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\section{An arithmetic for the polynomial hierarchy}
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Our base language is $\{ 0, \succ{} , + , \times, \smsh , |\cdot| , \leq \}$.
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The $\basic$ axioms are as follows:
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\[
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\begin{array}{l}
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\safe (0) \\
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\forall x^\safe . \safe (\succ{} x) \\
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\forall x^\safe . 0 \neq \succ{} (x) \\
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\forall x^\safe , y^\safe . (\succ{} x = \succ{} y \cimp x = y) \\
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\forall x^\safe . (x = 0 \cor \exists y^\safe.\  x = \succ{} y   )
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\end{array}
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\]
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\anupam{in fact, we use essentially the same language, so just take Buss' Basic axioms after proper typing. Should also add the symbol $\hlf{\cdot}$ for binary predecessor then we have the full language of bounded arithmetic.}
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\begin{definition}
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[Derived functions and notations]
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We write $1,2,3,\dots$ for the terms $\succ{} 0, \succ{} \succ{} 0, \succ{} \succ{} \succ{} 0 \dots$, and frequently omit the $\times$ symbol.
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We define the functions $\succ 0 x , \succ 1 x$ as $2 x$ and $2x +1$ respectively.
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\end{definition}
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(Here use a variation of S12 with sharply bounded quantifiers and safe quantifiers)
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Use base theory + sharply bounded quantifiers.
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\begin{definition}
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[Quantifier hierarchy]
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We define:
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\begin{itemize}
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	\item $\Sigma^\safe_0 = \Pi^\safe_0 $ = sharply bounded formulae.
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	\item (Increase with predicative quantifiers)
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\end{itemize}
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\end{definition}
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\anupam{Collection principles for prenexing? Otherwise need to add closure under sharply bounded quantifiers.}
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\begin{definition}
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Define the theory $\arith^i$ consisting of the following axioms:
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\begin{itemize}
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	\item $\basic$;
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	\item $\cpind{\Sigma^\safe_i } $:
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\end{itemize}
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and an inference rule:
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\[
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 \dfrac{\forall \vec x^\normal . \exists  y^\safe .  A }{ \forall \vec x^\normal .\exists y^\normal . A}
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\]
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\end{definition}
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\anupam{In induction,for inductive cases, need $u\neq 0$ for $\succ 0$ case.}
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\begin{lemma}
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[Sharply bounded lemma]
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Let $f_A$ be the characteristic function of a predicate $A(u , \vec u ; \vec x)$.
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Then the characteristic functions of $\forall u \prefix v . A(u,\vec u ; \vec x)$ and $\exists u \prefix v . A(u , \vec u ; \vec x)$ are in $\bc(f_A)$.
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\end{lemma}
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\begin{proof}
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	We give the $\forall$ case, the $\exists$ case being dual.
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	The characteristic function $f(v , \vec u ; \vec x)$ is defined by predicative recursion on $v$ as:
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	\[
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	\begin{array}{rcl}
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	f(0, \vec u ; \vec x) & \dfn & f_A (0 , \vec u ; \vec x) \\
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	f(\succ i v , \vec u ; \vec x) & \dfn & \cond ( ; f_A (\succ i v, \vec u ; \vec x) , 0 , f(v , \vec u ; \vec x) )
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	\end{array}
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	\]
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\end{proof}
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Notice that $\prefix$ suffices to encode usual sharply bounded inequalities,
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since $\forall u \leq |t| . A(u , \vec u ; \vec x) \ciff \forall u \prefix t . A(|u|, \vec u ; \vec x)$.
