Biomedical Entity Recognition by Detection and Matching

Biomedical named entity recognition (BNER) serves as the foundation for numerous biomedical text mining tasks. Unlike general NER, BNER require a comprehensive grasp of the domain, and incorporating external knowledge beyond training data poses a significant challenge. In this study, we propose a novel BNER framework called DMNER. By leveraging existing entity representation models SAPBERT, we tackle BNER as a two-step process: entity boundary detection and biomedical entity matching. DMNER exhibits applicability across multiple NER scenarios: 1) In supervised NER, we observe that DMNER effectively rectifies the output of baseline NER models, thereby further enhancing performance. 2) In distantly supervised NER, combining MRC and AutoNER as span boundary detectors enables DMNER to achieve satisfactory results. 3) For training NER by merging multiple datasets, we adopt a framework similar to DS-NER but additionally leverage ChatGPT to obtain high-quality phrases in the training. Through extensive experiments conducted on 10 benchmark datasets, we demonstrate the versatility and effectiveness of DMNER.Comment: 9 pages content, 2 pages appendi

Phen2Disease

Phen2Disease: A Phenotype-driven Semantic Similarity-based Integrated Model for Disease and Gene Prioritization </p

Research progress of improving subclinical atherosclerosis with exercise

Atherosclerosis is the main cause of cardiovascular diseases， while Carotid intima-media thickness is a biomarker of subclinical atherosclerosis. Numerous studies have confirmed that exercise can slow down or even reverse the formation and progression of carotid Intima-Media thickness. This paper provides a review of the effects of different exercise modalities， intensities， and populations on the vascular structure to provide a reference for the prevention of atherosclerosis with exercise

Ultrasensitive and Accurate Assay of Human Methyltransferase Activity at the Single-Cell Level Based on a Single Integrated Magnetic Microprobe

Human DNA methyltransferase (MTase) activity expression patterns and inhibition response are linked to related cancer initiation, progression, and therapeutic responses. Sensitive and accurate human MTase activity assay in cancer cells, especially at the single-cell level, is essential for biological study, clinical diagnosis, and therapy. Here, we developed an ultrasensitive and accurate DNA (cytosine-5)-methyltransferase 1 (Dnmt1) activity assay at the single-cell level based on a single integrated magnetic microprobe of functionalized double-stranded DNA (dsDNA) anchored to a single magnetic microbead surface. Functionalized dsDNA is designed with a hemimethylated DNA site for Dnmt1 recognition and a single-stranded tail to trigger in situ rolling circle amplification (RCA). Under the action of Dnmt1, hemimethylated dsDNA could be recognized and catalyzed to fully methylated dsDNA, which would protect them from the cleavage of BssHII. However, the dsDNA without full methylation would be cut by BssHII, making single-stranded tail separated from the single integrated microprobe. Subsequently, full methylation-protected in situ RCA could be performed, and multiple signal probes were hybridized to the single integrated microprobe for amplified signal accumulation. Finally, Dnmt1 activity could be evaluated by reading the fluorescence of the single integrated microprobe. Meanwhile, to minimize matrix interferences, magnetic separation was performed in the process. In this strategy, the single integrated magnetic microprobe was provided with integrated capacities of target recognition, signal amplification, signal accumulation, and matrix isolation. Therefore, an ultralow detection limit of 0.007 U/mL Dnmt1 was obtained, and accurate Dnmt1 activity assays in multiple cell lysates at the single-cell level were achieved. Furthermore, the inhibition effect of RG108 was evaluated conveniently. These results indicate that the single integrated magnetic microprobe-based strategy is an excellent candidate for sensitive monitoring of Dnmt1 activity and screening of anticancer drugs

Clinical characteristics and reaction to dopaminergic treatment of drug-naïve patients with Parkinson's disease in central China: A cross sectional study

