Rapeseed (Brassica napus) is the second most important oilseed crop in the world but the genetic diversity underlying its massive phenotypic variations remains largely unexplored. Here, we report the sequencing, de novo assembly and annotation of eight B. napus accessions. Using pan-genome comparative analysis, millions of small variations and 77.2–149.6 megabase presence and absence variations (PAVs) were identified. More than 9.4% of the genes contained large-effect mutations or structural variations. PAV-based genome-wide association study (PAV-GWAS) directly identified causal structural variations for silique length, seed weight and flowering time in a nested association mapping population with ZS11 (reference line) as the donor, which were not detected by single-nucleotide polymorphisms-based GWAS (SNP-GWAS), demonstrating that PAV-GWAS was complementary to SNP-GWAS in identifying associations to traits. Further analysis showed that PAVs in three FLOWERING LOCUS C genes were closely related to flowering time and ecotype differentiation. This study provides resources to support a better understanding of the genome architecture and acceleration of the genetic improvement of B. napus.

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Summary The social difficulties that are a hallmark of autism spectrum disorder (ASD) are thought to arise, at least in part, from atypical attention towards stimuli and their features. To investigate this hypothesis comprehensively, we characterized 700 complex natural scene images with a novel 3-layered saliency model that incorporated pixel-level (e.g., contrast), object-level (e.g., shape), and semantic-level attributes (e.g., faces) on 5551 annotated objects. Compared to matched controls, people with ASD had a stronger image center bias regardless of object distribution, reduced saliency for faces and for locations indicated by social gaze, yet a general increase in pixel-level saliency at the expense of semantic-level saliency. These results were further corroborated by direct analysis of fixation characteristics and investigation of feature interactions. Our results for the first time quantify atypical visual attention in ASD across multiple levels and categories of objects.

Online class imbalance learning is a new learning problem that combines the challenges of both online learning and class imbalance learning. It deals with data streams having very skewed class distributions. This type of problems commonly exists in real-world applications, such as fault diagnosis of real-time control monitoring systems and intrusion detection in computer networks. In our earlier work, we defined class imbalance online, and proposed two learning algorithms OOB and UOB that build an ensemble model overcoming class imbalance in real time through resampling and time-decayed metrics. In this paper, we further improve the resampling strategy inside OOB and UOB, and look into their performance in both static and dynamic data streams. We give the first comprehensive analysis of class imbalance in data streams, in terms of data distributions, imbalance rates and changes in class imbalance status. We find that UOB is better at recognizing minority-class examples in static data streams, and OOB is more robust against dynamic changes in class imbalance status. The data distribution is a major factor affecting their performance. Based on the insight gained, we then propose two new ensemble methods that maintain both OOB and UOB with adaptive weights for final predictions, called WEOB1 and WEOB2. They are shown to possess the strength of OOB and UOB with good accuracy and robustness.

Differences in cardiac and aortic structure and function are associated with cardiovascular diseases and a wide range of other types of disease. Here we analyzed cardiovascular magnetic resonance images from a population-based study, the UK Biobank, using an automated machine learning-based analysis pipeline. We report a comprehensive range of structural and functional phenotypes for the heart and aorta across 26,893 participants and explore how these phenotypes vary according to sex, age and major cardiovascular risk factors. We extended this analysis with a phenome-wide association study, in which we tested for correlations of a wide range of non-imaging phenotypes of the participants with imaging phenotypes. We further explored the associations of imaging phenotypes with early-life factors, mental health and cognitive function using both observational analysis and Mendelian randomization. Our study illustrates how population-based cardiac and aortic imaging phenotypes can be used to better define cardiovascular disease risks as well as heart-brain health interactions, highlighting new opportunities for studying disease mechanisms and developing image-based biomarkers.Cardiac and aortic structure and function are associated with cardiovascular diseases (CVDs) 1, 2 and a wide range of other types of disease [3][4][5][6] . Quantitative phenotypes derived from cardiovascular magnetic resonance (CMR) images enable us to assess cardiac and aortic structure and function in a non-invasive way and provide important biomarkers for the determination of pathological states in CVDs. For example, the left ventricular ejection fraction (LVEF) is an important clinical biomarker for the diagnosis and treatment of heart failure 1 . The left ventricular myocardial mass (LVM) is widely used for classifying hypertrophy and predicting risks of cardiovascular events 7 . Although CMR imaging phenotypes clearly play an important role in disease research and diagnosis, extracting these phenotypes demand significant involvement of experienced image analysts. This has become a limiting factor for applying CMR in large-scale studies and exploiting imaging phenotypes at a population level.Large-scale imaging studies potentially provide a wealth of information for investigating disease risk factors and discovering early-stage image-based biomarkers. Recent large-scale imaging studies collecting CMR images include the Framingham Heart

Rice (Oryza sativa), a major staple throughout the world and a model system for plant genomics and breeding, was the first crop genome sequenced almost two decades ago. However, reference genomes for all higher organisms to date contain gaps and missing sequences. Here, we report the assembly and analysis of gap-free reference genome sequences for two elite O. sativa xian/indica rice varieties, Zhenshan 97 and Minghui 63, which are being used as a model system for studying heterosis and yield. Gapfree reference genomes provide the opportunity for a global view of the structure and function of centromeres. We show that all rice centromeric regions share conserved centromere-specific satellite motifs with different copy numbers and structures. In addition, the similarity of CentO repeats in the same chromosome is higher than across chromosomes, supporting a model of local expansion and homogenization. Both genomes have over 395 non-TE genes located in centromere regions, of which $41% are actively transcribed. Two large structural variants at the end of chromosome 11 affect the copy number of resistance genes between the two genomes. The availability of the two gap-free genomes lays a solid foundation for further understanding genome structure and function in plants and breeding climate-resilient varieties.

Face recognition has witnessed significant progress due to the advances of deep convolutional neural networks (CNNs), the central task of which is how to improve the feature discrimination. To this end, several margin-based (e.g., angular, additive and additive angular margins) softmax loss functions have been proposed to increase the feature margin between different classes. However, despite great achievements have been made, they mainly suffer from three issues: 1) Obviously, they ignore the importance of informative features mining for discriminative learning; 2) They encourage the feature margin only from the ground truth class, without realizing the discriminability from other non-ground truth classes; 3) The feature margin between different classes is set to be same and fixed, which may not adapt the situations very well. To cope with these issues, this paper develops a novel loss function, which adaptively emphasizes the mis-classified feature vectors to guide the discriminative feature learning. Thus we can address all the above issues and achieve more discriminative face features. To the best of our knowledge, this is the first attempt to inherit the advantages of feature margin and feature mining into a unified loss function. Experimental results on several benchmarks have demonstrated the effectiveness of our method over state-of-the-art alternatives. Our code is available at http://www.cbsr.ia.ac.cn/users/xiaobowang/.