Signal binding at both modules of its dCache domain enables the McpA chemoreceptor of Bacillus velezensis to sense different ligands.

Bacteria have evolved multiple signal transduction systems that permit an adaptation to changing environmental conditions. Chemoreceptor-based signaling cascades are very abundant in bacteria and are among the most complex signaling systems. Currently, our knowledge on the molecular features that determine signal recognition at chemoreceptors is limited. Chemoreceptor McpA of Bacillus velezensis SQR9 has been shown to mediate chemotaxis to a broad range of different ligands. Here we show that its ligand binding domain binds directly 13 chemoattractants. We provide support that organic acids and amino acids bind to the membrane-distal and membrane-proximal module of the dCache domain, respectively, whereas binding of sugars/sugar alcohols occurred at both modules. Structural biology studies combined with site-directed mutagenesis experiments have permitted to identify 10 amino acid residues that play key roles in the recognition of multiple ligands. Residues in membrane-distal and membrane-proximal regions were central for sensing organic acids and amimo acids, respectively, whereas all residues participated in sugars/sugar alcohol sensing. Most characterized chemoreceptors possess a narrow and well-defined ligand spectrum. We propose here a sensing mechanism involving both dCache modules that allows the integration of very diverse signals by a single chemoreceptor.

MiRLoc: predicting miRNA subcellular localization by incorporating miRNA-mRNA interactions and mRNA subcellular localization.

Subcellular localization of microRNAs (miRNAs) is an important reflection of their biological functions. Considering the spatio-temporal specificity of miRNA subcellular localization, experimental detection techniques are expensive and time-consuming, which strongly motivates an efficient and economical computational method to predict miRNA subcellular localization. In this paper, we describe a computational framework, MiRLoc, to predict the subcellular localization of miRNAs. In contrast to existing methods, MiRLoc uses the functional similarity between miRNAs instead of sequence features and incorporates information about the subcellular localization of the corresponding target mRNAs. The results show that miRNA functional similarity data can be effectively used to predict miRNA subcellular localization, and that inclusion of subcellular localization information of target mRNAs greatly improves prediction performance.

Predicting the structure of unexplored novel fentanyl analogues by deep learning model.

Fentanyl and its analogues are psychoactive substances and the concern of fentanyl abuse has been existed in decades. Because the structure of fentanyl is easy to be modified, criminals may synthesize new fentanyl analogues to avoid supervision. The drug supervision is based on the structure matching to the database and too few kinds of fentanyl analogues are included in the database, so it is necessary to find out more potential fentanyl analogues and expand the sample space of fentanyl analogues. In this study, we introduced two deep generative models (SeqGAN and MolGPT) to generate potential fentanyl analogues, and a total of 11 041 valid molecules were obtained. The results showed that not only can we generate molecules with similar property distribution of original data, but the generated molecules also contain potential fentanyl analogues that are not pretty similar to any of original data. Ten molecules based on the rules of fentanyl analogues were selected for NMR, MS and IR validation. The results indicated that these molecules are all unreported fentanyl analogues. Furthermore, this study is the first to apply the deep learning to the generation of fentanyl analogues, greatly expands the exploring space of fentanyl analogues and provides help for the supervision of fentanyl.

NcPath: a novel platform for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways.

