Gallic Acid-Modified Polyethylenimine-Polypropylene Carbonate-Polyethylenimine Nanoparticles: Synthesis, Characterization, and Anti-Periodontitis Evaluation.

The aim of the research was to develop novel gallic acid (GA)-modified amphiphilic nanoparticles of polyethylenimine (PEI)-polypropylene carbonate (PPC)-PEI (PEPE) and comprehensively assess its properties as an antiperiodontitis nanoparticle targeting the Toll-like receptor (TLR). The first step is to evaluate the binding potential of GA to the core trigger receptors TLR2 and TLR4/MD2 for periodontitis using molecular docking techniques. Following this, we conducted NMR, transmission electron microscopy, and dynamic light scattering analyses on the synthesized PEPE nanoparticles. As the final step, we investigated the synthetic results and in vitro antiperiodontitis properties of GA-PEPE nanoparticles. The investigation revealed that GA exhibits potential for targeted binding to TLR2 and the TLR4/MD2 complex. Furthermore, we successfully developed 91.19 nm positively charged PEPE nanoparticles. Spectroscopic analysis indicated the successful synthesis of GA-modified PEPE. Additionally, CCK8 results demonstrated that GA modification significantly reduced the biotoxicity of PEPE. The in vitro antiperiodontitis properties assessment illustrated that 6.25 µM of GA-PEPE nanoparticles significantly reduced the expression of pro-inflammatory factors TNF-α, IL-1ß, and IL-6. The GA-PEPE nanoparticles, with their targeted TLR binding capabilities, were found to possess excellent biocompatibility and antiperiodontitis properties. GA-PEPE nanoparticles will provide highly innovative input into the development of anti- periodontitis nanoparticles.

Crosstalk between endothelial progenitor cells and HCC through periostin/CCL2/CD36 supports formation of the pro-metastatic microenvironment in HCC.

Metastasis causes most cancer-related deaths, and the role and mechanism of periostin (POSTN) in the metastasis of hepatocellular carcinoma (HCC) remain undiscovered. In this study, DEN and HTVi HCC models were performed in hepatic-specific Postn ablation and Postn knock-in mouse to reveal the role of POSTN in HCC metastasis. Furthermore, POSTN was positively correlated with circulating EPCs level and promoted EPC mobilization and tumour infiltration. POSTN also mediated the crosstalk between HCC and EPCs, which promoted metastasis ability and upregulated CD36 expression in HCC through indirect crosstalk. Chemokine arrays further revealed that hepatic-derived POSTN induced elevated CCL2 expression and secretion in EPCs, and CCL2 promoted prometastatic traits in HCC. Mechanistic studies showed that POSTN upregulated CCL2 expression in EPCs via the αvß3/ILK/NF-κB pathway. CCL2 further induced CD36 expression via the CCR2/STAT3 pathway by directly binding to the promoter region of CD36. Finally, CD36 was verified to have a prometastatic role in vitro and to be correlated with POSTN expression, metastasis and recurrence in HCC in clinical samples. Our findings revealed that crosstalk between HCC and EPCs is mediated by periostin/CCL2/CD36 signalling which promotes HCC metastasis and emphasizes a potential therapeutic strategy for preventing HCC metastasis.

BID-seq for transcriptome-wide quantitative sequencing of mRNA pseudouridine at base resolution.

Pseudouridine (Ψ) is an abundant RNA modification that is present in and affects the functions of diverse non-coding RNA species, including rRNA, tRNA and small nuclear RNA. Ψ also exists in mammalian mRNA and probably exhibits functional roles; however, functional investigations of mRNA Ψ modifications in mammals have been hampered by the lack of a quantitative method that detects Ψ at base precision. We have recently developed bisulfite-induced deletion sequencing (BID-seq), which provides the community with a quantitative method to map RNA Ψ distribution transcriptome-wide at single-base resolution. Here, we describe an optimized BID-seq protocol for mapping Ψ distribution across cellular mRNAs, which includes fast steps in both library preparation and data analysis. This protocol generates highly reproducible results by inducing high deletion ratios at Ψ modification within diverse sequence contexts, and meanwhile displayed almost zero background deletions at unmodified uridines. When used for transcriptome-wide Ψ profiling in mouse embryonic stem cells, the current protocol uncovered 8,407 Ψ sites from as little as 10 ng of polyA+ RNA input. This optimized BID-seq workflow takes 5 days to complete and includes four main sections: RNA preparation, library construction, next-generation sequencing (NGS) and data analysis. Library construction can be completed by researchers who have basic knowledge and skills in molecular biology and genetics. In addition to the experimental protocol, we provide BID-pipe ( https://github.com/y9c/pseudoU-BIDseq ), a user-friendly data analysis pipeline for Ψ site detection and modification stoichiometry quantification, requiring only basic bioinformatic and computational skills to uncover Ψ signatures from BID-seq data.

