Tracking the hologenome dynamics in aquatic invertebrates by the holo-2bRAD approach.

The "hologenome" concept is an increasingly popular way of thinking about microbiome-host for marine organisms. However, it is challenging to track hologenome dynamics because of the large amount of material, with tracking itself usually resulting in damage or death of the research object. Here we show the simple and efficient holo-2bRAD approach for the tracking of hologenome dynamics in marine invertebrates (i.e., scallop and shrimp) from one holo-2bRAD library. The stable performance of our approach was shown with high genotyping accuracy of 99.91% and a high correlation of r > 0.99 for the species-level profiling of microorganisms. To explore the host-microbe association underlying mass mortality events of bivalve larvae, core microbial species changed with the stages were found, and two potentially associated host SNPs were identified. Overall, our research provides a powerful tool with various advantages (e.g., cost-effective, simple, and applicable for challenging samples) in genetic, ecological, and evolutionary studies.

Venous thromboembolism and severe COVID-19: a Mendelian randomization trial and transcriptomic analysis.

Introduction: Venous thromboembolism (VTE) is known to be intricately linked to severe COVID-19 (sCOVID-19) occurrence. Herein, we employed univariable Mendelian randomization (MR) and transcriptome analysis to predict the causal association and associated signaling networks between VTE and sCOVID-19. Methods: Potential VTE and sCOVID-19 association was assessed using MR-Egger, weighted median, simple mode, weighted mode, and inverse variance weighted (IVW) regression. We conducted independent univariable analyses involving VTE and sCOVID-19. Using heterogeneity, pleiotropy, and the Leave-One-Out examinations, we performed sensitivity analyses. Thereafter, we performed transcriptome analysis of the GSE164805 dataset to identify differentially expressed genes (DEGs) linked to single nucleotide polymorphisms (SNPs). Lastly, we conducted immune analyses. Results: Based on our univariable analysis, VTE was a strong indicator of sCOVID-19 development, and it was intricately linked to sCOVID-19. We further conducted sensitivity analysis to demonstrate the reliability of our results. Using differential analysis, we identified 15 major genes, namely, ACSS2, CEP250, CYP4V2, DDB2, EIF6, GBGT1, GSS, MADD, MAPK8IP1, MMP24, YBPC3, NT5DC3, PROCR, SURF6, and YIPF2, which were strongly connected to suppressive adaptive immune as well as augmented inflammatory cells. In addition, we uncovered strong associations with most differential immunologic gene sets, such as, the Major Histocompatibility Complex (MHC), immunoactivators, and immunosuppressors. Conclusion: Herein, we demonstrated we strong association between VTE and enhanced sCOVID-19 risk. We also identified 15 DEGs which potentially contribute to the shared immunologic pathogenesis between VTE and sCOVID-19.

Safe Food Supply Chain as Health Network: An Evolutionary Game Analysis of Behavior Strategy for Quality Investment.

There is a natural relation between human health and the quality of their food and drinks, and elevating the quality input level of food production for all enterprises within the food supply chain system forms the foundation for preventing various potential food safety risks that may be encountered. Unlike the previous research on quality investment of food production by enterprises, this paper probes into the evolutionary routes of the behavior strategy selection of subjects in the food supply chain and the preconditions for the equilibrium points of the social co-governance system. It takes the approach of establishing a tripartite evolutionary game model of food suppliers, food manufacturers and consumers on the basis of the social co-governance framework, in view of the above, this paper focuses on the influence of the reputation mechanism and the market contracts among supply chain subjects on the selection of a behavior strategy for quality investment by enterprises under the condition of lawful regulation by government. The results show that every subject selects their own behavior strategy on the basis of the balance of their respective interests. The net disbursement incurred by enterprises for quality investment and the costs of participation in governance by consumers constitute the dominant factors that influence both enterprises' selection of a behavior strategy and the level of social co-governance. Compared with the increase in economic punishment imposed on suppliers for production of risky food raw materials, it is more efficient to control food safety risks by lowering the costs of quality investment by suppliers. Accordingly, this paper proposes advice on policy in an attempt to provide inspiration for preventing and controlling food safety risks.

