University of Chinese Academy of Sciences

Abstract Since the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large number of SARS-related coronaviruses (SARSr-CoVs) have been discovered in their natural reservoir host, bats 1–4 . Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans 5–7 . Here we report the identification and characterization of a new coronavirus (2019-nCoV), which caused an epidemic of acute respiratory syndrome in humans in Wuhan, China. The epidemic, which started on 12 December 2019, had caused 2,794 laboratory-confirmed infections including 80 deaths by 26 January 2020. Full-length genome sequences were obtained from five patients at an early stage of the outbreak. The sequences are almost identical and share 79.6% sequence identity to SARS-CoV. Furthermore, we show that 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus. Pairwise protein sequence analysis of seven conserved non-structural proteins domains show that this virus belongs to the species of . In addition, 2019-nCoV virus isolated from the bronchoalveolar lavage fluid of a critically ill patient could be neutralized by sera from several patients. Notably, we confirmed that 2019-nCoV uses the same cell entry receptor—angiotensin converting enzyme II (ACE2)—as SARS-CoV.

The central building block of convolutional neural networks (CNNs) is the convolution operator, which enables networks to construct informative features by fusing both spatial and channel-wise information within local receptive fields at each layer. A broad range of prior research has investigated the spatial component of this relationship, seeking to strengthen the representational power of a CNN by enhancing the quality of spatial encodings throughout its feature hierarchy. In this work, we focus instead on the channel relationship and propose a novel architectural unit, which we term the "Squeeze-and-Excitation" (SE) block, that adaptively recalibrates channel-wise feature responses by explicitly modelling interdependencies between channels. We show that these blocks can be stacked together to form SENet architectures that generalise extremely effectively across different datasets. We further demonstrate that SE blocks bring significant improvements in performance for existing state-of-the-art CNNs at slight additional computational cost. Squeeze-and-Excitation Networks formed the foundation of our ILSVRC 2017 classification submission which won first place and reduced the top-5 error to 2.251 percent, surpassing the winning entry of 2016 by a relative improvement of ∼ 25 percent. Models and code are available at https://github.com/hujie-frank/SENet.

Context. We present the second Gaia data release, Gaia DR2, consisting of astrometry, photometry, radial velocities, and information on astrophysical parameters and variability, for sources brighter than magnitude 21. In addition epoch astrometry and photometry are provided for a modest sample of minor planets in the solar system. Aims. A summary of the contents of Gaia DR2 is presented, accompanied by a discussion on the differences with respect to Gaia DR1 and an overview of the main limitations which are still present in the survey. Recommendations are made on the responsible use of Gaia DR2 results. Methods. The raw data collected with the Gaia instruments during the first 22 months of the mission have been processed by the Gaia Data Processing and Analysis Consortium (DPAC) and turned into this second data release, which represents a major advance with respect to Gaia DR1 in terms of completeness, performance, and richness of the data products. Results. Gaia DR2 contains celestial positions and the apparent brightness in G for approximately 1.7 billion sources. For 1.3 billion of those sources, parallaxes and proper motions are in addition available. The sample of sources for which variability information is provided is expanded to 0.5 million stars. This data release contains four new elements: broad-band colour information in the form of the apparent brightness in the G BP (330–680 nm) and G RP (630–1050 nm) bands is available for 1.4 billion sources; median radial velocities for some 7 million sources are presented; for between 77 and 161 million sources estimates are provided of the stellar effective temperature, extinction, reddening, and radius and luminosity; and for a pre-selected list of 14 000 minor planets in the solar system epoch astrometry and photometry are presented. Finally, Gaia DR2 also represents a new materialisation of the celestial reference frame in the optical, the Gaia -CRF2, which is the first optical reference frame based solely on extragalactic sources. There are notable changes in the photometric system and the catalogue source list with respect to Gaia DR1, and we stress the need to consider the two data releases as independent. Conclusions. Gaia DR2 represents a major achievement for the Gaia mission, delivering on the long standing promise to provide parallaxes and proper motions for over 1 billion stars, and representing a first step in the availability of complementary radial velocity and source astrophysical information for a sample of stars in the Gaia survey which covers a very substantial fraction of the volume of our galaxy.

