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IntroductionThis study aimed to assess the diagnostic values of bronchoalveolar lavage fluid (BALF) real-time polymerase chain reaction (PCR) and BALF metagenomic next-generation sequencing (mNGS) for Pneumocystis jirovecii pneumonia (PJP) in patients infected with human immunodeficiency virus (HIV).MethodsA total of 99 HIV-infected PJP patients and 61 HIV-infected patients diagnosed with non-PJP pneumonia between March 2019 and December 2022 were enrolled. P. jirovecii and multiple other co-pathogens detected in BALF by mNGS were analyzed. The clinical final diagnosis was employed as a benchmark. We compared the diagnostic performance of mNGS in PJP with serum BDG and BALF real-time PCR. The mixed infections detected by mNGS and modifications of antimicrobial treatment were also analyzed.ResultsThe sensitivity of mNGS test of BALF samples reached 85.86%, which was significantly higher than serum BDG (39.39%, P < 0.001). The sensitivity of BALF P. jirovecii PCR (84.85%) was similar with mNGS (P > 0.05). The specificity of mNGS (100%) was also same as PCR (100.0%), and superior to serum BDG (88.52%, P < 0.001). Besides, mNGS performs remarkably well in identifying co-pathogens of PJP patients infected with HIV. In addition to P. jirovecii, 82 cases (82.83%) of other co-pathogens were identified based on mNGS. Moreover, thirty-four patients (34.34%) increased therapeutic dose of trimethoprim-sulfamethoxazole (TMP-SMZ) based on BALF P. jirovecii PCR. Based on the mNGS results, initial antimicrobial treatment was modified in 86.87% (86/99) of PJP patients.ConclusionBALF mNGS and real-time PCR are two powerful techniques for rapid diagnosis of PJP with high specificity and sensitivity. Moreover, the benefit of mNGS is that it may identify other organisms besides PJP and it may benefit proper and prompt treatment.

Abstract Long noncoding RNAs (lncRNAs) play important roles in regulating HIV-1 infection and virus-host interactions. However, it is unclear whether and how ART alters lncRNAs in HIV-infected patients. In the present study, we investigated changes of lncRNAs in PBMCs from HIV-1 patients pre- and post-ART. We identified a total of 974 lncRNAs whose expression was restored to normal levels after ART. Cis-acting analysis showed that six lncRNAs have cis-regulated target genes, among which RP11-290F5.1 and interferon regulatory factor 2 (IRF2) were reported to promote HIV replication. Furthermore, we found that lncRNA CTB-119C2.1, which regulates most mRNAs with differential expression in PBMCs from HIV-1 infected patients after ART, was significantly upregulated by RNA-seq and qRT-PCR assays. KEGG analysis of CTB-119C2.1-associated genes revealed that most of the genes are involved in the p53 signaling pathway and pathways related to cell cycle and DNA replication. Our findings thus reveal the dynamic change of lncRNAs in people living with HIV-1 pre- and post-ART and warrant further investigation of the role of lncRNAs in HIV-1 pathogenesis and treatment.

Global climate changes have led to severe and frequent drought stress in many areas, seriously threatening the stability of yield in wheat. Exploring the quantitative trait loci for yield stability under drought condition is needed for wheat molecular breeding. In this study, we collected a panel of 432 diverse wheat accessions from different regions around the world and evaluated the drought stress susceptibility index of wheat yield-related phenotypes under drought stress and genotyped the panel with the wheat660K SNP array. Genome-wide association analysis has identified 40 yield stability-related loci, which distribute on various chromosomes. Four loci on Chromosome 1 A, 2B, 3 A and 7B are associate with more than two phenotypic indicators, explaining 1.59% − 8.07% of the phenotypic variation. Among them, Qgns.cas-3A.2 is a novel QTL for wheat yield stability under drought stress. Venn diagram analysis on the drought-responsive expression patterns of Qtgw.cas-3A genes in drought-tolerant and sensitive cultivars, and linkage disequilibrium analysis of the 57Kb region flanking SNP marker AX-108784842 on chromosomes 3 A which displays the highest confidence identified the same candidate gene, which encodes a glycosyl hydrolases family 17 protein. Haplotype analysis indicated that GG allele of this gene is the favorable allele for wheat yield stability under drought. Taken together, these results provide new insights on understanding the genetic basis of wheat yield stability under drought stress and new tools for developing molecular markers to engineer drought-tolerant wheat cultivars.