SUMMARY: Non-coding RNAs play important roles in transcriptional processes and participate in the regulation of various biological functions, in particular miRNAs and lncRNAs. Despite their importance for several biological functions, the existing signaling pathway databases do not include information on miRNA and lncRNA. Here, we redesigned a novel pathway database named NcPath by integrating and visualizing a total of 178 308 human experimentally validated miRNA-target interactions (MTIs), 32 282 experimentally verified lncRNA-target interactions (LTIs) and 4837 experimentally validated human ceRNA networks across 222 KEGG pathways (including 27 sub-categories). To expand the application potential of the redesigned NcPath database, we identified 556 798 reliable lncRNA-protein-coding genes (PCG) interaction pairs by integrating co-expression relations, ceRNA relations, co-TF-binding interactions, co-histone-modification interactions, cis-regulation relations and lncPro Tool predictions between lncRNAs and PCG. In addition, to determine the pathways in which miRNA/lncRNA targets are involved, we performed a KEGG enrichment analysis using a hypergeometric test. The NcPath database also provides information on MTIs/LTIs/ceRNA networks, PubMed IDs, gene annotations and the experimental verification method used. In summary, the NcPath database will serve as an important and continually updated platform that provides annotation and visualization of the pathways on which non-coding RNAs (miRNA and lncRNA) are involved, and provide support to multimodal non-coding RNAs enrichment analysis. The NcPath database is freely accessible at http://ncpath.pianlab.cn/. AVAILABILITY AND IMPLEMENTATION: NcPath database is freely available at http://ncpath.pianlab.cn/. The code and manual to use NcPath can be found at https://github.com/Marscolono/NcPath/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Dissection of rhizosphere microbiome and exploiting strategies for sustainable agriculture.

The rhizosphere microbiome plays critical roles in plant growth and provides promising solutions for sustainable agriculture. While the rhizosphere microbiome frequently fluctuates with the soil environment, recent studies have demonstrated that a small proportion of the microbiome is consistently assembled in the rhizosphere of a specific plant genotype regardless of the soil condition, which is determined by host genetics. Based on these breakthroughs, which involved exploiting the plant-beneficial function of the rhizosphere microbiome, we propose to divide the rhizosphere microbiome into environment-dominated and plant genetic-dominated components based on their different assembly mechanisms. Subsequently, two strategies to explore the different rhizosphere microbiome components for agricultural production are suggested, that is, the precise management of the environment-dominated rhizosphere microbiome by agronomic practices, and the elucidation of the plant genetic basis of the plant genetic-dominated rhizosphere microbiome for breeding microbiome-assisted crop varieties. We finally present the major challenges that need to be overcome to implement strategies for modulating these two components of the rhizosphere microbiome.

m6A mRNA modification promotes chilling tolerance and modulates gene translation efficiency in Arabidopsis.

N 6-methyladenosine (m6A), the most prevalent mRNA modification in eukaryotes, is an emerging player of gene regulation at transcriptional and translational levels. Here, we explored the role of m6A modification in response to low temperature in Arabidopsis (Arabidopsis thaliana). Knocking down mRNA adenosine methylase A (MTA), a key component of the modification complex, by RNA interference (RNAi) led to drastically reduced growth at low temperature, indicating a critical role of m6A modification in the chilling response. Cold treatment reduced the overall m6A modification level of mRNAs especially at the 3' untranslated region. Joint analysis of the m6A methylome, transcriptome and translatome of the wild type (WT) and the MTA RNAi line revealed that m6A-containing mRNAs generally had higher abundance and translation efficiency than non-m6A-containing mRNAs under normal and low temperatures. In addition, reduction of m6A modification by MTA RNAi only moderately altered the gene expression response to low temperature but led to dysregulation of translation efficiencies of one third of the genes of the genome in response to cold. We tested the function of the m6A-modified cold-responsive gene ACYL-COA:DIACYLGLYCEROL ACYLTRANSFERASE 1 (DGAT1) whose translation efficiency but not transcript level was reduced in the chilling-susceptible MTA RNAi plant. The dgat1 loss-of-function mutant exhibited reduced growth under cold stress. These results reveal a critical role of m6A modification in regulating growth under low temperature and suggest an involvement of translational control in chilling responses in Arabidopsis.

The beneficial rhizobacterium Bacillus velezensis SQR9 regulates plant nitrogen uptake via an endogenous signaling pathway.

