SEAOP: a statistical ensemble approach for outlier detection in quantitative proteomics data.

Quality control in quantitative proteomics is a persistent challenge, particularly in identifying and managing outliers. Unsupervised learning models, which rely on data structure rather than predefined labels, offer potential solutions. However, without clear labels, their effectiveness might be compromised. Single models are susceptible to the randomness of parameters and initialization, which can result in a high rate of false positives. Ensemble models, on the other hand, have shown capabilities in effectively mitigating the impacts of such randomness and assisting in accurately detecting true outliers. Therefore, we introduced SEAOP, a Python toolbox that utilizes an ensemble mechanism by integrating multi-round data management and a statistics-based decision pipeline with multiple models. Specifically, SEAOP uses multi-round resampling to create diverse sub-data spaces and employs outlier detection methods to identify candidate outliers in each space. Candidates are then aggregated as confirmed outliers via a chi-square test, adhering to a 95% confidence level, to ensure the precision of the unsupervised approaches. Additionally, SEAOP introduces a visualization strategy, specifically designed to intuitively and effectively display the distribution of both outlier and non-outlier samples. Optimal hyperparameter models of SEAOP for outlier detection were identified by using a gradient-simulated standard dataset and Mann-Kendall trend test. The performance of the SEAOP toolbox was evaluated using three experimental datasets, confirming its reliability and accuracy in handling quantitative proteomics.

The elite eating quality alleles Wxb and ALKb are regulated by OsDOF18 and coordinately improve head rice yield.

Head rice yield (HRY) measures rice milling quality and determines final grain yield and commercial value. Here, we report that two major quantitative trait loci for milling quality in rice, qMq-1 and qMq-2, represent allelic variants of Waxylv /Waxyb (hereafter Wx) encoding Granule-Bound Starch Synthase I (GBSSI) and Alkali Spreading Value ALKc /ALKb encoding Soluble Starch Synthase IIa (SSIIa), respectively. Complementation and overexpression transgenic lines in indica and japonica backgrounds confirmed that Wx and ALK coordinately regulate HRY by affecting amylose content, the number of amylopectin branches, amyloplast size, and thus grain filling and hardness. The transcription factor OsDOF18 acts upstream of Wx and ALK by activating their transcription. Furthermore, rice accessions with Wxb and ALKb alleles showed improved HRY over those with Wxlv and ALKc . Our study not only reveals the novel molecular mechanism underlying the formation of HRY but also provides a strategy for breeding rice cultivars with improved HRY.

Global Research Status Regarding Uveitis in the Last Decade.

PURPOSE: To provide an overview on global uveitis research in the last decade in terms of countries/regions, organizations, scholars, journals, trending topics, and fundings. METHODS: This cross-sectional bibliometric analysis yielded 10656 uveitis publications in English for subsequent bibliometric analysis. RESULTS: In terms of the number of publications, the leading country/region was the USA (3007). The most productive organization was the University College London (420). The most productive research team was Professor Yang's group (146). A higher h-index was noted in University College London (48). Professor Rosenbaum was the first h-index holder (32). Keywords of interest included topics such as biologics, COVID and OCT. Publications by Ocular Immunology and Inflammation (968) ranked the first position. CONCLUSIONS: The USA is the leading force in uveitis study. Asian countries/regions, such as China (mainland) and India, are exerting a substantial role worldwide. Trendy topics cover COVID-19, OCTA.

Revealing Academic Evolution and Frontier Pattern in the Field of Uveitis Using Bibliometric Analysis, Natural Language Processing, and Machine Learning.

