Generation of oxygen vacancies in CuO/TiO2 heterojunction induced by diatomite for highly efficient UV-Vis-IR driven photothermal catalytic oxidation of HCHO.

Photothermal catalytic oxidation is a promising and sustainable method for the degradation of indoor formaldehyde (HCHO). However, the excessively high surface temperature of existing photothermal catalysts during catalysis hinders the effective adsorption and degradation of formaldehyde under static conditions. Catalyst loading and oxygen vacancies (OVs) modulation are commonly employed strategies to reduce the photothermal catalytic temperature and enhance the efficiency of photothermal catalytic oxidation. In this work, a p-n type CuO/TiO2 heterojunction is successfully loaded onto diatomite using a wet precipitation method. Under the irradiation of a 300W xenon lamp, the prepared composite material achieved a 100% removal rate of HCHO within 2 h, with a 98% conversion rate to CO2, surpassing the performance of both individual photocatalysts and thermocatalysts. Additionally, by adjusting conditions such as light irradiation and temperature, we have demonstrated that this material exhibits synergistic photothermal catalytic properties. Based on HRTEM, XPS, Raman, and EPR analyses, the introduction of diatomite as a catalyst support was shown to effectively increase the number of OVs. Experimental results, along with O2-TPD, photoelectrochemical characterization, and radical detection, demonstrate that the presence of OVs enhances the oxidative efficiency of both photocatalysis and thermocatalysis, as well as the UV-Vis-IR photothermal catalytic performance. The ternary composite material generates weak hydroxyl (•OH) and superoxide (•O2-) radical under high-temperature with dark conditions, indicating its catalytic oxidation activity under this condition. The increase in temperature and the expansion of the spectral range both enhance the generation of these radicals. In summary, this work demonstrates that the use of diatomite as a support increases the material's specific surface area and OVs content, thereby enhancing adsorption and photothermal catalysis. It elucidates the enhanced catalytic degradation mechanism of this mineral-based photothermal catalyst.

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.

The stabilization ability of NaA zeolite derived from fly ash for lead and cadmium in soil: Mechanisms and evaluation of effectiveness.

Developing technologies aimed at ecologically restoring is of great significance in addressing the problem of heavy metal pollution. In this study, NaA zeolites (FAZ) originated from fly ash with outstanding performance were prepared by alkali fusion hydrothermal method and used for the solidification and stabilization of heavy metals in soil. After systematic evaluation, it was found that FAZ may lower the leaching concentration of lead (Pb) in soil to <1 mg/kg and increase the stabilization rate of Pb to 80 % in the single Pb-contaminated soil, lower the leaching concentration of cadmium (Cd) in soil to <3 mg/kg and increase the stabilization rate of Cd to 60 % in the single Cd-contaminated soil, and lower the leaching concentration of Pb to 0.15 mg/kg and the leaching concentration of Cd to 0.74 mg/kg in PbCd complex polluted soil. Additionally, Pb stabilization rates reach 60 % and Cd stabilization rates reach 30 %, respectively. Ion exchange is primarily responsible for the adsorption and solidification of Pb and Cd in soil by FAZ. Generally, FAZ has a wide range of applications in the rehabilitation of contaminated soil and significantly lowers the level of heavy metal pollution in soil.

Programmable, Self-Healable, and Photochromic Liquid Crystal Elastomers Based on Dynamic Hindered Urea Bonds for Biomimetic Flowers.

Recently, researchers have been exploring the use of dynamic covalent bonds (DCBs) in the construction of exchangeable liquid crystal elastomers (LCEs) for biomimetic actuators and devices. However, a significant challenge remains in achieving LCEs with both excellent dynamic properties and superior mechanical strength and stability. In this study, a diacrylate-functionalized monomer containing dynamic hindered urea bonds (DA-HUB) is employed to prepare exchangeable LCEs through a self-catalytic Michael addition reaction. By incorporating DA-HUB, the LCE system benefits from DCBs and hydrogen bonding, leading to materials with high mechanical strength and a range of dynamic properties such as programmability, self-healing, and recyclability. Leveraging these characteristics, bilayer LCE actuators with controlled reversible thermal deformation and outstanding dimensional stability are successfully fabricated using a simple welding method. Moreover, a biomimetic triangular plum, inspired by the blooming of flowers, is created to showcase reversible color and shape changes triggered by light and heat. This innovative approach opens new possibilities for the development of biomimetic and smart actuators and devices with multiple functionalities.

