Corrigendum to "Identification of gene regulatory networks associated with breast cancer patient survival using an interpretable deep neural network model" [Expert Syst. Appl. 262 (2025) 125632].

[This corrects the article PMC11643596.].

Host plant and soil nutrient filters mediate long-term grazing on arbuscular mycorrhizal fungi in desert grasslands.

Arbuscular mycorrhizal fungi (AMF) enhance plant performance through improved nutrient acquisition, stress resilience, and pathogen resistance while strengthening ecosystem functions through soil structure stabilization and carbon sequestration. Livestock grazing is the dominant grassland land-use globally, but the effects of increased grazing intensity on AMF remain debated. Importantly, the mechanistic drivers of AMF responses to grazing intensity remain poorly understood, particularly in arid grasslands.

Robustness and resilience of computational deconvolution methods for bulk RNA sequencing data.

This study benchmarks the robustness and resilience of computational deconvolution methods for estimating cell-type proportions in bulk tissues, with a focus on comparing reference-based and reference-free methods. Robustness is evaluated by generating in silico pseudo-bulk tissue RNA sequencing data from cell-level gene expression profiles derived from four different tissue types, with simulated cellular composition at varying levels of heterogeneity. To assess resilience, we intentionally alter single-cell RNA profiles to create pseudo-bulk tissue RNA-seq data.

An augmented GSNMF model for complete deconvolution of bulk RNA-seq data.

Performing complete deconvolution analysis for bulk RNA-seq data to obtain both cell type specific gene expression profiles (GEP) and relative cell abundances is a challenging task. One of the fundamental models used, the nonnegative matrix factorization (NMF), is mathematically ill-posed. Although several of complete deconvolution methods have been developed and their estimates compared to ground truth for some datasets appear promising, a comprehensive understanding of how to circumvent the ill-posedness and improve solution accuracy is still lacking.

Photocatalytic Pyridyl-carbamoylation of Alkenes for Accessing β-Pyridyl Amides.

The β-pyridyl amide is a critical scaffold in medical discovery yet lacks efficient synthetic methods. Here, we describe, for the first time, a visible-light-induced, redox-neutral radical cross-coupling reaction involving alkenes, oxamic acids, and cyanopyridines that offers a versatile assembly of β-pyridylamides. This approach features mild reaction conditions, high step efficiency, and substrate breadth, providing a green and efficient strategy for alkene pyridyl-carbamoylation.

Phosphoric Acid-Catalyzed Enantioselective Synthesis of Axially Chiral Cyclobutanamides.

Chiral cyclobutanamide is a privileged scaffold in drug discovery. Here, we describe, for the first time, the synthesis of axially chiral cyclobutanamides via phosphoric acid-catalyzed enantioselective condensation between -arylcarbamyl cyclobutanones and hydroxylamines. Rational substrate design, incorporating an amide moiety (CONHR) into the cyclobutanone backbone and the formation of a multi-hydrogen bonding network involving the N-H of this amide portion, is responsible for the excellent enantioselectivity achieved in the stereodetermining dehydration process, which is supported by a detailed mechanistic study.

Identification of Gene Regulatory Networks Associated with Breast Cancer Patient Survival Using an Interpretable Deep Neural Network Model.

Artificial neural networks have recently gained significant attention in biomedical research. However, their utility in survival analysis still faces many challenges. In addition to designing models for high accuracy, it is essential to optimize models that provide biologically meaningful insights.

Soil deterioration due to long-term grazing of desert-steppe promotes stress-tolerant ecological strategies in plants.

Predicting the impact of grazing on desert steppes' vegetation is crucial for sustainable management. The competitor, stress-tolerator and ruderal (CSR) theory has offer valuable insights into plant adaptive capacity and predicting changes in vegetation structure. However, whether adaptive strategy of desert steppe change with grazing intensity is not understood yet.

Linkage between soil stoichiometric imbalance and microbial carbon use efficiency in desert steppe under different grazing intensities.

