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Anthocyanin is one important nutrition composition in Tartary buckwheat (Fagopyrum tataricum) sprouts, a component missing in its seeds. Although anthocyanin biosynthesis requires light, the mechanism of light-induced anthocyanin accumulation in Tartary buckwheat is unclear. Here, comparative transcriptome analysis of Tartary buckwheat sprouts under light and dark treatments and biochemical approaches were performed to identify the roles of one B-box protein BBX22 and ELONGATED HYPOCOTYL 5 (HY5). The overexpression assay showed that FtHY5 and FtBBX22 could both promote anthocyanin synthesis in red-flower tobacco. Additionally, FtBBX22 associated with FtHY5 to form a complex that activates the transcription of MYB transcription factor genes FtMYB42 and FtDFR, leading to anthocyanin accumulation. These findings revealed the regulation mechanism of light-induced anthocyanin synthesis and provide excellent gene resources for breeding high-quality Tartary buckwheat. [ABSTRACT FROM AUTHOR]

The red panda (Ailurus fulgens) is a distinctive mammal known for its reliance on a diet primarily consisting of bamboo. The gut microbiota and overall health of animals are strongly influenced by diets and environments. Therefore, conducting research to explore the taxonomical and functional variances within the gut microbiota of red pandas exposed to various dietary and environmental conditions could shed light on the dynamic complexities of their microbial communities. In this study, normal fecal samples were obtained from red pandas residing in captive and semi‐free environments under different dietary regimes and used for metabolomic, 16S rRNA, and metagenomic sequencing analysis, with the pandas classified into four distinct cohorts according to diet and environment. In addition, metagenomic sequencing was conducted on mucus fecal samples to elucidate potential etiological agents of disease. Results revealed an increased risk of gastrointestinal diseases in red pandas consuming bamboo shoots due to the heightened presence of pathogenic bacteria, although an increased presence of microbiota‐derived tryptophan metabolites appeared to facilitate intestinal balance. The red pandas fed bamboo leaves also exhibited a decrease in gut microbial diversity, which may be attributed to the antibacterial flavonoids and lower protein levels in leaves. Notably, red pandas residing in semi‐free environments demonstrated an enriched gut microbial diversity. Moreover, the occurrence of mucus secretion may be due to an increased presence of species associated with diarrhea and a reduced level of microbiota‐derived tryptophan metabolites. In summary, our findings substantiate the influential role of diet and environment in modulating the gut microbiota of red pandas, offering potential implications for improved captive breeding practices. [ABSTRACT FROM AUTHOR]

Purpose: This study conducted an phenotypic and whole-genome sequencing analysis with Klebsiella aerogenes to elucidate its clinical epidemiological characteristics, antimicrobial resistance (AMR) phenotype, biofilm formation ability and hemolytic activity testing, AMR genes and phylogenetic relationships, so as to provide a further understanding of the intra-hospital strain transmission. Methods: Samples were collected from a hospital in Beijing between 2020 and 2022. All strains underwent bacterial identification, antimicrobial susceptibility testing (AST) using the VITEK-2 compact system. Biofilm formation ability and hemolytic activity were tested. Second-generation sequencing was applied to all strains, with those carrying the blaKPC gene were selected for third-generation sequencing. Whole-genome analysis identified resistance genes, plasmid types, MLST typing, and phylogenetic relationships. Plasmids were assembled to detect plasmid structures and AMR gene location. Results: Among the 42 K. aerogenes isolates, 21 were carbapenem-resistant K. aerogenes (CRKA). All strains exhibited strong biofilm formation and no hemolytic activity. Most were sourced from sputum (83.3%). CRKA demonstrated extensive resistance to antibiotics, particularly β-lactamase inhibitors and Cefotetan. This resistance pattern was closely associated with the presence of an IncFII(pHN7A8) plasmid, which carried multiple resistance genes, including blaKPC-2, blaCTX-M-65, blaTEM-1, rmtB and a large number of mobile elements. The majority of CRKA strains clustered within the same branch of the phylogenetic tree, exhibiting minimal single nucleotide polymorphism (0– 13 SNPs) differences, and they shared the same sequence type (ST292), resistance genes, and plasmids, originating from different departments, suggesting clonal transmission among the hospital. Conclusion: Our research reveals that the clonal transmission of CRKA occurs across various departments within the hospital. The widespread resistance observed in CRKA, attributed to the presence of blaKPC and ESBLs genes, underscores the need for heightened vigilance to prevent the further dissemination of CRKA within the hospital and, potentially, throughout the wider community. [ABSTRACT FROM AUTHOR]

Hypersaline lakes in arid and semi-arid areas are unique ecosystems that harbour unique extremophile organisms such as Artemia , the paradigmatic example of adaptation to harsh living conditions. We assessed the mitogenomic biodiversity of Artemia species from the Tibetan Plateau, China, a remote and yet minimally disturbed ecosystem with a variety of hypersaline lakes. Analysis of ten Tibetan salt lakes demonstrated the occurrence of two regionally endemic species, Artemia tibetiana and Artemia sorgeloosi , with the latter being the dominant species with eight localities. Both species coexist in Jingyu and Jibu lakes, representing the first case of natural distribution overlap between sexual Artemia species. Artemia sorgeloosi exhibits higher genetic diversity and interpopulation differences, a result consistent with the heterogeneity of local salt lakes, local Artemia population demographics, and their adaptive potentials. Significant F ST values demonstrate a gene flow barrier between A. sorgeloosi populations that is compatible with an 'island biogeography' distribution pattern, making the Tibetan Plateau a sort of natural laboratory to study intraspecific population differences. Artemia sorgeloosi and the exotic Artemia franciscana were found coexisting in Yangnapen Lake, demonstrating the ability of this invasive species to colonize high-altitude inland habitats, and the need to monitor its presence and eventual expansion. [ABSTRACT FROM AUTHOR]

Tartary buckwheat (Fagopyrum tataricum) is an important plant, utilized for both medicine and food. It has become a current research hotspot due to its rich content of flavonoids, which are beneficial for human health. Anthocyanins (ATs) and proanthocyanidins (PAs) are the two main kinds of flavonoid compounds in Tartary buckwheat, which participate in the pigmentation of some tissue as well as rendering resistance to many biotic and abiotic stresses. Additionally, Tartary buckwheat anthocyanins and PAs have many health benefits for humans and the plant itself. However, little is known about the regulation mechanism of the biosynthesis of anthocyanin and PA in Tartary buckwheat. In the present study, a bHLH transcription factor (TF) FtTT8 was characterized to be homologous with AtTT8 and phylogenetically close to bHLH proteins from other plant species. Subcellular location and yeast two-hybrid assays suggested that FtTT8 locates in the nucleus and plays a role as a transcription factor. Complementation analysis in Arabidopsis tt8 mutant showed that FtTT8 could not recover anthocyanin deficiency but could promote PAs accumulation. Overexpression of FtTT8 in red-flowering tobacco showed that FtTT8 inhibits anthocyanin biosynthesis and accelerates proanthocyanidin biosynthesis. QRT-PCR and yeast one-hybrid assay revealed that FtTT8 might bind to the promoter of NtUFGT and suppress its expression, while binding to the promoter of NtLAR and upregulating its expression in K326 tobacco. This displayed the bidirectional regulating function of FtTT8 that negatively regulates anthocyanin biosynthesis and positively regulates proanthocyanidin biosynthesis. The results provide new insights on TT8 in Tartary buckwheat, which is inconsistent with TT8 from other plant species, and FtTT8 might be a high-quality gene resource for Tartary buckwheat breeding. [ABSTRACT FROM AUTHOR]