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\subsection{Graphs of some basic functions}
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Todo: $+1$,
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\subsection{Encoding sequences in the arithmetic}
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\todo{}
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\anupam{Assume we have a $\Sigma^\safe_1$ predicate $\beta(i,x,y)$, expressing that the $i$th element of the sequence $x$ is $y$, such that $\arith^1 \proves \forall i^\normal , x^\safe . \exists ! y^\safe . \beta (i,x,y)$.}
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\subsection{A sequent calculus presentation}
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\todo{Write out usual first-order sequent calculus}
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\begin{figure}
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\[
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\small
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\begin{array}{l}
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\begin{array}{cccc}
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%\vlinf{\lefrul{\bot}}{}{p, \lnot{p} \seqar }{}
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%& \vlinf{\id}{}{p \seqar p}{}
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%& \vlinf{\rigrul{\bot}}{}{\seqar p, \lnot{p}}{}
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%& \vliinf{\cut}{}{\Gamma, \Sigma \seqar \Delta , \Pi}{ \Gamma \seqar \Delta, A }{\Sigma, A \seqar \Pi}
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 \vlinf{id}{}{p \seqar p}{}
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& \vliinf{cut}{}{\Gamma \seqar \Delta }{ \Gamma \seqar \Delta, A }{\Gamma, A \seqar \Delta}
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&&
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\\
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\noalign{\bigskip}
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%\noalign{\bigskip}
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\vliinf{\lefrul{\cor}}{}{\Gamma, A \cor B \seqar \Delta}{\Gamma , A \seqar \Delta}{\Gamma, B \seqar \Delta}
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&
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\vlinf{\lefrul{\cand}}{}{\Gamma, A\cand B \seqar \Delta}{\Gamma, A , B \seqar \Delta}
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&
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%\vlinf{\lefrul{\laand}}{}{\Gamma, A\laand B \seqar \Delta}{\Gamma, B \seqar \Delta}
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%\quad
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\vlinf{\rigrul{\cor}}{}{\Gamma \seqar \Delta, A \cor B}{\Gamma \seqar \Delta, A, B}
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&
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%\vlinf{\rigrul{\laor}}{}{\Gamma \seqar \Delta, A\laor B}{\Gamma \seqar \Delta, B}
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%\quad
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\vliinf{\rigrul{\cand}}{}{\Gamma \seqar \Delta, A \cand B }{\Gamma \seqar \Delta, A}{\Gamma \seqar \Delta, B}
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\\
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\noalign{\bigskip}
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\vliinf{\lefrul{\cimp}}{}{\Gamma, A \cimp B \seqar \Delta}{\Gamma \seqar A, \Delta}{\Gamma, B \seqar \Delta}
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&
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\vlinf{\lefrul{\neg}}{}{\Gamma, \neg A \seqar \Delta}{\Gamma \seqar A, \Delta}
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&
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\vlinf{\rigrul{\cimp}}{}{\Gamma \seqar \Delta, A \cimp B}{\Gamma, A \seqar \Delta,  B}
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&
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\vlinf{\lefrul{\neg}}{}{\Gamma, \seqar \neg A, \Delta}{\Gamma, A \seqar  \Delta}
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\\
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\noalign{\bigskip}
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%\text{Structural:} & & & \\
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%\noalign{\bigskip}
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\vlinf{\lefrul{\wk}}{}{\Gamma, A \seqar \Delta}{\Gamma \seqar \Delta}
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&
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\vlinf{\lefrul{\cntr}}{}{\Gamma, A \seqar \Delta}{\Gamma, A, A \seqar \Delta}
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&
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\vlinf{\rigrul{\wk}}{}{\Gamma \seqar \Delta, A }{\Gamma \seqar \Delta}
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&
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\vlinf{\rigrul{\cntr}}{}{\Gamma \seqar \Delta, A}{\Gamma \seqar \Delta, A, A}
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\\
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\noalign{\bigskip}
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\vlinf{\lefrul{\exists}}{}{\Gamma, \exists x . A(x) \seqar \Delta}{\Gamma, A(a) \seqar \Delta}
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&
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\vlinf{\lefrul{\forall}}{}{\Gamma, \forall x. A(x) \seqar \Delta}{\Gamma, A(t) \seqar \Delta}
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&
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\vlinf{\rigrul{\exists}}{}{\Gamma \seqar \Delta, \exists x . A(x)}{ \Gamma \seqar \Delta, A(t)}
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&
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\vlinf{\rigrul{\forall}}{}{\Gamma \seqar \Delta, \forall x . A(x)}{ \Gamma \seqar \Delta, A(a) } \\
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%\noalign{\bigskip}
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% \vliinf{mix}{}{\Gamma, \Sigma \seqar \Delta , \Pi}{ \Gamma \seqar \Delta}{\Sigma \seqar \Pi} &&&
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\end{array}
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\end{array}
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\]
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\caption{Sequent calculus rules}\label{fig:sequentcalculus}
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\end{figure}
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 We denote sequence as $\Gamma \seqar \Delta$ where $\Gamma$, $\Delta$ are multi sets of formulas. The sequent calculus rules are displayed on Fig. \ref{fig:sequentcalculus},  where $p$ is atomic, $i \in \{ 1,2 \}$, $t$ is a term and the eigenvariable $a$ does not occur free in $\Gamma$ or $\Delta$.
