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One of the key tasks of multi-modal sentiment classification is to accurately extract and fuse complementary information from two different modes of text and vision in order to detect the affective tendency of the mentioned aspect words in the text. Most of the existing methods only use a single context information combined with picture information for analysis, and there are problems such as insensitive recognition of the correlation between aspects, context information and visual information, and insufficient local extraction of aspects related information in vision. In addition, when the feature fusion is carried out, some modal information is not sufficient, which leads to the general fusion effect. In order to fully carry out fine-grained information interaction between multiple modes, a multi-modal sentiment classification based on graph neural network and multi-head cross-attention mechanism for education emotion analysis is proposed in this paper. Firstly, cross-attention is used to obtain the global representation of aspect-oriented objects in text and images. Then a multi-modal interaction graph is established to connect the local and global representation nodes of different modes. Finally, the graph attention network is used to fully integrate the features in the two granularity. Numerous experiments on popular multi-modal sentiment analysis datasets demonstrate the advantages of the proposed framework in this paper compared to state-of-the-art methods.

Abstract Background M1 macrophages are closely associated with cardiac injury after myocardial infarction (MI). Increasing evidence shows that exosomes play a key role in pathophysiological regulation after MI, but the role of M1 macrophage-derived exosomes (M1-Exos) in myocardial regeneration remains unclear. In this study, we explored the impact of M1 macrophage-derived exosomes on cardiomyocytes regeneration in vitro and in vivo. Methods M0 macrophages were induced to differentiate into M1 macrophages with GM-CSF (50 ng/mL) and IFN-γ (20 ng/mL). Then M1-Exos were isolated and co-incubated with cardiomyocytes. Cardiomyocyte proliferation was detected by pH3 or ki67 staining. Quantitative real-time PCR (qPCR) was used to test the level of miR-155 in macrophages, macrophage-derived exosomes and exosome-treated cardiomyocytes. MI model was constructed and LV-miR-155 was injected around the infarct area, the proliferation of cardiomyocytes was counted by pH3 or ki67 staining. The downstream gene and pathway of miR-155 were predicted and verified by dual-luciferase reporter gene assay, qPCR and immunoblotting analysis. IL-6 (50 ng/mL) was added to cardiomyocytes transfected with miR-155 mimics, and the proliferation of cardiomyocytes was calculated by immunofluorescence. The protein expressions of IL-6R, p-JAK2 and p-STAT3 were detected by Western blot. Results The results showed that M1-Exos suppressed cardiomyocytes proliferation. Meanwhile, miR-155 was highly expressed in M1-Exos and transferred to cardiomyocytes. miR-155 inhibited the proliferation of cardiomyocytes and antagonized the pro-proliferation effect of interleukin 6 (IL-6). Furthermore, miR-155 targeted gene IL-6 receptor (IL-6R) and inhibited the Janus kinase 2(JAK)/Signal transducer and activator of transcription (STAT3) signaling pathway. Conclusion M1-Exos inhibited cardiomyocyte proliferation by delivering miR-155 and inhibiting the IL-6R/JAK/STAT3 signaling pathway. This study provided new insight and potential treatment strategy for the regulation of myocardial regeneration and cardiac repair by macrophages.

This paper focuses on the automatic detection of industrial storage tanks in urban areas using deep learning-based algorithms. Industrial storage tanks are critical for storing raw materials, finished products, and intermediate products in industries such as petroleum, chemical, and metallurgy. However, they can leak and cause environmental damage, making it important to monitor them in cities. The challenge lies in the large number and dispersed distribution of these tanks throughout the city. To address this, high-resolution remote sensing images and deep learning algorithms are used to improve the accuracy of industrial storage tank detection at the city scale. We construct a city scale industrial storage tank object detection dataset using high-resolution remote sensing images and explore the effect of deep learning object detection algorithm optimization on industrial storage tank detection. Techniques including ResNet50, FPN, and dilated convolution are utilized in this work for improving the model detection accuracy. Furthermore, we construct multiple city industrial storage tank datasets based on high-resolution remote sensing images enriched by integrating point-of-interest data and land use data of each city. The integration from multiple data sources provides an accurate and efficient solution for the identification of industrial storage tanks within urban areas.

ObjectivesThrough a longitudinal study, we explored the relationship between sensory impairments and depression in the elderly, and examined the mediating roles of daily activity capability and social participation within this relationship.MethodsBased on data from the China Health and Retirement Longitudinal Study (CHARLS) collected in 2015 and 2018, a total of 4,419 individuals aged 60 and above were selected as research participants. Sensory impairments (predictor variables) were assessed in 2015 through self-rated visual and hearing capabilities. Daily activity capability and social participation (mediator variables) were also assessed in 2015, with daily activities assessed using the Basic Activities of Daily Living (BADL) and Instrumental Activities of Daily Living (IADL), and social participation assessed by the quantity of social activity participation. Depression status (outcome variable) was assessed in 2018 using the Center for Epidemiologic Studies Depression Scale (CESD-10). Statistical analysis was conducted using logistic regression and SPSS Macro PROCESS.ResultsFirst, there is a significant correlation between sensory impairments and an increased risk of depression among the elderly, including visual impairment (VI), hearing impairment (HI), and dual sensory impairment (DSI), all of which increase the likelihood of depression. Second, DSI indirectly affect depression through the cascading mediating effects of daily activity capability and social participation. Finally, in contrast to DSI, when there is only a single sensory impairment, either VI or HI, the cascading mediating effects of daily activity capability and social participation on depression are not statistically significant.ConclusionThe elderly population with dual sensory impairments requires continued attention to help these individuals adopt preventive measures to halt the onset and worsening of depression.

In the field of remote sensing image denoising, the current mainstream methods usually only consider using clean or noisy images to guide the network in the training phase. Most of them only apply to specific types of noise, and the denoising effect is not satisfactory enough, with problems such as artifacts and noise residues. In this article, we endeavor to deal with a wide range of noise types, preserving as much detailed information in the image as possible and aiming to address the relevant limitations. Inspired by contrastive learning, we propose a remote sensing image denoising framework based on contrastive learning, named RSID-CR, which constructs positive and negative sample pairs between clean, noisy, and denoised images. Then, we construct a joint loss function consisting of reconstruction loss and contrastive regularization as a guide signal to train the denoising network, such that the denoised image is pushed closer to the clean image and farther away from the noisy image in the feature space. We conduct extensive experiments on two public datasets for five types of noise often present in remote sensing images. In addition, we validate our method using two real noisy remote sensing datasets. The experimental results indicate that our proposed method achieves satisfactory outcomes.

Fugitive dust is an important source of total suspended particulate matter in urban ambient air. The existing segmentation methods for dust sources face challenges in distinguishing key and secondary features, and they exhibit poor segmentation at the image edge. To address these issues, this paper proposes the Dust Source U-Net (DSU-Net), enhancing the U-Net model by incorporating VGG16 for feature extraction, and integrating the shuffle attention module into the jump connection branch to enhance feature acquisition. Furthermore, we combine Dice Loss, Focal Loss, and Activate Boundary Loss to improve the boundary extraction accuracy and reduce the loss oscillation. To evaluate the effectiveness of our model, we selected Jingmen City, Jingzhou City, and Yichang City in Hubei Province as the experimental area and established two dust source datasets from 0.5 m high-resolution remote sensing imagery acquired by the Jilin-1 satellite. Our created datasets include dataset HDSD-A for dust source segmentation and dataset HDSD-B for distinguishing the dust control measures. Comparative analyses of our proposed model with other typical segmentation models demonstrated that our proposed DSU-Net has the best detection performance, achieving a mIoU of 93% on dataset HDSD-A and 92% on dataset HDSD-B. In addition, we verified that it can be successfully applied to detect dust sources in urban areas.