TFTG: A comprehensive database for human transcription factors and their targets.

Transcription factors (TFs) are major contributors to gene transcription, especially in controlling cell-specific gene expression and disease occurrence and development. Uncovering the relationship between TFs and their target genes is critical to understanding the mechanism of action of TFs. With the development of high-throughput sequencing techniques, a large amount of TF-related data has accumulated, which can be used to identify their target genes. In this study, we developed TFTG (Transcription Factor and Target Genes) database (http://tf.liclab.net/TFTG), which aimed to provide a large number of available human TF-target gene resources by multiple strategies, besides performing a comprehensive functional and epigenetic annotations and regulatory analyses of TFs. We identified extensive available TF-target genes by collecting and processing TF-associated ChIP-seq datasets, perturbation RNA-seq datasets and motifs. We also obtained experimentally confirmed relationships between TF and target genes from available resources. Overall, the target genes of TFs were obtained through integrating the relevant data of various TFs as well as fourteen identification strategies. Meanwhile, TFTG was embedded with user-friendly search, analysis, browsing, downloading and visualization functions. TFTG is designed to be a convenient resource for exploring human TF-target gene regulations, which will be useful for most users in the TF and gene expression regulation research.

Chemical inertness conversion of carbon fraction in coal gangue via N-doping for efficient benzo(a)pyrene degradation.

Efficient degradation of organic pollutants in complex media via advanced oxidation processes (AOPs) is still critical and challenging. Herein, nitrogen (N)-doped coal gangue (CG) catalysts (N-CG) with economic competitiveness and environmental friendliness were successfully synthesized to activate peroxymonosulfate (PMS), exhibiting ultrafast degradation performance toward benzo(a)pyrene (BaP) with 100.00 % and 93.21 % in contaminated solution and soil under optimized condition, respectively. In addition, 0.4 N-CG possessed excellent reusability toward BaP degradation with over 80.00 % after five cycles. However, BaP removal efficiency was significantly affected by some co-existing anions (HCO3- and SO42-) and humic acid (HA) in solution and soil, as well as inhibited under alkaline conditions, especially pH ≥ 9. According to the characterizations, N-doping could promote the generation of pyridinic N and graphitic N in N-CG via high-temperature calcination, which was conducive to produce hydroxyl radical (•OH), sulfate radical (SO4•-), superoxide radical (•O2-) and single oxygen (1O2). In 0.4 N-CG/PMS system, 1O2 and •O2- were proved to be the predominant reactive oxygen species (ROSs) in BaP degradation, as well as •OH and SO4•- made certain contributions. To sum up, this work provided a promising strategy for synthesis of CG-based catalysts by chemical inertness conversion of carbon fracture via N-doping for PMS activation and opened a novel perspective for environmental remediation of hydrophobic and hydrophilic contaminants pollution.

Development and validation of a multi-modality fusion deep learning model for differentiating glioblastoma from solitary brain metastases. / åŒºåˆ†èƒ¶è´¨æ¯ç»†èƒžç˜¤å’Œå•å‘æ€§è„‘è½¬ç§»ç˜¤çš„å¤šæ¨¡æ€èžåˆæ·±åº¦å­¦ä¹ æ¨¡åž‹çš„å¼€å‘å’ŒéªŒè¯.

