DORE: Document Ordered Relation Extraction based on Generative Framework

In recent years, there is a surge of generation-based information extraction work, which allows a more direct use of pre-trained language models and efficiently captures output dependencies. However, previous generative methods using lexical representation do not naturally fit document-level relation extraction (DocRE) where there are multiple entities and relational facts. In this paper, we investigate the root cause of the underwhelming performance of the existing generative DocRE models and discover that the culprit is the inadequacy of the training paradigm, instead of the capacities of the models. We propose to generate a symbolic and ordered sequence from the relation matrix which is deterministic and easier for model to learn. Moreover, we design a parallel row generation method to process overlong target sequences. Besides, we introduce several negative sampling strategies to improve the performance with balanced signals. Experimental results on four datasets show that our proposed method can improve the performance of the generative DocRE models. We have released our code at https://github.com/ayyyq/DORE.Comment: Findings of EMNLP 202

A Systematic Study of Dysregulated MicroRNA in Type 2 Diabetes Mellitus.

MicroRNAs (miRNAs) are small noncoding RNAs that modulate the cellular transcriptome at the post-transcriptional level. miRNA plays important roles in different disease manifestation, including type 2 diabetes mellitus (T2DM). Many studies have characterized the changes of miRNAs in T2DM, a complex systematic disease; however, few studies have integrated these findings and explored the functional effects of the dysregulated miRNAs identified. To investigate the involvement of miRNAs in T2DM, we obtained and analyzed all relevant studies published prior to 18 October 2016 from various literature databases. From 59 independent studies that met the inclusion criteria, we identified 158 dysregulated miRNAs in seven different major sample types. To understand the functional impact of these deregulated miRNAs, we performed targets prediction and pathway enrichment analysis. Results from our analysis suggested that the altered miRNAs are involved in the core processes associated with T2DM, such as carbohydrate and lipid metabolisms, insulin signaling pathway and the adipocytokine signaling pathway. This systematic survey of dysregulated miRNAs provides molecular insights on the effect of deregulated miRNAs in different tissues during the development of diabetes. Some of these miRNAs and their mRNA targets may have diagnostic and/or therapeutic utilities in T2DM

Seasonal variation and nutrient jointly drive the community structure of macrophytes in lakes with different trophic states

IntroductionMacrophytes are essential for maintaining the health of shallow lake ecosystems, however, the driving and responsive relationship between ecological factors (such as seasonal changes and nutrition, etc.) and plant communities is not yet clear.MethodsIn this study, we conducted seasonal surveys of macrophyte community composition in lakes with different nutrient states, aiming to understand the incidence relation between macrophyte community diversity, seasonal changes and environmental factors.ResultsAccording to the classification criteria of comprehensive nutritional index, there were significant differences in the trophic status of the three lakes. Among them, the Xihu Lake has reached mild eutrophication with a TLI value of 56.33, both Cibi Lake and Haixihai Lake are mesotrophic with TLI value of 36.03 and 33.48, respectively. The results of diversity analysis showed a significant negative correlation between α-diversity (include Species richness, Shannon-Wiener index, Simpson index and Pielou index) and lake nutrient status. Among them, Xihu Lake showed the lowest α-diversity in all seasons, Haixihai Lake exhibited the middle α-diversity, Cibi Lake indicated the highest α-diversity. Non-metric multidimensional ordination showed that there were obvious spatial structures differences among the macrophyte communities in the three lakes. Macrophyte community composition in the three lakes was more similar in summer and autumn, but there was a wider gap in spring and winter. The redundancy analysis indicated distinct differences between diversity index and ecological factors, the eigenvalues of Axis 1 and Axis 2 being, respectively, 36.13% and 8.15%. Environmental factors could explain 44.8% of the total variation in macrophyte communities structure. Among these, nitrogen, phosphorus, water transparency and water temperature contributed 50.2%, 3.5%, 3.8% and 27.5%, respectively.ConclusionsIn summary, the community structure of macrophytes in plateau shallow lakes is co-regulated by seasons and nutrients