Nitrogen fertilizer is widely used in agriculture to boost crop yields. Plant growth-promoting rhizobacteria (PGPRs) can increase plant nitrogen use efficiency through nitrogen fixation and organic nitrogen mineralization. However, it is not known whether they can activate plant nitrogen uptake. In this study, we investigated the effects of volatile compounds (VCs) emitted by the PGPR strain Bacillus velezensis SQR9 on plant nitrogen uptake. Strain SQR9 VCs promoted nitrogen accumulation in both rice and Arabidopsis. In addition, isotope labeling experiments showed that strain SQR9 VCs promoted the absorption of nitrate and ammonium. Several key nitrogen-uptake genes were up-regulated by strain SQR9 VCs, such as AtNRT2.1 in Arabidopsis and OsNAR2.1, OsNRT2.3a, and OsAMT1 family members in rice, and the deletion of these genes compromised the promoting effect of strain SQR9 VCs on plant nitrogen absorption. Furthermore, calcium and the transcription factor NIN-LIKE PROTEIN 7 play an important role in nitrate uptake promoted by strain SQR9 VCs. Taken together, our results indicate that PGPRs can promote nitrogen uptake through regulating plant endogenous signaling and nitrogen transport pathways.

GSDMD mediated pyroptosis induced inflammation of Graves' orbitopathy via the NF-κB/ AIM2/ Caspase-1 pathway.

Gasdermin D (GSDMD) is a key executor which triggers pyroptosis as well as an attractive checkpoint in various inflammatory and autoimmune diseases but it has yet to prove its function in Graves'orbitopathy (GO). Our aim was to investigate GSDMD levels in orbital connective tissue and serum of GO patients and then assess the association between serum levels and patients' clinical activity score (CAS). Further, GSDMD-mediated pyroptosis and the underlying mechanism in inflammatory pathogenesis in the cultured orbital fibroblasts (OFs) of GO patients were examined. OFs were collected after tumor necrosis factor (TNF)-α or interferon (IFN)-γ treatment or combination treatment at different times, and the expression of GSDMD and related molecular mechanisms were analyzed. Then, we constructed the GSDMD knockout system with siRNA and the system was further exposed to the medium with or without IFN-γ and TNF-α for a specified time. Finally, we evaluated the production of interleukin (IL)-1ß and IL-18. We found that serum GSDMD levels were elevated and positively correlated with the CAS in GO patients. Meanwhile, the expression of GSDMD and N-terminal domain (NT-GSDMD) in orbital connective tissue of GO patients was augmented. Also, increased expression of GSDMD and related pyroptosis factors was observed in vitro model of GO. We further demonstrated that GSDMD-mediated pyroptosis induced inflammation via the nuclear factor kB (NF-κB)/absent in melanoma-2 (AIM-2)/caspase-1 pathway. In addition, blocking GSDMD suppressed proinflammatory cytokine production in GO. We concluded that GSDMD may be a biomarker as well as a potential target for the evaluation and treatment of inflammation related with GO.

Efficacy and safety of tibial nerve stimulation using a wearable device for overactive bladder.

