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In this paper, by modeling a narrowband interference (NBI) as a wide-sense stationary (WSS), zero-mean Gaussian bandpass random process, a systematic theoretical framework is developed for the first time to characterize the operation and performance improvement of energy detection (ED) based impulse radio ultra-wideband (IR-UWB) receivers that employ a nonlinear Teager-Kaiser operator (TKO) and a highpass filter. Furthermore, through both theoretical analysis and simulations, we have identified (1) that the TKO technique can effectively mitigate not only the performance degradation caused by an NBI but also that caused by additive white Gaussian noise and (2) that a larger bandwidth of the UWB signal leads to better mitigation. Therefore, the TKO technique is considered as a very promising technique to improve the overall performance of ED-based IR-UWB receivers no matter an NBI is present or not. [ABSTRACT FROM PUBLISHER]

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). To deal with the multipath effects, we adopt the DBscan spatiotemporal clustering algorithm with adaptive parameters. In addition, the time-continuous angle of arrival information is obtained by interpolating and supplementing points to extract the dynamic signal paths better. Finally, the least-squares method is used for linear fitting to obtain the final angle information of a moving target. Experiments are conducted with the tracking data set presented with Tsinghua's Widar 2.0. The results show that the average angle estimation error with the proposed algorithm is smaller than Widar2.0. The average angle error is about 7.18° in the classroom environment, 3.62° in the corridor environment, and 12.16° in the office environment; they are smaller than the errors of the existing system. [ABSTRACT FROM AUTHOR]

• Microbial eukaryotic community (MEC) in Zhe-Min Coastal Current (ZMCC) was studied. • MEC in the Hong Kong coastal water were strongly influenced by ZMCC in winter. • Abundant and rare MEC shared similar biogeographic distribution along ZMCC. • Neutral process dominated the MEC in ZMCC with weak dispersal limitation. One interesting question in the study of marine microbial ecology is how ocean currents affect the geographic distributions of microorganisms. The Zhe-Min Coastal Current (ZMCC) is strong in winter and could influence the plankton communities in Hong Kong coastal waters by bringing species from far north. In this study, we investigated the spatial distribution of microbial eukaryotic communities (MEC) in the ZMCC and evaluated the relative contribution of environmental and spatial factors on the variations of MEC. The results showed that diverse taxa of diatoms (Bacillariophyceae) and Dinophyceae (Dinoflagellata) dominated the sequences in all samples. MEC compositions in the Hong Kong coastal waters were closer to the communities in the ZMCC than other adjacent areas. Abundant and rare taxa exhibited a similar geographic pattern of distribution. Environmental factors alone explained 14.1% and 27.6% of the variations in the entire and abundant communities, respectively, which were higher than pure spatial factors (8.3% and 19.5%, respectively). The lower importance of spatial factors (dispersal limitation) might be explained by the passive dispersal favored by current transportation and was further supported by the high immigration rate computed in the neutral community model (NCM). High fitness to the NCM (R2 = 0.74) indicated the predominant role of neutral process in shaping the MEC. The large proportion of unexplained variations in rare taxa suggested the importance of other potential factors, especially biotic interactions. Our study demonstrates the influences of coastal current on local and regional structures of MEC. [ABSTRACT FROM AUTHOR]

Background: Although several studies have investigated the effects of mobile health (mHealth) interventions on depression among people living with HIV, few studies have explored mediators of mHealth-based interventions to improve mental health in people living with HIV. Identifying influential mediators may enhance and refine effective components of mHealth interventions to improve mental health of people living with HIV. Objective: This study aimed to examine mediating factors of the effects of a mHealth intervention, Run4Love , designed to reduce depression among people living with HIV using 4 time-point measurement data. Methods: This study used data from a randomized controlled trial of a mHealth intervention among people living with HIV with elevated depressive symptoms in Guangzhou, China. A total of 300 patients were assigned to receive either the mHealth intervention (n=150) or a waitlist control group (n=150) through computer-generated block randomization. Depressive symptoms, coping, and HIV-related stigma were measured at baseline, 3-, 6-, and 9-month follow-ups. The latent growth curve model was used to examine the effects of the intervention on depressive symptoms via potential mediators. Mediating effects were estimated using bias-corrected 95% bootstrapped CIs (BCIs) with resampling of 5000. Results: Enhanced positive coping and reduced HIV-related stigma served as effective treatment mediators in the mHealth intervention. Specially, there was a significant indirect effect of the mHealth intervention on the slope of depressive symptoms via the slope of positive coping (beta=–2.86; 95% BCI –4.78 to –0.94). The indirect effect of the mHealth intervention on the slope of depressive symptoms via the slope of HIV-related stigma was also statistically significant (beta=–1.71; 95% BCI –3.03 to –0.40). These findings indicated that enhancement of positive coping and reduction of HIV-related stigma were important mediating factors of the mHealth intervention in reducing depression among people living with HIV. Conclusions: This study revealed the underlying mediators of a mHealth intervention to reduce depression among people living with HIV using latent growth curve model and 4 time-point longitudinal measurement data. The study results underscored the importance of improving positive coping skills and mitigating HIV-related stigma in mHealth interventions to reduce depression among people living with HIV. [ABSTRACT FROM AUTHOR]