Surface Passivation by Embedment of Polyphosphate Inhibits the Aragonite-to-Calcite Thermodynamic Pump.

We monitored the conversion of aragonite to calcite in water by comparing single and mixed polymorph suspensions. We demonstrate that the enhanced aragonite-to-calcite conversion in mixed polymorph suspensions is dramatically inhibited by adding polyphosphate (sodium hexametaphosphate). 13C and 31P solid-state magic angle spinning (MAS) NMR and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectra allow us to follow quantitatively these effects as imparted by the dissolution-recrystallization processes. 31P{13C} and 13C{31P} rotational echo double resonance (REDOR)NMR experiments reveal coprecipitated phosphate that is embedded only within the surfaces of both polymorphs during the initial dissolution and recrystallization processes, causing passivation that arrests phase conversion.

Anti-inflammatory effect and mechanism of catalpol in various inflammatory diseases.

Catalpol is a kind of iridoid glucoside, widely found in a variety of plants, mostly extracted from the rhizome of the traditional medicinal herb rehmanniae. It has various biological activities such as anti-inflammatory, antioxidant, and antitumor. The anti-inflammatory effects of catalpol have been demonstrated in a variety of diseases, such as neurological diseases, atherosclerosis, renal diseases, respiratory diseases, digestive diseases, bone and joint diseases, eye diseases, and periodontitis. The purpose of this review is to summarize the existing literature on the anti-inflammatory effects of catalpol in a variety of inflammatory diseases over the last decade and to focus on the anti-inflammatory mechanisms of catalpol.

RBFOX2 recognizes N6-methyladenosine to suppress transcription and block myeloid leukaemia differentiation.

N6-methyladenosine (m6A) methylation can be deposited on chromatin-associated RNAs (caRNAs) by the RNA methyltransferase complex (MTC) to regulate chromatin state and transcription. However, the mechanism by which MTC is recruited to distinct genomic loci remains elusive. Here we identify RBFOX2, a well-studied RNA-binding protein, as a chromatin factor that preferentially recognizes m6A on caRNAs. RBFOX2 can recruit RBM15, an MTC component, to facilitate methylation of promoter-associated RNAs. RBM15 also physically interacts with YTHDC1 and recruits polycomb repressive complex 2 (PRC2) to the RBFOX2-bound loci for chromatin silencing and transcription suppression. Furthermore, we found that this RBFOX2/m6A/RBM15/YTHDC1/PRC2 axis plays a critical role in myeloid leukaemia. Downregulation of RBFOX2 notably inhibits survival/proliferation of acute myeloid leukaemia cells and promotes their myeloid differentiation. RBFOX2 is also required for self-renewal of leukaemia stem/initiation cells and acute myeloid leukaemia maintenance. Our study presents a pathway of m6A MTC recruitment and m6A deposition on caRNAs, resulting in locus-selective chromatin regulation, which has potential therapeutic implications in leukaemia.

RBM33 is a unique m6A RNA-binding protein that regulates ALKBH5 demethylase activity and substrate selectivity.