A series of palladium-modified (Pd-modified) CuO-ZnO-Al2O3 (CZA) catalysts with various Pd loadings (0.3 wt% to 2.4 wt%) were prepared using the wetness impregnation method, on two CZA supports with different structures that are CZA-aged precursor composed of a mixture of zincian-malachite and hydrotalcite-like phases (CZA-zH), and CuO-ZnO-Al2O3 metal oxide nanoparticles (CZA-MO). Enhancement on catalytic activity can be observed on both Pd-modified CZA catalysts in a temperature range of 180–240 °C for methanol synthesis via CO2 hydrogenation. Pd/CZA-zH catalysts exhibited a more efficient and stable production of methanol at a relatively low reaction temperature of 180 °C for 100 hrs of reaction. The improvement of activity is mainly ascribed to a higher surface area and abundant oxygen-containing functional groups (e.g., –OH) of CZA-zH support, which is beneficial for better adsorption and distribution of Pd promoter. Hydrogen temperature programmed reduction and X-ray photoelectron spectroscopy results demonstrated a better interaction between Pd and Cu on Pd/CZA-zH catalysts via enhanced reducibility of CuO, and peak shift of Cu to a lower binding energy. The difference in the efficient utilization of hydrogen spillover effect of Pd promoter over two CZA supports resulted in the different performances for methanol synthesis under mild reaction conditions.

Abstract Purpose The extracellular electron transfer (EET) capability enables electroactive microorganisms have a wide range of applications in energy production, wastewater treatment, bioremediation and chemical synthesis. Because the oxygen levels will sharply affect the EET process, we integrated transcriptome changes under different oxygen levels with protein–protein interaction (PPI) network to study the specific changes under these conditions in a typical electroactive microorganism Shewanella oneidensis MR-1 (S. oneidensis MR-1). Methods First, the mRNA expression data of S. oneidensis MR-1 under different oxygen levels were integrated into its PPI network to construct the active protein networks. Then, we studied the changes of key proteins and their interactions by comparative analysis of multiple pairs of active networks. Results The analysis of node centrality and its changes in the active networks under high and low oxygen levels shows that most of the key nodes in the network are ribosomes or proteins closely related to ribosomes. The results of our centrality versus centrality change analysis of nodes show that the two proteins FlgB and PetA are the largest changed proteins. Among these proteins, the FlgB protein is the structural component of flagella, while PetA protein is closely related to cytochrome c. Furthermore, we also analyzed the changes in protein–protein interactions in the active networks under different oxygen levels, identified the key interactions in each pair of active networks, and finally screened out the key interaction Tig-RplX that exists in three pairs of active networks. Conclusion Our results indicate that the translational processes of proteins and the corresponding translation efficiency may play an important role before and after the activation of the EET process of S. oneidensis MR-1. Furthermore, this study can also provide some guidance for identifying key proteins and interactions under different conditions for this species.

Abstract We present multiPrime, a novel tool that automatically designs minimal primer sets for targeted next‐generation sequencing, tailored to specific microbiomes or genes. MultiPrime enhances primer coverage by designing primers with mismatch tolerance and ensures both high compatibility and specificity. We evaluated the performance of multiPrime using a data set of 43,016 sequences from eight viruses. Our results demonstrated that multiPrime outperformed conventional tools, and the primer set designed by multiPrime successfully amplified the target amplicons. Furthermore, we expanded the application of multiPrime to 30 types of viruses and validated the work efficacy of multiPrime‐designed primers in 80 clinical specimens. The subsequent sequencing outcomes from these primers indicated a sensitivity of 94% and a specificity of 89%.

IntroductionInterspecies interactions are a crucial driving force of species evolution. The genes of each coexisting species play a pivotal role in shaping the structure and function within the community, but how to identify them at the genome-wide level has always been challenging.MethodsIn this study, we embed the Lotka-Volterra ordinary differential equations in the theory of community ecology into the systems mapping model, so that this model can not only describe how the quantitative trait loci (QTL) of a species directly affects its own phenotype, but also describe the QTL of the species how to indirectly affect the phenotype of its interacting species, and how QTL from different species affects community behavior through epistatic interactions.ResultsBy designing and implementing a co-culture experiment for 100 pairs of Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus), we mapped 244 significant QTL combinations in the interaction process of the two bacteria using this model, including 69 QTLs from E. coli and 59 QTLs from S. aureus, respectively. Through gene annotation, we obtained 57 genes in E. coli, among which the genes with higher frequency were ypdC, nrfC, yphH, acrE, dcuS, rpnE, and ptsA, while we obtained 43 genes in S. aureus, among which the genes with higher frequency were ebh, SAOUHSC_00172, capF, gdpP, orfX, bsaA, and phnE1.DiscussionBy dividing the overall growth into independent growth and interactive growth, we could estimate how QTLs modulate interspecific competition and cooperation. Based on the quantitative genetic model, we can obtain the direct genetic effect, indirect genetic effect, and genome-genome epistatic effect related to interspecific interaction genes, and then further mine the hub genes in the QTL networks, which will be particularly useful for inferring and predicting the genetic mechanisms of community dynamics and evolution. Systems mapping can provide a tool for studying the mechanism of competition and cooperation among bacteria in co-culture, and this framework can lay the foundation for a more comprehensive and systematic study of species interactions.

Background: Prenatal exposure to per- and polyfluoroalkyl substances (PFAS) may adversely affect fetal brain development, yet no study has investigated the potential association between prenatal PFAS exposure and infant sleep. Objectives: To explore the associations of prenatal PFAS exposure with infant sleep disturbances during the first year of life in a prospective cohort study. Methods: We recruited 4127 pregnant women from the Shanghai Birth Cohort (SBC) and followed their children from birth to 12 months old. A total of 2366 infants were included in the 6-month analyses, and 2466 infants in the 12-month analyses. Ten PFAS were quantified in blood serum collected in the first trimester. Sleep quality was measured using the Brief Infant Sleep Questionnaire. We used multiple linear regression and multinomial logistic regression to estimate the individual effects of PFAS on sleep outcomes. We utilized a quantile-based g-computation model to determine the joint effects of the PFAS mixture on infant sleep outcomes. Additionally, generalized estimating equation (GEE) models were performed to examine the longitudinal effects of PFAS exposure during pregnancy. Results: In infants aged 6 months, perfluorooctane sulfonate and perfluoroheptanoic acid were associated with a more than 2-fold risk of parent-reported sleep problems as severe. Perfluorodecanoic acid was associated with an increased risk of often or almost always snoring in one-year-old infants (relative risk ratios, 1.79; 95% CI, 1.12–2.86). PFAS mixtures were positively associated with nighttime awakenings both among infants aged 6 months (β, 0.11; 95% CI, 0.04–0.19) and 12 months (β, 0.11; 95% CI, 0.05–0.18). Prenatal exposure to PFAS were associated with longer sleep latency, increased nighttime awakenings, longer nocturnal wakefulness hours, snoring, and earlier sleep-onset time in infants aged 6–12 months, according to GEE models. Conclusions: Our study suggests that prenatal exposure to PFAS may increase the risk of sleep disturbance in infants.

