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For such an \\(u\\), the authors prove the following inequality in Theorem 1.1: \\N\\[\\N\\int_{S^1}\\Big( \\int_{\\Sigma_{\\theta}}\\frac{1}{2}(|du|^{-2}|\\mathrm{Hess}(u)|^2+R_N) +\\int_{\\partial \\Sigma_{\\theta}}H_{\\partial N}\\Big)\\leq 2\\pi \\int_{S^1}\\chi(\\Sigma_{\\theta}).\\N\\]\\NHere \\(R_N\\) denotes the scalar curvature of \\(N\\), \\(H_{\\partial N}\\) denotes the mean curvature of \\(\\partial N\\), \\(\\Sigma_{\\theta}\\) denotes the level set \\(u^{-1}(\\theta)\\), and \\(\\chi(\\Sigma_{\\theta})\\) denotes the Euler characteristic of \\(\\Sigma_{\\theta}\\). This inequality generalizes the second author's work in [J. Differential Geom. 122, No. 2, 259--269 (2022; Zbl 1514.53110)] for closed \\(3\\)-manifolds. The proof of Theorem 1.1 is similar to the computation in the second author's aforementioned paper.\\N\\NThe authors also give two applications of Theorem 1.1. The first one gives the following upper bound of the Thurston norm of a non-zero element \\(\\alpha \\in H_2(N,\\partial N;\\mathbb{Z})\\cong H^1(N;\\mathbb{Z})\\), under the assumption that every \\((\\Sigma,\\partial \\Sigma)\\subset (N,\\partial N)\\) with \\(\\chi(\\Sigma)>0\\) represents \\(0\\in H_2(N,\\partial N;\\mathbb{Z})\\): \\N\\[\\N4\\pi\\|\\alpha\\|_{Th}\\leq \\|du\\|_{L^2(N)}\\|R_N^-\\|_{L^2(N)}+2\\|du\\|_{L^2(\\partial N)}\\|H_{\\partial N}^-\\|_{L^2(\\partial N)}.\\]\\NHere \\(u:N\\to S^1\\) is the energy minimizer dual to \\(\\alpha\\), and \\(R_N^-\\) and \\(H_{\\partial N}^-\\) denote the negative parts of the scalar curvature of \\(N\\) and the mean curvature of \\(\\partial N\\), respectively.\\N\\NThe second application gives an upper bound for the Thurston norm of any closed, oriented \\(3\\)-manifold \\(M\\): for any \\(\\alpha\\in H_2(M;\\mathbb{Z})\\), we have \\N\\[\\N4\\pi\\|\\alpha\\|_{Th}\\leq \\|\\alpha\\|_H\\|R_g^-\\|_{L^2}.\\N\\]\\NHere \\(\\|\\cdot \\|_H\\) denotes the \\(L^2\\)-norm of the harmonic representative of \\(du\\), for \\(u:N\\to S^1\\) dual to \\(\\alpha\\). This result also generalizes a result of the second author in the aforementioned paper. This result is proved by cutting \\(M\\) along a maximal disjoint family of non-separating embedded minimal spheres, to obtain a \\(3\\)-manifold \\(N\\) with sphere boundary components. The authors study the behavior of two involved norms of \\(M\\) and \\(N\\), and applies the inequality in the previous application to \\(N\\).\\N\\NThe authors also study the case when the equalities hold in the above two 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