OBJECTIVE: To evaluate the efficacy and safety of a wearable, smartphone-controlled, rechargeable transcutaneous tibial nerve stimulation (TTNS) device in patients with overactive bladder (OAB). PATIENTS AND METHODS: This multicentre, prospective, single-blind, randomised clinical trial included eligible patients with OAB symptoms who were randomly assigned to the stimulation group or sham group. The primary efficacy outcome was change from baseline in voiding frequency/24 h after 4 weeks of treatment. The secondary efficacy outcomes included changes in bladder diary outcomes (urgency score/void, nocturia episodes/day, micturition volume/void, and incontinence episodes/day), questionnaires on Overactive Bladder Symptom Score (OABSS), Patient Perception of Bladder Condition (PPBC), and American Urological Association Symptom Index Quality of Life Score (AUA-SI-QoL) at baseline and after 4 weeks of treatment. Device-related adverse events (AEs) were also evaluated. RESULTS: In the full analysis set (FAS), the mean (sd) change of voiding frequency/24 h in the stimulation group and sham group at 4 weeks were -3.5 (2.9) and -0.6 (2.4), respectively (P < 0.01). Similar results were obtained in the per-protocol set (PPS): -3.5 (2.9) vs -0.4 (2.3) (P < 0.01). In the FAS and PPS, micturition volume/void significantly improved at 4 weeks (P = 0.01 and P = 0.02). PPBC improvement almost reached significance in the FAS (P = 0.05), while it was significant in the PPS (P = 0.02). In the FAS and PPS, AUA-SI-QoL significantly improved at 4 weeks in the two groups (P < 0.01 and P < 0.01), whereas there were no significant differences in urgency score/void, nocturia episodes/day or OABSS between the groups. Also, no device-related serious AEs were reported. CONCLUSIONS: The non-invasive neuromodulation technique using the novel ambulatory TTNS device is effective and safe for treating OAB. Its convenience and easy maintenance make it a new potential home-based treatment modality. Future studies are warranted to confirm its longer-term efficacy.

MnO4--Triggered Immediate-Stable Real-Time Fluorescence Immunosensor with High Response Speed and Low Steady-State Error.

Real-time chemical and biological sensing in vitro is important for application in health and environmental monitoring. Thus, a more rapid and stable detection method is urgently needed. Herein, an immediate-stable real-time fluorescent immunosensor with a high response speed (∼100%, <1 s) and approximately zero steady-state error is constructed. The developed sensor is based on the MnO4--triggered in situ immediate-stable fluorogenic reaction between dopamine and orcinol monohydrate to produce azamonardine (DMTM). The obtained DMTM is identified and characterized by high-resolution mass spectrometry, 1H NMR spectroscopy, 13C NMR spectroscopy, and theoretical calculations. The present sensor achieves a highly sensitive detection of dopamine (DA) with a limit of detection (LOD) of 10 nM as well as alkaline phosphates (ALP) with an LOD of 0.1 mU/mL by using orcinol monohydrate phosphate sodium salt as a substrate. As a proof of concept, ALP-triggered fluorescence ELISA using cardiac troponin I (cTnI) as a model antigen target is further constructed. The developed real-time sensor achieves the detection of cTnI with an LOD of 0.05 ng/mL. Moreover, the sensor proposed by us is successfully applied to assess the cTnI level in clinical serum specimens and yields results consistent with those obtained by the commercial ELISA method. The immediate-stable real-time fluorescence immunosensor provides a promising and powerful platform for the trace detection of biomolecules in clinical diagnosis.

Multicomponent Hybridization Transition Metal Oxide Electrode Enriched with Oxygen Vacancy for Ultralong-Life Supercapacitor.

Transition metal oxide electrode materials for supercapacitors suffer from poor electrical conductivity and stability, which are the research focus of the energy storage field. Herein, multicomponent hybridization Ni-Cu oxide (NCO-Ar/H2 -10) electrode enriched with oxygen vacancy and high electrical conductivity including the Cu0.2 Ni0.8 O, Cu2 O and CuO is prepared by introducing Cu element into Ni metal oxide with hydrothermal, annealing, and plasma treatment. The NCO-Ar/H2 -10 electrode exhibits high specific capacity (1524 F g-1 at 3 A g-1 ), good rate performance (72%) and outstanding cyclic stability (109% after 40,000 cycles). The NCO-Ar/H2 -10//AC asymmetric supercapacitor (ASC) achieves high energy density of 48.6 Wh kg-1 at 799.6 W kg-1 while exhibiting good cycle life (117.5% after 10,000 cycles). The excellent electrochemical performance mainly comes from the round-trip valence change of Cu+ /Cu2+ in the multicomponent hybridization enhance the surface capacitance during the redox process, and the change of electronic microstructure triggered by a large number of oxygen vacancies reduce the adsorption energy of OH- ions of thin nanosheet with crack of surface edge, ensuring electron and ion-transport processes and remitting the structural collapse of material. This work provides a new strategy for improving the cycling stability of transition metal oxide electrode materials.