Background: The symptoms of early Parkinson's disease (PD) are complex and hidden. The aim of this study is to explore and summarize the characteristics of the symptoms of drug naïve patients with PD. Objectives: and Methods Drug-naïve patients with PD and age-matched healthy controls were recruited from the outpatient clinic of Wuhan Union Hospital. The motor and non-motor symptoms were evaluated for further analysis using Unified Parkinson's Disease Rating Scale (UPDRS) I, II, and III; Sniffin’ Sticks Screening 12 test; Mini-Mental State Exam (MMSE); Montreal Cognitive Assessment (MoCA); Hamilton Anxiety Scale (HAMA); and Hamilton Depression Scale (HAMD) scores. The acute levodopa challenge test (ALCT) was adopted to assess the reaction to dopaminergic treatment. Results: We recruited 80 drug-naïve patients with PD and 40 age-matched healthy controls (HCs). Approximately 53.7% of the patients were females. The mean onset age was 59.96 ± 10.40 years. The mean UPDRS I, II, and III were 2.01 ± 1.90, 6.18 ± 3.68, and 26.13 ± 12.09, respectively. Compared with HCs, PD patients had lower scores in MMSE and MoCA; and higher scores in HAMA and HAMD (p < 0.05). In ALCT, 54 patients showed good responses to levodopa while 26 patients did not. The mean improvement rate of UPDRS III was 34.09% at 120 min. Conclusion: The motor symptoms of patients with early PD were mild but virous. They also suffered from different non-motor symptoms. In ALCT, about two thirds of patients (54/80) with early PD showed good response to levodopa. Among four aspects of motor symptoms, bradykinesia reacted best to ALCT, while axial symptoms were the worst

Kinetics and Size Effects on Adsorption of Cu(II), Cr(III), and Pb(II) Onto Polyethylene, Polypropylene, and Polyethylene Terephthalate Microplastic Particles

Due to its small size, large specific surface area and hydrophobicity, microplastics, and the adsorbed contaminants may together cause potential negative effects on ecosystems and human beings. In this study, kinetics and size effects on adsorption of Cu(II), Cr(III), and Pb(II) onto PE, PP and PET microplastic particles were explored. Results indicated that the PE and PET microplastics have the higher adsorption capacity for Cu(II), Cr(III), and Pb(II) than that for PP microplastic. The adsorption capacity was affected by microplastic types and metal species. Among the three metals, Pb(II) had the largest adsorption amount on microplastic particles, especially on PET particles. Moreover, the adsorption capacities of microplastics increase with the decrease of particle size. The metal adsorption capacity of &amp;lt;0.9 mm microplastics is greater than that of 0.9–2 mm and 2–5 mm microplastics. The size effect on metal adsorption was largest for PE microplastic. More attention should be paid in case of the coexistence of heavy metals and tiny PE and PET microplastics in the environment

Kinetics and Size Effects on Adsorption of Cu(II), Cr(III), and Pb(II) Onto Polyethylene, Polypropylene, and Polyethylene Terephthalate Microplastic Particles

Due to its small size, large specific surface area and hydrophobicity, microplastics, and the adsorbed contaminants may together cause potential negative effects on ecosystems and human beings. In this study, kinetics and size effects on adsorption of Cu(II), Cr(III), and Pb(II) onto PE, PP and PET microplastic particles were explored. Results indicated that the PE and PET microplastics have the higher adsorption capacity for Cu(II), Cr(III), and Pb(II) than that for PP microplastic. The adsorption capacity was affected by microplastic types and metal species. Among the three metals, Pb(II) had the largest adsorption amount on microplastic particles, especially on PET particles. Moreover, the adsorption capacities of microplastics increase with the decrease of particle size. The metal adsorption capacity of <0.9 mm microplastics is greater than that of 0.9–2 mm and 2–5 mm microplastics. The size effect on metal adsorption was largest for PE microplastic. More attention should be paid in case of the coexistence of heavy metals and tiny PE and PET microplastics in the environment

Mesoporous Zeolite-Supported Ruthenium Nanoparticles as Highly Selective Fischer-Tropsch Catalysts for the Production of C-5-C-11 Isoparaffins

NSF of China [20625310, 20923004, 21033006]; National Basic Program of China [2010CB732303]; Key Scientific Project of Fujian Province [2009HZ0002-1]; Doctoral Program of Higher Education [20090121110007