OBJECTIVES: Glioblastoma (GBM) and brain metastases (BMs) are the two most common malignant brain tumors in adults. Magnetic resonance imaging (MRI) is a commonly used method for screening and evaluating the prognosis of brain tumors, but the specificity and sensitivity of conventional MRI sequences in differential diagnosis of GBM and BMs are limited. In recent years, deep neural network has shown great potential in the realization of diagnostic classification and the establishment of clinical decision support system. This study aims to apply the radiomics features extracted by deep learning techniques to explore the feasibility of accurate preoperative classification for newly diagnosed GBM and solitary brain metastases (SBMs), and to further explore the impact of multimodality data fusion on classification tasks. METHODS: Standard protocol cranial MRI sequence data from 135 newly diagnosed GBM patients and 73 patients with SBMs confirmed by histopathologic or clinical diagnosis were retrospectively analyzed. First, structural T1-weight, T1C-weight, and T2-weight were selected as 3 inputs to the entire model, regions of interest (ROIs) were manually delineated on the registered three modal MR images, and multimodality radiomics features were obtained, dimensions were reduced using a random forest (RF)-based feature selection method, and the importance of each feature was further analyzed. Secondly, we used the method of contrast disentangled to find the shared features and complementary features between different modal features. Finally, the response of each sample to GBM and SBMs was predicted by fusing 2 features from different modalities. RESULTS: The radiomics features using machine learning and the multi-modal fusion method had a good discriminatory ability for GBM and SBMs. Furthermore, compared with single-modal data, the multimodal fusion models using machine learning algorithms such as support vector machine (SVM), Logistic regression, RF, adaptive boosting (AdaBoost), and gradient boosting decision tree (GBDT) achieved significant improvements, with area under the curve (AUC) values of 0.974, 0.978, 0.943, 0.938, and 0.947, respectively; our comparative disentangled multi-modal MR fusion method performs well, and the results of AUC, accuracy (ACC), sensitivity (SEN) and specificity(SPE) in the test set were 0.985, 0.984, 0.900, and 0.990, respectively. Compared with other multi-modal fusion methods, AUC, ACC, and SEN in this study all achieved the best performance. In the ablation experiment to verify the effects of each module component in this study, AUC, ACC, and SEN increased by 1.6%, 10.9% and 15.0%, respectively after 3 loss functions were used simultaneously. CONCLUSIONS: A deep learning-based contrast disentangled multi-modal MR radiomics feature fusion technique helps to improve GBM and SBMs classification accuracy.

scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse.

Gene regulatory networks (GRNs) are interpretable graph models encompassing the regulatory interactions between transcription factors (TFs) and their downstream target genes. Making sense of the topology and dynamics of GRNs is fundamental to interpreting the mechanisms of disease etiology and translating corresponding findings into novel therapies. Recent advances in single-cell multi-omics techniques have prompted the computational inference of GRNs from single-cell transcriptomic and epigenomic data at an unprecedented resolution. Here, we present scGRN (https://bio.liclab.net/scGRN/), a comprehensive single-cell multi-omics gene regulatory network platform of human and mouse. The current version of scGRN catalogs 237 051 cell type-specific GRNs (62 999 692 TF-target gene pairs), covering 160 tissues/cell lines and 1324 single-cell samples. scGRN is the first resource documenting large-scale cell type-specific GRN information of diverse human and mouse conditions inferred from single-cell multi-omics data. We have implemented multiple online tools for effective GRN analysis, including differential TF-target network analysis, TF enrichment analysis, and pathway downstream analysis. We also provided details about TF binding to promoters, super-enhancers and typical enhancers of target genes in GRNs. Taken together, scGRN is an integrative and useful platform for searching, browsing, analyzing, visualizing and downloading GRNs of interest, enabling insight into the differences in regulatory mechanisms across diverse conditions.

eRNAbase: a comprehensive database for decoding the regulatory eRNAs in human and mouse.