Seagrass is a group of flowering plants capable of completing their life cycle in a marine environment. It not only provides a refuge for biodiversity and essential fish spawning and nursery grounds, but also provides ecologically and socioeconomically important services for urban coasts. Seagrass is widely distributed along temperate and tropical coastlines globally. The biodiversity corresponds with differences in the relative importance of sexual (seed production) and asexual (clonal growth) life history strategies in the maintenance of seagrass populations. Sexual reproduction in predominantly clonal marine plants increases recombination favoring adaptation and enhancing species resilience to environmental change. Flowering induction is an important link in the transition from vegetative growth to reproductive growth of seagrasses. Recent studies on seagrasses suggest that flowering intensity and frequency are correlated with global climate change, and the response of seagrasses will be more complex, and potentially more resilient than previously imagined.Seagrass environments are characterized by physical conditions, such as temperature, salinity, currents, waves, turbulence, and light. Each of these parameters has the potential to affect vegetation from the smallest (molecular and physiological) to the largest (ecosystem as well as global) scale. Based on bibliometric methods, this study summarized the development trend of seagrass flowering formation research. The SCIE database of the Web of Science core collection of the Institute for Scientific Information (ISI) was chosen as the retrieval source, and select published international journals were chosen as the research object. With "seagrass flowering" as the search keyword, a total of 300 related publications were retrieved. In terms of the number of relevant publications each year, there was an overall increasing trend, indicating that this topic has gradually received more attention in recent years, which has great research potential.This review summarizes the research progress of flowering inducement in the sexual reproduction of seagrasses and discusses the influence of physical factors on the flowering induction of seagrasses. It was previously thought that the flowering pathway initiated by seagrasses in response to environmental factors and endogenous signals may focus on the photoperiod, vernalization, and spontaneous pathways. However, the sexual reproduction of different species is different, and studying the interaction between seagrasses and their physical environment may improve understanding of the processes that influence their biology. This review focuses on the following aspects: 1) Clarifying the period of concentrated flowering of the seagrass bed, which is conducive to studying the inducement of flowering of seagrass and protecting the seagrass seed bank. 2) Discussing whether more genotypes of seagrass should be introduced for planting in the process of seagrass bed repair to avoid large-scale clonal reproduction of a single genotype of seagrass. 3) How sexual reproduction of seagrasses under adverse environments can be used to indicate changes in the climate and environment. However, existing studies have paid little attention to the sexual reproduction of seagrass beds, and do not consider the sexual reproduction rate as a long-term monitoring indicator. It is suggested that the sexual reproduction rate should be combined with environmental factors in the future long-term monitoring and assessment of the health status of seagrass beds to jointly assess their pressure status.

Abstract To evaluate clinical value of metagenomic next-generation sequencing (mNGS) in people living with HIV/AIDS (PLWHA) who had CNS disorders. Cerebrospinal fluid (CSF) samples from 48 PLWHA presenting with CNS disorders were sequenced using mNGS and compared with clinical conventional diagnostic methods. In total, 36/48 ss(75%) patients were diagnosed with pathogen(s) infection by mNGS, and the positive detection proportion by mNGS was higher than that by clinical conventional diagnostic methods (75% vs 52.1%, X 2 = 5.441, P = 0.020). Thirteen out of 48 patients (27.1%) were detected with 3–7 pathogens by mNGS. Moreover, 77 pathogen strains were detected, of which 94.8% (73/77) by mNGS and 37.0% (30/77) by clinical conventional methods (X 2 = 54.206, P

BackgroundSevere fever with thrombocytopenia syndrome (SFTS) is an emerging zoonosis caused by a novel bunyavirus. Until recently, the SFTS related acute kidney injury (AKI) was largely unexplored. This study aimed to investigate the clinical characteristics and outcomes of AKI in patients with SFTS.MethodsThe non-AKI and AKI groups were compared in terms of general characteristics, clinical features, laboratory parameters and cumulative survival rate. The independent risk factors for in-hospital mortality in patients with SFTS were analyzed by multivariate logistic regression to identify the population with poor prognosis.ResultsA total of 208 consecutive patients diagnosed with SFTS were enrolled, including 153 (73.6%) patients in the non-AKI group and 55 (26.4%) patients in the AKI group. Compared with patients without AKI, patients with AKI were older and had a higher frequency of diabetes. Among these laboratory parameters, platelet count, albumin and fibrinogen levels of patients with AKI were identified to be significantly lower than those of patients without AKI, while ALT, AST, ALP, triglyceride, LDH, BUN, uric acid, creatine, Cys-C, β2-MG, potassium, AMY, lipase, CK-MB, TnI, BNP, APTT, thrombin time, D-dimer, CRP, IL-6, PCT and ESR levels were significantly higher in patients with AKI. A higher SFTS viral load was also detected in the AKI patients than in the non-AKI patients. The cumulative survival rates of patients at AKI stage 2 or 3 were significantly lower than those of patients without AKI or at AKI stage 1. However, there was no significant difference in the cumulative survival rates between patients without AKI and those with stage 1 AKI. Univariate and multivariate binary logistic regression analyses demonstrated that stage 2 or 3 AKI was an independent risk factor for in-hospital mortality in patients with SFTS.ConclusionAKI is associated with poor outcomes in patients with SFTS, especially patients at AKI stage 2 or 3, who generally have high mortality. Our findings support the importance of early identification and timely treatment of AKI in patients with SFTS.

The current use of elastography ultrasound faces challenges, including vulnerability to subjective manipulation, echo signal attenuation, unknown risks of elastic pressure and high imaging hardware cost. Here, the author shows a virtual elastography to empower low-end ultrasound devices with state-of-art elastography function.