Regulation of RNA substrate selectivity of m6A demethylase ALKBH5 remains elusive. Here, we identify RNA-binding motif protein 33 (RBM33) as a previously unrecognized m6A-binding protein that plays a critical role in ALKBH5-mediated mRNA m6A demethylation of a subset of mRNA transcripts by forming a complex with ALKBH5. RBM33 recruits ALKBH5 to its m6A-marked substrate and activates ALKBH5 demethylase activity through the removal of its SUMOylation. We further demonstrate that RBM33 is critical for the tumorigenesis of head-neck squamous cell carcinoma (HNSCC). RBM33 promotes autophagy by recruiting ALKBH5 to demethylate and stabilize DDIT4 mRNA, which is responsible for the oncogenic function of RBM33 in HNSCC cells. Altogether, our study uncovers the mechanism of selectively demethylate m6A methylation of a subset of transcripts during tumorigenesis that may explain demethylation selectivity in other cellular processes, and we showed its importance in the maintenance of tumorigenesis of HNSCC.

METTL14 is a chromatin regulator independent of its RNA N6-methyladenosine methyltransferase activity.

METTL3 and METTL14 are two components that form the core heterodimer of the main RNA m6A methyltransferase complex (MTC) that installs m6A. Surprisingly, depletion of METTL3 or METTL14 displayed distinct effects on stemness maintenance of mouse embryonic stem cell (mESC). While comparable global hypo-methylation in RNA m6A was observed in Mettl3 or Mettl14 knockout mESCs, respectively. Mettl14 knockout led to a globally decreased nascent RNA synthesis, whereas Mettl3 depletion resulted in transcription upregulation, suggesting that METTL14 might possess an m6A-independent role in gene regulation. We found that METTL14 colocalizes with the repressive H3K27me3 modification. Mechanistically, METTL14, but not METTL3, binds H3K27me3 and recruits KDM6B to induce H3K27me3 demethylation independent of METTL3. Depletion of METTL14 thus led to a global increase in H3K27me3 level along with a global gene suppression. The effects of METTL14 on regulation of H3K27me3 is essential for the transition from self-renewal to differentiation of mESCs. This work reveals a regulatory mechanism on heterochromatin by METTL14 in a manner distinct from METTL3 and independently of m6A, and critically impacts transcriptional regulation, stemness maintenance, and differentiation of mESCs.

Transport of Microplastic and Dispersed Oil Co-contaminants in the Marine Environment.

Microplastics (MPs) and oil pollution are major concerns in oceans. Although their coexistence in oceans and the associated MP-oil-dispersant agglomerates (MODAs) have been reported, limited attention is given to the behavior of the co-contaminants. This study investigated MODA transport in a simulated ocean system and explored related mechanisms under various oil types, salinities, and mineral concentrations. We found that more than 90% of the heavy oil-formed MODAs stayed at the seawater surface, while the light oil-formed MODAs were widely distributed throughout the seawater column. The increased salinity promoted MODAs formed by 7 and 90 µm MPs to transport from the seawater surface to the column. This was elucidated by the Derjaguin-Landau-Verwey-Overbeek theory as more MODAs formed under higher salinities and dispersants kept them stable in the seawater column. Minerals facilitated the sinking of large MP-formed MODAs (e.g., 40 µm) as minerals were adsorbed on the MODA surface, but their impact on small MP-formed MODAs (e.g., 7 µm) was negligible. A MODA-mineral system was proposed to explain their interaction. Rubey's equation was recommended to predict the sinking velocity of MODAs. This study is the first attempt to reveal MODA transport. Findings will contribute to the model development to facilitate their environmental risk evaluation in oceans.

Efficacy of IL-23 inhibitors and IL-12/23 inhibitors in the induction treatment of Crohn's disease: A meta-analysis based on randomized controlled trials.