In this paper, we address the scene segmentation task by capturing rich contextual dependencies based on the self-attention mechanism. Unlike previous works that capture contexts by multi-scale features fusion, we propose a Dual Attention Networks (DANet) to adaptively integrate local features with their global dependencies. Specifically, we append two types of attention modules on top of traditional dilated FCN, which model the semantic interdependencies in spatial and channel dimensions respectively. The position attention module selectively aggregates the features at each position by a weighted sum of the features at all positions. Similar features would be related to each other regardless of their distances. Meanwhile, the channel attention module selectively emphasizes interdependent channel maps by integrating associated features among all channel maps. We sum the outputs of the two attention modules to further improve feature representation which contributes to more precise segmentation results. We achieve new state-of-the-art segmentation performance on three challenging scene segmentation datasets, i.e., Cityscapes, PASCAL Context and COCO Stuff dataset. In particular, a Mean IoU score of 81.5% on Cityscapes test set is achieved without using coarse data.

Transfer learning aims at improving the performance of target learners on target domains by transferring the knowledge contained in different but related source domains. In this way, the dependence on a large number of target-domain data can be reduced for constructing target learners. Due to the wide application prospects, transfer learning has become a popular and promising area in machine learning. Although there are already some valuable and impressive surveys on transfer learning, these surveys introduce approaches in a relatively isolated way and lack the recent advances in transfer learning. Due to the rapid expansion of the transfer learning area, it is both necessary and challenging to comprehensively review the relevant studies. This survey attempts to connect and systematize the existing transfer learning research studies, as well as to summarize and interpret the mechanisms and the strategies of transfer learning in a comprehensive way, which may help readers have a better understanding of the current research status and ideas. Unlike previous surveys, this survey article reviews more than 40 representative transfer learning approaches, especially homogeneous transfer learning approaches, from the perspectives of data and model. The applications of transfer learning are also briefly introduced. In order to show the performance of different transfer learning models, over 20 representative transfer learning models are used for experiments. The models are performed on three different data sets, that is, Amazon Reviews, Reuters-21578, and Office-31, and the experimental results demonstrate the importance of selecting appropriate transfer learning models for different applications in practice.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible and pathogenic coronavirus that emerged in late 2019 and has caused a pandemic of acute respiratory disease, named ‘coronavirus disease 2019’ (COVID-19), which threatens human health and public safety. In this Review, we describe the basic virology of SARS-CoV-2, including genomic characteristics and receptor use, highlighting its key difference from previously known coronaviruses. We summarize current knowledge of clinical, epidemiological and pathological features of COVID-19, as well as recent progress in animal models and antiviral treatment approaches for SARS-CoV-2 infection. We also discuss the potential wildlife hosts and zoonotic origin of this emerging virus in detail. In this Review, Shi and colleagues summarize the exceptional amount of research that has characterized acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease 2019 (COVID-19) since this virus has swept around the globe. They discuss what we know so far about the emergence and virology of SARS-CoV-2 and the pathogenesis and treatment of COVID-19.

A novel non-fullerene electron acceptor (ITIC) that overcomes some of the shortcomings of fullerene acceptors, for example, weak absorption in the visible spectral region and limited energy-level variability, is designed and synthesized. Fullerene-free polymer solar cells (PSCs) based on the ITIC acceptor are demonstrated to exhibit power conversion efficiencies of up to 6.8%, a record for fullerene-free PSCs. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

