Uncovering topologically associating domains from three-dimensional genome maps with TADGATE.

Topologically associating domains (TADs) are essential components of three-dimensional (3D) genome organization and significantly influence gene transcription regulation. However, accurately identifying TADs from sparse chromatin contact maps and exploring the structural and functional elements within TADs remain challenging. To this end, we develop TADGATE, a graph attention auto-encoder that can generate imputed maps from sparse Hi-C contact maps while adaptively preserving or enhancing the underlying topological structures, thereby facilitating TAD identification.

Reconstruction of a Closed-Loop Ecological Cycle System Anchored by Large-Scale Load-balancing Biogas and its economic viability assessment.

Biogas can be used for complementary load-balancing with renewable intermittent power, thus maintaining overall energy output stability. However, biogas load balancing load balancing is typically used in small-scale distributed energy systems, constrained by factors such as technology and land requirements, making it challenging to scale up. Therefore, this study proposes a closed-loop ecological cycle system, where biogas provides load leveling support for large-scale intermittent power sources in desertified regions dominated by animal husbandry.

Single-nucleus multi-omics analyses reveal cellular and molecular innovations in the anterior cingulate cortex during primate evolution.

The anterior cingulate cortex (ACC) of the human brain is involved in higher-level cognitive functions such as emotion and self-awareness. We generated profiles of human and macaque ACC gene expression and chromatin accessibility at single-nucleus resolution. We characterized the conserved patterns of gene expression, chromatin accessibility, and transcription factor binding in different cell types.

The E3 ubiquitin ligase RNF220 maintains hindbrain expression patterns through regulation of WDR5 stability.

The spatial and temporal linear expression of genes establishes a regional code, which is crucial for the antero-posterior (A-P) patterning, segmentation, and neuronal circuit development of the hindbrain. RNF220, an E3 ubiquitin ligase, is widely involved in neural development via targeting of multiple substrates. Here, we found that the expression of genes in the pons was markedly up-regulated at the late developmental stage (post-embryonic day E15.

The Decoupling Concept Bottleneck Model.

The Concept Bottleneck Model (CBM) is an interpretable neural network that leverages high-level concepts to explain model decisions and conduct human-machine interaction. However, in real-world scenarios, the deficiency of informative concepts can impede the model's interpretability and subsequent interventions. This paper proves that insufficient concept information can lead to an inherent dilemma of concept and label distortions in CBM.

Statistical batch-aware embedded integration, dimension reduction, and alignment for spatial transcriptomics.

Motivation: Spatial transcriptomics (ST) technologies provide richer insights into the molecular characteristics of cells by simultaneously measuring gene expression profiles and their relative locations. However, each slice can only contain limited biological variation, and since there are almost always non-negligible batch effects across different slices, integrating numerous slices to account for batch effects and locations is not straightforward. Performing multi-slice integration, dimensionality reduction, and other downstream analyses separately often results in suboptimal embeddings for technical artifacts and biological variations.

Visualization of metabolite distribution based on matrix-assisted laser desorption/ionization-mass spectrometry imaging of tea seedlings ().

Tea seedlings () have a well-developed root system with a strong taproot and lateral roots. Compared with ordinary cuttings, tea has stronger vitality and environmental adaptability, thus facilitating the promotion of good varieties. However, there is less of detailed research on the rooting and germination process of tea seeds.

ImputeHiFI: An Imputation Method for Multiplexed DNA FISH Data by Utilizing Single-Cell Hi-C and RNA FISH Data.

Although multiplexed DNA fluorescence in situ hybridization (FISH) enables tracking the spatial localization of thousands of genomic loci using probes within individual cells, the high rates of undetected probes impede the depiction of 3D chromosome structures. Current data imputation methods neither utilize single-cell Hi-C data, which elucidate 3D genome architectures using sequencing nor leverage multimodal RNA FISH data that reflect cell-type information, limiting the effectiveness of these methods in complex tissues such as the mouse brain. To this end, a novel multiplexed DNA FISH imputation method named ImputeHiFI is proposed, which fully utilizes the complementary structural information from single-cell Hi-C data and the cell type signature from RNA FISH data to obtain a high-fidelity and complete spatial location of chromatin loci.

U-Match: Exploring Hierarchy-Aware Local Context for Two-View Correspondence Learning.

Rejecting outlier correspondences is one of the critical steps for successful feature-based two-view geometry estimation, and contingent heavily upon local context exploration. Recent advances focus on devising elaborate local context extractors whereas typically adopting explicit neighborhood relationship modeling at a specific scale, which is intrinsically flawed and inflexible, because 1) severe outliers often populated in putative correspondences and 2) the uncertainty in the distribution of inliers and outliers make the network incapable of capturing adequate and reliable local context from such neighborhoods, therefore resulting in the failure of pose estimation. This prospective study proposes a novel network called U-Match that has the flexibility to enable implicit local context awareness at multiple levels, naturally circumventing the aforementioned issues that plague most existing studies.

Whole brain alignment of spatial transcriptomics between humans and mice with BrainAlign.

The increasing utilization of mouse models in human neuroscience research places higher demands on computational methods to translate findings from the mouse brain to the human one. In this study, we develop BrainAlign, a self-supervised learning approach, for the whole brain alignment of spatial transcriptomics (ST) between humans and mice. BrainAlign encodes spots and genes simultaneously in two separated shared embedding spaces by a heterogeneous graph neural network.

