Deciphering mechanism of Buyang Huanwu Decoction in regulating macrophage polarization to alleviate atherosclerosis via virtual screening and experimental verification.

Ethnopharmacological Relevance: Buyang Huanwu Decoction (BYHWD), a traditional prescription known for its Supplementing Qi and Promoting Blood Circulation, has demonstrated noteworthy therapeutic roles in regulating macrophage polarization to atherosclerosis (AS). However, its underlying mechanisms remain unknown.

Aim Of The Study: The purpose of this paper was to decipher mechanism of BYHWD in regulating macrophage polarization to alleviate AS.

Specialists regulate microbial network and community assembly in subtropical seagrass sediments under differing land use conditions.

Microorganisms in the sediment play a pivotal role in the functioning and stability of seagrass ecosystems and their dynamics are influenced by the nutrient acquisition strategies of host plants. While the distinct impacts of microbial generalists and specialists on community dynamics are recognized, their distribution patterns and ecological roles within seagrass ecosystems remain largely unexplored. To address this issue, we conducted an analysis of community assembly processes and co-occurrence relationships of both microbial generalists and specialists within sediment profiles (0-100 cm) from seagrass habitats subjected to differing land use conditions.

Transcriptomic insights into the shift of trophic strategies in mixotrophic dinoflagellate in the warming ocean.

The shift between photoautotrophic and phagotrophic strategies in mixoplankton significantly impacts the planktonic food webs and biogeochemical cycling. Considering the projected global warming, studying how temperature impacts this shift is crucial. Here, we combined the transcriptome of in-lab cultures (mixotrophic dinoflagellate sp.

Composition, diel dynamic and biotic-abiotic interaction of marine neustonic zooplankton in the oligotrophic South China Sea.

Neuston, situated at the air-sea interface, stands as a crucial frontier in the realm of the global warming. Despite its unique habitat, there remains a need to substantiate the composition, diel dynamic and biotic-abiotic interaction of neustonic zooplankton in the tropical seas. In this study, we present rare observational data on neustonic zooplankton (0-20 cm) in the oligotrophic tropical South China Sea (SCS) during the summer of 2022.

Latitudinal pronounced variations in tintinnid (Ciliophora) community at surface waters from the South China Sea to the Yellow Sea: Oceanic-to-neritic species shift, biotic-abiotic interaction and future prediction.

The oceanic-to-neritic species shift of microzooplanktonic tintinnids and their interaction with relevant abiotic variables are two crucial processes in the marine ecosystem. However, these processes remain poorly documented in China's marginal seas. In the summer of 2022, we investigated the community structure of pelagic tintinnids in surface waters from the South China Sea (SCS) to the Yellow Sea (YS), passing through the East China Sea (ECS).

Inoculation with plant growth-promoting rhizobacteria improves seagrass Thalassia hemprichii photosynthesis performance and shifts rhizosphere microbiome.

Plant growth-promoting rhizobacteria (PGPR) inoculation is a crucial strategy for maintaining the sustainability of agriculture and presents a promising solution for seagrass ecological restoration in the face of disturbances. However, the possible roles and functions of PGPRs in the seagrass rhizosphere remain unclear. Here, we isolated rhizosphere bacterial strains from both reef and coastal regions and screened two PGPR isolates regarding their in vivo functional traits.

Insights into the structure of the pelagic microbial food web in the oligotrophic tropical Western Pacific: Examining trophic interactions and relationship with abiotic variables.

Microbial food webs (MFW) play an indispensable role in marine pelagic ecosystem, yet their composition and response to abiotic variables were poorly documented in the oligotrophic tropical Western Pacific. During winter of 2015, we conducted a survey to examine key components of MFW, including Synechococcus, Prochlorococcus, picoeukaryotes, heterotrophic prokaryotes (HP), heterotrophic/pigmented nanoflagellates and ciliates, across water column from surface to 2000 m. Each MFW component exhibited unique vertical distribution pattern, with abundance ratio varying over six and three orders of magnitude across Pico/Microplankton (1.

DeepAIR: A deep learning framework for effective integration of sequence and 3D structure to enable adaptive immune receptor analysis.

Structural docking between the adaptive immune receptors (AIRs), including T cell receptors (TCRs) and B cell receptors (BCRs), and their cognate antigens are one of the most fundamental processes in adaptive immunity. However, current methods for predicting AIR-antigen binding largely rely on sequence-derived features of AIRs, omitting the structure features that are essential for binding affinity. In this study, we present a deep learning framework, termed DeepAIR, for the accurate prediction of AIR-antigen binding by integrating both sequence and structure features of AIRs.

Explore the dominant factor in prime editing via a view of DNA processing.

Prime editing is a revolutionary gene-editing method that is capable of introducing insertions, deletions and base substitutions into the genome. However, the editing efficiency of Prime Editor (PE) is limited by the DNA repair process. Here, we show that overexpression of the flap structure-specific endonuclease 1 (FEN1) and the DNA ligase 1 (LIG1) increases the efficiency of prime editing, which is similar to the dominant negative mutL homolog 1 (MLH1dn).

SC-AIR-BERT: a pre-trained single-cell model for predicting the antigen-binding specificity of the adaptive immune receptor.