Diabetic wounds may become chronic if left untreated. In the current study, a potential wound dressing was developed by incorporating fumaria officinalis extract-loaded chitosan nanoparticles (FOE-CHNPs) into calcium alginate hydrogel. The produced hydrogel was evaluated regarding its microarchitecture, cytotoxicity, cell migration activity, cytoprotective potential, porosity, in vitro anti-inflammatory activity, and drug release profile. Then, the healing function of FOE-CHNPs/calcium alginate hydrogel was compared with a marketed wound care product in a rat model of diabetic wound. In vitro study showed that the hydrogel system promoted skin cells viability and migration. In vivo wound healing assay showed that the animals treated with the FOE-CHNPs/calcium alginate hydrogel had comparable wound healing potential with the GranuGEL® as the marketed wound care hydrogel. Gene expression studies showed that FOE-CHNPs/calcium alginate hydrogel upregulated the tissue expression levels of collagen type 1, collagen type 2, VEGF, b-FGF and TGF-B genes. This preclinical research, suggests potential use of FOE-loaded calcium alginate hydrogel system in treating diabetic wounds in the clinic.

Background: The adverse perinatal outcome caused by adenomyosis has been widely concerned recently, but little attention has been paid to whether the positional relationship between placenta and adenomyotic lesion influences the maternal and perinatal outcomes. Methods: A total of 311 women with adenomyosis who were pregnant greater than 20 weeks gestation and delivered at Women’s Hospital, Zhejiang University School of Medicine between January 2010 and December 2021 were recruited. The positional relationships between placenta and adenomyotic lesions were determined. The patients were divided into two subgroups: group 1, placenta located on or above the adenomyotic lesion; and group 2, placenta located far away from the adenomyotic lesion. The clinical data of two groups were retrospectively analyzed. Results: We found a higher rate of diffuse adenomyosis (62.65% vs. 46.21%, p = 0.01), coexisting endometriosis (31.93% vs. 15.86%, p = 0.002), preterm delivery (34.94% vs.15.17%, p < 0.001) and placenta malposition (19.88% vs. 6.90%, p = 0.002) in group I compared to group II. Compared with group II, group I had lower birth weight (p = 0.02). After adjustment using multiple logistic regression analysis, maternal adverse outcome was only correlated with age (p = 0.02). Neonatal adverse outcomes were closely correlated with group I (p = 0.004), including pregnancy induced hypertension (p = 0.01), placenta malposition (p = 0.02), placental abruption (p = 0.003), and scarred uterus (p = 0.02). Conclusions: The positional relationships between the placenta and adenomyotic lesions were graphically presented. Placental position near or above adenomyosis lesions might correlate to the adverse perinatal outcomes of pregnant women with adenomyosis and thereby deserve more attention.

BackgroundThis study aimed to objectively evaluate the severity of impulsivity [behavior inhibitory control (BIC) impairment] among adolescents with depression. In particular, those involved in non-suicidal self-injury (NSSI) behaviors, compared with those engaged in suicidal behaviors and adolescents without any self-injury behavior, using event-related potentials (ERPs) and event-related spectral perturbation (ERSP) within the two-choice oddball paradigm.MethodsParticipants with a current diagnosis of major depressive disorder (MDD) engaged in repetitive NSSI for five or more days in the past year (n = 53) or having a history of at least one prior complete suicidal behavior (n = 31) were recruited in the self-injury group. Those without self-injury behavior were recruited in the MDD group (n = 40). They completed self-report scales and a computer-based two-choice oddball paradigm during which a continuous electroencephalogram was recorded. The difference waves in P3d were derived from the deviant minus standard wave, and the target index was the difference between the two conditions. We focused on latency and amplitude, and time-frequency analyses were conducted in addition to the conventional index.ResultsParticipants with self-injury, compared to those with depression but without self-injury, exhibited specific deficits in BIC impairment, showing a significantly larger amplitude. Specifically, the NSSI group showed the highest value in amplitude and theta power, and suicidal behavior showed a high value in amplitude but the lowest value in theta power. These results may potentially predict the onset of suicide following repetitive NSSI.ConclusionThese findings contribute to substantial progress in exploring neuro-electrophysiological evidence of self-injury behaviors. Furthermore, the difference between the NSSI and suicide groups might be the direction of prediction of suicidality.

BackgroundNonsuicidal self-injury (NSSI) is a common mental health threat in adolescents, peaking in adolescence with a lifetime prevalence of ~17%–60%, making it a high-risk risk factor for suicide. In this study, we compared changes in microstate parameters in depressed adolescents with NSSI, depressed adolescents, and healthy adolescents during exposure to negative emotional stimuli, and further explored the improvement of clinical symptoms and the effect of microstate parameters of repetitive transcranial magnetic stimulation (rTMS) in depressed adolescents with NSSI, and more evidence was provided for potential mechanisms and treatment optimization for the occurrence of NSSI behaviors in adolescents.MethodsSixty-six patients with major depressive disorder (MDD) exhibiting NSSI behavior (MDD + NSSI group), 52 patients with MDD (MDD group), and 20 healthy subjects (HC group) were recruited to perform neutral and negative emotional stimulation task. The age range of all subjects was 12–17 years. All participants completed the Hamilton Depression Scale, the Patient Health Questionnaire-9, the Ottawa Self-Injury Scale and a self-administered questionnaire to collect demographic information. We provided two different treatments to 66 MDD adolescents with NSSI; 31 patients received medication and completed post-treatment scale assessments and EEG acquisitions, and 21 patients received medication combined with rTMS and completed post-treatment scale assessments and EEG acquisitions. Multichannel EEG was recorded continuously from 64 scalp electrodes using the Curry 8 system. EEG signal preprocessing and analysis was performed offline, using the EEGLAB toolbox in MATLAB. Use the Microstate Analysis Toolbox in EEGLAB for segmentation and computation of microstates, and calculate a topographic map of the microstate segmentation of the EEG signal for a single subject in each dataset, and four parameters were obtained for each microstate classification: global explained variance (GEV), mean duration (Duration), average number of occurrences per second (Occurrence), and average percentage of total analysis time occupied (Coverage), which were then statistically analyzed.ResultsOur results indicate that MDD adolescents with NSSI exhibit abnormalities in MS 3, MS 4, and MS 6 parameters when exposed to negative emotional stimuli compared to MDD adolescents and healthy adolescents. The results also showed that medication combined with rTMS treatment improved depressive symptoms and NSSI performance more significantly in MDD adolescents with NSSI compared to medication treatment, and affected MS 1, MS 2, and MS 4 parameters in MDD adolescents with NSSI, providing microstate evidence for the moderating effect of rTMS.ConclusionMDD adolescents with NSSI showed abnormal changes in several microstate parameters when receiving negative emotional stimuli, and compared to those not receiving rTMS treatment, MDD adolescents with NSSI treated with rTMS showed more significant improvements in depressive symptoms and NSSI performance, as well as improvements in EEG microstate abnormalities.

This study aims to optimize the teaching content of ideological and political courses and guide students to establish correct values. Inspired by Artificial Intelligence, the K-means clustering algorithm was applied to the neural collaborative filtering algorithm through temporal data. Besides, a deep learning algorithm was designed for the improved matrix factorization. The evaluation indicators were selected through experiments. The relevant data sets were used for simulation and testing. The test results indicated that the Root Mean Square Error of this scheme was 1.251, and the Mean Absolute Error was 0.625. These index measurement values were better than those of similar algorithms, indicating this model has better performance after optimization and can recommend suitable courses. The innovative algorithm designed to construct the classroom teaching model of social and political education can accurately recommend proper courses according to the students’ learning situation reflecting their psychological states. The research provides adaptive teaching for students, enables interaction between teachers and students, and helps students form correct values. It also has an important role in improving the teaching strategies.