Omega-3 (n-3) and omega-6 (n-6) polyunsaturated fatty acids (PUFAs) play critical roles in human health. Prior genome-wide association studies (GWAS) of n-3 and n-6 PUFAs in European Americans from the CHARGE Consortium have documented strong genetic signals in/near the FADS locus on chromosome 11. We performed a GWAS of four n-3 and four n-6 PUFAs in Hispanic American (n = 1454) and African American (n = 2278) participants from three CHARGE cohorts. Applying a genome-wide significance threshold of P < 5 × 10−8, we confirmed association of the FADS signal and found evidence of two additional signals (in DAGLA and BEST1) within 200 kb of the originally reported FADS signal. Outside of the FADS region, we identified novel signals for arachidonic acid (AA) in Hispanic Americans located in/near genes including TMX2, SLC29A2, ANKRD13D and POLD4, and spanning a > 9 Mb region on chromosome 11 (57.5 Mb ~ 67.1 Mb). Among these novel signals, we found associations unique to Hispanic Americans, including rs28364240, a POLD4 missense variant for AA that is common in CHARGE Hispanic Americans but absent in other race/ancestry groups. Our study sheds light on the genetics of PUFAs and the value of investigating complex trait genetics across diverse ancestry populations. A genome-wide association study highlights the shared or unique genetic etiology of polyunsaturated fatty acids across diverse ancestry groups. [ABSTRACT FROM AUTHOR]

Human adenovirus (HAdV) is a highly virulent respiratory pathogen that poses clinical challenges in terms of diagnostics and treatment. Currently, no effective therapeutic drugs or prophylactic vaccines are available for HAdV infections. One factor contributing to this deficiency is that existing animal models, including wild‐type and single‐receptor transgenic mice, are unsuitable for HAdV proliferation and pathology testing. In this study, a tri‐receptor transgenic mouse model expressing the three best‐characterized human cellular receptors for HAdV (hCAR, hCD46, and hDSG2) was generated and validated via analysis of transgene insertion, receptor mRNA expression, and protein abundance distribution. Following HAdV‐7 infection, the tri‐receptor mice exhibited high transcription levels at the early and late stages of the HAdV gene, as well as viral protein expression. Furthermore, the tri‐receptor mice infected with HAdV exhibited dysregulated cytokine responses and multiple tissue lesions. This transgenic mouse model represents human HAdV infection and pathogenesis with more accuracy than any other reported animal model. As such, this model facilitates the comprehensive investigation of HAdV pathogenesis as well as the evaluation of potential vaccines and therapeutic modalities for HAdV. [ABSTRACT FROM AUTHOR]

Tartary buckwheat (Fagopyrum tataricum Gaertn.) belongs to the family of Polygonaceae and is used as a multi-functional plant. R2R3-MYB transcription factors play a crucial part in plant growth and are involved in many biological processes where they regulate their internal environment. To date, there is no documented systematic research on the R2R3-MYB gene family in Tartary buckwheat. Here, domain features, chromosomal location, motif prediction, gene structure, cis-acting elements, as well as the expression pattern of R2R3-MYB transcription factors were analyzed comprehensively in Tartary buckwheat using a bioinformatic approach. Additionally, one R2R3-MYB gene was verified by transgenic Arabidopsis. Results indicate that a total of 152 R2R3-MYB genes were identified with special R2R3 domains and were distributed on 8 chromosomes of Tartary buckwheat. They were further classified into 25 sub-categories via phylogenetic analysis in terms of the R2R3-MYB gene family classification principles of Arabidopsis thaliana. This classification was further supported by analysis of exon–intron structure, motif, and cis-elements. Tandem and segmental duplication existed among the R2R3-MYB gene family of Tartary buckwheat, and there were 5, 8, 27, and 36 FtR2R3-MYB homologous genes, respectively, when comparing with Zea mays, Oryza sativa, Arabidopsis thaliana, and Solanum melongena by synteny analysis. The expression pattern of FtR2R3-MYB genes in different tissue and under salt stress and different light condition showed that members had tissue-specific expression levels and that these members may play diverse functions in plant growth and adaptation to varying environments. In addition, one of the FtR2R3-MYB gene families, FtMYB43, a homologue of AtTT2, clustered with R2R3-MYB from other plant species, which were reported to be involved in the regulation of anthocyanin or proanthocyanidin biosynthesis. This gene was located in the nucleus, and had transcriptional activation activity, indicating that FtMYB43 may be a positive transcript factor of anthocyanin or proanthocyadin biosynthesis. Moreover, the function of FtMYB43 was further verified to improve the production of anthocyanin in transgenic Arabidopsis by overexpression, and qRT-PCR assay implied that FtMYB43 may regulate the expression levels of most structural genes of the anthocyanin biosynthesis pathway in Arabidopsis seedlings. These results provide more insights into the structure and function of the R2R3-MYB gene family and may accelerate the breeding of ornamental buckwheat cultivars. [ABSTRACT FROM AUTHOR]

Linoleic acid (LA) is a primary n-6 polyunsaturated fatty acid (PUFA), which is of interest to nutritional professionals as it has been associated with health outcomes. However, as some LA-rich foods offer protection against chronic diseases such as CVD (e.g., fatty fish), while others increase risk (e.g., red meat), the individual foods contributing to LA intake may be an important factor to consider. Therefore, this analysis sought to examine whether there are racial/ethnic differences in the proportion of overall LA intake accounted for by individual food groups, via a cross-sectional analysis of 3815 adults participating in the National Health and Nutrition Examination Survey (NHANES; 2017–2018 cycle). Separate multivariable linear regressions models specified the proportion of overall LA intake attributable to each of the nine food groups (dairy, eggs, fat, fish, fruits and vegetables, grains, meat, nuts, and sweets) as the outcome, and race/ethnicity as the predictor, with age, gender, and socioeconomic status (SES) as covariates, in order to estimate whether there were mean differences by race/ethnicity in the proportion of overall LA intake attributable to each of these foods seperately. After a Bonferroni correction for multiple testing, eggs, grains, fruits and vegetables, meat, and fish each accounted for a different proportion of overall LA intake according to racial/ethnic grouping (all p < 0.006 after a Bonferroni correction). These findings indicate the food sources of LA in the diet differ by race/ethnicity, and warrant future investigations into whether this plays a role in health disparities. [ABSTRACT FROM AUTHOR]

Species of Artemia are regionally endemic branchiopod crustaceans composed of sexual species and parthenogenetic lineages, and represent an excellent model for studying adaptation and speciation to extreme and heterogeneous hypersaline environments. We tested hypotheses of whether populations from the Tibetan Plateau belong to A. tibetiana Abatzopoulos, Zhang & Sorgeloos,1998 and whether a population from Kazakhstan is a new species, using other Asian species of Artemia as outgroups. We conducted a multitrait phylogenetic study based on the complete mitogenome, mitochondrial (COI, 12S, 16S) and nuclear (microsatellites, ITS1) markers, and a suit of uni- and multivariate morphological traits. Our results led to the discovery of two new species, one from the Tibetan Plateau (Haiyan Lake) in China (Artemia sorgeloosi n. sp.) and a second from Kazakhstan (Artemia amati n. sp.). Our analysis demonstrate that A. tibetiana and A. amati n. sp. are monophyletic, whereas A. sorgeloosi n. sp. , and A. tibetiana are polyphyletic. Evolutionary relationships based on mitochondrial and nSSR markers suggest that A. tibetiana may have arisen from a past hybridization event of a maternal ancestor of A. tibetiana with A. sorgeloosi n. sp. or its ancestor. We present the complete mitogenome of A. tibetiana , A. amati n. sp. , and A. sorgeloosi n. sp. We also provide a novel taxonomic identification key based on morphology, emphasizing the phenotype as a necessary component of the species concept. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome (mitogenome) of the soft coral Sinularia acuta Manuputty and van Ofwegen, 2007 was sequenced and annotated using Illumina next-generation sequencing (NGS). The mitogenome of S. acuta was 18,730 bp in length and consisted of 14 protein-coding genes (PCGs), two ribosomal RNA genes (rRNA), and only one transfer RNA gene (tRNA-Met). The base composition was 30.18% A, 16.46% C, 19.35% G, and 34.00% T, with a total A + T content of 64.19%. The phylogenetic analysis demonstrated a close evolutionary relationship among Sinularia acuta, Sinularia penghuensis, and Sinularia maxima. [ABSTRACT FROM AUTHOR]