Enhancer RNAs (eRNAs) transcribed from distal active enhancers serve as key regulators in gene transcriptional regulation. The accumulation of eRNAs from multiple sequencing assays has led to an urgent need to comprehensively collect and process these data to illustrate the regulatory landscape of eRNAs. To address this need, we developed the eRNAbase (http://bio.liclab.net/eRNAbase/index.php) to store the massive available resources of human and mouse eRNAs and provide comprehensive annotation and analyses for eRNAs. The current version of eRNAbase cataloged 10 399 928 eRNAs from 1012 samples, including 858 human samples and 154 mouse samples. These eRNAs were first identified and uniformly processed from 14 eRNA-related experiment types manually collected from GEO/SRA and ENCODE. Importantly, the eRNAbase provides detailed and abundant (epi)genetic annotations in eRNA regions, such as super enhancers, enhancers, common single nucleotide polymorphisms, expression quantitative trait loci, transcription factor binding sites, CRISPR/Cas9 target sites, DNase I hypersensitivity sites, chromatin accessibility regions, methylation sites, chromatin interactions regions, topologically associating domains and RNA spatial interactions. Furthermore, the eRNAbase provides users with three novel analyses including eRNA-mediated pathway regulatory analysis, eRNA-based variation interpretation analysis and eRNA-mediated TF-target gene analysis. Hence, eRNAbase is a powerful platform to query, browse and visualize regulatory cues associated with eRNAs.

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.

KnockTF 2.0: a comprehensive gene expression profile database with knockdown/knockout of transcription (co-)factors in multiple species.

Transcription factors (TFs), transcription co-factors (TcoFs) and their target genes perform essential functions in diseases and biological processes. KnockTF 2.0 (http://www.licpathway.net/KnockTF/index.html) aims to provide comprehensive gene expression profile datasets before/after T(co)F knockdown/knockout across multiple tissue/cell types of different species. Compared with KnockTF 1.0, KnockTF 2.0 has the following improvements: (i) Newly added T(co)F knockdown/knockout datasets in mice, Arabidopsis thaliana and Zea mays and also an expanded scale of datasets in humans. Currently, KnockTF 2.0 stores 1468 manually curated RNA-seq and microarray datasets associated with 612 TFs and 172 TcoFs disrupted by different knockdown/knockout techniques, which are 2.5 times larger than those of KnockTF 1.0. (ii) Newly added (epi)genetic annotations for T(co)F target genes in humans and mice, such as super-enhancers, common SNPs, methylation sites and chromatin interactions. (iii) Newly embedded and updated search and analysis tools, including T(co)F Enrichment (GSEA), Pathway Downstream Analysis and Search by Target Gene (BLAST). KnockTF 2.0 is a comprehensive update of KnockTF 1.0, which provides more T(co)F knockdown/knockout datasets and (epi)genetic annotations across multiple species than KnockTF 1.0. KnockTF 2.0 facilitates not only the identification of functional T(co)Fs and target genes but also the investigation of their roles in the physiological and pathological processes.

LncSEA 2.0: an updated platform for long non-coding RNA related sets and enrichment analysis.

Long non-coding RNAs (lncRNAs) possess a wide range of biological functions, and research has demonstrated their significance in regulating major biological processes such as development, differentiation, and immune response. The accelerating accumulation of lncRNA research has greatly expanded our understanding of lncRNA functions. Here, we introduce LncSEA 2.0 (http://bio.liclab.net/LncSEA/index.php), aiming to provide a more comprehensive set of functional lncRNAs and enhanced enrichment analysis capabilities. Compared with LncSEA 1.0, we have made the following improvements: (i) We updated the lncRNA sets for 11 categories and extremely expanded the lncRNA scopes for each set. (ii) We newly introduced 15 functional lncRNA categories from multiple resources. This update not only included a significant amount of downstream regulatory data for lncRNAs, but also covered numerous epigenetic regulatory data sets, including lncRNA-related transcription co-factor binding, chromatin regulator binding, and chromatin interaction data. (iii) We incorporated two new lncRNA set enrichment analysis functions based on GSEA and GSVA. (iv) We adopted the snakemake analysis pipeline to track data processing and analysis. In summary, LncSEA 2.0 offers a more comprehensive collection of lncRNA sets and a greater variety of enrichment analysis modules, assisting researchers in a more comprehensive study of the functional mechanisms of lncRNAs.

Efficient benzo(a)pyrene degradation by coal gangue-based catalytic material for peroxymonosulfate activation.