ABSTRACT: Objective: To compare the intestinal microbiota profiles in infants following rotavirus (RV) and human norovirus (HNoV) infection.Methods: Faecal specimens from 18 infants {mean age 11.8 months [standard deviation (SD) 3.0] months} with acute gastroenteritis caused by RV (G9P8) and 24 infants [mean age 8.8 (SD 6.4) months] with acute gastroenteritis caused by HNoV (GII) infection were collected prospectively. The faecal microbiome was assessed by 16S rRNA amplicon pyrosequencing. Alpha diversity, beta diversity, deferentially abundant taxa and microbial functions were assessed by bioinformatic analysis.Results: The Chao1 index for the HNoV group was significantly higher compared with the control group (P=0.0003), and was lower for the RV group compared with the HNoV group (P=0.0078). No significant difference in beta diversity was observed between the RV and HNoV groups. The RV group showed greater abundance of Actinobacteria at phylum level and Bifidobacterium spp., Streptococcus spp., Enterococcus spp. and Lactobacillus spp. at genus level. The HNoV group showed richness in Fusobacteria and Cyanobacteria at phylum level, and Enterococcus spp. and Streptococcus spp. at genus level. Bacillus was the characteristic genus in infected infants. In comparison with the control group, the viral group (P≤0.01), the RV group (P=0.002) and the HNoV group (P≤0.01) showed significant differences in potentially pathogenic bacteria.Conclusions: Changes in microbiotic structure were observed in infants following RV and HNoV infection. The Chao 1 index of alpha diversity increased significantly in the HNoV group. Bacillus was the characteristic genus in infected infants. An increase in pathogenic bacteria, particularly Streptococcus spp. and Enterococcus spp., was detected in infected infants.

Abstract Robust statistical tools such as the Skellam model and Bayesian networks can capture the count properties of transcriptome sequencing data and clusters of genes among treatments, thereby improving our knowledge of gene functions and networks. In this study, we successfully implemented a model to analyze a transcriptome dataset of Cucumis sativus and Botrytis cinerea before and after their interaction. First, 4200 differentially expressed genes (DEGs) from C. sativus were clustered into 17 distinct groups, and 670 DEGs from B. cinerea were clustered into 12 groups. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were applied on these DEGs to assess the interactions between C. sativus and B. cinerea. In C. sativus, more DEGs were divided into terms in the molecular function and biological process domains than into cellular components, and 277 DEGs were allocated to 19 KEGG pathways. In B. cinerea, more DEGs were divided into terms in the biological process and cellular component domains than into molecular functions, and 150 DEGs were allocated to 26 KEGG pathways. In this study, we constructed networks of genes that interact with each other to screen hub genes based on a directed graphical model known as Bayesian networks. Through a detailed GO analysis, we excavated hub genes which were biologically meaningful. These results verify that availability of Skellam model and Bayesian networks in clustering gene expression data and sorting out hub genes. These models are instrumental in increasing our knowledge of gene functions and networks in plant–pathogen interaction.

The leaf microbiota plays a key role in plant development, but a detailed mechanism of microbe-plant relationships remains elusive. Many genome-wide association studies (GWAS) have begun to map leaf microbes, but few have systematically characterized the genetics of how microbes act and interact. Previously, we integrated behavioral ecology and game theory to define four types of microbial interactions – mutualism, antagonism, aggression, and altruism, in a microbial community assembly. Here, we apply network mapping to identify specific plant genes that mediate the topological architecture of microbial networks. Analyzing leaf microbiome data from an Arabidopsis GWAS, we identify several heritable hub microbes for leaf microbial communities and detect 140–728 SNPs (Single nucleotide polymorphisms) responsible for emergent properties of microbial network. We reconstruct Bayesian genetic networks from which to identify 22–43 hub genes found to code molecular pathways related to leaf growth, abiotic stress responses, disease resistance and nutrition uptake. A further path analysis visualizes how genetic variants of Arabidopsis affect its fecundity through the internal workings of the leaf microbiome. We find that microbial networks and their genetic control vary along spatiotemporal gradients. Our study provides a new avenue to reveal the “endophenotype” role of microbial networks in linking genotype to end-point phenotypes in plants. Our integrative theory model provides a powerful tool to understand the mechanistic basis of structural-functional relationships within the leaf microbiome and supports the need for future research on plant breeding and synthetic microbial consortia with a specific function.

Misgurnus anguillicaudatus, also known as oriental weather loach, is widely consumed and favored in East Asia due to its superior nutritional values and excellent flavor. In this study, a crude Misgurnus anguillicaudatus carbohydrates (MAC) was isolated from Misgurnus anguillicaudatus. Subsequently, two parts, which were named MAO and MAP, respectively, were separated from MAC, and their primary structures and immunomodulatory activity were investigated. The results showed that MAO had a molecular weight of 2854 Da, and principally consisted of arabinose (77.11%) and rhamnose (21.97%), together with minor levels of fucose (0.92%); MAP, with a molecular weight of 3873 Da, was mainly composed of fucose (87.55%) and a small amount of rhamnose (8.86%) and galactose (3.59%). The in vitro assay showed that MAC could significantly enhance the proliferation of macrophages without cytotoxicity and increase the production of immune substances (TNF-α, IL-6). Together with Western blot results, we speculated that MAC could stimulate RAW264.7 murine macrophage cells to secrete TNF-α and IL-6 through up-regulating TLR4-MAPK-p38 signaling pathways. The results indicated that MAC could be a potential immune agent and might provide meaningful information for further chain conformation and immune mechanism research.

Genetic plasticity drives phenotypic differences. Here, the authors develop a framework to quantify the individual and combinatorial contributions of SNPs on a phenotype of interest and use it to identify SNP-SNP interactions associated with variations in bacteria’s response to external changes.

Abstract Understanding how plants interact with their colonizing microbiota to determine plant phenotypes is a fundamental question in modern plant science. Existing approaches for genome-wide association studies (GWAS) are often focused on the association analysis between host genes and the abundance of individual microbes, failing to characterize the genetic bases of microbial interactions that are thought to be important for microbiota structure, organization, and function. Here, we implement a behavioral model to quantify various patterns of microbe-microbe interactions, i.e., mutualism, antagonism, aggression, and altruism, and map host genes that modulate microbial networks constituted by these interaction types. We reanalyze a root-microbiome data involving 179 accessions of Arabidopsis thaliana and find that the four networks differ structurally in the pattern of bacterial-fungal interactions and microbiome complexity. We identify several fungus and bacterial hubs that play a central role in mediating microbial community assembly surrounding A. thaliana root systems. We detect 1142 significant host genetic variants throughout the plant genome and then implement Bayesian networks (BN) to reconstruct epistatic networks involving all significant SNPs, of which 91 are identified as hub QTLs. Results from gene annotation analysis suggest that most of the hub QTLs detected are in proximity to candidate genes, executing a variety of biological functions in plant growth and development, resilience against pathogens, root development, and abiotic stress resistance. This study provides a new gateway to understand how genetic variation in host plants influences microbial communities and our results could help improve crops by harnessing soil microbes.

This study aimed to evaluate the value of neutrophil-to-platelet ratio (NPR) in predicting all-cause mortality in patients with ST-elevation myocardial infarction (STEMI) after primary percutaneous coronary intervention (PCI). We enrolled 186 patients with STEMI who underwent primary PCI in the Third Affiliated Hospital of Guangzhou Medical University between January 2017 and December 2018. Based on the NPR values, the patients were divided into two groups: the NPR >0.035 group (n = 82) and the NPR ≤0.035 group (n = 104). All-cause mortality of the patients was followed up for 3 years. By the end of 3 years, 109 (58.6%) patients survived, 53 (28.5%) died, and 24 (12.9%) were lost to follow-up. Univariate analyses found that NPR was associated with all-cause mortality (p < 0.05). In COX regression analyses, patients in the high NPR group had a higher risk of all-cause death than those in the low NPR group (HR = 2.296, 95% CI: 1.150–4.582). These results indicate that NPR could predict all-cause death in 3 years after primary PCI in patients STEMI. NPR values may be useful in risk stratification and in specifying individualized treatment in patients with STEMI. In addition, NPR is a low-cost and easily accessible indicator, if its strong predictive value is confirmed in further studies of other large populations, it can be introduced into clinical practice for effective application.