Introduction: A growing number of randomized controlled trials (RCTs) have demonstrated the effectiveness of interleukin (IL)-23 and IL-12/23 inhibitors in treating Crohn's disease (CD). This study evaluated the efficacy of IL-23 and IL-12/23 inhibitors in the induction phase for the treatment of CD. Material and methods: We searched the following databases from inception until December, 2022: Medline, Embase, Web of Science and the Cochrane Library. The primary outcome was the proportion of CD patients who achieved clinical remission at the end of the induction therapy period. Secondary outcomes included clinical response, endoscopic remission, endoscopic response and normalized C-reactive protein (CRP). Results: After screening, 7 RCTs were included in our study. The meta-analysis showed that, in the induction period, more patients treated with IL-23 inhibitors and IL-12/23 inhibitors achieved clinical remission than patients with placebo therapy (RR = 2.11, 95% CI: 1.83-2.44; RR = 1.94, 95% CI: 1.64-2.29; respectively). The IL-23 inhibitor group and the IL-12/23 inhibitor group showed higher clinical response rates than the placebo group (RR = 1.92, 95% CI: 1.74-2,11; RR = 1.83, 95% CI: 1.61-2.09; respectively). In addition, the IL-23 inhibitor group had a higher endoscopic remission rate and endoscopic response rate than the placebo group; the corresponding pooled RRs were 3.40 (95% CI: 2.57-4.50) and 2.65 (95% CI: 2.65-3.12), respectively. Conclusions: IL-23 and IL-12/23 inhibitors were efficient methods in the induction treatment of CD.

FTO mediates LINE1 m6A demethylation and chromatin regulation in mESCs and mouse development.

N6-methyladenosine (m6A) is the most abundant internal modification on mammalian messenger RNA. It is installed by a writer complex and can be reversed by erasers such as the fat mass and obesity-associated protein FTO. Despite extensive research, the primary physiological substrates of FTO in mammalian tissues and development remain elusive. Here, we show that FTO mediates m6A demethylation of long-interspersed element-1 (LINE1) RNA in mouse embryonic stem cells (mESCs), regulating LINE1 RNA abundance and the local chromatin state, which in turn modulates the transcription of LINE1-containing genes. FTO-mediated LINE1 RNA m6A demethylation also plays regulatory roles in shaping chromatin state and gene expression during mouse oocyte and embryonic development. Our results suggest broad effects of LINE1 RNA m6A demethylation by FTO in mammals.

matExplorer: Visual Exploration on Predicting Ionic Conductivity for Solid-state Electrolytes.

Lithium ion batteries (LIBs) are widely used as important energy sources for mobile phones, electric vehicles, and drones. Experts have attempted to replace liquid electrolytes with solid electrolytes that have wider electrochemical window and higher stability due to the potential safety risks, such as electrolyte leakage, flammable solvents, poor thermal stability, and many side reactions caused by liquid electrolytes. However, finding suitable alternative materials using traditional approaches is very difficult due to the incredibly high cost in searching. Machine learning (ML)-based methods are currently introduced and used for material prediction. However, learning tools designed for domain experts to conduct intuitive performance comparison and analysis of ML models are rare. In this case, we propose an interactive visualization system for experts to select suitable ML models and understand and explore the predication results comprehensively. Our system uses a multifaceted visualization scheme designed to support analysis from various perspectives, such as feature distribution, data similarity, model performance, and result presentation. Case studies with actual lab experiments have been conducted by the experts, and the final results confirmed the effectiveness and helpfulness of our system.

Phase separation of RNA-binding protein promotes polymerase binding and transcription.

An RNA-involved phase-separation model has been proposed for transcription control. However, the molecular links that connect RNA to the transcription machinery remain missing. Here we find that RNA-binding proteins (RBPs) constitute half of the chromatin proteome in embryonic stem cells (ESCs), some being colocalized with RNA polymerase (Pol) II at promoters and enhancers. Biochemical analyses of representative RBPs show that the paraspeckle protein PSPC1 inhibits the RNA-induced premature release of Pol II, and makes use of RNA as multivalent molecules to enhance the formation of transcription condensates and subsequent phosphorylation and release of Pol II. This synergistic interplay enhances polymerase engagement and activity via the RNA-binding and phase-separation activities of PSPC1. In ESCs, auxin-induced acute degradation of PSPC1 leads to genome-wide defects in Pol II binding and nascent transcription. We propose that promoter-associated RNAs and their binding proteins synergize the phase separation of polymerase condensates to promote active transcription.

Impact of consumption frequency on generations of sensory product profiles using CATA questions: Case studies with two drink categories.