Application of microRNA-mediated mRNA expression in treatment of diverse cancers has been documented. The current study was explored to study the role of miR-217 in breast cancer (BC) progression and the related downstream factors. Clinical tissue samples, BC cell lines and the established xenograft models were prepared for ectopic expression and depletion experiments to discern the regulatory roles of miR-217-mediated NF1 in BC cell proliferation, metastasis and chemoresistance as well as tumorigenic ability of BC cells in nude mice. miR-217 was upregulated in BC, which was a predictor of poor prognosis of BC patients. NF1 could be targeted by miR-217. miR-217 promoted malignant characteristics of BC cells through enhancing ATF3-MMP13 interaction by inhibiting NF1. miR-217 repressed sensitivity against anti-cancer drugs by inducing autophagy of BC cells through the NF1/HSF1/ATG7 axis. Also, miR-217 could inhibit NF1 to facilitate tumorigenic ability of BC cells in vivo. Our study emphasized that miR-217 could potentially inhibit NF1 expression to activate the c-Jun, thus enhancing the expression and interaction of ATF3/MMP13 and promoting the malignant features of BC cells. Furthermore, miR-217 conferred chemoresistance on BC by enhancing BC cell autophagy, which was achieved by limiting NF1 expression to induce the HSF1/ATG7 pathway. [ABSTRACT FROM AUTHOR]

Human adenoviruses (HAdVs) can cause acute respiratory diseases (ARDs) worldwide, and HAdV‐55 is a reemergent pathogen in recent years. In the study, we investigated an outbreak of ARD at a school due to HAdV‐55 in Beijing, China, during the early outbreak of coronavirus disease 2019 (COVID‐19). The epidemic prevention team was dispatched to the school to collect epidemiologic data and nasopharyngeal samples. Then, real‐time reverse transcription polymerase chain reaction (PCR) and multiplex PCR assays were used to detect severe acute respiratory syndrome coronavirus 2 and other respiratory pathogens, respectively. One representative HAdV‐55 isolate was selected and submitted for whole‐genome sequencing using a MiSeq system and the whole‐genome phylogenetic tree was conducted based on the maximum likelihood method. The outbreak lasted from January 27 to February 6, 2020, and 108 students developed fever, among whom 60 (55.56%) cases were diagnosed with HAdV‐55 infection in the laboratory using real‐time PCR and 56 cases were hospitalized. All the confirmed cases had a fever and 11 cases (18.33%) presented with a fever above 39°C. Other main clinical symptoms included sore throat (43.33%) and headache (43.33%). We obtained and assembled the full genome of one isolate, BJ‐446, with 34 761 nucleotides in length. HAdV‐55 isolate BJ‐446 was 99.85% identical to strain QS‐DLL, which was the first HAdV‐55 strain in China isolated from an ARD outbreak in Shanxi in 2006. One and four amino acid mutations were observed in the hexon gene and the coding region of L2 pV 40.1 kDa protein, respectively. We identified the first HAdV‐55 infection associated with the ARD outbreak in Beijing since the emergence of COVID‐19. The study suggests that improved surveillance of HAdV is needed, although COVID‐19 is still prevalent in the world. [ABSTRACT FROM AUTHOR]

Antimicrobial resistance of Shigella sonnei has become a global concern. Here, we report a phylogenetic group of S. sonnei with extensive drug resistance, including a combination of multidrug resistance, coresistance to ceftriaxone and azithromycin (cefRaziR), reduced susceptibility to fluoroquinolones, and even colistin resistance (colR). This distinct clone caused six waterborne shigellosis outbreaks in China from 2015 to 2020. We collect 155 outbreak isolates and 152 sporadic isolates. The cefRaziR isolates, including outbreak strains, are mainly distributed in a distinct clade located in global Lineage III. The outbreak strains form a recently derived monophyletic group that may have emerged circa 2010. The cefRaziR and colR phenotypes are attributed to the acquisition of different plasmids, particularly the IncB/O/K/Z plasmid coharboring the blaCTX-M-14, mphA, aac(3)-IId, dfrA17, aadA5, and sul1 genes and the IncI2 plasmid with an mcr-1 gene. Genetic analyses identify 92 accessory genes and 60 single-nucleotide polymorphisms associated with the cefRaziR phenotype. Surveillance of this clone is required to determine its dissemination and threat to global public health. Shigella sonnei is a major contributor to the global burden of dysenteric diarrhoea in developed countries. In this work, authors report a S. sonnei clone which has caused numerous waterborne shigellosis outbreaks in China from 2015 to 2020. [ABSTRACT FROM AUTHOR]

To survey the virulence gene carrying status, drug sensitivity, and genetic characteristics of Vibrio parahaemolyticus, 26 seafood samples from three canteens in the Beidaihe area, as well as self-collected samples, were analyzed in August 2021. Four major virulence genes (tdh, trh, tlh, and toxR) were screened from ten strains of V. parahaemolyticus using PCR and the BD automatic microbial identification and drug susceptibility analysis system. Next-generation genome sequencing was performed on the isolates. A phylogenetic tree, drug resistance genes, and virulence genes were constructed based on core SNP sites. The gene carrying rates of tlh, toxR, were 100.00%, 100.00%; none of the isolates carried tdh or trh. Ten isolates were resistant to aztreonam and moderately sensitive to ampicillin. All the isolates contained the β-lactam resistance gene (CARB-18), corresponding to the resistance phenotype. One isolate was found to contain mexE, a virulence gene rarely reported in similar studies. Nine sequence types were identified. Several V . parahaemolyticus isolates exhibited high homology with local and foreign marine organism isolates. Local V. parahaemolyticus may pose a threat to human health, and its sources are complex and highly genetically diverse. There may be foreign sources of V. parahaemolyticus contamination; hence,monitoring needs to be strengthened. [ABSTRACT FROM AUTHOR]

Little is known about the characteristics of respiratory tract microbiome in Coronavirus disease 2019 (COVID‐19) inpatients with different severity. We conducted a study that expected to clarify these characteristics as much as possible. A cross‐sectional study was conducted to characterize respiratory tract microbial communities of 69 COVID‐19 inpatients from 64 nasopharyngeal swabs and 5 sputum specimens using 16S ribosomal RNA gene V3‐V4 region sequencing. The bacterial profiles were analyzed to find potential biomarkers by the two‐step method, the combination of random forest model and the linear discriminant analysis effect size, and explore the connections with clinical characteristics by Spearman's rank test. Compared with mild COVID‐19 patients, severe patients had significantly decreased bacterial diversity (p‐values were less than 0.05 in the alpha and beta diversity) and relative lower abundance of opportunistic pathogens, including Actinomyces, Prevotella, Rothia, Streptococcus, Veillonella. Eight potential biomarkers including Treponema, Leptotrichia, Lachnoanaerobaculum, Parvimonas, Alloprevotella, Porphyromonas, Gemella, and Streptococcus were found to distinguish the mild COVID‐19 patients from the severe COVID‐19 patients. The genera of Actinomyces and Prevotella were negatively correlated with age in two groups. Intensive care unit admission, neutrophil count, and lymphocyte count were significantly correlated with different genera in the two groups. In addition, there was a positive correlation between Klebsiella and white blood cell count in two groups. The respiratory tract microbiome had significant differences in COVID‐19 patients with different severity. The value of the respiratory tract microbiome as predictive biomarkers for COVID‐19 severity deserves further exploration. [ABSTRACT FROM AUTHOR]