Although Cas9 nucleases are remarkably diverse in microorganisms, the range of genomic sequences targetable by a CRISPR/Cas9 system is restricted by the requirement of a short protospacer adjacent motif (PAM) at the target site. Here, we generate a group of chimeric Cas9 (cCas9) variants by replacing the key region in the PAM interaction (PI) domain of Staphylococcus aureus Cas9 (SaCas9) with the corresponding region in a panel of SaCas9 orthologs. By using a functional assay at target sites with different nucleotide recombinations at PAM position 3-6, we identify several cCas9 variants with expanded recognition capability at NNVRRN, NNVACT, NNVATG, NNVATT, NNVGCT, NNVGTG, and NNVGTT PAM sequences. In summary, we provide a panel of cCas9 variants accessible up to 1/4 of all the possible genomic targets in mammalian cells. The genomic locations that can be targeted for editing by CRISPR are limited by the presence of the nuclease-specific PAM sequence. Here, the authors show PAM recognition can be expanded by replacing the key region in the PAM interaction domain of SaCas9 with the corresponding region of SaCas9 orthologs. [ABSTRACT FROM AUTHOR]

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. SC-AIR-BERT first learns the 'language' of AIR sequences through self-supervised pre-training on a large cohort of paired AIR chains from multiple single-cell resources. The model is then fine-tuned with a multilayer perceptron head for binding specificity prediction, employing the K-mer strategy to enhance sequence representation learning. Extensive experiments demonstrate the superior AUC performance of SC-AIR-BERT compared with current methods for TCR- and BCR-binding specificity prediction. [ABSTRACT FROM AUTHOR]

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. The purpose of this paper was to explore the action and mechanism of COS in alleviating RF. First, an acute unilateral ureteral obstruction operation (UUO) in male BALB/c mice was performed to induce RF, and COS or fosinopril (positive control drug) were administered for 7 consecutive days. Data from our experiments indicated that COS treatment can significantly alleviate kidney injury and decrease the levels of blood urea nitrogen (BUN) and serum creatinine (SCr) in the UUO mouse model. More importantly, our results show that COS can reduce collagen deposition and decrease the expression of fibrosis proteins, such as collagen IV, fibronectin, collagen I, α-smooth muscle actin (α-SMA) and E-cadherin, ameliorating experimental renal fibrosis in vivo. In addition, we also found that COS suppressed oxidative stress and inflammation in RF model mice. Further studies indicated that the mechanism by which COS alleviates renal fibrosis is closely related to the regulation of the TGF-β1/Smad pathway. COS has a therapeutic effect on ameliorating renal fibrosis similar to that of the positive control drug fosinopril. Taken together, COS can alleviate renal fibrosis induced by UUO by reducing oxidative stress damage and regulating the TGF-β1/Smad pathway. [ABSTRACT FROM AUTHOR]

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. The exact close-form forward and numerical inverse solutions are derived respectively using the generalized Snell's law of refraction. Given the orientations of the double metalenses, the pointing position can be accurately determined. If the desired pointing position is given, the required metalenses' orientations can be obtained by applied global optimization algorithms to solve nonlinear equations related to the inverse problem. The relationships of the scan region and blind zone with the system parameters are derived. The method to eliminate the blind zone is given. Comparison with double Risley-prism systems is also conducted. This work provides a new approach to control light beams. [ABSTRACT FROM AUTHOR]