Prevention of food fraud and fraud emulation among companies in the supply chain based on a social Co-governance framework.

This study develops a three-party evolutionary game model among upstream raw material producers, midstream food producers, and downstream distributors in the food supply chain, and investigates food fraud and fraud emulation among companies in the same group based on a food safety social co-governance framework. Moreover, the equilibrium points are divided into four scenarios according to the number of groups of companies committing fraud in the supply chain and whether companies in the same group emulate each other's fraudulent behavior. The stability conditions of these scenarios are also discussed and verified by numerical simulation in MATLAB. The results show that the behavioral strategy choices of different groups of food companies in the supply chain are closely related to the level of social co-governance involving the government, market, and consumers. Government regulation, supervision between companies, and consumer reporting can all change companies' behavioral strategies. Although the level of fraud emulation among companies in the same group does not change their behavioral strategy choice, it affects the time it takes for their behavioral strategy to evolve to a stable state. Moreover, the level of social co-governance directly affects companies' behavioral strategy choices at different emulation levels.

Identification of apoptosis-related gene signatures as potential biomarkers for differentiating active from latent tuberculosis via bioinformatics analysis.

Background: Apoptosis is associated with the pathogenesis of Mycobacterium tuberculosis infection. This study aims to identify apoptosis-related genes as biomarkers for differentiating active tuberculosis (ATB) from latent tuberculosis infection (LTBI). Methods: The tuberculosis (TB) datasets (GSE19491, GSE62525, and GSE28623) were downloaded from the Gene Expression Omnibus (GEO) database. The diagnostic biomarkers differentiating ATB from LTBI were identified by combining the data of protein-protein interaction network, differentially expressed gene, Weighted Gene Co-Expression Network Analysis (WGCNA), and receiver operating characteristic (ROC) analyses. Machine learning algorithms were employed to validate the diagnostic ability of the biomarkers. Enrichment analysis for biomarkers was established, and potential drugs were predicted. The association between biomarkers and N6-methyladenosine (m6A) or 5-methylated cytosine (m5C) regulators was evaluated. Results: Six biomarkers including CASP1, TNFSF10, CASP4, CASP5, IFI16, and ATF3 were obtained for differentiating ATB from LTBI. They showed strong diagnostic performances, with area under ROC (AUC) values > 0.7. Enrichment analysis demonstrated that the biomarkers were involved in immune and inflammation responses. Furthermore, 24 drugs, including progesterone and emricasan, were predicted. The correlation analysis revealed that biomarkers were positively correlated with most m6A or m5C regulators. Conclusion: The six ARGs can serve as effective biomarkers differentiating ATB from LTBI and provide insight into the pathogenesis of Mycobacterium tuberculosis infection.

Food manufacturer willingness to employ blockchain technology system under the social Co-governance framework: China's situation.

The blockchain technology system has gradually come to be employed in the food supply chain system, and it has emerged that the system offers the unique function of effectively curbing counterfeiting by food manufacturers. Unlike previous research on adoption by enterprises of new technology, this paper probes into the specific evolutionary routes of game subjects from the perspective of the precondition for enterprises' willingness to employ blockchain technology on the basis of China's social co-governance framework and by establishing a tripartite evolutionary game model of food manufacturer, government and consumer. The study then tests and verifies the stability conditions of equilibrium points and the relationship between these equilibrium points and the social co-governance level through numerical simulation analysis. On the above basis, the expected market proceeds of food producers employing blockchain technology and the influence of government and consumer behavior on enterprises' selection of a behavior strategy and the level of social co-governance are analyzed. The results show that every subject selects their own behavior strategy on the basis of the balance of their respective interests, and the final stability condition of the system is independent of their initial intentions. Rather, the expected sales volume of foods employing blockchain technology, governmental behavior (e.g., supervision, casual inspection, economic punishment, and fiscal subsidies), and complaints made by consumers constitute the main factors that influence food enterprises' selection of a behavior strategy. The level of social co-governance and the behavior of both government and consumers will ultimately be accomplished by influencing enterprises' expected economic returns, and the selection of an enterprise behavior strategy internally depends on the expected economic returns from producing foods employing blockchain technology. Therefore, this paper makes relevant proposals in an attempt to assist the Chinese government to better promote and popularize the blockchain technology system among food manufacturing enterprises.

