Overcoming artificial structures in resolution-enhanced Hi-C data by signal decomposition and multi-scale attention.

Computational enhancement is an important strategy for inferring high-resolution features from genome-wide chromosome conformation capture (Hi-C) data, which typically have limited resolution. Deep learning has been highly successful in this task but we show that it creates prevalent artificial structures in the enhanced data due to the need to divide the large contact matrix into small patches. In addition, previous deep learning methods largely focus on local patterns, which cannot fully capture the complexity of Hi-C data.

CircABCC1 reduces endometrial receptivity via METTL3/FAM155B axis.

Objective: Impaired endometrial receptivity is the main cause of embryo implantation failure. Little information is available on the role of circRNAs in endometrial receptivity. Here, the effect of circABCC1 on endometrial receptivity and its mechanism were investigated.

Transcriptome-Optimized Hydrogel Design of a Stem Cell Niche for Enhanced Tendon Regeneration.

Bioactive hydrogels have emerged as promising artificial niches for enhancing stem cell-mediated tendon repair. However, a substantial knowledge gap remains regarding the optimal combination of niche features for targeted cellular responses, which often leads to lengthy development cycles and uncontrolled healing outcomes. To address this critical gap, an innovative, data-driven materiomics strategy is developed.

Development and validation of a prognostic score for TIPS placement in patients with viral hepatitis cirrhosis-related portal hypertension: a multi-center retrospective study.

Introduction: There is no established scoring model focused on viral hepatitis patients to predict the prognosis after transjugular intrahepatic portosystemic shunt (TIPS). We aimed to develop and validate a novel model based on the largest cohort for better prediction of both short-term (1 year) and long-term (3 years) postoperative prognoses after TIPS in viral hepatitis cirrhosis-related portal hypertension patients.

Methods: A total of 925 viral hepatitis cirrhosis-related portal hypertension patients who underwent TIPS from nine hospitals were divided into the training and external validation cohorts.

Rapid diagnosis of infection in acute very severe aplastic anemia with metagenomic next-generation sequencing: a case report and literature review.

Infection remains the leading cause of mortality in severe aplastic anemia (SAA) patients, with invasive fungal infections being the great threat. accounts for most of the reported fungal infection cases. Here, we present a case of infection in a patient with acute very severe aplastic anemia (VSAA) despite persistently negative clinical fungal tests.

Self-Sacrificed Additive in Preparing PbI Film Enables the Oriented Growth of Perovskite Crystals for Improved Solar Cell Performance.

Due to the limitation of the diffusion kinetics of organic amine salts on the PbI layer in the two-step method, prepared perovskite particles are small in size, have many defects, and are randomly oriented, and the cell efficiency and stability are difficult to guarantee due to PbI residues. Here, we added a volatile additive, ,,','-tetramethylethylenediamine (TMEDA), to the PbI precursor solution and formed preaggregated atomic clusters with PbI through TMEDA, which reduced the Gibbs free energy of nucleation to obtain a porous PbI layer, and finally obtained a perovskite film with large particles, few defects, ideal crystal plane orientation, and no additive residues. The results show that the photoelectric conversion efficiency of the optimized device is increased by 1.

Gut microbiome pattern impacts treatment response in primary biliary cholangitis.

Background: Primary biliary cholangitis (PBC) is a progressive autoimmune liver disease. An inadequate response to ursodeoxycholic acid (UDCA) poses a high risk of progression toward end-stage liver disease. Gut dysbiosis has been implicated in PBC.

Molecular architecture of the assembly of Bacillus spore coat protein GerQ revealed by cryo-EM.

Protein filaments are ubiquitous in nature and have diverse biological functions. Cryo-electron microscopy (cryo-EM) enables the determination of atomic structures, even from native samples, and is capable of identifying previously unknown filament species through high-resolution cryo-EM maps. In this study, we determine the structure of an unreported filament species from a cryo-EM dataset collected from Bacillus amyloiquefaciens biofilms.

A magnetic resonance imaging-based lymph node regression grading scheme for nasopharyngeal carcinoma after radiotherapy.

Background: Among patients with nasopharyngeal carcinoma (NPC), there is no established method to distinguish between patients with residual disease that may eventually progress and those who have achieved cured. We thus aimed to assess the prognostic value of magnetic resonance imaging (MRI)-based lymph node regression grade (LRG) in the risk stratification of patients with NPC following radiotherapy (RT).

Methods: This study retrospectively enrolled 387 patients newly diagnosed with NPC between January 2010 and January 2013.

Targeted metabolomics study of fatty-acid metabolism in lean metabolic-associated fatty liver disease patients.

Background: The annual incidence of metabolic-associated fatty liver disease (MAFLD) in China has been increasing and is often overlooked owing to its insidious characteristics. Approximately 50% of the patients have a normal weight or are not obese. They are said to have lean-type MAFLD, and few studies of such patients are available.

Age and estimated glomerular filtration rate in Chinese older adults: a cohort study from 2014 to 2020.

Objectives: This study aimed to fill the data gap of the course of renal function decline in old age and explore changes in renal function across different health states with increasing age.

Methods: This observational, retrospective, single-center cohort study included 5,112 Chinese older adults (3,321 men and 1,791 women, range 60-104 years). The individual rate of estimated glomerular filtration rate (eGFR) decline was analyzed using linear mixed-effects model to account for repeated measures over the years.

Commonly used software tools produce conflicting and overly-optimistic AUPRC values.