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. Subsequently, we conducted microcosm experiments to elucidate how PGPR inoculation affected seagrass photosynthesis and shape within each rhizosphere microbiome. Both screened PGPR strains, Raoultella terrigena NXT28 and Bacillus aryabhattai XT37, excelled at expressing a specific subset of plant-beneficial functions and increased the photosynthetic rates of the seagrass host. PGPR inoculation not only decreased the abundance of sulfur-cycling bacteria, it also improved the abundance of putative iron-cycling bacteria in the seagrass rhizosphere. Strain XT37 successfully colonized the seagrass rhizosphere and displayed a leading role in microbial network structure. As a nitrogen-fixing bacteria, NXT28 showed potential to change the microbial nitrogen cycle with denitrification in the rhizosphere and alter dissimilatory and assimilatory nitrate reduction in bulk sediment. These findings have implications for the development of eco-friendly strategies aimed at exploiting microbial communities to confer sulfide tolerance in coastal seagrass ecosystem. • Two PGPR strains were screened from different seagrass species in both reef and coastal regions. • PGPR strains increased the photosynthetic rates of seagrass host. • PGPR inoculation inhibited and enriched the abundance of iron- and sulfur-cycling bacterial taxa, respectively. • The colonization of the seagrass rhizosphere by Bacillus aryabhattai XT37 played a leading role in the microbial network. [ABSTRACT FROM AUTHOR]

[Display omitted] • Isohaline ∼31.5 is the geographic boundary of P-limited Pearl River Diluted Water and N-limited South China Sea Water. • Increased phosphorus inputs promote the dominance of nano-sized Chlorophyta in the Pearl River Estuary in summer. • Increased phosphorus inputs induce species competitions among pigmented protists in the Pearl River Estuary in summer. • Increased phosphorus inputs stabilize microeukaryotic plankton co-occurrence network in the Pearl River Estuary in summer. The size structure of microeukaryotic plankton communities exerts a fundamental control on marine ecosystem functions, such as food web dynamics and element flows. The global expansion of nitrogen (N) and phosphorus (P) nutrient pollutants into estuaries and coastal waters is causing public health and environmental concerns associated with microeukaryotic plankton activities. In the context of eutrophication, understanding how size structure and biotic activities of microeukaryotic plankton communities responds to anthropogenic nutrient inputs is vital to evaluate the future fate of coastal ecosystems. Here, we conducted onboard incubation experiments to provide the first investigation of how size structure and co-occurrence network of microeukaryotic plankton communities change under the dynamic nutrient conditions in the Pearl River Estuary. Our study revealed (1) a transition from P limitation to N limitation or potential NP co-limitation for the growth of pigmented protists along the Pearl River-South China Sea continuum, and isohaline ∼ 31.5 being the geographic boundary; (2) P availability drove the microeukaryotic plankton community size structure that the increased P inputs favored the dominance of nano-sized (3–20 μm) protists due to the increased relative abundance of Chlorophyta; (3) increased P inputs enhanced the species competition among phototrophic protists and improved the network stability of microeukaryotic plankton communities. In the future, if there is an increase in anthropogenic input of P in the Pearl River Estuary during summer, which would alleviate the pressure of P-deficiency, it is expected to increase the biomass of microeukaryotic plankton, with a dominance of nano-sized Chlorophyta. Altogether, this study advances our understanding of the geographic nutrient limitation pattern for pigmented protist plankton in the Pearl River Estuary, an urbanized estuarine ecosystem. Moreover, it enhances our knowledge regarding the response of marine microeukaryotic plankton communities to future environmental changes. [ABSTRACT FROM AUTHOR]

Solar ultraviolet B (UVB) irradiance at the Earth's surface is increasing due to anthropogenic influences. To evaluate the effects of enhanced UVB radiation on photosynthetic characteristics of the marine diatom Phaeodactylum tricornutum, the species was exposed to four levels of UVB radiation, 0, 0.25, 0.75, and 1.50 KJ m day for 7 days. Effects of UVB stress on net photosynthetic rate, net respiration rate, variable chlorophyll (Chl) fluorescence parameters, Chl a and carotenoid contents, and UV-absorbing compounds (UVACs) were investigated. Results showed that there were no significant differences in terms of net respiration rate or maximal photochemical efficiency of photosystem II (F/F) between the treatments in the short or long term. However, enhanced UVB radiation at an intensity of 0.16 W m had a negative effect on the net photosynthetic rate, electron transport rate, and on the pathway of excess energy dissipation over the short term (1 to 5 days). Carotenoid and UVACs content increased under UVB radiation. Photosynthetic parameters were unaffected by UVB radiation on the seventh day indicating that P. tricornutum can adapt to UVB radiation in the long term. Results of the present study indicate that there is a dynamic balance between damage and adaptation in microalgae that enables them to adapt to UVB-induced photosystem alterations during both short-term and long-term exposure. [ABSTRACT FROM AUTHOR]