BackgroundTo analyze the changing characteristics of continuous monitoring of refined lymphocyte subsets in people living with HIV/AIDS (PLWHA) during ART period.MethodsRefined lymphocyte subsets was continuously monitored using flow cytometry for 173 PLWHA, who were hospitalized in Zhongnan Hospital of Wuhan University from August 17, 2021 to September 14, 2022. The effect of ART status and duration of ART on changes of refined lymphocyte subsets were compared in different groups. Then, the levels of refined lymphocyte subsets in PLWHA treated for more than 10 years were compared to those of 1086 healthy individuals.ResultsIn addition to conventional CD4+ T lymphocytes and CD4+/CD8+ ratio, gradually increasing in numbers of CD3+CD4+CD45RO cells, CD3+CD4+CD45RA cells, CD45RA+CD3+CD4+CD25+CD127low and CD45RO+CD3+CD4+CD25+CD127low cells were found with the increase of ART duration. The number of CD4+CD28+ cells and CD8+CD28+ cells were 174/ul and 233/ul at 6 months post-ART, which gradually increased to 616/ul and 461/ul after ART initiation more than 10 years. Moreover, in ART ≤ 6 months, 6 months-3years, 3-10 years and >10 years groups, the percentage of CD3+CD8+HLA-DR+/CD8 were 79.66%, 69.73%, 60.19% and 57.90%, respectively, and the differences between groups showed statistical significance (F=5.727, P=0.001). For those PLWHA with ART more than 10 years, the levels of CD4+ T lymphocytes, CD3+CD4+CD45RO cells, CD3+CD4+CD45RA cells, CD4+CD28+ cells and CD8+CD28+ cells can increase to levels similar to those of healthy control. However, for those PLWHA with ART more than 10 years, CD4+/CD8+ ratio was 0.86 ± 0.47, which was lower than that of healthy control (0.86 ± 0.47 vs 1.32 ± 0.59, t=3.611, P=0.003); absolute counts and percentage of CD3+CD8+HLA-DR+ cells were 547/ul and 57.90%, which were higher than those of healthy control(547/ul vs 135/ul, t=3.612, P=0.003; 57.90% vs 22.38%, t=6.959, P

Mangrove distribution along shorelines shows distinct zonation patterns; thus, different communities may face various influences from sea level rise (SLR) and land use. However, long-term change predictions are usually based only on the total extent of mangroves. Few studies have revealed how SLR and land development such as agriculture, aquaculture, and urbanization jointly affect different intertidal mangrove communities. This study proposed a novel framework combining SLAMM (Sea Level Affecting Marshes Model) and the CLUE-S (Conversion of Land Use and its Effect at Small regional extent) model to assess the potential impacts on upper and lower intertidal mangrove communities. Maoweihai in Guangxi, China, was selected as the study area and the potential impacts from the squeeze effect and mangrove expansion potential were evaluated. We established three scenarios combining SLR and land use patterns to predict mangrove coverage projections by 2070. The results showed that, under a single SLR driver, the upper intertidal mangroves would be more adaptive to rapid SLR than the lower intertidal mangroves. However, under the combined influence of the two drivers, the upper intertidal mangroves would experience larger squeeze effects than the lower intertidal mangroves, with up to 80.5% of suitable habitat lost. Moreover, the expansion potential of upper intertidal mangroves would be considerably more limited than that of lower intertidal mangroves. The length of the expandable habitat patch boundary of upper intertidal mangroves only reached 1.4–1.8 ​km, while that of the lower intertidal mangroves reached up to 99.2–111.2 ​km. Further, we found that aquaculture ponds and cropland are the top two land development types that could occupy suitable habitat and restrict the mangrove expansion potential. Our results highlight that timely improvement of land use policies to create available landward accommodation space for mangrove migration is essential to maintain the coverage and diversity of mangrove communities under SLR. The proposed method can be a helpful tool for adaptive mangrove conservation and management under climate change.

Global change has generated challenges for oceans, from individuals to the entire ecosystem, and has raised contemporary issues related to ocean conservation and management. Specifically, coral reef ecosystems have been exposed to various environmental and human disturbances. In this study, the Ecopath with Ecosim model was used to explore the impacts of ocean warming and fishing on Xisha Islands coral reef ecosystem in the South China Sea. The variables in this model included two ocean warming scenarios and three fishing scenarios. The model consisted of 23 functional groups including algae, coral, sea birds, and sharks. Our results showed that by the middle of the century, ocean warming and fishing led to a 3.79% and 4.74% decrease in total catch compared with 2009, respectively. In addition, the combined effects of ocean warming and fishing caused a 4.79% decrease in total catch, and the mean trophic level of catch was predicted to decrease by 6.01% under the SSP585-High fishing scenario. Reducing the fishing effort mitigates the effects of ocean warming on some species, such as large carnivorous fish and medium carnivorous fish; however, under low fishing effort, some functional groups, such as small carnivorous and omnivorous fish, have low biomass because of higher predation mortality.

Abstract Comorbidities are important for the disease outcome of COVID‐19, however, which underlying diseases that contribute the most to aggravate the conditions of COVID‐19 patients are still unclear. Viral clearance is the most important laboratory test for defining the recovery of COVID‐19 infections. To better understand which underlying diseases that are risk factors for delaying the viral clearance, we retrospectively analyzed 161 COVID‐19 clinical cases in the Zhongnan Hospital of Wuhan University, Wuhan, China between January 5 and March 13, 2020. The demographic, clinical and laboratory data, as well as patient treatment records were collected. Univariable and multivariable analysis were performed to explore the association between delayed viral clearance and other factors by using logistic regression. Survival analyses by Kaplan‐Meier and Cox regression modeling were employed to identify factors negatively influencing the viral clearance negatively. We found that hypertension and intravenous immunoglobulin adversely affected the time of viral RNA shedding. Hypertension was the most important risk factor to delay the SARS‐CoV‐2 virus clearance, however, the use of Angiotensin‐Converting Enzyme Inhibitors(ACEI)/Angiotensin Receptor Blockers(ARB) did not shorten the time for virus clearance in these hypertensive patients’ virus clearance. We conclude that patients having hypertension and intravenous immunoglobulin may delay the viral clearance in COVID‐19 patients.

