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The application of DNA barcoding has been significantly limited by the scarcity of reliable specimens and inadequate coverage and replication across all species. The deficiency of DNA barcode reference coverage is particularly striking for highly biodiverse subtropical and tropical regions. In this study, we present a comprehensive barcode library for woody plants in tropical and subtropical China. Our dataset includes a standard barcode library comprising the four most widely used barcodes (rbcL, matK, ITS, and ITS2) for 2,520 species from 4,654 samples across 49 orders, 144 families, and 693 genera, along with 79 samples identified at the genus level. This dataset also provides a super-barcode library consisting of 1,239 samples from 1,139 species, 411 genera, 113 families, and 40 orders. This newly developed library will serve as a valuable resource for DNA barcoding research in tropical and subtropical China and bordering countries, enable more accurate species identification, and contribute to the conservation and management of tropical and subtropical forests. [ABSTRACT FROM AUTHOR]

The identification of additional Echinococcus granulosus sensu lato (s.l.) complex species/genotypes in recent years raises the possibility that there might be more variation among this species in China than is currently understood. The aim of this study was to explore intra- and inter-species variation and population structure of Echinococcus species isolated from sheep in three areas of Western China. Of the isolates, 317, 322, and 326 were successfully amplified and sequenced for cox1, nad1, and nad5 genes, respectively. BLAST analysis revealed that the majority of the isolates were E. granulosus s.s., and using the cox1, nad1, and nad5 genes, respectively, 17, 14, and 11 isolates corresponded to Elodea canadensis (genotype G6/G7). In the three study areas, G1 genotypes were the most prevalent. There were 233 mutation sites along with 129 parsimony informative sites. A transition/transversion ratio of 7.5, 8, and 3.25, respectively, for cox1, nad1, and nad5 genes was obtained. Every mitochondrial gene had intraspecific variations, which were represented in a star-like network with a major haplotype with observable mutations from other distant and minor haplotypes. The Tajima's D value was significantly negative in all populations, indicating a substantial divergence from neutrality and supporting the demographic expansion of E. granulosus s.s. in the study areas. The phylogeny inferred by the maximum likelihood (ML) method using nucleotide sequences of cox1–nad1–nad5 further confirmed their identity. The nodes assigned to the G1, G3, and G6 clades as well as the reference sequences utilized had maximal posterior probability values (1.00). In conclusion, our study confirms the existence of a significant major haplotype of E. granulosus s.s. where G1 is the predominant genotype causing of CE in both livestock and humans in China. [ABSTRACT FROM AUTHOR]

To explore the relationship between physical exercise and smoking behavior among Chinese residents aged 16 years and older. Analysis based on 29,466 validated cases in the 2018 China Family Panel Studies (CFPS 2018). The chi-square test and Mann–Whitney U test were used for comparative analysis between groups. Logistic regression analysis was used to explore the relationship between physical exercise and smoking behavior. Gender and birth cohort differences in the relationship between physical exercise and smoking behavior were explored based on stratified regression analysis using gender and birth cohort as stratified variables, respectively. Robustness testing based on multiple linear regression analysis using a replacement data approach. There were 8735 cases of smokers among the respondents. After controlling for relevant confounders, there was a significant negative association between physical exercise and smoking behavior among residents [OR 0.718, 95% CI (0.673, 0.765), P < 0.01]. Physical exercise was more significantly associated with smoking behavior among male residents [OR 0.694, 95% CI (0.649, 0.743), P < 0.01], while it was not significantly associated with smoking behavior among female residents [OR 0.901, 95% CI (0.743, 1.093), P > 0.05]. Physical exercise was more significantly associated with smoking behavior in the pre-1948 (OR 0.748), 1959–1968 (OR 0.748), 1969–1978 (OR 0.812), 1989–1998 (OR 0.576) and post-1999 (OR 0.411) birth cohorts, and the association decreased over time and with social change. The results of the robustness test showed that frequency of exercise was significantly and negatively associated with smoking behavior among residents [OR 0.961, 95% CI (0.951, 0.970), P < 0.01]. Physical exercise is negatively associated with smoking behavior among Chinese residents aged 16 years and older, especially among male residents. There is a cohort effect between physical exercise and smoking behavior of the population, that is, the relationship between the two decreases with social change. [ABSTRACT FROM AUTHOR]