Due to rapid temperature rise and insulation moisture, bubbles can generate in the oil-paper insulation of oil-immersed power transformers, which can reduce the dielectric strength of oil-paper insulation and even bring about the risk of insulation breakdown. In order to accurately evaluate the conditions of bubble formation, the physical process of bubble formation in oil-paper insulation is studied in this article. Considering the effects of water vaporization, gas dissolution in oil, and moisture migration on bubble formation, a bubble formation prediction model is constructed. Based on Henry’s law, the dissolution equilibrium of gas in oil is taken into consideration and the upper boundary of the initial temperature of bubble effect (ITBE) envelope is obtained in this model. Based on the moisture equilibrium in oil-paper insulation, the bubble formation process caused by the emergence and rapid evaporation of free water is analyzed, and then, the lower boundary of the ITBE envelope is obtained in this model. The model results show that the moisture content of the pressboard and the presence of free water have a great impact on ITBE. Specifically, the higher the moisture content, the lower the ITBE value. In addition, with the further increase of moisture content, the upper and lower boundaries of the ITBE envelope gradually tend to be the same. However, once free water is present on the surface of cellulose, ITBE decreases rapidly to below 120 °C. The model built in this article is of great significance to study the temperature limit of the power transformer. Hence the ITBE envelope can provide an important theoretical reference for reducing the risk of bubble formation during power transformer operation. [ABSTRACT FROM AUTHOR]

Gymnocypris eckloni is widely distributed in isolated lakes and the upper reaches of the Yellow River and play significant roles in the trophic web of freshwater communities. In this study, we generated a chromosome-level genome of G. eckloni using PacBio, Illumina and Hi-C sequencing data. The genome consists of 23 pseudo-chromosomes that contain 918.68 Mb of sequence, with a scaffold N50 length of 43.54 Mb. In total, 23,157 genes were annotated, representing 94.80% of the total predicted protein-coding genes. The phylogenetic analysis showed that G. eckloni was most closely related to C. carpio with an estimated divergence time of ~34.8 million years ago. For G. eckloni, we identified a high-quality genome at the chromosome level. This genome will serve as a valuable genomic resource for future research on the evolution and ecology of the schizothoracine fish in the Qinghai-Tibetan Plateau. Measurement(s) Genome Technology Type(s) Whole Genome Sequencing Sample Characteristic - Organism Gymnocypris eckloni Sample Characteristic - Environment fresh water Sample Characteristic - Location Little Yellow River [ABSTRACT FROM AUTHOR]

In this paper, we present a class of hybrid coupled serially concatenated codes (HC-SCC), in which coupling is achieved by re-encoding partial outputs from both the outer and the inner encoders. Firstly, we derive the exact density evolution (DE) equations over the binary erasure channels (BECs) for the HC-SCCs, which can be used to analyze the impact of the coupling ratios and the coupling memories on the performances of the HC-SCCs. Secondly, we present a genie-aided lower bound for the proposed HC-SCCs to estimate their error-floors. Thirdly, we use the DE equations to design randomly punctured HC-SCCs, including rate-compatible HC-SCCs. The analytical and the numerical results show that: 1) for comparable coupling memories, the iterative decoding thresholds of the proposed HC-SCC ensembles are better than those of the recently introduced spatially coupled serially concatenated code (SC-SCC) ensembles and the partially parity-coupled turbo code (PPC-TC) ensembles; 2) with outer coupling memory five and inner coupling memory five, the iterative decoding thresholds of the rate-compatible HC-SCCs over the BECs are 0.0003 away from the corresponding channel capacities for a wide range of coding rates; 3) simulation results over the additive white Gaussian noise (AWGN) channels and the BECs are provided to confirm the performance advantages of the HC-SCCs. Particularly, the simulation results show that the HC-SCCs admit lower error-floor than the SC-SCCs and the rate-compatible HC-SCCs perform better than the PPC-TCs, which are consistent with the results of DE analysis. [ABSTRACT FROM AUTHOR]

Deficiency of the immune checkpoint lymphocyte activation gene-3 (LAG3) protein is significantly associated with both elevated HDL-cholesterol (HDL-C) and myocardial infarction risk. We determined the association of genetic variants within ±500 kb of LAG3 with plasma LAG3 and defined LAG3-associated plasma proteins with HDL-C and clinical outcomes. Whole genome sequencing and plasma proteomics were obtained from the Multi-Ethnic Study of Atherosclerosis (MESA) and the Framingham Heart Study (FHS) cohorts as part of the Trans-Omics for Precision Medicine program. In situ Hi-C chromatin capture was performed in EBV-transformed cell lines isolated from four MESA participants. Genetic association analyses were performed in MESA using multivariate regression models, with validation in FHS. A LAG3-associated protein network was tested for association with HDL-C, coronary heart disease, and all-cause mortality. We identify an association between the LAG3 rs3782735 variant and plasma LAG3 protein. Proteomics analysis reveals 183 proteins significantly associated with LAG3 with four proteins associated with HDL-C. Four proteins discovered for association with all-cause mortality in FHS shows nominal associations in MESA. Chromatin capture analysis reveals significant cis interactions between LAG3 and C1S, LRIG3, TNFRSF1A, and trans interactions between LAG3 and B2M. A LAG3-associated protein network has significant associations with HDL-C and mortality. Rodriguez et al. use whole genome sequencing and plasma proteomics from the Multi-Ethnic Study of Atherosclerosis (MESA) and the Framingham Heart Study (FHS) cohorts of the Trans-Omics for Precision Medicine program and perform in situ Hi-C chromatin capture in cell lines isolated from four MESA participants. They demonstrate that lymphocyte activation gene-3 protein networks are associated with HDL-cholesterol and mortality, which could guide the development of precision medicine. [ABSTRACT FROM AUTHOR]

Ecopath model is a snapshot of a particular ecosystem at a time to quickly reflect the real‐time status, characteristics and nutritional relationships of remaining systems in the water. Based on Aoshan Bay fishery resource data collected in 2006, 2013 and 2018, Ecopath models of the Aoshan Bay ecosystem were constructed for these 3 years using EwE 6.6 software. The models of the Aoshan Bay ecosystem included 15 functional groups. Based on the 3 models, we compared and analysed changes in ecosystem structure and phylogenetic characteristics. The trophic interactions between the 15 functional groups were aggregated within four effective trophic levels at 2006, 2013 and 2018. Most of the functional groups were laid within the trophic levels TL 2 and TL 3. The average trophic levels in 2006, 2013 and 2018 were 2.318, 2.444 and 2.410, respectively. The calculated ecotrophic efficiency (EE) value for this ecosystem was highest for Zooplankton (EE = 0.898, 2006), Nibea albiflora (EE = 0.857, 2013) and other demersal fishes (EE = 0.963, 2018). In this study, the calculated TPP/TR was 4.572 (2006), 4.484(2013), 5.347(2018), which indicates the ecosystem is in a developmental stage (not fully mature), the highest mature ecosystem is 2013 and gradually decrease in 2018. In 2013, the FCI is 4.814 and higher ecosystem's maturity than 2006 and 2018, indicating high utilization of primary productivity and detritus. Through analysis of Ecopath models for different years, the characteristics of ecosystem changes in the Aoshan Bay over the past decade were revealed, indicating that the Aoshan Bay ecosystem is still in an unstable and immature state, which provides scientific reference materials for the restoration of fishery resources in this sea area. [ABSTRACT FROM AUTHOR]

Visualizing the progression of fatty liver disease in vivo is of great significance in biomedical research of fatty liver, but hindered by the lack of suitable approaches with deep penetration, high specificity, and real‐time observability for fatty liver imaging. Herein, two bright NIR‐I/NIR‐II fluorophores with D–π–A–π–D structures are designed and synthesized for fatty liver tracking in vivo. Such fluorophores show an ultrahigh quantum yield of 49.2% and 17.3% at the emission maximum of 930 and 975 nm, respectively. Most interestingly, these two fluorophores display ultrasensitive fluorescence response (over 100‐fold enhancement) toward the variations of environment polarity. Accordingly, further doping of these fluorophores into amphiphilic organic matrix allows the formation of ultrabright NIR‐I/NIR‐II fluorescent nanoprobes for high‐resolution fluorescence imaging of the vessels. Additionally, with the assistance of such nanoprobes and NIR‐II fluorescence imaging, real‐time monitoring of heartbeat rate and the respiratory rate, accurate identification, and imaging‐guided surgery of the submillimeter scale lymph nodes are successfully realized. Moreover, the as‐designed fluorophores show superior performance for indicating lipid droplets (LDs) in living cells. Ultimately, precise monitoring of fatty liver with NIR‐I/NIR‐II fluorescent LDs probe is first confirmed, demonstrating the possibility for staging fatty liver disease with a contact‐free method. [ABSTRACT FROM AUTHOR]

