span></p>
<p style="  margin: 12.0pt 0in 8.0pt 1.0in;"><span style="font-family: 'Times New Roman',serif;">Figure 2.6<span>         </span> Free energy landscape representations of the substrate radical rearrangement process in EAL</span></p>
<p><span style="font-family: 'Times New Roman',serif;">Figure 2.7<span>         </span>Arrhenius plot of the microscopic rate constants.</span></p>
<p><span style="font-family: 'Times New Roman',serif;">Figure 2.8<span>         </span> Numerical simulations of the amplitude versus time data at different T values.</span></p>
<p style="  margin: 12.0pt 0in 8.0pt 1.0in;"><span style="font-family: 'Times New Roman',serif;">Figure 2.9<span>         </span>Comparison of the rate constants from the empirical fitting of the substrate radical decay data with the rate constants obtained by fitting the numerical simulation</span></p>
<p style="  margin: 12.0pt 0in 8.0pt 1.0in;"><span style="font-family: 'Times New Roman',serif;"> </span></p>
<p style="  margin: 12.0pt 0in 8.0pt 1.0in;"><span style="font-family: 'Times New Roman',serif;">Figure 2.10<span>       </span>Arrhenius plot of observed rate constants for substrate radical decay in EAL and dynamical parameters from other protein systems.</span></p>
<p> </p>```
no-reply commented 6 years ago

I can reproduce easily enough with str = # the string in the previous comment Etd.create(title: ['Very long ToC'], table_of_contents: [str]).

no-reply commented 6 years ago

I have a fix incoming. The new config breaks fedora before breaking Solr.

I can safely save objects with table of contents up to about 10 million (10_000_000) characters.