scATAC-Ref: a reference of scATAC-seq with known cell labels in multiple species.

Chromatin accessibility profiles at single cell resolution can reveal cell type-specific regulatory programs, help dissect highly specialized cell functions and trace cell origin and evolution. Accurate cell type assignment is critical for effectively gaining biological and pathological insights, but is difficult in scATAC-seq. Hence, by extensively reviewing the literature, we designed scATAC-Ref (https://bio.liclab.net/scATAC-Ref/), a manually curated scATAC-seq database aimed at providing a comprehensive, high-quality source of chromatin accessibility profiles with known cell labels across broad cell types. Currently, scATAC-Ref comprises 1 694 372 cells with known cell labels, across various biological conditions, >400 cell/tissue types and five species. We used uniform system environment and software parameters to perform comprehensive downstream analysis on these chromatin accessibility profiles with known labels, including gene activity score, TF enrichment score, differential chromatin accessibility regions, pathway/GO term enrichment analysis and co-accessibility interactions. The scATAC-Ref also provided a user-friendly interface to query, browse and visualize cell types of interest, thereby providing a valuable resource for exploring epigenetic regulation in different tissues and cell types.

SEanalysis 2.0: a comprehensive super-enhancer regulatory network analysis tool for human and mouse.

Super-enhancers (SEs) play an essential regulatory role in various biological processes and diseases through their specific interaction with transcription factors (TFs). Here, we present the release of SEanalysis 2.0 (http://licpathway.net/SEanalysis), an updated version of the SEanalysis web server for the comprehensive analyses of transcriptional regulatory networks formed by SEs, pathways, TFs, and genes. The current version added mouse SEs and further expanded the scale of human SEs, documenting 1 167 518 human SEs from 1739 samples and 550 226 mouse SEs from 931 samples. The SE-related samples in SEanalysis 2.0 were more than five times that in version 1.0, which significantly improved the ability of original SE-related network analyses ('pathway downstream analysis', 'upstream regulatory analysis' and 'genomic region annotation') for understanding context-specific gene regulation. Furthermore, we designed two novel analysis models, 'TF regulatory analysis' and 'Sample comparative analysis' for supporting more comprehensive analyses of SE regulatory networks driven by TFs. Further, the risk SNPs were annotated to the SE regions to provide potential SE-related disease/trait information. Hence, we believe that SEanalysis 2.0 has significantly expanded the data and analytical capabilities of SEs, which helps researchers in an in-depth understanding of the regulatory mechanisms of SEs.

Clinical Effect of Dermatologic Trephination Combined With Radiotherapy in the Treatment of Keloids.

BACKGROUND: Keloids are excessive formations of scar tissue that develop at the site of a skin injury. Due to their invasive nature, they have a negative impact on the skin's appearance and are prone to recurrence, making them a challenging condition to treat with regard to skin aesthetics. OBJECTIVES: The objective of this article was to compare the long-term effects of dermatologic trephination with nonsurgical treatments for scars and evaluate the clinical value of the treatments. METHODS: A retrospective analysis was conducted of 48 patients who received keloid treatment in the Department of Dermatology and Department of Thoracic Surgery at our hospital from January 2021 to October 2023. Twenty-four patients received dermatologic trephination, and 24 patients received nonsurgical treatment. Outcome measures included scar appearance, scar healing time, pain and itching levels, and patient satisfaction. RESULTS: The healing time of patients receiving dermatologic trephination was significantly shorter than that of patients in the nonsurgical group. The degree of itching in patients undergoing dermatologic trephination was significantly lower than that of patients in the nonsurgical group. The satisfaction of patients who received dermatologic trephination was significantly higher than that of patients in the nonsurgical group. CONCLUSIONS: In this study we demonstrated that trephination achieves better long-term results in keloid revision, including improved keloid appearance, itching symptoms, and patient satisfaction.

VARAdb: a comprehensive variation annotation database for human.