Visualizing the progression of fatty liver disease in vivo is of great significance in biomedical research of fatty liver, but hindered by the lack of suitable approaches with deep penetration, high specificity, and real‐time observability for fatty liver imaging. Herein, two bright NIR‐I/NIR‐II fluorophores with D–π–A–π–D structures are designed and synthesized for fatty liver tracking in vivo. Such fluorophores show an ultrahigh quantum yield of 49.2% and 17.3% at the emission maximum of 930 and 975 nm, respectively. Most interestingly, these two fluorophores display ultrasensitive fluorescence response (over 100‐fold enhancement) toward the variations of environment polarity. Accordingly, further doping of these fluorophores into amphiphilic organic matrix allows the formation of ultrabright NIR‐I/NIR‐II fluorescent nanoprobes for high‐resolution fluorescence imaging of the vessels. Additionally, with the assistance of such nanoprobes and NIR‐II fluorescence imaging, real‐time monitoring of heartbeat rate and the respiratory rate, accurate identification, and imaging‐guided surgery of the submillimeter scale lymph nodes are successfully realized. Moreover, the as‐designed fluorophores show superior performance for indicating lipid droplets (LDs) in living cells. Ultimately, precise monitoring of fatty liver with NIR‐I/NIR‐II fluorescent LDs probe is first confirmed, demonstrating the possibility for staging fatty liver disease with a contact‐free method. [ABSTRACT FROM AUTHOR]

With the rapid emergence of plasmid-mediated colistin resistance gene mcr-1 , the increased resistance of Salmonella has attracted extensive attention. This study reports on 11 multidrug-resistant Salmonella enterica serovar Typhimurium strains harboring mcr-1 in China. They all presented resistance to colistin, and additionally, one that was isolated from a child's stool sample was also resistant to ceftriaxone and azithromycin. We screened 1454 strains of Salmonella for mcr-1 gene through PCR, and these strains are all preserved in our laboratory. Antimicrobial sensitivity analysis was carried out for the screened mcr-1 positive strains. Genetic polymorphism analysis of S. Typhimurium was performed by using the Pulsed-Field Gel Electrophoresis (PFGE). The plasmids harboring mcr-1 were identified by S1-PFGE and southern blotting. Plasmid conjugation assays were used to analyze the transferability of colistin resistance. The plasmids harboring mcr-1 were characterized by sequencing and bioinformatic analysis. Eleven S. Typhimurium strains harboring mcr-1 with colistin resistance (MICs 4μg/ml) were detected, which were isolated from children and pig offal in China. All of them were multidrug-resistant strains. PFGE results revealed that the strains isolated from different samples or locations have identical genotypes. S1-PFGE and southern blotting experiments showed that three plasmids of different sizes (33, 60, and 250 kb) all carried the mcr-1 gene. The plasmid conjugation assays revealed that Salmonella acquired mcr-1 harboring plasmids by horizontal transfer. Sequencing and plasmid type analysis revealed that these plasmids were types IncX4, IncI2, and IncHI2. Among them, IncX4 and IncI2 plasmids had extremely similar backbones and contained one resistant gene mcr-1. IncHI2 plasmid contained multiple resistant genes including bla CTX–M, oqxB , sul , aph , aadA , and bla TEM. We identified 11 mcr-1 harboring S. Typhimurium strains in China and described their characteristics. Our findings indicate that the mcr-1 gene can effectively spread among intestinal bacteria by horizontal transfer of three types of plasmids. Moreover, the IncHI2 plasmid can also mediate the transfer of other drug resistance genes. These results reveal that constant surveillance of mcr-1 harboring S Typhimurium is imperative to prevent the spread of colistin resistance. [ABSTRACT FROM AUTHOR]

In multiregional randomized clinical trials (MRCTs), determining the regional treatment effect of a new treatment over an existing one is important to both the sponsor and related regulatory agencies. Also of particular interest is to test the null hypothesis that the treatment benefit is the same among all the regions. Existing methods are mainly for continuous endpoint and use parametric models, which are not robust. MRCTs are known for facing increased variation and heterogeneity and a robust model for its design and analysis would be desirable. We consider clinical trials with a binary primary endpoint and propose a robust semiparametric logistic model which has a known parametric and an unknown nonparametric component. The parametric component represents our prior knowledge about the model, and the nonparametric part reflects uncertainty. Compared to the classic logistic model for this problem, the proposed model has the following advantages: robust to model assumption, more flexible and accurate to model the relationship between the response and covariates, and possibly more accurate parameter estimates. The model parameters are estimated by profile maximum likelihood approach, and the null hypothesis of regional treatment difference being the same is tested by the profile likelihood ratio statistic. Asymptotic properties of the estimates are derived. Simulation studies are conducted to evaluate the performance of the proposed model, which demonstrated clear advantages over the classic logistic model. The method is then applied to analyzing a real MRCT. [ABSTRACT FROM AUTHOR]

Summary: Coronavirus disease 2019 (COVID‐19) pandemic has caused high number of infections and deaths of healthcare workers globally. Distribution and possible transmission route of SARS‐CoV‐2 in hospital environment should be clarified. We herein collected 431 environmental (391 surface and 40 air) samples in the intensive care unit (ICU) and general wards (GWs) of three hospitals in Wuhan, China from February 21 to March 4, 2020, and detected SARS‐CoV‐2 RNA by real‐time quantitative PCR. The viral positive rate in the contaminated areas was 17.8% (28/157), whereas there was no virus detected in the clean areas. Higher positive rate (22/59, 37.3%) was found in ICU than that in GWs (3/63, 4.8%). The surfaces of computer keyboards and mouse in the ICU were the most contaminated (8/10, 80.0%), followed by the ground (6/9, 66.7%) and outer glove (2/5, 40.0%). From 17 air samples in the contaminated areas, only one sample collected at a distance of around 30 cm from the patient was positive. Enhanced surface disinfection and hand hygiene effectively decontaminated the virus from the environment. This finding might help understand the transmission route and contamination risk of SARS‐CoV‐2 and evaluate the effectiveness of infection prevention and control measures in healthcare facilities. [ABSTRACT FROM AUTHOR]

Salmonella contamination of eggs and egg shells has been identified as a public health problem worldwide. Here, we reported an outbreak of severe gastrointestinal symptoms caused by Salmonella enterica serovar Enteritidis (S. enteritidis) in China. We evaluated the outbreak by using epidemiological surveys, routine laboratory testing methods, and whole genome sequencing (WGS). This outbreak occurred in a canteen in Beijing, during March 9–11, 2021, 225 of the 324 diners who have eaten at the canteen showed gastrointestinal symptoms. The outbreak had characteristical epidemiological and clinical features. It caused a very high attack rate (69.4%) in a short incubation time. All patients developed diarrhea and high fever, accompanied by abdominal pain (62.3%), nausea (50.4%), and vomiting (62.7%). The average frequency of diarrhea was 12.4 times/day, and the highest frequency of diarrhea was as high as 50 times/day. The average fever temperature was 39.4°C, and the highest fever temperature was 42°C. Twenty strains of S. enteritidis were recovered, including 19 from the patients samples, and one from remained egg fried rice. Antibiotic susceptibility test showed that the 20 outbreak strains all had the same resistance pattern. PFGE results demonstrated that all 20 strains bore completely identical bands. Phylogenetic analysis based on WGS revealed that all 20 outbreak strains were tightly clustered together. So the pathogenic source of this food poisoning incident may was contaminated egg fried rice. Resistance gene analysis showed that the outbreak strains are all multi-drug resistant strains. Virulence gene analysis indicated that these outbreak strains carried a large number of virulence genes, including 2 types of Salmonella pathogenicity islands (SPI-1 and SPI-2). Other important virulence genes were also carried by the outbreak strains, such as pef ABCD, rck and shd A. And the shd A gene was not in other strains located in the same evolutionary branch as the outbreak strain. We speculated that this is a significant reason for the serious symptoms of gastroenteritis in this outbreak. This outbreak caused by S. enteritidis suggested government should strengthen monitoring of the prevalence of outbreak clone strains, and take measures to mitigate the public health threat posed by contaminated eggs. [ABSTRACT FROM AUTHOR]

