Self-distillation framework for document-level relation extraction in low-resource environments.

The objective of document-level relation extraction is to retrieve the relations existing between entities within a document. Currently, deep learning methods have demonstrated superior performance in document-level relation extraction tasks. However, to enhance the model's performance, various methods directly introduce additional modules into the backbone model, which often increases the number of parameters in the overall model. Consequently, deploying these deep models in resource-limited environments presents a challenge. In this article, we introduce a self-distillation framework for document-level relational extraction. We partition the document-level relation extraction model into two distinct modules, namely, the entity embedding representation module and the entity pair embedding representation module. Subsequently, we apply separate distillation techniques to each module to reduce the model's size. In order to evaluate the proposed framework's performance, two benchmark datasets for document-level relation extraction, namely GDA and DocRED are used in this study. The results demonstrate that our model effectively enhances performance and significantly reduces the model's size.

The tolerance of two marine diatoms to diurnal pH fluctuation under dynamic light condition and ocean acidification scenario.

Coastal waters undergo dynamic changes in seawater carbonate chemistry due to natural and anthropogenic factors. Despite this, our current understanding of how coastal phytoplankton respond to fluctuating pH is limited. In the present study, we investigated the physiological responses of two coastal diatoms Thalassiosira pseudonana and Thalassiosira weissflogii to seawater acidification and diurnally fluctuating pH under natural solar irradiance. Seawater acidification did not significantly impact the growth, maximum and effective quantum yield of PSII, and photosynthetic rates of the two species. However, it did increase the maximum relative electron transport rate of T. weissflogii by 11%. Overall, fluctuating pH had neutral or positive effects on both species. It enhanced the light-saturated photosynthetic rate of T. weissflogii by 20% compared to cells grown under seawater acidification condition. Results from the short-term pH exposure experiment revealed that the photosynthetic rates of both species remained unaffected by acute pH changes, indicating their tolerance to varying pH. Nevertheless, it is crucial to consider dynamic pH when predicting changes in primary production in coastal waters, given the interplay of various environmental drivers.

Overexpression of KLHL22 correlates with poor prognosis in patients with triple-negative breast cancer.

Background: Kelch-like family member 22 (KLHL22) is a protein-coding gene that is responsible for several Mendelian diseases and has been reported to promote tumorigenesis and aging. The purpose of this study was to investigate its expression in triple-negative breast cancer (TNBC) and its prognostic significance. Methods: Immunohistochemistry (IHC) was performed to examine the expression levels of KLHL22 in 146 patients with TNBC. The Chi-squared test was used to analyze the correlations between KLHL22 expression level and clinicopathological features, and the Kaplan-Meier survival analysis and Cox multivariate regression model were used to analyze the prognostic significance of KLHL22 in patients with TNBC. Results: The results of immunohistochemical analysis showed that the high expression rate of KLHL22 protein in TNBC was 56.85% (83/146). Further analysis revealed a significantly positive correlation (P<0.05) between KLHL22 expression and primary tumor and regional lymph node status, clinical stage, and relapse. Kaplan-Meier survival analysis revealed that patients with low KLHL22 expression had a longer mean survival time than those with high KLHL22 expression (147.93 vs. 90.1 months; P<0.05). In the multivariate analysis, KLHL22 level, P53 expression, and clinical stage were found to be independent prognostic factors for overall survival (P<0.05), while clinical stage and KLHL22 level were independent prognostic factors for progression-free survival (P<0.05). Conclusions: The present study concludes that KLHL22 may serve as a biomarker for poor prognosis in patients with TNBC.

HnRNPR-mediated UPF3B mRNA splicing drives hepatocellular carcinoma metastasis.

INTRODUCTION: Abnormal alternative splicing (AS) contributes to aggressive intrahepatic invasion and metastatic spread, leading to the high lethality of hepatocellular carcinoma (HCC). OBJECTIVES: This study aims to investigate the functional implications of UPF3B-S (a truncated oncogenic splice variant) in HCC metastasis. METHODS: Basescope assay was performed to analyze the expression of UPF3B-S mRNA in tissues and cells. RNA immunoprecipitation, and in vitro and in vivo models were used to explore the role of UPF3B-S and the underlying mechanisms. RESULTS: We show that splicing factor HnRNPR binds to the pre-mRNA of UPF3B via its RRM2 domain to generate an exon 8 exclusion truncated splice variant UPF3B-S. High expression of UPF3B-S is correlated with tumor metastasis and unfavorable overall survival in patients with HCC. The knockdown of UPF3B-S markedly suppresses the invasive and migratory capacities of HCC cells in vitro and in vivo. Mechanistically, UPF3B-S protein targets the 3'-UTR of CDH1 mRNA to enhance the degradation of CDH1 mRNA, which results in the downregulation of E-cadherin and the activation of epithelial-mesenchymal transition. Overexpression of UPF3B-S enhances the dephosphorylation of LATS1 and the nuclear accumulation of YAP1 to trigger the Hippo signaling pathway. CONCLUSION: Our findings suggest that HnRNPR-induced UPF3B-S promotes HCC invasion and metastasis by exhausting CDH1 mRNA and modulating YAP1-Hippo signaling. UPF3B-S could potentially serve as a promising biomarker for the clinical management of invasive HCC.