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., Materials and Methods: A comprehensive virtual screening strategy, incorporating network pharmacology and batch molecular docking, combined with experimental validation techniques, was employed to systematically elucidate the underlying mechanism of BYHWD regulating macrophage polarization to alleviate AS., Results: Firstly, based on high-fat diet induced AS model in apolipoprotein E-deficient mice, it was found that BYHWD can significantly regulate macrophage polarization to alleviate AS. Then, the network pharmacological analysis revealed that the core targets of BYHWD regulating macrophage polarization to alleviate AS mainly involved TP53, AKT1 and BCL2. The mitochondrial function and metabolism were the main biological processes. Meanwhile, the main chemical components were identified as 3-O-p-coumaroylquinic acid, D-mandelonitrile, Ellagic acid, Ferulic acid, 5-hydroxy-L-tryptophan zwitterion, Isoliquiritigenin, Senkyunolide-F, Anofinic acid, Trimethylhydroquinone and Senkyunolide-E by batch molecular docking strategy. Further, the in vitro experiments demonstrated that BYHWD not only regulated macrophage polarization and alleviated macrophage foam formation but also modulated mitochondrial function and the expression of TP53, p-AKT, and BCL2 proteins. Finally, multivariate statistical analysis confirmed that the ameliorative effect of BYHWD on AS was closely related to mitochondrial function and macrophage polarization regulated by TP53, AKT1 and BCL2., Conclusions: BYHWD could activate key targets, including TP53, AKT1, and BCL2, to alleviate mitochondrial dysfunction and regulate macrophage polarization, thereby improving AS. The 10 active compounds of BYHWD, including 5-hydroxy-L-tryptophan zwitterion and Isoliquiritigenin, played an important role in regulating macrophages polarization to alleviate AS., Competing Interests: Declaration of Competing Interest ☒The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. ☐The authors declare the following financial interests/personal relationships which may be considered as potential competing interests, (Copyright © 2024. Published by Elsevier B.V.)

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. The results revealed that seagrasses in Yifeng Estuary experienced the large proportion of cultivated land and exhibited higher organic carbon content in the 0-20 cm surface sediment layer. Nitrogen-cycling bacteria were predominantly associated with seagrasses from Yifeng Estuary, whereas Vibrio spp. was more prevalent in seagrasses from Liusha Bay. Notably, seagrass Halophia beccarii (YHB) in Yifeng Estuary harbored higher niche breadths for both microbial generalist and specialist compared to Halodule uninervis (LHU) and Halophia ovalis (LHO) from Liusha Bay. Stochastic processes were pivotal in shaping seagrass sediment microbial communities, with a higher immigration rate observed in YHB, suggesting greater microbial turnover in this area. Additionally, YHB sediment presented lower drift and higher dispersal limitation among generalists compared to LHU and LHO, whereas the pattern was reversed among specialists. Specialists were found to play a crucial role in shaping microbial interactions within YHB sediment, with genera Halioglobus identified as keystone species in the network. The specialists were further found to significantly influence microbial β-diversity in seagrass sediment directly. Overall, our findings illustrated how microbial generalists and specialists were distributed in seagrass sediments in response to land use changes and provided new insights into the potential roles of microbial regulation in degraded seagrass ecosystems., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

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 Lepidodinium sp.) and the metatranscriptome dataset of the global ocean to investigate the mechanisms underlying the shift of trophic strategies and its relationship with increasing temperatures. Our results showed that phagocytosis-related pathways, including focal adhesion, regulation of actin cytoskeleton, and oxidative phosphorylation, were significantly stimulated in Lepidodinium sp. when cryptophyte prey were added. We further compared the expression profiles of photosynthesis and phagocytosis genes in Lepidodinium sp. in the global sunlit ocean. Our results indicated that Lepidodinium sp. became more phagotrophic with increasing temperatures when the ambient chlorophyll concentration was >0.3 mg.m -3 (~20.58% of the ocean surface) but became more photoautotrophic with increasing temperatures when the chlorophyll concentration was between 0.2 and 0.3 mg.m -3 (~11.47% of the ocean surface). Overall, we emphasized the crucial role of phagocytosis in phago-mixotrophy and suggested that the expression profile of phagocytosis genes can be a molecular marker to target the phagotrophic activity of mixoplankton in situ., Competing Interests: The authors declare that they have no competing interests., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