Accurately predicting the antigen-binding specificity of adaptive immune receptors (AIRs), such as T-cell receptors (TCRs) and B-cell receptors (BCRs), is essential for discovering new immune therapies. However, the diversity of AIR chain sequences limits the accuracy of current prediction methods. This study introduces SC-AIR-BERT, a pre-trained model that learns comprehensive sequence representations of paired AIR chains to improve binding specificity prediction.

Hypoxia and warming take sides with small marine protists: An integrated laboratory and field study.

Hypoxia and ocean warming are two mounting global environmental threats influencing marine ecosystems. However, the interactive effects of rising temperature and depleted dissolved oxygen (DO) on marine protists remains unknown. Here, we conducted a series of laboratory experiments on four protozoa with distinct cell sizes to investigate the combined effects of temperature (19, 22, 25, 28, and 31 °C) and oxygen availability (hypoxia, 2 mg DO L and normoxia, 7 mg DO L) on their physiological performances (i.

High Microeukaryotic Diversity in the Cold-Seep Sediment.

Microeukaryotic diversity, community structure, and their regulating mechanisms remain largely unclear in chemosynthetic ecosystems. Here, using high-throughput sequencing data of 18S rRNA genes, we explored microeukaryotic communities from the Haima cold seep in the northern South China Sea. We compared three distinct habitats: active, less active, and non-seep regions, with vertical layers (0-25 cm) from sediment cores.

Genomic Insights into Niche Partitioning across Sediment Depth among Anaerobic Methane-Oxidizing Archaea in Global Methane Seeps.

Marine sediments are important methane reservoirs. Methane efflux from the seabed is significantly restricted by anaerobic methanotrophic (ANME) archaea through a process known as anaerobic oxidation of methane (AOM). Different clades of ANME archaea occupy distinct niches in methane seeps, but their underlying molecular mechanisms still need to be fully understood.

Disentangling the Functional Role of Fungi in Cold Seep Sediment.

Cold seeps are biological oases of the deep sea fueled by methane, sulfates, nitrates, and other inorganic sources of energy. Chemolithoautotrophic bacteria and archaea dominate seep sediment, and their diversity and biogeochemical functions are well established. Fungi are likewise diverse, metabolically versatile, and known for their ability to capture and oxidize methane.

Changes in community structures and functions of the gut microbiomes of deep-sea cold seep mussels during in situ transplantation experiment.

Background: Many deep-sea invertebrates largely depend on chemoautotrophic symbionts for energy and nutrition, and some of them have reduced functional digestive tracts. By contrast, deep-sea mussels have a complete digestive system although symbionts in their gills play vital roles in nutrient supply. This digestive system remains functional and can utilise available resources, but the roles and associations among gut microbiomes in these mussels remain unknown.

SODB facilitates comprehensive exploration of spatial omics data.

Spatial omics technologies generate wealthy but highly complex datasets. Here we present Spatial Omics DataBase (SODB), a web-based platform providing both rich data resources and a suite of interactive data analytical modules. SODB currently maintains >2,400 experiments from >25 spatial omics technologies, which are freely accessible as a unified data format compatible with various computational packages.

Interpretable artificial intelligence model for accurate identification of medical conditions using immune repertoire.

Underlying medical conditions, such as cancer, kidney disease and heart failure, are associated with a higher risk for severe COVID-19. Accurate classification of COVID-19 patients with underlying medical conditions is critical for personalized treatment decision and prognosis estimation. In this study, we propose an interpretable artificial intelligence model termed VDJMiner to mine the underlying medical conditions and predict the prognosis of COVID-19 patients according to their immune repertoires.

Chitosan oligosaccharide alleviates renal fibrosis through reducing oxidative stress damage and regulating TGF-β1/Smads pathway.

Renal fibrosis (RF) is the common pathway for a variety of chronic kidney diseases that progress to end-stage renal disease. Chitosan oligosaccharide (COS) has been identified as possessing many health functions. However, it is not clear whether COS can prevent RF.

Analytic solution for double optical metasurface beam scanners.

Optical metasurfaces are researched more and more intensively for the possible realization of lightweight and compact optical devices with novel functionalities. In this paper, a new beam-steering system based on double metasurface lenses (metalenses) is proposed and developed. The proposed system is lightweight, small volume, low cost, and easy to integrate.

Disentangling the Ecological Processes Shaping the Latitudinal Pattern of Phytoplankton Communities in the Pacific Ocean.

Phytoplankton diversity and community compositions vary across spaces and are fundamentally affected by several deterministic (e.g., environmental selection) and stochastic (e.

An Angle Recognition Algorithm for Tracking Moving Targets Using WiFi Signals with Adaptive Spatiotemporal Clustering.

An angle estimation algorithm for tracking indoor moving targets with WiFi is proposed. First, phase calibration and static path elimination are proposed and performed on the collected channel state information signals from different antennas. Then, the angle of arrival information is obtained with the joint estimation algorithm of the angle of arrival (AOA) and time of flight (TOF).

Dose-Response Effects of Patient Engagement on Health Outcomes in an mHealth Intervention: Secondary Analysis of a Randomized Controlled Trial.

Background: The dose-response relationship between patient engagement and long-term intervention effects in mobile health (mHealth) interventions are understudied. Studies exploring long-term and potentially changing relationships between patient engagement and health outcomes in mHealth interventions are needed.

Objective: This study aims to examine dose-response relationships between patient engagement and 3 psychosocial outcomes in an mHealth intervention, Run4Love, using repeated measurements of outcomes at baseline and 3, 6, and 9 months.