Sharks play an important role in marine ecosystems as top predators and have been increasingly accepted in recent years as a group for priority conservation worldwide. However, as one of the regions with the highest marine shark species richness, there is still a limited understanding of shark diversity patterns and conservation needs in China and the Association of Southeast Asian Nations (ASEAN) seas. In this study, we applied an ensemble species distribution model of five algorithms to investigate the diversity distribution patterns of 149 shark species in China and the ASEAN seas for the first time. A systematic conservation planning approach involving diversity, scarcity, and biogeographical distinctiveness was used to identify and compare conservation priority settings. Our results showed that bathymetry and dissolved oxygen were the most important variables contributing to shark distribution. The distribution pattern of shark species richness peaked on the continental shelves at 22–26°N, and a hotspot of shark diversity was identified around the Taiwan Strait. The spatial distribution of shark species in the nine orders and the 72 threatened shark species varied considerably. The existing marine protected area network only protects 2.1% of the ocean, 32.9% of the shark species, and 43.1% of the threatened species, highlighting a substantial conservation gap. Among the conservation priorities identified, the high conservation target scenario (30%) protects only 10%–15% more species than the low conservation target scenario (10%). However, under the high conservation target scenario, the conservation range of species tripled. Our results show that low conservation targets were only suitable for addressing the number of protected species, and that high targets would bring about improved outcomes for the number of protected species and the protected range of threatened species. Furthermore, planned priorities with a large clump pattern had slightly higher conservation achievements than those with small clumps. The results of this study will contribute to the development of a priority area network for sharks and provide a scientific basis for shark conservation and management in the China and ASEAN seas.

Although China possesses a large number of islands, knowledge of their overall ecological condition is limited on a national scale. Accordingly, this study developed a comprehensive and quantitative island ecosystem assessment framework that incorporates environmental quality, biological structure, and landscape patterns. The framework was applied to 42 typical, representative islands within China’s coastal regions, including different climatic zones, area sizes, populations, and substratum lithologies. Results showed that the value range of the comprehensive index of island ecosystem condition (CIisland) was significant (from 52.33 to 89.53, 71.72 average), and 85.4% of islands scored either “high” or “good,” indicative of their exceptional condition. However, conditions varied among different island components, indicating different challenges. Environmental quality index (Ienv) values ranged from 60.70 to 94.80 (79.72 average), where primary threats were seawater nutrient pollution, petroleum, and marine organism metal contamination. Biological structure index (Ibio) values ranged from 43.50 to 89.40 (66.10 average), where primary threats were vegetation destruction and a reduction in marine biodiversity within intertidal and subtidal zones. Landscape pattern index (Iland) values varied significantly (from 6 to 100, 72.36 average), where a key characteristic of highly developed islands was low natural landscape (vegetation) coverage. Conditions also varied among island climate zones, lithologies, area sizes, and levels of human habitation. Additionally, island ecosystem conditions were influenced by both natural and anthropogenic factors as well as area size, population, and GDP. Although distance to the mainland significantly correlated to (Ibio), and (CIisland), these parameters did not significantly correlate to (Ienv), which might be explained by that environmental quality was generally conditional on large-scale environments. This assessment is intended to provide a holistic perspective on island conditions in China while identifying key challenges and associated driving factors, which will greatly aid in establishing island-specific sustainable management practices.

The effective and reliable monitoring of fish communities is important for the management and protection of marine ecosystems. Environmental DNA (eDNA) metabarcoding is a relatively new method that has been widely used in recent years, while traditional sampling via fish catching (i.e., gillnets) is one of the most common and reliable fish monitoring methods used to date. We compared the taxonomic and functional diversity of fish detected within a mangrove–seagrass–coral reef continuum using both survey methods. One liter seawater and gillnet samples were collected in August 2021 from mangrove forests, seagrass meadows and coral reef habitats (n = 3 each) in Hainan, China. Surveys using eDNA and gillnets identified 139 genera belonging to 66 families and 58 genera belonging to 42 families, respectively. Regardless of the survey method, fish detected in mangrove, seagrass and coral reef habitats were heterogeneous in their communities; however, the shared species between habitats suggest some degree of connectivity. There were no significant differences between habitats in terms of taxonomic and functional diversity, but a higher taxonomic diversity was detected using eDNA. Both methods were able to distinguish fish assemblages between different habitats; however, gillnet surveys performed better than eDNA surveys for distinguishing mangrove from seagrass assemblages. Therefore, the concurrent use of eDNA and gillnet survey methods provides a more comprehensive approach to understanding the heterogeneity of fish taxonomic and functional diversity along mangrove–seagrass–coral reef continuums.

The data provided in this article are partial fragments of the Cytochrome c oxidase subunit 1 mitochondrial gene (CO1) sequences of 175 tissues sampled from sharks and batoids collected from Malaysian waters, from June 2015 to June 2022. The barcoding was done randomly for six specimens from each species, so as to authenticate the code. We generated barcodes for 67 different species in 20 families and 11 orders. DNA was extracted from the tissue samples following the Chelex protocols and amplified by polymerase chain reaction (PCR) using the barcoding universal primers FishF2 and FishR2. A total of 654 base pairs (bp) of barcode CO1 gene from 175 samples were sequenced and analysed. The genetic sequences were blasted into the NCBI GenBank and Barcode of Life Data System (BOLD). A review of the blast search confirmed that there were 68 valid species of sharks and batoids that occurred in Malaysian waters. We provided the data of the COI gene mid-point rooting phylogenetic relation trees and analysed the genetic distances among infra-class and order, intra-species, inter-specific, inter-genus, inter-familiar, and inter-order. We confirmed the addition of Squalus edmundsi, Carcharhinus amboinensis, Alopias superciliosus, and Myliobatis hamlyni as new records for Malaysia. The establishment of a comprehensive CO1 database for sharks and batoids will help facilitate the rapid monitoring and assessment of elasmobranch fisheries using environmental DNA methods.