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. A total of eighteen samples were collected and analyzed, revealing the presence of fourteen taxa from eight phyla. The most prevalent group was Cypridina, accounting for 33.7% of the total abundance, followed by copepods (29.0%) and jellyfish (10.9%). Within copepods, the genus Pontella exhibited the highest relative abundance (38.0%). Additionally, each neuston taxon displayed unique diel distribution patterns. Cypridina was the most abundant taxon during the night (40.4%), while it shifted to copepod dominance during the day (50.4%). Among copepods, genus Pontella and larvae were dominant groups at night (44.7%) and during the day (30.0%), respectively. Moreover, a multivariate biota-environment analysis demonstrated that temperature, pH, dissolved oxygen and Si(OH) 4 significantly impacted neuston composition. Notably, both jellyfish and sea snails showed a significant positive correlation with temperature, suggesting their potential dominance in the neuston community in response to future global warming in the oligotrophic tropical seas. This study lays a robust foundation for recognizing the neuston community in the oceanic SCS, and helps evaluate the long-term risks to neuston habitats under climate changes., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

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 (1.6 ± 1.0 × 10 6 ) and Nano/Microplankton (3.2 ± 2.8 × 10 3 ), respectively. Furthermore, HP was main component for MFW in the bathypelagic (>1000 m) zone. Multivariate biota-environment analysis demonstrated that environmental variables, particularly temperature, significantly impacted MFW composition, suggesting that bottom-up control (resource availability) dominated the water column. Our study provides benchmark information for future environmental dynamics forcing on MFW in the oligotrophic tropical seas., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Ltd.)

Background and Aims: NAFLD has become a major metabolic disease worldwide. A few studies have reported the potential relationship between mitochondrial pyruvate carrier 1 (MPC1) and inflammation, fibrosis, and insulin sensitivity in obese or NASH mouse models. However, the impact of MPC1 on NAFLD-related liver lipid metabolism and its role in the NAFLD progression require further investigation., Approach and Results: MPC1 expression was measured in liver tissues from normal controls and patients with NAFLD. We characterized the metabolic phenotypes and expression of genes involved in hepatic lipid accumulation in MPC1 systemic heterozygous knockout (MPC1 +/- ) mice. Hepatic protein lactylation was detected using Tandem Mass Tags proteomics and verified by the overexpression of lactylation mutants in cells. Finally, the effect of MPC1 inhibition on liver inflammation was examined in mice and AML-12 cells. Here, we found that MPC1 expression was positively correlated to liver lipid deposition in patients with NAFLD. MPC1 +/- mice fed with high-fat diet had reduced hepatic lipid accumulation but no change in the expression of lipid synthesis-related genes. MPC1 knockout affected the lactylation of several proteins, especially fatty acid synthase, through the regulation of lactate levels in hepatocytes. Lactylation at the K673 site of fatty acid synthase inhibited fatty acid synthase activity, which mediated the downregulation of liver lipid accumulation by MPC1. Moreover, although MPC1 knockout caused lactate accumulation, inflammation level was controlled because of mitochondrial protection and macrophage polarization., Conclusions: In NAFLD, MPC1 levels are positively correlated with hepatic lipid deposition; the enhanced lactylation at fatty acid synthase K673 site may be a downstream mechanism., (Copyright © 2023 American Association for the Study of Liver Diseases.)