Multigene and genomic data sets have become commonplace in the field of phylogenetics, but many existing tools are not designed for such data sets, which often makes the analysis time-consuming and tedious. Here, we present PhyloSuite, a (cross-platform, open-source, stand-alone Python graphical user interface) user-friendly workflow desktop platform dedicated to streamlining molecular sequence data management and evolutionary phylogenetics studies. It uses a plugin-based system that integrates several phylogenetic and bioinformatic tools, thereby streamlining the entire procedure, from data acquisition to phylogenetic tree annotation (in combination with iTOL). It has the following features: (a) point-and-click and drag-and-drop graphical user interface; (b) a workplace to manage and organize molecular sequence data and results of analyses; (c) GenBank entry extraction and comparative statistics; and (d) a phylogenetic workflow with batch processing capability, comprising sequence alignment (mafft and macse), alignment optimization (trimAl, HmmCleaner and Gblocks), data set concatenation, best partitioning scheme and best evolutionary model selection (PartitionFinder and modelfinder), and phylogenetic inference (MrBayes and iq-tree). PhyloSuite is designed for both beginners and experienced researchers, allowing the former to quick-start their way into phylogenetic analysis, and the latter to conduct, store and manage their work in a streamlined way, and spend more time investigating scientific questions instead of wasting it on transferring files from one software program to another.

The rapid and unpredictable expansion of urban areas poses a major challenge to humanity in adapting to climate change in the coming decades.Therefore, the presence of urban forests promotes climate change adaptation through their geographic location in cities.This systematic literature review (SLR) analyzed the existing research on ecosystem services provided by urban forests for climate change adaptation.The bibliographic databases Web of Science and Scopus were used for the study according to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) statement.There were 484 publications found that were published between 2011 and 2021 using specific terms in both search engines.However, there were only 59 articles from 26 different countries that met the inclusion criteria.When analyzing these 59 articles, the majority focused on carbon storage, while less than a quarter examined other services such as climate regulation and air purification.Hence, research should focus on the less studied or potential ecosystem services for climate change adaptation.Because the results provide a comprehensive overview of the role of urban forests in climate change adaptation, they should provide insights for policymakers, urban planners, and researchers seeking to improve urban resilience through the sustainable use of urban forest ecosystem services.

A central goal in systems neuroscience is the parcellation of the cerebral cortex into discrete neurobiological "atoms". Resting-state functional magnetic resonance imaging (rs-fMRI) offers the possibility of in vivo human cortical parcellation. Almost all previous parcellations relied on 1 of 2 approaches. The local gradient approach detects abrupt transitions in functional connectivity patterns. These transitions potentially reflect cortical areal boundaries defined by histology or visuotopic fMRI. By contrast, the global similarity approach clusters similar functional connectivity patterns regardless of spatial proximity, resulting in parcels with homogeneous (similar) rs-fMRI signals. Here, we propose a gradient-weighted Markov Random Field (gwMRF) model integrating local gradient and global similarity approaches. Using task-fMRI and rs-fMRI across diverse acquisition protocols, we found gwMRF parcellations to be more homogeneous than 4 previously published parcellations. Furthermore, gwMRF parcellations agreed with the boundaries of certain cortical areas defined using histology and visuotopic fMRI. Some parcels captured subareal (somatotopic and visuotopic) features that likely reflect distinct computational units within known cortical areas. These results suggest that gwMRF parcellations reveal neurobiologically meaningful features of brain organization and are potentially useful for future applications requiring dimensionality reduction of voxel-wise fMRI data. Multiresolution parcellations generated from 1489 participants are publicly available (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal).

In object detection, keypoint-based approaches often experience the drawback of a large number of incorrect object bounding boxes, arguably due to the lack of an additional assessment inside cropped regions. This paper presents an efficient solution that explores the visual patterns within individual cropped regions with minimal costs. We build our framework upon a representative one-stage keypoint-based detector named CornerNet. Our approach, named CenterNet, detects each object as a triplet, rather than a pair, of keypoints, which improves both precision and recall. Accordingly, we design two customized modules, cascade corner pooling, and center pooling, that enrich information collected by both the top-left and bottom-right corners and provide more recognizable information from the central regions. On the MS-COCO dataset, CenterNet achieves an AP of 47.0 %, outperforming all existing one-stage detectors by at least 4.9%. Furthermore, with a faster inference speed than the top-ranked two-stage detectors, CenterNet demonstrates a comparable performance to these detectors. Code is available at https://github.com/Duankaiwen/CenterNet.

