TRIAGE: an R package for regulatory gene analysis.

Regulatory genes are critical determinants of cellular responses in development and disease, but standard RNA sequencing (RNA-seq) analysis workflows, such as differential expression analysis, have significant limitations in revealing the regulatory basis of cell identity and function. To address this challenge, we present the TRIAGE R package, a toolkit specifically designed to analyze regulatory elements in both bulk and single-cell RNA-seq datasets. The package is built upon TRIAGE methods, which leverage consortium-level H3K27me3 data to enrich for cell-type-specific regulatory regions.

The Use of Omics in Untangling the Effect of Lifestyle Factors in Pregnancy and Gestational Diabetes: A Systematic Review.

Aim: To synthesise the evidence from clinical trials and observational studies using omics techniques to investigate the impact of diet and lifestyle factors on metabolite profile in pregnancy, and in the prevention and management of gestational diabetes mellitus (GDM).

Materials And Methods: A systematic literature search was performed using PubMed, Ovid, CINAHL, and Web of Science databases in October 2023 and updated in September 2024. Inclusion criteria were randomised controlled trials (RCT) or non-RCTs in pregnant women with or without GDM, that measured diet and lifestyle factors, and which applied post-transcriptional omics approaches.

Replication Study and Meta-Analysis of the Contribution of Seven Genetic Polymorphisms in Immune-Related Genes to the Risk of Gastric and Colorectal Cancers.

Recently, it has been realized that immune processes participate in the pathogenesis of human cancers. A large number of genetic polymorphisms in immune-related genes have been extensively examined for their roles in the susceptibility of gastric cancer (GC) and colorectal cancer (CRC), including IL4 gene rs2070874, IL4RA gene rs1801275, IL18 gene rs187238, IL18RAP gene rs917997, IL17A gene rs8193036, IL23R gene rs1884444 and IL23R gene rs10889677. However, there is no consistent conclusion, which calls for further research.

Evaluation of Enrichment Approaches for the Study of the Viromes in Mollusk Species.

Invasive alien species such as freshwater snails have significantly affected the food, environment, and the health of humans and animals, which have unfortunately received insufficient attention. To facilitate the study of viromes in snail species, we compared the enrichment effect of cesium chloride (CsCl) and sucrose density gradient ultracentrifugations in the recovery of diverse viruses in Pomacea canaliculata and Achatina fulica. First, we showed that CsCl-based ultracentrifugation enriched more virus contigs and reduced the nucleic acid background of the Pomacea canaliculata and was thus beneficial for virus recovery.

Degraded products generated by iron stent inhibit the vascular smooth muscle cell proliferation by downregulating AP-1.

In-stent restenosis (ISR) following interventional therapy is a fatal clinical complication. Current evidence indicates that neointimal hyperplasia driven by uncontrolled proliferation of vascular smooth muscle cells (VSMC) is a major cause of restenosis. This implies that inhibiting VSMC proliferation may be an attractive approach for preventing in-stent restenosis.

Prognostic impact and risk factors of severe neutropenia in the early phase of treatment with trifluridine-tipiracil for metastatic colorectal cancer patients: a single-center retrospective study.

Purpose: We aimed to identify the risk factors for severe neutropenia in the early phase of trifluridine-tipiracil (FTD/TPI) treatment, and their impact on overall survival (OS).

Methods: This single-center retrospective study included patients with unresectable metastatic colorectal cancer who were treated with FTD/TPI. The primary endpoint was OS, and the secondary endpoint was severe neutropenia during the first and second cycles of FTD/TPI.

Life stage impact on the human skin ecosystem: lipids and the microbial community.

Sebaceous free fatty acids are metabolized by multiple skin microbes into bioactive lipid mediators termed oxylipins. This study investigated correlations between skin oxylipins and microbes on the superficial skin of pre-pubescent children (N = 36) and adults (N = 100), including pre- (N = 25) and post-menopausal females (N = 25). Lipidomics and metagenomics revealed that Malassezia restricta positively correlated with the oxylipin 9,10-DiHOME on adult skin and negatively correlated with its precursor, 9,10-EpOME, on pre-pubescent skin.

Blackcurrant (Ribes nigrum L.) and Its Association with Donepezil Restore Cognitive Impairment, Suppress Oxidative Stress and Pro-inflammatory Responses, and Improve Purinergic Signaling in a Scopolamine-Induced Amnesia Model in Mice.