Comprehensive analysis of 33 human cancers reveals clinical implications and immunotherapeutic value of the solute carrier family 35 member A2.

Background: Solute carrier family 35 member A2 (SLC35A2), which belongs to the SLC35 solute carrier family of human nucleoside sugar transporters, has shown regulatory roles in various tumors and neoplasms. However, the function of SLC35A2 across human cancers remains to be systematically assessed. Insights into the prediction ability of SLC35A2 in clinical practice and immunotherapy response remains limited. Materials and methods: We obtained the gene expression and protein levels of SLC35A2 in a variety of tumors from Molecular Taxonomy of Breast Cancer International Consortium, The Cancer Genome Atlas, Gene Expression Omnibus, Chinese Glioma Genome Atlas, and Human Protein Atlas databases. The SLC35A2 level was validated by immunohistochemistry. The predictive value for prognosis was evaluated by Kaplan-Meier survival and Cox regression analyses. Correlations between SLC35A2 expression and DNA methylation, genetic alterations, tumor mutation burden (TMB), microsatellite instability (MSI), and tumor microenvironment were performed using Spearman's correlation analysis. The possible downstream pathways of SLC35A2 in different human cancers were explored using gene set variation analysis. The potential role of SLC35A2 in the tumor immune microenvironment was evaluated via EPIC, CIBERSORT, MCP-counter, CIBERSORT-ABS, quanTIseq, TIMER, and xCell algorithms. The difference in the immunotherapeutic response of SLC35A2 under different expression conditions was evaluated by the tumor immune dysfunction and exclusion (TIDE) score as well as four independent immunotherapy cohorts, which includes patients with bladder urothelial carcinoma (BLCA, N = 299), non-small cell lung cancer (NSCLC, N = 72 and N = 36) and skin cutaneous melanoma (SKCM, N = 25). Potential drugs were identified using the CellMiner database and molecular docking. Results: SLC35A2 exhibited abnormally high or low expression in 23 cancers and was significantly associated with the prognosis. In various cancers, SLC35A2 expression and mammalian target of rapamycin complex 1 signaling were positively correlated. Multiple algorithmic immune infiltration analyses suggested an inverse relation between SLC35A2 expression and infiltrating immune cells, which includes CD4+T cells, CD8+T cells, B cells, and natural killer cells (NK) in various tumors. Furthermore, SLC35A2 expression was significantly correlated with pan-cancer immune checkpoints, TMB, MSI, and TIDE genes. SLC35A2 showed significant predictive value for the immunotherapy response of patients with diverse cancers. Two drugs, vismodegib and abiraterone, were identified, and the free binding energy of cytochrome P17 with abiraterone was higher than that of SLC35A2 with abiraterone. Conclusion: Our study revealed that SLC35A2 is upregulated in 20 types of cancer, including lung adenocarcinoma (LUAD), breast invasive carcinoma (BRCA), colon adenocarcinoma (COAD), and lung squamous cell carcinoma (LUSC). The upregulated SLC35A2 in five cancer types indicates a poor prognosis. Furthermore, there was a positive correlation between the overexpression of SLC35A2 and reduced lymphocyte infiltration in 13 cancer types, including BRCA and COAD. Based on data from several clinical trials, patients with LUAD, LUSC, SKCM, and BLCA who exhibited high SLC35A2 expression may experience improved immunotherapy response. Therefore, SLC35A2 could be considered a potential predictive biomarker for the prognosis and immunotherapy efficacy of various tumors. Our study provides a theoretical basis for further investigating its prognostic and therapeutic potentials.

Carrier-free multifunctional nanomedicine for intraperitoneal disseminated ovarian cancer therapy.

BACKGROUND: Ovarian cancer is the most lethal gynecological cancer which is characterized by extensive peritoneal implantation metastasis and malignant ascites. Despite advances in diagnosis and treatment in recent years, the five-year survival rate is only 25-30%. Therefore, developing multifunctional nanomedicine with abilities of promoting apoptosis and inhibiting migration on tumor cells would be a promising strategy to improve the antitumor effect. METHODS AND RESULTS: In this study, we developed a novel ACaT nanomedicine composed of alendronate, calcium ions and cyclin-dependent kinase 7 (CDK7) inhibitor THZ1. With the average size of 164 nm and zeta potential of 12.4 mV, the spherical ACaT nanoparticles were selectively internalized by tumor cells and effectively accumulated in the tumor site. Results of RNA-sequencing and in vitro experiments showed that ACaT promoted tumor cell apoptosis and inhibited tumor cell migration by arresting the cell cycle, increasing ROS and affecting calcium homeostasis. Weekly intraperitoneally administered of ACaT for 8 cycles significantly inhibited the growth of tumor and prolonged the survival of intraperitoneal xenograft mice. CONCLUSION: In summary, this study presents a new self-assembly nanomedicine with favorable tumor targeting, antitumor activity and good biocompatibility, providing a novel therapeutic strategy for advanced ovarian cancer.

