Systematic evaluation of methylation-based cell type deconvolution methods for plasma cell-free DNA.

Background: Plasma cell-free DNA (cfDNA) is derived from cellular death in various tissues. Investigating the tissue origin of cfDNA through cell type deconvolution, we can detect changes in tissue homeostasis that occur during disease progression or in response to treatment. Consequently, cfDNA has emerged as a valuable noninvasive biomarker for disease detection and treatment monitoring.

A genus-specific R2R3 MYB transcription factor, CsMYB34, regulates galloylated catechin biosynthesis in Camellia sinensis.

Galloylated catechins are the dominant polyphenols in Camellia sinensis (L.) O. Kuntze.

Dissecting gene expression heterogeneity: generalized Pearson correlation squares and the -lines clustering algorithm.

Motivated by the pressing needs for dissecting heterogeneous relationships in gene expression data, here we generalize the squared Pearson correlation to capture a mixture of linear dependences between two real-valued variables, with or without an index variable that specifies the line memberships. We construct the generalized Pearson correlation squares by focusing on three aspects: variable exchangeability, no parametric model assumptions, and inference of population-level parameters. To compute the generalized Pearson correlation square from a sample without a line-membership specification, we develop a -lines clustering algorithm to find clusters that exhibit distinct linear dependences, where can be chosen in a data-adaptive way.

Functional analysis of yak alveolar type II epithelial cells at high and low altitudes based on single-cell sequencing.

The adaptation of lung cells to high-altitude environments represents a notable gap in our understanding of how animals cope with hypoxic conditions. Alveolar epithelial cells type II (AEC II) are crucial for lung development and repair. However, their, specific role in the adaptation of yaks to high-altitude environments remains unclear.

Self-Cross-Linked Collagen Sponge from the Scale for Hemostasis and Wound Healing Applications.

Type I collagen, a crucial component maintaining the structural integrity and physiological function of various tissues, is widely regarded as one of the most suitable biomaterials for healthcare applications. In this study, shad scales, used for treating ulcers, scalds, and burns in traditional Chinese medicine, were exploited for type I collagen extraction. After self-assembly into hydrogels, the extracted collagen was subsequently freeze-dried to form collagen sponges.

CRISPR-Cas9-based genome-editing technologies in engineering bacteria for the production of plant-derived terpenoids.

Terpenoids are widely used as medicines, flavors, and biofuels. However, the use of these natural products is largely restricted by their low abundance in native plants. Fortunately, heterologous biosynthesis of terpenoids in microorganisms offers an alternative and sustainable approach for efficient production.

Association between serum uric acid and prediabetes in a normal Chinese population: A cross-sectional study.

Cardiovascular events are frequent among individuals with prediabetes. And the relationship between cardiovascular diseases and elevated serum uric acid (SUA) levels has been supported by extensive scientific evidence. However, there remains controversy regarding the correlation between elevated SUA and prediabetes.

Combination of DMDD with Nanoparticles Effective Against Diabetic Kidney Disease in vitro.

Purpose: 2-Dodecyl-6-methoxy-2,5-diene-1,4-cyclohexanedione (DMDD), isolated from . root, has demonstrated the potential to reduce blood sugar levels. However, DMDD has poor solubility and bioavailability.

Wnt signaling aberrant activation drives ameloblastoma invasion and recurrence: bioinformatics and in vitro insights.

Objective: This study aims to explore the regulatory mechanisms of Wnt signaling in the invasion and recurrence of ameloblastoma (AM) to provide a new theoretical basis for its treatment.

Methods: Bulk RNA sequencing was employed to analyze samples from AM patients, and identify differentially expressed genes. Subsequently, bioinformatics methods such as Weighted Gene Co-Expression Network Analysis (WGCNA), DESeq2, and KEGG enrichment analysis were utilized to construct gene co-expression networks and identify pathways associated with invasion and recurrence.

Integrated molecular and functional characterization of the intrinsic apoptotic machinery identifies therapeutic vulnerabilities in glioma.

Genomic profiling often fails to predict therapeutic outcomes in cancer. This failure is, in part, due to a myriad of genetic alterations and the plasticity of cancer signaling networks. Functional profiling, which ascertains signaling dynamics, is an alternative method to anticipate drug responses.

Epigenetic modifications involving ncRNAs in digestive system cancers: focus on histone modification.

In recent years, epigenetic modifications have been strongly linked to tumor development, with histone modifications representing a key epigenetic mechanism. In addition, non-coding RNAs (ncRNAs) play a critical role in regulating cancer-related pathways. The abnormal interaction between histone modifications and ncRNAs, both pivotal epigenetic regulators, has been widely observed across various cancer types.

Soil community history strengthens belowground multitrophic functioning across plant diversity levels in a grassland experiment.

