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Any person who is found by the Secretary, after notice and an opportunity for a hearing, to have violated subchapters I through III or this subchapter or a regulation issued under subchapters I through III or this subchapter shall be liable to the United States for a civil penalty, not to exceed $25,000 for each violation. Each day of a continuing violation shall constitute a separate violation. The amount of such civil penalty shall be assessed by the Secretary, or the Secretary’s designee, by written notice. In determining the amount of such penalty, the Secretary shall take into account the nature, circumstances, extent, and gravity of the prohibited acts committed and, with respect to the violator, the degree of culpability, any history of prior offenses, ability to pay, and such other matters as justice may require. The Secretary may compromise, modify, or remit, with or without conditions, any civil penalty that is subject to imposition or that has been imposed under this section. If any person fails to pay an assessment of a civil penalty after it has become final, the Secretary may refer the matter to the Attorney General of the United States, for collection in any appropriate district court of the United States. Any person who willfully and knowingly violates subchapters I through III or this subchapter or any regulation issued thereunder commits a class D felony. Any person who, in the willful and knowing violation of subchapters I through III or this subchapter or of any regulation issued thereunder, uses a dangerous weapon, or engages in conduct that causes bodily injury or fear of imminent bodily injury to any officer authorized to enforce the provisions of such a subchapter or the regulations issued under such subchapter, commits a class C felony. Any vessel that is used in violation of subchapters I, II, or III or this subchapter, or any regulations issued under such subchapter, shall be liable in rem for any civil penalty assessed pursuant to subsection (a) and may be proceeded against in the United States district court for any district in which such vessel may be found. The United States district courts shall have jurisdiction to restrain violations of subchapter I, II, or III or this subchapter or of regulations issued under such subchapter, for cause shown. into the navigable waters of the United States; or to any port or place under the jurisdiction of the United States. If any owner, operator, or individual in charge of a vessel is liable for a penalty or fine under this section, or if reasonable cause exists to believe that the owner, operator, or individual in charge may be subject to a penalty or fine under this section, the Secretary of the Treasury, upon the request of the Secretary, shall with respect to such vessel refuse or revoke any clearance required by section 60105 of title 46 . Clearance refused or revoked under this subsection may be granted upon filing of a bond or other surety satisfactory to the Secretary.