A robust and efficient AI assistant for breast tumor segmentation from DCE-MRI via a spatial-temporal framework.

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) allows screening, follow up, and diagnosis for breast tumor with high sensitivity. Accurate tumor segmentation from DCE-MRI can provide crucial information of tumor location and shape, which significantly influences the downstream clinical decisions. In this paper, we aim to develop an artificial intelligence (AI) assistant to automatically segment breast tumors by capturing dynamic changes in multi-phase DCE-MRI with a spatial-temporal framework. The main advantages of our AI assistant include (1) robustness, i.e., our model can handle MR data with different phase numbers and imaging intervals, as demonstrated on a large-scale dataset from seven medical centers, and (2) efficiency, i.e., our AI assistant significantly reduces the time required for manual annotation by a factor of 20, while maintaining accuracy comparable to that of physicians. More importantly, as the fundamental step to build an AI-assisted breast cancer diagnosis system, our AI assistant will promote the application of AI in more clinical diagnostic practices regarding breast cancer.

Assessment of ferroptosis-associated gene signatures as potential biomarkers for differentiating latent from active tuberculosis in children.

Ferroptotic cell death is a regulated process that is governed by iron-dependent membrane lipid peroxide accumulation that plays a pathogenic role in several disease-related settings. The use of ferroptosis-related genes (FRGs) to distinguish active tuberculosis (ATB) from latent tuberculosis infection (LTBI) among children, however, remains to be analysed. Tuberculosis-related gene expression data and FRG lists were obtained, respectively, from Gene Expression Omnibus (GEO) and FerrDb. Differentially expressed FRGs (DE-FRGs) detected when comparing samples from paediatric ATB and LTBI patients were explored using appropriate bioinformatics techniques, after which enrichment analyses were performed for these genes and hub genes were identified, with these genes then being used to explore potential drug interactions and construct competing endogenous RNA (ceRNA) networks. The GSE39939 dataset yielded 124 DE-FRGs that were primarily related to responses to oxidative, chemical and extracellular stimulus-associated stress. In total, the LASSO and SVM-RFE algorithms enabled the identification of nine hub genes (MAPK14, EGLN2, IDO1, USP11, SCD, CBS, PARP8, PARP16, CDC25A) that exhibited good diagnostic utility. Functional enrichment analyses of these genes suggested that they may govern ATB transition from LTBI through the control of many pathways, including the immune response, DNA repair, transcription, RNA degradation, and glycan and energy metabolism pathways. The CIBERSORT algorithm suggested that these genes were positively correlated with inflammatory and myeloid cell activity while being negatively correlated with the activity of lymphocytes. A total of 50 candidate drugs targeting 6 hub DE-FRGs were also identified, and a ceRNA network was used to explore the complex interplay among these hub genes. The nine hub FRGs defined in this study may serve as valuable biomarkers differentiating between ATB and LTBI in young patients.

The impact of capitalist profit-seeking behavior by online food delivery platforms on food safety risks and government regulation strategies.

Capital monopolized platforms that have emerged based on the new "Internet Plus" economic form will undoubtedly distort market competition. Taking the Meituan online food delivery platform in China as an example, this study (1) investigates the game of interests between the platform and restaurants and the resulting impact on food safety risks, and (2) explores the interactions among government regulations, platform profit strategy, and restaurant behavior. An evolutionary game model between the capital-monopolized online food delivery platform and the restaurants was developed with an optional promotion fee and government regulation level as variables. Analysis of four equilibrium situations derived from the evolutionary game model showed that the platform always pursued high overall profit in every equilibrium situation. This capitalist profit-seeking behavior will most likely reduce the profit margins and even the survival space of restaurants on the platform, forcing them to engage in opportunistic behavior and illegal production, thereby resulting in increased food safety risks in online food delivery and consequently increased government regulation costs. Although increased government regulation can change the production strategy of restaurants, it cannot change the platform's capitalist profit-seeking behavior. The platform's overall payoff is not reduced due to increased regulation, which once again proves the profit-seeking nature of capital. The strategy of low commissions but high promotion fees may require greater government regulation to restrain the opportunistic behavior of restaurants. Therefore, the Chinese government regulators can achieve a win-win situation of improved government regulation efficiency and reduced regulation costs by designing new regulatory strategies that do not reduce the platform's overall payoff.