PURPOSE: Numerous uveitis articles were published in this century, underneath which hides valuable intelligence. We aimed to characterize the evolution and patterns in this field. METHODS: We divided the 15,994 uveitis papers into four consecutive time periods for bibliometric analysis, and applied latent Dirichlet allocation topic modeling and machine learning techniques to the latest period. . RESULTS: The yearly publication pattern fitted the curve: 1.21335x2 - 4,848.95282x + 4,844,935.58876 (R2 = 0.98311). The USA, the most productive country/region, focused on topics like ankylosing spondylitis and biologic therapy, whereas China (mainland) focused on topics like OCT and Behcet disease. The logistic regression showed the highest accuracy (71.6%) in the test set. CONCLUSION: In this century, a growing number of countries/regions/authors/journals are involved in the uveitis study, promoting the scientific output and thematic evolution. Our pioneering study uncovers the evolving academic trends and frontier patterns in this field using bibliometric analysis and AI algorithms.

Recent progress and research trend of anti-cataract pharmacology therapy: A bibliometric analysis and literature review.

Cataract is the leading cause of blindness worldwide. Cataract phacoemulsification combined with intraocular lens implantation causes great burden to global healthcare, especially for low- and middle-income countries. Such burden would be significantly relieved if cataracts can effectively be treated or delayed by non-surgical means. Excitingly, novel drugs have been developed to treat cataracts in recent decades. For example, oxysterols are found to be able to innovatively reverse lens clouding, novel nanotechnology-loaded drugs improve anti-cataract pharmacological effect, and traditional Chinese medicine demonstrates promising therapeutic effects against cataracts. In the present review, we performed bibliometric analysis to provide an overview perspective regarding the research status, hot topics, and academic trends in the field of anti-cataract pharmacology therapy. We further reviewed the curative effects and molecular mechanisms of anti-cataract drugs such as lanosterol, metformin, resveratrol and curcumin, and prospected the possibility of their clinical application in future.

Nanoparticles in ocular applications and their potential toxicity.

Nanotechnology has been developed rapidly in recent decades and widely applied in ocular disease therapy. Nano-drug delivery systems overcome the bottlenecks of current ophthalmic drug delivery and are characterized with strong biocompatibility, stability, efficiency, sustainability, controllability, and few side effects. Nanoparticles have been identified as a promising and generally safe ophthalmic drug-delivery system based on the toxicity assessment in animals. Previous studies have found that common nanoparticles can be toxic to the cornea, conjunctiva, and retina under certain conditions. Because of the species differences between humans and animals, advanced in vitro cell culture techniques, such as human organoids, can mimic the human organism to a certain extent, bringing nanoparticle toxicity assessment to a new stage. This review summarizes the advanced application of nanoparticles in ocular drug delivery and the potential toxicity, as well as some of the current challenges and future opportunities in nanotoxicological evaluation.

Fullerenol protects cornea from ultraviolet B exposure.

The eyes are highly susceptible to the oxidative stress induced by ultraviolet B (UVB, wavelength between 280 ∼ 320 nm), which could cause severe damage to the cornea. Fullerenols are effective antioxidants to alleviate UVB-induced injury, while their application for the eyes is still rare. In present study, we investigated the protective performance and mechanism of fullerenols on cornea under UVB radiation in vivo and in vitro. The synthesized fullerenols exhibited broad-spectrum free radical scavenging properties (applicable to both reactive oxygen species (ROS) and reactive nitrogen species (RNS)) and photo-stability. When compared with another widely used antioxidant glutathione (GSH), the administration of fullerenols markedly decreased the injured area, corneal edema, cell death, and increased the cell proliferation in UVB-induced rat cornea. The effects of fullerenols were confirmed in UVB-exposed human corneal epithelial cells (hCECs), where elevated cell viability and proliferation, decreased oxidative free radical production, repaired mitochondrial dysfunction and DNA lesions were observed. RNA sequencing (RNA-Seq) analysis demonstrated that fullerenol alleviated UVB-induced corneal injury through down-regulation of oxidative stress-related genes and up-regulation of proliferation-associated genes. Our results demonstrate the suitability of fullerenols as a potential exogenous treatment in ameliorating UVB-induced cornea damage.

