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| 1 | Generation and characterization of stable pig pregastrulation epiblast stem cell lines显示文摘Pig epiblast-derived pluripotent stem cells are considered to have great potential and broad prospects for human therapeutic model developme nt and livestock breeding.Despite on going attempts since the 1990s,no stably defined pig epiblast-derived stem cell line has bee n established.Here,guided by in sights from a large-scale sin gle-cell tran scriptome an alysis of pig embryos from embryonic day(E)0 to E14,specifically,the tracing of pluripotency changes during epiblast development,we developed an in vitro culture medium for establishing and maintaining stable pluripotent stem cell lines from pig E10 pregastrulation epiblasts(pgEpiSCs).Enabled by chemical inhibition of WNT-related signaling in combination with growth factors in the FGF/ERK,JAK/STAT3,and Activin/Nodal pathways,pgEpiSCs maintain their pluripotency transcriptome features,similar to those of E10 epiblast cells,and normal karyotypes after more than 240 passages and have the potential to differentiate into three germ layers.Strikingly,ultradeep in situ Hi-C analysis revealed functional impacts of chromatin 3D-spatial associations on the transcriptional regulation of pluripote ncy marker genes in pgEpiSCs.I n practice,we con firmed that pgEpiSCs readily tolerate at least three rounds of successive gene editi ng and gene rated cloned gen e-edited live piglets.Our findings deliver on the long-a nticipated promise of pig pluripote nt stem cells and open new avenues for biological research,animal husbandry,and regenerative biomedicine. | Minglei Zhi Jinying Zhang Qianzi Tang Dawei Yu Shuai Gao Dengfeng Gao Pengliang Liu Jianxiong Guo Tang Hai Jie Gao Suying Cao Zimo Zhao Chongyang Li Xiaogang Weng Mengnan He Tianzhi Chen Yingjie Wang Keren Long Deling Jiao Guanglei Li Jiaman Zhang Yan Liu Yu Lin Daxin Pang Qianqian Zhu Naixin Chen Jingjing Huang Xinze Chen Yixuan Yao Jingcang Yang Zicong Xie Xianya Huang Mengxin Liu Ran Zhang Qiuyan Li Yiliang Miao Jianhui Tian Xingxu Huang Hongsheng Ouyang Bofeng Liu Wei Xie Qi Zhou Zhonghua Liu Caihong Zheng Mingzhou Li Jianyong Han | 2022 | Cell Research2022，32，4： | 3 |
| 2 | Reorganization of 3D genome architecture across wild boar and Bama pig adipose tissues显示文摘Background:A growing body of evidence has revealed that the mammalian genome is organized into hierarchical layers that are closely correlated with and may even be causally linked with variations in gene expression.Recent studies have characterized chromatin organization in various porcine tissues and cell types and compared them among species and during the early development of pigs.However,how chromatin organization differs among pig breeds is poorly understood.Results:In this study,we investigated the 3D genome organization and performed transcriptome characterization of two adipose depots(upper layer of backfat[ULB]and greater omentum[GOM])in wild boars and Bama pigs;the latter is a typical indigenous pig in China.We found that over 95%of the A/B compartments and topologically associating domains(TADs)are stable between wild boars and Bama pigs.In contrast,more than 70%of promoterenhancer interactions(PEIs)are dynamic and widespread,involving over a thousand genes.Alterations in chromatin structure are associated with changes in the expression of genes that are involved in widespread biological functions such as basic cellular functions,endocrine function,energy metabolism and the immune response.Approximately 95%and 97%of the genes associated with reorganized A/B compartments and PEIs in the two pig breeds differed between GOM and ULB,respectively.Conclusions:We reported 3D genome organization in adipose depots from different pig breeds.In a comparison of Bama pigs and wild boar,large-scale compartments and TADs were mostly conserved,while fine-scale PEIs were extensively reorganized.The chromatin architecture in these two pig breeds was reorganized in an adipose depotspecific manner.These results contribute to determining the regulatory mechanism of phenotypic differences between Bama pigs and wild boar. | Jiaman Zhang Pengliang Liu Mengnan He Yujie Wang Hua Kui Long Jin Diyan Li Mingzhou Li | 2022 | Journal of Animal Science and Biotechnology2022，13，4： | 2 |
| 3 | Efficient 3D Hilbert Curve Encoding and Decoding Algorithms显示文摘Hilbert curve describes a one-to-one mapping between multidimensional space and 1 D space.Most traditional 3D Hilbert encoding and decoding algorithms work on order-wise manner and are not aware of the difference between different input data and spend equivalent computing costs on them,thus resulting in a low efficiency.To solve this problem,in this paper we design efficient 3D state views for fast encoding and decoding.Based on the state views designed,a new encoding algorithm(JFK-3HE)and a new decoding algorithm(JFK-3HD)are proposed.JFK-3HE and JFK-3HD can avoid executing iteratively encoding or decoding each order by skipping the first 0 s in input data,thus decreasing the complexity and improving the efficiency.Experimental results show that JFK-3HE and JFK-3HD outperform the state-of-the-arts algorithms for both uniform and skew-distributed data. | JIA Lianyin LIANG Binbin LI Mengjuan LIU Yong CHEN Yinong DING Jiaman | 2022 | Chinese Journal of Electronics2022，31，2： | 1 |