Study on effect of collaborative governance participation willingness of online food delivery platform restaurants and consumers from perspective of control theory: Based on moderating effects of perceived risks.

The popularization of the Internet and the convenience of e-commerce are driving the online restaurant industry's rapid development of worldwide. However, serious information asymmetries in online food delivery (OFD) transactions not only aggravate food safety risks, resulting in simultaneous government and market failures, but also intensify consumers' perceived risks. This paper innovatively constructs a research framework for the governance participation willingness of OFD platform restaurants and consumers under the moderating effects of perceived risks from the perspective of control theory and then develops scales for analyzing the governance willingness of both restaurants and consumers. Using data collected through a survey, this paper explores the effect of control elements on governance participation by restaurants and consumers and analyzes the moderating effects of perceived food safety risks. Results showed that both government regulations and restaurant reputation (formal control elements) and online complaints and restaurant management response (informal control elements) can increase governance participation willingness among both platform restaurants and consumers. The moderating effects of perceived risks are partially significant. When the risks perceived by restaurants and consumers are strong, government regulation and online complaints can more effectively boost the governance participation willingness of restaurants and consumers, respectively. At this moment, consumers' willingness to pursue problem solving through online complaints is evidently enhanced. Accordingly, the perceived risks and the online complaints jointly motivate restaurants and consumers to participate in governance activities.

Nutritional quality and consumer health perception of online delivery food in the context of China.

BACKGROUND: Today, the popularization of mobile internet technology has enabled the public's need for food convenience and diversity arising from modern fast-paced lifestyles to be met at a relatively low cost. The digital age of the restaurant industry has arrived. Online food delivery (OFD) is rapidly developing globally. However, the public's awareness of the nutritional quality of food through OFD and their knowledge of dietary nutrition remain to be investigated. METHODS: In the context of China, this study attempts to evaluate the nutritional quality of best-selling OFD set meals (i.e., meal combos) based on the current official Chinese dietary guidelines 2022. It accomplishes this by collecting data on popular OFD restaurants among consumers in 115 Chinese universities from the restaurants' delivery addresses. Moreover, 20,430 valid questionnaires were collected online from undergraduates, graduate students, and other young groups aged 18-30 throughout China for descriptive analysis to investigate consumers' perceptions of the nutritional quality of food through OFD and its health impact. RESULTS: The results of the nutritional quality evaluation of the OFD set meals ranged widely from 15 to 85, with a mean of 36.57 out of a possible maximum score of 100; and 89.56% scored less than 50. The nutritional quality of OFD foods was thus generally low. The nutritional quality of foods was negatively correlated with their popularity among consumers. CONCLUSIONS: Young OFD consumers generally paid low attention to dietary nutrition knowledge and seldom paid attention to nutritional quality when choosing OFD foods while the nutritional quality of OFD foods was generally low. Respondents subjectively reported that long-term consumption of OFD food caused weight gain, increased blood lipids, and gastrointestinal discomfort. They thought that the reason might be excessive oil, salt, and sugar in the food, while ignoring the balance between different types of food.

Decoding the byssus fabrication by spatiotemporal secretome analysis of scallop foot.