With the study of human diseases and biological processes increasing, a large number of non-coding variants have been identified and facilitated. The rapid accumulation of genetic and epigenomic information has resulted in an urgent need to collect and process data to explore the regulation of non-coding variants. Here, we developed a comprehensive variation annotation database for human (VARAdb, http://www.licpathway.net/VARAdb/), which specifically considers non-coding variants. VARAdb provides annotation information for 577,283,813 variations and novel variants, prioritizes variations based on scores using nine annotation categories, and supports pathway downstream analysis. Importantly, VARAdb integrates a large amount of genetic and epigenomic data into five annotation sections, which include 'Variation information', 'Regulatory information', 'Related genes', 'Chromatin accessibility' and 'Chromatin interaction'. The detailed annotation information consists of motif changes, risk SNPs, LD SNPs, eQTLs, clinical variant-drug-gene pairs, sequence conservation, somatic mutations, enhancers, super enhancers, promoters, transcription factors, chromatin states, histone modifications, chromatin accessibility regions and chromatin interactions. This database is a user-friendly interface to query, browse and visualize variations and related annotation information. VARAdb is a useful resource for selecting potential functional variations and interpreting their effects on human diseases and biological processes.

SEanalysis: a web tool for super-enhancer associated regulatory analysis.

Super-enhancers (SEs) have prominent roles in biological and pathological processes through their unique transcriptional regulatory capability. To date, several SE databases have been developed by us and others. However, these existing databases do not provide downstream or upstream regulatory analyses of SEs. Pathways, transcription factors (TFs), SEs, and SE-associated genes form complex regulatory networks. Therefore, we designed a novel web server, SEanalysis, which provides comprehensive SE-associated regulatory network analyses. SEanalysis characterizes SE-associated genes, TFs binding to target SEs, and their upstream pathways. The current version of SEanalysis contains more than 330 000 SEs from more than 540 types of cells/tissues, 5042 TF ChIP-seq data generated from these cells/tissues, DNA-binding sequence motifs for ∼700 human TFs and 2880 pathways from 10 databases. SEanalysis supports searching by either SEs, samples, TFs, pathways or genes. The complex regulatory networks formed by these factors can be interactively visualized. In addition, we developed a customizable genome browser containing >6000 customizable tracks for visualization. The server is freely available at http://licpathway.net/SEanalysis.

Application of valence-variable transition-metal-oxide-based nanomaterials in electrochemical analysis: A review.

The construction of materials with rapid electron transfer is considered an effective method for enhancing electrochemical activity in electroanalysis. It has been widely demonstrated that valence changes in transition metal ions can promote electron transfer and thus increase electrochemical activity. Recently, valence-variable transition metal oxides (TMOs) have shown popular application in electrochemical analysis by using their abundant valence state changes to accelerate electron transfer during electrochemical detection. In this review, we summarize recent research advances in valence changes of TMOs and their application in electrochemical analysis. This includes the definition and mechanism of valence change, the association of valence changes with electronic structure, and their applications in electrochemical detection, along with the use of density functional theory (DFT) to simulate the process of electron transfer during valence changes. Finally, the challenges and opportunities for developing and applying valence changes in electrochemical analysis are also identified.

High efficiency Hg(II) electrochemical detection based on the number of defect engineering on MoS2: Insight in synergistic action of sulfur vacancies and undercoordinated Mo.

Defects on nanomaterials can effectively enhance the performance of electrochemical detection, but an excessive number of defects may have an adverse effect. In this study, MoS2 nanosheets were synthesized using a hydrothermal synthesis method. By controlling the calcination temperature, MoS2-7H, calcined at 700 °C under H2/Ar2, exhibited an optimal ratio of "point" defects to "plane" defects, resulting in excellent detection performance for mercury ions (Hg(II)). In general, the sulfur vacancies (SV) and undercoordinated Mo generated after calcination of MoS2 significantly promotes the adsorption process and redox of Hg(II) by increasing surface chemical activity, providing additional adsorption sites and adjusting surface charge status to accelerate the catalytic redox of Hg(II). The prepared MoS2-7H-modified electrode showed a sensitivity of 18.25 µA µM-1 and a low limit of detection (LOD) of 6.60 nM towards Hg(II). MoS2-7H also demonstrated a good anti-interference, stability, and exhibited a strong current response in real water samples. The modulation to obtain appropriate number of defects in MoS2 holds promise as a prospective electrode modification material for the electroanalysis.

scBlood: A comprehensive single-cell accessible chromatin database of blood cells.