The emergence of two dimensional ferromagnetism suffers from an inherent fragility to thermal fluctuations, which typically restricts the Curie temperature to below room temperature. Here, Zhang et al present CrTe2 thin films grown via molecular beam epitaxy with a Curie temperature exceeding 300 K.

Green diopside is currently popular in the jewelry market due to its attractive color and excellent transparency. Gem-quality diopsides are mainly sourced from Pakistan, Italy, Russia, and other places. The color, geographic origin, and formation mechanism are the main factors affecting the value of gemstones, which can be determined by examining their gemology and composition characteristics. This study systematically characterizes the standard gemology of green diopsides from Pakistan and Russia and compares them with the blue diopsides produced within the skarn process and the diopsides from the nearby region in Russia from previous studies by gemological microscopy, spectral testing (infrared, Raman and ultraviolet-visible spectroscopy), and chemical analyses (electron probe and laser ablation inductively coupled plasma mass spectrometry). The results show that the spectral characteristics and phase composition of the green diopside samples from Pakistan and Russia have excellent uniformity and similarity. The high Cr, Fe, V, and Ni contents are the reasons why they appear as green. Meanwhile, the elemental characteristics of the diopside are effective tools for distinguishing different origins of different diopsides. The Russian green diopsides have higher contents of Sr, Sc, Zr, and rare earth elements (REE), indicating that they are related to alkaline ultrabasic rocks, and the source of the diopside sample from Pakistan is metamorphic rock.

Abstract To accurately explore the interaction mechanism between Escherichia coli and Staphylococcus aureus, we designed an ecological experiment to monoculture and co-culture E. coli and S. aureus. We co-cultured 45 strains of E. coli and S. aureus, as well as each species individually to measure growth over 36 h. We implemented a genome wide association study (GWAS) based on growth parameters (λ, R, A and s) to identify significant single nucleotide polymorphisms (SNPs) of the bacteria. Three commonly used growth regression equations, Logistic, Gompertz, and Richards, were used to fit the bacteria growth data of each strain. Then each equation’s Akaike’s information criterion (AIC) value was calculated as a commonly used information criterion. We used the optimal growth equation to estimate the four parameters above for strains in co-culture. By plotting the estimates for each parameter across two strains, we can visualize how growth parameters respond ecologically to environment stimuli. We verified that different genotypes of bacteria had different growth trajectories, although they were the same species. We reported 85 and 52 significant SNPs that were associated with interaction in E. coli and S. aureus, respectively. Many significant genes might play key roles in interaction, such as yjjW, dnaK, aceE, tatD, ftsA, rclR, ftsK, fepA in E. coli, and scdA, trpD, sdrD, SAOUHSC_01219 in S. aureus. Our study illustrated that there were multiple genes working together to affect bacterial interaction, and laid a solid foundation for the later study of more complex inter-bacterial interaction mechanisms.

ObjectiveThe aim of the research is to study the association between the serum levels of autoantibodies against one important epitope (168FMILPVGAANFREAMR183, designated as P6) of α-enolase (ENO1-P6Abs) and miscarriage among euthyroid females with thyroid autoimmunity (TAI).MethodsAnti-ENO1-P6 total IgG was investigated in 432 euthyroid women, and its four subclasses were analyzed in 184 euthyroid women. The serum FT4, TSH, TgAb, and TPOAb levels were determined using an electrochemiluminescence immunoassay. The serum ENO1-P6Ab and anti-protein disulfide isomerase A3 autoantibody (PDIA3Ab) levels were determined using an enzyme-linked immunosorbent assay.ResultsThe serum levels of anti-ENO1-P6 total IgG, IgG2, IgG3, and IgG4 were significantly higher in euthyroid TAI females than in non-TAI controls. Additionally, anti-ENO1-P6 total IgG and its 4 subtypes were all markedly higher in euthyroid TAI females with pregnancy loss than those without miscarriage. Moreover, logistic regression analysis showed that highly expressed anti-ENO1-P6 total IgG, IgG1, IgG2, and IgG3 subtypes in the serum were all independent risk factors for euthyroid TAI-related miscarriage, and its IgG1 was also for non-TAI-related abortion. According to the trend test, the prevalence of miscarriage was increased in a titer-dependent manner with the raised levels of serum anti-ENO1-P6 total IgG and IgG1, IgG2, and IgG3 subtypes among euthyroid TAI females. The receiver operating characteristic curve analysis of anti-ENO1-P6 total IgG and IgG1, IgG2, and IgG3 subclass expressions in the serum for miscarriage prediction in euthyroid TAI females exhibited that the total areas under the curves were 0.773 ± 0.041, 0.761 ± 0.053, 0.827 ± 0.043, and 0.760 ± 0.050, respectively (all P

BackgroundThe coronavirus disease (COVID-19) pandemic has impacted HIV prevention strategies globally. However, changes in pre-exposure prophylaxis (PrEP) adherence and HIV-related behaviors, and their associations with medication adherence among men who have sex with men (MSM) PrEP users remain unclear since the onset of the COVID-19 pandemic.MethodsA Retrospective Cohort Study of HIV-negative MSM PrEP users was conducted in four Chinese metropolises from December 2018 to March 2020, assessing the changes in PrEP adherence and HIV-related behaviors before and during the COVID-19. The primary outcome was poor PrEP adherence determined from self-reported missing at least one PrEP dose in the previous month. We used multivariable logistic regression to determine factors correlated with poor adherence during COVID-19.ResultsWe enrolled 791 eligible participants (418 [52.8%] in daily PrEP and 373 [47.2%] in event-driven PrEP). Compared with the data conducted before the COVID-19, the proportion of PrEP users decreased from 97.9 to 64.3%, and the proportion of poor PrEP adherence increased from 23.6 to 50.1% during the COVID-19 [odds ratio (OR) 3.24, 95% confidence interval (CI) 2.62–4.02]. While the percentage of condomless anal intercourse (CAI) with regular partners (11.8 vs. 25.7%) and with casual partners (4.4 vs. 9.0%) both significantly increased. The proportion of those who were tested for HIV decreased from 50.1 to 25.9%. Factors correlated with poor PrEP adherence during the COVID-19 included not being tested for HIV (adjusted odds ratio [aOR] = 1.38 [95% CI: 1.00, 1.91]), using condoms consistently with regular partners (vs. never, aOR = 2.19 [95% CI: 1.16, 4.13]), and being married or cohabitating with a woman (vs. not married, aOR = 3.08 [95% CI: 1.60, 5.95]).ConclusionsIncreased poor PrEP adherence and CAI along with the decrease in HIV testing can lead to an increase in HIV acquisition and drug resistance to PrEP. Targeted interventions are needed to improve PrEP adherence and HIV prevention strategies.

Abstract Background Ovarian teratoma-associated anti-N-methyl-D-aspartate receptor encephalitis (NMDAR-E) is a severe autoimmune neurological disorder, and the influence of teratoma-induced autoantibodies on the pathogenesis remains unclear. Methods Ovarian teratoma tissues were collected from teratoma patients with and without NMDAR-E. Proteins were extracted and then analyzed using iTRAQ-coupled LC–MS/MS, which was followed by bioinformatics analysis. Candidate proteins were verified by Western blotting and immunohistochemistry. Results In total, 36 differentially expressed proteins (DEPs) were identified between the control group and NMDAR-E group, and the bioinformatics analysis revealed that the DEPs were mainly involved in immune-related pathways, especially HLA-A and HLA-DRB1. The western blotting results for HLA-A and HLA-DRB1 were consistent with the results of the iTRAQ analysis. Additionally, the immunohistochemical data revealed that the aggregation of HLA-A (+) and HLA-DRB1 (+) cells was more apparent in the teratoma tissues of NMDAR-E patients compared with that in the tissues of controls. Conclusion Our investigation indicated that HLA-A and HLA-DRB1 might be involved in mediating ovarian teratoma-associated NMDAR-E. These findings provide new insights into the pathophysiological mechanisms and provide information for the functional exploration of proteins in the future.