Secretome is involved in almost all physiological, developmental, and pathological processes, but to date there is still a lack of highly-efficient research strategy to comprehensively study the secretome of invertebrates. Adhesive secretion is a ubiquitous and essential physiological process in aquatic invertebrates with complicated protein components and unresolved adhesion mechanisms, making it a good subject for secretome profiling studies. Here we proposed a computational pipeline for systematic profiling of byssal secretome based on spatiotemporal transcriptomes of scallop. A total of 186 byssus-related proteins (BRPs) were identified, which represented the first characterized secretome of scallop byssal adhesion. Scallop byssal secretome covered almost all of the known structural elements and functional domains of aquatic adhesives, which suggested this secretome-profiling strategy had both high efficiency and accuracy. We revealed the main components of scallop byssus (including EGF-like domain containing proteins, the Tyr-rich proteins and 4C-repeats containing proteins) and the related modification enzymes primarily contributing to the rapid byssus assembly and adhesion. Spatiotemporal expression and co-expression network analyses of BRPs suggested a simultaneous secretion pattern of scallop byssal proteins across the entire region of foot and revealed their diverse functions on byssus secretion. In contrast to the previously proposed "root-initiated secretion and extension-based assembly" model, our findings supported a novel "foot-wide simultaneous secretion and in situ assembly" model of scallop byssus secretion and adhesion. Systematic analysis of scallop byssal secretome provides important clues for understanding the aquatic adhesive secretion process, as well as a common framework for studying the secretome of non-model invertebrates.

IAPs Gene Expansion in the Scallop Patinopecten yessoensis and Their Expression Profiles After Exposure to the Toxic Dinoflagellate.

Inhibitors of apoptosis proteins (IAPs) are conserved regulators involved in cell cycle, cell migration, cell death, immunity and inflammation, should be due to the fact that they can assist with the ability to cope with different kinds of extrinsic or intrinsic stresses. Bivalve molluscs are well adapted to highly complex marine environments. As free-living filter feeders that may take toxic dinoflagellates as food, bivalves can accumulate and put up with significant levels of paralytic shellfish toxins (PSTs). PSTs absorption and accumulation could have a deleterious effect on bivalves, causing negative impact on their feeding and digestion capabilities. In the present study, we analyzed IAP genes (PyIAPs) in Yesso scallop (Patinopecten yessoensis), a major fishery and aquaculture species in China. Forty-seven PyIAPs from five sub-families were identified, and almost half of the PyIAP genes were localized in clusters on two chromosomes. Several sites under positive selection was revealed in the significantly expanded sub-families BIRC4 and BIRC5. After exposure to PST-producing dinoflagellates, Alexandrium catenella, fourteen PyIAPs showed significant responses in hepatopancreas and kidney, and more than eighty-five percent of them were from the expanded sub-families BIRC4 and BIRC5. The regulation pattern of PyIAPs was similar between the two tissues, with more than half exhibited expression suppression within three days after exposure. In contrast to hepatopancreas, more acute changes of PyIAPs expression could be detected in kidney, suggesting the possible involvement of these PyIAPs in tissue-specific PST tolerance. These findings also imply the adaptive expansion of bivalve IAP genes in response to algae derived biotoxins.

A novel fluorescent probe with extremely low background fluorescence for sensing hypochlorite in zebrafish.

Development of an efficient fluorescent probe for sensing hypochlorite in water samples and biological samples is highly demanded. However, the currently reported fluorescent probes for hypochlorite frequently suffered from the problem of high background fluorescence. Herein, based on the combined effect of two different fluorescence quenching groups, we rationally developed a novel fluorescent probe for hypochlorite with extremely low background fluorescence. Notably, due to the doubly quenching groups, the probe could even keep low background fluorescence in a solution with high viscosity. Furthermore, the probe displayed highly sensitive and selective response to hypochlorite, with the detection limits calculated to be 10.5 nM. Practical application demonstrated that the probe was able to quantitatively detect hypochlorite in various water samples with good recovery. Significantly, the probe showed extremely low background fluorescence in living cells and was capable of detecting minor variation of endogenous hypochlorite in RAW 264.7 cells. Moreover, the fluorescence imaging different concentration of hypochlorite in zebrafish has been successfully conducted. The probe developed herein will be widely used as a reliable tool to accurately monitor the variation of hypochlorite in living organism.

Publisher Correction: Evolutionary transcriptomics of metazoan biphasic life cycle supports a single intercalation origin of metazoan larvae.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Evolutionary transcriptomics of metazoan biphasic life cycle supports a single intercalation origin of metazoan larvae.