A low cost and green peroxymonosulfate (PMS) activation catalyst (CG-Ca-N) was successfully prepared with coal gangue (CG), calcium chloride, and melamine as activator. Under the optimal conditions, the CG-Ca-N can remove 100 % for benzo(a)pyrene (Bap) in an aqueous solution after 20 min and 72.06 % in soil slurry medium within 60 min, which also display excellent reuse ability toward Bap after three times. The removal of Bap is significantly decreased when the initial pH value was greater than 9 and obviously inhibited in the presence of HCO3- or SO42-. The characterization results indicated that the addition of calcium chloride could stabilize and increase the content of pyridinic N during thermal annealing, resulting in the production of •OH, SO4•- and 1O2. Based on electron paramagnetic resonance (EPR) and active radical scavenging experiments, 1O2 could be identified to be the dominant role in Bap degradation. Overall, this work opened a new perspective for the low cost and green PMS catalysts and offered great promise in the practical remediation of organic pollution of groundwater and soil.

SCInter: A comprehensive single-cell transcriptome integration database for human and mouse.

Single-cell RNA sequencing (scRNA-seq), which profiles gene expression at the cellular level, has effectively explored cell heterogeneity and reconstructed developmental trajectories. With the increasing research on diseases and biological processes, scRNA-seq datasets are accumulating rapidly, highlighting the urgent need for collecting and processing these data to support comprehensive and effective annotation and analysis. Here, we have developed a comprehensive Single-Cell transcriptome integration database for human and mouse (SCInter, https://bio.liclab.net/SCInter/index.php), which aims to provide a manually curated database that supports the provision of gene expression profiles across various cell types at the sample level. The current version of SCInter includes 115 integrated datasets and 1016 samples, covering nearly 150 tissues/cell lines. It contains 8016,646 cell markers in 457 identified cell types. SCInter enabled comprehensive analysis of cataloged single-cell data encompassing quality control (QC), clustering, cell markers, multi-method cell type automatic annotation, predicting cell differentiation trajectories and so on. At the same time, SCInter provided a user-friendly interface to query, browse, analyze and visualize each integrated dataset and single cell sample, along with comprehensive QC reports and processing results. It will facilitate the identification of cell type in different cell subpopulations and explore developmental trajectories, enhancing the study of cell heterogeneity in the fields of immunology and oncology.

Synergistic Promotion System of Montmorillonite with Cu2+ and Benzalkonium Chloride for Efficient and Broad-Spectrum Antibacterial Activity.

By intercalating montmorillonite (MMT) with Cu2+ and benzalkonium chloride (BAC), the present work constructed a synergistic promotion system (Cu2+/BAC/MMT). MMT not only enhances the thermal stability of Cu2+ and BAC but also facilitates the controlled release of Cu2+ and BAC. Concurrently, the introduction of BAC improves the material's organic compatibility. In vitro assays show that the "MIC+" of Cu2+/BAC/MMT against Staphylococcus aureus is merely 7.32 mg/L and 55.56 mg/L against Escherichia coli. At concentrations of 10 and 25 mg/L, Cu2+/BAC/MMT inactivates 100% of S. aureus and E. coli within 2 h, respectively. Furthermore, it is confirmed that the prepared Cu2+/BAC/MMT exhibits a long-term antibacterial ability through antibacterial experiments and release tests. Also, the biosafety of this material was also substantiated by in vitro cytotoxicity tests. These comprehensive findings indisputably portend that Cu2+/BAC/MMT holds promise to supplant antibiotics as an efficacious treatment modality for bacterial infections.

Cis-Cardio: A comprehensive analysis platform for cardiovascular-relavant cis-regulation in human and mouse.