Symbiotic microbiomes of Sphagnum have been confirmed to play a fundamental role in carbon and nitrogen cycles, however, little is known about microbiomes associated with other bryophytes in subtropical peatland ecosystems. To explore the differences in community structure, metabolic potential and interaction relationship of bacterial microbiomes associated with different bryophytes species, the gametophytes of three bryophyte species (Sphagnum palustre, Aulacomnium androgynum, and Polytrichum commune) and their underlying peat sediments were collected from the subtropical Dajiuhu Peatland and subjected to Illumina high-throughout sequencing of 16S rRNA gene. Results showed that bacterial diversity was lowest in S. palustre, the dominant moss species, among the three moss species investigated in Dajiuhu Peatland. Bacterial communities from bryophytes clearly separated with those from sediments as indicated by both phylogenetic and taxonomical approaches. Linear discriminant analysis effect size (LEfSe) identified 30 and 36 indicator taxa in mosses and peat sediments. Bacteroidetes, Verrucomicrobia and Thermoleophilia significantly enriched in S. palustre, A. androgynum and P. commune, Chloroflexi, Proteobacteria and Acidobacteria subgroup 6 was indicator taxa for corresponding underlying sediments, respectively. Despite of these differences in compositions, bacterial functional structures were similar among all bryophytes, such as abundant aerobic heterotrophs, rare nitrifiers and denitrifiers. This phenomenon was also observed among the underlying sediments. Network analysis indicated that Proteobacteria and Acidobacteria located in the center of network and exerted strong interactions to other taxa. The sub-network of bacterial communities in sediments was more connected and microbial groups were more competitive than those in bryophytes subnetwork. Our results offer new insight into the community structure, ecological function and interaction pattern of bacterial microbiomes in the Dajiuhu Peatland across different habitats. [ABSTRACT FROM AUTHOR]

In the "treat all" era, the high rate of late HIV diagnosis (LHD) worldwide remains an impediment to ending the HIV epidemic. In this study, we analyzed LHD in newly diagnosed people living with HIV (PLWH) and its impact on HIV transmission in Northeast China. Sociodemographic information, baseline clinical data, and plasma samples obtained from all newly diagnosed PLWH in Shenyang, the largest city in Northeast China, between 2016 and 2019 were evaluated. Multivariate logistic regression analysis was performed to identify risk factors associated with LHD. A molecular network based on the HIV pol gene was constructed to assess the risk of HIV transmission with LHD. A total of 2882 PLWH, including 882 (30.6%) patients with LHD and 1390 (48.2%) patients with non-LHD, were enrolled. The risk factors for LHD were older age (≥ 30 years: p <.01) and diagnosis in the general population through physical examination (p <.0001). Moreover, the molecular network analysis revealed that the clustering rate (p <.0001), the fraction of individuals with ≥ 4 links (p =.0847), and the fraction of individuals linked to recent HIV infection (p <.0001) for LHD were significantly or marginally significantly lower than those recorded for non-LHD. Our study indicates the major risk factors associated with LHD in Shenyang and their limited contribution to HIV transmission, revealing that the peak of HIV transmission of LHD at diagnosis may have been missed. Early detection, diagnosis, and timely intervention for LHD may prevent HIV transmission. [ABSTRACT FROM AUTHOR]