Plant immunity suppressor SKRP encodes a novel RNA-binding protein that targets exon 3' end of unspliced RNA.

The regulatory roles of RNA splicing in plant immunity are emerging but still largely obscure. We reported previously that Phytophthora pathogen effector Avr3c targets a soybean protein SKRP (serine/lysine/arginine-rich protein) to impair soybean basal immunity by regulating host pre-mRNA alternative splicing, while the biochemical nature of SKRP remains unknown. Here, by using Arabidopsis as a model, we studied the mechanism of SKRP in regulating pre-mRNA splicing and plant immunity. AtSKRP confers impaired plant immunity against Phytophthora capsici and associates with spliceosome component PRP8 and splicing factor SR45, which positively and negatively regulate plant immunity, respectively. Enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP-seq) showed AtSKRP is a novel RNA-binding protein that targets exon 3' end of unspliced RNA. Such position-specific binding of SKRP is associated with its activity in suppressing intron retention, including at positive immune regulatory genes UBP25 and RAR1. In addition, we found AtSKRP self-interact and forms oligomer, and these properties are associated with its function in plant immunity. Overall, our findings reveal that the immune repressor SKRP is a spliceosome-associated protein that targets exon 3' end to regulate pre-mRNA splicing in Arabidopsis.

Listening to plant's Esperanto via root exudates: reprogramming the functional expression of plant growth-promoting rhizobacteria.

Rhizomicrobiome plays important roles in plant growth and health, contributing to the sustainable development of agriculture. Plants recruit and assemble the rhizomicrobiome to satisfy their functional requirements, which is widely recognized as the 'cry for help' theory, but the intrinsic mechanisms are still limited. In this study, we revealed a novel mechanism by which plants reprogram the functional expression of inhabited rhizobacteria, in addition to the de novo recruitment of soil microbes, to satisfy different functional requirements as plants grow. This might be an efficient and low-cost strategy and a substantial extension to the rhizomicrobiome recruitment theory. We found that the plant regulated the sequential expression of genes related to biocontrol and plant growth promotion in two well-studied rhizobacteria Bacillus velezensis SQR9 and Pseudomonas protegens CHA0 through root exudate succession across the plant developmental stages. Sixteen key chemicals in root exudates were identified to significantly regulate the rhizobacterial functional gene expression by high-throughput qPCR. This study not only deepens our understanding of the interaction between the plant-rhizosphere microbiome, but also provides a novel strategy to regulate and balance the different functional expression of the rhizomicrobiome to improve plant health and growth.

Nitrogen fertilization modulates beneficial rhizosphere interactions through signaling effect of nitric oxide.

Chemical nitrogen (N) fertilization is customary for increasing N inputs in agroecosystems. The nutritional effects of N fertilization on plants and soil microbes have been well studied. However, the signaling effects of N fertilization on rhizosphere plant-microbe interactions and the following feedback to plant performance remain unknown. Here, we investigated the effect of different N fertilizations on the behavior of the plant growth-promoting rhizobacteria (PGPR) Bacillus velezensis SQR9 in the cucumber (Cucumis sativus L.) rhizosphere. Moderate N fertilization promoted higher rhizosphere colonization of strain SQR9 than insufficient or excessive N input. Nitric oxide (NO) produced through the denitrification process under N fertilization was identified as the signaling molecule that dominates the root colonization of PGPR, and this effect could be neutralized by the NO-specific scavenger 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxy-3-oxide. Gene expression analysis demonstrated that NO regulated the biofilm formation of strain SQR9 by affecting the synthesis of extracellular matrix γ-polyglutamic acid, consequently impacting its root colonization. Finally, we demonstrated that moderate N fertilization-modulated enhanced PGPR root colonization can significantly promote plant growth and nitrogen use efficiency. This study provides insights into our understanding of the beneficial rhizosphere plant-microbe interactions under N fertilization and suggests that rational fertilization is critical to promote beneficial rhizosphere interactions for sustainable agricultural production.