Background: Chikungunya fever, caused by the Chikungunya virus (CHIKV), has become a major global health concern, causing unexpected large outbreaks in Africa, Asia, Europe, and the Americas. CHIKV is not indigenous to China, and its origin in the country is poorly understood. In particular, there is limited understanding of the recent global spread of CHIKV in the context of the CHIKV epidemic. Methods: Here we investigated a novel Chikungunya patient who came from Myanmar to China in August, 2019. Direct genome sequencing was performed via combined MinION sequencing and BGISEQ-500 sequencing. A complete CHIKV genome dataset, including 727 CHIKV genomes retrieved from GenBank and the genome sequenced in this study, was constructed. An updated and comprehensive phylogenetic analysis was conducted to understand the virus's origin, evolution, transmission routes and genetic adaptation. Results: All globally distributed CHIKV genomes were divided into West Africa, East/Central/South African and Asian genotypes. The genome sequenced in this study was located in the Indian Ocean lineage, and was closely related to a strain isolated from an Australian patient who returned from Bangladesh in 2017. A comprehensive phylogenetic analysis showed that the Chinese strains mainly originated from the Indian subcontinent and Southeast Asia. Further analyses indicated that the Indian subcontinent and Southeast Asia may act as major hubs for the recent global spread of CHIKV, leading to multiple outbreaks and epidemics. Moreover, we identified 179 distinct sites, including some undescribed sites in the structural and non-structural proteins, which exhibited apparent genetic variations associated with different CHIKV lineages. Conclusions: Here we report a novel CHIKV isolate from a chikungunya patient who came from Myanmar to China in 2019, and summarize the source and evolution of Chinese CHIKV strains. Our present findings provide a better understanding of the recent global evolution of CHIKV, highlighting the urgent need for strengthened surveillance against viral diversity. [ABSTRACT FROM AUTHOR]

In this study, the complete mitochondrial genome (mitogenome) of Sinularia humilis van Ofwegen, 2008 was determined using next-generation sequencing (NGS) method. The mitogenome of S. humilis is 18,743 bp in length, containing 14 protein-coding genes (PCGs), two ribosomal RNAs (rRNA) and one tRNA (tRNA-Met), which has same gene order with other species of Sinularia. ATG was determined as start codon in all 14 PCGs. Eight TAG, five TAA, and one incomplete codons (T-) were found as stop codon. Phylogenetic analysis of the small number of available mitogenomes showed that S. humilis is closely related to Sinularia ceramensis and Sinularia peculiaris. [ABSTRACT FROM AUTHOR]

Long chain polyunsaturated fatty acids (LC-PUFAs) have critical signaling roles that regulate dyslipidemia and inflammation. Genetic variation in the FADS gene cluster accounts for a large portion of interindividual differences in circulating and tissue levels of LC-PUFAs, with the genotypes most strongly predictive of low LC-PUFA levels at strikingly higher frequencies in Amerind ancestry populations. In this study, we examined relationships between genetic ancestry and FADS variation in 1102 Hispanic American participants from the Multi-Ethnic Study of Atherosclerosis. We demonstrate strong negative associations between Amerind genetic ancestry and LC-PUFA levels. The FADS rs174537 single nucleotide polymorphism (SNP) accounted for much of the AI ancestry effect on LC-PUFAs, especially for low levels of n-3 LC-PUFAs. Rs174537 was also strongly associated with several metabolic, inflammatory and anthropomorphic traits including circulating triglycerides (TGs) and E-selectin in MESA Hispanics. Our study demonstrates that Amerind ancestry provides a useful and readily available tool to identify individuals most likely to have FADS-related n-3 LC-PUFA deficiencies and associated cardiovascular risk. Yang et al. examine whether genetic ancestry is associated with genetic variation in fatty acid desaturases and plasma phospholipid levels of long chain polyunsaturated fatty acids (LC-PUFAs) in Hispanic Americans. They find strong associations between Amerind genetic ancestry and LC-PUFA levels; and report that the well-known FADS rs174537 variant was associated with several metabolic, inflammatory and anthropomorphic traits including circulating triglycerides. [ABSTRACT FROM AUTHOR]

Coronavirus disease 2019 (COVID‐19) has rapidly evolved into a global pandemic. A total of 1578 patients admitted into a newly built hospital specialized for COVID‐19 treatment in Wuhan, China, were enrolled. Clinical features and the levels of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) immunoglobulin (Ig)M and IgG were analyzed. In total, 1532 patients (97.2%) were identified as laboratory‐confirmed cases. Seventy‐seven patients were identified as asymptomatic carriers (n = 64) or SARS‐CoV‐2 RNA positive before symptom onset (n = 13). The positive rates of SARS‐CoV‐2 IgM and IgG were 80.4% and 96.8%, respectively. The median of IgM and IgG titers were 37.0A U/ml (interquartile range [IQR]: 13.4–81.1 AU/ml) and 156.9 AU/ml (IQR: 102.8–183.3 AU/ml), respectively. The IgM and IgG levels of asymptomatic patients (median titers, 8.3 AU/ml and 100.3 AU/ml) were much lower than those in symptomatic patients (median titers, 38.0 AU/ml and 158.2 AU/ml). A much lower IgG level was observed in critically ill patients 42–60 days after symptom onset. There were 153 patients with viral RNA shedding after IgG detection. These patients had a higher proportion of critical illness during hospitalization (p <.001) and a longer hospital stay (p <.001) compared to patients with viral clearance after IgG detection. Coronary heart disease (odds ratio [OR], 1.89 [95% confidence interval [CI], 1.11–3.24]; p =.020), and intensive care unit admission (OR, 2.47 [95% CI, 1.31–4.66]; p =.005) were independent risk factors associated with viral RNA shedding after IgG detection. Symptomatic patients produced more antibodies than asymptomatic patients. The patients who had SARS‐CoV‐2 RNA shedding after developing IgG were more likely to be sicker patients. Highlights: The IgM and IgG levels of asymptomatic COVID‐19 patients were much lower than those in symptomatic COVID‐19 patients Coronary heart disease and ICU admission were independent risk factors associated with SARS‐CoV‐2 RNA shedding after IgG detection [ABSTRACT FROM AUTHOR]

In integrated cyber-physical power systems (CPPS), the malfunctions of cyber system deeply affect the dispatcher's remedial action scheme, and thus have a significant impact on the reliability of the physical power system. The random failures of electrical devices in physical power system and the random outages of measurement and remote control in cyber system are both considered for the CPPS reliability evaluation in this paper. Firstly, the component outage models in physical, access, backbone and application layers are presented. Then, a linearized DC state estimation (SE) model is introduced and the SE errors incurred by measurement failures, i.e. bad and lost measurements, are interpreted. Moreover, the impact of SE errors and remote control failures on the corrective action scheme of the control center during the fault recovery process is simulated by a novel modification of the classical optimal load shedding (OLS) model. Finally, to verify the effectiveness and validity of the proposed CPPS reliability evaluation method, the communication network topologies of the cyber system for the RBTS and IEEE-RTS96 are designed, and then the reliability evaluation based on the presented component outage models and the novel modified OLS model are conducted by the non-sequential Monte Carlo simulation (NMCS). [ABSTRACT FROM AUTHOR]