PurposeTo develop a risk stratification system that can predict axillary lymph node (LN) metastasis in invasive breast cancer based on the combination of shear wave elastography (SWE) and conventional ultrasound.Materials and MethodsA total of 619 participants pathologically diagnosed with invasive breast cancer underwent breast ultrasound examinations were recruited from a multicenter of 17 hospitals in China from August 2016 to August 2017. Conventional ultrasound and SWE features were compared between positive and negative LN metastasis groups. The regression equation, the weighting, and the counting methods were used to predict axillary LN metastasis. The sensitivity, specificity, and the areas under the receiver operating characteristic curve (AUC) were calculated.ResultsA significant difference was found in the Breast Imaging Reporting and Data System (BI-RADS) category, the “stiff rim” sign, minimum elastic modulusof the internal tumor and peritumor region of 3 mm between positive and negative LN groups (p < 0.05 for all). There was no significant difference in the diagnostic performance of the regression equation, the weighting, and the counting methods (p > 0.05 for all). Using the counting method, a 0–4 grade risk stratification system based on the four characteristics was established, which yielded an AUC of 0.656 (95% CI, 0.617–0.693, p < 0.001), a sensitivity of 54.60% (95% CI, 46.9%–62.1%), and a specificity of 68.99% (95% CI, 64.5%–73.3%) in predicting axillary LN metastasis.ConclusionA 0–4 grade risk stratification system was developed based on SWE characteristics and BI-RADS categories, and this system has the potential to predict axillary LN metastases in invasive breast cancer.

Abstract Aim To explore the effect of miR-296-5p on the metastasis of nasopharyngeal carcinoma (NPC) cells and investigate the underlying mechanism. Methods The expressions of miR-296-5p in NPC tissues and cells were determined using GSE32920 database analysis and real-time PCR and miRNA microarray assays. An miR-296-5p mimic and inhibitor were transfected into NPC cells. Then, immunofluorescence imaging, scratch wound-healing, transwell migration and invasion assays were used to observe the effects of miR-296-5p on cell metastasis and invasion. Real-time PCR and western blotting were carried out to detect the expressions of genes and proteins related to epithelial–mesenchymal transition (EMT). A dual luciferase reporter assay was used to identify whether TGF-β is the target gene of miR-296-5p. Finally, TGF-β expression plasmids were transfected into NPC cells to verify the role of TGF-β in the miR-296-5p-mediated inhibition of nasopharyngeal carcinoma cell metastasis. Results Our results show that miR-296-5p inhibits the migratory and invasive capacities of NPC cells by targeting TGF-β, which suppresses EMT. Importantly, the miR-296-5p level was significantly lower in human NPC tissues than in adjacent normal tissues. It also negatively correlated with TGF-β and was significantly associated with the lymph node metastasis of patients with NPC. Conclusions Our findings show that miR-296-5p represses the EMT-related metastasis of NPC by targeting TGF-β. This provides new insight into the role of miR-296-5p in regulating NPC metastasis and invasiveness.

ABSTRACTCirculating in China and 158 other countries and areas, the ongoing COVID-19 outbreak has caused devastating mortality and posed a great threat to public health. However, efforts to identify effectively supportive therapeutic drugs and treatments has been hampered by our limited understanding of host immune response for this fatal disease. To characterize the transcriptional signatures of host inflammatory response to SARS-CoV-2 (HCoV-19) infection, we carried out transcriptome sequencing of the RNAs isolated from the bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cells (PBMC) specimens of COVID-19 patients. Our results reveal distinct host inflammatory cytokine profiles to SARS-CoV-2 infection in patients, and highlight the association between COVID-19 pathogenesis and excessive cytokine release such as CCL2/MCP-1, CXCL10/IP-10, CCL3/MIP-1A, and CCL4/MIP1B. Furthermore, SARS-CoV-2 induced activation of apoptosis and P53 signalling pathway in lymphocytes may be the cause of patients’ lymphopenia. The transcriptome dataset of COVID-19 patients would be a valuable resource for clinical guidance on anti-inflammatory medication and understanding the molecular mechansims of host response.

ABSTRACTQuantitative real time PCR (RT-PCR) is widely used as the gold standard for clinical detection of SARS-CoV-2. However, due to the low viral load specimens and the limitations of RT-PCR, significant numbers of false negative reports are inevitable, which results in failure to timely diagnose, cut off transmission, and assess discharge criteria. To improve this situation, an optimized droplet digital PCR (ddPCR) was used for detection of SARS-CoV-2, which showed that the limit of detection of ddPCR is significantly lower than that of RT-PCR. We further explored the feasibility of ddPCR to detect SARS-CoV-2 RNA from 77 patients, and compared with RT-PCR in terms of the diagnostic accuracy based on the results of follow-up survey. 26 patients of COVID-19 with negative RT-PCR reports were reported as positive by ddPCR. The sensitivity, specificity, PPV, NPV, negative likelihood ratio (NLR) and accuracy were improved from 40% (95% CI: 27–55%), 100% (95% CI: 54–100%), 100%, 16% (95% CI: 13–19%), 0.6 (95% CI: 0.48–0.75) and 47% (95% CI: 33–60%) for RT-PCR to 94% (95% CI: 83–99%), 100% (95% CI: 48–100%), 100%, 63% (95% CI: 36–83%), 0.06 (95% CI: 0.02–0.18), and 95% (95% CI: 84–99%) for ddPCR, respectively. Moreover, 6/14 (42.9%) convalescents were detected as positive by ddPCR at 5–12 days post discharge. Overall, ddPCR shows superiority for clinical diagnosis of SARS-CoV-2 to reduce the false negative reports, which could be a powerful complement to the RT-PCR.