Elevated serum uric acid level is associated with adverse reproductive outcomes in women with polycystic ovary syndrome undergoing in vitro fertilization or intracytoplasmic sperm injection embryo transfer cycles: a retrospective cohort study.

BACKGROUND: Serum uric acid levels are elevated in polycystic ovary syndrome, however, the relationship between serum uric acid level and reproductive outcomes in women with polycystic ovary syndrome remains unclear. OBJECTIVE: This study aimed to investigate the association between serum uric acid level and the reproductive outcomes in women with polycystic ovary syndrome undergoing in vitro fertilization or intracytoplasmic sperm injection embryo transfer cycles. STUDY DESIGN: This was a retrospective cohort study performed at a university-affiliated reproductive medicine center. A total of 1903 women with polycystic ovary syndrome undergoing their first in vitro fertilization or intracytoplasmic sperm injection embryo transfer cycles between January 2010 and January 2021 were initially included. The trends for reproductive outcomes in polycystic ovary syndrome across quartiles of serum uric acid levels were assessed. A logistic regression analysis was performed to obtain the odds ratios for in vitro fertilization outcomes based on the quartiles of serum uric acid with or without adjusting for potential confounding variables. Using generalized additive models, serum uric acid was further treated as its original continuous property to visualize its nonlinear relationship with in vitro fertilization outcomes. The live birth rate was the main outcome. RESULTS: After exclusions, a total of 883 women with polycystic ovary syndrome with their first fresh-embryo transfer cycles were included. In quartiles of serum uric acid levels, there was a significant decreasing trend in the live birth rate from the lowest quartile (Q1: 61.8%) to the highest (Q4: 45.9%) (Ptrend=.002). The percentage of low birthweight increased from Q1 (22.3%) to Q4 (31.7%) (Ptrend=.049). Compared with those in Q1, women in Q4 showed a significant lower probability of live birth and clinical pregnancy and a higher risk for low birthweight (all P<.05). Both the unadjusted and adjusted generalized additive models indicated that as the serum uric acid level increased, the probability of clinical pregnancy and the live birth rate exhibited an overall decreasing profile, and the risk for low birthweight showed an increasing profile. CONCLUSION: An elevated serum uric acid level is associated with decreased probabilities of live birth and clinical pregnancy and an increased risk for low birthweight in women with polycystic ovary syndrome. However, these associations may be confounded by other factors and more well-designed studies are needed to confirm these findings in the future.

Randomized controlled trial of intravesical electrical stimulation for underactive bladder.

AIM: To evaluate the efficacy and safety of intravesical electrical stimulation (IVES) performed with a novel device in patients with underactive bladder (UAB). PATIENTS AND METHODS: This was a multicentre, prospective, single-blind, randomized controlled clinical trial of patients with UAB in China. Eligible patients were randomly assigned in a 1:1 ratio to receive conventional IVES (n = 38) or IVES with an open circuit (n = 38). The primary efficacy measure was change from baseline in post-void residual urine volume (PVR) after 4 weeks of treatment. Secondary efficacy measures included changes in maximum urinary flow rate (Qmax ), bladder voiding efficiency (BVE), number of 24-h clean intermittent catheterization (CIC) procedures, and Patient Perception of Bladder Condition-Scale (PPBC-S) and American Urological Association Symptom Index Quality of Life (AUA-SI-QoL) scores from baseline after 4 weeks of treatment. Adverse events (AEs) were monitored throughout the trial. RESULTS: In the full analysis set (FAS), the mean (sd) PVR changes in the trial and control groups at 4 weeks were -97.1 (107.5) mL and -10.5 (86.7) mL, respectively (P < 0.01). Similar results were obtained in the per-protocol set (PPS): -102.9 (100.0) mL vs 0.7 (82.5) mL (P < 0.01). In the FAS and PPS, Qmax improved significantly at 4 weeks (P = 0.04 and P = 0.03). In the FAS and PPS, BVE was significantly improved at 4 weeks in the two groups (P < 0.01 and P < 0.01), whereas no significant differences in the number of 24-h CIC procedures, PPBC-S score or AUA-SI-QoL score were observed between the groups. Six possible therapy-related AEs occurred in six patients (four in the trial group and two in the control group; P = 0.67), all of which were urinary tract infections. No severe AEs were reported. CONCLUSIONS: The results of this clinical study strongly demonstrate that UAB patients benefit from this novel IVES device. More research is needed to validate the clinical utility of this device.