Abstract Background Tuberculosis (Tb) is the most frequent opportunistic infection among people living with HIV infection. The impact of Tb co-infection in the establishment and maintenance of the HIV reservoir is unclear. Method We enrolled 13 HIV-infected patients with microbiologically confirmed Tb and 10 matched mono-HIV infected controls. Total HIV DNA in peripheral blood mononuclear cells (PBMCs), plasma interleukin-7 (IL-7) concentrations and the activities of indoleamine 2,3-dioxygenase (IDO) were measured for all the participants prior to therapy and after antiretroviral therapy (ART). Results After a duration of 16 (12, 22) months’ ART, patients co-infected with Tb who were cured of Tb maintained higher levels of HIV DNA compared with mono-HIV infected patients [2.89 (2.65- 3.05) log10 copies/106 cells vs. 2.30 (2.11–2.84) log10 copies/106 cells, P = 0.008]. The levels of on-ART HIV DNA were positively correlated with the baseline viral load (r = 0.64, P = 0.02) in Tb co-infected group. However, neither plasma IL-7 concentration nor plasma IDO activity was correlated with the level of on-ART HIV DNA. Conclusions Tb co-infection was associated with the increased surrogate marker of the HIV reservoir, while its mechanism warrants further examination.

Abstract Background Pre-exposure prophylaxis (PrEP) is an effective biomedical strategy to prevent transmission of HIV infection, although medication adherence remains a challenge. We present the protocol for a multicentre randomised controlled trial to measure the effectiveness of a real-time monitoring and just-in-time intervention on medication adherence among PrEP users in China. Methods Study participants will include 1000 men who have sex with men (MSM) from four cites in China (Shenyang, Beijing, Chongqing and Shenzhen) attending a tenofovir disoproxil fumarate/emtricitabine (TDF/FTC) PrEP project as part of a real-world, prospective multicentre cohort study (CROPrEP). Participants will be randomised into the intervention and control arms in a 1:1 ratio. Participants in the intervention arm will be provided with remote real-time monitoring equipment that triggers twice just-in-time SMS (Short Messaging Service) medication reminders to PrEP users every half an hour when a scheduled dosage is missed, and followed with just-in-time SMS medication reminders to clinicians half an hour when there is no supplement after the second just-in-time SMS reminder to PrEP users. Clinicians will initiate individualised telephone intervention as soon as possible upon receipt of the just-in-time SMS missed dose alert. Those in the control arm will only receive generic weekly SMS reminders. The study will last 6 months. Participants will be seen at follow-up visits at three and 6 months. Trial outcomes to be measured include self-reported adherence assessed via questionnaire and pill counts, as well as drug concentration test results. Discussion Medication adherence is critical to achieve optimal benefits from PrEP. This study will be the first individualised behaviour intervention using real-time technology to increase adherence among MSM PrEP users globally. If found effective, a real-time monitoring and just-in-time intervention system may be utilized for improving adherence and thus effectiveness of global PrEP application. Trial registration This study registered at ClinicalTrials.gov ( ChiCTR1900025604 ) on September 2, 2019.

Abstract Background Pneumocystis pneumonia (PCP) is a common acquired immune deficiency syndrome (AIDS)-related opportunistic infection. Recent reports estimate that more than 400,000 patients with human immunodeficiency virus (HIV) develop PCP each year globally. However, the timing of antiretroviral therapy (ART) initiation for HIV-infected patients with PCP is still controversial, and the benefits and risks of early initiation of ART are not completely clear. We thus designed this study in order to determine the optimal timing for ART initiation for HIV-positive patients with moderate to severe PCP. Methods This study will be an open-label, multi-centre, prospective randomised controlled trial. A total of 200 subjects will be randomly assigned to an early ART initiation group (≤14 days after PCP diagnosis) and a deferred ART initiation group (>14 days after PCP diagnosis) at a 1:1 ratio. All subjects will be followed up for 48 weeks after starting ART. The primary endpoint is incidence of disease progression (including new or relapsing opportunistic infections and death) at week 48. The secondary endpoints are the changes in CD4 counts from baseline at weeks 12, 24 and 48; the degree of virological suppression (HIV RNA

Nano-scale coatings are important for controlling the functional behavior of surfaces. Here, a deposition process in liquid hydrocarbons is reported for metal oxides, in which a thin water coating on the substrate reacts with chemical precursors, forming a nano-scale layer.

At present, low teaching efficiency has been the common problem of ideological and political education in colleges and universities in China. It is essential to improve the teaching efficiency and realize the intelligent information transformation of the ideological and political courses in colleges and universities. First, the relationship between ideological and political courses and the educational psychology of college students was analyzed based on the theoretical characteristics of educational psychology and college ideological and political courses. Additionally, the teaching efficiency of ideological and political courses based on deep learning (DL) was analyzed through a literature survey. Combined with online teaching modes such as the flipped classroom and Massive Open Online Courses, a comprehensive online teaching mode of college ideological and political courses was proposed via educational psychology and the Single Shot MutiBox Detector networks of DL. Then, a total of 100 research subjects were selected randomly from the freshmen and sophomores of the Southwest University of Science and Technology, and their acceptability to the online ideological and political courses was analyzed by a questionnaire survey. The results show that the adopted questionnaire had high reliability and validity, and the proportion of respondents of different genders, grades, and majors was essentially balanced. More than half of the students had a good understanding of the comprehensive ideological and political courses and made progress in their values, ideology, morals, and knowledge reserves. More than half of the students had a positive attitude to the course, and they thought that the class atmosphere of the course was active, which was conducive to a satisfactory learning effect. This indicates that the teaching strategy of ideological and political courses in colleges and universities that integrates educational psychology, DL, and online information can attract students. The contribution of this study is that the research outcome can be applied to the concrete formulation of the teaching strategies of ideological and political courses for college students.

Phenotypic plasticity is the exhibition of various phenotypic traits produced by a single genotype in response to environmental changes, enabling organisms to adapt to environmental changes by maintaining growth and reproduction. Despite its significance in evolutionary studies, we still know little about the genetic control of phenotypic plasticity. In this study, we designed and conducted a genome-wide association study (GWAS) to reveal genetic architecture of how Staphylococcus aureus strains respond to increasing concentrations of vancomycin (0, 2, 4, and 6 μg/mL) in a time course. We implemented functional mapping, a dynamic model for genetic mapping using longitudinal data, to map specific loci that mediate the growth trajectories of abundance of vancomycin-exposed S. aureus strains. 78 significant single nucleotide polymorphisms were identified following analysis of the whole growth and development process, and seven genes might play a pivotal role in governing phenotypic plasticity to the pressure of vancomycin. These seven genes, SAOUHSC_00020 (walR), SAOUHSC_00176, SAOUHSC_00544 (sdrC), SAOUHSC_02998, SAOUHSC_00025, SAOUHSC_00169, and SAOUHSC_02023, were found to help S. aureus regulate antibiotic pressure. Our dynamic gene mapping technique provides a tool for dissecting the phenotypic plasticity mechanisms of S. aureus under vancomycin pressure, emphasizing the feasibility and potential of functional mapping in the study of bacterial phenotypic plasticity.