Visual object tracking has been a fundamental topic in recent years and many deep learning based trackers have achieved state-of-the-art performance on multiple benchmarks. However, most of these trackers can hardly get top performance with real-time speed. In this paper, we propose the Siamese region proposal network (Siamese-RPN) which is end-to-end trained off-line with large-scale image pairs. Specifically, it consists of Siamese subnetwork for feature extraction and region proposal subnetwork including the classification branch and regression branch. In the inference phase, the proposed framework is formulated as a local one-shot detection task. We can pre-compute the template branch of the Siamese subnetwork and formulate the correlation layers as trivial convolution layers to perform online tracking. Benefit from the proposal refinement, traditional multi-scale test and online fine-tuning can be discarded. The Siamese-RPN runs at 160 FPS while achieving leading performance in VOT2015, VOT2016 and VOT2017 real-time challenges.

A new polymer donor (PBDB-T-SF) and a new small molecule acceptor (IT-4F) for fullerene-free organic solar cells (OSCs) were designed and synthesized. The influences of fluorination on the absorption spectra, molecular energy levels, and charge mobilities of the donor and acceptor were systematically studied. The PBDB-T-SF:IT-4F-based OSC device showed a record high efficiency of 13.1%, and an efficiency of over 12% can be obtained with a thickness of 100-200 nm, suggesting the promise of fullerene-free OSCs in practical applications.

, much of which is attributable to common risk alleles. Here, in a two-stage genome-wide association study of up to 76,755 individuals with schizophrenia and 243,649 control individuals, we report common variant associations at 287 distinct genomic loci. Associations were concentrated in genes that are expressed in excitatory and inhibitory neurons of the central nervous system, but not in other tissues or cell types. Using fine-mapping and functional genomic data, we identify 120 genes (106 protein-coding) that are likely to underpin associations at some of these loci, including 16 genes with credible causal non-synonymous or untranslated region variation. We also implicate fundamental processes related to neuronal function, including synaptic organization, differentiation and transmission. Fine-mapped candidates were enriched for genes associated with rare disruptive coding variants in people with schizophrenia, including the glutamate receptor subunit GRIN2A and transcription factor SP4, and were also enriched for genes implicated by such variants in neurodevelopmental disorders. We identify biological processes relevant to schizophrenia pathophysiology; show convergence of common and rare variant associations in schizophrenia and neurodevelopmental disorders; and provide a resource of prioritized genes and variants to advance mechanistic studies.

autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

Siamese network based trackers formulate tracking as convolutional feature cross-correlation between target template and searching region. However, Siamese trackers still have accuracy gap compared with state-of-the-art algorithms and they cannot take advantage of feature from deep networks, such as ResNet-50 or deeper. In this work we prove the core reason comes from the lack of strict translation invariance. By comprehensive theoretical analysis and experimental validations, we break this restriction through a simple yet effective spatial aware sampling strategy and successfully train a ResNet-driven Siamese tracker with significant performance gain. Moreover, we propose a new model architecture to perform depth-wise and layer-wise aggregations, which not only further improves the accuracy but also reduces the model size. We conduct extensive ablation studies to demonstrate the effectiveness of the proposed tracker, which obtains currently the best results on four large tracking benchmarks, including OTB2015, VOT2018, UAV123, and LaSOT. Our model will be released to facilitate further studies based on this problem.