Relationship between Vitamin D Concentration and Lipid Concentration in Patients with NAFLD in the Hulunbuir Region of China.

Background: We aimed to characterize the relationship between the serum 25-hydroxyvitamin D concentration and the circulating lipid concentrations of patients with NAFLD in the Hulunbuir region of China.

Methods: One hundred fifty-six patients, who were diagnosed with NAFLD in the Physical Examination Department of the Second Clinical College of Inner Mongolia University for the Nationalities between January 2021 and March 2023, were recruited as NAFLD group, and 160 healthy people were recruited as a control group during the same period. The serum 25(OH)VitD, TBIL, TG, TC, LDL-C, HDL-C, AST, ALT, GGT, and FPG activities of the participants were measured, and hepatic ultrasonography was performed.

Exploring the promoting effect of nitrilotriacetic acid on hydroxyl radical and humification during magnetite-amended composting of sewage sludge.

The OH production by adding magnetite (MGT) alone has been reported in composting. However, the potential of nitrilotriacetic acid (NTA) addition for magnetite-amended sludge composting remained unclear. Three treatments with different addition [control check (CK); T1: 5 % MGT; T2: 5 % MGT + 5 % NTA] were investigated to characterize hydroxyl radical, humification and bacterial community response.

Divacancy and resonance level enables high thermoelectric performance in n-type SnSe polycrystals.

N-type polycrystalline SnSe is considered as a highly promising candidates for thermoelectric applications due to facile processing, machinability, and scalability. However, existing efforts do not enable a peak ZT value exceeding 2.0 in n-type polycrystalline SnSe.

Characteristics of humification, functional enzymes and bacterial community metabolism during manganese dioxide-added composting of municipal sludge.

The aim of this study was to assess effects of MnO addition (CK-0%, T1-2% and T2-5%) on humification and bacterial community during municipal sludge (MS) composting. The results suggested that MnO addition inhibited the growth of Nitrospira but stimulated Nonomuraea, Actinomadura, Streptomyces and Thermopolyspora, facilitating the lignocellulose degradation and humification with the increase in organic matter degradation by 13.8%-19.

High-density generation of spatial transcriptomics with STAGE.

Spatial transcriptome technologies have enabled the measurement of gene expression while maintaining spatial location information for deciphering the spatial heterogeneity of biological tissues. However, they were heavily limited by the sparse spatial resolution and low data quality. To this end, we develop a spatial location-supervised auto-encoder generator STAGE for generating high-density spatial transcriptomics (ST).

CdSe Quantum Dots Enable High Thermoelectric Performance in Solution-Processed Polycrystalline SnSe.

Here, a high peak ZT of ≈2.0 is reported in solution-processed polycrystalline Ge and Cd codoped SnSe. Microstructural characterization reveals that CdSe quantum dots are successfully introduced by solution process method.

LncRNA 51325 Alleviates Bone Cancer Induced Hyperalgesia Through Inhibition of Pum2.

Background: Bone cancer pain (BCP) represents one of the most challenging comorbidities associated with cancer metastasis. Long non-coding RNAs (lncRNAs) have garnered attention as potential therapeutic agents in managing neuropathic pain. However, their role in the regulation of nociceptive information processing remains poorly understood.

Integrating spatial transcriptomics data across different conditions, technologies and developmental stages.

With the rapid generation of spatial transcriptomics (ST) data, integrative analysis of multiple ST datasets from different conditions, technologies and developmental stages is becoming increasingly important. Here we present a graph attention neural network called STAligner for integrating and aligning ST datasets, enabling spatially aware data integration, simultaneous spatial domain identification and downstream comparative analysis. We apply STAligner to ST datasets of the human cortex slices from different samples, the mouse olfactory bulb slices generated by two profiling technologies, the mouse hippocampus tissue slices under normal and Alzheimer's disease conditions, and the spatiotemporal atlases of mouse organogenesis.

Effects of adding steel slag on humification and characteristics of bacterial community during phosphate-amended composting of municipal sludge.

This study aimed to investigate the effects of different proportions (0%, 5%, 7.5%, and 10%) of steel slag (SS) on humification and bacterial community characteristics during phosphate-amended composting of municipal sludge. Compared with adding KHPO alone, co-adding SS significantly promoted the temperature, pH, nitrification, and critical enzyme activities (polyphenol oxidase, cellulase, laccase); especially organic matter (OM) degradation rate (25.

The involvement of the gut microbiota in postoperative cognitive dysfunction based on integrated metagenomic and metabolomics analysis.

As the population ages and medical technology advances, anesthesia procedures for elderly patients are becoming more common, leading to an increased prevalence of postoperative cognitive dysfunction. However, the etiology and correlation between the gut microbiota and cognitive dysfunction are poorly understood, and research in this area is limited. In this study, mice with postoperative cognitive dysfunction were found to have reduced levels of fatty acid production and anti-inflammatory flora in the gut, and was associated with increased depression, leading to cognitive dysfunction and depression.

ConvMatch: Rethinking Network Design for Two-View Correspondence Learning.

Multilayer perceptron (MLP) has become the de facto backbone in two-view correspondence learning, for it can extract effective deep features from unordered correspondences individually. However, the problem of natively lacking context information limits its performance although many context-capturing modules are appended in the follow-up studies. In this paper, from a novel perspective, we design a correspondence learning network called ConvMatch that for the first time can leverage a convolutional neural network (CNN) as the backbone, inherently capable of context aggregation.