In this article our main goal is to establish an L2 version of the twisted invariance of plurigenera. We equally simplify the original “two towers” approach of Yum-Tong Siu.

Due to vast sequence divergence among different viral groups, sequence alignment is not directly applicable to genome-wide comparative analysis of viruses. More and more attention has been paid to alignment-free methods for whole genome comparison and phylogenetic tree reconstruction. Among alignment-free methods, the recently proposed ‘‘Natural Vector (NV) representation” has successfully been used to study the phylogeny of multi-segmented viruses based on a 12-dimensional genome space derived from the nucleotide sequence structure. But the preference of proteomes over genomes for the determination of viral phylogeny was not deeply investigated. As the translated products of genes, proteins directly form the shape of viral structure and are vital for all metabolic pathways. In this study, using the NV representation of a protein sequence along with the Hausdorff distance suitable to compare point sets, we construct a 60-dimensional protein space to analyze the evolutionary relationships of 4021 viruses by whole-proteomes in the current NCBI Reference Sequence Database (RefSeq). We also take advantage of the previously developed natural graphical representation to recover viral phylogeny. Our results demonstrate that the proposed method is efficient and accurate for classifying viruses. The accuracy rates of our predictions such as for Baltimore II viruses are as high as 95.9% for family labels, 95.7% for subfamily labels and 96.5% for genus labels. Finally, we discover that proteomes lead to better viral classification when reliable protein sequences are abundant. In other cases, the accuracy rates using proteomes are still comparable to that of genomes.

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We study a certain discrete differentiation of piecewise-constant functions on the adjoint of the braid hyperplane arrangement, defined by taking finite-differences across hyperplanes. In terms of Aguiar-Mahajan's Lie theory of hyperplane arrangements, we show that this structure is equivalent to the action of Lie elements on faces. We use layered binary trees to encode flags of adjoint arrangement faces, allowing for the representation of certain Lie elements by antisymmetrized layered binary forests. This is dual to the well-known use of (delayered) binary trees to represent Lie elements of the braid arrangement. The discrete derivative then induces an action of layered binary forests on piecewise-constant functions, which we call the forest derivative. Our main result states that forest derivatives of functions factorize as external products of functions precisely if one restricts to functions which satisfy the Steinmann relations, which are certain four-term linear relations appearing in the foundations of axiomatic quantum field theory. We also show that the forest derivative satisfies the Lie properties of antisymmetry the Jacobi identity. It follows from these Lie properties, and also crucially factorization, that functions which satisfy the Steinmann relations form a left comodule of the Lie cooperad, with the coaction given by the forest derivative. Dually, this endows the adjoint braid arrangement modulo the Steinmann relations with the structure of a Lie algebra internal to the category of vector species. This work is a first step towards describing new connections between Hopf theory in species and quantum field theory.

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