Purinergic signaling plays a major role in aging and neurodegenerative diseases, which are associated with memory decline. Blackcurrant (BC), an anthocyanin-rich berry, is renowned for its antioxidant and neuroprotective activities. However, evidence on the effects of BC on purinergic signaling is lacking.

Pulmonary Delivery of Nonviral Nucleic Acid-Based Vaccines With Spotlight on Gold Nanoparticles.

Nucleic acid-based vaccines are leading-edge tools in developing next-generation preventative care. Much research has been done to convert vaccine gene therapy from an invasive to a noninvasive administration approach. The lung's large surface area and permeability make the pulmonary route a promising noninvasive delivery option for vaccines, with systemic and local applications.

Sugar conditioning combined with nectar nonsugar compounds enhances honey bee pollen foraging in a nectarless diocious crop.

Recently, it has been shown that sugar‑conditioned honey bees can be biased towards a nectarless dioecious crop as kiwifruit. The challenges for an efficient pollination service in this crop species are its nectarless flowers and its short blooming period. It is known that combined non-sugar compounds (NSCs) present in the floral products of different plants, such as caffeine and arginine, enhance olfactory memory retention in honey bees.

Proteomic signature of HIV-associated subclinical left atrial remodeling and incident heart failure.

People living with HIV are at higher risk of heart failure and associated left atrial remodeling compared to people without HIV. Mechanisms are unclear but have been linked to inflammation and premature aging. Here we obtain plasma proteomics concurrently with cardiac magnetic resonance imaging in two independent study populations to identify parallels between HIV-related and aging-related immune dysfunction that could contribute to atrial remodeling and clinical heart failure.

Improved conversion of carbon dioxide to methane via photohydrogenation using GdNiMnO with a dendritic fibrous architecture.

The conversion of diluted CO₂ into high-energy fuels is increasingly central to renewable energy research. This study investigates the efficacy of a Gd₂NiMnO₆ dendritic nanofibrous (DNF) photocatalyst in transforming carbon dioxide to methane through photoreduction. Gd₂NiMnO₆ DNF was found to provide active adsorption sites and control the strand dimensions for metal groups, facilitating the chemical absorption of CO₂.

Developing novel Lin28 inhibitors by computer aided drug design.

Lin28 is a key regulator of cancer stem cell gene network that promotes therapy-resistant tumor progression in various tumors. However, no Lin28 inhibitor has been approved to treat cancer patients, urging exploration of novel compounds as candidates to be tested for clinical trials. In this contribution, we applied computer-aided drug design (CADD) in combination with quantitative biochemical and biological assays.

A broadly neutralizing antibody against the SARS-CoV-2 Omicron sub-variants BA.1, BA.2, BA.2.12.1, BA.4, and BA.5.

The global spread of Severe Acute Respiratory Syndrome Coronavirus 2. (SARS-CoV-2) and its variant strains, including Alpha, Beta, Gamma, Delta, and now Omicron, pose a significant challenge. With the constant evolution of the virus, Omicron and its subtypes BA.

NVP-2, in combination with Orlistat, represents a promising therapeutic strategy for acute myeloid leukemia.

Cell cycle dysregulation and the corresponding metabolic reprogramming play significant roles in tumor development and progression. CDK9, a kinase that regulates gene transcription and cell cycle, also induces oncogene transcription and abnormal cell cycle in AML cells. The function of CDK9 for gene regulation in AML cells requires further exploration.

The Calicophoron daubneyi genome provides new insight into mechanisms of feeding, eggshell synthesis and parasite-microbe interactions.

Background: The rumen fluke, Calicophoron daubneyi, is the major paramphistome species infecting ruminants within Europe. Adult flukes reside within the rumen where they are in direct contact with a unique collection of microorganisms. Here, we report a 1.

The world's most venomous spider is a species complex: systematics of the Sydney funnel-web spider (Atracidae: Atrax robustus).

The Sydney funnel-web spider Atrax robustus O. Pickard-Cambridge, 1877 is an iconic Australian species and considered among the most dangerously venomous spiders for humans. Originally described in 1877 from a single specimen collected in "New Holland", this spider has a complex taxonomic history.