METTL16 promotes cell proliferation by up-regulating cyclin D1 expression in gastric cancer.

N6-methyladenosine (m6A) is a well-known modification of RNA. However, as a key m6A methyltransferase, METTL16 has not been thoroughly studied in gastric cancer (GC). Here, the biological role of METTL16 in GC and its underlying mechanism was studied. Immunohistochemistry was used to detect the expression of METTL16 and relationship between METTL16 level and prognosis of GC was analysed. CCK8, colony formation assay, EdU assay and xenograft mouse model were used to study the effect of METTL16. Regulatory mechanism of METTL16 in the progression of GC was studied through flow cytometry analysis, RNA degradation assay, methyltransferase inhibition assay, RT-qPCR and Western blotting. METTL16 was highly expressed in GC cells and tissues and was associated with prognosis. In vitro and in vivo experiments confirmed that METTL16 promoted proliferation of GC cells and tumour growth. Furthermore, down-regulation of METTL16 inhibited proliferation by G1/S blocking. Significantly, we identified cyclin D1 as a downstream effector of METTL16. Knock-down METTL16 decreased the overall level of m6A and the stability of cyclin D1 mRNA in GC cells. Meanwhile, inhibition of methyltransferase activity reduced the level of cyclin D1. METTL16-mediated m6A methylation promotes proliferation of GC cells through enhancing cyclin D1 expression.

Combined effects of seawater acidification and benzo(a)pyrene on the physiological performance of the marine bloom-forming diatom Skeletonema costatum.

The combined effects of polycyclic aromatic hydrocarbons and seawater acidification are poorly understood. Hence, we exposed the bloom-forming diatom Skeletonema costatum to four concentrations (0, 0.1, 1 and 10 µg L-1) of benzo(a)pyrene and two pCO2 levels (400 and 1000 µatm) to investigate its physiological performance. The growth and photosynthesis of S. costatum were tolerant to low and moderate benzo(a)pyrene concentrations regardless of the pCO2 level. However, the highest benzo(a)pyrene concentration had remarkably adverse effects on most parameters, decreasing the growth rate by 69%. Seawater acidification increased the sensitivity to high light stress, as shown by the lower maximum relative electron transport rate and light saturation point at the highest benzo(a)pyrene concentration. Our results suggested that benzo(a)pyrene could be detrimental to diatoms at a habitat-relevant level, and seawater acidification might further decrease its light tolerance, which would have important ramifications for the community structure and primary production in coastal waters.

Which Way to Choose for the Treatment of Metastatic Prostate Cancer: A Case Report and Literature Review.

BACKGROUND: Prostate cancer (PCa) is the second most common cancer among males in the world and the majority of patients will eventually progress to the metastatic phase. How to choose an effective way for the treatment of metastatic PCa, especially in the later stage of the disease is still confusing. Herein we reported the case of a patient diagnosed with metastatic PCa and conducted a literature review on this issue. CASE PRESENTATION: A 57-year-old man with metastatic PCa had been managed by Dr. J.P. since April 2012 when the patient was admitted to the Third Affiliated Hospital of Sun Yat-sen University by aggravating frequent urination and dysuria. The prostate-specific antigen (PSA) concentration was 140 ng/ml, and the diagnosis of PCa was confirmed by prostate biopsy, with Gleason score 4 + 5 = 9. Chest CT and bone scan indicated multiple metastases in the lungs and bones. Triptorelin, bicalutamide, zoledronic acid, and docetaxel were then administered, six cycles later, the metastatic tumors in the lungs disappeared and those in the bones lessened significantly, along with a remarkable reduction in PSA level (< 2 ng/ml). Intermittent androgen deprivation was subsequently conducted until August 2018, when the serum PSA level was found to be 250 ng/ml, again docetaxel 75 mg/m2 was administered immediately but the patient was intolerant this time. Instead, abiraterone was administered until March 2019 because of intolerable gastrointestinal side-effects and increasing PSA level. In October 2019, the patient came to our center, a modified approach of docetaxel (day 1 40 mg/m2 + day 8 35 mg/m2) was administered. Luckily, the PSA level decreased rapidly, the bone pain was greatly relieved, and no obvious side effects occurred. However, four cycles later, docetaxel failed to work anymore, the metastatic tumor in the liver progressed. We proposed several regimens as alternatives, but they were soon denied due to the high prices or unavailability or uncertain effect of the drugs. In addition, the patient's condition deteriorated speedily and can no longer bear any aggressive treatment. Finally, the patient died of multiple organ failure in August 2020. CONCLUSION: The experiences of this case provide valuable evidence and reference for the treatment choices of metastatic PCa, in some circumstances modified and advanced regimens may produce unexpected effects.