Check-All-That-Apply (CATA) is a very popular tool for rapid sensory profiling in consumer research. Yet, consumers' dietary habits, such as consumption frequency, has been neglected in regard to the impact, if any, on CATA question responses. The present work aimed to fill this gap, by focusing on the effect of different consumption frequencies with four studies (N = 686). Two categories of drink products were involved, chrysanthemum tea and instant coffee. For each category, two sets of products were prepared to constitute two levels of difference between samples (larger vs. smaller). Consumers were classified into high- and low-consumption groups according to their consumption frequencies of each focal product; the size of these subgroups ranged from 54 to 130. Overall, the two groups did not produce large discrepancies from each other when constructing sensory profiling of the tested samples with CATA questions as well as the stability of sample configurations. However, there were some nuances between them. In the evaluation of chrysanthemum tea samples, the higher-consumption group of consumers presented better discrimination than the lower-consumption group while this was reversed for coffee samples. This might be mainly attributed to the fact infrequent consumers were more sensitive to such negative attributes as "strong chrysanthemum smell for chrysanthemum samples, earthy for coffee samples". Further, despite the higher stability obtained with larger sizes of difference between samples in Studies 3 and 4, in general, the effect of size of differences within sample sets was not significant between different consumption groups. To more effectively contribute to refinement of methodological guidelines for CATA questions, more validation work is needed.

Paired preference tests and placebo placement: 2. Unraveling the effects of stimulus variance.

From the literature on paired preference testing, there has been disagreement regarding whether a placebo pair would have a significantly higher frequency of 'no preference' responses if it were to be placed for assessment after its corresponding target pair rather than before. This can be important, because the higher the frequency of 'no preference' responses in the placebo pair, the more powerful will be any chi-squared related analysis, which determines whether the target pair indicates a significant preference or not. In the first paper in this series, it was shown, that indeed a placebo placed after the target pair induced a higher proportion of consumers to respond with a 'no preference'. However, the response was uneven. For some stimuli, the response was strong and significant, for others it was weaker and not significant. It was hypothesized that the weak response could be due to greater variance among the individual stimuli in the placebo sample to be tasted. The effect was confirmed using a priori chosen high and low variance stimuli. Further evidence was obtained from predictions for preference tau criterion levels and frequency of preference changes between two target pairs. All these indicated that the weaker response of some stimuli was due to a higher level of variance among the individual stimuli.

Visual and Semantic Knowledge Transfer for Large Scale Semi-Supervised Object Detection.

Deep CNN-based object detection systems have achieved remarkable success on several large-scale object detection benchmarks. However, training such detectors requires a large number of labeled bounding boxes, which are more difficult to obtain than image-level annotations. Previous work addresses this issue by transforming image-level classifiers into object detectors. This is done by modeling the differences between the two on categories with both image-level and bounding box annotations, and transferring this information to convert classifiers to detectors for categories without bounding box annotations. We improve this previous work by incorporating knowledge about object similarities from visual and semantic domains during the transfer process. The intuition behind our proposed method is that visually and semantically similar categories should exhibit more common transferable properties than dissimilar categories, e.g. a better detector would result by transforming the differences between a dog classifier and a dog detector onto the cat class, than would by transforming from the violin class. Experimental results on the challenging ILSVRC2013 detection dataset demonstrate that each of our proposed object similarity based knowledge transfer methods outperforms the baseline methods. We found strong evidence that visual similarity and semantic relatedness are complementary for the task, and when combined notably improve detection, achieving state-of-the-art detection performance in a semi-supervised setting.

Visual affective classification by combining visual and text features.

Affective analysis of images in social networks has drawn much attention, and the texts surrounding images are proven to provide valuable semantic meanings about image content, which can hardly be represented by low-level visual features. In this paper, we propose a novel approach for visual affective classification (VAC) task. This approach combines visual representations along with novel text features through a fusion scheme based on Dempster-Shafer (D-S) Evidence Theory. Specifically, we not only investigate different types of visual features and fusion methods for VAC, but also propose textual features to effectively capture emotional semantics from the short text associated to images based on word similarity. Experiments are conducted on three public available databases: the International Affective Picture System (IAPS), the Artistic Photos and the MirFlickr Affect set. The results demonstrate that the proposed approach combining visual and textual features provides promising results for VAC task.