The elicitor VP2 from Verticillium dahliae triggers defence response in cotton

Summary: Verticillium dahliae is a widespread and destructive soilborne vascular pathogenic fungus that causes serious diseases in dicot plants. Here, comparative transcriptome analysis showed that the number of genes upregulated in defoliating pathotype V991 was significantly higher than in the non‐defoliating pathotype 1cd3‐2 during the early response of cotton. Combined with analysis of the secretome during the V991–cotton interaction, an elicitor VP2 was identified, which was highly upregulated at the early stage of V991 invasion, but was barely expressed during the 1cd3‐2‐cotton interaction. Full‐length VP2 could induce cell death in several plant species, and which was dependent on NbBAK1 but not on NbSOBIR1 in N. benthamiana. Knock‐out of VP2 attenuated the pathogenicity of V991. Furthermore, overexpression of VP2 in cotton enhanced resistance to V. dahliae without causing abnormal plant growth and development. Several genes involved in JA, SA and lignin synthesis were significantly upregulated in VP2‐overexpressing cotton. The contents of JA, SA, and lignin were also significantly higher than in the wild‐type control. In summary, the identified elicitor VP2, recognized by the receptor in the plant membrane, triggers the cotton immune response and enhances disease resistance

CoLLiE: Collaborative Training of Large Language Models in an Efficient Way

Large language models (LLMs) are increasingly pivotal in a wide range of natural language processing tasks. Access to pre-trained models, courtesy of the open-source community, has made it possible to adapt these models to specific applications for enhanced performance. However, the substantial resources required for training these models necessitate efficient solutions. This paper introduces CoLLiE, an efficient library that facilitates collaborative training of large language models using 3D parallelism, parameter-efficient fine-tuning (PEFT) methods, and optimizers such as Lion, Adan, Sophia, LOMO and AdaLomo. With its modular design and comprehensive functionality, CoLLiE offers a balanced blend of efficiency, ease of use, and customization. CoLLiE has proven superior training efficiency in comparison with prevalent solutions in pre-training and fine-tuning scenarios. Furthermore, we provide an empirical evaluation of the correlation between model size and GPU memory consumption under different optimization methods, as well as an analysis of the throughput. Lastly, we carry out a comprehensive comparison of various optimizers and PEFT methods within the instruction-tuning context. CoLLiE is available at https://github.com/OpenLMLab/collie.Comment: To appear at EMNLP 2023 Demo; Code is available at https://github.com/OpenLMLab/colli

Polyethyleneimine-coated MXene quantum dots improve cotton tolerance to Verticillium dahliae by maintaining ROS homeostasis

Verticillium dahliae is a soil-borne hemibiotrophic fungal pathogen that threatens cotton production worldwide. In this study, we assemble the genomes of two V. dahliae isolates: the more virulence and defoliating isolate V991 and nondefoliating isolate 1cd3-2. Transcriptome and comparative genomics analyses show that genes associated with pathogen virulence are mostly induced at the late stage of infection (Stage II), accompanied by a burst of reactive oxygen species (ROS), with upregulation of more genes involved in defense response in cotton. We identify the V991-specific virulence gene SP3 that is highly expressed during the infection Stage II. V. dahliae SP3 knock-out strain shows attenuated virulence and triggers less ROS production in cotton plants. To control the disease, we employ polyethyleneimine-coated MXene quantum dots (PEI-MQDs) that possess the ability to remove ROS. Cotton seedlings treated with PEI-MQDs are capable of maintaining ROS homeostasis with enhanced peroxidase, catalase, and glutathione peroxidase activities and exhibit improved tolerance to V. dahliae. These results suggest that V. dahliae trigger ROS production to promote infection and scavenging ROS is an effective way to manage this disease. This study reveals a virulence mechanism of V. dahliae and provides a means for V. dahliae resistance that benefits cotton production

Berberine Ameliorates Hepatic Steatosis and Suppresses Liver and Adipose Tissue Inflammation in Mice with Diet-induced Obesity