Three new transition metal complexes, [Zn(L1)2(OTs)(CH3OH)](TsO)·CH3OH (1), {[Zn(L2)(H2O)4](SiF6)·H2O}n (2) and {[Cd(L2)2(OTs)2]·2DMF}n (3), were prepared from pyridine thiazolone derivatives (where L1 = 2-[4-(2-pyridinyl)-2-thiazolyl]hydrazone, L2 = 2-[4-(3-pyridinyl)-2-thiazolyl]hydrazone) and characterized by 1H-NMR, elemental analysis (EA), and infrared spectra (IR). The crystalline behavior of L1 and 1–3 were analyzed by X-ray diffraction. In the structure of 1, L1 acts as a bidentate agent coordinating the Zn2+ ion through the pyridine nitrogen and thiazole nitrogen, while L2 bonded in a 2D structure by coordinating Zn2+ through the nitrogen atoms of two pyridine rings in the structure of 2. Additionally, with Cd2+ ions as connection points and the spatial extension of L2, 3 possesses an intricate 3D metal–organic framework. The luminescent properties for the ligands and complexes were investigated. The in vitro antimicrobial and antitumor activities were evaluated against ten pathogenic bacterial strains and four human cancer cell lines. [ABSTRACT FROM AUTHOR]

Chronic obstructive pulmonary disease (COPD), diagnosed by reduced lung function, is a leading cause of morbidity and mortality. We performed whole genome sequence (WGS) analysis of lung function and COPD in a multi-ethnic sample of 11,497 participants from population- and family-based studies, and 8499 individuals from COPD-enriched studies in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program. We identify at genome-wide significance 10 known GWAS loci and 22 distinct, previously unreported loci, including two common variant signals from stratified analysis of African Americans. Four novel common variants within the regions of PIAS1, RGN (two variants) and FTO show evidence of replication in the UK Biobank (European ancestry n ~ 320,000), while colocalization analyses leveraging multi-omic data from GTEx and TOPMed identify potential molecular mechanisms underlying four of the 22 novel loci. Our study demonstrates the value of performing WGS analyses and multi-omic follow-up in cohorts of diverse ancestry. Chronic obstructive pulmonary disease is a leading cause of morbidity and mortality. Here, the authors analyse whole genome sequence data and find new loci associated with lung function and COPD. [ABSTRACT FROM AUTHOR]

Background: At present, azithromycin has become an effective treatment for severe diarrhea caused by Enterotoxigenic Escherichia coli (ETEC) infection. However, enterobacteria have begun to develop resistance to azithromycin and have attracted attention in recent years. This study conducted to described the emergence of a high proportion of azithromycin-resistant ETEC serogroup O6 strains in Shanghai and to analyzed the mechanisms of azithromycin resistance. Results: Strains from adult diarrhea patients with ETEC serogroup O6 infections were collected by Shanghai Diarrhea Surveillance Network and the Foodborne Surveillance Network from 2016 to 2018. We tested 30 isolates of ETEC O6 serogroup, 26 of which were resistant to azithromycin. Phylogenetic analysis revealed that these ETEC serogroup O6 strains have formed an independent dominant clone. S1-PFGE and southern blotting revealed the presence of the mphA gene on the 103 kb plasmid. Illumina and Nanopore sequencing and plasmid coverage analysis further confirmed that azithromycin-resistant strains carried a novel IncFII plasmid harboring mphA and blaTEM-1 resistance genes. Conclusions: This is the first study to report a high proportion of azithromycin resistance in a particular ETEC serogroup due to a specific plasmid carrying mphA. Our findings indicate the rapid spread of azithromycin resistance, highlighting the urgency of stringent surveillance and control measure. [ABSTRACT FROM AUTHOR]

Background: Salmonella enterica subsp. enterica serovar Typhimurium infections continue to be a significant public health threat worldwide. The aim of this study was to investigate antibiotic resistance among 147 S. Typhimurium isolates collected from patients in Henan, China from 2006 to 2015.Methods: 147 S. Typhimurium isolates were collected from March 2006 to November 2015 in Henan Province, China. Antimicrobial susceptibility testing was performed, and the resistant genes of ciprofloxacin, cephalosporins (ceftriaxone and cefoxitin) and azithromycin were detected and sequenced. Clonal relationships were assessed by multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE).Results: Of the 147 isolates, 91.1% were multidrug resistant (MDR), with 4.1% being resistant to all antibiotic classes tested. Of concern, 13 MDR isolates were co-resistant to the first-line treatments cephalosporins and ciprofloxacin, while three were also resistant to azithromycin. Seven PFGE patterns were identified among the 13 isolates. All of the isolates could be assigned to one of four main groups, with a similarity value of 89%. MLST assigned the 147 isolates into five STs, including two dominant STs (ST19 and ST34). Of the 43 ciprofloxacin-resistant isolates, 39 carried double gyrA mutations (Ser83Phe, Asp87Asn/Tyr/Gly) and a single parC (Ser80Arg) mutation, including 1 isolate with four mutations (gyrA: Ser83Phe, Asp87Gly; parC: Ser80Arg; parE: Ser458Pro). In addition, 12 isolates not only carried mutations in gyrA and parC but also had at least one plasmid-mediated quinolone resistance (PMQR) gene. Among the 32 cephalosporin-resistant isolates, the most common extended-spectrum β-lactamase (ESBL) gene was blaOXA-1, followed by blaCTX-M, blaTEM-1, and blaCMY-2. Moreover, the mphA gene was identified in 5 of the 15 azithromycin-resistant isolates. Four MDR isolates contained ESBL and PMQR genes, and one of them also carried mphA in addition.Conclusion: The high level of antibiotic resistance observed in S. Typhimurium poses a great danger to public health, so continuous surveillance of changes in antibiotic resistance is necessary. [ABSTRACT FROM AUTHOR]

The rapid emergence of multidrug resistant Salmonella is a global public-health concern as outbreaks in recent years have mostly been caused by multidrug resistant strains. Here, we evaluated an outbreak in China caused by multidrug resistant Salmonella enterica serovar Typhimurium (S. Typhimurium) by employing an epidemiological and laboratory investigation using conventional methods and whole genome sequencing (WGS). Eleven of the 12 people who participated in a banquet showed gastrointestinal symptoms, and 8 S. Typhimurium strains were recovered. Isolated outbreak strains showed multidrug resistance (MDR), and decreased susceptibility to ciprofloxacin, a first-line drug recommended by WHO for clinical treatment of intestinal infections. Antimicrobial resistance (AMR) gene analysis indicated that the MDR phenotype of these outbreak strains may be due to the presence of a number of AMR genes, including the bla OXA-1 and bla TEM-1 β-lactamase genes, which are often plasmid-borne and easily transferred. Further virulence gene analysis indicated that these outbreak strains also carried a large number of virulence genes, including 2 types of Salmonella pathogenicity islands (SPI-1 and SPI-2) and many adhesion-related virulence genes. Cluster analysis based on pulse-field gel electrophoresis data and phylogenetic analysis based on WGS revealed that the outbreak clone was closely related to and thus probably derived from local strains. This outbreak caused by multidrug resistant S. Typhimurium highlights the need for government improved strategies for the prevention and control of Salmonella infections. [ABSTRACT FROM AUTHOR]