| 4 | Study on Reproductive Growth Characteristics and Seed Germination of Eucalyptus dunnii in Sichuan Province显示文摘Studying the flowering development and seed germination of Eucalyptu dunnii and mastering the reproductive growth law can provide a theoretical basis for seed garden construction. In this study,a blooming plant growing in Zitong County was selected as the experiment subject. The results were as follows: florescence date of Eucalyptus dunnii was Mid-late February to mid to late October. Depending on morphologic change,flowering can be divided into 6 phases: Flower bud differentiation stage,inflorescence formation stage,opercle color change stage,capsule enlargement and shedding ring formation stage,flowering period,seed development stage. The development process of the buds on the same inflorescence was basically the same,the growth of buds near the base of the same branch was faster than that of the top buds,and the development of flower buds in different positions was random. There were 3-4 ovary cavities in a capsule. The number of shriveled seeds was far more than the number of effective seeds,and the average of each capsule contained five normal seeds which could develop into seedlings. | Zhen HUANG Lihua WANG Zhi CHEN Jiaman LI Hongying GUO | 2018 | Agricultural Biotechnology2018，7，3： | 1 |
| 5 | A cell transcriptomic profile p ovides insights into adipocytes of porcine mammary gland across development显示文摘Background Studying the composition and developmental mechanisms in mammary gland is crucial for healthy growth of newborns. The mammary gland is inherently heterogeneous, and its physiological function dependents on the gene expression of multiple cell types. Most studies focused on epithelial cells, disregarding the role of neighboring adipocytes.Results Here, we constructed the largest transcriptomic dataset of porcine mammary gland cells thus far. The dataset captured 126,829 high-quality nuclei from physiological mammary glands across five developmental stages(d 90 of gestation, G90;d 0 after lactation, L0;d 20 after lactation, L20;2 d post natural involution, PI2;7 d post natural involution, PI7). Seven cell types were identified, including epithelial cells, adipocytes, endothelial cells, fibroblasts cells, immune cells, myoepithelial cells and precursor cells. Our data indicate that mammary glands at different developmental stages have distinct phenotypic and transcriptional signatures. During late gestation(G90), the differentiation and proliferation of adipocytes were inhibited. Meanwhile, partly epithelial cells were completely differentiated. Pseudo-time analysis showed that epithelial cells undergo three stages to achieve lactation, including cellular differentiation, hormone sensing, and metabolic activation. During lactation(L0 and L20), adipocytes area accounts for less than 0.5% of mammary glands. To maintain their own survival, the adipocyte exhibited a poorly differentiated state and a proliferative capacity. Epithelial cells initiate lactation upon hormonal stimulation. After fulfilling lactation mission, their undergo physiological death under high intensity lactation. Interestingly, the physiological dead cells seem to be actively cleared by immune cells via CCL21-ACKR4 pathway. This biological process may be an important mechanism for maintaining homeostasis of the mammary gland. During natural involution(PI2 and PI7), epithelial cell populations dedifferentiate into mesenchymal stem cells to maintain the lactation potential of mammary glands for the next lactation cycle.Conclusion The molecular mechanisms of dedifferentiation, proliferation and redifferentiation of adipocytes and epithelial cells were revealed from late pregnancy to natural involution. This cell transcriptomic profile constitutes an essential reference for future studies in the development and remodeling of the mammary gland at different stages. | Yongliang Fan Long Jin Zhiping He Tiantian Wei Tingting Luo Jiaman Zhang Can Liu Changjiu Dai Chao A Yan Liang Xuan Tao Xuebin Lv Yiren Gu Mingzhou Li | 2024 | Journal of Animal Science and Biotechnology2024，15，1： | 0 |