Integrated Biogeography and Assembly Mechanisms of Microeukaryotic Communities in Coastal Waters Near Shellfish Cultivation.

The Lianjiang coast in the East China Sea is a typical subtropical marine ecosystem, and shellfish cultivation occupies almost all of the available tidal flats. Many studies have investigated the effects of shellfish cultivation on benthic organisms and sediments, while the impact of shellfish cultivation on plankton ecosystems is still poorly understood. This study investigated the biogeographical patterns of microeukaryotic communities from Lianjiang coastal waters in four seasons using 18S ribosomal RNA gene amplicon sequencing. Microeukaryotes were mainly comprised of Dinoflagellata, Diatomea, Arthropoda, Ciliophora, Chlorophyta, Protalveolata, Cryptophyceae, and Ochrophyta, and presented significant differences in three habitats (the aquaculture area, confluent area, and offshore area) and four seasons. Similarity percentage analysis revealed that Paracalanus parvus, Heterocapsa rotundata, Bestiolina similis, and five additional key taxa contributed to spatio-temporal differences. Seasonal environmental and spatial factors explained 27.47% of microeukaryotic community variation on average, with 11.11% of the variation shared. Environmental variables, particularly depth, pH, and nitrite concentration, were strongly associated with the microeukaryotic community compositions. The neutral community model further demonstrated that stochastic processes were sufficient in shaping substantial variation in microeukaryotic communities across four seasons, which may reveal the remaining unexplained microeukaryotic community variation. We further divided four seasons into the aquaculture stages and non-aquaculture stages, and speculated that aquaculture activities may increase the dispersal limitation of microeukaryotes in coastal waters, especially for the big bodied-microbes like Arthropoda. The results provide a better understanding of the biogeographical patterns, processes, and mechanisms of microeukaryotic communities near shellfish cultivation.

Genetic characterization of HIV-1 viruses among cases with antiretroviral therapy failure in Suzhou City, China.

BACKGROUND: This retrospective study aimed to characterize the distribution of HIV-1 genotypes and the prevalence of drug resistance mutations in people with antiretroviral treatment (ART) failure in Suzhou City, China. METHODS: Pol gene of HIV-1 viruses in blood samples of EDTA anticoagulants from 398 patients with failed antiviral treatment was successfully amplified by using an in-house assay. Drug resistance mutations were analyzed by using the Stanford HIV Drug Resistance Database system ( https://hivdb.stanford.edu/hivdb/by-mutations/ ). HIV-1 genotypes were determined by the REGA HIV subtyping tool (version 3.46, https://www.genomedetective.com/app/typingtool/hiv ). Near full-length genomes (NFLG) of HIV-1 viruses were obtained by next generation sequencing method. RESULTS: Sequences analysis of the pol gene revealed that CRF 01_AE (57.29%, 228/398) was the dominant subtype circulating in Suzhou City, followed by CRF 07_BC (17.34%, 69/398), subtype B (7.54%, 30/398), CRF 08_BC (6.53%, 26/398), CRF 67_01B (3.02%, 12/398) and CRF55_01B (2.51%, 10/398). The overall prevalence of drug-resistant mutations in cases with ART failure was 64.57% (257/398), including 45.48% (181/398) for nucleotide reverse transcriptase inhibitors (NRTIs) mutations, 63.32% (252/398) for non-nucleoside reverse transcriptase inhibitors (NNRTIs) mutations, and 3.02% (12/398) for protease inhibitors (PIs) mutations. Ten near full-length genomes (NFLG) of HIV-1 viruses were identified, including six recombinants of CRF 01_AE and subtype B, two recombinants of CRF 01_AE, subtype B and subtype C sequences, one recombinant of CRF 01_AE and subtype C and one recombinant of CRF 01_AE, subtype A1 and subtype C. CONCLUSIONS: The high prevalence of drug-resistant HIV-1 viruses was a serious challenge for HIV prevention and treatment of people with HIV infection. Treatment regimens for ART failure patients should be adjusted over time based on the outcome of drug resistance tests. NFLG sequencing facilitates the identification of new recombinants of HIV-1.