Erchen plus Huiyanzhuyu decoction (EHD), a Chinese herbal medicine (CHM) formula that consists of Erchen decoction and Huiyanzhuyu decoction, has achieved satisfactory results in the clinic. The main function of EHD is to remove phlegm and blood stasis, and EHD is suitable for phlegm-coagulation-blood-stasis (PCBS) syndrome in laryngeal cancer (LC). In this study, a xenograft mouse model of LC with PCBS syndrome was constructed by feeding a high-fat diet, swimming in ice water, and subcutaneously injecting epinephrine hydrochloride for 2 weeks. Based on the successful Chinese medicine syndrome model, Hep2-luciferase-GFP cells were injected subcutaneously under the armpit of the right upper limb in mice to form tumours. A mouse model of LC with PCBS syndrome was established via heterotopic transplantation. Then, the mice received intragastric administration of different concentrations of EHD daily, and cisplatin (DDP) was intraperitoneally injected every week for 21 days. Tumour fluorescence in mice was measured with a living animal imager on days 7, 14, 21, and 28 during treatment. The results of this experiment confirmed that a mouse model of Chinese medicine syndrome was successfully constructed. Moreover, EHD slowed the growth of xenograft tumours in nude mice; decreased the expression levels of STAT3, p-STAT3, and cyclin D1; and upregulated the expression level of P27. In brief, EHD inhibited laryngeal tumour growth in a xenograft mouse model of PCBS syndrome and regulated the STAT3/cyclin D1 signalling pathway. This study was the first to construct a Chinese medicine xenograft mouse model of LC with PCBS syndrome; in addition, this study clarified that EHD regulated the STAT3/cyclin D1 signalling pathway to inhibit the growth of LC and that EHD may be a promising novel therapeutic compound for the treatment of patients with LC. [ABSTRACT FROM AUTHOR]

Background: Coinfection with influenza virus and bacteria is a major cause of high mortality during flu pandemics. Understanding the mechanisms behind such coinfections is of utmost importance both for the clinical treatment of influenza and the prevention and control of epidemics. Methods: To investigate the cause of high mortality during flu pandemics, we performed coinfection experiments with H1N1 influenza virus and Staphylococcus aureus in which mice were infected with bacteria at time points ranging from 0 to 7 days after infection with influenza virus. Results: The mortality rates of mice infected with bacteria were highest 0–3 days after infection with influenza virus; lung tissues extracted from these co-infected mice showed higher infiltrating cells and thicker lung parenchyma than lung samples from coinfected mice in which influenza virus was introduced at other times and sequences. The levels of interferon (IFN)-γ, tumor necrosis factor (TNF)-α, interleukin (IL)-8, and IL-6 in the 0–3 day coinfected group were significantly higher than those in the other groups (p < 0.01), as were the mRNA levels of IFN-γ, IL-6, and TNF-α. Coinfection with influenza virus and S. aureus led to high mortality rates that are directly dependent on the sequence and timing of infection by both pathogens. Moreover, coinfection following this particular schedule induced severe pneumonia, leading to increased mortality. Conclusions: Our data suggest that prevention of bacterial co-infection in the early stage of influenza virus infection is critical to reducing the risk of clinical mortality. [ABSTRACT FROM AUTHOR]

The recently introduced spatially coupled turbo‐like codes are attractive in trading‐off performances between the error‐floor region and the water‐fall region. This letter is concerned with the construction of spatially coupled serially concatenated codes. Particularly, a new construction of spatially coupled serially concatenated codes is presented, in which a portion of the encoding output of the previous inner encoder is taken as the input of the current inner encoder. The authors show that by proper selection of the component codes and the re‐encoding ratio, performance gain about 0.25 dB is obtained with the proposed construction. [ABSTRACT FROM AUTHOR]

In this study, we discovered a novel mobilized colistin resistance (mcr-1) gene variant, named mcr-1.9, which was identified in a colistin-resistant enterotoxigenic Escherichia coli (ETEC) strain from a clinical diarrhea case. The mcr-1.9 gene differs from mcr-1 at position 1036 due to a single nucleotide polymorphism (G→A), which results in an aspartic acid residue being replaced by an asparagine residue (Asp346→Asn) in the MCR-1 protein sequence. Antimicrobial susceptibility testing showed that the mcr-1.9- harboring ETEC strain is resistant to colistin at a minimum inhibitory concentration of 4 µg/ml. Plasmid profiling and conjugation experiments also suggest that the mcr-1.9 variant can be successfully transferred into the E. coli strain J53, indicating that the gene is located on a transferable plasmid. Bioinformatics analysis of data obtained from genome sequencing indicates that the mcr-1.9 gene is located on a 64,005 bp plasmid which has been named pEC26. This plasmid was found to have high similarity to the mcr-1-bearing IncI2-type plasmids pWF-5-19C (99% identity and 99% coverage) and pmcr1-IncI2 (99% identity and 98% coverage). The mcr-1.9-harboring ETEC also shows multidrug resistance to nine classes of antibiotics, and contains several virulence and antimicrobial-resistance genes suggested by the genome sequence analysis. Our report is the first to identify a new mcr-1 variant in an ETEC isolated from a human fecal sample, raising concerns about the existence of more such variants in human intestinal flora. Therefore, we believe that an undertaking to identify new mcr-1 variants in the bacterial communities of human intestines is of utmost importance, and that measures need to be taken to control the spread of mcr-1 and its variants in human intestinal microflora. [ABSTRACT FROM AUTHOR]

Shigella represents one of the major diarrhea-inducing pathogens threatening public health, but its prevalence and antimicrobial resistance profile in Xinjiang Uygur Autonomous region, China, remains unclear. We conducted comprehensive investigation of Shigella serotype distribution and antimicrobial resistance pattern in Xinjiang, identifying 458 Shigella isolates between 2008 to 2014. Shigella flexneri was identified as predominant species, and several S. flexneri serotypes were isolated, including atypical serotypes 1c, 2c, and 4s. Dominant S. flexneri serotypes were 2a, 1b, 2b, and Xv, different from those generally dominant in China. A hybrid serotype pattern was observed, which included the major Chinese serotypes (2a, Xv) and those predominant in Pakistan (1b, 2b). Shigella sonnei was shown to have a lower frequency compared with that generally observed in China, but an increasing trend of infections associated with this pathogen was observed. Furthermore, a high frequency of drug resistance and different Shigella antimicrobial resistance patterns were demonstrated as well, including very severe resistance phenotypes, such as multidrug resistance and resistance to frontline antibiotics. Seventy-five cephalosporin-resistant Shigella isolates were frequently identified with the resistance determinants that can undergo horizontal transfer, such as blaOXA, blaTEM, blaCTX-M, and integrons, facilitating the development of cephalosporin resistance among Shigella subtypes. Additionally, genetic analyses demonstrated that all 86 quinolone-resistant S. flexneri isolates possess 3–4 mutation sites in quinolone resistance-determining regions, primarily contributing to their resistance to quinolone. However, S. sonnei isolates were not shown to be quinolone resistant. Co-resistance to cephalosporins and quinolones was detected in 17 S. flexneri isolates, and these isolates were additionally multidrug resistant and carried β-lactamase genes and quinolone-resistance determinants. As is demonstrated in this study, dominant serotypes of Shigella were distributed in unique trend with dangerous drug resistance patterns. Novel strategies are urgently required to prevent the development of drug resistance among diarrhea-inducing pathogens. [ABSTRACT FROM AUTHOR]

Human adenovirus 7 (HAdV-7) strains are a major cause of acute respiratory disease (ARD) among adults and children, associated with fatal pneumonia. An ARD outbreak caused by HAdV-7 that involved 739 college students was reported in this article. To better understand the underlying cause of this large-scale epidemic, virus strains were isolated from infected patients and sequence variations of the whole genome sequence were detected. Evolutionary trees and alignment results indicated that the major capsid protein genes hexon and fibre were strongly conserved among serotype 7 strains in China at that time. Instead, the HAdV-7 strains presented three thymine deletions in the virus associated RNA (VA RNA) II terminal region. We also found that the mutation might lead to increased mRNA expression of an adjacent gene, L1 52/55K, and thus promoted faster growth. These findings suggest that sequence variation of VA RNA II gene was a potential cause of such a severe HAdV-7 infection and this gene should be a new-emerging factor to be monitored for better understanding of HAdV-7 infection. [ABSTRACT FROM AUTHOR]