Homologous haplotypes, expression, genetic effects and geographic distribution of the wheat yield gene TaGW2

BACKGROUND: TaGW2-6A, cloned in earlier research, strongly influences wheat grain width and TKW. Here, we mainly analyzed haplotypes of TaGW2-6B and their effects on TKW and interaction with haplotypes at TaGW2-6A. RESULTS: About 2.9 kb of the promoter sequences of TaGW2-6B and TaGW2-6D were cloned in 34 bread wheat cultivars. Eleven SNPs were detected in the promoter region of TaGW2-6B, forming 4 haplotypes, but no divergence was detected in the TaGW2-6D promoter or coding region. Three molecular markers including CAPS, dCAPS and ACAS, were developed to distinguish the TaGW2-6B haplotypes. Haplotype association analysis indicated that TaGW2-6B has a stronger influence than TaGW2-6A on TKW, and Hap-6B-1 was a favored haplotype increasing grain width and weight that had undergone strong positive selection in global wheat breeding. However, clear geographic distribution differences for TaGW2-6A haplotypes were found; Hap-6A-A was favored in Chinese, Australian and Russian cultivars, whereas Hap-6A-G was preferred in European, American and CIMMYT cultivars. This difference might be caused by a flowering and maturity time difference between the two haplotypes. Hap-6A-A is the earlier type. Haplotype interaction analysis between TaGW2-6A and TaGW2-6B showed additive effects between the favored haplotypes. Hap-6A-A/Hap-6B-1 was the best combination to increase TKW. Relative expression analysis of the three TaGW2 homoeologous genes in 22 cultivars revealed that TaGW2-6A underwent the highest expression. TaGW2-6D was the least expressed during grain development and TaGW2-6B was intermediate. Diversity of the three genes was negatively correlated with their effect on TKW. CONCLUSIONS: Genetic effects, expression patterns and historic changes of haplotypes at three homoeologous genes of TaGW2 influencing yield were dissected in wheat cultivars. Strong and constant selection to favored haplotypes has been found in global wheat breeding during the past century. This research also provides a valuable case for understanding interaction of genes that control complex traits in polyploid species

Iteratively Coupled Multiple Instance Learning from Instance to Bag Classifier for Whole Slide Image Classification

Whole Slide Image (WSI) classification remains a challenge due to their extremely high resolution and the absence of fine-grained labels. Presently, WSIs are usually classified as a Multiple Instance Learning (MIL) problem when only slide-level labels are available. MIL methods involve a patch embedding process and a bag-level classification process, but they are prohibitively expensive to be trained end-to-end. Therefore, existing methods usually train them separately, or directly skip the training of the embedder. Such schemes hinder the patch embedder's access to slide-level labels, resulting in inconsistencies within the entire MIL pipeline. To overcome this issue, we propose a novel framework called Iteratively Coupled MIL (ICMIL), which bridges the loss back-propagation process from the bag-level classifier to the patch embedder. In ICMIL, we use category information in the bag-level classifier to guide the patch-level fine-tuning of the patch feature extractor. The refined embedder then generates better instance representations for achieving a more accurate bag-level classifier. By coupling the patch embedder and bag classifier at a low cost, our proposed framework enables information exchange between the two processes, benefiting the entire MIL classification model. We tested our framework on two datasets using three different backbones, and our experimental results demonstrate consistent performance improvements over state-of-the-art MIL methods. Code will be made available upon acceptance

Hairy root transgene expression analysis of a secretory peroxidase (PvPOX1) from common bean infected by Fusarium wilt

Plant peroxidases (POXs) are one of the most important redox enzymes in the defense responses. However, the large number of different plant POX genes makes it necessary to carefully confirm the function of each paralogous POX gene in specific tissues and disease interactions. Fusarium wilt is a devastating disease of common bean caused by Fusarium oxysporum f. sp. phaseoli. In this study, we evaluated a peroxidase gene, PvPOX1, from a resistant common bean genotype, CAAS260205 and provided direct evidence for PvPOX1’s role in resistance by transforming the resistant allele into a susceptible common bean genotype, BRB130, via hairy root transformation using Agrobacterium rhizogenes. Analysis of PvPOX1 gene over-expressing hairy roots showed it increased resistance to Fusarium wilt both in the roots and the rest of transgenic plants. Meanwhile, the PvPOX1 expressive level, the peroxidase activity and hydrogen peroxide (H2O2) accumulation were also enhanced in the interaction. The result showed that the PvPOX1 gene played an essential role in Fusarium wilt resistance through the occurrence of reactive oxygen species (ROS) induced hypersensitive response. Therefore, PvPOX1 expression was proven to be a valuable gene for further analysis which can strengthen host defense response against Fusarium wilt through a ROS activated resistance mechanism