Physicochemical and sensory characterization of functional synbiotic Labneh fortified with the bacteriocin-producing Lactiplantibacillus plantarum strain GA7 and nano-encapsulated Tirmania pinoyi extract.

Background: Functional foods and dairy products are gaining global attention due to their nutritional value and health-promoting characteristics. Lactic acid bacteria (LAB) are one of the promising components included in these products, thanks to their probiotic properties and ability to produce bioactive compounds such as bacteriocins. On the other hand, ectomycorrhizal wild mushrooms (truffles) are known for their ethnomycological importance.

N6-methyladenosine RNA modification regulates the transcription of SLC7A11 through KDM6B and GATA3 to modulate ferroptosis.

Background: Recent studies indicate that N6-methyladenosine (mA) RNA modification may regulate ferroptosis in cancer cells, while its molecular mechanisms require further investigation.

Methods: Liquid Chromatography-Tandem Mass Spectrometry (HPLC/MS/MS) was used to detect changes in mA levels in cells. Transmission electron microscopy and flow cytometry were used to detect mitochondrial reactive oxygen species (ROS).

Enantioselective Degradation and Processing Factors of Seven Chiral Pesticides During the Processing of Wine and Rice Wine.

Chiral pesticides often undergo enantioselective degradation during food fermentation. In this study, the enantioselective fates of seven chiral pesticides during processing of wine and rice wine were investigated. The results revealed that R-metalaxyl, R-mefentrifluconazole and S-hexaconazole were preferentially degraded during wine processing with EF values of 0.

CeO2 Modification Promotes the Oxidation Kinetics for Adipic Acid Electrosynthesis from KA Oil Oxidation at 200 mA cm-2.

Electrocatalytic oxidation of cyclohexanol/cyclohexanonein water provides a promising strategy for obtaining adipic acid (AA), which is an essential feedstock in the polymer industry. However, this process is impeded by slow kinetics and limited Faradaic efficiency (FE) due to a poor understanding of the reaction mechanism. Herein, NiCo2O4/CeO2 is developed to enable the electrooxidation of cyclohexanol to AA with a 0.

A Low-Symmetry Copper Benzenehexathiol Coordination Polymer with In-Plane Electrical Anisotropy.

Electrically conductive coordination polymers (ECCPs), particularly those incorporating benzenehexathiol (BHT) ligands, are emerging as a distinctive class of electronic materials with tunable semiconducting and metallic properties. However, the exploration of novel ECCPs with low-symmetry structures and electrical anisotropy remains under development. Here, we report the on-water surface synthesis of a novel ECCP, namely Cu5BHT, which exhibits a low-symmetry structure and unique in-plane electrical anisotropy that differs from the well-known Cu3BHT phase.

Molecular Design for Dual Circularity: Polyester with Complementary Mechanical and Chemical Recyclability under Mild Conditions.

The plastic waste accumulation requires facile yet effective solutions. Currently mechanical recycling typically leads to downcycling, while the environmental footprint of chemical recycling is often unacceptable. Here, we introduce a dual circularity concept, where rational molecular design paves the way for complementary closed-loop mechanical and chemical recyclability under mild conditions.

Evaluation of Multispecific Drugs Based on Patient-derived Immunocompetent Tumor Organoids.

The evolution of antitumor drug development has transitioned from single-agent chemotherapy to targeted therapy, immunotherapy, and more recently, multispecific drugs. These innovative drugs target multiple cellular or molecular pathways simultaneously, offering a more comprehensive anticancer approach and addressing some of the limitations inherent in traditional monotherapies. However, preclinical assessment of multispecific drugs remains challenging, as conventional tumor models often lack the necessary complexity to accurately reflect the interactions between various cell types and targets.

Buffered Hydroxyl Radical for Photocatalytic Non-Oxidative Methane Coupling.

Hydroxy radical (•OH) is a prestigious oxidant that allows the cleavage of strong chemical bonds of methane but is untamed, leading to over-oxidation of methane and waste of oxidants, especially at high methane conversion. Here, we managed to buffer •OH in an aqueous solution of photo-irradiated Fe3+, where •OH almost participates in methane oxidation. Due to the interaction between Fe3+ and SO42-, the electron transfer from OH- to excited-state Fe3+ for •OH generation is retarded, while excessive •OH is consumed by generated Fe2+ to restore Fe3+.