Cis-regulatory elements are important molecular switches in controlling gene expression and are regarded as determinant hubs in the transcriptional regulatory network. Collection and processing of large-scale cis-regulatory data are urgent to decipher the potential mechanisms of cardiovascular diseases from a cis-regulatory element aspect. Here, we developed a novel web server, Cis-Cardio, which aims to document a large number of available cardiovascular-related cis-regulatory data and to provide analysis for unveiling the comprehensive mechanisms at a cis-regulation level. The current version of Cis-Cardio catalogs a total of 45,382,361 genomic regions from 1,013 human and mouse epigenetic datasets, including ATAC-seq, DNase-seq, Histone ChIP-seq, TF/TcoF ChIP-seq, RNA polymerase ChIP-seq, and Cohesin ChIP-seq. Importantly, Cis-Cardio provides six analysis tools, including region overlap analysis, element upstream/downstream analysis, transcription regulator enrichment analysis, variant interpretation, and protein-protein interaction-based co-regulatory analysis. Additionally, Cis-Cardio provides detailed and abundant (epi-) genetic annotations in cis-regulatory regions, such as super-enhancers, enhancers, transcription factor binding sites (TFBSs), methylation sites, common SNPs, risk SNPs, expression quantitative trait loci (eQTLs), motifs, DNase I hypersensitive sites (DHSs), and 3D chromatin interactions. In summary, Cis-Cardio is a valuable resource for elucidating and analyzing regulatory cues of cardiovascular-specific cis-regulatory elements. The platform is freely available at http://www.licpathway.net/Cis-Cardio/index.html.

Landscape and significance of human super enhancer-driven core transcription regulatory circuitry.

A core transcription regulatory circuitry (CRC) is an interconnected self-regulatory circuitry that is formed by a group of core transcription factors (TFs). These core TFs collectively regulate gene expression by binding not only to their own super enhancers (SEs) but also to the SEs of one another. For most human tissue/cell types, a global view of CRCs and core TFs has not been generated. Here, we identified numerous CRCs using two identification methods and detailed the landscape of the CRCs driven by SEs in large cell/tissue samples. The comprehensive biological analyses, including sequence conservation, CRC activity and genome binding affinity were conducted for common TFs, moderate TFs, and specific TFs, which exhibit different biological features. The local module located from the common CRC network highlighted the essential functions and prognostic performance. The tissue-specific CRC network was highly related to cell identity. Core TFs in tissue-specific CRC networks exhibited disease markers, and had regulatory potential for cancer immunotherapy. Moreover, a user-friendly resource named CRCdb (http://www.licpathway.net/crcdb/index.html) was developed, which contained the detailed information of CRCs and core TFs used in this study, as well as other interesting results, such as the most representative CRC, frequency of TFs, and indegree/outdegree of TFs.

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.

Optimal design of a 4 × 4 MMI thermal optical switch with trapezoidal air trenches.

Optical switches are important in signal routing and switching. In this paper, a thermal optical switch with trapezoidal air trenches is proposed. The proposed structure consists of two cascaded 4×4 multimode interference (MMI) couplers. The beam propagation method is used to optimize the dimension and analyze the characteristics. Simulation results show excess loss (EL) and insertion loss (IL) are less than 0.14 dB and 0.22 dB at the wavelength of 1550 nm, respectively. Besides, the extinction ratio (ER) is higher than 21 dB. This design has the advantages of small size, low loss, and high flexibility, which is promising for application to all-optical network routing.

SENIES: DNA Shape Enhanced Two-Layer Deep Learning Predictor for the Identification of Enhancers and Their Strength.

Identifying enhancers is a critical task in bioinformatics due to their primary role in regulating gene expression. For this reason, various computational algorithms devoted to enhancer identification have been put forward over the years. More features are extracted from the single DNA sequences to boost the performance. Nevertheless, DNA structural information is neglected, which is an essential factor affecting the binding preferences of transcription factors to regulatory elements like enhancers. Here, we propose SENIES, a DNA shape enhanced deep learning predictor, to identify enhancers and their strength. The predictor consists of two layers where the first layer is for enhancer and non-enhancer identification, and the second layer is for predicting the strength of enhancers. Apart from two common sequence-derived features (i.e., one-hot and k-mer), DNA shape is introduced to describe the 3D structures of DNA sequences. Performance comparison with state-of-the-art methods conducted on public datasets demonstrates the effectiveness and robustness of our predictor. The code implementation of SENIES is publicly available at https://github.com/hlju-liye/SENIES.