ABSTRACTDifferent primers/probes sets have been developed all over the world for the nucleic acid detection of SARS-CoV-2 by quantitative real time polymerase chain reaction (qRT-PCR) as a standard method. In our recent study, we explored the feasibility of droplet digital PCR (ddPCR) for clinical SARS-CoV-2 nucleic acid detection compared with qRT-PCR using the same primer/probe sets issued by Chinese Center for Disease Control and Prevention (CDC) targeting viral ORF1ab or N gene, which showed that ddPCR could largely minimize the false negatives reports resulted by qRT-PCR [Suo T, Liu X, Feng J, et al. ddPCR: a more sensitive and accurate tool for SARS-CoV-2 detection in low viral load specimens. medRxiv [Internet]. 2020;2020.02.29.20029439. Available from: https://medrxiv.org/content/early/2020/03/06/2020.02.29.20029439.abstract]. Here, we further stringently compared the performance of qRT-PCR and ddPCR for 8 primer/probe sets with the same clinical samples and conditions. Results showed that none of 8 primer/probe sets used in qRT-PCR could significantly distinguish true negatives and positives with low viral load (10−4 dilution). Moreover, false positive reports of qRT-PCR with UCDC-N1, N2 and CCDC-N primers/probes sets were observed. In contrast, ddPCR showed significantly better performance in general for low viral load samples compared to qRT-PCR. Remarkably, the background readouts of ddPCR are relatively lower, which could efficiently reduce the production of false positive reports.

Coastal bays, situated within Earth’s critical zone, play important ecological and socioeconomic roles. This study developed an integrated ecosystem health assessment framework based on ecosystem services specific to coastal bays, particularly exploring approaches to determine critical indicators and establish a reference benchmark. The framework was applied to two typical coastal bays (Jiaozhou Bay and Daya Bay) to ascertain significant health differences, subsequent challenges and prospective management. Comparatively, Daya Bay was healthier. Daya Bay received an overall comprehensive index ecosystem health score of 69.42 (good); however, its ecosystem services scores differed significantly (supporting services = 71.34, regulating services = 87.29, provisioning services = 3.59, cultural services = 74.30), indicating severe degradation in its ecosystem food provisioning function. Jiaozhou Bay received corresponding score of 55.79 (moderate), and its ecosystem services scores were relatively lower (supporting services = 63.31, regulating service = 54.30, provisioning services = 6.18, and cultural services = 54.74), indicating widespread ecosystem degradation. The health status of coastal bays is closely associated with both natural characteristics and human interventions. The narrow bay mouth of Jiaozhou Bay, its limited enclosed seawater area, and the intensive land reclamation that has taken place since the 1950s have directly or indirectly led to the low score of most of its indicators, particularly regarding the significant reductions in its water area and shoreline. The geological advantages of Daya Bay is its large area of water and that it is open to the outer sea, which have contributed to its comparatively healthier status, wherein scores of only a few indicators were bad (i.e., biological indicators of sensitive organisms in the upper food chain). Results from this study provide important information for prospective bay management. For Jiaozhou Bay, more effort should be paid to improving ecosystem health in a comprehensive way, particularly fishing control, land reclamation control and habitat restoration. For Daya Bay, overfishing should be better controlled, while more emphasis should be paid to protecting and restoring certain moderately specific habitats and species. For effective management, we highlight that ecosystem management strategies needs to be differentiated among different bays based on their significant natural and social features. Our approach provides a practical ecosystem health assessment tool that can be applied to other coastal bays to better inform sustainable management and conservation initiatives.

Long-term habitat shifts in marine fishes under climate change have been discussed over the last few decades. However, there is still a limited understanding of how fish distribution and biodiversity patterns will change in the offshore areas of China over time. In the present study, the potential distributions of 21 important marine fishes under current conditions and two climate change scenarios up to the 2050 s were projected using the maximum entropy (MaxEnt) model. The predicted habitat shifts were further used to observe how future environmental changes would affect communities. By the 2050 s, nine out of 21 fish species may have reduced habitats, which were considered as potential loser species in adapting to climate change, while the other 12 fish species were considered as winner species. The habitats of 20 species were predicted to move northward, with a mean habitat centroid shifting distance from 110 to 206.5 km. A novel discovery is that the Yangtze River Estuary is probably a geographical barrier for the northward migration of some species. An asymmetry in the habitat range shift was observed within the study region, wherein the leading edge moved 1° faster than the trailing edge. The Beibu Gulf, Pearl River Estuary, Southwest Taiwan Strait, and Yangtze River Estuary were identified as fish refuges, indicating that large river estuaries and upwelling systems may have positive effects on reducing the vulnerability of biological communities to climate change. At the community level, species richness would be reduced at lower latitudes, while it would be increased at higher latitudes, and species turnover was the main component of temporal beta diversity. Our study provides an informative outlook on the impact of climate change on the distribution and biodiversity of marine fish species in China, supporting the adaptive conservation and management of fish habitats.