BackgroundRoutine HIV testing accompanied with pre-exposure prophylaxis (PrEP) requires innovative support in a real-world setting. ObjectiveThis study aimed to determine the usage of HIV self-testing (HIVST) kits and their secondary distribution to partners among men who have sex with men (MSM) in China, who use PrEP, in an observational study between 2018 and 2019. MethodsIn 4 major cities in China, we prospectively followed-up MSM from the China Real-world oral PrEP demonstration study, which provides daily or on-demand PrEP for 12 months, to assess the usage and secondary distribution of HIVST on quarterly follow-ups. Half of the PrEP users were randomized to receive 2 HIVSTs per month in addition to quarterly facility-based HIV testing. We evaluated the feasibility of providing HIVST to PrEP users. ResultsWe recruited 939 MSM and randomized 471 to receive HIVST, among whom 235 (49.9%) were daily and 236 (50.1%) were on-demand PrEP users. At baseline, the median age was 29 years, 390 (82.0%) men had at least college-level education, and 119 (25.3%) had never undergone facility-based HIV testing before. Three months after PrEP initiation, 341 (74.5%) men had used the HIVST provided to them and found it very easy to use. Among them, 180 of 341 (52.8%) men had distributed the HIVST kits it to other MSM, and 132 (51.6%) among the 256 men who returned HIVST results reported that used it with their sexual partners at the onset of intercourse. Participants on daily PrEP were more likely to use HIVST (adjusted hazard ratio=1.3, 95% CI 1.0-1.6) and distribute HIVST kits (adjusted hazard ratio=1.3, 95% CI 1.1-1.7) than those using on-demand PrEP. ConclusionsMSM who used PrEP had a high rate of usage and secondary distribution of HIVST kits, especially among those on daily PrEP, which suggested high feasibility and necessity for HIVST after PrEP initiation. Assuming that fourth-generation HIVST kits are available, HIVST may be able to replace facility-based HIV testing to a certain extent. Trial RegistrationChinese Clinical Trial Registry ChiCTR1800020374; https://www.chictr.org.cn/showprojen.aspx?proj=32481 International Registered Report Identifier (IRRID)RR2-10.1136/bmjopen-2019-036231

The purpose of the study is to analyze the current situation of ideological and political education and psychological education of college students, and explore the challenges faced by these two kinds of education in the information age. First, different research methods, such as literature research, questionnaire survey, and interdisciplinary research, are used to investigate and study the current situation of ideological and political education and psychological education of college students. Second, the survey data are analyzed to reveal the challenges they have encountered. The results show that there are many problems in ideological and political education, which need to be improved and strengthened. The Internet has a strong attraction for college students, but the purpose of getting online of many college students is not clear. Although it plays an important role in improving teaching quality by helping college students establish correct attitudes toward their study, values, life, and society, ideological and political education lack strong pertinence and effectiveness due to the professionalism of the teachers. And the negative impact of network information on ideological and political education of college students is also obvious. About 11.4% of the respondents believe that network information affects their physical and mental health. About 8.4% of the respondents believe that harmful information on the network is easy to induce students to behave wrongly. About 41% believe that computer games distract them from learning, which indicates that the negative impact of network information on college students cannot be underestimated, and it is imperative to strengthen the ideological and political education of college students. The research provides a useful reference for the ideological and political and psychological education in the information environment and helps to solve the problem in the ideological and political education and psychological education of college students.

Interactions between individuals are thought to shape evolution and speciation through natural selection, but little is known about how an individual (or player) strategically interacts with others to maximize its payoff. We develop a simple decision-theoretic model that generates four hypotheses about the choice of an optimal behavioral strategy by a player in response to the strategies of other players. The golden threshold hypothesis suggests that 62% is the critical threshold determining the transition of a larger player's strategy in reaction to its smaller dove-like partner. Below this critical point, the larger one exploits the smaller one, whereas above it, the larger one chooses to cooperate with the smaller one. The competition-to-cooperation shift hypothesis states that a larger player never cooperates with a smaller hawk-like player unless the former is reversely surpassed in size by the latter by 75%. The Fibonacci retracement mark hypothesis proposes that, faced with a larger dove-like player, a smaller player chooses to either cooperate or cheat, depending on whether its size relative to the larger player is less or more than 38%. The surrender-resistance hypothesis suggests that, in reaction to a larger hawk-like player, a smaller player can either gain some benefit from resistance or is sacrificed by choosing to surrender. We test these hypotheses by re-analyzing body mass data of full-sib fishes that were co-cultured in a common water pool. Pairwise analysis of these co-existing fishes broadly suggests the prediction of our hypotheses. Taken together, our model unveils detectable yet previously unknown quantitative mechanisms that mediate the strategic choice of animal behavior in populations or communities. Given the ubiquitous nature of biological interactions occurring at different levels of organizations and the paucity of quantitative approaches to understand them, results by our decision-theoretic model represent an initial step towards the deeper understanding of how biological entities interact with each other to drive their evolution.

Background: People living with HIV (PLWH) are aging worldwide, and different management strategies may be required for older and younger PLWH. However, demographic characteristics, illness distribution, mortality, and independent risk factors in the PLWH population in China are not yet fully understood, especially in patients aged 50 years or older.Methods: We conducted a retrospective analysis of 4445 HIV-positive Chinese inpatients in Chongqing, China.Results: The mortality rate in patients 50 years or older (the older group) was significantly higher than that in those under 50 years (the younger group) (p < 0.001). In the younger group, independent risk factors for death included: nadir CD4+ T-cell counts

The gut microbiota may play an important role in affecting human health. To explore the genetic mechanisms underlying microbiota-host relationships, many genome-wide association studies have begun to identify host genes that shape the microbial composition of the gut. It is becoming increasingly clear that the gut microbiota impacts host processes not only through the action of individual microbes but also their interaction networks. However, a systematic characterization of microbial interactions that occur in densely packed aggregates of the gut bacteria has proven to be extremely difficult. We develop a computational rule of thumb for addressing this issue by integrating ecological behavioral theory and genetic mapping theory. We introduce behavioral ecology theory to derive mathematical descriptors of how each microbe interacts with every other microbe through a web of cooperation and competition. We estimate the emergent properties of gut-microbiota networks reconstructed from these descriptors and map host-driven mutualism, antagonism, aggression, and altruism QTLs. We further integrate path analysis and mapping theory to detect and visualize how host genetic variants affect human diseases by perturbing the internal workings of the gut microbiota. As the proof of concept, we apply our model to analyze a published dataset of the gut microbiota, showing its usefulness and potential to gain new insight into how microbes are organized in human guts. The new model provides an analytical tool for revealing the “endophenotype” role of microbial networks in linking genotype to end-point phenotypes.

Introduction In recent years, due to various factors, the rate of infertility in China has increased and now affects over 10% of women of reproductive age. Hysterosalpingography (HSG) is a common diagnostic procedure during fertility examinations. However, there is no consensus on the choice of contrast agents and their effects. As the largest multicentre, randomised controlled trial (H2Oil trial from the Netherlands) has shown that oil-soluble contrast at HSG can enhance fertility compared with water-soluble contrast, we propose this study to examine whether the use of oil-soluble contrast media results in increased rates of pregnancy in Chinese women undergoing HSG.Methods and analysis This study is a single-centre, randomised, controlled, parallel-group, superiority trial. Patients with low risk of tubal disease will be randomised to undergo HSG using iodinated oil injection (OSCM group, oil-soluble contrast media) or ioversol injection (WSCM group, water-soluble contrast media). To evaluate the potential superiority of the OSCM group, with 1:1 allocation ratio, 90% statistical power and a two-sided significance level of 5%, we have calculated a sample of 520 women per group to be enrolled, for a total of 1040 including 10% loss to follow-up or protocol variation. The primary outcome is the rate of ongoing pregnancy during 6 months after randomisation. The secondary outcomes will consist of thyroid function of patients and newborns, pain scores during HSG, rate of live birth, clinical pregnancies, miscarriages, ectopic pregnancy, time to ongoing pregnancy, time to live birth, cost calculations of the OSCM group/WSCM group, and assisted reproductive technology treatments between the two groups.Ethics and dissemination This protocol received authorisation from the Medical Research Ethics Committee of International Peace Maternity and Child Health Hospital on 18 January 2020 (approval no GKLW2020-02). The findings will be reported in peer-reviewed publications and presentations at international scientific meetings.Trial registration number ChiCTR2000031612.