Integrative analyses identified ion channel genes GJB2 and SCNN1B as prognostic biomarkers and therapeutic targets for lung adenocarcinoma.

OBJECTIVES: Abnormal expressions of ion channel genes are associated with the occurrence and progression of tumors. At present, their roles in the carcinogenesis of lung adenocarcinoma (LUAD) are not clear. MATERIALS AND METHODS: Differentially expressed (DE) genes in the tumorigenesis were identified from 328 ion channel genes in 102 LUAD and paired adjacent normal samples. Similar analyses were performed between 177 metastatic and 286 non-metastatic LUAD samples to identify DE ion channel genes in the progression of LUAD. Independent prognostic factors selected from DE ion channel genes were used to construct a prognostic model. Correlation analysis and drugs-drug targets interaction network were used to screen the potential drugs for LUAD patients stratified by GJB2 or SCNN1B. RESULTS: Six ion channel genes (GJB2, CACNA1D, KCNQ1, SCNN1B, SCNN1G and TRPV6) were continuous differentially expressed in the tumorigenesis and progression of LUAD. The survival analysis in four datasets with 522 LUAD samples showed that GJB2 and SCNN1B were independent prognostic biomarkers. Patients with overexpression of GJB2 or underexpression of SCNN1B had shorter overall survival. Moreover, multi-omics analysis showed that hypomethylation of GJB2 and hypermethylation of SCNN1B in the promoter region may contribute to their aberrant expressions. KEGG enrichment analysis showed that the overexpressed genes in the group with high GJB2 or low SCNN1B were enriched in cancer-related pathways, while the underexpressed genes were enriched in metabolism-related pathways. The prognostic model with GJB2 and SCNN1B can stratify all LUAD patients into two groups with significantly different survival. Correlation analysis and drugs-drug targets interaction network suggested that GJB2 and SCNN1B expression might have indicative therapeutic values for LUAD patients. Finally, pan-cancer analysis in other eight cancer types showed that GJB2 and SCNN1B might be also potential prognostic factors for KIRC. CONCLUSIONS: GJB2 and SCNN1B were identified as prognostic biomarkers and therapeutic targets for LUAD.

Arbuscular Mycorrhizal Fungi Alleviate Drought Stress in C3 (Leymus chinensis) and C4 (Hemarthria altissima) Grasses via Altering Antioxidant Enzyme Activities and Photosynthesis.

As one of the most important limiting factors of grassland productivity, drought is predicted to increase in intensity and frequency. Greenhouse studies suggest that arbuscular mycorrhizal fungi (AMF) can improve plant drought resistance. However, whether AMF can improve plant drought resistance in field conditions and whether the effects of AMF on drought resistance differ among plants with different photosynthetic pathways remain unclear. To evaluate the effect of indigenous AMF on plant drought resistance, an in situ rainfall exclusion experiment was conducted in a temperate meadow in northeast China. The results showed that AMF significantly reduced the negative effects of drought on plant growth. On average, AMF enhanced plant biomass, photosynthetic rate (A), stomatal conductance (g s), intrinsic water use efficiency (iWUE), and superoxide dismutase (SOD) activity of the C3 species Leymus chinensis by 58, 63, 38, 15, and 45%, respectively, and reduced levels of malondialdehyde (MDA) by 32% under light and moderate drought (rainfall exclusion of 30 and 50%, respectively). However, under extreme drought (rainfall exclusion of 70%), AMF elevated only aboveground biomass and catalase (CAT) activities. Averagely, AMF increased the aboveground biomass, A, and CAT activity of Hemarthria altissima (C4) by 37, 28, and 30%, respectively, under light and moderate droughts. The contribution of AMF to plant drought resistance was higher for the C3 species than that for the C4 species under both light and moderate drought conditions. The results highlight potential photosynthetic type differences in the magnitude of AMF-associated enhancement in plant drought resistance. Therefore, AMF may determine plant community structure under future climate change scenarios by affecting the drought resistance of different plant functional groups.