Bathyarchaeota are believed to have roles in the carbon cycle in marine systems. However, the ecological knowledge of Bathyarchaeota is limited in peatland ecosystems. Here, we investigated the vertical distribution of Bathyarchaeota community structure using quantitative PCR and high-throughput sequencing technology of ribosomal 16S rRNA gene integrated with detailed chemical profiling in the Dajiuhu Peatland, central China. Eight archaeal phyla were observed in peat samples, which mainly composed of Bathyarchaeota with a mean relative abundance about 88%, followed by Thaumarchaeota (9%). Bathyarchaeota were further split into 17 subgroups, and some subgroups showed habitat specificity to peat horizons with distinct lithological and physicochemical properties, for example, Bathy-6 and Bathy-15 had preference for the acrotelm, Bathy-5b, Bathy-16, and Bathy-19 were enriched in the catotelm, Bathy-5a, Bathy-8, and Bathy-11 were specific for the clay horizon. This spatial distribution pattern of archaeal communities along peat profile was mainly influenced by water content as indicated by RDA ordination and permutational MANOVA, whereas organic matter content exclusively affected Bathyarchaeota distribution along the peat profile significantly. The abundance of archaeal 16S rRNA genes ranged from 105 to 107 copies per gram dry sediment, and the highest archaeal biomass was observed in the periodically oxic mesotelm horizon with more dynamic archaeal interaction relationship as indicated by the network analysis. Bathyarchaeota dominated the archaeal interaction network with 82% nodes, 96% edges, and 71% keystone species. Our results provide an overview of the archaeal population, community structure, and relationship with environmental factors that affect the vertical distribution of archaeal communities and emphasize the ecology of bathyarchaeotal lineages in terrestrial peatland ecosystems. [ABSTRACT FROM AUTHOR]

Parasitic infection is one of the many challenges facing livestock production globally. Cysticercosis tenuicollis is a common parasitic disease in domestic and wild ruminants (intermediate host) caused by the larval stage of Taenia hydatigena that primarily infects dogs (definitive host). Although genetic studies on this parasite exist, only a few describe the genetic variation of this parasite in Mongolia. Our aim was thus, to identify the mitochondrial differences in ovine isolates of Cysticercus tenuicollis entering China from Mongolia and comparison with existing Chinese isolates from sheep and goats based on the recently described PCR–RFLP method and mitochondrial genes of NADH dehydrogenase subunit 4 (nad4) and the NADH dehydrogenase subunit 5 (nad5). Sixty-nine isolates were collected during routine veterinary meat inspections from sheep that originated from Mongolia, at the modern slaughterhouses in Erenhot City, Inner Mongolia. Additional 114 cysticerci were also retrieved from sheep and goats from northern (Inner Mongolia Autonomous Region, Ningxia Hui Autonomous Region, and Gansu Province), western (Tibet Autonomous Region), and southern (Jiangxi Province and Guangxi Province) China. The PCR–RFLP approach of the nad5 showed nine mitochondrial subclusters A1, A2, A3, A5, A8, A9, A10, A11, and B of T. hydatigena isolates from sheep and goats from Mongolia and China. Meanwhile, haplogroup A1 RFLP profile was more widespread than other variants. These data supplements existing information on the molecular epidemiology of T. hydatigena in China and Mongolia and demonstrate the occurrence of similar genetic population structures in both countries. [ABSTRACT FROM AUTHOR]

Purpose: Chronic granulomatous disease (CGD) is the most common phagocyte defect disease. Here, we describe 114 CGD patients in our center and report a rare female infant with XL-CGD to provide a better understanding of diagnosis, treatment, and prenatal diagnosis of CGD. Method: Patients were diagnosed by DHR-1,2,3 flow cytometry assays and gene analysis. X chromosome inactivation analysis and gp91phox protein test were used for a female infant with XL-CGD. Results: XL-CGD accounts for the majority of cases in China and results in higher susceptibility to some infections than AR-CGD. The DHR assay can help diagnose CGD quickly, and atypical results should be combined with clinical manifestations, genetic analysis, and regular follow-up. For prenatal diagnosis, both gDNA and cDNA genotypes of amniotic fluid cells should be identified, and cord blood DHR assays should be performed to identify female XL-CGD patients. [ABSTRACT FROM AUTHOR]