The methyltransferase like 3 (METTL3)-containing methyltransferase complex catalyzes the N6-methyladenosine (m6A) formation, a novel epitranscriptomic marker; however, the nature of this complex remains largely unknown. Here we report two new components of the human m6A methyltransferase complex, Wilms' tumor 1-associating protein (WTAP) and methyltransferase like 14 (METTL14). WTAP interacts with METTL3 and METTL14, and is required for their localization into nuclear speckles enriched with pre-mRNA processing factors and for catalytic activity of the m6A methyltransferase in vivo. The majority of RNAs bound by WTAP and METTL3 in vivo represent mRNAs containing the consensus m6A motif. In the absence of WTAP, the RNA-binding capability of METTL3 is strongly reduced, suggesting that WTAP may function to regulate recruitment of the m6A methyltransferase complex to mRNA targets. Furthermore, transcriptomic analyses in combination with photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) illustrate that WTAP and METTL3 regulate expression and alternative splicing of genes involved in transcription and RNA processing. Morpholino-mediated knockdown targeting WTAP and/or METTL3 in zebrafish embryos caused tissue differentiation defects and increased apoptosis. These findings provide strong evidence that WTAP may function as a regulatory subunit in the m6A methyltransferase complex and play a critical role in epitranscriptomic regulation of RNA metabolism.

Reactive oxygen species (ROS) play an essential role in regulating various physiological functions of living organisms. The intrinsic biochemical properties of ROS, which underlie the mechanisms necessary for the growth, fitness, or aging of living organisms, have been driving researchers to take full advantage of these active chemical species for contributing to medical advances. Thanks to the remarkable advances in nanotechnology, great varieties of nanomaterials with unique ROS-regulating properties have been explored to guide the temporospatial dynamic behaviors of ROS in biological milieu, which contributes to the emergence of a new-generation therapeutic methodology, i.e., nanomaterial-guided in vivo ROS evolution for therapy. The interdependent relationship between ROS and their corresponding chemistry, biology, and nanotherapy leads us to propose the concept of "ROS science", which is believed to be an emerging scientific discipline that studies the chemical mechanisms, biological effects, and nanotherapeutic applications of ROS. In this review, state-of-art studies concerning recent progresses on ROS-based nanotherapies have been summarized in detail, with an emphasis on underlying material chemistry of nanomaterials by which ROS are generated or scavenged for improved therapeutic outcomes. Furthermore, key scientific issues in the evolution of ROS-based cross-disciplinary fields have also been discussed, aiming to unlock the innate powers of ROS for optimized therapeutic efficacies. We expect that our demonstration on this evolving field will be beneficial to the further development of ROS-based fundamental researches and clinical applications.

-methyladenosine (m6A) is the most prevalent, abundant and conserved internal cotranscriptional modification in eukaryotic RNAs, especially within higher eukaryotic cells. m6A modification is modified by the m6A methyltransferases, or writers, such as METTL3/14/16, RBM15/15B, ZC3H3, VIRMA, CBLL1, WTAP, and KIAA1429, and, removed by the demethylases, or erasers, including FTO and ALKBH5. It is recognized by m6A-binding proteins YTHDF1/2/3, YTHDC1/2 IGF2BP1/2/3 and HNRNPA2B1, also known as "readers". Recent studies have shown that m6A RNA modification plays essential role in both physiological and pathological conditions, especially in the initiation and progression of different types of human cancers. In this review, we discuss how m6A RNA methylation influences both the physiological and pathological progressions of hematopoietic, central nervous and reproductive systems. We will mainly focus on recent progress in identifying the biological functions and the underlying molecular mechanisms of m6A RNA methylation, its regulators and downstream target genes, during cancer progression in above systems. We propose that m6A RNA methylation process offer potential targets for cancer therapy in the future.

Exosomes are 40-100 nm nano-sized vesicles that are released from many cell types into the extracellular space. Such vesicles are widely distributed in various body fluids. Recently, mRNAs and microRNAs (miRNAs) have been identified in exosomes, which can be taken up by neighboring or distant cells and subsequently modulate recipient cells. This suggests an active sorting mechanism of exosomal miRNAs, since the miRNA profiles of exosomes may differ from those of the parent cells. Exosomal miRNAs play an important role in disease progression, and can stimulate angiogenesis and facilitate metastasis in cancers. In this review, we will introduce the origin and the trafficking of exosomes between cells, display current research on the sorting mechanism of exosomal miRNAs, and briefly describe how exosomes and their miRNAs function in recipient cells. Finally, we will discuss the potential applications of these miRNA-containing vesicles in clinical settings.