DNA methylation plays an important role in a wide range of developmental and physiological processes in plants. It is primarily catalyzed and regulated by cytosine-5 DNA methyltransferases (C5-MTases) and a group of DNA glycosylases that act as demethylases. To date, no genome-scale analysis of the two kiwifruit (Actinidia chinensis) families has been undertaken. In our study, nine C5-MTases and seven DNA demethylase genes were identified in the kiwifruit genome. Through selective evolution analysis, we found that there were gene duplications in C5-MTases and demethylases, which may have arisen during three genome doubling events followed by selection during evolution of kiwifruit. Expression analysis of DNA methylases (C5-MTases) and demethylases identified changes in transcripts of DNA methylation and demethylation genes during both vegetative and reproductive development. Moreover, we found that some members of the two methylase/demethylase families may also be involved in fruit ripening and the regulation of softening. Our results help to better understand the complex roles of methylation/demethylation in plants and provide a foundation for analyzing the role of DNA methylation modification in kiwifruit growth, development and ripening.

Introduction Pre-exposure prophylaxis (PrEP) reduces the risk of HIV infection among men who have sex with men by up to 99%. However, in real-world settings, PrEP users may exhibit risk compensation after uptake of PrEP, including more condomless anal intercourse (CAI) and increased sexually transmitted infection (STI) acquisition. HIV self-testing (HIVST) decreases CAI among men who have sex with men (MSM) by providing awareness of the HIV status of oneself and one’s sexual partners. Here, we describe the rationale and design of a randomised waitlist-controlled trial to examine the impact of HIVST on risk compensation among PrEP users.Methods and analysis The study is a two-arm randomised waitlist-controlled trial with 1000 HIV-negative MSM in four major cities in China who will be taking oral PrEP (involving tenofovir disoproxil fumarate/emtricitabine) either daily (n=500) or in an event-driven regimen (n=500). The participants will be randomised (1:1) to either the immediate HIVST intervention arm (HIVST plus standard facility-based counselling and testing from 0 to 12 months) or the waitlist arm (standard facility-based counselling and testing from 0 to 6 months, then crossover to receive the HIVST intervention in months 7–12). Participants will provide blood samples to assess the incidence of syphilis and herpes simplex virus type 2 (HSV-2) during a follow-up. The primary outcomes will be the occurrence of CAI, number of sexual partners and incidence of syphilis and HSV-2 during a follow-up. The secondary outcomes will be the HIV and STI testing frequency and STI treatment adherence during a follow-up. The planned start and end dates for the study is 26 December 2018 and 31 December 2020.Ethics and dissemination The Medical Science Research Ethics Committee of The First Affiliated Hospital of China Medical University has approved the study (IRB(2018)273).Trial registration number ChiCTR1800020374

Genetic variation from coexisting species influences interspecific interactions in a community. Here, the authors develop a framework for identifying quantitative trait loci (QTLs) underlying community dynamics and validate the tool using data from co-culturing of two bacterial species.

Bacteriophages are viruses that specifically infect target bacteria. Recently, bacteriophages have been considered potential biological control agents for bacterial pathogens due to their host specificity. Pseudomonas syringae pv. actinidiae (Psa) is a reemerging pathogen that causes bacterial canker of kiwifruit (Actinidia sp.). The economic impact of this pest and the development of resistance to antibiotics and copper sprays in Psa and other pathovars have led to investigation of alternative management strategies. Phage therapy may be a useful alternative to conventional treatments for controlling Psa infections. Although the efficacy of bacteriophage φ6 was evaluated for the control of Psa, the characteristics of other DNA bacteriophages infecting Psa remain unclear. In this study, the PHB09 lytic bacteriophage specific to Psa was isolated from kiwifruit orchard soil. Extensive host range testing using Psa isolated from kiwifruit orchards and other Pseudomonas strains showed PHB09 has a narrow host range. It remained stable over a wide range of temperatures (4–50 °C) and pH values (pH 3–11) and maintained stability for 50 min under ultraviolet irradiation. Complete genome sequence analysis indicated PHB09 might belong to a new myovirus genus in Caudoviricetes. Its genome contains a total of 94,844 bp and 186 predicted genes associated with phage structure, packaging, host lysis, DNA manipulation, transcription, and additional functions. The isolation and identification of PHB09 enrich the research on Pseudomonas phages and provide a promising biocontrol agent against kiwifruit bacterial canker.

Phenotypic plasticity enables individuals to develop different phenotypes in a changing environment and promotes adaptive evolution. Genome-wide association study (GWAS) facilitates the study of the genetic basis of bacterial phenotypes, and provides a new opportunity for bacterial phenotypic plasticity research. To investigate the relationship between growth plasticity and genotype in bacteria, 41 Staphylococcus aureus strains, including 29 vancomycin-intermediate S. aureus (VISA) strains, were inoculated in the absence or presence of vancomycin for 48 h. Growth curves and maximum growth rates revealed that strains with the same minimum inhibitory concentration (MIC) showed different levels of plasticity in response to vancomycin. A bivariate GWAS was performed to map single-nucleotide polymorphisms (SNPs) associated with growth plasticity. In total, 227 SNPs were identified from 14 time points, while 15 high-frequency SNPs were mapped to different annotated genes. The P-values and growth variations between the two cultures suggest that non-coding region (SNP 738836), ebh (SNP 1394043), drug transporter (SNP 264897), and pepV (SNP 1775112) play important roles in the growth plasticity of S. aureus. Our study provides an alternative strategy for dissecting the adaptive growth of S. aureus in vancomycin and highlights the feasibility of bivariate GWAS in bacterial phenotypic plasticity research.

How a species responds to such a biotic environment in the community, ultimately leading to its evolution, has been a topic of intense interest to ecological evolutionary biologists. Until recently, limited knowledge was available regarding the genotypic changes that underlie phenotypic changes. Our study implemented GWAS (Genome-Wide Association Studies) to illustrate the genetic architecture of ecological interactions that take place in microbial populations. By choosing 45 such interspecific pairs of Escherichia coli and Staphylococcus aureus strains that were all genotyped throughout the entire genome, we employed Q-ROADTRIPS to analyze the association between single SNPs and microbial abundance measured at each time point for bacterial populations reared in monoculture and co-culture, respectively. We identified a large number of SNPs and indels across the genomes (35.69 G clean data of E. coli and 50.41 G of S. aureus). We reported 66 and 111 SNPs that were associated with interaction in E. coli and S. aureus, respectively. 23 out of 66 polymorphic changes resulted in amino acid alterations.12 significant genes, such as murE, treA, argS, and relA, which were also identified in previous evolutionary studies. In S. aureus, 111 SNPs detected in coding sequences could be divided into 35 non-synonymous and 76 synonymous SNPs. Our study illustrated the potential of genome-wide association methods for studying rapidly evolving traits in bacteria. Genetic association study methods will facilitate the identification of genetic elements likely to cause phenotypes of interest and provide targets for further laboratory investigation.