«Conselho de amigo, aviso do céu»: contributos para a análise semântico-pragmática dos atos ilocutórios de conselho e de aviso em confronto com o de ameaça

Com base em exemplos de um corpus oral de Português Europeu, o presente texto discute a organização e funcionamento do ato ilocutório de conselho e de aviso, destacando as semelhanças e diferenças entre eles e os atos de discursos como ameaças e promessas, avisos hipotéticos e ameaças condicionais. Depois da análise das noções do “querer dizer NN” de Grice e de “uptake” de Austin, destacamos a importância da relação entre intenção e convenção na análise dos atos ilocutórios de Searle com o levantamento das regras que determinam os indicadores de força ilocutória. A interpretação dos valores ilocutórios na sequencialidade das intervenções destaca a relação entre práticas discursivas e figuração.info:eu-repo/semantics/publishedVersio

Super-Resolution Based Patch-Free 3D Image Segmentation with High-Frequency Guidance

High resolution (HR) 3D images are widely used nowadays, such as medical images like Magnetic Resonance Imaging (MRI) and Computed Tomography (CT). However, segmentation of these 3D images remains a challenge due to their high spatial resolution and dimensionality in contrast to currently limited GPU memory. Therefore, most existing 3D image segmentation methods use patch-based models, which have low inference efficiency and ignore global contextual information. To address these problems, we propose a super-resolution (SR) based patch-free 3D image segmentation framework that can realize HR segmentation from a global-wise low-resolution (LR) input. The framework contains two sub-tasks, of which semantic segmentation is the main task and super resolution is an auxiliary task aiding in rebuilding the high frequency information from the LR input. To furthermore balance the information loss with the LR input, we propose a High-Frequency Guidance Module (HGM), and design an efficient selective cropping algorithm to crop an HR patch from the original image as restoration guidance for it. In addition, we also propose a Task-Fusion Module (TFM) to exploit the inter connections between segmentation and SR task, realizing joint optimization of the two tasks. When predicting, only the main segmentation task is needed, while other modules can be removed for acceleration. The experimental results on two different datasets show that our framework has a four times higher inference speed compared to traditional patch-based methods, while its performance also surpasses other patch-based and patch-free models.Comment: Version #2 uploaded in Jul 10, 202

HAP: Structure-Aware Masked Image Modeling for Human-Centric Perception

Model pre-training is essential in human-centric perception. In this paper, we first introduce masked image modeling (MIM) as a pre-training approach for this task. Upon revisiting the MIM training strategy, we reveal that human structure priors offer significant potential. Motivated by this insight, we further incorporate an intuitive human structure prior - human parts - into pre-training. Specifically, we employ this prior to guide the mask sampling process. Image patches, corresponding to human part regions, have high priority to be masked out. This encourages the model to concentrate more on body structure information during pre-training, yielding substantial benefits across a range of human-centric perception tasks. To further capture human characteristics, we propose a structure-invariant alignment loss that enforces different masked views, guided by the human part prior, to be closely aligned for the same image. We term the entire method as HAP. HAP simply uses a plain ViT as the encoder yet establishes new state-of-the-art performance on 11 human-centric benchmarks, and on-par result on one dataset. For example, HAP achieves 78.1% mAP on MSMT17 for person re-identification, 86.54% mA on PA-100K for pedestrian attribute recognition, 78.2% AP on MS COCO for 2D pose estimation, and 56.0 PA-MPJPE on 3DPW for 3D pose and shape estimation.Comment: Accepted by NeurIPS 202

The transcriptional coactivator TAZ regulates reciprocal differentiation of T(h)17 cells and T(reg) cells