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. The results showed that seep regions harbored more abundant and diverse parasitic microeukaryotes (e.g., Apicomplexa and Syndiniales) as indicator species, compared to nearby non-seep region. Microeukaryotic community heterogeneity was larger between habitats than within habitat, and greatly increased when considering molecular phylogeny, suggesting the local diversification in cold-seep sediments. Microeukaryotic α-diversity at cold seeps was positively increased by metazoan richness and dispersal rate of microeukaryotes, while its β-diversity was promoted by heterogeneous selection mainly from metazoan communities (as potential hosts). Their combined effects led to the significant higher γ-diversity (i.e., total diversity in a region) at cold seeps than non-seep regions, suggesting cold-seep sediment as a hotspot for microeukaryotic diversity. Our study highlights the importance of microeukaryotic parasitism in cold-seep sediment and has implications for the roles of cold seep in maintaining and promoting marine biodiversity., (© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

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. DeepAIR achieves a Pearson's correlation of 0.813 in predicting the binding affinity of TCR, and a median area under the receiver-operating characteristic curve (AUC) of 0.904 and 0.942 in predicting the binding reactivity of TCR and BCR, respectively. Meanwhile, using TCR and BCR repertoire, DeepAIR correctly identifies every patient with nasopharyngeal carcinoma and inflammatory bowel disease in test data. Thus, DeepAIR improves the AIR-antigen binding prediction that facilitates the study of adaptive immunity.

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). In addition, MLH1 is still the dominant factor over FEN1 and LIG1 in prime editing. Our results help to further understand the relationship of proteins involved in prime editing and envisage future directions for the development of PE., Competing Interests: A patent application on the method of overexpressing FEN1 or LIG1 for genome editing is pending in State Intellectual Property Office of China., (© 2023 The Authors.)

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. To provide genetic explanations for the niche partitioning of ANME archaea, we applied comparative genomic analysis to ANME archaeal genomes retrieved from global methane seeps. Our results showed that ANME-2 archaea are more prevalent than ANME-1 archaea in shallow sediments because they carry genes that encode a significantly higher number of outer membrane multiheme c -type cytochromes and flagellar proteins. These features make ANME-2 archaea perform direct interspecies electron transfer better and benefit more from electron acceptors in AOM. Besides, ANME-2 archaea carry genes that encode extra peroxidase compared to ANME-1 archaea, which may lead to ANME-2 archaea better tolerating oxygen toxicity. In contrast, ANME-1 archaea are more competitive in deep layers than ANME-2 archaea because they carry extra genes ( mtb and mtt ) for methylotrophic methanogenesis and a significantly higher number of frh and mvh genes for hydrogenotrophic methanogenesis. Additionally, ANME-1 archaea carry exclusive genes ( sqr , TST , and mddA ) involved in sulfide detoxification compared to ANME-2 archaea, leading to stronger sulfide tolerance. Overall, this study reveals the genomic mechanisms shaping the niche partitioning among ANME archaea in global methane seeps. IMPORTANCE Anaerobic methanotrophic (ANME) archaea are important methanotrophs in marine sediment, controlling the flux of biologically generated methane, which plays an essential role in the marine carbon cycle and climate change. So far, no strain of this lineage has been isolated in pure culture, which makes metagenomics one of the fundamental approaches to reveal their metabolic potential. Although the niche partitioning of ANME archaea was frequently reported in different studies, whether this pattern was consistent in global methane seeps had yet to be verified, and little was known about the genetic mechanisms underlying it. Here, we reviewed and analyzed the community structure of ANME archaea in global methane seeps and indicated that the niche partitioning of ANME archaea was statistically supported. Our comparative genomic analysis indicated that the capabilities of interspecies electron transfer, methanogenesis, and the resistance of oxygen and hydrogen sulfide could be critical in defining the distribution of ANME archaea in methane 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. Still, no study has ever explored the functional role of the mycobiota in the cold seep biome. To assess the complex role of fungi and fill in the gaps, we performed network analysis on 147 samples to disentangle fungal-prokaryotic interactions (fungal 18S and prokaryotic 16S) in the Haima cold seep region. We demonstrated that fungi are central species with high connectivity at the epicenter of prokaryotic networks, reduce their random-attack vulnerability by 60%, and enhance information transfer efficiency by 15%. We then scavenged a global metagenomic and metatranscriptomic data set from 10 cold seep regions for fungal genes of interest (hydrophobins, cytochrome P450s, and ligninolytic family of enzymes); this is the first study to report active transcription of 2,500+ fungal genes in the cold seep sediment. The genera Fusarium and Moniliella were of notable importance and directly correlated with high methane abundance in the sulfate-methane transition zone (SMTZ), likely due to their ability to degrade and solubilize methane and oils. Overall, our results highlight the essential yet overlooked contribution of fungi to cold seep biological networks and the role of fungi in regulating cold seep biogeochemistry. IMPORTANCE The challenges we face when analyzing eukaryotic metagenomic and metatranscriptomic data sets have hindered our understanding of cold seep fungi and microbial eukaryotes. This fact does not make the mycobiota any less critical in mediating cold seep biogeochemistry. On the contrary, many fungal genera can oxidize and solubilize methane, produce methane, and play a unique role in nutrient recycling via saprotrophic enzymatic activity. In this study, we used network analysis to uncover key fungal-prokaryotic interactions that can mediate methane biogeochemistry and metagenomics and metatranscriptomics to report that fungi are transcriptionally active in the cold seep sediment. With concerns over rising methane levels and cold seeps being a pivotal source of global methane input, our holistic understanding of methane biogeochemistry with all domains of life is essential. We ultimately encourage scientists to utilize state-of-the-art tools and multifaceted approaches to uncover the role of microeukaryotic organisms in understudied systems.