Seagrass meadows provide important ecosystem services, but are among the least conserved marine ecosystems. The Southern bioregion of China has the nation’s largest seagrass distribution. However, lack of information on the distribution of seagrasses and the threats they face pose a significant obstacle to their conservation and restoration. Accordingly, a framework for prioritizing conservation and restoration objectives was proposed in the present study. First, we modeled the suitable habitats with MaxEnt, random forest (RF), and ensemble models to obtain a reliable basis map of seagrass distribution. A potentially suitable area of approximately 3,536–4,852 km2 was mapped in the coastal sea of South China, with the greatest area occurring between 18 °N and 22 °N. The anthropogenic pressures on the seagrass habitat were then estimated using an integrated exposure index consisting of four indicators, namely, population density, fishery economy, aquaculture, and shipping. The results indicated 48% of the coastal seas were under intensive anthropogenic pressures, with a higher exposure in the north than the south. The current conservation status suggests that there is a large seagrass conservation gap. By coupling the two dimensions of habitat suitability and integrated exposure, priority sites for seagrass management in South China were identified for the first time. Our work will not only provide basic information for coastal ecosystem management, but also serve as a tool to support the conservation and restoration planning of seagrass, thus, ultimately promoting the sustainability of seagrasses habitats.

Background/Aims Inflammatory bowel disease (IBD) is associated with considerable impairment of patients’ health-related quality of life (HRQoL). Knowledge of factors that significantly affect IBD patients’ HRQoL can contribute to better patient care. However, the HRQoL of IBD patients in non-Western countries are limited. Hence, we assessed the HRQoL of Singaporean IBD patients and identified its determinants. Methods A prospective, cross-sectional study was conducted at Singapore General Hospital outpatient IBD Centre. The HRQoL of IBD patients was assessed using the short IBD questionnaire (SIBDQ), Short Form-36 physical and mental component summary (SF-36 PCS/MCS) and EuroQol 5-dimensions 3-levels (EQ-5D-3L) and visual analogue scale (VAS). Independent samples t-test was used to compare HRQoL between Crohn’s disease (CD) and ulcerative colitis (UC). Determinants of HRQoL were identified through multiple linear regression. Results A total of 195 IBD patients (103 UC, 92 CD) with a mean disease duration of 11.2 years were included. There was no significant difference in HRQoL between patients with UC and CD. Factors that significantly worsened HRQoL were presence of active disease (b=−6.293 [SIBDQ], −9.409 [PCS], −9.743 [MCS], −7.254 [VAS]), corticosteroids use (b=−7.392 [SIBDQ], −10.390 [PCS], −8.827 [MCS]), poor medication adherence (b=−4.049 [SIBDQ], −1.320 [MCS], −8.961 [VAS]), presence of extraintestinal manifestations (b=−13.381 [PCS]), comorbidities (b=−4.531 [PCS]), non-employment (b=−9.738 [MCS], −0.104 [EQ-5D-3L]) and public housing (b=−8.070 [PCS], −9.207 [VAS]). Conclusions The HRQoL is impaired in this Asian cohort of IBD. The magnitude of HRQoL impairment was similar in UC and CD. Clinical characteristics were better determinants of patients’ HRQoL than socio-demographic factors. Recognizing the factors that impact patients’ HRQoL would improve the holistic management of IBD patients.

Tropical seagrass meadows and coral reefs often function as interconnected marine habitats, but they are often studied and managed as homogenous units. As macrohabitats, seagrass meadows provide important benefits to adjacent reef ecosystems by acting as natural filters of sediments and nutrients, and by providing critical feeding, nursery, and refuge habitats for reef fishes and other fauna. Whilst the macrohabitat functions of seagrass meadows have been often acknowledged, their microhabitats functions have largely been neglected. The purpose of the study is to explore how seagrass meadows provide multiple benefits to adjacent coral reefs through various microhabitat functions. The paper reveals some of the diversity of microhabitats that seagrass meadows contain, such as macroalgal mats, rubble cavities, sand patches with sparse seagrass, anemone gardens, hard substratum, and sponges mixed with seagrass. We highlight the ways in which reef creatures have diversified and specialized in using these different microhabitats, and postulate that seagrass microhabitat diversity enhances the habitat function and faunal diversity of seagrass meadows.

There are many challenges in biodiversity conservation, especially for migratory waterbirds because their survival depends on the availability of a suite of interconnected sites at different stages of their annual cycle. Due to habitat loss and degradation, the population of Baer’s Pochard (Aythya baeri), a migratory diving-duck, has declined to an extent that it has been listed as a critically endangered species by the IUCN Red List. To better understand the habitat requirements of this threatened waterbird for its effective conservation, we conducted seven years of field surveys within its historical distribution range in the East Asian–Australasian Flyway including China and neighbouring countries, covering 563 observation sites at 185 locations. Twelve new locations were identified as habitats for this species. By combining our surveys with literature and citizen science birding records, 171 Baer’s Pochard’s presence sites have classified as migratory stopovers, wintering grounds and breeding and potential breeding habitats. We then used Maxent model to estimate the potential distribution range and updated and refined the current IUCN distribution map. Finally, we identified the key conservation gaps by overlaying the distribution with a recent remotely acquired global landcover map. Our results show that: (1) The southernmost breeding site is about 1400 km south of its current IUCN breeding range; (2) the northern most wintering site is 800 km north of the IUCN wintering range; (3) Six newly discovered sites in Hebei, Henan, Shandong, Jiangxi and Hubei provinces, China are confirmed to be used all year round; (4) Most sites (81.8%) are not located in protected areas (PAs), and the majority of the suitable habitats (90%) are not protected by the current PA network. Our findings reveal that great changes have taken place in the distribution of Baer’s Pochard and that there are many distribution overlaps throughout its annual migration circle (e.g., many historical stopover sites become breeding habitats). Moreover, the key habitats have retreated into eastern Asia, and most of the habitats overlap with urban developed areas and are outside of current PA network. Our study suggests that the existing PA network may be less effective for the conservation of this critically endangered species under predicted global climate change, and other effective area-based conservation measures should be part of the conservation strategy. More importantly, as the distribution of Baer’s Pochard covers at least 15 countries, closely coordinated cross-border cooperation would be critical for its future survival.

