Research on the structure function recognition of PLOS

PurposeThe present study explores and investigates the efficiency of deep learning models in identifying discourse structure and functional features and explores the potential application of natural language processing (NLP) techniques in text mining, information measurement, and scientific communication.MethodThe PLOS literature series has been utilized to obtain full-text data, and four deep learning models, including BERT, RoBERTa, SciBERT, and SsciBERT, have been employed for structure-function recognition.ResultThe experimental findings reveal that the SciBERT model performs outstandingly, surpassing the other models, with an F1 score. Additionally, the performance of different paragraph structures has been analyzed, and it has been found that the model performs well in paragraphs such as method and result.ConclusionThe study's outcomes suggest that deep learning models can recognize the structure and functional elements at the discourse level, particularly for scientific literature, where the SciBERT model performs remarkably. Moreover, the NLP techniques have extensive prospects in various fields, including text mining, information measurement, and scientific communication. By automatically parsing and identifying structural and functional information in text, the efficiency of literature management and retrieval can be improved, thereby expediting scientific research progress. Therefore, deep learning and NLP technologies hold significant value in scientific research

GujiBERT and GujiGPT: Construction of Intelligent Information Processing Foundation Language Models for Ancient Texts

In the context of the rapid development of large language models, we have meticulously trained and introduced the GujiBERT and GujiGPT language models, which are foundational models specifically designed for intelligent information processing of ancient texts. These models have been trained on an extensive dataset that encompasses both simplified and traditional Chinese characters, allowing them to effectively handle various natural language processing tasks related to ancient books, including but not limited to automatic sentence segmentation, punctuation, word segmentation, part-of-speech tagging, entity recognition, and automatic translation. Notably, these models have exhibited exceptional performance across a range of validation tasks using publicly available datasets. Our research findings highlight the efficacy of employing self-supervised methods to further train the models using classical text corpora, thus enhancing their capability to tackle downstream tasks. Moreover, it is worth emphasizing that the choice of font, the scale of the corpus, and the initial model selection all exert significant influence over the ultimate experimental outcomes. To cater to the diverse text processing preferences of researchers in digital humanities and linguistics, we have developed three distinct categories comprising a total of nine model variations. We believe that by sharing these foundational language models specialized in the domain of ancient texts, we can facilitate the intelligent processing and scholarly exploration of ancient literary works and, consequently, contribute to the global dissemination of China's rich and esteemed traditional culture in this new era.Comment: 22pages,0 figur

An in vitro vesicle formation assay reveals cargo clients and factors that mediate vesicular trafficking

The fidelity of protein transport in the secretory pathway relies on the accurate sorting of proteins to their correct destinations. To deepen our understanding of the underlying molecular mechanisms, it is important to develop a robust approach to systematically reveal cargo proteins that depend on specific sorting machinery to be enriched into transport vesicles. Here, we used an in vitro assay that reconstitutes packaging of human cargo proteins into vesicles to quantify cargo capture. Quantitative mass spectrometry (MS) analyses of the isolated vesicles revealed cytosolic proteins that are associated with vesicle membranes in a GTP-dependent manner. We found that two of them, FAM84B (also known as LRAT domain containing 2 or LRATD2) and PRRC1, contain proline-rich domains and regulate anterograde trafficking. Further analyses revealed that PRRC1 is recruited to endoplasmic reticulum (ER) exit sites, interacts with the inner COPII coat, and its absence increases membrane association of COPII. In addition, we uncovered cargo proteins that depend on GTP hydrolysis to be captured into vesicles. Comparing control cells with cells depleted of the cargo receptors, SURF4 or ERGIC53, we revealed specific clients of each of these two export adaptors. Our results indicate that the vesicle formation assay in combination with quantitative MS analysis is a robust and powerful tool to uncover novel factors that mediate vesicular trafficking and to uncover cargo clients of specific cellular factors.</p

Coexistence of Histologically Confirmed Hashimoto's Thyroiditis with Different Stages of Papillary Thyroid Carcinoma in a Consecutive Chinese Cohort

Purpose. To determine the relationship between Hashimoto's thyroiditis (HT) and all stages of papillary thyroid carcinoma (PTC) with or without local lymph node metastasis (LNM). Methods:. We conducted a retrospective study of thyroidectomies from 2008–2013 in First Affiliated Hospital of Nanjing Medical University. We categorized patients according to the presence of histopathologically proven HT. The prevalence of mPTC (maximum diameter ≤ 10 mm) and crPTC (clinical relevant PTC) and local LNM rates were compared. Results:. We evaluated 6,432 consecutive thyroidectomies. In total, 1,328 specimens were confirmed as HT. The prevalence of PTC in this HT cohort was 43.8%, significantly higher than non-HT group. After adjustment of gender and age, the prevalence of PTC was still higher in HT group. HT was a risk factor for PTC in multivariate analysis with odds ratio 2.725 (95% CI, 2.390–3.109) (P < 0.001). However, no correlation was found between HT and LNM of PTC. Conclusion:. HT was associated with an increased prevalence of all stages of PTC, independent of tumor size, gender, and age. In contrast, locally advanced disease defined by LNM was unrelated to HT. These data suggest an association of HT with low risk PTC and a potential protective immunologic effect from further disease progression

ROS-scavenging hydrogel as protective carrier to regulate stem cells activity and promote osteointegration of 3D printed porous titanium prosthesis in osteoporosis