Long-term grazing alters soil resource availability and microbial biomass stoichiometry in grassland ecosystems. Exploring the relationship between soil stoichiometric imbalance and microbial carbon use efficiency (CUE) in grazed desert steppe can help understand soil carbon dynamics from a microbial perspective. Based on a long-term grazing platform in desert steppe of Inner Mongolia established in 2004, taking heavy, moderate and light grazing intensities, using no grazing as a control, we measured soil available nutrients, microbial biomass and associated enzyme activities for their acquisition, and calculated soil microbial CUE using ecological stoichiometry.

Impact of climate warming on soil microbial communities during the restoration of the inner Mongolian desert steppe.

Introduction: Grazer exclosure is widely regarded as an effective measure for restoring degraded grasslands, having positive effects on soil microbial diversity. The Intergovernmental Panel on Climate Change (IPCC) predicts that global surface temperatures will increase by 1.5-4.

Novel PDI-NH/PDI-COOH Supramolecular Junction for Enhanced Visible-Light Photocatalytic Phenol Degradation.

The development of efficient and environmentally friendly photocatalysts is crucial for addressing global energy and environmental challenges. Perylene diimide, an organic supramolecular material, holds great potential for applications in mineralized phenol. In this study, through the integration of different mass ratios of unmodified perylenimide (PDI-NH) into the self-assembly of amino acid-substituted perylenimide (PDI-COOH), a novel supramolecular organic heterojunction (PDICOOH/PDINH) was fabricated.

Enhanced 1,2-dichloroethane removal using g-CN/Blue TiO nanotube array photoanode in microbial photoelectrochemical cells.

The compound 1,2-dichloroethane (1,2-DCA), a persistent and ubiquitous pollutant, is often found in groundwater and can strongly affect the ecological environment. However, the extreme bio-impedance of C-Cl bonds means that a high energy input is needed to drive biological dechlorination. Biotechnology techniques based on microbial photoelectrochemical cell (MPEC) could potentially convert solar energy into electricity and significantly reduce the external energy inputs currently needed to treat 1,2-DCA.

Phosphoric Acid-Catalyzed Alkene Difunctionalization of 2-Vinylpyridines via HOMO/LUMO Biactivated Diels-Alder Reaction.

The difunctionalization of vinylpyridines based on the cyclization strategy remains rare and underdeveloped, in contrast to the well-developed hydrogen functionalization. Current exploration on [4 + 2] cyclization of vinylpyridines mainly relies on extremely high temperatures and the LUMO activation of vinylpyridines using boron trifluoride as a strong Lewis acid. Herein, we established a phosphoric acid-catalyzed [4 + 2] cyclization reaction of 3-vinyl-1H-indoles and 2-vinylpyridines by means of the LUMO/HOMO bifunctional activation model.

High stocking rates effects in continuous season long grazing reduces the contribution of microbial necromass to soil organic carbon in a semi-arid grassland in Inner Mongolia.

Livestock grazing strongly influences the accumulation of soil organic carbon (SOC) in grasslands. However, whether the changes occurring in SOC content under different intensities of continuous summer long grazing are associated with the changes in microbially-derived necromass C remains unclear. Here, we established a sheep grazing experiment in northern China in 2004 with four different stocking rates.

Effects of inhaled fine particulate matter on the lung injury as well as gut microbiota in broilers.

Fine particulate matter (PM) has been widely regarded as an important environmental risk factor that has widely influenced health of both animals and humans. Lung injury is the main cause of PM affecting respiratory tract health. Gut microbiota participates in the development of lung injury in many pathological processes.

Comparative transcriptomics reveal differential gene expression among Plasmodium vivax geographical isolates and implications on erythrocyte invasion mechanisms.

The documentation of Plasmodium vivax malaria across Africa especially in regions where Duffy negatives are dominant suggests possibly alternative erythrocyte invasion mechanisms. While the transcriptomes of the Southeast Asian and South American P. vivax are well documented, the gene expression profile of P.

