Epigenetic Modifications in Distinction: Histone versus DNA Methylation in ESCs

In this issue of Cell Stem Cell, Karimi et al. (2011) show that DNA methylation and histone H3 lysine 9 trimethylation (H3K9me3) have distinct genomic targets in mouse ESCs. In particular, loss of H3K9me3 leads to derepression of select endogenous retroviruses and subsequent ectopic transcription of adjacent genes

Transcribing Content from Structural Images with Spotlight Mechanism

Transcribing content from structural images, e.g., writing notes from music scores, is a challenging task as not only the content objects should be recognized, but the internal structure should also be preserved. Existing image recognition methods mainly work on images with simple content (e.g., text lines with characters), but are not capable to identify ones with more complex content (e.g., structured symbols), which often follow a fine-grained grammar. To this end, in this paper, we propose a hierarchical Spotlight Transcribing Network (STN) framework followed by a two-stage "where-to-what" solution. Specifically, we first decide "where-to-look" through a novel spotlight mechanism to focus on different areas of the original image following its structure. Then, we decide "what-to-write" by developing a GRU based network with the spotlight areas for transcribing the content accordingly. Moreover, we propose two implementations on the basis of STN, i.e., STNM and STNR, where the spotlight movement follows the Markov property and Recurrent modeling, respectively. We also design a reinforcement method to refine the framework by self-improving the spotlight mechanism. We conduct extensive experiments on many structural image datasets, where the results clearly demonstrate the effectiveness of STN framework.Comment: Accepted by KDD2018 Research Track. In proceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD'18

Indexing the Human-Nature Relationship in Cities

Since the globalization of the world’s economy, there has been a surge in studies ranking international cities by quantitative indices. This paper examines various city indices and identifies the transition from an economy-centric approach towards a sustainability-oriented approach through the lens of those contributing variables used in different indices.  The paper then introduces a new Biophilic City Index as a way to examine the human-nature relationship, i.e. biophilia, in cities. It is structured at three different levels: from nature service to ecological integrity to human-nature interaction. This index enriches existing city indices and encourages city planners and policy-makers to make cities more biophilic

Advances in metabolomics profiling of pediatric kidney diseases

Pediatric renal diseases encompass a diverse array of pathological conditions, often engendering enduring ramifications. Metabolomics, an emergent branch of omics sciences, endeavors to holistically delineate alterations in metabolite compositions through the amalgamation of sophisticated analytical chemistry techniques and robust statistical methodologies. Recent advancements in metabolomics research within the realm of pediatric nephrology have been substantial, offering promising avenues for the identification of robust biomarkers, the elaboration of novel therapeutic targets, and the intricate elucidation of molecular mechanisms. The present discourse aims to critically review the progress in metabolomics profiling pertinent to pediatric renal disorders over the previous 12 years