The advent of single cell transposase-accessible chromatin sequencing (scATAC-seq) technology enables us to explore the genomic characteristics and chromatin accessibility of blood cells at the single-cell level. To fully make sense of the roles and regulatory complexities of blood cells, it is critical to collect and analyze these rapidly accumulating scATAC-seq datasets at a system level. Here, we present scBlood (https://bio.liclab.net/scBlood/), a comprehensive single-cell accessible chromatin database of blood cells. The current version of scBlood catalogs 770,907 blood cells and 452,247 non-blood cells from ∼400 high-quality scATAC-seq samples covering 30 tissues and 21 disease types. All data hosted on scBlood have undergone preprocessing from raw fastq files and multiple standards of quality control. Furthermore, we conducted comprehensive downstream analyses, including multi-sample integration analysis, cell clustering and annotation, differential chromatin accessibility analysis, functional enrichment analysis, co-accessibility analysis, gene activity score calculation, and transcription factor (TF) enrichment analysis. In summary, scBlood provides a user-friendly interface for searching, browsing, analyzing, visualizing, and downloading scATAC-seq data of interest. This platform facilitates insights into the functions and regulatory mechanisms of blood cells, as well as their involvement in blood-related diseases.

MiR-124 targets Slug to regulate epithelial-mesenchymal transition and metastasis of breast cancer.

MicroRNAs (miRNAs or miR) have been integrated into tumorigenic programs as either oncogenes or tumor suppressor genes. The miR-124 was reported to be attenuated in several tumors, such as glioma, medulloblastoma and hepatocellular carcinoma. However, its role in cancer remains greatly elusive. In this study, we show that the miR-124 expression is significantly suppressed in human breast cancer specimens, which is reversely correlated to histological grade of the cancer. More intriguingly, ectopic expression of miR-124 in aggressive breast cancer cell lines MDA-MB-231 and BT-549 strongly inhibits cell motility and invasive capacity, as well as the epithelial-mesenchymal transition process. Also, lentivirus-delivered miR-124 endows MDA-MB-231 cells with the ability to suppress cell colony formation in vitro and pulmonary metastasis in vivo. Further studies have identified the E-cadherin transcription repressor Slug as a direct target gene of miR-124; its downregulation by miR-124 increases the expression of E-cadherin, a hallmark of epithelial cells and a repressor of cell invasion and metastasis. Moreover, knockdown of Slug notably impairs the motility of MDA-MB-231 cells, whereas re-expression of Slug abrogates the reduction of motility and invasion ability induced by miR-124 in MDA-MB-231 cells. These findings highlight an important role for miR-124 in the regulation of invasive and metastatic potential of breast cancer and suggest a potential application of miR-124 in cancer treatment.

Sensitive sensing of Hg(II) based on lattice B and surface F co-doped CeO2: Synergies of catalysis and adsorption brought by doping site engineering.

Transition metal oxides are widely used in the detection of heavy metal ions (HMIs), and the co-doping strategy that introducing a variety of different dopant atoms to modify them can obtain a better detection performance. However, there is very little research on the co-doped transition metal oxides by non-metallic elements for electrochemical detection. Herein, boron (B) and fluorine (F) co-doped CeO2 nanomaterial (BFC) is constructed to serve as the electrochemically sensitive interface for the detection of Hg(II). B and F affect the sensitivity of CeO2 to HMIs when they were introduced at different doping sites. Through a variety of characterization, it is proved that B is successfully doped into the lattice and F is doped on the surface of the material. Through the improvement of the catalytic properties and adsorption capacity of CeO2 by different doping sites, this B and F co-doped CeO2 exhibits excellent square wave anodic stripping voltammetry (SWASV) current responses to Hg(II). Both the high sensitivity of 906.99 µA µM-1 cm-2 and the low limit of detection (LOD) of 0.006 µM are satisfactory. Besides, this BFC glassy carbon electrode (GCE) also has good anti-interference property, which has been successfully used in the detection of Hg(II) in actual water. This discovery provides a useful strategy for designing a variety of non-metallic co-doped transition metal oxides to construct trace heavy metal ion-sensitive interfaces.