Stem cell-based therapy has drawn attention as an alternative option for promoting prosthetic osteointegration in osteoporosis by virtue of its unique characteristics. However, estrogen deficiency is the main mechanism of postmenopausal osteoporosis. Estrogen, as an effective antioxidant, deficienncy also results in the accumulation of reactive oxygen species (ROS) in the body, affecting the osteogenic differentiation of stem cells and the bone formation i osteoporosis. In this study, we prepared a ROS-scavenging hydrogel by crosslinking of epigallocatechin-3-gallate (EGCG), 3-acrylamido phenylboronic acid (APBA) and acrylamide. The engineered hydrogel can scavenge ROS efficiently, enabling it to be a cell carrier of bone marrow-derived mesenchymal stem cells (BMSCs) to protect delivered cells from ROS-mediated death and osteogenesis inhibition, favorably enhancing the tissue repair potential of stem cells. Further in vivo investigations seriously demonstrated that this ROS-scavenging hydrogel encapsulated with BMSCs can prominently promote osteointegration of 3D printed microporous titanium alloy prosthesis in osteoporosis, including scavenging accumulated ROS, inducing macrophages to polarize toward M2 phenotype, suppressing inflammatory cytokines expression, and improving osteogenesis related markers (e.g., ALP, Runx-2, COL-1, BSP, OCN, and OPN). This work provides a novel strategy for conquering the challenge of transplanted stem cells cannot fully function in the impaired microenvironment, and enhancing prosthetic osteointegration in osteoporosis

LUBAC assembles a ubiquitin signaling platform at mitochondria for signal amplification and transport of NF-κB to the nucleus

Mitochondria are increasingly recognized as cellular hubs to orchestrate signaling pathways that regulate metabolism, redox homeostasis, and cell fate decisions. Recent research revealed a role of mitochondria also in innate immune signaling; however, the mechanisms of how mitochondria affect signal transduction are poorly understood. Here, we show that the NF-κB pathway activated by TNF employs mitochondria as a platform for signal amplification and shuttling of activated NF-κB to the nucleus. TNF treatment induces the recruitment of HOIP, the catalytic component of the linear ubiquitin chain assembly complex (LUBAC), and its substrate NEMO to the outer mitochondrial membrane, where M1- and K63-linked ubiquitin chains are generated. NF-κB is locally activated and transported to the nucleus by mitochondria, leading to an increase in mitochondria-nucleus contact sites in a HOIP-dependent manner. Notably, TNF-induced stabilization of the mitochondrial kinase PINK1 furthermore contributes to signal amplification by antagonizing the M1-ubiquitin-specific deubiquitinase OTULIN. Overall, our study reveals a role for mitochondria in amplifying TNF-mediated NF-κB activation, both serving as a signaling platform, as well as a transport mode for activated NF-κB to the nuclear

Systematic Synthesis of Polyimide@inorganics Core-shell Microspheres via Ion-exchange and Interfacial Reaction

Uniform and stable core-shell microspheres composed of a polyimide (PI) core and thin metal/oxide/sulphide shells were prepared by an interfacial reaction of metal-ion-doped polymeric cores in reduction or in the air or sodium sulphide solutions, respectively. The silver shells on polyimide microspheres were prepared by the introduction of silver ions into ion-exchangeable surface-modified polyimide, and subsequently an in situ reduction of the silver ions in solution. Oxides shells such as SnO2, Co3O4, NiO, CuO or ZnO were prepared by thermally treating the ion-doped microspheres in air, while amorphous sulphides shells such as CuS, ZnS, CoS or Ag2S were prepared by an interfacial reaction of metal-ion-doped microspheres in its corresponding sodium sulphide solutions. The adhesion properties between the copper sulphide and PI substrates are demonstrated superior. This simple strategy is promising in the fabrication of a whole range of inorganic shells on polyimide microspheres, which may offer tailor-designed multi-functionalities based on the distinctive species of these inorganic shells

Double-edged sword: China’s free trade agreements reinforces embodied greenhouse gas transfers in agricultural products

Abstract China, as the world’s largest importer, heavily relies on agricultural products. However, the impact of China’s free trade agreements (FTAs) on greenhouse gas (GHG) emissions embodied in agricultural product imports has been overlooked. It’s crucial to analyze changes in embodied GHG emissions resulting from FTAs. We categorize 367 agricultural products into 15 categories and construct a dataset on the embodied GHG emissions of these products imported by China from 119 countries between 2000 and 2015. Using the Propensity Score Matching (PSM)-progressive difference-in-differences (DID) method, our findings indicate that China’s FTAs have double-edged impact on agricultural product imports. It has positively influenced imports, with a 12.22% annual growth rate, promoting economic integration. However, it has negatively affected GHG emissions, leading to a 53.00% increase in emissions from agricultural imports. These findings highlight the importance of addressing production and consumption in reducing GHG strategies with agricultural products

The Role of CXC Chemokines in Cancer Progression

CXC chemokines are small chemotactic and secreted cytokines. Studies have shown that CXC chemokines are dysregulated in multiple types of cancer and are closely correlated with tumor progression. The CXC chemokine family has a dual function in tumor development, either tumor-promoting or tumor-suppressive depending on the context of cellular signaling. Recent evidence highlights the pro-tumorigenic properties of CXC chemokines in most human cancers. CXC chemokines were found to play pivotal roles in promoting angiogenesis, stimulating inflammatory responses, and facilitating tumor metastases. Enhanced expression of CXC chemokines is always signatured with inferior survival and prognosis. The levels of CXC chemokines in cancer patients are in dynamic change according to the tumor contexts (e.g., chemotherapy resistance and tumor recurrence after surgery). Thus, CXC chemokines have great potential to be used as diagnostic and prognostic biomarkers and therapeutic targets. Currently, the molecular mechanisms underlying the effect of CXC chemokines on tumor inflammation and metastasis remain unclear and application of antagonists and neutralizing antibodies of CXC chemokines signaling for cancer therapy is still not fully established. This article will review the roles of CXC chemokines in promoting tumorigenesis and progression and address the future research directions of CXC chemokines for cancer treatment