Increasing evidence demonstrates that berberine (BBR) is beneficial for obesity-associated nonalcoholic fatty liver disease (NAFLD). However, it remains to be elucidated how BBR improves aspects of NAFLD. Here we revealed an AMP-activated protein kinase (AMPK)-independent mechanism for BBR to suppress obesity-associated inflammation and improve hepatic steatosis. In C57BL/6J mice fed a high-fat diet (HFD), treatment with BBR decreased inflammation in both the liver and adipose tissue as indicated by reduction of the phosphorylation state of JNK1 and the mRNA levels of proinflammatory cytokines. BBR treatment also decreased hepatic steatosis, as well as the expression of acetyl-CoA carboxylase and fatty acid synthase. Interestingly, treatment with BBR did not significantly alter the phosphorylation state of AMPK in both the liver and adipose tissue of HFD-fed mice. Consistently, BBR treatment significantly decreased the phosphorylation state of JNK1 in both hepatoma H4IIE cells and mouse primary hepatocytes in both dose-dependent and time-dependent manners, which was independent of AMPK phosphorylation. BBR treatment also caused a decrease in palmitate-induced fat deposition in primary mouse hepatocytes. Taken together, these results suggest that BBR actions on improving aspects of NAFLD are largely attributable to BBR suppression of inflammation, which is independent of AMPK.National Institutes of Health [HL108922, HL095556, R01DK095828, R01DK095862]; National Natural Science Foundation of China [81100562/H0711]; Hatch Program of the National Institutes of Food and Agriculture (NIFA)SCI(E)[email protected]; [email protected]

Metformin Ameliorates Hepatic Steatosis and Inflammation without Altering Adipose Phenotype in Diet-Induced Obesity

Non-alcoholic fatty liver disease (NAFLD) is closely associated with obesity and insulin resistance. To better understand the pathophysiology of obesity-associated NAFLD, the present study examined the involvement of liver and adipose tissues in metformin actions on reducing hepatic steatosis and inflammation during obesity. C57BL/6J mice were fed a high-fat diet (HFD) for 12 weeks to induce obesity-associated NAFLD and treated with metformin (150 mg/kg/d) orally for the last four weeks of HFD feeding. Compared with HFD-fed control mice, metformin-treated mice showed improvement in both glucose tolerance and insulin sensitivity. Also, metformin treatment caused a significant decrease in liver weight, but not adiposity. As indicated by histological changes, metformin treatment decreased hepatic steatosis, but not the size of adipocytes. In addition, metformin treatment caused an increase in the phosphorylation of liver AMP-activated protein kinase (AMPK), which was accompanied by an increase in the phosphorylation of liver acetyl-CoA carboxylase and decreases in the phosphorylation of liver c-Jun N-terminal kinase 1 (JNK1) and in the mRNA levels of lipogenic enzymes and proinflammatory cytokines. However, metformin treatment did not significantly alter adipose tissue AMPK phosphorylation and inflammatory responses. In cultured hepatocytes, metformin treatment increased AMPK phosphorylation and decreased fat deposition and inflammatory responses. Additionally, in bone marrow-derived macrophages, metformin treatment partially blunted the effects of lipopolysaccharide on inducing the phosphorylation of JNK1 and nuclear factor kappa B (NF-κB) p65 and on increasing the mRNA levels of proinflammatory cytokines. Taken together, these results suggest that metformin protects against obesity-associated NAFLD largely through direct effects on decreasing hepatocyte fat deposition and on inhibiting inflammatory responses in both hepatocytes and macrophages

In vivo partial cellular reprogramming enhances liver plasticity and regeneration.

Mammals have limited regenerative capacity, whereas some vertebrates, like fish and salamanders, are able to regenerate their organs efficiently. The regeneration in these species depends on cell dedifferentiation followed by proliferation. We generate a mouse model that enables the inducible expression of the four Yamanaka factors (Oct-3/4, Sox2, Klf4, and c-Myc, or 4F) specifically in hepatocytes. Transient in vivo 4F expression induces partial reprogramming of adult hepatocytes to a progenitor state and concomitantly increases cell proliferation. This is indicated by reduced expression of differentiated hepatic-lineage markers, an increase in markers of proliferation and chromatin modifiers, global changes in DNA accessibility, and an acquisition of liver stem and progenitor cell markers. Functionally, short-term expression of 4F enhances liver regenerative capacity through topoisomerase2-mediated partial reprogramming. Our results reveal that liver-specific 4F expression in vivo induces cellular plasticity and counteracts liver failure, suggesting that partial reprogramming may represent an avenue for enhancing tissue regeneration