The transient larva-bearing biphasic life cycle is the hallmark of many metazoan phyla, but how metazoan larvae originated remains a major enigma in animal evolution. There are two hypotheses for larval origin. The 'larva-first' hypothesis suggests that the first metazoans were similar to extant larvae, with later evolution of the adult-added biphasic life cycle; the 'adult-first' hypothesis suggests that the first metazoans were adult forms, with the biphasic life cycle arising later via larval intercalation. Here, we investigate the evolutionary origin of primary larvae by conducting ontogenetic transcriptome profiling for Mollusca-the largest marine phylum characterized by a trochophore larval stage and highly variable adult forms. We reveal that trochophore larvae exhibit rapid transcriptome evolution with extraordinary incorporation of novel genes (potentially contributing to adult shell evolution), and that cell signalling/communication genes (for example, caveolin and innexin) are probably crucial for larval evolution. Transcriptome age analysis of eight metazoan species reveals the wide presence of young larval transcriptomes in both trochozoans and other major metazoan lineages, therefore arguing against the prevailing larva-first hypothesis. Our findings support an adult-first evolutionary scenario with a single metazoan larval intercalation, and suggest that the first appearance of proto-larva probably occurred after the divergence of direct-developing Ctenophora from a metazoan ancestor.

A quality improvement method for lung LDCT images.

BACKGROUND: Low dose computed tomography (LDCT) reduces radiation damage to patients. However, with the decrease of radiation dose, LDCT images of the lung often appear some serious problems such as poor contrast, noise and streak artifacts. OBJECTIVE: To improve the quality of lung LDCT images, this study proposed and investigated a new denoising method based on classification training structure combined dictionary for lung LDCT images. METHODS: First, top-hat transform and anisotropic diffusion with a shock filter (ADSF) algorithm are used to enhance the image contrast and image details. Second, an adaptive dictionary is trained and used for noise reduction. Third, more image details are extracted from the residual image by using the atom activity measurement. The final result is obtained by combining the dictionary denoising result with the extracted detail information. The proposed method is then validated by both simulated and clinical lung LDCT images. Four metrics including Contrast-to-Noise Ratio (CNR), Noise Suppression Index (NSI), Edge Preserving Index (EPI), and Blurring Index (BI) are computed to quantitatively evaluate image quality. RESULTS: The results showed that the CNR, NSI, EPI, and BI of our method reached 8.953, 0.9500, 0.7230 and 0.0170, respectively. Noise and streak artifacts can be removed from lung LDCT images while keeping and retaining more details. CONCLUSIONS: Comparing with the results of other methods tested using the same dataset, this study demonstrated that our new method significantly improved quality of the lung LDCT images.

Integration of Biochemical, Cellular, and Genetic Indicators for Understanding the Aging Process in a Bivalve Mollusk Chlamys farreri.

The major causal factors for the irreversible decline in physical vitality during organismal aging are postulated to be a chronic state of cellular redox imbalance, metabolic toxicity, and impaired energy homeostasis. We assessed whether the relevant enzyme activity, oxidative stress, and intracellular ATP might be causally involved in the aging of short-lived Chlamys farreri (life span 4~5 years). A total of eight related biochemical and cellular indicators were chosen for the subsequent analysis. All the indicators were measured in seven different tissues from scallops aged one to four years, and our data support that the aging of C. farreri is associated with attenuated tissue enzyme activity as well as a decreased metabolic rate. Through principal component analysis, we developed an integrated vigor index for each tissue for comprehensive age-related fitness evaluation. Remarkably, all tissue-integrated vigor indexes significantly declined with age, and the kidney was observed to be the most representative tissue. Further transcriptional profiling of the enzymatic genes provided additional detail on the molecular responses that may underlie the corresponding biochemical results. Moreover, these critical molecular responses may be attributed to the conserved hierarchical regulators, e.g., FOXO, AMPKs, mTOR, and IGF1R, which were identified as potentially novel markers for chronic fitness decline with age in bivalves. The present study provides a systematic approach that could potentially benefit the global assessment of the aging process in C. farreri and provide detailed evaluation of the biochemical, cellular, and genetic indicators that might be involved. This information may assist in a better understanding of bivalve adaptability and life span.