LGALS3 Is a Poor Prognostic Factor in Diffusely Infiltrating Gliomas and Is Closely Correlated With CD163+ Tumor-Associated Macrophages.

Background: Glioma, the most common brain tumor, is a heterogeneous group of glia-derived tumors, the majority of which have characteristics of diffuse infiltration and immunosuppression. The LGALS protein family is a large class of sugar-binding proteins. Among them, LGALS3 has been reported to promote tumor development and progression in some cancers. However, the clinical significance and biological functions of LGALS3 in glioma remain virtually unknown. The purpose of our research is to detect LGALS3 expression and its prognostic value in glioma and reveal the relationship between its expression and the clinico/molecular-pathological features of patients and immune cell infiltration. Methods: LGALS3 protein expression was examined by immunohistochemistry. The mRNA expression data of LGALS3 was downloaded and analyzed from TCGA and Rembrandt datasets. The association between LGALS3 and glioma clinically relevant diagnostic/molecular markers (IDH, 1p19q, ATRX, MGMT, and TERT) was examined using the Chi-Squared (χ2) test. The correlation between LGALS3 expression and the infiltration of multiple intra-tumoral immune cell types, including B cells (CD20), T cells (CD4 and CD8), macrophages (CD68), and M2 tumor-associated macrophages (CD163), was evaluated by Spearman correlation analysis. Kaplan-Meier analysis and the Cox regression analysis were applied to evaluate the prognostic value of LGALS3 in glioma. The log-rank test was used to evaluate Kaplan-Meier results for significance. Results: Out of all 304 glioma cases, LGALS3 protein was expressed in 125 glioma cases (41.1%, 125/304), with 69.2% (9/13) in WHO I, 9.8% (8/82) in WHO II, 34.2% (26/76) in WHO III, and 61.7% (82/133) in WHO IV. The expression of LGALS3 was correlated with patient age, WHO grade, PHH3 (mitosis), Ki67 index, IDH, 1p/19q codeletion, and TERT promoter status. LGALS3 was an independent poor prognostic marker in diffusely infiltrating gliomas and was positively correlated with immune cell infiltration, particularly CD163+ tumor-associated macrophages in the TCGA dataset, Rembrandt dataset, and our SYSUCC cohort (R = 0.419, 0.627, and 0.724). Conclusion: LGALS3 was highly expressed in pilocytic astrocytoma, GBM, and IDH wild-type LGG. It served as a poor prognostic marker in diffusely infiltrating gliomas. Based on its prognostic significance and strong correlation with CD163+ TAMs, it may act as an important therapeutic target for human glioma.

The use of differential receptors to pattern peptide phosphorylation.

An array sensing scheme for the differentiation of small peptides and their phosphorylated analogues is introduced. The technique involves a series of receptors created by appending random peptides to a C(3v) symmetric scaffold that binds phosphomonoesters. Five specific peptide sequences were selected through a screening technique. In addition to cross reactivity being created by the peptides in the receptors, three metal ions and three pH indicators are used to create a suite of 45 indicator displacement assays. The colorimetric data from the 45 sensing ensembles is collected in a 96-well plate reader, and linear discriminant analysis gives patterns resulting in 100% classification of the peptides. The approach demonstrates a generalizable principle to create pattern-based recognition protocols for complex analytes.

Using an indicator displacement assay to monitor glucose oxidase activity in blood serum.

[diagram: see text] Using a boronic acid receptor that was previously found to have high affinity for gluconic acid, we created a colorimetric indicator displacement assay (IDA) that can report the concentration of the product of glucose oxidase (GOx) catalyzed glucose oxidation. The color change obtained directly reflects the concentration of glucose. Our sensing ensemble was then successfully applied to determine the glucose concentration in human serum, which offers a facile, colorimetric, sensitive, and accurate glucose test.

A colorimetric boronic acid based sensing ensemble for carboxy and phospho sugars.

[structure: see text] A cadmium-centered tris-boronic acid receptor was synthesized, and its binding properties toward various anionic sugars were determined. This receptor shows high affinity for different anionic sugars, especially gluconic acid, which has an association constant near approximately 10(7) M(-)(1) at neutral pH. Further, using an indicator displacement assay, a color change of pyrocatechol violet was observed upon addition of anionic sugars. This colorimetric test was used as a facile screening technique to qualitatively analyze guest affinities.