Biodiversity experiments revealed that plant diversity loss can decrease ecosystem functions across trophic levels. To address why such biodiversity-function relationships strengthen over time, we established experimental mesocosms replicating a gradient in plant species richness across treatments of shared versus non-shared history of (1) the plant community and (2) the soil fauna community. After 4 months, we assessed the multitrophic functioning of soil fauna via biomass stocks and energy fluxes across the food webs.

Research on information leakage in time series prediction based on empirical mode decomposition.

Time series analysis predicts the future based on existing historical data and has a wide range of applications in finance, economics, meteorology, biology, engineering, and other fields. Although the combination of decomposition techniques and machine learning algorithms can effectively solve the problem of predicting nonstationary sequences, this kind of decomposition-integration-prediction strategy of the prediction method has serious defects. After the decomposition of the division of the training set and the test set, the information of the test set in the process of decomposition of the information leakage ultimately shows a high accuracy of the prediction of the illusionary.

Sensitive detection of Hg(II) on MoS/NiS based on interfacial engineering to accelerate the Ni/Ni cycle: Identification the role of atomic-level heterojunction-induced electron transfer in electroanalysis.

The valence change of transition metal ions in nanomaterials can highly enhance the electrochemical detection performance toward heavy metal ions (HMIs), and how to further promote the valence change calls enormous concerns in electroanalysis. In this work, an interfacial engineering that combing the MoS and NiS together to form the MoS/NiS complex is proposed. The density functional theory (DFT) results reveals that the novel atomic-level heterojunction between MoS and NiS will build an internal electric field (IEF), which leads to an enhanced conductivity and valence change behavior of Ni atoms in MoS/NiS complex, resulting in a superior detection performance.

Zinc Oxide Nanoparticles Treatment Maintains the Postharvest Quality of Litchi Fruit by Inducing Antioxidant Capacity.

Pericarp browning and fruit decay severely reduce the postharvest quality of litchi. Improving the antioxidant capacity of the fruit is an effective way to solve these problems. In our study, the appropriate zinc oxide nanoparticles (ZnO NPs) treatment and its mechanism of action on the storability of litchi was investigated.

Nigenolides A-H, 13 new microperfuranones with ferroptosis inhibitory activity from the deep-sea-derived Aspergillus niger.

Thirteen new microperfuranones, including five pairs of enantiomers, (±)-nigenolides A-E (1a/1b-5a/5b), and three racemate nigenolides F-H (6-8), together with four known analogues (9-12) were isolated from a deep-sea-derived Aspergillus niger 3A00562. The absolute configurations of the five pairs of enantiomers were determined by the comparison of the calculated and experimental ECD spectra. Compounds 3a, 4a, 4b, and 12 were able to inhibit RSL3-induced ferroptosis.

Spatial transcriptomic landscape unveils immunoglobin-associated senescence as a hallmark of aging.

To systematically characterize the loss of tissue integrity and organ dysfunction resulting from aging, we produced an in-depth spatial transcriptomic profile of nine tissues in male mice during aging. We showed that senescence-sensitive spots (SSSs) colocalized with elevated entropy in organizational structure and that the aggregation of immunoglobulin-expressing cells is a characteristic feature of the microenvironment surrounding SSSs. Immunoglobulin G (IgG) accumulated across the aged tissues in both male and female mice, and a similar phenomenon was observed in human tissues, suggesting the potential of the abnormal elevation of immunoglobulins as an evolutionarily conserved feature in aging.

Alg-MFDL: A multi-feature deep learning framework for allergenic proteins prediction.

The escalating global incidence of allergy patients illustrates the growing impact of allergic issues on global health. Allergens are small molecule antigens that trigger allergic reactions. A widely recognized strategy for allergy prevention involves identifying allergens and avoiding re-exposure.

Response to "Neglecting normalization impact in semi-synthetic RNA-seq data simulation generates artificial false positives" and "Winsorization greatly reduces false positives by popular differential expression methods when analyzing human population samples".

Two correspondences raised concerns or comments about our analyses regarding exaggerated false positives found by differential expression (DE) methods. Here, we discuss the points they raise and explain why we agree or disagree with these points. We add new analysis to confirm that the Wilcoxon rank-sum test remains the most robust method compared to the other five DE methods (DESeq2, edgeR, limma-voom, dearseq, and NOISeq) in two-condition DE analyses after considering normalization and winsorization, the data preprocessing steps discussed in the two correspondences.

Cell-Shearing Chemistry Directed Closed-Pore Regeneration in Biomass-Derived Hard Carbons for Ultrafast Sodium Storage.

The closed-pore structure of hard carbons holds the key to high plateau capacity and rapid diffusion kinetics when applied as sodium-ion battery (SIB) anodes. However, understanding and establishing the structure-electrochemistry relationship still remains a significant challenge. This work, for the first time, introduces an innovative deep eutectic solvent (DES) cell-shearing strategy to precisely tailor the cell structure of natural bamboo and consequently the closed-pore in its derived hard carbons.