To investigate the vertical variation of microbial functional groups particular nitrogen fixers and ammonia oxidizers, sediment samples from a 155 cm deep peat profile were collected from the acidic Dajiuhu Peatland and subsequently subjected to clone library construction and quantification. Results showed that nifH gene abundance varied between 105–108 copies per gram dry sediment and reduced gradually with depth. The abundances of ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) abundance were generally comparable in each sample. More AOA was observed with a depth ≤55 cm, whereas AOB was more abundant with a depth >55 cm. Phylogenetically nifH could be divided into 94 OTUs which mainly affiliated with α-Proteobacteria. AOA were affiliated with Nitrosotalea from Group 1.1a associated (nearly 90%) and Nitrososphaera from Group I.1b. All AOB belonged to Nitrosospira. Notably, DJH11 with the depth of 50–55 cm was observed to have the highest abundance and the highest diversity of nitrogen fixers and ammonia oxidizers among all the samples. Pearson's correlation analysis showed a positive relationship between water content and pH with the nifH gene abundance. Our results offer the first insight about the microbial community composition and diversity involved in nitrogen cycles in the Dajiuhu Peatland. [ABSTRACT FROM AUTHOR]

Purpose: Chronic granulomatous disease (CGD) is an inherited disorder, with phagocytes failing to produce antimicrobial superoxide due to deficient NADPH oxidase activity. Mutations in the gene encoding CYBB are responsible for the majority of the CGD cases. To date, there have been no reports on large samples of children with CGD in China. Therefore, in this study, we described the clinical and molecular features of 38 suspected CGD patients from 36 unrelated Chinese families. Methods: Clinical diagnosis was performed using dihydrorhodamine assays detected by flow cytometry. Molecular analysis was used to identify underlying CGD-causative genes. Results: The mean age of onset in our 38 patients was 3.4 months, while the mean age at diagnosis was 31.7 months. Apart from recurrent pneumonia and abscesses, tuberculosis (TB) and Bacille Calmette-Guerin (BCG) infections were notable features in our cohort. Overall, 17 cases died and patient 1 did not participate in the follow-up period . In total, we identified 29 different CYBB gene mutations in 31 patients. We found NCF1 and CYBA mutations in 3 and 2 patients, respectively. In addition, we identified 31 carriers and prenatally diagnosed 4 CGD and 4 healthy fetuses. Conclusions: The results of our study demonstrate that children with BCG infections or recurrent TB infections should have immune function screening tests performed. Moreover, newborns with family histories of primary immunodeficiency diseases should avoid of BCG vaccination. Molecular analysis is an important tool for identifying patients, carriers, and high-risk CGD fetuses. [ABSTRACT FROM AUTHOR]

Doctoral graduate research performance (DRP) is recognized as one of the most critical indices for evaluation of the success of doctoral education. Doctoral graduates with high research performance directly reflect a higher ability in academic research and academic achievement. Consequently, identifying which factors influence DRP is potentially of great value. This topic is also challenging because of difficulties in identifying the impact factors on research performance and the feasibility of the relative data collection. This paper first examines the relationships between the indicators and DRP. After a review of previous literature, the focus is on the doctoral graduates' individual factors, advisor factors and learning performance. Data is collected from graduated doctors from the Science Schools of University of Science and Technology of China (USTC). Contrary to expectations, our findings indicate that, based on the Chinese context, learning performance does not appear to be strongly associated with research performance. Individual factors (status of academic origin) do have significant effect on DRP. The advisor factors (including academic status, academic experience and allocation of energy) show a relatively strong association with DRP, in terms of both the number of publications and the impact factor of Science Citation Index (SCI) cited journals. [ABSTRACT FROM AUTHOR]