自身免疫性疾病是一类机体对自身抗原发生免疫反应而导致自身多器官、组织受累的慢性炎症性疾病。目前大量研究表明机体内促炎症的TH17细胞和抑制炎症Treg细胞在类群数量和活化状态的失衡是造成自身免疫疾病的主要致病因素。陈兰芬教授和周大旺教授团队的前期研究发现小鼠中Hippo信号通路中激酶Mst1/2缺失导致免疫缺陷，机体易受病原体感染并伴随着严重自身免疫疾病。该研究揭示了Hippo 信号通路转录共激活因子TAZ在决定CD4+初始T细胞分化为促进炎症的TH17效应细胞和抑制免疫反应的Treg调节性细胞过程中发挥着关键作用，拓展了当前对于Hippo信号通路的相关研究内容。 陈兰芬，博士，厦门大学生命科学学院教授。【Abstraact】An imbalance in the lineages of immunosuppressive regulatory T cells (Treg cells) and the inflammatory TH17 subset of helper T cells leads to the development of autoimmune and/or inflammatory disease. Here we found that TAZ, a coactivator of TEAD transcription factors of Hippo signaling, was expressed under T H17 cell–inducing conditions and was required for TH17 differentiation and TH17 cell–mediated inflammatory diseases. TAZ was a critical co-activator of the TH17-defining transcription factor RORγt. In addition, TAZ attenuated Treg cell development by decreasing acetylation of the Treg cell master regulator Foxp3 mediated by the histone acetyltransferase Tip60, which targeted Foxp3 for proteasomal degradation. In contrast, under T regcell–skewing conditions, TEAD1 expression and sequestration of TAZ from the transcription factors RORγt and Foxp3 promoted Treg cell differentiation. Furthermore, deficiency in TAZ or overexpression of TEAD1 induced Treg cell differentiation, whereas expression of a transgene encoding TAZ or activation of TAZ directed TH17 cell differentiation. Our results demonstrate a pivotal role for TAZ in regulating the differentiation of Treg cells and TH17 cells.J. Avruch for comments on the manuscript.Supported by the National Basic Research Program (973) of China (2015CB910502 to L.C.), the National Natural Science Foundation of China (81422018 to L.C.; 31625010 and U1505224 to D.Z.; U1405225 and 81372617 to L.C.; J1310027 to D.Z.; 81472229 to L.H.; and 31600698 to J. Geng), the 111 Projects (B12001 and B06016), China's 1000 Young Talents Program (D.Z., and L.C.), the Fundamental Research Funds for the Central Universities of China-Xiamen University (20720160071 to D.Z. and 20720160054 to L.H.) and Major disease research projects of Xiamen (3502Z20149029 to L.C.)

Childhood Sexual Abuse and the Development of Recurrent Major Depression in Chinese Women

Background Our prior study in Han Chinese women has shown that women with a history of childhood sexual abuse (CSA) are at increased risk for developing major depression (MD). Would this relationship be found in our whole data set? Method Three levels of CSA (non-genital, genital, and intercourse) were assessed by self-report in two groups of Han Chinese women: 6017 clinically ascertained with recurrent MD and 5983 matched controls. Diagnostic and other risk factor information was assessed at personal interview. Odds ratios (ORs) were calculated by logistic regression. Results We confirmed earlier results by replicating prior analyses in 3,950 new recurrent MD cases. There were no significant differences between the two data sets. Any form of CSA was significantly associated with recurrent MD (OR 4.06, 95% confidence interval (CI) [3.19–5.24]). This association strengthened with increasing CSA severity: non-genital (OR 2.21, 95% CI 1.58–3.15), genital (OR 5.24, 95% CI 3.52–8.15) and intercourse (OR 10.65, 95% CI 5.56–23.71). Among the depressed women, those with CSA had an earlier age of onset, longer depressive episodes. Recurrent MD patients those with CSA had an increased risk for dysthymia (OR 1.60, 95%CI 1.11–2.27) and phobia (OR 1.41, 95%CI 1.09–1.80). Any form of CSA was significantly associated with suicidal ideation or attempt (OR 1.50, 95% CI 1.20–1.89) and feelings of worthlessness or guilt (OR 1.41, 95% CI 1.02–2.02). Intercourse (OR 3.47, 95%CI 1.66–8.22), use of force and threats (OR 1.95, 95%CI 1.05–3.82) and how strongly the victims were affected at the time (OR 1.39, 95%CI 1.20–1.64) were significantly associated with recurrent MD