The precision-recall curve (PRC) and the area under the precision-recall curve (AUPRC) are useful for quantifying classification performance. They are commonly used in situations with imbalanced classes, such as cancer diagnosis and cell type annotation. We evaluate 10 popular tools for plotting PRC and computing AUPRC, which were collectively used in more than 3000 published studies.

Tailoring the Buried Interface by Dipolar Halogen-Substituted Arylamine for Efficient and Stable Perovskite Solar Cells.

Improving the quality of the buried interface is decisive for achieving stable and high-efficiency perovskite solar cells. Herein, we report the interface engineering by using dipolar 2,4-difluoro-3,5-dichloroaniline (DDE) as the adhesive between titanium dioxide (TiO) and MAPbI. By manipulation of the anchoring groups of DDE, this molecule not only passivated defects of TiO but also optimized the energy level alignment.

Commonly used software tools produce conflicting and overly-optimistic AUPRC values.

The precision-recall curve (PRC) and the area under it (AUPRC) are useful for quantifying classification performance. They are commonly used in situations with imbalanced classes, such as cancer diagnosis and cell type annotation. We evaluated 10 popular tools for plotting PRC and computing AUPRC, which were collectively used in >3,000 published studies.

Evaluating the clinical performance of methylation for colorectal cancer detection.

The performance and clinical accuracy of combined methylation were evaluated in diagnosing colorectal cancer (CRC) and advanced adenoma.  A total of 2333 participants were enrolled to assess the sensitivity and specificity of biomarkers in diagnosing CRC in a multicenter clinical trial through feces DNA methylation tests. methylation showed excellent performance for CRC detection in biomarker research and the real world.

Simultaneous quantification of mirabegron and vibegron in human plasma by HPLC-MS/MS and its application in the clinical determination in patients with tumors associated with overactive bladder.

Mirabegron and vibegron, both newly identified beta-3 adrenergic agonists, have significantly improved the quality of life for patients suffering from overactive bladder. In order to comprehensively assess the plasma exposure levels of these agents, the development of a rapid and highly sensitive bioanalytical method becomes imperative. The primary objective of this study was to establish a robust high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method for the concurrent quantification of mirabegron and vibegron in human plasma.

Oxide Ion Conduction in Ca-Doped YbGaO Garnet.

Developing oxide ion conductors with new structural families is important for many energy conversion and storage techniques. Herein, a series of Ca-doped YbGaO garnet-type materials are prepared through a traditional solid-state reaction method, with their oxide ion conduction properties being reported for the first time. The results revealed that Ca substitution for Yb would significantly improve the conductivity of YbGaO from 3.

Artificial dermis combined with skin grafting for the treatment of hand skin and soft tissue defects and exposure of bone and tendon.

Background: The recovery time of hand wounds is long, which can easily result in chronic and refractory wounds, making the wounds unable to be properly repaired. The treatment cycle is long, the cost is high, and it is prone to recurrence and disability. Double layer artificial dermis combined with autologous skin transplantation has been used to repair hypertrophic scars, deep burn wounds, exposed bone and tendon wounds, and post tumor wounds.

Cryo-EM structures of the D290V mutant of the hnRNPA2 low-complexity domain suggests how D290V affects phase separation and aggregation.

Heterogeneous nuclear ribonucleoprotein A2 (hnRNPA2) is a human ribonucleoprotein that transports RNA to designated locations for translation via its ability to phase separate. Its mutated form, D290V, is implicated in multisystem proteinopathy known to afflict two families, mainly with myopathy and Paget's disease of bone. Here, we investigate this mutant form of hnRNPA2 by determining cryo-EM structures of the recombinant D290V low complexity domain.

Serine peptidase Vpr forms enzymatically active fibrils outside Bacillus bacteria revealed by cryo-EM.

Bacteria develop a variety of extracellular fibrous structures crucial for their survival, such as flagella and pili. In this study, we use cryo-EM to identify protein fibrils surrounding lab-cultured Bacillus amyloiquefaciens and discover an unreported fibril species in addition to the flagellar fibrils. These previously unknown fibrils are composed of Vpr, an extracellular serine peptidase.

Quantitative calculation of gases generation during low-temperature oxidation of coal.

The gases evolution during the low-temperature oxidation of coal is an essential parameter used to assess the state of coal oxidation and to estimate the gaseous pollutants. However, the current semi-quantitative method, which employs gas concentration as the measurement standard, is flawed. This paper presents a quantitative calculation method for gas products during coal oxidation.

Long-Read Sequencing Reveals Alternative Splicing-Driven, Shared Immunogenic Neoepitopes Regardless of SF3B1 Status in Uveal Melanoma.

Tumor-specific neoepitopes are promising targets in cancer immunotherapy. However, the identification of functional tumor-specific neoepitopes remains challenging. In addition to the most common source, single-nucleotide variants (SNV), alternative splicing (AS) represents another rich source of neoepitopes and can be utilized in cancers with low SNVs such as uveal melanoma (UM).

Transcriptomic and Functional Analyses of Two Cadmium Hyper-Enriched Duckweed Strains Reveal Putative Cadmium Tolerance Mechanisms.

Cadmium (Cd) is one of the most toxic metals in the environment and exerts deleterious effects on plant growth and production. Duckweed has been reported as a promising candidate for Cd phytoremediation. In this study, the growth, Cd enrichment, and antioxidant enzyme activity of duckweed were investigated.