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We consider \emph{systems} of `nonlogical' rules extending this sequent calculus, which we write as follows,
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 \[
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 \begin{array}{cc}
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    \vlinf{(R)}{}{ \Gamma , \Sigma' \seqar \Delta' , \Pi  }{ \{\Gamma , \Sigma_i \seqar \Delta_i , \Pi \}_{i \in I} }
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\end{array}
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\]
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 where, in each rule $(R)$, $I$ is a finite possibly empty set (indicating the number of premises) and we assume the following conditions and terminology:
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 \begin{enumerate}
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 \item In $(R)$ the formulas of $\Sigma', \Delta'$  are called \textit{principal}, those of $\Sigma_i, \Delta_i$ are called \textit{active}, and those of
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$ \Gamma,  \Pi$ are called \textit{context formulas}.
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\item Each rule $(R)$ comes with a list $a_1$, \dots, $a_k$ of eigenvariables such that each $a_j$ appears in exactly one $\Sigma_i, \Delta_i$ (so in some active formulas of exactly one premise)  and does not appear in  $\Sigma', \Delta'$ or $ \Gamma,  \Pi$.
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    \item A system $\mathcal{S}$ of rules must be closed under substitutions of free variables by terms (where these substitutions do not contain the eigenvariables $a_j$ in their domain or codomain).
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   \end{enumerate}
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%The distinction between modal and nonmodal formulae in $(R)$ induces condition 1
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 Conditions 2 and 3 are standard requirements for nonlogical rules, independently of the logical setting, cf.\ \cite{Beckmann11}. Condition 2 reflects the intuitive idea that, in our nonlogical rules, we often need a notion of \textit{bound} variables in the active formulas (typically for induction rules), for which we rely on eigenvariables. Condition 3 is needed for our proof system to admit elimination of cuts on quantified formulas.
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\subsection{Free-cut free normal form of proofs}
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\todo{State theorem, with references (Takeuti, Cook-Nguyen) and present the important corollaries for this work.}
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Since our nonlogical rules may have many principal formulae on which cuts may be anchored, we need a slightly more general notion of principality.
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    \begin{definition}\label{def:anchoredcut}
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  We define the notions of \textit{hereditarily principal formula} and \textit{anchored cut} in a $\system$-proof, for a system $\system$, by mutual induction as follows:
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  \begin{itemize}
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  \item A formula $A$ in a sequent $\Gamma \seqar \Delta$ is \textit{hereditarily principal} for a rule instance (S) if either (i) the sequent is in the conclusion of (S) and $A$ is principal in it, or
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(ii)  the sequent is in the conclusion of an anchored cut, the direct ancestor of $A$ in the corresponding premise is hereditarily principal for the rule instance (S), and the rule (S) is nonlogical.
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  \item A cut-step is an \textit{anchored cut} if the two occurrences of its cut-formula $A$ in each premise are hereditarily principal for nonlogical steps, or one is hereditarily principal for a nonlogical step and the other one is principal for a logical step.
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  \end{itemize}
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     A cut which is not anchored will also be called a \textit{free-cut}.
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  \end{definition}
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  As a consequence of this definition, an anchored cut on a formula $A$ has the following properties:
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  \begin{itemize}
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  \item At least one of the two premises of the cut has above it a sub-branch of the proof which starts (top-down) with a nonlogical step (R) with $A$ as one of its principal formulas, and then a sequence of anchored cuts in which $A$ is part of the context.
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  \item The other premise is either of the same form or is a logical step with principal formula $A$.
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  \end{itemize}
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   Now we have (see \cite{Takeuti87}):
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   \begin{theorem}
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   [Free-cut elimination]
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   \label{thm:free-cut-elim}
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    Given a system  $\mathcal{S}$, any  $\mathcal{S}$-proof $\pi$ can be transformed into a $\system$-proof $\pi'$ with same end sequent and without any free-cut.
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   \end{theorem}