Fine Particulate Matter Perturbs the Pulmonary Microbiota in Broiler Chickens.

(1) Fine particulate matter (PM) seriously affects the respiratory tract health of both animals and humans. Growing evidence indicates that the pulmonary microbiota is involved in the development of respiratory tract health; however, there is still much that is unknown about the specific changes of pulmonary microbiota caused by PM in broilers. (2) In this experiment, a total of 48 broilers were randomly divided into a control group and PM-exposure group.

Health Information on Pre-Exposure Prophylaxis From Search Engines and Twitter: Readability Analysis.

Background: Pre-exposure prophylaxis (PrEP) is proven to prevent HIV infection. However, PrEP uptake to date has been limited and inequitable. Analyzing the readability of existing PrEP-related information is important to understand the potential impact of available PrEP information on PrEP uptake and identify opportunities to improve PrEP-related education and communication.

Analysis of the Differential Expression and Antiviral Activity of Porcine Interferon-α In Vitro.

Porcine interferon α (poIFN-α) is a crucial cytokine that can prevent and treat viral infections. Seventeen functional porcine IFN-α subtypes were found in the porcine genome. In this study, multiple sequence alignment was performed to analyze IFN-α protein structure and function.

Comparative transcriptomics reveal differential gene expression in geographical isolates and implications on erythrocyte invasion mechanisms.

uses Duffy binding protein (PvDBP1) to bind to the Duffy Antigen-Chemokine Receptor (DARC) to invade human erythrocytes. Individuals who lack DARC expression (Duffy-negative) are thought to be resistance to . In recent years, malaria is becoming more prevalent in Africa with a portion of these cases detected in Duffy-negatives.

Biodiversity and soil pH regulate the recovery of ecosystem multifunctionality during secondary succession of abandoned croplands in northern China.

The 'Grain-for-Green' program in China provides a valuable opportunity to investigate whether spontaneous restoration can reverse the deterioration of grassland ecosystem functions. Previous studies have focused on individual ecosystem functions, but the response of and mechanisms driving variation in ecosystem multifunctionality (EMF) during restoration are poorly understood. Here, we quantified EMF using productivity, nutrient cycling, and water regulation functions along abandoned croplands in a recovery chronosequence (5, 15 and 20 years) and in natural grasslands in the desert steppe and typical steppe.

Accessing chiral sulfones bearing quaternary carbon stereocenters via photoinduced radical sulfur dioxide insertion and Truce-Smiles rearrangement.

From the viewpoint of synthetic accessibility and functional group compatibility, photoredox-catalyzed sulfur dioxide insertion strategy enables in situ generation of functionalized sulfonyl radicals from easily accessible starting materials under mild conditions, thereby conferring broader application potential. Here we present two complementary photoinduced sulfur dioxide insertion systems to trigger radical asymmetric Truce-Smiles rearrangements for preparing a variety of chiral sulfones that bear a quaternary carbon stereocenter. This protocol features broad substrate scope and excellent stereospecificity.

GEOMETRIC STRUCTURE GUIDED MODEL AND ALGORITHMS FOR COMPLETE DECONVOLUTION OF GENE EXPRESSION DATA.

Complete deconvolution analysis for bulk RNA-seq data is important and helpful to distinguish whether the differences of disease-associated GEPs (gene expression profiles) in tissues of patients and normal controls are due to changes in cellular composition of tissue samples, or due to GEPs changes in specific cells. One of the major techniques to perform complete deconvolution is nonnegative matrix factorization (NMF), which also has a wide-range of applications in the machine learning community. However, the NMF is a well-known strongly ill-posed problem, so a direct application of NMF to RNA-seq data will suffer severe difficulties in the interpretability of solutions.

Distance-Based Analysis with Quantile Regression Models.

Non-standard structured, multivariate data are emerging in many research areas, including genetics and genomics, ecology, and social science. Suitably defined pairwise distance measures are commonly used in distance-based analysis to study the association between the variables. In this work, we consider a linear quantile regression model for pairwise distances.