AGMN: Association Graph-based Graph Matching Network for Coronary Artery Semantic Labeling on Invasive Coronary Angiograms.

Semantic labeling of coronary arterial segments in invasive coronary angiography (ICA) is important for automated assessment and report generation of coronary artery stenosis in computer-aided coronary artery disease (CAD) diagnosis. However, separating and identifying individual coronary arterial segments is challenging because morphological similarities of different branches on the coronary arterial tree and human-to-human variabilities exist. Inspired by the training procedure of interventional cardiologists for interpreting the structure of coronary arteries, we propose an association graph-based graph matching network (AGMN) for coronary arterial semantic labeling. We first extract the vascular tree from invasive coronary angiography (ICA) and convert it into multiple individual graphs. Then, an association graph is constructed from two individual graphs where each vertex represents the relationship between two arterial segments. Thus, we convert the arterial segment labeling task into a vertex classification task; ultimately, the semantic artery labeling becomes equivalent to identifying the artery-to-artery correspondence on graphs. More specifically, the AGMN extracts the vertex features by the embedding module using the association graph, aggregates the features from adjacent vertices and edges by graph convolution network, and decodes the features to generate the semantic mappings between arteries. By learning the mapping of arterial branches between two individual graphs, the unlabeled arterial segments are classified by the labeled segments to achieve semantic labeling. A dataset containing 263 ICAs was employed to train and validate the proposed model, and a five-fold cross-validation scheme was performed. Our AGMN model achieved an average accuracy of 0.8264, an average precision of 0.8276, an average recall of 0.8264, and an average F1-score of 0.8262, which significantly outperformed existing coronary artery semantic labeling methods. In conclusion, we have developed and validated a new algorithm with high accuracy, interpretability, and robustness for coronary artery semantic labeling on ICAs.

Research on Photoacoustic Synthetic Aperture Focusing Technology Imaging Method of Internal Defects in Cylindrical Components.

Cylindrical components are parts with curved surfaces, and their high-precision defect testing is of great significance to industrial production. This paper proposes a noncontact internal defect imaging method for cylindrical components, and an automatic photoacoustic testing platform is built. A synthetic aperture focusing technology in the polar coordinate system based on laser ultrasonic (LU-pSAFT) is established, and the relationship between the imaging quality and position of discrete points is analyzed. In order to verify the validity of this method, small holes of Φ0.5 mm in the aluminum alloy rod are tested. During the imaging process, since a variety of waveforms can be excited by the pulsed laser synchronously, the masked longitudinal waves reflected by small holes need to be filtered and windowed to achieve high-quality imaging. In addition, the influence of ultrasonic beam angle and signal array spacing on imaging quality is analyzed. The results show that the method can accurately present the outline of the small hole, the circumferential resolution of the small hole is less than 1° and the dimensional accuracy and position error are less than 0.1 mm.