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. Specifically, how the gut microbiome reacts to environmental change is unclear., Results: The meta-pathway analysis showed the nutritional and metabolic roles of the deep-sea mussel gut microbiome. Comparative analyses of the gut microbiomes of original and transplanted mussels subjected to environmental change revealed shifts in bacterial communities. Gammaproteobacteria were enriched, whereas Bacteroidetes were slightly depleted. The functional response for the shifted communities was attributed to the acquisition of carbon sources and adjusting the utilisation of ammonia and sulphide. Self-protection was observed after transplantation., Conclusion: This study provides the first metagenomic insights into the community structure and function of the gut microbiome in deep-sea chemosymbiotic mussels and their critical mechanisms for adapting to changing environments and meeting of essential nutrient demand., (© 2023. The Author(s).)

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. SODB also provides multiple interactive data analytical modules, especially a unique module, Spatial Omics View (SOView). We conduct comprehensive statistical analyses and illustrate the utility of both basic and advanced analytical modules using multiple spatial omics datasets. We demonstrate SOView utility with brain spatial transcriptomics data and recover known anatomical structures. We further delineate functional tissue domains with associated marker genes that were obscured when analyzed using previous methods. We finally show how SODB may efficiently facilitate computational method development. The SODB website is https://gene.ai.tencent.com/SpatialOmics/ . The command-line package is available at https://pysodb.readthedocs.io/en/latest/ ., (© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Background: Nutrient stoichiometry of phytoplankton frequently changes with aquatic ambient nutrient concentrations, which is mainly influenced by anthropogenic water treatment and the ecosystem dynamics. Consequently, the stoichiometry of phytoplankton can markedly alter the metabolism and growth of zooplankton. However, the effects of nutrient-imbalanced prey on the interplay between zooplankton and their gut microbiota remain unknown. Using metatranscriptome, a 16 s rRNA amplicon-based neutral community model (NCM) and experimental validation, we investigated the interactions between Daphnia magna and its gut microbiota in a nutrient-imbalanced algal diet., Results: Our results showed that in nutrient-depleted water, the nutrient-enriched zooplankton gut stimulated the accumulation of microbial polyphosphate in fecal pellets under phosphorus limitation and the microbial assimilation of ammonia under nitrogen limitation. Compared with the nutrient replete group, both N and P limitation markedly promoted the gene expression of the gut microbiome for organic matter degradation but repressed that for anaerobic metabolisms. In the nutrient limited diet, the gut microbial community exhibited a higher fit to NCM (R 2  = 0.624 and 0.781, for N- and P-limitation, respectively) when compared with the Control group (R 2  = 0.542), suggesting increased ambient-gut exchange process favored by compensatory feeding. Further, an additional axenic grazing experiment revealed that the growth of D. magna can still benefit from gut microbiota under a nutrient-imbalanced diet., Conclusions: Together, these results demonstrated that under a nutrient-imbalanced diet, the microbes not only benefit themselves by absorbing excess nutrients inside the zooplankton gut but also help zooplankton to survive during nutrient limitation.