| 6 | TWE‐WSD: An effective topical word embedding based word sense disambiguation显示文摘Word embedding has been widely used in word sense disambiguation(WSD)and many other tasks in recent years for it can well represent the semantics of words.However,the existing word embedding methods mostly represent each word as a single vector,without considering the homonymy and polysemy of the word;thus,their performances are limited.In order to address this problem,an effective topical word embedding(TWE)‐based WSD method,named TWE‐WSD,is proposed,which integrates Latent Dirichlet Allocation(LDA)and word embedding.Instead of generating a single word vector(WV)for each word,TWE‐WSD generates a topical WV for each word under each topic.Effective integrating strategies are designed to obtain high quality contextual vectors.Extensive experiments on SemEval‐2013 and SemEval‐2015 for English all‐words tasks showed that TWE‐WSD outperforms other state‐of‐the‐art WSD methods,especially on nouns. | Lianyin Jia Jilin Tang Mengjuan Li Jinguo You Jiaman Ding Yinong Chen | 2021 | CAAI Transactions on Intelligence Technology2021，6，1： | 0 |
| 7 | GPU Based Hash Segmentation Index for Fast T-overlap Query显示文摘T-overlap query is the basis of set similarity query and has been applied in many important fields.Most existing approaches employ a pruning-and-verification framework,thus in low efficiency.Modern GPU has much higher parallelism as well as memory bandwidth than CPU and can be used to accelerate T-overlap query.In this paper,we use hash segmentation to divide inverted lists into segments,then design an efficient inverted index called GHSII on GPU using hash segmentation.Based on GHSII,a new segmentation parallel T-overlap algorithm,GSPS,is proposed.GSPS uses segment at a time to scan segments and uses shared memory to decrease the number of accesses to device memory.Furthermore,an optimized algorithm called GSPS-TLLO using a heuristic query order is proposed to solve the problem of load imbalance.Experiments are carried out on two real datasets and the results show that GSPS-TLLO outperforms the state-of-the-art GPU parallel T-overlap algorithms. | Lianyin Jia Yongbin Zhang Mengjuan Li Jiaman Ding Jinguo You | 2017 | 国际计算机前沿大会会议论文集2017，，1： | 0 |
| 8 | How do green product exports affect carbon emissions?Evidence from China显示文摘Green development has become an increasingly important global initiative.Therefore,this study focuses on the impact of green product exports on carbon emissions in China.Firm-level datasets are used to estimate provincial green product exports between 2001-2016.This study estimates the impact of green exports on carbon emissions using the system generalized method of moments methodology.In addition,heterogeneity and asymmetry of the nexus are explored.The following findings are highlighted:(1)China’s green product exports show a significant upward trend during the study period;(2)increased green product exports,especially those of high-technology manufacturers,can effectively mitigate CO_(2) emissions;(3)the influence of green product exports on carbon emissions is regional heterogeneous but consistent across quantiles;and(4)technique and scale effects are significant mediators,whereas the composition effect is not.These findings provide new evidence supporting methods to mitigate China’s CO_(2) emissions by adjusting green product export structures. | Kangyin Dong Jiaman Li Xiucheng Dong | 2023 | Chinese Journal of Population,Resources and Environment2023，21，2： | 0 |
| 9 | Dual Effects of Interfacial Interaction and Geometric Constraints on Structural Formation of Poly(butylene terephthalate)Nanorods显示文摘When the size of the material is smaller than the size of the molecular chain,new nanostructures can be formed by crystallizing polymers in nanoporous alumina.However,the effect of pore wall and geometric constraints on polymer nanostructures remains unclear.In this study,we demonstrate three new restricted nanostructures{upright-,flat-and tilting-ring}in polybutylene terephthalate(PBT)nanorods prepared from nanoporous alumina.The dual effects of geometrical constraints and interfacial interactions on the formation of PBT nanostructures were investigated for the first time by using X-ray diffraction and Cerius^(2) modeling packages.Under weak constraints,the interaction between pore wall and the PBT rings is dominant and the ring plane tends to be parallel to the pore wall and radiate outward to grow the upright-ring crystals.Surprisingly,in strong 2D confinement,a structural formation reversal occurs and geometrical constraints overpower the effect of pore wall.Rings tend to pile up vertically or obliquely along the long axis of the rod,so the flat-and tilting-ring crystals are predominate in the constrained system.In principle,our study of the nanostructure formation based on the geometrical constraints and the pore wall interfacial effects could provide a new route to manipulate the chain assembly at the nanoscale,further improving the performance of polymer nanomaterial. | Kaichao Wang Ziwei Lai Jiaman Huang Haiying Li Ziying Liang Junhao Liang Xing Ouyang Xiaoguang Li Yan Cao | 2022 | Chinese Journal of Polymer Science2022，40，6： | 0 |
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