Antibacterial and osteogenic functionalization of titanium (Ti) implants will greatly expand their clinical indications in immediate implant therapy, accelerate osteointegration, and enhance long-term prognosis. We had recently shown that the high-energy shot peening (HESP)-assisted micro-arc oxidation (MAO) significantly improved the bioactivity and coating stability of Ti-based substrates. In this study, we further functionalized Ti with antibacterial and osteogenic properties by doping silicon (Si) and/or copper (Cu) ions into HESP/MAO-treated coatings. Physicochemical characterization displayed that the doping of Si and Cu in HESP/MAO-treated coatings (Si/Cu-MAO) did not significantly change their surface topography, roughness, crystal structure, coating thickness, bonding strength, and wettability. The results of X-ray photoelectron spectroscopy (XPS) showed that Si and Cu in the Si/Cu-MAO coating was in the form of silicate radical (SiO32–) and bivalent copper (Cu2+), respectively. The total amounts of Si and Cu were about 13.5 and 5.8 μg/cm2, which released about 33.2 and 31.3% within 14 day, respectively. Compared with the control group (MAO), Si doping samples (MAO-Si) significantly increased the cell viability, alkaline phosphatase (ALP) activity, mineralization and osteogenic genes (ALP, collagen I and osteocalcin) expression of MC3T3-E1 cells. Furthermore, the addition of Cu presented good bactericidal property against both Staphylococcus aureus and Streptococcus mutans (even under the co-culture condition of bacteria and MC3T3-E1 cells): the bacteriostatic rate of both bacteria was over 95%. In conclusion, the novel bioactive Si/Cu-MAO coating with antibacterial and osteogenic properties is a promising functionalization method for orthopedic and dental implants, especially in the immediate implant treatment with an infected socket.

Background and aims: Aging-induced bone loss is a multifactorial, age-related, and progressive phenomenon among the general population and may further progress to osteoporosis and increase the risk of fractures. Cycloastragenol (CAG), currently the only compound reported that activates human telomerase, is thought to be able to alleviate or delay the symptoms of aging and chronic diseases. Previous research has suggested that CAG may have the potential to alleviate age-related bone loss. However, to date, no research has specifically focused on this aspect. In this study, we aimed to investigate whether CAG could prevent senile osteoporosis, and further reveal its underlying mechanism. Methods: CAG treatment was administrated into two bone loss rat models (D-galactose administration and aging) for 20 weeks and 33 weeks, respectively. Serum biomarkers analyses, bone biomechanical tests, micro-computed tomography assessment, and bone histomorphometry analyses were performed on the bone samples collected at the endpoint, to determine whether CAG could prevent or alleviate age-related bone loss. Proteomic analysis was performed to reveal the changes in protein profiles of the bones, and western blot was used to further verify the identity of the key proteins. The viability, osteoblastic differentiation, and mineralization of MC3T3-E1 cells were also evaluated after CAG treatment in vitro. Results: The results suggest that CAG treatment improves bone formation, reduces osteoclast number, alleviates the degradation of bone microstructure, and enhances bone biomechanical properties in both d-galactose- and aging-induced bone loss models. CAG treatment promotes viability, osteoblastic differentiation, and mineralization in MC3T3-E1 cells. Proteomic and western blot analyses revealed that CAG treatment increases osteoactivin (OA) expression to alleviate bone loss. Conclusion: The results revealed that CAG alleviates age-related bone loss and improves bone microstructure and biomechanical properties. This may due to CAG-induced increase in OA expression. In addition, the results support preclinical investigations of CAG as a potential therapeutic medicine for the treatment of senile osteoporosis.

Mangroves are important wetland ecosystems on tropical and subtropical coasts. There is an urgent need to better understand how the spatial distribution of mangroves varies with climate change factors. Species distribution models can be used to reveal the spatial change of mangroves; however, global models typically have a horizontal resolution of hundreds of kilometers and more than 1 km, even after downscaling. In the present study, a maximum entropy model was used to predict suitable areas for the northernmost mangroves in China in the 2050s. An approach was proposed to improve the resolution and credibility of suitability predictions by incorporating land-use potential. Predictions were made based on two CMIP6 scenarios (i.e., SSP1-2.6 and SSP5-8.5). The results show that the northern edge of the natural mangrove distribution in China would migrate from 27.20° N to 27.39° N–28.15° N, and the total extent of suitable mangrove habitats would expand. By integrating 30 m resolution land-use data to refine the model’s predictions, under the SSP1-2.6 scenario, the suitable habitats of mangroves are predicted to be 13,435 ha, which would increase by 33.9% compared with the current scenario. Under the SSP5-8.5 scenario, the suitable area would be 23,120 ha, with an increased rate of 96.5%. Approximately 40–44% of the simulated mangrove patches would be adjacent to aquacultural ponds, cultivated, and artificial land, which may restrict mangrove expansion. Collectively, our results showed how climate change and land use could influence mangrove distributions, providing a scientific basis for adaptive mangrove habitat management despite climate change.