Background: Although several studies have investigated the effects of mobile health (mHealth) interventions on depression among people living with HIV, few studies have explored mediators of mHealth-based interventions to improve mental health in people living with HIV. Identifying influential mediators may enhance and refine effective components of mHealth interventions to improve mental health of people living with HIV., Objective: This study aimed to examine mediating factors of the effects of a mHealth intervention, Run4Love, designed to reduce depression among people living with HIV using 4 time-point measurement data., Methods: This study used data from a randomized controlled trial of a mHealth intervention among people living with HIV with elevated depressive symptoms in Guangzhou, China. A total of 300 patients were assigned to receive either the mHealth intervention (n=150) or a waitlist control group (n=150) through computer-generated block randomization. Depressive symptoms, coping, and HIV-related stigma were measured at baseline, 3-, 6-, and 9-month follow-ups. The latent growth curve model was used to examine the effects of the intervention on depressive symptoms via potential mediators. Mediating effects were estimated using bias-corrected 95% bootstrapped CIs (BCIs) with resampling of 5000., Results: Enhanced positive coping and reduced HIV-related stigma served as effective treatment mediators in the mHealth intervention. Specially, there was a significant indirect effect of the mHealth intervention on the slope of depressive symptoms via the slope of positive coping (beta=-2.86; 95% BCI -4.78 to -0.94). The indirect effect of the mHealth intervention on the slope of depressive symptoms via the slope of HIV-related stigma was also statistically significant (beta=-1.71; 95% BCI -3.03 to -0.40). These findings indicated that enhancement of positive coping and reduction of HIV-related stigma were important mediating factors of the mHealth intervention in reducing depression among people living with HIV., Conclusions: This study revealed the underlying mediators of a mHealth intervention to reduce depression among people living with HIV using latent growth curve model and 4 time-point longitudinal measurement data. The study results underscored the importance of improving positive coping skills and mitigating HIV-related stigma in mHealth interventions to reduce depression among people living with HIV., (©Mengting Zhu, Weiping Cai, Linghua Li, Yan Guo, Aliza Monroe-Wise, Yiran Li, Chengbo Zeng, Jiaying Qiao, Zhimeng Xu, Hanxi Zhang, Yu Zeng, Cong Liu. Originally published in JMIR Mhealth and Uhealth (http://mhealth.jmir.org), 15.11.2019.)

Background: Most people living with HIV (PLWH) reside in middle- and low-income countries with limited access to health services. Thus, cost-effective interventions that can reach a large number of PLWH are urgently needed., Objective: The objective of our study was to assess the feasibility and acceptability of an mHealth intervention among PLWH in China., Methods: Based on previous formative research, we designed an mHealth intervention program that included sending weekly reminders to participants via text messages (short message service, SMS) and articles on HIV self-management three times a week via a popular social media app WeChat. A total of 62 PLWH recruited from an HIV outpatient clinic were randomly assigned to intervention or control group. The intervention lasted for 3 months, and all participants were assessed for their medication adherence, presence of depression, quality of life (QoL), and CD4 (cluster of differentiation 4) counts. Upon completing the intervention, we interviewed 31 participants to further assess the feasibility and acceptability of the study., Results: At baseline, the intervention and control groups did not differ in terms of demographic characteristics or any of the major outcome measures. About 85% (53/62) of the participants completed the intervention, and they provided valuable feedback on the design and content of the intervention. Participants preferred WeChat as the platform for receiving information and interactive communication for ease of access. Furthermore, they made specific recommendations about building trust, interactive features, and personalized feedback. In the follow-up assessment, the intervention and control groups did not differ in terms of major outcome measures., Conclusions: This pilot study represents one of the first efforts to develop a text messaging (SMS)- and WeChat-based intervention that focused on improving the medication adherence and QoL of PLWH in China. Our data indicates that an mHealth intervention is feasible and acceptable to this population. The data collected through this pilot study will inform the future designs and implementations of mHealth interventions in this vulnerable population. We recommend more innovative mHealth interventions with rigorous designs for the PLWH in middle- and low-income countries., Trial Registration: Chinese Clinical Trial Registry ChiCTR1800017987; http://www.chictr.org.cn/showprojen.aspx?proj=30448 (Archived by WebCite at http://www.webcitation.org/71zC7Pdzs)., Registered Report Ientifier: RR1-10.2196/., (©Yan Guo, Zhimeng Xu, Jiaying Qiao, Y Alicia Hong, Hanxi Zhang, Chengbo Zeng, Weiping Cai, Linghua Li, Cong Liu. Originally published in JMIR Mhealth and Uhealth (http://mhealth.jmir.org), 04.09.2018.)