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Molecular clocks are the basis for dating the divergence between lineages over macroevolutionary timescales (~10⁵to 10⁸years). However, classical DNA-based clocks tick too slowly to inform us about the recent past. Here, we demonstrate that stochastic DNA methylation changes at a subset of cytosines in plant genomes display a clocklike behavior. This “epimutation clock” is orders of magnitude faster than DNA-based clocks and enables phylogenetic explorations on a scale of years to centuries. We show experimentally that epimutation clocks recapitulate known topologies and branching times of intraspecies phylogenetic trees in the self-fertilizing plantArabidopsis thalianaand the clonal seagrassZostera marina, which represent two major modes of plant reproduction. This discovery will open new possibilities for high-resolution temporal studies of plant biodiversity. 

Abstract MotivationThe rapid development of scRNA-seq technologies enables us to explore the transcriptome at the cell level on a large scale. Recently, various computational methods have been developed to analyze the scRNAseq data, such as clustering and visualization. However, current visualization methods, including t-SNE and UMAP, are challenged by the limited accuracy of rendering the geometric relationship of populations with distinct functional states. Most visualization methods are unsupervised, leaving out information from the clustering results or given labels. This leads to the inaccurate depiction of the distances between the bona fide functional states. In particular, UMAP and t-SNE are not optimal to preserve the global geometric structure. They may result in a contradiction that clusters with near distance in the embedded dimensions are in fact further away in the original dimensions. Besides, UMAP and t-SNE cannot track the variance of clusters. Through the embedding of t-SNE and UMAP, the variance of a cluster is not only associated with the true variance but also is proportional to the sample size. ResultsWe present supCPM, a robust supervised visualization method, which separates different clusters, preserves the global structure and tracks the cluster variance. Compared with six visualization methods using synthetic and real datasets, supCPM shows improved performance than other methods in preserving the global geometric structure and data variance. Overall, supCPM provides an enhanced visualization pipeline to assist the interpretation of functional transition and accurately depict population segregation. Availability and implementationThe R package and source code are available at https://zenodo.org/record/5975977#.YgqR1PXMJjM. Supplementary informationSupplementary data are available at Bioinformatics online. 

Using a Lewis acid-quenched CF2Ph- reagent, we show C–C bond formation through nucleophilic addition reactions to prepare molecules containing internal –CF2– linkages. We demonstrate C(sp2)–C(sp3) coupling using both SNAr reactions and Pd-catalysis. Finally, C(sp3)–C(sp3) bonds are forged using operationally simple SN2 reactions that tolerate medicinally-relevant motifs. 

Work in computer vision and natural language processing involving images and text has been experiencing explosive growth over the past decade, with a particular boost coming from the neural network revolution. The present volume brings together five research articles from several different corners of the area: multilingual multimodal image description (Frank et al. ), multimodal machine translation (Madhyastha et al. , Frank et al. ), image caption generation (Madhyastha et al. , Tanti et al. ), visual scene understanding (Silberer et al. ), and multimodal learning of high-level attributes (Sorodoc et al. ). In this article, we touch upon all of these topics as we review work involving images and text under the three main headings of image description (Section 2), visually grounded referring expression generation (REG) and comprehension (Section 3), and visual question answering (VQA) (Section 4).